* -------------------------------------------------------------------------- * * CGenFF: Topology for the Charmm General Force Field v. 4.1 * * for Small Molecule Drug Design * * -------------------------------------------------------------------------- * * 36 1 ! -------------------------------------------------------------------------- ! ! References: - K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, ! ! J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and ! ! A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. ! ! - W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., ! ! J. Comput. Chem. 2012, 33, 2451-2468. ! ! -------------------------------------------------------------------------- ! ! IMPORTANT: This version contain new lone-pair definitions on aromatic ! ! halogens. NBFiX terms are introduced between the halogens and the carbonyl ! ! oxygen in amides. ! ! The following topology & parameter files should be read in the input files ! ! before reading top_all36_cgenff.rtf/par_all36_cgenff.prm for correctly ! ! implementing the NBFIX terms. ! ! 1) top_all36_prot.rtf/par_all36_prot.rtf ! ! 2) top_all36_na.rtf/par_all36_na.rtf ! ! 3) top_all36_carb.rtf/par_all36_carb.rtf ! ! ! ! -------------------------------------------------------------------------- ! ! Notes: - CGenFF is an ongoing project that is updated regularly. Please ! ! check http://mackerell.umaryland.edu/~kenno/cgenff/download.html ! ! and/or http://mackerell.umaryland.edu/ for updates! ! ! - As more functional groups will be introduced, small changes in ! ! existing parameters and/or charges may occur. ! ! - Comments in this file may be misleading. ! ! -------------------------------------------------------------------------- ! ! Contributors: abar = Arghya Barman ! ! adm = Alexander D. MacKerell Jr. ! ! alr = Ashley L. Ringer ! ! cacha = Chayan Acharya ! ! ctsai = Cheng-Chieh Tsai ! ! ed = Eva Darian ! ! ejd = Elizabeth J. Denning ! ! erh = Elizabeth R. Hatcher Frush ! ! fylin = Fang-Yu Lin ! ! gmu = Goutam MUkherjee ! ! isg = Ignacio Soteras Gutiérrez ! ! jal = Justin A. Lemkul ! ! jhs = JiHyun Shim ! ! jing = Jing Huang ! ! kevo = Kenno VanOmmeslaeghe ! ! kundu = Sibsankar Kundu ! ! lf = Lei Fang ! ! lsk = Lakkaraju Sirish Kaushik ! ! mcs = Meagan C. Small ! ! mnoon = Muhammad Noon ! ! my = Mingjun Yang ! ! oashi = Taiji Oashi ! ! og = Olgun Guvench ! ! peml = Pedro Lopes ! ! pram = E. Prabhu Raman ! ! rima = Madhurima Jana ! ! rting = Ting Ran ! ! sc = Sherry (Hua) Chen ! ! sna = Shanthi Nagarajan ! ! sz = Shijun Zhong ! ! viv = Igor Vorobyov ! ! xhe = Xibing He ! ! xxwy = Wenbo Yu ! ! yapol = Iakov Polyak ! ! yin = Daxu Yin ! ! yxu = You Xu ! ! -------------------------------------------------------------------------- ! ! All comments to ADM jr. via the CHARMM web site: www.charmm.org ! ! parameter set discussion forum ! ! -------------------------------------------------------------------------- ! !hydrogens MASS -1 HGA1 1.00800 H ! alphatic proton, CH MASS -1 HGA2 1.00800 H ! alphatic proton, CH2 MASS -1 HGA3 1.00800 H ! alphatic proton, CH3 MASS -1 HGA4 1.00800 H ! alkene proton; RHC= MASS -1 HGA5 1.00800 H ! alkene proton; H2C=CR MASS -1 HGA6 1.00800 H ! aliphatic H on fluorinated C, monofluoro MASS -1 HGA7 1.00800 H ! aliphatic H on fluorinated C, difluoro MASS -1 HGAAM0 1.00800 H ! aliphatic H, NEUTRAL trimethylamine (#) MASS -1 HGAAM1 1.00800 H ! aliphatic H, NEUTRAL dimethylamine (#) MASS -1 HGAAM2 1.00800 H ! aliphatic H, NEUTRAL methylamine (#) !(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY !on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens MASS -1 HGP1 1.00800 H ! polar H MASS -1 HGP2 1.00800 H ! polar H, +ve charge MASS -1 HGP3 1.00800 H ! polar H, thiol MASS -1 HGP4 1.00800 H ! polar H, neutral conjugated -NH2 group (NA bases) MASS -1 HGP5 1.00800 H ! polar H on quarternary ammonium salt (choline) MASS -1 HGPAM1 1.00800 H ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H MASS -1 HGPAM2 1.00800 H ! polar H, NEUTRAL methylamine (#) MASS -1 HGPAM3 1.00800 H ! polar H, NEUTRAL ammonia (#) !(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY !on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens MASS -1 HGR51 1.00800 H ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene MASS -1 HGR52 1.00800 H ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge MASS -1 HGR53 1.00800 H ! nonpolar H, +ve charge HIS he1(+1) MASS -1 HGR61 1.00800 H ! aromatic H MASS -1 HGR62 1.00800 H ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom MASS -1 HGR63 1.00800 H ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens MASS -1 HGR71 1.00800 H ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo !carbons MASS -1 CG1T1 12.01100 C ! internal alkyne R-C#C MASS -1 CG1T2 12.01100 C ! terminal alkyne H-C#C MASS -1 CG1N1 12.01100 C ! C for cyano group MASS -1 CG2D1 12.01100 C ! alkene; RHC= ; imine C MASS -1 CG2D2 12.01100 C ! alkene; H2C= MASS -1 CG2D1O 12.01100 C ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1. MASS -1 CG2D2O 12.01100 C ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2. MASS -1 CG2DC1 12.01100 C ! conjugated alkenes, R2C=CR2 MASS -1 CG2DC2 12.01100 C ! conjugated alkenes, R2C=CR2 MASS -1 CG2DC3 12.01100 C ! conjugated alkenes, H2C= MASS -1 CG2N1 12.01100 C ! conjugated C in guanidine/guanidinium MASS -1 CG2N2 12.01100 C ! conjugated C in amidinium cation MASS -1 CG2O1 12.01100 C ! carbonyl C: amides MASS -1 CG2O2 12.01100 C ! carbonyl C: esters, [neutral] carboxylic acids MASS -1 CG2O3 12.01100 C ! carbonyl C: [negative] carboxylates MASS -1 CG2O4 12.01100 C ! carbonyl C: aldehydes MASS -1 CG2O5 12.01100 C ! carbonyl C: ketones MASS -1 CG2O6 12.01100 C ! carbonyl C: urea, carbonate MASS -1 CG2O7 12.01100 C ! CO2 carbon MASS -1 CG2R51 12.01100 C ! 5-mem ring, his CG, CD2(0), trp MASS -1 CG2R52 12.01100 C ! 5-mem ring, double bound to N, PYRZ, pyrazole MASS -1 CG2R53 12.01100 C ! 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO, kevo MASS -1 CG2R57 12.01100 C ! 5-mem ring, bipyrroles MASS -1 CG25C1 12.01100 C ! same as CG2DC1 but in 5-membered ring with exocyclic double bond MASS -1 CG25C2 12.01100 C ! same as CG2DC2 but in 5-membered ring with exocyclic double bond MASS -1 CG251O 12.01100 C ! same as CG2D1O but in 5-membered ring with exocyclic double bond MASS -1 CG252O 12.01100 C ! same as CG2D2O but in 5-membered ring with exocyclic double bond MASS -1 CG2R61 12.01100 C ! 6-mem aromatic C MASS -1 CG2R62 12.01100 C ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA) MASS -1 CG2R63 12.01100 C ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?) MASS -1 CG2R64 12.01100 C ! 6-mem aromatic amidine and guanidine carbon (between 2 or 3 Ns and double-bound to one of them), NA, PYRM MASS -1 CG2R66 12.01100 C ! 6-mem aromatic carbon bound to F MASS -1 CG2R67 12.01100 C ! 6-mem aromatic carbon of biphenyl MASS -1 CG2RC0 12.01100 C ! 6/5-mem ring bridging C, guanine C4,C5, trp MASS -1 CG2R71 12.01100 C ! 7-mem ring arom C, AZUL, azulene, kevo MASS -1 CG2RC7 12.01100 C ! sp2 ring connection with single bond(!), AZUL, azulene, kevo MASS -1 CG301 12.01100 C ! aliphatic C, no hydrogens, neopentane MASS -1 CG302 12.01100 C ! aliphatic C, no hydrogens, trifluoromethyl MASS -1 CG311 12.01100 C ! aliphatic C with 1 H, CH MASS -1 CG312 12.01100 C ! aliphatic C with 1 H, difluoromethyl MASS -1 CG314 12.01100 C ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+) MASS -1 CG321 12.01100 C ! aliphatic C for CH2 MASS -1 CG322 12.01100 C ! aliphatic C for CH2, monofluoromethyl MASS -1 CG323 12.01100 C ! aliphatic C for CH2, thiolate carbon MASS -1 CG324 12.01100 C ! aliphatic C for CH2, adjacent to positive N (piperidine) (+) MASS -1 CG331 12.01100 C ! aliphatic C for methyl group (-CH3) MASS -1 CG334 12.01100 C ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+) MASS -1 CG3AM0 12.01100 C ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#) MASS -1 CG3AM1 12.01100 C ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#) MASS -1 CG3AM2 12.01100 C ! aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#) !(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY !on NEUTRAL METHYLAMINE groups, NOT ETHYL, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens MASS -1 CG3C31 12.01100 C ! cyclopropyl carbon MASS -1 CG3C41 12.01100 C ! cyclobutyl carbon MASS -1 CG3C50 12.01100 C ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids) MASS -1 CG3C51 12.01100 C ! 5-mem ring aliphatic CH (proline CA, furanoses) MASS -1 CG3C52 12.01100 C ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose) MASS -1 CG3C53 12.01100 C ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+) MASS -1 CG3C54 12.01100 C ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+) MASS -1 CG3RC1 12.01100 C ! bridgehead in bicyclic systems containing at least one 5-membered or smaller ring !(+) Includes protonated Shiff base (NG3D5, NG2R52 in 2HPP) but NOT amidinium (NG2R52 in IMIM), guanidinium !nitrogens MASS -1 NG1T1 14.00700 N ! N for cyano group !MASS -1 NG1D1 14.00700 N ! terminal N in azides, lsk MASS -1 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine) MASS -1 NG2S0 14.00700 N ! N,N-disubstituted amide, proline N (CO=NRR') MASS -1 NG2S1 14.00700 N ! peptide nitrogen (CO=NHR) MASS -1 NG2S2 14.00700 N ! terminal amide nitrogen (CO=NH2) MASS -1 NG2S3 14.00700 N ! external amine ring nitrogen (planar/aniline), phosphoramidate !MASS -1 NG2S4 14.00700 N ! neutral hydroxamic acid MASS -1 NG2O1 14.00700 N ! NITB, nitrobenzene MASS -1 NG2P1 14.00700 N ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium) MASS -1 NG2R43 14.00700 N ! amide in 4-memebered ring (planar), AZDO, lsk MASS -1 NG2R50 14.00700 N ! double bound neutral 5-mem planar ring, purine N7 MASS -1 NG2R51 14.00700 N ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused) MASS -1 NG2R52 14.00700 N ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo MASS -1 NG2R53 14.00700 N ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo MASS -1 NG2R57 14.00700 N ! 5-mem ring, bipyrroles MASS -1 NG2R60 14.00700 N ! double bound neutral 6-mem planar ring, pyr1, pyzn MASS -1 NG2R61 14.00700 N ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage MASS -1 NG2R62 14.00700 N ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm MASS -1 NG2R67 14.00700 N ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.) MASS -1 NG2RC0 14.00700 N ! 6/5-mem ring bridging N, indolizine, INDZ, kevo MASS -1 NG301 14.00700 N ! neutral trimethylamine nitrogen MASS -1 NG311 14.00700 N ! neutral dimethylamine nitrogen MASS -1 NG321 14.00700 N ! neutral methylamine nitrogen MASS -1 NG331 14.00700 N ! neutral ammonia nitrogen MASS -1 NG3C51 14.00700 N ! secondary sp3 amine in 5-membered ring MASS -1 NG3N1 14.00700 N ! N in hydrazine, HDZN MASS -1 NG3P0 14.00700 N ! quarternary N+, choline MASS -1 NG3P1 14.00700 N ! tertiary NH+ (PIP) MASS -1 NG3P2 14.00700 N ! secondary NH2+ (proline) MASS -1 NG3P3 14.00700 N ! primary NH3+, phosphatidylethanolamine !oxygens MASS -1 OG2D1 15.99940 O ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera MASS -1 OG2D2 15.99940 O ! carbonyl O: negative groups: carboxylates, carbonate MASS -1 OG2D3 15.99940 O ! carbonyl O: ketones MASS -1 OG2D4 15.99940 O ! 6-mem aromatic carbonyl oxygen (nucleic bases) MASS -1 OG2D5 15.99940 O ! CO2 oxygen MASS -1 OG2N1 15.99940 O ! NITB, nitrobenzene MASS -1 OG2P1 15.99940 O ! =O in phosphate or sulfate MASS -1 OG2R50 15.99940 O ! FURA, furan MASS -1 OG3R60 15.99940 O ! O in 6-mem cyclic enol ether (PY01, PY02) or ester MASS -1 OG301 15.99940 O ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60??? MASS -1 OG302 15.99940 O ! ester -O- MASS -1 OG303 15.99940 O ! phosphate/sulfate ester oxygen MASS -1 OG304 15.99940 O ! linkage oxygen in pyrophosphate/pyrosulphate MASS -1 OG311 15.99940 O ! hydroxyl oxygen MASS -1 OG312 15.99940 O ! ionized alcohol oxygen MASS -1 OG3C31 15.99940 O ! epoxide oxygen, 1EOX, 1BOX, sc MASS -1 OG3C51 15.99940 O ! 5-mem furanose ring oxygen (ether) MASS -1 OG3C61 15.99940 O ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60??? !sulphurs MASS -1 SG2D1 32.06000 S ! thiocarbonyl S MASS -1 SG2R50 32.06000 S ! THIP, thiophene MASS -1 SG311 32.06000 S ! sulphur, SH, -S- MASS -1 SG301 32.06000 S ! sulfur C-S-S-C type MASS -1 SG302 32.06000 S ! thiolate sulfur (-1) MASS -1 SG3O1 32.06000 S ! sulfate -1 sulfur MASS -1 SG3O2 32.06000 S ! neutral sulfone/sulfonamide sulfur MASS -1 SG3O3 32.06000 S ! neutral sulfoxide sulfur !halogens MASS -1 CLGA1 35.45300 Cl ! CLET, DCLE, chloroethane, 1,1-dichloroethane MASS -1 CLGA3 35.45300 Cl ! TCLE, 1,1,1-trichloroethane MASS -1 CLGR1 35.45300 Cl ! CHLB, chlorobenzene MASS -1 BRGA1 79.90400 Br ! BRET, bromoethane MASS -1 BRGA2 79.90400 Br ! DBRE, 1,1-dibromoethane MASS -1 BRGA3 79.90400 Br ! TBRE, 1,1,1-dibromoethane MASS -1 BRGR1 79.90400 Br ! BROB, bromobenzene MASS -1 IGR1 126.90447 I ! IODB, iodobenzene MASS -1 FGA1 18.99800 F ! aliphatic fluorine, monofluoro MASS -1 FGA2 18.99800 F ! aliphatic fluorine, difluoro MASS -1 FGA3 18.99800 F ! aliphatic fluorine, trifluoro MASS -1 FGP1 18.99800 F ! anionic F, for ALF4 AlF4- MASS -1 FGR1 18.99800 F ! aromatic flourine !miscellaneous MASS -1 PG0 30.97380 P ! neutral phosphate MASS -1 PG1 30.97380 P ! phosphate -1 MASS -1 PG2 30.97380 P ! phosphate -2 MASS -1 ALG1 26.98154 Al ! Aluminum, for ALF4, AlF4- MASS -1 LPH 0.00000 X ! Lone pair for halogens MASS -1 SG2P1 32.06000 ! mono-thio S-P bond MASS -1 OG2S1 15.99940 ! mono-thio S-P bond modulated oxygen MASS -1 SG2P2 32.06000 ! di-thio S-P bond DEFA FIRS NONE LAST NONE AUTO ANGLES DIHE PATCH DRUDE !RESI TIP3 0.00 ! tip3p water model, generate using noangle nodihedral !GROUP !ATOM OH2 OGTIP3 -0.834 !ATOM H1 HGTIP3 0.417 !ATOM H2 HGTIP3 0.417 !BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake !ANGLE H1 OH2 H2 ! required !ACCEPTOR OH2 !PATCHING FIRS NONE LAST NONE !protein model compounds !toppar_all22_model_aliphatic.str RESI ACET -1.00 ! C2H3O2 acetate, K. Kuczera GROUP ATOM C1 CG331 -0.37 ATOM C2 CG2O3 0.62 ! H1 O1 (-) ATOM H1 HGA3 0.09 ! | / ATOM H2 HGA3 0.09 ! H2--C1--C2 ATOM H3 HGA3 0.09 ! | \\ ATOM O1 OG2D2 -0.76 ! H3 O2 ATOM O2 OG2D2 -0.76 BOND C1 H1 C1 H2 C1 H3 BOND C1 C2 C2 O1 DOUBLE C2 O2 IMPR C2 O2 O1 C1 IC O1 C2 C1 H1 0.00 0.00 0.0 0.00 0.00 IC C2 H1 *C1 H2 0.00 0.00 120.0 0.00 0.00 IC C2 H1 *C1 H3 0.00 0.00 -120.0 0.00 0.00 IC C1 O1 *C2 O2 0.00 0.00 180.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI PROA -1.00 ! C3H5O2 propionic acid GROUP ATOM C2 CG321 -0.28 ATOM C1 CG2O3 0.62 ! H21 O1 (-) ATOM H21 HGA2 0.09 ! | / ATOM H22 HGA2 0.09 ! H22-C2--C1 ! | \\ ATOM O1 OG2D2 -0.76 ! | O2 ATOM O2 OG2D2 -0.76 !H31--C3 GROUP ! | \ ATOM C3 CG331 -0.27 ! H32 H33 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 C2 C2 C3 C1 O1 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 C3 H33 DOUBLE C1 O2 IMPR C1 O2 O1 C2 IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 O2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC O1 C2 *C1 O2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI GUAN 1.00 ! CH6N3 guandinium, K. Kuczera GROUP ATOM C CG2N1 0.64 ! H11 H12 ATOM N1 NG2P1 -0.80 ! \ / ATOM H11 HGP2 0.46 ! N1 (+) ATOM H12 HGP2 0.46 ! || ATOM N2 NG2P1 -0.80 ! C ATOM H21 HGP2 0.46 ! / \ ATOM H22 HGP2 0.46 ! H21-N2 N3-H31 ATOM N3 NG2P1 -0.80 ! | | ATOM H31 HGP2 0.46 ! H22 H32 ATOM H32 HGP2 0.46 BOND C N2 C N3 DOUBLE C N1 BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 H32 IMPR C N2 N1 N3 IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 IC H32 N3 C N2 0.00 0.00 0.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI MGUA 1.00 ! C2H8N3 methyl-guanidinium GROUP ATOM C CG2N1 0.64 ! H11 H12 ATOM N1 NG2P1 -0.80 ! \ / ATOM H11 HGP2 0.46 ! N1 (+) ATOM H12 HGP2 0.46 ! || ATOM N2 NG2P1 -0.80 ! C HC1 ATOM H21 HGP2 0.46 ! / \ / ATOM H22 HGP2 0.46 ! H21-N2 N3--C2-HC2 ATOM N3 NG2P1 -0.70 ! | | \ ATOM H31 HGP2 0.44 ! H22 H31 HC3 ATOM C2 CG334 0.11 ATOM HC1 HGA3 0.09 ATOM HC2 HGA3 0.09 ATOM HC3 HGA3 0.09 BOND C N2 C N3 DOUBLE C N1 BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2 BOND C2 HC1 C2 HC2 C2 HC3 IMPR C N2 N1 N3 IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 IC C2 N3 C N1 0.00 0.00 180.0 0.00 0.00 IC C N3 C2 HC1 0.00 0.00 0.0 0.00 0.00 IC C N3 C2 HC2 0.00 0.00 120.0 0.00 0.00 IC C N3 C2 HC3 0.00 0.00 240.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI GLYN 0.00 ! C2H5NO2 neutral glycine GROUP ATOM N NG321 -0.96 ATOM HT1 HGPAM2 0.34 ! HT1 HT2 ATOM HT2 HGPAM2 0.34 ! \ / ATOM CA CG321 0.18 ! N ATOM HA1 HGA2 0.05 ! | ATOM HA2 HGA2 0.05 ! HA1-CA-HA2 GROUP ! | ATOM C CG2O2 0.75 ! C ATOM OT1 OG2D1 -0.55 ! // \ ATOM OT2 OG311 -0.63 ! OT1 OT2 ATOM HO2 HGP1 0.43 ! | ! HO2 BOND N CA CA C C OT2 OT2 HO2 BOND N HT1 N HT2 CA HA1 CA HA2 DOUBLE OT1 C DONO HT1 N DONO HT2 N DONO HO2 OT2 IMPR C CA OT1 OT2 IC N CA C OT1 1.5010 119.00 88.76 126.10 1.2218 IC N CA C OT2 1.5010 119.00 -111.57 113.44 1.3958 IC OT1 OT2 *C CA 1.2218 117.44 -161.57 113.44 1.5780 IC CA C OT2 HO2 1.5780 113.44 -168.97 107.16 0.9565 IC C CA N HT1 1.5780 119.00 164.86 110.99 1.0023 IC C CA N HT2 1.5780 119.00 -77.98 111.22 1.0030 IC N C *CA HA1 1.5010 119.00 120.0 110.0 1.1 IC N C *CA HA2 1.5010 119.00 -120.0 110.0 1.1 PATCHING FIRS NONE LAST NONE RESI MAMM 1.00 ! CH6N methylammonium, K. Kuczera GROUP ATOM CE CG334 0.16 ATOM NZ NG3P3 -0.30 ! HE1 HZ1 ATOM HE1 HGA3 0.05 ! \ (+) | ATOM HE2 HGA3 0.05 !HE2-CE---NZ--HZ2 ATOM HE3 HGA3 0.05 ! / | ATOM HZ1 HGP2 0.33 ! HE3 HZ3 ATOM HZ2 HGP2 0.33 ATOM HZ3 HGP2 0.33 BOND CE HE1 CE HE2 CE HE3 BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 IC NZ HE3 *CE HE1 0.0000 0.00 120.00 0.00 0.0000 IC NZ HE3 *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 IC HE3 CE NZ HZ3 0.0000 0.00 180.00 0.00 0.0000 IC CE HZ3 *NZ HZ1 0.0000 0.00 120.00 0.00 0.0000 IC CE HZ3 *NZ HZ2 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI EAMM 1.00 ! C2H8N ethylammonium, adm jr. GROUP ATOM CE CG324 0.21 ATOM NZ NG3P3 -0.30 ! HE1 HZ1 ATOM HE1 HGA2 0.05 ! \ (+) | ATOM HE2 HGA2 0.05 !HE2-CE---NZ--HZ2 ! / | ATOM HZ1 HGP2 0.33 ! / HZ3 ATOM HZ2 HGP2 0.33 ! C1-H13 ATOM HZ3 HGP2 0.33 ! / \ GROUP !H11 H12 ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 BOND CE HE1 CE HE2 CE C1 BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 BOND C1 H11 C1 H12 C1 H13 IC H11 C1 CE NZ 0.0000 0.00 180.00 0.00 0.0000 IC C1 NZ *CE HE1 0.0000 0.00 120.00 0.00 0.0000 IC HE1 NZ *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 IC HE1 CE NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 IC HZ1 CE *NZ HZ2 0.0000 0.00 120.00 0.00 0.0000 IC HZ1 CE *NZ HZ3 0.0000 0.00 -120.00 0.00 0.0000 IC HE1 CE C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 CE *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 CE *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI ACEH 0.00 ! C2H4O2 acetic acid, ADM jr. GROUP ATOM C2 CG331 -0.30 ATOM C1 CG2O2 0.75 ! H21 O2 ATOM H21 HGA3 0.09 ! \ // ATOM H22 HGA3 0.09 ! H22-C2--C1 ATOM H23 HGA3 0.09 ! / \ ATOM O2 OG2D1 -0.55 ! H23 O1-HO1 ATOM O1 OG311 -0.60 ATOM HO1 HGP1 0.43 BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 DOUBLE C1 O2 IMPR C1 C2 O2 O1 DONO BLNK HO1 ! O1 ACCE O1 ACCE O2 IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 RESI MEOH 0.00 ! CH4O methanol, adm jr. GROUP ATOM CB CG331 -0.04 ! H11 ATOM OG OG311 -0.65 ! \ ATOM HG1 HGP1 0.42 ! H12--C1--O1 ATOM HB1 HGA3 0.09 ! / \ ATOM HB2 HGA3 0.09 ! H13 HO1 ATOM HB3 HGA3 0.09 BOND CB OG OG HG1 BOND CB HB1 CB HB2 CB HB3 DONO HG1 OG ACCE OG ! only for analysis IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG HB1 *CB HB2 0.0000 0.0000 120.0000 0.0000 0.0000 IC OG HB1 *CB HB3 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI METO -1.00 ! CH3O methoxide, adm jr. GROUP ! order of atoms to match that used in ab initio ATOM CB CG331 -0.41 ! HB1 ATOM OG OG312 -0.92 ! \ ! HB2--CB--OG (-) ATOM HB1 HGA3 0.11 ! / ATOM HB2 HGA3 0.11 ! HB3 ATOM HB3 HGA3 0.11 BOND CB OG BOND CB HB1 CB HB2 CB HB3 ACCE OG ! only for analysis IC HB2 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG HB2 *CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 RESI ETOH 0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1 CG321 0.05 ! H21 H11 H12 ATOM O1 OG311 -0.65 ! \ \ / ATOM HO1 HGP1 0.42 ! H22--C2--C1 ATOM H11 HGA2 0.09 ! / \ ATOM H12 HGA2 0.09 ! H23 O1--HO1 GROUP ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 BOND C2 H21 C2 H22 C2 H23 DONO HO1 O1 ACCE O1 ! for ic build IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1 H21 *C2 H23 0.0000 0.0000 240.0000 0.0000 0.0000 IC O1 C2 *C1 H11 0.0000 0.0000 240.0000 0.0000 0.0000 IC O1 C2 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000 RESI ETO -1.00 ! C2H5O Ethoxide, adm jr. GROUP ATOM OG OG312 -0.92 ! HA1 HB1 HB2 ATOM CB CG321 -0.30 ! \ \ / ATOM CA CG331 -0.27 ! HA2--CA--CB ATOM HB1 HGA2 0.11 ! / \ ATOM HB2 HGA2 0.11 ! HA3 OG (-) ATOM HA1 HGA3 0.09 ATOM HA2 HGA3 0.09 ATOM HA3 HGA3 0.09 BOND CA CB CB OG CB HB1 CB HB2 BOND CA HA1 CA HA2 CA HA3 ACCE OG ! for ic build IC CB CA HA1 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA OG CB HB2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA OG CB HB3 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 IC HA1 CA CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HA1 CA CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 RESI PRO2 0.00 ! C3H8O 2-propanol, adm jr. GROUP ATOM C2 CG311 0.14 ! H12 H13 H33 H32 ATOM O2 OG311 -0.65 ! \ / \ / ATOM HO2 HGP1 0.42 ! H11--C1 C3--H31 ATOM H21 HGA1 0.09 ! \ / GROUP ! C2 ATOM C1 CG331 -0.27 ! / \ ATOM H11 HGA3 0.09 ! O2 H21 ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! HO2 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 C2 C2 C3 C2 O2 C2 H21 O2 HO2 BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 DONO HO2 O2 ACCE O2 IC C1 C2 C3 H31 0.0000 0.000 180.0000 0.000 0.0000 IC C2 H31 *C3 H32 0.0000 0.000 120.0000 0.000 0.0000 IC C2 H31 *C3 H33 0.0000 0.000 -120.0000 0.000 0.0000 IC C3 C2 C1 H11 0.0000 0.000 180.0000 0.000 0.0000 IC C2 H11 *C1 H12 0.0000 0.000 120.0000 0.000 0.0000 IC C2 H11 *C1 H13 0.0000 0.000 -120.0000 0.000 0.0000 IC C1 C3 *C2 O2 0.0000 0.000 120.0000 0.000 0.0000 IC C1 C3 *C2 H21 0.0000 0.000 -120.0000 0.000 0.0000 IC C3 C2 O2 HO2 0.0000 0.000 180.0000 0.000 0.0000 RESI FORM 0.00 ! CH3NO formamide, adm jr. GROUP ATOM HA HGR52 0.08 ATOM C CG2O1 0.42 ! O Hc ATOM N NG2S2 -0.69 ! \\ / ATOM HC HGP1 0.35 ! C--N ATOM HT HGP1 0.35 ! / \ ATOM O OG2D1 -0.51 ! HA Ht BOND C HA C N N HC N HT DOUBLE C O !BOND O DUM IMPR C N O HA ! GAS PHASE GEOMETRY !IC DUM O C N 1.00 90.0 0. 124.70 1.352 !Gives strange error: !IC O C N HC 1.2190 124.70 0. 118.50 1.0016 ! variable 1 !IC HC N C HA 1.0016 118.50 180. 112.70 1.0980 ! variable 2 !IC O C N HT 1.2190 124.70 180. 120.00 1.0015 ! variable 3 !Works with IC param: IC O C N HT 0.0000 0.0000 180.0000 0.0000 0.0000 IC O N *C HA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C HT *N HC 0.0000 0.0000 180.0000 0.0000 0.0000 RESI ACEM 0.00 ! C2H5NO acetamide, adm jr. ! the amide charges listed below are used in asparagine and glutamine ! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32 GROUP ATOM CC CG331 -0.27 ATOM C CG2O1 0.55 ! HC1 Ht ATOM N NG2S2 -0.62 ! \ / ATOM HC HGP1 0.32 ! HC2--CC--C---N ATOM HT HGP1 0.30 ! / || \ ATOM O OG2D1 -0.55 ! HC3 O Hc ATOM HC1 HGA3 0.09 ATOM HC2 HGA3 0.09 ATOM HC3 HGA3 0.09 !atom dum dum 0.0 ! dummy for ic build BOND C N N HC N HT DOUBLE C O BOND C CC CC HC1 CC HC2 CC HC3 !BOND O DUM IMPR C CC N O ! GAS PHASE GEOMETRY IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 IC O C CC HC1 1.2012 123.27 0. 113.80 1.0832 IC O C CC HC2 1.2012 123.27 120. 108.52 1.0836 IC O C CC HC3 1.2012 123.27 300. 108.52 1.0836 RESI PRAM 0.00 ! C3H7NO propionamide, adm jr. ! the amide charges listed below are used in asparagine and glutamine ! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32 GROUP ATOM CC CG321 -0.18 ATOM C CG2O1 0.55 ! HC1 Ht ATOM N NG2S2 -0.62 ! \ / ATOM HC HGP1 0.32 ! HC2--CC--C---N ATOM HT HGP1 0.30 ! / || \ ATOM O OG2D1 -0.55 ! / O Hc ATOM HC1 HGA2 0.09 ! C1-H13 ATOM HC2 HGA2 0.09 ! / \ GROUP !H11 H12 ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 !atom dum dum 0.0 ! dummy for ic build BOND C N N HC N HT DOUBLE C O BOND C CC CC HC1 CC HC2 CC C1 BOND C1 H11 C1 H12 C1 H13 !BOND O DUM IMPR C CC N O ! GAS PHASE GEOMETRY IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 IC O C CC HC1 1.2012 123.27 60. 113.80 1.0832 IC O C CC HC2 1.2012 123.27 300. 108.52 1.0836 IC O C CC C1 1.2012 123.27 180. 108.52 1.5000 IC C CC C1 H11 0.0 0.0 180. 0.0 0.0 IC C CC C1 H12 0.0 0.0 60. 0.0 0.0 IC C CC C1 H13 0.0 0.0 300. 0.0 0.0 RESI NMA 0.00 ! C3H7NO N-methylacetamide, Louis Kuchnir GROUP ATOM CL CG331 -0.27 ATOM HL1 HGA3 0.09 ATOM HL2 HGA3 0.09 ATOM HL3 HGA3 0.09 ATOM C CG2O1 0.51 ATOM O OG2D1 -0.51 ATOM N NG2S1 -0.47 ATOM H HGP1 0.31 ATOM CR CG331 -0.11 ATOM HR1 HGA3 0.09 ATOM HR2 HGA3 0.09 ATOM HR3 HGA3 0.09 BOND HL1 CL HL2 CL HL3 CL ! N-Methylacetamide: BOND CL C C N N CR ! HL1\ O /HR1 BOND N H ! HL2-- CL -- C -- N -- CR --HR2 BOND HR1 CR HR2 CR HR3 CR ! HL3/ H \HR3 DOUBLE C O IMPR C CL N O IC O C N H 1.2233 122.84 180. 119.23 0.9933 ! variable 1 IC H N C CL 0.9933 119.23 0. 116.25 1.5118 ! variable 8 IC O C N CR 1.2233 122.84 0. 122.57 1.4488 ! variable 8 IC N C CL HL1 1.3418 116.25 180. 109.3 1.109 ! variable 2 IC N C CL HL2 1.3418 116.25 60. 109.3 1.109 ! variable 3 IC N C CL HL3 1.3418 116.25 300. 109.3 1.109 ! variable 4 IC C N CR HR1 1.3418 122.57 180. 110.7 1.113 ! variable 5 IC C N CR HR2 1.3418 122.57 60. 110.7 1.113 ! variable 6 IC C N CR HR3 1.3418 122.57 300. 110.7 1.113 ! variable 7 RESI AANM 0.00 ! C6H12N2O2 Ac-Ala-NMe, aka. alanine dipeptide GROUP ATOM CL CG331 -0.27 ATOM HL1 HGA3 0.09 ATOM HL2 HGA3 0.09 ATOM HL3 HGA3 0.09 GROUP ATOM CLP CG2O1 0.51 ATOM OL OG2D1 -0.51 GROUP ATOM NL NG2S1 -0.47 ATOM HL HGP1 0.31 ATOM CA CG311 0.07 ATOM HA HGA1 0.09 GROUP ATOM CB CG331 -0.27 ! HL1 OL OR HR1 ATOM HB1 HGA3 0.09 ! \ || HL HA || HR / ATOM HB2 HGA3 0.09 ! \ || | | || | / ATOM HB3 HGA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 GROUP ! / | \ ATOM CRP CG2O1 0.51 ! / HB1--CB--HB3 \ ATOM OR OG2D1 -0.51 ! HL3 | HR3 GROUP ! HB2 ATOM NR NG2S1 -0.47 ATOM HR HGP1 0.31 ATOM CR CG331 -0.11 ATOM HR1 HGA3 0.09 ATOM HR2 HGA3 0.09 ATOM HR3 HGA3 0.09 BOND CL CLP CLP NL NL CA BOND CA CRP CRP NR NR CR DOUBLE CLP OL CRP OR BOND NL HL NR HR BOND CA HA CA CB BOND CL HL1 CL HL2 CL HL3 BOND CB HB1 CB HB2 CB HB3 BOND CR HR1 CR HR2 CR HR3 IMPR CLP CL NL OL IMPR CRP CA NR OR IC CLP NL CA CRP 0.0 0.0 180.0 0.0 0.0 ! Phi IC CA CLP *NL HL 0.0 0.0 180.0 0.0 0.0 IC HL NL CA CRP 0.0 0.0 0.0 0.0 0.0 IC NL CA CRP NR 0.0 0.0 180.0 0.0 0.0 ! Psi IC CA NR *CRP OR 0.0 0.0 180.0 0.0 0.0 IC NL CA CRP OR 0.0 0.0 0.0 0.0 0.0 IC CL CLP NL CA 0.0 0.0 180.0 0.0 0.0 ! Omega Left IC NL CL *CLP OL 0.0 0.0 180.0 0.0 0.0 IC OL CLP NL CA 0.0 0.0 0.0 0.0 0.0 IC CA CRP NR CR 0.0 0.0 180.0 0.0 0.0 ! Omega Right IC CRP CR *NR HR 0.0 0.0 180.0 0.0 0.0 IC NL CRP *CA HA 0.0 0.0 240.0 0.0 0.0 IC NL CRP *CA CB 0.0 0.0 120.0 0.0 0.0 IC HL1 CL CLP NL 0.0 0.0 180.0 0.0 0.0 IC HL2 CL CLP NL 0.0 0.0 60.0 0.0 0.0 IC HL3 CL CLP OL 0.0 0.0 120.0 0.0 0.0 IC HA CA CB HB1 0.0 0.0 180.0 0.0 0.0 IC NL CA CB HB2 0.0 0.0 180.0 0.0 0.0 IC CRP CA CB HB3 0.0 0.0 180.0 0.0 0.0 IC CRP NR CR HR1 0.0 0.0 180.0 0.0 0.0 IC CRP NR CR HR2 0.0 0.0 60.0 0.0 0.0 IC HR NR CR HR3 0.0 0.0 120.0 0.0 0.0 IC CA CLP *NL HL 0.0 0.0 180.0 0.0 0.0 IC CA NR *CRP OR 0.0 0.0 180.0 0.0 0.0 IC HB1 HB2 *CB HB3 0.0 0.0 120.0 0.0 0.0 IC HL1 HL2 *CL HL3 0.0 0.0 240.0 0.0 0.0 IC HR1 HR2 *CR HR3 0.0 0.0 240.0 0.0 0.0 IC HA CA NL HL 0.0 0.0 240.0 0.0 0.0 RESI MESH 0.00 ! CH4S methanethiol, DZUNG NGUYEN GROUP ATOM H1 HGA3 0.09 ! H1 ATOM H2 HGA3 0.09 ! \ ATOM H3 HGA3 0.09 ! H2--CM--S ATOM CM CG331 -0.20 ! / \ ATOM S SG311 -0.23 ! H3 H4 ATOM H4 HGP3 0.16 BOND CM H1 CM H2 CM H3 BOND CM S S H4 IC H1 CM S H4 0.00 0.00 0.0 0.00 0.00 IC H2 CM S H4 0.00 0.00 120.0 0.00 0.00 IC H3 CM S H4 0.00 0.00 240.0 0.00 0.00 IC CM S H4 H1 0.00 0.00 0.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI MES1 -1.00 ! CH3S methylthiolate, adm jr. GROUP ATOM S SG302 -0.80 ! H11 ATOM C1 CG323 -0.47 ! \ ATOM H11 HGA3 0.09 ! H12--C1--S (-) ATOM H12 HGA3 0.09 ! / ATOM H13 HGA3 0.09 ! H13 BOND S C1 C1 H11 C1 H12 C1 H13 IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC S H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI ETSH 0.00 ! C2H6S ethanethiol, Dzung Nguyen GROUP ATOM H1 HGA3 0.09 ! H1 H4 H5 ATOM H2 HGA3 0.09 ! \ \ / ATOM H3 HGA3 0.09 ! H2-CM1--CM2 ATOM CM1 CG331 -0.27 ! / \ GROUP ! H3 S3--H6 ATOM H4 HGA2 0.09 ATOM H5 HGA2 0.09 ATOM CM2 CG321 -0.11 ATOM S3 SG311 -0.23 ATOM H6 HGP3 0.16 BOND CM1 H1 CM1 H2 CM1 H3 BOND CM1 CM2 CM2 H4 CM2 H5 BOND CM2 S3 S3 H6 IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0 IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0 IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0 IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0 IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0 IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0 IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0 IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0 IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0 IC CM1 CM2 S3 H6 0.00 0.00 60.0 0.0 0.0 IC H4 CM2 S3 H6 0.00 0.00 180.0 0.0 0.0 IC H5 CM2 S3 H6 0.00 0.00 300.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI ES1 -1.00 ! C2H5S ethylthiolate, adm jr. GROUP ATOM S SG302 -0.80 ! H21 H11 H12 ATOM C1 CG323 -0.38 ! \ \ / ATOM C2 CG331 -0.27 ! H22--C2--C1 ATOM H21 HGA3 0.09 ! / \ ATOM H22 HGA3 0.09 ! H23 S (-) ATOM H23 HGA3 0.09 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 BOND S C1 C1 H11 C1 H12 C1 C2 BOND C2 H21 C2 H22 C2 H23 IC BLNK H11 C1 S 0.0000 0.00 0.00 109.72 1.8281 IC S H11 *C1 H12 1.8281 109.72 118.35 105.91 1.1131 IC S H11 *C1 C2 1.8281 109.72 -125.21 108.57 1.5315 IC H12 C2 *C1 H11 1.1131 108.57 -114.71 108.57 1.1131 IC S C1 C2 H21 1.8281 114.02 -180.00 110.65 1.1089 IC S C1 C2 H22 1.8281 114.02 59.57 109.98 1.1111 IC S C1 C2 H23 1.8281 114.02 -59.57 109.98 1.1111 PATCH FIRST NONE LAST NONE RESI DMDS 0.00 ! C2H6S2 dimethyldisulfide, Dzung Nguyen GROUP ATOM H1 HGA3 0.09 ATOM H2 HGA3 0.09 ! H1 ATOM H3 HGA3 0.09 ! \ ATOM CM1 CG331 -0.19 ! H2-CM1 ATOM S2 SG301 -0.08 ! / \ GROUP ! H3 S2--S3 H4 ATOM S3 SG301 -0.08 ! \ / ATOM CM4 CG331 -0.19 ! CM4-H5 ATOM H4 HGA3 0.09 ! \ ATOM H5 HGA3 0.09 ! H6 ATOM H6 HGA3 0.09 BOND H1 CM1 H2 CM1 H3 CM1 CM1 S2 BOND S2 S3 S3 CM4 CM4 H4 CM4 H5 BOND CM4 H6 IC H1 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 IC H2 CM1 S2 S3 0.00 0.00 180.0 0.0 0.0 IC H3 CM1 S2 S3 0.00 0.00 300.0 0.0 0.0 IC CM1 S2 S3 CM4 0.00 0.00 90.0 0.0 0.0 IC S2 S3 CM4 H4 0.00 0.00 60.0 0.0 0.0 IC S2 S3 CM4 H5 0.00 0.00 180.0 0.0 0.0 IC S2 S3 CM4 H6 0.00 0.00 300.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI DEDS 0.00 ! C4H10S2 diethyldisulfide, adm jr. GROUP ATOM H1 HGA2 0.09 ATOM H2 HGA2 0.09 ! H1 ! \ ATOM CM1 CG321 -0.10 ! H2-CM1 ATOM S2 SG301 -0.08 ! / \ GROUP ! CM0 S2--S3 H4 ATOM S3 SG301 -0.08 ! / | \ \ / ATOM CM4 CG321 -0.10 !H01| H03 CM4-H5 ATOM H4 HGA2 0.09 ! H02 \ ATOM H5 HGA2 0.09 ! CM5-H53 GROUP ! / \ ATOM CM0 CG331 -0.27 ! H51 H52 ATOM H01 HGA3 0.09 ATOM H02 HGA3 0.09 ATOM H03 HGA3 0.09 GROUP ATOM CM5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND H1 CM1 H2 CM1 CM1 CM0 CM1 S2 BOND S2 S3 S3 CM4 CM4 H4 CM4 H5 BOND CM4 CM5 BOND CM0 H01 CM0 H02 CM0 H03 BOND CM5 H51 CM5 H52 CM5 H53 IC CM0 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 IC H1 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 IC H2 CM1 S2 S3 0.00 0.00 300.0 0.0 0.0 IC CM0 CM1 S2 S3 0.00 0.00 180.0 0.0 0.0 IC S2 CM1 CM0 H01 0.00 0.00 180.0 0.0 0.0 IC S2 CM1 CM0 H02 0.00 0.00 60.0 0.0 0.0 IC S2 CM1 CM0 H03 0.00 0.00 300.0 0.0 0.0 IC CM1 S2 S3 CM4 0.00 0.00 90.0 0.0 0.0 IC S2 S3 CM4 H4 0.00 0.00 60.0 0.0 0.0 IC S2 S3 CM4 H5 0.00 0.00 300.0 0.0 0.0 IC S2 S3 CM4 CM5 0.00 0.00 180.0 0.0 0.0 IC S3 CM4 CM5 H51 0.00 0.00 180.0 0.0 0.0 IC S3 CM4 CM5 H52 0.00 0.00 60.0 0.0 0.0 IC S3 CM4 CM5 H53 0.00 0.00 300.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI EMS 0.00 ! C3H8S ethylmethylsulfide, Dzung Nguyen GROUP ATOM H1 HGA3 0.09 ATOM H2 HGA3 0.09 ! H1 H4 H5 ATOM H3 HGA3 0.09 ! \ \ / ATOM CM1 CG331 -0.27 ! H2-CM1--CM2 H6 GROUP ! \ / ATOM H4 HGA2 0.09 ! S3--CM4-H7 ATOM H5 HGA2 0.09 ! \ ATOM CM2 CG321 -0.13 ! kevo: symmetrized H8 ATOM S3 SG311 -0.10 ! kevo: symmetrized ATOM CM4 CG331 -0.22 ATOM H6 HGA3 0.09 ATOM H7 HGA3 0.09 ATOM H8 HGA3 0.09 BOND CM1 H1 CM1 H2 CM1 H3 BOND CM1 CM2 CM2 H4 CM2 H5 BOND CM2 S3 S3 CM4 BOND CM4 H6 CM4 H7 CM4 H8 IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0 IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0 IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0 IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0 IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0 IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0 IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0 IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0 IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0 IC CM1 CM2 S3 CM4 0.00 0.00 60.0 0.0 0.0 IC H4 CM2 S3 CM4 0.00 0.00 180.0 0.0 0.0 IC H5 CM2 S3 CM4 0.00 0.00 300.0 0.0 0.0 IC CM2 S3 CM4 H6 0.00 0.00 60.0 0.0 0.0 IC CM2 S3 CM4 H7 0.00 0.00 180.0 0.0 0.0 IC CM2 S3 CM4 H8 0.00 0.00 300.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI IMIA 0.00 ! C3H4N2 Imidazole, adm jr. GROUP ATOM CG CG2R51 -0.05 ! HD1 HE1 ATOM HG HGR52 0.09 ! | / ATOM CD2 CG2R51 0.22 ! ND1--CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.36 ! HG-CG || ATOM HD1 HGP1 0.32 ! \\ || ATOM CE1 CG2R53 0.25 ! CD2--NE2 ATOM HE1 HGR52 0.13 ! | ATOM NE2 NG2R50 -0.70 ! HD2 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG HG DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 DONO HD1 ND1 ACCE NE2 ! for analysis DONO HE1 CE1 DONO HG CG ACCE CE1 ACCE ND1 ACCE CD2 IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 RESI MIMI 0.00 ! C4H6N2 4-methylimidazole, adm jr. GROUP ATOM ND1 NG2R51 -0.36 ! HD1 HE1 ATOM HD1 HGP1 0.32 ! | / ATOM CG CG2R51 -0.05 ! HB1 ND1--CE1 ATOM CB CG331 -0.18 ! | / || ATOM HB1 HGA3 0.09 ! HB2-CB-CG || ATOM HB2 HGA3 0.09 ! | \\ || ATOM HB3 HGA3 0.09 ! HB3 CD2--NE2 GROUP ! | ATOM NE2 NG2R50 -0.70 ! HD2 ATOM CD2 CG2R51 0.22 ATOM HD2 HGR52 0.10 ATOM CE1 CG2R53 0.25 ATOM HE1 HGR52 0.13 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB HB3 DONO HD1 ND1 ACCE NE2 IC CB CG ND1 CE1 1.5421 122.67 180.0 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CD2 NE2 CE1 HE1 1.3165 105.82 180.0 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 180.0 123.39 0.9770 IC CB CG CD2 HD2 1.5421 131.52 0.0 118.30 1.0902 IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 IC CD2 CG CB HB3 0.0 0.0 240.0 0.0 0.0 !IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 !IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 !IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 !IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 !Multiple errors corrected. RESI EIMI 0.00 ! C5H8N2 4-ethylimidazole, adm jr. GROUP ATOM CA CG331 -0.27 ! Optimized charges to minimize group size ATOM HA1 HGA3 0.09 ATOM HA2 HGA3 0.09 ATOM HA3 HGA3 0.09 GROUP ATOM ND1 NG2R51 -0.36 ! HD1 HE1 ATOM HD1 HGP1 0.32 ! | / ATOM CG CG2R51 -0.05 ! HA1 HB1 ND1--CE1 ATOM CB CG321 -0.09 ! \ | / || ATOM HB1 HGA2 0.09 ! HA2-CA--CB-CG || ATOM HB2 HGA2 0.09 ! / | \\ || GROUP ! HA3 HB2 CD2--NE2 ATOM NE2 NG2R50 -0.70 ! | ATOM CD2 CG2R51 0.22 ! HD2 ATOM HD2 HGR52 0.10 ATOM CE1 CG2R53 0.25 ATOM HE1 HGR52 0.13 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 DONO HD1 ND1 ACCE NE2 IC CB CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC CG NE2 *CD2 HD2 0.0 0.0 180.0 0.0 0.0 IC ND1 CD2 *CG CB 0.0 0.0 180.0 0.0 0.0 IC CD2 CG CB CA 0.0 0.0 240.0 0.0 0.0 IC CA CG *CB HB1 0.0 0.0 120.0 0.0 0.0 IC CA CG *CB HB2 0.0 0.0 -120.0 0.0 0.0 IC CG CB CA HA1 0.0 0.0 180.0 0.0 0.0 IC HA1 CB *CA HA2 0.0 0.0 120.0 0.0 0.0 IC HA1 CB *CA HA3 0.0 0.0 -120.0 0.0 0.0 RESI IMIM 1.00 ! C3H5N2 Imidazolium, adm jr. GROUP ATOM CG CG2R51 0.19 ! HD1 HE1 ATOM HG HGR52 0.13 ! | / ATOM CD2 CG2R51 0.19 ! ND1--CE1 ATOM HD2 HGR52 0.13 ! / || GROUP ! HG-CG || ATOM ND1 NG2R52 -0.51 ! \\ || ATOM HD1 HGP2 0.44 ! CD2--NE2 (+) ATOM NE2 NG2R52 -0.51 ! | \ ATOM HE2 HGP2 0.44 ! HD2 HE2 ATOM CE1 CG2R53 0.32 ATOM HE1 HGR53 0.18 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG HG DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 DONO HD1 ND1 DONO HE2 NE2 IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 IC HE1 CE1 NE2 HE2 1.0879 125.00 0.00 125.00 1.0000 RESI EIMM 1.00 ! C5H9N2 Ethyl-Imidazolium, adm jr. GROUP ATOM CA CG331 -0.27 ATOM HA1 HGA3 0.09 ATOM HA2 HGA3 0.09 ATOM HA3 HGA3 0.09 GROUP ATOM CB CG321 -0.05 ! HD1 HE1 ATOM HB1 HGA2 0.09 ! | / ATOM HB2 HGA2 0.09 ! HA1 HB1 ND1--CE1 ATOM CG CG2R51 0.19 ! \ | / || ATOM CD2 CG2R51 0.19 ! HA2-CA--CB-CG || ATOM HD2 HGR52 0.13 ! / | \\ || GROUP ! HA3 HB2 CD2--NE2(+) ATOM ND1 NG2R52 -0.51 ! | \ ATOM HD1 HGP2 0.44 ! HD2 HE2 ATOM NE2 NG2R52 -0.51 ATOM HE2 HGP2 0.44 ATOM CE1 CG2R53 0.32 ATOM HE1 HGR53 0.18 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB NE2 HE2 DOUBLE CD2 CG NE2 CE1 BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 DONO HD1 ND1 ACCE NE2 IC CA CB CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC HA1 CB *CA HA2 0.0000 0.00 120.00 0.00 0.0000 IC HA1 CB *CA HA3 0.0000 0.00 -120.00 0.00 0.0000 IC HA1 CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CG CA *CB HB1 0.0000 0.00 120.00 0.00 0.0000 IC CG CA *CB HB2 0.0000 0.00 -120.00 0.00 0.0000 IC CA CB CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC ND1 CB *CG CD2 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD2 NE2 0.0000 0.00 180.00 0.00 0.0000 IC NE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC CB CG ND1 CE1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC NE2 ND1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 RESI BENZ 0.00 ! C6H6 benzene, adm jr. GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 ATOM CD1 CG2R61 -0.115 ! | | ATOM HD1 HGR61 0.115 ! CD1--CE1 ATOM CD2 CG2R61 -0.115 ! / \ ATOM HD2 HGR61 0.115 ! HG--CG CZ--HZ ATOM CE1 CG2R61 -0.115 ! \ / ATOM HE1 HGR61 0.115 ! CD2--CE2 ATOM CE2 CG2R61 -0.115 ! | | ATOM HE2 HGR61 0.115 ! HD2 HE2 ATOM CZ CG2R61 -0.115 ATOM HZ HGR61 0.115 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ HZ IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 RESI EBEN 0.00 ! C8H10 ethylbenzene, adm jr. GROUP ATOM CG CG2R61 0.000 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 !HA1 HB1 CD1--CE1 ATOM HD1 HGR61 0.115 ! \ | / \ GROUP !HA2-CA--CB--CG CZ--HZ ATOM CD2 CG2R61 -0.115 ! / | \ / ATOM HD2 HGR61 0.115 !HA3 HB2 CD2--CE2 GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 -0.115 ATOM HZ HGR61 0.115 GROUP ATOM CB CG321 -0.18 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CA CG331 -0.27 ATOM HA1 HGA3 0.09 ATOM HA2 HGA3 0.09 ATOM HA3 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ HZ BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 RESI PHEN 0.00 ! C6H6O phenol, adm jr. GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 ATOM HD1 HGR61 0.115 ! // \\ GROUP ! HG--CG CZ--OH ATOM CD2 CG2R61 -0.115 ! \ / \ ATOM HD2 HGR61 0.115 ! CD2==CE2 HH GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 0.11 ATOM OH OG311 -0.53 ATOM HH HGP1 0.42 BOND CD2 CG CE1 CD1 BOND CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OH OH HH DOUBLE CD1 CG CE2 CD2 CZ CE1 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 RESI EPHE 0.00 ! C8H10O p-ethylphenol, adm jr. GROUP ATOM CG CG2R61 0.00 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 !HA1 HB1 CD1--CE1 ATOM HD1 HGR61 0.115 ! \ | / \ GROUP !HA2-CA--CB--CG CZ--OH ATOM CD2 CG2R61 -0.115 ! / | \ / \ ATOM HD2 HGR61 0.115 !HA3 HB2 CD2--CE2 HH GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 0.11 ATOM OH OG311 -0.53 ATOM HH HGP1 0.42 GROUP ATOM CB CG321 -0.18 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CA CG331 -0.27 ATOM HA1 HGA3 0.09 ATOM HA2 HGA3 0.09 ATOM HA3 HGA3 0.09 BOND CD2 CG CE1 CD1 BOND CZ CE2 BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OH OH HH BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 DOUBLE CD1 CG CE2 CD2 CZ CE1 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 RESI PHEO -1.00 ! C6H5O phenoxide, adm jr. GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 ATOM HD1 HGR61 0.115 ! / \ GROUP ! HG--CG CZ--OH (-) ATOM CD2 CG2R61 -0.115 ! \ / ATOM HD2 HGR61 0.115 ! CD2--CE2 GROUP ! | | ATOM CE1 CG2R61 -0.60 ! HD2 HE2 ATOM HE1 HGR61 0.28 ATOM CE2 CG2R61 -0.60 ATOM HE2 HGR61 0.28 ATOM CZ CG2R61 0.40 ATOM OH OG312 -0.76 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OH IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 RESI APNH 0.00 ! C7H12N2O2 acetyl-prolineamide (aka AP2, APAM), R. Dunbrack !HY1 HY2 HY3 ATOM N NG2S0 -0.29 ! \ | / ATOM CA CG3C51 0.02 ! CAY ATOM CB CG3C52 -0.18 ! | ATOM CG CG3C52 -0.18 ! OY=CY HD1 HD2 ATOM CD CG3C52 0.00 ! \ \ / ATOM CY CG2O1 0.51 ! N---CD HG1 ATOM OY OG2D1 -0.51 ! | \ / ATOM C CG2O1 0.51 ! | CG ATOM HA HGA1 0.09 ! | / \ ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 ATOM HB2 HGA2 0.09 ! | / \ ATOM HG1 HGA2 0.09 ! | HB1 HB2 ATOM HG2 HGA2 0.09 ! O=C ATOM HD1 HGA2 0.09 ! | ATOM HD2 HGA2 0.09 ! NT ATOM CAY CG331 -0.27 ! / \ ATOM HY1 HGA3 0.09 ! HT1 HT2 ATOM HY2 HGA3 0.09 ATOM HY3 HGA3 0.09 ATOM O OG2D1 -0.51 ATOM NT NG2S2 -0.62 ATOM HT1 HGP1 0.31 ATOM HT2 HGP1 0.31 BOND CY N CAY HY1 CAY HY2 CAY HY3 BOND CY CAY N CA CA CB CB CG CG CD CD N BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND C CA C NT NT HT1 NT HT2 DOUBLE C O CY OY IMPR CY CAY N OY IMPR C CA NT O DONOR HT1 NT DONOR HT2 NT ACCEPTOR OY CY ACCEPTOR O C ! Improper ICs IC CY CA *N CD 0.00 0.00 180.00 0.00 0.00 IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 IC N CAY *CY OY 0.00 0.00 180.00 0.00 0.00 ! Backbone + Peptide bond IC's IC OY CY N CA 0.00 0.00 0.00 0.00 0.00 !Omega IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !Omega IC CY N CA C 0.00 120.64 -60.00 0.00 0.00 !Psi IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi IC CAY CY N CD 0.00 0.00 0.00 120.64 0.00 IC CY N CD CG 0.00 0.00 168.60 103.28 0.00 IC CY N CA CB 0.00 0.00 168.64 103.34 0.00 ! Ring IC's IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 ! Carbonyl IC's IC CD N CA C 0.00 112.90 120.00 108.00 0.00 ! Hydrogen IC's IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 IC OY CY CAY HY1 0.00 0.00 90.00 0.00 0.00 IC CY HY1 *CAY HY2 0.00 0.00 120.00 0.00 0.00 IC CY HY1 *CAY HY3 0.00 0.00 -120.00 0.00 0.00 RESI PDIP 0.00 ! C8H14N2O2 proline dipeptide !HY1 HY2 HY3 ATOM N NG2S0 -0.29 ! \ | / ATOM CA CG3C51 0.02 ! CAY ATOM CB CG3C52 -0.18 ! | ATOM CG CG3C52 -0.18 ! OY=CY HD1 HD2 ATOM CD CG3C52 0.00 ! \ \ / ATOM CY CG2O1 0.51 ! N---CD HG1 ATOM OY OG2D1 -0.51 ! | \ / ATOM C CG2O1 0.51 ! | CG ATOM HA HGA1 0.09 ! | / \ ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 ATOM HB2 HGA2 0.09 ! | / \ ATOM HG1 HGA2 0.09 ! | HB1 HB2 ATOM HG2 HGA2 0.09 ! O=C ATOM HD1 HGA2 0.09 ! | ATOM HD2 HGA2 0.09 ! NT ATOM CAY CG331 -0.27 ! / \ ATOM HY1 HGA3 0.09 ! HT1 CR-HR3 ATOM HY2 HGA3 0.09 ! / \ ATOM HY3 HGA3 0.09 ! HR1 HR2 ATOM O OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT1 HGP1 0.31 ATOM CR CG331 -0.11 ATOM HR1 HGA3 0.09 ATOM HR2 HGA3 0.09 ATOM HR3 HGA3 0.09 BOND CY N CAY HY1 CAY HY2 CAY HY3 BOND CY CAY N CA CA CB CB CG CG CD CD N BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND C CA C NT NT HT1 NT CR BOND CR HR1 CR HR2 CR HR3 DOUBLE C O CY OY IMPR CY CAY N OY IMPR C CA NT O DONOR HT1 NT ACCEPTOR OY CY ACCEPTOR O C IC CAY CY N CA 1.4871 118.91 174.70 123.38 1.4590 IC CY N CA C 1.3234 123.38 -72.54 111.46 1.5357 IC N CA C NT 1.4590 111.46 117.46 121.78 1.3479 IC CY CA *N CD 1.3234 123.38 176.71 112.56 1.4667 IC N C *CA CB 1.4590 111.46 114.78 112.03 1.5409 IC N C *CA HA 1.4590 111.46 -122.11 109.86 1.0785 IC N CAY *CY OY 1.3234 118.91 -179.24 119.14 1.2260 IC OY CY N CA 1.2260 121.95 -6.08 123.38 1.4590 IC CAY CY N CA 1.4871 118.91 174.70 123.38 1.4590 IC CY N CA C 1.3234 123.38 -72.54 111.46 1.5357 IC N CA C NT 1.4590 111.46 117.46 121.78 1.3479 IC CAY CY N CD 1.4871 118.91 -1.63 123.97 1.4667 IC CY N CD CG 1.3234 123.97 171.81 105.08 1.5319 IC CY N CA CB 1.3234 123.38 167.19 102.97 1.5409 IC N CA CB CG 1.4590 102.97 30.57 104.52 1.5340 IC CA CB CG CD 1.5409 104.52 -33.72 103.37 1.5319 IC CB CG CD N 1.5340 103.37 23.86 105.08 1.4667 IC CG CD N CA 1.5319 105.08 -4.88 112.56 1.4590 IC CD N CA CB 1.4667 112.56 -16.10 102.97 1.5409 IC CD N CA C 1.4667 112.56 104.17 111.46 1.5357 IC CD N CA HA 1.4667 112.56 -133.77 109.94 1.0785 IC N CA CB HB1 1.4590 102.97 153.44 113.27 1.1091 IC N CA CB HB2 1.4590 102.97 -85.51 108.72 1.1129 IC CA CB CG HG1 1.5409 104.52 82.51 109.30 1.1137 IC CA CB CG HG2 1.5409 104.52 -155.89 112.80 1.1079 IC CB CG CD HD1 1.5340 103.37 144.10 110.20 1.1134 IC CB CG CD HD2 1.5340 103.37 -93.57 110.40 1.1126 IC NT CA *C O 1.3479 121.78 179.58 119.57 1.2276 IC CA C NT HT1 1.5357 121.78 -178.24 114.38 0.9952 IC N CY CAY HY1 1.3234 118.91 177.72 108.99 1.1118 IC HY1 CY *CAY HY2 1.1118 108.99 119.00 110.21 1.1099 IC HY1 CY *CAY HY3 1.1118 108.99 -119.34 110.53 1.1094 IC C HT1 *NT CR 1.3479 114.38 -176.13 117.94 1.4463 IC C NT CR HR1 1.3479 127.54 -178.11 110.27 1.1125 IC C NT CR HR2 1.3479 127.54 62.09 110.97 1.1130 IC C NT CR HR3 1.3479 127.54 -58.81 110.79 1.1141 RESI PNH2 1.00 ! C5H11N2O prolineamide (aka TP2, PAMD), R. Dunbrack ATOM N NG3P2 -0.07 ATOM HN1 HGP2 0.24 ATOM HN2 HGP2 0.24 ATOM CD CG3C54 0.16 ATOM CB CG3C52 -0.18 ! HN1 HD1 HD2 ATOM CG CG3C52 -0.18 ! \ \ / ATOM CA CG3C53 0.16 ! HN2--N---CD HG1 ATOM C CG2O1 0.51 ! |(+) \ / ATOM O OG2D1 -0.51 ! | CG ATOM HA HGA1 0.09 ! | / \ ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 ATOM HB2 HGA2 0.09 ! | / \ ATOM HG1 HGA2 0.09 ! | HB1 HB2 ATOM HG2 HGA2 0.09 ! O=C ATOM HD1 HGA2 0.09 ! | ATOM HD2 HGA2 0.09 ! NT ATOM NT NG2S2 -0.62 ! / \ ATOM HT1 HGP1 0.31 ! HT1 HT2 ATOM HT2 HGP1 0.31 BOND HN1 N HN2 N N CA CA CB CB CG CG CD CD N BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND C CA C NT NT HT1 NT HT2 DOUBLE C O IMPR C CA NT O DONOR HT1 NT DONOR HT2 NT DONOR HN1 N DONOR HN2 N ACCEPTOR O C ! Improper ICs IC HN1 CA *N CD 0.00 0.00 120.00 0.00 0.00 IC HN2 CA *N HN1 0.00 0.00 120.00 0.00 0.00 IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 ! Backbone + Peptide bond IC's IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi ! Ring IC's IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 ! Carbonyl IC's IC CD N CA C 0.00 112.90 120.00 108.00 0.00 ! Hydrogen IC's IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 RESI ETHA 0.00 ! C2H6 ethane GROUP ATOM H11 HGA3 0.09 ! H11 H21 ATOM H12 HGA3 0.09 ! \ / ATOM H13 HGA3 0.09 ! H12-C1--C2-H22 ATOM C1 CG331 -0.27 ! / \ GROUP ! H13 H23 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 ATOM C2 CG331 -0.27 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 C2 H21 C2 H22 C2 H23 IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 IC C1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 IC C1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 RESI PRPA 0.00 ! C3H8 propane, adm jr. GROUP ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C1 CG331 -0.27 ! H11 H21 H31 ATOM C2 CG321 -0.18 ! \ | / ATOM H21 HGA2 0.09 ! H12-C1--C2--C3-H32 ATOM H22 HGA2 0.09 ! / | \ ATOM H31 HGA3 0.09 ! H13 H22 H33 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 ATOM C3 CG331 -0.27 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 C3 H33 IC C1 C2 C3 H31 0.00 0.00 180.0 0.0 0.0 IC C2 H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 IC C2 H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 IC C3 C2 C1 H11 0.00 0.00 180.0 0.0 0.0 IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.0 0.0 IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.0 0.0 RESI BUTA 0.00 ! C4H10 butane GROUP ATOM H11 HGA3 0.09 ! H11 H21 H31 H41 ATOM H12 HGA3 0.09 ! \ | | / ATOM H13 HGA3 0.09 ! H12-C1--C2--C3--C4-H42 ATOM C1 CG331 -0.27 ! / | | \ GROUP ! H13 H22 H33 H43 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C2 CG321 -0.18 GROUP ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C3 CG321 -0.18 GROUP ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 ATOM C4 CG331 -0.27 BOND H11 C1 H12 C1 H13 C1 C1 C2 BOND H21 C2 H22 C2 C2 C3 BOND H31 C3 H32 C3 C3 C4 BOND H41 C4 H42 C4 H43 C4 IC C1 C2 C3 C4 0.00 0.00 180.0 0.0 0.0 IC C3 C2 C1 H11 0.00 0.00 180.0 0.0 0.0 IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.0 0.0 IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.0 0.0 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.0 0.0 IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.0 0.0 IC C2 C3 C4 H41 0.00 0.00 180.0 0.0 0.0 IC C3 H41 *C4 H42 0.00 0.00 120.0 0.0 0.0 IC C3 H41 *C4 H43 0.00 0.00 -120.0 0.0 0.0 RESI IBUT 0.00 ! C4H10 Iso-butane, S. Fischer GROUP ATOM CT CG311 -0.09 ! H12 ATOM HT HGA1 0.09 ! | GROUP ! H11-C1-H13 ATOM C1 CG331 -0.27 ! | ATOM H11 HGA3 0.09 ! CT-HT ATOM H12 HGA3 0.09 ! / \ ATOM H13 HGA3 0.09 ! / \ GROUP ! H21-C2 C3-H31 ATOM C2 CG331 -0.27 ! / | | \ ATOM H21 HGA3 0.09 ! H22 H23 H33 H32 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND CT C1 CT C2 CT C3 CT HT BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC C1 C2 *CT C3 0.00 0.00 120.0 0.0 0.0 IC C1 C2 *CT HT 0.00 0.00 -120.0 0.0 0.0 IC C2 CT C1 H11 0.00 0.00 180.0 0.0 0.0 IC CT H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC CT H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC C1 CT C2 H21 0.00 0.00 180.0 0.0 0.0 IC CT H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 IC CT H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 IC C1 CT C3 H31 0.00 0.00 180.0 0.0 0.0 IC CT H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 IC CT H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 RESI PENT 0.00 ! C5H12 pentane, adm jr. GROUP ATOM C1 CG331 -0.27 ! H11 H21 H31 H41 H51 ATOM H11 HGA3 0.09 ! \ | | | / ATOM H12 HGA3 0.09 ! H12-C1--C2--C3--C4--C5-H52 ATOM H13 HGA3 0.09 ! / | | | \ GROUP ! H13 H22 H33 H42 H53 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 BOND C5 H52 C5 H53 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 IC C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI OCOH 0.00 ! C8H18O OCTANOL GROUP ATOM C1 CG321 0.05 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM O1 OG311 -0.65 ATOM HO1 HGP1 0.42 GROUP ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 GROUP ATOM C6 CG321 -0.18 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 GROUP ATOM C7 CG321 -0.18 ATOM H71 HGA2 0.09 ATOM H72 HGA2 0.09 GROUP ATOM C8 CG331 -0.27 ATOM H81 HGA3 0.09 ATOM H82 HGA3 0.09 ATOM H83 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C1 O1 O1 HO1 BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 BOND C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 BOND C8 H81 C8 H82 C8 H83 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 H83 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 O1 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC C6 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 IC C7 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 IC C7 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI CO2 0.00 ! CO2 Carbon Dioxide, John Straub GROUP ATOM C CG2O7 0.60 ATOM OC1 OG2D5 -0.30 ATOM OC2 OG2D5 -0.30 BOND OC1 C OC2 C RESI CO3 -2.00 ! CO3 ionized carbonate, adm jr., aug 2001 !As organic carbonates and carbamates are uncharged, we definitely want to use !other (ester respectively amide?) atom typing for those. This leaves the atom !typing for their (-1) counterparts undefined, but these are unstable anyway... GROUP ATOM C1 CG2O6 1.42 ATOM O1 OG2D2 -1.14 ATOM O2 OG2D2 -1.14 ATOM O3 OG2D2 -1.14 BOND C1 O1 C1 O2 C1 O3 ! required for out-of-plane vibrations IMPR C1 O1 O2 O3 IC O2 O1 *C1 O3 0.0000 0.00 180.00 0.00 0.0000 IC O3 O2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 !redundant definition needed to enable seeding. RESI C3 0.00 ! C3H6 Cyclopropane Model Compound GROUP ! JMW and CBP 16 April 2004 ATOM C1 CG3C31 -0.18 ATOM H11 HGA2 0.09 ! H11 H12 ATOM H12 HGA2 0.09 ! \ / GROUP ! C1 ATOM C2 CG3C31 -0.18 ! / \ ATOM H21 HGA2 0.09 ! H21--C2----C3--H31 ATOM H22 HGA2 0.09 ! | | GROUP ! H22 H32 ATOM C3 CG3C31 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 BOND C1 C2 C2 C3 C3 C1 BOND C1 H11 C1 H12 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 IC C1 C2 C3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C3 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC C2 C1 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C1 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 PATCHING FIRST NONE LAST NONE !toppar_all22_prot_aldehydes.str !acetaldehyde additions, ssc & adm, jr., 2/01 RESI AALD 0.00 ! C2H4O Acetaldehyde, adm, Oct 2008 GROUP ATOM HA HGR52 0.09 ! HB3 ATOM C CG2O4 0.20 ! | ATOM O OG2D1 -0.40 !HB1-CB-HB2 ATOM CB CG331 -0.16 ! | ATOM HB1 HGA3 0.09 ! O=C ATOM HB2 HGA3 0.09 ! | ATOM HB3 HGA3 0.09 ! HA BOND HA C C CB CB HB1 CB HB2 CB HB3 DOUB C O IMPR C CB O HA ACCE O IC O C CB HB1 1.2074 123.73 -0.46 108.58 1.1053 IC HB2 CB C O 1.0625 110.65 118.23 123.73 1.2074 IC HB3 CB C O 1.0898 105.98 -126.83 123.73 1.2074 IC HA O *C CB 1.1347 126.86 -176.51 123.73 1.5462 PATCHING FIRST NONE LAST NONE RESI PALD 0.00 ! C3H6O Propionaldehyde GROUP ATOM O OG2D1 -0.40 ! HG3 ATOM C CG2O4 0.20 ! | ATOM CB CG321 -0.07 !HG1-CG-HG2 ATOM HB1 HGA2 0.09 ! | ATOM HB2 HGA2 0.09 !HB1-CB-HB2 ATOM HA HGR52 0.09 ! | GROUP ! O=C ATOM CG CG331 -0.27 ! | ATOM HG1 HGA3 0.09 ! HA ATOM HG2 HGA3 0.09 ATOM HG3 HGA3 0.09 BOND HA C C CB CB HB1 CB HB2 BOND CB CG CG HG1 CG HG3 CG HG2 DOUBLE C O IMPR C CB O HA ACCE O IC O C CB CG 0.0 0.0 0.0 0.0 0.0 IC CG CB C HA 0.0 0.0 180.0 0.0 0.0 IC HB1 CB C O 0.0 0.0 120.0 0.0 0.0 IC HB2 CB C O 0.0 0.0 -120.0 0.0 0.0 IC C CB CG HG1 0.0 0.0 180.0 0.0 0.0 IC C CB CG HG2 0.0 0.0 60.0 0.0 0.0 IC C CB CG HG3 0.0 0.0 -60.0 0.0 0.0 PATCHING FIRST NONE LAST NONE RESI CALD 0.00 ! C2H3ClO Chloroacetaldehyde !KEVO: charges adjusted to reflect updated aldehyde AND aliphatic chlorine L-J. !==> RE-OPTIMIZE!!! GROUP ! CL ATOM O OG2D1 -0.40 ! | ATOM C CG2O4 0.20 !HB1-CB-HB2 ATOM CB CG321 -0.03 ! | ATOM HB1 HGA2 0.09 ! O=C ATOM HB2 HGA2 0.09 ! | ATOM CL CLGA1 -0.04 ! HA ATOM HA HGR52 0.09 BOND HA C C CB CB HB1 CB HB2 BOND CB CL DOUBLE C O IMPR C CB O HA ACCE O IC O C CB CL 0.0 0.0 180.0 0.0 0.0 IC CL CB C HA 0.0 0.0 0.0 0.0 0.0 IC HA O *C CB 0.0 0.0 0.0 0.0 0.0 IC CL C *CB HB1 0.0 0.0 120.0 0.0 0.0 IC HB1 C *CB HB2 0.0 0.0 120.0 0.0 0.0 PATCHING FIRST NONE LAST NONE !benzaldehyde additions, ssc & adm, jr., 2/01 RESI BALD 0.00 ! C7H6O Benzaldehyde GROUP ATOM HA HGR52 0.08 ! HZ ATOM C CG2O4 0.24 ! | ATOM O OG2D1 -0.41 ! CZ ATOM CG CG2R61 0.09 ! // \ GROUP !HE1-CE1 CE2-HE2 ATOM CD1 CG2R61 -0.115 ! | || ATOM HD1 HGR61 0.115 !HD1-CD1 CD2-HD2 GROUP ! \\ / ATOM CE1 CG2R61 -0.115 ! CG ATOM HE1 HGR61 0.115 ! | GROUP ! O=C ATOM CZ CG2R61 -0.115 ! | ATOM HZ HGR61 0.115 ! HA GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 BOND HA C C CG CG CD1 CG CD2 BOND CD1 HD1 CD2 HD2 CD1 CE1 CD2 CE2 BOND CE1 HE1 CE2 HE2 CE1 CZ CE2 CZ BOND CZ HZ DOUBLE C O IMPR C CG O HA ACCE O IC O C CG CD1 0.0 0.0 0.0 0.0 0.0 IC HA O *C CG 0.0 0.0 180.0 0.0 0.0 IC CD1 C *CG CD2 0.0 0.0 -177.9600 0.0 0.0 IC C CG CD1 CE1 0.0 0.0 -177.3700 0.0 0.0 IC CE1 CG *CD1 HD1 0.0 0.0 179.7000 0.0 0.0 IC C CG CD2 CE2 0.0 0.0 177.2000 0.0 0.0 IC CE2 CG *CD2 HD2 0.0 0.0 -178.6900 0.0 0.0 IC CG CD1 CE1 CZ 0.0 0.0 -0.1200 0.0 0.0 IC CZ CD1 *CE1 HE1 0.0 0.0 -179.6900 0.0 0.0 IC CZ CD2 *CE2 HE2 0.0 0.0 -179.9300 0.0 0.0 IC CE1 CE2 *CZ HZ 0.0 0.0 179.5100 0.0 0.0 PATCHING FIRST NONE LAST NONE !toppar_all22_prot_fluoro_alkanes.str RESI FETH 0.00 ! C2H5F fluoroethane, adm jr., 4/99 GROUP ATOM H13 HGA3 0.09 ATOM C1 CG331 -0.21 ATOM C2 CG322 -0.06 ATOM F21 FGA1 -0.22 ATOM H22 HGA6 0.11 ATOM H23 HGA6 0.11 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 BOND C2 F21 C2 H22 C2 H23 IC H13 C1 C2 F21 1.1111 110.55 180.00 109.78 1.3721 IC H13 C1 C2 H22 1.1111 110.55 60.02 111.56 1.0839 IC H13 C1 C2 H23 1.1111 110.55 -60.02 111.56 1.0839 IC C1 C2 H22 H23 1.5188 111.56 -122.50 36.33 1.7464 IC H13 C2 *C1 H11 1.1111 110.55 -120.29 110.55 1.1111 IC H13 C2 *C1 H12 1.1111 110.55 120.29 110.55 1.1111 PATC FIRS NONE LAST NONE RESI DFET 0.00 ! C2H4F2 difluoroethane, adm jr., 4/99 GROUP ATOM H13 HGA3 0.09 ATOM C1 CG331 -0.23 ATOM C2 CG312 0.24 ATOM H21 HGA7 0.10 ATOM F22 FGA2 -0.19 ATOM F23 FGA2 -0.19 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 BOND C2 F23 C2 F22 C2 H21 IC H13 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 IC C1 C2 F23 F22 0.00 0.00 0.0 0.0 0.0 IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0 IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0 IC H12 C1 C2 H21 0.00 0.00 -60.0 0.0 0.0 IC H11 C1 C2 H21 0.00 0.00 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TFET 0.00 ! C2H3F3 trifluoroethane GROUP ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C1 CG331 -0.20 ATOM F21 FGA3 -0.15 ATOM F22 FGA3 -0.15 ATOM F23 FGA3 -0.15 ATOM C2 CG302 0.38 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 C2 F21 C2 F22 C2 F23 IC H13 C1 C2 F21 0.00 0.00 180.0 0.0 0.0 IC C1 C2 F22 F23 0.00 0.00 0.0 0.0 0.0 IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0 IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0 IC H11 C1 C2 F21 0.00 0.00 60.0 0.0 0.0 IC H12 C1 C2 F21 0.00 0.00 -60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TFE 0.00 ! C2H3F3O trifluoroethanol GROUP ATOM O1 OG311 -0.59 ATOM HO1 HGP1 0.41 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C1 CG321 0.08 ATOM F21 FGA3 -0.14 ATOM F22 FGA3 -0.14 ATOM F23 FGA3 -0.14 ATOM C2 CG302 0.34 BOND C1 H11 C1 H12 C1 O1 O1 HO1 BOND C1 C2 C2 F21 C2 F22 C2 F23 IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 C2 F21 0.0000 0.00 180.00 0.00 0.0000 IC F21 C1 *C2 F22 0.0000 0.00 120.00 0.00 0.0000 IC F21 C1 *C2 F23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE !toppar_all22_prot_pyridines.str RESI PYR1 0.00 ! C5H5N pyridine, yin GROUP ATOM N1 NG2R60 -0.600 ATOM C2 CG2R61 0.180 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R61 -0.115 ATOM C5 CG2R61 -0.115 ATOM C6 CG2R61 0.180 ATOM H2 HGR62 0.120 ATOM H3 HGR61 0.115 ATOM H4 HGR61 0.115 ATOM H5 HGR61 0.115 ATOM H6 HGR62 0.120 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 N1 BOND C2 H2 C3 H3 C4 H4 C5 H5 C6 H6 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI 4AP2 0.00 ! C5H6N2 4-aminopyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 -0.115 ATOM CG CG2R61 0.050 ATOM CE2 CG2R61 0.180 ATOM CD2 CG2R61 -0.115 ATOM NG NG2S3 -0.850 ATOM HE1 HGR62 0.120 ATOM HD1 HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM HG11 HGP4 0.400 ATOM HG12 HGP4 0.400 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 BOND CG NG NG HG11 NG HG12 IMPR NG HG12 HG11 CG IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3APY 0.00 ! C5H6N2 3-aminopyridine, yin GROUP ! HD11 HD12 ATOM CG CG2R61 -0.115 ! \ / ATOM HG HGR61 0.115 ! ND1 HE1 GROUP ! \ | ATOM CD1 CG2R61 0.090 ! CD1--CE1 ATOM ND1 NG2S3 -0.840 ! / \ ATOM HD11 HGP4 0.370 ! HG--CG NZ ATOM HD12 HGP4 0.380 ! \ / GROUP ! CD2--CE2 ATOM CD2 CG2R61 -0.115 ! | | ATOM HD2 HGR61 0.115 ! HD2 HE2 GROUP ATOM CE1 CG2R61 0.180 ATOM HE1 HGR62 0.120 ATOM CE2 CG2R61 0.180 ATOM HE2 HGR62 0.120 ATOM NZ NG2R60 -0.600 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 CE1 HE1 BOND CE2 HE2 BOND CD1 ND1 ND1 HD11 ND1 HD12 IMPR ND1 HD12 HD11 CD1 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 IC HD11 CD1 *ND1 HD12 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 RESI 34AP 0.00 ! C5H7N3 3,4-diaminopyridine, adm jr. GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.120 ATOM CG CG2R61 0.070 ATOM CE2 CG2R61 0.180 ATOM CD2 CG2R61 -0.115 ATOM ND1 NG2S3 -0.850 ATOM NG NG2S3 -0.850 ATOM HE1 HGR62 0.120 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM HD11 HGP4 0.350 ATOM HD12 HGP4 0.380 ATOM HG11 HGP4 0.390 ATOM HG12 HGP4 0.390 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CD2 HD2 CE1 HE1 BOND CE2 HE2 BOND CD1 ND1 ND1 HD11 ND1 HD12 BOND CG NG NG HG11 NG HG12 IMPR ND1 HD12 HD11 CD1 IMPR NG HG12 HG11 CG IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 IC HD11 CD1 *ND1 HD12 0.0000 0.0000 120.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3CPY -1.00 ! C6H4NO2 pyridine-3-carboxylate (niacinate), yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 -0.10 ATOM CG CG2R61 -0.155 ATOM CE2 CG2R61 0.180 ! O1 HG ATOM CD2 CG2R61 -0.115 ! \ | ATOM HE1 HGR62 0.120 ! (-) ) CD3 CG ATOM HG HGR61 0.155 ! / \ / \\ ATOM HD2 HGR61 0.115 ! O2 CD1 CD2--HD2 ATOM HE2 HGR62 0.120 ! || | ATOM CD3 CG2O3 0.62 ! HE1--CE1 CE2--HE2 ATOM O1 OG2D2 -0.76 ! \ // ATOM O2 OG2D2 -0.76 ! NZ BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 CE1 HE1 BOND CE2 HE2 BOND CD1 CD3 CD3 O1 DOUB CD3 O2 IMPR CD3 O2 O1 CD1 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 RESI 3CB -1.00 ! C7H5O2 benzoate GROUP ATOM CZ CG2R61 -0.115 ATOM CE1 CG2R61 -0.115 ATOM CD1 CG2R61 -0.100 ATOM CG CG2R61 -0.115 ATOM CE2 CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR61 0.115 ATOM HZ HGR61 0.115 ATOM CD3 CG2O3 0.620 ATOM O1 OG2D2 -0.760 ATOM O2 OG2D2 -0.760 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 CD3 CD3 O1 BOND CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ HZ DOUB CD3 O2 IMPR CD3 O2 O1 CD1 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 RESI 3FLP 0.00 ! C5H4FN 3-fluoropyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.220 ATOM CD1 CG2R66 0.170 ATOM CG CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM CD2 CG2R61 -0.115 ATOM HE1 HGR62 0.120 ATOM F1 FGR1 -0.210 !charge similar to difluorotoluene ATOM HG HGR62 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD1 F1 CD2 HD2 CE1 HE1 BOND CE2 HE2 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 F1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3ALP 0.00 ! C6H5NO 3-pyridinecarboxaldehyde, 3-formylpyridine, nicotinaldehyde, yin GROUP ATOM NZ NG2R60 -0.600 ! H3 HG ATOM CE1 CG2R61 0.180 ! \ | ATOM CD1 CG2R61 0.09 ! CD3 CG ATOM CG CG2R61 -0.115 ! // \ / \\ ATOM CD2 CG2R61 -0.115 ! O1 CD1 CD2--HD2 ATOM CE2 CG2R61 0.180 ! || | ATOM HE1 HGR62 0.120 ! HE1--CE1 CE2--HE2 ATOM HG HGR61 0.115 ! \ // ATOM HD2 HGR61 0.115 ! NZ ATOM HE2 HGR62 0.120 ATOM CD3 CG2O4 0.24 !benzaldehyde ATOM O1 OG2D1 -0.41 !benzaldehyde ATOM H3 HGR52 0.08 !benzaldehyde BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 CE1 HE1 BOND CE2 HE2 BOND CD1 CD3 CD3 H3 DOUB CD3 O1 IMPR CD3 CD1 O1 H3 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 IC O1 CD1 *CD3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 RESI 3HOP 0.000 ! C5H5NO 3-hydroxypyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CG CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM HE1 HGR62 0.120 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM CD1 CG2R61 0.11 !phenol ATOM OH OG311 -0.53 !phenol ATOM HO1 HGP1 0.42 !phenol BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD1 OH CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HO1 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 OH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 OH CD2 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3MEP 0.00 ! C6H7N 3-methylpyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.000 ! H32 H33 ATOM CG CG2R61 -0.115 ! \ / ATOM CD2 CG2R61 -0.115 ! H31--CD3 HE1 ATOM CE2 CG2R61 0.180 ! \ | ATOM HE1 HGR62 0.120 ! CD1--CE1 ATOM HG HGR61 0.115 ! / \ ATOM HD2 HGR61 0.115 ! HG--CG NZ ATOM HE2 HGR62 0.120 ! \ / ATOM CD3 CG331 -0.27 ! CD2--CE2 ATOM H31 HGA3 0.09 ! | | ATOM H32 HGA3 0.09 ! HD2 HE2 ATOM H33 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD1 CD3 CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD3 H31 CD3 H32 CD3 H33 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CD1 CD3 H31 0.0000 0.0000 60.0000 0.0000 0.0000 IC CE1 CD1 CD3 H32 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 H33 0.0000 0.0000 300.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3ETP 0.00 ! C7H9N ethylpyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.000 ATOM CG CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM HE1 HGR62 0.120 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM CD3 CG321 -0.18 !aliphatic, corresponds to new CT2, HA2 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG331 -0.27 !aliphatic, corresponds to new CT3, HA3 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD1 CD3 CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD3 H11 CD3 H12 CD3 C2 BOND H21 C2 H22 C2 H23 C2 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CD1 CD3 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD3 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD3 H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3BPY 0.00 ! C9H13N butylpyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.000 ATOM CG CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM CD2 CG2R61 -0.115 ATOM HE1 HGR62 0.120 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM CD3 CG321 -0.18 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 CE1 HE1 CE2 HE2 BOND CD1 CD3 CD3 H11 CD3 H12 BOND CD3 C2 C2 C3 C3 C4 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 C4 H43 IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CD1 CD3 C2 C3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD3 C3 *C2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC CD3 C3 *C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CD3 C2 C3 C4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H31 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C4 *C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2 C3 C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3CYP 0.00 ! C6H4N2 3-Cyanopyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ! N3C ATOM CD1 CG2R61 0.100 ! \\\ ATOM CG CG2R61 -0.115 ! C3N HE1 ATOM CD2 CG2R61 -0.115 ! \ | ATOM CE2 CG2R61 0.180 ! CD1--CE1 ATOM HE1 HGR62 0.120 ! / \ ATOM HG HGR61 0.115 ! HG--CG NZ ATOM HD2 HGR61 0.115 ! \ / ATOM HE2 HGR62 0.120 ! CD2--CE2 ATOM C3N CG1N1 0.360 ! | | ATOM N3C NG1T1 -0.460 ! HD2 HE2 ! Original charges after bringing HE1 and HE2 in line with the other pyridines. !ATOM NZ NG2R60 -0.600 !ATOM CE1 CG2R61 0.180 ! N3C !ATOM CD1 CG2R61 0.080 ! \\\ !ATOM CG CG2R61 -0.120 ! C3N HE1 !ATOM CD2 CG2R61 -0.115 ! \ | !ATOM CE2 CG2R61 0.180 ! CD1--CE1 !ATOM HE1 HGR62 0.120 ! / \ !ATOM HG HGR61 0.140 ! HG--CG NZ !ATOM HD2 HGR61 0.115 ! \ / !ATOM HE2 HGR62 0.120 ! CD2--CE2 !ATOM C3N CG1N1 0.360 ! | | !ATOM N3C NG1T1 -0.460 ! HD2 HE2 !! Partially optimized charges with !! - Dipoles and H2O interactions substantially better !! - DHvap slightly worse (but not really significant) !! - Not transferable BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 C3N BOND C3N N3C IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 C3N 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3C C3N CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3ACP 0.00 ! C7H7NO 3-acetylpyridine, yin GROUP ATOM NZ NG2R60 -0.600 ! HC2 HC3 ATOM CE1 CG2R61 0.180 ! \ / ATOM CD1 CG2R61 0.070 ! HC1--CH3 HG ATOM CG CG2R61 -0.115 ! \ | ATOM CD2 CG2R61 -0.115 ! C CG ATOM CE2 CG2R61 0.180 ! //\ / \\ ATOM HE1 HGR62 0.120 ! O CD1 CD2--HD2 ATOM HG HGR61 0.115 ! || | ATOM HD2 HGR61 0.115 ! HE1--CE1 CE2--HE2 ATOM HE2 HGR62 0.120 ! \ // ATOM C CG2O5 0.360 ! NZ ATOM O OG2D3 -0.470 ATOM CH3 CG331 -0.230 !aliphatic, corresponds to new CT3, HA3 ATOM HC1 HGA3 0.090 ATOM HC2 HGA3 0.090 ATOM HC3 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 C C CH3 BOND HC1 CH3 HC2 CH3 HC3 CH3 DOUB C O IMPR C CD1 CH3 O IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CH3 C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CH3 CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC O C CH3 HC1 0.0000 0.0000 180.0000 0.0000 0.0000 IC O C CH3 HC2 0.0000 0.0000 60.0000 0.0000 0.0000 IC O C CH3 HC3 0.0000 0.0000 -60.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3NAP 0.00 ! C6H6N2O Really just unprotonated oxidized nicotinamide, GROUP ! aka. "nicotinamide". Other correct names include: ATOM NZ NG2R60 -0.600 ! 3-pyridinecarboxamide, 3-amidopyridine, ATOM CE1 CG2R61 0.180 ! 3-(aminocarbonyl)pyridine, yin ATOM CD1 CG2R61 -0.020 ATOM CG CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ! HT ATOM CE2 CG2R61 0.180 ! / ATOM HE1 HGR62 0.120 ! Hc--N HG ATOM HG HGR61 0.115 ! \ | ATOM HD2 HGR61 0.115 ! C CG ATOM HE2 HGR62 0.120 ! //\ / \\ ATOM C CG2O1 0.630 ! O CD1 CD2--HD2 ATOM O OG2D1 -0.460 ! || | ATOM N NG2S2 -0.900 ! HE1--CE1 CE2--HE2 ATOM HC HGP1 0.390 ! \ // ATOM HT HGP1 0.360 ! NZ BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 C C N BOND HC N HT N DOUB C O IMPR C CD1 N O IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC HC N C O 0.0000 0.0000 0.0000 0.0000 0.0000 IC HT N C O 0.0000 0.0000 180.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3CAP 0.00 ! C6H7NO carbinol-pyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.000 ATOM CG CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM HE1 HGR62 0.120 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 GROUP ATOM CD3 CG321 0.05 !aliphatic, corresponds to new CT2, HA2 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM OH OG311 -0.65 ATOM HO HGP1 0.42 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 CD3 CD3 OH OH HO BOND CD3 H11 CD3 H12 IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC NZ CE1 CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CD1 CD3 OH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CD3 OH HO 0.0000 0.0000 180.0000 0.0000 0.0000 IC OH CD1 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 IC OH CD1 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3PHP 0.00 ! C11H9N 3-phenyl-pyridine, yin GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R67 0.000 ATOM CG CG2R61 -0.115 ATOM CD2 CG2R61 -0.115 ATOM CE2 CG2R61 0.180 ATOM HE1 HGR62 0.120 ATOM HG HGR61 0.115 ATOM HD2 HGR61 0.115 ATOM HE2 HGR62 0.120 ATOM CA1 CG2R67 0.000 ATOM CA2 CG2R61 -0.115 ATOM CA3 CG2R61 -0.115 ATOM CA4 CG2R61 -0.115 ATOM CA5 CG2R61 -0.115 ATOM CA6 CG2R61 -0.115 ATOM HA2 HGR61 0.115 ATOM HA3 HGR61 0.115 ATOM HA4 HGR61 0.115 ATOM HA5 HGR61 0.115 ATOM HA6 HGR61 0.115 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 CA1 CA1 CA2 CA2 CA3 BOND CA3 CA4 CA4 CA5 CA6 CA5 BOND CA6 CA1 BOND CA2 HA2 CA3 HA3 CA4 HA4 BOND CA5 HA5 CA6 HA6 IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 CA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA2 CA1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA3 CA2 CA1 CD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA4 CA3 CA2 CA1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA5 CA4 CA3 CA2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA6 CA5 CA4 CA3 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI 3BNP 0.00 ! C12H11N 3-benzyl-pyridine, yin GROUP !methylene between rings ATOM NZ NG2R60 -0.600 !1 ATOM CE1 CG2R61 0.180 !2 ATOM CD1 CG2R61 0.000 !3 ATOM CG CG2R61 -0.115 !4 ATOM CD2 CG2R61 -0.115 !5 ATOM CE2 CG2R61 0.180 !6 ATOM HE1 HGR62 0.120 !7 ATOM HG HGR61 0.115 !8 ATOM HD2 HGR61 0.115 !9 ATOM HE2 HGR62 0.120 !10 ATOM C CG321 -0.180 !11 ATOM HC1 HGA2 0.090 !12 ATOM HC2 HGA2 0.090 !13 ATOM CA1 CG2R61 0.000 !14 ATOM CA2 CG2R61 -0.115 !15 ATOM CA3 CG2R61 -0.115 !16 ATOM CA4 CG2R61 -0.115 !17 ATOM CA5 CG2R61 -0.115 !18 ATOM CA6 CG2R61 -0.115 !19 ATOM HA2 HGR61 0.115 !20 ATOM HA3 HGR61 0.115 !21 ATOM HA4 HGR61 0.115 !22 ATOM HA5 HGR61 0.115 !23 ATOM HA6 HGR61 0.115 !24 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG HG CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND CD1 C C CA1 BOND C HC1 C HC2 BOND CA1 CA2 CA2 CA3 BOND CA3 CA4 CA4 CA5 CA6 CA5 BOND CA6 CA1 BOND CA2 HA2 CA3 HA3 CA4 HA4 BOND CA5 HA5 CA6 HA6 IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CD1 C CA1 0.0000 0.0000 90.0000 0.0000 0.0000 IC CD1 C CA1 CA2 0.0000 0.0000 90.0000 0.0000 0.0000 IC CA1 CD1 *C HC1 0.0000 0.0000 120.0000 0.0000 0.0000 IC CA1 CD1 *C HC2 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C CA1 CA2 CA3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA1 CA2 CA3 CA4 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA2 CA3 CA4 CA5 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA3 CA4 CA5 CA6 0.0000 0.0000 0.0000 0.0000 0.0000 IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE !toppar_all27_lipid_cholesterol.str RESI CLOL 0.00 ! C27H46O cholesterol (name to avoid conflict with choline) ! atoms names correspond to the correct cholesterol nomenclature GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ATOM H4B HGA2 0.09 GROUP ATOM C5 CG2D1 0.00 ATOM C6 CG2D1 -0.15 ATOM H6 HGA4 0.15 GROUP ATOM C7 CG321 -0.18 ATOM H7A HGA2 0.09 ATOM H7B HGA2 0.09 GROUP ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ! OH Me21 C22 C24 Me26 ATOM H2A HGA2 0.09 ! | \ / \ / \ / ATOM H2B HGA2 0.09 ! C12 Me18 C20 C23 C25--Me27 GROUP ! / \ | / ATOM C20 CG311 -0.09 ! C11 C13---C17 ATOM H20 HGA1 0.09 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM C21 CG331 -0.27 ! / \|/ \ / \ / ATOM H21A HGA3 0.09 ! C2 C10 C8 C15 ATOM H21B HGA3 0.09 ! | | | ATOM H21C HGA3 0.09 ! C3 C5 C7 GROUP ! / \ / \\ / ATOM C22 CG321 -0.18 ! HO C4 C6 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 ! Cholesterol (CHL1) GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM C24 CG321 -0.18 !beyond this nomenclature may not be correct ATOM H24A HGA2 0.09 ATOM H24B HGA2 0.09 GROUP ATOM C25 CG311 -0.09 !c25 ATOM H25 HGA1 0.09 GROUP ATOM C26 CG331 -0.27 !terminal methyl, c26 ATOM H26A HGA3 0.09 ATOM H26B HGA3 0.09 ATOM H26C HGA3 0.09 GROUP ATOM C27 CG331 -0.27 !terminal methyl, c27 ATOM H27A HGA3 0.09 ATOM H27B HGA3 0.09 ATOM H27C HGA3 0.09 BOND C3 O3 C3 H3 O3 H3' BOND C3 C2 C2 H2A C2 H2B BOND C2 C1 C1 H1A C1 H1B BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 BOND C5 C10 BOND C10 C1 BOND C10 C19 C19 H19A C19 H19B C19 H19C DOUBLE C5 C6 BOND C6 H6 BOND C6 C7 C7 H7A C7 H7B BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C13 C18 C18 H18A C18 H18B C18 H18C BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 BOND C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 C24 C24 H24A C24 H24B BOND C24 C25 C25 H25 BOND C25 C26 C26 H26A C26 H26B C26 H26C BOND C25 C27 C27 H27A C27 H27B C27 H27C !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5383 110.44 55.92 110.66 1.5367 IC C4 C2 *C3 O3 1.5367 110.66 120.28 109.14 1.4158 IC O3 C2 *C3 H3 1.4158 109.14 118.92 109.40 1.1155 IC C2 C3 O3 H3' 1.5311 109.14 -58.51 105.39 0.9593 IC C2 C3 C4 C5 1.5311 110.66 -55.96 111.70 1.5156 IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 IC C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304 IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 IC C4 C5 C6 C7 1.5156 121.28 -178.39 123.88 1.5018 IC C7 C5 *C6 H6 1.5018 123.88 177.19 119.54 1.1001 IC C5 C6 C7 C8 1.3432 123.88 14.50 112.36 1.5506 IC C8 C6 *C7 H7A 1.5506 112.36 122.18 110.84 1.1114 IC H7A C6 *C7 H7B 1.1114 110.84 118.17 109.17 1.1124 IC C6 C7 C8 C14 1.5018 112.36 -165.89 110.02 1.5202 IC C14 C7 *C8 C9 1.5202 110.02 121.07 110.84 1.5327 IC C9 C7 *C8 H8 1.5327 110.84 119.34 108.18 1.1123 IC C7 C8 C14 C13 1.5506 110.02 179.73 115.21 1.5247 IC C13 C8 *C14 C15 1.5247 115.21 126.69 117.86 1.5382 IC C13 C8 *C14 H14 1.5247 115.21 -116.05 105.83 1.1205 IC C8 C14 C15 C16 1.5202 117.86 -163.10 103.40 1.5360 IC C16 C14 *C15 H15A 1.5360 103.40 117.45 109.62 1.1113 IC H15A C14 *C15 H15B 1.1113 109.62 121.32 111.94 1.1082 IC C14 C15 C16 C17 1.5382 103.40 7.85 106.79 1.5620 IC C17 C15 *C16 H16A 1.5620 106.79 118.96 109.25 1.1107 IC H16A C15 *C16 H16B 1.1107 109.25 120.76 111.65 1.1090 IC C13 C16 *C17 C20 1.5401 104.94 132.02 112.36 1.5633 IC C13 C16 *C17 H17 1.5401 104.94 -111.76 106.42 1.1153 IC C17 C14 *C13 C12 1.5401 100.27 122.68 106.98 1.5408 IC C12 C14 *C13 C18 1.5408 106.98 122.91 110.83 1.5518 IC C14 C13 C18 H18A 1.5247 110.83 60.33 111.48 1.1077 IC H18A C13 *C18 H18B 1.1077 111.48 119.80 110.01 1.1086 IC H18A C13 *C18 H18C 1.1077 111.48 -121.00 111.71 1.1067 IC C14 C13 C12 C11 1.5247 106.98 56.78 111.10 1.5422 IC C11 C13 *C12 H12A 1.5422 111.10 121.37 111.21 1.1067 IC H12A C13 *C12 H12B 1.1067 111.21 118.82 108.68 1.1119 IC C9 C12 *C11 H11A 1.5593 113.54 121.67 107.06 1.1093 IC H11A C12 *C11 H11B 1.1093 107.06 115.98 108.75 1.1100 IC C10 C8 *C9 H9 1.5531 112.73 -114.54 104.68 1.1185 IC C9 C5 *C10 C19 1.5531 111.91 -120.04 108.03 1.5524 IC C19 C5 *C10 C1 1.5524 108.03 -119.87 109.26 1.5579 IC C5 C10 C19 H19A 1.5304 108.03 -172.88 110.67 1.1082 IC H19A C10 *C19 H19B 1.1082 110.67 118.48 111.77 1.1080 IC H19A C10 *C19 H19C 1.1082 110.67 -120.66 110.97 1.1095 IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 IC C16 C17 C20 C22 1.5620 112.36 55.21 110.55 1.5476 IC C22 C17 *C20 C21 1.5476 110.55 125.88 113.32 1.5349 IC C21 C17 *C20 H20 1.5349 113.32 118.87 107.27 1.1157 IC C17 C20 C21 H21A 1.5633 113.32 64.90 110.93 1.1077 IC H21A C20 *C21 H21B 1.1077 110.93 -121.00 110.41 1.1104 IC H21A C20 *C21 H21C 1.1077 110.93 118.40 111.29 1.1085 IC C17 C20 C22 C23 1.5633 110.55 -174.59 115.12 1.5394 IC C23 C20 *C22 H22A 1.5394 115.12 120.23 109.35 1.1116 IC H22A C20 *C22 H22B 1.1116 109.35 117.13 108.75 1.1121 IC C20 C22 C23 C24 1.5476 115.12 172.50 112.25 1.5377 IC C24 C22 *C23 H23A 1.5377 112.25 121.13 109.69 1.1108 IC H23A C22 *C23 H23B 1.1108 109.69 118.14 108.99 1.1129 IC C22 C23 C24 C25 1.5394 112.25 -176.23 114.06 1.5418 IC C25 C23 *C24 H24A 1.5418 114.06 120.56 108.44 1.1132 IC H24A C23 *C24 H24B 1.1132 108.44 117.11 109.39 1.1121 IC C23 C24 C25 C26 1.5377 114.06 174.26 111.24 1.5378 IC C26 C24 *C25 C27 1.5378 111.24 119.63 112.86 1.5381 IC C26 C24 *C25 H25 1.5378 111.24 -119.50 108.47 1.1151 IC C24 C25 C26 H26A 1.5418 111.24 -178.53 110.52 1.1105 IC H26A C25 *C26 H26B 1.1105 110.52 120.00 110.36 1.1105 IC H26A C25 *C26 H26C 1.1105 110.52 -120.09 110.33 1.1106 IC C24 C25 C27 H27A 1.5418 112.86 -178.28 110.40 1.1105 IC H27A C25 *C27 H27B 1.1105 110.40 119.95 110.31 1.1105 IC H27A C25 *C27 H27C 1.1105 110.40 -119.82 110.77 1.1097 RESI CLNS 0.00 ! C20H32O cholesterol with sidechain beyond c18(c20) omitted ! atoms names after the comments correspond to the ! correct cholesterol nomenclature GROUP ATOM C1 CG311 0.14 !c3 ATOM O1 OG311 -0.65 ATOM HO1 HGP1 0.42 ATOM H1 HGA1 0.09 ATOM C2 CG321 -0.18 !c4 ATOM H2 HGA2 0.09 ATOM H2' HGA2 0.09 ATOM C3 CG2D1 0.00 !c5 ATOM C4 CG2D1 -0.15 !c6 ATOM H4 HGA4 0.15 ATOM C5 CG321 -0.18 !c7 ATOM H5 HGA2 0.09 ATOM H5' HGA2 0.09 ATOM C6 CG311 -0.09 !c8 ATOM H6 HGA1 0.09 GROUP ATOM C7 CG3RC1 -0.09 !c14 ATOM H7 HGA1 0.09 ATOM C8 CG3C52 -0.18 !c15 ATOM H8 HGA2 0.09 ATOM H8' HGA2 0.09 ATOM C9 CG3C52 -0.18 !c16 ATOM H9 HGA2 0.09 ATOM H9' HGA2 0.09 ATOM C10 CG3C51 -0.09 !c17 ATOM H10 HGA1 0.09 ATOM C11 CG3RC1 0.00 !c13 GROUP ATOM CC11 CG331 -0.27 !c18, methyl at c13 ATOM H111 HGA3 0.09 ATOM H112 HGA3 0.09 ATOM H113 HGA3 0.09 ATOM C12 CG321 -0.18 !c12 ATOM H12 HGA2 0.09 ATOM H12' HGA2 0.09 ATOM C13 CG321 -0.18 !c11 ATOM H13 HGA2 0.09 ATOM H13' HGA2 0.09 ATOM C14 CG311 -0.09 !c9 ATOM H14 HGA1 0.09 ATOM C15 CG301 0.00 !c10: no hydrogen GROUP ATOM CC15 CG331 -0.27 !c19, methyl at c10 ATOM H151 HGA3 0.09 ATOM H152 HGA3 0.09 ATOM H153 HGA3 0.09 ATOM C16 CG321 -0.18 !c1 ATOM H16 HGA2 0.09 ATOM H16' HGA2 0.09 ATOM C17 CG321 -0.18 !c2 ATOM H17 HGA2 0.09 ATOM H17' HGA2 0.09 ATOM C18 CG331 -0.27 !c20 ATOM H181 HGA3 0.09 ATOM H182 HGA3 0.09 ATOM H183 HGA3 0.09 BOND C1 O1 C1 H1 C1 C2 BOND O1 HO1 BOND C2 C3 C2 H2 C2 H2' DOUBLE C3 C4 BOND C4 C5 C4 H4 BOND C5 C6 C5 H5 C5 H5' BOND C6 C7 C6 H6 BOND C7 C8 C7 H7 BOND C8 C9 C8 H8 C8 H8' BOND C9 C10 C9 H9 C9 H9' BOND C10 C18 C10 C11 C10 H10 BOND C11 CC11 C11 C7 C11 C12 BOND CC11 H111 CC11 H112 CC11 H113 BOND C12 C13 C12 H12 C12 H12' BOND C13 C14 C13 H13 C13 H13' BOND C14 C15 C14 C6 C14 H14 BOND C15 C16 C15 C3 C15 CC15 BOND CC15 H151 CC15 H152 CC15 H153 BOND C16 C17 C16 H16 C16 H16' BOND C17 C1 C17 H17 C17 H17' BOND C18 H181 C18 H182 C18 H183 !DONO HO1 O1 !ACCE O1 IC O1 C1 C2 C3 1.4158 109.24 -176.17 111.80 1.5153 IC C1 C2 C3 C4 1.5368 111.80 -123.48 121.41 1.3430 IC C2 C3 C4 C5 1.5153 121.41 -178.76 123.84 1.5019 IC C3 C4 C5 C6 1.3430 123.84 14.64 112.44 1.5504 IC C4 C5 C6 C7 1.5019 112.44 -166.16 109.90 1.5192 IC C5 C6 C7 C8 1.5504 109.90 -54.73 118.74 1.5447 IC C6 C7 C8 C9 1.5192 118.74 -161.90 103.72 1.5418 IC C7 C8 C9 C10 1.5447 103.72 5.69 105.45 1.5530 IC C8 C9 C10 C11 1.5418 105.45 21.50 105.85 1.5300 IC C9 C10 C11 C12 1.5530 105.85 -155.90 116.00 1.5351 IC C7 C12 *C11 CC11 1.5194 108.58 -123.00 111.88 1.5530 IC C10 C11 C12 C13 1.5300 116.00 167.75 110.42 1.5414 IC C10 C11 C7 C8 1.5300 99.46 43.93 105.86 1.5447 IC C11 C12 C13 C14 1.5351 110.42 -52.28 113.50 1.5626 IC CC11 C11 C12 C13 1.5530 111.88 -66.16 110.42 1.5414 IC CC11 C11 C7 C8 1.5530 111.12 -70.96 105.86 1.5447 IC C12 C13 C14 C15 1.5414 113.50 179.43 114.52 1.5524 IC C13 C14 C15 CC15 1.5626 114.52 -50.80 109.07 1.5522 IC C13 C14 C15 C16 1.5626 114.52 69.29 108.64 1.5574 IC C13 C14 C6 C7 1.5626 113.16 -48.42 109.31 1.5192 IC CC15 C15 C16 C17 1.5522 110.15 -68.75 114.54 1.5383 IC C14 C15 C16 C17 1.5524 108.64 171.83 114.54 1.5383 IC C14 C15 C3 C4 1.5524 111.86 7.71 123.46 1.3430 IC C15 C16 C17 C1 1.5574 114.54 -54.68 110.51 1.5312 IC C11 C9 *C10 C18 1.5300 105.85 126.88 114.22 1.5413 IC O1 C2 *C1 H1 1.4158 109.24 -119.02 109.53 1.1156 IC C2 C1 O1 HO1 1.5368 109.24 62.69 105.39 0.9593 IC C3 C1 *C2 H2 1.5153 111.80 121.88 109.11 1.1100 IC C3 C1 *C2 H2' 1.5153 111.80 -123.05 107.36 1.1142 IC C5 C3 *C4 H4 1.5019 123.84 177.13 119.55 1.1001 IC C6 C4 *C5 H5 1.5504 112.44 122.17 110.88 1.1114 IC C6 C4 *C5 H5' 1.5504 112.44 -119.69 109.16 1.1124 IC C7 C5 *C6 H6 1.5192 109.90 -119.58 108.19 1.1122 IC C8 C6 *C7 H7 1.5447 118.74 117.73 105.77 1.1205 IC C9 C7 *C8 H8 1.5418 103.72 117.51 109.61 1.1108 IC C9 C7 *C8 H8' 1.5418 103.72 -121.25 111.67 1.1078 IC C10 C8 *C9 H9 1.5530 105.45 118.45 109.64 1.1105 IC C10 C8 *C9 H9' 1.5530 105.45 -120.18 112.16 1.1085 IC C18 C9 *C10 H10 1.5413 114.22 119.69 107.07 1.1162 IC C7 C11 CC11 H111 1.5194 111.12 -178.60 110.01 1.1092 IC H111 C11 *CC11 H112 1.1092 110.01 118.82 111.63 1.1068 IC H111 C11 *CC11 H113 1.1092 110.01 -120.26 111.66 1.1075 IC C13 C11 *C12 H12 1.5414 110.42 122.09 109.96 1.1102 IC C13 C11 *C12 H12' 1.5414 110.42 -119.49 108.88 1.1120 IC C14 C12 *C13 H13 1.5626 113.50 121.59 107.14 1.1091 IC C14 C12 *C13 H13' 1.5626 113.50 -122.38 108.79 1.1098 IC C13 C6 *C14 H14 1.5626 113.16 113.80 104.59 1.1184 IC C3 C15 CC15 H151 1.5435 107.81 -172.81 110.68 1.1082 IC H151 C15 *CC15 H152 1.1082 110.68 118.52 111.71 1.1081 IC H151 C15 *CC15 H153 1.1082 110.68 -120.68 110.98 1.1094 IC C17 C15 *C16 H16 1.5383 114.54 122.43 109.27 1.1104 IC C17 C15 *C16 H16' 1.5383 114.54 -120.70 108.26 1.1134 IC C16 C1 *C17 H17 1.5383 110.51 121.12 109.37 1.1120 IC C16 C1 *C17 H17' 1.5383 110.51 -120.62 109.70 1.1111 IC C9 C10 C18 H181 0.0000 0.00 180.00 0.00 0.0000 IC C10 H181 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 IC C10 H181 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 RESI CLM1 0.00 ! C11H18O cholesterol analog with only rings 1 and 2 !and the position 19 methyl ! atoms names after the comments correspond to the ! correct cholesterol nomenclature ! ring 1 GROUP ATOM C1 CG311 0.14 !c3 ATOM O1 OG311 -0.65 ATOM HO1 HGP1 0.42 ATOM H1 HGA1 0.09 ATOM C2 CG321 -0.18 !c4 ATOM H2 HGA2 0.09 ATOM H2' HGA2 0.09 ATOM C3 CG2D1 0.00 !c5 ATOM C15 CG301 0.00 !c10: no hydrogen ATOM C16 CG321 -0.18 !c1 ATOM H16 HGA2 0.09 ATOM H16' HGA2 0.09 ATOM C17 CG321 -0.18 !c2 ATOM H17 HGA2 0.09 ATOM H17' HGA2 0.09 ATOM CC15 CG331 -0.27 !c19, methyl at c10 ATOM H151 HGA3 0.09 ATOM H152 HGA3 0.09 ATOM H153 HGA3 0.09 ! ring 2 GROUP ATOM C4 CG2D1 -0.15 !c6 ATOM H4 HGA4 0.15 ATOM C5 CG321 -0.18 !c7 ATOM H5 HGA2 0.09 ATOM H5' HGA2 0.09 ATOM C6 CG321 -0.18 !c8 ATOM H6 HGA2 0.09 ATOM H6' HGA2 0.09 ATOM C14 CG321 -0.18 !c9 ATOM H14 HGA2 0.09 ATOM H14' HGA2 0.09 BOND C1 C2 C2 C3 C3 C15 C15 C16 C16 C17 C17 C1 BOND C1 O1 O1 HO1 C1 H1 BOND C2 H2 C2 H2' BOND C15 CC15 CC15 H151 CC15 H152 CC15 H153 BOND C16 H16 C16 H16' BOND C17 H17 C17 H17' DOUB C3 C4 BOND C4 C5 C5 C6 C6 C14 C14 C15 BOND C4 H4 BOND C5 H5 C5 H5' BOND C6 H6 C6 H6' BOND C14 H14 C14 H14' IC C1 C2 C3 C15 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C15 C16 0.0000 0.00 0.00 0.00 0.0000 IC C17 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 C17 *C1 O1 0.0000 0.00 120.00 0.00 0.0000 IC C2 C17 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 IC C17 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H2' 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 15.00 0.00 0.0000 IC C4 C5 C6 C14 0.0000 0.00 -45.00 0.00 0.0000 IC C14 C3 *C15 CC15 0.0000 0.00 -120.00 0.00 0.0000 IC C17 C15 *C16 H16 0.0000 0.00 120.00 0.00 0.0000 IC C17 C15 *C16 H16' 0.0000 0.00 -120.00 0.00 0.0000 IC C16 C1 *C17 H17 0.0000 0.00 120.00 0.00 0.0000 IC C16 C1 *C17 H17' 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C15 CC15 H151 0.0000 0.00 180.00 0.00 0.0000 IC H151 C15 *CC15 H152 0.0000 0.00 120.00 0.00 0.0000 IC H151 C15 *CC15 H153 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 IC C6 C4 *C5 H5' 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C5 *C6 H6 0.0000 0.00 120.00 0.00 0.0000 IC C14 C5 *C6 H6' 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C15 *C14 H14 0.0000 0.00 120.00 0.00 0.0000 IC C6 C15 *C14 H14' 0.0000 0.00 -120.00 0.00 0.0000 !toppar_all27_lipid_model.str RESI MAS 0.00 ! C3H6O2 methylacetate GROUP ATOM C1 CG331 -0.31 ! H22 ATOM C CG2O2 0.90 ! | ATOM OM OG302 -0.49 ! H21-C2-H23 ATOM C2 CG331 -0.01 ! \ ATOM O OG2D1 -0.63 ! OM ATOM H11 HGA3 0.09 ! / ATOM H12 HGA3 0.09 ! O=C ATOM H13 HGA3 0.09 ! | ATOM H21 HGA3 0.09 ! H11-C1-H13 ATOM H22 HGA3 0.09 ! | ATOM H23 HGA3 0.09 ! H12 BOND C1 C C OM OM C2 DOUBLE C O BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IMPR C C1 O OM ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 RESI ETAC 0.00 ! C4H8O2 Ethylacetate ! ! H213 GROUP ! | ATOM C1 CG331 -0.31 ! H211-C21-H212 ATOM C CG2O2 0.90 ! / ATOM OM OG302 -0.49 ! H22-C2-H23 ATOM C2 CG321 0.08 ! \ ATOM O OG2D1 -0.63 ! OM ATOM H11 HGA3 0.09 ! / ATOM H12 HGA3 0.09 ! O=C ATOM H13 HGA3 0.09 ! \ ATOM H22 HGA2 0.09 ! H11-C1-H13 ATOM H23 HGA2 0.09 ! | GROUP ! H12 ATOM C21 CG331 -0.27 ATOM H211 HGA3 0.09 ATOM H212 HGA3 0.09 ATOM H213 HGA3 0.09 BOND C1 C C OM OM C2 BOND C1 H11 C1 H12 C1 H13 BOND C2 C21 C2 H22 C2 H23 BOND C21 H211 C21 H212 C21 H213 DOUBLE C O IMPR C C1 O OM ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC C21 C2 OM C 1.520 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 IC H211 C21 C2 OM 1.1 108.90 180.0 116.7 1.437 IC H212 C21 C2 OM 1.1 108.90 60.0 116.7 1.437 IC H213 C21 C2 OM 1.1 108.90 -60.0 116.7 1.437 RESI MPRO 0.00 ! C4H8O2 Methylpropionate GROUP ATOM C1 CG321 -0.22 ! H22 ATOM C CG2O2 0.90 ! | ATOM OM OG302 -0.49 ! H21-C2-H23 ATOM C2 CG331 -0.01 ! \ ATOM O OG2D1 -0.63 ! OM ATOM H12 HGA2 0.09 ! / ATOM H13 HGA2 0.09 ! O=C ATOM H21 HGA3 0.09 ! \ ATOM H22 HGA3 0.09 ! H12-C1-H13 ATOM H23 HGA3 0.09 ! / GROUP ! H112-C11-H111 ATOM C11 CG331 -0.27 ! | ATOM H111 HGA3 0.09 ! H113 ATOM H112 HGA3 0.09 ATOM H113 HGA3 0.09 BOND C1 C C OM C O OM C2 BOND C1 C11 C1 H12 C1 H13 BOND C11 H111 C11 H112 C11 H113 BOND C2 H21 C2 H22 C2 H23 IMPR C C1 O OM ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC C11 C1 C OM 1.520 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 IC H111 C11 C1 C 1.1 109.75 180.0 109.0 1.520 IC H112 C11 C1 C 1.1 109.75 60.4 109.0 1.520 IC H113 C11 C1 C 1.1 109.75 -60.4 109.0 1.520 RESI MSO4 -1.00 ! CH3O4S Methylsulfate GROUP ATOM S SG3O1 1.33 ! OS2(-1) ATOM OS1 OG303 -0.28 ! | ATOM OS2 OG2P1 -0.65 ! (-1) OS2--S(+2)--OS4 (-1) ATOM OS3 OG2P1 -0.65 ! | ATOM OS4 OG2P1 -0.65 ! OS1 ATOM C1 CG331 -0.37 ! \ ATOM H11 HGA3 0.09 ! H11-C1-H13 ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! H12 BOND S OS1 S OS2 S OS3 S OS4 OS1 C1 BOND C1 H11 C1 H12 C1 H13 ACCE OS1 ACCE OS2 ACCE OS3 ACCE OS4 IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000 IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000 IC C1 OS1 S OS2 0.0000 0.0000 60.0000 0.0000 0.0000 IC S OS1 C1 OS3 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS4 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS2 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS3 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 RESI HEXA 0.00 ! C6H14 hexane GROUP ATOM H11 HGA3 0.09 ! H2 ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! H1-C1-H3 ATOM C1 CG331 -0.27 ! | GROUP ! | ATOM H21 HGA2 0.09 ! H4-C2-H5 ATOM H22 HGA2 0.09 ! | ATOM C2 CG321 -0.18 ! | GROUP ! | ATOM H31 HGA2 0.09 ! H6-C3-H7 ATOM H32 HGA2 0.09 ! | ATOM C3 CG321 -0.18 ! | GROUP ! | ATOM H41 HGA2 0.09 ! H8-C4-H10 ATOM H42 HGA2 0.09 ! | ATOM C4 CG321 -0.18 ! | GROUP ! | ATOM H51 HGA2 0.09 ! H51-C5-H152 ATOM H52 HGA2 0.09 ! | ATOM C5 CG321 -0.18 ! | GROUP ! | ATOM H61 HGA3 0.09 ! H61-C4-H62 ATOM H62 HGA3 0.09 ! | ATOM H63 HGA3 0.09 ! H63 ATOM C6 CG331 -0.27 BOND H11 C1 H12 C1 H13 C1 C1 C2 BOND H21 C2 H22 C2 C2 C3 BOND H31 C3 H32 C3 C3 C4 BOND H41 C4 H42 C4 C4 C5 BOND H51 C5 H52 C5 C5 C6 BOND H61 C6 H62 C6 C6 H63 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC H11 C2 *C1 H12 0.00 0.00 120.0 0.00 0.00 IC H11 C2 *C1 H13 0.00 0.00 240.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 IC C1 C3 *C2 H22 0.00 0.00 240.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 IC C2 C4 *C3 H32 0.00 0.00 240.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 240.0 0.00 0.00 IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 IC C4 C6 *C5 H52 0.00 0.00 240.0 0.00 0.00 IC C4 C5 C6 H61 0.00 0.00 180.0 0.00 0.00 IC H61 C5 *C6 H62 0.00 0.00 120.0 0.00 0.00 IC H61 C5 *C6 H63 0.00 0.00 240.0 0.00 0.00 RESI ETHE 0.00 ! C2H4 ethylene, yin/adm jr. GROUP ATOM C1 CG2D2 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 ATOM H12 HGA5 0.21 ! \ / GROUP ! C1=C2 ATOM C2 CG2D2 -0.42 ! / \ ATOM H21 HGA5 0.21 ! H12 H22 ATOM H22 HGA5 0.21 BOND C1 H11 C1 H12 DOUBLE C1 C2 BOND C2 H21 C2 H22 IC H11 C1 C2 H21 1.1036 121.37 180.00 121.37 1.1036 IC H12 C2 *C1 H11 1.1036 121.37 180.00 121.37 1.1036 IC H22 C1 *C2 H21 1.1036 121.37 180.00 121.37 1.1036 IC C1 C2 H21 H22 1.3370 121.37 -180.00 31.37 1.8845 PATC FIRS NONE LAST NONE RESI PRPE 0.00 ! C3H6 propene, yin/adm jr. GROUP ATOM C1 CG2D2 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 ATOM H12 HGA5 0.21 ! \ / GROUP ! C1=C2 H31 ATOM C2 CG2D1 -0.15 ! / \ / ATOM H21 HGA4 0.15 ! H12 C3 GROUP ! / \ ATOM C3 CG331 -0.27 ! H33 H32 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 H11 C1 H12 DOUBLE C1 C2 BOND C2 H21 BOND C2 C3 BOND C3 H31 C3 H32 C3 H33 IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 IC H12 C2 *C1 H11 0.00 0.00 180.0 0.0 0.0 IC C3 C1 *C2 H21 0.00 0.00 180.0 0.0 0.0 IC H31 C3 C2 C1 0.00 0.00 0.0 0.0 0.0 IC H32 C3 C2 C1 0.00 0.00 120.0 0.0 0.0 IC H33 C3 C2 C1 0.00 0.00 -120.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI BTE1 0.00 ! C4H8 1-Butene, yin/adm jr. GROUP ATOM C1 CG2D2 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 H41 ATOM H12 HGA5 0.21 ! \ / | GROUP ! C1=C2 C4-H42 ATOM C2 CG2D1 -0.15 ! / \ / \ ATOM H21 HGA4 0.15 ! H12 C3 H43 GROUP ! / \ ATOM C3 CG321 -0.18 ! H31 H32 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 DOUBLE C1 C2 BOND C2 H21 BOND C2 C3 BOND C3 H31 C3 H32 BOND C3 C4 BOND C4 H41 C4 H42 C4 H43 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC H11 C1 C2 C3 0.00 0.00 180.0 0.00 0.00 IC H12 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 IC H31 C2 *C3 C4 0.00 0.00 120.0 0.00 0.00 IC H32 C2 *C3 C4 0.00 0.00 -120.0 0.00 0.00 IC H41 C4 C3 C2 0.00 0.00 180.0 0.00 0.00 IC H42 C4 C3 C2 0.00 0.00 60.0 0.00 0.00 IC H43 C4 C3 C2 0.00 0.00 -60.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI BTE2 0.00 ! C4H8 2-Butene, yin/adm jr. GROUP ATOM C1 CG331 -0.27 ! H12 H13 ATOM H11 HGA3 0.09 ! \ | ATOM H12 HGA3 0.09 ! H13-C1 H31 ATOM H13 HGA3 0.09 ! \ / GROUP ! C2=C3 ATOM C2 CG2D1 -0.15 ! / \ ATOM H21 HGA4 0.15 ! H21 C4-H41 GROUP ! | \ ATOM C3 CG2D1 -0.15 ! H43 H42 ATOM H31 HGA4 0.15 GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 BOND C2 H21 DOUBLE C2 C3 BOND C3 H31 BOND C3 C4 BOND C4 H41 C4 H42 C4 H43 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC H11 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 IC H12 C1 C2 C3 0.00 0.00 120.0 0.00 0.00 IC H13 C1 C2 C3 0.00 0.00 -120.0 0.00 0.00 IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 IC H31 C4 *C3 C2 0.00 0.00 180.0 0.00 0.00 IC H41 C4 C3 C2 0.00 0.00 0.0 0.00 0.00 IC H42 C4 C3 C2 0.00 0.00 120.0 0.00 0.00 IC H43 C4 C3 C2 0.00 0.00 -120.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI DIPE 0.00 ! C5H8 1,4-dipentene, adm jr. GROUP ATOM C1 CG2D2 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 H41 H51 ATOM H12 HGA5 0.21 ! \ / | / GROUP ! C1=C2 C4=C5 ATOM C2 CG2D1 -0.15 ! / \ / \ ATOM H21 HGA4 0.15 ! H12 C3 H52 GROUP ! / \ ATOM C3 CG321 -0.18 ! H31 H32 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG2D1 -0.15 ATOM H41 HGA4 0.15 GROUP ATOM C5 CG2D2 -0.42 ATOM H51 HGA5 0.21 ATOM H52 HGA5 0.21 BOND C1 H11 C1 H12 DOUBLE C1 C2 BOND C2 H21 BOND C2 C3 BOND C3 H31 C3 H32 BOND C3 C4 BOND C4 H41 DOUBLE C4 C5 BOND C5 H51 C5 H52 IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI DIHE 0.00 ! C7H12 2,5-diheptene, adm jr. GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 GROUP ATOM C2 CG2D1 -0.15 ! H21 H31 H51 H61 ATOM H21 HGA4 0.15 ! \ / | / GROUP ! C2=C3 C5=C6 ATOM C3 CG2D1 -0.15 ! / \ / \ ATOM H31 HGA4 0.15 ! H11-C1 C4 C7-H71 GROUP ! / \ / \ / \ ATOM C4 CG321 -0.18 ! H12 H13 H41 H42 H73 H72 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG2D1 -0.15 ATOM H51 HGA4 0.15 GROUP ATOM C6 CG2D1 -0.15 ATOM H61 HGA4 0.15 GROUP ATOM C7 CG331 -0.27 ATOM H71 HGA3 0.09 ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 C2 H21 DOUBLE C2 C3 BOND C3 H31 BOND C3 C4 C4 H41 C4 H42 BOND C4 C5 C5 H51 DOUBLE C5 C6 BOND C6 H61 BOND C6 C7 C7 H71 C7 H72 C7 H73 IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C7 C5 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6 C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC H71 C6 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 IC H71 C6 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI HXE2 0.00 ! C6H12 2-hexene, yin/adm jr. GROUP ATOM C1 CG331 -0.27 ! H12 H13 ATOM H11 HGA3 0.09 ! \ | ATOM H12 HGA3 0.09 ! H13-C1 H31 H51 H52 ATOM H13 HGA3 0.09 ! \ / \ / GROUP ! C2=C3 C5 H61 ATOM C2 CG2D1 -0.15 ! / \ / \ / ATOM H21 HGA4 0.15 ! H21 C4 C6-H62 GROUP ! / \ \ ATOM C3 CG2D1 -0.15 ! H41 H42 H63 ATOM H31 HGA4 0.15 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 GROUP ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 C2 BOND C2 H21 DOUBLE C2 C3 BOND C3 H31 BOND C3 C4 BOND C4 H41 C4 H42 BOND C4 C5 C5 H51 C5 H52 BOND C5 C6 C6 H61 C6 H62 C6 H63 ! all trans IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC H11 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 IC H12 C1 C2 C3 0.00 0.00 120.0 0.00 0.00 IC H13 C1 C2 C3 0.00 0.00 -120.0 0.00 0.00 IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 IC H31 C4 *C3 C2 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 IC C4 C6 *C5 H52 0.00 0.00 -120.0 0.00 0.00 IC H61 C6 C5 C4 0.00 0.00 180.0 0.00 0.00 IC H62 C6 C5 C4 0.00 0.00 60.0 0.00 0.00 IC H63 C6 C5 C4 0.00 0.00 300.0 0.00 0.00 PATC FIRS NONE LAST NONE RESI NC4 1.00 ! C4H12N tetramethylammonium GROUP ATOM N NG3P0 -0.60 ! H32 ATOM C1 CG334 -0.35 ! | ATOM C2 CG334 -0.35 ! H31-C3-H33 ATOM C3 CG334 -0.35 ! H23 | H41 ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! H22-C2------N------C4-H42 (+) ATOM H12 HGP5 0.25 ! | | | ATOM H13 HGP5 0.25 ! H21 | H43 ATOM H21 HGP5 0.25 ! H11-C1-H13 ATOM H22 HGP5 0.25 ! | ATOM H23 HGP5 0.25 ! H12 ATOM H31 HGP5 0.25 ATOM H32 HGP5 0.25 ATOM H33 HGP5 0.25 ATOM H41 HGP5 0.25 ATOM H42 HGP5 0.25 ATOM H43 HGP5 0.25 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 *N C4 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3 N C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C4 N C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C1 N C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI NC5 1.00 ! C5H14N tetramethylammonium ethyl analog GROUP ATOM N NG3P0 -0.60 ATOM C1 CG324 -0.10 ! | ATOM C2 CG334 -0.35 ! -C3- ATOM C3 CG334 -0.35 ! | ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) ATOM H12 HGP5 0.25 ! | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H23 HGP5 0.25 ! | ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! -C5- ATOM H33 HGP5 0.25 ! | ATOM H41 HGP5 0.25 ATOM H42 HGP5 0.25 ATOM H43 HGP5 0.25 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 C5 H53 ! ab-initio HF/6-31G* structure IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797 IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797 IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793 IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 RESI CHOL 1.00 ! C5H14NO choline GROUP ATOM N NG3P0 -0.60 ATOM C1 CG324 -0.10 ! | ATOM C2 CG334 -0.35 ! -C3- ATOM C3 CG334 -0.35 ! | ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) ATOM H12 HGP5 0.25 ! | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H23 HGP5 0.25 ! | ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! | ATOM H33 HGP5 0.25 ! | ATOM H41 HGP5 0.25 ! | ATOM H42 HGP5 0.25 ! | ATOM H43 HGP5 0.25 ! | GROUP ! | ATOM C5 CG321 0.05 ! | ATOM H51 HGA2 0.09 ! -C5- ATOM H52 HGA2 0.09 ! | ATOM OH1 OG311 -0.65 ! OH1---HO1 ATOM HO1 HGP1 0.42 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND C5 OH1 OH1 HO1 ! ab-initio HF/6-31G* geometry of gauche conformer IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208 IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031 IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945 IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947 IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491 IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796 IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746 IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794 IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794 IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800 IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773 IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793 IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796 IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794 IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 RESI ACHO 1.00 ! C7H16NO2 acetylcholine GROUP ATOM N NG3P0 -0.60 ATOM C1 CG324 -0.10 ! | ATOM C2 CG334 -0.35 ! -C3- ATOM C3 CG334 -0.35 ! | ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) ATOM H12 HGP5 0.25 ! | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H23 HGP5 0.25 ! | ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! | ATOM H33 HGP5 0.25 ! | ATOM H41 HGP5 0.25 ! | ATOM H42 HGP5 0.25 ! | ATOM H43 HGP5 0.25 ! | GROUP ! | ATOM C5 CG321 0.08 ! -C5- ATOM OM OG302 -0.49 ! | ATOM C CG2O2 0.90 ! OM ATOM C7 CG331 -0.31 ! / ATOM O OG2D1 -0.63 ! O==C ATOM H51 HGA2 0.09 ! | ATOM H52 HGA2 0.09 ! --C7-- ATOM H71 HGA3 0.09 ! | ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND C7 C C OM OM C5 DOUBLE C O BOND C7 H71 C7 H72 C7 H73 IMPR C C7 O OM IC C4 N C1 C5 0.0000 000.00 161.60 000.00 0.0000 IC C5 C1 N C2 0.0000 000.00 -80.13 000.00 0.0000 IC C5 C1 N C3 0.0000 000.00 42.05 000.00 0.0000 IC C2 N C1 H11 0.0000 000.00 158.76 000.00 0.0000 IC C3 N C1 H12 0.0000 000.00 165.25 000.00 0.0000 IC C1 N C2 H21 0.0000 000.00 -179.38 000.00 0.0000 IC C3 N C2 H22 0.0000 000.00 -63.85 000.00 0.0000 IC C4 N C2 H23 0.0000 000.00 57.69 000.00 0.0000 IC C1 N C3 H31 0.0000 000.00 173.42 000.00 0.0000 IC C2 N C3 H32 0.0000 000.00 177.22 000.00 0.0000 IC C4 N C3 H33 0.0000 000.00 174.14 000.00 0.0000 IC C1 N C4 H41 0.0000 000.00 175.04 000.00 0.0000 IC C2 N C4 H42 0.0000 000.00 -64.86 000.00 0.0000 IC C3 N C4 H43 0.0000 000.00 56.40 000.00 0.0000 IC N C1 C5 H51 0.0000 000.00 180.00 000.00 0.0000 IC N C1 C5 H52 0.0000 000.00 -60.0 000.00 0.0000 IC N C1 C5 OM 0.0000 000.00 72.0 000.00 0.0000 IC C1 C5 OM C 0.0000 000.00 166.9 000.00 0.0000 IC C7 C OM C5 0.0000 000.00 20.0 000.00 0.0000 IC O C OM C5 0.0000 000.00 -160.0 000.00 0.0000 IC H71 C7 C OM 0.0000 000.00 180.0 000.00 0.0000 IC H72 C7 C OM 0.0000 000.00 60.4 000.00 0.0000 IC H73 C7 C OM 0.0000 000.00 -60.4 000.00 0.0000 RESI PC 0.00 ! C6H16NO4P phosphatidylcholine GROUP ATOM N NG3P0 -0.60 ATOM C1 CG324 -0.10 ! | ATOM C2 CG334 -0.35 ! -C3- ATOM C3 CG334 -0.35 ! | ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) ATOM H12 HGP5 0.25 ! | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H23 HGP5 0.25 ! | ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! | ATOM H33 HGP5 0.25 ! | ATOM H41 HGP5 0.25 ! | ATOM H42 HGP5 0.25 ! | ATOM H43 HGP5 0.25 ! | GROUP ! | ATOM C5 CG321 -0.08 ! | ATOM H51 HGA2 0.09 ! H52---C5---H51 ATOM H52 HGA2 0.09 ! | GROUP ! | ATOM P1 PG1 1.50 ! (-) O3 O1 ATOM O3 OG2P1 -0.78 ! \ / ATOM O4 OG2P1 -0.78 ! P1 (+) ATOM O1 OG303 -0.57 ! / \ ATOM O2 OG303 -0.57 ! (-) O4 O2 GROUP ! | ATOM C6 CG331 -0.17 ! | ATOM H61 HGA3 0.09 ! H63-C6-H62 ATOM H62 HGA3 0.09 ! | ATOM H63 HGA3 0.09 ! H61 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 BOND C6 H61 C6 H62 C6 H63 IC C4 N C1 C5 0.0000 000.00 112.00 000.00 0.0000 IC C5 C1 N C2 0.0000 000.00 -121.00 000.00 0.0000 IC C5 C1 N C3 0.0000 000.00 0.00 000.00 0.0000 IC C2 N C1 H11 0.0000 000.00 120.00 000.00 0.0000 IC C3 N C1 H12 0.0000 000.00 120.00 000.00 0.0000 IC C1 N C2 H21 0.0000 000.00 180.00 000.00 0.0000 IC C3 N C2 H22 0.0000 000.00 -60.00 000.00 0.0000 IC C4 N C2 H23 0.0000 000.00 60.00 000.00 0.0000 IC C1 N C3 H31 0.0000 000.00 180.00 000.00 0.0000 IC C2 N C3 H32 0.0000 000.00 180.00 000.00 0.0000 IC C4 N C3 H33 0.0000 000.00 180.00 000.00 0.0000 IC C1 N C4 H41 0.0000 000.00 180.00 000.00 0.0000 IC C2 N C4 H42 0.0000 000.00 -60.00 000.00 0.0000 IC C3 N C4 H43 0.0000 000.00 60.00 000.00 0.0000 IC N C1 C5 H51 0.0000 000.00 -150.00 000.00 0.0000 IC N C1 C5 H52 0.0000 000.00 100.00 000.00 0.0000 IC N C1 C5 O1 0.0000 000.00 -30.00 000.00 0.0000 IC C1 C5 O1 P1 0.0000 000.00 130.00 000.00 0.0000 IC C5 O1 P1 O2 0.0000 000.00 -160.0 000.00 0.0000 IC O3 P1 O1 C5 0.0000 000.00 80.00 000.00 0.0000 IC O4 P1 O1 C5 0.0000 000.00 -60.00 000.00 0.0000 IC O1 P1 O2 C6 0.0000 000.00 180.00 000.00 0.0000 IC H61 C6 O2 P1 0.0000 000.00 0.00 000.00 0.0000 IC H62 C6 O2 P1 0.0000 000.00 120.00 000.00 0.0000 IC H63 C6 O2 P1 0.0000 000.00 -120.00 000.00 0.0000 RESI GPC 0.00 ! C8H20NO6P glycerolphosphorylcholine GROUP ATOM N NG3P0 -0.60 ATOM C1 CG324 -0.10 ! | ATOM C2 CG334 -0.35 ! -C3- ATOM C3 CG334 -0.35 ! | ATOM C4 CG334 -0.35 ! | | | ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) ATOM H12 HGP5 0.25 ! | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H23 HGP5 0.25 ! | ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! | ATOM H33 HGP5 0.25 ! | ATOM H41 HGP5 0.25 ! | ATOM H42 HGP5 0.25 ! | ATOM H43 HGP5 0.25 ! | GROUP ! | ATOM C5 CG321 -0.08 ! | ATOM H51 HGA2 0.09 ! H51---C5---H52 ATOM H52 HGA2 0.09 ! | ATOM P PG1 1.50 ! (-) O3 O1 ATOM O3 OG2P1 -0.78 ! \ / ATOM O4 OG2P1 -0.78 ! P (+) ATOM O1 OG303 -0.57 ! / \ ATOM O2 OG303 -0.57 ! (-) O4 O2 ATOM CG1 CG321 -0.08 ! | ATOM HG11 HGA2 0.09 ! HG11-CG1-HG12 ATOM HG12 HGA2 0.09 ! | GROUP ! | ATOM CG2 CG311 0.14 ! | ATOM HG21 HGA1 0.09 ! HG21-CG2-OG2-HO2 ATOM OG2 OG311 -0.65 ! | ATOM HO2 HGP1 0.42 ! | GROUP ! | ATOM CG3 CG321 0.05 ! | ATOM HG31 HGA2 0.09 ! HG31-CG3-OG3-HO3 ATOM HG32 HGA2 0.09 ! | ATOM OG3 OG311 -0.65 ! HG32 ATOM HO3 HGP1 0.42 BOND CG1 O2 CG1 HG11 CG1 HG12 BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2 BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND P O1 P O2 P O3 P O4 O1 C5 ! internal coordinates for analysis ! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981) ! glycerol backbone IC O2 CG1 CG2 CG3 0. 0. 0. 0. 0. ! t1 IC O2 CG1 CG2 OG2 0. 0. 0. 0. 0. ! t2 IC CG1 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 IC OG2 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 ! zwitterionic headgroup IC P O2 CG1 CG2 0. 0. 0. 0. 0. ! a1 IC O1 P O2 CG1 0. 0. 0. 0. 0. ! a2 IC O2 P O1 C5 0. 0. 0. 0. 0. ! a3 IC C1 C5 O1 P 0. 0. 0. 0. 0. ! a4 IC N C1 C5 O1 0. 0. 0. 0. 0. ! a5 IC C2 N C1 C5 0. 0. 0. 0. 0. ! a6 IC C3 N C1 C5 0. 0. 0. 0. 0. ! a6 IC C4 N C1 C5 0. 0. 0. 0. 0. ! a6 IC O1 O2 *P O3 0. 0. 120. 0. 0. IC O1 O2 *P O4 0. 0. -120. 0. 0. PATCH FIRST NONE LAST NONE RESI TEA 1.00 ! C8H20N tetra ethylammonium (TEA) ! S. Crouzy, S. Berneche and B. Roux ! calc F.E. solvation = -51 kcal/mol ! versus experiment = -49 kcal/mol ! | GROUP ! -C7- ATOM N NG3P0 -0.60 ! | ATOM C1 CG324 -0.10 ! | ATOM C2 CG324 -0.10 ! -C3- ATOM C3 CG324 -0.10 ! | ATOM C4 CG324 -0.10 ! | | | | | ATOM H11 HGP5 0.25 ! -C6--C2---N---C4--C8- (+) ATOM H12 HGP5 0.25 ! | | | | | ATOM H21 HGP5 0.25 ! | ATOM H22 HGP5 0.25 ! -C1- ATOM H31 HGP5 0.25 ! | ATOM H32 HGP5 0.25 ! -C5- ATOM H41 HGP5 0.25 ! | ATOM H42 HGP5 0.25 ! in the following methyl groups, the atom type HAL ! has been changed to HGA3 . adm jr. GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 GROUP ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 GROUP ATOM C7 CG331 -0.27 ATOM H71 HGA3 0.09 ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 GROUP ATOM C8 CG331 -0.27 ATOM H81 HGA3 0.09 ATOM H82 HGA3 0.09 ATOM H83 HGA3 0.09 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 C6 BOND C3 H31 C3 H32 C3 C7 BOND C4 H41 C4 H42 C4 C8 BOND C5 H51 C5 H52 C5 H53 BOND C6 H61 C6 H62 C6 H63 BOND C7 H71 C7 H72 C7 H73 BOND C8 H81 C8 H82 C8 H83 ! ab-initio HF/6-31G* structure IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 IC C3 N C2 C6 1.4967 107.80 180.00 115.98 1.5217 IC N C1 C6 H61 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C6 H62 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C6 H63 1.5176 115.98 -62.29 112.91 1.0820 IC C2 N C3 C7 1.4967 107.80 180.00 115.98 1.5217 IC N C1 C7 H71 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C7 H72 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C7 H73 1.5176 115.98 -62.29 112.91 1.0820 IC C1 N C4 C8 1.4967 107.80 180.00 115.98 1.5217 IC N C1 C8 H81 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C8 H82 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C8 H83 1.5176 115.98 -62.29 112.91 1.0820 RESI ETAM 1.00 ! C2H8NO ethanolamine GROUP ATOM N NG3P3 -0.30 ! HN2 ATOM HN1 HGP2 0.33 ! | ATOM HN2 HGP2 0.33 ! (+) HN1---N---HN3 ATOM HN3 HGP2 0.33 ! | ATOM C1 CG324 0.13 ! | ATOM H11 HGA2 0.09 ! H12---C1---H11 ATOM H12 HGA2 0.09 ! | GROUP ! | ATOM C5 CG321 0.05 ! | ATOM H51 HGA2 0.09 ! H52---C5---H51 ATOM H52 HGA2 0.09 ! | ATOM OH1 OG311 -0.65 ! OH1---HO1 ATOM HO1 HGP1 0.42 BOND N HN1 N HN2 N HN3 N C1 BOND C1 H11 C1 H12 C1 C5 BOND C5 H51 C5 H52 BOND C5 OH1 OH1 HO1 ! HF/6-31G* OPTIMIZED STRUCTURE: IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987 IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495 IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191 IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191 IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191 IC N C5 *C1 H11 0.0000 000.00 120.00 000.00 0.0000 IC N C5 *C1 H12 0.0000 000.00 -120.00 000.00 0.0000 IC OH1 C1 *C5 H51 0.0000 000.00 120.00 000.00 0.0000 IC OH1 C1 *C5 H52 0.0000 000.00 -120.00 000.00 0.0000 RESI GLYC 0.00 ! C7H12O4 Model compound for glycerol headgroup the ! aliphatic tail linker region GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 GROUP ATOM C1 CG321 0.08 ! H12 H21 H31 ATOM H11 HGA2 0.09 ! | | | ATOM H12 HGA2 0.09 ! H11--C1--C2--C3--H32 ATOM O4 OG302 -0.49 ! / | | ATOM C5 CG2O2 0.90 ! O4 O8 H33 ATOM O6 OG2D1 -0.63 ! / \ ATOM C7 CG331 -0.31 ! O6=C5 C9=O10 ATOM H71 HGA3 0.09 ! / \ ATOM H72 HGA3 0.09 ! H71-C7-H73 H113-C11-H111 ATOM H73 HGA3 0.09 ! | | GROUP ! H72 H112 ATOM C2 CG311 0.17 ATOM H21 HGA1 0.09 ATOM O8 OG302 -0.49 ATOM C9 CG2O2 0.90 ATOM O10 OG2D1 -0.63 ATOM C11 CG331 -0.31 ATOM H111 HGA3 0.09 ATOM H112 HGA3 0.09 ATOM H113 HGA3 0.09 BOND C1 C2 C2 C3 BOND C1 O4 O4 C5 C5 C7 C5 O6 BOND C2 O8 O8 C9 C9 C11 C9 O10 BOND C1 H11 C1 H12 BOND C2 H21 BOND C3 H31 C3 H32 C3 H33 BOND C7 H71 C7 H72 C7 H73 BOND C11 H111 C11 H112 C11 H113 IMPR C5 C7 O6 O4 IMPR C9 C11 O10 O8 ! internal coordinates IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 IC H31 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C1 O4 C5 O6 0.0000 0.00 0.00 0.00 0.0000 IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 O8 C9 0.0000 0.00 90.00 0.00 0.0000 IC C2 O8 C9 O10 0.0000 0.00 0.00 0.00 0.0000 IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 RESI AAPM -1.00 ! C8H14O8P acetyl,acetyl-phosphatidylmethanol GROUP ! Model compound for glycerol headgroup the ATOM P1 PG1 1.50 ! aliphatic tail linker region, phosphorylated ATOM OP3 OG2P1 -0.78 ATOM OP4 OG2P1 -0.78 ! HP11 ATOM OP1 OG303 -0.57 ! | ATOM OP2 OG303 -0.57 ! HP13-CP1-HP12 ! \ ATOM CP1 CG331 -0.17 ! (-)OP3 OP1 ATOM HP11 HGA3 0.09 ! \ / ATOM HP12 HGA3 0.09 ! P1 (+) ATOM HP13 HGA3 0.09 ! / \ ! (-)OP4 OP2 ! \ ATOM C3 CG321 -0.08 ! \ Combining DMEP and GLYC lead to omission ATOM H31 HGA2 0.09 ! \ of the C2 methylene group ATOM H32 HGA2 0.09 ! \ GROUP ! | ATOM C1 CG321 0.08 ! H12 H21 | ATOM H11 HGA2 0.09 ! | | | ATOM H12 HGA2 0.09 ! H11--C1--C2--C3--H31 ATOM O4 OG302 -0.49 ! / | | ATOM C5 CG2O2 0.90 ! O4 O8 H32 ATOM O6 OG2D1 -0.63 ! / \ ATOM C7 CG331 -0.31 ! O6=C5 C9=O10 ATOM H71 HGA3 0.09 ! / \ ATOM H72 HGA3 0.09 ! H71-C7-H73 H113-C11-H111 ATOM H73 HGA3 0.09 ! | | GROUP ! H72 H112 ATOM C2 CG311 0.17 ATOM H21 HGA1 0.09 ATOM O8 OG302 -0.49 ATOM C9 CG2O2 0.90 ATOM O10 OG2D1 -0.63 ATOM C11 CG331 -0.31 ATOM H111 HGA3 0.09 ATOM H112 HGA3 0.09 ATOM H113 HGA3 0.09 BOND P1 OP1 P1 OP2 P1 OP3 P1 OP4 OP1 CP1 BOND CP1 HP11 CP1 HP12 CP1 HP13 OP2 C3 BOND C1 C2 C2 C3 BOND C1 O4 O4 C5 C5 C7 C5 O6 BOND C2 O8 O8 C9 C9 C11 C9 O10 BOND C1 H11 C1 H12 C2 H21 C3 H31 C3 H32 BOND C7 H71 C7 H72 C7 H73 BOND C11 H111 C11 H112 C11 H113 IMPR C5 C7 O6 O4 IMPR C9 C11 O10 O8 ! internal coordinates from ic generate, dihedrals corrected IC CP1 OP1 P1 OP2 0.0000 0.00 60.00 0.00 0.0000 IC OP1 OP2 *P1 OP3 0.0000 0.00 120.00 0.00 0.0000 IC OP1 OP2 *P1 OP4 0.0000 0.00 -120.00 0.00 0.0000 IC OP2 P1 OP1 CP1 0.0000 0.00 60.00 0.00 0.0000 IC P1 OP1 CP1 HP11 0.0000 0.00 180.00 0.00 0.0000 IC HP11 OP1 *CP1 HP12 0.0000 0.00 120.00 0.00 0.0000 IC HP11 OP1 *CP1 HP13 0.0000 0.00 -120.00 0.00 0.0000 IC OP1 P1 OP2 C3 0.0000 0.00 -120.00 0.00 0.0000 IC P1 OP2 C3 C2 0.0000 0.00 180.00 0.00 0.0000 IC C2 OP2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 OP2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC OP2 C3 C2 C1 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C1 O4 C5 O6 0.0000 0.00 180.00 0.00 0.0000 IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 O8 C9 0.0000 0.00 60.00 0.00 0.0000 IC C2 O8 C9 O10 0.0000 0.00 180.00 0.00 0.0000 IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 !Small corrections RESI MBUT 0.00 ! C5H10O2 methyl-butyrate GROUP ATOM C4 CG331 -0.27 ! H42 ATOM H41 HGA3 0.09 ! | ATOM H42 HGA3 0.09 ! H41-C4-H43 ATOM H43 HGA3 0.09 ! | GROUP ! | ATOM C3 CG321 -0.18 ! H31-C3-H32 ATOM H31 HGA2 0.09 ! | ATOM H32 HGA2 0.09 ! | GROUP ! H21-C2-H22 ATOM C2 CG321 -0.22 ! | ATOM H21 HGA2 0.09 ! | ATOM H22 HGA2 0.09 ! C1 HM1 ATOM C1 CG2O2 0.90 ! // \ / ATOM O1 OG2D1 -0.63 ! O1 OM-CM-HM2 ATOM OM OG302 -0.49 ! \ ATOM CM CG331 -0.01 ! HM3 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND C1 OM OM CM CM HM1 CM HM2 CM HM3 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 BOND C3 C4 C4 H41 C4 H42 C4 H43 DOUBLE C1 O1 IMPR C1 C2 O1 OM IC C1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 IC H41 C4 C3 C2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 IC OM C2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C1 OM CM 0.0000 0.00 180.00 0.00 0.0000 IC C1 OM CM HM1 0.0000 0.00 180.00 0.00 0.0000 IC HM1 OM *CM HM2 0.0000 0.00 120.00 0.00 0.0000 IC HM1 OM *CM HM3 0.0000 0.00 -120.00 0.00 0.0000 !toppar_all27_na_base_modifications.str RESI DFT 0.00 ! C7H6F2 2,4-difluorotoluene GROUP ! adm jr. w/Daniel Barsky ATOM C1 CG2R61 -0.24 ATOM C2 CG2R66 0.28 ATOM C3 CG2R61 -0.24 ! F4 ATOM C4 CG2R66 0.22 ! | ATOM C5 CG2R61 0.10 ! H51 C4 H3 ATOM C6 CG2R61 -0.28 ! \ / \\ / ATOM H1 HGR62 0.21 ! H52--C5M-C5 C3 ATOM F2 FGR1 -0.21 ! / || | ATOM H3 HGR62 0.19 ! H52 C6 C2 ATOM F4 FGR1 -0.21 ! / \ // \ ATOM C5M CG331 -0.24 ! H6 C1 F2 ATOM H51 HGA3 0.07 ! | ATOM H52 HGA3 0.07 ! H1 ATOM H53 HGA3 0.07 ATOM H6 HGR61 0.21 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 C5M C6 H6 BOND C5M H51 C5M H52 C5M H53 IC C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 IC C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 IC C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 IC C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 IC C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 IC C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 IC C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 IC C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 IC C3 C4 C5 C5M 0.00 0.00 180.00 0.00 0.00 IC C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 IC C4 C5 C5M H51 0.00 0.00 180.00 0.00 0.00 IC H51 C5 *C5M H52 0.00 0.00 60.00 0.00 0.00 IC H51 C5 *C5M H53 0.00 0.00 240.00 0.00 0.00 RESI DFB 0.00 ! C6H4F2 1,3-difluorobenzene aka m-difluorobenzene ! adm jr. w/Daniel Barsky GROUP ! atom numbering based in difluorotoluene ATOM C1 CG2R61 -0.26 ATOM H1 HGR62 0.23 ! F4 ATOM C2 CG2R66 0.27 ! | ATOM F2 FGR1 -0.19 ! H5 C4 H3 ATOM C3 CG2R61 -0.23 ! \ / \\ / ATOM H3 HGR62 0.19 ! C5 C3 ATOM C4 CG2R66 0.27 ! || | ATOM F4 FGR1 -0.19 ! C6 C2 ATOM C5 CG2R61 -0.26 ! / \ // \ ATOM H5 HGR62 0.23 ! H6 C1 F2 ATOM C6 CG2R61 -0.32 ! | ATOM H6 HGR61 0.26 ! H1 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 H5 C6 H6 IC C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 IC C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 IC C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 IC C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 IC C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 IC C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 IC C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 IC C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 IC C3 C4 C5 H5 0.00 0.00 180.00 0.00 0.00 IC C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 !toppar_all27_na_bkb_modifications.str RESI BPET -2.00 ! C4H10O8P2 Bis-methylphosphate-ethane ! adm jr., w/Daniel Barsky GROUP ATOM C1 CG331 -0.17 ! H11 ATOM H11 HGA3 0.09 ! | ATOM H12 HGA3 0.09 ! H13-C1-H12 ATOM H13 HGA3 0.09 ! \ ATOM O2 OG303 -0.57 ! O31 O2 ATOM P3 PG1 1.50 ! \\ / ATOM O31 OG2P1 -0.78 ! (-) P3 ATOM O32 OG2P1 -0.78 ! // \ ATOM O4 OG303 -0.57 ! O32 O4 ATOM C5 CG321 -0.08 ! / ATOM H51 HGA2 0.09 ! H51-C5-H52 ATOM H52 HGA2 0.09 ! | ATOM C6 CG321 -0.08 ! H51-C6-H52 ATOM H61 HGA2 0.09 ! \ ATOM H62 HGA2 0.09 ! O81 O7 ATOM O7 OG303 -0.57 ! \\ / ATOM P8 PG1 1.50 ! (-) P8 ATOM O81 OG2P1 -0.78 ! // \ ATOM O82 OG2P1 -0.78 ! O82 O9 ATOM O9 OG303 -0.57 ! / ATOM C10 CG331 -0.17 ! H101-C10-H102 ATOM H101 HGA3 0.09 ! | ATOM H102 HGA3 0.09 ! H103 ATOM H103 HGA3 0.09 BOND C1 O2 O2 P3 P3 O4 O4 C5 C5 C6 C6 O7 BOND O7 P8 P8 O9 O9 C10 P3 O31 P3 O32 BOND P8 O81 P8 O82 BOND C1 H11 C1 H12 C1 H13 C5 H51 C5 H52 BOND C6 H61 C6 H62 C10 H101 C10 H102 C10 H103 !from IC generate IC H11 C1 O2 P3 0.0000 0.00 180.00 0.00 0.0000 IC C1 O2 P3 O4 0.0000 0.00 180.00 0.00 0.0000 IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC O4 O2 *P3 O31 0.0000 0.00 120.00 0.00 0.0000 IC O4 O2 *P3 O32 0.0000 0.00 -120.00 0.00 0.0000 IC O2 P3 O4 C5 0.0000 0.00 180.00 0.00 0.0000 IC P3 O4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C6 O4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 O4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC O4 C5 C6 O7 0.0000 0.00 180.00 0.00 0.0000 IC O7 C5 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC O7 C5 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C6 O7 P8 0.0000 0.00 180.00 0.00 0.0000 IC C6 O7 P8 O9 0.0000 0.00 180.00 0.00 0.0000 IC O9 O7 *P8 O81 0.0000 0.00 120.00 0.00 0.0000 IC O9 O7 *P8 O82 0.0000 0.00 -120.00 0.00 0.0000 IC O7 P8 O9 C10 0.0000 0.00 180.00 0.00 0.0000 IC P8 O9 C10 H101 0.0000 0.00 180.00 0.00 0.0000 IC H101 O9 *C10 H102 0.0000 0.00 120.00 0.00 0.0000 IC H101 O9 *C10 H103 0.0000 0.00 -120.00 0.00 0.0000 RESI ABNS 0.00 ! C5H10O3 abasic deoxyribose nucleoside (susil) ! adm jr., w/Daniel Barsky GROUP ATOM H5T HGP1 0.42 ATOM O5' OG311 -0.65 ATOM C5' CG321 0.05 ! H5T ATOM H51' HGA2 0.09 ! \ ATOM H52' HGA2 0.09 ! H51' O5' ATOM C4' CG3C51 0.11 ! \ / ATOM H42' HGA1 0.09 ! H52'--C5' O4' H11' ATOM O4' OG3C51 -0.40 ! \ / \ / ATOM C1' CG3C52 0.02 ! H42'-C4' C1'-H12' ATOM H11' HGA2 0.09 ! | | ATOM H12' HGA2 0.09 ! C3'---C2'-H21' ATOM C2' CG3C52 -0.18 ! / | \ ATOM H21' HGA2 0.09 ! O3' H31' H22' ATOM H22' HGA2 0.09 ! | ATOM C3' CG3C51 0.14 ! H32' ATOM H31' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 BOND O4' C4' O4' C1' C4' C5' C4' H42' C4' C3' BOND C1' H11' C1' H12' C1' C2' C2' H21' C2' H22' BOND C3' H31' C3' O3' O3' H32' C5' O5' C5' H51' BOND C5' H52' O5' H5T C2' C3' IC O4' C1' C2' C3' 1.433 104.1 41.2 100.9 1.525 IC C1' C2' C3' C4' 1.521 100.9 325.1 102.6 1.533 IC C2' C3' C4' C5' 1.525 102.6 257.8 113.7 1.513 IC C3' C4' C5' O5' 1.534 113.7 46.5 108.2 1.428 IC C4' C5' O5' H5T 1.513 108.2 170.4 107.7 0.971 IC C3' C4' C5' H52' 1.534 113.7 167.5 108.4 1.098 IC C3' C4' C5' H51' 1.534 113.7 285.5 109.1 1.101 IC C2' C3' C4' H42' 1.525 102.6 135.9 108.6 1.099 IC C1' C2' C3' H31' 1.521 100.9 204.2 113.0 1.097 IC C1' C2' C3' O3' 1.521 100.9 78.3 111.7 1.434 IC C2' C3' O3' H32' 1.525 111.7 65.4 107.1 0.973 IC O4' C1' C2' H22' 1.433 104.1 162.1 113.9 1.096 IC O4' C1' C2' H21' 1.433 104.1 285.5 110.1 1.093 IC O4' C1' C2' H11' 1.433 104.1 243.2 26.8 2.209 IC O4' C1' C2' H12' 1.433 104.1 119.0 28.2 2.173 ! May need to revisit the phosphoramidates when we get to the anionic sulfamates and try an aromatic one. -- Kenno RESI PHA -1.00 ! C2H7NO3P Phosphoramidate (backbone for DNA) GROUP ATOM P1 PG1 1.57 ATOM O3 OG2P1 -0.82 ATOM O4 OG2P1 -0.82 ATOM O2 OG303 -0.56 ! H11 ATOM N1 NG2S3 -0.86 ! | ATOM H1 HGP1 0.33 ! H13- C1-H12 ! \ ATOM C1 CG331 -0.19 ! (-)O3 N1-H1 ATOM H11 HGA3 0.09 ! \ / ATOM H12 HGA3 0.09 ! P1(+1) ATOM H13 HGA3 0.09 ! / \ ! (-)O4 O2 ATOM C2 CG331 -0.19 ! / ATOM H21 HGA3 0.09 ! H23-C2-H22 ATOM H22 HGA3 0.09 ! | ATOM H23 HGA3 0.09 ! H21 BOND P1 N1 P1 O2 P1 O3 P1 O4 N1 C2 N1 H1 O2 C1 BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 ! IC FOR THE g,g crystal conformation (6-31G* opt. structure) IC O3 P1 N1 C2 1.4816 107.70 342.80 123.13 1.4559 IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 IC O4 P1 O2 C1 1.4812 105.80 43.90 118.08 1.4331 IC N1 P1 O2 C1 1.6728 99.90 158.10 118.08 1.4331 IC O2 P1 N1 C2 1.6480 99.90 96.20 123.13 1.4559 IC H11 C1 O2 P1 1.0913 113.30 253.00 123.13 1.6728 IC H12 C1 O2 P1 1.0790 106.20 12.40 123.13 1.6728 IC H13 C1 O2 P1 1.0898 111.90 131.00 123.13 1.6728 IC H21 C2 N1 P1 1.0841 108.20 196.00 118.08 1.6480 IC H22 C2 N1 P1 1.0805 109.90 316.40 118.08 1.6480 IC H23 C2 N1 P1 1.0862 111.20 76.70 118.08 1.6480 PATC FIRS NONE LAST NONE RESI TPHC -1.00 ! C5H11NO4P monoanionic 3'phosphoramidate-tetrahydrofuran ! used to fit epsilon ! Charges and atom types for the monoanionic phosphate groups were ! transfered from residue PHA ! Atom types for aliphatic hydrogens are a mess GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM H41' HGA2 0.09 ! H42'-C4' C1'-H12' ATOM H42' HGA2 0.09 ! | | GROUP ! H31'-C3'-C2'-H21' ATOM C2' CG3C52 -0.18 ! / \ ATOM H21' HGA2 0.09 ! H1-N1 O3 H22' ATOM H22' HGA2 0.09 ! \ / GROUP ! P1 ATOM C3' CG3C51 -0.01 ! / \ ATOM H31' HGA1 0.09 ! O2 O4 ATOM N1 NG2S3 -0.86 ! | ATOM H1 HGP1 0.33 ! H51'-C5-H52' ATOM P1 PG1 1.57 ! | ATOM O3 OG2P1 -0.82 ! H53' ATOM O4 OG2P1 -0.82 ATOM O2 OG303 -0.56 ATOM C5' CG331 -0.19 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' N1 BOND N1 H1 C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' BOND C4' H41' C4' H42' N1 P1 P1 O3 P1 O4 P1 O2 BOND O2 C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC O4' C2' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 IC O4' C2' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 IC C1' C3' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 IC C1' C3' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 IC P1 N1 C3' C4' 1.7190 119.98 185.77 110.95 1.5332 IC O3 P1 N1 C3' 1.4771 109.35 14.75 120.00 1.4525 IC O4 P1 N1 C3' 1.4818 105.19 150.42 120.00 1.4525 IC O2 P1 N1 C3' 1.6379 101.65 263.47 120.00 1.4525 IC C5' O2 P1 N1 1.3955 119.61 286.08 101.65 1.7190 IC H51' C5' O2 P1 1.0859 107.43 179.85 119.61 1.6379 IC H52' C5' O2 P1 1.0835 111.18 299.56 119.61 1.6379 IC H53' C5' O2 P1 1.0868 111.29 60.84 119.61 1.6379 PATC FIRS NONE LAST NONE RESI THNI 0.00 ! C8H13N3O2 tetrahydrofuran with 3'-NH2, 5'-CH2OH, 1'-imidazole GROUP ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons. ATOM C4' CG3C51 0.11 ! Abs. config is arbitrary. ATOM H42' HGA1 0.09 ATOM C1' CG3C51 0.11 ATOM H12' HGA1 0.09 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! HE1 ATOM HG HGR52 0.09 ! / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / | ATOM ND1 NG2R51 -0.04 ! HG-CG | ATOM CE1 CG2R53 0.25 ! \ | ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM N1 NG321 -0.91 ATOM H1 HGPAM2 0.34 ATOM H2 HGPAM2 0.34 GROUP ! Methyl group on C4' ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5' HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' N1 N1 H1 N1 H2 C1' H12' C2' H21' C2' H22' BOND C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5' BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 BOND CE1 HE1 CD2 HD2 CG HG ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC N1 C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H1 N1 C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H2 N1 C3' C2' 0.0 0.0 60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 PATC FIRS NONE LAST NONE RESI THNP -1.00 ! C9H15N3O5P Tetrahydrofuran with 3'-NH-PO2-OCH3, 5'-CH2OH, 1'-imidazole GROUP ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons. ATOM C4' CG3C51 0.11 ! Abs. config is arbitrary. ATOM H42' HGA1 0.09 ATOM C1' CG3C51 0.11 ATOM H12' HGA1 0.09 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! HE1 ATOM HG HGR52 0.09 ! / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / | ATOM ND1 NG2R51 -0.04 ! HG-CG | ATOM CE1 CG2R53 0.25 ! \ | ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 GROUP ! Methyl group on C4' ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5' HGP1 0.42 GROUP ! phosphoramidate group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 -0.01 ATOM N1 NG2S3 -0.86 ATOM H1 HGP1 0.33 ATOM P1 PG1 1.57 ATOM O3 OG2P1 -0.82 ATOM O4 OG2P1 -0.82 ATOM O5 OG303 -0.56 ATOM C5 CG331 -0.19 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' N1 N1 H1 C1' H12' C2' H21' C2' H22' BOND C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5' BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 BOND CE1 HE1 CD2 HD2 CG HG BOND P1 N1 P1 O5 P1 O3 P1 O4 O5 C5 BOND C5 H51 C5 H52 C5 H53 ! This IC table is only an initial guess: IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC ND1 C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P1 N1 C3' C4' 0.0000 000.00 180.00 000.00 0.0000 IC C3' N1 P1 O5 0.0000 000.00 -95.22 000.00 0.0000 IC O5 N1 *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 IC O5 N1 *P1 O4 0.0000 000.00 115.90 000.00 0.0000 IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 IC C5 O5 P1 N1 0.0000 000.00 -46.90 000.00 0.0000 IC H51 C5 O5 P1 0.0000 000.00 180.00 000.00 0.0000 IC H52 C5 O5 P1 0.0000 000.00 60.00 000.00 0.0000 IC H53 C5 O5 P1 0.0000 000.00 -60.00 000.00 0.0000 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 PATC FIRS NONE LAST NONE !toppar_all27_na_carbocyclic.str RESI CPEN 0.00 ! C5H10 cyclopentane, adm jr. ! with north atom types ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C1 CG3C52 -0.18 ! H51 H52 ATOM H11 HGA2 0.09 ! \ / ATOM H12 HGA2 0.09 ! C5 GROUP ! H41 / \ H11 ATOM C2 CG3C52 -0.18 ! \ / \ / ATOM H21 HGA2 0.09 ! H42-C4 C1-H12 ATOM H22 HGA2 0.09 ! | | GROUP ! H31-C3------C2-H21 ATOM C3 CG3C52 -0.18 ! | | ATOM H31 HGA2 0.09 ! H32 H22 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG3C52 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG3C52 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 BOND C5 H51 C5 H52 ! internal coordinates from parameter file, note initial planar geometry IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 PATC FIRS NONE LAST NONE RESI CPES 0.00 ! C5H10 cyclopentane, adm jr. ! with south atom types ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C1 CG3C52 -0.18 ! H51 H52 ATOM H11 HGA2 0.09 ! \ / ATOM H12 HGA2 0.09 ! C5 GROUP ! H41 / \ H11 ATOM C2 CG3C52 -0.18 ! \ / \ / ATOM H21 HGA2 0.09 ! H42-C4 C1-H12 ATOM H22 HGA2 0.09 ! | | GROUP ! H31-C3------C2-H21 ATOM C3 CG3C52 -0.18 ! | | ATOM H31 HGA2 0.09 ! H32 H22 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG3C52 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG3C52 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 BOND C5 H51 C5 H52 ! internal coordinates from parameter file, note initial planar geometry IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 PATC FIRS NONE LAST NONE RESI BPNP -1.00 ! C7H12O4P North carbocyclic sugar with 3'-OPOCH3 ! used to parameterize epsilon ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C2 CG3C51 0.01 ! This charge changed from -0.09 to make it ATOM H21 HGA1 0.09 ! compatible with -OPOCH3 ATOM O3' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O5' OG303 -0.57 ATOM C5' CG331 -0.17 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 ! H61 H62 ! \ / ! C6 GROUP ! / \ H11 ATOM C4 CG3C52 -0.18 ! / \ / ATOM H41 HGA2 0.09 ! H51-C5-----C1 H51' ATOM H42 HGA2 0.09 ! | | / GROUP ! H41-C4 C2--O3'--P--O5'-C5'-H52' ATOM C3 CG3C52 -0.18 ! / \ / \ // \ _ \ ATOM H31 HGA2 0.09 ! H42 \ / H21 O1P O2P H53' ATOM H32 HGA2 0.09 ! C3 GROUP ! / \ ATOM C1 CG3RC1 -0.09 ! H31 H32 ATOM H11 HGA1 0.09 GROUP ATOM C5 CG3RC1 -0.09 ATOM H51 HGA1 0.09 GROUP ATOM C6 CG3C31 -0.18 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C1 C5 C6 C6 C1 C5 H51 BOND C2 H21 C4 H42 C3 H31 C3 H32 BOND C4 H41 C6 H61 C1 H11 BOND C6 H62 C2 O3' O3' P P O1P BOND P O2P P O5' O5' C5' C5' H51' BOND C5' H52' C5' H53' ! internal coordinates from parameter file, note initial planar geometry IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C2 C5 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 240.0 0.00 0.0000 IC C1 C3 *C2 O3' 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C1 C4 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 C6 0.0000 0.00 120.0 0.00 0.0000 IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 IC O3' C2 C1 C5 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C2 C1 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C2 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C2 0.0 0.0 60.0 0.0 0.0 IC O5' P O3' C2 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI BPSP -1.00 ! C7H12O4P south carbcyclic sugar with 3'-OPOCH3 ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C1 CG3RC1 -0.09 ! H31 H32 ATOM H11 HGA1 0.09 ! \ / ! C6 GROUP ! / \ ATOM C2 CG3C52 -0.18 ! / \ ATOM H21 HGA2 0.09 ! H51-C5------C1-H11 ATOM H22 HGA2 0.09 ! | | GROUP ! H41-C4 C2-H22 ATOM C6 CG3C31 -0.18 ! / \ / \ ATOM H61 HGA2 0.09 ! H42 \ / H21 ATOM H62 HGA2 0.09 ! C3-H31 GROUP ! | ATOM C4 CG3C52 -0.18 ! O3' H51' ATOM H41 HGA2 0.09 ! \ / ATOM H42 HGA2 0.09 ! P--O5'-C5'-H52' ! // \ _ \ GROUP ! O1P O2P H53' ATOM C5 CG3RC1 -0.09 ATOM H51 HGA1 0.09 GROUP ATOM C3 CG3C51 0.01 ! This charge changed from -0.09 to make it ATOM H31 HGA1 0.09 ! compatible with -OPOCH3 ATOM O3' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O5' OG303 -0.57 ATOM C5' CG331 -0.17 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C1 C5 C6 C6 C1 C4 H42 BOND C1 H11 C2 H21 C2 H22 BOND C6 H61 C6 H62 C4 H41 BOND C5 H51 C3 H31 C3 O3' O3' P BOND P O1P P O2P P O5' O5' C5' BOND C5' H51' C5' H52' C5' H53' ! internal coordinates IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C2 C5 *C1 C6 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 O3' 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 IC O3' C3 C4 C5 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3 C4 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3 0.0 0.0 60.0 0.0 0.0 IC O5' P O3' C3 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI CSAD 0.00 ! C11H13N5 carbocyclic sugar with adenine base, south ! base attached to C1 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C52 -0.18 ! / \ ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* ATOM H22S HGA2 0.09 ! | | GROUP ! H41S-C4S C2S-H22S ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 0.00 ATOM C5 CG2RC0 0.28 ! H61 H62 ATOM N7 NG2R50 -0.71 ! \ / ATOM C8 CG2R53 0.34 ! N6 ATOM H8 HGR52 0.12 ! | ATOM N9 NG2R51 -0.05 ! C6 ! // \ ATOM N1 NG2R62 -0.74 ! N1 C5--N7\\ ATOM C2 CG2R64 0.50 ! | || C8-H8 ATOM H2 HGR62 0.13 ! C2 C4--N9/ ATOM N3 NG2R62 -0.75 ! / \\ / \ ATOM C4 CG2RC0 0.43 ! H2 N3 \ ATOM C6 CG2R64 0.46 ! \ ATOM N6 NG2S3 -0.77 ! \ ATOM H61 HGP4 0.38 ! \ ATOM H62 HGP4 0.38 ! * BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C2S H21S C2S H22S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C1S N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 BOND C6 N6 N6 H61 N6 H62 C6 C5 BOND C5 N7 C8 H8 C2 H2 DOUB N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S N9 0.0000 108.00 140.0 120.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C3S C2S C1S N9 1.5284 101.97 147.80 120.00 1.4896 !N9 is already defined IC C5S C1S N9 C4 1.5251 120.00 -150.0 125.59 1.3783 !chi IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI CSGU 0.00 ! C11H13N5O carbocyclic sugar with guanine base, south ! base attached to C1 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C52 -0.18 ! / \ ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* ATOM H22S HGA2 0.09 ! | | GROUP ! H41S-C4S C2S-H22S ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 0.00 GROUP ATOM N9 NG2R51 -0.02 ! O6 ATOM C4 CG2RC0 0.26 ! || ATOM N3 NG2R62 -0.74 ! C6 ATOM C2 CG2R64 0.75 ! / \ ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ ATOM H1 HGP1 0.26 ! | || C8-H8 ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ ATOM H21 HGP4 0.32 ! / \\ / \ ATOM H22 HGP4 0.35 ! H21-N2 N3 \ ATOM C6 CG2R63 0.54 ! | \ ATOM O6 OG2D4 -0.51 ! H22 \ ATOM C5 CG2RC0 0.00 ! * ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C2S H21S C2S H22S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C1S N9 BOND N9 C4 N9 C8 C4 N3 C8 H8 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 IMPR C2 N1 N3 N2 IMPR N2 H22 H21 C2 IMPR C6 C5 N1 O6 DONO H21 N2 DONO H22 N2 DONO H1 N1 ACCE O6 C6 ACCE N3 ACCE N7 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S N9 0.0000 108.00 140.0 120.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C3S C2S C1S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C5S C1S N9 C4 1.5251 120.00 -150.0 125.59 1.3783 !chi IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI CSTH 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, south ! base attached to C1 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C52 -0.18 ! / \ ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* ATOM H22S HGA2 0.09 ! | | GROUP ! H41S-C4S C2S-H22S ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 0.00 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! * ATOM H53 HGA3 0.07 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C2S H21S C2S H22S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C1S N1 BOND N1 C2 N1 C6 C2 O2 C4 C5 BOND C2 N3 N3 H3 N3 C4 C4 O4 BOND C5 C5M C5 C6 C6 H6 C5M H51 BOND C5M H52 C5M H53 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S N1 0.0000 108.00 140.0 120.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C3S C2S C1S N1 1.5284 101.97 147.80 120.00 1.4896 !N9 is already defined IC C5S C1S N1 C2 0.0000 120.00 -130.0 125.59 1.3783 !chi IC C1S C2 *N1 C6 0.0000 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0000 0.0 -0.02 0.0 0.0 IC C6 N1 C2 N3 0.0000 0.0 0.06 0.0 0.0 IC N1 N3 *C2 O2 0.0000 0.0 -179.95 0.0 0.0 IC N1 C2 N3 C4 0.0000 0.0 -0.07 0.0 0.0 IC C5 N3 *C4 O4 0.0000 0.0 179.98 0.0 0.0 IC C2 C4 *N3 H3 0.0000 0.0 180.00 0.0 0.0 IC C4 C6 *C5 C5M 0.0000 0.0 -179.94 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 90.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI CSCY 0.00 ! C10H13N3O carbocyclic sugar with cytosine base, south ! base attached to C1 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C52 -0.18 ! / \ ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* ATOM H22S HGA2 0.09 ! | | GROUP ! H41S-C4S C2S-H22S ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 0.00 ! H42 H41 GROUP ! \ / ATOM N1 NG2R61 -0.13 ! N4 ATOM C6 CG2R62 0.05 ! | ATOM H6 HGR62 0.17 ! C4 ATOM C2 CG2R63 0.52 ! / \\ ATOM O2 OG2D4 -0.49 ! H5-C5 N3 ATOM N3 NG2R62 -0.66 ! || | ATOM C4 CG2R64 0.65 ! H6-C6 C2 ATOM N4 NG2S3 -0.75 ! \ / \\ ATOM H41 HGP4 0.37 ! N1 O2 ATOM H42 HGP4 0.33 ! \ ATOM C5 CG2R62 -0.13 ! \ ATOM H5 HGR62 0.07 ! * BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C2S H21S C2S H22S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C1S N1 BOND N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C5 H5 C6 H6 IMPR C4 C5 N3 N4 IMPR C2 N1 N3 O2 IMPR N4 H42 H41 C4 DONO H42 N4 DONO H41 N4 ACCE O2 C2 ACCE N3 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S N1 0.0000 108.00 140.0 120.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C3S C2S C1S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C5S C1S N1 C2 0.0000 120.00 -130.0 125.59 1.3783 !chi IC C1S C2 *N1 C6 0.0000 0.00 -180.00 0.00 0.0000 IC C2 N1 C6 C5 0.0000 0.00 0.0 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.0 0.00 0.0000 IC N1 N3 *C2 O2 0.0000 0.00 180.0 0.00 0.0000 IC N1 C2 N3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C5 N3 *C4 N4 0.0000 0.00 180.00 0.00 0.0000 IC N3 C4 N4 H41 0.0000 0.00 0.00 0.00 0.0000 IC H41 C4 *N4 H42 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI CNAD 0.00 ! C11H13N5 carbocyclic sugar with adenine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM C5 CG2RC0 0.28 ! H61 H62 ATOM N7 NG2R50 -0.71 ! \ / ATOM C8 CG2R53 0.34 ! N6 ATOM H8 HGR52 0.12 ! | ATOM N9 NG2R51 -0.05 ! C6 ! // \ ATOM N1 NG2R62 -0.74 ! N1 C5--N7\\ ATOM C2 CG2R64 0.50 ! | || C8-H8 ATOM H2 HGR62 0.13 ! C2 C4--N9/ ATOM N3 NG2R62 -0.75 ! / \\ / \ ATOM C4 CG2RC0 0.43 ! H2 N3 \ ATOM C6 CG2R64 0.46 ! \ ATOM N6 NG2S3 -0.77 ! \ ATOM H61 HGP4 0.38 ! \ ATOM H62 HGP4 0.38 ! * BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUB N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N9 C4 1.5251 113.71 -120.0 125.59 1.3783 !chi IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNGU 0.00 ! C11H13N5O carbocyclic sugar with guanine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM N9 NG2R51 -0.02 ! O6 ATOM C4 CG2RC0 0.26 ! || ATOM N3 NG2R62 -0.74 ! C6 ATOM C2 CG2R64 0.75 ! / \ ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ ATOM H1 HGP1 0.26 ! | || C8-H8 ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ ATOM H21 HGP4 0.32 ! / \\ / \ ATOM H22 HGP4 0.35 ! H21-N2 N3 \ ATOM C6 CG2R63 0.54 ! | \ ATOM O6 OG2D4 -0.51 ! H22 \ ATOM C5 CG2RC0 0.00 ! * ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N9 BOND N9 C4 N9 C8 C4 N3 C8 H8 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 IMPR C2 N1 N3 N2 IMPR N2 H22 H21 C2 IMPR C6 C5 N1 O6 DONO H21 N2 DONO H22 N2 DONO H1 N1 ACCE O6 C6 ACCE N3 ACCE N7 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N9 C4 1.5251 113.71 -120.00 125.59 1.3783 !chi IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNTH 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! * ATOM H53 HGA3 0.07 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N1 BOND N1 C2 N1 C6 C2 O2 C4 C5 BOND C2 N3 N3 H3 N3 C4 C4 O4 BOND C5 C5M C5 C6 C6 H6 C5M H51 BOND C5M H52 C5M H53 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N1 C2 0.0 0.0 -160.0 0.0 0.0 !chi IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNT1 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! * ATOM H53 HGA3 0.07 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N1 BOND N1 C2 N1 C6 C2 O2 C4 C5 BOND C2 N3 N3 H3 N3 C4 C4 O4 BOND C5 C5M C5 C6 C6 H6 C5M H51 BOND C5M H52 C5M H53 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNT2 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! * ATOM H53 HGA3 0.07 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N1 BOND N1 C2 N1 C6 C2 O2 C4 C5 BOND C2 N3 N3 H3 N3 C4 C4 O4 BOND C5 C5M C5 C6 C6 H6 C5M H51 BOND C5M H52 C5M H53 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNT3 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! * ATOM H53 HGA3 0.07 BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N1 BOND N1 C2 N1 C6 C2 O2 C4 C5 BOND C2 N3 N3 H3 N3 C4 C4 O4 BOND C5 C5M C5 C6 C6 H6 C5M H51 BOND C5M H52 C5M H53 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI CNCY 0.00 ! C10H13N3O carbocyclic sugar with cytosine base, north ! base attached to C2 of carbocyclic sugar ! used to parameterize chi ! the atom types used correspond to those used in the NA ! ribose/deoxyribose moieties GROUP ATOM C4S CG3C52 -0.18 ! H61S H62S ATOM H41S HGA2 0.09 ! \ / ATOM H42S HGA2 0.09 ! C6S GROUP ! / \ ATOM C2S CG3C51 -0.09 ! / \ ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S ! | | GROUP ! H41S-C4S C2S---------* ATOM C3S CG3C52 -0.18 ! / \ / \ ATOM H31S HGA2 0.09 ! H42S \ / H21S ATOM H32S HGA2 0.09 ! C3S ! / \ GROUP ! H31S H32S ATOM C5S CG3RC1 -0.09 ATOM H51S HGA1 0.09 GROUP ATOM C6S CG3C31 -0.18 ATOM H61S HGA2 0.09 ATOM H62S HGA2 0.09 GROUP ATOM C1S CG3RC1 -0.09 ATOM H11S HGA1 0.09 ! H42 H41 GROUP ! \ / ATOM N1 NG2R61 -0.13 ! N4 ATOM C6 CG2R62 0.05 ! | ATOM H6 HGR62 0.17 ! C4 ATOM C2 CG2R63 0.52 ! / \\ ATOM O2 OG2D4 -0.49 ! H5-C5 N3 ATOM N3 NG2R62 -0.66 ! || | ATOM C4 CG2R64 0.65 ! H6-C6 C2 ATOM N4 NG2S3 -0.75 ! \ / \\ ATOM H41 HGP4 0.37 ! N1 O2 ATOM H42 HGP4 0.33 ! \ ATOM C5 CG2R62 -0.13 ! \ ATOM H5 HGR62 0.07 ! * BOND C1S C2S C2S C3S C3S C4S C4S C5S BOND C5S C1S C5S C6S C6S C1S BOND C1S H11S C2S H21S C3S H31S C3S H32S BOND C4S H41S C4S H42S C5S H51S C6S H61S BOND C6S H62S C2S N1 BOND N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C5 H5 C6 H6 IMPR C4 C5 N3 N4 IMPR C2 N1 N3 O2 IMPR N4 H42 H41 C4 DONO H42 N4 DONO H41 N4 ACCE O2 C2 ACCE N3 ! internal coordinates IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 !IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 IC C2 N1 C6 C5 0.0 0.0 0.0 0.0 0.0 IC C6 N1 C2 N3 0.0 0.0 0.0 0.0 0.0 IC N1 N3 *C2 O2 0.0 0.0 180.0 0.0 0.0 IC N1 C2 N3 C4 0.0 0.0 0.0 0.0 0.0 IC C5 N3 *C4 N4 0.0 0.0 180.00 0.0 0.0 IC N3 C4 N4 H41 0.0 0.0 0.00 0.0 0.0 IC H41 C4 *N4 H42 0.0 0.0 180.00 0.0 0.0 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 PATCH FIRST NONE LAST NONE RESI B5NP -1.00 ! C8H14O5P carbocyclic sugar with 5' OPOCH3 ! north conformation ! used to parameterize gamma GROUP ! Note : C1 charge changed from -0.09 to 0.00 to ATOM C5' CG321 -0.08 ! accomodate the CH2-OPOCH3 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O3' OG303 -0.57 ATOM C3' CG331 -0.17 ATOM H31' HGA3 0.09 ! H31' ATOM H32' HGA3 0.09 ! H61 H62 / ATOM H33' HGA3 0.09 ! \ / H51' O1P C3'-H32' ! C6 | | / \ GROUP ! / \ C5'-O5'-P-O3' H33' ATOM C4 CG3C52 -0.18 ! / \ / \ | ATOM H41 HGA2 0.09 ! H51-C5-----C1 H52' O2P ATOM H42 HGA2 0.09 ! | | GROUP ! H41-C4 C2--H21 ATOM C3 CG3C52 -0.18 ! / \ / \ ATOM H31 HGA2 0.09 ! H42 \ / O3T-H3T ATOM H32 HGA2 0.09 ! C3 GROUP ! / \ ATOM C1 CG3RC1 0.00 ! H31 H32 GROUP ATOM C2 CG3C51 0.14 ! changed from -0.18 to accomodate O3'-H ATOM H21 HGA1 0.09 ATOM O3T OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5 CG3RC1 -0.09 ATOM H51 HGA1 0.09 GROUP ATOM C6 CG3C31 -0.18 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C1 C5 C6 C6 C1 C5 H51 BOND C2 H21 C4 H42 C3 H31 C3 H32 BOND C4 H41 C6 H61 C1 C5' C2 O3T BOND C6 H62 C5' O5' O5' P P O1P BOND P O2P P O3' O3' C3' C3' H31' BOND C3' H32' C3' H33' C5' H51' C5' H52' BOND O3T H3T ! internal coordinates from parameter file, note initial planar geometry IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C5 C2 *C1 C5' 0.0000 0.00 240.0 0.00 0.0000 IC C1 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 IC C1 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C2 O3T 0.0000 0.00 240.0 0.00 0.0000 IC C1 C2 O3T H3T 0.0000 0.00 -60.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C1 C4 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 C6 0.0000 0.00 120.0 0.00 0.0000 IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 IC C5' C1 C2 O3T 0.0000 0.00 70.0 0.00 0.0000 IC O5' C5' C1 C2 0.0000 0.00 50.0 0.00 0.0000 IC P O5' C5' C1 0.0 0.0 -105.0 0.0 0.0 IC C5' O5' P O3' 0.0 0.0 140.0 0.0 0.0 IC O5' O3' *P O1P 0.0 0.0 120.0 0.0 0.0 IC O5' O3' *P O2P 0.0 0.0 240.0 0.0 0.0 IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI B5SP -1.00 ! C8H14O5P south carbcyclic sugar with C5'-OPOCH3 GROUP ATOM C1 CG3RC1 -0.09 ATOM H11 HGA1 0.09 ! H61 H62 GROUP ! \ / ATOM C3 CG3C51 0.14 ! C6 ATOM H31 HGA1 0.09 ! / \ ATOM O3T OG311 -0.65 ! H51-C5------C1-H11 H51' O1P H31' ATOM H3T HGP1 0.42 ! | | / | / GROUP ! H41-C4 C2-----C5'-O5'-P-O3'-C3'-H32' ATOM C6 CG3C31 -0.18 ! / \ / \ \ | \ ATOM H61 HGA2 0.09 ! H42 \ / H21 H52' O2P H33' ATOM H62 HGA2 0.09 ! C3-H31 GROUP ! | ATOM C4 CG3C52 -0.18 ! O3T ATOM H41 HGA2 0.09 ! \ ATOM H42 HGA2 0.09 ! H3T GROUP ATOM C5 CG3RC1 -0.09 ATOM H51 HGA1 0.09 GROUP ATOM C2 CG3C51 -0.09 ! This charge changed from -0.18 to make it ATOM H21 HGA1 0.09 ! compatible with C5'-OPOCH3 ATOM C5' CG321 -0.08 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O3' OG303 -0.57 ATOM C3' CG331 -0.17 ATOM H31' HGA3 0.09 ATOM H32' HGA3 0.09 ATOM H33' HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C1 C5 C6 C6 C1 C2 C5' BOND C4 H41 C4 H42 C5' H51' C1 H11 BOND C5' H52' C6 H61 C6 H62 C2 H21 BOND C5 H51 C3 H31 C3 O3T C5' O5' BOND O5' P O3T H3T BOND P O1P P O2P P O3' O3' C3' BOND C3' H31' C3' H32' C3' H33' ! internal coordinates IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 IC C4 C5 C1 C6 1.5000 60.00 120.0 60.00 1.5000 IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 120.0 0.00 0.0000 IC C4 C3 O3T H3T 0.0000 0.00 270.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 240.0 0.00 0.0000 IC C2 C4 *C3 O3T 0.0000 0.00 120.0 0.00 0.0000 IC C3 C1 *C2 C5' 0.0000 0.00 120.0 0.00 0.0000 IC C2 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 IC C2 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 IC C5 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C1 C4 *C5 C6 1.5000 0.00 120.0 60.00 1.5000 IC C1 C5 *C6 H61 0.0000 60.00 120.0 0.00 0.0000 IC C1 C5 *C6 H62 0.0000 60.00 240.0 0.00 0.0000 IC C5' C2 C3 O3T 0.0000 0.00 150.0 0.00 0.0000 IC O5' C5' C2 C3 0.0000 0.00 60.0 0.00 0.0000 IC P O5' C5' C2 0.0 0.0 180.00 0.0 0.0 IC O1P P O5' C5' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O5' C5' 0.0 0.0 60.0 0.0 0.0 IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE !toppar_all27_na_model.str RESI DMEP -1.00 ! C2H6O4P Dimethylphosphate GROUP ATOM P1 PG1 1.50 ! H11 ATOM O3 OG2P1 -0.78 ! | ATOM O4 OG2P1 -0.78 ! H13- C1-H12 ATOM O1 OG303 -0.57 ! \ ATOM O2 OG303 -0.57 ! O3 O1 ATOM C1 CG331 -0.17 ! \\ / ATOM H11 HGA3 0.09 ! (-) P1 ATOM H12 HGA3 0.09 ! // \ ATOM H13 HGA3 0.09 ! O4 O2 ATOM C2 CG331 -0.17 ! / ATOM H21 HGA3 0.09 ! H23-C2-H22 ATOM H22 HGA3 0.09 ! | ATOM H23 HGA3 0.09 ! H21 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 ! IC FOR THE g,g conformation (3-21G* opt. structure) IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 RESI MP_0 0.00 ! CH5O4P Methylphosphate, neutral GROUP ! atom order for molvib ATOM C1 CG331 -0.17 ATOM O1 OG303 -0.56 ! H11 ATOM P1 PG0 1.50 ! | ATOM O2 OG311 -0.62 ! H13--C1--H12 ATOM O3 OG311 -0.62 ! | ATOM O4 OG2P1 -0.64 ! O1 ATOM H11 HGA3 0.09 ! | ATOM H12 HGA3 0.09 ! O4==P1--O3 ATOM H13 HGA3 0.09 ! | \ ATOM H2 HGP1 0.42 ! O2 H3 ATOM H3 HGP1 0.42 ! \ ! H2 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 O3 H3 IC H11 C1 O1 P1 0.0000 0.00 180.00 0.00 0.0000 IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 IC H11 O1 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O1 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 IC O1 P1 O2 H2 0.0000 0.00 180.00 0.00 0.0000 IC O1 P1 O3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI MP_1 -1.00 ! CH4O4P Methylphosphate, anionic GROUP ATOM C1 CG331 -0.170 ! H11 ATOM O1 OG303 -0.620 ! | ATOM P1 PG1 1.500 ! H13--C1--H12 ATOM O2 OG311 -0.670 ! | ATOM O3 OG2P1 -0.820 ! O1 ATOM O4 OG2P1 -0.820 ! | ATOM H11 HGA3 0.090 ! O4==P1==O3 (-) ATOM H12 HGA3 0.090 ! | ATOM H13 HGA3 0.090 ! O2 ATOM H2 HGP1 0.330 ! \ ! H2 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 IC P1 O1 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC O1 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC O1 H11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 IC O1 O2 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 IC O1 O2 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 IC O1 P1 O2 H2 0.0000 0.00 90.00 0.00 0.0000 ! asymm RESI MP_2 -2.00 ! CH3O4P Methylphosphate, dianionic GROUP ATOM P1 PG2 1.100 ATOM O1 OG303 -0.400 ! H11 ATOM O2 OG2P1 -0.900 ! | ATOM O3 OG2P1 -0.900 ! H13--C1--H12 ATOM O4 OG2P1 -0.900 ! | GROUP ! O1 ATOM C1 CG331 -0.270 ! | ATOM H11 HGA3 0.090 ! (-) O4==P1==O3 (-) ATOM H12 HGA3 0.090 ! || ATOM H13 HGA3 0.090 ! O2 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 IC P1 O1 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC O1 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC O1 H11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 IC O1 O2 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 IC O1 O2 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 ! below are residues and patches added for the 97/98 optimization ! and extension of the na all-atom parameters RESI THF 0.00 ! C4H8O tetrahydrofuran, for MOLVIB GROUP ATOM O4' OG3C51 -0.40 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM C3' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM C2' CG3C52 -0.18 ! | | ATOM C1' CG3C52 0.02 ! H31'--C3'--C2'--H21' ATOM H11' HGA2 0.09 ! / \ ATOM H12' HGA2 0.09 ! H32' H22' ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 ATOM H41' HGA2 0.09 ATOM H42' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' IC C1' O4' C4' C3' 0.0000 0.00 45.00 0.00 0.0000 IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 IC C4' O4' C1' C2' 0.0000 0.00 -45.00 0.00 0.0000 IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 IC C2' C4' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI THFM 0.00 ! C5H10O Methyl-tetrahydrofuran GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM C2' CG3C52 -0.18 ATOM C3' CG3C52 -0.18 ! H52' H53' ATOM C4' CG3C51 0.11 ! \ / ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' ATOM H12' HGA2 0.09 ! \ / \ / ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H22' HGA2 0.09 ! | | ATOM H31' HGA2 0.09 ! H31'--C3'--C2'--H21' ATOM H32' HGA2 0.09 ! / \ ATOM H42' HGA1 0.09 ! H32' H22' GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H42' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 0.0000 0.00 45.00 0.00 0.0000 IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 IC O4' C1' C2' C3' 0.0000 0.00 -25.00 0.00 0.0000 IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 IC C4' C2' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 IC C4' C2' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 IC O4' C4' C5' H51' 0.0000 0.00 180.00 0.00 0.0000 IC H51' C4' *C5' H52' 0.0000 0.00 120.00 0.00 0.0000 IC H51' C4' *C5' H53' 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI THFO 0.00 ! C4H8O2 3'-hydroxyl-tetrahydrofuran ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM C2' CG3C52 -0.18 ATOM C4' CG3C52 0.02 ! H41' O4' H11' ATOM H11' HGA2 0.09 ! \ / \ / ATOM H12' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' ATOM H41' HGA2 0.09 ! / \ ATOM H42' HGA2 0.09 ! O3' H22' GROUP ! | ATOM C3' CG3C51 0.14 ! H32' ATOM H31' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI THFI 0.00 ! C7H10N2O imidazole analog with THF ring ! Sugar: transferred from thf; used for optimization of chi, therefore ! the sugar carbon atom types are not rigorously correct ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C51 0.11 ! Abs. config is arbitrary. ATOM H12' HGA1 0.09 ATOM C4' CG3C52 0.02 ! H41' O4' Imidazole ATOM H41' HGA2 0.09 ! \ / \ / ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' GROUP ! | | ATOM C2' CG3C52 -0.18 ! H31'--C3'--C2'--H21' ATOM H21' HGA2 0.09 ! / \ ATOM H22' HGA2 0.09 ! H32' H22' GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / | ATOM ND1 NG2R51 -0.04 ! HG-CG | ATOM CE1 CG2R53 0.25 ! \ | ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 BOND CE1 HE1 CD2 HD2 CG HG ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI THMI 0.00 ! C8H12N2O thf-ch3-imidazole ! C5' has been declared as CN8, and C3' as CN7, for compatibility ! with DNA, but these carbons are rigorously CG331 and CG321 respectively ! Atom types for aliphatic hydrogens based on nucleotide GROUP ! Sugar: transferred from thf ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. ATOM C1' CG3C51 0.11 ! Abs. config is arbitrary. ATOM H12' HGA1 0.09 ATOM C4' CG3C51 0.11 ! H52' H53' ATOM H42' HGA1 0.09 ! \ / GROUP ! H51'-C5' O4' Imidazole ATOM C2' CG3C52 -0.18 ! \ / \ / ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H22' HGA2 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C3' CG3C52 -0.18 ! / \ ATOM H31' HGA2 0.09 ! H32' H22' ATOM H32' HGA2 0.09 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H42' C4' C5' C5' H51' C5' H52' C5' H53' BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI THFC 0.00 ! C5H10O2 THF-3'-OH-4'-CH3 ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H52' H53' ATOM C4' CG3C51 0.11 ! \ / ATOM H42' HGA1 0.09 ! H51'-C5' O4' H11' GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM H31' HGA1 0.09 ! O3' H22' ATOM C3' CG3C51 0.14 ! | ATOM O3' OG311 -0.65 ! H32' ATOM H32' HGP1 0.42 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' BOND C1' H11' C1' H12' BOND C2' H21' C2' H22' BOND C3' H31' BOND C4' H42' BOND C5' H51' C5' H52' C5' H53' BOND O3' H32' IC C4' O4' C1' C2' 0.0000 0.00 180.00 0.00 0.0000 IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 IC C1' O4' C4' C3' 0.0000 0.00 180.00 0.00 0.0000 IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 IC C2' C4' *C3' O3' 0.0000 0.00 120.00 0.00 0.0000 IC C2' C4' *C3' H31' 0.0000 0.00 -120.00 0.00 0.0000 IC C4' C3' O3' H32' 0.0000 0.00 180.00 0.00 0.0000 IC O4' C4' C5' H51' 0.0000 0.00 180.00 0.00 0.0000 IC H51' C4' *C5' H52' 0.0000 0.00 120.00 0.00 0.0000 IC H51' C4' *C5' H53' 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI TH5P -2.00 ! C5H9O5P 5'-phosphate-methyl-tetrahydrofuran (phosphate -2) ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H1' HGA2 0.09 ATOM H1'' HGA2 0.09 ! O1P (-2) ATOM C4' CG3C51 0.11 ! || ATOM H4'' HGA1 0.09 ! O2P==P==O2P GROUP ! | ATOM C2' CG3C52 -0.18 ! H5'' O5' ATOM H2' HGA2 0.09 ! \ | ATOM H2'' HGA2 0.09 ! H5'--C5' O4' H1' GROUP ! \ / \ / ATOM C3' CG3C52 -0.18 ! H4'--C4' C1'--H1'' ATOM H3' HGA2 0.09 ! | | ATOM H3'' HGA2 0.09 ! H3'--C3'--C2'--H2' GROUP ! / \ ATOM C5' CG321 -0.18 ! H3'' H2'' ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 GROUP ATOM O5' OG303 -0.40 ATOM P PG2 1.10 ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TH5H 0.00 ! C5H10O2 5'-hydroxy-methyl-tetrahydrofuran (phosphate -2) ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H1' HGA2 0.09 ATOM H1'' HGA2 0.09 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H4'' HGA1 0.09 ! H5'' O5' GROUP ! \ | ATOM C2' CG3C52 -0.18 ! H5'--C5' O4' H1' ATOM H2' HGA2 0.09 ! \ / \ / ATOM H2'' HGA2 0.09 ! H4'--C4' C1'--H1'' GROUP ! | | ATOM C3' CG3C52 -0.18 ! H3'--C3'--C2'--H2' ATOM H3' HGA2 0.09 ! / \ ATOM H3'' HGA2 0.09 ! H3'' H2'' GROUP ATOM C5' CG321 0.05 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H5' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H5'' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' H5T 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T5PH -1.00 ! C5H10O5P 5'-phosphate-methyl-tetrahydrofuran (phosphate -1) ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM C5' CG321 -0.08 ! Note: has 1 asymmetric carbon. ATOM H5' HGA2 0.09 ! Abs. config is arbitrary. ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.62 ! O1P H5T ATOM P PG1 1.50 ! || / ATOM O1P OG2P1 -0.82 ! O2P==P==O3P ATOM O2P OG2P1 -0.82 ! | ATOM O3P OG311 -0.67 ! O5' ATOM H5T HGP1 0.33 ! | GROUP ! H5'' | ATOM O4' OG3C51 -0.40 ! \ | ATOM C1' CG3C52 0.02 ! H5'--C5' O4' H1' ATOM H1' HGA2 0.09 ! \ / \ / ATOM H1'' HGA2 0.09 ! H4'--C4' C1'--H1'' ATOM C4' CG3C51 0.11 ! | | ATOM H4'' HGA1 0.09 ! H3'--C3'--C2'--H2' GROUP ! / \ ATOM C2' CG3C52 -0.18 ! H3'' H2'' ATOM H2' HGA2 0.09 ATOM H2'' HGA2 0.09 GROUP ATOM C3' CG3C52 -0.18 ATOM H3' HGA2 0.09 ATOM H3'' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P O3P H5T IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC O4' C4' C5' H5' 0.0 0.0 180.0 0.0 0.0 IC O4' C4' C5' H5'' 0.0 0.0 -60.0 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 IC O5' P O3P H5T 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TH3P -2.00 ! C4H7O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -2) ! used to fit epsilon ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H42' HGA2 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C52 -0.18 ! / \ ATOM H21' HGA2 0.09 ! O3' H22' ATOM H22' HGA2 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CG3C51 -0.09 ! || ATOM H31' HGA1 0.09 ! O3P (-2) GROUP ATOM O3' OG303 -0.40 ATOM P PG2 1.10 ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T3PH -1.00 ! C4H8O5P monoanionic 3'phosphate-tetrahydrofuran ! used to fit epsilon ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H42' HGA2 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C52 -0.18 ! / \ ATOM H21' HGA2 0.09 ! O3' H22' ATOM H22' HGA2 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CG3C51 0.01 ! | ATOM H31' HGA1 0.09 ! O3T (-1) ATOM O3' OG303 -0.62 ! \ ATOM P PG1 1.50 ! H3T ATOM O1P OG2P1 -0.82 ATOM O2P OG2P1 -0.82 ATOM O3T OG311 -0.67 ATOM H3T HGP1 0.33 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI R3PH -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA ! Atom types for aliphatic hydrogens based on RNA nucleotide GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H42' HGA2 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C51 0.14 ! / \ ATOM H21' HGA1 0.09 ! O3' O2' ATOM O2' OG311 -0.65 ! | | ATOM H22' HGP1 0.42 ! O1P==P==O2P H22' GROUP ! | ATOM C3' CG3C51 0.01 ! O3T (-1) ATOM H31' HGA1 0.09 ! \ ATOM O3' OG303 -0.62 ! H3T ATOM P PG1 1.50 ATOM O1P OG2P1 -0.82 ATOM O2P OG2P1 -0.82 ATOM O3T OG311 -0.67 ATOM H3T HGP1 0.33 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC O2' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 IC H22' O2' C2' C3' 1.0822 110.88 0.00 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI A3PH -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran ! with O2' hydroxyl in an arabinose (beta) conformation. ! The furanose ring contains atom type CG311 , specific of arabinose GROUP ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.02 ATOM H11' HGA2 0.09 ! H41' O4' H11' ATOM H12' HGA2 0.09 ! \ / \ / ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' ATOM H41' HGA2 0.09 ! | | ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CG3C51 0.14 ! O3' O2' O2' is beta ATOM H22' HGA1 0.09 ! | | ATOM O2' OG311 -0.65 ! O1P==P==O2P H22' ATOM H21' HGP1 0.42 ! | GROUP ! O3T (-1) ATOM C3' CG3C51 0.01 ! \ ATOM H31' HGA1 0.09 ! H3T ATOM O3' OG303 -0.62 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.82 ATOM O2P OG2P1 -0.82 ATOM O3T OG311 -0.67 ATOM H3T HGP1 0.33 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H22' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 IC O2' C2' C3' C4' 1.0846 110.65 120.00 100.86 1.5211 IC H21' O2' C2' C3' 1.0822 110.88 120.00 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T3PM -1.00 ! C5H10O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1) ! capped with a methyl group. This is to investigate the differences ! between BI and BII forms of DNA ! C3T is defined as CG321 to miminck DNA GROUP ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM C4' CG3C52 0.02 ! \ / \ / ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H42' HGA2 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C52 -0.18 ! / \ ATOM H21' HGA2 0.09 ! O3' H22' ATOM H22' HGA2 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CG3C51 0.01 ! | ATOM H31' HGA1 0.09 ! O3T (-1) GROUP ! \ ATOM O3' OG303 -0.57 ! C3T--H3T3 ATOM P PG1 1.50 ! / \ ATOM O1P OG2P1 -0.78 ! H3T1 H3T2 ATOM O2P OG2P1 -0.78 ATOM O3T OG303 -0.57 ATOM C3T CG331 -0.17 ATOM H3T1 HGA3 0.09 ATOM H3T2 HGA3 0.09 ATOM H3T3 HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T BOND C3T H3T1 C3T H3T2 C3T H3T3 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 PATC FIRS NONE LAST NONE RESI TM3P -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) ! This is the DNA version (the RNA version is RM3P, see below) GROUP ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H52' H53' ATOM C4' CG3C51 0.11 ! \ / ATOM H42' HGA1 0.09 ! H51'-C5' O4' H11' GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C3' CG3C51 -0.09 ! O3' H22' ATOM H31' HGA1 0.09 ! | GROUP ! O1P==P==O2P ATOM O3' OG303 -0.40 ! || ATOM P PG2 1.10 ! O3P (-2) ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RM3P -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) ! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to ! allow for the determination of the influence of the ring dihedrals on the ! sugar puckering energetics in the absence of the 2' hydroxyl GROUP ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ATOM C4' CG3C51 0.11 ATOM H42' HGA1 0.09 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C51 -0.09 ATOM H31' HGA1 0.09 GROUP ATOM O3' OG303 -0.40 ATOM P PG2 1.10 ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T2FU -2.00 ! C4H6FO5P THF with PO3 on c3, F (beta, up) on c2 GROUP ! Charges by analogy ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.05 ! Note: has 2 asymmetric carbons. ATOM C4' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM H41' HGA2 0.09 ! \ / \ / ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM C2' CG3C51 0.05 ! | | ATOM H22' HGA6 0.11 ! H31'--C3'--C2'--F2' (beta) ATOM F2' FGA1 -0.22 ! / \ ATOM C3' CG3C51 -0.06 ! O3' H22' ATOM H31' HGA1 0.09 ! | GROUP ! O1P==P==O2P ATOM O3' OG303 -0.40 ! || ATOM P PG2 1.10 ! O3P (-2) ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' F2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC F2' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TMFU -2.00 ! C5H8FO5P THF with ch3 on c4', opo3 on c3', F (beta, up) on c2' GROUP ! Charges by analogy ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.05 ! Note: has 3 asymmetric carbons. ATOM H11' HGA2 0.09 ! Abs. config is arbitrary. ATOM H12' HGA2 0.09 ATOM C4' CG3C51 0.11 ! H52' H53' ATOM H42' HGA1 0.09 ! \ / ATOM C2' CG3C51 0.05 ! H51'-C5' O4' H11' ATOM H22' HGA6 0.11 ! \ / \ / ATOM F2' FGA1 -0.22 ! H42'--C4' C1'--H12' ATOM C3' CG3C51 -0.06 ! | | ATOM H31' HGA1 0.09 ! H31'--C3'--C2'--F2' (beta) GROUP ! / \ ATOM O3' OG303 -0.40 ! O3' H22' ATOM P PG2 1.10 ! | ATOM O1P OG2P1 -0.90 ! O1P==P==O2P ATOM O2P OG2P1 -0.90 ! || ATOM O3P OG2P1 -0.90 ! O3P (-2) GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' H22' C2' F2' BOND C3' O3' C3' H31' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC F2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI T2FD -2.00 ! C4H6FO5P THF with PO3 on c3, F (alpha, down) on c2 GROUP ! Charges by analogy ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.05 ! Note: has 2 asymmetric carbons. ATOM C4' CG3C52 0.02 ! Abs. config is arbitrary. ATOM H11' HGA2 0.09 ATOM H12' HGA2 0.09 ! H41' O4' H11' ATOM H41' HGA2 0.09 ! \ / \ / ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM C2' CG3C51 0.05 ! | | ATOM H21' HGA6 0.11 ! H31'--C3'--C2'--F2' (beta) ATOM F2' FGA1 -0.22 ! / \ ATOM C3' CG3C51 -0.06 ! O3' H22' ATOM H31' HGA1 0.09 ! | GROUP ! O1P==P==O2P ATOM O3' OG303 -0.40 ! || ATOM P PG2 1.10 ! O3P (-2) ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' F2' C2' H21' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC F2' C2' C3' C4' 1.0846 110.65 -148.45 100.86 1.5211 IC H21' C2' C3' C4' 1.0822 110.88 91.68 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TMFD -2.00 ! C5H8FO5P Flourine on C2' (alpha, down) with ch3 on c4', opo3 on c3', oh on c2' GROUP ! Charges by analogy ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.05 ! Note: has 3 asymmetric carbons. ATOM H11' HGA2 0.09 ! Abs. config is arbitrary. ATOM H12' HGA2 0.09 ATOM C4' CG3C51 0.11 ! H52' H53' ATOM H42' HGA1 0.09 ! \ / ATOM C2' CG3C51 0.05 ! H51'-C5' O4' H11' ATOM H21' HGA6 0.11 ! \ / \ / ATOM F2' FGA1 -0.22 ! H42'--C4' C1'--H12' ATOM C3' CG3C51 -0.06 ! | | ATOM H31' HGA1 0.09 ! H31'--C3'--C2'--F2' (beta) GROUP ! / \ ATOM O3' OG303 -0.40 ! O3' H22' ATOM P PG2 1.10 ! | ATOM O1P OG2P1 -0.90 ! O1P==P==O2P ATOM O2P OG2P1 -0.90 ! || ATOM O3P OG2P1 -0.90 ! O3P (-2) GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' F2' C2' H21' BOND C3' O3' C3' H31' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC F2' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI ARMO 0.00 ! C5H10O3 ribose, thfch3ohoh, with the c2' hydroxyl in the beta configuration GROUP ATOM O4' OG3C51 -0.40 ! H52' H53' ATOM C1' CG3C52 0.02 ! \ / ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' ATOM H12' HGA2 0.09 ! \ / \ / ATOM C4' CG3C51 0.11 ! H42'--C4' C1'--H12' ATOM H42' HGA1 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C51 0.14 ! / \ ATOM H22' HGA1 0.09 ! O3' O2' ATOM O2' OG311 -0.65 ! | | (beta) ATOM H21' HGP1 0.42 ! H32' H22' GROUP ATOM C3' CG3C51 0.14 ATOM H31' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' O2' C2' H22' O2' H21' BOND C3' O3' O3' H32' C3' H31' BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC H21' O2' C2' C3' 0.0 0.0 90.00 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC H32' O3' C3' C4' 0.0 0.0 44.72 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI THFA 0.00 ! C8H12N2O2 THF-OH-CH3-IM GROUP ! Note: has 3 asymmetric carbons. ATOM O4' OG3C51 -0.40 ! Abs. config is arbitrary. ATOM C4' CG3C51 0.11 ATOM H42' HGA1 0.09 ! H52' H53' ATOM C1' CG3C51 0.11 ! \ / ATOM H12' HGA1 0.09 ! H51'-C5' O4' Imidazole GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM H31' HGA1 0.09 ! O3' H22' ATOM C3' CG3C51 0.14 ! | ATOM O3' OG311 -0.65 ! H32' ATOM H32' HGP1 0.42 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' H53' BOND O3' H32' BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 PATC FIRS NONE LAST NONE RESI ARAO 0.00 ! C4H8O3 arabinose sugar, oh alpha on c3', oh beta on c2' GROUP ATOM O4' OG3C51 -0.40 ATOM C1' CG3C52 0.02 ATOM H11' HGA2 0.09 ! H41' O4' H11' ATOM H12' HGA2 0.09 ! \ / \ / ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' ATOM H41' HGA2 0.09 ! | | ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CG3C51 0.14 ! O3' O2' ATOM H22' HGA1 0.09 ! | | (beta) ATOM O2' OG311 -0.65 ! H32' H22' ATOM H21' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H31' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O2' H21' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC O2' C2' C3' C4' 0.0000 0.00 91.68 0.0000 0.0000 IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI ARIM 0.00 ! C7H10N2O2 arabinose sugar with imidazole ! transferred from thf GROUP ATOM O4' OG3C51 -0.40 ATOM C1' CG3C51 0.11 ! H41' O4' Imidazole ATOM H12' HGA1 0.09 ! \ / \ / ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' ATOM H41' HGA2 0.09 ! | | ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C3' CG3C52 -0.18 ! H32' O2' ATOM H31' HGA2 0.09 ! | (beta) ATOM H32' HGA2 0.09 ! H22' GROUP ATOM C2' CG3C51 0.14 ATOM H22' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H21' HGP1 0.42 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C2' O2' C1' H12' C2' H22' C3' H31' C3' H32' O2' H21' BOND C4' H41' C4' H42' BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 1.532 101.886 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI AR3P -2.00 ! C4H7O6P arabinose sugar with phosphate on 3' (phosphate -2) GROUP ATOM O4' OG3C51 -0.40 ! H41' O4' H11' ATOM C1' CG3C52 0.02 ! \ / \ / ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' ATOM H11' HGA2 0.09 ! | | ATOM H12' HGA2 0.09 ! H31'--C3'--C2'--H22' (alpha) ATOM H41' HGA2 0.09 ! / \ ATOM H42' HGA2 0.09 ! O3' O2' GROUP ! | | ATOM C2' CG3C51 0.14 ! O1P==P==O2P H21' ATOM H22' HGA1 0.09 ! || ATOM O2' OG311 -0.65 ! O3P (-2) ATOM H21' HGP1 0.42 GROUP ATOM C3' CG3C51 -0.09 ATOM H31' HGA1 0.09 GROUP ATOM O3' OG303 -0.40 ATOM P PG2 1.10 ATOM O1P OG2P1 -0.90 ATOM O2P OG2P1 -0.90 ATOM O3P OG2P1 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O2' H21' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 6.07 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 -25.13 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 33.40 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 -30.20 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 14.98 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 91.77 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -144.31 103.11 1.5346 IC O2' C2' C3' C4' 1.0846 110.65 152.51 100.86 1.5211 IC H21' O2' C2' C3' 0.0 0.0 60.0 0.0 0.0 IC H22' C2' C3' C4' 1.0822 110.88 -84.13 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 87.99 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 136.35 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -102.74 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -151.73 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RIBO 0.00 ! C4H8O3 ribose, both c2' and c3' hydroxyls are alpha GROUP ATOM O4' OG3C51 -0.40 ! H41' O4' H11' ATOM C1' CG3C52 0.02 ! \ / \ / ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' ATOM H11' HGA2 0.09 ! | | ATOM H12' HGA2 0.09 ! H31'--C3'--C2'--H22' ATOM H41' HGA2 0.09 ! / \ ATOM H42' HGA2 0.09 ! O3' O2' GROUP ! | | ATOM C2' CG3C51 0.14 ! H32' H21' ATOM H21' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H22' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H31' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H21' C3' H31' C4' H41' BOND C4' H42' O2' H22' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H22' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI TMPM -1.00 ! C6H12O5P 4'-methyl,3'-methylphosphate tetrahydrofuran (phosphate -1) !charges corrected by adm jr. 9/98 GROUP ATOM O4' OG3C51 -0.40 ! H52' H53' ATOM C1' CG3C52 0.02 ! \ / ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' ATOM H12' HGA2 0.09 ! \ / \ / ATOM C4' CG3C51 0.11 ! H42'--C4' C1'--H12' ATOM H42' HGA1 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CG3C52 -0.18 ! / \ ATOM H21' HGA2 0.09 ! O3' H22' ATOM H22' HGA2 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CG3C51 0.01 ! | ATOM H31' HGA1 0.09 ! O3P (-1) GROUP ! \ ATOM O3' OG303 -0.57 ! C3T--H3T3 ATOM P PG1 1.50 ! / \ ATOM O1P OG2P1 -0.78 ! H3T1 H3T2 ATOM O2P OG2P1 -0.78 ATOM O3P OG303 -0.57 ATOM C3T CG331 -0.17 ATOM H3T1 HGA3 0.09 ATOM H3T2 HGA3 0.09 ATOM H3T3 HGA3 0.09 GROUP ATOM C5' CG331 -0.27 ATOM H51' HGA3 0.09 ATOM H52' HGA3 0.09 ATOM H53' HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TADE 0.00 ! C9H11N5O thf with adenine ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 9-m-ade GROUP ATOM C5 CG2RC0 0.28 ! H61 H62 ATOM N7 NG2R50 -0.71 ! \ / ATOM C8 CG2R53 0.34 ! N6 ATOM H8 HGR52 0.12 ! | ATOM N9 NG2R51 -0.05 ! C6 ATOM N1 NG2R62 -0.74 ! // \ ATOM C2 CG2R64 0.50 ! N1 C5--N7\\ ATOM H2 HGR62 0.13 ! | || C8-H8 ATOM N3 NG2R62 -0.75 ! C2 C4--N9/ ATOM C4 CG2RC0 0.43 ! / \\ / \ ATOM C6 CG2R64 0.46 ! H2 N3 \ ATOM N6 NG2S3 -0.77 ! \ ATOM H61 HGP4 0.38 ! \ ATOM H62 HGP4 0.38 ! \ ATOM O4' OG3C51 -0.40 ! H42' O4' \ ATOM C1' CG3C51 0.11 ! \ / \ \ ATOM H12' HGA1 0.09 ! H41'-C4' C1' ATOM C4' CG3C52 0.02 ! \ / \ ATOM H41' HGA2 0.09 ! H31'--C3'--C2' H12' ATOM H42' HGA2 0.09 ! / / \ GROUP ! H32' H21' H22' ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TCYT 0.00 ! C8H11N3O2 THF with cytosine ! Atom types for aliphatic atoms based on nucleotide !atom order to be consistent with 1-m-cyt GROUP ATOM N1 NG2R61 -0.13 ATOM C6 CG2R62 0.05 ! H42 H41 ATOM H6 HGR62 0.17 ! \ / ATOM C2 CG2R63 0.52 ! N4 ATOM O2 OG2D4 -0.49 ! | ATOM N3 NG2R62 -0.66 ! C4 ATOM C4 CG2R64 0.65 ! / \\ ATOM N4 NG2S3 -0.75 ! H5-C5 N3 ATOM H41 HGP4 0.37 ! || | ATOM H42 HGP4 0.33 ! H6-C6 C2 ATOM C5 CG2R62 -0.13 ! \ / \\ ATOM H5 HGR62 0.07 ! N1 O2 ATOM O4' OG3C51 -0.40 ! \ ATOM C1' CG3C51 0.11 ! \ ATOM H12' HGA1 0.09 ! \ ATOM C4' CG3C52 0.02 ! H42' O4' \ ATOM H41' HGA2 0.09 ! \ / \ \ ATOM H42' HGA2 0.09 ! H41'-C4' C1' GROUP ! \ / \ ATOM C2' CG3C52 -0.18 ! H31'--C3'--C2' H12' ATOM H21' HGA2 0.09 ! / / \ ATOM H22' HGA2 0.09 ! H32' H21' H22' GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 BOND C2 N3 C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C4 C5 N3 N4 IMPR C2 N1 N3 O2 IMPR N4 H42 H41 C4 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TGUA 0.00 ! C9H11N5O2 thf with guanine ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 9-m-gua GROUP ATOM N9 NG2R51 -0.02 ! O6 ATOM C4 CG2RC0 0.26 ! || ATOM N3 NG2R62 -0.74 ! C6 ATOM C2 CG2R64 0.75 ! / \ ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ ATOM H1 HGP1 0.26 ! | || C8-H8 ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ ATOM H21 HGP4 0.32 ! / \\ / \ ATOM H22 HGP4 0.35 ! H21-N2 N3 \ ATOM C6 CG2R63 0.54 ! | \ ATOM O6 OG2D4 -0.51 ! H22 \ ATOM C5 CG2RC0 0.00 ! \ ATOM N7 NG2R50 -0.60 ! H42' O4' \ ATOM C8 CG2R53 0.25 ! \ / \ \ ATOM H8 HGR52 0.16 ! H41'-C4' C1' ATOM O4' OG3C51 -0.40 ! \ / \ ATOM C1' CG3C51 0.11 ! H31'--C3'--C2' H12' ATOM H12' HGA1 0.09 ! / / \ ATOM C4' CG3C52 0.02 ! H32' H21' H22' ATOM H41' HGA2 0.09 ATOM H42' HGA2 0.09 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N1 N3 N2 IMPR N2 H22 H21 C2 IMPR C6 C5 N1 O6 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TTHY 0.00 ! C9H12N2O3 THF with thymine on C1' ! Atom type for N1 changed from NN2 to NN2B, to adjust ! chi in thymine independantly of cytosine. ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 1-m-thy GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! \ ATOM H51 HGA3 0.07 ! \ ATOM H52 HGA3 0.07 ! H42' O4' \ ATOM H53 HGA3 0.07 ! \ / \ \ ATOM O4' OG3C51 -0.40 ! H41'-C4' C1' ATOM C1' CG3C51 0.11 ! \ / \ ATOM H12' HGA1 0.09 ! H31'--C3'--C2' H12' ATOM C4' CG3C52 0.02 ! / / \ ATOM H41' HGA2 0.09 ! H32' H21' H22' ATOM H42' HGA2 0.09 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TURA 0.00 ! C8H10N2O3 THF with uracil on C1' ! Atom type for N1 changed from NN2 to NN2B, in order to adjust ! chi in uracil/thymine independantly of cytosine. ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 1-m-thy GROUP ATOM N1 NG2R61 -0.34 ! O4 ATOM C6 CG2R62 0.20 ! || ATOM H6 HGR62 0.14 ! C4 H3 ATOM C2 CG2R63 0.55 ! / \ / ATOM O2 OG2D4 -0.45 ! H5-C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.53 ! \ / \\ ATOM O4 OG2D4 -0.48 ! N1 O2 ATOM C5 CG2R62 -0.15 ! \ ATOM H5 HGR62 0.10 ! \ ATOM O4' OG3C51 -0.40 ! \ ATOM C1' CG3C51 0.11 ! H42' O4' \ ATOM H12' HGA1 0.09 ! \ / \ \ ATOM C4' CG3C52 0.02 ! H41'-C4' C1' ATOM H41' HGA2 0.09 ! \ / \ ATOM H42' HGA2 0.09 ! H31'--C3'--C2' H12' GROUP ! / / \ ATOM C2' CG3C52 -0.18 ! H32' H21' H22' ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C52 -0.18 ATOM H31' HGA2 0.09 ATOM H32' HGA2 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 H5 C6 H6 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC C4 C6 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI THAO 0.00 ! C8H12N2O3 Nucleoside analogue with imidazole GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Imidazole GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM H31' HGA1 0.09 ! O3' H22' ATOM C3' CG3C51 0.14 ! | ATOM O3' OG311 -0.65 ! H32' ATOM H32' HGP1 0.42 GROUP ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CG 0.0 0.0 90.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSA 0.00 ! C10H13N5O3 deoxy-nucleoside with adenine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Adenine GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' ! Adenine atoms ! / \ GROUP ! O3' H22' ATOM C5 CG2RC0 0.28 ! | ATOM N7 NG2R50 -0.71 ! H32' ATOM C8 CG2R53 0.34 ATOM H8 HGR52 0.12 ATOM N9 NG2R51 -0.05 ATOM N1 NG2R62 -0.74 ATOM C2 CG2R64 0.50 ATOM H2 HGR62 0.13 ATOM N3 NG2R62 -0.75 ATOM C4 CG2RC0 0.43 ATOM C6 CG2R64 0.46 ATOM N6 NG2S3 -0.77 ATOM H61 HGP4 0.38 ATOM H62 HGP4 0.38 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! Methyl group on C4' ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSG 0.00 ! C10H13N5O4 nucleoside with guanine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Guanine GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' !Guanine atoms ! / \ GROUP ! O3' H22' ATOM N9 NG2R51 -0.02 ! | ATOM C4 CG2RC0 0.26 ! H32' ATOM N3 NG2R62 -0.74 ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM N2 NG2S3 -0.68 ATOM H21 HGP4 0.32 ATOM H22 HGP4 0.35 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N1 N3 N2 IMPR N2 H22 H21 C2 IMPR C6 C5 N1 O6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSC 0.00 ! C9H13N3O4 nucleoside with cytosine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Cytosine GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' ! Cytosine atoms ! / \ GROUP ! O3' H22' ATOM N1 NG2R61 -0.13 ! | ATOM C6 CG2R62 0.05 ! H32' ATOM H6 HGR62 0.17 ATOM C2 CG2R63 0.52 ATOM O2 OG2D4 -0.49 ATOM N3 NG2R62 -0.66 ATOM C4 CG2R64 0.65 ATOM N4 NG2S3 -0.75 ATOM H41 HGP4 0.37 ATOM H42 HGP4 0.33 ATOM C5 CG2R62 -0.13 ATOM H5 HGR62 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 BOND C2 N3 C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C4 C5 N3 N4 IMPR C2 N1 N3 O2 IMPR N4 H42 H41 C4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUST 0.00 ! C10H14N2O5 nucleoside with thymine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Thymine GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' ! Atoms for thymine ! / \ GROUP ! O3' H22' ATOM N1 NG2R61 -0.34 ! | ATOM C6 CG2R62 0.17 ! H32' ATOM H6 HGR62 0.17 ATOM C2 CG2R63 0.51 ATOM O2 OG2D4 -0.41 ATOM N3 NG2R61 -0.46 ATOM H3 HGP1 0.36 ATOM C4 CG2R63 0.50 ATOM O4 OG2D4 -0.45 ATOM C5 CG2R62 -0.15 ATOM C5M CG331 -0.11 ATOM H51 HGA3 0.07 ATOM H52 HGA3 0.07 ATOM H53 HGA3 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSU 0.00 ! C9H12N2O5 nucleoside with uracil GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Uracil GROUP ! \ / \ / ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HGA2 0.09 ! | | ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' ! Atoms for uracil ! / \ GROUP ! O3' H22' ATOM N1 NG2R61 -0.34 ! | ATOM C6 CG2R62 0.20 ! H32' ATOM H6 HGR62 0.14 ATOM C2 CG2R63 0.55 ATOM O2 OG2D4 -0.45 ATOM N3 NG2R61 -0.46 ATOM H3 HGP1 0.36 ATOM C4 CG2R63 0.53 ATOM O4 OG2D4 -0.48 ATOM C5 CG2R62 -0.15 ATOM H5 HGR62 0.10 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C5 H5 C6 H6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUS 0.00 ! C8H12N2O4 Ribonucleoside analogue with imidazole GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Imidazole GROUP ! \ / \ / ATOM C2' CG3C51 0.14 ! H42'--C4' C1'--H12' ATOM H21' HGA1 0.09 ! | | ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' ATOM H22' HGP1 0.42 ! / \ GROUP ! O3' O2' ATOM H31' HGA1 0.09 ! | | ATOM C3' CG3C51 0.14 ! H32' H22' ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H22' O2' C2' C3' 0.0 0.0 -60.00 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUA 0.00 ! C10H13N5O4 ribo-nucleoside with adenine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Adenine GROUP ! \ / \ / ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' ATOM C2' CG3C51 0.14 ! | | ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' ATOM H22' HGP1 0.42 ! / \ ! Adenine atoms ! O3' O2' GROUP ! | | ATOM C5 CG2RC0 0.28 ! H32' H22' ATOM N7 NG2R50 -0.71 ATOM C8 CG2R53 0.34 ATOM H8 HGR52 0.12 ATOM N9 NG2R51 -0.05 ATOM N1 NG2R62 -0.74 ATOM C2 CG2R64 0.50 ATOM H2 HGR62 0.13 ATOM N3 NG2R62 -0.75 ATOM C4 CG2RC0 0.43 ATOM C6 CG2R64 0.46 ATOM N6 NG2S3 -0.77 ATOM H61 HGP4 0.38 ATOM H62 HGP4 0.38 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 150.8 113.71 1.4896 IC O4' C1' N9 C4 1.5251 108.6 229.5 125.5 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUG 0.00 ! C10H13N5O5 ribo-nucleoside with guanine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Guanine GROUP ! \ / \ / ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' ATOM C2' CG3C51 0.14 ! | | ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' ATOM H22' HGP1 0.42 ! / \ ! Guanine atoms ! O3' O2' GROUP ! | | ATOM N9 NG2R51 -0.02 ! H32' H22' ATOM C4 CG2RC0 0.26 ATOM N3 NG2R62 -0.74 ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM N2 NG2S3 -0.68 ATOM H21 HGP4 0.32 ATOM H22 HGP4 0.35 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! C5' hydroxyl ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N1 N3 N2 IMPR N2 H22 H21 C2 IMPR C6 C5 N1 O6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUC 0.00 ! C9H13N3O5 ribo-nucleoside with cytosine GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C4' CG3C51 0.11 ! / ATOM H42' HGA1 0.09 ! H51' O5' ATOM C1' CG3C51 0.11 ! \ | ATOM H12' HGA1 0.09 !H52'--C5' O4' Cytosine GROUP ! \ / \ / ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' ATOM C2' CG3C51 0.14 ! | | ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' ATOM H22' HGP1 0.42 ! / \ ! Cytosine atoms ! O3' O2' GROUP ! | | ATOM N1 NG2R61 -0.13 ! H32' H22' ATOM C6 CG2R62 0.05 ATOM H6 HGR62 0.17 ATOM C2 CG2R63 0.52 ATOM O2 OG2D4 -0.49 ATOM N3 NG2R62 -0.66 ATOM C4 CG2R64 0.65 ATOM N4 NG2S3 -0.75 ATOM H41 HGP4 0.37 ATOM H42 HGP4 0.33 ATOM C5 CG2R62 -0.13 ATOM H5 HGR62 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HGA1 0.09 ATOM C3' CG3C51 0.14 ATOM O3' OG311 -0.65 ATOM H32' HGP1 0.42 GROUP ! Methyl group on C4' ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM O5' OG311 -0.65 ATOM H5T HGP1 0.42 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C4 C5 N3 N4 IMPR C2 N1 N3 O2 IMPR N4 H42 H41 C4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUCL -1.00 ! C9H14N2O6P !WARNING: - The charge distribution on the imidazole is identical ! to the charge distribution on the imidazole in THFI, which is ! different from the charge distribution on the equivalent moiety ! in adenine. ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is in non-terminal residues in DNA. GROUP ATOM O4' OG3C51 -0.40 ATOM C1' CG3C51 0.11 ATOM H12' HGA1 0.09 ATOM C4' CG3C51 0.11 ATOM H42' HGA1 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ! The following atom types use the parameters specifically developed ! for the imidazole ! Atom types for aliphatic atoms based on nucleotide ATOM CG CG2R51 -0.05 ! C1' HE1 ATOM HG HGR52 0.09 ! \ / ATOM CD2 CG2R51 0.22 ! ND1---CE1 ATOM HD2 HGR52 0.10 ! / || ATOM ND1 NG2R51 -0.04 ! HG-CG || ATOM CE1 CG2R53 0.25 ! \\ || ATOM HE1 HGR52 0.13 ! CD2---NE2 ATOM NE2 NG2R50 -0.70 ! | ! HD2 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ! H5T ATOM H22' HGA2 0.09 ! | GROUP ! H52' O5' ATOM C3' CG3C51 0.01 ! \ / ATOM H31' HGA1 0.09 ! H51'-C5' O4' Imidazole ATOM O3' OG303 -0.57 ! \ / \ / ATOM P PG1 1.50 ! H42'--C4' C1'--H12' ATOM O1P OG2P1 -0.78 ! | | ATOM O2P OG2P1 -0.78 ! H31'--C3'--C2'--H21' ATOM O3P OG303 -0.57 ! / \ ATOM C3T CG331 -0.17 ! O3' H22' ATOM H3T1 HGA3 0.09 ! | ATOM H3T2 HGA3 0.09 ! O1P==P==O2P ATOM H3T3 HGA3 0.09 ! | GROUP ! O3P (-1) ATOM C5' CG321 0.05 ! \ ATOM H51' HGA2 0.09 ! C3T--H3T3 ATOM H52' HGA2 0.09 ! / \ ATOM H5T HGP1 0.42 ! H3T1 H3T2 ATOM O5' OG311 -0.65 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 90.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI NADE -1.00 ! C11H15N5O6P ! NADE is a nucleotide analogue similar to NUCL, except that the imidazole ! has been replaced by an adenine ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is actuallly in non-terminal residues in the ! DNA. GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C1' CG3C51 0.11 ! | ATOM H12' HGA1 0.09 ! H52' O5' ATOM C4' CG3C51 0.11 ! \ / ATOM H42' HGA1 0.09 ! H51'-C5' O4' Adenine GROUP ! \ / \ / ATOM C5 CG2RC0 0.30 ! H42'--C4' C1'--H12' ATOM N7 NG2R50 -0.69 ! | | ATOM C8 CG2R53 0.34 ! H31'--C3'--C2'--H21' ATOM H8 HGR52 0.10 ! / \ ATOM N9 NG2R51 -0.06 ! O3' H22' ATOM N1 NG2R62 -0.74 ! | ATOM C2 CG2R64 0.50 ! O1P==P==O2P ATOM H2 HGR62 0.13 ! | ATOM N3 NG2R62 -0.75 ! O3P (-1) ATOM C4 CG2RC0 0.43 ! \ ATOM C6 CG2R64 0.44 ! C3T--H3T3 ATOM N6 NG2S3 -0.75 ! / \ ATOM H61 HGP4 0.38 ! H3T1 H3T2 ATOM H62 HGP4 0.37 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C51 0.01 ATOM H31' HGA1 0.09 ATOM O3' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O3P OG303 -0.57 ATOM C3T CG331 -0.17 ATOM H3T1 HGA3 0.09 ATOM H3T2 HGA3 0.09 ATOM H3T3 HGA3 0.09 GROUP ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM H5T HGP1 0.42 ATOM O5' OG311 -0.65 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NTHY -1.00 ! C11H16N2O8P ! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole ! has been replaced by a thymine ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is actuallly in non-terminal residues in the ! DNA. GROUP ATOM O4' OG3C51 -0.40 ! H5T ATOM C1' CG3C51 0.11 ! | ATOM H12' HGA1 0.09 ! H52' O5' ATOM C4' CG3C51 0.11 ! \ / ATOM H42' HGA1 0.09 ! H51'-C5' O4' Thymine GROUP ! \ / \ / ATOM N1 NG2R61 -0.34 ! H42'--C4' C1'--H12' ATOM C6 CG2R62 0.17 ! | | ATOM H6 HGR62 0.17 ! H31'--C3'--C2'--H21' ATOM C2 CG2R63 0.51 ! / \ ATOM O2 OG2D4 -0.41 ! O3' H22' ATOM N3 NG2R61 -0.46 ! | ATOM H3 HGP1 0.36 ! O1P==P==O2P ATOM C4 CG2R63 0.50 ! | ATOM O4 OG2D4 -0.45 ! O3P (-1) ATOM C5 CG2R62 -0.15 ! \ ATOM C5M CG331 -0.11 ! C3T--H3T3 ATOM H51 HGA3 0.07 ! / \ ATOM H52 HGA3 0.07 ! H3T1 H3T2 ATOM H53 HGA3 0.07 GROUP ATOM C2' CG3C52 -0.18 ATOM H21' HGA2 0.09 ATOM H22' HGA2 0.09 GROUP ATOM C3' CG3C51 0.01 ATOM H31' HGA1 0.09 ATOM O3' OG303 -0.57 ATOM P PG1 1.50 ATOM O1P OG2P1 -0.78 ATOM O2P OG2P1 -0.78 ATOM O3P OG303 -0.57 ATOM C3T CG331 -0.17 ATOM H3T1 HGA3 0.09 ATOM H3T2 HGA3 0.09 ATOM H3T3 HGA3 0.09 GROUP ATOM C5' CG321 0.05 ATOM H51' HGA2 0.09 ATOM H52' HGA2 0.09 ATOM H5T HGP1 0.42 ATOM O5' OG311 -0.65 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE !toppar_all27_na_nad_ppi.str RESI NIC 1.00 ! C6H7N2O oxidized nicotinamide (protonated), jjp1/adm jr. ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! H15 GROUP ! \ ATOM H1 HGP2 0.45 ! H16-N14 H8 ATOM N2 NG2R61 -0.52 ! \ | ATOM C3 CG2R62 0.16 ! C12 C7 ATOM H4 HGR63 0.19 ! // \ / \\ ATOM C5 CG2R62 -0.10 ! O13 C9 C5-H6 ATOM H6 HGR63 0.16 ! || | ATOM C7 CG2R62 -0.05 ! H11-C10 C3-H4 ATOM H8 HGR63 0.16 ! \+ // ATOM C9 CG2R62 0.05 ! N2 ATOM C10 CG2R62 0.18 ! | ATOM H11 HGR63 0.16 ! H1 ATOM C12 CG2O1 0.68 ATOM O13 OG2D1 -0.40 ATOM N14 NG2S2 -0.82 ATOM H15 HGP1 0.34 ! trans to O13 ATOM H16 HGP1 0.36 ! cis to O13 BOND N2 H1 C3 H4 C3 C5 C5 H6 BOND C7 H8 C7 C9 N2 C10 BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 DOUBLE C12 O13 C9 C10 C5 C7 N2 C3 IMPR C12 C9 N14 O13 ! ic table for analysis IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 PATCH FIRST NONE LAST NONE RESI NICH 0.00 ! C6H8N2O reduced nicotinamide, jjp1/adm jr. ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98 ! H15 GROUP ! \ ATOM H1 HGPAM1 0.42 ! H16-N14 H8 H17 ATOM N2 NG311 -0.69 ! \ \ / ATOM C3 CG2D1O -0.06 ! C12 C7 ATOM H4 HGA4 0.17 ! / \ / \ ATOM C5 CG2D1 -0.18 ! O13 C9 C5-H6 ATOM H6 HGA4 0.14 ! || || ATOM C7 CG321 -0.28 ! H11-C10 C3-H4 ATOM H8 HGA2 0.09 ! \ / ATOM H17 HGA2 0.09 ! N2 ATOM C10 CG2D1O -0.10 ! | ATOM H11 HGA4 0.14 ! H1 ATOM C9 CG2DC1 0.36 ATOM C12 CG2O1 0.55 ATOM O13 OG2D1 -0.51 ATOM N14 NG2S2 -0.72 ATOM H15 HGP1 0.26 ! trans to O13 ATOM H16 HGP1 0.32 ! cis to O13 BOND N2 H1 N2 C3 C3 H4 C5 H6 BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10 BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 DOUBLE C12 O13 C9 C10 C3 C5 IMPR C3 C5 N2 H4 IMPR C10 C9 N2 H11 IMPR C12 C9 N14 O13 ! new IC table by kevo. Deliberately slightly distorted. IC C10 C9 C7 C5 0.0000 0.00 10.00 0.00 0.0000 IC C7 C9 C10 N2 0.0000 0.00 0.00 0.00 0.0000 IC C10 C7 *C9 C12 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 C5 C3 0.0000 0.00 -10.00 0.00 0.0000 IC C10 C9 C12 N14 0.0000 0.00 180.00 0.00 0.0000 IC C9 N14 *C12 O13 0.0000 0.00 180.00 0.00 0.0000 IC C9 C12 N14 H15 0.0000 0.00 0.00 0.00 0.0000 IC C12 H15 *N14 H16 0.0000 0.00 180.00 0.00 0.0000 IC C9 N2 *C10 H11 0.0000 0.00 180.00 0.00 0.0000 IC C10 C3 *N2 H1 0.0000 0.00 175.00 0.00 0.0000 IC N2 C5 *C3 H4 0.0000 0.00 180.00 0.00 0.0000 IC C3 C7 *C5 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 C9 *C7 H8 0.0000 0.00 120.00 0.00 0.0000 IC C5 C9 *C7 H17 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PPI1 -3.00 ! CH3O7P2 Inorganic phosphate, jjp1/adm jr. GROUP ATOM C1 CG331 -0.17 ATOM O11 OG303 -0.62 ATOM P1 PG1 1.50 ! H11 ATOM O12 OG304 -0.74 ! | ATOM O13 OG2P1 -0.82 ! H13--C1--H12 ATOM O14 OG2P1 -0.82 ! | ! O11 ATOM P2 PG2 1.10 ! | ATOM O22 OG2P1 -0.90 ! O14==P1==O13 (-) ATOM O23 OG2P1 -0.90 ! | ATOM O24 OG2P1 -0.90 ! O12 ! | ATOM H11 HGA3 0.09 ! (-) O24==P2==O23 (-) ATOM H12 HGA3 0.09 ! || ATOM H13 HGA3 0.09 ! O22 BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 BOND C1 H11 C1 H12 C1 H13 BOND O12 P2 P2 O22 P2 O23 P2 O24 IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 IC O11 O12 *P1 O13 0.0000 000.00 120.0 000.00 0.0000 IC O11 O12 *P1 O14 0.0000 000.00 -120.0 000.00 0.0000 IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 IC P1 O12 P2 O22 0.0000 000.00 0.0 000.00 0.0000 IC O12 O22 *P2 O23 0.0000 000.00 120.0 000.00 0.0000 IC O12 O22 *P2 O24 0.0000 000.00 -120.0 000.00 0.0000 IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 IC O11 H11 *C1 H12 0.0000 000.00 120.0 000.00 0.0000 IC O11 H11 *C1 H13 0.0000 000.00 -120.0 000.00 0.0000 PATC FIRS NONE LAST NONE RESI PPI2 -2.00 ! CH4O7P2 Inorganic phosphate, protonated, adm jr. ! terminal P charges based on neutral GROUP ! methylphosphate ATOM C1 CG331 -0.17 ATOM O11 OG303 -0.62 ATOM P1 PG1 1.46 ! H11 ATOM O12 OG304 -0.63 ! | ATOM O13 OG2P1 -0.83 ! H13--C1--H12 ATOM O14 OG2P1 -0.83 ! | ! O11 ATOM P2 PG1 1.34 ! | ATOM O22 OG311 -0.71 ! -0.60 , kevo O14==P1==O13 (-) ATOM H22 HGP1 0.44 ! 0.33 , kevo | ATOM O23 OG2P1 -0.86 ! | ATOM O24 OG2P1 -0.86 ! O12 ! | ATOM H11 HGA3 0.09 ! O24==P2==O23 (-) ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! O22 ! \ ! H22 BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 BOND C1 H11 C1 H12 C1 H13 BOND O12 P2 P2 O22 P2 O23 P2 O24 O22 H22 ! IC Table IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 IC O12 P2 O22 H22 0.0000 000.00 180.0 000.00 0.0000 PATC FIRS NONE LAST NONE RESI AMP -2.00 ! C10H12N5O7P adenosine monophosphate, jjp1/adm jr. ! atom names correspond to pdb nomenclature GROUP ATOM C4' CG3C51 0.11 ! H61 H62 ATOM H4' HGA1 0.09 ! \ / ATOM O4' OG3C51 -0.40 ! N6 ATOM C1' CG3C51 0.11 ! | ATOM H1' HGA1 0.09 ! C6 GROUP ! // \ ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ ATOM N7 NG2R50 -0.71 ! | || C8-H8 ATOM C8 CG2R53 0.34 ! C2 C4--N9/ ATOM H8 HGR52 0.12 ! / \\ / \ ATOM N9 NG2R51 -0.05 ! H2 N3 \ ! \ ATOM N1 NG2R62 -0.74 ! \ ATOM C2 CG2R64 0.50 ! \ ATOM H2 HGR62 0.13 ! O1A H5' H4' O4' \ ATOM N3 NG2R62 -0.75 ! | | \ / \ \ ATOM C4 CG2RC0 0.43 ! O3A=PA-O5'-C5'---C4' C1' ATOM C6 CG2R64 0.46 ! | | \ / \ ! O2A H5'' C3'--C2' H1' ATOM N6 NG2S3 -0.77 ! / \ / \ ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' ATOM H62 HGP4 0.38 ! | | GROUP ! H3T H2' ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.18 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 GROUP ATOM O5' OG303 -0.40 ATOM PA PG2 1.10 ATOM O1A OG2P1 -0.90 ATOM O2A OG2P1 -0.90 ATOM O3A OG2P1 -0.90 BOND PA O1A PA O2A PA O3A PA O5' O3' H3T BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O3A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 !IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 !IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 !IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 !IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI ADP -3.00 ! C10H12N5O10P2 adenosine diphosphate, jjp1/adm jr. ! atom names correspond to pdb nomenclature GROUP ATOM C4' CG3C51 0.11 ! H61 H62 ATOM H4' HGA1 0.09 ! \ / ATOM O4' OG3C51 -0.40 ! N6 ATOM C1' CG3C51 0.11 ! | ATOM H1' HGA1 0.09 ! C6 GROUP ! // \ ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ ATOM N7 NG2R50 -0.71 ! | || C8-H8 ATOM C8 CG2R53 0.34 ! C2 C4--N9/ ATOM H8 HGR52 0.12 ! / \\ / \ ATOM N9 NG2R51 -0.05 ! H2 N3 \ ! \ ATOM N1 NG2R62 -0.74 ! \ ATOM C2 CG2R64 0.50 ! \ ATOM H2 HGR62 0.13 ! O3B O1A H5' H4' O4' \ ATOM N3 NG2R62 -0.75 ! | | | \ / \ \ ATOM C4 CG2RC0 0.43 ! O1B=PB-O3A--PA-O5'-C5'---C4' C1' ATOM C6 CG2R64 0.46 ! | | | \ / \ ! O2B O2A H5'' C3'--C2' H1' ATOM N6 NG2S3 -0.77 ! / \ / \ ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' ATOM H62 HGP4 0.38 ! | | GROUP ! H3T H2' ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.62 ATOM PA PG1 1.50 ATOM O1A OG2P1 -0.82 ATOM O2A OG2P1 -0.82 ATOM O3A OG304 -0.74 ATOM PB PG2 1.10 ATOM O1B OG2P1 -0.90 ATOM O2B OG2P1 -0.90 ATOM O3B OG2P1 -0.90 BOND PB O3A PB O1B PB O2B PB O3B O3A PA BOND PA O1A PA O2A PA O5' O3' H3T BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O3B ACCE O2B ACCE O1B IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 IC PB O3A PA O5' 0.0000 000.00 120.0 000.00 0.0000 IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 IC O3A O3B *PB O1B 0.0000 000.00 120.0 000.00 0.0000 IC O3A O3B *PB O2B 0.0000 000.00 -120.0 000.00 0.0000 IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 !IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 !IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 !IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 !IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI ATP -4.00 ! C10H12N5O13P3 adenosine triphosphate , jjp1/adm jr. !atom names correspond to pdb nomenclature GROUP ATOM C4' CG3C51 0.11 ! H61 H62 ATOM H4' HGA1 0.09 ! \ / ATOM O4' OG3C51 -0.40 ! N6 ATOM C1' CG3C51 0.11 ! | ATOM H1' HGA1 0.09 ! C6 GROUP ! // \ ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ ATOM N7 NG2R50 -0.71 ! | || C8-H8 ATOM C8 CG2R53 0.34 ! C2 C4--N9/ ATOM H8 HGR52 0.12 ! / \\ / \ ATOM N9 NG2R51 -0.05 ! H2 N3 \ ! \ ATOM N1 NG2R62 -0.74 ! \ ATOM C2 CG2R64 0.50 ! \ ATOM H2 HGR62 0.13 ! (-)O3G O2B O1A H5' H4' O4' \ ATOM N3 NG2R62 -0.75 ! | | | | \ / \ \ ATOM C4 CG2RC0 0.43 !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4' C1' ATOM C6 CG2R64 0.46 ! | | | | \ / \ ! (-)O2G (-)O1B (-)O2A H5'' C3'--C2' H1' ATOM N6 NG2S3 -0.77 ! / \ / \ ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' ATOM H62 HGP4 0.38 ! | | GROUP ! H3T H2' ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.62 ATOM PA PG1 1.50 ATOM O1A OG2P1 -0.82 ATOM O2A OG2P1 -0.82 ATOM O3A OG304 -0.74 ATOM PB PG1 1.50 ATOM O1B OG2P1 -0.82 ATOM O2B OG2P1 -0.82 ATOM O3B OG304 -0.86 ! charge adjusted to yield total triP of -4.0 ATOM PG PG2 1.10 ATOM O1G OG2P1 -0.90 ATOM O2G OG2P1 -0.90 ATOM O3G OG2P1 -0.90 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG O2G PG O3G BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O2B ACCE O1B ACCE O3B ACCE O3G ACCE O1G ACCE O2G IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 IC PB O3A PA O5' 0.0000 000.00 120.0 000.00 0.0000 IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 IC O3A O3B *PB O1B 0.0000 000.00 120.0 000.00 0.0000 IC O3A O3B *PB O2B 0.0000 000.00 -120.0 000.00 0.0000 IC O3A PB O3B PG 0.0000 000.00 150.0 000.00 0.0000 IC PB O3B PG O1G 0.0000 000.00 150.0 000.00 0.0000 IC O3B O1G *PG O2G 0.0000 000.00 120.0 000.00 0.0000 IC O3B O1G *PG O3G 0.0000 000.00 -120.0 000.00 0.0000 IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 !IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 !IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 !IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 !IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NAD -1.00 ! C21H26N7O14P2 oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params GROUP ATOM AC4' CG3C51 0.11 ! AH61 AH62 ATOM AH4' HGA1 0.09 ! \ / ATOM AO4' OG3C51 -0.40 ! AN6 ATOM AC1' CG3C51 0.11 ! | ATOM AH1' HGA1 0.09 ! AC6 GROUP ! // \ ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ ATOM AH8 HGR52 0.12 ! / \\ / \ ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NG2R62 -0.74 ! \ ATOM AC2 CG2R64 0.50 ! \ ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NG2S3 -0.77 ! \ / \ / \ ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HGP4 0.38 ! \ | | GROUP ! \ AH3T AH2T ATOM AC2' CG3C51 0.14 ! \ NH71 ATOM AH2' HGA1 0.09 ! \ \ ATOM AO2' OG311 -0.65 ! \ NH72-NN7 NH4 ATOM AH2T HGP1 0.42 ! \ \ | GROUP ! \ NC7 NC4 ATOM AC3' CG3C51 0.14 ! \ // \ / \\ ATOM AH3' HGA1 0.09 ! \ NO7 NC3 NC5-NH5 ATOM AO3' OG311 -0.65 ! \ || | ATOM AH3T HGP1 0.42 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 GROUP ! \ | \ / \ \+// ATOM AC5' CG321 -0.08 ! NC5'--NC4' NC1'---------NN1 ATOM AH5' HGA2 0.09 ! | \ / \ ATOM AH5S HGA2 0.09 ! NH5' NC3'-NC2'NH1' ATOM AP PG1 1.50 ! / \ / \ ATOM AO1 OG2P1 -0.82 ! NO3' NH3'NO2'NH2' ATOM AO2 OG2P1 -0.82 ! | | ATOM AO5' OG303 -0.62 ! NH3T NH2T ATOM O3 OG304 -0.68 ATOM NP PG1 1.50 ATOM NO1 OG2P1 -0.82 ATOM NO2 OG2P1 -0.82 ATOM NO5' OG303 -0.62 ATOM NC5' CG321 -0.08 ATOM NH5S HGA2 0.09 ATOM NH5' HGA2 0.09 GROUP ATOM NC2' CG3C51 0.14 ATOM NH2' HGA1 0.09 ATOM NO2' OG311 -0.65 ATOM NH2T HGP1 0.42 GROUP ATOM NC3' CG3C51 0.14 ATOM NH3' HGA1 0.09 ATOM NO3' OG311 -0.65 ATOM NH3T HGP1 0.42 GROUP ATOM NC1' CG3C53 0.11 ATOM NH1' HGA1 0.09 ATOM NC4' CG3C51 0.11 ATOM NH4' HGA1 0.09 ATOM NO4' OG3C51 -0.40 GROUP ATOM NN1 NG2R61 -0.07 ATOM NC6 CG2R62 0.16 ATOM NH6 HGR63 0.19 ATOM NC5 CG2R62 -0.10 ATOM NH5 HGR63 0.16 ATOM NC4 CG2R62 -0.05 ATOM NH4 HGR63 0.16 ATOM NC3 CG2R62 0.05 ATOM NC2 CG2R62 0.18 ATOM NH2 HGR63 0.16 ATOM NC7 CG2O1 0.68 ATOM NO7 OG2D1 -0.40 ATOM NN7 NG2S2 -0.82 ATOM NH71 HGP1 0.34 ! trans to amide O ATOM NH72 HGP1 0.36 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC5 NC6 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 IMPR AC6 AC5 AN1 AN6 IMPR AN6 AH62 AH61 AC6 IMPR NC7 NC3 NN7 NO7 DONO AH61 AN6 DONO AH62 AN6 DONO AH2T AO2' DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 IC NO7 NC7 NN7 NH71 1.2300 120.00 180.00 120.00 1.0000 IC NO7 NC7 NN7 NH72 1.2300 120.00 0.00 120.00 1.0000 IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 PATCH FIRST NONE LAST NONE RESI NADH -2.00 ! C21H27N7O14P2 reduced nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params GROUP ATOM AC4' CG3C51 0.11 ! AH61 AH62 ATOM AH4' HGA1 0.09 ! \ / ATOM AO4' OG3C51 -0.40 ! AN6 ATOM AC1' CG3C51 0.11 ! | ATOM AH1' HGA1 0.09 ! AC6 GROUP ! // \ ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ ATOM AH8 HGR52 0.12 ! / \\ / \ ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NG2R62 -0.74 ! \ ATOM AC2 CG2R64 0.50 ! \ ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NG2S3 -0.77 ! \ / \ / \ ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HGP4 0.38 ! \ | | GROUP ! \ AH3T AH2T ATOM AC2' CG3C51 0.14 ! \ NH71 ATOM AH2' HGA1 0.09 ! \ \ ATOM AO2' OG311 -0.65 ! \ NH72-NN7 NH4 NH42 ATOM AH2T HGP1 0.42 ! \ \ \ / GROUP ! \ NC7 NC4 ATOM AC3' CG3C51 0.14 ! \ / \ / \ ATOM AH3' HGA1 0.09 ! \ NO7 NC3 NC5-NH5 ATOM AO3' OG311 -0.65 ! \ || || ATOM AH3T HGP1 0.42 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 GROUP ! \ | \ / \ \ / ATOM AC5' CG321 -0.08 ! NC5'--NC4' NC1'---------NN1 ATOM AH5' HGA2 0.09 ! | \ / \ ATOM AH5S HGA2 0.09 ! NH5' NC3'-NC2'NH1' ATOM AP PG1 1.50 ! / \ / \ ATOM AO1 OG2P1 -0.82 ! NO3' NH3'NO2'NH2' ATOM AO2 OG2P1 -0.82 ! | | ATOM AO5' OG303 -0.62 ! NH3T NH2T ATOM O3 OG304 -0.68 ATOM NP PG1 1.50 ATOM NO1 OG2P1 -0.82 ATOM NO2 OG2P1 -0.82 ATOM NO5' OG303 -0.62 ATOM NC5' CG321 -0.08 ATOM NH5S HGA2 0.09 ATOM NH5' HGA2 0.09 GROUP ATOM NC2' CG3C51 0.14 ATOM NH2' HGA1 0.09 ATOM NO2' OG311 -0.65 ATOM NH2T HGP1 0.42 GROUP ATOM NC3' CG3C51 0.14 ATOM NH3' HGA1 0.09 ATOM NO3' OG311 -0.65 ATOM NH3T HGP1 0.42 GROUP ATOM NC1' CG3C51 0.11 ATOM NH1' HGA1 0.09 ATOM NC4' CG3C51 0.11 ATOM NH4' HGA1 0.09 ATOM NO4' OG3C51 -0.40 GROUP ATOM NN1 NG301 -0.27 !N2 ATOM NC6 CG2D1O -0.06 !C3 ATOM NH6 HGA4 0.17 !H4 ATOM NC5 CG2D1 -0.18 !C5 ATOM NH5 HGA4 0.14 !H6 ATOM NC4 CG321 -0.28 !C7 ATOM NH4 HGA2 0.09 !H8 ATOM NH42 HGA2 0.09 !H17 ATOM NC3 CG2DC1 0.36 !C9 ATOM NC2 CG2D1O -0.10 !C10 ATOM NH2 HGA4 0.14 !H11 ATOM NC7 CG2O1 0.55 !C12 ATOM NO7 OG2D1 -0.51 !O13 ATOM NN7 NG2S2 -0.72 !N14 ATOM NH71 HGP1 0.26 !H15 ! trans to amide O ATOM NH72 HGP1 0.32 !H16 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC4 NC5 NC6 NN1 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 DOUBLE NC2 NC3 NC5 NC6 IMPR AC6 AC5 AN1 AN6 IMPR AN6 AH62 AH61 AC6 IMPR NC6 NC5 NN1 NH6 IMPR NC2 NC3 NN1 NH2 IMPR NC7 NC3 NN7 NO7 DONO AH61 AN6 DONO AH62 AN6 DONO AH2T AO2' DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 ! IC table was beyond repair ==> replaced (kevo) IC AP O3 NP NO5' 1.6011 92.88 167.64 96.12 1.6600 IC AP O3 NP NO1 1.6011 92.88 62.12 118.93 1.5360 IC AP O3 NP NO2 1.6011 92.88 -85.34 112.47 1.5263 IC NP O3 AP AO5' 1.6074 92.88 169.27 93.16 1.6636 IC O3 AO5' *AP AO1 1.6011 93.16 -115.15 102.32 1.5255 IC O3 AO5' *AP AO2 1.6011 93.16 120.82 100.53 1.5378 IC O3 AP AO5' AC5' 1.6011 93.16 -65.25 117.89 1.4434 IC AP AO5' AC5' AC4' 1.6636 117.89 -111.08 111.72 1.5437 IC AC4' AO5' *AC5' AH5' 1.5437 111.72 121.91 113.03 1.1186 IC AC4' AO5' *AC5' AH5S 1.5437 111.72 -120.24 108.95 1.1118 IC AO5' AC5' AC4' AC3' 1.4434 111.72 32.23 115.30 1.5403 IC AC5' AC4' AC3' AO3' 1.5437 115.30 82.44 113.07 1.4340 IC AH3T AO3' AC3' AC4' 0.9956 102.19 -78.33 113.07 1.5403 IC AO4' AC3' *AC4' AC5' 1.4436 105.34 -122.02 115.30 1.5437 IC AC2' AC4' *AC3' AO3' 1.5312 103.02 -124.10 113.07 1.4340 IC AC4' AC3' AC2' AC1' 1.5403 103.02 34.98 101.18 1.5414 IC AC3' AC2' AC1' AN9 1.5312 101.18 88.32 111.78 1.4609 IC AO4' AC1' AN9 AC4 1.4336 105.95 -149.10 127.35 1.3682 IC AC1' AC4 *AN9 AC8 1.4609 127.35 179.89 106.85 1.3818 IC AC4 AN9 AC8 AN7 1.3682 106.85 0.34 112.92 1.3338 IC AC8 AN9 AC4 AC5 1.3818 106.85 -0.12 105.55 1.3970 IC AC8 AN7 AC5 AC6 1.3338 103.64 -179.39 132.41 1.4083 IC AN7 AC5 AC6 AN1 1.3924 132.41 179.90 118.87 1.3616 IC AC5 AC6 AN1 AC2 1.4083 118.87 -0.29 119.53 1.3626 IC AN9 AC5 *AC4 AN3 1.3682 105.55 -179.81 125.91 1.3450 IC AC5 AN1 *AC6 AN6 1.4083 118.87 179.60 117.11 1.3448 IC AN1 AC6 AN6 AH61 1.3616 117.11 -176.96 119.87 0.9980 IC AH61 AC6 *AN6 AH62 0.9980 119.87 174.83 117.95 0.9930 IC AN9 AN7 *AC8 AH8 1.3818 112.92 -179.84 125.33 1.0978 IC AN1 AN3 *AC2 AH2 1.3626 125.37 -179.78 117.21 1.0932 IC AO4' AC2' *AC1' AH1' 1.4336 107.49 -118.51 111.70 1.1012 IC AC1' AC3' *AC2' AH2' 1.5414 101.18 120.60 111.56 1.0994 IC AC2' AC4' *AC3' AH3' 1.5312 103.02 114.75 109.97 1.1020 IC AC3' AO4' *AC4' AH4' 1.5403 105.34 -116.63 105.95 1.1009 IC NC5' NO5' NP NO2 1.4353 125.45 -110.33 103.18 1.5263 IC NP NO5' NC5' NC4' 1.6600 125.45 -100.01 114.36 1.5573 IC NO5' NC5' NC4' NC3' 1.4353 114.36 42.03 115.36 1.5403 IC NC5' NC4' NC3' NC2' 1.5573 115.36 -91.03 101.62 1.5376 IC NC4' NC3' NC2' NC1' 1.5403 101.62 -39.21 100.72 1.5399 IC NC3' NC2' NC1' NO4' 1.5376 100.72 35.40 105.65 1.4395 IC NO2' NC2' NC1' NO4' 1.4392 115.62 158.69 105.65 1.4395 IC NH2T NO2' NC2' NC1' 0.9686 102.30 157.15 115.62 1.5399 IC NO4' NC2' *NC1' NH1' 1.4395 105.65 -114.11 109.56 1.1015 IC NC1' NC3' *NC2 NH2' 2.4605 9.08 131.65 26.20 3.7695 IC NC2' NC4' *NC3 NH3' 4.7247 22.53 -7.48 17.99 6.8615 IC NC3' NO4' *NC4 NH4' 6.4634 19.31 -56.73 2.93 7.0769 IC NC4' NO5' *NC5 NH5' 5.1412 29.29 35.30 14.10 6.2151 IC NC4' NO5' *NC5 NH5S 5.1412 29.29 55.33 24.87 4.9161 IC NC3' NC2' NC1' NN1 1.5376 100.72 153.61 113.06 1.4871 IC NO3' NC3' NC2' NC1' 1.4390 111.69 79.56 100.72 1.5399 IC NH3T NO3' NC3' NC2' 0.9633 102.31 55.04 111.69 1.5376 IC NC2' NC1' NN1 NC2 1.5399 113.06 115.33 119.55 1.3595 IC NC1' NN1 NC2 NC3 1.4871 119.55 179.60 123.83 1.3763 IC NN1 NC2 NC3 NC4 1.3595 123.83 5.03 118.94 1.5428 IC NC2 NC3 NC4 NC5 1.3763 118.94 -6.70 111.53 1.5189 IC NC3 NC4 NC5 NC6 1.5428 111.53 5.08 122.32 1.3550 IC NN1 NC2 NC3 NC7 1.3595 123.83 -158.70 118.33 1.5212 IC NC2 NC3 NC7 NO7 1.3763 118.33 -160.59 120.47 1.2354 IC NC2 NC3 NC7 NN7 1.3763 118.33 20.47 119.04 1.3683 IC NO7 NC7 NN7 NH71 1.2354 120.48 -176.29 120.56 0.9982 IC NO7 NC7 NN7 NH72 1.2354 120.48 0.52 116.91 0.9963 IC NC2 NC3 NC4 NH4 1.3763 118.94 -136.51 113.66 1.1068 IC NC2 NC3 NC4 NH42 1.3763 118.94 108.33 105.96 1.1115 IC NC3 NC4 NC5 NH5 1.5428 111.53 -149.76 116.93 1.0907 IC NC4 NC5 NC6 NH6 1.5189 122.32 179.97 119.29 1.0969 IC NC6 NN1 NC2 NH2 1.3589 121.05 177.95 116.69 1.0900 IC AC1' AC3' *AC2' AO2' 1.5414 101.18 -118.90 110.89 1.4319 IC AC3' AC2' AO2' AH2T 1.5312 110.89 -28.83 100.98 0.9715 PATCH FIRST NONE LAST NONE RESI NADP -2.00 ! C21H26N7O17P3 oxidized nicotinamide adenine dinucleotide, ! NADP+, adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params GROUP ATOM AC4' CG3C51 0.11 ! AH61 AH62 ATOM AH4' HGA1 0.09 ! \ / ATOM AO4' OG3C51 -0.40 ! AN6 ATOM AC1' CG3C51 0.11 ! | ATOM AH1' HGA1 0.09 ! AC6 GROUP ! // \ ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ ATOM AH8 HGR52 0.12 ! / \\ / \ ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NG2R62 -0.74 ! \ ATOM AC2 CG2R64 0.50 ! \ ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NG2S3 -0.77 ! \ / \ / \ ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HGP4 0.38 ! \ | | GROUP ! \ AH3T AO1P=AP2==AO2P (-) ATOM AC2' CG3C51 0.01 ! \ | NH71 ATOM AH2' HGA1 0.09 ! \ AH2T-AO2T / ATOM AO2' OG303 -0.62 ! \ NH72-NN7 NH4 ATOM AP2 PG1 1.50 ! \ \ | ATOM AO1P OG2P1 -0.82 ! \ NC7 NC4 ATOM AO2P OG2P1 -0.82 ! \ / \ / \\ ATOM AO2T OG311 -0.67 ! \ NO7 NC3 NC5-NH5 ATOM AH2T HGP1 0.33 ! \ || | GROUP ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 ATOM AC3' CG3C51 0.14 ! \ | \ / \ \+ // ATOM AH3' HGA1 0.09 ! NC5'--NC4' NC1'---------NN1 ATOM AO3' OG311 -0.65 ! | \ / \ ATOM AH3T HGP1 0.42 ! NH5' NC3'-NC2'NH1' GROUP ! / \ / \ ATOM AC5' CG321 -0.08 ! NO3' NH3'NO2'NH2' ATOM AH5' HGA2 0.09 ! | | ATOM AH5S HGA2 0.09 ! NH3T NH2T ATOM AP PG1 1.50 ATOM AO1 OG2P1 -0.82 ATOM AO2 OG2P1 -0.82 ATOM AO5' OG303 -0.62 ATOM O3 OG304 -0.68 ATOM NP PG1 1.50 ATOM NO1 OG2P1 -0.82 ATOM NO2 OG2P1 -0.82 ATOM NO5' OG303 -0.62 ATOM NC5' CG321 -0.08 ATOM NH5S HGA2 0.09 ATOM NH5' HGA2 0.09 GROUP ATOM NC2' CG3C51 0.14 ATOM NH2' HGA1 0.09 ATOM NO2' OG311 -0.65 ATOM NH2T HGP1 0.42 GROUP ATOM NC3' CG3C51 0.14 ATOM NH3' HGA1 0.09 ATOM NO3' OG311 -0.65 ATOM NH3T HGP1 0.42 GROUP ATOM NC1' CG3C53 0.11 ATOM NH1' HGA1 0.09 ATOM NC4' CG3C51 0.11 ATOM NH4' HGA1 0.09 ATOM NO4' OG3C51 -0.40 GROUP ATOM NN1 NG2R61 -0.07 ATOM NC6 CG2R62 0.16 ATOM NH6 HGR63 0.19 ATOM NC5 CG2R62 -0.10 ATOM NH5 HGR63 0.16 ATOM NC4 CG2R62 -0.05 ATOM NH4 HGR63 0.16 ATOM NC3 CG2R62 0.05 ATOM NC2 CG2R62 0.18 ATOM NH2 HGR63 0.16 ATOM NC7 CG2O1 0.68 ATOM NO7 OG2D1 -0.40 ATOM NN7 NG2S2 -0.82 ATOM NH71 HGP1 0.34 ! trans to amide O ATOM NH72 HGP1 0.36 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC5 NC6 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 IMPR AC6 AC5 AN1 AN6 IMPR AN6 AH62 AH61 AC6 IMPR NC7 NC3 NN7 NO7 DONO AH61 AN6 DONO AH62 AN6 DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 DONO AH2T AO2T ACCE AO2T ACCE AO1P ACCE AO2P ACCE AO2' IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 !IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 PATCH FIRST NONE LAST NONE RESI NDPH -3.00 ! C21H27N7O17P3 reduced nicotinamide adenine dinucleotide ! NADPH, VARNAI/adm jr. ! from RESI NADH and 3PHO ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params GROUP ATOM AC4' CG3C51 0.11 ! AH61 AH62 ATOM AH4' HGA1 0.09 ! \ / ATOM AO4' OG3C51 -0.40 ! AN6 ATOM AC1' CG3C51 0.11 ! | ATOM AH1' HGA1 0.09 ! AC6 GROUP ! // \ ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ ATOM AH8 HGR52 0.12 ! / \\ / \ ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NG2R62 -0.74 ! \ ATOM AC2 CG2R64 0.50 ! \ ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NG2S3 -0.77 ! \ / \ / \ ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HGP4 0.38 ! \ | | GROUP ! \ AH3T AO1P=AP2==AO2P (-) ATOM AC2' CG3C51 0.01 ! \ | NH71 ATOM AH2' HGA1 0.09 ! \ AH2T-AO2T / ATOM AO2' OG303 -0.62 ! \ NH72-NN7 NH4 NH42 ATOM AP2 PG1 1.50 ! \ \ \ / ATOM AO1P OG2P1 -0.82 ! \ NC7 NC4 ATOM AO2P OG2P1 -0.82 ! \ / \ / \ ATOM AO2T OG311 -0.67 ! \ NO7 NC3 NC5-NH5 ATOM AH2T HGP1 0.33 ! \ || || GROUP ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 ATOM AC3' CG3C51 0.14 ! \ | \ / \ \ / ATOM AH3' HGA1 0.09 ! NC5'--NC4' NC1'---------NN1 ATOM AO3' OG311 -0.65 ! | \ / \ ATOM AH3T HGP1 0.42 ! NH5' NC3'-NC2'NH1' GROUP ! / \ / \ ATOM AC5' CG321 -0.08 ! NO3' NH3'NO2'NH2' ATOM AH5' HGA2 0.09 ! | | ATOM AH5S HGA2 0.09 ! NH3T NH2T ATOM AP PG1 1.50 ATOM AO1 OG2P1 -0.82 ATOM AO2 OG2P1 -0.82 ATOM AO5' OG303 -0.62 ATOM O3 OG304 -0.68 ATOM NP PG1 1.50 ATOM NO1 OG2P1 -0.82 ATOM NO2 OG2P1 -0.82 ATOM NO5' OG303 -0.62 ATOM NC5' CG321 -0.08 ATOM NH5S HGA2 0.09 ATOM NH5' HGA2 0.09 GROUP ATOM NC2' CG3C51 0.14 ATOM NH2' HGA1 0.09 ATOM NO2' OG311 -0.65 ATOM NH2T HGP1 0.42 GROUP ATOM NC3' CG3C51 0.14 ATOM NH3' HGA1 0.09 ATOM NO3' OG311 -0.65 ATOM NH3T HGP1 0.42 GROUP ATOM NC1' CG3C51 0.11 ATOM NH1' HGA1 0.09 ATOM NC4' CG3C51 0.11 ATOM NH4' HGA1 0.09 ATOM NO4' OG3C51 -0.40 GROUP ATOM NN1 NG301 -0.27 !N2 ATOM NC6 CG2D1O -0.06 !C3 ATOM NH6 HGA4 0.17 !H4 ATOM NC5 CG2D1 -0.18 !C5 ATOM NH5 HGA4 0.14 !H6 ATOM NC4 CG321 -0.28 !C7 ATOM NH4 HGA2 0.09 !H8 ATOM NH42 HGA2 0.09 !H17 ATOM NC3 CG2DC1 0.36 !C9 ATOM NC2 CG2D1O -0.10 !C10 ATOM NH2 HGA4 0.14 !H11 ATOM NC7 CG2O1 0.55 !C12 ATOM NO7 OG2D1 -0.51 !O13 ATOM NN7 NG2S2 -0.72 !N14 ATOM NH71 HGP1 0.26 !H15 ! trans to amide O ATOM NH72 HGP1 0.32 !H16 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC4 NC5 NC6 NN1 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T DOUBLE NC2 NC3 NC5 NC6 IMPR AC6 AC5 AN1 AN6 IMPR AN6 AH62 AH61 AC6 IMPR NC6 NC5 NN1 NH6 IMPR NC2 NC3 NN1 NH2 IMPR NC7 NC3 NN7 NO7 DONO AH61 AN6 DONO AH62 AN6 DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 DONO AH2T AO2T ACCE AO2T ACCE AO1P ACCE AO2P ACCE AO2' ! IC table was beyond repair ==> replaced (kevo) IC AP O3 NP NO5' 1.5954 101.60 146.76 97.71 1.6612 IC AP O3 NP NO1 1.5954 101.60 37.78 120.83 1.5331 IC AP O3 NP NO2 1.5954 101.60 -103.74 108.35 1.5264 IC NP O3 AP AO5' 1.6061 101.60 164.74 96.46 1.6655 IC O3 AO5' *AP AO1 1.5954 96.46 -112.08 103.67 1.5327 IC O3 AO5' *AP AO2 1.5954 96.46 120.37 104.32 1.5300 IC O3 AP AO5' AC5' 1.5954 96.46 -55.54 115.61 1.4409 IC AP AO5' AC5' AC4' 1.6655 115.61 -176.43 112.56 1.5479 IC AC4' AO5' *AC5' AH5' 1.5479 112.56 120.22 110.27 1.1161 IC AC4' AO5' *AC5' AH5S 1.5479 112.56 -120.20 110.70 1.1158 IC AO5' AC5' AC4' AC3' 1.4409 112.56 51.86 114.73 1.5409 IC AC5' AC4' AC3' AO3' 1.5479 114.73 138.72 111.81 1.4297 IC AH3T AO3' AC3' AC4' 0.9769 98.08 131.19 111.81 1.5409 IC AO4' AC3' *AC4' AC5' 1.4383 107.54 -123.87 114.73 1.5479 IC AC2' AC4' *AC3' AO3' 1.5457 105.32 -117.01 111.81 1.4297 IC AC4' AC3' AC2' AC1' 1.5409 105.32 -20.11 102.83 1.5465 IC AC3' AC2' AC1' AN9 1.5457 102.83 133.28 112.16 1.4587 IC AO4' AC1' AN9 AC4 1.4312 106.95 -116.73 127.46 1.3677 IC AC1' AC4 *AN9 AC8 1.4587 127.46 -179.84 106.79 1.3782 IC AC4 AN9 AC8 AN7 1.3677 106.79 0.68 113.34 1.3348 IC AC8 AN9 AC4 AC5 1.3782 106.79 -0.37 105.46 1.3976 IC AC8 AN7 AC5 AC6 1.3348 103.19 179.17 132.19 1.4074 IC AN7 AC5 AC6 AN1 1.3939 132.19 -179.58 119.12 1.3630 IC AC5 AC6 AN1 AC2 1.4074 119.12 -0.76 119.15 1.3635 IC AN9 AC5 *AC4 AN3 1.3677 105.46 179.47 125.74 1.3491 IC AC5 AN1 *AC6 AN6 1.4074 119.12 -178.70 117.19 1.3459 IC AN1 AC6 AN6 AH61 1.3630 117.19 175.38 119.41 0.9983 IC AH61 AC6 *AN6 AH62 0.9983 119.41 -173.82 118.04 0.9911 IC AN9 AN7 *AC8 AH8 1.3782 113.34 -179.89 124.72 1.0924 IC AN1 AN3 *AC2 AH2 1.3635 125.66 -177.12 116.89 1.0924 IC AO4' AC2' *AC1' AH1' 1.4312 109.65 -115.54 110.14 1.1011 IC AC1' AC3' *AC2' AH2' 1.5465 102.83 118.17 107.40 1.1056 IC AC2' AC4' *AC3' AH3' 1.5457 105.32 120.87 111.10 1.0996 IC AC3' AO4' *AC4' AH4' 1.5409 107.54 -117.93 106.34 1.1019 IC NC5' NO5' NP NO2 1.4347 124.65 -95.76 105.77 1.5264 IC NP NO5' NC5' NC4' 1.6612 124.65 -102.77 115.34 1.5645 IC NO5' NC5' NC4' NC3' 1.4347 115.34 72.35 114.08 1.5406 IC NC5' NC4' NC3' NC2' 1.5645 114.08 -96.03 100.78 1.5383 IC NC4' NC3' NC2' NC1' 1.5406 100.78 -41.51 100.30 1.5383 IC NC3' NC2' NC1' NO4' 1.5383 100.30 39.58 104.62 1.4444 IC NO2' NC2' NC1' NO4' 1.4360 117.19 163.91 104.62 1.4444 IC NH2T NO2' NC2' NC1' 0.9842 100.86 159.27 117.19 1.5383 IC NO4' NC2' *NC1' NH1' 1.4444 104.62 -113.82 109.33 1.1012 IC NC1' NC3' *NC2 NH2' 2.4561 9.02 118.36 26.48 3.8155 IC NC2' NC4' *NC3 NH3' 4.7358 22.19 -3.45 17.84 6.8914 IC NC3' NO4' *NC4 NH4' 6.4975 19.19 -28.86 1.80 7.1052 IC NC4' NO5' *NC5 NH5' 5.2257 29.02 -4.03 10.68 6.4109 IC NC4' NO5' *NC5 NH5S 5.2257 29.02 51.20 19.04 5.7156 IC NC3' NC2' NC1' NN1 1.5383 100.30 157.86 113.54 1.4868 IC NO3' NC3' NC2' NC1' 1.4402 112.92 77.43 100.30 1.5383 IC NH3T NO3' NC3' NC2' 0.9765 102.62 77.94 112.92 1.5383 IC NC2' NC1' NN1 NC2 1.5383 113.54 116.11 119.27 1.3589 IC NC1' NN1 NC2 NC3 1.4868 119.27 179.46 123.90 1.3767 IC NN1 NC2 NC3 NC4 1.3589 123.90 5.63 118.97 1.5415 IC NC2 NC3 NC4 NC5 1.3767 118.97 -6.62 111.44 1.5185 IC NC3 NC4 NC5 NC6 1.5415 111.44 4.92 122.41 1.3553 IC NN1 NC2 NC3 NC7 1.3589 123.90 -157.15 117.98 1.5220 IC NC2 NC3 NC7 NO7 1.3767 117.98 -162.23 120.57 1.2364 IC NC2 NC3 NC7 NN7 1.3767 117.98 18.92 119.12 1.3682 IC NO7 NC7 NN7 NH71 1.2364 120.30 -176.87 120.26 0.9992 IC NO7 NC7 NN7 NH72 1.2364 120.30 1.04 117.08 0.9956 IC NC2 NC3 NC4 NH4 1.3767 118.97 -136.44 113.82 1.1070 IC NC2 NC3 NC4 NH42 1.3767 118.97 108.13 105.93 1.1113 IC NC3 NC4 NC5 NH5 1.5415 111.44 -151.27 117.50 1.0907 IC NC4 NC5 NC6 NH6 1.5185 122.41 178.77 119.10 1.0963 IC NC6 NN1 NC2 NH2 1.3587 120.94 176.28 116.55 1.0900 IC AC1' AC3' *AC2' AO2' 1.5465 102.83 -119.62 111.15 1.4465 IC AC3' AC2' AO2' AP2 1.5457 111.15 -174.33 121.36 1.5853 IC AC2' AO2' AP2 AO2T 1.4465 121.36 -92.28 103.37 1.5606 IC AO2T AO2' *AP2 AO1P 1.5606 103.37 -113.56 111.24 1.4737 IC AO2T AO2' *AP2 AO2P 1.5606 103.37 109.47 111.16 1.4708 IC AO2' AP2 AO2T AH2T 1.5853 103.37 81.16 108.83 0.9674 PATCH FIRST NONE LAST NONE !toppar_amines.str RESI AMM1 0.00 ! NH3 Ammonia GROUP ATOM N1 NG331 -1.125 ATOM H11 HGPAM3 0.375 ATOM H12 HGPAM3 0.375 ATOM H13 HGPAM3 0.375 BOND N1 H11 N1 H12 N1 H13 IC H11 H12 *N1 H13 0.0 0.0 120. 0.0 0.0 IC H13 H11 *N1 H12 0.0 0.0 120. 0.0 0.0 !redundant definition needed to enable seeding. RESI MAM1 0.00 ! CH5N methylamine GROUP ATOM N1 NG321 -0.99 ATOM C1 CG3AM2 -0.06 ! HC1 HN1 ATOM HN1 HGPAM2 0.39 ! \ / ATOM HN2 HGPAM2 0.39 ! HC2-C1---N1 ATOM HC1 HGAAM2 0.09 ! / \ ATOM HC2 HGAAM2 0.09 ! HC3 HN2 ATOM HC3 HGAAM2 0.09 BOND N1 C1 N1 HN1 N1 HN2 BOND C1 HC1 C1 HC2 C1 HC3 IC N1 HC1 *C1 HC2 0.00 0.00 120.0 0.0 0.0 IC N1 HC1 *C1 HC3 0.00 0.00 -120.0 0.0 0.0 IC HC1 C1 N1 HN1 0.00 0.00 180.0 0.0 0.0 IC C1 HN1 *N1 HN2 0.00 0.00 120.0 0.0 0.0 RESI DMAM 0.00 ! C2H7N dimethylamine GROUP ATOM N1 NG311 -0.82 ATOM HN1 HGPAM1 0.40 ATOM C1 CG3AM1 -0.06 ! H11 HN1 ATOM C2 CG3AM1 -0.06 ! \ / ATOM H11 HGAAM1 0.09 ! H12-C1---N1 ATOM H12 HGAAM1 0.09 ! / \ ATOM H13 HGAAM1 0.09 ! H13 C2-H23 ATOM H21 HGAAM1 0.09 ! / \ ATOM H22 HGAAM1 0.09 ! H21 H22 ATOM H23 HGAAM1 0.09 BOND N1 HN1 N1 C1 N1 C2 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IC C1 N1 C2 H21 0.00 0.00 180.0 0.0 0.0 IC N1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 IC N1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 IC C1 C2 *N1 HN1 0.00 0.00 120.0 0.0 0.0 IC C2 N1 C1 H11 0.00 0.00 180.0 0.0 0.0 IC N1 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC N1 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 RESI TMAM 0.00 ! C3H9N trimethylamine, adm jr. GROUP ! H31 H32 ATOM N1 NG301 -0.63 ! \ / ATOM C1 CG3AM0 -0.06 ! H11 C3-H33 ATOM C2 CG3AM0 -0.06 ! \ / ATOM C3 CG3AM0 -0.06 ! H12-C1---N1 ATOM H11 HGAAM0 0.09 ! / \ ATOM H12 HGAAM0 0.09 ! H13 C2-H23 ATOM H13 HGAAM0 0.09 ! / \ ATOM H21 HGAAM0 0.09 ! H21 H22 ATOM H22 HGAAM0 0.09 ATOM H23 HGAAM0 0.09 ATOM H31 HGAAM0 0.09 ATOM H32 HGAAM0 0.09 ATOM H33 HGAAM0 0.09 BOND N1 C1 N1 C2 N1 C3 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC C1 C2 *N1 C3 0.00 0.00 120.0 0.0 0.0 IC C2 N1 C1 H11 0.00 0.00 180.0 0.0 0.0 IC N1 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC N1 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC C1 N1 C2 H21 0.00 0.00 180.0 0.0 0.0 IC N1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 IC N1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 IC C1 N1 C3 H31 0.00 0.00 180.0 0.0 0.0 IC N1 H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 IC N1 H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 !toppar_prot_na_all.str RESI PPH1 -1.00 ! C6H6O4P phenol phosphate residue GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 ATOM HD1 HGR61 0.115 ! // \\ GROUP ! HG--CG CZ--OH O2-H2 ATOM CD2 CG2R61 -0.115 ! \ __ / \ / ATOM HD2 HGR61 0.115 ! CD2--CE2 P1 (-) GROUP ! | | // \\ ATOM CE1 CG2R61 -0.21 ! HD2 HE2 O4 O3 ATOM HE1 HGR61 0.21 GROUP ATOM CE2 CG2R61 -0.21 ATOM HE2 HGR61 0.21 GROUP ATOM CZ CG2R61 -0.16 ATOM OH OG303 -0.36 ATOM P1 PG1 1.40 ATOM O2 OG311 -0.75 ATOM H2 HGP1 0.39 ATOM O3 OG2P1 -0.76 ATOM O4 OG2P1 -0.76 BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 BOND CE1 CZ CE2 CZ CZ OH BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND P1 OH P1 O2 P1 O3 P1 O4 BOND O2 H2 ! IC table IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CE1 *CZ OH 1.3750 120.00 180.00 120.00 1.3800 IC CE1 CZ OH P1 1.3750 120.00 90.00 120.00 1.6100 IC CZ OH P1 O2 1.3800 120.00 300.00 108.00 1.5800 IC O2 OH *P1 O3 1.5800 108.00 120.00 103.00 1.4800 IC O2 OH *P1 O4 1.5800 108.00 -120.00 103.00 1.4800 IC OH P1 O2 H2 1.6100 108.00 180.00 115.00 0.9600 RESI BMPH -1.00 ! C7H8O3P Benzylphosphonate GROUP ATOM CG CG2R61 -0.115 ! HD1 HE1 ATOM HG HGR61 0.115 ! | | GROUP ! CD1--CE1 HH1 O2-H2 ATOM CD1 CG2R61 -0.115 ! // \\ \ / ATOM HD1 HGR61 0.115 ! HG--CG CZ---CH---P1 (-) GROUP ! \ __ / / //\\ ATOM CD2 CG2R61 -0.115 ! CD2--CE2 HH2 O4 O3 ATOM HD2 HGR61 0.115 ! | | GROUP ! HD2 HE2 ATOM CE1 CG2R61 -0.21 ATOM HE1 HGR61 0.24 ATOM CE2 CG2R61 -0.21 ATOM HE2 HGR61 0.24 ATOM CZ CG2R61 -0.44 ATOM CH CG321 -0.18 ATOM HH1 HGA2 0.09 ATOM HH2 HGA2 0.09 ATOM P1 PG1 1.53 ATOM O2 OG311 -0.79 ATOM H2 HGP1 0.36 ATOM O3 OG2P1 -0.86 ATOM O4 OG2P1 -0.86 ! NA ATOM TYPE BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 BOND CE1 CZ CE2 CZ CZ CH BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 BOND P1 O4 O2 H2 ! IC table IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 IC CE2 CE1 *CZ CH 1.3750 120.00 180.00 122.30 1.4900 IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CZ CH P1 1.3750 122.30 270.00 111.00 1.8800 IC P1 CZ *CH HH1 1.8800 111.00 120.00 107.50 1.1110 IC HH1 CZ *CH HH2 1.1110 107.50 -120.00 107.50 1.1110 IC CZ CH P1 O2 1.4900 111.00 180.00 93.00 1.5800 IC O2 CH *P1 O3 1.5800 93.00 120.00 103.00 1.4800 IC O2 CH *P1 O4 1.5800 93.00 -120.00 103.00 1.4800 IC CH P1 O2 H2 1.8800 93.00 120.00 115.00 0.9600 RESI BMPD -2.00 ! C7H7O3P Benzylphosphonate dianionic GROUP ATOM CG CG2R61 -0.115 ! HD1 HE1 ATOM HG HGR61 0.115 ! | | GROUP ! CD1--CE1 HH1 O2 ATOM CD1 CG2R61 -0.115 ! // \\ \ / ATOM HD1 HGR61 0.115 ! HG--CG CZ---CH---P1 (-2) GROUP ! \ __ / / //\\ ATOM CD2 CG2R61 -0.115 ! CD2--CE2 HH2 O4 O3 ATOM HD2 HGR61 0.115 ! | | GROUP HD2 HE2 ATOM CE1 CG2R61 -0.24 ATOM HE1 HGR61 0.26 ATOM CE2 CG2R61 -0.24 ATOM HE2 HGR61 0.26 ATOM CZ CG2R61 -0.45 ATOM CH CG321 -0.28 ATOM HH1 HGA2 0.09 ATOM HH2 HGA2 0.09 ATOM P1 PG2 1.90 ATOM O2 OG2P1 -1.13 ATOM O3 OG2P1 -1.13 ATOM O4 OG2P1 -1.13 BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 BOND CE1 CZ CE2 CZ CZ CH BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 BOND P1 O4 ! IC table IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 IC CD1 CE1 CZ CH 0.0000 000.00 180.00 000.00 0.0000 IC HD1 CD1 CG CD2 0.0000 000.00 180.00 000.00 0.0000 IC CG CD1 CE1 CZ 0.0000 000.00 0.00 000.00 0.0000 IC HG CG CD1 CE1 0.0000 000.00 180.00 000.00 0.0000 IC CD2 CG CD1 CE1 0.0000 000.00 0.00 000.00 0.0000 IC HD2 CD2 CG HG 0.0000 000.00 0.00 000.00 0.0000 IC CE2 CD2 CG CD1 0.0000 000.00 0.00 000.00 0.0000 IC HH1 CH P1 O3 0.0000 000.00 180.00 000.00 0.0000 IC HH2 CH P1 O3 0.0000 000.00 0.00 000.00 0.0000 IC HE1 CE1 CD1 HD1 0.0000 000.00 0.00 000.00 0.0000 IC HE2 CE2 CD2 HD2 0.0000 000.00 0.00 000.00 0.0000 RESI BDFP -1.00 ! C7H6F2O3P Difuorobenzylphosphonate GROUP ATOM CG CG2R61 -0.115 ! HD1 HE1 ATOM HG HGR61 0.115 ! | | GROUP CD1--CE1 F1 O2-H2 ATOM CD1 CG2R61 -0.115 ! // \\ \ / ATOM HD1 HGR61 0.115 ! HG--CG CZ---CF---P1 (-) GROUP \ __ / / //\\ ATOM CD2 CG2R61 -0.115 ! CD2--CE2 F2 O4 O3 ATOM HD2 HGR61 0.115 ! | | GROUP HD2 HE2 ATOM CE1 CG2R61 -0.21 ATOM HE1 HGR61 0.24 ATOM CE2 CG2R61 -0.21 ATOM HE2 HGR61 0.24 ATOM CZ CG2R61 -0.40 ATOM CF CG312 0.21 ATOM F1 FGA2 -0.17 ATOM F2 FGA2 -0.17 ATOM P1 PG1 1.43 ATOM O2 OG311 -0.72 ATOM H2 HGP1 0.36 ATOM O3 OG2P1 -0.80 ATOM O4 OG2P1 -0.80 BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 BOND CE1 CZ CE2 CZ CZ CF BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 BOND P1 O4 O2 H2 ! IC table IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CZ CF P1 1.3750 120.00 270.00 115.00 1.8800 IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 IC CZ CF P1 O2 1.4500 115.00 180.00 86.00 1.5800 IC O2 CF *P1 O3 1.5800 86.00 120.00 95.00 1.4800 IC O2 CF *P1 O4 1.5800 86.00 -120.00 95.00 1.4800 IC CF P1 O2 H2 1.8800 86.00 180.00 115.00 0.9600 RESI BDFD -2.00 ! C7H5F2O3P Difuorobenzylphosphonate dianionic, chris GROUP ATOM CG CG2R61 -0.115 ! HD1 HE1 ATOM HG HGR61 0.115 ! | | GROUP CD1--CE1 F1 O2 ATOM CD1 CG2R61 -0.115 ! // \\ \ / ATOM HD1 HGR61 0.115 ! HG--CG CZ---CF---P1 (-2) GROUP \ __ / / //\\ ATOM CD2 CG2R61 -0.115 ! CD2--CE2 F2 O4 O3 ATOM HD2 HGR61 0.115 ! | | GROUP HD2 HE2 ATOM CE1 CG2R61 -0.24 ATOM HE1 HGR61 0.26 ATOM CE2 CG2R61 -0.24 ATOM HE2 HGR61 0.26 ATOM CZ CG2R61 -0.36 ATOM CF CG312 0.24 ATOM F1 FGA2 -0.28 ATOM F2 FGA2 -0.28 ATOM P1 PG2 2.00 ATOM O2 OG2P1 -1.12 ATOM O3 OG2P1 -1.12 ATOM O4 OG2P1 -1.12 BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 BOND CE1 CZ CE2 CZ CZ CF BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 BOND P1 O4 ! IC table IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 IC CE1 CZ CF P1 1.3750 120.00 90.00 115.00 1.8800 IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 IC CZ CF P1 O2 1.4500 115.00 180.00 95.00 1.4800 IC O2 CF *P1 O3 1.4800 95.00 120.00 95.00 1.4800 IC O2 CF *P1 O4 1.4800 95.00 -120.00 95.00 1.4800 RESI EP_2 -2.00 ! C2H5O4P Ethylphosphate, dianionic !test CT3-CT2-ON2-P dihedral without complications from phosphate proton GROUP ! H21 ATOM P1 PG2 1.10 ! | ATOM O1 OG303 -0.40 ! H23--C2--H22 ATOM O2 OG2P1 -0.90 ! | ATOM O3 OG2P1 -0.90 ! H11--C1--H12 ATOM O4 OG2P1 -0.90 ! | GROUP ! O1 ATOM C1 CG321 -0.18 ! | ATOM H11 HGA2 0.09 ! (-) O4==P1==O3 (-) ATOM H12 HGA2 0.09 ! || GROUP ! O2 ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 C2 BOND C2 H21 C2 H22 C2 H23 IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 IC O2 P1 O1 C1 0.0000 0.00 180.00 0.00 0.0000 IC P1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 RESI IP_2 -2.00 ! C3H7O4P isopropylphosphate, dianionic !test CT3-CT1-ON2-P dihedral without complications from phosphate proton GROUP ! H21 ATOM P1 PG2 1.10 ! | ATOM O1 OG303 -0.40 ! H23--C2--H22 H31 ATOM O2 OG2P1 -0.90 ! | / ATOM O3 OG2P1 -0.90 ! H11--C1----C3--H32 ATOM O4 OG2P1 -0.90 ! | \ GROUP ! O1 H33 ATOM C1 CG311 -0.09 ! | ATOM H11 HGA1 0.09 ! (-) O4==P1==O3 (-) ! || GROUP ! O2 ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 C2 C1 C3 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC C1 O1 P1 O2 0.0000 0.00 60.00 0.00 0.0000 IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 IC O2 P1 O1 C1 0.0000 0.00 60.00 0.00 0.0000 IC P1 O1 C1 C2 0.0000 0.00 220.00 0.00 0.0000 IC C2 O1 *C1 C3 0.0000 0.00 -120.00 0.00 0.0000 IC C3 O1 *C1 H11 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 C2 H21 0.0000 0.00 -60.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H31 C1 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 C1 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 RESI SAH 0.00 ! C14H20N6O5S S-adenosyl-homocysteine GROUP ATOM N NG3P3 -0.30 ATOM HT1 HGP2 0.33 ! (2) HT1 ATOM HT2 HGP2 0.33 ! | / ATOM HT3 HGP2 0.33 !(1)--CA--N--HT2 (+) ATOM CA CG314 0.21 ! | \ ATOM HA HGA1 0.10 ! HA HT3 GROUP ATOM CB CG321 -0.18 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 ! HB1 HG1 H5' H4' O4' Adenine GROUP ! | | | \ / \ / ATOM CG CG321 -0.13 ! (1)--CB--CG--SD--C5'----C4' C1'-H1' ATOM HG1 HGA2 0.09 ! | | | | | ATOM HG2 HGA2 0.09 ! HB2 HG2 H5'' H3'-C3'--C2'-H21' ATOM SD SG311 -0.10 ! kevo: symmetrized | | ATOM C5' CG321 -0.13 ! H3T--O3' O2'-H2' ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ! OT2(-) GROUP ! / ATOM C CG2O3 0.34 !(2)-C ATOM OT1 OG2D2 -0.67 ! \\ ATOM OT2 OG2D2 -0.67 ! OT1 GROUP ATOM C4' CG3C51 0.16 ATOM H4' HGA1 0.09 ATOM O4' OG3C51 -0.50 ATOM C1' CG3C51 0.16 ATOM H1' HGA1 0.09 GROUP ATOM N9 NG2R51 -0.05 ATOM C5 CG2RC0 0.28 ATOM N7 NG2R50 -0.71 ATOM C8 CG2R53 0.34 ATOM H8 HGR52 0.12 ATOM N1 NG2R62 -0.74 ATOM C2 CG2R64 0.50 ATOM H2 HGR62 0.13 ATOM N3 NG2R62 -0.75 ATOM C4 CG2RC0 0.43 ATOM C6 CG2R64 0.46 ATOM N6 NG2S3 -0.77 ATOM H61 HGP4 0.38 ATOM H62 HGP4 0.38 GROUP ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 BOND N CA O3' H3T BOND CB CA CG CB SD CG C5' SD C CA BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND HT1 N HT2 N HT3 N OT2 C DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 DOUBLE C OT1 IMPR N6 C6 H61 H62 C6 N1 C5 N6 IMPR OT1 CA OT2 C IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC N CA CB CG 1.4863 111.52 -68.05 114.80 1.5438 IC CA CB CG SD 1.5495 114.80 -169.85 111.97 1.8249 IC HT1 CA *N HT2 1.0633 98.00 113.14 109.99 1.0338 IC HT1 CA *N HT3 1.0633 98.00 -117.28 113.48 1.0305 IC HT1 N CA CB 1.0633 98.00 -136.27 111.52 1.5495 IC CB N *CA C 1.5495 111.52 123.39 106.34 1.5395 IC CB N *CA HA 1.5495 111.52 -122.64 109.49 1.0806 IC CG CA *CB HB1 1.5438 114.80 125.78 110.22 1.1112 IC CG CA *CB HB2 1.5438 114.80 -119.31 106.97 1.1179 IC SD CB *CG HG1 1.8249 111.97 120.25 107.22 1.1112 IC SD CB *CG HG2 1.8249 111.97 -122.78 110.68 1.1101 IC CB CG SD C5' 1.5438 111.97 149.65 104.32 1.8303 IC CG SD C5' C4' 1.8249 104.32 -59.34 117.91 1.5403 IC C4' SD *C5' H5' 1.5403 117.91 122.31 108.22 1.1127 IC C4' SD *C5' H5'' 1.5403 117.91 -122.71 108.62 1.1118 IC N CA C OT1 1.4863 106.34 -166.34 117.88 1.2492 IC OT1 CA *C OT2 1.2492 117.88 -178.37 117.42 1.2654 IC SD C5' C4' O4' 1.8303 117.91 169.12 108.69 1.4591 IC O4' C5' *C4' C3' 1.4591 108.69 118.83 122.55 1.5499 IC O4' C5' *C4' H4' 1.4591 108.69 -116.07 109.38 1.1099 IC C5' C4' O4' C1' 1.5403 108.69 133.30 108.22 1.4240 IC C4' O4' C1' N9 1.4591 108.22 -159.13 111.15 1.4614 IC N9 O4' *C1' C2' 1.4614 111.15 124.24 102.39 1.5135 IC N9 O4' *C1' H1' 1.4614 111.15 -119.53 107.46 1.1156 IC C4 C1' *N9 C8 1.3837 126.86 175.00 127.05 1.3697 IC C1' N9 C4 C5 1.4614 126.86 176.84 105.37 1.3831 IC C5 N9 *C4 N3 1.3831 105.37 179.25 128.02 1.3472 IC N9 C4 C5 C6 1.3837 105.37 179.94 116.97 1.4115 IC C6 C4 *C5 N7 1.4115 116.97 179.52 110.80 1.3914 IC N7 N9 *C8 H8 1.3073 113.91 -179.74 121.60 1.0918 IC C4 C5 C6 N1 1.3831 116.97 -0.21 118.01 1.3524 IC N1 C5 *C6 N6 1.3524 118.01 -179.35 123.62 1.3438 IC N3 N1 *C2 H2 1.3403 129.44 -179.97 115.20 1.0945 IC C5 C6 N6 H61 1.4115 123.62 179.97 117.15 0.9949 IC C3' C1' *C2' O2' 1.5132 95.49 115.41 113.17 1.4151 IC C3' C1' *C2' H2'' 1.5132 95.49 -116.10 112.79 1.1120 IC C1' C2' O2' H2' 1.5135 113.17 177.31 109.89 0.9633 IC C4' C3' O3' H3T 1.5499 116.35 167.44 110.25 0.9629 RESI INDO 0.00 ! C8H7N indole, adm jr., atm GROUP ATOM HG HGR51 0.14 ! HE3 ATOM CG CG2R51 -0.17 ! | ATOM CD2 CG2RC0 0.11 ! HG CE3 ATOM CD1 CG2R51 -0.15 ! \ / \\ ATOM HD1 HGR52 0.22 ! CG-----CD2 CZ3-HZ3 ATOM NE1 NG2R51 -0.51 ! || || | ATOM HE1 HGP1 0.37 ! CD1 CE2 CH2-HH2 ATOM CE2 CG2RC0 0.24 ! / \ / \ // ATOM CE3 CG2R61 -0.25 ! HD1 NE1 CZ2 ATOM HE3 HGR61 0.17 ! | | ATOM CZ2 CG2R61 -0.27 ! HE1 HZ2 ATOM HZ2 HGR61 0.16 ATOM CZ3 CG2R61 -0.20 ATOM HZ3 HGR61 0.14 ATOM CH2 CG2R61 -0.14 ATOM HH2 HGR61 0.14 BOND CG HG CD2 CG NE1 CD1 BOND CZ2 CE2 BOND CZ3 CH2 CD2 CE3 NE1 CE2 BOND CD1 HD1 NE1 HE1 CE3 HE3 BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 DONOR HE1 NE1 IC CG CD1 NE1 CE2 1.3650 110.50 0.00 112.00 1.3700 IC CD1 CG CD2 CE2 1.3650 106.40 0.00 108.00 1.3850 IC CD2 CG CD1 NE1 1.4300 106.40 0.00 110.50 1.3700 IC CE2 CG *CD2 CE3 1.3850 108.00 180.00 133.50 1.3600 IC CE2 CD2 CE3 CZ3 1.3850 110.00 0.00 113.20 1.3750 IC CD2 CE3 CZ3 CH2 1.3600 113.20 0.00 120.00 1.3750 IC CE3 CZ3 CH2 CZ2 1.3750 120.00 0.00 120.00 1.3750 IC CZ3 CD2 *CE3 HE3 1.3750 113.20 180.00 122.00 1.0800 IC CH2 CE3 *CZ3 HZ3 1.3750 120.00 180.00 120.00 1.0800 IC CZ2 CZ3 *CH2 HH2 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CH2 *CZ2 HZ2 1.3600 113.20 180.00 120.00 1.0800 IC CD1 CE2 *NE1 HE1 1.3700 112.00 180.00 126.00 0.9760 IC CG NE1 *CD1 HD1 1.3650 110.50 180.00 125.00 1.0800 IC CD1 CD2 *CG HG 1.3650 106.40 180.00 126.40 1.0800 PATCH FIRST NONE LAST NONE RESI MIND 0.00 ! C9H9N 3-methylindole, adm jr., atm GROUP ATOM CB CG331 -0.27 ATOM HB1 HGA3 0.09 ATOM HB2 HGA3 0.09 ATOM HB3 HGA3 0.09 GROUP ATOM CG CG2R51 -0.03 ATOM CD2 CG2RC0 0.11 ATOM CD1 CG2R51 -0.15 ATOM HD1 HGR52 0.22 ATOM NE1 NG2R51 -0.51 ATOM HE1 HGP1 0.37 ATOM CE2 CG2RC0 0.24 ATOM CE3 CG2R61 -0.25 ATOM HE3 HGR61 0.17 ATOM CZ2 CG2R61 -0.27 ATOM HZ2 HGR61 0.16 ATOM CZ3 CG2R61 -0.20 ATOM HZ3 HGR61 0.14 ATOM CH2 CG2R61 -0.14 ATOM HH2 HGR61 0.14 BOND CB HB1 CB HB2 CB HB3 BOND CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND CZ3 CH2 CD2 CE3 NE1 CE2 BOND CD1 HD1 NE1 HE1 CE3 HE3 BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 DONOR HE1 NE1 IC CB CG CD1 NE1 1.4920 127.00 180.00 110.50 1.3700 IC CG CD1 NE1 CE2 1.3650 110.50 0.00 112.00 1.3700 IC CD1 CG CD2 CE2 1.3650 106.40 0.00 108.00 1.3850 IC CD2 CB *CG CD1 1.4300 126.70 180.00 127.00 1.3650 IC HB1 CB CG CD1 1.1110 109.50 0.00 127.00 1.3650 IC HB2 CB CG CD1 1.1110 109.50 120.00 127.00 1.3650 IC HB3 CB CG CD1 1.1110 109.50 240.00 127.00 1.3650 IC CD2 CG CD1 NE1 1.4300 106.40 0.00 110.50 1.3700 IC CE2 CG *CD2 CE3 1.3850 108.00 180.00 133.50 1.3600 IC CE2 CD2 CE3 CZ3 1.3850 110.00 0.00 113.20 1.3750 IC CD2 CE3 CZ3 CH2 1.3600 113.20 0.00 120.00 1.3750 IC CE3 CZ3 CH2 CZ2 1.3750 120.00 0.00 120.00 1.3750 IC CZ3 CD2 *CE3 HE3 1.3750 113.20 180.00 122.00 1.0800 IC CH2 CE3 *CZ3 HZ3 1.3750 120.00 180.00 120.00 1.0800 IC CZ2 CZ3 *CH2 HH2 1.3750 120.00 180.00 120.00 1.0800 IC CE2 CH2 *CZ2 HZ2 1.3600 113.20 180.00 120.00 1.0800 IC CD1 CE2 *NE1 HE1 1.3700 112.00 180.00 126.00 0.9760 IC CG NE1 *CD1 HD1 1.3650 110.50 180.00 125.00 1.0800 RESI EIND 0.00 ! C10H11N ethylindole, adm jr., atm GROUP ATOM CA CG331 -0.27 ! HA2 ATOM HA1 HGA3 0.09 ! | ATOM HA2 HGA3 0.09 ! HA1-CA-HA3 HE3 ATOM HA3 HGA3 0.09 ! | | GROUP ! HB1-CB-HB2 CE3 ATOM CB CG321 -0.18 ! \ / \\ ATOM HB1 HGA2 0.09 ! CG-----CD2 CZ3-HZ3 ATOM HB2 HGA2 0.09 ! || || | GROUP ! CD1 CE2 CH2-HH2 ATOM CG CG2R51 -0.03 ! / \ / \ // ATOM CD2 CG2RC0 0.11 ! HD1 NE1 CZ2 ATOM CD1 CG2R51 -0.15 ! | | ATOM HD1 HGR52 0.22 ! HE1 HZ2 ATOM NE1 NG2R51 -0.51 ATOM HE1 HGP1 0.37 ATOM CE2 CG2RC0 0.24 ATOM CE3 CG2R61 -0.25 ATOM HE3 HGR61 0.17 ATOM CZ2 CG2R61 -0.27 ATOM HZ2 HGR61 0.16 ATOM CZ3 CG2R61 -0.20 ATOM HZ3 HGR61 0.14 ATOM CH2 CG2R61 -0.14 ATOM HH2 HGR61 0.14 BOND CA HA1 CA HA2 CA HA3 BOND CA CB CB HB1 CB HB2 BOND CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND CZ3 CH2 CD2 CE3 NE1 CE2 BOND CD1 HD1 NE1 HE1 CE3 HE3 BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 DONOR HE1 NE1 IC CA CB CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CB CG CD1 NE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HA1 CB *CA HA2 0.0000 0.0000 120.0000 0.0000 0.0000 IC HA1 CB *CA HA3 0.0000 0.0000 240.0000 0.0000 0.0000 IC CA CG *CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 IC CA CG *CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 CG *CD2 CE3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CD2 CE3 CZ3 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CE3 CZ3 CH2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE3 CZ3 CH2 CZ2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CZ3 CD2 *CE3 HE3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CH2 CE3 *CZ3 HZ3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ2 CZ3 *CH2 HH2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CH2 *CZ2 HZ2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CE2 *NE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CG NE1 *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 !IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 !reset default patches DEFA FIRS NONE LAST NONE RESI BFL 0.00 ! C12H10 biphenyl, peml. GROUP ATOM CG1 CG2R67 0.000 ATOM CG2 CG2R67 0.000 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ! HE1 HD1 HD3 HE3 ATOM CE2 CG2R61 -0.115 ! \ / \ / ATOM HE2 HGR61 0.115 ! CE1--CD1 CD3--CE3 ATOM CZ1 CG2R61 -0.115 ! / \ / \ ATOM HZ1 HGR61 0.115 ! HZ1--CZ1 CG1---CG2 CZ2--HZ2 ATOM CD3 CG2R61 -0.115 ! \ / \ / ATOM HD3 HGR61 0.115 ! CE2--CD2 CD4--CE4 ATOM CD4 CG2R61 -0.115 ! / \ / \ ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 ATOM CZ2 CG2R61 -0.115 ATOM HZ2 HGR61 0.115 BOND CD1 CG1 CG1 CD2 CG1 CG2 BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 HZ1 CZ2 HZ2 IC CG2 CG1 CD1 CE1 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CG2 *CG1 CD2 0.0000 0.00 180.00 0.00 0.0000 IC CG2 CG1 CD1 CE1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CG2 CG1 CD2 CE2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG1 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CD1 CE1 CZ1 0.0000 0.00 180.00 0.00 0.0000 IC CZ1 CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CZ1 CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CE1 *CZ1 HZ1 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CG1 CG2 CD4 0.0000 0.00 180.00 0.00 0.0000 IC CD4 CG1 *CG2 CD3 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CG2 CD3 CE3 0.0000 0.00 180.00 0.00 0.0000 IC CE3 CG2 *CD3 HD3 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CG2 CD4 CE4 0.0000 0.00 180.00 0.00 0.0000 IC CE4 CG2 *CD4 HD4 0.0000 0.00 180.00 0.00 0.0000 IC CG2 CD3 CE3 CZ2 0.0000 0.00 180.00 0.00 0.0000 IC CZ2 CD3 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 IC CZ2 CD4 *CE4 HE4 0.0000 0.00 180.00 0.00 0.0000 IC CE4 CE3 *CZ2 HZ2 0.0000 0.00 180.00 0.00 0.0000 RESI BF6 -2.00 ! C16H12O6 biphenyl analog, peml. !KEVO: charges adjusted to reflect updated acetone L-J. !Resulting charges are unlikey to be good ==> re-optimize? GROUP ATOM CG1 CG2R67 0.000 ATOM CG2 CG2R67 0.000 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ! HE1 HD1 HD3 HE3 ATOM HE1 HGR61 0.115 ! \ / \ / ATOM CE2 CG2R61 -0.115 ! CE1--CD1 CD3--CE3 ATOM HE2 HGR61 0.115 ! / \ / \ ATOM CZ1 CG2R61 0.000 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS ATOM CD3 CG2R61 -0.115 ! \ / \ / ATOM HD3 HGR61 0.115 ! CE2--CD2 CD4--CE4 ATOM CD4 CG2R61 -0.115 ! / \ / \ ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 ATOM CZ2 CG2R61 0.000 GROUP ATOM C1 CG2O5 0.38 ATOM O1 OG2D3 -0.48 ! O1 ATOM C2 CG311 0.17 ! // ATOM H2 HGA1 0.09 !Ring--C1 H2 ATOM O2A OG311 -0.60 ! \ / ATOM H2A HGP1 0.32 ! C2--O2A--H2A ATOM O2B OG312 -0.88 ! \ ! O2B (-) GROUP ATOM C3 CG2O5 0.38 ATOM O3 OG2D3 -0.48 ATOM C4 CG311 0.17 ATOM H4 HGA1 0.09 ATOM O4A OG311 -0.60 ATOM H4A HGP1 0.32 ATOM O4B OG312 -0.88 BOND CD1 CG1 CG1 CD2 CG1 CG2 BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 C1 O1 C1 C2 BOND C2 H2 C2 O2A O2A H2A BOND C2 O2B BOND CZ2 C3 C3 O3 C3 C4 BOND C4 H4 C4 O4A O4A H4A BOND C4 O4B IMPR C1 CZ1 C2 O1 IMPR C3 CZ2 C4 O3 IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 IC O2A C1 *C2 H2 1.4000 110.00 -120.00 110.00 1.1000 IC C1 C2 O2A H2A 1.4000 110.00 180.00 110.00 0.9000 IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 IC O4A C3 *C4 H4 1.4000 110.00 -120.00 110.00 1.1000 IC C3 C4 O4A H4A 1.4000 110.00 180.00 110.00 0.9000 RESI BF7 -2.00 ! C16H8O6 biphenyl analog, peml. !KEVO: charges adjusted to reflect updated acetone L-J. !Resulting charges are probably not that bad. GROUP ATOM CG1 CG2R67 0.00 ATOM CG2 CG2R67 0.00 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ! HE1 HD1 HD3 HE3 GROUP ! \ / \ / ATOM CZ1 CG2R61 0.000 ! CE1--CD1 CD3--CE3 GROUP ! / \ / \ ATOM CD3 CG2R61 -0.115 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS ATOM HD3 HGR61 0.115 ! \ / \ / GROUP ! CE2--CD2 CD4--CE4 ATOM CD4 CG2R61 -0.115 ! / \ / \ ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 GROUP ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 GROUP ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 GROUP ATOM CZ2 CG2R61 0.000 GROUP ATOM C1 CG2O5 0.38 ! O ATOM O1 OG2D3 -0.48 ! // ATOM C2 CG2O3 0.62 ! Ring-C ATOM O2A OG2D2 -0.76 ! \ ATOM O2B OG2D2 -0.76 ! C==O GROUP ! | ATOM C3 CG2O5 0.38 ! O (-) ATOM O3 OG2D3 -0.48 ATOM C4 CG2O3 0.62 ATOM O4A OG2D2 -0.76 ATOM O4B OG2D2 -0.76 BOND CD1 CG1 CG1 CD2 CG1 CG2 BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 CZ2 C3 BOND C1 O1 C1 C2 C2 O2A BOND C2 O2B BOND C3 O3 C3 C4 C4 O4A BOND C4 O4B IMPR C1 C2 CZ1 O1 IMPR C2 O2B O2A C1 IMPR C3 C4 CZ2 O3 IMPR C4 O4B O4A C3 IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 RESI BCA -2.00 ! C14H8O4 biphenyl analog, peml., acid analog GROUP ATOM CG1 CG2R67 0.000 ATOM CG2 CG2R67 0.000 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ! HE1 HD1 HD3 HE3 ATOM CE1 CG2R61 -0.115 ! \ / \ / ATOM HE1 HGR61 0.115 ! CE1--CD1 CD3--CE3 GROUP ! / \ / \ ATOM CE2 CG2R61 -0.115 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS ATOM HE2 HGR61 0.115 ! \ / \ / GROUP ! CE2--CD2 CD4--CE4 ATOM CD3 CG2R61 -0.115 ! / \ / \ ATOM HD3 HGR61 0.115 ! HE2 HD2 HD4 HE4 GROUP ATOM CD4 CG2R61 -0.115 ATOM HD4 HGR61 0.115 GROUP ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 GROUP ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 GROUP ATOM CZ1 CG2R61 -0.10 ! O ATOM C1 CG2O3 0.62 ! // ATOM O1A OG2D2 -0.76 ! Ring-C (-) ATOM O1B OG2D2 -0.76 ! \ GROUP ! O ATOM CZ2 CG2R61 -0.10 ATOM C2 CG2O3 0.62 ATOM O2A OG2D2 -0.76 ATOM O2B OG2D2 -0.76 BOND CD1 CG1 CG1 CD2 CG1 CG2 BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 C1 O1A C1 O1B BOND CZ2 C2 C2 O2A C2 O2B IMPR C1 O1B O1A CZ1 IMPR C2 O2B O2A CZ2 IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 O1A 1.4000 120.00 180.00 120.00 1.4000 IC O1A CZ1 *C1 O1B 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CE3 *CZ2 C2 1.4000 120.00 180.00 120.00 1.4000 IC CE3 CZ2 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 IC O2A CZ2 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 RESI C36 -2.00 ! C16H12O7 biphenyl with bridging O analog, peml. !KEVO: charges adjusted to reflect updated acetone L-J. !Resulting charges are unlikey to be good ==> re-optimize? GROUP ! hydrated aldehyde analog (ionized) ATOM CG1 CG2R61 0.215 ATOM O OG301 -0.430 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ! HE3 ATOM CD2 CG2R61 -0.115 ! \ / ATOM HD2 HGR61 0.115 ! CD3--CE3 ATOM CE1 CG2R61 -0.115 ! / \ ATOM HE1 HGR61 0.115 ! HD1 O ---CG2 CZ2--SUBS ATOM CE2 CG2R61 -0.115 ! \ / \ / ATOM HE2 HGR61 0.115 ! CD1--CG1 CD4--CE4 ATOM CZ1 CG2R61 0.000 ! / \ / \ ATOM CG2 CG2R61 0.215 ! HE1--CE1 CD2--HD2 HD4 HE4 ATOM CD3 CG2R61 -0.115 ! \ / ATOM HD3 HGR61 0.115 ! CZ1--CE2 ATOM CD4 CG2R61 -0.115 ! / \ ATOM HD4 HGR61 0.115 ! SUBS HE2 ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 ATOM CZ2 CG2R61 0.000 GROUP ATOM C1 CG2O5 0.38 ! O1 ATOM O1 OG2D3 -0.48 ! // ATOM C2 CG311 0.17 !Ring--C1 H2 ATOM H2 HGA1 0.09 ! \ / ATOM O2A OG311 -0.60 ! C2--OH ATOM H2A HGP1 0.32 ! \ ATOM O2B OG312 -0.88 ! O (-) GROUP ATOM C3 CG2O5 0.38 ATOM O3 OG2D3 -0.48 ATOM C4 CG311 0.17 ATOM H4 HGA1 0.09 ATOM O4A OG311 -0.60 ATOM H4A HGP1 0.32 ATOM O4B OG312 -0.88 BOND CD1 CG1 CG1 CD2 CG1 O BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 CG2 O BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 C1 O1 C1 C2 BOND C2 H2 C2 O2A O2A H2A BOND C2 O2B BOND CZ2 C3 C3 O3 C3 C4 BOND C4 H4 C4 O4A O4A H4A BOND C4 O4B IMPR C1 CZ1 C2 O1 IMPR C3 CZ2 C4 O3 IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 IC CG1 O CG2 CD4 1.3820 120.00 40.00 120.00 1.4000 IC CD4 O *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 IC O2A C1 *C2 H2 1.4000 110.00 -120.00 110.00 1.1000 IC C1 C2 O2A H2A 1.4000 110.00 180.00 110.00 0.9000 IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 IC O4A C3 *C4 H4 1.4000 110.00 -120.00 110.00 1.1000 IC C3 C4 O4A H4A 1.4000 110.00 180.00 110.00 0.9000 RESI C37 -2.00 ! C16H8O7 biphenyl analog, peml. !KEVO: charges adjusted to reflect updated acetone L-J. !Resulting charges are probably not that bad. GROUP ATOM CG1 CG2R61 0.215 ATOM O OG301 -0.430 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ! HE3 ATOM CD2 CG2R61 -0.115 ! \ / ATOM HD2 HGR61 0.115 ! CD3--CE3 ATOM CE1 CG2R61 -0.115 ! / \ ATOM HE1 HGR61 0.115 ! HD1 O ---CG2 CZ2--SUBS ATOM CE2 CG2R61 -0.115 ! \ / \ / ATOM HE2 HGR61 0.115 ! CD1--CG1 CD4--CE4 ATOM CZ1 CG2R61 0.000 ! / \ / \ ATOM CG2 CG2R61 0.215 ! HE1--CE1 CD2--HD2 HD4 HE4 ATOM CD3 CG2R61 -0.115 ! \ / ATOM HD3 HGR61 0.115 ! CZ1--CE2 ATOM CD4 CG2R61 -0.115 ! / \ ATOM HD4 HGR61 0.115 ! SUBS HE2 ATOM CE3 CG2R61 -0.115 ATOM HE3 HGR61 0.115 ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 ATOM CZ2 CG2R61 0.000 GROUP ATOM C1 CG2O5 0.38 ATOM O1 OG2D3 -0.48 ! O ATOM C2 CG2O3 0.62 ! // ATOM O2A OG2D2 -0.76 ! Ring--C ATOM O2B OG2D2 -0.76 ! \ GROUP ! C--O (-) ATOM C3 CG2O5 0.38 ! // ATOM O3 OG2D3 -0.48 ! O ATOM C4 CG2O3 0.62 ATOM O4A OG2D2 -0.76 ATOM O4B OG2D2 -0.76 BOND CD1 CG1 CG1 CD2 CG1 O BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 CG2 O BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 C1 O1 C1 C2 BOND C2 O2A BOND C2 O2B BOND CZ2 C3 C3 O3 C3 C4 BOND C4 O4A BOND C4 O4B IMPR C1 C2 CZ1 O1 IMPR C2 O2B O2A C1 IMPR C3 C4 CZ2 O3 IMPR C4 O4B O4A C3 IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 IC CG1 O CG2 CD4 1.3820 120.00 40.00 120.00 1.4000 IC CD4 O *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 IC CZ1 C1 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 IC O2A C1 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 IC CZ2 C3 C4 O4A 1.4000 120.00 180.00 120.00 1.4000 IC O4A C3 *C4 O4B 1.4000 120.00 180.00 120.00 1.4000 RESI C3C -2.00 ! C14H8O5 GROUP ATOM CG1 CG2R61 0.215 ATOM O OG301 -0.430 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ! HE3 ATOM HD2 HGR61 0.115 ! \ / ATOM CE1 CG2R61 -0.115 ! CD3--CE3 ATOM HE1 HGR61 0.115 ! / \ ATOM CE2 CG2R61 -0.115 ! HD1 O ---CG2 CZ2--SUBS ATOM HE2 HGR61 0.115 ! \ / \ / ATOM CZ1 CG2R61 -0.100 ! CD1--CG1 CD4--CE4 ATOM CG2 CG2R61 0.215 ! / \ / \ ATOM CD3 CG2R61 -0.115 ! HE1--CE1 CD2--HD2 HD4 HE4 ATOM HD3 HGR61 0.115 ! \ / ATOM CD4 CG2R61 -0.115 ! CZ1--CE2 ATOM HD4 HGR61 0.115 ! / \ ATOM CE3 CG2R61 -0.115 ! SUBS HE2 ATOM HE3 HGR61 0.115 ATOM CE4 CG2R61 -0.115 ATOM HE4 HGR61 0.115 ATOM CZ2 CG2R61 -0.100 GROUP ATOM C1 CG2O3 0.62 ATOM O1A OG2D2 -0.76 ! O ATOM O1B OG2D2 -0.76 ! // GROUP ! Ring-C (-) ATOM C2 CG2O3 0.62 ! \ ATOM O2A OG2D2 -0.76 ! O ATOM O2B OG2D2 -0.76 BOND CD1 CG1 CG1 CD2 CG1 O BOND CD2 CE2 CE2 CZ1 CZ1 CE1 BOND CE1 CD1 CG2 CD3 CD3 CE3 BOND CE3 CZ2 CZ2 CE4 CE4 CD4 BOND CD4 CG2 CG2 O BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CD3 HD3 BOND CD4 HD4 CE3 HE3 CE4 HE4 BOND CZ1 C1 C1 O1A C1 O1B BOND CZ2 C2 C2 O2A C2 O2B IMPR C1 O1B O1A CZ1 IMPR C2 O2B O2A CZ2 IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 IC CG1 O CG2 CD3 1.3820 120.00 0.00 120.00 1.4000 IC CD3 O *CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 IC CE1 CZ1 C1 O1A 1.4000 120.00 180.00 120.00 1.4000 IC O1A CZ1 *C1 O1B 1.4000 120.00 180.00 120.00 1.4000 IC CE4 CE3 *CZ2 C2 1.4000 120.00 180.00 120.00 1.4000 IC CE3 CZ2 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 IC O2A CZ2 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 PATCHING FIRST NONE LAST NONE !toppar_retinol_2.str RESI HEX3 0.00 ! C6H8 1,3,5-hexatriene GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 ATOM H12 HGA5 0.21 ! \ / ATOM C2 CG2DC2 -0.15 ! C1=C2 H41 ATOM H21 HGA4 0.15 ! / \ / GROUP ! H12 C3=C4 H61 ATOM C3 CG2DC1 -0.15 ! / \ / ATOM H31 HGA4 0.15 ! H31 C5=C6 ATOM C4 CG2DC1 -0.15 ! / \ ATOM H41 HGA4 0.15 ! H51 H62 GROUP ATOM C5 CG2DC2 -0.15 ATOM H51 HGA4 0.15 GROUP ATOM C6 CG2DC3 -0.42 ATOM H61 HGA5 0.21 ATOM H62 HGA5 0.21 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C1 H11 C1 H12 C2 H21 C3 H31 BOND C4 H41 C5 H51 C6 H61 C6 H62 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI 13DB 0.00 ! C4H6 1,3-dibutene GROUP ATOM C1 CG2DC3 -0.42 ! H11 H21 ATOM H11 HGA5 0.21 ! \ / ATOM H12 HGA5 0.21 ! C1=C2 H41 GROUP ! / \ / ATOM C2 CG2DC2 -0.15 ! H12 C3=C4 ATOM H21 HGA4 0.15 ! / \ ATOM C3 CG2DC1 -0.15 ! H31 H42 ATOM H31 HGA4 0.15 GROUP ATOM C4 CG2DC3 -0.42 ATOM H41 HGA5 0.21 ATOM H42 HGA5 0.21 BOND C1 C2 C2 C3 C3 C4 BOND C1 H11 C1 H12 C2 H21 C3 H31 BOND C4 H41 C4 H42 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI 13DP 0.00 ! C5H8 1,3-dipentene GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 ATOM H12 HGA5 0.21 ! \ / ATOM C2 CG2DC2 -0.15 ! C1=C2 H41 ATOM H21 HGA4 0.15 ! / \ / GROUP ! H12 C3=C4 H51 ATOM C3 CG2DC1 -0.15 ! / \ / ATOM H31 HGA4 0.15 ! H31 C5-H52 ATOM C4 CG2DC1 -0.15 ! \ ATOM H41 HGA4 0.15 ! H53 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C1 H11 C1 H12 C2 H21 C3 H31 BOND C4 H41 C5 H51 C5 H52 C5 H53 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C5 H51 0.00 0.00 0.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI DMB1 0.00 ! C5H8 2-methyl-1,3-butadiene GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ! H2M1 H2M2 ATOM H12 HGA5 0.21 ! \ / GROUP ! H11 C2M-H2M3 ATOM C2 CG2DC2 0.00 ! \ / ATOM C2M CG331 -0.27 ! C1=C2 H41 ATOM H2M1 HGA3 0.09 ! / \ / ATOM H2M2 HGA3 0.09 ! H12 C3=C4 ATOM H2M3 HGA3 0.09 ! / \ GROUP ! H31 H42 ATOM C3 CG2DC1 -0.15 ATOM H31 HGA4 0.15 GROUP ATOM C4 CG2DC3 -0.42 ATOM H41 HGA5 0.21 ATOM H42 HGA5 0.21 BOND C1 C2 C2 C3 C3 C4 C2 C2M BOND C1 H11 C1 H12 C3 H31 C4 H41 C4 H42 BOND C2M H2M1 C2M H2M2 C2M H2M3 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI DMP1 0.00 ! C6H10 4-methyl-1,3-pentadiene GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ! H11 H21 H4M1 H4M2 ATOM H12 HGA5 0.21 ! \ / \ / GROUP ! C1=C2 C4M-H4M3 ATOM C2 CG2DC2 -0.15 ! / \ / ATOM H21 HGA4 0.15 ! H12 C3=C4 H51 ATOM C3 CG2DC1 -0.15 ! / \ / ATOM H31 HGA4 0.15 ! H31 C5-H52 GROUP ! \ ATOM C4 CG2DC1 0.00 ! H53 ATOM C4M CG331 -0.27 ATOM H4M1 HGA3 0.09 ATOM H4M2 HGA3 0.09 ATOM H4M3 HGA3 0.09 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C4 C4M BOND C1 H11 C1 H12 C2 H21 C3 H31 BOND C4M H4M1 C4M H4M2 C4M H4M3 BOND C5 H51 C5 H52 C5 H53 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 IC C3 C5 *C4 C4M 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C4M H4M1 0.00 0.00 180.0 0.00 0.00 IC C4 H4M1 *C4M H4M2 0.00 0.00 120.0 0.00 0.00 IC C4 H4M1 *C4M H4M3 0.00 0.00 -120.0 0.00 0.00 IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI DMP2 0.00 ! C6H10 2-methyl-1,3-pentadiene GROUP ! H2M1 H2M2 ATOM C1 CG2DC3 -0.42 ! \ / ATOM H11 HGA5 0.21 ! H11 C2M-H2M3 ATOM H12 HGA5 0.21 ! \ / GROUP ! C1=C2 H41 ATOM C2 CG2DC2 0.00 ! / \ / ATOM C2M CG331 -0.27 ! H12 C3=C4 H51 ATOM H2M1 HGA3 0.09 ! / \ / ATOM H2M2 HGA3 0.09 ! H31 C5-H52 ATOM H2M3 HGA3 0.09 ! \ ATOM C3 CG2DC1 -0.15 ! H53 ATOM H31 HGA4 0.15 GROUP ATOM C4 CG2DC1 -0.15 ATOM H41 HGA4 0.15 ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C2 C2M BOND C1 H11 C1 H12 C3 H31 C4 H41 BOND C2M H2M1 C2M H2M2 C2M H2M3 BOND C5 H51 C5 H52 C5 H53 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI CROT 0.00 ! C6H11NO N,3-dimethyl-2-buteneamide, (N,3-dimethylcrotonamide) ! numbering as in fennretinide ! note different atom types for N21 and C15: this is consistent ! with differences in NMA and acetamide GROUP ATOM C12 CG331 -0.27 ATOM H121 HGA3 0.09 ! H202 H203 ATOM H122 HGA3 0.09 ! \ / ATOM H123 HGA3 0.09 ! H201-C20 GROUP ! | ATOM C13 CG2DC2 0.00 !H121-C12--C13 O29 ATOM C14 CG2DC2 -0.15 ! / | \\ || ATOM H141 HGA4 0.15 !H122 H123 C14--C15 GROUP ! / \ ATOM C15 CG2O1 0.51 ! H141 N21-H211 (cis) ATOM O29 OG2D1 -0.51 ! | GROUP ! H132-C16-H131 ATOM N21 NG2S1 -0.47 ! | ATOM H211 HGP1 0.28 ! H133 ATOM C16 CG331 -0.08 ATOM H131 HGA3 0.09 ATOM H132 HGA3 0.09 ATOM H133 HGA3 0.09 GROUP ATOM C20 CG331 -0.27 ATOM H201 HGA3 0.09 ATOM H202 HGA3 0.09 ATOM H203 HGA3 0.09 BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C16 BOND C13 C20 C15 O29 C14 H141 N21 H211 BOND C16 H131 C16 H132 C16 H133 BOND C12 H121 C12 H122 C12 H123 BOND C20 H201 C20 H202 C20 H203 IMPR C15 C14 N21 O29 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 IC C14 C15 N21 C16 0.0000 0.00 180.00 0.00 0.0000 IC H121 C13 *C12 H122 0.0000 0.00 120.00 0.00 0.0000 IC H121 C13 *C12 H123 0.0000 0.00 -120.00 0.00 0.0000 IC H121 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 IC C16 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 IC C15 N21 C16 H131 0.0000 0.00 180.00 0.00 0.0000 IC H131 N21 *C16 H132 0.0000 0.00 120.00 0.00 0.0000 IC H131 N21 *C16 H133 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PACP 0.00 ! C8H9NO2 p-acetamide-phenol ! numbering as in fennretinide ATOM C14 CG331 -0.27 ! H142 ATOM H141 HGA3 0.09 ! | ATOM H142 HGA3 0.09 ! H141-C14-H143 ATOM H143 HGA3 0.09 ! | GROUP ! C15=O29 ATOM C15 CG2O1 0.52 ! | ATOM O29 OG2D1 -0.52 ! N21-H211 GROUP ! | ATOM N21 NG2S1 -0.47 ! C22 ATOM H211 HGP1 0.33 ! // \ ATOM C22 CG2R61 0.14 ! H231-C23 C27-H271 GROUP ! | || ATOM C23 CG2R61 -0.115 ! H241-C24 C26-H261 ATOM H231 HGR61 0.115 ! \\ / GROUP ! C25 ATOM C24 CG2R61 -0.115 ! | ATOM H241 HGR61 0.115 ! O28 GROUP ! \ ATOM C26 CG2R61 -0.115 ! H281 ATOM H261 HGR61 0.115 GROUP ATOM C27 CG2R61 -0.115 ATOM H271 HGR61 0.115 GROUP ATOM C25 CG2R61 0.11 ATOM O28 OG311 -0.53 ATOM H281 HGP1 0.42 BOND C14 C15 C15 N21 N21 C22 C22 C23 C15 O29 BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 BOND C25 O28 O28 H281 N21 H211 BOND C14 H141 C14 H142 C14 H143 BOND C23 H231 C24 H241 C26 H261 C27 H271 IMPR C15 C14 N21 O29 IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 IC C15 N21 C22 C27 0.0000 0.00 0.00 0.00 0.0000 IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 IC H141 C15 *C14 H142 0.0000 0.00 120.00 0.00 0.0000 IC H141 C15 *C14 H143 0.0000 0.00 -120.00 0.00 0.0000 IC H141 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI MECH 0.00 ! C11H18 1,6,6-trimethyl-2-ethenyl-cyclohexene ! using retinol numbering GROUP ATOM C1 CG301 0.00 !H162 H163 H171 H172 ATOM C2 CG321 -0.18 ! \ | | / ATOM H21 HGA2 0.09 !H161-C16 C17-H173 H81 ATOM H22 HGA2 0.09 ! \ / | ATOM C3 CG321 -0.18 ! H21 C1 C8-H82 ATOM H31 HGA2 0.09 ! \ / \ // ATOM H32 HGA2 0.09 ! H22-C2 C6------C7 ATOM C4 CG321 -0.18 ! | || \ ATOM H41 HGA2 0.09 ! H31-C3 C5 H181 H71 ATOM H42 HGA2 0.09 ! / \ / \ / ATOM C5 CG2DC2 0.00 ! H32 C4 C18-H18 ATOM C6 CG2DC2 0.00 ! / \ \ GROUP ! H41 H42 H183 ATOM C7 CG2DC1 -0.15 ATOM H71 HGA4 0.15 ATOM C8 CG2DC3 -0.42 ATOM H81 HGA5 0.21 ATOM H82 HGA5 0.21 GROUP ATOM C16 CG331 -0.27 ATOM H161 HGA3 0.09 ATOM H162 HGA3 0.09 ATOM H163 HGA3 0.09 GROUP ATOM C17 CG331 -0.27 ATOM H171 HGA3 0.09 ATOM H172 HGA3 0.09 ATOM H173 HGA3 0.09 GROUP ATOM C18 CG331 -0.27 ATOM H181 HGA3 0.09 ATOM H182 HGA3 0.09 ATOM H183 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C7 C8 C1 C16 C1 C17 C5 C18 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C7 H71 C8 H81 C8 H82 C18 H181 C18 H182 C18 H183 !initial ring geometry is planar IC C1 C2 C3 C4 0.00 0.00 63.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 -46.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 15.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 IC C5 C6 C7 C8 0.00 0.00 60.0 0.00 0.00 IC C6 C8 *C7 H71 0.00 0.00 180.0 0.00 0.00 IC C6 C7 C8 H81 0.00 0.00 180.0 0.00 0.00 IC C7 H81 *C8 H82 0.00 0.00 180.0 0.00 0.00 IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI TMCH 0.00 ! C10H18 1,2,6,6-tetramethylcyclohexene ! using retinol numbering GROUP ATOM C1 CG301 0.00 !H162 H163 H171 H172 ATOM C2 CG321 -0.18 ! \ | | / ATOM H21 HGA2 0.09 !H161-C16 C17-H173 ATOM H22 HGA2 0.09 ! \ / ATOM C3 CG321 -0.18 ! H21 C1 H71 H72 ATOM H31 HGA2 0.09 ! \ / \ | / ATOM H32 HGA2 0.09 ! H22-C2 C6------C7-H73 ATOM C4 CG321 -0.18 ! | || ATOM H41 HGA2 0.09 ! H31-C3 C5 H181 ATOM H42 HGA2 0.09 ! / \ / \ / ATOM C5 CG2D1 0.00 ! H32 C4 C18-H18 ATOM C6 CG2D1 0.00 ! / \ \ GROUP ! H41 H42 H183 ATOM C7 CG331 -0.27 ATOM H71 HGA3 0.09 ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 GROUP ATOM C16 CG331 -0.27 ATOM H161 HGA3 0.09 ATOM H162 HGA3 0.09 ATOM H163 HGA3 0.09 GROUP ATOM C17 CG331 -0.27 ATOM H171 HGA3 0.09 ATOM H172 HGA3 0.09 ATOM H173 HGA3 0.09 GROUP ATOM C18 CG331 -0.27 ATOM H181 HGA3 0.09 ATOM H182 HGA3 0.09 ATOM H183 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C1 C16 C1 C17 C5 C18 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C7 H71 C7 H72 C7 H73 C18 H181 C18 H182 C18 H183 !initial geometry is planar IC C1 C2 C3 C4 0.00 0.00 -63.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 46.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 -13.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 IC C5 C6 C7 H71 0.00 0.00 180.0 0.00 0.00 IC C6 H71 *C7 H72 0.00 0.00 120.0 0.00 0.00 IC C6 H71 *C7 H73 0.00 0.00 -120.0 0.00 0.00 IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI FRET 0.00 ! C26H33NO2 fennretinide, nomenclature consistent with retinol GROUP ATOM C1 CG301 0.00 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 ATOM C5 CG2DC2 0.00 ATOM C6 CG2DC2 0.00 GROUP ATOM C7 CG2DC1 -0.15 ATOM H71 HGA4 0.15 ATOM C8 CG2DC1 -0.15 ATOM H81 HGA4 0.15 ATOM C9 CG2DC2 0.00 ATOM C10 CG2DC2 -0.15 ATOM H101 HGA4 0.15 GROUP ATOM C11 CG2DC1 -0.15 !H162 H163 H171 H172 ATOM H111 HGA4 0.15 ! \ | | / ATOM C12 CG2DC1 -0.15 !H161-C16 C17-H173 H191 H192 ATOM H121 HGA4 0.15 ! \ / \ / ATOM C13 CG2DC2 0.00 ! H21 C1 H71 H81 C19 ATOM C14 CG2DC2 -0.15 ! \ / \ | | / \ ATOM H141 HGA4 0.15 ! H22-C2 C6------C7=====C8----C9 H193 GROUP ! | || || ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 ATOM H161 HGA3 0.09 ! / \ / \ / | ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 ATOM H163 HGA3 0.09 ! / \ \ || GROUP ! H41 H42 H183 C12-H121 H201 ATOM C17 CG331 -0.27 ! | / ATOM H171 HGA3 0.09 ! C13---C20-H202 ATOM H172 HGA3 0.09 ! || \ ATOM H173 HGA3 0.09 ! C14-H141 H203 GROUP ! | ATOM C18 CG331 -0.27 ! C15=O29 ATOM H181 HGA3 0.09 ! | ATOM H182 HGA3 0.09 ! N21-H211 ATOM H183 HGA3 0.09 ! | GROUP ! C22 ATOM C19 CG331 -0.27 ! // \ ATOM H191 HGA3 0.09 ! H231-C23 C27-H271 ATOM H192 HGA3 0.09 ! | || ATOM H193 HGA3 0.09 ! H241-C24 C26-H261 GROUP ! \\ / ATOM C20 CG331 -0.27 ! C25 ATOM H201 HGA3 0.09 ! | ATOM H202 HGA3 0.09 ! O28 ATOM H203 HGA3 0.09 ! \ GROUP ! H281 ATOM C15 CG2O1 0.51 ! charges from CROT ATOM O29 OG2D1 -0.51 GROUP ATOM N21 NG2S1 -0.47 ATOM H211 HGP1 0.33 ! charges from PACP ATOM C22 CG2R61 0.14 GROUP ATOM C23 CG2R61 -0.115 ATOM H231 HGR61 0.115 GROUP ATOM C24 CG2R61 -0.115 ATOM H241 HGR61 0.115 GROUP ATOM C26 CG2R61 -0.115 ATOM H261 HGR61 0.115 GROUP ATOM C27 CG2R61 -0.115 ATOM H271 HGR61 0.115 GROUP ATOM C25 CG2R61 0.11 ATOM O28 OG311 -0.53 ATOM H281 HGP1 0.42 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C22 C22 C23 BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 C15 O29 BOND C25 O28 O28 H281 N21 H211 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 BOND C20 H201 C20 H202 C20 H203 BOND C23 H231 C24 H241 C26 H261 C27 H271 IMPR C15 C14 N21 O29 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 IC C15 N21 C22 C27 0.0000 0.00 180.00 0.00 0.0000 IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI RTOL 0.00 ! C20H30O retinol, nomenclature from PDB GROUP ATOM C1 CG301 0.00 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 ATOM C5 CG2DC2 0.00 ATOM C6 CG2DC2 0.00 GROUP ATOM C7 CG2DC1 -0.15 ATOM H71 HGA4 0.15 ATOM C8 CG2DC1 -0.15 ATOM H81 HGA4 0.15 GROUP ATOM C9 CG2DC2 0.00 ATOM C10 CG2DC2 -0.15 ATOM H101 HGA4 0.15 GROUP ATOM C11 CG2DC1 -0.15 ATOM H111 HGA4 0.15 GROUP ATOM C12 CG2DC1 -0.15 ATOM H121 HGA4 0.15 GROUP ATOM C13 CG2DC2 0.00 ATOM C14 CG2DC2 -0.15 ATOM H141 HGA4 0.15 !H162 H163 H171 H172 GROUP ! \ | | / ATOM C15 CG321 0.05 !H161-C16 C17-H173 H191 H192 ATOM H151 HGA2 0.09 ! \ / \ / ATOM H152 HGA2 0.09 ! H21 C1 H71 H81 C19 ATOM OR OG311 -0.65 ! \ / \ | | / \ ATOM HR HGP1 0.42 ! H22-C2 C6------C7=====C8----C9 H193 GROUP ! | || || ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 ATOM H161 HGA3 0.09 ! / \ / \ / | ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 ATOM H163 HGA3 0.09 ! / \ \ || GROUP ! H41 H42 H183 C12-H121 H201 ATOM C17 CG331 -0.27 ! | / ATOM H171 HGA3 0.09 ! C13---C20-H202 ATOM H172 HGA3 0.09 ! || \ ATOM H173 HGA3 0.09 ! C14-H141 H203 GROUP ! | ATOM C18 CG331 -0.27 ! H151-C15-H152 ATOM H181 HGA3 0.09 ! | ATOM H182 HGA3 0.09 ! OR ATOM H183 HGA3 0.09 ! \ GROUP ! HR ATOM C19 CG331 -0.27 ATOM H191 HGA3 0.09 ATOM H192 HGA3 0.09 ATOM H193 HGA3 0.09 GROUP ATOM C20 CG331 -0.27 ATOM H201 HGA3 0.09 ATOM H202 HGA3 0.09 ATOM H203 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 BOND C12 C13 C13 C14 C14 C15 C15 OR BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 BOND C15 H151 C15 H152 OR HR BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 BOND C20 H201 C20 H202 C20 H203 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 IC C13 C14 C15 OR 0.0000 0.00 180.00 0.00 0.0000 IC OR C14 *C15 H151 0.0000 0.00 120.00 0.00 0.0000 IC OR C14 *C15 H152 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C15 OR HR 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI RTAL 0.00 ! C20H28O retinal, nomenclature from PDB based on retinol GROUP ATOM C1 CG301 0.00 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 ATOM C5 CG2DC2 0.00 ATOM C6 CG2DC2 0.00 GROUP ATOM C7 CG2DC1 -0.15 ATOM H71 HGA4 0.15 ATOM C8 CG2DC1 -0.15 ATOM H81 HGA4 0.15 ATOM C9 CG2DC2 0.00 ATOM C10 CG2DC2 -0.15 ATOM H101 HGA4 0.15 GROUP ATOM C11 CG2DC1 -0.15 ATOM H111 HGA4 0.15 ATOM C12 CG2DC1 -0.15 ATOM H121 HGA4 0.15 ATOM C13 CG2DC2 0.00 !H162 H163 H171 H172 GROUP ! \ | | / ATOM C14 CG2DC2 -0.04 !H161-C16 C17-H173 H191 H192 ATOM H141 HGA4 0.15 ! \ / \ / ATOM C15 CG2O4 0.27 ! H21 C1 H71 H81 C19 ATOM O15 OG2D1 -0.51 ! \ / \ | | / \ ATOM H15 HGR52 0.13 ! H22-C2 C6------C7=====C8----C9 H193 GROUP ! | || || ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 ATOM H161 HGA3 0.09 ! / \ / \ / | ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 ATOM H163 HGA3 0.09 ! / \ \ || GROUP ! H41 H42 H183 C12-H121 H201 ATOM C17 CG331 -0.27 ! | / ATOM H171 HGA3 0.09 ! C13---C20-H202 ATOM H172 HGA3 0.09 ! || \ ATOM H173 HGA3 0.09 ! C14-H141 H203 GROUP ! | ATOM C18 CG331 -0.27 ! C15 ATOM H181 HGA3 0.09 ! / \\ ATOM H182 HGA3 0.09 ! H15 O15 ATOM H183 HGA3 0.09 GROUP ATOM C19 CG331 -0.27 ATOM H191 HGA3 0.09 ATOM H192 HGA3 0.09 ATOM H193 HGA3 0.09 GROUP ATOM C20 CG331 -0.27 ATOM H201 HGA3 0.09 ATOM H202 HGA3 0.09 ATOM H203 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 BOND C12 C13 C13 C14 C14 C15 C15 O15 C15 H15 BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 BOND C20 H201 C20 H202 C20 H203 IMPR C15 C14 O15 H15 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 IC C13 C14 C15 O15 0.0000 0.00 180.00 0.00 0.0000 IC O15 C14 *C15 H15 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI RTAC -1.00 ! C20H27O2 all-trans-retinoic acid, nomenclature from PDB GROUP ATOM C1 CG301 0.00 ATOM C16 CG331 -0.27 ATOM H161 HGA3 0.09 ATOM H162 HGA3 0.09 ATOM H163 HGA3 0.09 ATOM C17 CG331 -0.27 ATOM H171 HGA3 0.09 ATOM H172 HGA3 0.09 ATOM H173 HGA3 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG2DC2 0.00 ATOM C6 CG2DC2 0.00 GROUP ATOM C18 CG331 -0.27 ATOM H181 HGA3 0.09 ATOM H182 HGA3 0.09 ATOM H183 HGA3 0.09 GROUP ATOM C7 CG2DC1 -0.15 ATOM H71 HGA4 0.15 ATOM C8 CG2DC1 -0.15 ATOM H81 HGA4 0.15 GROUP ATOM C9 CG2DC2 0.00 ATOM C19 CG331 -0.27 !H162 H163 H171 H172 ATOM H191 HGA3 0.09 ! \ | | / ATOM H192 HGA3 0.09 !H161-C16 C17-H173 H191 H192 ATOM H193 HGA3 0.09 ! \ / \ / ATOM C10 CG2DC2 -0.15 ! H21 C1 H71 H81 C19 ATOM H101 HGA4 0.15 ! \ / \ | | / \ GROUP ! H22-C2 C6------C7=====C8----C9 H193 ATOM C11 CG2DC1 -0.15 ! | || || ATOM H111 HGA4 0.15 ! H31-C3 C5 H181 C10-H101 ATOM C12 CG2DC1 -0.15 ! / \ / \ / | ATOM H121 HGA4 0.15 ! H32 C4 C18-H182 C11-H111 GROUP ! / \ \ || ATOM C13 CG2DC2 0.00 ! H41 H42 H183 C12-H121 H201 ATOM C20 CG331 -0.27 ! | / ATOM H201 HGA3 0.09 ! C13---C20-H202 ATOM H202 HGA3 0.09 ! || \ ATOM H203 HGA3 0.09 ! C14-H141 H203 GROUP ! | ATOM C14 CG2DC2 -0.25 ! C15=O29 ATOM H141 HGA4 0.15 ! | (-) ATOM C15 CG2O3 0.62 ! O29B ATOM O29 OG2D2 -0.76 ATOM O29B OG2D2 -0.76 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 BOND C12 C13 C13 C14 C14 C15 C15 O29 C15 O29B BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 BOND C20 H201 C20 H202 C20 H203 IMPR C15 O29B O29 C14 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 IC C13 C14 C15 O29 0.0000 0.00 180.00 0.00 0.0000 IC O29 C14 *C15 O29B 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PRAC -1.00 ! C3H3O2 2-propenoic acid GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ATOM H12 HGA5 0.21 ! H11 OD1 GROUP ! \ || ATOM C2 CG2DC1 -0.25 ! C1 CG ATOM H21 HGA4 0.15 ! / \\ / \ ATOM CG CG2O3 0.62 ! H12 C2 OD2 (-) ATOM OD1 OG2D2 -0.76 ! | ATOM OD2 OG2D2 -0.76 ! H21 BOND C1 H11 C1 H12 C1 C2 C2 H21 BOND C2 CG CG OD1 CG OD2 IMPR CG OD2 OD1 C2 IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 IC OD1 C2 *CG OD2 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PROL 0.00 ! C3H6O 3-propenol (1-hydroxy-2-propene) GROUP ATOM C1 CG2D2 -0.42 ATOM H11 HGA5 0.21 ! H11 H31 ATOM H12 HGA5 0.21 ! \ | ATOM C2 CG2D1 -0.15 ! C1 C3-OR ATOM H21 HGA4 0.15 ! / \\ / | \ GROUP ! H12 C2 H32 HR ATOM C3 CG321 0.05 ! | ATOM H31 HGA2 0.09 ! H21 ATOM H32 HGA2 0.09 ATOM OR OG311 -0.65 ATOM HR HGP1 0.42 BOND C1 C2 C2 C3 C3 OR OR HR BOND H11 C1 H12 C1 H21 C2 H31 C3 BOND H32 C3 IC C1 C2 C3 OR 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 OR HR 0.0000 0.00 60.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC OR C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC OR C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PRAL 0.00 ! C3H4O 2-propenal (acrolein) GROUP ATOM C1 CG2DC3 -0.42 ATOM H11 HGA5 0.21 ! H11 OD1 ATOM H12 HGA5 0.21 ! \ || ATOM C2 CG2DC1 -0.04 ! C1 CG ATOM H21 HGA4 0.15 ! / \\ / \ ATOM CG CG2O4 0.27 ! H12 C2 H ATOM OD1 OG2D1 -0.51 ! | ATOM H HGR52 0.13 ! H21 BOND C1 H11 C1 H12 C1 C2 C2 H21 BOND C2 CG CG OD1 CG H IMPR CG C2 OD1 H IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC OD1 C2 *CG H 0.0000 0.00 180.00 0.00 0.0000 RESI SCH1 0.00 ! C3H7N Schiff's base model compound 1, deprotonated GROUP ATOM C1 CG331 -0.05 ! H11 H31 ATOM H11 HGA3 0.09 ! \ / ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H41 ATOM H13 HGA3 0.09 ! / \ / ATOM N2 NG2D1 -0.60 ! H13 C4--H42 ATOM C3 CG2D1 0.23 ! \ ATOM H31 HGA4 0.15 ! H43 GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 N2 N2 C3 C3 H31 BOND C3 C4 C4 H41 C4 H42 C4 H43 IMPR C3 C4 N2 H31 IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI SCH2 1.00 ! C3H8N Schiff's base model compound 2, protonated GROUP ATOM C1 CG334 0.18 ! H11 H21 H31 ATOM H11 HGA3 0.09 ! \ | / ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H41 ATOM H13 HGA3 0.09 ! / (+) \ / ATOM N2 NG2P1 -0.40 ! H13 C4--H42 ATOM H21 HGP2 0.38 ! \ ATOM C3 CG2D1 0.37 ! H43 ATOM H31 HGR52 0.20 ! hydrogen with intermediate VDW radius GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 N2 N2 H21 N2 C3 C3 H31 BOND C3 C4 C4 H41 C4 H42 C4 H43 IMPR C3 C4 N2 H31 IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI SCH3 1.00 ! C4H8N Schiff's base model compound 3, protonated GROUP ATOM C1 CG334 0.18 ! H11 H21 H31 ATOM H11 HGA3 0.09 ! \ | / ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H51 ATOM H13 HGA3 0.09 ! / (+) \ / ATOM N2 NG2P1 -0.40 ! H13 C4=C5 ATOM H21 HGP2 0.38 ! / \ ATOM C3 CG2DC1 0.37 ! H41 H52 ATOM H31 HGR52 0.20 ! hydrogen with intermediate VDW radius GROUP ATOM C4 CG2DC2 -0.15 ATOM H41 HGA4 0.15 ATOM C5 CG2DC3 -0.42 ATOM H51 HGA5 0.21 ATOM H52 HGA5 0.21 BOND C1 H11 C1 H12 C1 H13 BOND C1 N2 N2 H21 N2 C3 C3 H31 BOND C3 C4 C4 H41 BOND C4 C5 C5 H51 C5 H52 IMPR C3 C4 N2 H31 IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC N2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 N2 C3 0.0000 0.00 180.00 0.00 0.0000 IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 !/home/alex/param/general/Cyprus/toppar !toppar_all22_flavopyridol_apr05.str !piperidine models only RESI PIP1 1.00 ! C6H14N N-methyl piperidinium !methyl axial to ring !Note that PIP1 and 2 only differ by the configuration about the N GROUP ATOM C1 CG334 0.15 ATOM H1A HGA3 0.09 ATOM H1B HGA3 0.09 ! C15--C16 ATOM H1C HGA3 0.09 ! / \ ATOM N1 NG3P1 -0.40 ! C14 (+) N1--C1 ATOM HNA HGP2 0.32 ! \ / ATOM C12 CG324 0.15 ! C13--C12 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 ATOM C16 CG324 0.15 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C13 CG321 -0.18 ATOM H13A HGA2 0.09 ATOM H13B HGA2 0.09 GROUP ATOM C14 CG321 -0.18 ATOM H14A HGA2 0.09 ATOM H14B HGA2 0.09 GROUP ATOM C15 CG321 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 BOND C1 H1A C1 H1B C1 H1C C1 N1 BOND N1 HNA BOND N1 C16 N1 C12 C12 H12A C12 H12B BOND C12 C13 C13 H13A C13 H13B BOND C13 C14 C14 H14A C14 H14B C14 C15 BOND C15 H15A C15 H15B C15 C16 C16 H16A BOND C16 H16B IC C16 N1 C12 C13 0.0000 0.00 -60.00 0.00 0.0000 IC N1 C12 C13 C14 0.0000 0.00 60.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 -60.00 0.00 0.0000 IC C13 C14 C15 C16 0.0000 0.00 60.00 0.00 0.0000 IC C12 C16 *N1 C1 0.0000 0.00 -120.00 0.00 0.0000 IC H1A N1 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 IC H1A N1 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 IC H1A C1 N1 C16 0.0000 0.00 180.00 0.00 0.0000 IC C16 C1 *N1 C12 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C1 *N1 HNA 0.0000 0.00 -120.00 0.00 0.0000 IC C13 N1 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 IC H12A N1 *C12 H12B 0.0000 0.00 120.00 0.00 0.0000 IC C15 N1 *C16 H16A 0.0000 0.00 120.00 0.00 0.0000 IC C15 N1 *C16 H16B 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000 IC H13A C12 *C13 H13B 0.0000 0.00 120.00 0.00 0.0000 IC C15 C13 *C14 H14A 0.0000 0.00 -120.00 0.00 0.0000 IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C16 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000 IC C14 C16 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PIP2 1.00 ! C6H14N N-methyl piperidinium !methyl equitorial to ring GROUP ATOM C1 CG334 0.15 ATOM H1A HGA3 0.09 ATOM H1B HGA3 0.09 ! C15--C16 ATOM H1C HGA3 0.09 ! / \ ATOM N1 NG3P1 -0.40 ! C14 (+) N1--C1 ATOM HNA HGP2 0.32 ! \ / ATOM C12 CG324 0.15 ! C13--C12 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 ATOM C16 CG324 0.15 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C13 CG321 -0.18 ATOM H13A HGA2 0.09 ATOM H13B HGA2 0.09 GROUP ATOM C14 CG321 -0.18 ATOM H14A HGA2 0.09 ATOM H14B HGA2 0.09 GROUP ATOM C15 CG321 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 BOND C1 H1A C1 H1B C1 H1C C1 N1 BOND N1 HNA BOND N1 C16 N1 C12 C12 H12A C12 H12B BOND C12 C13 C13 H13A C13 H13B BOND C13 C14 C14 H14A C14 H14B C14 C15 BOND C15 H15A C15 H15B C15 C16 C16 H16A BOND C16 H16B IC C16 N1 C12 C13 0.0000 0.00 -60.00 0.00 0.0000 IC N1 C12 C13 C14 0.0000 0.00 60.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 -60.00 0.00 0.0000 IC C13 C14 C15 C16 0.0000 0.00 60.00 0.00 0.0000 IC C12 C16 *N1 C1 0.0000 0.00 120.00 0.00 0.0000 IC H1A N1 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 IC H1A N1 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 IC H1A C1 N1 C16 0.0000 0.00 180.00 0.00 0.0000 IC C16 C1 *N1 C12 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C1 *N1 HNA 0.0000 0.00 120.00 0.00 0.0000 IC C13 N1 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 IC H12A N1 *C12 H12B 0.0000 0.00 120.00 0.00 0.0000 IC C15 N1 *C16 H16A 0.0000 0.00 120.00 0.00 0.0000 IC C15 N1 *C16 H16B 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000 IC H13A C12 *C13 H13B 0.0000 0.00 120.00 0.00 0.0000 IC C15 C13 *C14 H14A 0.0000 0.00 -120.00 0.00 0.0000 IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C16 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000 IC C14 C16 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI PIP3 1.00 ! C6H14NO 3-hydroxy-N-methyl piperidinium GROUP ATOM C1 CG334 0.15 ! group charge should be 1.0 ATOM H1A HGA3 0.09 ATOM H1B HGA3 0.09 ! C15--C16 ATOM H1C HGA3 0.09 ! / \ ATOM N1 NG3P1 -0.40 ! ----C14 (+) N1--C1 ATOM HNA HGP2 0.32 ! \ / ATOM C12 CG324 0.15 ! C13--C12 ATOM H12A HGA2 0.09 ! / ATOM H12B HGA2 0.09 ! H-O3 ATOM C16 CG324 0.15 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C13 CG311 0.14 ATOM H13 HGA1 0.09 ATOM O3 OG311 -0.65 ATOM HO3 HGP1 0.42 GROUP ATOM C14 CG321 -0.18 ATOM H14A HGA2 0.09 ATOM H14B HGA2 0.09 GROUP ATOM C15 CG321 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 BOND C1 H1A C1 H1B C1 H1C C1 N1 BOND N1 HNA BOND N1 C16 N1 C12 C12 H12A C12 H12B BOND C12 C13 C13 H13 C13 O3 O3 HO3 BOND C13 C14 C14 H14A C14 H14B C14 C15 BOND C15 H15A C15 H15B C15 C16 C16 H16A BOND C16 H16B IC C14 C15 C16 N1 .0000 .00 -60.00 .00 .0000 IC C15 C16 N1 C12 .0000 .00 60.00 .00 .0000 IC C16 N1 C12 C13 .0000 .00 -60.00 .00 .0000 IC N1 C12 C13 C14 .0000 .00 60.00 .00 .0000 IC C12 C16 *N1 C1 .0000 .00 120.00 .00 .0000 IC C12 C16 *N1 HNA .0000 .00 -120.00 .00 .0000 IC C16 N1 C1 H1A .0000 .00 120.00 .00 .0000 IC H1A N1 *C1 H1B .0000 .00 120.00 .00 .0000 IC H1A N1 *C1 H1C .0000 .00 -120.00 .00 .0000 IC C13 N1 *C12 H12A .0000 .00 120.00 .00 .0000 IC C13 N1 *C12 H12B .0000 .00 -120.00 .00 .0000 IC C15 N1 *C16 H16A .0000 .00 120.00 .00 .0000 IC C15 N1 *C16 H16B .0000 .00 -120.00 .00 .0000 IC C12 C14 *C13 O3 .0000 .00 120.00 .00 .0000 IC C12 C14 *C13 H13 .0000 .00 -120.00 .00 .0000 IC C12 C13 O3 HO3 .0000 .00 60.00 .00 .0000 IC C15 C13 *C14 H14A .0000 .00 120.00 .00 .0000 IC C15 C13 *C14 H14B .0000 .00 -120.00 .00 .0000 IC C14 C16 *C15 H15A .0000 .00 120.00 .00 .0000 IC C14 C16 *C15 H15B .0000 .00 -120.00 .00 .0000 PATCH FIRST NONE LAST NONE !RESI DUM 0.00 ! DUMMY ATOM !GROUP !ATOM DUM DUM 0.00 !PATCHING FIRST NONE LAST NONE !RESI HE 0.00 ! helium !GROUP !ATOM HE HE 0.00 !PATCHING FIRST NONE LAST NONE !RESI NE 0.00 ! neon !GROUP !ATOM NE NE 0.00 !PATCHING FIRST NONE LAST NONE !adm jr(?), july2006 RESI ALF4 -1.00 ! AlF4 Aluminum tetraflouride, tetrahedral geometry GROUP ATOM AL1 ALG1 1.16 ATOM F1 FGP1 -0.54 ATOM F2 FGP1 -0.54 ATOM F3 FGP1 -0.54 ATOM F4 FGP1 -0.54 BOND AL1 F1 AL1 F2 AL1 F3 AL1 F4 IC F2 F1 *AL1 F3 0.0000 0.00 120.00 0.00 0.0000 IC F2 F1 *AL1 F4 0.0000 0.00 -120.00 0.00 0.0000 RESI FLUB 0.00 ! C6H5F fluorobenzene, adm jr. GROUP ! atom numbering based on difluorotoluene ATOM C1 CG2R61 -0.10 ATOM H1 HGR62 0.15 ! H5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! F6--C6 C3--H3 ATOM C4 CG2R61 -0.115 ! \\ // ATOM H4 HGR61 0.115 ! C1---C2 ATOM C5 CG2R61 -0.10 ! / \ ATOM H5 HGR62 0.15 ! H1 H2 ATOM C6 CG2R66 0.11 ATOM F6 FGR1 -0.21 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 BOND C6 C1 C6 F6 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 F6 0.0000 0.00 180.00 0.00 0.0000 RESI UREA 0.00 ! CH4N2O Urea, adm GROUP ATOM N1 NG2S2 -0.69 ATOM H11 HGP1 0.34 ATOM H12 HGP1 0.34 ATOM C2 CG2O6 0.60 ATOM O2 OG2D1 -0.58 ATOM N3 NG2S2 -0.69 ATOM H31 HGP1 0.34 ATOM H32 HGP1 0.34 BOND C2 O2 C2 N1 C2 N3 BOND N1 H11 N1 H12 BOND N3 H31 N3 H32 IMPR C2 N1 N3 O2 IC O2 C2 N1 H11 0.0000 0.00 0.00 0.00 0.0000 IC H11 C2 *N1 H12 0.0000 0.00 180.00 0.00 0.0000 IC H11 N1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC N1 C2 N3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H31 C2 *N3 H32 0.0000 0.00 180.00 0.00 0.0000 RESI PY01 0.000 ! C5H6O 4H-Pyran, maybridge list, adm GROUP ATOM O1 OG3R60 -0.32 ! new atom type!! ATOM C2 CG2D1O -0.04 ! new atom type!! ATOM H21 HGA4 0.20 ! O1 ATOM C3 CG2D1 -0.15 ! / \ ATOM H31 HGA4 0.15 ! H21-C2 C6-H61 ATOM C4 CG321 -0.18 ! || || ATOM H41 HGA2 0.09 ! H31-C3 C5-H51 ATOM H42 HGA2 0.09 ! \ / ATOM C5 CG2D1 -0.15 ! C4 ATOM H51 HGA4 0.15 ! / \ ATOM C6 CG2D1O -0.04 ! H41 H42 ATOM H61 HGA4 0.20 BOND O1 C2 C2 H21 C2 C3 C3 H31 BOND C3 C4 C4 H41 C4 H42 C4 C5 C5 H51 BOND C5 C6 C6 H61 C6 O1 IC C6 O1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 O1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 RESI PY02 0.000 ! C5H6O 2H-Pyran, maybridge list, adm GROUP ! Note use of conjugated C types ATOM O1 OG3R60 -0.37 ATOM C2 CG321 0.00 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ! H21 O1 ATOM C3 CG2DC2 -0.15 ! \ / \ ATOM H31 HGA4 0.15 ! H22-C2 C6-H61 ATOM C4 CG2DC2 -0.15 ! | || ATOM H41 HGA4 0.15 ! H31-C3 C5-H51 ATOM C5 CG2DC1 -0.15 ! \\ / ATOM H51 HGA4 0.15 ! C4 ATOM C6 CG2D1O 0.00 ! | ATOM H61 HGA4 0.19 ! H41 BOND O1 C2 C2 H21 C2 H22 C2 C3 C3 H31 BOND C3 C4 C4 H41 C4 C5 C5 H51 BOND C5 C6 C6 H61 C6 O1 !mp2/6-31g* ring IC C6 O1 C2 C3 0.0000 0.00 51.00 0.00 0.0000 IC O1 C2 C3 C4 0.0000 0.00 -42.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 8.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 18.00 0.00 0.0000 IC C4 C5 C6 O1 0.0000 0.00 -8.00 0.00 0.0000 IC C5 C6 O1 C2 0.0000 0.00 -27.00 0.00 0.0000 IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 O1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 RESI NITB 0.000 ! C6H5NO2 nitrobenzene GROUP ATOM C1 CG2R61 -0.18 ATOM H1 HGR61 0.16 ! H5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! O6A C5---C4 ATOM C3 CG2R61 -0.115 ! \ + / \ ATOM H3 HGR61 0.115 ! - N6--C6 C3--H3 ATOM C4 CG2R61 -0.115 ! / \\ // ATOM H4 HGR61 0.115 ! O6B C1---C2 ATOM C5 CG2R61 -0.18 ! / \ ATOM H5 HGR61 0.16 ! H1 H2 ATOM C6 CG2R61 0.32 ATOM N6 NG2O1 0.40 ATOM O6A OG2N1 -0.34 ATOM O6B OG2N1 -0.34 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 BOND C6 C1 C6 N6 N6 O6A N6 O6B IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 IC C1 C6 N6 O6A 0.0000 0.00 180.00 0.00 0.0000 IC O6A C6 *N6 O6B 0.0000 0.00 180.00 0.00 0.0000 RESI PYRL 0.000 ! C4H5N pyrrole GROUP ! H2 H1 ATOM C1 CG2R51 -0.04 ! \ ____ / ATOM H1 HGR52 0.14 ! C2----C1 ATOM C2 CG2R51 -0.25 ! | \ ATOM H2 HGR51 0.15 ! | N5--H5 ATOM C3 CG2R51 -0.25 ! |____ / ATOM H3 HGR51 0.15 ! C3----C4 ATOM C4 CG2R51 -0.04 ! / \ ATOM H4 HGR52 0.14 ! H3 H4 ATOM N5 NG2R51 -0.35 ATOM H5 HGP1 0.35 BOND C1 H1 C1 C2 C2 H2 C2 C3 C3 H3 BOND C3 C4 C4 H4 C4 N5 N5 H5 N5 C1 IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI FURA 0.00 ! C4H4O furan GROUP ! H2 H1 ATOM C1 CG2R51 0.10 ! \ ____ / ATOM H1 HGR52 0.14 ! C2----C1 ATOM C2 CG2R51 -0.25 ! | \ ATOM H2 HGR51 0.15 ! | O5 ATOM C3 CG2R51 -0.25 ! |____ / ATOM H3 HGR51 0.15 ! C3----C4 ATOM C4 CG2R51 0.10 ! / \ ATOM H4 HGR52 0.14 ! H3 H4 ATOM O5 OG2R50 -0.28 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 O5 O5 C1 IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC O5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC O5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 RESI THIP 0.000 ! C4H4S thiophene GROUP ATOM C1 CG2R51 -0.06 ! H2 H1 ATOM H1 HGR52 0.18 ! \ ____ / ATOM C2 CG2R51 -0.24 ! C2----C1 ATOM H2 HGR51 0.17 ! | \ ATOM C3 CG2R51 -0.24 ! | S5 ATOM H3 HGR51 0.17 ! |____ / ATOM C4 CG2R51 -0.06 ! C3----C4 ATOM H4 HGR52 0.18 ! / \ ATOM S5 SG2R50 -0.10 ! H3 H4 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 S5 S5 C1 IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC S5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC S5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 RESI OXAZ 0.000 ! C3H3NO oxazole GROUP ! H2 H1 ATOM C1 CG2R51 0.11 ! \ ____ / ATOM H1 HGR52 0.12 ! C2----C1 ATOM C2 CG2R51 0.15 ! | \ ATOM H2 HGR52 0.11 ! | O5 ATOM N3 NG2R50 -0.61 ! |____ / ATOM C4 CG2R53 0.22 ! N3----C4 ATOM H4 HGR52 0.19 ! \ ATOM O5 OG2R50 -0.29 ! H4 BOND C1 H1 C1 C2 C2 H2 C2 N3 BOND N3 C4 C4 H4 C4 O5 O5 C1 IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC O5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC O5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 RESI ISOX 0.000 ! C3H3NO isoxazole GROUP ! H2 H1 ATOM C1 CG2R51 0.28 ! \ ____ / ATOM H1 HGR52 0.13 ! C2----C1 ATOM C2 CG2R51 -0.43 ! | \ ATOM H2 HGR51 0.18 ! | O5 ATOM C3 CG2R52 0.35 ! |____ / ATOM H3 HGR52 0.11 ! C3----N4 ATOM N4 NG2R50 -0.45 ! / ATOM O5 OG2R50 -0.17 ! H3 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 N4 C3 H3 N4 O5 O5 C1 IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC O5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI THAZ 0.000 ! C3H3NS thiazole GROUP ! H2 H1 ATOM C1 CG2R51 -0.30 ! \ ____ / ATOM H1 HGR52 0.21 ! C2----C1 ATOM C2 CG2R51 0.20 ! | \ ATOM H2 HGR52 0.13 ! | S5 ATOM N3 NG2R50 -0.61 ! |____ / ATOM C4 CG2R53 0.22 ! N3----C4 ATOM H4 HGR52 0.14 ! \ ATOM S5 SG2R50 0.01 ! H4 BOND C1 H1 C1 C2 C2 H2 C2 N3 BOND N3 C4 C4 H4 C4 S5 S5 C1 IC C1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC S5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC S5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 RESI ISOT 0.000 ! C3H3NS isothiazole GROUP ! H2 H1 ATOM C1 CG2R51 -0.04 ! \ ____ / ATOM H1 HGR52 0.16 ! C2----C1 ATOM C2 CG2R51 -0.20 ! | \ ATOM H2 HGR51 0.13 ! | S5 ATOM C3 CG2R52 0.23 ! |____ / ATOM H3 HGR52 0.11 ! C3----N4 ATOM N4 NG2R50 -0.53 ! / ATOM S5 SG2R50 0.14 ! H3 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 N4 C3 H3 N4 S5 S5 C1 IC S5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI PYRZ 0.000 ! C3H4N2 pyrazole GROUP ATOM C1 CG2R51 -0.03 ! H2 H1 ATOM H1 HGR52 0.15 ! \ ____ / ATOM C2 CG2R51 -0.24 ! C2----C1 ATOM H2 HGR51 0.14 ! | \ ATOM C3 CG2R52 0.14 ! | N5--H5 ATOM H3 HGR52 0.13 ! |____ / ATOM N4 NG2R50 -0.57 ! C3----N4 ATOM N5 NG2R51 -0.05 ! / ATOM H5 HGP1 0.33 ! H3 BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 N4 N4 N5 N5 H5 N5 C1 IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC N5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI OXAD 0.000 ! C2H2N2O oxadiazole123 GROUP ! H2 H1 ATOM C1 CG2R51 0.17 ! \ ____ / ATOM H1 HGR52 0.14 ! C2----C1 ATOM C2 CG2R51 0.19 ! | \ ATOM H2 HGR52 0.10 ! | O5 ATOM N3 NG2R50 -0.32 ! |____ / ATOM N4 NG2R50 -0.10 ! N3----N4 ATOM O5 OG2R50 -0.18 BOND C1 H1 C1 C2 C2 H2 C2 N3 BOND N3 N4 N4 O5 O5 C1 IC C1 C2 N3 N4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 N4 O5 0.0000 0.00 0.00 0.00 0.0000 IC N3 N4 O5 C1 0.0000 0.00 0.00 0.00 0.0000 IC O5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 RESI TRZ3 0.000 ! C2H3N3 triazole123 GROUP ! H2 H1 ATOM C1 CG2R51 -0.35 ! \ ____ / ATOM H1 HGR52 0.20 ! C2----C1 ATOM C2 CG2R51 0.25 ! | \ ATOM H2 HGR52 0.11 ! | N5--H5 ATOM N3 NG2R50 -0.41 ! |____ / ATOM N4 NG2R50 -0.37 ! N3----N4 ATOM N5 NG2R51 0.28 ATOM H5 HGP1 0.29 BOND C1 H1 C1 C2 C2 H2 C2 N3 BOND N3 N4 N4 N5 N5 H5 N5 C1 IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 N3 N4 0.0000 0.00 0.00 0.00 0.0000 IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI PYRD 0.000 ! C4H4N2 pyridazine GROUP ATOM N1 NG2R62 -0.44 ATOM N2 NG2R62 -0.44 ! H5 H6 ATOM C3 CG2R61 0.31 ! \ / ATOM H3 HGR62 0.11 ! C5----C6 ATOM C4 CG2R61 -0.16 ! / \ ATOM H4 HGR61 0.18 ! H4--C4 N1 ATOM C5 CG2R61 -0.16 ! \\ // ATOM H5 HGR61 0.18 ! C3----N2 ATOM C6 CG2R61 0.31 ! / ATOM H6 HGR62 0.11 ! H3 BOND N1 N2 N2 C3 C3 C4 C4 C5 C5 C6 C6 N1 BOND C3 H3 C4 H4 C5 H5 C6 H6 IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI PYZN 0.000 ! C4H4N2 pyrazine GROUP ATOM N1 NG2R60 -0.56 ! H5 H6 ATOM C2 CG2R61 0.18 ! \ ____ / ATOM H2 HGR62 0.10 ! C5----C6 ATOM C3 CG2R61 0.18 ! / \ ATOM H3 HGR62 0.10 ! N4 N1 ATOM N4 NG2R60 -0.56 ! \\ // ATOM C5 CG2R61 0.18 ! C3----C2 ATOM H5 HGR62 0.10 ! / \ ATOM C6 CG2R61 0.18 ! H3 H2 ATOM H6 HGR62 0.10 BOND C6 H6 C6 C5 C5 H5 C5 N4 N4 C3 BOND C3 H3 C3 C2 C2 H2 C2 N1 N1 C6 IC N1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 N4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C2 N1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI PYRM 0.00 ! C4H4N2 pyrimidine GROUP ATOM N1 NG2R62 -0.73 ! H5 H6 ATOM C2 CG2R64 0.50 ! \ ___ / ATOM H2 HGR62 0.14 ! C5---C6 ATOM N3 NG2R62 -0.73 ! / \ ATOM C4 CG2R61 0.29 ! H4--C4 N1 ATOM H4 HGR62 0.12 ! \\ // ATOM C5 CG2R61 -0.115 ! N3---C2 ATOM H5 HGR61 0.115 ! \ ATOM C6 CG2R61 0.29 ! H2 ATOM H6 HGR62 0.12 BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 BOND C2 H2 C4 H4 C5 H5 C6 H6 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI TRIA 0.00 ! C3H3N3 1,3,5-triazine GROUP ATOM N1 NG2R62 -0.88 ! H6 ATOM C2 CG2R64 0.78 ! ___ / ATOM H2 HGR62 0.10 ! N5---C6 ATOM N3 NG2R62 -0.88 ! / \ ATOM C4 CG2R64 0.78 ! H4--C4 N1 ATOM H4 HGR62 0.10 ! \\ // ATOM N5 NG2R62 -0.88 ! N3---C2 ATOM C6 CG2R64 0.78 ! \ ATOM H6 HGR62 0.10 ! H2 BOND C6 H6 C6 N5 N5 C4 C4 H4 C4 N3 BOND N3 C2 C2 H2 C2 N1 N1 C6 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 N5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C4 N5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI TRIB 0.00 ! C3H3N3 1,2,4-triazine GROUP ATOM N1 NG2R62 -0.41 ! H5 H6 ATOM N2 NG2R62 -0.53 ! \ ___ / ATOM C3 CG2R64 0.72 ! C5---C6 ATOM H3 HGR62 0.09 ! / \ ATOM N4 NG2R62 -0.75 ! N4 N1 ATOM C5 CG2R61 0.36 ! \\ // ATOM H5 HGR62 0.09 ! C3---N2 ATOM C6 CG2R61 0.36 ! / ATOM H6 HGR62 0.07 ! H3 BOND N1 N2 N2 C3 C3 N4 N4 C5 C5 C6 C6 N1 BOND C3 H3 C5 H5 C6 H6 IC C6 N1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 IC N4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI THP 0.00 ! C5H10O tetrahydropyran sng GROUP ATOM O1 OG3C61 -0.40 ATOM C2 CG321 0.02 ! O1 ATOM H21 HGA2 0.09 ! / \ ATOM H22 HGA2 0.09 ! C6 C2 ATOM C6 CG321 0.02 ! | | ATOM H61 HGA2 0.09 ! C5 C3 ATOM H62 HGA2 0.09 ! \ / GROUP ! C4 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 IC C6 O1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 IC O1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 IC C2 O1 C6 C5 0.0000 0.00 60.00 0.00 0.0000 IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 O1 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 BOND C5 H51 C5 H52 BOND C6 H61 C6 H62 PATC FIRS NONE LAST NONE RESI DIOX 0.00 ! C4H8O2 dioxane14 GROUP ATOM O1 OG3C61 -0.40 ATOM C2 CG321 0.02 ATOM H21 HGA2 0.09 ! H52 H61 H62 ATOM H22 HGA2 0.09 ! \ \ / ATOM C3 CG321 0.02 ! H51--C5---C6 ATOM H31 HGA2 0.09 ! / \ ATOM H32 HGA2 0.09 ! O4 O1 ATOM O4 OG3C61 -0.40 ! \ / ATOM C5 CG321 0.02 ! H31--C3---C2 ATOM H51 HGA2 0.09 ! / / \ ATOM H52 HGA2 0.09 ! H32 H21 H22 ATOM C6 CG321 0.02 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND O1 C2 C2 C3 C3 O4 O4 C5 C5 C6 C6 O1 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND C6 H61 C6 H62 C5 H51 C5 H52 IC O1 C2 C3 O4 0.0000 0.00 60.00 0.00 0.0000 IC C2 C3 O4 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C3 O4 C5 C6 0.0000 0.00 60.00 0.00 0.0000 IC O4 C5 C6 O1 0.0000 0.00 -60.00 0.00 0.0000 IC O1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 O4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 O4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC O4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC O4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI DIXB 0.00 ! C4H8O2 1,3-dioxane GROUP ATOM O1 OG3C61 -0.40 ATOM C2 CG321 0.22 ATOM H21 HGA2 0.09 ! H52 H61 H62 ATOM H22 HGA2 0.09 ! \ \ / ATOM O3 OG3C61 -0.40 ! H51--C5---C6 ATOM C4 CG321 0.02 ! / \ ATOM H41 HGA2 0.09 ! H42-C4 O1 ATOM H42 HGA2 0.09 ! / \ / ATOM C5 CG321 -0.18 ! H41 O3---C2 ATOM H51 HGA2 0.09 ! / \ ATOM H52 HGA2 0.09 ! H21 H22 ATOM C6 CG321 0.02 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND O1 C2 C2 O3 O3 C4 C4 C5 C5 C6 C6 O1 BOND C2 H21 C2 H22 C4 H41 C4 H42 BOND C6 H61 C6 H62 C5 H51 C5 H52 IC C6 O1 C2 O3 0.0000 0.00 -60.00 0.00 0.0000 IC O1 C2 O3 C4 0.0000 0.00 60.00 0.00 0.0000 IC C2 O3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 IC O3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 O3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI PIP 1.00 ! C5H12N piperidine GROUP ATOM N1 NG3P2 -0.40 ATOM H11 HGP2 0.32 ATOM H12 HGP2 0.32 ! C5---C6 H11 ATOM C2 CG324 0.20 ! / \ / ATOM H21 HGA2 0.09 ! C4 (+) N1 ATOM H22 HGA2 0.09 ! \ / \ ATOM C6 CG324 0.20 ! C3---C2 H12 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 N1 BOND N1 H11 N1 H12 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 BOND C5 H51 C5 H52 BOND C6 H61 C6 H62 IC C6 N1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 IC N1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 IC C2 N1 C6 C5 0.0000 0.00 60.00 0.00 0.0000 IC C2 C6 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *N1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C5 N1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 N1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 RESI THPS 0.00 ! C5H10S tetrahydro-thiopyran (thiane) GROUP ATOM S1 SG311 -0.24 ! from ethylmethylsulfide (-0.09) ATOM C2 CG321 -0.06 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG321 -0.18 ! H52 H61 H62 ATOM H31 HGA2 0.09 ! \ \ / ATOM H32 HGA2 0.09 ! H51--C5---C6 ATOM C4 CG321 -0.18 ! H41 / \ ATOM H41 HGA2 0.09 ! \ / \ ATOM H42 HGA2 0.09 ! C4 S1 ATOM C5 CG321 -0.18 ! / \ / ATOM H51 HGA2 0.09 ! H42 \ / ATOM H52 HGA2 0.09 ! H31--C3---C2 ATOM C6 CG321 -0.06 ! / / \ ATOM H61 HGA2 0.09 ! H32 H21 H22 ATOM H62 HGA2 0.09 BOND S1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 S1 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND C6 H61 C6 H62 IC S1 C2 C3 C4 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 -60.00 0.00 0.0000 IC C6 S1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI DITH 0.00 ! C4H8S2 1,4-dithiane GROUP ATOM S1 SG311 -0.22 ! from ethylmethylsulfide (-0.09) ATOM C2 CG321 -0.07 ATOM H21 HGA2 0.09 ! H52 H61 H62 ATOM H22 HGA2 0.09 ! \ \ / ATOM C3 CG321 -0.07 ! H51--C5---C6 ATOM H31 HGA2 0.09 ! / \ ATOM H32 HGA2 0.09 ! / \ ATOM S4 SG311 -0.22 ! S4 S1 ATOM C5 CG321 -0.07 ! \ / ATOM H51 HGA2 0.09 ! \ / ATOM H52 HGA2 0.09 ! H31--C3---C2 ATOM C6 CG321 -0.07 ! / / \ ATOM H61 HGA2 0.09 ! H32 H21 H22 ATOM H62 HGA2 0.09 BOND S1 C2 C2 C3 C3 S4 S4 C5 C5 C6 C6 S1 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND C5 H51 C5 H52 BOND C6 H61 C6 H62 IC S1 C2 C3 S4 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C3 S4 C5 0.0000 0.00 60.00 0.00 0.0000 IC C3 S4 C5 C6 0.0000 0.00 -60.00 0.00 0.0000 IC C6 S1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC S4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC S4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C6 S4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 S4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI TRIT 0.00 ! C3H6S3 trithiane135 GROUP ATOM S1 SG311 -0.18 ATOM C2 CG321 0.00 ! H61 H62 ATOM H21 HGA2 0.09 ! \ / ATOM H22 HGA2 0.09 ! H41 S5---C6 ATOM S3 SG311 -0.18 ! \ / \ ATOM C4 CG321 0.00 ! C4 S1 ATOM H41 HGA2 0.09 ! / \ / ATOM H42 HGA2 0.09 ! H42 S3---C2 ATOM S5 SG311 -0.18 ! / \ ATOM C6 CG321 0.00 ! H21 H22 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND S1 C2 C2 S3 S3 C4 C4 S5 S5 C6 C6 S1 BOND C2 H21 C2 H22 C4 H41 C4 H42 BOND C6 H61 C6 H62 IC S1 C2 S3 C4 0.0000 0.00 60.00 0.00 0.0000 IC C2 S3 C4 S5 0.0000 0.00 -60.00 0.00 0.0000 IC S3 C4 S5 C6 0.0000 0.00 60.00 0.00 0.0000 IC C6 S1 C2 S3 0.0000 0.00 -60.00 0.00 0.0000 IC S3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC S3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC S5 S3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC S5 S3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC S5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC S5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI MORP 1.00 ! C4H10NO morpholine ATOM O1 OG3C61 -0.28 ATOM C2 CG321 -0.04 ATOM H21 HGA2 0.09 ! H52 H61 H62 ATOM H22 HGA2 0.09 ! \ \ / ATOM C3 CG324 0.20 ! H51--C5---C6 ATOM H31 HGA2 0.09 !H41 / \ ATOM H32 HGA2 0.09 ! \ / \ ATOM N4 NG3P2 -0.46 ! N4 (+) O1 ATOM H41 HGP2 0.35 ! / \ / ATOM H42 HGP2 0.35 !H42 \ / ATOM C5 CG324 0.20 ! H31--C3---C2 ATOM H51 HGA2 0.09 ! / / \ ATOM H52 HGA2 0.09 ! H32 H21 H22 ATOM C6 CG321 -0.04 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND O1 C2 C2 C3 C3 N4 N4 C5 C5 C6 C6 O1 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND N4 H41 N4 H42 BOND C5 H51 C5 H52 C6 H61 C6 H62 IC O1 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 IC C2 C3 N4 C5 0.0000 0.00 -30.00 0.00 0.0000 IC C3 N4 C5 C6 0.0000 0.00 -30.00 0.00 0.0000 IC C6 O1 C2 C3 0.0000 0.00 -30.00 0.00 0.0000 IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC N4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *N4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *N4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C6 N4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 N4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI TMOR 1.00 ! C4H10NS thiomorpholine ATOM S1 SG311 -0.12 ATOM C2 CG321 -0.12 ATOM H21 HGA2 0.09 ! H52 H61 H62 ATOM H22 HGA2 0.09 ! \ \ / ATOM C3 CG324 0.20 ! H51--C5---C6 ATOM H31 HGA2 0.09 !H41 / \ ATOM H32 HGA2 0.09 ! \ / \ ATOM N4 NG3P2 -0.40 ! N4 (+) S1 ATOM H41 HGP2 0.32 ! / \ / ATOM H42 HGP2 0.32 !H42 \ / ATOM C5 CG324 0.20 ! H31--C3---C2 ATOM H51 HGA2 0.09 ! / / \ ATOM H52 HGA2 0.09 ! H32 H21 H22 ATOM C6 CG321 -0.12 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 BOND S1 C2 C2 C3 C3 N4 N4 C5 C5 C6 C6 S1 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND N4 H41 N4 H42 BOND C5 H51 C5 H52 C6 H61 C6 H62 IC S1 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 IC C2 C3 N4 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C3 N4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C6 S1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC N4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *N4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *N4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C6 N4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 N4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI MGU1 0.00 ! C2H7N3 deprotonated methyl-guanidinium GROUP ! Ne deprotonated ATOM C CG2N1 0.66 ! H11 H12 ATOM N1 NG321 -0.60 ! \ / ATOM H11 HGPAM2 0.29 ! N1 ATOM H12 HGPAM2 0.29 ! | ATOM N2 NG321 -0.60 ! C H41 ATOM H21 HGPAM2 0.29 ! / \\ / ATOM H22 HGPAM2 0.29 ! H21-N2 N3--C4-H42 ATOM N3 NG2D1 -0.86 ! | \ ATOM C4 CG331 -0.03 ! H22 H43 !extra charge on C4 to neutralize ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C N1 C N2 C N3 N3 C4 BOND N1 H11 N1 H12 N2 H21 N2 H22 BOND C4 H41 C4 H42 C4 H43 IMPR C N1 N2 N3 IC N3 C N1 H11 0.0000 0.00 150.00 0.00 0.0000 IC H11 C *N1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 IC N3 C N2 H21 0.0000 0.00 150.00 0.00 0.0000 IC H21 C *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C N3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C N3 C4 H41 0.0000 0.00 -170.00 0.00 0.0000 IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI MGU2 0.00 ! C2H7N3 deprotonated methyl-guanidinium GROUP ! NH1-H12 (outer) deprotonated ATOM C CG2N1 0.59 ATOM N1 NG2D1 -0.91 ! H11 ATOM H11 HGP1 0.37 ! \ ATOM N2 NG321 -0.60 ! N1 ATOM H21 HGPAM2 0.33 ! || ATOM H22 HGPAM2 0.33 ! C H41 ATOM N3 NG311 -0.54 ! / \ / ATOM H31 HGPAM1 0.36 ! H21-N2 N3--C4-H42 ATOM C4 CG331 -0.20 ! | | \ !carbon charge to neutralize ATOM H41 HGA3 0.09 ! H22 H31 H43 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C N1 C N2 C N3 N3 C4 BOND N1 H11 N2 H21 N2 H22 N3 H31 BOND C4 H41 C4 H42 C4 H43 IMPR C N1 N3 N2 IC N3 C N1 H11 0.0000 0.00 180.00 0.00 0.0000 IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 IC N3 C N2 H21 0.0000 0.00 150.00 0.00 0.0000 IC H21 C *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C N3 C4 0.0000 0.00 -120.00 0.00 0.0000 IC C C4 *N3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC C N3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE !end adm jr(?), jul2006 !start adm jr(?), dec2006 RESI HDZ1 0.00 ! C4H8N2O Hydrazone model compound GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ! C1 H3 ATOM H12 HGA3 0.09 ! \ | ATOM H13 HGA3 0.09 ! C2--N3 H5 GROUP ! // \ / ATOM C2 CG2O1 0.58 ! O2 N4=C5 ATOM O2 OG2D1 -0.49 ! \ ATOM N3 NG2S1 -0.34 ! C6 ATOM H3 HGP1 0.31 ATOM N4 NG2D1 -0.31 ATOM C5 CG2D1 -0.24 ATOM H5 HGA4 0.24 ATOM C6 CG331 -0.02 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 C2 N3 N3 H3 BOND N3 N4 C5 H5 C5 C6 C6 H61 C6 H62 C6 H63 BOND N4 C5 IMPR C2 C1 N3 O2 IMPR C5 C6 N4 H5 IC C1 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 IC N3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 IC N3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 RESI HDZ2 0.00 ! C16H13N3O2 Hydrazone containing drug-like molecule GROUP ATOM HG HGR51 0.14 ! HE3 ATOM CG CG2R51 -0.17 ! | ATOM CD2 CG2RC0 0.11 ! HG CE3 ATOM CD1 CG2R51 -0.15 ! \ / \\ ATOM HD1 HGR52 0.22 ! CG-----CD2 CZ3-HZ3 ATOM NE1 NG2R51 -0.51 ! || || | ATOM HE1 HGP1 0.37 ! CD1 CE2 CH2-HH2 ATOM CE2 CG2RC0 0.24 ! / \ / \ // ATOM CE3 CG2R61 -0.25 ! HD1 NE1 CZ2 ATOM HE3 HGR61 0.17 ! | / ATOM CZ2 CG2R61 -0.11 ! HE1 / ATOM CZ3 CG2R61 -0.20 ! / ATOM HZ3 HGR61 0.14 ! / ATOM CH2 CG2R61 -0.14 ! / ATOM HH2 HGR61 0.14 ! ___________/ GROUP ! \ ATOM C2 CG2O1 0.58 ! \ H3 ATOM O2 OG2D1 -0.49 ! \ | ATOM N3 NG2S1 -0.34 ! C2--N3 H5 ATOM H3 HGP1 0.31 ! // \ / ATOM N4 NG2D1 -0.31 ! O2 N4=C5 ATOM C5 CG2DC1 -0.24 ! \ ATOM H5 HGA4 0.24 ! ________________\ ! | !Phenol moiety: P added to atom names to avoid conflicts with indole ! | ATOM CPG CG2R61 0.25 ! | HPD1 HPE1 GROUP ! | | | ATOM CPD1 CG2R61 -0.115 ! | CPD1--CPE1 ATOM HPD1 HGR61 0.115 ! | // \\ GROUP ! |--CPG CPZ--OPH ATOM CPD2 CG2R61 -0.115 ! \ / \ ATOM HPD2 HGR61 0.115 ! CPD2==CPE2 HPH GROUP ! | | ATOM CPE1 CG2R61 -0.115 ! HPD2 HPE2 ATOM HPE1 HGR61 0.115 GROUP ATOM CPE2 CG2R61 -0.115 ATOM HPE2 HGR61 0.115 GROUP ATOM CPZ CG2R61 0.11 ATOM OPH OG311 -0.53 ATOM HPH HGP1 0.42 !indole section BOND CG HG CD2 CG NE1 CD1 CZ2 CE2 BOND CZ3 CH2 CD2 CE3 NE1 CE2 BOND CD1 HD1 NE1 HE1 CE3 HE3 BOND CZ3 HZ3 CH2 HH2 BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 BOND CZ2 C2 BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5 BOND N4 C5 C5 CPG BOND CPD2 CPG CPE1 CPD1 CPZ CPE2 BOND CPD1 HPD1 CPD2 HPD2 CPE1 HPE1 BOND CPE2 HPE2 CPZ OPH OPH HPH BOND CPD1 CPG CPE2 CPD2 CPZ CPE1 IMPR C2 CZ2 N3 O2 IMPR C5 CPG N4 H5 IC CG CD1 NE1 CE2 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 IC CD2 HG *CG CD1 0.0000 0.00 180.00 0.00 0.0000 IC HG CG CD1 NE1 0.0000 0.00 180.00 0.00 0.0000 IC NE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CD1 *NE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG *CD2 CE3 0.0000 0.00 180.00 0.00 0.0000 IC CG CD2 CE3 CZ3 0.0000 0.00 180.00 0.00 0.0000 IC CZ3 CD2 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 IC CD2 NE1 *CE2 CZ2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CE3 CZ3 CH2 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 IC CH2 CE3 *CZ3 HZ3 0.0000 0.00 180.00 0.00 0.0000 IC CZ2 CZ3 *CH2 HH2 0.0000 0.00 180.00 0.00 0.0000 IC CH2 CE2 *CZ2 C2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CZ2 C2 N3 0.0000 0.00 180.00 0.00 0.0000 IC N3 CZ2 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC CZ2 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 IC N3 N4 C5 CPG 0.0000 0.00 180.00 0.00 0.0000 IC CPG N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N4 C5 CPG CPD1 0.0000 0.00 180.00 0.00 0.0000 IC CPD1 C5 *CPG CPD2 0.0000 0.00 180.00 0.00 0.0000 IC C5 CPG CPD1 CPE1 0.0000 0.00 180.00 0.00 0.0000 IC CPE1 CPG *CPD1 HPD1 0.0000 0.00 180.00 0.00 0.0000 IC C5 CPG CPD2 CPE2 0.0000 0.00 180.00 0.00 0.0000 IC CPE2 CPG *CPD2 HPD2 0.0000 0.00 180.00 0.00 0.0000 IC CPG CPD1 CPE1 CPZ 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 IC CPZ CPD1 *CPE1 HPE1 0.0000 0.00 180.00 0.00 0.0000 IC CPZ CPD2 *CPE2 HPE2 0.0000 0.00 180.00 0.00 0.0000 IC CPE2 CPE1 *CPZ OPH 0.0000 0.00 180.00 0.00 0.0000 IC CPE1 CPZ OPH HPH 0.0000 0.00 180.00 0.00 0.0000 !end adm jr(?), dec2006 !Continuation of Maybridge list, kevo, dec2006 RESI INDZ 0.00 ! C8H7N indolizine, kevo GROUP ATOM C1 CG2R51 -0.28 ! H5 ATOM H1 HGR51 0.23 ! | ATOM C2 CG2R51 -0.23 ! H3 C5 ATOM H2 HGR51 0.19 ! \ / \\ ATOM C3 CG2R51 0.07 ! C3----N4 C6-H6 ATOM H3 HGR52 0.14 ! || | | ATOM N4 NG2RC0 -0.28 ! C2 C9 C7-H7 ATOM C5 CG2R61 -0.10 ! / \ // \ // ATOM H5 HGR62 0.24 ! H2 C1 C8 ATOM C6 CG2R61 -0.14 ! | | ATOM H6 HGR61 0.17 ! H1 H8 ATOM C7 CG2R61 -0.15 ATOM H7 HGR61 0.18 ATOM C8 CG2R61 -0.22 ATOM H8 HGR61 0.24 ATOM C9 CG2RC0 -0.06 BOND C1 C2 C2 C3 C3 N4 N4 C9 C9 C1 BOND N4 C5 C5 C6 C6 C7 C7 C8 C8 C9 BOND C1 H1 C2 H2 C3 H3 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC C9 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC C3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC N4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C2 C9 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C9 C3 *N4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI ISOI 0.00 ! C8H7N isoindole, kevo GROUP ATOM HG HGR52 0.15 ! HE3 ATOM CG CG2R51 -0.16 ! | ATOM CD2 CG2RC0 0.17 ! HG CE3 ATOM ND1 NG2R51 -0.29 ! \ _____ / \\ ATOM HD1 HGP1 0.35 ! CG-----CD2 CZ3-HZ3 ATOM CE1 CG2R51 -0.16 ! | | | ATOM HE1 HGR52 0.15 ! ND1 CE2 CH2-HH2 ATOM CE2 CG2RC0 0.17 ! / \ // \ // ATOM CE3 CG2R61 -0.36 ! HD1 CE1 CZ2 ATOM HE3 HGR61 0.23 ! | | ATOM CZ2 CG2R61 -0.36 ! HE1 HZ2 ATOM HZ2 HGR61 0.23 ATOM CZ3 CG2R61 -0.30 ATOM HZ3 HGR61 0.24 ATOM CH2 CG2R61 -0.30 ATOM HH2 HGR61 0.24 BOND CD2 CE2 BOND CE1 ND1 ND1 CG BOND CD2 CE3 CZ3 CH2 CZ2 CE2 BOND CE1 HE1 ND1 HD1 CG HG BOND CE3 HE3 CZ3 HZ3 CH2 HH2 CZ2 HZ2 DOUBLE CE2 CE1 CG CD2 CE3 CZ3 CH2 CZ2 DONOR HD1 ND1 IC CG ND1 CE1 CE2 0.0000 0.00 0.00 0.00 0.0000 IC ND1 CG CD2 CE2 0.0000 0.00 0.00 0.00 0.0000 IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC CE2 CG *CD2 CE3 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CD2 CE3 CZ3 0.0000 0.00 0.00 0.00 0.0000 IC CD2 CE3 CZ3 CH2 0.0000 0.00 0.00 0.00 0.0000 IC CE3 CZ3 CH2 CZ2 0.0000 0.00 0.00 0.00 0.0000 IC CZ3 CD2 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 IC CH2 CE3 *CZ3 HZ3 0.0000 0.00 180.00 0.00 0.0000 IC CZ2 CZ3 *CH2 HH2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CH2 *CZ2 HZ2 0.0000 0.00 180.00 0.00 0.0000 IC ND1 CE2 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CG CE1 *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC ND1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI INDA 0.00 ! C7H6N2 1H-indazole, kevo GROUP ATOM N1 NG2R51 -0.05 ! H5 ATOM H1 HGP1 0.28 ! | ATOM N2 NG2R50 -0.60 ! H3 C5 ATOM C3 CG2R52 0.28 ! \ / \\ ATOM H3 HGR52 0.09 ! C3-----C4 C6 -H6 ATOM C4 CG2RC0 -0.11 ! || || | ATOM C5 CG2R61 -0.43 ! N2 C9 C7 -H7 ATOM H5 HGR61 0.30 ! \ / \ // ATOM C6 CG2R61 -0.38 ! N1 C8 ATOM H6 HGR61 0.28 ! | | ATOM C7 CG2R61 -0.26 ! H1 H8 ATOM H7 HGR61 0.24 ATOM C8 CG2R61 -0.20 ATOM H8 HGR61 0.15 ATOM C9 CG2RC0 0.41 BOND C3 H3 C4 C3 N1 N2 BOND C8 C9 BOND C6 C7 C4 C5 N1 C9 BOND N1 H1 C5 H5 C6 H6 BOND C7 H7 C8 H8 DOUBLE N2 C3 C9 C4 C7 C8 C6 C5 DONOR H1 N1 IC C3 N2 N1 C9 0.0000 0.00 0.00 0.00 0.0000 IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC N2 C9 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI ZIMI 0.00 ! C7H6N2 benzimidazole, kevo GROUP ATOM N1 NG2R51 -0.28 ! H5 ATOM H1 HGP1 0.31 ! | ATOM C2 CG2R53 0.24 ! C5 ATOM H2 HGR52 0.14 ! / \\ ATOM N3 NG2R50 -0.72 ! N3----C4 C6 -H6 ATOM C4 CG2RC0 0.45 ! || || | ATOM C5 CG2R61 -0.35 ! C2 C9 C7 -H7 ATOM H5 HGR61 0.23 ! / \ / \ // ATOM C6 CG2R61 -0.19 ! H2 N1 C8 ATOM H6 HGR61 0.20 ! | | ATOM C7 CG2R61 -0.34 ! H1 H8 ATOM H7 HGR61 0.24 ATOM C8 CG2R61 -0.32 ATOM H8 HGR61 0.22 ATOM C9 CG2RC0 0.17 BOND N1 H1 C2 H2 BOND C5 H5 C6 H6 C7 H7 C8 H8 BOND C9 N1 N1 C2 N3 C4 BOND C4 C5 C6 C7 C8 C9 DOUBLE C2 N3 C4 C9 C5 C6 C7 C8 DONOR H1 N1 IC N3 C2 N1 C9 0.0000 0.00 0.00 0.00 0.0000 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 N3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C2 C9 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI 2HPR 0.000 ! C4H5N 2H-pyrrole, kevo GROUP ATOM N1 NG2R50 -0.72 ! H5 ATOM C2 CG3C52 0.45 ! \ ____ ATOM H21 HGA2 0.09 ! C5----N1 H21 ATOM H22 HGA2 0.09 ! | \ / ATOM C3 CG2R51 -0.75 ! | C2 ATOM H3 HGR51 0.33 ! |____ / \ ATOM C4 CG2R51 0.05 ! C4----C3 H22 ATOM H4 HGR51 0.15 ! / \ ATOM C5 CG2R52 0.20 ! H4 H3 ATOM H5 HGR52 0.11 BOND C2 H21 C2 H22 C3 H3 C4 H4 C5 H5 BOND N1 C2 C2 C3 C4 C5 DOUBLE C3 C4 C5 N1 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI 2PRL 0.000 ! C4H7N 2-pyrroline, kevo GROUP ATOM N1 NG3C51 -0.60 ATOM H1 HGP1 0.32 ! H3 H41 H42 ATOM C2 CG2R51 -0.01 ! \ | / ATOM H2 HGR52 0.17 ! C3----C4 ATOM C3 CG2R51 -0.36 ! || | ATOM H3 HGR51 0.20 ! C2 C5--H51 ATOM C4 CG3C52 -0.10 ! / \ / \ ATOM H41 HGA2 0.09 ! H2 N1 H52 ATOM H42 HGA2 0.09 ! | ATOM C5 CG3C52 0.02 ! H1 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 H1 C2 H2 C3 H3 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 C3 C4 C4 C5 C5 N1 DOUBLE C2 C3 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 RESI 2PRZ 0.000 ! C3H6N2 2-pyrazoline, kevo GROUP ATOM N1 NG3C51 -0.46 ATOM H1 HGP1 0.34 ! H3 H41 H42 ATOM N2 NG2R50 -0.49 ! \ | / ATOM C3 CG2R52 0.32 ! C3----C4 ATOM H3 HGR52 0.06 ! || | ATOM C4 CG3C52 -0.15 ! N2 C5--H51 ATOM H41 HGA2 0.09 ! \ / \ ATOM H42 HGA2 0.09 ! N1 H52 ATOM C5 CG3C52 0.02 ! | ATOM H51 HGA2 0.09 ! H1 ATOM H52 HGA2 0.09 !H[45][12] constrained at +0.09, pre1g BOND N1 H1 C3 H3 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 N2 C3 C4 C4 C5 C5 N1 DOUBLE N2 C3 IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 IC N2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 RESI 2IMI 0.000 ! C3H6N2 2-imidazoline, kevo GROUP ATOM N1 NG3C51 -0.68 ATOM H1 HGP1 0.32 ! H41 H42 ATOM C2 CG2R53 0.61 ! | / ATOM H2 HGR52 0.06 ! N3----C4 ATOM N3 NG2R50 -0.79 ! || | ATOM C4 CG3C52 0.12 ! C2 C5--H51 ATOM H41 HGA2 0.09 ! / \ / \ ATOM H42 HGA2 0.09 ! H2 N1 H52 ATOM C5 CG3C52 0.00 ! | ATOM H51 HGA2 0.09 ! H1 ATOM H52 HGA2 0.09 BOND N1 H1 C2 H2 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 N3 C4 C4 C5 C5 N1 DOUBLE C2 N3 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 N3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 !end continuation of Maybridge list, kevo, dec2006 !Continuation of Maybridge list, kevo, may2007 RESI PRLD 0.000 ! C4H9N pyrrolidine, kevo GROUP ATOM N1 NG3C51 -0.86 ATOM H1 HGP1 0.36 ATOM C2 CG3C52 0.10 ! H32 H42 ATOM H21 HGA2 0.09 ! \ / ATOM H22 HGA2 0.09 ! H31--C3----C4--H41 ATOM C3 CG3C52 -0.21 ! | | ATOM H31 HGA2 0.09 ! H21--C2 C5--H51 ATOM H32 HGA2 0.09 ! / \ / \ ATOM C4 CG3C52 -0.21 ! H22 N1 H52 ATOM H41 HGA2 0.09 ! | ATOM H42 HGA2 0.09 ! H1 ATOM C5 CG3C52 0.10 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 BOND N1 H1 C2 H21 C2 H22 C3 H31 C3 H32 BOND C4 H41 C4 H42 C5 H51 C5 H52 IC C2 C3 C4 C5 0.0000 0.00 10.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 15.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 RESI 3PRL 0.000 ! C4H7N 3-pyrroline, kevo GROUP ATOM N1 NG3C51 -0.89 ATOM H1 HGP1 0.37 ! H3 H4 ATOM C2 CG3C52 0.17 ! \ ____ / ATOM H21 HGA2 0.09 ! C3----C4 ATOM H22 HGA2 0.09 ! | | ATOM C3 CG2R51 -0.28 ! H21--C2 C5--H52 ATOM H3 HGR51 0.19 ! / \ / \ ATOM C4 CG2R51 -0.28 ! H22 N1 H51 ATOM H4 HGR51 0.19 ! | ATOM C5 CG3C52 0.17 ! H1 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 H1 C2 H21 C2 H22 BOND C3 H3 C4 H4 C5 H51 C5 H52 BOND N1 C2 C2 C3 C4 C5 C5 N1 DOUBLE C3 C4 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 20.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 RESI PRLP 1.000 ! C4H10N pyrrolidine protonated, kevo GROUP ATOM N1 NG3P2 -0.22 ATOM H11 HGP2 0.34 ATOM H12 HGP2 0.34 ATOM C2 CG3C54 -0.35 ! H32 H42 ATOM H21 HGA2 0.28 ! \ / ATOM H22 HGA2 0.28 ! H31--C3----C4--H41 ATOM C3 CG3C52 -0.12 ! | | ATOM H31 HGA2 0.09 ! H21--C2 C5--H51 ATOM H32 HGA2 0.09 ! / \ / \ ATOM C4 CG3C52 -0.12 ! H22 N1(+) H52 ATOM H41 HGA2 0.09 ! / \ ATOM H42 HGA2 0.09 ! H11 H12 ATOM C5 CG3C54 -0.35 ATOM H51 HGA2 0.28 ATOM H52 HGA2 0.28 BOND N1 H11 N1 H12 C2 H21 C2 H22 C3 H31 BOND C3 H32 C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 IC C2 C3 C4 C5 0.0000 0.00 40.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 330.00 0.00 0.0000 IC C2 C5 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C2 C5 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 RESI 3PRP 1.000 ! C4H8N 3-pyrroline protonated, kevo GROUP ATOM N1 NG3P2 -0.40 ATOM H11 HGP2 0.39 ATOM H12 HGP2 0.39 ! H3 H4 ATOM C2 CG3C54 -0.17 ! \ ____ / ATOM H21 HGA2 0.28 ! C3----C4 ATOM H22 HGA2 0.28 ! | | ATOM C3 CG2R51 -0.33 ! H21--C2 C5--H51 ATOM H3 HGR51 0.25 ! / \ / \ ATOM C4 CG2R51 -0.33 ! H22 N1(+) H52 ATOM H4 HGR51 0.25 ! / \ ATOM C5 CG3C54 -0.17 ! H11 H12 ATOM H51 HGA2 0.28 ATOM H52 HGA2 0.28 BOND N1 H11 N1 H12 C2 H21 C2 H22 BOND C3 H3 C4 H4 C5 H51 C5 H52 BOND N1 C2 C2 C3 C4 C5 C5 N1 BOND C3 C4 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 20.00 0.00 0.0000 IC C5 C2 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C5 C2 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 RESI 2PRP 1.000 ! C4H8N 2-pyrroline protonated, kevo GROUP ATOM N1 NG3P2 -0.13 ATOM H11 HGP2 0.33 ATOM H12 HGP2 0.33 ! H3 H41 H42 ATOM C2 CG2R51 -0.18 ! \ | / ATOM H2 HGR52 0.22 ! C3----C4 ATOM C3 CG2R51 -0.06 ! || | ATOM H3 HGR51 0.20 ! C2 C5--H51 ATOM C4 CG3C52 -0.12 ! / \ / \ ATOM H41 HGA2 0.09 ! H2 N1(+) H52 ATOM H42 HGA2 0.09 ! / \ ATOM C5 CG3C54 -0.33 ! H11 H12 ATOM H51 HGA2 0.28 ATOM H52 HGA2 0.28 BOND N1 H11 N1 H12 C2 H2 C3 H3 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 C3 C4 C4 C5 C5 N1 BOND C2 C3 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 IC C2 C5 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C2 C5 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 RESI 2IMP 1.000 ! C3H7N2 2-imidazoline protonated, kevo GROUP ATOM N1 NG2R52 -0.35 ATOM H1 HGP2 0.38 ATOM C2 CG2R53 0.52 ! H3 H41 H42 ATOM H2 HGR53 0.12 ! \ | / ATOM N3 NG2R52 -0.35 ! (+) N3----C4 ATOM H3 HGP2 0.38 ! || | ATOM C4 CG3C54 -0.41 ! C2 C5--H51 ATOM H41 HGA2 0.28 ! / \ / \ ATOM H42 HGA2 0.28 ! H2 N1 H52 ATOM C5 CG3C54 -0.41 ! | ATOM H51 HGA2 0.28 ! H1 ATOM H52 HGA2 0.28 !H[2-5][12] constrained, pre1g BOND N1 H1 C2 H2 N3 H3 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 N3 C4 C4 C5 C5 N1 DOUBLE C2 N3 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 -12.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 N3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 RESI 2HPP 1.000 ! C4H6N 2H-pyrrole protonated, kevo GROUP ATOM N1 NG2R52 -0.27 ATOM H1 HGP2 0.39 ! H5 H1 ATOM C2 CG3C54 -0.19 ! \ ____ / ATOM H21 HGA2 0.28 ! C5----N1 H21 ATOM H22 HGA2 0.28 ! | (+) \ / ATOM C3 CG2R51 -0.08 ! | C2 ATOM H3 HGR51 0.25 ! |____ / \ ATOM C4 CG2R51 -0.27 ! C4----C3 H22 ATOM H4 HGR51 0.25 ! / \ ATOM C5 CG2R52 0.07 ! H4 H3 ATOM H5 HGR52 0.29 BOND N1 H1 C2 H21 C2 H22 C3 H3 C4 H4 C5 H5 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 !End continuation of Maybridge list, kevo, may2007 !Bile acids and related compounds, chayan, jul2006 RESI BAM1 0.00 ! C13H24 Bile Acid Model cmpd 1, cacha (to estimate dihedral rotational surface energy) GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ! C21 ATOM H11B HGA2 0.09 ! | GROUP ! C12 C18 C20--C22 ATOM C9 CG321 -0.18 ! / \ | | ATOM H9A HGA2 0.09 ! C11 C13--C17 ATOM H9B HGA2 0.09 ! | | | GROUP ! C9 C14 C16 ATOM C8 CG321 -0.18 ! \ / \ / ATOM H8A HGA2 0.09 ! C8 C15 ATOM H8B HGA2 0.09 GROUP ! Model Compound ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C18 CG331 -0.27 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG331 -0.27 ATOM H22A HGA3 0.09 ATOM H22B HGA3 0.09 ATOM H22C HGA3 0.09 BOND C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 C9 H9A C9 H9B BOND C9 C8 C8 H8A C8 H8B BOND C8 C14 C14 H14 C14 C13 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 C13 C12 BOND C13 C18 C18 H18A C18 H18B C18 H18C BOND C17 C20 C20 H20 BOND C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B C22 H22C ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) IC C12 C11 C9 C8 1.5465 113.07 53.26 111.97 1.5369 IC C11 C9 C8 C14 1.5370 111.97 -54.31 108.19 1.5301 IC C9 C8 C14 C15 1.5369 108.19 179.63 117.07 1.5242 IC C8 C14 C15 C16 1.5301 117.07 -157.35 103.25 1.5463 IC C14 C15 C16 C17 1.5242 103.25 -1.62 106.76 1.5545 IC C15 C16 C17 C13 1.5463 106.76 32.90 98.76 1.5707 IC C16 C17 C13 C12 1.5545 98.76 -165.58 115.64 1.5392 IC C8 C14 C13 C12 1.5301 113.89 -59.62 108.36 1.5392 IC C8 C14 C13 C17 1.5301 113.89 -179.99 97.80 1.5707 IC C14 C13 C12 C11 1.5400 108.36 54.13 111.30 1.5465 IC C13 C8 *C14 C15 1.5400 113.89 120.29 117.07 1.5242 IC C17 C14 *C13 C12 1.5707 97.80 120.38 108.36 1.5392 IC C14 C9 *C8 H8A 1.5301 108.19 121.59 109.97 1.1090 IC H8A C9 *C8 H8B 1.1090 109.97 118.57 109.82 1.1117 IC C8 C11 *C9 H9A 1.5369 111.97 -119.77 108.41 1.1138 IC H9A C11 *C9 H9B 1.1138 108.41 -117.69 109.98 1.1118 IC C9 C12 *C11 H11A 1.5370 113.07 120.55 109.08 1.1127 IC H11A C12 *C11 H11B 1.1127 109.08 117.14 109.30 1.1121 IC C14 C13 C12 H12A 1.5400 108.36 174.66 111.17 1.1064 IC H12A C13 *C12 H12B 1.1064 111.17 119.56 108.93 1.1115 IC C13 C8 *C14 H14 1.5400 113.89 -118.75 106.87 1.1175 IC C16 C14 *C15 H15A 1.5463 103.25 119.82 111.17 1.0999 IC H15A C14 *C15 H15B 1.0999 111.17 119.44 111.12 1.0993 IC C17 C15 *C16 H16A 1.5545 106.76 121.20 110.63 1.0991 IC H16A C15 *C16 H16B 1.0991 110.63 117.46 111.19 1.0988 IC C13 C16 *C17 H17 1.5707 98.76 -113.04 109.96 1.1005 IC C12 C14 *C13 C18 1.5392 108.36 121.36 113.50 1.5528 IC C14 C13 C18 H18A 1.5400 113.50 109.24 111.90 1.1059 IC H18A C13 *C18 H18B 1.1059 111.90 119.52 110.40 1.1089 IC H18A C13 *C18 H18C 1.1059 111.90 -120.42 111.60 1.1063 IC C13 C16 *C17 C20 1.5707 98.76 126.23 112.96 1.5593 IC C16 C17 C20 C22 1.5545 112.96 61.62 107.68 1.5428 IC C22 C17 *C20 C21 1.5428 107.68 119.44 112.55 1.5383 IC C21 C17 *C20 H20 1.5383 112.55 122.44 110.57 1.1109 IC C17 C20 C21 H21A 1.5593 112.55 76.43 111.01 1.1069 IC H21A C20 *C21 H21B 1.1069 111.01 -121.83 110.68 1.1100 IC H21A C20 *C21 H21C 1.1069 111.01 118.41 110.01 1.1108 IC C17 C20 C22 H22A 1.5593 107.68 177.17 110.13 1.1105 IC H22A C20 *C22 H22B 1.1105 110.13 119.59 111.27 1.1091 IC H22A C20 *C22 H22C 1.1105 110.13 -119.58 110.32 1.1103 RESI CA -1.00 ! C24H39O5 Cholic Acid, cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ATOM H4B HGA2 0.09 GROUP ATOM C5 CG311 -0.09 ATOM H5 HGA1 0.09 GROUP ATOM C6 CG321 -0.18 ATOM H6A HGA2 0.09 ATOM H6B HGA2 0.09 ! OE1 GROUP ! || ATOM C7 CG311 0.14 ! OH Me21 C22 CD ATOM O7 OG311 -0.65 ! | \ / \ / \ ATOM H7' HGP1 0.42 ! C12 Me18 C20 CG OE2(-1) ATOM H7 HGA1 0.09 ! / \ | / GROUP ! C11 C13---C17 ATOM C8 CG311 -0.09 ! Me19 | | | ATOM H8 HGA1 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C14 CG3RC1 -0.09 ! C2 C10 C8 C15 ATOM H14 HGA1 0.09 ! | | | GROUP ! C3 C5 C7 ATOM C15 CG3C52 -0.18 ! / \ / \ / \ ATOM H15A HGA2 0.09 ! HO C4 C6 OH ATOM H15B HGA2 0.09 GROUP ! Cholic Acid (CA) ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG311 0.14 ATOM H12 HGA1 0.09 ATOM O12 OG311 -0.65 ATOM H12' HGP1 0.42 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM CD CG2O3 0.52 ATOM OE1 OG2D2 -0.76 ATOM OE2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12 C12 O12 O12 H12' BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 CD CD OE1 CD OE2 IMPR CD OE2 OE1 C23 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5324 111.68 -49.58 111.85 1.5384 IC C2 C3 C4 C5 1.5336 111.85 43.65 115.86 1.5602 IC C3 C4 C5 C6 1.5384 115.86 -174.25 108.84 1.5528 IC C4 C5 C6 C7 1.5602 108.84 86.42 115.04 1.5449 IC C5 C6 C7 C8 1.5528 115.04 38.94 113.04 1.5297 IC C7 C8 C9 C10 1.5297 113.41 59.71 109.57 1.5432 IC C8 C9 C10 C1 1.5223 109.57 178.73 111.89 1.5560 IC C9 C10 C1 C2 1.5432 111.89 63.50 113.76 1.5324 IC O3 C3 C4 C5 1.4163 109.08 161.75 115.86 1.5602 IC C4 C2 *C3 O3 1.5384 111.85 -119.36 106.95 1.4163 IC C4 C2 *C3 H3 1.5384 111.85 121.41 109.41 1.1143 IC C9 C5 *C10 C19 1.5432 109.52 -123.19 109.67 1.5560 IC C2 C3 O3 H3' 1.5336 106.95 64.94 104.68 0.9611 IC C5 C3 *C4 H4A 1.5602 115.86 122.86 108.65 1.1110 IC H4A C3 *C4 H4B 1.1110 108.65 115.61 108.72 1.1114 IC C10 C4 *C5 H5 1.5283 114.75 116.75 105.10 1.1173 IC C7 C5 *C6 H6A 1.5449 115.04 -124.17 109.40 1.1112 IC H6A C5 *C6 H6B 1.1112 109.40 -115.79 108.30 1.1112 IC C2 C10 *C1 H1A 1.5324 113.76 119.42 107.87 1.1135 IC C2 C10 *C1 H1B 1.5324 113.76 -124.15 110.13 1.1095 IC C1 C3 *C2 H2A 1.5324 111.68 121.97 110.22 1.1118 IC H2A C3 *C2 H2B 1.1118 110.22 117.25 108.75 1.1127 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5449 113.04 -167.24 109.07 1.5517 IC C14 C7 *C8 C9 1.5517 109.07 119.23 113.41 1.5223 IC C7 C8 C14 C13 1.5297 109.07 -171.16 112.73 1.5504 IC C13 C8 *C14 C15 1.5504 112.73 117.19 114.03 1.5268 IC C8 C14 C15 C16 1.5517 114.03 -155.98 103.48 1.5369 IC C14 C15 C16 C17 1.5268 103.48 2.71 107.62 1.5513 IC C17 C14 *C13 C12 1.5748 98.26 120.41 106.82 1.5557 IC C14 C13 C12 C11 1.5504 106.82 50.62 112.18 1.5515 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 O7 1.5297 113.04 -126.79 108.12 1.4213 IC O7 C6 *C7 H7 1.4213 108.12 -113.65 106.95 1.1162 IC C6 C7 O7 H7' 1.5449 108.12 170.74 104.84 0.9615 IC C9 C7 *C8 H8 1.5223 113.41 122.31 106.89 1.1063 IC C10 C8 *C9 H9 1.5432 109.57 -116.33 105.86 1.1163 IC C9 C12 *C11 H11A 1.5553 117.58 122.21 106.83 1.1096 IC H11A C12 *C11 H11B 1.1096 106.83 114.26 107.91 1.1115 IC C14 C13 C12 O12 1.5504 106.82 -74.73 114.67 1.4228 IC O12 C13 *C12 H12 1.4228 114.67 -118.14 108.61 1.1119 IC C13 C12 O12 H12' 1.5557 114.67 -49.37 105.00 0.9629 IC C13 C8 *C14 H14 1.5504 112.73 -119.72 109.55 1.1139 IC C16 C14 *C15 H15A 1.5369 103.48 119.05 111.22 1.1006 IC H15A C14 *C15 H15B 1.1006 111.22 119.83 112.45 1.0988 IC C17 C15 *C16 H16A 1.5513 107.62 120.90 110.48 1.1007 IC H16A C15 *C16 H16B 1.1007 110.48 117.28 111.71 1.1003 IC C13 C16 *C17 H17 1.5748 100.22 -113.28 108.29 1.1013 IC C12 C14 *C13 C18 1.5557 106.82 122.03 113.69 1.5568 IC C14 C13 C18 H18A 1.5504 113.69 3.50 112.14 1.1055 IC H18A C13 *C18 H18B 1.1055 112.14 119.59 111.31 1.1063 IC H18A C13 *C18 H18C 1.1055 112.14 -120.84 110.78 1.1084 IC C5 C10 C19 H19A 1.5283 109.67 9.75 111.22 1.1077 IC H19A C10 *C19 H19B 1.1077 111.22 120.95 111.67 1.1070 IC H19A C10 *C19 H19C 1.1077 111.22 -119.64 110.71 1.1092 IC C13 C16 *C17 C20 1.5748 100.22 127.99 112.63 1.5616 IC C16 C17 C20 C22 1.5513 112.63 71.02 108.94 1.5487 IC C22 C17 *C20 C21 1.5487 108.94 122.52 113.13 1.5408 IC C21 C17 *C20 H20 1.5408 113.13 121.15 109.02 1.1123 IC C17 C20 C21 H21A 1.5616 113.13 67.60 111.00 1.1068 IC H21A C20 *C21 H21B 1.1068 111.00 -122.83 111.01 1.1085 IC H21A C20 *C21 H21C 1.1068 111.00 118.17 109.90 1.1107 IC C17 C20 C22 C23 1.5616 108.94 -161.91 113.97 1.5494 IC C23 C20 *C22 H22A 1.5494 113.97 119.29 109.76 1.1125 IC H22A C20 *C22 H22B 1.1125 109.76 117.37 110.00 1.1113 IC C20 C22 C23 CD 1.5487 113.97 176.94 113.05 1.5299 IC CD C22 *C23 H23A 1.5299 113.05 119.90 111.01 1.1071 IC CD C22 *C23 H23B 1.5299 113.05 -119.56 110.12 1.1084 IC C22 C23 CD OE1 1.5494 113.05 -178.02 116.54 1.2584 IC OE1 C23 *CD OE2 1.2584 116.54 175.48 119.00 1.2572 RESI DCA -1.00 ! C24H39O4 deoxycholic acid(DCA), cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ! OE1 ATOM H4B HGA2 0.09 ! || GROUP ! OH Me21 C22 CD ATOM C5 CG311 -0.09 ! | \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) GROUP ! / \ | / ATOM C6 CG321 -0.18 ! C11 C13---C17 ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG321 -0.18 ! C2 C10 C8 C15 ATOM H7A HGA2 0.09 ! | | | ATOM H7B HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / ATOM C8 CG311 -0.09 ! OH C4 C6 ATOM H8 HGA1 0.09 GROUP ATOM C14 CG3RC1 -0.09 ! Deoxycholic acid (DCA) ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG311 0.14 ATOM H12 HGA1 0.09 ATOM O12 OG311 -0.65 ATOM H12' HGP1 0.42 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM CD CG2O3 0.52 ATOM OE1 OG2D2 -0.76 ATOM OE2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7A C7 H7B BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12 C12 O12 O12 H12' BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 CD CD OE1 CD OE2 IMPR CD OE2 OE1 C23 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5324 111.68 -49.58 111.85 1.5384 IC C2 C3 C4 C5 1.5336 111.85 43.65 115.86 1.5602 IC C3 C4 C5 C6 1.5384 115.86 -174.25 108.84 1.5528 IC C4 C5 C6 C7 1.5602 108.84 86.42 115.04 1.5449 IC C5 C6 C7 C8 1.5528 115.04 38.94 113.04 1.5297 IC C7 C8 C9 C10 1.5297 113.41 59.71 109.57 1.5432 IC C8 C9 C10 C1 1.5223 109.57 178.73 111.89 1.5560 IC C9 C10 C1 C2 1.5432 111.89 63.50 113.76 1.5324 IC O3 C3 C4 C5 1.4163 109.08 161.75 115.86 1.5602 IC C4 C2 *C3 O3 1.5384 111.85 -119.36 106.95 1.4163 IC C4 C2 *C3 H3 1.5384 111.85 121.41 109.41 1.1143 IC C9 C5 *C10 C19 1.5432 109.52 -123.19 109.67 1.5560 IC C2 C3 O3 H3' 1.5336 106.95 64.94 104.68 0.9611 IC C5 C3 *C4 H4A 1.5602 115.86 122.86 108.65 1.1110 IC H4A C3 *C4 H4B 1.1110 108.65 115.61 108.72 1.1114 IC C10 C4 *C5 H5 1.5283 114.75 116.75 105.10 1.1173 IC C7 C5 *C6 H6A 1.5449 115.04 -124.17 109.40 1.1112 IC H6A C5 *C6 H6B 1.1112 109.40 -115.79 108.30 1.1112 IC C2 C10 *C1 H1A 1.5324 113.76 119.42 107.87 1.1135 IC C2 C10 *C1 H1B 1.5324 113.76 -124.15 110.13 1.1095 IC C1 C3 *C2 H2A 1.5324 111.68 121.97 110.22 1.1118 IC H2A C3 *C2 H2B 1.1118 110.22 117.25 108.75 1.1127 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5449 113.04 -167.24 109.07 1.5517 IC C14 C7 *C8 C9 1.5517 109.07 119.23 113.41 1.5223 IC C7 C8 C14 C13 1.5297 109.07 -171.16 112.73 1.5504 IC C13 C8 *C14 C15 1.5504 112.73 117.19 114.03 1.5268 IC C8 C14 C15 C16 1.5517 114.03 -155.98 103.48 1.5369 IC C14 C15 C16 C17 1.5268 103.48 2.71 107.62 1.5513 IC C17 C14 *C13 C12 1.5748 98.26 120.41 106.82 1.5557 IC C14 C13 C12 C11 1.5504 106.82 50.62 112.18 1.5515 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 H7A 1.5383 113.44 -126.79 109.41 1.1119 IC H7A C6 *C7 H7B 1.1119 109.41 -113.65 109.70 1.1112 IC C9 C7 *C8 H8 1.5223 113.41 122.31 106.89 1.1063 IC C10 C8 *C9 H9 1.5432 109.57 -116.33 105.86 1.1163 IC C9 C12 *C11 H11A 1.5553 117.58 122.21 106.83 1.1096 IC H11A C12 *C11 H11B 1.1096 106.83 114.26 107.91 1.1115 IC C14 C13 C12 O12 1.5504 106.82 -74.73 114.67 1.4228 IC O12 C13 *C12 H12 1.4228 114.67 -118.14 108.61 1.1119 IC C13 C12 O12 H12' 1.5557 114.67 -49.37 105.00 0.9629 IC C13 C8 *C14 H14 1.5504 112.73 -119.72 109.55 1.1139 IC C16 C14 *C15 H15A 1.5369 103.48 119.05 111.22 1.1006 IC H15A C14 *C15 H15B 1.1006 111.22 119.83 112.45 1.0988 IC C17 C15 *C16 H16A 1.5513 107.62 120.90 110.48 1.1007 IC H16A C15 *C16 H16B 1.1007 110.48 117.28 111.71 1.1003 IC C13 C16 *C17 H17 1.5748 100.22 -113.28 108.29 1.1013 IC C12 C14 *C13 C18 1.5557 106.82 122.03 113.69 1.5568 IC C14 C13 C18 H18A 1.5504 113.69 3.50 112.14 1.1055 IC H18A C13 *C18 H18B 1.1055 112.14 119.59 111.31 1.1063 IC H18A C13 *C18 H18C 1.1055 112.14 -120.84 110.78 1.1084 IC C5 C10 C19 H19A 1.5283 109.67 9.75 111.22 1.1077 IC H19A C10 *C19 H19B 1.1077 111.22 120.95 111.67 1.1070 IC H19A C10 *C19 H19C 1.1077 111.22 -119.64 110.71 1.1092 IC C13 C16 *C17 C20 1.5748 100.22 127.99 112.63 1.5616 IC C16 C17 C20 C22 1.5513 112.63 71.02 108.94 1.5487 IC C22 C17 *C20 C21 1.5487 108.94 122.52 113.13 1.5408 IC C21 C17 *C20 H20 1.5408 113.13 121.15 109.02 1.1123 IC C17 C20 C21 H21A 1.5616 113.13 67.60 111.00 1.1068 IC H21A C20 *C21 H21B 1.1068 111.00 -122.83 111.01 1.1085 IC H21A C20 *C21 H21C 1.1068 111.00 118.17 109.90 1.1107 IC C17 C20 C22 C23 1.5616 108.94 -161.91 113.97 1.5494 IC C23 C20 *C22 H22A 1.5494 113.97 119.29 109.76 1.1125 IC H22A C20 *C22 H22B 1.1125 109.76 117.37 110.00 1.1113 IC C20 C22 C23 CD 1.5487 113.97 176.94 113.05 1.5299 IC CD C22 *C23 H23A 1.5299 113.05 119.90 111.01 1.1071 IC CD C22 *C23 H23B 1.5299 113.05 -119.56 110.12 1.1084 IC C22 C23 CD OE1 1.5494 113.05 -178.02 116.54 1.2584 IC OE1 C23 *CD OE2 1.2584 116.54 175.48 119.00 1.2572 RESI LCA -1.00 ! C24H39O3 LITHOCHOLIC ACID (LCA), cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ! OE1 ATOM H4B HGA2 0.09 ! || GROUP ! H Me21 C22 CD ATOM C5 CG311 -0.09 ! | \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) GROUP ! / \ | / ATOM C6 CG321 -0.18 ! C11 C13---C17 ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG321 -0.18 ! C2 C10 C8 C15 ATOM H7A HGA2 0.09 ! | | | ATOM H7B HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / ATOM C8 CG311 -0.09 ! OH C4 C6 ATOM H8 HGA1 0.09 GROUP ! Lithocholic acid (LCA) ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM CD CG2O3 0.52 ATOM OE1 OG2D2 -0.76 ATOM OE2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7A C7 H7B BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 CD CD OE1 CD OE2 IMPR CD OE2 OE1 C23 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5337 112.03 -49.25 111.84 1.5388 IC C2 C3 C4 C5 1.5350 111.84 44.83 114.98 1.5580 IC C3 C4 C5 C6 1.5388 114.98 -175.73 110.26 1.5462 IC C4 C5 C6 C7 1.5580 110.26 75.60 112.05 1.5329 IC C5 C6 C7 C8 1.5462 112.05 52.55 111.32 1.5462 IC C7 C8 C9 C10 1.5462 111.19 57.34 111.05 1.5448 IC C8 C9 C10 C1 1.5356 111.05 -177.00 112.40 1.5563 IC C9 C10 C1 C2 1.5448 112.40 64.20 114.05 1.5337 IC O3 C3 C4 C5 1.4166 109.16 163.09 114.98 1.5580 IC C4 C2 *C3 O3 1.5388 111.84 -119.52 107.04 1.4166 IC C4 C2 *C3 H3 1.5388 111.84 121.28 109.34 1.1145 IC C9 C5 *C10 C19 1.5448 110.02 -122.97 109.85 1.5545 IC C2 C3 O3 H3' 1.5350 107.04 60.89 105.08 0.9602 IC C5 C3 *C4 H4A 1.5580 114.98 122.28 108.66 1.1112 IC H4A C3 *C4 H4B 1.1112 108.66 116.01 108.59 1.1102 IC C10 C4 *C5 H5 1.5336 114.85 117.05 105.40 1.1171 IC C7 C5 *C6 H6A 1.5329 112.05 -122.19 109.68 1.1114 IC H6A C5 *C6 H6B 1.1114 109.68 -117.56 109.38 1.1121 IC C2 C10 *C1 H1A 1.5337 114.05 119.68 107.55 1.1136 IC C2 C10 *C1 H1B 1.5337 114.05 -124.22 110.15 1.1090 IC C1 C3 *C2 H2A 1.5337 112.03 122.06 110.32 1.1113 IC H2A C3 *C2 H2B 1.1113 110.32 117.22 108.67 1.1129 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5329 111.32 -170.02 106.39 1.5454 IC C14 C7 *C8 C9 1.5454 106.39 115.37 111.19 1.5356 IC C7 C8 C14 C13 1.5462 106.39 -177.38 112.55 1.5432 IC C13 C8 *C14 C15 1.5432 112.55 118.10 116.48 1.5277 IC C8 C14 C15 C16 1.5454 116.48 -154.70 103.50 1.5439 IC C14 C15 C16 C17 1.5277 103.50 -1.82 106.89 1.5535 IC C17 C14 *C13 C12 1.5722 98.05 120.18 108.13 1.5348 IC C14 C13 C12 C11 1.5432 108.13 53.76 111.21 1.5444 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 H7A 1.5462 111.32 -120.76 109.56 1.1112 IC H7A C6 *C7 H7B 1.1112 109.56 -117.60 109.24 1.1114 IC C9 C7 *C8 H8 1.5356 111.19 124.30 109.39 1.1045 IC C10 C8 *C9 H9 1.5448 111.05 -116.65 106.44 1.1137 IC C9 C12 *C11 H11A 1.5521 113.16 121.96 109.10 1.1097 IC H11A C12 *C11 H11B 1.1097 109.10 116.39 107.43 1.1100 IC C14 C13 C12 H12A 1.5432 108.13 -66.12 108.72 1.1120 IC H12A C13 *C12 H12B 1.1120 108.72 -119.32 111.59 1.1062 IC C13 C8 *C14 H14 1.5432 112.55 -119.67 108.40 1.1145 IC C16 C14 *C15 H15A 1.5439 103.50 119.46 111.24 1.0997 IC H15A C14 *C15 H15B 1.0997 111.24 119.60 111.35 1.0990 IC C17 C15 *C16 H16A 1.5535 106.89 121.34 110.90 1.0992 IC H16A C15 *C16 H16B 1.0992 110.90 117.31 111.27 1.0993 IC C13 C16 *C17 H17 1.5722 98.51 -112.99 110.29 1.1004 IC C12 C14 *C13 C18 1.5348 108.13 121.73 113.93 1.5529 IC C14 C13 C18 H18A 1.5432 113.93 -4.01 111.83 1.1058 IC H18A C13 *C18 H18B 1.1058 111.83 120.17 111.33 1.1067 IC H18A C13 *C18 H18C 1.1058 111.83 -120.74 110.60 1.1083 IC C5 C10 C19 H19A 1.5336 109.85 -8.12 111.07 1.1083 IC H19A C10 *C19 H19B 1.1083 111.07 120.82 111.82 1.1063 IC H19A C10 *C19 H19C 1.1083 111.07 -119.70 110.58 1.1092 IC C13 C16 *C17 C20 1.5722 98.51 127.11 111.95 1.5637 IC C16 C17 C20 C22 1.5535 111.95 70.28 109.13 1.5506 IC C22 C17 *C20 C21 1.5506 109.13 121.97 112.87 1.5401 IC C21 C17 *C20 H20 1.5401 112.87 121.21 109.11 1.1116 IC C17 C20 C21 H21A 1.5637 112.87 73.29 110.62 1.1071 IC H21A C20 *C21 H21B 1.1071 110.62 -122.03 110.43 1.1097 IC H21A C20 *C21 H21C 1.1071 110.62 118.43 110.33 1.1098 IC C17 C20 C22 C23 1.5637 109.13 -161.00 114.04 1.5502 IC C23 C20 *C22 H22A 1.5502 114.04 119.37 110.02 1.1115 IC H22A C20 *C22 H22B 1.1115 110.02 117.32 109.74 1.1112 IC C20 C22 C23 CD 1.5506 114.04 177.56 113.25 1.5303 IC CD C22 *C23 H23A 1.5303 113.25 119.99 110.96 1.1070 IC CD C22 *C23 H23B 1.5303 113.25 -119.65 110.01 1.1083 IC C22 C23 CD OE1 1.5502 113.25 -178.85 116.56 1.2588 IC OE1 C23 *CD OE2 1.2588 116.56 177.44 119.16 1.2573 RESI CDCA -1.00 ! C24H39O4 CHENODEOXYCHOLIC ACID, cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ! OE1 ATOM H4B HGA2 0.09 ! || GROUP ! H Me21 C22 CD ATOM C5 CG311 -0.09 ! | \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) GROUP ! / \ | / ATOM C6 CG321 -0.18 ! C11 C13---C17 ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM H7' HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! Chenodeoxycholic acid (CDCA) GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM CD CG2O3 0.52 ATOM OE1 OG2D2 -0.76 ATOM OE2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 CD CD OE1 CD OE2 IMPR CD OE2 OE1 C23 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5325 111.74 -49.21 111.88 1.5385 IC C2 C3 C4 C5 1.5341 111.88 43.74 115.69 1.5597 IC C3 C4 C5 C6 1.5385 115.69 -175.10 109.04 1.5520 IC C4 C5 C6 C7 1.5597 109.04 85.37 114.98 1.5440 IC C5 C6 C7 C8 1.5520 114.98 38.83 113.15 1.5290 IC C7 C8 C9 C10 1.5290 114.20 57.90 109.53 1.5437 IC C8 C9 C10 C1 1.5325 109.53 179.78 112.01 1.5562 IC C9 C10 C1 C2 1.5437 112.01 63.19 113.83 1.5325 IC O3 C3 C4 C5 1.4164 109.06 161.96 115.69 1.5597 IC C4 C2 *C3 O3 1.5385 111.88 -119.42 107.04 1.4164 IC C4 C2 *C3 H3 1.5385 111.88 121.34 109.37 1.1144 IC C9 C5 *C10 C19 1.5437 109.64 -123.44 109.56 1.5561 IC C2 C3 O3 H3' 1.5341 107.04 68.70 104.78 0.9606 IC C5 C3 *C4 H4A 1.5597 115.69 122.74 108.67 1.1111 IC H4A C3 *C4 H4B 1.1111 108.67 115.74 108.84 1.1112 IC C10 C4 *C5 H5 1.5278 114.69 116.72 105.05 1.1175 IC C7 C5 *C6 H6A 1.5440 114.98 -124.18 109.41 1.1112 IC H6A C5 *C6 H6B 1.1112 109.41 -115.81 108.31 1.1113 IC C2 C10 *C1 H1A 1.5325 113.83 119.45 107.75 1.1136 IC C2 C10 *C1 H1B 1.5325 113.83 -124.31 110.15 1.1092 IC C1 C3 *C2 H2A 1.5325 111.74 122.10 110.26 1.1113 IC H2A C3 *C2 H2B 1.1113 110.26 117.21 108.67 1.1128 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5440 113.15 -166.48 108.55 1.5543 IC C14 C7 *C8 C9 1.5543 108.55 119.88 114.20 1.5325 IC C7 C8 C14 C13 1.5290 108.55 -174.00 113.09 1.5423 IC C13 C8 *C14 C15 1.5423 113.09 118.54 116.41 1.5290 IC C8 C14 C15 C16 1.5543 116.41 -154.98 103.52 1.5436 IC C14 C15 C16 C17 1.5290 103.52 -2.21 106.91 1.5527 IC C17 C14 *C13 C12 1.5726 98.14 119.76 107.63 1.5335 IC C14 C13 C12 C11 1.5423 107.63 55.01 111.17 1.5432 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 O7 1.5290 113.15 -126.97 108.08 1.4217 IC O7 C6 *C7 H7 1.4217 108.08 -113.63 107.20 1.1165 IC C6 C7 O7 H7' 1.5440 108.08 176.29 104.82 0.9615 IC C9 C7 *C8 H8 1.5325 114.20 122.49 107.19 1.1068 IC C10 C8 *C9 H9 1.5437 109.53 -117.14 106.58 1.1136 IC C9 C12 *C11 H11A 1.5549 114.17 122.57 108.68 1.1092 IC H11A C12 *C11 H11B 1.1092 108.68 115.77 107.30 1.1109 IC C14 C13 C12 H12A 1.5423 107.63 -64.93 108.84 1.1122 IC H12A C13 *C12 H12B 1.1122 108.84 -119.33 111.64 1.1063 IC C13 C8 *C14 H14 1.5423 113.09 -118.19 108.50 1.1148 IC C16 C14 *C15 H15A 1.5436 103.52 118.98 111.14 1.1003 IC H15A C14 *C15 H15B 1.1003 111.14 119.93 112.23 1.0983 IC C17 C15 *C16 H16A 1.5527 106.91 121.32 110.94 1.0995 IC H16A C15 *C16 H16B 1.0995 110.94 117.27 111.30 1.0996 IC C13 C16 *C17 H17 1.5726 98.49 -113.15 110.37 1.1004 IC C12 C14 *C13 C18 1.5335 107.63 121.99 114.21 1.5526 IC C14 C13 C18 H18A 1.5423 114.21 -3.87 111.99 1.1055 IC H18A C13 *C18 H18B 1.1055 111.99 120.12 111.33 1.1067 IC H18A C13 *C18 H18C 1.1055 111.99 -120.94 110.59 1.1084 IC C5 C10 C19 H19A 1.5278 109.56 4.64 111.20 1.1078 IC H19A C10 *C19 H19B 1.1078 111.20 121.08 112.01 1.1062 IC H19A C10 *C19 H19C 1.1078 111.20 -119.52 110.63 1.1093 IC C13 C16 *C17 C20 1.5726 98.49 127.01 111.91 1.5638 IC C16 C17 C20 C22 1.5527 111.91 69.89 109.15 1.5504 IC C22 C17 *C20 C21 1.5504 109.15 122.01 112.87 1.5400 IC C21 C17 *C20 H20 1.5400 112.87 121.24 109.18 1.1115 IC C17 C20 C21 H21A 1.5638 112.87 73.30 110.64 1.1072 IC H21A C20 *C21 H21B 1.1072 110.64 -122.05 110.45 1.1097 IC H21A C20 *C21 H21C 1.1072 110.64 118.42 110.32 1.1099 IC C17 C20 C22 C23 1.5638 109.15 -160.90 114.01 1.5501 IC C23 C20 *C22 H22A 1.5501 114.01 119.25 110.01 1.1115 IC H22A C20 *C22 H22B 1.1115 110.01 117.37 109.82 1.1111 IC C20 C22 C23 CD 1.5504 114.01 177.00 113.21 1.5306 IC CD C22 *C23 H23A 1.5306 113.21 120.02 110.96 1.1069 IC CD C22 *C23 H23B 1.5306 113.21 -119.58 110.04 1.1084 IC C22 C23 CD OE1 1.5501 113.21 -177.88 116.45 1.2588 IC OE1 C23 *CD OE2 1.2588 116.45 173.57 119.02 1.2574 RESI UDCA -1.00 ! C24H39O4 URSODEOXYCHOLIC ACID (UDCA), cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ! OE1 ATOM H4B HGA2 0.09 ! || GROUP ! H Me21 C22 CD ATOM C5 CG311 -0.09 ! | \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) GROUP ! / \ | / ATOM C6 CG321 -0.18 ! C11 C13---C17 ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM H7' HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH (above the plane of the ring) ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! Ursodeoxycholic acid (UDCA) GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM CD CG2O3 0.52 ATOM OE1 OG2D2 -0.76 ATOM OE2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 CD CD OE1 CD OE2 IMPR CD OE2 OE1 C23 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on CHARMM optimized structure IC C1 C2 C3 C4 1.5325 111.74 -49.21 111.88 1.5385 IC C2 C3 C4 C5 1.5341 111.88 43.74 115.69 1.5597 IC C3 C4 C5 C6 1.5385 115.69 -175.10 109.04 1.5520 IC C4 C5 C6 C7 1.5597 109.04 85.37 114.98 1.5440 IC C5 C6 C7 C8 1.5520 114.98 38.83 113.15 1.5290 IC C7 C8 C9 C10 1.5290 114.20 57.90 109.53 1.5437 IC C8 C9 C10 C1 1.5325 109.53 179.78 112.01 1.5562 IC C9 C10 C1 C2 1.5437 112.01 63.19 113.83 1.5325 IC O3 C3 C4 C5 1.4164 109.06 161.96 115.69 1.5597 IC C4 C2 *C3 O3 1.5385 111.88 -119.42 107.04 1.4164 IC C4 C2 *C3 H3 1.5385 111.88 121.34 109.37 1.1144 IC C9 C5 *C10 C19 1.5437 109.64 -123.44 109.56 1.5561 IC C2 C3 O3 H3' 1.5341 107.04 68.70 104.78 0.9606 IC C5 C3 *C4 H4A 1.5597 115.69 122.74 108.67 1.1111 IC H4A C3 *C4 H4B 1.1111 108.67 115.74 108.84 1.1112 IC C10 C4 *C5 H5 1.5278 114.69 116.72 105.05 1.1175 IC C7 C5 *C6 H6A 1.5440 114.98 -124.18 109.41 1.1112 IC H6A C5 *C6 H6B 1.1112 109.41 -115.81 108.31 1.1113 IC C2 C10 *C1 H1A 1.5325 113.83 119.45 107.75 1.1136 IC C2 C10 *C1 H1B 1.5325 113.83 -124.31 110.15 1.1092 IC C1 C3 *C2 H2A 1.5325 111.74 122.10 110.26 1.1113 IC H2A C3 *C2 H2B 1.1113 110.26 117.21 108.67 1.1128 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5440 113.15 -166.48 108.55 1.5543 IC C14 C7 *C8 C9 1.5543 108.55 119.88 114.20 1.5325 IC C7 C8 C14 C13 1.5290 108.55 -174.00 113.09 1.5423 IC C13 C8 *C14 C15 1.5423 113.09 118.54 116.41 1.5290 IC C8 C14 C15 C16 1.5543 116.41 -154.98 103.52 1.5436 IC C14 C15 C16 C17 1.5290 103.52 -2.21 106.91 1.5527 IC C17 C14 *C13 C12 1.5726 98.14 119.76 107.63 1.5335 IC C14 C13 C12 C11 1.5423 107.63 55.01 111.17 1.5432 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 H7 1.5322 112.88 -121.61 108.52 1.1146 IC H7 C6 *C7 O7 1.1146 108.52 -118.80 106.42 1.4215 IC C6 C7 O7 H7' 1.5418 106.42 -178.10 104.63 0.9612 IC C9 C7 *C8 H8 1.5325 114.20 122.49 107.19 1.1068 IC C10 C8 *C9 H9 1.5437 109.53 -117.14 106.58 1.1136 IC C9 C12 *C11 H11A 1.5549 114.17 122.57 108.68 1.1092 IC H11A C12 *C11 H11B 1.1092 108.68 115.77 107.30 1.1109 IC C14 C13 C12 H12A 1.5423 107.63 -64.93 108.84 1.1122 IC H12A C13 *C12 H12B 1.1122 108.84 -119.33 111.64 1.1063 IC C13 C8 *C14 H14 1.5423 113.09 -118.19 108.50 1.1148 IC C16 C14 *C15 H15A 1.5436 103.52 118.98 111.14 1.1003 IC H15A C14 *C15 H15B 1.1003 111.14 119.93 112.23 1.0983 IC C17 C15 *C16 H16A 1.5527 106.91 121.32 110.94 1.0995 IC H16A C15 *C16 H16B 1.0995 110.94 117.27 111.30 1.0996 IC C13 C16 *C17 H17 1.5726 98.49 -113.15 110.37 1.1004 IC C12 C14 *C13 C18 1.5335 107.63 121.99 114.21 1.5526 IC C14 C13 C18 H18A 1.5423 114.21 -3.87 111.99 1.1055 IC H18A C13 *C18 H18B 1.1055 111.99 120.12 111.33 1.1067 IC H18A C13 *C18 H18C 1.1055 111.99 -120.94 110.59 1.1084 IC C5 C10 C19 H19A 1.5278 109.56 4.64 111.20 1.1078 IC H19A C10 *C19 H19B 1.1078 111.20 121.08 112.01 1.1062 IC H19A C10 *C19 H19C 1.1078 111.20 -119.52 110.63 1.1093 IC C13 C16 *C17 C20 1.5726 98.49 127.01 111.91 1.5638 IC C16 C17 C20 C22 1.5527 111.91 69.89 109.15 1.5504 IC C22 C17 *C20 C21 1.5504 109.15 122.01 112.87 1.5400 IC C21 C17 *C20 H20 1.5400 112.87 121.24 109.18 1.1115 IC C17 C20 C21 H21A 1.5638 112.87 73.30 110.64 1.1072 IC H21A C20 *C21 H21B 1.1072 110.64 -122.05 110.45 1.1097 IC H21A C20 *C21 H21C 1.1072 110.64 118.42 110.32 1.1099 IC C17 C20 C22 C23 1.5638 109.15 -160.90 114.01 1.5501 IC C23 C20 *C22 H22A 1.5501 114.01 119.25 110.01 1.1115 IC H22A C20 *C22 H22B 1.1115 110.01 117.37 109.82 1.1111 IC C20 C22 C23 CD 1.5504 114.01 177.00 113.21 1.5306 IC CD C22 *C23 H23A 1.5306 113.21 120.02 110.96 1.1069 IC CD C22 *C23 H23B 1.5306 113.21 -119.58 110.04 1.1084 IC C22 C23 CD OE1 1.5501 113.21 -177.88 116.45 1.2588 IC OE1 C23 *CD OE2 1.2588 116.45 173.57 119.02 1.2574 PRES GYCO -1.00 ! C3H3NO3 previously PRES GLYC, cacha ! patch combination: ! core residue cholic acid (CA) >> glycocholic acid (GCA) ! core residue deoxycholic acid (DCA) >> glycodeoxycholic acid (GDCA) ! core residue lithocholic acid (LCA) >> glycolithocholic acid (GLCA) ! core residue chenodeoxycholic acid (CDCA) >> glycochenodeoxycholic acid (GCDCA) ! core residue ursodeoxycholic acid (UDCA) >> glycoursodeoxycholic acid (GUDCA) ! OEG1 ! || ! OE1 CDG--OEG2(-1) ! || | DELETE ATOM OE2 ! OH Me21 C22 CD CG ATOM CD CG2O1 0.51 ! | \ / \ / \ / ATOM OE1 OG2D1 -0.51 ! C12 Me18 C20 C23 NH ATOM N NG2S1 -0.47 ! / \ | / ATOM HN HGP1 0.47 ! C11 C13---C17 ATOM CG CG321 -0.28 ! Me19 | | | ATOM HG1 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG2 HGA2 0.09 ! / \|/ \ / \ / ATOM CDG CG2O3 0.62 ! C2 C10 C8 C15 ATOM OEG1 OG2D2 -0.76 ! | | | ATOM OEG2 OG2D2 -0.76 ! C3 C5 C7 ! / \ / \ / \ ! HO C4 C6 OH BOND CD N N HN BOND N CG CG HG1 CG HG2 ! Glycocholic acid (GCA) BOND CG CDG CDG OEG1 CDG OEG2 IMPR CD C23 N OE1 IMPR CDG OEG1 OEG2 CG IC OE1 C23 *CD N 1.2267 119.93 177.01 116.52 1.3368 IC C23 CD N CG 1.5039 116.52 -173.26 130.72 1.4497 IC CG CD *N HN 1.4497 130.72 170.32 124.06 1.0161 IC CD N CG CDG 1.3368 130.72 168.60 104.28 1.5483 IC CDG N *CG HG1 1.5483 104.28 117.38 111.67 1.1092 IC CDG N *CG HG2 1.5483 104.28 -117.58 112.23 1.1082 IC N CG CDG OEG1 1.4497 104.28 148.60 116.21 1.2549 IC OEG1 CG *CDG OEG2 1.2549 116.21 -149.85 112.75 1.2749 !end bile acid related compounds, chayan, jul2006 !bile acid related compounds, chayan, dec2006 RESI GA -2.00 ! C29H45NO7 GLUTAMIC ACID CDCA AMIDE, cacha GROUP ATOM C3 CG311 0.14 ATOM O3 OG311 -0.65 ATOM H3' HGP1 0.42 ATOM H3 HGA1 0.09 GROUP ! OA2(-0.5) ATOM C4 CG321 -0.18 ! | ATOM H4A HGA2 0.09 ! O24 CA--OA1(-0.5) ATOM H4B HGA2 0.09 ! || | GROUP ! H Me21 C22 C24 CC1 CC3 OG1(-0.5) ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ / \ / ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CC2 CG GROUP ! / \ | / \ ATOM C6 CG321 -0.18 ! C11 C13---C17 OG2(-0.5) ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM H7' HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! Glutamic Acid CDCA Amide (GA) GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 ! no hydrogen GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 ! no hydrogen GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM C24 CG2O1 0.51 ATOM O24 OG2D1 -0.51 ATOM N NG2S1 -0.47 ATOM HN HGP1 0.47 GROUP ATOM CC1 CG311 -0.19 ATOM HC1 HGA1 0.09 ATOM CA CG2O3 0.62 ATOM OA1 OG2D2 -0.76 ATOM OA2 OG2D2 -0.76 GROUP ATOM CC2 CG321 -0.18 ATOM HC2A HGA2 0.09 ATOM HC2B HGA2 0.09 GROUP ATOM CC3 CG321 -0.28 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ATOM CG CG2O3 0.62 ATOM OG1 OG2D2 -0.76 ATOM OG2 OG2D2 -0.76 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 C24 C24 O24 BOND C24 N N HN BOND N CC1 CC1 HC1 CC1 CA CA OA1 CA OA2 BOND CC1 CC2 CC2 HC2A CC2 HC2B CC2 CC3 BOND CC3 HC3A CC3 HC3B CC3 CG CG OG1 CG OG2 IMPR C24 C23 N O24 IMPR CA OA2 OA1 CC1 IMPR CG OG2 OG1 CC3 ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on arbitrary CHARMM optimized structure IC C1 C2 C3 C4 1.5325 111.83 -48.81 111.97 1.5386 IC C2 C3 C4 C5 1.5343 111.97 43.31 115.75 1.5595 IC C3 C4 C5 C6 1.5386 115.75 -175.01 109.03 1.5520 IC C4 C5 C6 C7 1.5595 109.03 85.21 115.02 1.5438 IC C5 C6 C7 C8 1.5520 115.02 38.61 113.11 1.5276 IC C7 C8 C9 C10 1.5276 114.59 57.44 109.36 1.5436 IC C8 C9 C10 C1 1.5364 109.36 -179.93 112.02 1.5561 IC C9 C10 C1 C2 1.5436 112.02 62.99 113.75 1.5325 IC O3 C3 C4 C5 1.4166 108.95 161.43 115.75 1.5595 IC C4 C2 *C3 O3 1.5386 111.97 -119.29 106.97 1.4166 IC C4 C2 *C3 H3 1.5386 111.97 121.36 109.36 1.1143 IC C9 C5 *C10 C19 1.5436 109.73 -123.35 109.59 1.5558 IC C2 C3 O3 H3' 1.5343 106.97 70.81 104.29 0.9610 IC C5 C3 *C4 H4A 1.5595 115.75 122.78 108.78 1.1109 IC H4A C3 *C4 H4B 1.1109 108.78 115.85 108.94 1.1114 IC C10 C4 *C5 H5 1.5280 114.66 116.76 105.20 1.1172 IC C7 C5 *C6 H6A 1.5438 115.02 -124.32 109.59 1.1107 IC H6A C5 *C6 H6B 1.1107 109.59 -115.96 108.35 1.1117 IC C2 C10 *C1 H1A 1.5325 113.75 119.62 107.69 1.1133 IC C2 C10 *C1 H1B 1.5325 113.75 -124.21 109.99 1.1093 IC C1 C3 *C2 H2A 1.5325 111.83 121.96 110.22 1.1114 IC H2A C3 *C2 H2B 1.1114 110.22 117.27 108.72 1.1125 !IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config !IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config !IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config !IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config !IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config IC C6 C7 C8 C14 1.5438 113.11 -165.92 108.46 1.5523 IC C14 C7 *C8 C9 1.5523 108.46 119.72 114.59 1.5364 IC C7 C8 C14 C13 1.5276 108.46 -173.32 111.50 1.5366 IC C13 C8 *C14 C15 1.5366 111.50 118.16 117.80 1.5346 IC C8 C14 C15 C16 1.5523 117.80 -150.82 103.90 1.5511 IC C14 C15 C16 C17 1.5346 103.90 -5.86 105.47 1.5512 IC C17 C14 *C13 C12 1.5566 98.22 118.19 109.26 1.5283 IC C14 C13 C12 C11 1.5366 109.26 55.66 110.30 1.5429 !IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config !IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config !IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config !IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config !IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config !IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config !IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config !IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config !IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config !IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config !IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config !IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config IC C8 C6 *C7 O7 1.5276 113.11 -126.99 108.31 1.4225 IC O7 C6 *C7 H7 1.4225 108.31 -113.92 107.38 1.1176 IC C6 C7 O7 H7' 1.5438 108.31 -176.31 103.73 0.9623 IC C9 C7 *C8 H8 1.5364 114.59 122.91 107.14 1.1079 IC C10 C8 *C9 H9 1.5436 109.36 -116.93 106.27 1.1129 IC C9 C12 *C11 H11A 1.5599 114.19 122.19 108.67 1.1091 IC H11A C12 *C11 H11B 1.1091 108.67 115.84 107.52 1.1100 IC C14 C13 C12 H12A 1.5366 109.26 -63.53 108.77 1.1119 IC H12A C13 *C12 H12B 1.1119 108.77 -118.49 110.35 1.1099 IC C13 C8 *C14 H14 1.5366 111.50 -117.92 108.42 1.1139 IC C16 C14 *C15 H15A 1.5511 103.90 118.25 111.42 1.1022 IC H15A C14 *C15 H15B 1.1022 111.42 120.29 112.58 1.0964 IC C17 C15 *C16 H16A 1.5512 105.47 121.54 108.43 1.1009 IC H16A C15 *C16 H16B 1.1009 108.43 116.18 112.44 1.0973 IC C13 C16 *C17 H17 1.5566 98.62 -112.31 108.27 1.1016 IC C12 C14 *C13 C18 1.5283 109.26 123.58 114.19 1.5536 IC C14 C13 C18 H18A 1.5366 114.19 4.73 112.02 1.1075 IC H18A C13 *C18 H18B 1.1075 112.02 118.46 111.31 1.1080 IC H18A C13 *C18 H18C 1.1075 112.02 -121.96 111.70 1.1059 IC C5 C10 C19 H19A 1.5280 109.59 4.28 111.26 1.1078 IC H19A C10 *C19 H19B 1.1078 111.26 120.71 111.90 1.1071 IC H19A C10 *C19 H19C 1.1078 111.26 -119.86 110.79 1.1088 IC C13 C16 *C17 C20 1.5566 98.62 124.35 118.99 1.5606 IC C16 C17 C20 C22 1.5512 118.99 -1.33 112.57 1.5470 IC C22 C17 *C20 C21 1.5470 112.57 123.04 107.65 1.5439 IC C21 C17 *C20 H20 1.5439 107.65 117.51 109.34 1.1119 IC C17 C20 C21 H21A 1.5606 107.65 56.27 110.43 1.1095 IC H21A C20 *C21 H21B 1.1095 110.43 -120.25 109.86 1.1109 IC H21A C20 *C21 H21C 1.1095 110.43 120.00 110.54 1.1093 IC C17 C20 C22 C23 1.5606 112.57 -177.70 114.81 1.5506 IC C23 C20 *C22 H22A 1.5506 114.81 119.77 108.00 1.1166 IC H22A C20 *C22 H22B 1.1166 108.00 116.45 108.68 1.1124 IC C20 C22 C23 C24 1.5470 114.81 166.35 110.40 1.4987 IC C24 C22 *C23 H23A 1.4987 110.40 121.19 111.13 1.1081 IC C24 C22 *C23 H23B 1.4987 110.40 -118.13 109.46 1.1111 IC C22 C23 C24 N 1.5506 110.40 46.22 115.40 1.3366 IC N C23 *C24 O24 1.3366 115.40 -179.81 120.30 1.2285 IC C23 C24 N CC1 1.4987 115.40 -163.64 129.84 1.4417 IC CC1 C24 *N HN 1.4417 129.84 178.15 124.42 1.0052 IC C24 N CC1 CA 1.3366 129.84 -156.03 104.17 1.5535 IC CA N *CC1 HC1 1.5535 104.17 116.15 110.25 1.1093 IC HC1 N *CC1 CC2 1.1093 110.25 122.36 109.79 1.5587 IC N CC1 CA OA1 1.4417 104.17 160.24 120.14 1.2563 IC OA1 CC1 *CA OA2 1.2563 120.14 -176.18 115.58 1.2715 IC N CC1 CC2 CC3 1.4417 109.79 58.95 114.87 1.5576 IC CC3 CC1 *CC2 HC2A 1.5576 114.87 122.98 109.65 1.1108 IC HC2A CC1 *CC2 HC2B 1.1108 109.65 116.68 107.14 1.1137 IC CC1 CC2 CC3 CG 1.5587 114.87 -160.82 114.28 1.5329 IC CG CC2 *CC3 HC3A 1.5329 114.28 119.62 110.64 1.1056 IC HC3A CC2 *CC3 HC3B 1.1056 110.64 118.51 109.05 1.1085 IC CC2 CC3 CG OG1 1.5576 114.28 -112.88 118.59 1.2602 IC OG1 CC3 *CG OG2 1.2602 118.59 -177.02 117.98 1.2616 PRES AMGA 0.00 ! C3H4O2 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha-Methyl Glu Acid CDCA Amide ! OA1 ! || ! O24 CA--OA2--CH3(M) ! || | ! OH Me21 C22 C24 CC1 CC3 OG1(-0.5) ATOM CC1 CG311 0.17 ! | \ / \ / \ / \ / \ / ATOM HC1 HGA1 0.09 ! C12 Me18 C20 C23 NH CC2 CG ATOM CA CG2O2 0.90 ! / \ | / \ ATOM OA1 OG2D1 -0.63 ! C11 C13---C17 OG2(-0.5) ATOM OA2 OG302 -0.49 ! Me19 | | | ATOM CM CG331 -0.31 ! C1 | C9 C14 C16 ATOM HM1 HGA3 0.09 ! / \|/ \ / \ / ATOM HM2 HGA3 0.09 ! C2 C10 C8 C15 ATOM HM3 HGA3 0.09 ! | | | ! C3 C5 C7 ! / \ / \ / \ ! HO C4 C6 OH ! Alpha-Methyl Glutamic Acid CDCA Amide BOND OA2 CM BOND CM HM1 CM HM2 CM HM3 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CM 1.5285 111.09 -178.91 115.08 1.4371 IC HM1 CM OA2 CA 1.1113 109.28 179.56 115.08 1.3429 IC HM2 CM OA2 CA 1.1136 110.99 60.48 115.08 1.3429 IC HM3 CM OA2 CA 1.1135 110.99 -61.17 115.08 1.3429 PRES GMGA 0.00 ! C3H5O2 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Methyl Glu Acid CDCA Amide ! OA1(-0.5) ! | ! O24 CA--OA2(-0.5) ! || | ! OH Me21 C22 C24 CC1 CC3 OG1 ! | \ / \ / \ / \ / \ // ATOM CC3 CG321 0.08 ! C12 Me18 C20 C23 NH CC2 CG ATOM HC3A HGA2 0.09 ! / \ | / \ ATOM HC3B HGA2 0.09 ! C11 C13---C17 OG2--CM3(M) ATOM CG CG2O2 0.90 ! Me19 | | | ATOM OG1 OG2D1 -0.63 ! C1 | C9 C14 C16 ATOM OG2 OG302 -0.49 ! / \|/ \ / \ / ATOM CM CG331 -0.31 ! C2 C10 C8 C15 ATOM HM1 HGA3 0.09 ! | | | ATOM HM2 HGA3 0.09 ! C3 C5 C7 ATOM HM3 HGA3 0.09 ! / \ / \ / \ ! HO C4 C6 OH ! Gamma-Methyl Glutamic Acid CDCA Amide BOND OG2 CM BOND CM HM1 CM HM2 CM HM3 DELETE IMPR CG OG2 OG1 CC3 DELETE IMPR CG OG2 OG1 CC3 IMPR CG CC3 OG1 OG2 IC CC3 CG OG2 CM 1.5001 109.42 178.80 114.93 1.4378 IC HM1 CM OG2 CG 1.1114 109.43 179.48 114.93 1.3439 IC HM2 CM OG2 CG 1.1140 110.99 60.32 114.93 1.3439 IC HM3 CM OG2 CG 1.1136 111.06 -61.13 114.93 1.3439 PRES DMGA 0.00 ! C6H9O4 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dimethyl Glu Acid CDCA Amide ATOM CC1 CG311 0.17 ! OA1 ATOM HC1 HGA1 0.09 ! || ATOM CA CG2O2 0.90 ! O24 CA--OA2--CH3(M) ATOM OA1 OG2D1 -0.63 ! || | ATOM OA2 OG302 -0.49 ! OH Me21 C22 C24 CC1 CC3 OG1 ATOM CM CG331 -0.31 ! | \ / \ / \ / \ / \ // ATOM HM1 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG ATOM HM2 HGA3 0.09 ! / \ | / \ ATOM HM3 HGA3 0.09 ! C11 C13---C17 OG2--CM3(N) ATOM CC3 CG321 0.08 ! Me19 | | | ATOM HC3A HGA2 0.09 ! C1 | C9 C14 C16 ATOM HC3B HGA2 0.09 ! / \|/ \ / \ / ATOM CG CG2O2 0.90 ! C2 C10 C8 C15 ATOM OG1 OG2D1 -0.63 ! | | | ATOM OG2 OG302 -0.49 ! C3 C5 C7 ATOM CN CG331 -0.31 ! / \ / \ / \ ATOM HN1 HGA3 0.09 ! HO C4 C6 OH ATOM HN2 HGA3 0.09 ATOM HN3 HGA3 0.09 ! Alpha,Gamma-Dimethyl Glutamic Acid CDCA Amide BOND OA2 CM BOND CM HM1 CM HM2 CM HM3 BOND OG2 CN BOND CN HN1 CN HN2 CN HN3 DELETE IMPR CA OA2 OA1 CC1 DELETE IMPR CG OG2 OG1 CC3 IMPR CA CC1 OA1 OA2 IMPR CG CC3 OG1 OG2 IC CC1 CA OA2 CM 1.5215 109.43 -179.14 114.39 1.4397 IC HM1 CM OA2 CA 1.1119 109.81 179.92 114.39 1.3481 IC HM2 CM OA2 CA 1.1147 111.25 60.55 114.39 1.3481 IC HM3 CM OA2 CA 1.1148 111.21 -60.74 114.39 1.3481 IC CC3 CG OG2 CN 1.5036 109.18 178.54 114.99 1.4389 IC HN1 CN OG2 CG 1.1119 109.57 179.75 114.99 1.3378 IC HN2 CN OG2 CG 1.1144 111.15 60.57 114.99 1.3378 IC HN3 CN OG2 CG 1.1141 111.21 -60.90 114.99 1.3378 PRES AMGT 0.00 ! C9H15O4 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Methyl, Gamma Tert.Butyl Glu Acid CDCA Amide ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ! OA1 ATOM CA CG2O2 0.90 ! || ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH3(M) ATOM OA2 OG302 -0.49 ! || | ATOM CM CG331 -0.31 ! OH Me21 C22 C24 CC1 CC3 OG1 ATOM HM1 HGA3 0.09 ! | \ / \ / \ / \ / \ // ATOM HM2 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG CB1 ATOM HM3 HGA3 0.09 ! / \ | / \ | ATOM CC3 CG321 0.08 ! C11 C13---C17 OG2--CT--CB2 ATOM HC3A HGA2 0.09 ! Me19 | | | | ATOM HC3B HGA2 0.09 ! C1 | C9 C14 C16 CB3 ATOM CG CG2O2 0.90 ! / \|/ \ / \ / ATOM OG1 OG2D1 -0.63 ! C2 C10 C8 C15 ATOM OG2 OG302 -0.49 ! | | | ATOM CT CG301 -0.04 ! C3 C5 C7 ATOM CB1 CG331 -0.27 ! / \ / \ / \ ATOM HB11 HGA3 0.09 ! HO C4 C6 OH ATOM HB12 HGA3 0.09 ATOM HB13 HGA3 0.09 ! Alpha Methyl,Gamma Tert.Butyl Glutamic Acid CDCA Amide ATOM CB2 CG331 -0.27 ATOM HB21 HGA3 0.09 ATOM HB22 HGA3 0.09 ATOM HB23 HGA3 0.09 ATOM CB3 CG331 -0.27 ATOM HB31 HGA3 0.09 ATOM HB32 HGA3 0.09 ATOM HB33 HGA3 0.09 BOND OA2 CM BOND CM HM1 CM HM2 CM HM3 BOND OG2 CT BOND CT CB1 CB1 HB11 CB1 HB12 CB1 HB13 BOND CT CB2 CB2 HB21 CB2 HB22 CB2 HB23 BOND CT CB3 CB3 HB31 CB3 HB32 CB3 HB33 DELETE IMPR CA OA2 OA1 CC1 DELETE IMPR CG OG2 OG1 CC3 IMPR CA CC1 OA1 OA2 IMPR CG CC3 OG1 OG2 IC CC1 CA OA2 CM 1.5216 109.43 -179.07 114.39 1.4397 IC HM1 CM OA2 CA 1.1119 109.81 179.90 114.39 1.3481 IC HM2 CM OA2 CA 1.1147 111.24 60.54 114.39 1.3481 IC HM3 CM OA2 CA 1.1147 111.21 -60.74 114.39 1.3481 IC CC3 CG OG2 CT 1.5056 108.23 179.34 121.50 1.4254 IC CB1 CT OG2 CG 1.5308 105.14 179.25 121.50 1.3210 IC CB2 CT OG2 CG 1.5354 111.04 62.01 121.50 1.3210 IC CB3 CT OG2 CG 1.5354 110.89 -63.42 121.50 1.3210 IC HB11 CB1 CT OG2 1.1097 110.37 -179.27 105.14 1.4254 IC HB12 CB1 CT OG2 1.1088 110.29 60.60 105.14 1.4254 IC HB13 CB1 CT OG2 1.1105 110.19 -59.24 105.14 1.4254 IC HB21 CB2 CT OG2 1.1098 109.96 171.88 111.04 1.4254 IC HB22 CB2 CT OG2 1.1099 110.24 52.17 111.04 1.4254 IC HB23 CB2 CT OG2 1.1092 111.27 -68.59 111.04 1.4254 IC HB31 CB3 CT OG2 1.1098 109.90 -171.74 110.89 1.4254 IC HB32 CB3 CT OG2 1.1094 111.09 68.88 110.89 1.4254 IC HB33 CB3 CT OG2 1.1092 110.31 -51.87 110.89 1.4254 PRES ATGM 0.00 ! C9H15O4 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Gamma Methyl, Alpha Tert.Butyl Glu Acid CDCA Amide ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ! OA1 CB1 CB2 ATOM OA1 OG2D1 -0.63 ! || \ / ATOM OA2 OG302 -0.49 ! O24 CA--OA2--CT--CB3 ATOM CT CG301 -0.04 ! || | ATOM CB1 CG331 -0.27 ! OH Me21 C22 C24 CC1 CC3 OG1 ATOM HB11 HGA3 0.09 ! | \ / \ / \ / \ / \ // ATOM HB12 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG ATOM HB13 HGA3 0.09 ! / \ | / \ ATOM CB2 CG331 -0.27 ! C11 C13---C17 OG2--CH3(M) ATOM HB21 HGA3 0.09 ! Me19 | | | ATOM HB22 HGA3 0.09 ! C1 | C9 C14 C16 ATOM HB23 HGA3 0.09 ! / \|/ \ / \ / ATOM CB3 CG331 -0.27 ! C2 C10 C8 C15 ATOM HB31 HGA3 0.09 ! | | | ATOM HB32 HGA3 0.09 ! C3 C5 C7 ATOM HB33 HGA3 0.09 ! / \ / \ / \ ATOM CC3 CG321 0.08 ! HO C4 C6 OH ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ! Gamma Methyl, Alpha Tert.Butyl Glutamic Acid CDCA Amide ATOM CG CG2O2 0.90 ATOM OG1 OG2D1 -0.63 ATOM OG2 OG302 -0.49 ATOM CM CG331 -0.31 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND OA2 CT BOND CT CB1 CB1 HB11 CB1 HB12 CB1 HB13 BOND CT CB2 CB2 HB21 CB2 HB22 CB2 HB23 BOND CT CB3 CB3 HB31 CB3 HB32 CB3 HB33 BOND OG2 CM BOND CM HM1 CM HM2 CM HM3 DELETE IMPR CA OA2 OA1 CC1 DELETE IMPR CG OG2 OG1 CC3 IMPR CA CC1 OA1 OA2 IMPR CG CC3 OG1 OG2 IC CC1 CA OA2 CT 1.5243 108.15 -178.31 121.38 1.4251 IC CB1 CT OA2 CA 1.5313 105.10 179.75 121.38 1.3318 IC CB2 CT OA2 CA 1.5354 111.03 62.52 121.38 1.3318 IC CB3 CT OA2 CA 1.5351 111.02 -62.94 121.38 1.3318 IC HB11 CB1 CT OA2 1.1105 110.10 -179.76 105.10 1.4251 IC HB12 CB1 CT OA2 1.1099 110.43 60.50 105.10 1.4251 IC HB13 CB1 CT OA2 1.1100 110.42 -60.01 105.10 1.4251 IC HB21 CB2 CT OA2 1.1101 109.87 172.54 111.03 1.4251 IC HB22 CB2 CT OA2 1.1093 110.56 52.80 111.03 1.4251 IC HB23 CB2 CT OA2 1.1095 111.28 -68.22 111.03 1.4251 IC HB31 CB3 CT OA2 1.1101 109.93 -172.01 111.02 1.4251 IC HB32 CB3 CT OA2 1.1095 111.24 68.69 111.02 1.4251 IC HB33 CB3 CT OA2 1.1095 110.50 -52.18 111.02 1.4251 IC CC3 CG OG2 CM 1.5032 109.19 178.53 114.98 1.4389 IC HM1 CM OG2 CG 1.1119 109.57 179.56 114.98 1.3378 IC HM2 CM OG2 CG 1.1145 111.16 60.39 114.98 1.3378 IC HM3 CM OG2 CG 1.1141 111.21 -61.08 114.98 1.3378 PRES ABGA 0.00 ! C9H8O2 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha-Benzyl Glu Acid CDCA Amide ATOM CC1 CG311 0.17 ! OA1 CD1--CE1 ATOM HC1 HGA1 0.09 ! || // \\ ATOM CA CG2O2 0.90 ! O24 CA--OA2--CB--CZ CP ATOM OA1 OG2D1 -0.63 ! || | \ __ / ATOM OA2 OG302 -0.49 ! OH Me21 C22 C24 CM1 CC3 CD2--CE2 ATOM CB CG321 -0.22 ! | \ / \ / \ / \ / \ ATOM HB1 HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CG--OG1(-0.5) ATOM HB2 HGA2 0.09 ! / \ | / | ATOM CZ CG2R61 0.00 ! C11 C13---C17 OG2(-0.5) ATOM CD1 CG2R61 -0.115 ! Me19 | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 ATOM CE1 CG2R61 -0.115 ! | | | ATOM HE1 HGR61 0.115 ! C3 C5 C7 ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ ATOM HE2 HGR61 0.115 ! HO C4 C6 OH ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 ! Alpha-Benzyl Glutamic Acid CDCA Amide BOND OA2 CB BOND CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5276 110.26 -175.22 115.99 1.4474 IC HB1 CB OA2 CA 1.1152 110.81 49.30 115.99 1.3364 IC HB2 CB OA2 CA 1.1140 109.30 -69.99 115.99 1.3364 IC CZ CB OA2 CA 1.5060 114.53 168.41 115.99 1.3364 IC CD2 CZ CB OA2 1.4042 119.63 -39.76 114.53 1.4474 IC CD1 CZ CB OA2 1.4055 120.89 141.67 114.53 1.4474 IC CD1 CD2 *CZ CB 1.4055 119.47 -178.59 119.63 1.5060 IC CD2 CZ CB HB1 1.4042 119.63 82.33 105.44 1.1152 IC CD2 CZ CB HB2 1.4042 119.63 -161.94 108.22 1.1140 IC CB CZ CD1 CE1 1.5060 120.89 178.93 120.21 1.4022 IC CB CZ CD2 CE2 1.5060 119.63 -178.66 120.33 1.4001 IC CZ CD1 CE1 CP 1.4055 120.21 -0.33 119.99 1.4018 IC CD1 CE1 CP CE2 1.4022 119.99 0.00 119.98 1.4008 IC CE1 CP CE2 CD2 1.4018 119.98 0.28 120.02 1.4001 IC CE1 CZ *CD1 HD1 1.4022 120.21 179.92 119.72 1.0791 IC CE2 CZ *CD2 HD2 1.4001 120.33 -179.34 119.97 1.0825 IC CP CD1 *CE1 HE1 1.4018 119.99 -179.96 120.00 1.0797 IC CP CD2 *CE2 HE2 1.4008 120.02 -179.26 119.27 1.0807 IC CE1 CE2 *CP HP 1.4018 119.98 -179.91 119.82 1.0797 PRES GBGA 0.00 ! C9H9O2 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Benzyl Glu Acid CDCA Amide ATOM CC3 CG321 0.08 ! OA1(-0.5) ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2(-0.5) ATOM CG CG2O2 0.90 ! || | ATOM OG1 OG2D1 -0.63 ! OH Me21 C22 C24 CC1 CC3 CD1--CE1 ATOM OG2 OG302 -0.49 ! | \ / \ / \ / \ / \ // \\ ATOM CB CG321 -0.22 ! C12 Me18 C20 C23 NH CC2 CG--OG2--CB--CZ CP ATOM HB1 HGA2 0.09 ! / \ | / || \ __ / ATOM HB2 HGA2 0.09 ! C11 C13---C17 OG1 CD2--CE2 ATOM CZ CG2R61 0.00 ! Me19 | | | ATOM CD1 CG2R61 -0.115 ! C1 | C9 C14 C16 ATOM HD1 HGR61 0.115 ! / \|/ \ / \ / ATOM CD2 CG2R61 -0.115 ! C2 C10 C8 C15 ATOM HD2 HGR61 0.115 ! | | | ATOM CE1 CG2R61 -0.115 ! C3 C5 C7 ATOM HE1 HGR61 0.115 ! / \ / \ / \ ATOM CE2 CG2R61 -0.115 ! HO C4 C6 OH ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ! Gamma-Benzyl Glutamic Acid CDCA Amide ATOM HP HGR61 0.115 BOND OG2 CB BOND CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CG OG2 OG1 CC3 IMPR CG CC3 OG1 OG2 IC CC3 CG OG2 CB 1.5019 110.25 -178.87 116.50 1.4500 IC HB1 CB OG2 CG 1.1166 111.80 -40.89 116.50 1.3367 IC HB2 CB OG2 CG 1.1126 107.85 -156.53 116.50 1.3367 IC CZ CB OG2 CG 1.5090 115.77 84.56 116.50 1.3367 IC CD2 CZ CB OG2 1.4043 120.63 -105.67 115.77 1.4500 IC CD1 CZ CB OG2 1.4036 119.72 73.22 115.77 1.4500 IC CD1 CD2 *CZ CB 1.4036 119.63 178.88 120.63 1.5090 IC CD2 CZ CB HB1 1.4043 120.63 21.27 108.88 1.1166 IC CD2 CZ CB HB2 1.4043 120.63 134.60 106.33 1.1126 IC CB CZ CD1 CE1 1.5090 119.72 -179.56 120.22 1.4014 IC CB CZ CD2 CE2 1.5090 120.63 179.55 120.19 1.4015 IC CZ CD1 CE1 CP 1.4036 120.22 0.20 119.95 1.4016 IC CD1 CE1 CP CE2 1.4014 119.95 0.28 120.04 1.4017 IC CE1 CP CE2 CD2 1.4016 120.04 -0.28 119.96 1.4015 IC CE1 CZ *CD1 HD1 1.4014 120.22 179.19 119.50 1.0802 IC CE2 CZ *CD2 HD2 1.4015 120.19 -178.97 119.56 1.0802 IC CP CD1 *CE1 HE1 1.4016 119.95 179.43 119.88 1.0801 IC CP CD2 *CE2 HE2 1.4017 119.96 -179.44 119.89 1.0800 IC CE1 CE2 *CP HP 1.4016 120.04 -179.29 120.00 1.0800 PRES DBGA 0.00 ! C18H17O4 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dibenzyl Glu Acid CDCA Amide ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ! OA1 CJ1--CK1 ATOM CA CG2O2 0.90 ! || // \\ ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH2(B)--CY CQ ATOM OA2 OG302 -0.49 ! || | \ __ / ATOM CB CG321 -0.22 ! OH Me21 C22 C24 CC1 CC3 CJ2--CK2 CD1--CE1 ATOM HB1 HGA2 0.09 ! | \ / \ / \ / \ / \ // \\ ATOM HB2 HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CG--OG2--CH2(N)--CZ CP ATOM CY CG2R61 0.00 ! / \ | / || \ __ / ATOM CJ1 CG2R61 -0.115 ! C11 C13---C17 OG1 CD2--CE2 ATOM HJ1 HGR61 0.115 ! Me19 | | | ATOM CJ2 CG2R61 -0.115 ! C1 | C9 C14 C16 ATOM HJ2 HGR61 0.115 ! / \|/ \ / \ / ATOM CK1 CG2R61 -0.115 ! C2 C10 C8 C15 ATOM HK1 HGR61 0.115 ! | | | ATOM CK2 CG2R61 -0.115 ! C3 C5 C7 ATOM HK2 HGR61 0.115 ! / \ / \ / \ ATOM CQ CG2R61 -0.115 ! HO C4 C6 OH ATOM HQ HGR61 0.115 ATOM CC3 CG321 0.08 ! Alpha,Gamma-Dibenzyl Glutamic Acid CDCA Amide ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ATOM CG CG2O2 0.90 ATOM OG1 OG2D1 -0.63 ATOM OG2 OG302 -0.49 ATOM CN CG321 -0.22 ATOM HN1 HGA2 0.09 ATOM HN2 HGA2 0.09 ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND OG2 CN BOND CN HN1 CN HN2 CN CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 DELETE IMPR CG OG2 OG1 CC3 IMPR CA CC1 OA1 OA2 IMPR CG CC3 OG1 OG2 IC CC1 CA OA2 CB 1.5206 108.90 105.00 116.86 1.4507 IC HB1 CB OA2 CA 1.1132 108.27 147.25 116.86 1.3434 IC HB2 CB OA2 CA 1.1177 112.85 31.14 116.86 1.3434 IC CY CB OA2 CA 1.5069 114.70 -93.16 116.86 1.3434 IC CJ2 CY CB OA2 1.4050 120.48 -91.04 114.70 1.4507 IC CJ1 CY CB OA2 1.4039 119.88 87.42 114.70 1.4507 IC CJ1 CJ2 *CY CB 1.4039 119.62 178.47 120.48 1.5069 IC CJ2 CY CB HB1 1.4050 120.48 29.17 107.16 1.1132 IC CJ2 CY CB HB2 1.4050 120.48 142.14 108.03 1.1177 IC CB CY CJ1 CK1 1.5069 119.88 -178.91 120.21 1.4011 IC CB CY CJ2 CK2 1.5069 120.48 178.97 120.16 1.4016 IC CY CJ1 CK1 CQ 1.4039 120.21 0.12 119.97 1.4012 IC CJ1 CK1 CQ CK2 1.4011 119.97 0.13 120.06 1.4013 IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.07 119.97 1.4016 IC CK1 CY *CJ1 HJ1 1.4011 120.21 179.67 119.77 1.0809 IC CK2 CY *CJ2 HJ2 1.4016 120.16 179.94 119.94 1.0795 IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.94 119.95 1.0807 IC CQ CJ2 *CK2 HK2 1.4013 119.97 179.97 120.09 1.0805 IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.96 120.02 1.0806 IC CC3 CG OG2 CN 1.5035 108.85 -165.00 116.75 1.4498 IC HN1 CN OG2 CG 1.1127 108.18 -45.00 116.75 1.3348 IC HN2 CN OG2 CG 1.1172 112.24 75.00 116.75 1.3348 IC CZ CN OG2 CG 1.5070 115.12 -165.00 116.75 1.3348 IC CD2 CZ CN OG2 1.4041 120.43 180.00 115.12 1.4498 IC CD1 CZ CN OG2 1.4041 119.89 0.00 115.12 1.4498 IC CD1 CD2 *CZ CN 1.4041 119.66 178.41 120.43 1.5070 IC CD2 CZ CN HB1 1.4041 120.43 -88.94 130.32 7.6318 IC CD2 CZ CN HB2 1.4041 120.43 -83.96 118.87 8.2110 IC CN CZ CD1 CE1 1.5070 119.89 -179.11 120.18 1.4013 IC CN CZ CD2 CE2 1.5070 120.43 179.10 120.17 1.4013 IC CZ CD1 CE1 CP 1.4041 120.18 0.23 119.96 1.4014 IC CD1 CE1 CP CE2 1.4013 119.96 0.23 120.06 1.4014 IC CE1 CP CE2 CD2 1.4014 120.06 -0.23 119.97 1.4013 IC CE1 CZ *CD1 HD1 1.4013 120.18 179.46 119.82 1.0792 IC CE2 CZ *CD2 HD2 1.4013 120.17 -179.25 119.77 1.0805 IC CP CD1 *CE1 HE1 1.4014 119.96 179.64 120.04 1.0805 IC CP CD2 *CE2 HE2 1.4014 119.97 -179.65 119.97 1.0805 IC CE1 CE2 *CP HP 1.4014 120.06 -179.54 119.96 1.0805 PRES AL 1.00 ! C3H9N cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Lysine CDCA Amide ! OA1(-0.5) ! | ! O24 CA--OA2(-0.5) DELETE ATOM CG ! || | DELETE ATOM OG1 ! OH Me21 C22 C24 CC1 CC3 CC5 DELETE ATOM OG2 ! | \ / \ / \ / \ / \ / \ ATOM CC3 CG321 -0.18 ! C12 Me18 C20 C23 NH CC2 CC4 NH3(+1) ATOM HC3A HGA2 0.09 ! / \ | / ATOM HC3B HGA2 0.09 ! C11 C13---C17 ATOM CC4 CG321 -0.18 ! Me19 | | | ATOM HC4A HGA2 0.09 ! C1 | C9 C14 C16 ATOM HC4B HGA2 0.09 ! / \|/ \ / \ / ATOM CC5 CG324 0.13 ! C2 C10 C8 C15 ATOM HC5A HGA2 0.09 ! | | | ATOM HC5B HGA2 0.09 ! C3 C5 C7 ATOM NL NG3P3 -0.30 ! / \ / \ / \ ATOM HL1 HGP2 0.33 ! HO C4 C6 OH ATOM HL2 HGP2 0.33 ATOM HL3 HGP2 0.33 ! Alpha Lysine CDCA Amide BOND CC3 CC4 CC4 HC4A CC4 HC4B BOND CC4 CC5 CC5 HC5A CC5 HC5B BOND CC5 NL NL HL1 NL HL2 NL HL3 IC CC1 CC2 CC3 CC4 1.5561 114.54 179.98 116.18 1.5479 IC CC2 CC3 CC4 CC5 1.5463 116.18 -57.56 115.63 1.5430 IC CC5 CC3 *CC4 HC4A 1.5430 115.63 -123.18 108.29 1.1129 IC HC4A CC3 *CC4 HC4B 1.1129 108.29 -115.77 107.94 1.1143 IC CC3 CC4 CC5 NL 1.5479 115.63 -52.00 111.91 1.4822 IC NL CC4 *CC5 HC5A 1.4822 111.91 119.56 110.77 1.1051 IC NL CC4 *CC5 HC5B 1.4822 111.91 -121.02 110.60 1.1019 IC HL1 NL CC5 CC4 1.0369 112.46 -11.49 111.91 1.5430 IC HL2 NL CC5 CC4 1.0708 105.60 100.09 111.91 1.5430 IC HL3 NL CC5 CC4 1.0308 115.27 -141.75 111.91 1.5430 PRES ALME 1.00 ! C6H13NO2 cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Lysine Methyl Ester CDCA Amide DELETE ATOM CG DELETE ATOM OG1 DELETE ATOM OG2 ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ! OA1 ATOM CA CG2O2 0.90 ! || ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH3(M) ATOM OA2 OG302 -0.49 ! || | ATOM CM CG331 -0.31 ! OH Me21 C22 C24 CC1 CC3 CC5 ATOM HM1 HGA3 0.09 ! | \ / \ / \ / \ / \ / \ ATOM HM2 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CC4 NH3(+1) ATOM HM3 HGA3 0.09 ! / \ | / ATOM CC3 CG321 -0.18 ! C11 C13---C17 ATOM HC3A HGA2 0.09 ! Me19 | | | ATOM HC3B HGA2 0.09 ! C1 | C9 C14 C16 ATOM CC4 CG321 -0.18 ! / \|/ \ / \ / ATOM HC4A HGA2 0.09 ! C2 C10 C8 C15 ATOM HC4B HGA2 0.09 ! | | | ATOM CC5 CG324 0.13 ! C3 C5 C7 ATOM HC5A HGA2 0.09 ! / \ / \ / \ ATOM HC5B HGA2 0.09 ! HO C4 C6 OH ATOM NL NG3P3 -0.30 ATOM HL1 HGP2 0.33 ! Alpha Lysine Methyl Ester CDCA Amide ATOM HL2 HGP2 0.33 ATOM HL3 HGP2 0.33 BOND OA2 CM CM HM1 CM HM2 CM HM3 BOND CC3 CC4 CC4 HC4A CC4 HC4B BOND CC4 CC5 CC5 HC5A CC5 HC5B BOND CC5 NL NL HL1 NL HL2 NL HL3 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CM 1.5257 109.81 -179.93 115.57 1.4395 IC HM1 CM OA2 CA 1.1130 109.51 -178.65 115.57 1.3318 IC HM2 CM OA2 CA 1.1137 111.53 62.15 115.57 1.3318 IC HM3 CM OA2 CA 1.1147 111.32 -60.00 115.57 1.3318 IC CC1 CC2 CC3 CC4 1.5577 114.43 -162.39 114.31 1.5433 IC CC2 CC3 CC4 CC5 1.5429 114.31 -58.57 113.71 1.5434 IC CC5 CC3 *CC4 HC4A 1.5434 113.71 -122.33 108.53 1.1138 IC HC4A CC3 *CC4 HC4B 1.1138 108.53 -116.24 108.97 1.1147 IC CC3 CC4 CC5 NL 1.5433 113.71 -46.10 111.29 1.4903 IC NL CC4 *CC5 HC5A 1.4903 111.29 119.98 110.79 1.1033 IC NL CC4 *CC5 HC5B 1.4903 111.29 -120.90 110.69 1.1030 IC HL1 NL CC5 CC4 1.0382 110.29 -57.73 111.29 1.5434 IC HL2 NL CC5 CC4 1.0532 109.68 61.17 111.29 1.5434 IC HL3 NL CC5 CC4 1.0388 111.18 -179.42 111.29 1.5434 !end bile acids, chayan, dec2006 !Bile acids and related compounds, chayan, may2007 RESI BAB1 -1.00 ! C29H47N2O6 Bile Acid Basic moiety 1 (BASE FOR NEW COMPOUNDS), cacha GROUP ATOM C3 CG311 0.14 ! OG ATOM O3 OG311 -0.65 ! || ATOM H3' HGP1 0.42 ! CG--NT--HT2 ATOM H3 HGA1 0.09 ! / HT1 GROUP ! CC3 ATOM C4 CG321 -0.18 ! \ ATOM H4A HGA2 0.09 ! O24 CC2 ATOM H4B HGA2 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) GROUP ! / \ | / | ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM H7' HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! BAB1 GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM C24 CG2O1 0.51 ATOM O24 OG2D1 -0.51 ATOM N NG2S1 -0.47 ATOM HN HGP1 0.47 GROUP ATOM CC1 CG311 -0.19 ATOM HC1 HGA1 0.09 ATOM CA CG2O3 0.62 ATOM OA1 OG2D2 -0.76 ATOM OA2 OG2D2 -0.76 GROUP ATOM CC2 CG321 -0.18 ATOM HC2A HGA2 0.09 ATOM HC2B HGA2 0.09 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 GROUP ATOM CG CG2O1 0.55 ATOM OG OG2D1 -0.55 ATOM NT NG2S2 -0.62 ATOM HT1 HGP1 0.32 ATOM HT2 HGP1 0.30 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 C24 C24 O24 BOND C24 N N HN BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 BOND CC2 HC2A CC2 HC2B CC2 CC3 BOND CC3 HC3A CC3 HC3B CC3 CG BOND CG OG CG NT NT HT1 NT HT2 IMPR C24 C23 N O24 IMPR CA OA2 OA1 CC1 IMPR CG CC3 NT OG ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on arbitrary CHARMM optimized structure IC C1 C2 C3 C4 1.5325 111.68 -49.45 111.84 1.5383 IC C2 C3 C4 C5 1.5339 111.84 43.93 115.68 1.5598 IC C3 C4 C5 C6 1.5383 115.68 -175.10 109.02 1.5521 IC C4 C5 C6 C7 1.5598 109.02 85.47 114.98 1.5441 IC C5 C6 C7 C8 1.5521 114.98 39.04 113.05 1.5290 IC C7 C8 C9 C10 1.5290 114.08 58.26 109.48 1.5439 IC C8 C9 C10 C1 1.5323 109.48 179.67 111.99 1.5563 IC C9 C10 C1 C2 1.5439 111.99 63.33 113.83 1.5325 IC O3 C3 C4 C5 1.4163 109.09 162.18 115.68 1.5598 IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C2 C3 O3 H3' 1.5339 107.07 70.05 104.87 0.9608 IC C5 C3 *C4 H4A 1.5598 115.68 122.75 108.69 1.1111 IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 IC C10 C4 *C5 H5 1.5279 114.70 116.72 105.03 1.1175 IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 IC C6 C7 C8 C14 1.5441 113.05 -166.95 108.56 1.5542 IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.08 1.5323 IC C7 C8 C14 C13 1.5290 108.56 -174.20 113.13 1.5425 IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5533 IC C17 C14 *C13 C12 1.5731 98.18 119.81 107.46 1.5340 IC C14 C13 C12 C11 1.5425 107.46 55.26 111.18 1.5432 IC C8 C6 *C7 O7 1.5290 113.05 -126.94 107.98 1.4218 IC O7 C6 *C7 H7 1.4218 107.98 -113.62 107.19 1.1164 IC C6 C7 O7 H7' 1.5441 107.98 177.77 105.26 0.9614 IC C9 C7 *C8 H8 1.5323 114.08 122.47 107.18 1.1067 IC C10 C8 *C9 H9 1.5439 109.48 -117.10 106.56 1.1138 IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.88 1.1059 IC H12A C13 *C12 H12B 1.1059 111.88 119.47 108.82 1.1125 IC C13 C8 *C14 H14 1.5425 113.13 -118.30 108.46 1.1150 IC C16 C14 *C15 H15A 1.5435 103.56 119.15 111.17 1.1002 IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 IC C17 C15 *C16 H16A 1.5533 106.91 121.49 110.78 1.0992 IC H16A C15 *C16 H16B 1.0992 110.78 117.20 110.97 1.0999 IC C13 C16 *C17 H17 1.5731 98.41 -112.89 110.39 1.1009 IC C12 C14 *C13 C18 1.5340 107.46 121.97 114.21 1.5526 IC C14 C13 C18 H18A 1.5425 114.21 116.84 111.38 1.1064 IC H18A C13 *C18 H18B 1.1064 111.38 119.04 110.59 1.1085 IC H18A C13 *C18 H18C 1.1064 111.38 -120.17 111.91 1.1058 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C5 C10 C19 H19A 1.5279 109.53 5.08 111.17 1.1079 IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1061 IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 IC C13 C16 *C17 C20 1.5731 98.41 127.01 111.83 1.5649 IC C16 C17 C20 C22 1.5533 111.83 71.96 108.75 1.5519 IC C22 C17 *C20 C21 1.5519 108.75 122.38 112.90 1.5396 IC C21 C17 *C20 H20 1.5396 112.90 120.78 108.89 1.1119 IC C17 C20 C21 H21A 1.5649 112.90 71.88 110.45 1.1079 IC H21A C20 *C21 H21B 1.1079 110.45 -121.55 110.43 1.1103 IC H21A C20 *C21 H21C 1.1079 110.45 118.45 110.89 1.1089 IC C17 C20 C22 C23 1.5649 108.75 -163.10 113.67 1.5524 IC C23 C20 *C22 H22A 1.5524 113.67 119.92 108.15 1.1127 IC H22A C20 *C22 H22B 1.1127 108.15 116.44 108.31 1.1133 IC C20 C22 C23 C24 1.5519 113.67 176.63 114.01 1.5029 IC C24 C22 *C23 H23A 1.5029 114.01 120.77 110.50 1.1097 IC H23A C22 *C23 H23B 1.1097 110.50 118.82 109.42 1.1112 IC C22 C23 C24 N 1.5524 114.01 0.05 116.58 1.3364 IC N C23 *C24 O24 1.3364 116.58 -179.90 119.94 1.2265 IC C23 C24 N CC1 1.5029 116.58 178.79 130.40 1.4446 IC CC1 C24 *N HN 1.4446 130.40 -174.70 123.77 1.0138 IC C24 N CC1 CA 1.3364 130.40 -170.40 102.83 1.5482 IC CA N *CC1 HC1 1.5482 102.83 114.75 109.50 1.1102 IC HC1 N *CC1 CC2 1.1102 109.50 123.68 113.47 1.5536 IC N CC1 CA OA1 1.4446 102.83 178.79 119.90 1.2534 IC OA1 CC1 *CA OA2 1.2534 119.90 177.56 115.53 1.2691 IC N CC1 CC2 CC3 1.4446 113.47 60.10 115.05 1.5552 IC CC3 CC1 *CC2 HC2A 1.5552 115.05 126.07 109.17 1.1118 IC HC2A CC1 *CC2 HC2B 1.1118 109.17 114.51 106.60 1.1142 IC CC1 CC2 CC3 CG 1.5536 115.05 107.73 115.32 1.5034 IC CG CC2 *CC3 HC3A 1.5034 115.32 119.05 108.25 1.1125 IC HC3A CC2 *CC3 HC3B 1.1125 108.25 117.32 110.47 1.1095 IC CC2 CC3 CG NT 1.5552 115.32 -46.42 118.71 1.3503 IC NT CC3 *CG OG 1.3503 118.71 -179.05 119.96 1.2327 IC CC3 CG NT HT2 1.5034 118.71 -177.78 118.60 0.9905 IC HT2 CG *NT HT1 0.9905 118.60 177.52 119.35 1.0169 PRES G4MP 1.00 ! C7H14N2O (01OH03), cacha ! This compund has 4-methylamine piperidine at gamma-position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! OG CG2--CG3 HG41 ATOM OG OG2D1 -0.51 ! || / \ / ATOM NT NG2S1 -0.47 ! CG---NT--CGT--CG1 NG4 (+) ATOM HT1 HGP1 0.47 ! / HT1 \ / \ GROUP ! CC3 CG6--CG5 HG42 ATOM CGT CG321 -0.18 ! \ ATOM HGT1 HGA2 0.09 ! O24 CC2 ATOM HGT2 HGA2 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 ATOM CG1 CG311 -0.09 ! | \ / \ / \ / \ ATOM HG1 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) GROUP ! / \ | / | ATOM CG2 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) ATOM HG21 HGA2 0.09 ! Me19 | | | ATOM HG22 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CG3 CG324 0.20 ! C2 C10 C8 C15 ATOM HG31 HGA2 0.09 ! | | | ATOM HG32 HGA2 0.09 ! C3 C5 C7 ATOM NG4 NG3P2 -0.40 ! / \ / \ / \ ATOM HG41 HGP2 0.32 ! HO C4 C6 OH ATOM HG42 HGP2 0.32 ATOM CG5 CG324 0.20 ! G4MP (01OH03) ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 GROUP ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 NG4 BOND NG4 HG41 NG4 HG42 NG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CGT 1.2271 121.41 13.20 121.99 1.4538 IC CG NT CGT HGT1 1.3456 121.99 88.64 107.55 1.1142 IC HGT1 NT *CGT HGT2 1.1142 107.55 -116.19 111.07 1.1174 IC HGT1 NT *CGT CG1 1.1142 107.55 121.44 115.04 1.5450 IC NT CGT CG1 HG1 1.4538 115.04 77.21 107.27 1.1164 IC HG1 CGT *CG1 CG2 1.1164 107.27 -117.50 111.92 1.5436 IC HG1 CGT *CG1 CG6 1.1164 107.27 118.24 109.86 1.5466 IC CGT CG1 CG2 CG3 1.5450 111.92 -173.65 113.31 1.5201 IC CG3 CG1 *CG2 HG21 1.5201 113.31 123.02 108.94 1.1140 IC CG3 CG1 *CG2 HG22 1.5201 113.31 -119.66 109.16 1.1145 IC CG1 CG2 CG3 NG4 1.5436 113.31 55.01 108.23 1.5017 IC NG4 CG2 *CG3 HG31 1.5017 108.23 116.95 112.61 1.1038 IC NG4 CG2 *CG3 HG32 1.5017 108.23 -117.23 113.22 1.1028 IC CG2 CG3 NG4 CG5 1.5201 108.23 -61.48 112.36 1.5048 IC CG5 CG3 *NG4 HG41 1.5048 112.36 118.67 107.00 1.0106 IC CG5 CG3 *NG4 HG42 1.5048 112.36 -125.21 110.67 1.0050 IC CG3 NG4 CG5 CG6 1.5017 112.36 62.10 109.26 1.5264 IC CG6 NG4 *CG5 HG51 1.5264 109.26 121.78 105.74 1.1029 IC CG6 NG4 *CG5 HG52 1.5264 109.26 -121.65 105.59 1.1034 IC CG5 CG1 *CG6 HG61 1.5264 111.91 -121.76 108.69 1.1133 IC CG5 CG1 *CG6 HG62 1.5264 111.91 121.65 108.91 1.1129 PRES G4MPAB 1.00 ! C16H22N2O3 (010203D), cacha ! This compound has 4-methylamine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ! OG CG2--CG3 HG41 ATOM NT NG2S1 -0.47 ! || / \ / ATOM HT1 HGP1 0.47 ! CG---NT--CGT--CG1 NG4 (+) GROUP ! / HT1 \ / \ ATOM CGT CG321 -0.18 ! CC3 CG6--CG5 HG42 ATOM HGT1 HGA2 0.09 ! \ ATOM HGT2 HGA2 0.09 ! O24 CC2 GROUP ! || / ATOM CG1 CG311 -0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG1 HGA1 0.09 ! | \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CA--OA2--CB--CZ CP ATOM CG2 CG321 -0.18 ! / \ | / || \ __ / ATOM HG21 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 ATOM HG22 HGA2 0.09 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CG3 CG324 0.20 ! / \|/ \ / \ / ATOM HG31 HGA2 0.09 ! C2 C10 C8 C15 ATOM HG32 HGA2 0.09 ! | | | ATOM NG4 NG3P2 -0.40 ! C3 C5 C7 ATOM HG41 HGP2 0.32 ! / \ / \ / \ ATOM HG42 HGP2 0.32 ! HO C4 C6 OH ATOM CG5 CG324 0.20 ATOM HG51 HGA2 0.09 ! G4MPAB (010203D) ATOM HG52 HGA2 0.09 GROUP ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 NG4 BOND NG4 HG41 NG4 HG42 NG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5235 109.54 -176.41 116.53 1.4472 IC CA OA2 CB HB1 1.3360 116.53 -64.48 110.30 1.1156 IC CA OA2 CB CZ 1.3360 116.53 176.13 113.68 1.5063 IC CA OA2 CB HB2 1.3360 116.53 54.52 110.72 1.1160 IC OA2 CB CZ CD2 1.4472 113.68 -117.39 121.22 1.4060 IC OA2 CB CZ CD1 1.4472 113.68 62.45 119.30 1.4048 IC CD1 CD2 *CZ CB 1.4048 119.48 179.84 121.22 1.5063 IC CD2 CZ CB HB1 1.4060 121.22 121.02 106.39 1.1156 IC CD2 CZ CB HB2 1.4060 121.22 5.79 107.87 1.1160 IC CB CZ CD1 CE1 1.5063 119.30 179.52 120.29 1.4015 IC CB CZ CD2 CE2 1.5063 121.22 -179.50 120.19 1.4018 IC CZ CD1 CE1 CP 1.4048 120.29 0.00 119.94 1.4007 IC CD1 CE1 CP CE2 1.4015 119.94 0.62 120.09 1.4005 IC CE1 CP CE2 CD2 1.4007 120.09 -0.61 120.00 1.4018 IC CE1 CZ *CD1 HD1 1.4015 120.29 -179.48 119.81 1.0800 IC CE2 CZ *CD2 HD2 1.4018 120.19 179.40 120.20 1.0796 IC CP CD1 *CE1 HE1 1.4007 119.94 -179.57 120.13 1.0809 IC CP CD2 *CE2 HE2 1.4005 120.00 179.35 120.25 1.0815 IC CE1 CE2 *CP HP 1.4007 120.09 -179.52 119.77 1.0816 IC OG CG NT CGT 1.2237 121.80 2.70 123.40 1.4463 IC CG NT CGT HGT1 1.3437 123.40 165.76 109.15 1.1140 IC HGT1 NT *CGT HGT2 1.1140 109.15 -116.48 109.48 1.1169 IC HGT1 NT *CGT CG1 1.1140 109.15 121.76 113.44 1.5425 IC NT CGT CG1 HG1 1.4463 113.44 57.56 106.98 1.1180 IC HG1 CGT *CG1 CG2 1.1180 106.98 -118.28 112.49 1.5449 IC HG1 CGT *CG1 CG6 1.1180 106.98 116.87 111.08 1.5446 IC CGT CG1 CG2 CG3 1.5425 112.49 179.28 110.63 1.5296 IC CG3 CG1 *CG2 HG21 1.5296 110.63 122.32 109.32 1.1119 IC CG3 CG1 *CG2 HG22 1.5296 110.63 -120.00 109.52 1.1129 IC CG1 CG2 CG3 NG4 1.5449 110.63 55.35 110.03 1.5090 IC NG4 CG2 *CG3 HG31 1.5090 110.03 117.95 113.07 1.1028 IC NG4 CG2 *CG3 HG32 1.5090 110.03 -117.03 112.44 1.1041 IC CG2 CG3 NG4 CG5 1.5296 110.03 -57.44 113.44 1.5087 IC CG5 CG3 *NG4 HG41 1.5087 113.44 120.02 108.22 1.0087 IC CG5 CG3 *NG4 HG42 1.5087 113.44 -123.98 110.17 1.0071 IC CG3 NG4 CG5 CG6 1.5090 113.44 57.59 109.66 1.5282 IC CG6 NG4 *CG5 HG51 1.5282 109.66 122.28 105.76 1.1029 IC CG6 NG4 *CG5 HG52 1.5282 109.66 -121.41 105.40 1.1040 IC CG5 CG1 *CG6 HG61 1.5282 110.78 -122.43 109.37 1.1120 IC CG5 CG1 *CG6 HG62 1.5282 110.78 120.30 108.99 1.1138 PRES G4P 1.00 ! C6H12N2O (01OH02), cacha ! This compound has 4-amine piperidine at gamma position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! OG CG2--CG3 HG41 ATOM OG OG2D1 -0.51 ! || / \ / ATOM NT NG2S1 -0.47 ! CG--NT--CG1 NG4 ATOM HT1 HGP1 0.47 ! / HT1 \ / \ GROUP ! CC3 CG6--CG5 HG42 ATOM CG1 CG311 -0.09 ! \ ATOM HG1 HGA1 0.09 ! O24 CC2 GROUP ! || / ATOM CG2 CG321 -0.18 ! H Me21 C22 C24 CC1 ATOM HG21 HGA2 0.09 ! | \ / \ / \ / \ ATOM HG22 HGA2 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) GROUP ! / \ | / | ATOM CG3 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) ATOM HG31 HGA2 0.09 ! Me19 | | | ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 ATOM NG4 NG3P2 -0.40 ! / \|/ \ / \ / ATOM HG41 HGP2 0.32 ! C2 C10 C8 C15 ATOM HG42 HGP2 0.32 ! | | | ATOM CG5 CG324 0.20 ! C3 C5 C7 ATOM HG51 HGA2 0.09 ! / \ / \ / \ ATOM HG52 HGA2 0.09 ! HO C4 C6 OH GROUP ATOM CG6 CG321 -0.18 ! G4P (01OH02) ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 BOND NT CG1 CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 NG4 BOND NG4 HG41 NG4 HG42 NG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CG1 1.2252 121.32 5.10 125.38 1.4376 IC CG NT CG1 HG1 1.3388 125.38 -51.92 107.87 1.1178 IC HG1 NT *CG1 CG2 1.1178 107.87 -118.28 109.63 1.5451 IC HG1 NT *CG1 CG6 1.1178 107.87 120.36 111.16 1.5418 IC NT CG1 CG2 CG3 1.4376 109.63 -92.37 112.88 1.5415 IC CG3 CG1 *CG2 HG21 1.5415 112.88 121.50 108.63 1.1130 IC CG3 CG1 *CG2 HG22 1.5415 112.88 -121.67 109.79 1.1112 IC CG1 CG2 CG3 NG4 1.5451 112.88 27.90 112.58 1.5035 IC NG4 CG2 *CG3 HG31 1.5035 112.58 118.55 112.20 1.1031 IC NG4 CG2 *CG3 HG32 1.5035 112.58 -117.34 112.10 1.1033 IC CG2 CG3 NG4 CG5 1.5415 112.58 -56.71 115.17 1.5102 IC CG5 CG3 *NG4 HG41 1.5102 115.17 117.55 107.51 1.0298 IC CG5 CG3 *NG4 HG42 1.5102 115.17 -129.75 113.29 1.0008 IC CG3 NG4 CG5 CG6 1.5035 115.17 21.27 111.60 1.5345 IC CG6 NG4 *CG5 HG51 1.5345 111.60 121.58 104.25 1.1051 IC CG6 NG4 *CG5 HG52 1.5345 111.60 -123.20 105.77 1.1005 IC CG5 CG1 *CG6 HG61 1.5345 110.88 -120.54 109.69 1.1126 IC CG5 CG1 *CG6 HG62 1.5345 110.88 122.25 109.27 1.1110 PRES G4PAB 1.00 ! C15H20N2O3 (010202D), cacha ! This compound has 4-amine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ! OG CG2--CG3 HG41 ATOM NT NG2S1 -0.47 ! || / \ / ATOM HT1 HGP1 0.47 ! CG--NT--CG1 NG4 (+) GROUP ! / HT1 \ / \ ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 HG42 ATOM HG1 HGA1 0.09 ! \ GROUP ! O24 CC2 ATOM CG2 CG321 -0.18 ! || / ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CA--OA2--CB--CZ CP ATOM CG3 CG324 0.20 ! / \ | / || \ __ / ATOM HG31 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 ATOM HG32 HGA2 0.09 ! Me19 | | | ATOM NG4 NG3P2 -0.40 ! C1 | C9 C14 C16 ATOM HG41 HGP2 0.32 ! / \|/ \ / \ / ATOM HG42 HGP2 0.32 ! C2 C10 C8 C15 ATOM CG5 CG324 0.20 ! | | | ATOM HG51 HGA2 0.09 ! C3 C5 C7 ATOM HG52 HGA2 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ! G4PAB (010202D) ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CG1 CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 NG4 BOND NG4 HG41 NG4 HG42 NG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB BOND CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5231 109.59 -176.73 116.72 1.4465 IC HB1 CB OA2 CA 1.1156 110.71 55.90 116.72 1.3350 IC HB2 CB OA2 CA 1.1156 110.36 -63.25 116.72 1.3350 IC CZ CB OA2 CA 1.5059 113.59 177.35 116.72 1.3350 IC CD2 CZ CB OA2 1.4060 121.17 -112.96 113.59 1.4465 IC CD1 CZ CB OA2 1.4048 119.33 66.62 113.59 1.4465 IC CD1 CD2 *CZ CB 1.4048 119.49 179.58 121.17 1.5059 IC CD2 CZ CB HB1 1.4060 121.17 10.10 107.80 1.1156 IC CD2 CZ CB HB2 1.4060 121.17 125.42 106.41 1.1156 IC CB CZ CD1 CE1 1.5059 119.33 179.62 120.28 1.4015 IC CB CZ CD2 CE2 1.5059 121.17 -179.61 120.18 1.4018 IC CZ CD1 CE1 CP 1.4048 120.28 0.06 119.94 1.4006 IC CD1 CE1 CP CE2 1.4015 119.94 0.67 120.09 1.4005 IC CE1 CP CE2 CD2 1.4006 120.09 -0.65 120.00 1.4018 IC CE1 CZ *CD1 HD1 1.4015 120.28 -179.55 119.88 1.0800 IC CE2 CZ *CD2 HD2 1.4018 120.18 179.50 120.27 1.0795 IC CP CD1 *CE1 HE1 1.4006 119.94 -179.64 120.14 1.0810 IC CP CD2 *CE2 HE2 1.4005 120.00 179.44 120.29 1.0816 IC CE1 CE2 *CP HP 1.4006 120.09 -179.41 119.77 1.0817 IC OG CG NT CG1 1.2229 121.22 -0.98 123.49 1.4328 IC CG NT CG1 HG1 1.3417 123.49 42.04 108.39 1.1209 IC HG1 NT *CG1 CG2 1.1209 108.39 -119.14 110.90 1.5409 IC HG1 NT *CG1 CG6 1.1209 108.39 118.05 110.60 1.5391 IC NT CG1 CG2 CG3 1.4328 110.90 179.86 110.81 1.5271 IC CG3 CG1 *CG2 HG21 1.5271 110.81 122.78 109.51 1.1117 IC CG3 CG1 *CG2 HG22 1.5271 110.81 -120.05 109.07 1.1144 IC CG1 CG2 CG3 NG4 1.5409 110.81 56.29 109.54 1.5089 IC NG4 CG2 *CG3 HG31 1.5089 109.54 117.78 113.14 1.1028 IC NG4 CG2 *CG3 HG32 1.5089 109.54 -116.99 112.54 1.1039 IC CG2 CG3 NG4 CG5 1.5271 109.54 -57.03 113.50 1.5096 IC CG5 CG3 *NG4 HG41 1.5096 113.50 120.09 108.06 1.0087 IC CG5 CG3 *NG4 HG42 1.5096 113.50 -124.10 110.07 1.0071 IC CG3 NG4 CG5 CG6 1.5089 113.50 56.82 110.03 1.5304 IC CG6 NG4 *CG5 HG51 1.5304 110.03 122.41 105.69 1.1028 IC CG6 NG4 *CG5 HG52 1.5304 110.03 -121.42 105.25 1.1040 IC CG5 CG1 *CG6 HG61 1.5304 110.58 -122.01 109.49 1.1127 IC CG5 CG1 *CG6 HG62 1.5304 110.58 120.54 109.24 1.1133 PRES G3PR 1.00 ! C6H12N2O (01OH04(R)), cacha ! Check IC table ! This compound has 3-amine piperidine at gamma position ! core residue Bile Acid Basic moiety 1 (BAB1) ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! HG31 ATOM OG OG2D1 -0.51 ! | ATOM NT NG2S1 -0.47 ! OG CG2--NG3(+1)--HG32 ATOM HT1 HGP1 0.47 ! || / \ GROUP ! CG--NT--CG1 CG4 ATOM CG1 CG311 -0.09 ! / HT1 \ / ATOM HG1 HGA1 0.09 ! CC3 CG6--CG5 GROUP ! \ ATOM CG2 CG324 0.20 ! O24 CC2 ATOM HG21 HGA2 0.09 ! || / ATOM HG22 HGA2 0.09 ! H Me21 C22 C24 CC1 ATOM NG3 NG3P2 -0.40 ! | \ / \ / \ / \ ATOM HG31 HGP2 0.32 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) ATOM HG32 HGP2 0.32 ! / \ | / | ATOM CG4 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) ATOM HG41 HGA2 0.09 ! Me19 | | | ATOM HG42 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CG5 CG321 -0.18 ! C2 C10 C8 C15 ATOM HG51 HGA2 0.09 ! | | | ATOM HG52 HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CG6 CG321 -0.18 ! HO C4 C6 OH ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 ! G3PR (01OH04(R)) BOND NT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC CC3 CG NT CG1 1.5047 118.90 -176.48 124.61 1.4438 IC CG NT CG1 HG1 1.3378 124.61 -36.75 108.87 1.1179 IC HG1 NT *CG1 CG2 1.1179 108.87 119.19 110.98 1.5420 ! for R config IC HG1 NT *CG1 CG6 1.1179 108.87 -118.11 109.81 1.5506 ! for R config IC NT CG1 CG2 NG3 1.4438 110.98 74.30 110.11 1.5058 ! for R config IC NG3 CG1 *CG2 HG21 1.5058 110.11 118.33 113.56 1.0998 IC NG3 CG1 *CG2 HG22 1.5058 110.11 -116.73 111.83 1.1032 IC CG1 CG2 NG3 CG4 1.5420 110.11 58.73 115.65 1.5046 IC CG4 CG2 *NG3 HG31 1.5046 115.65 131.36 112.19 1.0010 IC CG4 CG2 *NG3 HG32 1.5046 115.65 -117.57 105.76 1.0308 IC CG2 NG3 CG4 CG5 1.5058 115.65 -9.08 111.13 1.5355 IC CG5 NG3 *CG4 HG41 1.5355 111.13 123.33 105.76 1.1009 IC CG5 NG3 *CG4 HG42 1.5355 111.13 -121.08 104.21 1.1056 IC NG3 CG4 CG5 CG6 1.5046 111.13 -47.06 110.56 1.5411 IC CG6 CG4 *CG5 HG51 1.5411 110.56 122.13 110.68 1.1119 IC CG6 CG4 *CG5 HG52 1.5411 110.56 -120.28 109.02 1.1129 IC CG5 CG1 *CG6 HG61 1.5411 113.66 -123.82 109.48 1.1121 IC CG5 CG1 *CG6 HG62 1.5411 113.66 119.91 108.64 1.1155 PRES G3PS 1.00 ! C6H12N2O (01OH04(S)), cacha ! Check IC table ! This compound has 3-amine piperidine at gamma position ! core residue Bile Acid Basic moiety 1 (BAB1) ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! HG31 ATOM OG OG2D1 -0.51 ! | ATOM NT NG2S1 -0.47 ! OG CG2--NG3(+1)--HG32 ATOM HT1 HGP1 0.47 ! || / \ GROUP ! CG--NT--CG1 CG4 ATOM CG1 CG311 -0.09 ! / HT1 \ / ATOM HG1 HGA1 0.09 ! CC3 CG6--CG5 GROUP ! \ ATOM CG2 CG324 0.20 ! O24 CC2 ATOM HG21 HGA2 0.09 ! || / ATOM HG22 HGA2 0.09 ! H Me21 C22 C24 CC1 ATOM NG3 NG3P2 -0.40 ! | \ / \ / \ / \ ATOM HG31 HGP2 0.32 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) ATOM HG32 HGP2 0.32 ! / \ | / | ATOM CG4 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) ATOM HG41 HGA2 0.09 ! Me19 | | | ATOM HG42 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CG5 CG321 -0.18 ! C2 C10 C8 C15 ATOM HG51 HGA2 0.09 ! | | | ATOM HG52 HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CG6 CG321 -0.18 ! HO C4 C6 OH ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 ! G3PS (01OH04(S)) BOND NT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC CC3 CG NT CG1 1.5067 118.82 -168.68 125.46 1.4406 IC CG NT CG1 HG1 1.3336 125.46 -54.62 108.34 1.1153 IC HG1 NT *CG1 CG2 1.1153 108.34 -120.60 110.10 1.5378 ! for S config IC HG1 NT *CG1 CG6 1.1153 108.34 119.57 110.63 1.5471 ! for S config IC NT CG1 CG2 NG3 1.4406 110.10 -175.03 112.25 1.5062 ! for S config IC NG3 CG1 *CG2 HG21 1.5062 112.25 116.92 111.42 1.1050 IC NG3 CG1 *CG2 HG22 1.5062 112.25 -120.00 112.62 1.1009 IC CG1 CG2 NG3 CG4 1.5378 112.25 58.60 112.03 1.5047 IC CG4 CG2 *NG3 HG31 1.5047 112.03 122.85 109.11 1.0062 IC CG4 CG2 *NG3 HG32 1.5047 112.03 -120.61 108.23 1.0067 IC CG2 NG3 CG4 CG5 1.5062 112.03 -59.03 109.25 1.5284 IC CG5 NG3 *CG4 HG41 1.5284 109.25 120.95 105.28 1.1051 IC CG5 NG3 *CG4 HG42 1.5284 109.25 -122.37 105.83 1.1021 IC NG3 CG4 CG5 CG6 1.5047 109.25 57.37 110.27 1.5380 IC CG6 CG4 *CG5 HG51 1.5380 110.27 120.37 109.44 1.1129 IC CG6 CG4 *CG5 HG52 1.5380 110.27 -121.28 110.59 1.1129 IC CG5 CG1 *CG6 HG61 1.5380 112.70 -121.55 108.33 1.1151 IC CG5 CG1 *CG6 HG62 1.5380 112.70 122.04 109.35 1.1123 PRES G3PABR 1.00 ! C15H20N2O3 (010204(R)D), cacha ! check IC table ! This compound has 3-amine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ! HG31 ATOM HT1 HGP1 0.47 ! | GROUP ! OG CG2--NG3(+1)--HG32 ATOM CG1 CG311 -0.09 ! || / \ ATOM HG1 HGA1 0.09 ! CG---NT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG2 CG324 0.20 ! CC3 CG6--CG5 ATOM HG21 HGA2 0.09 ! \ ATOM HG22 HGA2 0.09 ! O24 CC2 ATOM NG3 NG3P2 -0.40 ! || / ATOM HG31 HGP2 0.32 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG32 HGP2 0.32 ! | \ / \ / \ / \ // \\ ATOM CG4 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG41 HGA2 0.09 ! / \ | / || \ __ / ATOM HG42 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 GROUP ! Me19 | | | ATOM CG5 CG321 -0.18 ! C1 | C9 C14 C16 ATOM HG51 HGA2 0.09 ! / \|/ \ / \ / ATOM HG52 HGA2 0.09 ! C2 C10 C8 C15 GROUP ! | | | ATOM CG6 CG321 -0.18 ! C3 C5 C7 ATOM HG61 HGA2 0.09 ! / \ / \ / \ ATOM HG62 HGA2 0.09 ! HO C4 C6 OH GROUP ATOM CC1 CG311 0.17 ! G3PABR (010204(R)D) ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CG1 CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5247 109.30 -176.15 116.76 1.4477 IC HB1 CB OA2 CA 1.1153 110.11 -68.10 116.76 1.3346 IC HB2 CB OA2 CA 1.1158 110.89 51.00 116.76 1.3346 IC CZ CB OA2 CA 1.5068 113.78 172.70 116.76 1.3346 IC CD2 CZ CB OA2 1.4048 119.29 56.49 113.78 1.4477 IC CD1 CZ CB OA2 1.4063 121.26 -123.70 113.78 1.4477 IC CD1 CD2 *CZ CB 1.4063 119.45 179.81 119.29 1.5068 IC CD2 CZ CB HB1 1.4048 119.29 -64.86 106.30 1.1153 IC CD2 CZ CB HB2 1.4048 119.29 179.89 107.79 1.1158 IC CB CZ CD1 CE1 1.5068 121.26 -179.38 120.20 1.4018 IC CB CZ CD2 CE2 1.5068 119.29 179.41 120.31 1.4014 IC CZ CD1 CE1 CP 1.4063 120.20 0.03 120.00 1.4005 IC CD1 CE1 CP CE2 1.4018 120.00 -0.52 120.09 1.4006 IC CE1 CP CE2 CD2 1.4005 120.09 0.55 119.94 1.4014 IC CE1 CZ *CD1 HD1 1.4018 120.20 179.30 120.24 1.0794 IC CE2 CZ *CD2 HD2 1.4014 120.31 -179.45 119.81 1.0801 IC CP CD1 *CE1 HE1 1.4005 120.00 179.28 120.29 1.0816 IC CP CD2 *CE2 HE2 1.4006 119.94 -179.51 120.12 1.0810 IC CE1 CE2 *CP HP 1.4005 120.09 179.59 120.13 1.0815 IC CC3 CG NT CG1 1.5011 116.88 179.73 129.61 1.4554 IC CG NT CG1 HG1 1.3471 129.61 -155.34 103.59 1.1192 IC HG1 NT *CG1 CG2 1.1192 103.59 116.28 117.90 1.5488 ! for R config IC HG1 NT *CG1 CG6 1.1192 103.59 -114.20 112.24 1.5460 ! for R config IC NT CG1 CG2 NG3 1.4554 117.90 78.28 110.69 1.5102 ! for R config IC NG3 CG1 *CG2 HG21 1.5102 110.69 116.99 112.30 1.1021 IC NG3 CG1 *CG2 HG22 1.5102 110.69 -118.04 112.47 1.1014 IC CG1 CG2 NG3 CG4 1.5488 110.69 56.48 114.54 1.5050 IC CG4 CG2 *NG3 HG31 1.5050 114.54 128.88 111.74 1.0037 IC CG4 CG2 *NG3 HG32 1.5050 114.54 -116.54 104.32 1.0232 IC CG2 NG3 CG4 CG5 1.5102 114.54 -57.39 109.28 1.5325 IC CG5 NG3 *CG4 HG41 1.5325 109.28 121.77 105.46 1.1028 IC CG5 NG3 *CG4 HG42 1.5325 109.28 -121.69 105.58 1.1031 IC NG3 CG4 CG5 CG6 1.5050 109.28 55.18 111.03 1.5405 IC CG6 CG4 *CG5 HG51 1.5405 111.03 121.20 109.59 1.1130 IC CG6 CG4 *CG5 HG52 1.5405 111.03 -121.12 109.77 1.1134 IC CG5 CG1 *CG6 HG61 1.5405 112.67 -120.64 108.98 1.1142 IC CG5 CG1 *CG6 HG62 1.5405 112.67 122.50 109.46 1.1133 PRES G3PABS 1.00 ! C15H20N2O3 (010204(S)D), cacha ! check IC table ! This compound has 3-amine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ! HG31 ATOM HT1 HGP1 0.47 ! | GROUP ! OG CG2--NG3(+1)--HG32 ATOM CG1 CG311 -0.09 ! || / \ ATOM HG1 HGA1 0.09 ! CG---NT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG2 CG324 0.20 ! CC3 CG6--CG5 ATOM HG21 HGA2 0.09 ! \ ATOM HG22 HGA2 0.09 ! O24 CC2 ATOM NG3 NG3P2 -0.40 ! || / ATOM HG31 HGP2 0.32 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG32 HGP2 0.32 ! | \ / \ / \ / \ // \\ ATOM CG4 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG41 HGA2 0.09 ! / \ | / || \ __ / ATOM HG42 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 GROUP ! Me19 | | | ATOM CG5 CG321 -0.18 ! C1 | C9 C14 C16 ATOM HG51 HGA2 0.09 ! / \|/ \ / \ / ATOM HG52 HGA2 0.09 ! C2 C10 C8 C15 GROUP ! | | | ATOM CG6 CG321 -0.18 ! C3 C5 C7 ATOM HG61 HGA2 0.09 ! / \ / \ / \ ATOM HG62 HGA2 0.09 ! HO C4 C6 OH GROUP ATOM CC1 CG311 0.17 ! G3PABS (010204(R)D) ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CG1 CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5355 110.33 173.10 116.65 1.4498 IC HB1 CB OA2 CA 1.1133 107.66 -159.94 116.65 1.3360 IC HB2 CB OA2 CA 1.1172 110.84 -45.26 116.65 1.3360 IC CZ CB OA2 CA 1.5124 117.67 81.14 116.65 1.3360 IC CD2 CZ CB OA2 1.4046 119.99 -124.81 117.67 1.4498 IC CD1 CZ CB OA2 1.4055 120.38 59.26 117.67 1.4498 IC CD1 CD2 *CZ CB 1.4055 119.50 -175.97 119.99 1.5124 IC CD2 CZ CB HB1 1.4046 119.99 115.14 105.50 1.1133 IC CD2 CZ CB HB2 1.4046 119.99 2.48 109.03 1.1172 IC CB CZ CD1 CE1 1.5124 120.38 174.84 120.09 1.4034 IC CB CZ CD2 CE2 1.5124 119.99 -174.60 120.33 1.4000 IC CZ CD1 CE1 CP 1.4055 120.09 0.17 120.04 1.4001 IC CD1 CE1 CP CE2 1.4034 120.04 0.53 120.04 1.4004 IC CE1 CP CE2 CD2 1.4001 120.04 -0.28 119.98 1.4000 IC CE1 CZ *CD1 HD1 1.4034 120.09 -177.48 119.41 1.0806 IC CE2 CZ *CD2 HD2 1.4000 120.33 177.84 119.72 1.0808 IC CP CD1 *CE1 HE1 1.4001 120.04 -177.24 120.45 1.0791 IC CP CD2 *CE2 HE2 1.4004 119.98 178.76 119.77 1.0812 IC CE1 CE2 *CP HP 1.4001 120.04 178.32 119.79 1.0802 IC CC3 CG NT CG1 1.4955 118.65 -174.99 125.29 1.4513 IC CG NT CG1 HG1 1.3420 125.29 72.25 106.27 1.1180 IC HG1 NT *CG1 CG2 1.1180 106.27 -120.59 116.06 1.5481 ! for S config IC HG1 NT *CG1 CG6 1.1180 106.27 116.21 109.65 1.5438 ! for S config IC NT CG1 CG2 NG3 1.4513 116.06 -178.87 111.82 1.5083 ! for S config IC NG3 CG1 *CG2 HG21 1.5083 111.82 118.34 112.32 1.1010 IC NG3 CG1 *CG2 HG22 1.5083 111.82 -117.38 113.04 1.1005 IC CG1 CG2 NG3 CG4 1.5481 111.82 58.07 113.36 1.5025 IC CG4 CG2 *NG3 HG31 1.5025 113.36 123.57 108.79 1.0183 IC CG4 CG2 *NG3 HG32 1.5025 113.36 -121.13 108.70 1.0090 IC CG2 NG3 CG4 CG5 1.5083 113.36 -55.74 109.81 1.5325 IC CG5 NG3 *CG4 HG41 1.5325 109.81 121.56 105.19 1.1030 IC CG5 NG3 *CG4 HG42 1.5325 109.81 -122.34 105.61 1.1031 IC NG3 CG4 CG5 CG6 1.5025 109.81 53.37 112.00 1.5423 IC CG6 CG4 *CG5 HG51 1.5423 112.00 121.73 109.45 1.1131 IC CG6 CG4 *CG5 HG52 1.5423 112.00 -121.07 109.56 1.1110 IC CG5 CG1 *CG6 HG61 1.5423 112.61 -121.49 109.20 1.1133 IC CG5 CG1 *CG6 HG62 1.5423 112.61 121.00 109.29 1.1144 !end bile acids, chayan, may2007 !fatty acid binding protein inhibitors, chayan, may2007 RESI FBIB -1.00 ! C12H15O3 Fatty acid Binding protein Inhibitor B, cacha ! This is a phenyl derivative having ! dimethyl at 2 and ethyl acetate at 4 position GROUP ATOM CG CG2R61 0.00 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! (-0.5)OD1 HA1 HB1 CD1--CE1 ATOM HD1 HGR61 0.115 ! \ | | // \\ GROUP ! CD--CA--CB--CG CZ--OH ATOM CD2 CG2R61 -0.115 ! / | | \ __ / \ ATOM HD2 HGR61 0.115 ! (-0.5)OD2 HA2 HB2 CD2--CE2 HH GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 CC--C1(Me) ATOM HE1 HGR61 0.115 ! | GROUP ! C2(Me) ATOM CE2 CG2R61 0.00 GROUP ! COMPOUND "FBIB" ATOM CC CG311 -0.09 ATOM HC HGA1 0.09 ATOM C1 CG331 -0.27 ATOM H1A HGA3 0.09 ATOM H1B HGA3 0.09 ATOM H1C HGA3 0.09 ATOM C2 CG331 -0.27 ATOM H2A HGA3 0.09 ATOM H2B HGA3 0.09 ATOM H2C HGA3 0.09 GROUP ATOM CZ CG2R61 0.11 ATOM OH OG311 -0.53 ATOM HH HGP1 0.42 GROUP ATOM CB CG321 -0.18 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CA CG321 -0.28 ATOM HA1 HGA2 0.09 ATOM HA2 HGA2 0.09 ATOM CD CG2O3 0.62 ATOM OD1 OG2D2 -0.76 ATOM OD2 OG2D2 -0.76 BOND CG CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ BOND CG CD2 CD2 HD2 CD2 CE2 CE2 CC CE2 CZ BOND CG CB CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA CD CD OD1 CD OD2 BOND CC HC CC C1 CC C2 BOND C1 H1A C1 H1B C1 H1C BOND C2 H2A C2 H2B C2 H2C BOND CZ OH OH HH IMPR CD OD2 OD1 CA IC CG CD1 CE1 CZ 1.4003 119.98 -0.26 120.25 1.3984 IC CD1 CE1 CZ CE2 1.4003 120.25 -0.01 120.56 1.4166 IC CE1 CZ CE2 CD2 1.3984 120.56 0.13 118.30 1.4085 IC CD1 CD2 *CG CB 1.4003 119.77 -179.27 119.58 1.5048 IC CE1 CG *CD1 HD1 1.4003 119.98 -179.56 119.47 1.0801 IC CE2 CG *CD2 HD2 1.4085 121.14 179.42 118.28 1.0793 IC CZ CD1 *CE1 HE1 1.3984 120.25 -179.58 119.97 1.0797 IC CZ CD2 *CE2 CC 1.4166 118.30 179.70 119.43 1.5244 IC CD2 CE2 CC C1 1.4085 119.43 -61.92 108.96 1.5426 IC C1 CE2 *CC C2 1.5426 108.96 122.45 109.20 1.5429 IC C1 CE2 *CC HC 1.5426 108.96 -118.75 112.03 1.1131 IC CE2 CC C1 H1A 1.5244 108.96 -177.62 110.22 1.1101 IC H1A CC *C1 H1B 1.1101 110.22 120.09 110.82 1.1111 IC H1A CC *C1 H1C 1.1101 110.22 -119.54 111.08 1.1110 IC CE2 CC C2 H2A 1.5244 109.20 177.34 110.11 1.1103 IC H2A CC *C2 H2B 1.1103 110.11 119.41 111.04 1.1107 IC H2A CC *C2 H2C 1.1103 110.11 -120.01 110.78 1.1110 IC CE1 CE2 *CZ OH 1.3984 120.56 179.54 121.85 1.4123 IC CE1 CZ OH HH 1.3984 117.60 176.63 106.54 0.9574 IC CD2 CG CB HB1 1.4003 119.58 -159.98 109.56 1.1132 IC CD2 CG CB HB2 1.4003 119.58 -41.93 108.74 1.1119 IC CD2 CG CB CA 1.4003 119.58 79.08 109.99 1.5472 IC CG CB CA HA1 1.5048 109.99 61.87 110.80 1.1089 IC CG CB CA HA2 1.5048 109.99 -59.13 110.94 1.1090 IC CG CB CA CD 1.5048 109.99 -179.13 111.18 1.5290 IC CB CA CD OD1 1.5472 111.18 124.07 117.29 1.2587 IC OD1 CA *CD OD2 1.2587 117.29 167.13 117.17 1.2586 PRES FBIA 0.00 ! CH3 Fatty acid Binding protein Inhibitor A, cacha ! This is a phenyl derivative having ! methyl at 2 and ethyl acetate at 4 position ! patch combination: ! core residue Compound "FBIB" >> Compound "FBIA" DELETE ATOM CC ! HD1 HE1 DELETE ATOM HC ! | | DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 DELETE ATOM H1A ! \ | | // \\ DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH DELETE ATOM H1C ! / | | \ __ / \ DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 HH DELETE ATOM H2A ! | | DELETE ATOM H2B ! HD2 CM(Me) DELETE ATOM H2C GROUP ! COMPOUND "FBIA" ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CE2 CM CM HM1 CM HM2 CM HM3 IC CZ CD2 *CE2 CM 1.4166 118.30 179.70 119.43 1.5244 IC CD2 CE2 CM HM1 1.4085 119.43 -118.92 108.96 1.1426 IC HM1 CE2 *CM HM2 1.1426 108.96 122.45 109.20 1.1429 IC HM1 CE2 *CM HM3 1.1426 108.96 -118.75 112.03 1.1131 !PRES FBICR 0.00 ! Fatty acid Binding protein Inhibitor, R-isomer, cacha PRES FBICS 0.00 ! C2H5 Fatty acid Binding protein Inhibitor, S-isomer, cacha ! This is a phenyl derivative having ! 2-methyl ethyl acetate at 4 position ! core residue "FBIB" >> Compound "FBICR" or Compound "FBICS" ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration ! Specific configuration can be obtained by commenting/uncommenting corresponding IC values ! as described in the IC table DELETE ATOM CB ! HD1 HE1 DELETE ATOM HB1 ! | | DELETE ATOM HB2 ! (-0.5)OD1 HA1 CM CD1--CE1 DELETE ATOM CC ! \ | | // \\ DELETE ATOM HC ! CD--CA--CBA--CG CZ--OH DELETE ATOM C1 ! / | | \ __ / \ DELETE ATOM H1A ! (-0.5)OD2 HA2 HBA CD2--CE2 HH DELETE ATOM H1B ! | | DELETE ATOM H1C ! HD2 HE2 DELETE ATOM C2 DELETE ATOM H2A ! COMPOUND "FBICR" OR "FBICS" DELETE ATOM H2B DELETE ATOM H2C GROUP ATOM HE2 HGR61 0.00 GROUP ATOM CBA CG311 -0.09 ATOM HBA HGA1 0.09 ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CE2 HE2 BOND CG CBA CBA HBA CBA CM CM HM1 CM HM2 CM HM3 BOND CBA CA IC CZ CD2 *CE2 HE2 1.4028 119.93 -179.94 119.66 1.0804 IC CD1 CD2 *CG CBA 1.4029 119.56 179.52 120.59 1.4978 !IC CD2 CG CBA CM 1.4036 120.59 178.00 110.88 1.1144 ! for r-isomer !IC CD2 CG CBA HBA 1.4036 120.59 -60.83 109.72 1.5424 ! for r-isomer IC CD2 CG CBA CM 1.4036 120.59 -60.83 109.72 1.5424 ! for s-isomer IC CD2 CG CBA HBA 1.4036 120.59 178.00 110.88 1.1144 ! for s-isomer IC CG CBA CM HM1 1.4978 109.72 65.78 111.17 1.1093 IC HM1 CBA *CM HM2 1.1093 111.17 120.55 110.04 1.1140 IC HM1 CBA *CM HM3 1.1093 111.17 -120.83 110.06 1.1096 !End fatty acid binding protein inhibitors, chayan, may2007 RESI 2PDO 0.000 ! C4H7NO 2-pyrrolidinone, kevo GROUP ATOM N1 NG2R53 -0.58 ATOM H1 HGP1 0.36 ATOM C2 CG2R53 0.30 ! H32 H42 ATOM O2 OG2D1 -0.49 ! \ / ATOM C3 CG3C52 -0.01 ! H31--C3----C4--H41 ATOM H31 HGA2 0.09 ! | | ATOM H32 HGA2 0.09 ! C2 C5--H51 ATOM C4 CG3C52 -0.19 ! // \ / \ ATOM H41 HGA2 0.09 ! O2 N1 H52 ATOM H42 HGA2 0.09 ! | ATOM C5 CG3C52 0.07 ! H1 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 H1 C2 O2 C3 H31 C3 H32 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 IMPR C2 C3 N1 O2 IC C5 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C2 C3 C4 0.0000 0.00 15.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 200.00 0.00 0.0000 IC C3 N1 *C2 O2 0.0000 0.00 181.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 !Acyclic ethers from top_all27_carb_jul2o.inp RESI DMEE 0.0000 ! C2H6O Dimethylether, viv 2006 GROUP ATOM C1 CG331 -0.10 ! H12 H32 ATOM H11 HGA3 0.09 ! | | ATOM H12 HGA3 0.09 ! H11--C1---O2---C3--H31 ATOM H13 HGA3 0.09 ! | | ATOM O2 OG301 -0.34 ! H13 H33 ATOM C3 CG331 -0.10 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 O2 O2 C3 BOND C1 H11 C1 H12 C1 H13 BOND C3 H31 C3 H32 C3 H33 IC C1 O2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H31 O2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 O2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 RESI METE 0.0000 ! C3H8O Methyl ethyl ether, viv 2006 GROUP ATOM C1 CG331 -0.27 ! H12 H21 H42 ATOM H11 HGA3 0.09 ! | | | ATOM H12 HGA3 0.09 ! H11--C1---C2---O3---C4--H41 ATOM H13 HGA3 0.09 ! | | | GROUP ! H13 H22 H43 ATOM C2 CG321 -0.01 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O3 OG301 -0.34 ATOM C4 CG331 -0.10 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C2 O3 O3 C4 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 BOND C4 H41 C4 H42 C4 H43 IC C4 O3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC H41 O3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 O3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 IC O3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 RESI DETE 0.0000 ! C4H10O Diethylether, viv 2006 GROUP ATOM C1 CG331 -0.27 ! H11 H21 H41 H51 ATOM H11 HGA3 0.09 ! | | | | ATOM H12 HGA3 0.09 ! H13--C1---C2---O3---C4---C5--H53 ATOM H13 HGA3 0.09 ! | | | | GROUP ! H12 H22 H42 H52 ATOM C2 CG321 -0.01 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O3 OG301 -0.34 ATOM C4 CG321 -0.01 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 C2 C2 O3 O3 C4 C4 C5 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 BOND C4 H41 C4 H42 BOND C5 H51 C5 H52 C5 H53 IC C1 C2 O3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 O3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 O3 0.0000 0.00 180.00 0.00 0.0000 IC O3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C5 O3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 O3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC O3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC H51 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 IC H51 C4 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 RESI DME 0.0000 ! C4H10O2 Dimethoxyethane, adm jr. GROUP ATOM C1 CG331 -0.10 ! H12 H11 ATOM H11 HGA3 0.09 ! \ / ATOM H12 HGA3 0.09 ! H13-C1 H31 H32 H61 H62 ATOM H13 HGA3 0.09 ! \ \ / \ / ATOM O2 OG301 -0.34 ! O2--C3 C6-H63 ATOM C3 CG321 -0.01 ! \ / ATOM H31 HGA2 0.09 ! H41-C4-O5 ATOM H32 HGA2 0.09 ! | GROUP ! H42 ATOM C4 CG321 -0.01 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 ATOM O5 OG301 -0.34 ATOM C6 CG331 -0.10 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 BOND C1 O2 O2 C3 BOND C3 H31 C3 H32 C3 C4 BOND C4 H41 C4 H42 BOND C4 O5 O5 C6 BOND C6 H61 C6 H62 C6 H63 IC C1 O2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 O2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C4 O2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 O2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 !corrected by kevo IC O2 C3 C4 O5 0.0000 0.00 180.00 0.00 0.0000 IC O5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC O5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 !corrected by kevo IC C3 C4 O5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 O5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC H61 O5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC H61 O5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 RESI MPRE 0.0000 ! C4H10O Methyl Propyl Ether, 9/29/06 viv GROUP ATOM C1 CG331 -0.10 ! H11 H31 H41 H51 ATOM H11 HGA3 0.09 ! | | | | ATOM H12 HGA3 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - H53 ATOM H13 HGA3 0.09 ! | | | | ATOM O2 OG301 -0.34 ! H12 H32 H42 H52 ATOM C3 CG321 -0.01 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 O2 BOND O2 C3 C3 H31 C3 H32 C3 C4 BOND C4 H41 C4 H42 C4 C5 BOND C5 H51 C5 H52 C5 H53 IC O2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C4 C3 O2 C1 0.0000 0.00 180.00 0.00 0.0000 IC O2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC O2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 IC C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 RESI MBUE 0.0000 ! C5H12O Methyl Butyl Ether, 9/30/06 viv GROUP ATOM C1 CG331 -0.10 ! H11 H31 H41 H51 H6A ATOM H11 HGA3 0.09 ! | | | | | ATOM H12 HGA3 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - C6 - H6C ATOM H13 HGA3 0.09 ! | | | | | ATOM O2 OG301 -0.34 ! H12 H32 H42 H52 H6B ATOM C3 CG321 -0.01 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 GROUP ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 O2 BOND O2 C3 C3 H31 C3 H32 C3 C4 BOND C4 H41 C4 H42 C4 C5 BOND C5 H51 C5 H52 C5 C6 BOND C6 H61 C6 H62 C6 H63 IC O2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C4 C3 O2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC O2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC O2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC C5 H61 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC C5 H61 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 RESI EPRE 0.0000 ! C5H12O Ethyl propyl ether, viv 9/30/06 GROUP ATOM C1 CG331 -0.27 ! H11 H21 H41 H51 H61 ATOM H11 HGA3 0.09 ! | | | | | ATOM H12 HGA3 0.09 ! H13 - C1 - C2 - O3 - C4 - C5 - C6 - H63 ATOM H13 HGA3 0.09 ! | | | | | GROUP ! H12 H22 H42 H52 H62 ATOM C2 CG321 -0.01 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O3 OG301 -0.34 ATOM C4 CG321 -0.01 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 GROUP ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 C2 C2 O3 O3 C4 BOND C4 C5 C5 C6 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 BOND C4 H41 C4 H42 BOND C5 H51 C5 H52 BOND C6 H61 C6 H62 C6 H63 IC C2 O3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C4 O3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC O3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC O3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC O3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC C5 H61 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC C5 H61 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 IC O3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 !<<<<<<<<<<<>>>>>>>>>>> DECL -C2 DECL -O1 DECL +C1 AUTOGENERATE ANGLE DIHE DEFAULT FIRST HYD1 LAST HYD2 RESI PEGM 0.0000 ! C2H4O Peg monomer for polymer construction, viv Nov 2006 GROUP ATOM C1 CG321 -0.01 ATOM H12 HGA2 0.09 ! H11 H21 ATOM H11 HGA2 0.09 ! | | ATOM O1 OG301 -0.34 ! (-C2) - C1 - O1 - C2 - ATOM C2 CG321 -0.01 ! | | ATOM H21 HGA2 0.09 ! H12 H22 ATOM H22 HGA2 0.09 BOND C1 H11 C1 H12 C1 O1 BOND O1 C2 C2 H21 C2 H22 BOND C1 -C2 IC -O1 -C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC -C2 C1 O1 C2 0.0000 0.00 180.00 0.00 0.0000 IC C1 O1 C2 +C1 0.0000 0.00 180.00 0.00 0.0000 IC -C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC -C2 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC O1 +C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 +C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 PRES HYD1 0.1700 ! CH3 Complete terminal methyl group adjacent to OCE ATOM H13 HGA3 0.09 ATOM C1 CG331 -0.10 ! H13 - ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 BOND H13 C1 IC C2 O1 C1 H13 0.0000 0.00 180.00 0.00 0.0000 IC H13 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC H13 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 PRES HYD2 0.1700 ! CH3 Complete terminal methyl group adjacent to OCE ATOM H23 HGA3 0.09 ATOM C2 CG331 -0.10 ! H23 - ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 BOND H23 C2 IC C1 O1 C2 H23 0.0000 0.00 180.00 0.00 0.0000 IC O1 H23 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 H23 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 PRES MET1 0.0000 ! CH3 Append terminal methyl group adjacent to CH2 ! HE2 ATOM CE CG331 -0.27 ! | ATOM HE1 HGA3 0.09 ! HE3 - CE - ATOM HE2 HGA3 0.09 ! | ATOM HE3 HGA3 0.09 ! HE1 BOND CE C1 CE HE1 CE HE2 CE HE3 IC C2 O1 C1 CE 0.0000 0.00 180.00 0.00 0.0000 IC CE O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC CE O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 CE HE3 0.0000 0.00 180.00 0.00 0.0000 IC HE3 C1 *CE HE1 0.0000 0.00 120.00 0.00 0.0000 IC HE3 C1 *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 PRES MET2 0.0000 ! CH3 Append terminal methyl group adjacent to CH2 ! HA3 ATOM CA CG331 -0.27 ! | ATOM HA1 HGA3 0.09 ! HA2 - CA - ATOM HA2 HGA3 0.09 ! | ATOM HA3 HGA3 0.09 ! HA1 BOND CA C2 CA HA1 CA HA2 CA HA3 IC C1 O1 C2 CA 0.0000 0.00 180.00 0.00 0.0000 IC O1 CA *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 CA *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C2 CA HA3 0.0000 0.00 180.00 0.00 0.0000 IC C2 HA3 *CA HA1 0.0000 0.00 120.00 0.00 0.0000 IC C2 HA3 *CA HA2 0.0000 0.00 -120.00 0.00 0.0000 DEFAULT FIRST NONE LAST NONE !<<<<<<<<<<<>>>>>>>>>>> !End acyclic ethers from top_all27_carb_jul2o.inp !New compounds from the sugar force field RESI ACO 0.0000 ! C3H6O Acetone, adm, Oct 08 GROUP ATOM O1 OG2D3 -0.48 ATOM C1 CG2O5 0.40 ATOM C2 CG331 -0.23 ! O1 ATOM C3 CG331 -0.23 ! || ATOM H21 HGA3 0.09 ! C1 ATOM H22 HGA3 0.09 ! / \ ATOM H23 HGA3 0.09 ! H21--C2 C3--H31 ATOM H31 HGA3 0.09 ! / | | \ ATOM H32 HGA3 0.09 ! H22 H32 H33 H32 ATOM H33 HGA3 0.09 BOND C1 C2 C1 C3 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 DOUBLE O1 C1 IMPR C1 C2 C3 O1 ACCE O1 IC C2 C1 C3 H31 1.5366 110.58 135.22 109.51 1.1328 IC O1 C1 C3 H31 1.2237 122.95 -42.47 109.51 1.1328 IC O1 C1 C3 H32 1.2237 122.95 77.28 104.63 1.1325 IC O1 C1 C3 H33 1.2237 122.95 -161.85 105.76 1.0732 IC C3 C1 C2 H21 1.5233 110.58 -153.74 111.52 1.1204 IC O1 C1 C2 H21 1.2237 126.42 23.85 111.52 1.1204 IC O1 C1 C2 H22 1.2237 126.42 148.26 114.11 1.1296 IC O1 C1 C2 H23 1.2237 126.42 -90.21 101.67 1.1375 RESI IPAA 0.00 ! C5H11NO og isopropyl acetamide, based on NMA GROUP ! n.b.: CL, HL, CR, HR vdw params != c22 ATOM CL CG331 -0.27 ! ??? this molecule needs optimization ATOM HL1 HGA3 0.09 ATOM HL2 HGA3 0.09 ! H211 H212 H213 ATOM HL3 HGA3 0.09 ! \ | / GROUP ! C21 ATOM C CG2O1 0.51 ! HL1\ O / ATOM O OG2D1 -0.51 ! HL2-- CL -- C -- N -- CR --HR ATOM N NG2S1 -0.47 ! HL3/ H \ ATOM H HGP1 0.31 ! C22 ATOM CR CG311 0.07 ! / | \ ATOM HR HGA1 0.09 ! H221 H222 H223 GROUP ATOM C21 CG331 -0.27 ATOM H211 HGA3 0.09 ATOM H212 HGA3 0.09 ATOM H213 HGA3 0.09 GROUP ATOM C22 CG331 -0.27 ATOM H221 HGA3 0.09 ATOM H222 HGA3 0.09 ATOM H223 HGA3 0.09 BOND HL1 CL HL2 CL HL3 CL BOND CL C C N N CR BOND N H BOND HR CR C21 CR C22 CR BOND C21 H211 C21 H212 C21 H213 BOND C22 H221 C22 H222 C22 H223 DOUBLE C O IMPR C CL N O ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) IC O C N H 1.2240 124.40 -180.00 118.74 0.9902 IC H N C CL 0.9902 118.74 0.00 115.46 1.4817 IC O C N CR 1.2240 124.40 0.00 125.23 1.4315 IC N C CL HL1 1.3414 115.46 180.00 109.20 1.1119 IC N C CL HL2 1.3414 115.46 60.56 110.24 1.1102 IC N C CL HL3 1.3414 115.46 -60.56 110.24 1.1102 IC C N CR HR 1.3414 125.23 180.00 105.39 1.1185 IC C N CR C21 1.3414 125.23 64.21 112.40 1.5343 IC C N CR C22 1.3414 125.23 -64.21 112.40 1.5343 IC N CR C21 H211 1.4315 112.40 53.31 110.44 1.1098 IC N CR C21 H212 1.4315 112.40 -66.48 110.16 1.1110 IC N CR C21 H213 1.4315 112.40 173.88 110.46 1.1098 IC N CR C22 H221 1.4315 112.40 66.48 110.16 1.1110 IC N CR C22 H222 1.4315 112.40 -53.31 110.44 1.1098 IC N CR C22 H223 1.4315 112.40 -173.88 110.46 1.1098 RESI AMOP -1.00 ! C4H7O3 alpha-methoxy-propionic acid, og GROUP ATOM C1 CG311 -0.02 ! CT1 HM1 HM2 HM3 ATOM C2 CG2O3 0.62 ! CC \ | / ATOM H1 HGA1 0.09 ! HA CM ATOM OM OG301 -0.34 ! ethers | ATOM CM CG331 -0.10 ! CT3 OM O1 (-) ATOM HM1 HGA3 0.09 ! HA | / ATOM HM2 HGA3 0.09 ! HA H1--C1--C2 ATOM HM3 HGA3 0.09 ! HA | \\ ATOM O1 OG2D2 -0.76 ! OC | O2 ATOM O2 OG2D2 -0.76 ! OC H01--C0 GROUP ! | \ ATOM C0 CG331 -0.27 ! CT3 H02 H03 ATOM H01 HGA3 0.09 ! HA ATOM H02 HGA3 0.09 ! HA ATOM H03 HGA3 0.09 ! HA BOND C1 H1 C1 OM C1 C0 BOND C1 C2 C2 O1 BOND C0 H01 C0 H02 C0 H03 BOND OM CM BOND CM HM1 CM HM2 CM HM3 DOUBLE C2 O2 IMPR C2 O2 O1 C1 IC C2 C1 OM CM 1.5370 107.76 -154.77 111.65 1.4194 IC OM C2 *C1 C0 1.4224 107.76 123.63 111.13 1.5565 IC OM C2 *C1 H1 1.4224 107.76 -117.54 106.67 1.1094 IC C1 OM CM HM1 1.4224 111.65 60.37 109.96 1.1106 IC HM1 OM *CM HM2 1.1106 109.96 -120.84 110.46 1.1094 IC HM1 OM *CM HM3 1.1106 109.96 119.38 109.38 1.1097 IC H1 C1 C2 O1 1.1094 106.67 177.14 118.57 1.2599 IC O1 C1 *C2 O2 1.2599 118.57 -179.67 117.64 1.2609 IC H1 C1 C0 H01 1.1094 109.13 -60.43 109.93 1.1106 IC H01 C1 *C0 H02 1.1106 109.93 -118.90 109.59 1.1115 IC H01 C1 *C0 H03 1.1106 109.93 120.54 111.13 1.1077 PATC FIRS NONE LAST NONE !End new compounds from the sugar force field !Special project, og, feb2008 RESI CUME 0.0000 ! C9H12 Cumene (aka. isopropylbenzene), Olgun Guvench GROUP ATOM CA1 CG2R61 -0.115 ! HA1 ATOM HA1 HGR61 0.115 ! | GROUP ! CA1 ATOM CA2 CG2R61 -0.115 ! // \ ATOM HA2 HGR61 0.115 ! HA6--CA6 CA2--HA2 GROUP ! | || ATOM CA3 CG2R61 -0.115 ! | || ATOM HA3 HGR61 0.115 ! HA5--CA5 CA3--HA3 GROUP ! \\ / ATOM CA4 CG2R61 0.0 ! CA4 GROUP ! | ATOM CA5 CG2R61 -0.115 ! | ATOM HA5 HGR61 0.115 ! | GROUP ! -------C4-------- ATOM CA6 CG2R61 -0.115 ! | | | ATOM HA6 HGR61 0.115 ! | H41 | GROUP ! H52-C5-H51 H31-C3-H32 ATOM C4 CG311 -0.09 ! | | ATOM H41 HGA1 0.09 ! H53 H33 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 BOND CA1 HA1 BOND CA1 CA2 CA2 HA2 BOND CA3 HA3 CA3 CA4 BOND CA5 HA5 CA5 CA6 BOND CA6 HA6 DOUBLE CA6 CA1 CA4 CA5 CA2 CA3 BOND C3 H31 C3 H32 C3 H33 BOND CA4 C4 BOND C3 C4 BOND C4 H41 BOND C4 C5 BOND C5 H51 C5 H52 C5 H53 IC CA6 HA1 *CA1 CA2 1.4195 121.85 177.84 121.53 1.4194 IC HA1 CA1 CA2 CA3 1.0800 121.53 -178.93 121.60 1.3982 IC CA3 CA1 *CA2 HA2 1.3982 121.60 -179.91 119.41 1.0825 IC CA1 CA2 CA3 CA4 1.4194 121.60 0.43 120.92 1.4029 IC CA4 CA2 *CA3 HA3 1.4029 120.92 179.85 119.25 1.0788 IC HA1 CA1 CA6 CA5 1.0800 121.85 178.93 121.61 1.3985 IC CA5 CA1 *CA6 HA6 1.3985 121.61 179.93 119.45 1.0824 IC CA4 CA6 *CA5 HA5 1.4036 120.87 -179.85 119.09 1.0786 IC CA5 CA3 *CA4 C4 1.4036 118.40 179.75 120.23 1.5147 IC CA3 CA4 C4 C3 1.4029 120.23 0.00 109.64 1.5411 IC C3 CA4 *C4 C5 1.5411 109.64 -124.08 109.66 1.5411 IC C3 CA4 *C4 H41 1.5411 109.64 117.96 107.55 1.1143 IC CA4 C4 C3 H31 1.5147 109.64 176.65 110.17 1.1098 IC H31 C4 *C3 H32 1.1098 110.17 119.90 110.84 1.1103 IC H31 C4 *C3 H33 1.1098 110.17 -119.93 110.47 1.1115 IC CA4 C4 C5 H51 1.5147 109.66 -176.66 110.16 1.1098 IC H51 C4 *C5 H52 1.1098 110.16 119.93 110.47 1.1114 IC H51 C4 *C5 H53 1.1098 110.16 -119.89 110.84 1.1103 PATCHING FIRST NONE LAST NONE RESI BSAT -1.0000 ! C6H5O3S Benzenesulfonate, Olgun Guvench GROUP ATOM S SG3O1 1.35 ! O1 ATOM O1 OG2P1 -0.65 ! | ATOM O2 OG2P1 -0.65 ! O2--S--O3 ATOM O3 OG2P1 -0.65 ! | ATOM CA1 CG2R61 -0.40 ! CA1 GROUP ! // \ ATOM CA2 CG2R61 -0.21 ! HA6--CA6 CA2--HA2 ATOM HA2 HGR61 0.21 ! | || GROUP ! | || ATOM CA3 CG2R61 -0.115 ! HA5--CA5 CA3--HA3 ATOM HA3 HGR61 0.115 ! \\ / GROUP ! CA4 ATOM CA4 CG2R61 -0.115 ! | ATOM HA4 HGR61 0.115 ! HA4 GROUP ATOM CA5 CG2R61 -0.115 ATOM HA5 HGR61 0.115 GROUP ATOM CA6 CG2R61 -0.21 ATOM HA6 HGR61 0.21 BOND S O1 S O2 S O3 BOND S CA1 BOND CA1 CA2 CA2 HA2 BOND CA3 HA3 CA3 CA4 BOND CA4 HA4 BOND CA5 HA5 CA5 CA6 BOND CA6 HA6 DOUBLE CA6 CA1 CA4 CA5 CA2 CA3 ACCEPTOR O1 S ACCEPTOR O2 S ACCEPTOR O3 S IC O1 CA1 *S O2 1.4520 103.94 119.83 106.18 1.4544 IC O1 CA1 *S O3 1.4520 103.94 -119.70 105.93 1.4543 IC O1 S CA1 CA6 1.4520 103.94 -90.93 121.85 1.4195 IC CA6 S *CA1 CA2 1.4195 121.85 177.84 121.53 1.4194 IC S CA1 CA2 CA3 1.6322 121.53 -178.93 121.60 1.3982 IC CA3 CA1 *CA2 HA2 1.3982 121.60 -179.91 119.41 1.0825 IC CA1 CA2 CA3 CA4 1.4194 121.60 0.43 120.92 1.4029 IC CA4 CA2 *CA3 HA3 1.4029 120.92 179.85 119.25 1.0788 IC S CA1 CA6 CA5 1.6322 121.85 178.93 121.61 1.3985 IC CA5 CA1 *CA6 HA6 1.3985 121.61 179.93 119.45 1.0824 IC CA4 CA6 *CA5 HA5 1.4036 120.87 -179.85 119.09 1.0786 IC CA5 CA3 *CA4 HA4 1.4036 118.40 179.75 120.23 1.0800 PATCHING FIRST NONE LAST NONE !End special project, og, feb2008 !Polli's bile acids, chayan, feb2008 RESI 2MPA 1.00 ! C8H17N2O 2-Methyl Piperidine Amide ! Made in order to build Polli's compounds (Pablo) GROUP ATOM CG1 CG314 0.29 ATOM HG1 HGA1 0.09 ! HG21 HG22 ATOM NG2 NG3P2 -0.40 ! \ / ATOM HG21 HGP2 0.32 ! OG HT (+1)NG2--CG3 ATOM HG22 HGP2 0.32 ! || | / \ ATOM CG3 CG324 0.20 ! CG---NT--CGT--CG1 CG4 ATOM HG31 HGA2 0.09 ! / \ / ATOM HG32 HGA2 0.09 ! HM1--CM--HM3 CG6--CG5 GROUP ! | ATOM CG4 CG321 -0.18 ! HM2 ATOM HG41 HGA2 0.09 ATOM HG42 HGA2 0.09 ! 2MPA GROUP ATOM CG5 CG321 -0.18 ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 GROUP ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 GROUP ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT HGP1 0.47 GROUP ATOM CGT CG321 -0.18 ATOM HGT1 HGA2 0.09 ATOM HGT2 HGA2 0.09 BOND CM HM1 CM HM2 CM HM3 CM CG BOND CG OG CG NT NT HT BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 NG2 BOND NG2 HG21 NG2 HG22 NG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IMPR CG CM NT OG IC CM CG NT CGT 1.4784 116.17 178.50 125.70 1.4627 IC CG NT CGT HGT1 1.3412 125.70 -174.52 107.65 1.1160 IC HGT1 NT *CGT HGT2 1.1160 107.65 114.70 109.82 1.1155 IC HGT1 NT *CGT CG1 1.1160 107.65 -119.46 116.84 1.5494 IC NT CG CM HM1 1.3412 116.17 -62.83 110.69 1.1111 IC HM1 CG *CM HM2 1.1111 110.69 -119.06 109.32 1.1131 IC HM1 CG *CM HM3 1.1111 110.69 121.66 110.83 1.1107 IC CM NT *CG OG 1.4784 116.17 170.21 122.13 1.2240 IC OG CG NT HT 1.2240 122.13 175.26 115.36 0.9985 IC CG NT CGT CG1 1.3412 125.70 66.02 116.84 1.5494 IC NT CGT CG1 HG1 1.4627 116.84 36.30 109.99 1.1056 IC HG1 CGT *CG1 NG2 1.1056 109.99 -114.94 109.74 1.5010 IC HG1 CGT *CG1 CG6 1.1056 109.99 124.49 113.69 1.5350 IC CGT CG1 NG2 CG3 1.5494 109.74 176.09 115.30 1.5001 IC CG3 CG1 *NG2 HG21 1.5001 115.30 122.39 107.69 1.0058 IC CG3 CG1 *NG2 HG22 1.5001 115.30 -125.48 107.03 1.0184 IC CG1 NG2 CG3 CG4 1.5010 115.30 59.26 108.63 1.5313 IC CG4 NG2 *CG3 HG31 1.5313 108.63 122.04 105.77 1.1032 IC CG4 NG2 *CG3 HG32 1.5313 108.63 -121.53 105.49 1.1034 IC NG2 CG3 CG4 CG5 1.5001 108.63 -54.12 110.88 1.5394 IC CG5 CG3 *CG4 HG41 1.5394 110.88 120.82 109.89 1.1138 IC CG5 CG3 *CG4 HG42 1.5394 110.88 -121.31 109.72 1.1134 IC CG3 CG4 CG5 CG6 1.5313 110.88 54.58 111.72 1.5411 IC CG6 CG4 *CG5 HG51 1.5411 111.72 121.65 109.56 1.1147 IC CG6 CG4 *CG5 HG52 1.5411 111.72 -121.21 109.32 1.1144 IC CG5 CG1 *CG6 HG61 1.5411 110.92 -121.44 110.01 1.1127 IC CG5 CG1 *CG6 HG62 1.5411 110.92 120.54 109.46 1.1130 !Pablo's Compounds RESI BPIP 1.00 ! C12H18N Model compound for N-benzyl piperidine, cacha GROUP ATOM CB CG324 0.15 ATOM HB1 HGA2 0.09 ! C3---C2 CD1--CE1 ATOM HB2 HGA2 0.09 ! / \ // \\ ATOM N1 NG3P1 -0.40 ! C4 N1--CB--CZ CP ATOM H1 HGP2 0.32 ! \ / \ __ / ATOM C2 CG324 0.15 ! C5---C6 CD2--CE2 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ! BPIP ATOM C6 CG324 0.15 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 GROUP ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 GROUP ATOM CZ CG2R61 0.090 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND N1 H1 N1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 BOND C3 C4 C4 H41 C4 H42 BOND C4 C5 C5 H51 C5 H52 BOND C5 C6 C6 H61 C6 H62 C6 N1 BOND N1 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 BOND CE1 CP CP HP CP CE2 IC C6 N1 C2 C3 1.5157 110.13 -60.42 110.11 1.5319 IC N1 C2 C3 C4 1.5157 110.11 57.37 110.44 1.5362 IC C2 C3 C4 C5 1.5319 110.44 -54.84 111.24 1.5362 IC C3 C4 C5 C6 1.5362 111.24 54.84 110.44 1.5319 IC C2 C6 *N1 CB 1.5157 110.13 135.82 116.61 1.5015 IC HB1 N1 *CB HB2 1.1028 107.08 -120.06 107.08 1.1028 IC HB1 N1 *CB CZ 1.1028 107.08 119.97 107.59 1.4889 IC HB1 CB N1 C6 1.1028 107.08 173.55 116.61 1.5157 IC C6 CB *N1 C2 1.5157 116.61 132.96 116.61 1.5157 IC C2 CB *N1 H1 1.5157 116.61 113.52 105.15 1.0496 IC C3 N1 *C2 H21 1.5319 110.11 121.51 105.72 1.1025 IC H21 N1 *C2 H22 1.1025 105.72 116.75 105.78 1.1018 IC C5 N1 *C6 H61 1.5319 110.11 121.75 105.78 1.1018 IC C5 N1 *C6 H62 1.5319 110.11 -121.51 105.72 1.1025 IC C4 C2 *C3 H31 1.5362 110.44 120.70 109.65 1.1137 IC H31 C2 *C3 H32 1.1137 109.65 118.12 110.23 1.1131 IC C5 C3 *C4 H41 1.5362 111.24 -121.82 109.83 1.1145 IC H41 C3 *C4 H42 1.1145 109.83 -117.39 109.30 1.1147 IC C4 C6 *C5 H51 1.5362 110.44 121.18 110.23 1.1131 IC C4 C6 *C5 H52 1.5362 110.44 -120.70 109.65 1.1137 IC C2 N1 CB CZ 1.5157 116.61 66.48 107.59 1.4889 IC N1 CB CZ CD2 1.5015 107.59 -92.75 120.51 1.4109 IC N1 CB CZ CD1 1.5015 107.59 92.75 120.51 1.4109 IC CD1 CD2 *CZ CB 1.4109 118.75 -174.60 120.51 1.4889 IC CD2 CZ CB HB1 1.4109 120.51 24.38 111.50 1.1028 IC CD2 CZ CB HB2 1.4109 120.51 150.12 111.50 1.1028 IC CB CZ CD1 CE1 1.4889 120.51 177.83 120.52 1.4001 IC CB CZ CD2 CE2 1.4889 120.51 -177.83 120.52 1.4001 IC CZ CD1 CE1 CP 1.4109 120.52 -1.31 120.00 1.3993 IC CD1 CE1 CP CE2 1.4001 120.00 -0.66 120.12 1.3993 IC CE1 CP CE2 CD2 1.3993 120.12 0.66 120.00 1.4001 IC CE1 CZ *CD1 HD1 1.4001 120.52 -179.79 120.55 1.0802 IC CE2 CZ *CD2 HD2 1.4001 120.52 179.79 120.55 1.0802 IC CP CD1 *CE1 HE1 1.3993 120.00 -179.18 120.30 1.0822 IC CP CD2 *CE2 HE2 1.3993 120.00 179.18 120.30 1.0822 IC CE1 CE2 *CP HP 1.3993 120.12 178.89 119.94 1.0821 PRES BPAB 1.00 ! C22H26N2O3 Gamma N-benzyl piperidine, alpha benzyl CDCA amide (010201P), cacha ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ! OG CG3--CG3 CJ1--CK1 ATOM CG CG2O1 0.51 ! || / \ // \\ ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 GROUP ! \ ATOM CG4 CG311 -0.09 ! O24 CC2 ATOM HG4 HGA1 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 CD1--CE1 ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ // \\ ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG32 HGA2 0.09 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OA1 CD2--CE2 ATOM CG2 CG324 0.15 ! Me19 | | | ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 ATOM HG1 HGP2 0.32 ! | | | ATOM CBG CG324 0.15 ! C3 C5 C7 ATOM HBG1 HGA2 0.09 ! / \ / \ / \ ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH ATOM CG6 CG324 0.15 ATOM HG61 HGA2 0.09 ! BPAB (010201P) ATOM HG62 HGA2 0.09 GROUP ATOM CG5 CG321 -0.18 ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 GROUP ATOM CY CG2R61 0.090 GROUP ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 GROUP ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 GROUP ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 GROUP ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 GROUP ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CG4 CG4 HG4 CG4 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG1 BOND NG1 HG1 NG1 CBG NG1 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG4 BOND CBG HBG1 CBG HBG2 CBG CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5234 109.38 -153.04 116.99 1.4484 IC HB1 CB OA2 CA 1.1167 112.82 -38.66 116.99 1.3347 IC HB2 CB OA2 CA 1.1142 108.54 -155.51 116.99 1.3347 IC CZ CB OA2 CA 1.5069 113.23 86.00 116.99 1.3347 IC CD2 CZ CB OA2 1.4041 120.59 -99.33 113.23 1.4484 IC CD1 CZ CB OA2 1.4045 119.58 76.21 113.23 1.4484 IC CD1 CD2 *CZ CB 1.4045 119.68 175.54 120.59 1.5069 IC CD2 CZ CB HB1 1.4041 120.59 27.27 109.20 1.1167 IC CD2 CZ CB HB2 1.4041 120.59 141.22 106.86 1.1142 IC CB CZ CD1 CE1 1.5069 119.58 -176.05 120.14 1.4008 IC CB CZ CD2 CE2 1.5069 120.59 175.62 120.15 1.4011 IC CZ CD1 CE1 CP 1.4045 120.14 0.56 119.98 1.4008 IC CD1 CE1 CP CE2 1.4008 119.98 -0.25 120.07 1.4012 IC CE1 CP CE2 CD2 1.4008 120.07 -0.13 119.97 1.4011 IC CE1 CZ *CD1 HD1 1.4008 120.14 179.88 120.03 1.0802 IC CE2 CZ *CD2 HD2 1.4011 120.15 -179.36 120.10 1.0785 IC CP CD1 *CE1 HE1 1.4008 119.98 -179.84 120.09 1.0803 IC CP CD2 *CE2 HE2 1.4012 119.97 179.92 120.22 1.0812 IC CE1 CE2 *CP HP 1.4008 120.07 179.63 119.91 1.0813 IC HT1 CG *NT CG4 1.0054 116.40 -172.83 124.61 1.4381 IC CG NT CG4 CG3 1.3416 124.61 170.00 110.67 1.5378 IC CG3 NT *CG4 HG4 1.5378 110.67 -117.93 107.34 1.1204 IC CG3 NT *CG4 CG5 1.5378 110.67 122.73 112.97 1.5408 IC NT CG4 CG3 CG2 1.4381 110.67 70.05 111.85 1.5352 IC CG4 CG2 *CG3 HG31 1.5378 111.85 121.71 109.54 1.1122 IC CG4 CG2 *CG3 HG32 1.5378 111.85 -120.95 109.60 1.1132 IC CG4 CG3 CG2 NG1 1.5378 111.85 55.34 111.06 1.5202 IC NG1 CG3 *CG2 HG21 1.5202 111.06 118.37 110.41 1.1001 IC NG1 CG3 *CG2 HG22 1.5202 111.06 -118.11 113.59 1.1007 IC CG3 CG2 NG1 CG6 1.5352 111.06 -56.33 110.73 1.5109 IC CG6 CG2 *NG1 HG1 1.5109 110.73 112.39 104.22 1.0469 IC CG6 CG2 *NG1 CBG 1.5109 110.73 -129.60 117.47 1.4972 IC CG2 CG3 CG4 CG5 1.5352 111.85 -54.87 109.15 1.5408 IC CG5 NG1 *CG6 HG61 1.5266 110.48 121.09 105.90 1.1028 IC CG5 NG1 *CG6 HG62 1.5266 110.48 -122.70 105.64 1.1023 IC CG6 CG4 *CG5 HG51 1.5266 111.10 121.26 109.77 1.1128 IC CG6 CG4 *CG5 HG52 1.5266 111.10 -122.01 109.21 1.1123 IC CG6 NG1 CBG HBG1 1.5109 111.45 -69.57 107.08 1.1032 IC HBG1 NG1 *CBG HBG2 1.1032 107.08 121.43 107.67 1.1023 IC CG2 NG1 CBG CY 1.5202 117.47 -60.45 105.98 1.4862 IC NG1 CBG CY CJ2 1.4972 105.98 -74.47 120.62 1.4104 IC NG1 CBG CY CJ1 1.4972 105.98 108.23 120.17 1.4090 IC CBG CY CJ1 CK1 1.4862 120.17 179.26 120.32 1.4003 IC CBG CY CJ2 CK2 1.4862 120.62 -179.21 120.29 1.4003 IC CY CJ1 CK1 CQ 1.4090 120.32 -0.80 120.02 1.3998 IC CJ1 CK1 CQ CK2 1.4003 120.02 -0.38 120.16 1.3998 IC CK1 CQ CK2 CJ2 1.3998 120.16 0.42 120.02 1.4003 IC CK1 CY *CJ1 HJ1 1.4003 120.32 179.90 120.54 1.0806 IC CK2 CY *CJ2 HJ2 1.4003 120.29 179.62 120.62 1.0803 IC CQ CJ1 *CK1 HK1 1.3998 120.02 -179.40 120.26 1.0821 IC CQ CJ2 *CK2 HK2 1.3998 120.02 179.37 120.29 1.0822 IC CK1 CK2 *CQ HQ 1.3998 120.16 179.20 119.92 1.0821 PRES BPAT 1.00 ! C19H28N2O3 Gamma N-benzyl piperidine, alpha tert.butyl CDCA amide (010101P), cacha ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ! OG CG3--CG3 CJ1--CK1 ATOM CG CG2O1 0.51 ! || / \ // \\ ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 GROUP ! \ ATOM CG4 CG311 -0.09 ! O24 CC2 ATOM HG4 HGA1 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 CT1 ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ / ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2---CT--CT2 ATOM HG32 HGA2 0.09 ! / \ | / || \ GROUP ! C11 C13---C17 OA1 CT3 ATOM CG2 CG324 0.15 ! Me19 | | | ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 ATOM HG1 HGP2 0.32 ! | | | ATOM CBG CG324 0.15 ! C3 C5 C7 ATOM HBG1 HGA2 0.09 ! / \ / \ / \ ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH ATOM CG6 CG324 0.15 ATOM HG61 HGA2 0.09 ! BPAT (010101P) ATOM HG62 HGA2 0.09 GROUP ATOM CG5 CG321 -0.18 ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 GROUP ATOM CY CG2R61 0.090 GROUP ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 GROUP ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 GROUP ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 GROUP ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 GROUP ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CT CG301 -0.04 ATOM CT1 CG331 -0.27 ATOM HT11 HGA3 0.09 ATOM HT12 HGA3 0.09 ATOM HT13 HGA3 0.09 ATOM CT2 CG331 -0.27 ATOM HT21 HGA3 0.09 ATOM HT22 HGA3 0.09 ATOM HT23 HGA3 0.09 ATOM CT3 CG331 -0.27 ATOM HT31 HGA3 0.09 ATOM HT32 HGA3 0.09 ATOM HT33 HGA3 0.09 BOND NT CG4 BOND CG4 HG4 CG4 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG1 BOND NG1 HG1 NG1 CBG NG1 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG4 BOND CBG HBG1 CBG HBG2 CBG CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND OA2 CT BOND CT CT1 CT1 HT11 CT1 HT12 CT1 HT13 BOND CT CT2 CT2 HT21 CT2 HT22 CT2 HT23 BOND CT CT3 CT3 HT31 CT3 HT32 CT3 HT33 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CT 1.5234 109.10 -173.96 122.03 1.4239 IC CT1 CT OA2 CA 1.5352 110.85 62.78 122.03 1.3222 IC CT2 CT OA2 CA 1.5347 111.07 -62.73 122.03 1.3222 IC CT3 CT OA2 CA 1.5307 105.00 179.91 122.03 1.3222 IC HT11 CT1 CT OA2 1.1112 109.61 171.34 110.85 1.4239 IC HT12 CT1 CT OA2 1.1067 111.59 -69.34 110.85 1.4239 IC HT13 CT1 CT OA2 1.1101 110.52 52.23 110.85 1.4239 IC HT21 CT2 CT OA2 1.1108 109.79 -171.93 111.07 1.4239 IC HT22 CT2 CT OA2 1.1080 111.70 68.38 111.07 1.4239 IC HT23 CT2 CT OA2 1.1104 110.28 -52.79 111.07 1.4239 IC HT31 CT3 CT OA2 1.1107 110.25 179.66 105.00 1.4239 IC HT32 CT3 CT OA2 1.1106 110.46 60.01 105.00 1.4239 IC HT33 CT3 CT OA2 1.1099 110.69 -60.47 105.00 1.4239 IC HT1 CG *NT CG4 1.0045 117.45 -173.12 124.06 1.4390 IC CG NT CG4 CG3 1.3436 124.06 168.56 110.90 1.5381 IC CG3 NT *CG4 HG4 1.5381 110.90 -117.89 107.42 1.1207 IC CG3 NT *CG4 CG5 1.5381 110.90 122.85 112.85 1.5408 IC NT CG4 CG3 CG2 1.4390 110.90 70.34 111.99 1.5350 IC CG4 CG2 *CG3 HG31 1.5381 111.99 121.82 109.60 1.1121 IC CG4 CG2 *CG3 HG32 1.5381 111.99 -120.93 109.55 1.1133 IC CG4 CG3 CG2 NG1 1.5381 111.99 55.21 111.05 1.5200 IC NG1 CG3 *CG2 HG21 1.5200 111.05 118.37 110.38 1.1001 IC NG1 CG3 *CG2 HG22 1.5200 111.05 -118.12 113.66 1.1004 IC CG3 CG2 NG1 CG6 1.5350 111.05 -56.35 110.70 1.5109 IC CG6 CG2 *NG1 HG1 1.5109 110.70 112.41 104.22 1.0468 IC CG6 CG2 *NG1 CBG 1.5109 110.70 -129.56 117.44 1.4972 IC CG2 CG3 CG4 CG5 1.5350 111.99 -54.61 109.17 1.5408 IC CG5 NG1 *CG6 HG61 1.5267 110.50 121.09 105.89 1.1029 IC CG5 NG1 *CG6 HG62 1.5267 110.50 -122.70 105.62 1.1023 IC CG6 CG4 *CG5 HG51 1.5267 111.14 121.28 109.72 1.1128 IC CG6 CG4 *CG5 HG52 1.5267 111.14 -122.01 109.20 1.1124 IC CG6 NG1 CBG HBG1 1.5109 111.46 -69.49 107.08 1.1032 IC HBG1 NG1 *CBG HBG2 1.1032 107.08 121.42 107.67 1.1023 IC CG2 NG1 CBG CY 1.5200 117.44 -60.42 105.99 1.4862 IC NG1 CBG CY CJ2 1.4972 105.99 -74.52 120.62 1.4104 IC NG1 CBG CY CJ1 1.4972 105.99 108.18 120.17 1.4090 IC CBG CY CJ1 CK1 1.4862 120.17 179.26 120.32 1.4003 IC CBG CY CJ2 CK2 1.4862 120.62 -179.21 120.29 1.4003 IC CY CJ1 CK1 CQ 1.4090 120.32 -0.80 120.02 1.3998 IC CJ1 CK1 CQ CK2 1.4003 120.02 -0.38 120.16 1.3998 IC CK1 CQ CK2 CJ2 1.3998 120.16 0.42 120.02 1.4003 IC CK1 CY *CJ1 HJ1 1.4003 120.32 179.88 120.54 1.0806 IC CK2 CY *CJ2 HJ2 1.4003 120.29 179.63 120.62 1.0803 IC CQ CJ1 *CK1 HK1 1.3998 120.02 -179.41 120.26 1.0821 IC CQ CJ2 *CK2 HK2 1.3998 120.02 179.38 120.29 1.0822 IC CK1 CK2 *CQ HQ 1.3998 120.16 179.21 119.92 1.0821 PRES GBP 1.00 ! C13H18N2O Gamma N-benzyl piperidine CDCA amide (01OH01), cacha ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ! OG CG3--CG3 CJ1--CK1 ATOM CG CG2O1 0.51 ! || / \ // \\ ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 GROUP ! \ ATOM CG4 CG311 -0.09 ! O24 CC2 ATOM HG4 HGA1 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2 ATOM HG32 HGA2 0.09 ! / \ | / || GROUP ! C11 C13---C17 OA1 ATOM CG2 CG324 0.15 ! Me19 | | | ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 ATOM HG1 HGP2 0.32 ! | | | ATOM CBG CG324 0.15 ! C3 C5 C7 ATOM HBG1 HGA2 0.09 ! / \ / \ / \ ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH ATOM CG6 CG324 0.15 ATOM HG61 HGA2 0.09 ! GBP (01OH01) ATOM HG62 HGA2 0.09 GROUP ATOM CG5 CG321 -0.18 ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 GROUP ATOM CY CG2R61 0.090 GROUP ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 GROUP ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 GROUP ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 GROUP ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 GROUP ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND NT CG4 BOND CG4 HG4 CG4 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG1 BOND NG1 HG1 NG1 CBG NG1 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG4 BOND CBG HBG1 CBG HBG2 CBG CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY IC HT1 CG *NT CG4 1.0266 118.64 -178.12 121.63 1.4492 IC CG NT CG4 CG3 1.3473 121.63 69.87 112.24 1.5369 IC CG3 NT *CG4 HG4 1.5369 112.24 -119.04 107.41 1.1206 IC CG3 NT *CG4 CG5 1.5369 112.24 122.72 113.59 1.5392 IC NT CG4 CG3 CG2 1.4492 112.24 63.89 110.04 1.5253 IC CG4 CG2 *CG3 HG31 1.5369 110.04 120.66 109.41 1.1118 IC CG4 CG2 *CG3 HG32 1.5369 110.04 -121.42 110.77 1.1110 IC CG4 CG3 CG2 NG1 1.5369 110.04 61.26 111.15 1.5205 IC NG1 CG3 *CG2 HG21 1.5205 111.15 118.11 110.13 1.0998 IC NG1 CG3 *CG2 HG22 1.5205 111.15 -118.76 113.26 1.0984 IC CG3 CG2 NG1 CG6 1.5253 111.15 -51.59 113.22 1.5195 IC CG6 CG2 *NG1 HG1 1.5195 113.22 114.22 104.34 1.0416 IC CG6 CG2 *NG1 CBG 1.5195 113.22 -126.12 117.02 1.4977 IC CG2 CG3 CG4 CG5 1.5253 110.04 -62.01 107.88 1.5392 IC CG5 NG1 *CG6 HG61 1.5363 113.88 122.63 105.32 1.1016 IC CG5 NG1 *CG6 HG62 1.5363 113.88 -123.87 104.60 1.0916 IC CG6 CG4 *CG5 HG51 1.5363 113.37 121.63 109.05 1.1130 IC CG6 CG4 *CG5 HG52 1.5363 113.37 -121.40 108.53 1.1122 IC CG6 NG1 CBG HBG1 1.5195 107.66 -53.18 106.80 1.1054 IC HBG1 NG1 *CBG HBG2 1.1054 106.80 120.32 107.39 1.1012 IC CG2 NG1 CBG CY 1.5205 117.02 -43.82 108.23 1.4811 IC NG1 CBG CY CJ2 1.4977 108.23 -74.54 121.06 1.4098 IC NG1 CBG CY CJ1 1.4977 108.23 108.39 119.67 1.4082 IC CBG CY CJ1 CK1 1.4811 119.67 177.88 120.36 1.3993 IC CBG CY CJ2 CK2 1.4811 121.06 -178.43 120.27 1.4006 IC CY CJ1 CK1 CQ 1.4082 120.36 0.02 120.02 1.4003 IC CJ1 CK1 CQ CK2 1.3993 120.02 -0.22 120.13 1.4003 IC CK1 CQ CK2 CJ2 1.4003 120.13 -0.37 120.00 1.4006 IC CK1 CY *CJ1 HJ1 1.3993 120.36 -179.98 119.89 1.0829 IC CK2 CY *CJ2 HJ2 1.4006 120.27 179.99 120.44 1.0799 IC CQ CJ1 *CK1 HK1 1.4003 120.02 179.98 119.90 1.0816 IC CQ CJ2 *CK2 HK2 1.4003 120.00 179.79 119.85 1.0816 IC CK1 CK2 *CQ HQ 1.4003 120.13 -179.96 120.17 1.0809 PRES 3MSB 1.00 ! C16H22N2O3 (010206(S)D), cacha ! This compound has 3-methylamine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT1 HGP1 0.47 ! HG31 HG32 GROUP ! \ / ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) ATOM HGT1 HGA2 0.09 ! || / \ ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 ATOM HG1 HGA1 0.09 ! \ GROUP ! O24 CC2 ATOM CG2 CG324 0.20 ! || / ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG31 HGP2 0.32 ! / \ | / || \ __ / ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 CD2--CE2 ATOM CG4 CG324 0.20 ! Me19 | | | ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CG5 CG321 -0.18 ! | | | ATOM HG51 HGA2 0.09 ! C3 C5 C7 ATOM HG52 HGA2 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ! 3MSB (010206(S)D) ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5242 109.43 -175.98 116.64 1.4476 IC CA OA2 CB HB1 1.3349 116.64 -66.79 110.19 1.1154 IC CA OA2 CB CZ 1.3349 116.64 173.93 113.76 1.5066 IC CA OA2 CB HB2 1.3349 116.64 52.26 110.81 1.1160 IC OA2 CB CZ CD2 1.4476 113.76 -121.85 121.23 1.4061 IC OA2 CB CZ CD1 1.4476 113.76 58.24 119.30 1.4048 IC CD1 CD2 *CZ CB 1.4048 119.46 -179.91 121.23 1.5066 IC CD2 CZ CB HB1 1.4061 121.23 116.69 106.33 1.1154 IC CD2 CZ CB HB2 1.4061 121.23 1.46 107.82 1.1160 IC CB CZ CD1 CE1 1.5066 119.30 179.43 120.30 1.4015 IC CB CZ CD2 CE2 1.5066 121.23 -179.39 120.20 1.4017 IC CZ CD1 CE1 CP 1.4048 120.30 -0.06 119.94 1.4007 IC CD1 CE1 CP CE2 1.4015 119.94 0.59 120.09 1.4005 IC CE1 CP CE2 CD2 1.4007 120.09 -0.55 120.00 1.4017 IC CE1 CZ *CD1 HD1 1.4015 120.30 -179.46 119.80 1.0800 IC CE2 CZ *CD2 HD2 1.4017 120.20 179.33 120.22 1.0796 IC CP CD1 *CE1 HE1 1.4007 119.94 -179.52 120.13 1.0809 IC CP CD2 *CE2 HE2 1.4005 120.00 179.30 120.26 1.0816 IC CE1 CE2 *CP HP 1.4007 120.09 -179.58 119.77 1.0816 IC OG CG NT CGT 1.2239 122.72 8.77 127.00 1.4536 IC CG NT CGT HGT1 1.3478 127.00 -166.41 108.33 1.1149 IC HGT1 NT *CGT HGT2 1.1149 108.33 -115.07 108.53 1.1163 IC HGT1 NT *CGT CG1 1.1149 108.33 122.64 117.09 1.5521 IC NT CGT CG1 HG1 1.4536 117.09 69.36 107.48 1.1153 IC HG1 CGT *CG1 CG2 1.1153 107.48 -120.14 111.66 1.5358 IC HG1 CGT *CG1 CG6 1.1153 107.48 117.07 111.60 1.5466 IC CGT CG1 CG2 NG3 1.5521 111.66 179.38 109.85 1.5116 IC NG3 CG1 *CG2 HG21 1.5116 109.85 117.59 112.64 1.1015 IC NG3 CG1 *CG2 HG22 1.5116 109.85 -116.95 113.19 1.1017 IC CG1 CG2 NG3 CG4 1.5358 109.85 58.38 113.58 1.5084 IC CG4 CG2 *NG3 HG31 1.5084 113.58 124.95 110.23 1.0062 IC CG4 CG2 *NG3 HG32 1.5084 113.58 -119.78 107.15 1.0101 IC CG2 NG3 CG4 CG5 1.5116 113.58 -56.76 109.83 1.5314 IC CG5 NG3 *CG4 HG41 1.5314 109.83 121.43 105.28 1.1036 IC CG5 NG3 *CG4 HG42 1.5314 109.83 -122.30 105.71 1.1029 IC NG3 CG4 CG5 CG6 1.5084 109.83 54.36 110.96 1.5395 IC CG6 CG4 *CG5 HG51 1.5395 110.96 121.27 109.75 1.1134 IC CG6 CG4 *CG5 HG52 1.5395 110.96 -120.76 109.94 1.1139 IC CG5 CG1 *CG6 HG61 1.5395 111.48 -121.73 109.49 1.1129 IC CG5 CG1 *CG6 HG62 1.5395 111.48 120.99 109.18 1.1142 PRES 3MPS 1.00 ! C7H14N2O (01OH06(S)D), cacha ! This compound has 3-methylamine piperidine at gamma position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT1 HGP1 0.47 ! HG31 HG32 GROUP ! \ / ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) ATOM HGT1 HGA2 0.09 ! || / \ ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 ATOM HG1 HGA1 0.09 ! \ GROUP ! O24 CC2 ATOM CG2 CG324 0.20 ! || / ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2 ATOM HG31 HGP2 0.32 ! / \ | / || ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 ATOM CG4 CG324 0.20 ! Me19 | | | ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CG5 CG321 -0.18 ! | | | ATOM HG51 HGA2 0.09 ! C3 C5 C7 ATOM HG52 HGA2 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ! 3MPS (01OH06(S)D) ATOM HG62 HGA2 0.09 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CGT 1.2256 121.47 0.79 124.59 1.4530 IC CG NT CGT HGT1 1.3392 124.59 149.80 107.85 1.1137 IC HGT1 NT *CGT HGT2 1.1137 107.85 -116.73 111.18 1.1160 IC HGT1 NT *CGT CG1 1.1137 107.85 120.07 112.47 1.5501 IC NT CGT CG1 HG1 1.4530 112.47 83.79 108.38 1.1140 IC HG1 CGT *CG1 CG2 1.1140 108.38 -117.58 107.80 1.5302 IC HG1 CGT *CG1 CG6 1.1140 108.38 121.37 112.80 1.5449 IC CGT CG1 CG2 NG3 1.5501 107.80 -170.55 116.62 1.5027 IC NG3 CG1 *CG2 HG21 1.5027 116.62 118.47 110.90 1.1061 IC NG3 CG1 *CG2 HG22 1.5027 116.62 -118.49 111.67 1.1051 IC CG1 CG2 NG3 CG4 1.5302 116.62 51.23 112.51 1.4981 IC CG4 CG2 *NG3 HG31 1.4981 112.51 122.69 105.66 1.0135 IC CG4 CG2 *NG3 HG32 1.4981 112.51 -123.39 108.44 1.0051 IC CG2 NG3 CG4 CG5 1.5027 112.51 -54.57 109.73 1.5348 IC CG5 NG3 *CG4 HG41 1.5348 109.73 121.15 105.11 1.1047 IC CG5 NG3 *CG4 HG42 1.5348 109.73 -122.63 105.65 1.1024 IC NG3 CG4 CG5 CG6 1.4981 109.73 58.52 111.11 1.5422 IC CG6 CG4 *CG5 HG51 1.5422 111.11 120.57 109.36 1.1130 IC CG6 CG4 *CG5 HG52 1.5422 111.11 -121.30 110.16 1.1129 IC CG5 CG1 *CG6 HG61 1.5422 112.06 -120.86 108.98 1.1136 IC CG5 CG1 *CG6 HG62 1.5422 112.06 122.05 109.12 1.1131 PRES 2MRB 1.00 ! C16H22N2O3 (010207(R)D), cacha ! This compound has 2-methylamine piperidine at gamma position ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! HG21 HG22 ATOM OG OG2D1 -0.51 ! \ / ATOM NT NG2S1 -0.47 ! OG (+1)NG2--CG3 ATOM HT1 HGP1 0.47 ! || / \ GROUP ! CG---NT--CGT--CG1 CG4 ATOM CGT CG321 -0.18 ! / HT1 \ / ATOM HGT1 HGA2 0.09 ! CC3 CG6--CG5 ATOM HGT2 HGA2 0.09 ! \ GROUP ! O24 CC2 ATOM CG1 CG314 0.29 ! || / ATOM HG1 HGA1 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM NG2 NG3P2 -0.40 ! | \ / \ / \ / \ // \\ ATOM HG21 HGP2 0.32 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG22 HGP2 0.32 ! / \ | / || \ __ / ATOM CG3 CG324 0.20 ! C11 C13---C17 OA1 CD2--CE2 ATOM HG31 HGA2 0.09 ! Me19 | | | ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CG4 CG321 -0.18 ! C2 C10 C8 C15 ATOM HG41 HGA2 0.09 ! | | | ATOM HG42 HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CG5 CG321 -0.18 ! HO C4 C6 OH ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 ! 2MRB (010207(R)D) GROUP ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 NG2 BOND NG2 HG21 NG2 HG22 NG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5251 109.19 -176.53 116.84 1.4475 IC CA OA2 CB HB1 1.3348 116.84 -68.03 110.09 1.1153 IC CA OA2 CB CZ 1.3348 116.84 172.79 113.76 1.5068 IC CA OA2 CB HB2 1.3348 116.84 51.08 110.88 1.1157 IC OA2 CB CZ CD2 1.4475 113.76 -124.12 121.29 1.4063 IC OA2 CB CZ CD1 1.4475 113.76 56.05 119.26 1.4048 IC CD1 CD2 *CZ CB 1.4048 119.45 -179.83 121.29 1.5068 IC CD2 CZ CB HB1 1.4063 121.29 114.56 106.29 1.1153 IC CD2 CZ CB HB2 1.4063 121.29 -0.72 107.81 1.1157 IC CB CZ CD1 CE1 1.5068 119.26 179.46 120.31 1.4013 IC CB CZ CD2 CE2 1.5068 121.29 -179.43 120.20 1.4018 IC CZ CD1 CE1 CP 1.4048 120.31 -0.08 119.94 1.4006 IC CD1 CE1 CP CE2 1.4013 119.94 0.52 120.09 1.4005 IC CE1 CP CE2 CD2 1.4006 120.09 -0.49 119.99 1.4018 IC CE1 CZ *CD1 HD1 1.4013 120.31 -179.47 119.81 1.0801 IC CE2 CZ *CD2 HD2 1.4018 120.20 179.31 120.24 1.0794 IC CP CD1 *CE1 HE1 1.4006 119.94 -179.52 120.12 1.0810 IC CP CD2 *CE2 HE2 1.4005 119.99 179.29 120.29 1.0816 IC CE1 CE2 *CP HP 1.4006 120.09 -179.60 119.79 1.0814 IC OG CG NT CGT 1.2258 121.77 -9.07 126.25 1.4608 IC CG NT CGT HGT1 1.3453 126.25 -63.13 109.68 1.1149 IC HGT1 NT *CGT HGT2 1.1149 109.68 -114.42 107.29 1.1157 IC HGT1 NT *CGT CG1 1.1149 109.68 125.80 116.89 1.5520 IC NT CGT CG1 HG1 1.4608 116.89 35.97 109.62 1.1148 IC HG1 CGT *CG1 NG2 1.1148 109.62 -115.37 110.19 1.4997 IC HG1 CGT *CG1 CG6 1.1148 109.62 123.79 114.12 1.5387 IC CGT CG1 NG2 CG3 1.5520 110.19 177.33 115.54 1.5017 IC CG3 CG1 *NG2 HG21 1.5017 115.54 122.50 107.57 1.0057 IC CG3 CG1 *NG2 HG22 1.5017 115.54 -125.48 106.76 1.0184 IC CG1 NG2 CG3 CG4 1.4997 115.54 58.81 109.20 1.5329 IC CG4 NG2 *CG3 HG31 1.5329 109.20 122.16 105.67 1.1031 IC CG4 NG2 *CG3 HG32 1.5329 109.20 -121.59 105.38 1.1034 IC NG2 CG3 CG4 CG5 1.5017 109.20 -54.65 110.62 1.5388 IC CG5 CG3 *CG4 HG41 1.5388 110.62 120.78 109.91 1.1136 IC CG5 CG3 *CG4 HG42 1.5388 110.62 -121.22 109.75 1.1132 IC CG3 CG4 CG5 CG6 1.5329 110.62 54.76 111.04 1.5388 IC CG6 CG4 *CG5 HG51 1.5388 111.04 121.50 109.70 1.1146 IC CG6 CG4 *CG5 HG52 1.5388 111.04 -121.04 109.48 1.1142 IC CG5 CG1 *CG6 HG61 1.5388 112.23 -121.77 109.64 1.1131 IC CG5 CG1 *CG6 HG62 1.5388 112.23 120.96 109.15 1.1133 PRES 2MPR 1.00 ! C7H14N2O (01OH07(R)D), cacha ! This compound has 3-methylamine piperidine at gamma position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ! HG31 HG32 ATOM HT1 HGP1 0.47 ! \ / GROUP ! OG (+1) NG2--CG3 ATOM CGT CG321 -0.18 ! || / \ ATOM HGT1 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 ATOM HGT2 HGA2 0.09 ! / HT1 \ / GROUP ! CC3 CG6--CG5 ATOM CG1 CG314 0.29 ! \ ATOM HG1 HGA1 0.09 ! O24 CC2 ATOM NG2 NG3P2 -0.40 ! || / ATOM HG21 HGP2 0.32 ! H Me21 C22 C24 CC1 ATOM HG22 HGP2 0.32 ! | \ / \ / \ / \ ATOM CG3 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2 ATOM HG31 HGA2 0.09 ! / \ | / || ATOM HG32 HGA2 0.09 ! C11 C13---C17 OA1 GROUP ! Me19 | | | ATOM CG4 CG321 -0.18 ! C1 | C9 C14 C16 ATOM HG41 HGA2 0.09 ! / \|/ \ / \ / ATOM HG42 HGA2 0.09 ! C2 C10 C8 C15 GROUP ! | | | ATOM CG5 CG321 -0.18 ! C3 C5 C7 ATOM HG51 HGA2 0.09 ! / \ / \ / \ ATOM HG52 HGA2 0.09 ! HO C4 C6 OH GROUP ATOM CG6 CG321 -0.18 ! 2MPR (01OH07(R)D) ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 NG2 BOND NG2 HG21 NG2 HG22 NG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CGT 1.2249 120.85 2.25 124.27 1.4568 IC CG NT CGT HGT1 1.3396 124.27 30.47 110.37 1.1163 IC HGT1 NT *CGT HGT2 1.1163 110.37 -116.64 108.59 1.1139 IC HGT1 NT *CGT CG1 1.1163 110.37 122.29 114.28 1.5472 IC NT CGT CG1 HG1 1.4568 114.28 59.06 109.88 1.1157 IC HG1 CGT *CG1 NG2 1.1157 109.88 -114.17 109.66 1.4973 IC HG1 CGT *CG1 CG6 1.1157 109.88 124.35 113.41 1.5401 IC CGT CG1 NG2 CG3 1.5472 109.66 -178.06 116.32 1.5005 IC CG3 CG1 *NG2 HG21 1.5005 116.32 127.76 109.81 1.0015 IC CG3 CG1 *NG2 HG22 1.5005 116.32 -119.58 107.88 1.0283 IC CG1 NG2 CG3 CG4 1.4973 116.32 55.95 110.16 1.5319 IC CG4 NG2 *CG3 HG31 1.5319 110.16 123.18 105.12 1.1032 IC CG4 NG2 *CG3 HG32 1.5319 110.16 -121.78 104.60 1.1046 IC NG2 CG3 CG4 CG5 1.5005 110.16 -54.81 110.24 1.5379 IC CG5 CG3 *CG4 HG41 1.5379 110.24 120.63 109.71 1.1131 IC CG5 CG3 *CG4 HG42 1.5379 110.24 -121.15 109.61 1.1124 IC CG3 CG4 CG5 CG6 1.5319 110.24 56.12 110.68 1.5379 IC CG6 CG4 *CG5 HG51 1.5379 110.68 121.42 109.84 1.1137 IC CG6 CG4 *CG5 HG52 1.5379 110.68 -120.66 109.46 1.1142 IC CG5 CG1 *CG6 HG61 1.5379 112.67 -121.48 109.11 1.1130 IC CG5 CG1 *CG6 HG62 1.5379 112.67 121.55 108.86 1.1125 !End of Pablo's compounds !Start of Rana's and Swan's compounds RESI 2AMP 0.00 ! C7H8N2O 2-acetamide pyridine, cacha ! Made in order to build Polli's compounds (Rana & Swan) GROUP ATOM NZ NG2R60 -0.600 GROUP ATOM CE1 CG2R64 0.600 ! O NZ---CE2 GROUP ! || // \\ ATOM CD1 CG2R61 -0.115 ! CM--C--NE--CE1 CD2 ATOM HD1 HGR61 0.115 ! | \ ___ / GROUP ! HE CD1---CG ATOM CE2 CG2R61 0.180 ATOM HE2 HGR62 0.120 ! 2AMP GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 GROUP ATOM NE NG2S1 -0.620 ATOM HE HGP1 0.320 ATOM C CG2O1 0.550 ATOM O OG2D1 -0.550 ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CG HG CG CD1 CD1 HD1 CD1 CE1 CE1 NZ BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CG BOND CE1 NE NE HE NE C C O BOND C CM CM HM1 CM HM2 CM HM3 IMPR C CM NE O IMPR CE1 CD1 NZ NE IC CG CD1 CE1 NZ 1.4062 118.77 0.00 121.31 1.3330 IC CD1 CE1 NZ CE2 1.4051 121.31 0.00 120.60 1.3284 IC CE1 NZ CE2 CD2 1.3330 120.60 0.00 122.45 1.4013 IC CD1 CD2 *CG HG 1.4062 118.83 -180.00 120.71 1.0807 IC CE1 CG *CD1 HD1 1.4051 118.77 180.00 119.96 1.0752 IC CE2 CG *CD2 HD2 1.4013 118.04 -180.00 121.24 1.0783 IC NZ CD1 *CE1 NE 1.3330 121.31 -180.00 127.83 1.3987 IC NZ CD2 *CE2 HE2 1.3284 122.45 -180.00 122.15 1.0814 IC CD1 CE1 NE C 1.4051 127.83 0.00 128.89 1.3256 IC C CE1 *NE HE 1.3256 128.89 180.00 109.18 0.9866 IC CE1 NE C CM 1.3987 128.89 180.00 115.52 1.4775 IC CM NE *C O 1.4775 115.52 -180.00 123.87 1.2197 IC O C CM HM1 1.2197 120.61 119.56 110.14 1.1102 IC O C CM HM2 1.2197 120.61 0.00 109.25 1.1117 IC O C CM HM3 1.2197 120.61 -119.56 110.14 1.1102 RESI 3AMP 0.00 ! C7H8N2O 3-acetamide pyridine, cacha ! Made in order to build Polli's compounds (Rana & Swan) ! Taken from Acetamide and 4-Amino pyridine GROUP ATOM NZ NG2R60 -0.600 GROUP ATOM CE1 CG2R61 0.180 ATOM HE1 HGR62 0.120 ! O CE1--NZ GROUP ! || // \\ ATOM CE2 CG2R61 0.180 ! CM--C--ND--CD1 CE2 ATOM HE2 HGR62 0.120 ! | \ ___ / GROUP ! HD CG---CD2 ATOM CD1 CG2R61 0.300 GROUP ! 3AMP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 GROUP ATOM ND NG2S1 -0.620 ATOM HD HGP1 0.320 ATOM C CG2O1 0.550 ATOM O OG2D1 -0.550 ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CG HG CG CD1 CD1 CE1 CE1 HE1 CE1 NZ BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CG BOND CD1 ND ND HD ND C C O BOND C CM CM HM1 CM HM2 CM HM3 IMPR C CM ND O IC CG CD1 CE1 NZ 1.4078 116.24 0.00 123.96 1.3381 IC CD1 CE1 NZ CE2 1.4129 123.96 0.00 118.93 1.3292 IC CE1 NZ CE2 CD2 1.3381 118.93 0.00 122.82 1.4035 IC CD1 CD2 *CG HG 1.4078 120.04 -180.00 120.23 1.0783 IC CE1 CG *CD1 ND 1.4129 116.24 -180.00 116.49 1.4213 IC CE2 CG *CD2 HD2 1.4035 118.00 180.00 121.42 1.0782 IC NZ CD1 *CE1 HE1 1.3381 123.96 180.00 121.22 1.0791 IC NZ CD2 *CE2 HE2 1.3292 122.82 -180.00 122.14 1.0813 IC CE1 CD1 ND C 1.4129 127.27 0.00 126.90 1.3351 IC C CD1 *ND HD 1.3351 126.90 -180.00 115.12 0.9890 IC CD1 ND C CM 1.4213 126.90 -180.00 115.67 1.4776 IC CM ND *C O 1.4776 115.67 180.00 123.60 1.2198 IC O C CM HM1 1.2198 120.73 119.43 110.22 1.1101 IC O C CM HM2 1.2198 120.73 0.00 109.14 1.1120 IC O C CM HM3 1.2198 120.73 -119.43 110.22 1.1101 RESI 2AMF 0.00 ! C8H9NO2 2-acetamide phenol, cacha ! Made in order to build Polli's compounds (Rana & Swan) GROUP ATOM CM CG331 -0.27 ! O CD2--CE2 ATOM HM1 HGA3 0.09 ! || // \\ ATOM HM2 HGA3 0.09 ! CM--C--N---CZ CP ATOM HM3 HGA3 0.09 ! | \ ___ / GROUP ! H CD1---CE2 ATOM C CG2O1 0.52 ! | ATOM O OG2D1 -0.52 ! OH(D) GROUP ATOM N NG2S1 -0.47 ! 2AMF ATOM H HGP1 0.33 ATOM CZ CG2R61 0.14 GROUP ATOM CD1 CG2R61 0.11 ATOM OD OG311 -0.53 ATOM HOD HGP1 0.42 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 BOND CM HM1 CM HM2 CM HM3 CM C BOND C O C N N H N CZ BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ IMPR C CM N O IC N C CM HM1 1.3407 115.20 180.00 109.20 1.1118 IC HM1 C *CM HM2 1.1118 109.20 119.48 110.20 1.1102 IC HM1 C *CM HM3 1.1118 109.20 -119.48 110.20 1.1102 IC N CM *C O 1.3407 115.20 -180.00 119.94 1.2226 IC CM C N CZ 1.4807 115.20 -180.00 130.65 1.4232 IC CZ C *N H 1.4232 130.65 180.00 118.72 0.9928 IC C N CZ CD1 1.3407 130.65 180.00 115.77 1.4149 IC CD1 N *CZ CD2 1.4149 115.77 -180.00 125.20 1.4017 IC N CZ CD1 CE1 1.4232 115.77 -180.00 120.37 1.4002 IC CE1 CZ *CD1 OD 1.4002 120.37 180.00 120.75 1.4188 IC CZ CD1 OD HOD 1.4149 120.75 -180.00 107.60 0.9602 IC CZ CD1 CE1 CP 1.4149 120.37 0.00 120.00 1.4013 IC CP CD1 *CE1 HE1 1.4013 120.00 180.00 120.56 1.0796 IC CD1 CE1 CP CE2 1.4002 120.00 0.00 119.97 1.3995 IC CE2 CE1 *CP HP 1.3995 119.97 180.00 120.14 1.0810 IC CD2 CP *CE2 HE2 1.4022 120.11 180.00 120.11 1.0811 IC CE2 CZ *CD2 HD2 1.4022 120.52 180.00 120.79 1.0784 IC HM1 C *CM HM2 1.1118 109.20 119.48 110.20 1.1102 IC HM1 C *CM HM3 1.1118 109.20 -119.48 110.20 1.1102 IC HM1 CM C N 1.1118 109.20 180.00 115.20 1.3407 IC N CM *C O 1.3407 115.20 -180.00 119.94 1.2226 IC CM C N CZ 1.4807 115.20 -180.00 130.65 1.4232 IC CZ C *N H 1.4232 130.65 180.00 118.72 0.9928 IC C N CZ CD1 1.3407 130.65 180.00 115.77 1.4149 IC CD1 N *CZ CD2 1.4149 115.77 -180.00 125.20 1.4017 IC N CZ CD1 CE1 1.4232 115.77 -180.00 120.37 1.4002 IC CE1 CZ *CD1 OD 1.4002 120.37 180.00 120.75 1.4188 IC CZ CD1 OD HOD 1.4149 120.75 -180.00 107.60 0.9602 IC CZ CD1 CE1 CP 1.4149 120.37 0.00 120.00 1.4013 IC CP CD1 *CE1 HE1 1.4013 120.00 180.00 120.56 1.0796 IC CD1 CE1 CP CE2 1.4002 120.00 0.00 119.97 1.3995 IC CE2 CE1 *CP HP 1.3995 119.97 180.00 120.14 1.0810 IC CD2 CP *CE2 HE2 1.4022 120.11 180.00 120.11 1.0811 IC CE2 CZ *CD2 HD2 1.4022 120.52 180.00 120.79 1.0784 PRES 2APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-2-Amino Pyridine GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ! CJ1--CK1 ATOM HC3B HGA2 0.09 ! // \\ GROUP ! OA1 CY CJ ATOM CG CG2O1 0.52 ! | / \ __ / ATOM OG OG2D1 -0.52 ! O24 CA--OA2---CB CJ2--CK2 GROUP ! || | ATOM NG NG2S1 -0.47 ! OH Me21 C22 C24 CC1 CC3 NG NZ---CE2 ATOM HG HGP1 0.33 ! | \ / \ / \ / \ / \ / \ // \\ ATOM CZ CG2R64 0.44 ! C12 Me18 C20 C23 NH CC2 CG CZ CP GROUP ! / \ | / || \ __ / ATOM CD1 CG2R61 -0.115 ! C11 C13---C17 OG CD1--CE1 ATOM HD1 HGR61 0.115 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CE1 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HE1 HGR61 0.115 ! C2 C10 C8 C15 GROUP ! | | | ATOM NZ NG2R60 -0.600 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CE2 CG2R61 0.180 ! HO C4 C6 OH ATOM HE2 HGR62 0.120 GROUP ! 2APP ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IMPR CZ CD1 NZ NG IC CC1 CA OA2 CB 1.5262 109.01 178.05 116.10 1.4465 IC HB1 CB OA2 CA 1.1154 110.02 65.56 116.10 1.3439 IC HB2 CB OA2 CA 1.1163 110.83 -53.21 116.10 1.3439 IC CY CB OA2 CA 1.5059 113.59 -172.68 116.10 1.3439 IC CJ2 CY CB OA2 1.4053 121.33 -117.38 113.59 1.4465 IC CJ1 CY CB OA2 1.4046 119.17 62.26 113.59 1.4465 IC CJ1 CJ2 *CY CB 1.4046 119.50 179.63 121.33 1.5059 IC CJ2 CY CB HB1 1.4053 121.33 5.26 108.43 1.1154 IC CJ2 CY CB HB2 1.4053 121.33 120.54 106.20 1.1163 IC CB CY CJ1 CK1 1.5059 119.17 180.00 120.30 1.4013 IC CB CY CJ2 CK2 1.5059 121.33 -179.83 120.18 1.4021 IC CY CJ1 CK1 CQ 1.4046 120.30 -0.04 119.97 1.4011 IC CJ1 CK1 CQ CK2 1.4013 119.97 0.26 120.01 1.4014 IC CK1 CQ CK2 CJ2 1.4011 120.01 -0.08 120.03 1.4021 IC CK1 CY *CJ1 HJ1 1.4013 120.30 -179.72 119.65 1.0800 IC CK2 CY *CJ2 HJ2 1.4021 120.18 179.57 120.00 1.0798 IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0806 IC CQ CJ2 *CK2 HK2 1.4014 120.03 179.68 120.00 1.0809 IC CK1 CK2 *CQ HQ 1.4011 120.01 179.51 120.01 1.0810 IC CC2 CC3 CG NG 1.5506 112.89 -51.60 116.27 1.3339 IC NG CC3 *CG OG 1.3339 116.27 -171.32 119.51 1.2231 IC CG CZ *NG HG 1.3339 129.72 179.61 108.48 0.9872 IC CC3 CG NG CZ 1.4983 116.27 -177.09 129.72 1.4019 IC CG NG CZ CD1 1.3339 129.72 -1.35 127.25 1.4046 IC NG CZ CD1 CE1 1.4019 127.25 -179.67 118.62 1.4059 IC CZ CD1 CE1 CP 1.4046 118.62 0.11 118.91 1.4033 IC CD1 CE1 CP CE2 1.4059 118.91 0.05 118.00 1.4015 IC CE1 CP CE2 NZ 1.4033 118.00 0.00 122.46 1.3291 IC CZ CE1 *CD1 HD1 1.4046 118.62 -179.85 120.00 1.0758 IC CD1 CP *CE1 HE1 1.4059 118.91 -179.93 120.66 1.0804 IC CE1 CE2 *CP HP 1.4033 118.00 -179.93 120.73 1.0781 IC CP NZ *CE2 HE2 1.4015 122.46 -179.90 115.36 1.0811 PRES 3APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-3-Amino Pyridine GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! CJ1--CK1 ATOM HC3A HGA2 0.09 ! // \\ ATOM HC3B HGA2 0.09 ! OA1 CY CJ GROUP ! | / \ __ / ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 ATOM HE1 HGR61 0.115 ! | | | GROUP ! C3 C5 C7 ATOM CP CG2R61 0.180 ! / \ / \ / \ ATOM HP HGR62 0.120 ! HO C4 C6 OH GROUP ATOM NZ NG2R60 -0.600 ! 3APP GROUP ATOM CD2 CG2R61 0.180 ATOM HD2 HGR62 0.120 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5266 108.91 178.06 116.23 1.4463 IC HC1 CC1 CA OA2 1.1142 106.59 -130.75 108.91 1.3434 IC HB1 CB OA2 CA 1.1155 110.00 65.28 116.23 1.3434 IC HB2 CB OA2 CA 1.1162 110.85 -53.55 116.23 1.3434 IC CY CB OA2 CA 1.5060 113.54 -173.02 116.23 1.3434 IC CJ2 CY CB OA2 1.4052 121.32 -119.04 113.54 1.4463 IC CJ1 CY CB OA2 1.4048 119.18 60.58 113.54 1.4463 IC CJ1 CJ2 *CY CB 1.4048 119.50 179.62 121.32 1.5060 IC CJ2 CY CB HB1 1.4052 121.32 3.54 108.43 1.1155 IC CJ2 CY CB HB2 1.4052 121.32 118.88 106.21 1.1162 IC CB CY CJ1 CK1 1.5060 119.18 -179.91 120.31 1.4013 IC CB CY CJ2 CK2 1.5060 121.32 -179.85 120.18 1.4020 IC CY CJ1 CK1 CQ 1.4048 120.31 -0.14 119.96 1.4010 IC CJ1 CK1 CQ CK2 1.4013 119.96 0.31 120.01 1.4014 IC CK1 CQ CK2 CJ2 1.4010 120.01 -0.07 120.03 1.4020 IC CK1 CY *CJ1 HJ1 1.4013 120.31 -179.69 119.67 1.0799 IC CK2 CY *CJ2 HJ2 1.4020 120.18 179.59 120.02 1.0799 IC CQ CJ1 *CK1 HK1 1.4010 119.96 -179.53 120.06 1.0806 IC CQ CJ2 *CK2 HK2 1.4014 120.03 179.71 119.99 1.0809 IC CK1 CK2 *CQ HQ 1.4010 120.01 179.51 120.00 1.0810 IC CC2 CC3 CG NG 1.5518 114.60 -1.21 117.28 1.3433 IC CG CZ *NG HG 1.3433 128.03 179.74 114.63 0.9895 IC NG CC3 *CG OG 1.3433 117.28 179.83 119.35 1.2229 IC CC3 CG NG CZ 1.5020 117.28 -180.00 128.03 1.4225 IC CG NG CZ CD2 1.3433 128.03 0.97 126.45 1.4111 IC NG CZ CD2 NZ 1.4225 126.45 -179.92 123.66 1.3358 IC CZ CD2 NZ CP 1.4111 123.66 0.08 119.08 1.3292 IC CD2 NZ CP CE1 1.3358 119.08 0.01 122.82 1.4031 IC NZ CP CE1 CD1 1.3292 122.82 -0.03 118.00 1.4059 IC CZ NZ *CD2 HD2 1.4111 123.66 179.94 114.79 1.0796 IC CZ CE1 *CD1 HD1 1.4072 119.79 179.97 120.05 1.0788 IC NZ CE1 *CP HP 1.3292 122.82 -179.97 122.13 1.0811 IC CP CD1 *CE1 HE1 1.4031 118.00 -179.98 121.40 1.0780 PRES 4APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-4-Amino Pyridine GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! CJ1--CK1 ATOM HC3A HGA2 0.09 ! // \\ ATOM HC3B HGA2 0.09 ! OA1 CY CJ GROUP ! | / \ __ / ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ NZ ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 0.180 ! C2 C10 C8 C15 ATOM HE1 HGR62 0.120 ! | | | GROUP ! C3 C5 C7 ATOM NZ NG2R60 -0.600 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CE2 CG2R61 0.180 ATOM HE2 HGR62 0.120 ! 4APP GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 NZ BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5239 109.11 -178.78 115.31 1.4471 IC HC1 CC1 CA OA2 1.1142 106.36 -134.92 109.11 1.3428 IC HB1 CB OA2 CA 1.1164 110.53 59.14 115.31 1.3428 IC HB2 CB OA2 CA 1.1163 110.59 -59.32 115.31 1.3428 IC CY CB OA2 CA 1.5039 113.58 179.91 115.31 1.3428 IC CJ2 CY CB OA2 1.4046 120.24 -90.36 113.58 1.4471 IC CJ1 CY CB OA2 1.4046 120.15 88.42 113.58 1.4471 IC CJ1 CJ2 *CY CB 1.4046 119.59 178.79 120.24 1.5039 IC CJ2 CY CB HB1 1.4046 120.24 32.16 107.39 1.1164 IC CJ2 CY CB HB2 1.4046 120.24 147.07 107.36 1.1163 IC CB CY CJ1 CK1 1.5039 120.15 -179.79 120.20 1.4015 IC CB CY CJ2 CK2 1.5039 120.24 179.88 120.19 1.4014 IC CY CJ1 CK1 CQ 1.4046 120.20 0.22 119.97 1.4011 IC CJ1 CK1 CQ CK2 1.4015 119.97 0.48 120.05 1.4013 IC CK1 CQ CK2 CJ2 1.4011 120.05 -0.39 119.98 1.4014 IC CK1 CY *CJ1 HJ1 1.4015 120.20 -179.58 119.84 1.0799 IC CK2 CY *CJ2 HJ2 1.4014 120.19 179.62 119.87 1.0801 IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0807 IC CQ CJ2 *CK2 HK2 1.4013 119.98 179.84 119.99 1.0807 IC CK1 CK2 *CQ HQ 1.4011 120.05 -179.99 119.97 1.0807 IC CC2 CC3 CG NG 1.5519 114.52 13.37 116.90 1.3446 IC CG CZ *NG HG 1.3446 129.26 179.52 114.04 0.9891 IC NG CC3 *CG OG 1.3446 116.90 179.10 119.13 1.2233 IC CC3 CG NG CZ 1.5018 116.90 -179.26 129.26 1.4198 IC CG NG CZ CD1 1.3446 129.26 13.81 125.21 1.4032 IC NG CZ CD1 CE1 1.4198 125.21 -179.01 118.21 1.4006 IC CZ CD1 CE1 NZ 1.4032 118.21 0.20 122.53 1.3294 IC CD1 CE1 NZ CE2 1.4006 122.53 0.20 119.84 1.3282 IC CE1 NZ CE2 CD2 1.3294 119.84 -0.22 122.41 1.4002 IC CE1 CZ *CD1 HD1 1.4006 118.21 -179.44 122.09 1.0759 IC CE2 CZ *CD2 HD2 1.4002 118.32 -179.68 121.19 1.0764 IC NZ CD1 *CE1 HE1 1.3294 122.53 180.00 122.17 1.0810 IC NZ CD2 *CE2 HE2 1.3282 122.41 -179.87 122.39 1.0812 PRES 2APD 0.00 ! C7H7N2O Gamma-2-Amino Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CM3 NG NZ---CE2 ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CGP CZ CP ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OGP CD1--CE1 ATOM CZ CG2R64 0.44 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM NZ NG2R60 -0.600 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CE2 CG2R61 0.180 ! | | | ATOM HE2 HGR62 0.120 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 -0.115 ! HO C4 C6 OH ATOM HP HGR61 0.115 GROUP ! 2APD ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IMPR CZ CD1 NZ NG IC CC2 CC3 CG NG 1.5492 112.40 -59.01 115.58 1.3349 IC CG CZ *NG HG 1.3349 129.91 179.75 110.72 0.9908 IC NG CC3 *CG OG 1.3349 115.58 -178.53 120.70 1.2263 IC CC3 CG NG CZ 1.4933 115.58 179.53 129.91 1.4027 IC CG NG CZ CD1 1.3349 129.91 -0.74 126.80 1.4060 IC NG CZ CD1 CE1 1.4027 126.80 -179.83 118.92 1.4057 IC CZ CD1 CE1 CP 1.4060 118.92 0.05 118.91 1.4029 IC CD1 CE1 CP CE2 1.4057 118.91 0.03 117.98 1.4010 IC CE1 CP CE2 NZ 1.4029 117.98 0.00 122.23 1.3271 IC CZ CE1 *CD1 HD1 1.4060 118.92 -179.87 119.87 1.0753 IC CD1 CP *CE1 HE1 1.4057 118.91 -179.95 120.76 1.0796 IC CE1 CE2 *CP HP 1.4029 117.98 -179.95 120.75 1.0774 IC CP NZ *CE2 HE2 1.4010 122.23 -179.94 115.28 1.0808 PRES 3APD 0.00 ! C7H7N2O Gamma-3-Amino Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CM3 NG CD2---NZ ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CGP CZ CP ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OGP CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 GROUP ! | | | ATOM NZ NG2R60 -0.600 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 0.180 ! HO C4 C6 OH ATOM HP HGR62 0.120 GROUP ! 3APD ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5535 114.91 -48.02 117.54 1.3422 IC CG CZ *NG HG 1.3422 128.46 -179.57 113.64 1.0156 IC NG CC3 *CG OG 1.3422 117.54 -179.06 119.46 1.2281 IC CC3 CG NG CZ 1.5030 117.54 -179.13 128.46 1.4197 IC CG NG CZ CD2 1.3422 128.46 -3.17 126.55 1.4108 IC NG CZ CD2 NZ 1.4197 126.55 179.85 124.13 1.3390 IC CZ CD2 NZ CP 1.4108 124.13 -0.43 118.24 1.3305 IC CD2 NZ CP CE1 1.3390 118.24 0.10 123.37 1.4034 IC NZ CP CE1 CD1 1.3305 123.37 0.07 117.85 1.4044 IC CZ NZ *CD2 HD2 1.4108 124.13 -179.72 114.91 1.0790 IC CZ CE1 *CD1 HD1 1.4056 119.87 -179.90 120.63 1.0809 IC NZ CE1 *CP HP 1.3305 123.37 179.97 121.76 1.0804 IC CP CD1 *CE1 HE1 1.4034 117.85 179.97 121.01 1.0770 PRES 4APD 0.00 ! C7H7N2O Gamma-4-Amino Pyridine GA CDCA Amide (alpha-deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CD1 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HD1 HGR61 0.115 ! C2 C10 C8 C15 GROUP ! | | | ATOM CE1 CG2R61 0.180 ! C3 C5 C7 ATOM HE1 HGR62 0.120 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM NZ NG2R60 -0.600 GROUP ! 4APD ATOM CE2 CG2R61 0.180 ATOM HE2 HGR62 0.120 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 NZ BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5535 114.98 -47.60 117.27 1.3441 IC CG CZ *NG HG 1.3441 129.78 -179.11 112.90 1.0148 IC NG CC3 *CG OG 1.3441 117.27 -178.79 119.11 1.2283 IC CC3 CG NG CZ 1.5032 117.27 -179.47 129.78 1.4177 IC CG NG CZ CD1 1.3441 129.78 -75.00 125.48 1.4027 IC NG CZ CD1 CE1 1.4177 125.48 178.96 118.11 1.4012 IC CZ CD1 CE1 NZ 1.4027 118.11 -0.21 123.10 1.3307 IC CD1 CE1 NZ CE2 1.4012 123.10 -0.04 118.95 1.3315 IC CE1 NZ CE2 CD2 1.3307 118.95 -0.04 122.87 1.3990 IC CE1 CZ *CD1 HD1 1.4012 118.11 179.50 121.85 1.0751 IC CE2 CZ *CD2 HD2 1.3990 118.37 179.96 120.58 1.0785 IC NZ CD1 *CE1 HE1 1.3307 123.10 -179.94 121.79 1.0804 IC NZ CD2 *CE2 HE2 1.3315 122.87 179.77 121.77 1.0804 PRES 2AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-2-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! CJ1--CK1 ATOM HC3A HGA2 0.09 ! // \\ ATOM HC3B HGA2 0.09 ! OA1 CY CJ GROUP ! | / \ __ / ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 0.11 ! Me19 | | | | ATOM OD OG311 -0.53 ! C1 | C9 C14 C16 OH(D) ATOM HOD HGP1 0.42 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CE1 CG2R61 -0.115 ! | | | ATOM HE1 HGR61 0.115 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 -0.115 ! HO C4 C6 OH ATOM HP HGR61 0.115 GROUP ! 2AFP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5213 109.18 176.21 116.81 1.4508 IC HC1 CC1 CA OA2 1.1144 106.26 -147.37 109.18 1.3426 IC HB1 CB OA2 CA 1.1133 108.22 148.39 116.81 1.3426 IC HB2 CB OA2 CA 1.1175 112.74 32.40 116.81 1.3426 IC CY CB OA2 CA 1.5072 114.91 -92.05 116.81 1.3426 IC CJ2 CY CB OA2 1.4049 120.41 -89.66 114.91 1.4508 IC CJ1 CY CB OA2 1.4040 119.97 89.00 114.91 1.4508 IC CJ1 CJ2 *CY CB 1.4040 119.61 178.67 120.41 1.5072 IC CJ2 CY CB HB1 1.4049 120.41 30.54 107.06 1.1133 IC CJ2 CY CB HB2 1.4049 120.41 143.47 108.08 1.1175 IC CB CY CJ1 CK1 1.5072 119.97 -179.11 120.21 1.4011 IC CB CY CJ2 CK2 1.5072 120.41 179.16 120.17 1.4015 IC CY CJ1 CK1 CQ 1.4040 120.21 0.12 119.97 1.4012 IC CJ1 CK1 CQ CK2 1.4011 119.97 0.14 120.06 1.4013 IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.07 119.97 1.4015 IC CK1 CY *CJ1 HJ1 1.4011 120.21 179.64 119.77 1.0808 IC CK2 CY *CJ2 HJ2 1.4015 120.17 179.97 119.92 1.0795 IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.91 119.96 1.0806 IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.99 120.08 1.0805 IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.91 120.01 1.0806 IC CC2 CC3 CG NG 1.5538 115.11 -15.46 117.38 1.3413 IC CG CZ *NG HG 1.3413 130.29 178.93 113.17 0.9900 IC HG NG CG OG 0.9900 116.53 176.72 123.61 1.2237 IC CC3 CG NG CZ 1.5004 117.38 175.23 130.29 1.4278 IC CG NG CZ CD1 1.3413 130.29 -22.14 127.51 1.4180 IC NG CZ CD1 OD 1.4278 127.51 -0.04 124.65 1.4137 IC CZ CD1 OD HOD 1.4180 124.65 20.40 106.30 0.9750 IC NG CZ CD1 CE1 1.4278 127.51 -178.75 119.88 1.4002 IC CZ CD1 CE1 CP 1.4180 119.88 -0.93 120.65 1.3996 IC CD1 CE1 CP CE2 1.4002 120.65 0.22 119.87 1.3982 IC CE1 CP CE2 CD2 1.3996 119.87 0.26 119.87 1.3997 IC CD1 CD2 *CP HP 2.4326 60.10 179.91 150.25 1.0810 IC CE2 CZ *CD2 HD2 1.3997 120.98 -179.92 119.69 1.0796 IC CP CD1 *CE1 HE1 1.3996 120.65 -179.71 119.51 1.0809 IC CP CD2 *CE2 HE2 1.3982 119.87 -179.89 120.17 1.0811 PRES 3AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-3-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! CJ1--CK1 ATOM HC3A HGA2 0.09 ! // \\ ATOM HC3B HGA2 0.09 ! OA1 CY CJ GROUP ! | / \ __ / ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 OH(E) GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 0.11 ! C2 C10 C8 C15 ATOM OE OG311 -0.53 ! | | | ATOM HOE HGP1 0.42 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 -0.115 ! HO C4 C6 OH ATOM HP HGR61 0.115 GROUP ! 3AFP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 OE OE HOE CE1 CP BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5213 109.19 176.53 116.82 1.4508 IC HC1 CC1 CA OA2 1.1144 106.19 -147.97 109.19 1.3424 IC HB1 CB OA2 CA 1.1133 108.20 148.28 116.82 1.3424 IC HB2 CB OA2 CA 1.1175 112.72 32.34 116.82 1.3424 IC CY CB OA2 CA 1.5073 114.94 -92.14 116.82 1.3424 IC CJ2 CY CB OA2 1.4049 120.41 -89.70 114.94 1.4508 IC CJ1 CY CB OA2 1.4040 119.97 89.00 114.94 1.4508 IC CJ1 CJ2 *CY CB 1.4040 119.61 178.70 120.41 1.5073 IC CJ2 CY CB HB1 1.4049 120.41 30.50 107.07 1.1133 IC CJ2 CY CB HB2 1.4049 120.41 143.43 108.09 1.1175 IC CB CY CJ1 CK1 1.5073 119.97 -179.14 120.22 1.4011 IC CB CY CJ2 CK2 1.5073 120.41 179.20 120.17 1.4015 IC CY CJ1 CK1 CQ 1.4040 120.22 0.11 119.97 1.4012 IC CJ1 CK1 CQ CK2 1.4011 119.97 0.14 120.06 1.4013 IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.08 119.97 1.4015 IC CK1 CY *CJ1 HJ1 1.4011 120.22 179.64 119.75 1.0808 IC CK2 CY *CJ2 HJ2 1.4015 120.17 179.98 119.90 1.0795 IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.91 119.95 1.0806 IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.99 120.07 1.0805 IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.90 120.01 1.0806 IC CC2 CC3 CG NG 1.5550 116.14 -6.99 117.40 1.3442 IC CG CZ *NG HG 1.3442 129.55 175.98 113.63 0.9888 IC HG NG CG OG 0.9888 116.71 177.69 124.09 1.2224 IC CC3 CG NG CZ 1.5026 117.40 171.67 129.55 1.4221 IC CG NG CZ CD1 1.3442 129.55 8.58 125.65 1.4019 IC NG CZ CD1 CE1 1.4221 125.65 -176.91 120.47 1.3983 IC CZ CD1 CE1 OE 1.4019 120.47 -179.93 119.61 1.4070 IC CD1 CE1 OE HOE 1.3983 119.61 173.29 107.72 0.9583 IC CZ CD1 CE1 CP 1.4019 120.47 0.29 120.28 1.3988 IC CD1 CE1 CP CE2 1.3983 120.28 0.19 119.83 1.4012 IC CE1 CP CE2 CD2 1.3988 119.83 -0.22 119.70 1.4012 IC CD1 CD2 *CP HP 2.4258 59.83 -179.40 149.86 1.0795 IC CE1 CZ *CD1 HD1 1.3983 120.47 -179.99 121.26 1.0774 IC CE2 CZ *CD2 HD2 1.4012 120.77 -179.35 119.71 1.0794 IC CP CD2 *CE2 HE2 1.4012 119.70 -179.76 120.15 1.0810 PRES 4AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-4-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! CJ1--CK1 ATOM HC3A HGA2 0.09 ! // \\ ATOM HC3B HGA2 0.09 ! OA1 CY CJ GROUP ! | / \ __ / ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--OH(P) ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 ATOM HE1 HGR61 0.115 ! | | | GROUP ! C3 C5 C7 ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ ATOM HE2 HGR61 0.115 ! HO C4 C6 OH GROUP ATOM CD2 CG2R61 -0.115 ! 4AFP ATOM HD2 HGR61 0.115 GROUP ATOM CP CG2R61 0.11 ATOM OP OG311 -0.53 ATOM HOP HGP1 0.42 GROUP ATOM CC1 CG311 0.17 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.90 ATOM OA1 OG2D1 -0.63 ATOM OA2 OG302 -0.49 ATOM CB CG321 -0.22 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ BOND CP OP OP HOP DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5236 109.09 -178.41 115.32 1.4470 IC HC1 CC1 CA OA2 1.1142 106.35 -136.56 109.09 1.3425 IC HB1 CB OA2 CA 1.1165 110.58 58.38 115.32 1.3425 IC HB2 CB OA2 CA 1.1162 110.53 -60.09 115.32 1.3425 IC CY CB OA2 CA 1.5038 113.57 178.93 115.32 1.3425 IC CJ2 CY CB OA2 1.4045 120.04 -86.50 113.57 1.4470 IC CJ1 CY CB OA2 1.4046 120.35 92.29 113.57 1.4470 IC CJ1 CJ2 *CY CB 1.4046 119.60 178.79 120.04 1.5038 IC CJ2 CY CB HB1 1.4045 120.04 35.94 107.19 1.1165 IC CJ2 CY CB HB2 1.4045 120.04 150.86 107.55 1.1162 IC CB CY CJ1 CK1 1.5038 120.35 -179.80 120.19 1.4015 IC CB CY CJ2 CK2 1.5038 120.04 179.88 120.20 1.4014 IC CY CJ1 CK1 CQ 1.4046 120.19 0.22 119.97 1.4011 IC CJ1 CK1 CQ CK2 1.4015 119.97 0.49 120.06 1.4013 IC CK1 CQ CK2 CJ2 1.4011 120.06 -0.40 119.97 1.4014 IC CK1 CY *CJ1 HJ1 1.4015 120.19 -179.59 119.87 1.0799 IC CK2 CY *CJ2 HJ2 1.4014 120.20 179.63 119.84 1.0802 IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.64 120.03 1.0807 IC CQ CJ2 *CK2 HK2 1.4013 119.97 179.84 119.99 1.0807 IC CK1 CK2 *CQ HQ 1.4011 120.06 -179.97 119.97 1.0807 IC CC2 CC3 CG NG 1.5522 114.66 9.31 116.85 1.3446 IC CG CZ *NG HG 1.3446 129.70 -179.80 113.69 0.9886 IC NG CC3 *CG OG 1.3446 116.85 179.97 118.95 1.2231 IC CC3 CG NG CZ 1.5020 116.85 178.94 129.70 1.4209 IC CG NG CZ CD1 1.3446 129.70 -12.00 125.34 1.4023 IC NG CZ CD1 CE1 1.4209 125.34 179.30 120.44 1.4040 IC CZ CD1 CE1 CP 1.4023 120.44 -0.30 120.10 1.3974 IC CD1 CE1 CP OP 1.4040 120.10 -179.94 119.57 1.4076 IC CE1 CP OP HOP 1.3974 119.57 179.31 107.83 0.9582 IC CD1 CE1 CP CE2 1.4040 120.10 0.00 120.00 1.3995 IC CE1 CP CE2 CD2 1.3974 120.00 0.08 119.77 1.4034 IC CE1 CZ *CD1 HD1 1.4040 120.44 179.44 120.86 1.0783 IC CE2 CZ *CD2 HD2 1.4034 120.68 179.81 119.68 1.0792 IC CP CD1 *CE1 HE1 1.3974 120.10 -179.87 120.20 1.0802 IC CP CD2 *CE2 HE2 1.3995 119.77 179.92 119.80 1.0794 PRES 2AFD 0.00 ! C8H8NO2 Gamma-2-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ! OA1 (-0.5) GROUP ! | ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 0.11 ! Me19 | | | | ATOM OD OG311 -0.53 ! C1 | C9 C14 C16 OH(D) ATOM HOD HGP1 0.42 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CE1 CG2R61 -0.115 ! | | | ATOM HE1 HGR61 0.115 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 -0.115 ! HO C4 C6 OH ATOM HP HGR61 0.115 GROUP ! 2AFD ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5527 114.79 -49.84 117.53 1.3436 IC CG CZ *NG HG 1.3436 131.49 -179.00 112.13 1.0158 IC HG NG CG OG 1.0158 116.38 178.36 123.50 1.2277 IC CC3 CG NG CZ 1.5021 117.53 -179.31 131.49 1.4281 IC CG NG CZ CD1 1.3436 131.49 -17.12 128.16 1.4178 IC NG CZ CD1 OD 1.4281 128.16 -0.87 124.84 1.4130 IC CZ CD1 OD HOD 1.4178 124.84 13.21 105.74 0.9771 IC NG CZ CD1 CE1 1.4281 128.16 -180.00 120.02 1.4012 IC CZ CD1 CE1 CP 1.4178 120.02 -0.79 120.69 1.3997 IC CD1 CE1 CP CE2 1.4012 120.69 0.09 119.77 1.3979 IC CE1 CP CE2 CD2 1.3997 119.77 0.21 119.83 1.3990 IC CD1 CD2 *CP HP 2.4340 59.99 -179.98 150.22 1.0801 IC CE2 CZ *CD2 HD2 1.3990 121.28 -179.74 119.14 1.0814 IC CP CD1 *CE1 HE1 1.3997 120.69 -179.78 119.40 1.0802 IC CP CD2 *CE2 HE2 1.3979 119.83 -179.85 119.73 1.0805 PRES 3AFD 0.00 ! C8H8NO2 Gamma-3-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ! OA1 (-0.5) GROUP ! | ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 OH(E) GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 0.11 ! C2 C10 C8 C15 ATOM OE OG311 -0.53 ! | | | ATOM HOE HGP1 0.42 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 -0.115 ! HO C4 C6 OH ATOM HP HGR61 0.115 GROUP ! 3AFD ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 OE OE HOE CE1 CP BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5535 114.97 -47.53 117.22 1.3441 IC CG CZ *NG HG 1.3441 129.77 -178.97 112.88 1.0143 IC HG NG CG OG 1.0143 117.35 177.56 123.74 1.2279 IC CC3 CG NG CZ 1.5033 117.22 -179.94 129.77 1.4190 IC CG NG CZ CD1 1.3441 129.77 -14.90 125.45 1.4020 IC NG CZ CD1 CE1 1.4190 125.45 179.05 120.37 1.3993 IC CZ CD1 CE1 OE 1.4020 120.37 179.48 120.07 1.4087 IC CD1 CE1 OE HOE 1.3993 120.07 179.46 107.22 0.9566 IC CZ CD1 CE1 CP 1.4020 120.37 -0.43 120.24 1.4003 IC CD1 CE1 CP CE2 1.3993 120.24 0.04 119.87 1.4014 IC CE1 CP CE2 CD2 1.4003 119.87 0.07 119.63 1.4004 IC CD1 CD2 *CP HP 2.4274 59.83 -179.94 149.75 1.0785 IC CE1 CZ *CD1 HD1 1.3993 120.37 179.29 120.63 1.0774 IC CE2 CZ *CD2 HD2 1.4004 120.84 -179.99 119.02 1.0816 IC CP CD2 *CE2 HE2 1.4014 119.63 179.99 119.74 1.0802 PRES 4AFD 0.00 ! C8H8NO2 Gamma-4-Amino Phenol GA CDCA Amide, cacha ! patch combination: ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 ! OA1 (-0.5) GROUP ! | ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) ATOM OG OG2D1 -0.52 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--OH(P) ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / GROUP ! C11 C13---C17 OG CD1--CE1 ATOM CD1 CG2R61 -0.115 ! Me19 | | | ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 ATOM HE1 HGR61 0.115 ! | | | GROUP ! C3 C5 C7 ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ ATOM HE2 HGR61 0.115 ! HO C4 C6 OH GROUP ATOM CD2 CG2R61 -0.115 ! 4AFP ATOM HD2 HGR61 0.115 GROUP ATOM CP CG2R61 0.11 ATOM OP OG311 -0.53 ATOM HOP HGP1 0.42 BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ BOND CP OP OP HOP IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5534 114.96 -47.72 117.22 1.3442 IC CG CZ *NG HG 1.3442 129.81 -179.00 112.85 1.0143 IC NG CC3 *CG OG 1.3442 117.22 -178.69 119.03 1.2282 IC CC3 CG NG CZ 1.5032 117.22 -179.68 129.81 1.4190 IC CG NG CZ CD1 1.3442 129.81 -13.97 125.44 1.4028 IC NG CZ CD1 CE1 1.4190 125.44 178.96 120.46 1.4048 IC CZ CD1 CE1 CP 1.4028 120.46 -0.32 120.02 1.3982 IC CD1 CE1 CP OP 1.4048 120.02 -179.99 120.03 1.4082 IC CE1 CP OP HOP 1.3982 120.03 -179.80 106.81 0.9579 IC CD1 CE1 CP CE2 1.4048 120.02 -0.03 120.03 1.3994 IC CE1 CP CE2 CD2 1.3982 120.03 0.06 119.74 1.4022 IC CE1 CZ *CD1 HD1 1.4048 120.46 179.35 120.40 1.0778 IC CE2 CZ *CD2 HD2 1.4022 120.80 179.99 119.04 1.0815 IC CP CD1 *CE1 HE1 1.3982 120.02 -179.92 120.17 1.0792 IC CP CD2 *CE2 HE2 1.3994 119.74 179.94 119.33 1.0788 RESI GABD -1.00 ! C35H51N2O6 Gamma amino benzene glutamic acid CDCA amide, cacha GROUP ATOM C3 CG311 0.14 ! OG CD1--CE1 ATOM O3 OG311 -0.65 ! || // \\ ATOM HO3 HGP1 0.42 ! CG--NG--CZ CP ATOM H3 HGA1 0.09 ! / HG \ __ / GROUP ! CC3 CD2--CE2 ATOM C4 CG321 -0.18 ! \ ATOM H4A HGA2 0.09 ! O24 CC2 ATOM H4B HGA2 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) GROUP ! / \ | / | ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM HO7 HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! GABD GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 GROUP ATOM C18 CG331 -0.27 !methyl at c13 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 GROUP ATOM C19 CG331 -0.27 !methyl at c10 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM C24 CG2O1 0.51 ATOM O24 OG2D1 -0.51 ATOM N NG2S1 -0.47 ATOM HN HGP1 0.47 GROUP ATOM CC1 CG311 -0.19 ATOM HC1 HGA1 0.09 ATOM CA CG2O3 0.62 ATOM OA1 OG2D2 -0.76 ATOM OA2 OG2D2 -0.76 GROUP ATOM CC2 CG321 -0.18 ATOM HC2A HGA2 0.09 ATOM HC2B HGA2 0.09 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 GROUP ATOM CG CG2O1 0.52 ATOM OG OG2D1 -0.52 GROUP ATOM NG NG2S1 -0.47 ATOM HG HGP1 0.33 ATOM CZ CG2R61 0.14 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 BOND C3 O3 C3 H3 O3 HO3 BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 HO7 BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 C24 C24 O24 BOND C24 N N HN BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 BOND CC2 HC2A CC2 HC2B CC2 CC3 BOND CC3 HC3A CC3 HC3B CC3 CG BOND CG OG CG NG NG HG NG CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ IMPR C24 C23 N O24 IMPR CA OA2 OA1 CC1 IMPR CG CC3 NG OG ! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) !ICs based on arbitrary CHARMM optimized structure IC C1 C2 C3 C4 1.5325 111.68 -49.44 111.84 1.5383 IC C2 C3 C4 C5 1.5339 111.84 43.92 115.68 1.5598 IC C3 C4 C5 C6 1.5383 115.68 -175.08 109.02 1.5521 IC C4 C5 C6 C7 1.5598 109.02 85.48 114.98 1.5441 IC C5 C6 C7 C8 1.5521 114.98 39.05 113.05 1.5291 IC C7 C8 C9 C10 1.5291 114.07 58.27 109.47 1.5439 IC C8 C9 C10 C1 1.5323 109.47 179.67 111.99 1.5563 IC C9 C10 C1 C2 1.5439 111.99 63.32 113.83 1.5325 IC O3 C3 C4 C5 1.4163 109.09 162.16 115.68 1.5598 IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C2 C3 O3 HO3 1.5339 107.07 70.15 104.87 0.9608 IC C5 C3 *C4 H4A 1.5598 115.68 122.76 108.69 1.1111 IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 IC C10 C4 *C5 H5 1.5279 114.71 116.72 105.03 1.1175 IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 IC C6 C7 C8 C14 1.5441 113.05 -166.97 108.56 1.5542 IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.07 1.5323 IC C7 C8 C14 C13 1.5291 108.56 -174.23 113.13 1.5425 IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5532 IC C17 C14 *C13 C12 1.5731 98.17 119.81 107.46 1.5340 IC C14 C13 C12 C11 1.5425 107.46 55.27 111.17 1.5431 IC C8 C6 *C7 O7 1.5291 113.05 -126.94 107.98 1.4218 IC O7 C6 *C7 H7 1.4218 107.98 -113.62 107.19 1.1164 IC C6 C7 O7 HO7 1.5441 107.98 178.15 105.27 0.9614 IC C9 C7 *C8 H8 1.5323 114.07 122.48 107.18 1.1067 IC C10 C8 *C9 H9 1.5439 109.47 -117.09 106.55 1.1138 IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.87 1.1059 IC H12A C13 *C12 H12B 1.1059 111.87 119.48 108.83 1.1125 IC C13 C8 *C14 H14 1.5425 113.13 -118.31 108.46 1.1150 IC C16 C14 *C15 H15A 1.5435 103.56 119.14 111.17 1.1002 IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 IC C17 C15 *C16 H16A 1.5532 106.91 121.49 110.78 1.0992 IC H16A C15 *C16 H16B 1.0992 110.78 117.18 110.97 1.0998 IC C13 C16 *C17 H17 1.5731 98.41 -112.88 110.39 1.1009 IC C12 C14 *C13 C18 1.5340 107.46 121.96 114.21 1.5526 IC C14 C13 C18 H18A 1.5425 114.21 116.77 111.39 1.1064 IC H18A C13 *C18 H18B 1.1064 111.39 119.05 110.59 1.1085 IC H18A C13 *C18 H18C 1.1064 111.39 -120.16 111.91 1.1058 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C5 C10 C19 H19A 1.5279 109.53 5.11 111.17 1.1079 IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1062 IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 IC C13 C16 *C17 C20 1.5731 98.41 127.02 111.84 1.5649 IC C16 C17 C20 C22 1.5532 111.84 71.76 108.71 1.5518 IC C22 C17 *C20 C21 1.5518 108.71 122.37 112.90 1.5396 IC C21 C17 *C20 H20 1.5396 112.90 120.80 108.91 1.1119 IC C17 C20 C21 H21A 1.5649 112.90 71.89 110.45 1.1079 IC H21A C20 *C21 H21B 1.1079 110.45 -121.56 110.44 1.1103 IC H21A C20 *C21 H21C 1.1079 110.45 118.40 110.88 1.1089 IC C17 C20 C22 C23 1.5649 108.71 -163.91 113.72 1.5524 IC C23 C20 *C22 H22A 1.5524 113.72 119.83 108.17 1.1129 IC H22A C20 *C22 H22B 1.1129 108.17 116.47 108.28 1.1132 IC C20 C22 C23 C24 1.5518 113.72 174.68 113.87 1.5026 IC C24 C22 *C23 H23A 1.5026 113.87 120.96 110.57 1.1095 IC H23A C22 *C23 H23B 1.1095 110.57 118.91 109.38 1.1114 IC C22 C23 C24 N 1.5524 113.87 6.38 116.55 1.3359 IC N C23 *C24 O24 1.3359 116.55 -179.98 120.03 1.2265 IC C23 C24 N CC1 1.5026 116.55 -179.82 130.34 1.4436 IC CC1 C24 *N HN 1.4436 130.34 -176.24 124.18 1.0134 IC C24 N CC1 CA 1.3359 130.34 -166.57 103.53 1.5637 IC CA N *CC1 HC1 1.5637 103.53 115.21 109.79 1.1100 IC HC1 N *CC1 CC2 1.1100 109.79 123.30 112.57 1.5529 IC N CC1 CA OA1 1.4436 103.53 -162.71 117.28 1.2563 IC OA1 CC1 *CA OA2 1.2563 117.28 152.11 113.14 1.2722 IC N CC1 CC2 CC3 1.4436 112.57 56.12 114.17 1.5540 IC CC3 CC1 *CC2 HC2A 1.5540 114.17 126.04 108.53 1.1120 IC HC2A CC1 *CC2 HC2B 1.1120 108.53 114.46 107.25 1.1137 IC CC1 CC2 CC3 CG 1.5529 114.17 119.76 114.11 1.4995 IC CG CC2 *CC3 HC3A 1.4995 114.11 120.83 109.21 1.1109 IC HC3A CC2 *CC3 HC3B 1.1109 109.21 118.15 110.34 1.1107 IC CC2 CC3 CG NG 1.5540 114.11 -53.86 116.06 1.3423 IC NG CC3 *CG OG 1.3423 116.06 -178.54 119.61 1.2286 IC CC3 CG NG HG 1.4995 116.06 0.87 115.97 1.0167 IC CC3 CG NG CZ 1.4995 116.06 -179.02 130.53 1.4189 IC CG NG CZ CD1 1.3423 130.53 -7.10 125.50 1.4022 IC NG CZ CD1 CE1 1.4189 125.50 179.36 120.55 1.4034 IC CZ CD1 CE1 CP 1.4022 120.55 -0.19 119.96 1.4008 IC CD1 CE1 CP CE2 1.4034 119.96 0.01 119.92 1.4004 IC CE1 CP CE2 CD2 1.4008 119.92 0.02 119.80 1.4007 IC CE1 CZ *CD1 HD1 1.4034 120.55 179.64 120.41 1.0774 IC CE2 CZ *CD2 HD2 1.4007 120.81 179.97 119.00 1.0814 IC CP CD1 *CE1 HE1 1.4008 119.96 -179.93 119.80 1.0798 IC CP CD2 *CE2 HE2 1.4004 119.80 179.93 119.74 1.0797 IC CE1 CE2 *CP HP 1.4008 119.92 179.95 119.93 1.0796 PRES 4FBD 0.00 ! C3H2F Gamma 4-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HP ATOM CE1 CG2R61 -0.100 ATOM HE1 HGR62 0.150 ATOM CP CG2R66 0.110 ATOM FP FGR1 -0.210 ATOM CE2 CG2R61 -0.100 ATOM HE2 HGR62 0.150 BOND CP FP IC CE1 CE2 *CP FP 1.4008 119.92 179.96 119.93 1.0796 PRES 3FBD 0.00 ! C3H2F Gamma 3-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HE1 ATOM CD1 CG2R61 -0.100 ATOM HD1 HGR62 0.150 ATOM CE1 CG2R66 0.110 ATOM FE1 FGR1 -0.210 ATOM CP CG2R61 -0.100 ATOM HP HGR62 0.150 BOND CE1 FE1 IC CP CD1 *CE1 FE1 1.4008 119.96 -179.93 119.80 1.0798 PRES 2FBD 0.14 ! C3HF Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HD1 ATOM CE1 CG2R61 -0.100 ATOM HE1 HGR62 0.150 ATOM CD1 CG2R66 0.110 ATOM FD1 FGR1 -0.210 ATOM CZ CG2R61 0.190 BOND CD1 FD1 IC CE1 CZ *CD1 FD1 1.3985 122.02 176.60 121.03 1.3368 PRES 4FBP 0.00 ! C12H10FO2 Alpha benzyl, Gamma 4-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HP GROUP ! OG CD1--CE1 ATOM CC1 CG311 0.17 ! || // \\ ATOM HC1 HGA1 0.09 ! CG--NG--CZ CP--FP ATOM CA CG2O2 0.90 ! / HG \ __ / ATOM OA1 OG2D1 -0.63 ! CC3 CD2--CE2 ATOM OA2 OG302 -0.49 ! \ ATOM CB CG321 -0.22 ! O24 CC2 ATOM HB1 HGA2 0.09 ! || / ATOM HB2 HGA2 0.09 ! H Me21 C22 C24 CC1 GROUP ! | \ / \ / \ / \ __ ATOM CY CG2R61 0.00 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 ATOM CJ1 CG2R61 -0.115 ! / \ | / | // \\ ATOM HJ1 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ ATOM CJ2 CG2R61 -0.115 ! Me19 | | | \ __ / ATOM HJ2 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 ATOM CK1 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HK1 HGR61 0.115 ! C2 C10 C8 C15 ATOM CK2 CG2R61 -0.115 ! | | | ATOM HK2 HGR61 0.115 ! C3 C5 C7 ATOM CQ CG2R61 -0.115 ! / \ / \ / \ ATOM HQ HGR61 0.115 ! HO C4 C6 OH GROUP ATOM CE1 CG2R61 -0.100 ! 4FBP ATOM HE1 HGR62 0.150 ATOM CP CG2R66 0.110 ATOM FP FGR1 -0.210 ATOM CE2 CG2R61 -0.100 ATOM HE2 HGR62 0.150 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CP FP DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5349 110.60 -171.93 114.63 1.4514 IC HB1 CB OA2 CA 1.1146 109.86 61.07 114.63 1.3430 IC HB2 CB OA2 CA 1.1156 110.43 -57.63 114.63 1.3430 IC CA OA2 CB CY 1.3430 114.63 -177.12 115.21 1.5061 IC CJ1 CY CB OA2 1.4037 119.63 48.09 115.21 1.4514 IC CB CY CJ1 CK1 1.5061 119.63 177.33 120.28 1.4016 IC CY CJ1 CK1 CQ 1.4037 120.28 0.19 119.99 1.4012 IC CJ1 CK1 CQ CK2 1.4016 119.99 -0.03 120.04 1.4009 IC CK1 CQ CK2 CJ2 1.4012 120.04 -0.22 119.92 1.4012 IC CB CY CJ2 CK2 1.5061 120.87 -177.55 120.33 1.4012 IC CK1 CY *CJ1 HJ1 1.4016 120.28 -179.34 119.52 1.0802 IC CK2 CY *CJ2 HJ2 1.4012 120.33 179.00 119.92 1.0789 IC CQ CJ1 *CK1 HK1 1.4012 119.99 -179.93 119.95 1.0805 IC CQ CJ2 *CK2 HK2 1.4009 119.92 179.15 120.02 1.0814 IC CK1 CK2 *CQ HQ 1.4012 120.04 179.61 119.92 1.0812 IC CE1 CE2 *CP FP 1.3937 122.13 178.58 118.94 1.3320 PRES 3FBP 0.00 ! C12H10FO2 Alpha benzyl, Gamma 3-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HE1 GROUP ! OG CD1--CE1--FE1 ATOM CC1 CG311 0.17 ! || // \\ ATOM HC1 HGA1 0.09 ! CG--NG--CZ CP ATOM CA CG2O2 0.90 ! / HG \ __ / ATOM OA1 OG2D1 -0.63 ! CC3 CD2--CE2 ATOM OA2 OG302 -0.49 ! \ ATOM CB CG321 -0.22 ! O24 CC2 ATOM HB1 HGA2 0.09 ! || / ATOM HB2 HGA2 0.09 ! H Me21 C22 C24 CC1 GROUP ! | \ / \ / \ / \ __ ATOM CY CG2R61 0.00 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 ATOM CJ1 CG2R61 -0.115 ! / \ | / | // \\ ATOM HJ1 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ ATOM CJ2 CG2R61 -0.115 ! Me19 | | | \ __ / ATOM HJ2 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 ATOM CK1 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HK1 HGR61 0.115 ! C2 C10 C8 C15 ATOM CK2 CG2R61 -0.115 ! | | | ATOM HK2 HGR61 0.115 ! C3 C5 C7 ATOM CQ CG2R61 -0.115 ! / \ / \ / \ ATOM HQ HGR61 0.115 ! HO C4 C6 OH GROUP ATOM CD1 CG2R61 -0.100 ! 3FBP ATOM HD1 HGR62 0.150 ATOM CE1 CG2R66 0.110 ATOM FE1 FGR1 -0.210 ATOM CP CG2R61 -0.100 ATOM HP HGR62 0.150 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CE1 FE1 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5310 110.63 -175.15 114.31 1.4534 IC HB1 CB OA2 CA 1.1151 110.56 55.87 114.31 1.3407 IC HB2 CB OA2 CA 1.1156 109.57 -63.30 114.31 1.3407 IC CA OA2 CB CY 1.3407 114.31 175.76 116.12 1.5054 IC CJ1 CY CB OA2 1.4053 119.56 164.70 116.12 1.4534 IC CB CY CJ1 CK1 1.5054 119.56 177.79 120.29 1.4017 IC CY CJ1 CK1 CQ 1.4053 120.29 -0.37 119.95 1.4010 IC CJ1 CK1 CQ CK2 1.4017 119.95 0.24 119.94 1.4000 IC CK1 CQ CK2 CJ2 1.4010 119.94 0.14 120.12 1.4002 IC CB CY CJ2 CK2 1.5054 120.97 -177.38 120.26 1.4002 IC CK1 CY *CJ1 HJ1 1.4017 120.29 -179.60 119.80 1.0797 IC CK2 CY *CJ2 HJ2 1.4002 120.26 178.59 119.81 1.0794 IC CQ CJ1 *CK1 HK1 1.4010 119.95 -179.67 120.07 1.0804 IC CQ CJ2 *CK2 HK2 1.4000 120.12 178.86 119.82 1.0784 IC CK1 CK2 *CQ HQ 1.4010 119.94 179.70 119.90 1.0807 IC CD1 CP *CE1 FE1 1.3934 122.09 178.24 118.96 1.3332 PRES 2FBP 0.14 ! C12H9FO2 Alpha benzyl, Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HD1 GROUP ! FD1 ATOM CC1 CG311 0.17 ! | ATOM HC1 HGA1 0.09 ! OG CD1--CE1 ATOM CA CG2O2 0.90 ! || // \\ ATOM OA1 OG2D1 -0.63 ! CG--NG--CZ CP ATOM OA2 OG302 -0.49 ! / HG \ __ / ATOM CB CG321 -0.22 ! CC3 CD2--CE2 ATOM HB1 HGA2 0.09 ! \ ATOM HB2 HGA2 0.09 ! O24 CC2 GROUP ! || / ATOM CY CG2R61 0.00 ! H Me21 C22 C24 CC1 ATOM CJ1 CG2R61 -0.115 ! | \ / \ / \ / \ __ ATOM HJ1 HGR61 0.115 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 ATOM CJ2 CG2R61 -0.115 ! / \ | / | // \\ ATOM HJ2 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ ATOM CK1 CG2R61 -0.115 ! Me19 | | | \ __ / ATOM HK1 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 ATOM CK2 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HK2 HGR61 0.115 ! C2 C10 C8 C15 ATOM CQ CG2R61 -0.115 ! | | | ATOM HQ HGR61 0.115 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CE1 CG2R61 -0.100 ! HO C4 C6 OH ATOM HE1 HGR62 0.150 ATOM CD1 CG2R66 0.110 ! 2FBP ATOM FD1 FGR1 -0.210 ATOM CZ CG2R61 0.190 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CD1 FD1 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5324 110.58 -171.81 114.58 1.4510 IC HB1 CB OA2 CA 1.1152 109.67 65.73 114.58 1.3429 IC HB2 CB OA2 CA 1.1162 110.77 -52.90 114.58 1.3429 IC CA OA2 CB CY 1.3429 114.58 -172.25 114.95 1.5055 IC CJ1 CY CB OA2 1.4051 121.08 -129.13 114.95 1.4510 IC CB CY CJ1 CK1 1.5055 121.08 -177.36 120.29 1.4015 IC CY CJ1 CK1 CQ 1.4051 120.29 0.38 119.93 1.4010 IC CJ1 CK1 CQ CK2 1.4015 119.93 -0.45 120.04 1.4010 IC CK1 CQ CK2 CJ2 1.4010 120.04 0.10 119.98 1.4014 IC CB CY CJ2 CK2 1.5055 119.39 177.05 120.28 1.4014 IC CK1 CY *CJ1 HJ1 1.4015 120.29 179.02 119.81 1.0790 IC CK2 CY *CJ2 HJ2 1.4014 120.28 -179.17 119.50 1.0802 IC CQ CJ1 *CK1 HK1 1.4010 119.93 179.08 120.10 1.0810 IC CQ CJ2 *CK2 HK2 1.4010 119.98 -179.89 119.95 1.0805 IC CK1 CK2 *CQ HQ 1.4010 120.04 -179.60 120.00 1.0812 IC CZ CE1 *CD1 FD1 1.4058 122.69 179.26 117.93 1.3368 !End Polli's bile acids, chayan, feb2008 !Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008 !Model compound to optimize aromatic-aliphatic ether RESI MEOB 0.00 ! C7H8O Methoxybenzene (aka anisole, phenyl-methyl ether), cacha ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 ATOM HD1 HGR61 0.115 ! / \ GROUP ! HG--CG CZ--OZ--CM ATOM CD2 CG2R61 -0.115 ! \ / ATOM HD2 HGR61 0.115 ! CD2--CE2 GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of ATOM OZ OG301 -0.39 ! RESI C36 and Igor's ethers should ATOM CM CG331 -0.10 ! be better than analogy to phenol! ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OZ OZ CM BOND CM HM1 CM HM2 CM HM3 IC CG CD1 CE1 CZ 1.3999 119.78 0.00 121.00 1.3997 IC CD1 CE1 CZ CE2 1.4007 121.00 0.00 118.94 1.4128 IC CE1 CZ CE2 CD2 1.3997 118.94 0.00 120.14 1.4039 IC CD1 CD2 *CG HG 1.3999 119.98 180.00 120.06 1.0805 IC CE1 CG *CD1 HD1 1.4007 119.78 180.00 120.21 1.0804 IC CE2 CG *CD2 HD2 1.4039 120.17 -180.00 119.86 1.0805 IC CZ CD1 *CE1 HE1 1.3997 121.00 -180.00 120.31 1.0797 IC CZ CD2 *CE2 HE2 1.4128 120.14 -180.00 117.62 1.0763 IC CE1 CE2 *CZ OZ 1.3997 118.94 -180.00 123.32 1.4094 IC CE2 CZ OZ CM 1.4128 123.32 0.00 117.32 1.4272 IC CZ OZ CM HM1 1.4094 117.32 -61.22 110.78 1.1121 IC HM1 OZ *CM HM2 1.1121 110.78 122.45 110.78 1.1121 IC HM1 OZ *CM HM3 1.1121 110.78 -118.78 108.75 1.1112 RESI ETOB 0.00 ! C8H10O Ethoxybenzene (aka phenetole, phenyl-ethyl ether), cacha ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 ATOM HD1 HGR61 0.115 ! / \ GROUP ! HG--CG CZ--OZ--C1--C2(Me) ATOM CD2 CG2R61 -0.115 ! \ / ATOM HD2 HGR61 0.115 ! CD2--CE2 GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of ATOM OZ OG301 -0.39 ! RESI C36 and Igor's ethers should ATOM C1 CG321 -0.01 ! be better than analogy to phenol! ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG331 -0.27 ATOM H2A HGA3 0.09 ATOM H2B HGA3 0.09 ATOM H2C HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OZ OZ C1 BOND C1 H1A C1 H1B C1 C2 BOND C2 H2A C2 H2B C2 H2C IC CG CD1 CE1 CZ 1.4001 119.79 0.00 120.95 1.3995 IC CD1 CE1 CZ CE2 1.4009 120.95 0.00 118.98 1.4120 IC CE1 CZ CE2 CD2 1.3995 118.98 0.00 120.18 1.4036 IC CD1 CD2 *CG HG 1.4001 119.98 -180.00 120.05 1.0805 IC CE1 CG *CD1 HD1 1.4009 119.79 180.00 120.21 1.0804 IC CE2 CG *CD2 HD2 1.4036 120.12 -180.00 119.88 1.0805 IC CZ CD1 *CE1 HE1 1.3995 120.95 180.00 120.34 1.0797 IC CZ CD2 *CE2 HE2 1.4120 120.18 180.00 117.95 1.0763 IC CE1 CE2 *CZ OZ 1.3995 118.98 -180.00 123.18 1.4086 IC CE2 CZ OZ C1 1.4120 123.18 0.00 117.39 1.4239 IC CZ OZ C1 H1A 1.4086 117.39 -60.67 110.26 1.1142 IC H1A OZ *C1 H1B 1.1142 110.26 121.34 110.26 1.1142 IC H1A OZ *C1 C2 1.1142 110.26 -119.33 107.48 1.5257 IC OZ C1 C2 H2A 1.4239 107.48 180.00 110.94 1.1094 IC H2A C1 *C2 H2B 1.1094 110.94 120.60 109.82 1.1110 IC H2A C1 *C2 H2C 1.1094 110.94 -120.60 109.82 1.1110 PRES FBID 0.00 ! C3H6O Fatty acid Binding protein Inhibitor D, cacha ! This is a phenyl-methyl ether derivative having ! methyl at 2 and ethyl acetate at 4 position ! patch combination: ! core residue Compound "FBIB" >> Compound "FBID" DELETE ATOM CC ! HD1 HE1 DELETE ATOM HC ! | | DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 DELETE ATOM H1A ! \ | | // \\ DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH DELETE ATOM H1C ! / | | \ __ / \ DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 CN(Me) DELETE ATOM H2A ! | | DELETE ATOM H2B ! HD2 CM(Me) DELETE ATOM H2C DELETE ATOM HH GROUP ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 GROUP ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should ATOM CN CG331 -0.10 ! be better than analogy to phenol! ATOM HN1 HGA3 0.09 ATOM HN2 HGA3 0.09 ATOM HN3 HGA3 0.09 BOND CE2 CM CM HM1 CM HM2 CM HM3 BOND OH CN CN HN1 CN HN2 CN HN3 IC CZ CD2 *CE2 CM 1.4150 119.45 178.47 118.38 1.5035 IC CD2 CE2 CM HM1 1.4035 118.38 -73.69 108.56 1.1101 IC HM1 CE2 *CM HM2 1.1101 108.56 120.14 109.17 1.1105 IC HM1 CE2 *CM HM3 1.1101 108.56 -119.98 109.71 1.1110 IC CE1 CZ OH CN 1.4096 121.48 33.49 115.06 1.4278 IC CZ OH CN HN1 1.4137 115.06 -76.12 110.63 1.1113 IC HN1 OH *CN HN2 1.1113 110.63 122.41 111.24 1.1132 IC HN1 OH *CN HN3 1.1113 110.63 -118.58 108.69 1.1108 PRES FBIE 0.00 ! C2H4O Fatty acid Binding protein Inhibitor D, cacha ! This is a phenyl-methyl ether derivative having ! ethyl acetate at 4 position ! patch combination: ! core residue Compound "FBIB" >> Compound "FBIE" DELETE ATOM CC ! HD1 HE1 DELETE ATOM HC ! | | DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 DELETE ATOM H1A ! \ | | // \\ DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH DELETE ATOM H1C ! / | | \ __ / \ DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 CM(Me) DELETE ATOM H2A ! | | DELETE ATOM H2B ! HD2 HE2 DELETE ATOM H2C DELETE ATOM HH GROUP ATOM HE2 HGR61 0.00 GROUP ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should ATOM CM CG331 -0.10 ! be better than analogy to phenol! ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CE2 HE2 BOND OH CM CM HM1 CM HM2 CM HM3 IC CZ CD2 *CE2 HE2 1.4159 120.13 -179.81 117.32 1.0785 IC CE1 CZ OH CM 1.4005 117.83 171.75 116.32 1.4272 IC CZ OH CM HM1 1.4145 116.32 -56.84 110.84 1.1126 IC HM1 OH *CM HM2 1.1126 110.84 122.15 110.67 1.1120 IC HM1 OH *CM HM3 1.1126 110.84 -118.98 108.83 1.1108 PRES FBIFR -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, R-isomer, cacha ! This is IBUPROFEN (phenyl derivative having ! 2-methyl ethyl acetate at 4 position) ! core residue "FBIB" >> Compound "FBIFR" ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration DELETE ATOM CA DELETE ATOM HA1 DELETE ATOM HA2 DELETE ATOM CB DELETE ATOM HB1 DELETE ATOM HB2 ! HD1 HE1 DELETE ATOM CC ! | | DELETE ATOM HC ! (-0.5)OD1 CMG CD1--CE1 CN1 DELETE ATOM C1 ! \ | // \\ / DELETE ATOM H1A ! CD--CBG--CG CZM--CM1--CM2 DELETE ATOM H1B ! / | \ __ / \ DELETE ATOM H1C ! (-0.5)OD2 HBG CD2--CE2 CN2 DELETE ATOM C2 ! | | DELETE ATOM H2A ! HD2 HE2 DELETE ATOM H2B DELETE ATOM H2C ! COMPOUND "FBIFR" OR "FBIFS" DELETE ATOM CZ DELETE ATOM OH DELETE ATOM HH GROUP ATOM HE2 HGR61 0.00 GROUP ATOM CBG CG311 -0.19 ATOM HBG HGA1 0.09 ATOM CMG CG331 -0.27 ATOM HMG1 HGA3 0.09 ATOM HMG2 HGA3 0.09 ATOM HMG3 HGA3 0.09 GROUP ATOM CZM CG2R61 0.00 GROUP ATOM CM1 CG321 -0.18 ATOM HM1A HGA2 0.09 ATOM HM1B HGA2 0.09 GROUP ATOM CM2 CG311 -0.09 ATOM HM2 HGA1 0.09 GROUP ATOM CN1 CG331 -0.27 ATOM HN1A HGA3 0.09 ATOM HN1B HGA3 0.09 ATOM HN1C HGA3 0.09 GROUP ATOM CN2 CG331 -0.27 ATOM HN2A HGA3 0.09 ATOM HN2B HGA3 0.09 ATOM HN2C HGA3 0.09 BOND CE2 HE2 BOND CG CBG CBG CD CBG HBG CBG CMG CMG HMG1 CMG HMG2 CMG HMG3 BOND CE1 CZM CE2 CZM CZM CM1 CM1 HM1A CM1 HM1B BOND CM1 CM2 CM2 HM2 CM2 CN1 CN1 HN1A CN1 HN1B CN1 HN1C BOND CM2 CN2 CN2 HN2A CN2 HN2B CN2 HN2C IMPR CD OD1 OD2 CBG IC CG CD1 CE1 CZM 1.4074 121.22 0.25 120.04 1.4018 IC CZM CD2 *CE2 HE2 1.4038 120.33 -179.97 119.65 1.0800 IC CE2 CD2 CG CBG 1.4008 120.74 178.69 123.82 1.5308 IC CD2 CG CBG CMG 1.4107 123.82 -15.87 111.99 1.5638 IC CD2 CG CBG HBG 1.4107 123.82 -132.75 108.39 1.1103 IC CG CBG CMG HMG1 1.5308 111.99 68.31 110.42 1.1099 IC HMG1 CBG *CMG HMG2 1.1099 110.42 118.37 109.28 1.1117 IC HMG1 CBG *CMG HMG3 1.1099 110.42 -121.91 110.96 1.1084 IC CMG CG *CBG CD 1.5638 111.99 126.26 113.97 1.5510 IC CG CBG CD OD1 1.5308 113.97 1.93 120.65 1.2585 IC OD1 CBG *CD OD2 1.2585 120.65 172.14 115.78 1.2623 IC CE1 CE2 CZM CM1 2.4229 30.26 178.92 120.81 1.5097 IC CE1 CZM CM1 HM1A 1.4018 119.74 50.63 107.54 1.1109 IC HM1A CZM *CM1 HM1B 1.1109 107.54 117.28 109.24 1.1111 IC HM1A CZM *CM1 CM2 1.1109 107.54 -120.94 111.69 1.5467 IC CZM CM1 CM2 HM2 1.5097 111.69 56.61 108.58 1.1171 IC HM2 CM1 *CM2 CN1 1.1171 108.58 117.56 110.34 1.5373 IC HM2 CM1 *CM2 CN2 1.1171 108.58 -119.29 112.25 1.5383 IC CM1 CM2 CN1 HN1A 1.5467 110.34 61.99 110.14 1.1105 IC HN1A CM2 *CN1 HN1B 1.1105 110.14 119.99 110.39 1.1102 IC HN1A CM2 *CN1 HN1C 1.1105 110.14 -119.88 110.33 1.1105 IC CM1 CM2 CN2 HN2A 1.5467 112.25 60.91 110.56 1.1111 IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.90 110.46 1.1099 IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.87 110.24 1.1101 PRES FBIFS -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, S-isomer, cacha ! This is IBUPROFEN (phenyl derivative having ! 2-methyl ethyl acetate at 4 position) ! core residue "FBIB" >> Compound "FBIFS" ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration DELETE ATOM CA DELETE ATOM HA1 DELETE ATOM HA2 DELETE ATOM CB DELETE ATOM HB1 DELETE ATOM HB2 DELETE ATOM CC ! HD1 HE1 DELETE ATOM HC ! | | DELETE ATOM C1 ! (-0.5)OD1 CMG CD1--CE1 CN1 DELETE ATOM H1A ! \ | // \\ / DELETE ATOM H1B ! CD--CBG--CG CZM--CM1--CM2 DELETE ATOM H1C ! / | \ __ / \ DELETE ATOM C2 ! (-0.5)OD2 HBG CD2--CE2 CN2 DELETE ATOM H2A ! | | DELETE ATOM H2B ! HD2 HE2 DELETE ATOM H2C DELETE ATOM CZ ! COMPOUND "FBIFR" OR "FBIFS" DELETE ATOM OH DELETE ATOM HH GROUP ATOM HE2 HGR61 0.00 GROUP ATOM CBG CG311 -0.19 ATOM HBG HGA1 0.09 ATOM CMG CG331 -0.27 ATOM HMG1 HGA3 0.09 ATOM HMG2 HGA3 0.09 ATOM HMG3 HGA3 0.09 GROUP ATOM CZM CG2R61 0.00 GROUP ATOM CM1 CG321 -0.18 ATOM HM1A HGA2 0.09 ATOM HM1B HGA2 0.09 GROUP ATOM CM2 CG311 -0.09 ATOM HM2 HGA1 0.09 GROUP ATOM CN1 CG331 -0.27 ATOM HN1A HGA3 0.09 ATOM HN1B HGA3 0.09 ATOM HN1C HGA3 0.09 GROUP ATOM CN2 CG331 -0.27 ATOM HN2A HGA3 0.09 ATOM HN2B HGA3 0.09 ATOM HN2C HGA3 0.09 BOND CE2 HE2 BOND CG CBG CBG HBG CBG CD CBG CMG CMG HMG1 CMG HMG2 CMG HMG3 BOND CE1 CZM CE2 CZM CZM CM1 CM1 HM1A CM1 HM1B BOND CM1 CM2 CM2 HM2 CM2 CN1 CN1 HN1A CN1 HN1B CN1 HN1C BOND CM2 CN2 CN2 HN2A CN2 HN2B CN2 HN2C IMPR CD OD1 OD2 CBG IC CG CD1 CE1 CZM 1.4067 120.82 0.59 120.10 1.4030 IC CZM CD2 *CE2 HE2 1.4050 120.15 -179.82 119.75 1.0799 IC CE2 CD2 CG CBG 1.3998 120.76 178.17 119.92 1.5233 IC CD2 CG CBG CMG 1.4058 119.92 -112.06 107.62 1.5610 ! S-isomer IC CD2 CG CBG HBG 1.4058 119.92 5.06 110.49 1.1095 ! S-isomer IC CG CBG CMG HMG1 1.5233 107.62 55.81 110.88 1.1088 IC HMG1 CBG *CMG HMG2 1.1088 110.88 119.89 109.40 1.1116 IC HMG1 CBG *CMG HMG3 1.1088 110.88 -121.32 110.59 1.1099 IC CMG CG *CBG CD 1.5610 107.62 -124.32 115.01 1.5504 IC CG CBG CD OD1 1.5233 115.01 -1.31 120.84 1.2583 IC OD1 CBG *CD OD2 1.2583 120.84 -175.49 115.85 1.2621 IC CE1 CE2 CZM CM1 2.4256 30.23 179.20 120.79 1.5096 IC CE1 CZM CM1 HM1A 1.4030 119.71 50.70 107.54 1.1109 IC HM1A CZM *CM1 HM1B 1.1109 107.54 117.31 109.24 1.1110 IC HM1A CZM *CM1 CM2 1.1109 107.54 -120.92 111.68 1.5467 IC CZM CM1 CM2 HM2 1.5096 111.68 56.65 108.57 1.1172 IC HM2 CM1 *CM2 CN1 1.1172 108.57 117.56 110.34 1.5373 IC HM2 CM1 *CM2 CN2 1.1172 108.57 -119.28 112.26 1.5383 IC CM1 CM2 CN1 HN1A 1.5467 110.34 62.00 110.14 1.1105 IC HN1A CM2 *CN1 HN1B 1.1105 110.14 119.98 110.39 1.1103 IC HN1A CM2 *CN1 HN1C 1.1105 110.14 -119.89 110.33 1.1105 IC CM1 CM2 CN2 HN2A 1.5467 112.26 60.95 110.56 1.1111 IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.89 110.46 1.1099 IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.88 110.25 1.1101 !End Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008 !Fundamental functional groups, kevo, feb2008 RESI ACN 0.000 ! C2H3N acetonitrile, kevo GROUP ATOM C1 CG331 -0.17 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG1N1 0.36 ATOM N3 NG1T1 -0.46 BOND C1 C2 C2 N3 BOND C1 H11 C1 H12 C1 H13 IC N3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 !End fundamental functional groups, kevo, feb2008 !Continuation of Maybridge list, kevo, feb2008 RESI 3HPR 0.000 ! C4H5N 3H-pyrrole, kevo GROUP ATOM N1 NG2R50 -0.60 ATOM C2 CG2R52 0.10 ATOM H2 HGR52 0.13 ! H31 H4 ATOM C3 CG3C52 0.05 ! \ / ATOM H31 HGA2 0.09 ! H32--C3---C4 ATOM H32 HGA2 0.09 ! | || ATOM C4 CG2R51 -0.30 ! C2 C5 ATOM H4 HGR51 0.18 ! / \\ / \ ATOM C5 CG2R51 0.12 ! H2 N1 H5 ATOM H5 HGR52 0.14 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 BOND C2 H2 C3 H31 C3 H32 C4 H4 C5 H5 IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI 3HIN 0.000 ! C8H7N 3H-indole, kevo GROUP ATOM N1 NG2R50 -0.61 ATOM C2 CG2R52 0.18 ATOM H2 HGR52 0.11 ATOM C3 CG3C52 -0.09 ! H5 ATOM H31 HGA2 0.09 ! | ATOM H32 HGA2 0.09 ! H31 C5 ATOM C4 CG2RC0 0.25 ! \ / \\ ATOM C5 CG2R61 -0.36 ! H32--C3---C4 C6--H6 ATOM H5 HGR61 0.20 ! | || | ATOM C6 CG2R61 -0.22 ! C2 C9 C7--H7 ATOM H6 HGR61 0.21 ! / \\ / \ // ATOM C7 CG2R61 -0.21 ! H2 N1 C8 ATOM H7 HGR61 0.21 ! | ATOM C8 CG2R61 -0.34 ! H8 ATOM H8 HGR61 0.26 ATOM C9 CG2RC0 0.23 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 N1 C4 C9 BOND C2 H2 C3 H31 C3 H32 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 RESI INDI 0.000 ! C8H9N indoline, kevo GROUP ATOM N1 NG3C51 -0.68 ATOM H1 HGP1 0.33 ATOM C2 CG3C52 0.00 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ! H5 ATOM C3 CG3C52 -0.12 ! | ATOM H31 HGA2 0.09 ! H31 C5 ATOM H32 HGA2 0.09 ! \ / \\ ATOM C4 CG2RC0 0.11 ! H32--C3---C4 C6--H6 ATOM C5 CG2R61 -0.40 ! | || | ATOM H5 HGR61 0.24 ! H22--C2 C9 C7--H7 ATOM C6 CG2R61 -0.27 ! / \ / \ // ATOM H6 HGR61 0.22 ! H21 N1 C8 ATOM C7 CG2R61 -0.20 ! | | ATOM H7 HGR61 0.20 ! H1 H8 ATOM C8 CG2R61 -0.29 ATOM H8 HGR61 0.21 ATOM C9 CG2RC0 0.29 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 N1 C4 C9 BOND N1 H1 C2 H21 C2 H22 C3 H31 C3 H32 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC N1 C2 C3 C4 0.0000 0.00 330.00 0.00 0.0000 IC C2 C3 C4 C9 0.0000 0.00 20.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C9 C2 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 RESI ZFUR 0.000 ! C8H6O benzofuran (there's only 1 benzofuran), kevo GROUP ATOM O1 OG2R50 -0.28 ATOM C2 CG2R51 0.02 ATOM H2 HGR52 0.18 ! H5 ATOM C3 CG2R51 -0.40 ! | ATOM H3 HGR51 0.25 ! H3 C5 ATOM C4 CG2RC0 0.15 ! \ / \\ ATOM C5 CG2R61 -0.33 ! C3---C4 C6--H6 ATOM H5 HGR61 0.24 ! || || | ATOM C6 CG2R61 -0.28 ! C2 C9 C7--H7 ATOM H6 HGR61 0.23 ! / \ / \ // ATOM C7 CG2R61 -0.21 ! H2 O1 C8 ATOM H7 HGR61 0.22 ! | ATOM C8 CG2R61 -0.34 ! H8 ATOM H8 HGR61 0.24 ATOM C9 CG2RC0 0.31 BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 O1 C4 C9 BOND C2 H2 C3 H3 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C3 O1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI ZTHP 0.000 ! C8H6S benzothiophene (there's only 1 benzothiophene), kevo GROUP ATOM S1 SG2R50 -0.16 ATOM C2 CG2R51 -0.09 ATOM H2 HGR52 0.18 ! H5 ATOM C3 CG2R51 -0.28 ! | ATOM H3 HGR51 0.21 ! H3 C5 ATOM C4 CG2RC0 0.17 ! \ / \\ ATOM C5 CG2R61 -0.34 ! C3---C4 C6--H6 ATOM H5 HGR61 0.24 ! || || | ATOM C6 CG2R61 -0.29 ! C2 C9 C7--H7 ATOM H6 HGR61 0.24 ! / \ / \ // ATOM C7 CG2R61 -0.21 ! H2 S1 C8 ATOM H7 HGR61 0.21 ! | ATOM C8 CG2R61 -0.23 ! H8 ATOM H8 HGR61 0.24 ATOM C9 CG2RC0 0.11 BOND S1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 S1 C4 C9 BOND C2 H2 C3 H3 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC S1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C3 S1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI ZTHZ 0.000 ! C7H5NS benzothiazole, kevo GROUP ATOM S1 SG2R50 -0.25 ATOM C2 CG2R53 0.16 ATOM H2 HGR52 0.18 ! H5 ATOM N3 NG2R50 -0.69 ! | ATOM C4 CG2RC0 0.64 ! C5 ATOM C5 CG2R61 -0.46 ! / \\ ATOM H5 HGR61 0.26 ! N3---C4 C6--H6 ATOM C6 CG2R61 -0.29 ! || || | ATOM H6 HGR61 0.26 ! C2 C9 C7--H7 ATOM C7 CG2R61 -0.38 ! / \ / \ // ATOM H7 HGR61 0.26 ! H2 S1 C8 ATOM C8 CG2R61 -0.24 ! | ATOM H8 HGR61 0.22 ! H8 ATOM C9 CG2RC0 0.33 BOND S1 C2 C2 N3 N3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 S1 C4 C9 BOND C2 H2 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC S1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 N3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC N3 S1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 RESI PUR9 0.00 ! C5H4N4 purine (N9H-tautomer), kevo GROUP ATOM C5 CG2RC0 0.30 ATOM N7 NG2R50 -0.73 ATOM C8 CG2R53 0.37 ! H6 ATOM H8 HGR52 0.09 ! | ATOM N9 NG2R51 -0.19 ! C6 ATOM H9 HGP1 0.29 ! // \ ATOM N1 NG2R62 -0.73 ! N1 C5--N7\\ ATOM C2 CG2R64 0.50 ! | || C8-H8 ATOM H2 HGR62 0.14 ! C2 C4--N9/ ATOM N3 NG2R62 -0.77 ! / \\ / \ ATOM C4 CG2RC0 0.44 ! H2 N3 H9 ATOM C6 CG2R61 0.09 ! Was: CG2R64. See: PYRM. ATOM H6 HGR62 0.20 BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 BOND C5 N7 N7 C8 C8 N9 N9 C4 BOND C2 H2 C6 H6 C8 H8 N9 H9 IC N7 C8 N9 C4 0.0000 0.00 0.00 0.00 0.0000 IC N9 C8 N7 C5 0.0000 0.00 0.00 0.00 0.0000 IC C8 N7 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 N7 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C8 C4 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI PUR7 0.00 ! C5H4N4 purine (N7H-tautomer), kevo GROUP ATOM C5 CG2RC0 0.23 ATOM N7 NG2R51 -0.22 ATOM H7 HGP1 0.26 ! H6 ATOM C8 CG2R53 0.32 ! | ATOM H8 HGR52 0.12 ! C6 H7 ATOM N9 NG2R50 -0.57 ! // \ / ATOM N1 NG2R62 -0.78 ! N1 C5--N7\ ATOM C2 CG2R64 0.48 ! | || C8-H8 ATOM H2 HGR62 0.13 ! C2 C4--N9// ATOM N3 NG2R62 -0.58 ! / \\ / ATOM C4 CG2RC0 0.21 ! H2 N3 ATOM C6 CG2R61 0.31 ATOM H6 HGR62 0.09 BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 BOND C5 N7 N7 C8 C8 N9 N9 C4 BOND C2 H2 C6 H6 C8 H8 N7 H7 IC N7 C8 N9 C4 0.0000 0.00 0.00 0.00 0.0000 IC N9 C8 N7 C5 0.0000 0.00 0.00 0.00 0.0000 IC C8 N7 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 N7 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C5 C8 *N7 H7 0.0000 0.00 180.00 0.00 0.0000 IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 !End continuation of Maybridge list, kevo, feb2008 !Continuation of Maybridge list, kevo and erh, jun2008 RESI CPDE 0.000 ! C5H6 cyclopentadiene, kevo ATOM C1 CG3C52 0.10 ATOM H11 HGA2 0.09 ! H3 H4 ATOM H12 HGA2 0.09 ! \ / ATOM C2 CG2R51 -0.36 ! C3----C4 ATOM H2 HGR51 0.22 ! || || ATOM C3 CG2R51 -0.22 ! C2 C5 ATOM H3 HGR51 0.22 ! / \ / \ ATOM C4 CG2R51 -0.22 ! H2 C1 H5 ATOM H4 HGR51 0.22 ! /\ ATOM C5 CG2R51 -0.36 ! H11 H12 ATOM H5 HGR51 0.22 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C1 C1 H11 C1 H12 BOND C2 H2 C3 H3 C4 H4 C5 H5 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C5 C2 *C1 H12 0.0000 0.00 240.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI INDE 0.00 ! C9H8 indene, kevo GROUP ATOM C1 CG3C52 0.02 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG2R51 -0.30 ! H5 ATOM H2 HGR51 0.22 ! | ATOM C3 CG2R51 -0.43 ! H3 C5 ATOM H3 HGR51 0.26 ! \ / \\ ATOM C4 CG2RC0 0.24 ! C3----C4 C6 -H6 ATOM C5 CG2R61 -0.33 ! || || | ATOM H5 HGR61 0.22 ! C2 C9 C7 -H7 ATOM C6 CG2R61 -0.19 ! / \ / \ // ATOM H6 HGR61 0.20 ! H2 C1 C8 ATOM C7 CG2R61 -0.22 ! /\ | ATOM H7 HGR61 0.21 ! H11 H12 H8 ATOM C8 CG2R61 -0.36 ATOM H8 HGR61 0.22 ATOM C9 CG2RC0 0.06 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C4 C9 C9 C1 BOND C1 H11 C1 H12 C2 H2 C3 H3 BOND C5 H5 C6 H6 C7 H7 C8 H8 IC C9 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C9 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C9 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C4 C1 *C9 C8 0.0000 0.00 180.00 0.00 0.0000 IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C9 C8 C7 0.0000 0.00 0.00 0.00 0.0000 IC C9 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C9 C2 *C1 H12 0.0000 0.00 240.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI CRBZ 0.00 ! C12H9N Carbazole, erh GROUP ATOM C1 CG2R61 -0.180 ATOM H1 HGR61 0.180 ATOM C2 CG2R61 -0.180 ATOM H2 HGR61 0.180 ATOM C3 CG2R61 -0.180 ATOM H3 HGR61 0.180 ATOM C4 CG2R61 -0.270 ! H4 H7 ATOM H4 HGR61 0.270 ! | | ATOM C5 CG2R67 -0.200 ! C4 C7 ATOM C6 CG2R67 -0.200 ! // \ / \\ ATOM C7 CG2R61 -0.270 ! H3--C3 C5----C6 C8--H8 ATOM H7 HGR61 0.270 ! | || || | ATOM C8 CG2R61 -0.180 ! H2--C2 C13 C11 C9--H9 ATOM H8 HGR61 0.180 ! \\ / \ / \ // ATOM C9 CG2R61 -0.180 ! C1 N12 C10 ATOM H9 HGR61 0.180 ! | | | ATOM C10 CG2R61 -0.180 ! H1 H12 H10 ATOM H10 HGR61 0.180 ATOM C11 CG2RC0 0.200 ATOM N12 NG2R51 -0.300 ATOM H12 HGP1 0.300 ATOM C13 CG2RC0 0.200 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 N12 N12 C13 C13 C1 C5 C13 C6 C11 BOND C1 H1 C2 H2 C3 H3 C4 H4 C7 H7 BOND C8 H8 C9 H9 C10 H10 N12 H12 IC C5 C13 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C13 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C13 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C13 N12 0.0000 0.00 180.00 0.00 0.0000 IC C4 C13 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C13 C5 C6 C11 0.0000 0.00 0.00 0.00 0.0000 IC N12 C6 *C11 C10 0.0000 0.00 180.00 0.00 0.0000 IC C5 C11 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C11 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C11 C10 C9 0.0000 0.00 0.00 0.00 0.0000 IC C13 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *N12 H12 0.0000 0.00 180.00 0.00 0.0000 RESI FLRN 0.00 ! C13H10 Fluorene, erh GROUP ATOM C1 CG2R61 -0.140 ATOM H1 HGR61 0.140 ATOM C2 CG2R61 -0.170 ATOM H2 HGR61 0.170 ATOM C3 CG2R61 -0.190 ATOM H3 HGR61 0.190 ATOM C4 CG2R61 -0.280 ! H4 H7 ATOM H4 HGR61 0.280 ! | | ATOM C5 CG2R67 -0.240 ! C4 C7 ATOM C6 CG2R67 -0.240 ! // \ / \\ ATOM C7 CG2R61 -0.280 ! H3--C3 C5----C6 C8--H8 ATOM H7 HGR61 0.280 ! | || || | ATOM C8 CG2R61 -0.190 ! H2--C2 C13 C11 C9--H9 ATOM H8 HGR61 0.190 ! \\ / \ / \ // ATOM C9 CG2R61 -0.170 ! C1 C12 C10 ATOM H9 HGR61 0.170 ! | / \ | ATOM C10 CG2R61 -0.140 ! H1 H21 H22 H10 ATOM H10 HGR61 0.140 ATOM C11 CG2RC0 0.240 ATOM C12 CG3C52 -0.180 ATOM H21 HGA2 0.090 ATOM H22 HGA2 0.090 ATOM C13 CG2RC0 0.240 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 C13 C13 C1 C5 C13 C6 C11 BOND C1 H1 C2 H2 C3 H3 C4 H4 C7 H7 BOND C8 H8 C9 H9 C10 H10 C12 H21 C12 H22 IC C5 C13 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C13 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C13 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C13 C12 0.0000 0.00 180.00 0.00 0.0000 IC C4 C13 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C13 C5 C6 C11 0.0000 0.00 5.00 0.00 0.0000 ! Deliberate distorsion! IC C5 C11 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 ! Deviating def to make above work IC C7 C6 C11 C10 0.0000 0.00 0.00 0.00 0.0000 ! Deviating def to make above work IC C11 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C11 C10 C9 0.0000 0.00 0.00 0.00 0.0000 IC C13 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *C12 H21 0.0000 0.00 120.00 0.00 0.0000 IC C11 C13 *C12 H22 0.0000 0.00 -120.00 0.00 0.0000 RESI NAFT 0.00 ! C10H8 Naphtalene, kevo GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ! H4 H6 ATOM H3 HGR61 0.115 ! | | ATOM C4 CG2R61 -0.115 ! C4 C6 ATOM H4 HGR61 0.115 ! // \ / \\ ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 ATOM C6 CG2R61 -0.115 ! | || | ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 ATOM C7 CG2R61 -0.115 ! \\ / \ // ATOM H7 HGR61 0.115 ! C1 C9 ATOM C8 CG2R61 -0.115 ! | | ATOM H8 HGR61 0.115 ! H1 H9 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.000 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 C1 C10 BOND C1 H1 C2 H2 C3 H3 C4 H4 BOND C6 H6 C7 H7 C8 H8 C9 H9 IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI QINL 0.00 ! C9H7N Quinoline, kevo and erh GROUP ATOM N1 NG2R60 -0.640 ATOM C2 CG2R61 0.160 ATOM H2 HGR62 0.140 ATOM C3 CG2R61 -0.115 ! H4 H6 ATOM H3 HGR61 0.115 ! | | ATOM C4 CG2R61 -0.115 ! C4 C6 ATOM H4 HGR61 0.115 ! // \ / \\ ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 ATOM C6 CG2R61 -0.115 ! | || | ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 ATOM C7 CG2R61 -0.115 ! \\ / \ // ATOM H7 HGR61 0.115 ! N1 C9 ATOM C8 CG2R61 -0.115 ! | ATOM H8 HGR61 0.115 ! H9 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.340 BOND N1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 N1 C10 BOND C2 H2 C3 H3 C4 H4 BOND C6 H6 C7 H7 C8 H8 C9 H9 IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI IQIN 0.00 ! C9H7N Isoquinoline, erh GROUP ATOM C1 CG2R61 0.17 ATOM H1 HGR62 0.15 ATOM N2 NG2R60 -0.61 ATOM C3 CG2R61 0.12 ! H4 H6 ATOM H3 HGR62 0.14 ! | | ATOM C4 CG2R61 -0.115 ! C4 C6 ATOM H4 HGR61 0.115 ! // \ / \\ ATOM C5 CG2R61 0.05 ! H3--C3 C5 C7--H7 ATOM C6 CG2R61 -0.115 ! | || | ATOM H6 HGR61 0.115 ! N2 C10 C8--H8 ATOM C7 CG2R61 -0.115 ! \\ / \ // ATOM H7 HGR61 0.115 ! C1 C9 ATOM C8 CG2R61 -0.115 ! | | ATOM H8 HGR61 0.115 ! H1 H9 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 -0.02 BOND C1 N2 N2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 C1 C10 BOND C1 H1 C3 H3 C4 H4 BOND C6 H6 C7 H7 C8 H8 C9 H9 IC C5 C10 C1 N2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI CINL 0.00 ! C8H6N2 Cinnoline, erh GROUP ATOM N1 NG2R62 -0.500 ATOM N2 NG2R62 -0.450 ATOM C3 CG2R61 0.350 ! H4 H6 ATOM H3 HGR62 0.070 ! | | ATOM C4 CG2R61 -0.160 ! C4 C6 ATOM H4 HGR61 0.180 ! // \ / \\ ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 ATOM C6 CG2R61 -0.115 ! | || | ATOM H6 HGR61 0.115 ! N2 C10 C8--H8 ATOM C7 CG2R61 -0.115 ! \\ / \ // ATOM H7 HGR61 0.115 ! N1 C9 ATOM C8 CG2R61 -0.115 ! | ATOM H8 HGR61 0.115 ! H9 ATOM C9 CG2R61 -0.160 ATOM H9 HGR61 0.180 ATOM C10 CG2R61 0.490 BOND N1 N2 N2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 N1 C10 BOND C3 H3 C4 H4 C6 H6 BOND C7 H7 C8 H8 C9 H9 IC C5 C10 N1 N2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI FTAZ 0.00 ! C8H6N2 Phthalazine, erh GROUP ATOM C1 CG2R61 0.340 ATOM H1 HGR62 0.080 ATOM N2 NG2R62 -0.490 ATOM N3 NG2R62 -0.490 ! H4 H6 ATOM C4 CG2R61 0.340 ! | | ATOM H4 HGR62 0.080 ! C4 C6 ATOM C5 CG2R61 0.070 ! // \ / \\ ATOM C6 CG2R61 -0.115 ! N3 C5 C7--H7 ATOM H6 HGR61 0.115 ! | || | ATOM C7 CG2R61 -0.115 ! N2 C10 C8--H8 ATOM H7 HGR61 0.115 ! \\ / \ // ATOM C8 CG2R61 -0.115 ! C1 C9 ATOM H8 HGR61 0.115 ! | | ATOM C9 CG2R61 -0.115 ! H1 H9 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.070 BOND C1 N2 N2 N3 N3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 C1 C10 BOND C1 H1 C4 H4 C6 H6 BOND C7 H7 C8 H8 C9 H9 IC C5 C10 C1 N2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI QINZ 0.00 ! C8H6N2 Quinazoline, erh GROUP ATOM N1 NG2R62 -0.810 ATOM C2 CG2R64 0.520 ATOM H2 HGR62 0.140 ATOM N3 NG2R62 -0.750 ! H4 H6 ATOM C4 CG2R61 0.280 ! | | ATOM H4 HGR62 0.130 ! C4 C6 ATOM C5 CG2R61 0.020 ! // \ / \\ ATOM C6 CG2R61 -0.115 ! N3 C5 C7--H7 ATOM H6 HGR61 0.115 ! | || | ATOM C7 CG2R61 -0.115 ! H2--C2 C10 C8--H8 ATOM H7 HGR61 0.115 ! \\ / \ // ATOM C8 CG2R61 -0.115 ! N1 C9 ATOM H8 HGR61 0.115 ! | ATOM C9 CG2R61 -0.115 ! H9 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.470 BOND N1 C2 C2 N3 N3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 N1 C10 BOND C2 H2 C4 H4 C6 H6 BOND C7 H7 C8 H8 C9 H9 IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI QINX 0.00 ! C8H6N2 Quinoxaline, erh GROUP ATOM N1 NG2R60 -0.580 ATOM C2 CG2R61 0.090 ATOM H2 HGR62 0.160 ATOM C3 CG2R61 0.090 ! H6 ATOM H3 HGR62 0.160 ! | ATOM N4 NG2R60 -0.580 ! N4 C6 ATOM C5 CG2R61 0.330 ! // \ / \\ ATOM C6 CG2R61 -0.115 ! H3--C3 C5 C7--H7 ATOM H6 HGR61 0.115 ! | || | ATOM C7 CG2R61 -0.115 ! H2--C2 C10 C8--H8 ATOM H7 HGR61 0.115 ! \\ / \ // ATOM C8 CG2R61 -0.115 ! N1 C9 ATOM H8 HGR61 0.115 ! | ATOM C9 CG2R61 -0.115 ! H9 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.330 BOND N1 C2 C2 C3 C3 N4 N4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 N1 C10 BOND C2 H2 C3 H3 C6 H6 BOND C7 H7 C8 H8 C9 H9 IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 N4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 N4 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC N4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 N4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI 18NFD 0.00 ! C8H6N2 1,8-naphthyridine, erh GROUP ATOM N1 NG2R62 -0.660 ATOM C2 CG2R61 0.330 ATOM H2 HGR62 0.090 ATOM C3 CG2R61 -0.115 ! H4 H6 ATOM H3 HGR61 0.115 ! | | ATOM C4 CG2R61 -0.115 ! C4 C6 ATOM H4 HGR61 0.115 ! // \ / \\ ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 ATOM C6 CG2R61 -0.115 ! | || | ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 ATOM C7 CG2R61 -0.115 ! \\ / \ // ATOM H7 HGR61 0.115 ! N1 N9 ATOM C8 CG2R61 0.330 ATOM H8 HGR62 0.090 ATOM N9 NG2R62 -0.660 ATOM C10 CG2R64 0.480 BOND N1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 N9 BOND N9 C10 C5 C10 N1 C10 BOND C2 H2 C3 H3 C4 H4 BOND C6 H6 C7 H7 C8 H8 IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 N9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 N9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI PTID 0.00 ! C6H4N4 pteridine, erh GROUP ATOM N1 NG2R62 -0.710 ATOM C2 CG2R64 0.500 ATOM H2 HGR62 0.140 ATOM N3 NG2R62 -0.700 ! H4 ATOM C4 CG2R61 0.110 ! | ATOM H4 HGR62 0.180 ! C4 N6 ATOM C5 CG2R61 0.450 ! // \ / \\ ATOM N6 NG2R60 -0.640 ! N3 C5 C7--H7 ATOM C7 CG2R61 0.185 ! | || | ATOM H7 HGR62 0.105 ! H2--C2 C10 C8--H8 ATOM C8 CG2R61 0.320 ! \\ / \ // ATOM H8 HGR62 0.090 ! N1 N9 ATOM N9 NG2R62 -0.650 ATOM C10 CG2R64 0.620 ! Manual init guess (analogy to PYZN, PYRM, PUR9 and PUR7) BOND N1 C2 C2 N3 N3 C4 C4 C5 BOND C5 N6 N6 C7 C7 C8 C8 N9 BOND N9 C10 C5 C10 N1 C10 BOND C2 H2 C4 H4 C7 H7 C8 H8 IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 IC N1 C5 *C10 N9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 N6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 N6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 N9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI ANTR 0.00 ! C14H10 Anthracene, kevo and erh GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 -0.115 ATOM H4 HGR61 0.115 ! H4 H6 H8 ATOM C5 CG2R61 0.000 ! | | | ATOM C6 CG2R61 -0.115 ! C4 C6 C8 ATOM H6 HGR61 0.115 ! // \ / \\ / \\ ATOM C7 CG2R61 0.000 ! H3--C3 C5 C7 C9--H9 ATOM C8 CG2R61 -0.115 ! | || | | ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // ATOM H9 HGR61 0.115 ! C1 C13 C11 ATOM C10 CG2R61 -0.115 ! | | | ATOM H10 HGR61 0.115 ! H1 H13 H11 ATOM C11 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C12 CG2R61 0.000 ATOM C13 CG2R61 -0.115 ATOM H13 HGR61 0.115 ATOM C14 CG2R61 0.000 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 C13 C13 C14 C14 C1 C5 C14 C7 C12 BOND C1 H1 C2 H2 C3 H3 C4 H4 C6 H6 BOND C8 H8 C9 H9 C10 H10 C11 H11 C13 H13 IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C14 C13 0.0000 0.00 180.00 0.00 0.0000 IC C4 C14 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C14 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C14 C13 C12 0.0000 0.00 0.00 0.00 0.0000 IC C13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C12 C14 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 RESI ACRD 0.00 ! C13H9N Acridine, erh GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 -0.115 ATOM H4 HGR61 0.115 ! H4 H6 H8 ATOM C5 CG2R61 0.000 ! | | | ATOM C6 CG2R61 -0.115 ! C4 C6 C8 ATOM H6 HGR61 0.115 ! // \ / \\ / \\ ATOM C7 CG2R61 0.000 ! H3--C3 C5 C7 C9--H9 ATOM C8 CG2R61 -0.115 ! | || | | ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // ATOM H9 HGR61 0.115 ! C1 N13 C11 ATOM C10 CG2R61 -0.115 ! | | ATOM H10 HGR61 0.115 ! H1 H11 ATOM C11 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C12 CG2R61 0.345 ATOM N13 NG2R60 -0.690 ATOM C14 CG2R61 0.345 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 BOND C1 H1 C2 H2 C3 H3 C4 H4 C6 H6 BOND C8 H8 C9 H9 C10 H10 C11 H11 IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 IC C4 C14 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C14 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C14 N13 C12 0.0000 0.00 0.00 0.00 0.0000 IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI FENZ 0.00 ! C12H8N2 Phenazine, erh GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 -0.115 ! H4 H8 ATOM H4 HGR61 0.115 ! | | ATOM C5 CG2R61 0.320 ! C4 N6 C8 ATOM N6 NG2R60 -0.640 ! // \ / \\ / \\ ATOM C7 CG2R61 0.320 ! H3--C3 C5 C7 C9--H9 ATOM C8 CG2R61 -0.115 ! | || | | ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // ATOM H9 HGR61 0.115 ! C1 N13 C11 ATOM C10 CG2R61 -0.115 ! | | ATOM H10 HGR61 0.115 ! H1 H11 ATOM C11 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C12 CG2R61 0.320 ATOM N13 NG2R60 -0.640 ATOM C14 CG2R61 0.320 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 N6 BOND N6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 BOND C1 H1 C2 H2 C3 H3 C4 H4 BOND C8 H8 C9 H9 C10 H10 C11 H11 IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 IC C4 C14 *C5 N6 0.0000 0.00 180.00 0.00 0.0000 IC C14 C5 N6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C14 N13 C12 0.0000 0.00 0.00 0.00 0.0000 IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 IC N6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI FEOZ 0.00 ! C12H9NO Phenoxazine, erh & kevo GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 -0.115 ! H4 H8 ATOM H4 HGR61 0.115 ! | | ATOM C5 CG2R61 0.130 ! C4 O6 C8 ATOM O6 OG3R60 -0.260 ! // \ / \ / \\ ATOM C7 CG2R61 0.130 ! H3--C3 C5 C7 C9--H9 ATOM C8 CG2R61 -0.115 ! | || || | ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 ATOM C9 CG2R61 -0.115 ! \\ / \ / \ // ATOM H9 HGR61 0.115 ! C1 N13 C11 ATOM C10 CG2R61 -0.115 ! | | | ATOM H10 HGR61 0.115 ! H1 H13 H11 ATOM C11 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C12 CG2R61 0.040 ATOM N13 NG311 -0.470 ATOM H13 HGPAM1 0.390 ATOM C14 CG2R61 0.040 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 O6 BOND O6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 BOND C1 H1 C2 H2 C3 H3 C4 H4 BOND C8 H8 C9 H9 C10 H10 C11 H11 N13 H13 IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 IC C4 C14 *C5 O6 0.0000 0.00 180.00 0.00 0.0000 IC C14 C5 O6 C7 0.0000 0.00 -30.00 0.00 0.0000 IC C5 C14 N13 C12 0.0000 0.00 30.00 0.00 0.0000 IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 IC O6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C12 C14 *N13 H13 0.0000 0.00 120.00 0.00 0.0000 RESI FETZ 0.00 ! C12H9NS Phenothiazine, erh GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 -0.115 ! H4 H8 ATOM H4 HGR61 0.115 ! | | ATOM C5 CG2R61 0.130 ! C4 S6 C8 ATOM S6 SG311 -0.240 ! // \ / \ / \\ ATOM C7 CG2R61 0.130 ! H3--C3 C5 C7 C9--H9 ATOM C8 CG2R61 -0.115 ! | || || | ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 ATOM C9 CG2R61 -0.115 ! \\ / \ / \ // ATOM H9 HGR61 0.115 ! C1 N13 C11 ATOM C10 CG2R61 -0.115 ! | | | ATOM H10 HGR61 0.115 ! H1 H13 H11 ATOM C11 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C12 CG2R61 -0.010 ATOM N13 NG311 -0.360 ATOM H13 HGPAM1 0.360 ATOM C14 CG2R61 -0.010 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 S6 BOND S6 C7 C7 C8 C8 C9 C9 C10 C10 C11 BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 BOND C1 H1 C2 H2 C3 H3 C4 H4 BOND C8 H8 C9 H9 C10 H10 C11 H11 N13 H13 IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 1.4300 IC C4 C14 *C5 S6 0.0000 0.00 180.00 0.00 0.0000 IC C14 C5 S6 C7 0.0000 0.00 -30.00 99.00 0.0000 IC C5 C14 N13 C12 0.0000 0.00 30.00 114.00 1.4300 IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C12 C14 *N13 H13 0.0000 0.00 120.00 0.00 0.0000 RESI DIOL 0.000 ! C3H6O2 1,3-Dioxolane, erh GROUP ATOM O1 OG3C51 -0.40 ATOM C2 CG3C52 0.16 ! H42 ATOM H21 HGA2 0.09 ! / ATOM H22 HGA2 0.09 ! O3----C4--H41 ATOM O3 OG3C51 -0.40 ! | | ATOM C4 CG3C52 0.05 ! H21--C2 C5--H51 ATOM H41 HGA2 0.09 ! / \ / \ ATOM H42 HGA2 0.09 ! H22 O1 H52 ATOM C5 CG3C52 0.05 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND O1 C2 C2 O3 O3 C4 BOND C4 C5 C5 O1 BOND C2 H21 C2 H22 C4 H41 C4 H42 BOND C5 H51 C5 H52 IC C4 C5 O1 C2 0.0000 0.00 30.00 0.00 0.0000 IC O1 C5 C4 O3 0.0000 0.00 0.00 0.00 0.0000 IC O1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC O3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC O3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC O1 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 RESI IMDP 1.000 ! C3H9N2 Imidazolidine protonated, erh and kevo GROUP ATOM N1 NG3C51 -0.89 !>=.89 ATOM H1 HGP1 0.50 !<=.50 ATOM C2 CG3C54 0.16 ATOM H21 HGA2 0.28 ! H32 H42 ATOM H22 HGA2 0.28 ! \(+) / ATOM N3 NG3P2 -0.89 ! H31--N3----C4--H41 ATOM H31 HGP2 0.54 !x | | ATOM H32 HGP2 0.54 !xH21--C2 C5--H51 ATOM C4 CG3C54 -0.22 ! / \ / \ ATOM H41 HGA2 0.28 ! H22 N1 H52 ATOM H42 HGA2 0.28 ! | ATOM C5 CG3C52 -0.04 ! H1 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 H1 C2 H21 C2 H22 N3 H31 N3 H32 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 C2 C2 N3 C4 C5 C5 N1 N3 C4 IC C2 N3 C4 C5 0.0000 0.00 -20.00 0.00 0.0000 IC N3 C4 C5 N1 0.0000 0.00 40.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *N3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *N3 H32 0.0000 0.00 120.00 0.00 0.0000 IC N3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC N3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC N1 N3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 N3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 RESI PRZP 1.000 ! C3H9N2 Pyrazolidine protonated, kevo GROUP ATOM N1 NG3C51 -0.47 ATOM H1 HGP1 0.35 ATOM N2 NG3P2 -0.18 ! H32 H42 ATOM H21 HGP2 0.37 ! \ / ATOM H22 HGP2 0.37 ! H31--C3----C4--H41 ATOM C3 CG3C54 -0.30 ! | | ATOM H31 HGA2 0.28 ! H21--N2(+) C5--H51 ATOM H32 HGA2 0.28 ! / \ / \ ATOM C4 CG3C52 -0.18 ! H22 N1 H52 ATOM H41 HGA2 0.09 ! | ATOM H42 HGA2 0.09 ! H1 ATOM C5 CG3C52 0.12 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND N1 H1 N2 H21 N2 H22 C3 H31 C3 H32 BOND C4 H41 C4 H42 C5 H51 C5 H52 BOND N1 N2 N2 C3 C4 C5 C5 N1 C3 C4 IC N2 C3 C4 C5 0.0000 0.00 -20.00 0.00 0.0000 IC C3 C4 C5 N1 0.0000 0.00 40.00 0.00 0.0000 IC N2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C4 N2 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC C4 N2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C3 *N2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N1 C3 *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 RESI QINU 1.00 ! C7H14N Quinuclidine, kevo GROUP ATOM N1 NG3P1 0.13 ATOM H1 HGP2 0.19 ATOM C2 CG324 0.03 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C6 CG324 0.03 ATOM H61 HGA2 0.09 ! C5---C6 ATOM H62 HGA2 0.09 ! / \ (+) ATOM C7 CG324 0.03 ! H4--C4--C8-C7--N1--H1 ATOM H71 HGA2 0.09 ! \ / ATOM H72 HGA2 0.09 ! C3---C2 ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG311 -0.04 ATOM H4 HGA1 0.09 ATOM C5 CG321 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 ATOM C8 CG321 -0.18 ATOM H81 HGA2 0.09 ATOM H82 HGA2 0.09 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 N1 N1 C7 C7 C8 C8 C4 BOND N1 H1 C4 H4 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND C5 H51 C5 H52 C6 H61 C6 H62 BOND C7 H71 C7 H72 C8 H81 C8 H82 IC C6 N1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N1 C6 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C6 *N1 C7 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *N1 H1 0.0000 0.00 -120.00 0.00 0.0000 IC C6 N1 C7 C8 0.0000 0.00 -60.00 0.00 0.0000 IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 N1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 N1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC N1 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 IC C7 C4 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 IC C7 C4 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 RESI NORB 0.00 ! C7H12 Norbornane, kevo GROUP ATOM C1 CG3RC1 -0.09 ATOM H1 HGA1 0.09 ATOM C2 CG3C52 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG3C52 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ! C5---C6 ATOM C4 CG3RC1 -0.09 ! / \ ATOM H4 HGA1 0.09 ! H4--C4---C7---C1--H1 ATOM C5 CG3C52 -0.18 ! \ / ATOM H51 HGA2 0.09 ! C3---C2 ATOM H52 HGA2 0.09 ATOM C6 CG3C52 -0.18 ATOM H61 HGA2 0.09 ATOM H62 HGA2 0.09 ATOM C7 CG3C52 -0.18 ATOM H71 HGA2 0.09 ATOM H72 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C1 C1 C7 C7 C4 BOND C1 H1 C4 H4 C7 H71 C7 H72 BOND C2 H21 C2 H22 C3 H31 C3 H32 BOND C5 H51 C5 H52 C6 H61 C6 H62 IC C6 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C1 C6 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C6 *C1 C7 0.0000 0.00 120.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C4 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC C1 C4 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 C1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 RESI ADAM 0.00 ! C10H16 Adamantane, kevo and erh GROUP ATOM C1 CG311 -0.09 ATOM H1 HGA1 0.09 ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG311 -0.09 ATOM H3 HGA1 0.09 ATOM C4 CG321 -0.18 ATOM H41 HGA2 0.09 ! _C1_ ATOM H42 HGA2 0.09 ! _- \ -_ ATOM C5 CG311 -0.09 ! C2 \ C8 ATOM H5 HGA1 0.09 ! | C10 | ATOM C6 CG321 -0.18 ! | | | ATOM H61 HGA2 0.09 ! C3_ |_C7 ATOM H62 HGA2 0.09 ! \ -_ _+ \ ATOM C7 CG311 -0.09 ! \ C9 | \ ATOM H7 HGA1 0.09 ! \ C5_ \ ATOM C8 CG321 -0.18 ! \ / -_ \ ATOM H81 HGA2 0.09 ! C4 -C6 ATOM H82 HGA2 0.09 ATOM C9 CG321 -0.18 ATOM H91 HGA2 0.09 ATOM H92 HGA2 0.09 ATOM C10 CG321 -0.18 ATOM H101 HGA2 0.09 ATOM H102 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C1 BOND C3 C9 C9 C7 C5 C10 C10 C1 BOND C1 H1 C3 H3 C5 H5 C7 H7 BOND C2 H21 C2 H22 C4 H41 C4 H42 BOND C6 H61 C6 H62 C8 H81 C8 H82 BOND C9 H91 C9 H92 C10 H101 C10 H102 IC C1 C2 C3 C9 0.0000 0.00 -60.00 0.00 0.0000 IC C3 C2 C1 C8 0.0000 0.00 60.00 0.00 0.0000 IC C2 C1 C8 C7 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C9 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C9 *C3 H3 0.0000 0.00 120.00 0.00 0.0000 IC C9 C8 *C7 C6 0.0000 0.00 -120.00 0.00 0.0000 IC C9 C8 *C7 H7 0.0000 0.00 120.00 0.00 0.0000 IC C8 C2 *C1 C10 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C2 *C1 H1 0.0000 0.00 120.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C7 C1 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 IC C7 C1 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C7 *C9 H91 0.0000 0.00 120.00 0.00 0.0000 IC C3 C7 *C9 H92 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C10 H101 0.0000 0.00 120.00 0.00 0.0000 IC C5 C1 *C10 H102 0.0000 0.00 -120.00 0.00 0.0000 RESI AZUL 0.00 ! C10H8 azulene, kevo !QM has exteremly low freq for 7-ring. In CHARMM, it's way too rigid, !despite drastically pulling down all force constants. However, !The final result is more or less in line with naftalene (NAFT). GROUP ATOM C1 CG2R51 -0.30 ATOM H1 HGR51 0.20 ATOM C2 CG2R51 -0.17 ATOM H2 HGR51 0.20 ATOM C3 CG2R51 -0.30 ! H5 ATOM H3 HGR51 0.20 ! H3 | H6 ATOM C4 CG2RC7 0.07 ! | C5-_ / ATOM C5 CG2R71 -0.24 ! C3-_ // -C6 ATOM H5 HGR71 0.23 ! // -C4 \\ ATOM C6 CG2R71 -0.15 ! H2--C2 | C7--H7 ATOM H6 HGR71 0.18 ! \ _=C10 / ATOM C7 CG2R71 -0.22 ! C1=- \ _=C8 ATOM H7 HGR71 0.21 ! | C9=- \ ATOM C8 CG2R71 -0.15 ! H1 | H8 ATOM H8 HGR71 0.18 ! H9 ATOM C9 CG2R71 -0.24 ATOM H9 HGR71 0.23 ATOM C10 CG2RC7 0.07 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C10 C1 C4 C10 BOND C1 H1 C2 H2 C3 H3 C5 H5 BOND C6 H6 C7 H7 C8 H8 C9 H9 IC C4 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C4 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C3 C10 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 !End continuation of Maybridge list, kevo and erh, jun2008 !Team Sugar, og, jun2008 RESI AMOL -1.00 ! C4H7O4 alpha-methoxy-lactic acid, og GROUP ATOM C1 CG301 0.30 ! CT1 HM1 HM2 HM3 ATOM C2 CG2O3 0.30 ! CC \ | / ATOM OH OG311 -0.65 ! OH1 CM ATOM HO HGP1 0.42 ! H | ATOM OM OG301 -0.34 ! ethers OM O1 (-) ATOM CM CG331 -0.10 ! CT3 | / ATOM HM1 HGA3 0.09 ! HA OH--C1--C2 ATOM HM2 HGA3 0.09 ! HA / | \\ ATOM HM3 HGA3 0.09 ! HA HO | O2 ATOM O1 OG2D2 -0.60 ! OC H01--C0 ATOM O2 OG2D2 -0.60 ! OC | \ GROUP ! H02 H03 ATOM C0 CG331 -0.27 ! CT3 ATOM H01 HGA3 0.09 ! HA ATOM H02 HGA3 0.09 ! HA ATOM H03 HGA3 0.09 ! HA BOND C1 OH OH HO C1 OM C1 C0 BOND C1 C2 C2 O1 BOND C0 H01 C0 H02 C0 H03 BOND OM CM BOND CM HM1 CM HM2 CM HM3 BOND C2 O2 IMPR C2 O2 O1 C1 IC C2 C1 OM CM 1.5530 103.90 -179.96 113.60 1.4233 IC OM C2 *C1 C0 1.4292 103.90 120.03 110.17 1.5625 IC OM C2 *C1 OH 1.4292 103.90 -122.26 107.58 1.4253 IC C2 C1 OH HO 1.5530 107.58 -175.04 105.92 0.9600 IC C1 OM CM HM1 1.4292 113.60 51.98 110.67 1.1100 IC HM1 OM *CM HM2 1.1100 110.67 -121.80 110.69 1.1095 IC HM1 OM *CM HM3 1.1100 110.67 119.24 109.06 1.1099 IC OH C1 C2 O1 1.4253 107.58 116.60 118.67 1.2616 IC O1 C1 *C2 O2 1.2616 118.67 -179.94 118.34 1.2627 IC OH C1 C0 H01 1.4253 108.18 -61.82 109.95 1.1112 IC H01 C1 *C0 H02 1.1112 109.95 -118.40 109.70 1.1104 IC H01 C1 *C0 H03 1.1112 109.95 120.36 111.60 1.1074 PATC FIRS NONE LAST NONE !End team Sugar, og, jun2008 !Opioid preparation, kevo, jun2008 RESI CHXE 0.00 ! C6H10 cyclohexene, kevo GROUP ! Based on RESI TMCH . ATOM C1 CG321 -0.18 ! We don't really want to optimize it. ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG321 -0.18 ! H11 H12 ATOM H21 HGA2 0.09 ! \ / ATOM H22 HGA2 0.09 ! H21 C1 H6 ATOM C3 CG321 -0.18 ! \ / \ / ATOM H31 HGA2 0.09 ! H22-C2 C6 ATOM H32 HGA2 0.09 ! | || ATOM C4 CG321 -0.18 ! H31-C3 C5 ATOM H41 HGA2 0.09 ! / \ / \ ATOM H42 HGA2 0.09 ! H32 C4 H5 ATOM C5 CG2D1 -0.15 ! / \ ATOM H5 HGA4 0.15 ! H41 H42 ATOM C6 CG2D1 -0.15 ATOM H6 HGA4 0.15 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C6 H6 C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H5 IC C1 C2 C3 C4 0.00 0.00 -63.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 46.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 -13.0 0.00 0.00 IC C6 C2 *C1 H11 0.00 0.00 120.0 0.00 0.00 IC C6 C2 *C1 H12 0.00 0.00 -120.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 IC C4 C6 *C5 H5 0.00 0.00 180.0 0.00 0.00 IC C1 C5 *C6 H6 0.00 0.00 180.0 0.00 0.00 PATCH FIRST NONE LAST NONE RESI 2DHF 0.000 ! C4H6O 2,3-dihydrofuran, kevo GROUP ATOM O1 OG3C51 -0.33 ATOM C2 CG2R51 -0.06 ATOM H2 HGR52 0.20 ! H3 H41 H42 ATOM C3 CG2R51 -0.41 ! \ | / ATOM H3 HGR51 0.24 ! C3----C4 ATOM C4 CG3C52 -0.08 ! || | ATOM H41 HGA2 0.09 ! C2 C5--H51 ATOM H42 HGA2 0.09 ! / \ / \ ATOM C5 CG3C52 0.08 ! H2 O1 H52 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 O1 BOND C2 H2 C3 H3 BOND C4 H41 C4 H42 C5 H51 C5 H52 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 IC C3 O1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 IC O1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC O1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 !End opioid preparation, kevo, jun2008 !Compounds for GSK/IBM collaboration, kevo, jun2008 RESI 9MAD 0.00 ! C6H7N5 9-Methyl-Adenine, kevo for gsk/ibm GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 GROUP ATOM N9 NG2R51 -0.05 ! H61 H62 ATOM C5 CG2RC0 0.28 ! \ / ATOM N7 NG2R50 -0.71 ! N6 ATOM C8 CG2R53 0.34 ! | ATOM H8 HGR52 0.12 ! C6 ATOM N1 NG2R62 -0.74 ! // \ ATOM C2 CG2R64 0.50 ! N1 C5--N7\\ ATOM H2 HGR62 0.13 ! | || C8-H8 ATOM N3 NG2R62 -0.75 ! C2 C4--N9/ ATOM C4 CG2RC0 0.43 ! / \\ / \ ATOM C6 CG2R64 0.46 ! H2 N3 C1--H13 ATOM N6 NG2S3 -0.77 ! / \ ATOM H61 HGP4 0.38 ! H11 H12 ATOM H62 HGP4 0.38 BOND C1 N9 C1 H11 C1 H12 C1 H13 BOND N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR C6 C5 N1 N6 IMPR N6 H62 H61 C6 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C4 C8 *N9 C1 0.0 0.0 180.0 0.0 0.0 IC C4 N9 C1 H11 0.0 0.0 180.0 0.0 0.0 IC N9 H11 *C1 H12 0.0 0.0 120.0 0.0 0.0 IC N9 H11 *C1 H13 0.0 0.0 -120.0 0.0 0.0 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 RESI 1MTH 0.00 ! C6H8N2O2 1-Methyl-Thymine, kevo for gsk/ibm GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 GROUP ATOM N1 NG2R61 -0.34 ! H51 O4 ATOM C6 CG2R62 0.17 ! | || ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 ATOM C2 CG2R63 0.51 ! | \ / \ / ATOM O2 OG2D4 -0.41 ! H53 C5 N3 ATOM N3 NG2R61 -0.46 ! || | ATOM H3 HGP1 0.36 ! H6-C6 C2 ATOM C4 CG2R63 0.50 ! \ / \\ ATOM O4 OG2D4 -0.45 ! N1 O2 ATOM C5 CG2R62 -0.15 ! | ATOM C5M CG331 -0.11 ! H11--C1--H13 ATOM H51 HGA3 0.07 ! | ATOM H52 HGA3 0.07 ! H12 ATOM H53 HGA3 0.07 BOND C1 N1 C1 H11 C1 H12 C1 H13 BOND N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 C6 H6 BOND C5 C5M C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0 IC C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 IC N1 H11 *C1 H12 0.0 0.0 120.0 0.0 0.0 IC N1 H11 *C1 H13 0.0 0.0 -120.0 0.0 0.0 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 RESI PROH 0.00 ! C3H8O n-propanol, kevo for gsk/ibm GROUP ATOM O1 OG311 -0.65 ATOM HO1 HGP1 0.42 ATOM C1 CG321 0.05 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND O1 HO1 O1 C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 C3 H33 IC C1 C2 C3 H33 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 IC O1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 RESI PRSH 0.00 ! C3H8S n-thiopropanol, kevo for gsk/ibm GROUP ATOM S1 SG311 -0.23 ATOM HS1 HGP3 0.16 ATOM C1 CG321 -0.11 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND S1 HS1 S1 C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 C3 H33 IC C1 C2 C3 H33 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 S1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C1 S1 HS1 0.0000 0.00 180.00 0.00 0.0000 IC S1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC S1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 RESI 2BOH 0.00 ! C4H10O (S)-2-butanol, kevo for gsk/ibm GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 GROUP ATOM O2 OG311 -0.65 ATOM HO2 HGP1 0.42 ATOM C2 CG311 0.14 ATOM H2 HGA1 0.09 GROUP ATOM C3 CG321 -0.18 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C1 H11 C1 H12 C1 H13 BOND O2 HO2 O2 C2 C2 H2 BOND C2 C3 C3 H31 C3 H32 BOND C3 C4 C4 H41 C4 H42 C4 H43 IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 IC C4 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 O2 0.0000 0.00 -120.00 0.00 0.0000 ! S IC C1 C3 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 ! S IC C3 C2 O2 HO2 0.0000 0.00 180.00 0.00 0.0000 IC H13 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC H13 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI NEOP 0.00 ! C5H12 neopentane, kevo for gsk/ibm GROUP ATOM C CG301 0.00 ATOM C1 CG331 -0.27 ATOM C2 CG331 -0.27 ATOM C3 CG331 -0.27 ! H32 ATOM C4 CG331 -0.27 ! | ATOM H11 HGA3 0.09 ! H31-C3-H33 ATOM H12 HGA3 0.09 ! H23 | H41 ATOM H13 HGA3 0.09 ! | | | ATOM H21 HGA3 0.09 ! H22-C2------C------C4-H42 ATOM H22 HGA3 0.09 ! | | | ATOM H23 HGA3 0.09 ! H21 | H43 ATOM H31 HGA3 0.09 ! H11-C1-H13 ATOM H32 HGA3 0.09 ! | ATOM H33 HGA3 0.09 ! H12 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C C1 C C2 C C3 C C4 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 IC C2 C C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC C H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2 C1 *C C3 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 *C C4 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3 C C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC C H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC C H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C4 C C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC C H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC C H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C1 C C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 IC C H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 IC C H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI MCPE 0.00 ! C6H12 methylcyclopentane, kevo for gsk/ibm GROUP ATOM C1 CG3C52 -0.18 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG3C52 -0.18 ! H61 H62 ATOM H21 HGA2 0.09 ! \ / ATOM H22 HGA2 0.09 ! H51 C6--H63 ATOM C3 CG3C52 -0.18 ! \ / ATOM H31 HGA2 0.09 ! H41 C5 H11 ATOM H32 HGA2 0.09 ! \ / \ / ATOM C4 CG3C52 -0.18 ! H42--C4 C1--H12 ATOM H41 HGA2 0.09 ! | | ATOM H42 HGA2 0.09 ! H31--C3----C2--H21 ATOM C5 CG3C51 -0.09 ! | | ATOM H51 HGA1 0.09 ! H32 H22 GROUP ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 BOND C5 H51 C5 C6 C6 H61 C6 H62 C6 H63 IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 -20.0 0.00 0.0000 ! equatorial IC C3 C4 C5 C1 0.0000 0.00 40.0 0.00 0.0000 ! equatorial IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 C6 0.0000 0.00 240.0 0.00 0.0000 IC C4 C5 C6 H63 0.0000 0.00 180.0 0.00 0.0000 IC C5 H63 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 IC C5 H63 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 RESI DMTF 0.00 ! C6H12O (S,R)-dimethyl-tetrahydrofuran GROUP ATOM O4' OG3C51 -0.40 ATOM C1' CG3C51 0.11 ATOM C2' CG3C52 -0.18 ! H52 H53 H11 H12 ATOM C3' CG3C52 -0.18 ! \ / \ / ATOM C4' CG3C51 0.11 ! H51--C5 O4' C1--H13 ATOM H11' HGA1 0.09 ! \ / \ / ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H11' ATOM H22' HGA2 0.09 ! | | ATOM H31' HGA2 0.09 ! H31'--C3'----C2'--H21' ATOM H32' HGA2 0.09 ! / \ ATOM H42' HGA1 0.09 ! H32' H22' GROUP ATOM C5 CG331 -0.27 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5 BOND C1' H11' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H42' C5 H51 C5 H52 C5 H53 BOND C1' C1 C1 H11 C1 H12 C1 H13 IC C4' O4' C1' C2' 0.0000 0.00 -40.00 0.00 0.0000 ! equatorial IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 ! S IC C2' O4' *C1' C1 0.0000 0.00 -120.00 0.00 0.0000 ! S IC O4' C1' C2' C3' 0.0000 0.00 20.00 0.00 0.0000 ! equatorial IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 IC C4' C2' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 IC C4' C2' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' O4' *C4' C5 0.0000 0.00 120.00 0.00 0.0000 ! R IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 ! R IC O4' C4' C5 H51 0.0000 0.00 180.00 0.00 0.0000 IC H51 C4' *C5 H52 0.0000 0.00 120.00 0.00 0.0000 IC H51 C4' *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 IC O4' C1' C1 H13 0.0000 0.00 180.00 0.00 0.0000 IC C1' H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C1' H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 RESI TOLU 0.00 ! C7H8 toluene, copied from pedro/toppar_aromatics.str for gsk/ibm GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ! HD1 HE1 ATOM HD1 HGR61 0.115 ! | | ATOM CD2 CG2R61 -0.115 ! CD1--CE1 H11 ATOM HD2 HGR61 0.115 ! / \ / ATOM CE1 CG2R61 -0.115 ! HG--CG CZ--CT--H12 ATOM HE1 HGR61 0.115 ! \ / \ ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 ATOM HE2 HGR61 0.115 ! | | ATOM CZ CG2R61 0.000 ! HD2 HE2 ATOM CT CG331 -0.270 ATOM H11 HGA3 0.090 ATOM H12 HGA3 0.090 ATOM H13 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ CT BOND CT H11 CT H12 CT H13 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 RESI BBEN 0.00 ! C10H14 butylbenzene, kevo for gsk/ibm GROUP ATOM CG CG2R61 0.000 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CZ CG2R61 -0.115 ATOM HZ HGR61 0.115 GROUP ATOM C1 CG321 -0.18 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ! HD1 HE1 ATOM C2 CG321 -0.18 ! | | ATOM H21 HGA2 0.09 ! H41 H31 H21 H11 CD1--CE1 ATOM H22 HGA2 0.09 ! | | | | / \ ATOM C3 CG321 -0.18 ! H43--C4---C3---C2---C1---CG CZ--HZ ATOM H31 HGA2 0.09 ! | | | | \ / ATOM H32 HGA2 0.09 ! H42 H32 H22 H12 CD2--CE2 ATOM C4 CG331 -0.27 ! | | ATOM H41 HGA3 0.09 ! HD2 HE2 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG C1 C1 C2 C2 C3 C3 C4 BOND CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 IC CG CD1 CE1 CZ 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CD2 *CG C1 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG C1 C2 0.0000 0.00 90.00 0.00 0.0000 IC CG C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CE2 *CZ HZ 0.0000 0.00 180.00 0.00 0.0000 IC CG C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC CG C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI OXYL 0.00 ! C8H10 o-xylene, kevo for gsk/ibm GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ! HD1 HE1 ATOM HD2 HGR61 0.115 ! | | ATOM CE1 CG2R61 -0.115 ! CD1--CE1 H11 ATOM HE1 HGR61 0.115 ! / \ / ATOM CE2 CG2R61 0.000 ! HG--CG CZ--C1--H12 ATOM CZ CG2R61 0.000 ! \ / \ ATOM C1 CG331 -0.270 ! CD2--CE2 H13 ATOM H11 HGA3 0.090 ! | \ ATOM H12 HGA3 0.090 ! HD2 C2--H21 ATOM H13 HGA3 0.090 ! | \ ATOM C2 CG331 -0.270 ! H23 H22 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 C2 CZ C1 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 C2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ C1 H11 1.4000 120.00 0.00 109.50 1.1100 IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 IC CZ CE2 C2 H21 1.4000 120.00 180.00 109.50 1.1100 IC CE2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 IC CE2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 RESI MXYL 0.00 ! C8H10 m-xylene, kevo for gsk/ibm GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 0.000 ! HD1 HE1 ATOM CE1 CG2R61 -0.115 ! | | ATOM HE1 HGR61 0.115 ! CD1--CE1 H11 ATOM CE2 CG2R61 -0.115 ! / \ / ATOM HE2 HGR61 0.115 ! HG--CG CZ--C1--H12 ATOM CZ CG2R61 0.000 ! \ / \ ATOM C1 CG331 -0.270 ! CD2--CE2 H13 ATOM H11 HGA3 0.090 ! / \ ATOM H12 HGA3 0.090 ! H21--C2 HE2 ATOM H13 HGA3 0.090 ! / | ATOM C2 CG331 -0.270 ! H22 H23 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 C2 CE1 HE1 BOND CE2 HE2 CZ C1 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 C2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 IC CE2 CD2 C2 H21 1.4000 120.00 -90.00 109.50 1.1100 IC CD2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 IC CD2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 RESI PXYL 0.00 ! C8H10 p-xylene, kevo for gsk/ibm GROUP ATOM CG CG2R61 0.000 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ! HD1 HE1 ATOM HE1 HGR61 0.115 ! | | ATOM CE2 CG2R61 -0.115 ! H21 CD1--CE1 H11 ATOM HE2 HGR61 0.115 ! \ / \ / ATOM CZ CG2R61 0.000 ! H22--C2--CG CZ--C1--H12 ATOM C1 CG331 -0.270 ! / \ / \ ATOM H11 HGA3 0.090 ! H23 CD2--CE2 H13 ATOM H12 HGA3 0.090 ! | | ATOM H13 HGA3 0.090 ! HD2 HE2 ATOM C2 CG331 -0.270 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG C2 CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ C1 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG C2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 IC CD2 CG C2 H21 1.4000 120.00 -90.00 109.50 1.1100 IC CG H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 IC CG H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 RESI PSCU 0.00 ! C9H12 pseudocumene (1,2,4-trimethylbenzene), kevo for gsk/ibm GROUP ATOM CG CG2R61 0.000 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ! HD1 HE1 ATOM HE1 HGR61 0.115 ! | | ATOM CE2 CG2R61 0.000 ! H31 CD1--CE1 H11 ATOM CZ CG2R61 0.000 ! \ / \ / ATOM C1 CG331 -0.270 ! H32--C3--CG CZ--C1--H12 ATOM H11 HGA3 0.090 ! / \ / \ ATOM H12 HGA3 0.090 ! H33 CD2--CE2 H13 ATOM H13 HGA3 0.090 ! | \ ATOM C2 CG331 -0.270 ! HD2 C2--H21 ATOM H21 HGA3 0.090 ! | \ ATOM H22 HGA3 0.090 ! H23 H22 ATOM H23 HGA3 0.090 ATOM C3 CG331 -0.270 ATOM H31 HGA3 0.090 ATOM H32 HGA3 0.090 ATOM H33 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG C3 CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 C2 CZ C1 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG C3 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 C2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ C1 H11 1.4000 120.00 0.00 109.50 1.1100 IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 IC CZ CE2 C2 H21 1.4000 120.00 180.00 109.50 1.1100 IC CE2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 IC CE2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 IC CD2 CG C3 H31 1.4000 120.00 90.00 109.50 1.1100 IC CG H31 *C3 H32 1.5000 109.50 120.00 109.50 1.1100 IC CG H31 *C3 H33 1.5000 109.50 -120.00 109.50 1.1100 RESI PCRO 0.00 ! C7H8O p-cresol, kevo for gsk/ibm GROUP ATOM CG CG2R61 0.110 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ! HD1 HE1 ATOM HE1 HGR61 0.115 ! | | ATOM CE2 CG2R61 -0.115 ! CD1--CE1 H11 ATOM HE2 HGR61 0.115 ! / \ / ATOM CZ CG2R61 0.000 ! H2--O2--CG CZ--C1--H12 ATOM C1 CG331 -0.270 ! \ / \ ATOM H11 HGA3 0.090 ! CD2--CE2 H13 ATOM H12 HGA3 0.090 ! | | ATOM H13 HGA3 0.090 ! HD2 HE2 ATOM O2 OG311 -0.530 ATOM H2 HGP1 0.420 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG O2 CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ C1 O2 H2 BOND C1 H11 C1 H12 C1 H13 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG O2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 IC CD2 CG O2 H2 1.4000 120.00 0.00 109.50 0.9600 RESI PNPO 0.000 ! C6H5NO3 p-nitrophenol, kevo for gsk/ibm GROUP ATOM C1 CG2R61 -0.18 ATOM H1 HGR61 0.16 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ! H5 H4 ATOM C3 CG2R61 0.110 ! \ ___ / ATOM O3 OG311 -0.53 ! O6A C5---C4 ATOM H3 HGP1 0.42 ! \ + / \ ATOM C4 CG2R61 -0.115 ! - N6--C6 C3--O3--H3 ATOM H4 HGR61 0.115 ! / \\ // ATOM C5 CG2R61 -0.18 ! O6B C1---C2 ATOM H5 HGR61 0.16 ! / \ ATOM C6 CG2R61 0.32 ! H1 H2 ATOM N6 NG2O1 0.40 ATOM O6A OG2N1 -0.34 ATOM O6B OG2N1 -0.34 BOND C1 H1 C1 C2 C2 H2 C2 C3 C3 O3 BOND O3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 BOND C6 C1 C6 N6 N6 O6A N6 O6B IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 O3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 IC C1 C6 N6 O6A 0.0000 0.00 180.00 0.00 0.0000 IC O6A C6 *N6 O6B 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 O3 H3 0.0000 0.00 0.00 0.00 0.0000 RESI 34MP 0.00 ! C7H9N 3,4-dimethylpyridine, kevo for gsk/ibm GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 0.000 ATOM CG CG2R61 0.000 ! H32 H33 ATOM CD2 CG2R61 -0.115 ! \ / ATOM CE2 CG2R61 0.180 ! H31--CD3 HE1 ATOM HE1 HGR62 0.120 ! \ | ATOM HD2 HGR61 0.115 ! H21 CD1--CE1 ATOM HE2 HGR62 0.120 ! \ / \ ATOM C3 CG331 -0.270 ! H22--C2--CG NZ ATOM H31 HGA3 0.090 ! / \ / ATOM H32 HGA3 0.090 ! H23 CD2--CE2 ATOM H33 HGA3 0.090 ! | | ATOM C2 CG331 -0.270 ! HD2 HE2 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG C2 CD1 C3 CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC CG CD1 CE1 NZ 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CD2 *CG C2 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *CD1 C3 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG C2 H21 0.0000 0.00 0.00 0.00 0.0000 IC CG H21 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC CG H21 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 IC CG CD1 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC CD1 H31 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC CD1 H31 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 RESI 4MEP 0.00 ! C6H7N 4-methylpyridine, kevo for gsk/ibm GROUP ATOM NZ NG2R60 -0.600 ATOM CE1 CG2R61 0.180 ATOM CD1 CG2R61 -0.115 ATOM CG CG2R61 0.000 ! HD1 HE1 ATOM CD2 CG2R61 -0.115 ! | | ATOM CE2 CG2R61 0.180 ! H21 CD1--CE1 ATOM HE1 HGR62 0.120 ! \ / \ ATOM HD1 HGR61 0.115 ! H22--C2--CG NZ ATOM HD2 HGR61 0.115 ! / \ / ATOM HE2 HGR62 0.120 ! H23 CD2--CE2 ATOM C2 CG331 -0.270 ! | | ATOM H21 HGA3 0.090 ! HD2 HE2 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 NZ CE1 NZ CE2 BOND CG C2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND C2 H21 C2 H22 C2 H23 IC CG CD1 CE1 NZ 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CE1 NZ CE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 NZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CD2 *CG C2 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC NZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC NZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG C2 H21 0.0000 0.00 90.00 0.00 0.0000 IC CG H21 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC CG H21 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 RESI 23MN 0.00 ! C12H12 2,3-dimethylnaphtalene, kevo for gsk/ibm GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 0.000 ATOM C3 CG2R61 0.000 ATOM C4 CG2R61 -0.115 ATOM H4 HGR61 0.115 ATOM C5 CG2R61 0.000 ATOM C6 CG2R61 -0.115 ! H4 H6 ATOM H6 HGR61 0.115 ! | | ATOM C7 CG2R61 -0.115 ! H312 H311 C4 C6 ATOM H7 HGR61 0.115 ! \ | // \ / \\ ATOM C8 CG2R61 -0.115 ! H313--C31---C3 C5 C7--H7 ATOM H8 HGR61 0.115 ! | || | ATOM C9 CG2R61 -0.115 ! H211--C21---C2 C10 C8--H8 ATOM H9 HGR61 0.115 ! / | \\ / \ // ATOM C10 CG2R61 0.000 ! H212 H213 C1 C9 ATOM C21 CG331 -0.270 ! | | ATOM H211 HGA3 0.090 ! H1 H9 ATOM H212 HGA3 0.090 ATOM H213 HGA3 0.090 ATOM C31 CG331 -0.270 ATOM H311 HGA3 0.090 ATOM H312 HGA3 0.090 ATOM H313 HGA3 0.090 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 C1 C10 BOND C1 H1 C2 C21 C3 C31 C4 H4 BOND C6 H6 C7 H7 C8 H8 C9 H9 BOND C21 H211 C21 H212 C21 H213 BOND C31 H311 C31 H312 C31 H313 IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 C21 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 C31 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C21 H211 0.0000 0.00 0.00 0.00 0.0000 IC C2 H211 *C21 H212 0.0000 0.00 120.00 0.00 0.0000 IC C2 H211 *C21 H213 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C3 C31 H311 0.0000 0.00 180.00 0.00 0.0000 IC C3 H311 *C31 H312 0.0000 0.00 120.00 0.00 0.0000 IC C3 H311 *C31 H313 0.0000 0.00 -120.00 0.00 0.0000 RESI 14MN 0.00 ! C12H12 1,4-dimethylnaphtalene, kevo for gsk/ibm GROUP ATOM C1 CG2R61 0.000 ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C4 CG2R61 0.000 ! H412 H411 ATOM C5 CG2R61 0.000 ! \ | ATOM C6 CG2R61 -0.115 ! H413--C41 H6 ATOM H6 HGR61 0.115 ! | | ATOM C7 CG2R61 -0.115 ! C4 C6 ATOM H7 HGR61 0.115 ! // \ / \\ ATOM C8 CG2R61 -0.115 ! H3--C3 C5 C7--H7 ATOM H8 HGR61 0.115 ! | || | ATOM C9 CG2R61 -0.115 ! H2--C2 C10 C8--H8 ATOM H9 HGR61 0.115 ! \\ / \ // ATOM C10 CG2R61 0.000 ! C1 C9 ATOM C11 CG331 -0.270 ! | | ATOM H111 HGA3 0.090 ! H111--C11 H9 ATOM H112 HGA3 0.090 ! / | ATOM H113 HGA3 0.090 ! H112 H113 ATOM C41 CG331 -0.270 ATOM H411 HGA3 0.090 ATOM H412 HGA3 0.090 ATOM H413 HGA3 0.090 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C8 C9 BOND C9 C10 C5 C10 C1 C10 BOND C1 C11 C2 H2 C3 H3 C4 C41 BOND C6 H6 C7 H7 C8 H8 C9 H9 BOND C11 H111 C11 H112 C11 H113 BOND C41 H411 C41 H412 C41 H413 IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 C2 *C1 C11 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 C41 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C10 C1 C11 H111 0.0000 0.00 180.00 0.00 0.0000 IC C1 H111 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 IC C1 H111 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C4 C41 H411 0.0000 0.00 0.00 0.00 0.0000 IC C4 H411 *C41 H412 0.0000 0.00 120.00 0.00 0.0000 IC C4 H411 *C41 H413 0.0000 0.00 -120.00 0.00 0.0000 !End compounds for GSK/IBM collaboration, kevo, jun2008 !Drug-like molecules, S. Zhong, jun2008 RESI FORA -1.00 ! CHO2 formate, from acetate, sz & kevo GROUP ATOM C1 CG2O3 0.52 ! H ATOM O2 OG2D2 -0.76 ! C ATOM O3 OG2D2 -0.76 ! / \\ ATOM H4 HGR52 0.00 ! -O O BOND C1 H4 BOND C1 O2 C1 O3 IMPR C1 O2 O3 H4 IC O3 O2 *C1 H4 0.00 0.00 180.0 0.0 0.0 IC H4 O3 *C1 O2 0.00 0.00 180.0 0.0 0.0 !redundant definition needed to enable seeding. !Hydrazine, E. Darian, jun2008 RESI HDZN 0.00 ! N2H4 Hydrazine neutral, ed GROUP ATOM N1 NG3N1 -0.78 ATOM H11 HGP1 0.39 ! H11 H21 ATOM H12 HGP1 0.39 ! \ / GROUP ! N1--N2 ATOM N2 NG3N1 -0.78 ! / \ ATOM H21 HGP1 0.39 ! H12 H22 ATOM H22 HGP1 0.39 BOND N1 H11 N1 H12 N1 N2 N2 H21 N2 H22 IC H11 N1 N2 H21 0.0000 0.0000 60.0000 0.0000 0.0000 IC N2 H11 *N1 H12 0.0000 0.0000 130.0000 0.0000 0.0000 IC H21 N1 *N2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 !End hydrazine, E. Darian, jun2008 !halogenated ethanes, Nov08, adm RESI CLET 0.00 ! C2H5Cl chloroethane, adm jr. GROUP ATOM C1 CG321 0.07 ! CL11 H12 H13 ATOM CL11 CLGA1 -0.10 ! \ | / ATOM H12 HGA2 0.14 ! C1 ATOM H13 HGA2 0.14 ! | ATOM C2 CG331 -0.52 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 CL11 C1 H12 C1 H13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 CL11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC C2 CL11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI DCLE 0.00 ! C2H4Cl2 1,1-dichloroethane, adm jr. GROUP ATOM C1 CG311 0.12 ! CL11 CL12 H13 ATOM CL11 CLGA1 -0.04 ! \ | / ATOM CL12 CLGA1 -0.04 ! C1 ATOM H13 HGA1 0.22 ! | ATOM C2 CG331 -0.53 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 CL11 C1 CL12 C1 H13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 CL11 *C1 CL12 0.0000 0.00 120.00 0.00 0.0000 IC C2 CL11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI TCLE 0.00 ! C2H3Cl3 1,1,1-trichloroethane, adm jr. GROUP ATOM C1 CG301 -0.24 ! CL11 CL12 CL13 ATOM CL11 CLGA3 0.14 ! \ | / ATOM CL12 CLGA3 0.14 ! C1 ATOM CL13 CLGA3 0.14 ! | ATOM C2 CG331 -0.45 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 CL11 C1 CL12 C1 CL13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 CL11 *C1 CL12 0.0000 0.00 120.00 0.00 0.0000 IC C2 CL11 *C1 CL13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI BRET 0.00 ! C2H5Br bromoethane, adm jr. GROUP ATOM C1 CG321 0.07 ! BR11 H12 H13 ATOM BR11 BRGA1 -0.10 ! \ | / ATOM H12 HGA2 0.14 ! C1 ATOM H13 HGA2 0.14 ! | ATOM C2 CG331 -0.52 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 BR11 C1 H12 C1 H13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 BR11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC C2 BR11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI DBRE 0.00 ! C2H4Br2 1,1-dibromoethane, adm jr. GROUP ATOM C1 CG311 0.10 ! BR11 BR12 H13 ATOM BR11 BRGA2 -0.04 ! \ | / ATOM BR12 BRGA2 -0.04 ! C1 ATOM H13 HGA1 0.22 ! | ATOM C2 CG331 -0.51 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 BR11 C1 BR12 C1 H13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 BR11 *C1 BR12 0.0000 0.00 120.00 0.00 0.0000 IC C2 BR11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI TBRE 0.00 ! C2H3Br3 1,1,1-tribromoethane, adm jr. GROUP ATOM C1 CG301 -0.12 ! BR11 BR12 BR13 ATOM BR11 BRGA3 -0.01 ! \ | / ATOM BR12 BRGA3 -0.01 ! C1 ATOM BR13 BRGA3 -0.01 ! | ATOM C2 CG331 -0.12 ! C2 ATOM H21 HGA3 0.09 ! / | \ ATOM H22 HGA3 0.09 ! H21 H22 H23 ATOM H23 HGA3 0.09 BOND C1 BR11 C1 BR12 C1 BR13 BOND C1 C2 BOND C2 H21 C2 H22 C2 H23 IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 BR11 *C1 BR12 0.0000 0.00 120.00 0.00 0.0000 IC C2 BR11 *C1 BR13 0.0000 0.00 -120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE !New compounds by "team CGenFF", Dec 09 RESI CYIN 0.000 ! C9H6N2 5-cyanoindole, alr GROUP ATOM N1 NG2R51 -0.45 ! H6 ATOM H1 HGP1 0.37 ! | ATOM C2 CG2RC0 0.23 ! H8 C6 ATOM C3 CG2R61 -0.29 ! \ / \\ __ ATOM H3 HGR61 0.17 ! C8-----C7 C5--C10==N10 ATOM C4 CG2R61 -0.13 ! || || | ATOM H4 HGR61 0.16 ! C9 C2 C4 ATOM C5 CG2R61 -0.08 ! / \ / \ // \ ATOM C6 CG2R61 -0.28 ! H9 N1 C3 H4 ATOM H6 HGR61 0.20 ! | | ATOM C7 CG2RC0 0.26 ! H1 H3 ATOM C8 CG2R51 -0.40 ATOM H8 HGR51 0.18 ATOM C9 CG2R51 -0.02 ATOM H9 HGR52 0.16 ATOM C10 CG1N1 0.39 ATOM N10 NG1T1 -0.47 BOND N1 C2 C2 C3 DOUBLE C3 C4 BOND C4 C5 DOUBLE C5 C6 BOND C6 C7 C7 C8 DOUBLE C7 C2 C8 C9 BOND C9 N1 BOND N1 H1 C3 H3 C4 H4 BOND C5 C10 TRIPLE C10 N10 BOND C6 H6 C8 H8 C9 H9 IC C8 C9 N1 C2 1.3650 110.50 0.00 112.00 1.3700 IC C9 C8 C7 C2 1.3650 106.40 0.00 108.00 1.3850 IC C7 C8 C9 N1 1.4300 106.40 0.00 110.50 1.3700 IC C2 C8 *C7 C6 1.3850 108.00 180.00 133.50 1.3600 IC C2 C7 C6 C5 1.3850 110.00 0.00 113.20 1.3750 IC C7 C6 C5 C4 1.3600 113.20 0.00 120.00 1.3750 IC C6 C5 C4 C3 1.3750 120.00 0.00 120.00 1.3750 IC C5 C7 *C6 H6 1.3750 113.20 180.00 122.00 1.0800 IC C4 C6 *C5 C10 1.3750 120.00 180.00 120.00 1.3750 IC C4 C5 C10 N10 1.3750 120.00 0.00 120.00 1.2800 IC C3 C5 *C4 H4 1.3750 120.00 180.00 120.00 1.0800 IC C2 C4 *C3 H3 1.3600 113.20 180.00 120.00 1.0800 IC C9 C2 *N1 H1 1.3700 112.00 180.00 126.00 0.9760 IC C8 N1 *C9 H9 1.3650 110.50 180.00 125.00 1.0800 IC C9 C7 *C8 H8 1.3650 106.40 180.00 126.40 1.0800 RESI PHHZ 0.00 ! C6H8N2 Phenylhydrazine (neutral), ed GROUP ATOM CG CG2R61 -0.115 ! HG ATOM HG HGR61 0.115 ! CG GROUP ! // \ ATOM CD1 CG2R61 -0.115 ! HD1--CD1 CD2--HD2 ATOM HD1 HGR61 0.115 ! | || GROUP ! | || ATOM CD2 CG2R61 -0.115 ! HE1--CE1 CE2--HE2 ATOM HD2 HGR61 0.115 ! \\ / GROUP ! C6 ATOM CE1 CG2R61 -0.115 ! | ATOM HE1 HGR61 0.115 ! N7--H71 GROUP ! / ATOM CE2 CG2R61 -0.115 ! N8 ATOM HE2 HGR61 0.115 ! / \ GROUP ! H81 H82 ATOM C6 CG2R61 0.24 ATOM N7 NG3N1 -0.74 ATOM H71 HGP1 0.48 ATOM N8 NG3N1 -0.74 ATOM H81 HGP1 0.38 ATOM H82 HGP1 0.38 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 C6 CE1 C6 CE2 BOND CG HG CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 BOND C6 N7 N7 H71 N7 N8 N8 H81 N8 H82 IC CG CD1 CE1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CD1 CG CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CE1 *C6 N7 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 C6 N7 N8 0.0000 0.0000 30.0000 0.0000 0.0000 IC N8 C6 *N7 H71 0.0000 0.0000 130.0000 0.0000 0.0000 IC C6 N7 N8 H81 0.0000 0.0000 -150.0000 0.0000 0.0000 IC H81 N7 *N8 H82 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI THF2 0.00 ! C5H10O2 THF-2'OME, delete H22'->OM neutral, ed GROUP ATOM O4' OG3C51 -0.40 ! Change C2' and H21' type ATOM C4' CG3C52 0.02 ATOM C3' CG3C52 -0.18 ! H41' O4' H11' ATOM C1' CG3C52 0.02 ! \ / \ / ATOM H11' HGA2 0.09 ! H42'--C4' C1'--H12' ATOM H12' HGA2 0.09 ! | | ATOM H31' HGA2 0.09 ! H31'--C3'--C2'--H21' ATOM H32' HGA2 0.09 ! / | ATOM H41' HGA2 0.09 ! H32' OM (changed OM to O2') ATOM H42' HGA2 0.09 ! | GROUP ! CM ATOM C2' CG3C51 0.08 ! / | \ ATOM H21' HGA1 0.09 ! HM1 HM2 HM3 ATOM O2' OG301 -0.34 ATOM CM CG331 -0.10 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C2' H21' O2' C2' O2' CM BOND CM HM1 CM HM2 CM HM3 IC C1' O4' C4' C3' 0.0000 0.00 36.00 0.00 0.0000 IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 IC C4' O4' C1' C2' 0.0000 0.00 -19.00 0.00 0.0000 IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' C1' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 IC C3' C1' *C2' O2' 0.0000 0.00 120.00 0.00 0.0000 IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 IC C2' C4' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 IC O2' C2' C1' O4' 0.0000 0.00 105.00 0.00 0.0000 IC C1' C2' O2' CM 0.0000 0.00 -165.00 0.00 0.0000 IC C2' O2' CM HM1 0.0000 0.00 55.00 0.00 0.0000 IC C1' O2' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 IC HM1 O2' *CM HM2 0.0000 0.00 118.00 0.00 0.0000 IC HM3 O2' *CM HM2 0.0000 0.00 -120.00 0.00 0.0000 RESI AMCP 1.00 ! C4H10N Aminomethyl Cyclopropane, jhs ATOM C1 CG3C31 -0.09 ! C6 ATOM H2 HGA1 0.09 ! / \ ATOM C3 CG3C31 -0.18 ! C3__C1 ATOM H4 HGA2 0.09 ! \ ATOM H5 HGA2 0.09 ! C9 ATOM C6 CG3C31 -0.18 ! \ ATOM H7 HGA2 0.09 ! N12+ ATOM H8 HGA2 0.09 ATOM C9 CG324 0.21 ATOM H10 HGA2 0.05 ATOM H11 HGA2 0.05 ATOM N12 NG3P3 -0.30 ! from ethylammonium ATOM H13 HGP2 0.33 ATOM H14 HGP2 0.33 ATOM H15 HGP2 0.33 BOND C1 C3 C1 C6 C1 C9 C1 H2 BOND C3 C6 C3 H4 C3 H5 BOND C6 H7 C6 H8 BOND C9 N12 C9 H10 C9 H11 BOND N12 H13 N12 H14 N12 H15 IC C3 C9 *C1 C6 0.0000 0.00 -60.00 0.00 0.0000 IC C3 C9 *C1 H2 0.0000 0.00 150.00 0.00 0.0000 IC C6 C1 *C3 H4 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C1 *C3 H5 0.0000 0.00 100.00 0.00 0.0000 IC C3 C1 *C6 H7 0.0000 0.00 100.00 0.00 0.0000 IC C3 C1 *C6 H8 0.0000 0.00 -100.00 0.00 0.0000 IC C3 C1 C9 N12 0.0000 0.00 150.00 0.00 0.0000 IC N12 C1 *C9 H10 0.0000 0.00 120.00 0.00 0.0000 IC N12 C1 *C9 H11 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C9 N12 H13 0.0000 0.00 -60.00 0.00 0.0000 IC H13 C9 *N12 H14 0.0000 0.00 -120.00 0.00 0.0000 IC H13 C9 *N12 H15 0.0000 0.00 120.00 0.00 0.0000 PATCH FIRST NONE LAST NONE RESI BTON 0.00 ! C4H8O Butanone, yapol GROUP ATOM O1 OG2D3 -0.48 ATOM C1 CG2O5 0.40 ATOM C2 CG331 -0.23 ! O1 H41 H42 ATOM C3 CG321 -0.14 ! || | / ATOM H21 HGA3 0.09 ! C1 C4--H43 ATOM H22 HGA3 0.09 ! / \ / ATOM H23 HGA3 0.09 ! H21--C2 C3--H31 ATOM H31 HGA2 0.09 ! / | \ ATOM H32 HGA2 0.09 ! H22 H23 H32 GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C1 C3 C3 C4 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 C4 H43 DOUBLE O1 C1 IMPR C1 C3 C2 O1 ACCE O1 IC C2 C1 C3 H31 1.5366 116.31 56.91 107.51 1.1328 IC O1 C1 C3 H31 1.2237 122.02 -123.36 107.51 1.1328 IC O1 C1 C3 H32 1.2237 122.02 124.49 107.48 1.1325 IC C3 C1 C2 H21 1.5233 110.58 -153.74 111.52 1.1204 IC O1 C1 C2 H21 1.2237 126.42 23.85 111.52 1.1204 IC O1 C1 C2 H22 1.2237 126.42 148.26 114.11 1.1296 IC O1 C1 C2 H23 1.2237 126.42 -90.21 101.67 1.1375 IC O1 C1 C3 C4 1.2237 122.02 0.50 114.19 1.5261 IC C2 C1 C3 C4 1.5366 116.31 -179.21 114.19 1.5261 IC C1 C3 C4 H41 1.5233 114.19 -60.64 111.01 1.0980 IC C1 C3 C4 H42 1.5233 114.19 178.91 110.72 1.0989 IC C1 C3 C4 H43 1.5233 114.19 58.43 111.02 1.0980 RESI CHON 0.00 ! C6H10O cyclohexanone, yapol GROUP ATOM O1 OG2D3 -0.48 ATOM C1 CG2O5 0.40 ATOM C6 CG321 -0.14 ! O1 ATOM C2 CG321 -0.14 ! || ATOM H6A HGA2 0.09 ! H6A C1 H2A ATOM H6B HGA2 0.09 ! \ / \ / ATOM H2A HGA2 0.09 ! H6B--C6 C2--H2B ATOM H2B HGA2 0.09 ! | | ! H5A--C5 C3--H3A GROUP ! / \ / \ ATOM C3 CG321 -0.18 ! H5B C4 H3B ATOM H3A HGA2 0.09 ! / \ ATOM H3B HGA2 0.09 ! H4A H4B GROUP ATOM C4 CG321 -0.18 ATOM H4A HGA2 0.09 ATOM H4B HGA2 0.09 GROUP ATOM C5 CG321 -0.18 ATOM H5A HGA2 0.09 ATOM H5B HGA2 0.09 BOND C1 C2 BOND C2 H2A C2 H2B C2 C3 BOND C3 H3A C3 H3B C3 C4 BOND C4 H4A C4 H4B C4 C5 BOND C5 H5A C5 H5B C5 C6 BOND C6 H6A C6 H6B C6 C1 DOUBLE O1 C1 IMPR C1 C2 C6 O1 ACCE O1 IC C1 C2 C3 C4 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC C6 C2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000 IC H2A C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C2 *C3 H3A 0.0000 0.00 -120.00 0.00 0.0000 IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C3 *C4 H4A 0.0000 0.00 -120.00 0.00 0.0000 IC H4A C3 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C4 *C5 H5A 0.0000 0.00 -120.00 0.00 0.0000 IC H5A C4 *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C1 *C6 H6A 0.0000 0.00 120.00 0.00 0.0000 IC C5 C1 *C6 H6B 0.0000 0.00 -120.00 0.00 0.0000 patc firs none last none RESI DMTT 0.000 ! C3H6S3 dimethyl trithiocarbonate, kevo GROUP ATOM C1 CG331 -0.09 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM S1 SG311 -0.17 ! H11 S H21 ATOM C CG2O6 0.22 ! | || | ATOM S SG2D1 -0.24 ! H12--C1---S1---C---S2---C2--H22 ATOM S2 SG311 -0.17 ! | | ATOM C2 CG331 -0.09 ! H13 H23 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 S1 S1 C C S2 S2 C2 C S BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 IMPR C S1 S2 S IC S1 C S2 C2 0.0000 0.00 185.00 0.00 0.0000 IC S2 C S1 C1 0.0000 0.00 180.00 0.00 0.0000 IC S1 S2 *C S 0.0000 0.00 185.00 0.00 0.0000 IC C S1 C1 H11 0.0000 0.00 185.00 0.00 0.0000 IC C S1 C1 H12 0.0000 0.00 65.00 0.00 0.0000 IC C S1 C1 H13 0.0000 0.00 305.00 0.00 0.0000 IC C S2 C2 H21 0.0000 0.00 185.00 0.00 0.0000 ! introduce IC C S2 C2 H22 0.0000 0.00 65.00 0.00 0.0000 ! 5deg asymmetry IC C S2 C2 H23 0.0000 0.00 305.00 0.00 0.0000 ! everywhere. PRES 3POMP -0.030 ! C8H8O 3-phenoxymethylpyrrolidine (aka alpha-(3-pyrrolidine)anisole), kevo DELETE ATOM H31 GROUP ATOM C3 CG3C51 -0.12 ATOM H32 HGA1 0.09 GROUP ATOM C31 CG321 -0.01 ATOM H311 HGA2 0.09 ATOM H312 HGA2 0.09 ATOM O32 OG301 -0.39 ATOM C1B CG2R61 -0.115 ! H5B H4B ATOM H1B HGR61 0.115 ! \ ___ / ATOM C2B CG2R61 -0.115 ! C5B---C4B H312 H32 H42 ATOM H2B HGR61 0.115 ! / \ \ \ / ATOM C3B CG2R61 0.22 ! H6B--C6B C3B---O32---C31----C3----C4--H41 ATOM C4B CG2R61 -0.115 ! \\ // / | | ATOM H4B HGR61 0.115 ! C1B---C2B H311 H21--C2 C5--H51 ATOM C5B CG2R61 -0.115 ! / \ / \ / \ ATOM H5B HGR61 0.115 ! H1B H2B H22 N1 H52 ATOM C6B CG2R61 -0.115 ! | ATOM H6B HGR61 0.115 ! H1 BOND C3 C31 C31 O32 C31 H311 C31 H312 O32 C3B BOND C1B H1B C1B C2B C2B H2B C2B C3B BOND C3B C4B C4B H4B C4B C5B C5B H5B C5B C6B BOND C6B H6B C6B C1B IC C4 C2 *C3 C31 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C3 C31 O32 0.0000 0.00 60.00 0.00 0.0000 ! folded (-120) is best for PES. 60="Axial" IC C3 O32 *C31 H311 0.0000 0.00 120.00 0.00 0.0000 IC C3 O32 *C31 H312 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C31 O32 C3B 0.0000 0.00 180.00 0.00 0.0000 ! folded (0) is best for PES. 180="Pointing away from ring" IC C31 O32 C3B C2B 0.0000 0.00 0.00 0.00 0.0000 ! folded (90) is best for PES. 0="in-plane" like MEOB (unlike EBEN) IC O32 C2B *C3B C4B 0.0000 0.00 180.00 0.00 0.0000 IC C4B C3B C2B C1B 0.0000 0.00 0.00 0.00 0.0000 IC C2B C3B C4B C5B 0.0000 0.00 0.00 0.00 0.0000 IC C3B C4B C5B C6B 0.0000 0.00 0.00 0.00 0.0000 IC C2B C6B *C1B H1B 0.0000 0.00 180.00 0.00 0.0000 IC C3B C1B *C2B H2B 0.0000 0.00 180.00 0.00 0.0000 IC C5B C3B *C4B H4B 0.0000 0.00 180.00 0.00 0.0000 IC C6B C4B *C5B H5B 0.0000 0.00 180.00 0.00 0.0000 IC C1B C5B *C6B H6B 0.0000 0.00 180.00 0.00 0.0000 RESI DMCB 0.00 ! C3H7NO2 dimethyl carbamate, kevo & xxwy GROUP ATOM C1 CG331 -0.04 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM N2 NG2S1 -0.38 ATOM H2 HGP1 0.32 ! H11 O31 H41 ATOM C3 CG2O6 0.20 ! | || | ATOM O31 OG2D1 -0.39 ! H12--C1---N2---C3---O32---C4--H42 ATOM O32 OG302 -0.32 ! | | | ATOM C4 CG331 0.07 ! H13 H2 H43 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 N2 BOND N2 H2 N2 C3 BOND C3 O31 C3 O32 O32 C4 BOND C4 H41 C4 H42 C4 H43 IMPR C3 N2 O31 O32 IC C1 N2 C3 O32 0.0000 0.00 -170.00 0.00 0.0000 IC C3 N2 C1 H11 0.0000 0.00 -150.00 0.00 0.0000 IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *N2 H2 0.0000 0.00 158.00 0.00 0.0000 IC O32 N2 *C3 O31 0.0000 0.00 -180.00 0.00 0.0000 IC N2 C3 O32 C4 0.0000 0.00 180.00 0.00 0.0000 IC C3 O32 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC H41 O32 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 O32 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI DECB 0.00 ! C5H11NO2 diethyl carbamate, kevo & xxwy GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG321 0.05 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM N3 NG2S1 -0.38 ATOM H3 HGP1 0.32 ! H11 H21 O41 H51 H61 ATOM C4 CG2O6 0.20 ! | | || | | ATOM O41 OG2D1 -0.39 ! H12--C1---C2---N3---C4---O42---C5---C6--H62 ATOM O42 OG302 -0.32 ! | | | | | ATOM C5 CG321 0.16 ! H13 H22 H3 H52 H63 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 C2 BOND C2 H21 C2 H22 C2 N3 N3 H3 N3 C4 BOND C4 O41 C4 O42 O42 C5 BOND C5 H51 C5 H52 C5 C6 BOND C6 H61 C6 H62 C6 H63 IMPR C4 N3 O41 O42 IC C1 C2 N3 C4 0.0000 0.00 80.00 0.00 0.0000 IC N3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 N3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC H21 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *N3 H3 0.0000 0.00 155.00 0.00 0.0000 IC C2 N3 C4 O41 0.0000 0.00 0.00 0.00 0.0000 IC O41 N3 *C4 O42 0.0000 0.00 180.00 0.00 0.0000 IC N3 C4 O42 C5 0.0000 0.00 180.00 0.00 0.0000 IC C4 O42 C5 C6 0.0000 0.00 -90.00 0.00 0.0000 IC C6 O42 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C6 O42 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC O42 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 RESI FORH 0.00 ! CH2O2 formic acid, xxwy GROUP ATOM C CG2O2 0.38 ! O2 ATOM H HGR52 0.11 ! // ATOM O2 OG2D1 -0.40 ! H--C ATOM O1 OG311 -0.49 ! \ ATOM HO1 HGP1 0.40 ! O1-HO1 BOND C O1 C H O1 HO1 DOUBLE C O2 IMPR C O2 O1 H DONO BLNK HO1 ! O1 ACCE O1 ACCE O2 IC O2 C O1 HO1 0.0000 0.0000 0.0000 0.0000 0.0000 IC O1 O2 *C H 0.0000 0.0000 180.0000 0.0000 0.0000 RESI DMA 0.00 ! C4H9NO Dimethylacetamide, xxwy GROUP ATOM C CG2O1 0.43 ! H33 ATOM O OG2D1 -0.52 ! | ATOM N NG2S0 -0.35 ! O C3--H32 ATOM C1 CG331 -0.19 ! \\ / \ ATOM H11 HGA3 0.09 ! C---N H31 ATOM H12 HGA3 0.09 ! / \ ATOM H13 HGA3 0.09 ! H11--C1 C2--H23 ATOM C2 CG331 -0.09 ! / | / | ATOM H21 HGA3 0.09 ! H12 H13 H21 H22 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 ATOM C3 CG331 -0.09 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND H11 C1 H12 C1 H13 C1 BOND H21 C2 H22 C2 H23 C2 BOND H31 C3 H32 C3 H33 C3 BOND C C1 C N N C2 N C3 DOUBLE C O IMPR C C1 N O IC O C N C2 0.0000 0.0000 180.0000 0.0000 0.0000 IC O N *C C1 0.0000 0.0000 180.0000 0.0000 0.0000 IC C C2 *N C3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N C C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC C H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C N C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C N C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI DMF 0.00 ! C3H7NO Dimethylformamide, xxwy GROUP ATOM HA HGR52 0.08 ATOM C CG2O1 0.43 ! HC3 ATOM O OG2D1 -0.54 ! | ATOM N NG2S0 -0.33 ! O CC--HC2 ATOM CC CG331 -0.09 ! \\ / \ ATOM HC1 HGA3 0.09 ! C--N HC1 ATOM HC2 HGA3 0.09 ! / \ ATOM HC3 HGA3 0.09 ! HA CT--HT3 ATOM CT CG331 -0.09 ! / | ATOM HT1 HGA3 0.09 ! HT1 HT2 ATOM HT2 HGA3 0.09 ATOM HT3 HGA3 0.09 BOND HT1 CT HT2 CT HT3 CT BOND C HA C N N CC N CT BOND HC1 CC HC2 CC HC3 CC DOUBLE C O IMPR C N O HA IC O C N CT 0.0000 0.0000 180.0000 0.0000 0.0000 IC O N *C HA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CT *N CC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C N CC HC1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N HC1 *CC HC2 0.0000 0.0000 120.0000 0.0000 0.0000 IC N HC1 *CC HC3 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C N CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N HT1 *CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 IC N HT1 *CT HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 !IC O C N CT 1.2287 125.40 -180.0000 120.95 1.4495 !IC O N *C HA 1.2287 125.40 180.0000 112.84 1.1003 !IC C CT *N CC 1.3646 120.95 -179.0000 117.80 1.4514 !IC C N CC HC1 1.3646 121.26 0.0000 110.77 1.1140 !IC N HC1 *CC HC2 1.4514 110.77 118.6600 110.23 1.1108 !IC N HC1 *CC HC3 1.4514 110.77 -118.6600 110.23 1.1108 !IC C N CT HT1 1.3646 120.95 0.0000 110.56 1.1133 !IC N HT1 *CT HT2 1.4495 110.56 118.5900 110.54 1.1115 !IC N HT1 *CT HT3 1.4495 110.56 -118.5900 110.54 1.1115 RESI HEXD 0.00 ! C6H14O2 1,6-hexanediol, xxwy GROUP ATOM H11 HGA2 0.09 ! O1-HO1 ATOM H12 HGA2 0.09 ! | ATOM HO1 HGP1 0.42 ! H11-C1-H12 ATOM C1 CG321 0.05 ! | ATOM O1 OG311 -0.65 ! | GROUP ! | ATOM H21 HGA2 0.09 ! H21-C2-H22 ATOM H22 HGA2 0.09 ! | ATOM C2 CG321 -0.18 ! | GROUP ! | ATOM H31 HGA2 0.09 ! H31-C3-H32 ATOM H32 HGA2 0.09 ! | ATOM C3 CG321 -0.18 ! | GROUP ! | ATOM H41 HGA2 0.09 ! H41-C4-H42 ATOM H42 HGA2 0.09 ! | ATOM C4 CG321 -0.18 ! | GROUP ! | ATOM H51 HGA2 0.09 ! H51-C5-H152 ATOM H52 HGA2 0.09 ! | ATOM C5 CG321 -0.18 ! | GROUP ! | ATOM H61 HGA2 0.09 ! H61-C6-H62 ATOM H62 HGA2 0.09 ! | ATOM HO6 HGP1 0.42 ! O6-HO6 ATOM C6 CG321 0.05 ATOM O6 OG311 -0.65 BOND H11 C1 H12 C1 O1 C1 C1 C2 BOND H21 C2 H22 C2 C2 C3 O1 HO1 BOND H31 C3 H32 C3 C3 C4 BOND H41 C4 H42 C4 C4 C5 BOND H51 C5 H52 C5 C5 C6 BOND H61 C6 H62 C6 C6 O6 O6 HO6 IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 IC C3 C2 C1 O1 0.00 0.00 180.0 0.00 0.00 IC C2 C1 O1 HO1 0.00 0.00 180.0 0.00 0.00 IC O1 C2 *C1 H11 0.00 0.00 120.0 0.00 0.00 IC O1 C2 *C1 H12 0.00 0.00 240.0 0.00 0.00 IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 IC C1 C3 *C2 H22 0.00 0.00 240.0 0.00 0.00 IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 IC C2 C4 *C3 H32 0.00 0.00 240.0 0.00 0.00 IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 IC C3 C5 *C4 H42 0.00 0.00 240.0 0.00 0.00 IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 IC C4 C6 *C5 H52 0.00 0.00 240.0 0.00 0.00 IC C4 C5 C6 O6 0.00 0.00 180.0 0.00 0.00 IC C5 C6 O6 HO6 0.00 0.00 180.0 0.00 0.00 IC O6 C5 *C6 H61 0.00 0.00 120.0 0.00 0.00 IC O6 C5 *C6 H62 0.00 0.00 240.0 0.00 0.00 RESI TBOH 0.00 ! C4H10O t-butanol, xxwy GROUP ATOM C CG301 0.23 ! H12 H13 H33 H32 ATOM O OG311 -0.65 ! \ / \ / ATOM HO HGP1 0.42 ! H11--C1 C3--H31 GROUP ! \ / ATOM C1 CG331 -0.27 ! C ATOM H11 HGA3 0.09 ! / \ ATOM H12 HGA3 0.09 ! O C2--H23 ATOM H13 HGA3 0.09 ! | | \ GROUP ! HO H21 H22 ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 C C2 C C3 C C O O HO BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 DONO HO O ACCE O IC C1 C C2 H21 0.0000 0.000 180.0000 0.000 0.0000 IC C H21 *C2 H22 0.0000 0.000 120.0000 0.000 0.0000 IC C H21 *C2 H23 0.0000 0.000 -120.0000 0.000 0.0000 IC C2 C C1 H11 0.0000 0.000 180.0000 0.000 0.0000 IC C H11 *C1 H12 0.0000 0.000 120.0000 0.000 0.0000 IC C H11 *C1 H13 0.0000 0.000 -120.0000 0.000 0.0000 IC C1 C C3 H31 0.0000 0.000 180.0000 0.000 0.0000 IC C H31 *C3 H32 0.0000 0.000 120.0000 0.000 0.0000 IC C H31 *C3 H33 0.0000 0.000 -120.0000 0.000 0.0000 IC C1 C2 *C O 0.0000 0.000 120.0000 0.000 0.0000 IC C1 C2 *C C3 0.0000 0.000 -120.0000 0.000 0.0000 IC C3 C O HO 0.0000 0.000 180.0000 0.000 0.0000 RESI TMAOP 1.00 ! C3H10NO protonated trimethylammoniumoxide (TMAO) GROUP ! (aka Hydroxy(trimethyl)Ammonium), xxwy ATOM N NG3P0 -0.53 ATOM C1 CG334 -0.35 ! H31 H32 ATOM C2 CG334 -0.35 ! \ / ATOM C3 CG334 -0.35 ! H11 C3-H33 ATOM H11 HGP5 0.25 ! \ | ATOM H12 HGP5 0.25 ! H12-C1---N---O-HO ATOM H13 HGP5 0.25 ! / | ATOM H21 HGP5 0.25 ! H1 C2-H23 ATOM H22 HGP5 0.25 ! / \ ATOM H23 HGP5 0.25 ! H21 H22 ATOM H31 HGP5 0.25 ATOM H32 HGP5 0.25 ATOM H33 HGP5 0.25 ATOM O OG311 -0.17 ATOM HO HGP1 0.50 BOND N C1 N C2 N C3 N O O HO BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC C2 N C1 H11 0.00 0.00 180.0 0.0 0.0 IC N H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 IC N H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 IC C1 N C2 H21 0.00 0.00 180.0 0.0 0.0 IC N H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 IC N H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 IC C1 N C3 H31 0.00 0.00 180.0 0.0 0.0 IC N H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 IC N H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 IC C1 C2 *N C3 0.00 0.00 120.0 0.0 0.0 IC C1 C2 *N O 0.00 0.00 -120.0 0.0 0.0 IC C3 N O HO 0.00 0.00 180.0 0.0 0.0 RESI MRDN 0.000 ! C4H3NOS2 methylidene rhodanine, kevo & xxwy GROUP ATOM S1 SG311 -0.14 ! H3 S2 ATOM C2 CG2R53 0.26 ! \ // ATOM S2 SG2D1 -0.27 ! N3----C2 ATOM N3 NG2R53 -0.25 ! | | ATOM H3 HGP1 0.32 ! C4 S1 ATOM C4 CG2R53 0.29 ! // \ / ATOM O4 OG2D1 -0.39 ! O4 C5 ATOM C5 CG252O 0.10 ! || ATOM C6 CG2DC3 -0.49 ! C6 ATOM H61 HGA5 0.24 ! / \ ATOM H62 HGA5 0.33 ! H61 H62 BOND S1 C2 C2 N3 N3 C4 C4 C5 BOND C5 S1 C2 S2 N3 H3 C4 O4 BOND C5 C6 C6 H61 C6 H62 IMPR C2 N3 S2 S1 IMPR C4 C5 N3 O4 IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C4 N3 C2 S1 0.0000 0.00 0.00 0.00 0.0000 IC N3 S1 *C2 S2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 IC S1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 RESI MEOI 0.000 ! C9H7NO methyleneoxindole, kevo & xxwy GROUP ATOM C5 CG2DC3 -0.52 ATOM H51 HGA5 0.29 ATOM H52 HGA5 0.24 ATOM C6 CG25C2 -0.10 ! H51 H52 ATOM C7 CG2R53 0.67 ! \ / ATOM O7 OG2D1 -0.57 ! H13 C5 ATOM N8 NG2R51 -0.45 ! | || ATOM H8 HGP1 0.32 ! C13 C6 O7 ATOM C9 CG2RC0 0.25 ! // \ / \ // ATOM C10 CG2R61 -0.34 ! H12--C12 C14 C7 ATOM H10 HGR61 0.24 ! | || | ATOM C11 CG2R61 -0.20 ! H11--C11 C9----N8 ATOM H11 HGR61 0.22 ! \\ / \ ATOM C12 CG2R61 -0.23 ! C10 H8 ATOM H12 HGR61 0.21 ! | ATOM C13 CG2R61 -0.32 ! H10 ATOM H13 HGR61 0.28 ATOM C14 CG2RC0 0.01 BOND C6 C7 C7 N8 N8 C9 C9 C10 C10 C11 BOND C11 C12 C12 C13 C13 C14 C14 C6 C9 C14 BOND C7 O7 N8 H8 C10 H10 C11 H11 C12 H12 BOND C13 H13 C6 C5 C5 H51 C5 H52 IMPR C7 C6 N8 O7 IC C6 C14 C9 N8 0.0000 0.00 0.00 0.00 0.0000 IC C14 C9 N8 C7 0.0000 0.00 0.00 0.00 0.0000 IC C6 C9 *C14 C13 0.0000 0.00 180.00 0.00 0.0000 IC C14 N8 *C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C14 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C14 C13 C12 0.0000 0.00 0.00 0.00 0.0000 IC N8 C6 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *N8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 IC C7 C14 *C6 C5 0.0000 0.00 180.00 0.00 0.0000 IC C14 C6 C5 H51 0.0000 0.00 0.00 0.00 0.0000 IC H51 C6 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 RESI BAB2 -1.00 ! C29H47N2O6 Bile Acid Basic moiety 1 (BASE FOR NEW COMPOUNDS), cacha ! Based on Glu-UDCA Amide GROUP ATOM C3 CG311 0.14 ! OG ATOM O3 OG311 -0.65 ! || ATOM H3' HGP1 0.42 ! CG--NT--HT2 ATOM H3 HGA1 0.09 ! / HT1 GROUP ! CC3 ATOM C4 CG321 -0.18 ! \ ATOM H4A HGA2 0.09 ! O24 CC2 ATOM H4B HGA2 0.09 ! || / GROUP ! H Me21 C22 C24 CC1 ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) GROUP ! / \ | / | ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) ATOM H6A HGA2 0.09 ! Me19 | | | ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM C7 CG311 0.14 ! C2 C10 C8 C15 ATOM O7 OG311 -0.65 ! | | | ATOM H7' HGP1 0.42 ! C3 C5 C7 ATOM H7 HGA1 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM C8 CG311 -0.09 ATOM H8 HGA1 0.09 ! BAB2 GROUP ATOM C14 CG3RC1 -0.09 ATOM H14 HGA1 0.09 GROUP ATOM C15 CG3C52 -0.18 ATOM H15A HGA2 0.09 ATOM H15B HGA2 0.09 GROUP ATOM C16 CG3C52 -0.18 ATOM H16A HGA2 0.09 ATOM H16B HGA2 0.09 GROUP ATOM C17 CG3C51 -0.09 ATOM H17 HGA1 0.09 GROUP ATOM C13 CG3RC1 0.00 GROUP ATOM C18 CG331 -0.27 ATOM H18A HGA3 0.09 ATOM H18B HGA3 0.09 ATOM H18C HGA3 0.09 GROUP ATOM C12 CG321 -0.18 ATOM H12A HGA2 0.09 ATOM H12B HGA2 0.09 GROUP ATOM C11 CG321 -0.18 ATOM H11A HGA2 0.09 ATOM H11B HGA2 0.09 GROUP ATOM C9 CG311 -0.09 ATOM H9 HGA1 0.09 GROUP ATOM C10 CG301 0.00 GROUP ATOM C19 CG331 -0.27 ATOM H19A HGA3 0.09 ATOM H19B HGA3 0.09 ATOM H19C HGA3 0.09 GROUP ATOM C1 CG321 -0.18 ATOM H1A HGA2 0.09 ATOM H1B HGA2 0.09 GROUP ATOM C2 CG321 -0.18 ATOM H2A HGA2 0.09 ATOM H2B HGA2 0.09 GROUP ATOM C20 CG311 -0.09 ATOM H20 HGA1 0.09 GROUP ATOM C21 CG331 -0.27 ATOM H21A HGA3 0.09 ATOM H21B HGA3 0.09 ATOM H21C HGA3 0.09 GROUP ATOM C22 CG321 -0.18 ATOM H22A HGA2 0.09 ATOM H22B HGA2 0.09 GROUP ATOM C23 CG321 -0.18 ATOM H23A HGA2 0.09 ATOM H23B HGA2 0.09 GROUP ATOM C24 CG2O1 0.51 ATOM O24 OG2D1 -0.51 ATOM N NG2S1 -0.47 ATOM HN HGP1 0.47 GROUP ATOM CC1 CG311 -0.19 ATOM HC1 HGA1 0.09 ATOM CA CG2O3 0.62 ATOM OA1 OG2D2 -0.76 ATOM OA2 OG2D2 -0.76 GROUP ATOM CC2 CG321 -0.18 ATOM HC2A HGA2 0.09 ATOM HC2B HGA2 0.09 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 GROUP ATOM CG CG2O1 0.55 ATOM OG OG2D1 -0.55 ATOM NT NG2S2 -0.62 ATOM HT1 HGP1 0.32 ATOM HT2 HGP1 0.30 BOND C3 O3 C3 H3 O3 H3' BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5 BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C BOND C10 C1 C1 H1A C1 H1B BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7 C7 O7 O7 H7' BOND C7 C8 C8 H8 BOND C8 C9 C9 H9 BOND C9 C10 BOND C8 C14 C14 H14 BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C BOND C13 C12 C12 H12A C12 H12B BOND C12 C11 C11 H11A C11 H11B BOND C11 C9 BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B BOND C16 C17 C17 H17 BOND C17 C13 BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C BOND C20 C22 C22 H22A C22 H22B BOND C22 C23 C23 H23A C23 H23B BOND C23 C24 C24 O24 BOND C24 N N HN BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 BOND CC2 HC2A CC2 HC2B CC2 CC3 BOND CC3 HC3A CC3 HC3B CC3 CG BOND CG OG CG NT NT HT1 NT HT2 IMPR C24 C23 N O24 IMPR CA OA2 OA1 CC1 IMPR CG CC3 NT OG IC C1 C2 C3 C4 1.5325 111.68 -49.45 111.84 1.5383 IC C2 C3 C4 C5 1.5339 111.84 43.93 115.68 1.5598 IC C3 C4 C5 C6 1.5383 115.68 -175.10 109.02 1.5521 IC C4 C5 C6 C7 1.5598 109.02 85.47 114.98 1.5441 IC C5 C6 C7 C8 1.5521 114.98 39.04 113.05 1.5290 IC C7 C8 C9 C10 1.5290 114.08 58.26 109.48 1.5439 IC C8 C9 C10 C1 1.5323 109.48 179.67 111.99 1.5563 IC C9 C10 C1 C2 1.5439 111.99 63.33 113.83 1.5325 IC O3 C3 C4 C5 1.4163 109.09 162.18 115.68 1.5598 IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C2 C3 O3 H3' 1.5339 107.07 70.05 104.87 0.9608 IC C5 C3 *C4 H4A 1.5598 115.68 122.75 108.69 1.1111 IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 IC C10 C4 *C5 H5 1.5279 114.70 116.72 105.03 1.1175 IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 IC C6 C7 C8 C14 1.5441 113.05 -166.95 108.56 1.5542 IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.08 1.5323 IC C7 C8 C14 C13 1.5290 108.56 -174.20 113.13 1.5425 IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5533 IC C17 C14 *C13 C12 1.5731 98.18 119.81 107.46 1.5340 IC C14 C13 C12 C11 1.5425 107.46 55.26 111.18 1.5432 IC C8 C6 *C7 O7 1.5290 113.05 119.58 107.98 1.4218 IC O7 C6 *C7 H7 1.4218 107.98 118.83 107.19 1.1164 IC C6 C7 O7 H7' 1.5441 107.98 178.44 105.26 0.9614 IC C9 C7 *C8 H8 1.5323 114.08 122.47 107.18 1.1067 IC C10 C8 *C9 H9 1.5439 109.48 -117.10 106.56 1.1138 IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.88 1.1059 IC H12A C13 *C12 H12B 1.1059 111.88 119.47 108.82 1.1125 IC C13 C8 *C14 H14 1.5425 113.13 -118.30 108.46 1.1150 IC C16 C14 *C15 H15A 1.5435 103.56 119.15 111.17 1.1002 IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 IC C17 C15 *C16 H16A 1.5533 106.91 121.49 110.78 1.0992 IC H16A C15 *C16 H16B 1.0992 110.78 117.20 110.97 1.0999 IC C13 C16 *C17 H17 1.5731 98.41 -112.89 110.39 1.1009 IC C12 C14 *C13 C18 1.5340 107.46 121.97 114.21 1.5526 IC C14 C13 C18 H18A 1.5425 114.21 116.84 111.38 1.1064 IC H18A C13 *C18 H18B 1.1064 111.38 119.04 110.59 1.1085 IC H18A C13 *C18 H18C 1.1064 111.38 -120.17 111.91 1.1058 IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 IC C5 C10 C19 H19A 1.5279 109.53 5.08 111.17 1.1079 IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1061 IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 IC C13 C16 *C17 C20 1.5731 98.41 127.01 111.83 1.5649 IC C16 C17 C20 C22 1.5533 111.83 71.96 108.75 1.5519 IC C22 C17 *C20 C21 1.5519 108.75 122.38 112.90 1.5396 IC C21 C17 *C20 H20 1.5396 112.90 120.78 108.89 1.1119 IC C17 C20 C21 H21A 1.5649 112.90 71.88 110.45 1.1079 IC H21A C20 *C21 H21B 1.1079 110.45 -121.55 110.43 1.1103 IC H21A C20 *C21 H21C 1.1079 110.45 118.45 110.89 1.1089 IC C17 C20 C22 C23 1.5649 108.75 -163.10 113.67 1.5524 IC C23 C20 *C22 H22A 1.5524 113.67 119.92 108.15 1.1127 IC H22A C20 *C22 H22B 1.1127 108.15 116.44 108.31 1.1133 IC C20 C22 C23 C24 1.5519 113.67 176.63 114.01 1.5029 IC C24 C22 *C23 H23A 1.5029 114.01 120.77 110.50 1.1097 IC H23A C22 *C23 H23B 1.1097 110.50 118.82 109.42 1.1112 IC C22 C23 C24 N 1.5524 114.01 0.05 116.58 1.3364 IC N C23 *C24 O24 1.3364 116.58 -179.90 119.94 1.2265 IC C23 C24 N CC1 1.5029 116.58 178.79 130.40 1.4446 IC CC1 C24 *N HN 1.4446 130.40 -174.70 123.77 1.0138 IC C24 N CC1 CA 1.3364 130.40 -170.40 102.83 1.5482 IC CA N *CC1 HC1 1.5482 102.83 114.75 109.50 1.1102 IC HC1 N *CC1 CC2 1.1102 109.50 123.68 113.47 1.5536 IC N CC1 CA OA1 1.4446 102.83 178.79 119.90 1.2534 IC OA1 CC1 *CA OA2 1.2534 119.90 177.56 115.53 1.2691 IC N CC1 CC2 CC3 1.4446 113.47 60.10 115.05 1.5552 IC CC3 CC1 *CC2 HC2A 1.5552 115.05 126.07 109.17 1.1118 IC HC2A CC1 *CC2 HC2B 1.1118 109.17 114.51 106.60 1.1142 IC CC1 CC2 CC3 CG 1.5536 115.05 107.73 115.32 1.5034 IC CG CC2 *CC3 HC3A 1.5034 115.32 119.05 108.25 1.1125 IC HC3A CC2 *CC3 HC3B 1.1125 108.25 117.32 110.47 1.1095 IC CC2 CC3 CG NT 1.5552 115.32 -46.42 118.71 1.3503 IC NT CC3 *CG OG 1.3503 118.71 -179.05 119.96 1.2327 IC CC3 CG NT HT2 1.5034 118.71 -177.78 118.60 0.9905 IC HT2 CG *NT HT1 0.9905 118.60 177.52 119.35 1.0169 PRES 3MRB 1.00 ! C16H22N2O3 (010206(R)D), cacha ! This compound has 3-methylamine piperidine at gamma position (R-isomer) ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT1 HGP1 0.47 ! HG31 HG32 GROUP ! \ / ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) ATOM HGT1 HGA2 0.09 ! || / \ ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 ATOM HG1 HGA1 0.09 ! \ GROUP ! O24 CC2 ATOM CG2 CG324 0.20 ! || / ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG31 HGP2 0.32 ! / \ | / || \ __ / ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 CD2--CE2 ATOM CG4 CG324 0.20 ! Me19 | | | ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CG5 CG321 -0.18 ! | | | ATOM HG51 HGA2 0.09 ! C3 C5 C7 ATOM HG52 HGA2 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ! 3MRB (010206(R)D) ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 -0.01 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.63 ATOM OA1 OG2D1 -0.51 ATOM OA2 OG302 -0.33 ATOM CB CG321 -0.05 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5303 108.41 178.95 117.49 1.4423 IC CA OA2 CB HB1 1.3389 117.49 -63.60 110.30 1.1151 IC CA OA2 CB CZ 1.3389 117.49 175.38 113.51 1.5040 IC CA OA2 CB HB2 1.3389 117.49 55.90 110.62 1.1128 IC OA2 CB CZ CD2 1.4423 113.51 -83.20 119.67 1.4050 IC OA2 CB CZ CD1 1.4423 113.51 96.00 120.74 1.4052 IC CD1 CD2 *CZ CB 1.4052 119.59 179.22 119.67 1.5040 IC CD2 CZ CB HB1 1.4050 119.67 154.34 107.75 1.1151 IC CD2 CZ CB HB2 1.4050 119.67 38.67 106.37 1.1128 IC CB CZ CD1 CE1 1.5040 120.74 179.42 120.16 1.4019 IC CB CZ CD2 CE2 1.5040 119.67 -179.26 120.19 1.4014 IC CZ CD1 CE1 CP 1.4052 120.16 0.10 119.97 1.4007 IC CD1 CE1 CP CE2 1.4019 119.97 1.03 120.10 1.4008 IC CE1 CP CE2 CD2 1.4007 120.10 -0.88 119.97 1.4014 IC CE1 CZ *CD1 HD1 1.4019 120.16 -179.61 120.14 1.0798 IC CE2 CZ *CD2 HD2 1.4014 120.19 179.65 119.92 1.0808 IC CP CD1 *CE1 HE1 1.4007 119.97 -179.69 120.14 1.0811 IC CP CD2 *CE2 HE2 1.4008 119.97 179.52 120.22 1.0812 IC CE1 CE2 *CP HP 1.4007 120.10 -179.21 119.80 1.0818 IC OG CG NT CGT 1.2255 122.02 -7.42 126.12 1.4473 IC CG NT CGT CG1 1.3372 126.12 -120.45 106.50 1.5345 IC CG1 NT *CGT HGT1 1.5345 106.50 -118.61 109.21 1.1138 IC CG1 NT *CGT HGT2 1.5345 106.50 121.47 112.52 1.1152 IC NT CGT CG1 HG1 1.4473 106.50 -49.08 105.00 1.1195 IC HG1 CGT *CG1 CG2 1.1195 105.00 117.96 109.91 1.5332 IC HG1 CGT *CG1 CG6 1.1195 105.00 -116.91 117.24 1.5386 IC CGT CG1 CG2 NG3 1.5345 109.91 -165.05 107.18 1.5040 IC NG3 CG1 *CG2 HG21 1.5040 107.18 115.15 114.00 1.1022 IC NG3 CG1 *CG2 HG22 1.5040 107.18 -117.58 113.73 1.0992 IC CG1 CG2 NG3 CG4 1.5332 107.18 -58.17 114.03 1.5040 IC CG4 CG2 *NG3 HG31 1.5040 114.03 121.47 103.04 1.0297 IC CG4 CG2 *NG3 HG32 1.5040 114.03 -128.31 110.60 1.0023 IC CG2 NG3 CG4 CG5 1.5040 114.03 49.95 112.77 1.5402 IC CG5 NG3 *CG4 HG41 1.5402 112.77 123.21 105.30 1.1028 IC CG5 NG3 *CG4 HG42 1.5402 112.77 -121.26 104.50 1.1039 IC NG3 CG4 CG5 CG6 1.5040 112.77 -47.23 111.99 1.5433 IC CG6 CG4 *CG5 HG51 1.5433 111.99 119.26 108.44 1.1152 IC CG6 CG4 *CG5 HG52 1.5433 111.99 -123.11 110.16 1.1110 IC CG5 CG1 *CG6 HG61 1.5433 108.29 -119.60 109.57 1.1132 IC CG5 CG1 *CG6 HG62 1.5433 108.29 121.59 110.16 1.1111 PRES 3MPR 1.00 ! C7H14N2O (01OH06(R)D), cacha ! This compound has 3-methylamine piperidine at gamma position (R-isomer) ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ATOM HT1 HGP1 0.47 ! HG31 HG32 GROUP ! \ / ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) ATOM HGT1 HGA2 0.09 ! || / \ ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 GROUP ! / HT1 \ / ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 ATOM HG1 HGA1 0.09 ! \ GROUP ! O24 CC2 ATOM CG2 CG324 0.20 ! || / ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2 ATOM HG31 HGP2 0.32 ! / \ | / || ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 ATOM CG4 CG324 0.20 ! Me19 | | | ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM CG5 CG321 -0.18 ! | | | ATOM HG51 HGA2 0.09 ! C3 C5 C7 ATOM HG52 HGA2 0.09 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ! 3MPR (01OH06(R)D) ATOM HG62 HGA2 0.09 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 CG2 BOND CG2 HG21 CG2 HG22 CG2 NG3 BOND NG3 HG31 NG3 HG32 NG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CGT 1.2255 122.02 -7.42 126.12 1.4473 IC CG NT CGT CG1 1.3372 126.12 -120.45 106.50 1.5345 IC CG1 NT *CGT HGT1 1.5345 106.50 -118.61 109.21 1.1138 IC CG1 NT *CGT HGT2 1.5345 106.50 121.47 112.52 1.1152 IC NT CGT CG1 HG1 1.4473 106.50 -49.08 105.00 1.1195 IC HG1 CGT *CG1 CG2 1.1195 105.00 117.96 109.91 1.5332 IC HG1 CGT *CG1 CG6 1.1195 105.00 -116.91 117.24 1.5386 IC CGT CG1 CG2 NG3 1.5345 109.91 -165.05 107.18 1.5040 IC NG3 CG1 *CG2 HG21 1.5040 107.18 115.15 114.00 1.1022 IC NG3 CG1 *CG2 HG22 1.5040 107.18 -117.58 113.73 1.0992 IC CG1 CG2 NG3 CG4 1.5332 107.18 -58.17 114.03 1.5040 IC CG4 CG2 *NG3 HG31 1.5040 114.03 121.47 103.04 1.0297 IC CG4 CG2 *NG3 HG32 1.5040 114.03 -128.31 110.60 1.0023 IC CG2 NG3 CG4 CG5 1.5040 114.03 49.95 112.77 1.5402 IC CG5 NG3 *CG4 HG41 1.5402 112.77 123.21 105.30 1.1028 IC CG5 NG3 *CG4 HG42 1.5402 112.77 -121.26 104.50 1.1039 IC NG3 CG4 CG5 CG6 1.5040 112.77 -47.23 111.99 1.5433 IC CG6 CG4 *CG5 HG51 1.5433 111.99 119.26 108.44 1.1152 IC CG6 CG4 *CG5 HG52 1.5433 111.99 -123.11 110.16 1.1110 IC CG5 CG1 *CG6 HG61 1.5433 108.29 -119.60 109.57 1.1132 IC CG5 CG1 *CG6 HG62 1.5433 108.29 121.59 110.16 1.1111 PRES 2MSB 1.00 ! C16H22N2O3 (010207(S)D), cacha ! This compound has 2-methylamine piperidine at gamma position (S-isomer) ! and benzyl at alpha position ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ! HG21 HG22 ATOM OG OG2D1 -0.51 ! \ / ATOM NT NG2S1 -0.47 ! OG (+1)NG2--CG3 ATOM HT1 HGP1 0.47 ! || / \ GROUP ! CG---NT--CGT--CG1 CG4 ATOM CGT CG321 -0.18 ! / HT1 \ / ATOM HGT1 HGA2 0.09 ! CC3 CG6--CG5 ATOM HGT2 HGA2 0.09 ! \ GROUP ! O24 CC2 ATOM CG1 CG314 0.29 ! || / ATOM HG1 HGA1 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 ATOM NG2 NG3P2 -0.40 ! | \ / \ / \ / \ // \\ ATOM HG21 HGP2 0.32 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP ATOM HG22 HGP2 0.32 ! / \ | / || \ __ / ATOM CG3 CG324 0.20 ! C11 C13---C17 OA1 CD2--CE2 ATOM HG31 HGA2 0.09 ! Me19 | | | ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CG4 CG321 -0.18 ! C2 C10 C8 C15 ATOM HG41 HGA2 0.09 ! | | | ATOM HG42 HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CG5 CG321 -0.18 ! HO C4 C6 OH ATOM HG51 HGA2 0.09 ATOM HG52 HGA2 0.09 ! 2MSB (010207(S)D) GROUP ATOM CG6 CG321 -0.18 ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 GROUP ATOM CC1 CG311 -0.01 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.63 ATOM OA1 OG2D1 -0.51 ATOM OA2 OG302 -0.33 ATOM CB CG321 -0.05 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CZ CG2R61 0.00 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 NG2 BOND NG2 HG21 NG2 HG22 NG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 BOND OA2 CB CB HB1 CB HB2 CB CZ BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IC CC1 CA OA2 CB 1.5236 109.54 -177.42 116.65 1.4465 IC CA OA2 CB HB1 1.3366 116.65 -64.52 110.23 1.1158 IC CA OA2 CB CZ 1.3366 116.65 176.07 113.61 1.5060 IC CA OA2 CB HB2 1.3366 116.65 54.51 110.79 1.1153 IC OA2 CB CZ CD2 1.4465 113.61 -112.74 121.20 1.4061 IC OA2 CB CZ CD1 1.4465 113.61 66.81 119.31 1.4047 IC CD1 CD2 *CZ CB 1.4047 119.49 179.56 121.20 1.5060 IC CD2 CZ CB HB1 1.4061 121.20 125.73 106.48 1.1158 IC CD2 CZ CB HB2 1.4061 121.20 10.45 107.83 1.1153 IC CB CZ CD1 CE1 1.5060 119.31 179.64 120.28 1.4014 IC CB CZ CD2 CE2 1.5060 121.20 -179.62 120.19 1.4018 IC CZ CD1 CE1 CP 1.4047 120.28 0.05 119.95 1.4006 IC CD1 CE1 CP CE2 1.4014 119.95 0.67 120.10 1.4005 IC CE1 CP CE2 CD2 1.4006 120.10 -0.64 119.99 1.4018 IC CE1 CZ *CD1 HD1 1.4014 120.28 -179.54 119.86 1.0801 IC CE2 CZ *CD2 HD2 1.4018 120.19 179.49 120.24 1.0792 IC CP CD1 *CE1 HE1 1.4006 119.95 -179.62 120.12 1.0810 IC CP CD2 *CE2 HE2 1.4005 119.99 179.44 120.33 1.0815 IC CE1 CE2 *CP HP 1.4006 120.10 -179.39 119.77 1.0816 IC OG CG NT CGT 1.2228 120.84 -7.65 123.20 1.4570 IC CG NT CGT CG1 1.3449 123.20 96.54 115.15 1.5486 IC CG1 NT *CGT HGT1 1.5486 115.15 -123.43 109.82 1.1176 IC CG1 NT *CGT HGT2 1.5486 115.15 121.48 107.78 1.1146 IC NT CGT CG1 HG1 1.4570 115.15 68.02 110.07 1.1142 IC HG1 CGT *CG1 NG2 1.1142 110.07 114.89 108.81 1.5039 IC HG1 CGT *CG1 CG6 1.1142 110.07 -124.38 114.33 1.5405 IC CGT CG1 NG2 CG3 1.5486 108.81 179.78 115.31 1.5090 IC CG3 CG1 *NG2 HG21 1.5090 115.31 125.72 109.31 1.0053 IC CG3 CG1 *NG2 HG22 1.5090 115.31 -120.05 106.24 1.0090 IC CG1 NG2 CG3 CG4 1.5039 115.31 -57.58 110.01 1.5313 IC CG4 NG2 *CG3 HG31 1.5313 110.01 121.64 105.32 1.1035 IC CG4 NG2 *CG3 HG32 1.5313 110.01 -122.17 105.62 1.1031 IC NG2 CG3 CG4 CG5 1.5090 110.01 55.45 110.22 1.5360 IC CG5 CG3 *CG4 HG41 1.5360 110.22 121.05 109.87 1.1134 IC CG5 CG3 *CG4 HG42 1.5360 110.22 -120.70 110.12 1.1138 IC CG3 CG4 CG5 CG6 1.5313 110.22 -55.61 110.75 1.5369 IC CG6 CG4 *CG5 HG51 1.5369 110.75 121.23 109.73 1.1140 IC CG6 CG4 *CG5 HG52 1.5369 110.75 -121.10 109.70 1.1150 IC CG5 CG1 *CG6 HG61 1.5369 112.98 -121.21 109.26 1.1128 IC CG5 CG1 *CG6 HG62 1.5369 112.98 122.27 109.31 1.1139 PRES 2MPS 1.00 ! C7H14N2O (01OH07(S)D), cacha ! This compound has 3-methylamine piperidine at gamma position (S-isomer) ! core residue Bile Acid Basic moiety 1 (BAB1) DELETE ATOM HT2 GROUP ATOM CG CG2O1 0.51 ATOM OG OG2D1 -0.51 ATOM NT NG2S1 -0.47 ! HG31 HG32 ATOM HT1 HGP1 0.47 ! \ / GROUP ! OG (+1) NG2--CG3 ATOM CGT CG321 -0.18 ! || / \ ATOM HGT1 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 ATOM HGT2 HGA2 0.09 ! / HT1 \ / GROUP ! CC3 CG6--CG5 ATOM CG1 CG314 0.29 ! \ ATOM HG1 HGA1 0.09 ! O24 CC2 ATOM NG2 NG3P2 -0.40 ! || / ATOM HG21 HGP2 0.32 ! H Me21 C22 C24 CC1 ATOM HG22 HGP2 0.32 ! | \ / \ / \ / \ ATOM CG3 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2 ATOM HG31 HGA2 0.09 ! / \ | / || ATOM HG32 HGA2 0.09 ! C11 C13---C17 OA1 GROUP ! Me19 | | | ATOM CG4 CG321 -0.18 ! C1 | C9 C14 C16 ATOM HG41 HGA2 0.09 ! / \|/ \ / \ / ATOM HG42 HGA2 0.09 ! C2 C10 C8 C15 GROUP ! | | | ATOM CG5 CG321 -0.18 ! C3 C5 C7 ATOM HG51 HGA2 0.09 ! / \ / \ / \ ATOM HG52 HGA2 0.09 ! HO C4 C6 OH GROUP ATOM CG6 CG321 -0.18 ! 2MPS (01OH07(S)D) ATOM HG61 HGA2 0.09 ATOM HG62 HGA2 0.09 BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 BOND CG1 HG1 CG1 NG2 BOND NG2 HG21 NG2 HG22 NG2 CG3 BOND CG3 HG31 CG3 HG32 CG3 CG4 BOND CG4 HG41 CG4 HG42 CG4 CG5 BOND CG5 HG51 CG5 HG52 CG5 CG6 BOND CG6 HG61 CG6 HG62 CG6 CG1 IC OG CG NT CGT 1.2255 120.76 -0.11 124.20 1.4535 IC CG NT CGT CG1 1.3396 124.20 89.00 113.92 1.5472 IC CG1 NT *CGT HGT1 1.5472 113.92 -122.19 110.38 1.1160 IC CG1 NT *CGT HGT2 1.5472 113.92 121.49 108.57 1.1134 IC NT CGT CG1 HG1 1.4535 113.92 -58.25 109.55 1.1156 IC HG1 CGT *CG1 NG2 1.1156 109.55 114.51 110.44 1.4973 IC HG1 CGT *CG1 CG6 1.1156 109.55 -123.47 112.81 1.5409 IC CGT CG1 NG2 CG3 1.5472 110.44 175.74 117.06 1.5009 IC CG3 CG1 *NG2 HG21 1.5009 117.06 121.42 108.94 1.0280 IC CG3 CG1 *NG2 HG22 1.5009 117.06 -127.82 109.50 1.0039 IC CG1 NG2 CG3 CG4 1.4973 117.06 -54.19 110.53 1.5314 IC CG4 NG2 *CG3 HG31 1.5314 110.53 121.79 104.60 1.1041 IC CG4 NG2 *CG3 HG32 1.5314 110.53 -123.22 105.06 1.1033 IC NG2 CG3 CG4 CG5 1.5009 110.53 54.50 110.14 1.5371 IC CG5 CG3 *CG4 HG41 1.5371 110.14 121.18 109.65 1.1124 IC CG5 CG3 *CG4 HG42 1.5371 110.14 -120.57 109.68 1.1132 IC CG3 CG4 CG5 CG6 1.5314 110.14 -56.74 110.53 1.5373 IC CG6 CG4 *CG5 HG51 1.5373 110.53 120.76 109.61 1.1141 IC CG6 CG4 *CG5 HG52 1.5373 110.53 -121.25 109.83 1.1138 IC CG5 CG1 *CG6 HG61 1.5373 112.98 -121.67 108.73 1.1128 IC CG5 CG1 *CG6 HG62 1.5373 112.98 121.47 109.00 1.1129 PRES 3A2MPD 0.00 ! C8H9N2O Gamma-3-Amino-2-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 Me(CM) GROUP ! || | | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CD2 CG2R61 0.300 ! / \|/ \ / \ / ATOM CM CG331 -0.270 ! C2 C10 C8 C15 ATOM HM1 HGA3 0.090 ! | | | ATOM HM2 HGA3 0.090 ! C3 C5 C7 ATOM HM3 HGA3 0.090 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM NZ NG2R60 -0.600 GROUP ! 3A2MPD ATOM CP CG2R61 0.180 ATOM HP HGR62 0.120 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 CM CM HM1 CM HM2 CM HM3 BOND CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5543 115.92 -36.64 118.00 1.3402 IC CG CZ *NG HG 1.3402 127.24 -172.12 113.52 1.0153 IC NG CC3 *CG OG 1.3402 118.00 -178.84 119.23 1.2279 IC CC3 CG NG CZ 1.5047 118.00 -177.11 127.24 1.4173 IC CG NG CZ CD2 1.3402 127.24 -53.74 126.63 1.4232 IC NG CZ CD2 NZ 1.4173 126.63 -179.11 121.18 1.3371 IC CZ CD2 NZ CP 1.4232 121.18 1.08 120.70 1.3284 IC CD2 NZ CP CE1 1.3371 120.70 0.72 122.63 1.3997 IC NZ CP CE1 CD1 1.3284 122.63 -1.05 117.83 1.4014 IC CZ NZ *CD2 CM 1.4232 121.18 -177.19 115.74 1.4939 IC CZ CD2 CM HM1 1.4232 123.02 84.73 108.13 1.1092 IC HM1 CD2 *CM HM2 1.1092 108.13 119.79 109.25 1.1096 IC HM1 CD2 *CM HM3 1.1092 108.13 -120.01 109.21 1.1094 IC CZ CE1 *CD1 HD1 1.4045 119.82 179.62 121.08 1.0815 IC NZ CE1 *CP HP 1.3284 122.63 -178.98 122.17 1.0800 IC CP CD1 *CE1 HE1 1.3997 117.83 179.97 121.02 1.0771 PRES 3A2MPP 0.00 ! C17H17N2O3 Gamma-3-Amino-2-methyl Pyridine GA CDCA Amide (alpha protected), cacha ! core residue Glutamic Acid CDCA Amide (GA) ! CJ1--CK1 DELETE ATOM OG1 ! // \\ DELETE ATOM OG2 ! CY CQ GROUP ! / \ __ / ATOM CC3 CG321 -0.18 ! OA2--CB CJ2--CK2 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA1 Me(CM) GROUP ! || | | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CD2 CG2R61 0.300 ! / \|/ \ / \ / ATOM CM CG331 -0.270 ! C2 C10 C8 C15 ATOM HM1 HGA3 0.090 ! | | | ATOM HM2 HGA3 0.090 ! C3 C5 C7 ATOM HM3 HGA3 0.090 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM NZ NG2R60 -0.600 GROUP ! 3A2MPP ATOM CP CG2R61 0.180 ATOM HP HGR62 0.120 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CC1 CG311 -0.01 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.63 ATOM OA1 OG2D1 -0.51 ATOM OA2 OG302 -0.33 ATOM CB CG321 -0.05 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 CM CM HM1 CM HM2 CM HM3 BOND CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5221 108.68 -175.12 115.77 1.4469 IC HC1 CC1 CA OA2 1.1139 106.96 -144.03 108.68 1.3393 IC HB1 CB OA2 CA 1.1164 110.99 52.62 115.77 1.3393 IC HB2 CB OA2 CA 1.1155 110.08 -66.34 115.77 1.3393 IC CY CB OA2 CA 1.5032 113.31 171.98 115.77 1.3393 IC CJ2 CY CB OA2 1.4045 119.10 -63.26 113.31 1.4469 IC CJ1 CY CB OA2 1.4049 121.26 115.57 113.31 1.4469 IC CJ1 CJ2 *CY CB 1.4049 119.63 178.85 119.10 1.5032 IC CJ2 CY CB HB1 1.4045 119.10 58.82 106.19 1.1164 IC CJ2 CY CB HB2 1.4045 119.10 174.18 108.48 1.1155 IC CB CY CJ1 CK1 1.5032 121.26 -179.06 120.12 1.4017 IC CB CY CJ2 CK2 1.5032 119.10 179.04 120.23 1.4010 IC CY CJ1 CK1 CQ 1.4049 120.12 0.13 120.01 1.4014 IC CJ1 CK1 CQ CK2 1.4017 120.01 0.02 120.07 1.4012 IC CK1 CQ CK2 CJ2 1.4014 120.07 -0.07 119.94 1.4010 IC CK1 CY *CJ1 HJ1 1.4017 120.12 179.89 120.04 1.0798 IC CK2 CY *CJ2 HJ2 1.4010 120.23 -179.86 119.77 1.0802 IC CQ CJ1 *CK1 HK1 1.4014 120.01 -179.98 120.02 1.0806 IC CQ CJ2 *CK2 HK2 1.4012 119.94 179.88 120.03 1.0807 IC CK1 CK2 *CQ HQ 1.4014 120.07 179.94 119.96 1.0807 IC CC2 CC3 CG NG 1.5542 114.91 -16.91 117.82 1.3394 IC CG CZ *NG HG 1.3394 123.27 -179.51 116.62 0.9904 IC NG CC3 *CG OG 1.3394 117.82 179.62 119.61 1.2236 IC CC3 CG NG CZ 1.4992 117.82 177.13 123.27 1.4197 IC CG NG CZ CD2 1.3394 123.27 -69.73 124.04 1.4247 IC NG CZ CD2 NZ 1.4197 124.04 -176.97 120.97 1.3327 IC CZ CD2 NZ CP 1.4247 120.97 0.50 121.13 1.3277 IC CD2 NZ CP CE1 1.3327 121.13 1.14 122.26 1.4005 IC NZ CP CE1 CD1 1.3277 122.26 -0.91 118.06 1.4035 IC CZ NZ *CD2 CM 1.4247 120.97 -178.59 116.57 1.4945 IC CZ CD2 CM HM1 1.4247 122.45 71.53 108.26 1.1096 IC HM1 CD2 *CM HM2 1.1096 108.26 119.36 109.30 1.1107 IC HM1 CD2 *CM HM3 1.1096 108.26 -120.51 109.27 1.1089 IC CZ CE1 *CD1 HD1 1.4037 119.50 -179.00 120.49 1.0791 IC NZ CE1 *CP HP 1.3277 122.26 -179.11 122.38 1.0810 IC CP CD1 *CE1 HE1 1.4005 118.06 179.76 121.28 1.0781 PRES 3A4MPD 0.00 ! C8H9N2O Gamma-3-Amino-4-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ! OA1 ATOM CC3 CG321 -0.18 ! | ATOM HC3A HGA2 0.09 ! O24 CA--OA2 ATOM HC3B HGA2 0.09 ! || | GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM CG CG2O1 0.52 ! | \ / \ / \ / \ / \ / \ // \\ ATOM OG OG2D1 -0.52 ! C12 Me18 C20 C23 NH CC2 CG CZ CP GROUP ! / \ | / || \ __ / ATOM NG NG2S1 -0.47 ! C11 C13---C17 OG CD1--CE1 ATOM HG HGP1 0.33 ! Me19 | | | | ATOM CZ CG2R61 0.14 ! C1 | C9 C14 C16 Me(CM) GROUP ! / \|/ \ / \ / ATOM CD2 CG2R61 0.180 ! C2 C10 C8 C15 ATOM HD2 HGR62 0.120 ! | | | GROUP ! C3 C5 C7 ATOM NZ NG2R60 -0.600 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM CP CG2R61 0.180 ATOM HP HGR62 0.120 ! 3A4MPD GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 0.000 ATOM CM CG331 -0.270 ATOM HM1 HGA3 0.090 ATOM HM2 HGA3 0.090 ATOM HM3 HGA3 0.090 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 BOND CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 CM BOND CM HM1 CM HM2 CM HM3 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5525 114.66 -48.60 118.08 1.3462 IC CG CZ *NG HG 1.3462 126.54 -178.10 115.39 1.0162 IC NG CC3 *CG OG 1.3462 118.08 -179.48 119.23 1.2283 IC CC3 CG NG CZ 1.5020 118.08 -178.29 126.54 1.4265 IC CG NG CZ CD2 1.3462 126.54 26.39 123.95 1.4120 IC NG CZ CD2 NZ 1.4265 123.95 -179.67 124.64 1.3366 IC CZ CD2 NZ CP 1.4120 124.64 1.51 118.03 1.3276 IC CD2 NZ CP CE1 1.3366 118.03 0.27 123.29 1.3997 IC NZ CP CE1 CD1 1.3276 123.29 -0.52 118.73 1.4069 IC CZ NZ *CD2 HD2 1.4120 124.64 178.81 114.94 1.0798 IC NZ CE1 *CP HP 1.3276 123.29 -179.59 121.83 1.0808 IC CP CD1 *CE1 HE1 1.3997 118.73 -179.92 120.40 1.0767 IC CZ NZ *CD1 CM 1.4166 60.12 161.97 177.14 1.5012 IC CZ CD1 CM HM1 1.4166 122.60 -76.39 108.52 1.1122 IC HM1 CD1 *CM HM2 1.1122 108.52 118.88 109.64 1.1117 IC HM1 CD1 *CM HM3 1.1122 108.52 -120.43 110.64 1.1100 PRES 3A5MPD 0.00 ! C8H9N2O Gamma-3-Amino-5-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | | GROUP ! C1 | C9 C14 C16 Me(CM) ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 GROUP ! | | | ATOM NZ NG2R60 -0.600 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 0.180 ! HO C4 C6 OH ATOM HP HGR62 0.120 GROUP ! 3A5MPD ATOM CE1 CG2R61 0.000 ATOM CM CG331 -0.270 ATOM HM1 HGA3 0.090 ATOM HM2 HGA3 0.090 ATOM HM3 HGA3 0.090 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP BOND CP CE1 CE1 CM CM HM1 CM HM2 CM HM3 BOND CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5534 114.93 -46.79 117.53 1.3423 IC CG CZ *NG HG 1.3423 128.66 -179.60 113.69 1.0157 IC NG CC3 *CG OG 1.3423 117.53 -179.09 119.44 1.2280 IC CC3 CG NG CZ 1.5029 117.53 -179.23 128.66 1.4204 IC CG NG CZ CD2 1.3423 128.66 -3.33 126.46 1.4112 IC NG CZ CD2 NZ 1.4204 126.46 -179.70 123.49 1.3393 IC CZ CD2 NZ CP 1.4112 123.49 -0.17 118.65 1.3332 IC CD2 NZ CP CE1 1.3393 118.65 -0.04 123.55 1.4122 IC NZ CP CE1 CD1 1.3332 123.55 0.33 116.91 1.4049 IC CZ NZ *CD2 HD2 1.4112 123.49 -179.82 117.24 1.0814 IC CZ CE1 *CD1 HD1 1.4037 120.52 -179.76 120.10 1.0806 IC NZ CE1 *CP HP 1.3332 123.55 179.99 119.15 1.0821 IC CP CD1 *CE1 CM 1.4122 116.91 -179.23 120.70 1.5005 IC CD1 CE1 CM HM1 1.4049 120.70 82.83 108.60 1.1108 IC HM1 CE1 *CM HM2 1.1108 108.60 120.58 109.86 1.1106 IC HM1 CE1 *CM HM3 1.1108 108.60 -119.40 109.06 1.1121 PRES 3A6MPD 0.00 ! C8H9N2O Gamma-3-Amino-6-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP--Me(CM) ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 GROUP ! | | | ATOM NZ NG2R60 -0.600 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CP CG2R61 0.300 ! HO C4 C6 OH ATOM CM CG331 -0.270 ATOM HM1 HGA3 0.090 ! 3A6MPD ATOM HM2 HGA3 0.090 ATOM HM3 HGA3 0.090 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 BOND CD2 NZ NZ CP CP CM CM HM1 CM HM2 CM HM3 BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5536 114.92 -47.92 117.56 1.3422 IC CG CZ *NG HG 1.3422 128.44 -179.56 113.65 1.0157 IC NG CC3 *CG OG 1.3422 117.56 -179.06 119.47 1.2281 IC CC3 CG NG CZ 1.5031 117.56 -179.10 128.44 1.4197 IC CG NG CZ CD2 1.3422 128.44 -3.17 126.56 1.4088 IC NG CZ CD2 NZ 1.4197 126.56 179.85 123.64 1.3373 IC CZ CD2 NZ CP 1.4088 123.64 -0.45 119.84 1.3272 IC CD2 NZ CP CE1 1.3373 119.84 0.10 121.50 1.4077 IC NZ CP CE1 CD1 1.3272 121.50 0.08 118.83 1.4038 IC CZ NZ *CD2 HD2 1.4088 123.64 -179.72 115.15 1.0789 IC CZ CE1 *CD1 HD1 1.4042 119.69 -179.90 120.71 1.0810 IC CP CD1 *CE1 HE1 1.4077 118.83 179.98 120.81 1.0765 IC NZ CE1 *CP CM 1.3272 121.50 179.95 121.15 1.4853 IC CE1 CP CM HM1 1.4077 121.15 120.74 108.01 1.1094 IC HM1 CD2 *CM HM2 1.1094 97.28 111.25 97.26 1.1094 IC HM1 CD2 *CM HM3 1.1094 97.28 -124.39 129.99 1.1093 PRES 4A2MPD 0.00 ! C8H9N2O Gamma-4-Amino-2-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ! OA1 ATOM HC3A HGA2 0.09 ! | ATOM HC3B HGA2 0.09 ! O24 CA--OA2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---CE2 ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | | GROUP ! C1 | C9 C14 C16 Me(CM) ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 GROUP ! | | | ATOM CE2 CG2R61 0.180 ! C3 C5 C7 ATOM HE2 HGR62 0.120 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM NZ NG2R60 -0.600 GROUP ! 4A2MPD ATOM CE1 CG2R61 0.300 ATOM CM CG331 -0.270 ATOM HM1 HGA3 0.090 ATOM HM2 HGA3 0.090 ATOM HM3 HGA3 0.090 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 CE2 NZ BOND NZ CE1 CE1 CM CM HM1 CM HM2 CM HM3 BOND CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5535 114.99 -47.53 117.29 1.3441 IC CG CZ *NG HG 1.3441 129.75 -179.09 112.92 1.0149 IC NG CC3 *CG OG 1.3441 117.29 -178.78 119.12 1.2283 IC CC3 CG NG CZ 1.5032 117.29 -179.46 129.75 1.4176 IC CG NG CZ CD2 1.3441 129.75 -11.88 125.49 1.4013 IC NG CZ CD2 CE2 1.4176 125.49 178.88 118.08 1.3986 IC CZ CD2 CE2 NZ 1.4013 118.08 -0.21 122.51 1.3287 IC CD2 CE2 NZ CE1 1.3986 122.51 0.05 120.56 1.3285 IC CE2 NZ CE1 CD1 1.3287 120.56 -0.23 121.12 1.4025 IC CZ CE2 *CD2 HD2 1.4013 118.08 -179.53 120.08 1.0753 IC CZ CE1 *CD1 HD1 1.4024 119.20 -179.99 120.55 1.0781 IC NZ CD2 *CE2 HE2 1.3287 122.51 -179.90 122.11 1.0803 IC NZ CD1 *CE1 CM 1.3285 121.12 179.43 121.32 1.4855 IC CD1 CE1 CM HM1 1.4025 121.32 126.89 108.18 1.1092 IC HM1 CE1 *CM HM2 1.1092 108.18 119.25 108.09 1.1089 IC HM1 CE1 *CM HM3 1.1092 108.18 -120.30 109.96 1.1104 PRES 4A2MPP 0.00 ! C17H17N2O3 Gamma-4-Amino-2-methyl Pyridine GA CDCA Amide (alpha protected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 ! CJ1--CK1 GROUP ! // \\ ATOM CC3 CG321 -0.18 ! OA1 CY CQ ATOM HC3A HGA2 0.09 ! | / \ __ / ATOM HC3B HGA2 0.09 ! O24 CA--OA2--CB CJ2--CK2 GROUP ! || | ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---CE2 ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 ATOM CZ CG2R61 0.14 ! Me19 | | | | GROUP ! C1 | C9 C14 C16 Me(CM) ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 GROUP ! | | | ATOM CE2 CG2R61 0.180 ! C3 C5 C7 ATOM HE2 HGR62 0.120 ! / \ / \ / \ GROUP ! HO C4 C6 OH ATOM NZ NG2R60 -0.600 GROUP ! 4A2MPP ATOM CE1 CG2R61 0.300 ATOM CM CG331 -0.270 ATOM HM1 HGA3 0.090 ATOM HM2 HGA3 0.090 ATOM HM3 HGA3 0.090 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 GROUP ATOM CC1 CG311 -0.01 ATOM HC1 HGA1 0.09 ATOM CA CG2O2 0.63 ATOM OA1 OG2D1 -0.51 ATOM OA2 OG302 -0.33 ATOM CB CG321 -0.05 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 CE2 NZ BOND NZ CE1 CE1 CM CM HM1 CM HM2 CM HM3 BOND CE1 CD1 CD1 HD1 CD1 CZ DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CG CC3 NG OG IC CC1 CA OA2 CB 1.5239 109.11 -178.78 115.31 1.4471 IC HC1 CC1 CA OA2 1.1142 106.36 -134.87 109.11 1.3428 IC HB1 CB OA2 CA 1.1164 110.53 59.15 115.31 1.3428 IC HB2 CB OA2 CA 1.1163 110.59 -59.31 115.31 1.3428 IC CY CB OA2 CA 1.5039 113.58 179.93 115.31 1.3428 IC CJ2 CY CB OA2 1.4046 120.25 -90.46 113.58 1.4471 IC CJ1 CY CB OA2 1.4046 120.15 88.33 113.58 1.4471 IC CJ1 CJ2 *CY CB 1.4046 119.59 178.79 120.25 1.5039 IC CJ2 CY CB HB1 1.4046 120.25 32.06 107.40 1.1164 IC CJ2 CY CB HB2 1.4046 120.25 146.97 107.35 1.1163 IC CB CY CJ1 CK1 1.5039 120.15 -179.79 120.20 1.4015 IC CB CY CJ2 CK2 1.5039 120.25 179.88 120.19 1.4014 IC CY CJ1 CK1 CQ 1.4046 120.20 0.22 119.97 1.4011 IC CJ1 CK1 CQ CK2 1.4015 119.97 0.48 120.05 1.4013 IC CK1 CQ CK2 CJ2 1.4011 120.05 -0.38 119.98 1.4014 IC CK1 CY *CJ1 HJ1 1.4015 120.20 -179.58 119.84 1.0799 IC CK2 CY *CJ2 HJ2 1.4014 120.19 179.61 119.87 1.0801 IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0807 IC CQ CJ2 *CK2 HK2 1.4013 119.98 179.84 119.99 1.0807 IC CK1 CK2 *CQ HQ 1.4011 120.05 -179.99 119.97 1.0807 IC CC2 CC3 CG NG 1.5519 114.50 13.96 116.90 1.3446 IC CG CZ *NG HG 1.3446 129.24 179.51 114.07 0.9892 IC NG CC3 *CG OG 1.3446 116.90 179.09 119.15 1.2233 IC CC3 CG NG CZ 1.5018 116.90 -179.29 129.24 1.4197 IC CG NG CZ CD2 1.3446 129.24 13.84 125.26 1.4018 IC NG CZ CD2 CE2 1.4197 125.26 -179.01 118.17 1.3982 IC CZ CD2 CE2 NZ 1.4018 118.17 0.19 121.97 1.3275 IC CD2 CE2 NZ CE1 1.3982 121.97 0.25 121.39 1.3249 IC CE2 NZ CE1 CD1 1.3275 121.39 -0.27 120.72 1.4039 IC CZ CE2 *CD2 HD2 1.4018 118.17 179.45 119.73 1.0761 IC CZ CE1 *CD1 HD1 1.4037 119.12 179.72 120.00 1.0760 IC NZ CD2 *CE2 HE2 1.3275 121.97 -179.97 122.47 1.0810 IC NZ CD1 *CE1 CM 1.3249 120.72 -179.86 121.70 1.4852 IC CD1 CE1 CM HM1 1.4039 121.70 120.68 108.10 1.1099 IC HM1 CE1 *CM HM2 1.1099 108.10 118.69 108.12 1.1099 IC HM1 CE1 *CM HM3 1.1099 108.10 -120.64 110.47 1.1094 PRES 3CPD 0.00 ! C9H11N2O Gamma-3-Amide Pyridine Lysine CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM CG DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ATOM HC3B HGA2 0.09 GROUP ! OA1 ATOM CC4 CG321 -0.18 ! | ATOM HC4A HGA2 0.09 ! O24 CA--OA2 OC ATOM HC4B HGA2 0.09 ! || | || GROUP ! OH Me21 C22 C24 CC1 CC3 CC5 CC CD2---NZ ATOM CC5 CG321 -0.02 ! | \ / \ / \ / \ / \ / \ / \ // \\ ATOM HC5A HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CC4 NG CZ CP ATOM HC5B HGA2 0.09 ! / \ | / \ __ / ATOM NG NG2S1 -0.47 ! C11 C13---C17 CD1--CE1 ATOM HG HGP1 0.31 ! Me19 | | | GROUP ! C1 | C9 C14 C16 ATOM CC CG2O1 0.52 ! / \|/ \ / \ / ATOM OC OG2D1 -0.52 ! C2 C10 C8 C15 GROUP ! | | | ATOM CZ CG2R61 0.00 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CD2 CG2R61 0.180 ! HO C4 C6 OH ATOM HD2 HGR62 0.120 GROUP ! 3CPD ATOM NZ NG2R60 -0.600 GROUP ATOM CP CG2R61 0.180 ATOM HP HGR62 0.120 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CC3 CC4 CC4 HC4A CC4 HC4B CC4 CC5 BOND CC5 HC5A CC5 HC5B CC5 NG NG HG BOND NG CC CC OC CC CZ BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CC CZ NG OC IC CC1 CC2 CC3 CC4 1.5507 114.34 180.00 115.13 1.5423 IC CC2 CC3 CC4 HC4A 1.5420 115.13 47.51 110.26 1.1108 IC HC4A CC3 *CC4 HC4B 1.1108 110.26 116.79 107.05 1.1139 IC CC2 CC3 CC4 CC5 1.5420 115.13 -77.09 115.20 1.5407 IC CC3 CC4 CC5 HC5A 1.5423 115.20 -159.28 108.95 1.1153 IC HC5A NG *CC5 HC5B 1.1153 110.83 -116.80 108.42 1.1148 IC CC3 CC4 CC5 NG 1.5423 115.20 76.82 113.35 1.4396 IC CC4 CC5 NG CC 1.5407 113.35 94.14 123.08 1.3465 IC CC5 CC *NG HG 1.4396 123.08 180.00 123.02 1.0168 IC CC5 NG CC CZ 1.4396 123.08 -179.48 120.02 1.4949 IC NG CZ *CC OC 1.3465 120.02 -179.84 119.11 1.2317 IC NG CC CZ CD2 1.3465 120.02 -0.44 123.04 1.4096 IC CC CZ CD2 NZ 1.4949 123.04 179.89 122.97 1.3360 IC CZ CD2 NZ CP 1.4096 122.97 -0.08 119.87 1.3266 IC CD2 NZ CP CE1 1.3360 119.87 0.09 122.66 1.4001 IC NZ CP CE1 CD1 1.3266 122.66 -0.04 117.99 1.4032 IC CZ NZ *CD2 HD2 1.4096 122.97 -179.95 114.38 1.0801 IC CZ CE1 *CD1 HD1 1.4162 119.80 -179.92 119.66 1.0810 IC NZ CE1 *CP HP 1.3266 122.66 -179.97 122.30 1.0805 IC CP CD1 *CE1 HE1 1.4001 117.99 179.95 121.24 1.0773 PRES 3A26PD 0.60 ! C4H6 Gamma-3-Amino-2,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! 1st patch Glutamic Acid CDCA Amide (GA); 2nd patch 3APD *** double patch *** DELETE ATOM HD2 DELETE ATOM HP ATOM CD2 CG2R61 0.300 ! CM2 ATOM CM1 CG331 -0.270 ! | ATOM HM11 HGA3 0.090 ! NG CD2---NZ ATOM HM12 HGA3 0.090 ! / \ // \\ ATOM HM13 HGA3 0.090 ! -----CGP CZ CP--CM2 ATOM CP CG2R61 0.300 ! || \ __ / ATOM CM2 CG331 -0.270 ! OGP CD1--CE1 ATOM HM21 HGA3 0.090 ATOM HM22 HGA3 0.090 ATOM HM23 HGA3 0.090 BOND CD2 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CP CM2 CM2 HM21 CM2 HM22 CM2 HM23 IC CZ NZ *CD2 CM1 1.4232 120.79 -176.99 115.58 1.4943 IC CZ CD2 CM1 HM11 1.4232 123.56 83.84 108.07 1.1092 IC HM11 CD2 *CM1 HM12 1.1092 108.07 119.91 109.35 1.1096 IC HM11 CD2 *CM1 HM13 1.1092 108.07 -119.82 109.06 1.1094 IC NZ CE1 *CP CM2 1.3247 120.93 -179.02 120.29 1.4852 IC NZ CP CM2 HM21 1.3247 118.78 121.68 108.66 1.1090 IC HM21 CP *CM2 HM22 1.1090 108.66 120.57 108.58 1.1091 IC HM21 CP *CM2 HM23 1.1090 108.66 -119.74 108.92 1.1105 PRES 3A46PD 0.00 ! C9H11N2O Gamma-3-Amino-4,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ! OA1 ATOM HC3B HGA2 0.09 ! | GROUP ! O24 CA--OA2 ATOM CG CG2O1 0.52 ! || | ATOM OG OG2D1 -0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ GROUP ! | \ / \ / \ / \ / \ / \ // \\ ATOM NG NG2S1 -0.47 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--CM2 ATOM HG HGP1 0.33 ! / \ | / || \ __ / ATOM CZ CG2R61 0.14 ! C11 C13---C17 OG CD1--CE1 GROUP ! Me19 | | | | ATOM CD2 CG2R61 0.180 ! C1 | C9 C14 C16 CM1 ATOM HD2 HGR62 0.120 ! / \|/ \ / \ / GROUP ! C2 C10 C8 C15 ATOM NZ NG2R60 -0.600 ! | | | GROUP ! C3 C5 C7 ATOM CP CG2R61 0.300 ! / \ / \ / \ ATOM CM2 CG331 -0.270 ! HO C4 C6 OH ATOM HM21 HGA3 0.090 ATOM HM22 HGA3 0.090 ATOM HM23 HGA3 0.090 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR62 0.115 GROUP ATOM CD1 CG2R61 0.000 ATOM CM1 CG331 -0.270 ATOM HM11 HGA3 0.090 ATOM HM12 HGA3 0.090 ATOM HM13 HGA3 0.090 BOND CG OG CG NG NG HG NG CZ BOND CZ CD2 CD2 HD2 BOND CD2 NZ NZ CP CP CM2 CM2 HM21 CM2 HM22 CM2 HM23 BOND CP CE1 CE1 HE1 CE1 CD1 BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5525 114.68 -48.50 118.09 1.3462 IC CG CZ *NG HG 1.3462 126.53 -178.06 115.39 1.0163 IC NG CC3 *CG OG 1.3462 118.09 -179.48 119.24 1.2283 IC CC3 CG NG CZ 1.5020 118.09 -178.28 126.53 1.4265 IC CG NG CZ CD2 1.3462 126.53 26.25 123.98 1.4099 IC NG CZ CD2 NZ 1.4265 123.98 -179.65 124.10 1.3349 IC CZ CD2 NZ CP 1.4099 124.10 1.50 119.63 1.3248 IC CD2 NZ CP CE1 1.3349 119.63 0.31 121.47 1.4025 IC NZ CP CE1 CD1 1.3248 121.47 -0.57 119.67 1.4057 IC CP CD1 *CE1 HE1 1.4025 119.67 -179.96 120.27 1.0763 IC CZ NZ *CD2 HD2 1.4099 124.10 178.82 115.20 1.0797 IC CZ CE1 *CD1 CM1 1.4153 118.74 -179.91 118.59 1.5010 IC CZ CD1 CM1 HM11 1.4153 122.67 42.43 109.65 1.1117 IC HM11 CD1 *CM1 HM12 1.1117 109.65 120.69 110.64 1.1101 IC HM11 CD1 *CM1 HM13 1.1117 109.65 -118.88 108.52 1.1122 IC NZ CE1 *CP CM2 1.3248 121.47 -179.55 119.98 1.4855 IC NZ CP CM2 HM21 1.3248 118.55 120.51 108.65 1.1091 IC HM21 CP *CM2 HM22 1.1091 108.65 120.62 108.66 1.1090 IC HM21 CP *CM2 HM23 1.1091 108.65 -119.67 108.93 1.1106 PRES 2A46PD 0.30 ! C4H6 Gamma-2-Amino 4,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! double patch ! 1st patch Glutamic Acid CDCA Amide (GA); 2nd patch 2APD DELETE ATOM HE1 DELETE ATOM HE2 ! CM2 ATOM CE1 CG2R61 0.000 ! | ATOM CM1 CG331 -0.270 ! NG NZ---CE2 ATOM HM11 HGA3 0.090 ! / \ // \\ ATOM HM12 HGA3 0.090 ! ----CG CZ CP ATOM HM13 HGA3 0.090 ! || \ __ / ATOM CE2 CG2R61 0.300 ! OG CD1--CE1 ATOM CM2 CG331 -0.270 ! | ATOM HM21 HGA3 0.090 ! CM1 ATOM HM22 HGA3 0.090 ATOM HM23 HGA3 0.090 BOND CE1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CE2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 IC CD1 CP *CE1 CM1 1.4049 118.22 -179.92 120.32 1.4954 IC CD1 CE1 CM1 HM11 1.4049 121.46 120.27 108.89 1.1107 IC HM11 CE1 *CM1 HM12 1.1107 108.89 120.08 108.88 1.1108 IC HM11 CE1 *CM1 HM13 1.1107 108.89 -119.97 109.96 1.1118 IC CP NZ *CE2 CM2 1.4031 120.54 -179.86 117.53 1.4848 IC CP CE2 CM2 HM21 1.4031 121.92 122.41 108.06 1.1100 IC HM21 CE2 *CM2 HM22 1.1100 108.06 118.55 108.05 1.1099 IC HM21 CE2 *CM2 HM23 1.1100 108.06 -120.69 110.40 1.1091 PRES 2AEPD 0.00 ! C9H11N2O Gamma-2-Aminoehtyl Pyridine GA CDCA Amide (alpha deprotected), cacha ! core residue Glutamic Acid CDCA Amide (GA) DELETE ATOM OG1 DELETE ATOM OG2 GROUP ATOM CC3 CG321 -0.18 ATOM HC3A HGA2 0.09 ! OA1 ATOM HC3B HGA2 0.09 ! | GROUP ! O24 CA--OA2 ATOM CG CG2O1 0.52 ! || | ATOM OG OG2D1 -0.52 ! OH Me21 C22 C24 CC1 CM3 NG CM2 NZ---CE2 GROUP ! | \ / \ / \ / \ / \ / \ / \ // \\ ATOM NG NG2S1 -0.47 ! C12 Me18 C20 C23 NH CC2 CG CM1 CZ CP ATOM HG HGP1 0.33 ! / \ | / || \ __ / ATOM CM1 CG321 -0.04 ! C11 C13---C17 OG CD1--CE1 ATOM HM11 HGA2 0.09 ! Me19 | | | ATOM HM12 HGA2 0.09 ! C1 | C9 C14 C16 GROUP ! / \|/ \ / \ / ATOM CM2 CG321 -0.18 ! C2 C10 C8 C15 ATOM HM21 HGA2 0.09 ! | | | ATOM HM22 HGA2 0.09 ! C3 C5 C7 GROUP ! / \ / \ / \ ATOM CZ CG2R61 0.300 ! HO C4 C6 OH GROUP ATOM NZ NG2R60 -0.600 GROUP ATOM CE2 CG2R61 0.180 ATOM HE2 HGR62 0.120 GROUP ATOM CP CG2R61 -0.115 ATOM HP HGR61 0.115 GROUP ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 GROUP ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 BOND CG OG CG NG NG HG NG CM1 BOND CM1 HM11 CM1 HM12 CM1 CM2 CM2 HM21 CM2 HM22 BOND CM2 CZ CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ IMPR CG CC3 NG OG IC CC2 CC3 CG NG 1.5538 114.55 -50.29 117.81 1.3379 IC CG CZ *NG HG 1.3379 146.97 179.36 93.64 1.0168 IC NG CC3 *CG OG 1.3379 117.81 -179.31 120.32 1.2286 IC CC3 CG NG CM1 1.5026 117.81 178.60 123.77 1.4341 IC CG NG CM1 CM2 1.3379 123.77 166.12 110.08 1.5334 IC NG CM2 *CM1 HM11 1.4341 110.08 121.55 109.20 1.1164 IC HM11 CM2 *CM1 HM12 1.1164 109.20 118.53 110.55 1.1139 IC NG CM1 CM2 CZ 1.4341 110.08 170.36 110.71 1.4960 IC CZ CM1 *CM2 HM21 1.4960 110.71 120.16 110.22 1.1105 IC HM21 CM1 *CM2 HM22 1.1105 110.22 119.17 110.33 1.1120 IC CM1 CM2 CZ CD1 1.5334 110.71 -84.87 118.37 1.4085 IC CM2 CZ CD1 CE1 1.4960 118.37 179.16 118.99 1.4033 IC CZ CD1 CE1 CP 1.4085 118.99 -0.20 118.79 1.4032 IC CD1 CE1 CP CE2 1.4033 118.79 -0.01 118.33 1.4035 IC CE1 CP CE2 NZ 1.4032 118.33 -0.05 121.73 1.3296 IC CZ CE1 *CD1 HD1 1.4085 118.99 -179.95 121.31 1.0780 IC CD1 CP *CE1 HE1 1.4033 118.79 179.91 120.78 1.0797 IC CE1 CE2 *CP HP 1.4032 118.33 179.95 120.52 1.0774 IC CP NZ *CE2 HE2 1.4035 121.73 179.81 117.68 1.0828 PRES 2A3HPD 0.00 ! CHO 2-Amino 3-Hydroxy Pyridine CDCA Amide (alpha deprotected), cacha ! core residue GA and it is the second patch to 2APD (use of double patch) ! NG NZ---CE2 DELETE ATOM HD1 ! / \ // \\ GROUP ! ----CG CZ CP ATOM CD1 CG2R61 0.110 ! || \ __ / ATOM OD1 OG311 -0.530 ! OG CD1--CE1 ATOM HOD1 HGP1 0.420 ! | BOND CD1 OD1 OD1 HOD1 ! OD1 IC CZ CE1 *CD1 OD1 1.4299 117.44 -179.97 114.67 1.4209 IC CZ CD1 OD1 HOD1 1.4299 127.89 0.53 106.95 0.9786 PRES 2MBD 0.00 ! C2H3 Gamma 2-methyl amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HD1 ! CM--CD1--CE1 ATOM CD1 CG2R61 0.000 ! // \ ATOM CM CG331 -0.270 !--CG--NG--CZ CP ATOM HM1 HGA3 0.090 ! || \ __ // ATOM HM2 HGA3 0.090 ! OG CD2--CE2 ATOM HM3 HGA3 0.090 BOND CD1 CM CM HM1 CM HM2 CM HM3 IC CZ CE1 *CD1 CM 1.4134 118.69 -178.93 119.09 1.5058 IC CZ CD1 CM HM1 2.8050 42.16 78.76 114.26 1.1110 IC HM1 CD1 *CM HM2 1.1110 114.26 112.67 91.29 1.1100 IC HM1 CD1 *CM HM3 1.1110 114.26 -133.69 120.46 1.1114 PRES 3MBD 0.00 ! C2H3 Gamma 3-methyl amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HE1 ! CD1--CE1--CM ATOM CE1 CG2R61 0.000 ! // \ ATOM CM CG331 -0.270 !--CG--NG--CZ CP ATOM HM1 HGA3 0.090 ! || \ __ // ATOM HM2 HGA3 0.090 ! OG CD2--CE2 ATOM HM3 HGA3 0.090 BOND CE1 CM CM HM1 CM HM2 CM HM3 IC CD1 CP *CE1 CM 1.4042 119.12 -179.98 121.22 1.4967 IC CD1 CE1 CM HM1 1.4042 119.66 58.53 108.62 1.1109 IC HM1 CE1 *CM HM2 1.1109 121.07 108.19 81.88 1.1106 IC HM1 CE1 *CM HM3 1.1109 121.07 -143.61 119.97 1.1108 PRES 4MBD 0.00 ! C2H3 Gamma 4-methyl amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HP ! CD1--CE1 ATOM CP CG2R61 0.000 ! // \ ATOM CM CG331 -0.270 !--CG--NG--CZ CP--CM ATOM HM1 HGA3 0.090 ! || \ __ // ATOM HM2 HGA3 0.090 ! OG CD2--CE2 ATOM HM3 HGA3 0.090 BOND CP CM CM HM1 CM HM2 CM HM3 IC CE1 CE2 *CP CM 1.4027 118.99 179.94 120.96 1.4962 IC CE1 CP CM HM1 1.4027 120.05 60.06 108.73 1.1106 IC HM1 CP *CM HM2 1.1106 108.73 120.04 109.93 1.1111 IC HM1 CP *CM HM3 1.1106 108.73 -119.90 108.74 1.1106 PRES 2XBD -1.00 ! C2O2 Gamma 2-carboxy phenyl GA CDCA amide, cacha ! To be patched with residue GABD ! OG CD1--CE1 DELETE ATOM HD2 ! || // \\ ATOM CD2 CG2R61 -0.100 ! | CG--NG--CZ CP ATOM CX CG2O3 0.620 ! |\ / HG \ __ / ATOM OX1 OG2D2 -0.760 ! CC3 CD2--CE2 ATOM OX2 OG2D2 -0.760 ! | ! (-0.5)OX1--CX--OX2(-0.5) BOND CD2 CX CX OX1 CX OX2 IMPR CX OX1 OX2 CD2 IC CZ CE2 *CD2 CX 1.4234 118.49 179.85 118.42 1.5417 IC CZ CD2 CX OX1 1.4234 123.10 90.24 120.07 1.2614 IC OX1 CD2 *CX OX2 1.2614 120.07 178.02 118.47 1.2663 PRES 3XBD -1.00 ! C2O2 Gamma 3-carboxy phenyl GA CDCA amide, cacha ! To be patched with residue GABD ! (-0.5)OX1--CX--OX1(-0.5) DELETE ATOM HE1 ! | ATOM CE1 CG2R61 -0.100 ! OG CD1--CE1 ATOM CX CG2O3 0.620 ! || // \\ ATOM OX1 OG2D2 -0.760 ! | CG--NG--CZ CP ATOM OX2 OG2D2 -0.760 ! |\ / HG \ __ / ! CC3 CD2--CE2 BOND CE1 CX CX OX1 CX OX2 IMPR CX OX1 OX2 CE1 IC CD1 CP *CE1 CX 1.4121 118.22 -175.98 121.14 1.5400 IC CD1 CE1 CX OX1 1.4121 120.51 3.27 118.27 1.2608 IC OX1 CE1 *CX OX2 1.2608 118.27 -167.99 118.42 1.2655 PRES 4XBD -1.00 ! C2O2 Gamma 4-carboxy phenyl GA CDCA amide, cacha ! To be patched with residue GABD DELETE ATOM HP ! OG CD1--CE1 OX1(-0.5) ATOM CP CG2R61 -0.100 ! || // \\ / ATOM CX CG2O3 0.620 ! | CG--NG--CZ CP--CX ATOM OX1 OG2D2 -0.760 ! |\ / HG \ __ / \ ATOM OX2 OG2D2 -0.760 ! CC3 CD2--CE2 OX2(-0.5) BOND CP CX CX OX1 CX OX2 IMPR CX OX1 OX2 CP IC CE1 CE2 *CP CX 1.4118 118.05 179.99 120.66 1.5407 IC CE1 CP CX OX1 1.4118 121.29 0.02 118.88 1.2647 IC OX1 CP *CX OX2 1.2647 118.88 179.99 118.86 1.2643 PRES 4XEBD -0.86 ! C9H8O2 Gamma 4-carboxy ethyl phenyl GA CDCA amide, cacha ! To be patched with residue GABD DELETE ATOM CZ DELETE ATOM CD1 DELETE ATOM HD1 DELETE ATOM CE1 ! OG CJ1--CK1 OX1(-0.5) DELETE ATOM HE1 ! || // \\ / DELETE ATOM CD2 ! CG--NG--CM1--CM2--CY CQ--CX DELETE ATOM HD2 ! / HG \ __ / \ DELETE ATOM CE2 ! CC3 CJ2--CK2 OX2(-0.5) DELETE ATOM HE2 DELETE ATOM CP DELETE ATOM HP ATOM CM1 CG321 -0.04 ATOM HM11 HGA2 0.09 ATOM HM12 HGA2 0.09 ATOM CM2 CG321 -0.18 ATOM HM21 HGA2 0.09 ATOM HM22 HGA2 0.09 GROUP ATOM CY CG2R61 0.000 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CQ CG2R61 -0.100 ATOM CX CG2O3 0.620 ATOM OX1 OG2D2 -0.760 ATOM OX2 OG2D2 -0.760 BOND NG CM1 CM1 HM11 CM1 HM12 CM1 CM2 BOND CM2 HM21 CM2 HM22 CM2 CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CQ CX CX OX1 CX OX2 IMPR CX OX1 OX2 CQ IC CC3 CG NG CM1 1.4988 116.82 -179.37 123.36 1.4381 IC CG NG CM1 CM2 1.3386 123.36 -179.46 111.10 1.5340 IC NG CM2 *CM1 HM11 1.4381 111.10 121.09 109.49 1.1152 IC HM11 CM2 *CM1 HM12 1.1152 109.49 117.77 109.51 1.1153 IC NG CM1 CM2 CY 1.4381 111.10 179.82 110.46 1.5095 IC CM1 CY *CM2 HM21 1.5340 110.46 121.17 109.19 1.1118 IC HM21 CY *CM2 HM22 1.1118 109.19 117.66 109.24 1.1120 IC CM1 CM2 CY CJ1 1.5340 110.46 90.37 120.27 1.4016 IC CM2 CY CJ1 CK1 1.5095 120.27 179.91 120.28 1.4008 IC CY CJ1 CK1 CQ 1.4016 120.28 0.12 121.07 1.4150 IC CJ1 CK1 CQ CK2 1.4008 121.07 0.22 117.79 1.4150 IC CK1 CQ CK2 CJ2 1.4150 117.79 -0.22 121.07 1.4007 IC CK1 CY *CJ1 HJ1 1.4008 120.28 -179.90 119.73 1.0789 IC CK2 CY *CJ2 HJ2 1.4007 120.28 179.91 119.73 1.0788 IC CQ CJ1 *CK1 HK1 1.4150 121.07 -179.94 119.81 1.0809 IC CQ CJ2 *CK2 HK2 1.4150 121.07 179.95 119.81 1.0809 IC CK1 CK2 *CQ CX 1.4150 117.79 179.95 121.10 1.5435 IC CK1 CQ CX OX1 1.4150 121.11 0.13 116.99 1.2633 IC OX1 CQ *CX OX2 1.2633 116.99 179.67 116.99 1.2633 PRES 3XBP -1.00 ! C11H8O4 Alpha benzyl, Gamma 3-carboxy phenyl GA CDCA amide, cacha ! To be patched with residue GABD DELETE ATOM HE1 ! OG CD1--CE1--CX--OX1(-0.5) ATOM CE1 CG2R61 -0.100 ! || // \\ \ ATOM CX CG2O3 0.620 ! CG--NG--CZ CP \ ATOM OX1 OG2D2 -0.760 ! / HG \ __ / OX2(-0.5) ATOM OX2 OG2D2 -0.760 ! CC3 CD2--CE2 GROUP ! \ ATOM CC1 CG311 -0.01 ! CC2 CJ1--CK1 ATOM HC1 HGA1 0.09 ! / // \\ ATOM CA CG2O2 0.63 !-CC1--CA--OA2--CB--CY CQ ATOM OA1 OG2D1 -0.51 ! | \ __ / ATOM OA2 OG302 -0.33 ! OA1 CJ2--CK2 ATOM CB CG321 -0.05 ATOM HB1 HGA2 0.09 ATOM HB2 HGA2 0.09 GROUP ATOM CY CG2R61 0.00 ATOM CJ1 CG2R61 -0.115 ATOM HJ1 HGR61 0.115 ATOM CJ2 CG2R61 -0.115 ATOM HJ2 HGR61 0.115 ATOM CK1 CG2R61 -0.115 ATOM HK1 HGR61 0.115 ATOM CK2 CG2R61 -0.115 ATOM HK2 HGR61 0.115 ATOM CQ CG2R61 -0.115 ATOM HQ HGR61 0.115 BOND OA2 CB BOND CB HB1 CB HB2 CB CY BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY BOND CE1 CX CX OX1 CX OX2 DELETE IMPR CA OA2 OA1 CC1 IMPR CA CC1 OA1 OA2 IMPR CX OX1 OX2 CE1 IC CC1 CA OA2 CB 1.5612 110.02 -169.48 113.80 1.4482 IC HC1 CC1 CA OA2 1.1143 105.31 -138.17 110.02 1.3340 IC HB1 CB OA2 CA 1.1146 109.13 70.79 113.80 1.3340 IC HB2 CB OA2 CA 1.1139 110.51 -47.32 113.80 1.3340 IC CY CB OA2 CA 1.5046 115.25 -167.09 113.80 1.3340 IC CJ2 CY CB OA2 1.4041 119.47 52.44 115.25 1.4482 IC CJ1 CY CB OA2 1.4047 120.95 -131.01 115.25 1.4482 IC CJ1 CJ2 *CY CB 1.4047 119.49 176.60 119.47 1.5046 IC CJ2 CY CB HB1 1.4041 119.47 174.99 108.34 1.1146 IC CJ2 CY CB HB2 1.4041 119.47 -69.92 105.73 1.1139 IC CB CY CJ1 CK1 1.5046 120.95 -176.57 120.28 1.4011 IC CB CY CJ2 CK2 1.5046 119.47 176.36 120.27 1.4016 IC CY CJ1 CK1 CQ 1.4047 120.28 0.43 119.97 1.4012 IC CJ1 CK1 CQ CK2 1.4011 119.97 -0.59 120.02 1.4013 IC CK1 CQ CK2 CJ2 1.4012 120.02 0.33 119.97 1.4016 IC CK1 CY *CJ1 HJ1 1.4011 120.28 179.19 120.09 1.0813 IC CK2 CY *CJ2 HJ2 1.4016 120.27 -179.48 119.40 1.0795 IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.04 119.50 1.0814 IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.73 120.01 1.0798 IC CK1 CK2 *CQ HQ 1.4012 120.02 -179.42 120.05 1.0805 IC CD1 CP *CE1 CX 1.4130 117.96 -179.80 121.26 1.5397 IC CD1 CE1 CX OX1 1.4130 120.79 0.27 116.51 1.2620 IC OX1 CE1 *CX OX2 1.2620 116.51 -179.55 116.84 1.2610 PRES 2AMFD 0.00 ! C2H3O Gamma-2-Amino Phenyl methyl ether GA CDCA Amide, cacha ! patch combination: ! core residue GABD DELETE ATOM HD1 GROUP ATOM CD1 CG2R61 0.11 ! OG CD2--CE2 ATOM OD OG301 -0.54 ! || // \\ ATOM CM CG331 0.16 ! --CG--NG--CZ CP ATOM HM1 HGA3 0.09 ! \ __ / ATOM HM2 HGA3 0.09 ! CM--OD--CD1--CE1 ATOM HM3 HGA3 0.09 BOND CD1 OD OD CM CM HM1 CM HM2 CM HM3 IC NG CZ CD1 OD 1.4205 124.52 -3.45 121.25 1.4058 IC CZ CD1 OD CM 1.4163 121.25 115.89 111.85 1.4241 IC CD1 OD CM HM1 1.4058 111.85 -165.29 108.54 1.1105 IC HM1 OD *CM HM2 1.1105 108.54 118.63 111.53 1.1137 IC HM1 OD *CM HM3 1.1105 108.54 -119.19 110.77 1.1105 PRES 3AMFD 0.00 ! C2H3O Gamma-3-Amino Phenyl methyl ether GA CDCA Amide, cacha ! patch combination: ! core residue GABD DELETE ATOM HE1 GROUP ATOM CE1 CG2R61 0.11 ! OG CD2--CE2 ATOM OE OG301 -0.54 ! || // \\ ATOM CM CG331 0.16 ! --CG--NG--CZ CP ATOM HM1 HGA3 0.09 ! \ __ / ATOM HM2 HGA3 0.09 ! CD1--CE1--OE--CM ATOM HM3 HGA3 0.09 BOND CE1 OE OE CM CM HM1 CM HM2 CM HM3 IC CZ CD1 CE1 OE 1.4015 120.67 -179.85 123.17 1.4121 IC CD1 CE1 OE CM 1.4124 123.17 4.14 116.52 1.4248 IC CE1 OE CM HM1 1.4121 116.52 -63.56 110.72 1.1124 IC HM1 OE *CM HM2 1.1124 110.72 122.02 110.86 1.1128 IC HM1 OE *CM HM3 1.1124 110.72 -118.94 108.92 1.1105 PRES 4AMFD 0.00 ! C2H3O Gamma-4-Amino Phenyl methyl ether GA CDCA Amide, cacha ! patch combination: ! core residue GABD DELETE ATOM HP GROUP ATOM CP CG2R61 0.11 ! OG CD2--CE2 ATOM OP OG301 -0.54 ! || // \\ ATOM CM CG331 0.16 ! --CG--NG--CZ CP--OP--CM ATOM HM1 HGA3 0.09 ! \ __ / ATOM HM2 HGA3 0.09 ! CD1--CE1 ATOM HM3 HGA3 0.09 BOND CP OP OP CM CM HM1 CM HM2 CM HM3 IC CD1 CE1 CP OP 1.4032 120.95 -179.94 117.95 1.4118 IC CE1 CP OP CM 1.3994 117.95 179.23 116.73 1.4232 IC CE1 OP CM HM1 2.4090 147.60 62.27 110.73 1.1123 IC HM1 OP *CM HM2 1.1123 110.73 118.86 108.79 1.1108 IC HM1 OP *CM HM3 1.1123 110.73 -122.28 110.75 1.1123 PRES 26MD 0.00 ! C4H6 Gamma 2,6-dimethyl amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HD2 DELETE ATOM HD1 ! CM1--CD1--CE1 ATOM CD1 CG2R61 0.000 ! // \ ATOM CM1 CG331 -0.270 !--CG--NG--CZ CP ATOM HM11 HGA3 0.090 ! || \ __ // ATOM HM12 HGA3 0.090 ! OG CM2--CD2--CE2 ATOM HM13 HGA3 0.090 ATOM CD2 CG2R61 0.000 ATOM CM2 CG331 -0.270 ATOM HM21 HGA3 0.090 ATOM HM22 HGA3 0.090 ATOM HM23 HGA3 0.090 BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CD2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 IC CZ CE1 *CD1 CM1 1.4107 119.12 -179.77 120.02 1.5047 IC CZ CD1 CM1 HM11 1.4107 120.86 60.39 108.71 1.1110 IC HM11 CD1 *CM1 HM12 1.1110 108.71 120.79 110.66 1.1098 IC HM11 CD1 *CM1 HM13 1.1110 108.71 -118.95 108.53 1.1134 IC CZ CE2 *CD2 CM2 1.4123 118.93 179.40 119.49 1.5054 IC CZ CD2 CM2 HM21 1.4123 121.57 52.53 108.64 1.1123 IC HM21 CD2 *CM2 HM22 1.1123 108.64 120.32 110.67 1.1099 IC HM21 CD2 *CM2 HM23 1.1123 108.64 -119.01 108.44 1.1111 PRES 23MD 0.00 ! C4H6 Gamma 2,3-dimethyl amino benzene glutamic acid CDCA amide, cacha !To be patched with residue GABD DELETE ATOM HE1 DELETE ATOM HD1 ! CM1--CD1--CE1--CM2 ATOM CD1 CG2R61 0.000 ! // \ ATOM CM1 CG331 -0.270 ! --CG--NG--CZ CP ATOM HM11 HGA3 0.090 ! || \ __ // ATOM HM12 HGA3 0.090 ! OG CD2--CE2 ATOM HM13 HGA3 0.090 ATOM CE1 CG2R61 0.000 ATOM CM2 CG331 -0.270 ATOM HM21 HGA3 0.090 ATOM HM22 HGA3 0.090 ATOM HM23 HGA3 0.090 BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CE1 CM2 CM2 HM21 CM2 HM22 CM2 HM23 IC CZ CE1 *CD1 CM1 1.4167 118.80 -179.20 119.49 1.5148 IC CZ CD1 CM1 HM11 1.4167 121.71 95.98 108.42 1.1105 IC HM11 CD1 *CM1 HM12 1.1105 108.42 121.46 110.56 1.1094 IC HM11 CD1 *CM1 HM13 1.1105 108.42 -119.35 109.76 1.1108 IC CD1 CP *CE1 CM2 1.4202 119.81 -179.88 118.34 1.5043 IC CD1 CE1 CM2 HM21 1.4202 121.85 48.66 109.10 1.1108 IC HM21 CE1 *CM2 HM22 1.1108 109.10 119.76 110.41 1.1118 IC HM21 CE1 *CM2 HM23 1.1108 109.10 -120.08 108.64 1.1104 PRES 24MFD 0.00 ! C4H6O2 Gamma-2,4 Dimethoxy amino benzene GA CDCA Amide, cacha ! patch core residue GABD DELETE ATOM HD1 DELETE ATOM HP ! OG CD2--CE2 GROUP ! || // \\ ATOM CD1 CG2R61 0.11 ! --CG--NG--CZ CP--OP--CN ATOM OD OG301 -0.54 ! \ __ / ATOM CM CG331 0.16 ! CM--OD--CD1--CE1 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 ATOM CP CG2R61 0.11 ATOM OP OG301 -0.54 ATOM CN CG331 0.16 ATOM HN1 HGA3 0.09 ATOM HN2 HGA3 0.09 ATOM HN3 HGA3 0.09 BOND CD1 OD OD CM CM HM1 CM HM2 CM HM3 BOND CP OP OP CN CN HN1 CN HN2 CN HN3 IC NG CZ CD1 OD 1.4201 124.87 -5.97 121.19 1.4059 IC CZ CD1 OD CM 1.4156 121.19 118.27 111.90 1.4248 IC CD1 OD CM HM1 1.4059 111.90 -164.26 108.54 1.1104 IC HM1 OD *CM HM2 1.1104 108.54 118.60 111.54 1.1140 IC HM1 OD *CM HM3 1.1104 108.54 -119.19 110.79 1.1105 IC CD1 CE1 CP OP 1.4029 121.13 -177.79 118.46 1.4038 IC CE1 CP OP CN 1.3967 118.46 -146.32 114.18 1.4295 IC CE1 OP CN HN1 2.4063 137.70 21.69 111.50 1.1134 IC HN1 OP *CN HN2 1.1134 111.50 119.29 108.75 1.1111 IC HN1 OP *CN HN3 1.1134 111.50 -122.48 110.76 1.1123 PRES 35MFD 0.00 ! C4H6O2 Gamma-3,5 Dimethoxy amino benzene GA CDCA Amide, cacha ! patch core residue GABD DELETE ATOM HE1 DELETE ATOM HE2 ! OG CD1--CE1--OE1--CM1 GROUP ! || // \\ ATOM CE1 CG2R61 0.11 ! --CG--NG--CZ CP ATOM OE1 OG301 -0.54 ! \ __ / ATOM CM1 CG331 0.16 ! CD2--CE2--OE2-CM2 ATOM HM11 HGA3 0.09 ATOM HM12 HGA3 0.09 ATOM HM13 HGA3 0.09 ATOM CE2 CG2R61 0.11 ATOM OE2 OG301 -0.54 ATOM CM2 CG331 0.16 ATOM HM21 HGA3 0.09 ATOM HM22 HGA3 0.09 ATOM HM23 HGA3 0.09 BOND CE1 OE1 OE1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 BOND CE2 OE2 OE2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 IC CZ CD1 CE1 OE1 1.3988 120.42 -179.28 123.08 1.4117 IC CD1 CE1 OE1 CM1 1.4113 123.08 5.94 116.55 1.4244 IC CE1 OE1 CM1 HM11 1.4117 116.55 57.38 110.88 1.1128 IC HM11 OE1 *CM1 HM12 1.1128 110.88 119.03 108.87 1.1105 IC HM11 OE1 *CM1 HM13 1.1128 110.88 -122.07 110.68 1.1123 IC CZ CD2 CE2 OE2 1.3995 120.87 -179.50 122.96 1.4111 IC CD2 CE2 OE2 CM2 1.4067 122.96 3.62 116.04 1.4273 IC CE2 OE2 CM2 HM21 1.4111 116.04 58.51 111.01 1.1134 IC HM21 OE2 *CM2 HM22 1.1134 111.01 119.14 109.03 1.1103 IC HM21 OE2 *CM2 HM23 1.1134 111.01 -121.82 110.85 1.1129 !New compounds by "team CGenFF" (mainly xxwy), Jul 10 RESI STYR 0.00 ! C8H8 styrene, xxwy & oashi GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CG2R61 -0.115 ! CD1--CE1 H21 ATOM HD1 HGR61 0.115 ! / \ / GROUP ! HG--CG CZ----C1=C2 ATOM CD2 CG2R61 -0.115 ! \ / / \ ATOM HD2 HGR61 0.115 ! CD2--CE2 H1 H22 GROUP ! | | ATOM CE1 CG2R61 -0.115 ! HD2 HE2 ATOM HE1 HGR61 0.115 GROUP ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 GROUP ATOM CZ CG2R61 0.0 GROUP ATOM C1 CG2DC1 -0.15 ATOM H1 HGA4 0.15 GROUP ATOM C2 CG2DC3 -0.42 ATOM H21 HGA5 0.21 ATOM H22 HGA5 0.21 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ C1 BOND C1 C2 BOND C1 H1 C2 H21 C2 H22 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ C1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CZ C1 C2 0.0000 0.0000 179.0000 0.0000 0.0000 ! Introduce asymmetry IC C2 CZ *C1 H1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC H21 C1 *C2 H22 0.0000 0.0000 180.0000 0.0000 0.0000 RESI DMCA 0.000 ! C3H6O3 dimethyl carbonate (CAS: 616-38-6), xxwy GROUP ATOM C1 CG331 0.05 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM O1 OG302 -0.24 ! H12 O H22 ATOM C CG2O6 0.23 ! | || | ATOM O OG2D1 -0.39 ! H11--C1---O1---C---O2---C2--H21 ATOM O2 OG302 -0.24 ! | | ATOM C2 CG331 0.05 ! H13 H23 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 O1 O1 C C O2 O2 C2 C O BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 IMPR C O1 O2 O IC O1 C O2 C2 0.0000 0.00 185.00 0.00 0.0000 IC O2 C O1 C1 0.0000 0.00 180.00 0.00 0.0000 IC O1 O2 *C O 0.0000 0.00 185.00 0.00 0.0000 IC C O1 C1 H11 0.0000 0.00 185.00 0.00 0.0000 IC H11 O1 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 O1 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C O2 C2 H21 0.0000 0.00 185.00 0.00 0.0000 ! introduce IC H21 O2 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 ! 5deg asymmetry IC H21 O2 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 RESI DECA 0.000 ! C5H10O3 diethyl carbonate (CAS: 105-58-8), xxwy GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG321 0.14 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O1 OG302 -0.24 ! H12 H21 O H31 H41 ATOM C CG2O6 0.23 ! | | || | | ATOM O OG2D1 -0.39 ! H11--C1---C2---O1---C---O2---C3---C4--H42 ATOM O2 OG302 -0.24 ! | | | | ATOM C3 CG321 0.14 ! H13 H22 H32 H43 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C2 O1 O1 C BOND C O2 O2 C3 C3 C4 C O BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 IMPR C O1 O2 O IC C1 C2 O1 C 0.0000 0.00 80.00 0.00 0.0000 IC O1 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 O1 C O2 0.0000 0.00 180.00 0.00 0.0000 IC O1 C O2 C3 0.0000 0.00 185.00 0.00 0.0000 IC O1 O2 *C O 0.0000 0.00 180.00 0.00 0.0000 IC C O2 C3 C4 0.0000 0.00 -80.00 0.00 0.0000 IC O2 C3 C4 H41 0.0000 0.00 185.00 0.00 0.0000 IC C4 O2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 O2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI URAC 0.000 ! C4H4N2O2 uracil, xxwy GROUP ATOM N1 NG2R61 -0.37 ! O4 ATOM C6 CG2R62 0.11 ! || ATOM H6 HGR62 0.18 ! C4 H3 ATOM C2 CG2R63 0.44 ! / \ / ATOM O2 OG2D4 -0.45 ! H5-C5 N3 ATOM N3 NG2R61 -0.53 ! || | ATOM H3 HGP1 0.38 ! H6-C6 C2 ATOM C4 CG2R63 0.40 ! \ / \\ ATOM O4 OG2D4 -0.46 ! N1 O2 ATOM C5 CG2R62 -0.20 ! | ATOM H5 HGR62 0.15 ! H1 ATOM H1 HGP1 0.35 BOND N1 C2 C2 N3 N3 C4 C4 C5 C6 N1 BOND N1 H1 N3 H3 C5 H5 C6 H6 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC C2 C6 *N1 H1 0.0000 0.00 179.00 0.00 0.0000 ! deliberately distorted for test case IC N1 N3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI 2PYO 0.000 ! C5H5NO 2-Pyridone, xxwy GROUP ATOM N1 NG2R61 -0.13 ! H4 ATOM H1 HGP1 0.28 ! | ATOM C2 CG2R63 0.16 ! C4 ATOM O2 OG2D4 -0.48 ! / \\ ATOM C3 CG2R62 -0.26 ! H5-C5 C3-H3 ATOM H3 HGR62 0.22 ! || | ATOM C4 CG2R62 -0.22 ! H6-C6 C2 ATOM H4 HGR62 0.22 ! \ / \\ ATOM C5 CG2R62 -0.22 ! N1 O2 ATOM H5 HGR62 0.15 ! | ATOM C6 CG2R62 0.15 ! H1 ATOM H6 HGR62 0.13 BOND N1 C2 C2 C3 C4 C5 C6 N1 BOND N1 H1 C3 H3 C4 H4 C5 H5 C6 H6 DOUBLE C2 O2 C3 C4 C5 C6 IMPR C2 C3 N1 O2 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC C2 C6 *N1 H1 0.0000 0.00 179.00 0.00 0.0000 ! deliberately distorted for test case IC N1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI RSRF 0.00 ! C6H10O3 4,6-dioxabicyclo[3.3.0]octan-8-ol; CID9942150, xxwy GROUP ! IUPAC: (3R,3aS,6aR)-2,3,3a,4,5,6a-hexahydrofuro[2,3-b]furan-3-ol ATOM C1 CG3RC1 0.07 ATOM H11 HGA1 0.09 ! H11 ATOM C2 CG3RC1 0.03 ! H41 O4 | O6 H61 ATOM H21 HGA1 0.09 ! \ / \ | / \ / ATOM O4 OG3C51 -0.34 ! H42--C4 C1 C6--H62 ATOM C4 CG3C52 0.02 ! | | | ATOM H41 HGA2 0.09 ! H31--C3----C2----C5--H51 ATOM H42 HGA2 0.09 ! / | \ ATOM O6 OG3C51 -0.34 ! O3 H21 H52 ATOM C6 CG3C52 0.02 ! | ATOM H61 HGA2 0.09 ! H32 ATOM H62 HGA2 0.09 ATOM C5 CG3C52 -0.18 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 !GROUP ATOM C3 CG3C51 0.14 ATOM H31 HGA1 0.09 ATOM O3 OG311 -0.65 ATOM H32 HGP1 0.42 BOND C1 O4 C1 C2 C2 C3 C3 C4 C4 O4 C3 O3 BOND C1 H11 C1 O6 C2 H21 C2 C5 C3 H31 C4 H41 BOND C4 H42 O3 H32 C5 C6 C6 O6 C5 H51 C5 H52 BOND C6 H61 C6 H62 IC C1 O4 C4 C3 0.0 0.0 15.00 0.0 0.0 IC C3 O4 *C4 H41 0.0 0.0 120.00 0.0 0.0 IC C3 O4 *C4 H42 0.0 0.0 -120.00 0.0 0.0 IC C4 O4 C1 C2 0.0 0.0 10.00 0.0 0.0 IC C2 O4 *C1 H11 0.0 0.0 120.00 0.0 0.0 IC C2 O4 *C1 O6 0.0 0.0 -120.00 0.0 0.0 IC C2 C1 O6 C6 0.0 0.0 43.00 0.0 0.0 IC C1 O6 C6 C5 0.0 0.0 -35.00 0.0 0.0 IC C5 O6 *C6 H61 0.0 0.0 120.00 0.0 0.0 IC C5 O6 *C6 H62 0.0 0.0 -120.00 0.0 0.0 IC C4 C2 *C3 H31 0.0 0.0 120.00 0.0 0.0 IC C4 C2 *C3 O3 0.0 0.0 -120.00 0.0 0.0 IC C4 C3 O3 H32 0.0 0.0 -60.00 0.0 0.0 IC C6 C2 *C5 H51 0.0 0.0 120.00 0.0 0.0 IC C6 C2 *C5 H52 0.0 0.0 -120.00 0.0 0.0 IC C3 C5 *C2 H21 0.0 0.0 -120.00 0.0 0.0 RESI OXD4 0.000 ! C2H2N2O oxadiazole124, xxwy GROUP ! H1 ATOM C1 CG2R53 0.45 ! ____ / ATOM H1 HGR52 0.17 ! N2----C1 ATOM N2 NG2R50 -0.64 ! | \ ATOM C3 CG2R53 0.49 ! | O5 ATOM H3 HGR52 0.13 ! |____ / ATOM N4 NG2R50 -0.42 ! C3----N4 ATOM O5 OG2R50 -0.18 ! / ! H3 BOND C1 H1 C1 N2 N2 C3 C3 H3 BOND C3 N4 N4 O5 O5 C1 IC C1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 N4 O5 0.0000 0.00 0.00 0.00 0.0000 IC C3 N4 O5 C1 0.0000 0.00 0.00 0.00 0.0000 IC N2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N2 N4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 RESI TRZ4 0.00 ! C2H3N3 triazole124 GROUP ! H1 ATOM C1 CG2R53 0.23 ! ____ / ATOM H1 HGR52 0.16 ! N2----C1 ATOM N2 NG2R50 -0.66 ! | \ ATOM C3 CG2R53 0.47 ! | N5--H5 ATOM H3 HGR52 0.11 ! |____ / ATOM N4 NG2R50 -0.58 ! C3----N4 ATOM N5 NG2R51 -0.05 ! / ATOM H5 HGP1 0.32 ! H3 BOND C1 H1 C1 N2 N2 C3 C3 H3 BOND C3 N4 N4 N5 N5 H5 N5 C1 IC C1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 IC N2 C3 N4 N5 0.0000 0.00 0.00 0.00 0.0000 IC N5 C1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 IC N2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI HDZ1B 0.00 ! C9H10N2O Hydrazone model compound for comparison with styrene GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 GROUP ATOM C2 CG2O1 0.58 ! C1 H3 ATOM O2 OG2D1 -0.49 ! \ | ATOM N3 NG2S1 -0.34 ! C2--N3 H5 ATOM H3 HGP1 0.31 ! // \ / ATOM N4 NG2D1 -0.31 ! O2 N4=C5 ATOM C5 CG2DC1 -0.24 ! _______________\ ATOM H5 HGA4 0.24 ! | ATOM C6G CG2R61 0.25 ! | H6D1 H6E1 GROUP ! | | | ATOM C6D1 CG2R61 -0.115 ! | C6D1--C6E1 ATOM H6D1 HGR61 0.115 ! | // \\ GROUP ! |--C6G C6Z--H6Z ATOM C6D2 CG2R61 -0.115 ! \ / ATOM H6D2 HGR61 0.115 ! C6D2==C6E2 GROUP ! | | ATOM C6E1 CG2R61 -0.115 ! H6D2 H6E2 ATOM H6E1 HGR61 0.115 GROUP ATOM C6E2 CG2R61 -0.115 ATOM H6E2 HGR61 0.115 GROUP ATOM C6Z CG2R61 -0.115 ATOM H6Z HGR61 0.115 BOND C1 H11 C1 H12 C1 H13 C1 C2 BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5 BOND N4 C5 C5 C6G BOND C6D2 C6G C6E1 C6D1 C6Z C6E2 BOND C6D1 H6D1 C6D2 H6D2 C6E1 H6E1 BOND C6E2 H6E2 C6Z H6Z BOND C6D1 C6G C6E2 C6D2 C6Z C6E1 IMPR C2 C1 N3 O2 IMPR C5 C6G N4 H5 IC C1 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 IC H11 C1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC N3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 IC N3 N4 C5 C6G 0.0000 0.00 180.00 0.00 0.0000 IC C6G N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N4 C5 C6G C6D1 0.0000 0.00 179.00 0.00 0.0000 ! Introduce asymmetry IC C6D1 C5 *C6G C6D2 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6G C6D1 C6E1 0.0000 0.00 180.00 0.00 0.0000 IC C6E1 C6G *C6D1 H6D1 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6G C6D2 C6E2 0.0000 0.00 180.00 0.00 0.0000 IC C6E2 C6G *C6D2 H6D2 0.0000 0.00 180.00 0.00 0.0000 IC C6G C6D1 C6E1 C6Z 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 IC C6Z C6D1 *C6E1 H6E1 0.0000 0.00 180.00 0.00 0.0000 IC C6Z C6D2 *C6E2 H6E2 0.0000 0.00 180.00 0.00 0.0000 IC C6E2 C6E1 *C6Z H6Z 0.0000 0.00 180.00 0.00 0.0000 RESI METP -4.00 ! CH3O10P3 Methyl triphosphate, kevo GROUP ATOM C1 CG331 -0.17 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM O1 OG303 -0.62 ATOM P2 PG1 1.50 ATOM O21 OG2P1 -0.82 ATOM O22 OG2P1 -0.82 ATOM O2 OG304 -0.74 ATOM P3 PG1 1.50 ATOM O31 OG2P1 -0.82 ATOM O32 OG2P1 -0.82 ATOM O3 OG304 -0.86 ATOM P4 PG2 1.10 ATOM O41 OG2P1 -0.90 ATOM O42 OG2P1 -0.90 ATOM O43 OG2P1 -0.90 BOND C1 H11 C1 H12 C1 H13 C1 O1 BOND O1 P2 P2 O21 P2 O22 P2 O2 BOND O2 P3 P3 O31 P3 O32 P3 O3 BOND O3 P4 P4 O41 P4 O42 P4 O43 IC P3 O3 P4 O43 0.0000 0.00 0.00 0.00 0.0000 IC P4 O3 P3 O2 0.0000 0.00 180.00 0.00 0.0000 IC O3 P3 O2 P2 0.0000 0.00 180.00 0.00 0.0000 IC P3 O2 P2 O1 0.0000 0.00 -90.00 0.00 0.0000 ! from QM IC O2 P2 O1 C1 0.0000 0.00 180.00 0.00 0.0000 IC P2 O1 C1 H13 0.0000 0.00 180.00 0.00 0.0000 IC O1 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC O1 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC O1 O2 *P2 O21 0.0000 0.00 120.00 0.00 0.0000 IC O1 O2 *P2 O22 0.0000 0.00 -120.00 0.00 0.0000 IC O2 O3 *P3 O31 0.0000 0.00 120.00 0.00 0.0000 IC O2 O3 *P3 O32 0.0000 0.00 -120.00 0.00 0.0000 IC O3 O43 *P4 O41 0.0000 0.00 120.00 0.00 0.0000 IC O3 O43 *P4 O42 0.0000 0.00 -120.00 0.00 0.0000 !New compounds by "team CGenFF", Dec 10 RESI 4CYT 0.00 ! C8H7N p-cyanotoluene, alr GROUP ATOM CG CG2R61 0.10 ATOM C3N CG1N1 0.36 ATOM N3C NG1T1 -0.46 ATOM CD1 CG2R61 -0.115 ! HD1 HE1 ATOM HD1 HGR61 0.115 ! | | ATOM CD2 CG2R61 -0.115 ! CD1--CE1 H11 ATOM HD2 HGR61 0.115 ! __ / \ / ATOM CE1 CG2R61 -0.115 ! N3C==C3N--CG CZ--CT--H12 ATOM HE1 HGR61 0.115 ! \ / \ ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 ATOM HE2 HGR61 0.115 ! | | ATOM CZ CG2R61 0.00 ! HD2 HE2 ATOM CT CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ CT BOND CT H11 CT H12 CT H13 BOND CG C3N BOND C3N N3C IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG C3N 1.4000 120.00 180.00 120.00 1.2000 IC N3C C3N CG CD1 1.1200 179.99 0.0000 120.00 1.4000 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 RESI TMAO 0.00 ! C3H9NO trimethylamine N-oxide, xxwy & ejd GROUP ATOM N NG3P0 -0.83 ! H32 ATOM C1 CG334 -0.35 ! | ATOM C2 CG334 -0.35 ! H31-C3-H33 ATOM C3 CG334 -0.35 ! H23 | ATOM O1 OG312 -0.37 ! | | (+) ATOM H11 HGP5 0.25 ! H22-C2------N------O1 (-) ATOM H12 HGP5 0.25 ! | | ATOM H13 HGP5 0.25 ! H21 | ATOM H21 HGP5 0.25 ! H11-C1-H13 ATOM H22 HGP5 0.25 ! | ATOM H23 HGP5 0.25 ! H12 ATOM H31 HGP5 0.25 ATOM H32 HGP5 0.25 ATOM H33 HGP5 0.25 BOND N C1 N C2 N C3 N O1 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 *N O1 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3 N C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 IC O1 N C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 !IC C1 N O1 H41 0.0000 0.0000 180.0000 0.0000 0.0000 !IC N H41 *O1 H42 0.0000 0.0000 120.0000 0.0000 0.0000 !IC N H41 *O1 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI PHMK 0.000 ! C8H8O phenyl methyl ketone, mcs GROUP ATOM C1 CG331 -0.23 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG2O5 0.36 ! H8 O2 ATOM O2 OG2D3 -0.47 ! | || ATOM C3 CG2R61 0.07 ! H7 C8 C2 H11 ATOM C4 CG2R61 -0.115 ! \ // \ / \ / ATOM H4 HGR61 0.115 ! C7 C3 C1-H12 ATOM C5 CG2R61 -0.115 ! | || \ ATOM H5 HGR61 0.115 ! H6-C6 C4-H4 H13 ATOM C6 CG2R61 -0.115 ! \\ / ATOM H6 HGR61 0.115 ! C5 ATOM C7 CG2R61 -0.115 ! | ATOM H7 HGR61 0.115 ! H5 ATOM C8 CG2R61 -0.115 ATOM H8 HGR61 0.115 BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 BOND C2 C3 C3 C4 C4 H4 C4 C5 C5 H5 BOND C5 C6 C6 H6 C6 C7 C7 H7 C7 C8 C8 H8 C8 C3 IMPR C2 C3 C1 O2 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C2 *C3 C4 0.0000 0.00 -180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 -180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 -180.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 -180.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 -180.00 0.00 0.0000 IC C7 C3 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI PHEK 0.000 ! C9H10O phenyl ethyl ketone, mcs GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG321 -0.17 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM C3 CG2O5 0.34 ! H9 O3 ATOM O3 OG2D3 -0.47 ! | || ATOM C4 CG2R61 0.12 ! H8 C9 C3 H21 H11 ATOM C5 CG2R61 -0.115 ! \ // \ / \ | / ATOM H5 HGR61 0.115 ! C8 C4 C2-C1-H12 ATOM C6 CG2R61 -0.115 ! | || | \ ATOM H6 HGR61 0.115 ! H7-C7 C5-H5 H22 H13 ATOM C7 CG2R61 -0.115 ! \\ / ATOM H7 HGR61 0.115 ! C6 ATOM C8 CG2R61 -0.115 ! | ATOM H8 HGR61 0.115 ! H6 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 H21 C2 H22 C2 C3 C3 O3 BOND C3 C4 C4 C5 C5 H5 C5 C6 C6 H6 C6 C7 C7 H7 BOND C7 C8 C8 H8 C8 C9 C9 H9 C9 C4 IMPR C3 C4 C2 O3 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 IC C1 H21 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 O3 0.0000 0.00 -180.00 0.00 0.0000 IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 IC C9 C3 *C4 C5 0.0000 0.00 -180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C4 *C9 H9 0.0000 0.00 -180.00 0.00 0.0000 RESI BEON 0.00 ! C4H6O butenone (there can be only one), mcs & kevo GROUP ATOM C1 CG331 -0.23 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ATOM C2 CG2O5 0.38 ! H41 H3 O2 H11 ATOM O2 OG2D3 -0.46 ! \ | || / ATOM C3 CG2DC1 -0.11 ! C4 = C3- C2 - C1 -H12 ATOM H3 HGA4 0.15 ! / \ ATOM C4 CG2DC3 -0.42 ! H42 H13 ATOM H41 HGA5 0.21 ATOM H42 HGA5 0.21 BOND C1 H11 C1 H12 C1 H13 C1 C2 BOND C2 O2 C2 C3 C3 H3 C3 C4 BOND C4 H41 C4 H42 IMPR C2 C3 C1 O2 !IMPR C3 C4 C2 H3 ! Just a test! IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 180.00 0.00 0.0000 RESI DMPR 0.00 ! C5H11NO Dimethylpropanamide, mnoon GROUP ATOM C CG2O1 0.43 ! H33 ATOM O OG2D1 -0.52 ! | ATOM N NG2S0 -0.35 ! O C3--H32 ATOM C1 CG321 -0.10 ! \\ / \ ATOM H11 HGA2 0.09 ! C---N H31 ATOM H12 HGA2 0.09 ! / \ ATOM C2 CG331 -0.09 ! H11--C1 C2--H23 ATOM H21 HGA3 0.09 ! / | / | ATOM H22 HGA3 0.09 ! C4 H12 H21 H22 ATOM H23 HGA3 0.09 ! /|\ ATOM C3 CG331 -0.09 ! / | \ ATOM H31 HGA3 0.09 ! H41 H42 H43 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 GROUP ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C1 C4 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C C1 C N N C2 N C3 BOND C4 H41 C4 H42 C4 H43 DOUBLE C O IMPR C C1 N O IC N C C1 C4 0.0000 0.00 180.00 0.00 0.0000 IC C C4 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C C4 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 N *C O 0.0000 0.00 180.00 0.00 0.0000 IC C1 C N C3 0.0000 0.00 180.00 0.00 0.0000 IC C C3 *N C2 0.0000 0.00 180.00 0.00 0.0000 IC C N C2 H23 0.0000 0.00 0.00 0.00 0.0000 IC N H23 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC N H23 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C N C3 H33 0.0000 0.00 0.00 0.00 0.0000 IC N H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC N H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C C1 C4 H43 0.0000 0.00 180.00 0.00 0.0000 IC C1 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C1 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI DMSO 0.00 ! C2H6OS dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz GROUP ATOM O1 OG2P1 -0.55 ATOM S2 SG3O3 0.31 ! charges: ML Strader, SE Feller, JPC-A106(6),1074(2002) ATOM C3 CG331 -0.15 ATOM H4 HGA3 0.09 ! O1 ATOM H5 HGA3 0.09 ! || ATOM H6 HGA3 0.09 ! S2 ATOM C7 CG331 -0.15 ! / \ ATOM H8 HGA3 0.09 ! H4--C3 C7--H10 ATOM H9 HGA3 0.09 ! / | | \ ATOM H10 HGA3 0.09 ! H5 H6 H8 H9 BOND O1 S2 S2 C3 S2 C7 BOND C3 H4 C3 H5 C3 H6 BOND C7 H8 C7 H9 C7 H10 !IMPR S2 C3 C7 O1 ! Just a test! IC C3 S2 C7 H8 0.0000 0.00 180.00 0.00 0.0000 IC S2 H8 *C7 H9 0.0000 0.00 120.00 0.00 0.0000 IC S2 H8 *C7 H10 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C7 *S2 O1 0.0000 0.00 120.00 0.00 0.0000 IC C7 S2 C3 H4 0.0000 0.00 180.00 0.00 0.0000 IC S2 H4 *C3 H5 0.0000 0.00 120.00 0.00 0.0000 IC S2 H4 *C3 H6 0.0000 0.00 -120.00 0.00 0.0000 RESI MESO 0.00 ! C3H8OS methylethylsulfoxide, xxwy & mnoon & kevo GROUP ATOM O OG2P1 -0.55 ATOM S SG3O3 0.31 ATOM C3 CG331 -0.15 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ! O H11 ATOM H33 HGA3 0.09 ! || / ATOM C2 CG321 -0.06 ! S C1--H12 ATOM H21 HGA2 0.09 ! / \ / \ ATOM H22 HGA2 0.09 ! H31--C3 C2 H13 ATOM C1 CG331 -0.27 ! / | | \ ATOM H11 HGA3 0.09 ! H32 H33 H21 H22 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 BOND S C3 S C2 BOND C3 H31 C3 H32 C3 H33 BOND C2 H21 C2 H22 C2 C1 BOND C1 H11 C1 H12 C1 H13 DOUBLE O S !IMPR S C2 C3 O ! Just a test! IC C3 C2 *S O 0.0000 0.00 120.00 0.00 0.0000 IC C2 S C3 H33 0.0000 0.00 180.00 0.00 0.0000 IC H33 S *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC H33 S *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 S C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C1 S *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 S *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC S C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 IC H13 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC H13 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 RESI AMDN 1.00 ! C2H7N2 amidinium cation, sz & pram GROUP ATOM C1 CG2N2 0.66 ATOM C2 CG331 -0.15 ! H3 H4 H5 ATOM H3 HGA3 0.09 ! \| / ATOM H4 HGA3 0.09 ! C2 ATOM H5 HGA3 0.09 ! | ATOM N6 NG2P1 -0.69 ! +) C1 ATOM H7 HGP2 0.40 ! // \ ATOM H8 HGP2 0.40 ! H7-N6 N9-H10 ATOM N9 NG2P1 -0.69 ! | | ATOM H10 HGP2 0.40 ! H8 H11 ATOM H11 HGP2 0.40 BOND C1 C2 C2 H3 C2 H4 C2 H5 BOND C1 N6 N6 H7 N6 H8 BOND C1 N9 N9 H10 N9 H11 IMPR C1 N6 N9 C2 IC N6 C1 C2 H3 0.0000 0.00 90.00 0.00 0.0000 IC C1 H3 *C2 H4 0.0000 0.00 120.00 0.00 0.0000 IC C1 H3 *C2 H5 0.0000 0.00 -120.00 0.00 0.0000 IC N6 C2 *C1 N9 0.0000 0.00 180.00 0.00 0.0000 IC H7 N6 C1 N9 0.0000 0.00 180.00 0.00 0.0000 IC H7 C1 *N6 H8 0.0000 0.00 180.00 0.00 0.0000 IC H10 N9 C1 N6 0.0000 0.00 180.00 0.00 0.0000 IC H10 C1 *N9 H11 0.0000 0.00 180.00 0.00 0.0000 RESI BAMI 1.00 ! C7H9N2 benzamidinium cation, sz & pram GROUP ATOM C1 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM C3 CG2R61 -0.115 ATOM H4 HGR61 0.115 ATOM C5 CG2R61 -0.115 ATOM H6 HGR61 0.115 ATOM C7 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM C9 CG2R61 -0.115 ATOM H10 HGR61 0.115 GROUP ATOM C11 CG2R61 0.19 ATOM C12 CG2N2 0.73 ATOM N13 NG2P1 -0.60 ATOM H14 HGP2 0.32 ATOM H15 HGP2 0.32 ATOM N16 NG2P1 -0.60 ATOM H17 HGP2 0.32 ATOM H18 HGP2 0.32 BOND C1 H2 BOND C1 C3 C3 H4 C3 C5 C5 H6 BOND C1 C7 C7 H8 C7 C9 C9 H10 BOND C11 C5 C11 C12 C11 C9 BOND C12 N13 N13 H14 N13 H15 C12 N16 N16 H17 N16 H18 IMPR C12 N13 N16 C11 IC C1 C3 C5 C11 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 C11 C9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C11 C9 C7 0.0000 0.00 0.00 0.00 0.0000 IC C11 C9 C7 C1 0.0000 0.00 0.00 0.00 0.0000 IC C9 C7 C1 C3 0.0000 0.00 0.00 0.00 0.0000 IC C7 C1 C3 C5 0.0000 0.00 0.00 0.00 0.0000 IC C7 C3 *C1 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C3 H4 0.0000 0.00 180.00 0.00 0.0000 IC C3 C11 *C5 H6 0.0000 0.00 180.00 0.00 0.0000 IC C11 C7 *C9 H10 0.0000 0.00 180.00 0.00 0.0000 IC C9 C1 *C7 H8 0.0000 0.00 180.00 0.00 0.0000 IC C5 C9 *C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C5 C11 C12 N13 0.0000 0.00 45.00 0.00 0.0000 IC N13 C11 *C12 N16 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 N13 H14 0.0000 0.00 0.00 0.00 0.0000 IC H14 C12 *N13 H15 0.0000 0.00 180.00 0.00 0.0000 IC C11 C12 N16 H17 0.0000 0.00 0.00 0.00 0.0000 IC H17 C12 *N16 H18 0.0000 0.00 180.00 0.00 0.0000 RESI PNTM 2.00 ! C19H26N4O2 1,5-bis(p-Amidinophenoxy)pentane, Pentamidine, sz & pram GROUP ! based on PENT, ETOB, PAMI/ARG, ATOM C1 CG321 -0.18 ATOM H2 HGA2 0.09 ATOM H3 HGA2 0.09 ! H11 H5 H2 H8 H32 ATOM C4 CG321 -0.18 ! \ | | | / ATOM H5 HGA2 0.09 ! H12-C10-C4--C1--C7--C31-H33 ATOM H6 HGA2 0.09 ! / | | | \ ATOM C7 CG321 -0.18 ! O13 H6 H3 H9 O34 ATOM H8 HGA2 0.09 ! | | ATOM H9 HGA2 0.09 ! H20-C19==C14 C35==C40-H41 GROUP ! / \ / \ ATOM C10 CG321 -0.01 ! H22-C21 C15-H16 H37-C36 C42-H43 ATOM H11 HGA2 0.09 ! \\ // \\ // ATOM H12 HGA2 0.09 ! C23--C17-H18 H39-C38--C44 ATOM O13 OG301 -0.39 ! / \ ATOM C14 CG2R61 0.22 ! (+) C24 C45 (+) GROUP ! // \ / \\ ATOM C15 CG2R61 -0.115 ! H29-N28 N25-H26 H47-N46 N49-H50 ATOM H16 HGR61 0.115 ! | | | | ATOM C17 CG2R61 -0.115 ! H30 H27 H48 H51 ATOM H18 HGR61 0.115 ATOM C19 CG2R61 -0.115 ATOM H20 HGR61 0.115 ATOM C21 CG2R61 -0.115 ATOM H22 HGR61 0.115 GROUP ! one positive charge on this group which is from PAMI ATOM C23 CG2R61 0.19 ATOM C24 CG2N2 0.73 ATOM N25 NG2P1 -0.60 ATOM H26 HGP2 0.32 ATOM H27 HGP2 0.32 ATOM N28 NG2P1 -0.60 ATOM H29 HGP2 0.32 ATOM H30 HGP2 0.32 GROUP ! This group is from ETOB ATOM C31 CG321 -0.01 ATOM H32 HGA2 0.09 ATOM H33 HGA2 0.09 ATOM O34 OG301 -0.39 ATOM C35 CG2R61 0.22 GROUP ATOM C36 CG2R61 -0.115 ATOM H37 HGR61 0.115 ATOM C38 CG2R61 -0.115 ATOM H39 HGR61 0.115 ATOM C40 CG2R61 -0.115 ATOM H41 HGR61 0.115 ATOM C42 CG2R61 -0.115 ATOM H43 HGR61 0.115 GROUP ! one positive charge on this group (PAMI) ATOM C44 CG2R61 0.19 ATOM C45 CG2N2 0.73 ATOM N46 NG2P1 -0.60 ATOM H47 HGP2 0.32 ATOM H48 HGP2 0.32 ATOM N49 NG2P1 -0.60 ATOM H50 HGP2 0.32 ATOM H51 HGP2 0.32 BOND C1 H2 C1 H3 C1 C4 C4 H5 C4 H6 C1 C7 C7 H8 C7 H9 BOND C4 C10 C10 H11 C10 H12 C10 O13 O13 C14 BOND C14 C15 C15 H16 C15 C17 C17 H18 BOND C14 C19 C19 H20 C19 C21 C21 H22 BOND C17 C23 C21 C23 C23 C24 C24 N25 C24 N28 BOND N25 H26 N25 H27 N28 H29 N28 H30 BOND C7 C31 C31 H32 C31 H33 C31 O34 O34 C35 BOND C35 C36 C36 H37 C36 C38 C38 H39 BOND C35 C40 C40 H41 C40 C42 C42 H43 BOND C38 C44 C42 C44 C44 C45 C45 N46 C45 N49 BOND N46 H47 N46 H48 N49 H50 N49 H51 IMPR C24 N25 N28 C23 IMPR C45 N46 N49 C44 IC C10 C4 C1 C7 0.0000 0.00 180.00 0.00 0.0000 IC O13 C10 C4 C1 0.0000 0.00 180.00 0.00 0.0000 IC C14 O13 C10 C4 0.0000 0.00 180.00 0.00 0.0000 IC C10 O13 C14 C15 0.0000 0.00 0.00 0.00 0.0000 IC C4 C1 C7 C31 0.0000 0.00 180.00 0.00 0.0000 IC C1 C7 C31 O34 0.0000 0.00 180.00 0.00 0.0000 IC C7 C31 O34 C35 0.0000 0.00 180.00 0.00 0.0000 IC C31 O34 C35 C36 0.0000 0.00 0.00 0.00 0.0000 IC C4 C7 *C1 H2 0.0000 0.00 120.00 0.00 0.0000 IC C4 C7 *C1 H3 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C10 *C4 H5 0.0000 0.00 120.00 0.00 0.0000 IC C1 C10 *C4 H6 0.0000 0.00 -120.00 0.00 0.0000 IC O13 C4 *C10 H11 0.0000 0.00 120.00 0.00 0.0000 IC O13 C4 *C10 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C31 C1 *C7 H8 0.0000 0.00 120.00 0.00 0.0000 IC C31 C1 *C7 H9 0.0000 0.00 -120.00 0.00 0.0000 IC C7 O34 *C31 H32 0.0000 0.00 120.00 0.00 0.0000 IC C7 O34 *C31 H33 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C15 C17 C23 0.0000 0.00 0.00 0.00 0.0000 IC C15 C17 C23 C21 0.0000 0.00 0.00 0.00 0.0000 IC C17 C23 C21 C19 0.0000 0.00 0.00 0.00 0.0000 IC C23 C21 C19 C14 0.0000 0.00 0.00 0.00 0.0000 IC C21 C19 C14 C15 0.0000 0.00 0.00 0.00 0.0000 IC C19 C14 C15 C17 0.0000 0.00 0.00 0.00 0.0000 IC C14 C17 *C15 H16 0.0000 0.00 180.00 0.00 0.0000 IC C15 C23 *C17 H18 0.0000 0.00 180.00 0.00 0.0000 IC C17 C21 *C23 C24 0.0000 0.00 180.00 0.00 0.0000 IC C23 C19 *C21 H22 0.0000 0.00 180.00 0.00 0.0000 IC C21 C14 *C19 H20 0.0000 0.00 180.00 0.00 0.0000 IC C19 C15 *C14 O13 0.0000 0.00 180.00 0.00 0.0000 IC C17 C23 C24 N25 0.0000 0.00 45.00 0.00 0.0000 IC C23 N25 *C24 N28 0.0000 0.00 180.00 0.00 0.0000 IC C23 C24 N25 H26 0.0000 0.00 0.00 0.00 0.0000 IC C24 H26 *N25 H27 0.0000 0.00 180.00 0.00 0.0000 IC C23 C24 N28 H29 0.0000 0.00 0.00 0.00 0.0000 IC C24 H29 *N28 H30 0.0000 0.00 180.00 0.00 0.0000 IC C35 C36 C38 C44 0.0000 0.00 0.00 0.00 0.0000 IC C36 C38 C44 C42 0.0000 0.00 0.00 0.00 0.0000 IC C38 C44 C42 C40 0.0000 0.00 0.00 0.00 0.0000 IC C44 C42 C40 C35 0.0000 0.00 0.00 0.00 0.0000 IC C42 C40 C35 C36 0.0000 0.00 0.00 0.00 0.0000 IC C40 C35 C36 C38 0.0000 0.00 0.00 0.00 0.0000 IC C35 C38 *C36 H37 0.0000 0.00 180.00 0.00 0.0000 IC C36 C44 *C38 H39 0.0000 0.00 180.00 0.00 0.0000 IC C38 C42 *C44 C45 0.0000 0.00 180.00 0.00 0.0000 IC C44 C40 *C42 H43 0.0000 0.00 180.00 0.00 0.0000 IC C42 C35 *C40 H41 0.0000 0.00 180.00 0.00 0.0000 IC C40 C36 *C35 O34 0.0000 0.00 180.00 0.00 0.0000 IC C38 C44 C45 N46 0.0000 0.00 45.00 0.00 0.0000 IC C44 N46 *C45 N49 0.0000 0.00 180.00 0.00 0.0000 IC C44 C45 N46 H47 0.0000 0.00 0.00 0.00 0.0000 IC C45 H47 *N46 H48 0.0000 0.00 180.00 0.00 0.0000 IC C44 C45 N49 H50 0.0000 0.00 0.00 0.00 0.0000 IC C45 H50 *N49 H51 0.0000 0.00 180.00 0.00 0.0000 RESI MHYO 0.000 ! C4H4N2O2 5-methylenehydantoin, xxwy GROUP ATOM N1 NG2R53 -0.18 ! H3 O2 ATOM C2 CG2R53 0.25 ! \ // ATOM O2 OG2D1 -0.43 ! N3----C2 ATOM N3 NG2R53 -0.25 ! | | ATOM H3 HGP1 0.35 ! C4 N1 ATOM C4 CG2R53 0.26 ! // \ / \ ATOM O4 OG2D1 -0.41 ! O4 C5 H1 ATOM C5 CG252O 0.09 ! || ATOM C6 CG2DC3 -0.46 ! C6 ATOM H61 HGA5 0.23 ! / \ ATOM H62 HGA5 0.24 ! H61 H62 ATOM H1 HGP1 0.31 BOND N1 C2 C2 N3 N3 C4 C4 C5 BOND C5 N1 C2 O2 N3 H3 C4 O4 BOND C5 C6 C6 H61 C6 H62 N1 H1 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 O4 IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C4 N3 C2 N1 0.0000 0.00 0.00 0.00 0.0000 IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 RESI MOET 0.00 ! C3H6O Methoxyethene, xxwy GROUP ATOM C1 CG2D2 -0.53 ATOM H11 HGA5 0.23 ATOM H12 HGA5 0.23 ! H41 ATOM C2 CG2D1O -0.14 ! / ATOM H21 HGA4 0.21 ! H11 O3---C4--H42 ATOM O3 OG301 -0.28 ! \ / \ ATOM C4 CG331 0.01 ! C1==C2 H43 ATOM H41 HGA3 0.09 ! / \ ATOM H42 HGA3 0.09 ! H12 H21 ATOM H43 HGA3 0.09 BOND C1 C2 C2 O3 O3 C4 C1 H11 BOND C1 H12 C2 H21 C4 H41 C4 H42 C4 H43 IMPR C2 C1 O3 H21 IC C1 C2 O3 C4 0.0000 0.00 180.00 0.00 0.0000 IC O3 C2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 IC C2 H11 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 IC C1 O3 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC O3 H41 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC O3 H41 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI MOBU 0.00 ! C5H8O 1-Methoxy-1,3-butadiene, CAS Num: 10034-09-0, xxwy GROUP ATOM C1 CG2D1O -0.14 ATOM H11 HGA4 0.21 ! H1 ATOM C2 CG2DC1 -0.30 ! / ATOM H21 HGA4 0.23 ! H21 O1---C--H2 ATOM O1 OG301 -0.28 ! \ / \ ATOM C CG331 0.01 ! H41 C2==C1 H3 ATOM H1 HGA3 0.09 ! \ / \ ATOM H2 HGA3 0.09 ! C4==C3 H11 ATOM H3 HGA3 0.09 ! / \ ATOM C3 CG2DC2 -0.15 ! H42 H31 ATOM H31 HGA4 0.15 ATOM C4 CG2DC3 -0.42 ATOM H41 HGA5 0.21 ATOM H42 HGA5 0.21 BOND C1 C2 C1 O1 O1 C C1 H11 BOND C2 H21 C H1 C H2 C H3 BOND C2 C3 C3 C4 C3 H31 C4 H41 C4 H42 IMPR C1 C2 O1 H11 IC C2 C1 O1 C 0.0000 0.00 180.00 0.00 0.0000 IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 O1 *C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 H41 0.0000 0.00 0.00 0.00 0.0000 IC C3 H41 *C4 H42 0.0000 0.00 180.00 0.00 0.0000 IC C1 O1 C H1 0.0000 0.00 180.00 0.00 0.0000 IC O1 H1 *C H2 0.0000 0.00 120.00 0.00 0.0000 IC O1 H1 *C H3 0.0000 0.00 -120.00 0.00 0.0000 RESI BSAM 0.00 ! C6H7NO2S Benzenesulfonamide, CAS Num: 98-10-2, xxwy GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ! HD1 HE1 ATOM HD2 HGR61 0.115 ! | __ | ATOM CE2 CG2R61 -0.115 ! CD1--CE1 O11 H21 ATOM HE2 HGR61 0.115 ! / \ || / ATOM CZ CG2R61 0.24 ! HG--CG CZ--S1--N2 ATOM S1 SG3O2 0.61 ! \\ // || \ ATOM O11 OG2P1 -0.42 ! CD2--CE2 O12 H22 ATOM O12 OG2P1 -0.42 ! | | ATOM N2 NG321 -0.77 ! HD2 HE2 ATOM H21 HGP1 0.38 ATOM H22 HGP1 0.38 BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 H22 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CZ S1 N2 0.0000 0.0000 90.0000 0.0000 0.0000 IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CZ S1 N2 H21 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 H21 *N2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 RESI MSAM 0.00 ! CH5NO2S Methanesulfonamide, CAS Num: 3144-09-0, xxwy GROUP ATOM C3 CG331 -0.07 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 ! H31 O11 H21 ATOM S1 SG3O2 0.65 ! \ || / ATOM O11 OG2P1 -0.42 ! H32--C3--S1--N2 ATOM O12 OG2P1 -0.42 ! / || \ ATOM N2 NG321 -0.77 ! H33 O12 H22 ATOM H21 HGP1 0.38 ATOM H22 HGP1 0.38 BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 H22 BOND C3 H31 C3 H32 C3 H33 IC C3 S1 N2 H21 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 H21 *N2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI MMSM 0.00 ! C2H7NO2S N-Methylmethanesulfonamide, xxwy GROUP ATOM C3 CG331 -0.05 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 ! H31 O11 H21 ATOM S1 SG3O2 0.60 ! \ || / ATOM O11 OG2P1 -0.42 ! H32--C3--S1--N2 H41 ATOM O12 OG2P1 -0.42 ! / || \ / ATOM N2 NG311 -0.57 ! H33 O12 C4--H42 ATOM H21 HGP1 0.35 ! \ ATOM C4 CG331 -0.03 ! H43 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 BOND C3 H31 C3 H32 C3 H33 C4 H41 C4 H42 C4 H43 IC C3 S1 N2 C4 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 N2 C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 IC N2 H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 IC N2 H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI EESM 0.00 ! C4H11NO2S N-Ethylethanesulfonamide, xxwy GROUP ATOM C3 CG321 0.04 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM S1 SG3O2 0.60 ATOM O11 OG2P1 -0.42 ATOM O12 OG2P1 -0.42 ATOM N2 NG311 -0.57 ATOM H21 HGP1 0.35 ! H51 H31 O11 H21 H41 H61 ATOM C4 CG321 0.06 ! | | || | | | ATOM H41 HGA2 0.09 ! H52--C5--C3--S1--N2--C4--C6--H62 ATOM H42 HGA2 0.09 ! | | || | | ATOM C5 CG331 -0.27 ! H53 H32 O12 H42 H63 ATOM H51 HGA3 0.09 ATOM H52 HGA3 0.09 ATOM H53 HGA3 0.09 ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 BOND C3 H31 C3 H32 C3 C5 C4 H41 C4 H42 C4 C6 BOND C5 H51 C5 H52 C5 H53 C6 H61 C6 H62 C6 H63 IC C3 S1 N2 C4 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC N2 S1 C3 C5 0.0000 0.0000 180.0000 0.0000 0.0000 IC S1 C5 *C3 H31 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 C5 *C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 N2 C4 C6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N2 C6 *C4 H41 0.0000 0.0000 120.0000 0.0000 0.0000 IC N2 C6 *C4 H42 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 C3 C5 H51 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 H51 *C5 H52 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 H51 *C5 H53 0.0000 0.0000 -120.0000 0.0000 0.0000 IC N2 C4 C6 H61 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4 H61 *C6 H62 0.0000 0.0000 120.0000 0.0000 0.0000 IC C4 H61 *C6 H63 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI MBSM 0.00 ! C7H9NO2S N-Methylbenzenesulfonamide, xxwy GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ! HD1 HE1 ATOM HD2 HGR61 0.115 ! | __ | ATOM CE2 CG2R61 -0.115 ! CD1--CE1 O11 H21 H31 ATOM HE2 HGR61 0.115 ! / \ || | / ATOM CZ CG2R61 0.24 ! HG--CG CZ--S1--N2--C3--H32 ATOM S1 SG3O2 0.58 ! \\ // || \ ATOM O11 OG2P1 -0.42 ! CD2--CE2 O12 H33 ATOM O12 OG2P1 -0.42 ! | | ATOM N2 NG311 -0.57 ! HD2 HE2 ATOM H21 HGP1 0.35 ATOM C3 CG331 -0.03 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C3 BOND C3 H31 C3 H32 C3 H33 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CZ S1 N2 0.0000 0.0000 120.0000 0.0000 0.0000 IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CZ S1 N2 C3 0.0000 0.0000 -80.0000 0.0000 0.0000 IC S1 C3 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 N2 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC H31 N2 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC H31 N2 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 RESI PMSM 0.00 ! C7H9NO2S N-Phenylmethanesulfonamide, xxwy GROUP ATOM C3 CG331 -0.03 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 ATOM S1 SG3O2 0.42 ATOM O11 OG2P1 -0.36 ATOM O12 OG2P1 -0.36 ! H51 H61 ATOM N2 NG311 -0.48 ! | __ | ATOM H21 HGP1 0.33 ! H31 O11 H21 C51--C61 ATOM C4 CG2R61 0.21 ! \ || | / \ ATOM C51 CG2R61 -0.115 ! H32--C3--S1--N2--C4 C7--H7 ATOM H51 HGR61 0.115 ! / || \\ // ATOM C52 CG2R61 -0.115 ! H33 O12 C52--C62 ATOM H52 HGR61 0.115 ! | | ATOM C61 CG2R61 -0.115 ! H52 H62 ATOM H61 HGR61 0.115 ATOM C62 CG2R61 -0.115 ATOM H62 HGR61 0.115 ATOM C7 CG2R61 -0.115 ATOM H7 HGR61 0.115 BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 BOND C3 H31 C3 H32 C3 H33 BOND C4 C51 C4 C52 C51 C61 C52 C62 C7 C61 C7 C62 BOND C51 H51 C52 H52 C61 H61 C62 H62 C7 H7 IC C3 S1 N2 C4 0.0000 0.0000 50.0000 0.0000 0.0000 IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 IC S1 N2 C4 C51 0.0000 0.0000 60.0000 0.0000 0.0000 IC N2 C51 *C4 C52 0.0000 0.0000 180.0000 0.0000 0.0000 IC C52 C4 C51 C61 0.0000 0.0000 0.0000 0.0000 0.0000 IC C51 C4 C52 C62 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4 C51 C61 C7 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4 C61 *C51 H51 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4 C62 *C52 H52 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C51 *C61 H61 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C52 *C62 H62 0.0000 0.0000 180.0000 0.0000 0.0000 IC C61 C62 *C7 H7 0.0000 0.0000 180.0000 0.0000 0.0000 RESI PBSM 0.00 ! C12H11NO2S N-Phenylbenzenesulfonamide, CAS Num: 1678-25-7, xxwy GROUP ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CE1 CG2R61 -0.115 ATOM HE1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CE2 CG2R61 -0.115 ATOM HE2 HGR61 0.115 ! HD1 HE1 H41 H51 ATOM CZ CG2R61 0.23 ! | __ | | __ | ATOM S1 SG3O2 0.58 ! CD1--CE1 O11 H21 C41--C51 ATOM O11 OG2P1 -0.40 ! / \ || | / \ ATOM O12 OG2P1 -0.40 ! HG--CG CZ--S1--N2--C3 C6--H6 ATOM N2 NG311 -0.57 ! \\ // || \\ // ATOM H21 HGP1 0.32 ! CD2--CE2 O12 C42--C52 ATOM C3 CG2R61 0.24 ! | | | | ATOM C41 CG2R61 -0.115 ! HD2 HE2 H42 H52 ATOM H41 HGR61 0.115 ATOM C42 CG2R61 -0.115 ATOM H42 HGR61 0.115 ATOM C51 CG2R61 -0.115 ATOM H51 HGR61 0.115 ATOM C52 CG2R61 -0.115 ATOM H52 HGR61 0.115 ATOM C6 CG2R61 -0.115 ATOM H6 HGR61 0.115 BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C3 BOND C3 C41 C3 C42 C41 C51 C42 C52 C6 C51 C6 C52 BOND C41 H41 C42 H42 C51 H51 C52 H52 C6 H6 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CZ S1 N2 0.0000 0.0000 90.0000 0.0000 0.0000 IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 IC CZ S1 N2 C3 0.0000 0.0000 50.0000 0.0000 0.0000 IC S1 C3 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 IC S1 N2 C3 C41 0.0000 0.0000 -110.0000 0.0000 0.0000 IC N2 C41 *C3 C42 0.0000 0.0000 180.0000 0.0000 0.0000 IC C42 C3 C41 C51 0.0000 0.0000 0.0000 0.0000 0.0000 IC C41 C3 C42 C52 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3 C41 C51 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3 C51 *C41 H41 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 C52 *C42 H42 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C41 *C51 H51 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C42 *C52 H52 0.0000 0.0000 180.0000 0.0000 0.0000 IC C51 C52 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 RESI MMST 0.00 ! C2H6O3S Methyl methanesulfonate, CAS Num: 66-27-3, xxwy GROUP ATOM S1 SG3O2 0.24 ATOM C2 CG331 0.05 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ! O3 O4 ATOM H23 HGA3 0.09 ! \\ // ATOM O3 OG2P1 -0.32 ! S1 H61 ATOM O4 OG2P1 -0.32 ! / \ / ATOM O5 OG303 -0.24 ! H21--C2 O5---C6--H62 ATOM C6 CG331 0.05 ! / | \ ATOM H61 HGA3 0.09 ! H22 H23 H63 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND S1 C2 C2 H21 C2 H22 C2 H23 BOND S1 O3 S1 O4 S1 O5 BOND O5 C6 C6 H61 C6 H62 C6 H63 IC C2 O5 *S1 O3 0.0000 0.00 113.00 0.00 0.0000 IC C2 O5 *S1 O4 0.0000 0.00 -113.00 0.00 0.0000 IC O5 S1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC H21 S1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 S1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 IC C2 S1 O5 C6 0.0000 0.00 180.00 0.00 0.0000 IC S1 O5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 IC H61 O5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 IC H61 O5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 RESI MSNA -1.00 ! CH3O3S methyl sulfonate, xhe GROUP ATOM S SG3O1 0.73 ! O1 ATOM O1 OG2P1 -0.55 ! | ATOM O2 OG2P1 -0.55 ! O2---S---O3 ATOM O3 OG2P1 -0.55 ! | ATOM C1 CG331 -0.35 ! | ATOM H11 HGA3 0.09 ! H11-C1-H12 ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! H13 BOND S O1 S O2 S O3 BOND S C1 C1 H11 C1 H12 BOND C1 H13 ACCEPTOR O1 S ACCEPTOR O2 S ACCEPTOR O3 S IC H13 C1 S O1 0.0 0.00 180.00 0.0 0.0 IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 IC S H13 *C1 H11 0.0 0.00 120.00 0.0 0.0 IC S H13 *C1 H12 0.0 0.00 -120.00 0.0 0.0 RESI ESNA -1.00 ! C2H5O3S ethyl sulfonate, xhe GROUP ATOM S SG3O1 0.73 ! O1 ATOM O1 OG2P1 -0.55 ! | ATOM O2 OG2P1 -0.55 ! O2---S---O3 ATOM O3 OG2P1 -0.55 ! | ATOM C1 CG321 -0.26 ! | ATOM H11 HGA2 0.09 ! H11-C1-H12 ATOM H12 HGA2 0.09 ! | GROUP ! | ATOM C2 CG331 -0.27 ! H21-C2-H22 ATOM H21 HGA3 0.09 ! | ATOM H22 HGA3 0.09 ! | ATOM H23 HGA3 0.09 ! H23 BOND S O1 S O2 S O3 BOND S C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 H23 ACCEPTOR O1 S ACCEPTOR O2 S ACCEPTOR O3 S IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 IC S C1 C2 H23 0.0 0.00 180.00 0.0 0.0 IC C1 H23 *C2 H21 0.0 0.00 120.00 0.0 0.0 IC C1 H23 *C2 H22 0.0 0.00 -120.00 0.0 0.0 RESI PSNA -1.00 ! C3H7O3S propyl sulfonate, xhe GROUP ATOM S SG3O1 0.73 ! O1 ATOM O1 OG2P1 -0.55 ! | ATOM O2 OG2P1 -0.55 ! O2---S---O3 ATOM O3 OG2P1 -0.55 ! | ATOM C1 CG321 -0.26 ! | ATOM H11 HGA2 0.09 ! H11-C1-H12 ATOM H12 HGA2 0.09 ! | GROUP ! | ATOM C2 CG321 -0.18 ! H21-C2-H22 ATOM H21 HGA2 0.09 ! | ATOM H22 HGA2 0.09 ! | GROUP ! | ATOM C3 CG331 -0.27 ! H31-C3-H32 ATOM H31 HGA3 0.09 ! | ATOM H32 HGA3 0.09 ! | ATOM H33 HGA3 0.09 ! H33 BOND S O1 S O2 S O3 BOND S C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 BOND C3 H33 ACCEPTOR O1 S ACCEPTOR O2 S ACCEPTOR O3 S IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 IC S C1 C2 C3 0.0 0.00 180.00 0.0 0.0 IC C1 C3 *C2 H21 0.0 0.00 120.00 0.0 0.0 IC C1 C3 *C2 H22 0.0 0.00 -120.00 0.0 0.0 IC C1 C2 C3 H31 0.0 0.00 180.00 0.0 0.0 IC C2 H31 *C3 H32 0.0 0.00 120.00 0.0 0.0 IC C2 H31 *C3 H33 0.0 0.00 -120.00 0.0 0.0 RESI DMSN 0.00 ! C2H6O2S dimethyl sulfone, xhe GROUP ATOM S SG3O2 0.14 ATOM O1 OG2P1 -0.36 ! H31 ATOM O2 OG2P1 -0.36 ! | ATOM C3 CG331 0.02 ! H32-C3-H33 ATOM H31 HGA3 0.09 ! | ATOM H32 HGA3 0.09 ! O1=S=O2 ATOM H33 HGA3 0.09 ! | ATOM C4 CG331 0.02 ! H42-C4-H43 ATOM H41 HGA3 0.09 ! | ATOM H42 HGA3 0.09 ! H41 ATOM H43 HGA3 0.09 BOND S O1 S O2 S C3 S C4 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 ACCEPTOR O1 S ACCEPTOR O2 S IC C3 C4 *S O1 0.00 0.0000 120.0 0.00 0.00 IC C3 C4 *S O2 0.00 0.0000 -120.0 0.00 0.00 IC C4 S C3 H31 0.00 0.0000 180.000 0.00 0.00 IC S H31 *C3 H32 0.00 0.0000 120.000 0.00 0.00 IC S H31 *C3 H33 0.00 0.0000 -120.000 0.00 0.00 IC C3 S C4 H41 0.00 0.0000 180.000 0.00 0.00 IC S H41 *C4 H42 0.00 0.0000 120.000 0.00 0.00 IC S H41 *C4 H43 0.00 0.0000 -120.000 0.00 0.00 RESI MESN 0.00 ! C3H8O2S methyl ethyl sulfone, xhe GROUP ATOM S SG3O2 0.14 ATOM O1 OG2P1 -0.36 ATOM O2 OG2P1 -0.36 ! H31 ATOM C3 CG331 0.02 ! | ATOM H31 HGA3 0.09 ! H32-C3-H33 ATOM H32 HGA3 0.09 ! | ATOM H33 HGA3 0.09 ! O1=S=O2 ATOM C4 CG321 0.11 ! | ATOM H41 HGA2 0.09 ! H42-C4-H43 ATOM H42 HGA2 0.09 ! | GROUP ! H51-C5-H52 ATOM C5 CG331 -0.270 ! | ATOM H51 HGA3 0.090 ! H53 ATOM H52 HGA3 0.090 ATOM H53 HGA3 0.090 BOND S O1 S O2 S C3 S C4 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 C5 BOND C5 H51 C5 H52 C5 H53 ACCEPTOR O1 S ACCEPTOR O2 S IC C3 C4 *S O1 0.00 0.0000 120.0 0.00 0.00 IC C3 C4 *S O2 0.00 0.0000 -120.0 0.00 0.00 IC C4 S C3 H31 0.00 0.0000 180.000 0.00 0.00 IC S H31 *C3 H32 0.00 0.0000 120.000 0.00 0.00 IC S H31 *C3 H33 0.00 0.0000 -120.000 0.00 0.00 IC C3 S C4 C5 0.00 0.0000 180.000 0.00 0.00 IC S C5 *C4 H41 0.00 0.0000 120.000 0.00 0.00 IC S C5 *C4 H42 0.00 0.0000 -120.000 0.00 0.00 IC S C4 C5 H51 0.00 0.0000 180.00 0.00 0.00 IC C4 H51 *C5 H52 0.00 0.0000 120.00 0.00 0.00 IC C4 H51 *C5 H53 0.00 0.0000 -120.00 0.00 0.00 RESI MTDO 0.000 ! C4H3NO2S 5-methylene-2,4-thiazolidinedione, kevo & xxwy & oashi GROUP ATOM S1 SG311 -0.15 ! H3 O2 ATOM C2 CG2R53 0.42 ! \ // ATOM O2 OG2D1 -0.46 ! N3----C2 ATOM N3 NG2R53 -0.36 ! | | ATOM H3 HGP1 0.44 ! C4 S1 ATOM C4 CG2R53 0.26 ! // \ / ATOM O4 OG2D1 -0.45 ! O4 C5 ATOM C5 CG252O 0.22 ! || ATOM C6 CG2DC3 -0.58 ! C6 ATOM H61 HGA5 0.33 ! / \ ATOM H62 HGA5 0.33 ! H61 H62 BOND S1 C2 C2 N3 N3 C4 C4 C5 BOND C5 S1 C2 O2 N3 H3 C4 O4 BOND C5 C6 C6 H61 C6 H62 IMPR C2 N3 O2 S1 IMPR C4 C5 N3 O4 IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C4 N3 C2 S1 0.0000 0.00 0.00 0.00 0.0000 IC N3 S1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 IC S1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 RESI ZDOL 0.000 ! C7H6O2 1,3-benzodioxole, pram & oashi & kevo GROUP ATOM C1 CG2RC0 0.03 ATOM O1 OG3C51 -0.31 ATOM C2 CG3C52 0.38 ! H7 ATOM H21 HGA2 0.09 ! | ATOM H22 HGA2 0.09 ! H6 C7 ATOM O2 OG3C51 -0.31 ! \ // \ H21 ATOM C3 CG2RC0 0.03 ! C6 C1--O1\ / ATOM C4 CG2R61 -0.32 ! | || C2 ATOM H4 HGR61 0.28 ! C5 C3--O2/ \ ATOM C5 CG2R61 -0.15 ! / \\ / H22 ATOM H5 HGR61 0.19 ! H5 C4 ATOM C6 CG2R61 -0.15 ! | ATOM H6 HGR61 0.19 ! H4 ATOM C7 CG2R61 -0.32 ATOM H7 HGR61 0.28 BOND C1 O1 O1 C2 C2 H21 C2 H22 C2 O2 BOND O2 C3 C3 C1 C3 C4 C4 H4 C4 C5 BOND C5 H5 C5 C6 C6 H6 C6 C7 C7 H7 BOND C7 C1 IC C1 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C1 0.0000 0.00 0.00 0.00 0.0000 IC C6 C7 C1 C3 0.0000 0.00 0.00 0.00 0.0000 IC C7 C1 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C7 C1 O1 C2 0.0000 0.00 160.00 0.00 0.0000 ! nonplanar IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C3 *C1 O1 0.0000 0.00 177.50 0.00 0.0000 ! nonplanar IC C4 C1 *C3 O2 0.0000 0.00 -177.50 0.00 0.0000 ! nonplanar IC O1 O2 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC O1 O2 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 !New compounds by "team CGenFF", Sep 11 RESI AMET 0.000 ! C2H5N ethenamine (CAS: 593-67-9), pram (parameters tweaked by kevo) GROUP ! Notes: - tautomer of ethanimine (CAS: 20729-41-3) ATOM C1 CG2D2 -0.50 ! - both tautomers predited to be basic (ACD) ATOM H2 HGA5 0.21 ! - probably unstable ATOM H3 HGA5 0.21 ATOM C4 CG2D1O -0.13 ! H2 H5 H7 ATOM H5 HGA4 0.24 ! \ | / ATOM N6 NG321 -0.81 ! C1==C4--N6 ATOM H7 HGPAM2 0.39 ! / \ ATOM H8 HGPAM2 0.39 ! H3 H8 BOND C1 H2 C1 H3 C1 C4 BOND C4 H5 C4 N6 N6 H7 N6 H8 IMPR C4 C1 N6 H5 IC C1 C4 N6 H7 0.0000 0.00 180.00 0.00 0.0000 IC H2 C1 C4 N6 0.0000 0.00 180.00 0.00 0.0000 IC H2 C4 *C1 H3 0.0000 0.00 180.00 0.00 0.0000 IC N6 C1 *C4 H5 0.0000 0.00 180.00 0.00 0.0000 IC H7 C4 *N6 H8 0.0000 0.00 180.00 0.00 0.0000 RESI DMOP 0.00 ! C5H12O2 dimethoxypropane, sna GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ! H52 ATOM H13 HGA3 0.09 ! | GROUP ! H51-C5-H53 ATOM C2 CG301 0.40 ! | ATOM O4 OG301 -0.38 ! H11 O4 H31 ATOM C5 CG331 -0.09 ! | | | ATOM H51 HGA3 0.09 ! H12-C1----C2----C3-H32 ATOM H52 HGA3 0.09 ! | | | ATOM H53 HGA3 0.09 ! H13 O6 H33 ATOM O6 OG301 -0.38 ! | ATOM C7 CG331 -0.09 ! H71-C7-H73 ATOM H71 HGA3 0.09 ! | ATOM H72 HGA3 0.09 ! H72 ATOM H73 HGA3 0.09 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 C2 C2 C3 C2 O4 O4 C5 C2 O6 O6 C7 BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 BOND C5 H51 C5 H52 C5 H53 C7 H71 C7 H72 C7 H73 IC C1 C2 C3 H31 0.0000 0.00 -177.05 0.00 0.0000 IC C1 C3 *C2 O4 0.0000 0.00 -119.46 0.00 0.0000 IC C1 C3 *C2 O6 0.0000 0.00 115.38 0.00 0.0000 IC C1 C2 O4 C5 0.0000 0.00 -145.11 0.00 0.0000 IC C1 C2 O6 C7 0.0000 0.00 -162.42 0.00 0.0000 IC C3 C2 C1 H11 0.0000 0.00 -59.81 0.00 0.0000 IC C2 O4 C5 H51 0.0000 0.00 -177.01 0.00 0.0000 IC C2 O6 C7 H71 0.0000 0.00 -178.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 IC H51 O4 *C5 H52 0.0000 0.00 118.35 0.00 0.0000 IC H51 O4 *C5 H53 0.0000 0.00 -123.77 0.00 0.0000 IC H71 O6 *C7 H72 0.0000 0.00 118.30 0.00 0.0000 IC H71 O6 *C7 H73 0.0000 0.00 -118.47 0.00 0.0000 RESI DMBU 0.00 ! C6H14O2 dimethoxybutane, sna GROUP ATOM C1 CG331 -0.27 ATOM H11 HGA3 0.09 ! H62 ATOM H12 HGA3 0.09 ! | ATOM H13 HGA3 0.09 ! H61-C6-H63 GROUP ! | ATOM C6 CG331 -0.06 ! | ATOM H61 HGA3 0.09 ! | ATOM H62 HGA3 0.09 ! H11 O5 H31 H41 ATOM H63 HGA3 0.09 ! | | | | ATOM O5 OG301 -0.34 ! H12-C1----C2----C3----C4-H42 ATOM C2 CG301 0.26 ! | | | | ATOM O7 OG301 -0.34 ! H13 O7 H32 H43 ATOM C8 CG331 -0.06 ! | ATOM H81 HGA3 0.09 ! | ATOM H82 HGA3 0.09 ! | ATOM H83 HGA3 0.09 ! H81-C8-H83 GROUP ! | ATOM C3 CG321 -0.18 ! H82 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C2 O5 O5 C6 C2 O7 BOND O7 C8 C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 BOND C4 H41 C4 H42 C4 H43 C6 H61 C6 H62 C6 H63 BOND C8 H81 C8 H82 C8 H83 IC C1 C2 C3 C4 0.0000 0.00 178.49 0.00 0.0000 IC C1 C3 *C2 O5 0.0000 0.00 116.78 0.00 0.0000 IC C1 C3 *C2 O7 0.0000 0.00 -116.78 0.00 0.0000 IC C1 C2 O5 C6 0.0000 0.00 60.00 0.00 0.0000 ! minimum used in parametrization. Try -69.33 -69.33 for two other minima. IC C1 C2 O7 C8 0.0000 0.00 -60.00 0.00 0.0000 ! minimum used in parametrization. Try -54.16 -175.82 for two other minima. IC C3 C2 C1 H11 0.0000 0.00 -170.79 0.00 0.0000 IC C2 C3 C4 H41 0.0000 0.00 -179.00 0.00 0.0000 IC C2 O5 C6 H61 0.0000 0.00 -177.12 0.00 0.0000 IC C2 O7 C8 H81 0.0000 0.00 -176.20 0.00 0.0000 IC C1 C2 C3 H31 0.0000 0.00 -61.01 0.00 0.0000 IC C1 C2 C3 H32 0.0000 0.00 56.69 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 -119.96 0.00 0.0000 IC H11 C2 *C1 H13 0.0000 0.00 118.92 0.00 0.0000 IC H41 C3 *C4 H42 0.0000 0.00 -119.43 0.00 0.0000 IC H41 C3 *C4 H43 0.0000 0.00 119.41 0.00 0.0000 IC H61 O5 *C6 H62 0.0000 0.00 -118.05 0.00 0.0000 IC H61 O5 *C6 H63 0.0000 0.00 118.28 0.00 0.0000 IC H81 O7 *C8 H82 0.0000 0.00 -117.74 0.00 0.0000 IC H81 O7 *C8 H83 0.0000 0.00 118.36 0.00 0.0000 !New compounds by "team CGenFF", Aug 13 RESI NIME 0.00 ! CH3NO2 nitromethane, abar GROUP ATOM C1 CG334 0.20 ATOM H11 HGA3 0.09 ! H11 O21 ATOM H12 HGA3 0.09 ! \ // ATOM H13 HGA3 0.09 ! H12--C1-N2 ATOM N2 NG2O1 0.11 ! / \\ ATOM O21 OG2N1 -0.29 ! H13 O22 ATOM O22 OG2N1 -0.29 BOND C1 H11 C1 H12 C1 H13 C1 N2 N2 O21 N2 O22 IMPR N2 O21 O22 C1 IC O21 N2 C1 H11 0.0000 0.00 -29.00 0.00 0.0000 IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O21 *N2 O22 0.0000 0.00 180.00 0.00 0.0000 RESI NIPR 0.00 ! C3H7NO2 nitropropane, abar GROUP ATOM C1 CG324 0.26 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM N1 NG2O1 0.14 ATOM O11 OG2N1 -0.29 ! H32 H22 H11 O11 ATOM O12 OG2N1 -0.29 ! \ | | // ATOM C2 CG321 -0.18 ! H31--C3--C2--C1--N1 ATOM H21 HGA2 0.09 ! / | | \\ ATOM H22 HGA2 0.09 ! H33 H21 H12 O12 ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 H11 C1 H12 C1 N1 C1 C2 N1 O11 N1 O12 BOND C2 H21 C2 H22 C2 C3 C3 H31 C3 H32 C3 H33 IMPR N1 O11 O12 C1 IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 C1 N1 0.0000 0.00 -180.00 0.00 0.0000 IC C2 N1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C2 N1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 N1 O11 0.0000 0.00 90.00 0.00 0.0000 IC O11 C1 *N1 O12 0.0000 0.00 180.00 0.00 0.0000 RESI CBU 0.00 ! C4H8 cyclobutane, lsk & kevo GROUP ATOM C1 CG3C41 -0.18 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 GROUP ATOM C2 CG3C41 -0.18 ! H12 H22 ATOM H21 HGA2 0.09 ! | | ATOM H22 HGA2 0.09 ! H11-C1--C2-H21 GROUP ! | | ATOM C3 CG3C41 -0.18 ! H41-C4--C3-H31 ATOM H31 HGA2 0.09 ! | | ATOM H32 HGA2 0.09 ! H42 H32 GROUP ATOM C4 CG3C41 -0.18 ATOM H41 HGA2 0.09 ATOM H42 HGA2 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C1 BOND C1 H11 C1 H12 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 IC C1 C2 C3 C4 0.0000 0.00 25.00 0.00 0.0000 IC C4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C1 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C1 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI AZDO 0.00 ! C3H5NO beta-lactam, 2-azetidinone, lsk & kevo GROUP ATOM N1 NG2R43 -0.54 ATOM H1 HGP1 0.36 GROUP ATOM C2 CG2R53 0.29 ! H32 H31 ATOM O2 OG2D1 -0.47 ! \ / GROUP ! C3 ATOM C3 CG3C41 -0.01 ! / \ ATOM H31 HGA2 0.09 ! H41--C4 C2=O2 ATOM H32 HGA2 0.09 ! / \ / GROUP ! H42 N1 ATOM C4 CG3C41 0.01 ! | ATOM H41 HGA2 0.09 ! H1 ATOM H42 HGA2 0.09 BOND N1 H1 C2 O2 BOND C3 H31 C3 H32 BOND C4 H41 C4 H42 BOND N1 C2 C2 C3 C3 C4 C4 N1 IMPR C2 C3 N1 O2 IC N1 C2 C3 C4 0.0000 0.00 15.00 0.00 0.0000 IC C2 C4 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 N1 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 N1 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI ZOIC 0.000 ! C7H6O2 neutral benzoic acid, jal GROUP ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ! H3 H2 ATOM C3 CG2R61 -0.115 ! \ ___ / ATOM H3 HGR61 0.115 ! C3---C2 O7 ATOM C4 CG2R61 -0.115 ! / \ // ATOM H4 HGR61 0.115 ! H4--C4 C1--C7 ATOM C5 CG2R61 -0.115 ! \\ // \ ATOM H5 HGR61 0.115 ! C5---C6 O8--H8 ATOM C6 CG2R61 -0.115 ! / \ ATOM H6 HGR61 0.115 ! H5 H6 GROUP ATOM C1 CG2R61 0.080 ATOM C7 CG2O2 0.460 ATOM O7 OG2D1 -0.460 ATOM O8 OG311 -0.510 ATOM H8 HGP1 0.430 BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 C5 C5 H5 C5 C6 C6 H6 C6 C1 BOND C1 C7 C7 O7 C7 O8 O8 H8 IMPR C7 C1 O7 O8 ! Seed can be either C1 C2 C3 (line 1-2) OR C6 C1 C2 (line 2-3) IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 C1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C2 *C1 C7 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C7 O8 0.0000 0.00 45.00 0.00 0.0000 IC C1 O8 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 IC C1 C7 O8 H8 0.0000 0.00 180.00 0.00 0.0000 RESI MBOA 0.000 ! C8H8O2 methylbenzoate, jal GROUP ATOM C2 CG2R61 -0.115 ATOM H2 HGR61 0.115 ! H3 H2 ATOM C3 CG2R61 -0.115 ! \ ___ / ATOM H3 HGR61 0.115 ! C3---C2 O7 ATOM C4 CG2R61 -0.115 ! / \ // ATOM H4 HGR61 0.115 ! H4--C4 C1--C7 H81 ATOM C5 CG2R61 -0.115 ! \\ // \ | ATOM H5 HGR61 0.115 ! C5---C6 O8--C8--H83 ATOM C6 CG2R61 -0.115 ! / \ | ATOM H6 HGR61 0.115 ! H5 H6 H82 GROUP ATOM C1 CG2R61 0.080 ATOM C7 CG2O2 0.460 ATOM O7 OG2D1 -0.460 ATOM O8 OG302 -0.310 ATOM C8 CG331 -0.040 ATOM H81 HGA3 0.090 ATOM H82 HGA3 0.090 ATOM H83 HGA3 0.090 BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 C5 C5 H5 C5 C6 C6 H6 C6 C1 BOND C1 C7 C7 O7 C7 O8 O8 C8 BOND C8 H81 C8 H82 C8 H83 IMPR C7 C1 O7 O8 ! Seed can be either C1 C2 C3 (line 1-2) OR C6 C1 C2 (line 2-3) IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C2 C1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C2 *C1 C7 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C7 O8 0.0000 0.00 45.00 0.00 0.0000 IC C1 O8 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 IC C1 C7 O8 C8 0.0000 0.00 180.00 0.00 0.0000 IC C7 O8 C8 H83 0.0000 0.00 180.00 0.00 0.0000 IC O8 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 IC O8 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 RESI 1EOX 0.00 ! C2H4O 1-ethylene oxide, sc GROUP ATOM O1 OG3C31 -0.40 ATOM C1 CG3C31 0.02 ! H2 H3 ATOM H1 HGA2 0.09 ! \ / ATOM H2 HGA2 0.09 ! H1--C1--C2--H4 ATOM C2 CG3C31 0.02 ! \ / ATOM H3 HGA2 0.09 ! O1 ATOM H4 HGA2 0.09 BOND C1 H1 C1 H2 C2 H3 C2 H4 BOND C1 O1 C2 O1 BOND C1 C2 IC C1 O1 *C2 H1 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H3 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H4 0.0000 0.00 -120.00 0.00 0.0000 RESI 1BOX 0.00 ! C4H8O 1-butene oxide, sc GROUP ATOM O1 OG3C31 -0.40 ATOM C1 CG3C31 0.02 ATOM H11 HGA2 0.09 ATOM H12 HGA2 0.09 ATOM C2 CG3C31 0.11 ATOM H2 HGA1 0.09 ATOM C3 CG321 -0.18 ! H12 H2 H31 H41 ATOM H31 HGA2 0.09 ! \ | | | ATOM H32 HGA2 0.09 ! H11--C1--C2--C3--C4--H42 ATOM C4 CG331 -0.27 ! \ / | | ATOM H41 HGA3 0.09 ! O1 H32 H43 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 H11 C1 H12 C2 H2 C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 BOND C1 O1 C2 O1 BOND C1 C2 C2 C3 C3 C4 IC C1 O1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 IC C1 O1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 -140.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 RESI PMST 0.00 ! C7H8O3S phenyl methanesulfonate, xxwy GROUP ATOM S1 SG3O2 0.24 ATOM C2 CG331 0.05 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ! O11 O12 HE1 HD1 ATOM H23 HGA3 0.09 ! \\ // | | ATOM O11 OG2P1 -0.32 ! S1 CE1--CD1 ATOM O12 OG2P1 -0.32 ! / \ // \\ ATOM O3 OG303 -0.24 ! H21--C2 O3---CZ CG--HG ATOM CZ CG2R61 0.32 ! / | \ __ / ATOM CE1 CG2R61 -0.115 ! H22 H23 CE2--CD2 ATOM HE1 HGR61 0.115 ! | | ATOM CE2 CG2R61 -0.115 ! HE2 HD2 ATOM HE2 HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 BOND S1 C2 C2 H21 C2 H22 C2 H23 BOND S1 O11 S1 O12 S1 O3 BOND O3 CZ CZ CE1 CZ CE2 CE1 HE1 CE2 HE2 BOND CE1 CD1 CE2 CD2 CD1 HD1 CD2 HD2 BOND CD1 CG CD2 CG CG HG IC C2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 IC C2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 IC O3 S1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 IC H21 S1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 IC H21 S1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 IC C2 S1 O3 CZ 0.0000 0.00 180.00 0.00 0.0000 IC S1 O3 CZ CE1 0.0000 0.00 90.00 0.00 0.0000 IC O3 CE1 *CZ CE2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CZ CE1 CD1 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 IC CZ CE1 CD1 CG 0.0000 0.00 0.00 0.00 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CG CE1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CG CE2 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 RESI MSMT 0.00 ! CH5NO3S methyl sulfamate, xxwy GROUP ATOM S1 SG3O2 0.22 ATOM N2 NG321 -0.46 ATOM H21 HGP1 0.35 ! O11 O12 ATOM H22 HGP1 0.35 ! \\ // ATOM O11 OG2P1 -0.28 ! S1 H41 ATOM O12 OG2P1 -0.28 ! / \ / ATOM O3 OG303 -0.24 ! H21--N2 O3---C4--H42 ATOM C4 CG331 0.07 ! / \ ATOM H41 HGA3 0.09 ! H22 H43 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND S1 N2 N2 H21 N2 H22 BOND S1 O11 S1 O12 S1 O3 BOND O3 C4 C4 H41 C4 H42 C4 H43 IC N2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 IC N2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 IC O3 S1 N2 H21 0.0000 0.00 -60.00 0.00 0.0000 IC H21 S1 *N2 H22 0.0000 0.00 120.00 0.00 0.0000 IC N2 S1 O3 C4 0.0000 0.00 180.00 0.00 0.0000 IC S1 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 IC H41 O3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC H41 O3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 RESI PSMT 0.00 ! C6H7NO3S phenyl sulfamate, xxwy GROUP ATOM S1 SG3O2 0.22 ATOM N2 NG321 -0.46 ATOM H21 HGP1 0.35 ! O11 O12 HE1 HD1 ATOM H22 HGP1 0.35 ! \\ // | | ATOM O11 OG2P1 -0.28 ! S1 CE1--CD1 ATOM O12 OG2P1 -0.28 ! / \ // \\ ATOM O3 OG303 -0.24 ! H21--N2 O3---CZ CG--HG ATOM CZ CG2R61 0.34 ! / \ __ / ATOM CE1 CG2R61 -0.115 ! H22 CE2--CD2 ATOM HE1 HGR61 0.115 ! | | ATOM CE2 CG2R61 -0.115 ! HE2 HD2 ATOM HE2 HGR61 0.115 ATOM CD1 CG2R61 -0.115 ATOM HD1 HGR61 0.115 ATOM CD2 CG2R61 -0.115 ATOM HD2 HGR61 0.115 ATOM CG CG2R61 -0.115 ATOM HG HGR61 0.115 BOND S1 N2 N2 H21 N2 H22 BOND S1 O11 S1 O12 S1 O3 BOND O3 CZ CZ CE1 CZ CE2 CE1 HE1 CE2 HE2 BOND CE1 CD1 CE2 CD2 CD1 HD1 CD2 HD2 BOND CD1 CG CD2 CG CG HG IC N2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 IC N2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 IC O3 S1 N2 H21 0.0000 0.00 -60.00 0.00 0.0000 IC H21 S1 *N2 H22 0.0000 0.00 120.00 0.00 0.0000 IC N2 S1 O3 CZ 0.0000 0.00 180.00 0.00 0.0000 IC S1 O3 CZ CE1 0.0000 0.00 90.00 0.00 0.0000 IC O3 CE1 *CZ CE2 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CZ CE1 CD1 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 IC CZ CE1 CD1 CG 0.0000 0.00 0.00 0.00 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 IC CG CE1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CG CE2 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 RESI OBTZ 0.00 ! C7H8N2O2S 1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine model compound for drug hydrochlorothiazide, xxwy GROUP ATOM S1 SG3O2 0.33 ATOM N2 NG311 -0.55 ATOM H2 HGP1 0.38 ! H6 H4 ATOM O11 OG2P1 -0.34 ! | | ATOM O12 OG2P1 -0.34 ! C6 N4 H31 ATOM C3 CG321 0.29 ! // \ / \ / ATOM H31 HGA2 0.09 ! H7---C7 C5 C3---H32 ATOM H32 HGA2 0.09 ! | || | ATOM N4 NG311 -0.76 ! H8---C8 C10 N2---H2 ATOM H4 HGPAM1 0.39 ! \\ / \ / ATOM C5 CG2R61 0.32 ! C9 S1 ATOM C6 CG2R61 -0.115 ! | // \\ ATOM H6 HGR61 0.115 ! H9 O11 O12 ATOM C7 CG2R61 -0.115 ATOM H7 HGR61 0.115 ATOM C8 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 0.100 BOND S1 N2 N2 C3 C3 N4 N4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 S1 BOND C5 C10 S1 O11 S1 O12 N2 H2 C3 H31 BOND C3 H32 N4 H4 C6 H6 C7 H7 C8 H8 C9 H9 IC C5 C10 S1 N2 0.0000 0.00 -20.00 0.00 0.0000 IC S1 C10 C5 N4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 N4 C3 0.0000 0.00 0.00 0.00 0.0000 IC S1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC N4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC C10 N2 *S1 O11 0.0000 0.00 -120.00 0.00 0.0000 IC C10 N2 *S1 O12 0.0000 0.00 120.00 0.00 0.0000 IC S1 C3 *N2 H2 0.0000 0.00 120.00 0.00 0.0000 IC N2 N4 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC N2 N4 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *N4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI AOBT 0.00 ! C8H12N2O2S acyclic model compound for OBTZ, xxwy GROUP ATOM S1 SG3O2 0.56 ATOM N2 NG311 -0.60 ATOM H2 HGP1 0.37 ATOM O11 OG2P1 -0.43 ! H6 H4 ATOM O12 OG2P1 -0.43 ! | | ATOM C3 CG321 0.21 ! C6 N4 H31 ATOM H31 HGA2 0.09 ! // \ / \ / ATOM H32 HGA2 0.09 ! H7---C7 C5 C3---H32 ATOM N4 NG311 -0.56 ! | || | ATOM H4 HGPAM1 0.37 ! H8---C8 C10 N2--H2 HS1 ATOM C5 CG2R61 0.05 ! \\ / | \ / ATOM C6 CG2R61 -0.115 ! C9 H10 S1---CS--HS2 ATOM H6 HGR61 0.115 ! | // \\ \ ATOM C7 CG2R61 -0.115 ! H9 O11 O12 HS3 ATOM H7 HGR61 0.115 ATOM C8 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM C9 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C10 CG2R61 -0.115 ATOM H10 HGR61 0.115 ATOM CS CG331 0.010 ATOM HS1 HGA3 0.090 ATOM HS2 HGA3 0.090 ATOM HS3 HGA3 0.090 BOND S1 N2 N2 C3 C3 N4 N4 C5 C5 C6 BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 H10 BOND C5 C10 S1 O11 S1 O12 N2 H2 C3 H31 BOND C3 H32 N4 H4 C6 H6 C7 H7 C8 H8 C9 H9 BOND S1 CS CS HS1 CS HS2 CS HS3 IC CS S1 N2 C3 0.0000 0.00 -60.00 0.00 0.0000 IC S1 N2 C3 N4 0.0000 0.00 180.00 0.00 0.0000 IC N2 C3 N4 C5 0.0000 0.00 60.00 0.00 0.0000 IC C3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC N4 C6 *C5 C10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C6 C5 C10 C9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC N2 S1 CS HS1 0.0000 0.00 180.00 0.00 0.0000 IC HS1 S1 *CS HS2 0.0000 0.00 120.00 0.00 0.0000 IC HS1 S1 *CS HS3 0.0000 0.00 -120.00 0.00 0.0000 IC CS N2 *S1 O11 0.0000 0.00 -120.00 0.00 0.0000 IC CS N2 *S1 O12 0.0000 0.00 120.00 0.00 0.0000 IC S1 C3 *N2 H2 0.0000 0.00 120.00 0.00 0.0000 IC N2 N4 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 IC N2 N4 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *N4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C5 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 !New compounds by "team CGenFF", Feb 15 RESI 2BTY 0.000 ! C4H6 2-butyne, kevo & rima GROUP ATOM C1 CG331 -0.19 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ATOM H13 HGA3 0.09 ! H11 H41 ATOM C2 CG1T1 -0.08 ! | __ | GROUP ! H12--C1--C2==C3--C4--H42 ATOM C3 CG1T1 -0.08 ! | | ATOM C4 CG331 -0.19 ! H13 H43 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 BOND C1 H11 C1 H12 C1 H13 BOND C4 H41 C4 H42 C4 H43 !!Just a test !DIHE H11 C2 C3 H41 !DIHE H11 C2 C3 H42 !DIHE H11 C2 C3 H43 !DIHE H12 C2 C3 H41 !DIHE H12 C2 C3 H42 !DIHE H12 C2 C3 H43 !DIHE H13 C2 C3 H41 !DIHE H13 C2 C3 H42 !DIHE H13 C2 C3 H43 IC C1 C2 C3 C4 0.0000 179.90 0.00 179.90 0.0000 IC C3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 IC C2 C3 C4 H41 0.0000 179.90 0.00 0.00 0.0000 IC C3 H41 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 IC C3 H41 *C4 H43 0.0000 0.00 240.00 0.00 0.0000 RESI PRPY 0.000 ! C3H4 propyne, xxwy, mnoon, rima & kevo GROUP ATOM C1 CG331 -0.14 ATOM H11 HGA3 0.09 ! H11 ATOM H12 HGA3 0.09 ! | __ ATOM H13 HGA3 0.09 ! H12--C1--C2==C3--H31 ATOM C2 CG1T1 -0.01 ! | ATOM C3 CG1T2 -0.41 ! H13 ATOM H31 HGPAM1 0.29 BOND C1 C2 C2 C3 C3 H31 BOND C1 H11 C1 H12 C1 H13 IC C1 C2 C3 H31 0.0000 179.90 0.00 179.90 0.0000 IC C3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 RESI CYPE 0.000 ! C5H8 cyclopentene abar & rima GROUP ATOM C1 CG2R51 -0.12 ATOM H1 HGR51 0.12 ATOM C2 CG2R51 -0.12 ! H2 H31 H32 ATOM H2 HGR51 0.12 ! \ \ / ATOM C3 CG3C52 -0.18 ! C2---C3 H41 ATOM H31 HGA2 0.09 ! || \ / ATOM H32 HGA2 0.09 ! || C4 ATOM C4 CG3C52 -0.18 ! || / \ ATOM H41 HGA2 0.09 ! C1---C5 H42 ATOM H42 HGA2 0.09 ! / / \ ATOM C5 CG3C52 -0.18 ! H1 H51 H52 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND C1 C2 C1 C5 C1 H1 C2 C3 C2 H2 BOND C3 C4 C3 H31 C3 H32 BOND C4 C5 C4 H41 C4 H42 C5 H51 C5 H52 IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 IC C5 C2 *C1 H1 0.0000 0.00 180.0 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.0 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.0 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.0 0.00 0.0000 IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 IC C4 C1 *C5 H52 0.0000 0.00 -120.0 0.00 0.0000 RESI 13BPO 0.00 ! C8H8N2 1,3-bipyrrole, lf GROUP ATOM N1 NG2R57 -0.35 ATOM C2 CG2R51 -0.04 ATOM H2 HGR52 0.14 ATOM C3 CG2R51 -0.25 ATOM H3 HGR51 0.15 ATOM C4 CG2R51 -0.25 ! H4 H5 H9 H10 ATOM H4 HGR51 0.15 ! \ / \ / ATOM C5 CG2R51 -0.04 ! C4==C5 C9==C10 ATOM H5 HGR52 0.14 ! | \ / | ATOM N6 NG2R51 -0.35 ! | N1--C8 | ATOM H6 HGP1 0.35 ! | / \ | ATOM C7 CG2R51 -0.04 ! C3==C2 C7--N6 ATOM H7 HGR52 0.14 ! / \ / \ ATOM C8 CG2R57 0.25 ! H3 H2 H7 H6 ATOM C9 CG2R51 -0.25 ATOM H9 HGR51 0.15 ATOM C10 CG2R51 -0.04 ATOM H10 HGR52 0.14 BOND N1 C5 N1 C2 N1 C8 C2 C3 C2 H2 BOND C3 C4 C3 H3 C4 C5 C4 H4 C5 H5 BOND N6 C10 N6 C7 N6 H6 C7 C8 C7 H7 BOND C8 C9 C9 C10 C9 H9 C10 H10 IC N1 C8 C7 N6 0.0000 0.00 180.00 0.00 0.0000 IC N1 C7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC N1 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C8 C2 *N1 C5 0.0000 0.00 180.00 0.00 0.0000 IC C8 N1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C8 N1 C5 C4 0.0000 0.00 180.00 0.00 0.0000 IC C8 N6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C10 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 RESI 11BPO 0.00 ! C8H8N2 1,1-bipyrrole, lf GROUP ATOM C2 CG2R51 -0.04 ATOM H2 HGR52 0.14 ATOM N1 NG2R57 0.00 ATOM C5 CG2R51 -0.04 ATOM H5 HGR52 0.14 ATOM C4 CG2R51 -0.25 ! H4 H5 H7 H8 ATOM H4 HGR51 0.15 ! \ / \ / ATOM C3 CG2R51 -0.25 ! C4==C5 C7==C8 ATOM H3 HGR51 0.15 ! | \ / | ATOM C8 CG2R51 -0.25 ! | N1--N6 | ATOM H8 HGR51 0.15 ! | / \ | ATOM C7 CG2R51 -0.04 ! C3==C2 C10==C9 ATOM H7 HGR52 0.14 ! / \ / \ ATOM N6 NG2R57 0.00 ! H3 H2 H10 H9 ATOM C10 CG2R51 -0.04 ATOM H10 HGR52 0.14 ATOM C9 CG2R51 -0.25 ATOM H9 HGR51 0.15 BOND C2 H2 C2 N1 C2 C3 N1 C5 N1 N6 BOND C5 H5 C5 C4 C4 H4 C4 C3 C3 H3 BOND C8 H8 C8 C7 C8 C9 C7 H7 BOND C7 N6 N6 C10 C10 H10 C10 C9 C9 H9 IC N1 N6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC N1 C7 *N6 C10 0.0000 0.00 180.00 0.00 0.0000 IC N1 N6 C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C7 N6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 IC N6 C2 *N1 C5 0.0000 0.00 180.00 0.00 0.0000 IC N6 N1 C5 C4 0.0000 0.00 180.00 0.00 0.0000 IC N6 N1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 RESI 33BPO 0.00 ! C8H8N2 3,3-bipyrrole, lf GROUP ATOM C5 CG2R51 -0.04 ATOM H5 HGR52 0.14 ATOM C4 CG2R57 -0.10 ATOM C3 CG2R51 -0.25 ATOM H3 HGR51 0.15 ATOM C2 CG2R51 -0.04 ! H2 H3 H9 H10 ATOM H2 HGR52 0.14 ! \ / \ / ATOM N1 NG2R51 -0.35 ! C2==C3 C9==C10 ATOM H1 HGP1 0.35 ! | \ / | ATOM C10 CG2R51 -0.04 ! | C4--C8 | ATOM H10 HGR52 0.14 ! | // \\ | ATOM C9 CG2R51 -0.25 ! N1--C5 C7--N6 ATOM H9 HGR51 0.15 ! / \ / \ ATOM C8 CG2R57 -0.10 ! H1 H5 H7 H6 ATOM C7 CG2R51 -0.04 ATOM H7 HGR52 0.14 ATOM N6 NG2R51 -0.35 ATOM H6 HGP1 0.35 BOND C5 H5 C5 C4 C5 N1 C4 C3 C4 C8 BOND C3 H3 C3 C2 C2 H2 C2 N1 N1 H1 BOND C10 H10 C10 C9 C10 N6 C9 H9 BOND C9 C8 C8 C7 C7 H7 C7 N6 N6 H6 IC C4 C8 C7 N6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C7 C8 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C8 C5 *C4 C3 0.0000 0.00 180.00 0.00 0.0000 IC C8 C4 C3 C2 0.0000 0.00 180.00 0.00 0.0000 IC C8 C4 C5 N1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C7 C10 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 RESI TRZ2 0.00 ! C2H3N3 2H-1,2,3-triazole, lf GROUP ! H4 ATOM C4 CG2R52 0.06 ! \ ATOM H4 HGR52 0.16 ! C4==N3 ATOM C5 CG2R52 0.06 ! | \ ATOM H5 HGR52 0.16 ! | N2--H2 ATOM N1 NG2R50 -0.55 ! | / ATOM N2 NG2R51 0.39 ! C5==N1 ATOM H2 HGP1 0.27 ! / ATOM N3 NG2R50 -0.55 ! H5 BOND C4 H4 C4 C5 C4 N3 C5 H5 BOND C5 N1 N1 N2 N2 H2 N2 N3 IC N1 N2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC N2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC N1 N3 *N2 H2 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 N1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI 22BPY 0.000 ! C10H8N2 2,2'-bipyridine, kevo GROUP ATOM N1 NG2R60 -0.600 ATOM C2 CG2R67 0.300 ! H5 ATOM C3 CG2R61 -0.115 ! | ATOM H3 HGR61 0.115 ! C5 ATOM C4 CG2R61 -0.115 ! // \ ATOM H4 HGR61 0.115 ! H6--C6 C4--H4 ATOM C5 CG2R61 -0.115 ! | || ATOM H5 HGR61 0.115 ! N1 C3--H3 ATOM C6 CG2R61 0.180 ! \\ / ATOM H6 HGR62 0.120 ! C2 GROUP ! | ATOM N7 NG2R60 -0.600 ! C8 ATOM C8 CG2R67 0.300 ! // \ ATOM C9 CG2R61 -0.115 ! H9--C9 N7 ATOM H9 HGR61 0.115 ! | || ATOM C10 CG2R61 -0.115 ! H10-C10 C12-H12 ATOM H10 HGR61 0.115 ! \\ / ATOM C11 CG2R61 -0.115 ! C11 ATOM H11 HGR61 0.115 ! | ATOM C12 CG2R61 0.180 ! H11 ATOM H12 HGR62 0.120 BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 BOND C6 N1 C3 H3 C4 H4 C5 H5 C6 H6 BOND C2 C8 BOND N7 C8 C8 C9 C9 C10 C10 C11 C11 C12 BOND C12 N7 C9 H9 C10 H10 C11 H11 C12 H12 !Special! Use IC SEED C2 C8 N7 for cleaner dipoles for asymmetric conformations! IC C8 N1 *C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C3 C2 N1 C6 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N1 C2 C8 N7 0.0000 0.00 175.00 0.00 0.0000 ! deliberate distortion IC C2 N7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 ! use in reverse order as IC SEED IC N7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.0000 IC C9 C8 N7 C12 0.0000 0.00 0.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C11 N7 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 RESI ETRZ 0.000 ! C4H7N3 1-ethyl-1,2,3-triazole, kevo GROUP ATOM N1 NG2R51 0.28 ATOM N2 NG2R50 -0.37 ATOM N3 NG2R50 -0.41 ATOM C4 CG2R51 0.25 ! H4 H5 H71 H72 ATOM H4 HGR52 0.11 ! \ ___ / | / ATOM C5 CG2R51 -0.35 ! C4---C5 C7--H73 ATOM H5 HGR52 0.20 ! | \ / ATOM C6 CG321 0.11 ! | N1---C6 ATOM H61 HGA2 0.09 ! |___ / | \ ATOM H62 HGA2 0.09 ! N3---N2 H61 H62 GROUP ATOM C7 CG331 -0.27 ATOM H71 HGA3 0.09 ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 BOND N1 C5 N1 N2 N1 C6 N2 N3 N3 C4 BOND C4 C5 C4 H4 C5 H5 C6 C7 C6 H61 BOND C6 H62 C7 H71 C7 H72 C7 H73 IC N1 N2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC N3 N2 N1 C5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 N1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N2 *N1 C6 0.0000 0.00 180.00 0.00 0.0000 IC N2 N1 C6 C7 0.0000 0.00 90.00 0.00 0.0000 ! rotatable bond IC N1 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC N1 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC N1 C6 C7 H73 0.0000 0.00 180.00 0.00 0.0000 IC C6 H73 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC C6 H73 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 RESI YTHY 0.00 ! C8H6N2O2 2,4(1H,3H)-quinazolinedione (CAS # 86-96-4), isg GROUP ATOM C1 CG2R61 -0.115 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R62 0.340 ATOM C5 CG2R62 -0.070 ! H6 O8 ATOM C6 CG2R61 -0.115 ! | || ATOM H6 HGR61 0.115 ! C6 C8 H9 ATOM C8 CG2R63 0.510 ! // \ / \ / ATOM N9 NG2R61 -0.570 ! H1--C1 C5 N9 ATOM C10 CG2R63 0.450 ! | || | ATOM N11 NG2R61 -0.490 ! H2--C2 C4 C10 ATOM H11 HGP1 0.360 ! \\ / \ / \\ ATOM O10 OG2D4 -0.450 ! C3 N11 O10 ATOM H9 HGP1 0.390 ! | | ATOM O8 OG2D4 -0.470 ! H3 H11 ATOM H3 HGR61 0.115 ATOM H2 HGR61 0.115 ATOM H1 HGR61 0.115 BOND C1 C2 C1 H1 C2 C3 C2 H2 C3 C4 C3 H3 BOND C4 C5 C5 C6 C5 C8 C6 C1 C6 H6 C8 N9 BOND C8 O8 N9 C10 N9 H9 C10 N11 C10 O10 N11 C4 N11 H11 IMPR C8 C5 N9 O8 IMPR C10 N9 N11 O10 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 -1.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI RIN 0.000 ! C9H6O2 coumarin (CAS # 91-64-5), isg GROUP ATOM C7 CG2R61 -0.115 ATOM C6 CG2R61 -0.115 ATOM C5 CG2R62 -0.010 ATOM C10 CG2R62 0.400 ! H6 H4 ATOM C9 CG2R61 -0.115 ! | | ATOM C8 CG2R61 -0.115 ! C6 C4 H3 ATOM H4 HGR62 0.230 ! // \ / \\ / ATOM H7 HGR61 0.115 ! H7--C7 C5 C3 ATOM H6 HGR61 0.115 ! | || | ATOM C4 CG2R62 -0.230 ! H8--C8 C10 C2 ATOM H9 HGR61 0.115 ! \\ / \ / \\ ATOM H8 HGR61 0.115 ! C9 O1 O2 ATOM C3 CG2R62 -0.260 ! | ATOM H3 HGR62 0.200 ! H9 ATOM O1 OG3R60 -0.360 ATOM C2 CG2R63 0.490 ATOM O2 OG2D4 -0.460 BOND C7 C6 C7 C8 C7 H7 C6 C5 C6 H6 C5 C10 C5 C4 BOND C10 C9 C10 O1 C9 C8 C9 H9 C8 H8 H4 C4 C4 C3 BOND C3 H3 C3 C2 O1 C2 C2 O2 IMPR C2 C3 O2 O1 IC C5 C10 O1 C2 0.0000 0.00 -1.00 0.00 0.0000 IC O1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 IC O1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 IC O1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 RESI YTS2 0.00 ! C8H6N2S2 2,4(1H,3H)-quinazolinedithione (CAS # 5993-69-1), isg GROUP ATOM C1 CG2R61 -0.115 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R61 0.490 ATOM C5 CG2R61 0.120 ! H6 S8 ATOM C6 CG2R61 -0.115 ! | || ATOM H1 HGR61 0.115 ! C6 C8 H9 ATOM H2 HGR61 0.115 ! // \ / \ / ATOM H3 HGR61 0.115 ! H1--C1 C5 N9 ATOM H6 HGR61 0.115 ! | || | ATOM C8 CG2R63 0.100 ! H2--C2 C4 C10 ATOM S8 SG2D1 -0.240 ! \\ / \ / \\ ATOM N9 NG2R61 -0.600 ! C3 N11 S10 ATOM H9 HGP1 0.420 ! | | ATOM C10 CG2R63 0.140 ! H3 H11 ATOM S10 SG2D1 -0.240 ATOM N11 NG2R61 -0.600 ATOM H11 HGP1 0.410 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 H1 C1 H2 C2 BOND H3 C3 H6 C6 C5 C8 C8 S8 C8 N9 N9 H9 N9 C10 BOND C10 S10 C10 N11 N11 H11 N11 C4 C6 C1 IMPR C8 C5 N9 S8 IMPR C10 N9 N11 S10 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 N9 *C8 S8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N9 N11 *C10 S10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI YT4S 0.00 ! C8H6N2OS 2,3-dihydro-2-thioxo-4(1H)-quinazolinone (CAS # 13906-09-7), isg GROUP ATOM C1 CG2R61 -0.115 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R62 0.360 ATOM C5 CG2R62 -0.050 ! H6 O8 ATOM C6 CG2R61 -0.115 ! | || ATOM H1 HGR61 0.115 ! C6 C8 H9 ATOM H2 HGR61 0.115 ! // \ / \ / ATOM H3 HGR61 0.115 ! H1--C1 C5 N9 ATOM H6 HGR61 0.115 ! | || | ATOM C8 CG2R63 0.500 ! H2--C2 C4 C10 ATOM O8 OG2D4 -0.460 ! \\ / \ / \\ ATOM N9 NG2R61 -0.410 ! C3 N11 S10 ATOM H9 HGP1 0.370 ! | | ATOM C10 CG2R63 -0.100 ! H3 H11 ATOM S10 SG2D1 -0.240 ATOM N11 NG2R61 -0.290 ATOM H11 HGP1 0.320 BOND C1 C2 C1 H1 C1 C6 C2 C3 C2 H2 C3 C4 C3 H3 C4 C5 BOND C4 N11 C5 C8 C5 C6 C6 H6 N11 H11 N11 C10 C10 S10 C10 N9 BOND N9 H9 N9 C8 C8 O8 IMPR C8 C5 N9 O8 IMPR C10 N11 N9 S10 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N9 N11 *C10 S10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI YT2S 0.00 ! C8H6N2OS 3,4-dihydro-4-thioxo-2(1H)-quinazolinone (CAS # 17796-47-3) isg GROUP ATOM C1 CG2R61 -0.115 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R62 0.340 ATOM C5 CG2R62 -0.040 ! H6 S8 ATOM C6 CG2R61 -0.115 ! | || ATOM C8 CG2R63 0.110 ! C6 C8 H9 ATOM S8 SG2D1 -0.280 ! // \ / \ / ATOM N9 NG2R61 -0.310 ! H1--C1 C5 N9 ATOM H9 HGP1 0.310 ! | || | ATOM C10 CG2R63 0.440 ! H2--C2 C4 C10 ATOM O10 OG2D4 -0.450 ! \\ / \ / \\ ATOM N11 NG2R61 -0.490 ! C3 N11 O10 ATOM H11 HGP1 0.370 ! | | ATOM H1 HGR61 0.115 ! H3 H11 ATOM H2 HGR61 0.115 ATOM H3 HGR61 0.115 ATOM H6 HGR61 0.115 BOND C1 C6 C1 H1 C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 BOND C4 C5 C4 N11 C5 C6 C6 H6 C5 C8 C8 S8 C8 N9 BOND N9 H9 N9 C10 C10 O10 C10 N11 N11 H11 IMPR C8 C5 N9 S8 IMPR C10 N9 N11 O10 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 N9 *C8 S8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI TC243C 0.00 ! C8H6N2O 4(3H)-quinazolinone (CAS # 491-36-1), isg GROUP ATOM H10 HGR62 0.150 ATOM H3 HGR61 0.115 ATOM H2 HGR61 0.115 ATOM H1 HGR61 0.115 ! H6 O8 ATOM H6 HGR61 0.115 ! | || ATOM H9 HGP1 0.350 ! C6 C8 H9 ATOM C10 CG2R64 0.440 ! // \ / \ / ATOM N11 NG2R62 -0.770 ! H1--C1 C5 N9 ATOM C4 CG2R62 0.340 ! | || | ATOM C3 CG2R61 -0.115 ! H2--C2 C4 C10 ATOM C2 CG2R61 -0.115 ! \\ / \ // \ ATOM C1 CG2R61 -0.115 ! C3 N11 H10 ATOM C6 CG2R61 -0.115 ! | ATOM C5 CG2R62 0.190 ! H3 ATOM C8 CG2R63 0.090 ATOM O8 OG2D4 -0.400 ATOM N9 NG2R61 -0.390 BOND C10 H10 C10 N11 C10 N9 N11 C4 C4 C3 C4 C5 C3 H3 BOND C3 C2 C2 H2 C2 C1 C1 H1 C1 C6 C6 H6 C6 C5 BOND C5 C8 C8 O8 C8 N9 N9 H9 IMPR C8 C5 N9 O8 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 IC N9 N11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 RESI 4PYO 0.00 ! C5H5NO 4(1H)-pyridinone (CAS # 108-96-3), isg GROUP ATOM O1 OG2D4 -0.57 ATOM C1 CG2R63 0.46 ATOM C21 CG2R62 -0.38 ! H22 H32 ATOM C31 CG2R62 -0.07 ! | | ATOM N1 NG2R61 -0.11 ! C22==C32 ATOM C32 CG2R62 -0.07 ! / \ ATOM C22 CG2R62 -0.38 ! O1==C1 N1--H1 ATOM H21 HGR62 0.22 ! \ / ATOM H22 HGR62 0.22 ! C21==C31 ATOM H32 HGR62 0.20 ! | | ATOM H31 HGR62 0.20 ! H21 H31 ATOM H1 HGP1 0.28 BOND O1 C1 C1 C21 C21 H21 C21 C31 C31 H31 C31 N1 N1 H1 BOND N1 C32 C32 H32 C32 C22 C22 H22 C22 C1 IMPR C1 C21 C22 O1 IC C1 C22 C32 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C22 C32 N1 C31 0.0000 0.0000 0.0000 0.0000 0.0000 IC C32 N1 C31 C21 0.0000 0.0000 0.0000 0.0000 0.0000 IC C22 C21 *C1 O1 0.0000 0.0000 180.0000 0.0000 0.0000 IC C32 C1 *C22 H22 0.0000 0.0000 180.0000 0.0000 0.0000 IC C31 C1 *C21 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C22 *C32 H32 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C21 *C31 H31 0.0000 0.0000 180.0000 0.0000 0.0000 IC C32 C31 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 1PH4PO 0.00 ! C11H9NO 1-phenyl-4(1H)-pyridinone (CAS # 39076-91-0), isg GROUP ATOM O4 OG2D4 -0.570 ATOM C4 CG2R63 0.460 ATOM C3 CG2R62 -0.380 ATOM C2 CG2R62 -0.070 ATOM N1 NG2R67 -0.110 ATOM C6 CG2R62 -0.070 ATOM C5 CG2R62 -0.380 ATOM H3 HGR62 0.220 ! H5 H6 H8 H9 ATOM H5 HGR62 0.220 ! | | | | ATOM H6 HGR62 0.200 ! C5==C6 C8==C9 ATOM H2 HGR62 0.200 ! / \ / \ ATOM C7 CG2R67 0.280 ! O4==C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! C3==C2 C12--C11 ATOM C10 CG2R61 -0.115 ! | | | | ATOM C11 CG2R61 -0.115 ! H3 H2 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND O4 C4 C4 C3 C4 C5 C3 C2 C3 H3 C5 H5 C2 N1 C2 H2 C5 C6 BOND C6 H6 C6 N1 N1 C7 C7 C8 C7 C12 C12 C11 C12 H12 C8 C9 C8 H8 BOND C11 C10 C11 H11 C9 C10 C9 H9 C10 H10 IMPR C4 C3 C5 O4 IC C4 C5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5 C3 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 21QU 0.00 ! C9H7NO 2(1H)-quinolinone (CAS # 59-31-4), isg GROUP ATOM C1 CG2R61 -0.115 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R62 0.280 ATOM C5 CG2R62 -0.090 ! H6 H8 ATOM C6 CG2R61 -0.115 ! | | ATOM H11 HGP1 0.300 ! C6 C8 H9 ATOM C8 CG2R62 -0.200 ! // \ / \\ / ATOM C9 CG2R62 -0.180 ! H1--C1 C5 C9 ATOM C10 CG2R63 0.240 ! | || | ATOM N11 NG2R61 -0.260 ! H2--C2 C4 C10 ATOM H6 HGR61 0.115 ! \\ / \ / \\ ATOM H1 HGR61 0.115 ! C3 N11 O10 ATOM H2 HGR61 0.115 ! | | ATOM H3 HGR61 0.115 ! H3 H11 ATOM H8 HGR62 0.220 ATOM H9 HGR62 0.180 ATOM O10 OG2D4 -0.490 BOND O10 C10 N11 C10 N11 H11 N11 C4 C10 C9 H3 C3 H2 C2 C4 C3 BOND C4 C5 C3 C2 C2 C1 H9 C9 C9 C8 C1 H1 C1 C6 C5 C8 BOND C5 C6 C8 H8 C6 H6 IMPR C10 C9 N11 O10 IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C3 C5 *C4 N11 0.0000 0.00 179.00 0.00 0.0000 IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C5 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 RESI 1PH2PO 0.00 ! C11H9NO 1-phenyl-2(1H)-pyridinone (CAS # 13131-02-7), isg GROUP ATOM N1 NG2R67 -0.130 ATOM C2 CG2R63 0.160 ATOM O2 OG2D4 -0.480 ATOM C3 CG2R62 -0.260 ATOM H3 HGR62 0.220 ATOM C4 CG2R62 -0.220 ATOM H4 HGR62 0.220 ATOM C5 CG2R62 -0.220 ! H3 O2 H8 H9 ATOM H5 HGR62 0.150 ! | || | | ATOM C6 CG2R62 0.150 ! C3--C2 C8==C9 ATOM H6 HGR62 0.130 ! // \ / \ ATOM C7 CG2R67 0.280 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! C5==C6 C12--C11 ATOM C10 CG2R61 -0.115 ! | | | | ATOM C11 CG2R61 -0.115 ! H5 H6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 BOND C5 C6 C6 H6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 IMPR C2 C3 N1 O2 IC C4 C5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 3PHURA 0.00 ! C10H8N2O2 3-phenyl-2,4(1H,3H)-pyrimidinedione (CAS # 4260-40-6), isg GROUP ATOM N1 NG2R67 -0.530 ATOM C2 CG2R63 0.400 ATOM O2 OG2D4 -0.460 ATOM C3 CG2R62 -0.200 ATOM H3 HGR62 0.150 ATOM C4 CG2R62 0.110 ATOM H4 HGR62 0.180 ATOM N5 NG2R61 -0.370 ! H3 O2 H8 H9 ATOM H5 HGP1 0.350 ! | || | | ATOM C6 CG2R63 0.440 ! C3--C2 C8==C9 ATOM O6 OG2D4 -0.450 ! // \ / \ ATOM C7 CG2R67 0.380 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 ATOM C10 CG2R61 -0.115 ! | || | | ATOM C11 CG2R61 -0.115 ! H5 O6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 BOND N5 C6 C6 O6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 IMPR C2 C3 N1 O2 IMPR C6 N5 N1 O6 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 O6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI URA2S 0.00 ! C4H4N2OS 2,3-dihydro-2-thioxo-4(1H)pyrimidinone (CAS # 141-90-2), isg GROUP ATOM C2 CG2R63 -0.04 ATOM C4 CG2R63 0.52 ! O4 ATOM C5 CG2R62 -0.24 ! || ATOM C6 CG2R62 0.08 ! C4 H3 ATOM H1 HGP1 0.33 ! / \ / ATOM H3 HGP1 0.37 ! H5--C5 N3 ATOM H5 HGR62 0.17 ! || | ATOM H6 HGR62 0.20 ! H6--C6 C2 ATOM O4 OG2D4 -0.49 ! \ / \\ ATOM S2 SG2D1 -0.30 ! N1 S2 ATOM N1 NG2R61 -0.22 ! | ATOM N3 NG2R61 -0.38 ! H1 BOND C2 S2 C2 N1 C2 N3 C4 C5 C4 O4 C4 N3 BOND C5 C6 C5 H5 C6 H6 C6 N1 H1 N1 H3 N3 IMPR C2 N1 N3 S2 IMPR C4 C5 N3 O4 IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C5 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 3PH2SR 0.00 ! C10H8N2OS 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone (CAS # 53632-80-7), isg GROUP ATOM N1 NG2R67 -0.380 ATOM C2 CG2R63 0.520 ATOM O2 OG2D4 -0.490 ATOM C3 CG2R62 -0.240 ATOM H3 HGR62 0.170 ATOM C4 CG2R62 0.080 ATOM H4 HGR62 0.200 ATOM N5 NG2R61 -0.220 ! H3 O2 H8 H9 ATOM H5 HGP1 0.330 ! | || | | ATOM C6 CG2R63 -0.040 ! C3--C2 C8==C9 ATOM S6 SG2D1 -0.300 ! // \ / \ ATOM C7 CG2R67 0.370 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 ATOM C10 CG2R61 -0.115 ! | || | | ATOM C11 CG2R61 -0.115 ! H5 S6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 BOND N5 C6 C6 S6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 IMPR C2 C3 N1 O2 IMPR C6 N5 N1 S6 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 S6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI URA4S 0.00 ! C4H4N2OS 3,4-dihydro-4-thioxo-2(1H)-pyrimidinone (CAS # 591-28-6), isg GROUP ATOM C2 CG2R63 0.41 ATOM C4 CG2R63 0.11 ! S4 ATOM C5 CG2R62 -0.31 ! || ATOM C6 CG2R62 0.04 ! C4 H3 ATOM H1 HGP1 0.35 ! / \ / ATOM H3 HGP1 0.34 ! H5--C5 N3 ATOM H5 HGR62 0.20 ! || | ATOM H6 HGR62 0.23 ! H6--C6 C2 ATOM S4 SG2D1 -0.28 ! \ / \\ ATOM O2 OG2D4 -0.44 ! N1 O2 ATOM N1 NG2R61 -0.30 ! | ATOM N3 NG2R61 -0.35 ! H1 BOND C2 O2 C2 N1 C2 N3 C4 C5 C4 S4 C4 N3 C5 C6 BOND C5 H5 C6 H6 C6 N1 H1 N1 H3 N3 IMPR C2 N1 N3 O2 IMPR C4 C5 N3 S4 IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C5 *C4 S4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 3PH4SR 0.00 ! C10H8N2OS 2,3-dihydro-3-phenyl-2-oxo-4(1H)pyrimidinethione, isg GROUP ATOM N1 NG2R67 -0.350 ATOM C2 CG2R63 0.110 ATOM S2 SG2D1 -0.280 ATOM C3 CG2R62 -0.310 ATOM H3 HGR62 0.200 ATOM C4 CG2R62 0.040 ATOM H4 HGR62 0.230 ATOM N5 NG2R61 -0.300 ! H3 S2 H8 H9 ATOM H5 HGP1 0.350 ! | || | | ATOM C6 CG2R63 0.410 ! C3--C2 C8==C9 ATOM O6 OG2D4 -0.440 ! // \ / \ ATOM C7 CG2R67 0.340 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 ATOM C10 CG2R61 -0.115 ! | || | | ATOM C11 CG2R61 -0.115 ! H5 O6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C2 N1 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 BOND N5 C6 C6 O6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 IMPR C2 C3 N1 S2 IMPR C6 N5 N1 O6 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 O6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI URA24S 0.00 ! C4H4N2S2 2,4(1H,3H)-pyrimidinedithione (CAS # 2001-93-6), isg GROUP ATOM N1 NG2R61 -0.12 ATOM C2 CG2R63 -0.13 ! S4 ATOM N3 NG2R61 -0.17 ! || ATOM C4 CG2R63 0.04 ! C4 H3 ATOM C5 CG2R61 -0.17 ! / \ / ATOM C6 CG2R61 -0.06 ! H5--C5 N3 ATOM H1 HGP1 0.33 ! || | ATOM H3 HGP1 0.32 ! H6--C6 C2 ATOM H5 HGR62 0.19 ! \ / \\ ATOM H6 HGR62 0.26 ! N1 S2 ATOM S4 SG2D1 -0.26 ! | ATOM S2 SG2D1 -0.23 ! H1 BOND N1 H1 N1 C2 N1 C6 C2 S2 C2 N3 N3 H3 N3 C4 BOND C4 S4 C4 C5 C5 H5 C5 C6 C6 H6 IMPR C2 N1 N3 S2 IMPR C4 C5 N3 S4 IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C5 *C4 S4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 3PH24S 0.00 ! C10H8N2S2 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione, isg GROUP ATOM N1 NG2R67 -0.170 ATOM C2 CG2R63 0.040 ATOM S2 SG2D1 -0.260 ATOM C3 CG2R61 -0.170 ATOM H3 HGR62 0.190 ATOM C4 CG2R61 -0.060 ATOM H4 HGR62 0.260 ATOM N5 NG2R61 -0.120 ! H3 S2 H8 H9 ATOM H5 HGP1 0.330 ! | || | | ATOM C6 CG2R63 -0.130 ! C3--C2 C8==C9 ATOM S6 SG2D1 -0.230 ! // \ / \ ATOM C7 CG2R67 0.320 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \\ // ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 ATOM C10 CG2R61 -0.115 ! | || | | ATOM C11 CG2R61 -0.115 ! H5 S6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C2 N1 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 BOND N5 C6 C6 S6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 IMPR C2 C3 N1 S2 IMPR C6 N5 N1 S6 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 S6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 43HPY 0.00 ! C4H4N2O 4(3H)-pyrimidinone (CAS # 4562-27-0), isg GROUP ATOM C6 CG2R62 -0.21 ATOM C5 CG2R62 0.35 ! O1 ATOM N4 NG2R62 -0.76 ! || ATOM C3 CG2R64 0.42 ! C1 H2 ATOM N2 NG2R61 -0.30 ! / \ / ATOM H2 HGP1 0.33 ! H6--C6 N2 ATOM C1 CG2R63 0.21 ! || | ATOM O1 OG2D4 -0.46 ! H5--C5 C3 ATOM H6 HGR62 0.15 ! \ // \ ATOM H5 HGR62 0.11 ! N4 H3 ATOM H3 HGR62 0.16 BOND C6 C1 C6 C5 C6 H6 C5 N4 C5 H5 BOND N4 C3 C3 N2 C3 H3 N2 H2 N2 C1 C1 O1 IMPR C1 C6 N2 O1 IC C1 N2 C3 N4 0.0000 0.0000 0.0000 0.0000 0.0000 IC N2 C3 N4 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3 N4 C5 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC N2 C6 *C1 O1 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 C1 *N2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N4 N2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N4 C6 *C5 H5 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 43PPY 0.00 ! C10H8N2O 3-phenyl-4(3H)-pyrimidinone (CAS # 52090-51-4), isg GROUP ATOM N1 NG2R67 -0.300 ATOM C2 CG2R63 0.210 ATOM O2 OG2D4 -0.460 ATOM C3 CG2R62 -0.210 ATOM H3 HGR62 0.150 ATOM C4 CG2R62 0.350 ATOM H4 HGR62 0.110 ! H3 O2 H8 H9 ATOM N5 NG2R62 -0.760 ! \ // \ / ATOM C6 CG2R64 0.420 ! C3--C2 C8--C9 ATOM H6 HGR62 0.160 ! // \ // \\ ATOM C7 CG2R67 0.330 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \ / ATOM C9 CG2R61 -0.115 ! N5==C6 C12==C11 ATOM C10 CG2R61 -0.115 ! \ / \ ATOM C11 CG2R61 -0.115 ! H6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND N1 C7 N1 C2 N1 C6 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 N5 N5 C6 C6 H6 C7 C8 C8 H8 C8 C9 C9 H9 BOND C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 C12 C7 IMPR C2 C3 N1 O2 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 43HSPY 0.00 ! C4H4N2S 4(3H)-pyrimidinethione (CAS # 1450-86-8), isg GROUP ATOM C6 CG2R61 -0.03 ATOM C5 CG2R61 0.21 ! S1 ATOM N4 NG2R62 -0.73 ! || ATOM C3 CG2R64 0.59 ! C1 H2 ATOM N2 NG2R61 -0.24 ! / \ / ATOM H2 HGP1 0.32 ! H6--C6 N2 ATOM C1 CG2R63 -0.37 ! || | ATOM S1 SG2D1 -0.21 ! H5--C5 C3 ATOM H6 HGR62 0.16 ! \ // \ ATOM H5 HGR62 0.17 ! N4 H3 ATOM H3 HGR62 0.13 BOND C1 S1 C1 N2 C1 C6 N2 H2 N2 C3 BOND C3 H3 C3 N4 N4 C5 C5 H5 C5 C6 C6 H6 IMPR C1 C6 N2 S1 IC C1 N2 C3 N4 0.0000 0.0000 0.0000 0.0000 0.0000 IC N2 C3 N4 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3 N4 C5 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC N2 C6 *C1 S1 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 C1 *N2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N4 N2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N4 C6 *C5 H5 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case RESI 43HSPP 0.00 ! C10H8N2S 3-phenyl-4(3H)-pyrimidinethione, isg GROUP ATOM N1 NG2R67 -0.240 ATOM C2 CG2R63 -0.370 ATOM S2 SG2D1 -0.210 ATOM C3 CG2R61 -0.030 ATOM H3 HGR62 0.160 ATOM C4 CG2R61 0.210 ATOM H4 HGR62 0.170 ! H3 S2 H8 H9 ATOM N5 NG2R62 -0.730 ! \ // \ / ATOM C6 CG2R64 0.590 ! C3--C2 C8--C9 ATOM H6 HGR62 0.130 ! // \ // \\ ATOM C7 CG2R67 0.320 ! H4--C4 N1--C7 C10--H10 ATOM C8 CG2R61 -0.115 ! \ / \ / ATOM C9 CG2R61 -0.115 ! N5==C6 C12==C11 ATOM C10 CG2R61 -0.115 ! \ / \ ATOM C11 CG2R61 -0.115 ! H6 H12 H11 ATOM C12 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND N1 C7 N1 C2 N1 C6 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 N5 N5 C6 C6 H6 C7 C8 C8 H8 C8 C9 C9 H9 BOND C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 C12 C7 IMPR C2 C3 N1 S2 IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 4O2SM 0.00 ! C5H6N2OS 2-(methylthio)-4(3H)-pyrimidinone (CAS # 5751-20-2), isg GROUP ATOM N1 NG2R62 -0.76 ATOM C2 CG2R64 0.58 ! O4 ATOM N3 NG2R61 -0.30 ! || ATOM C4 CG2R63 0.21 ! C4 H3 ATOM C5 CG2R62 -0.21 ! / \ / ATOM C6 CG2R62 0.35 ! H5--C5 N3 ATOM H3 HGP1 0.33 ! || | ATOM H5 HGR62 0.15 ! H6--C6 C2 ATOM H6 HGR62 0.11 ! \ // \ ATOM O4 OG2D4 -0.46 ! N1 S2 ATOM S2 SG311 -0.07 ! | ATOM C7 CG331 -0.20 ! H72--C7--H73 ATOM H71 HGA3 0.09 ! | ATOM H72 HGA3 0.09 ! H71 ATOM H73 HGA3 0.09 BOND N1 C2 N1 C6 C2 S2 C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 H5 C5 C6 C6 H6 S2 C7 C7 H71 C7 H72 C7 H73 IMPR C4 C5 N3 O4 IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C5 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case IC N3 C2 S2 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 S2 C7 H71 0.0000 0.0000 60.0000 0.0000 0.0000 IC C2 S2 C7 H72 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C2 S2 C7 H73 0.0000 0.0000 180.0000 0.0000 0.0000 RESI 2SMPYR 0.00 ! C5H6N2S 2-(methylthio)-pyrimidine (CAS # 823-09-6), isg GROUP ATOM N1 NG2R62 -0.730 ATOM C2 CG2R64 0.640 ! H6 ATOM N3 NG2R62 -0.730 ! | ATOM C4 CG2R61 0.290 ! C6 ATOM C5 CG2R61 -0.115 ! / \\ ATOM C6 CG2R61 0.290 ! H5--C5 N1 ATOM H4 HGR62 0.120 ! || | ATOM H5 HGR61 0.115 ! H4--C4 C2 ATOM H6 HGR62 0.120 ! \ // \ ATOM S7 SG311 -0.070 ! N3 S7 ATOM C8 CG331 -0.200 ! | ATOM H81 HGA3 0.090 ! H81--C8--H83 ATOM H82 HGA3 0.090 ! | ATOM H83 HGA3 0.090 ! H82 BOND N1 C2 N1 C6 C2 S7 C2 N3 N3 C4 C4 H4 C4 C5 BOND C5 H5 C5 C6 C6 H6 S7 C8 C8 H81 C8 H82 C8 H83 IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 IC N3 C5 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4 C6 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC N1 N3 *C2 S7 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case IC N3 C2 S7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 S7 C8 H81 0.0000 0.0000 60.0000 0.0000 0.0000 IC C2 S7 C8 H82 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C2 S7 C8 H83 0.0000 0.0000 180.0000 0.0000 0.0000 RESI NZAD 0.00 ! C9H11NO N-benzylacetamide (CAS # 588-46-5), isg GROUP ATOM C1 CG2R61 0.000 ATOM C2 CG2R61 -0.115 ATOM C3 CG2R61 -0.115 ATOM C4 CG2R61 -0.115 ATOM C5 CG2R61 -0.115 ATOM C6 CG2R61 -0.115 ATOM H2 HGR61 0.115 ATOM H3 HGR61 0.115 ATOM H4 HGR61 0.115 ! H5 H6 O9 H102 ATOM H5 HGR61 0.115 ! | | \\ | ATOM H6 HGR61 0.115 ! C5==C6 H71 C9--C10--H103 GROUP ! / \ | / | ATOM C7 CG321 -0.020 ! H4--C4 C1--C7--N8 H101 ATOM H71 HGA2 0.090 ! \\ // | | ATOM H72 HGA2 0.090 ! C3--C2 H72 H8 ATOM N8 NG2S1 -0.470 ! | | ATOM H8 HGP1 0.310 ! H3 H2 ATOM C9 CG2O1 0.510 ATOM O9 OG2D1 -0.510 GROUP ATOM C10 CG331 -0.270 ATOM H101 HGA3 0.090 ATOM H102 HGA3 0.090 ATOM H103 HGA3 0.090 BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 BOND C5 C6 C6 H6 C6 C1 C1 C7 C7 H71 C7 H72 C7 N8 N8 H8 BOND N8 C9 C9 O9 C9 C10 C10 H101 C10 H102 C10 H103 IMPR C9 C10 N8 O9 IC C4 C5 C6 C1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5 C6 C1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 C1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 IC C6 C2 *C1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 C1 *C2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4 C6 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4 C2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 IC C5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 IC C6 C1 C7 N8 0.0000 0.0000 70.0000 0.0000 0.0000 ! Orig 180 IC C1 N8 *C7 H71 0.0000 0.0000 120.0000 0.0000 0.0000 ! Orig 60 IC C1 N8 *C7 H72 0.0000 0.0000 -120.0000 0.0000 0.0000 ! Orig -60 IC C1 C7 N8 C9 0.0000 0.0000 -90.0000 0.0000 0.0000 ! Orig 180 IC C7 C9 *N8 H8 0.0000 0.0000 -160.0000 0.0000 0.0000 ! Orig 180 IC C7 N8 C9 C10 0.0000 0.0000 180.0000 0.0000 0.0000 ! Orig 180 IC N8 C10 *C9 O9 0.0000 0.0000 -180.0000 0.0000 0.0000 ! Orig 180 IC N8 C9 C10 H101 0.0000 0.0000 -150.0000 0.0000 0.0000 ! Orig 90 IC H101 C9 *C10 H102 0.0000 0.0000 -120.0000 0.0000 0.0000 ! Orig -30 IC H101 C9 *C10 H103 0.0000 0.0000 120.0000 0.0000 0.0000 ! Orig 150 RESI NMSM -1.00 ! CH4NO3S N-methyl-sulfamate, my & kevo GROUP ATOM S1 SG3O1 0.62 ATOM O11 OG2P1 -0.50 ATOM O12 OG2P1 -0.50 ATOM O13 OG2P1 -0.50 ! O11 H21 H31 ATOM N2 NG2S3 -0.52 ! \\ | / ATOM H21 HGP1 0.33 ! (-) O12=S1--N2--C3--H32 ATOM C3 CG331 -0.20 ! // \ ATOM H31 HGA3 0.09 ! O13 H33 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND S1 O11 S1 O12 S1 O13 S1 N2 N2 H21 BOND N2 C3 C3 H31 C3 H32 C3 H33 IC S1 N2 C3 H31 0.0000 0.00 -60.42 0.00 0.0000 IC N2 H31 *C3 H32 0.0000 0.00 117.9 0.00 0.0000 IC N2 H31 *C3 H33 0.0000 0.00 -123.1 0.00 0.0000 IC H31 C3 N2 H21 0.0000 0.00 -176.0 0.00 0.0000 IC C3 N2 S1 O11 0.0000 0.00 -51.92 0.00 0.0000 IC N2 O11 *S1 O12 0.0000 0.00 -112.5 0.00 0.0000 IC N2 O11 *S1 O13 0.0000 0.00 110.8 0.00 0.0000 RESI NESM -1.00 ! C2H6NO3S N-ethyl-sulfamate, my GROUP ATOM S1 SG3O1 0.62 ATOM O11 OG2P1 -0.50 ATOM O12 OG2P1 -0.50 ATOM O13 OG2P1 -0.50 ATOM N2 NG2S3 -0.52 ! O11 H21 H31 H41 ATOM H21 HGP1 0.33 ! \\ | / / ATOM C3 CG321 -0.11 ! (-) O12=S1--N2--C3 -- C4 - H42 ATOM H31 HGA2 0.09 ! // \ \ ATOM H32 HGA2 0.09 ! O13 H32 H43 ATOM C4 CG331 -0.27 ATOM H41 HGA3 0.09 ATOM H42 HGA3 0.09 ATOM H43 HGA3 0.09 BOND S1 O11 S1 O12 S1 O13 S1 N2 N2 H21 N2 C3 BOND C3 H31 C3 H32 C3 C4 C4 H41 C4 H42 C4 H43 IC S1 N2 C3 H31 0.0000 0.00 -60.42 0.00 0.0000 IC N2 H31 *C3 H32 0.0000 0.00 117.9 0.00 0.0000 IC N2 H31 *C3 C4 0.0000 0.00 -126.1 0.00 0.0000 IC H31 C3 N2 H21 0.0000 0.00 -176.0 0.00 0.0000 IC C3 N2 S1 O11 0.0000 0.00 -51.92 0.00 0.0000 IC N2 O11 *S1 O12 0.0000 0.00 -112.5 0.00 0.0000 IC N2 O11 *S1 O13 0.0000 0.00 110.8 0.00 0.0000 IC N2 C3 C4 H41 0.0000 0.00 -58.51 0.00 0.0000 IC C3 H41 *C4 H42 0.0000 0.00 122.1 0.00 0.0000 IC C3 H41 *C4 H43 0.0000 0.00 -120.4 0.00 0.0000 RESI MESI 0.000 ! C3H10N2O2S N-methyl,N'-ethylsulfamide, rting GROUP ATOM C1 CG331 -0.02 ATOM N2 NG311 -0.63 ATOM H2 HGP1 0.37 ! H11 H2 O31 H4 H51 H61 ATOM H11 HGA3 0.09 ! | | || | | / ATOM H13 HGA3 0.09 ! H12-C1-N2-S3-N4-C5-C6-H62 ATOM H12 HGA3 0.09 ! | || | \ ATOM S3 SG3O2 0.80 ! H13 O32 H52 H63 ATOM N4 NG311 -0.50 ATOM H4 HGP1 0.33 ATOM C5 CG321 0.06 ATOM C6 CG331 -0.27 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 ATOM O31 OG2P1 -0.43 ATOM O32 OG2P1 -0.43 BOND C1 N2 C1 H11 C1 H13 C1 H12 N2 H2 BOND N2 S3 S3 N4 S3 O31 S3 O32 N4 H4 BOND N4 C5 C5 C6 C5 H51 C5 H52 C6 H61 C6 H62 C6 H63 IC C1 N2 S3 O32 1.46875 116.231 -165.443 104.674 1.46516 IC C1 N2 S3 O31 1.46875 116.231 -32.882 113.246 1.46416 IC C1 N2 S3 N4 1.46875 116.231 77.486 97.671 1.67030 IC N2 S3 N4 C5 1.66703 97.671 -162.329 116.007 1.47543 IC N2 S3 N4 H4 1.66703 97.671 69.008 108.612 1.02191 IC O31 S3 N4 H4 1.46416 105.323 -174.260 108.612 1.02191 IC O32 S3 N4 H4 1.46516 113.734 -47.774 108.612 1.02191 IC H51 C5 N4 H4 1.09138 106.498 -178.564 113.090 1.02191 IC H52 C5 N4 H4 1.09413 105.601 -64.441 113.090 1.02191 IC H51 C5 C6 H61 1.09138 111.162 -178.617 110.870 1.09423 IC H51 C5 C6 H62 1.09138 111.162 -58.335 111.115 1.09210 IC H51 C5 C6 H63 1.09138 111.162 61.785 110.137 1.09428 IC H52 C5 C6 H61 1.09413 110.839 61.859 110.870 1.09423 IC H52 C5 C6 H62 1.09413 110.839 -177.859 111.115 1.09210 IC H52 C5 C6 H63 1.09413 110.839 -57.738 110.137 1.09428 IC S3 N2 C1 H11 1.66703 116.231 -59.314 108.009 1.08999 IC S3 N2 C1 H12 1.66703 116.231 61.802 113.066 1.09416 IC S3 N2 C1 H13 1.66703 116.231 -176.624 107.554 1.09122 IC H2 N2 C1 H11 1.02043 114.022 175.001 108.009 1.08999 IC H2 N2 C1 H12 1.02043 114.022 -63.884 113.066 1.09416 IC H2 N2 C1 H13 1.02043 114.022 57.691 107.554 1.09416 IC S3 N4 C5 C6 1.67030 116.007 -68.483 114.796 1.52388 IC S3 N4 C5 H51 1.67030 116.007 54.992 106.498 1.09138 IC S3 N4 C5 H52 1.67030 116.007 169.115 105.601 1.09413 IC N4 C5 C6 H61 1.47543 114.796 -57.668 110.870 1.09423 IC N4 C5 C6 H62 1.47543 114.796 62.614 111.115 1.09210 IC N4 C5 C6 H63 1.47543 114.796 -177.165 110.137 1.09428 RESI NACT -1.000 ! C4H8NO4S N-acetyltaurine, xxwy GROUP ATOM S SG3O1 0.73 ATOM O1 OG2P1 -0.55 ATOM O2 OG2P1 -0.55 ! O1 ATOM O3 OG2P1 -0.55 ! | ATOM C1 CG321 -0.26 ! O2---S---O3 ATOM H11 HGA2 0.09 ! | ATOM H12 HGA2 0.09 ! H11-C1-H12 ATOM C2 CG321 -0.02 ! | ATOM H21 HGA2 0.09 ! H21-C2-H22 ATOM H22 HGA2 0.09 ! | ATOM N NG2S1 -0.47 ! N-H ATOM H HGP1 0.31 ! | ATOM C CG2O1 0.51 ! C=O ATOM O OG2D1 -0.51 ! | ATOM C3 CG331 -0.27 ! H31-C3-H32 ATOM H31 HGA3 0.09 ! | ATOM H32 HGA3 0.09 ! H33 ATOM H33 HGA3 0.09 BOND S O1 S O2 S O3 BOND S C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 N N C N H BOND C C3 C3 H31 C3 H32 BOND C3 H33 DOUBLE C O IMPR C C3 N O IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 IC S C1 C2 N 0.0 0.00 180.00 0.0 0.0 IC C1 N *C2 H21 0.0 0.00 120.00 0.0 0.0 IC C1 N *C2 H22 0.0 0.00 -120.00 0.0 0.0 IC C1 C2 N C 0.0 0.00 180.00 0.0 0.0 IC C C2 *N H 0.0 0.00 180.00 0.0 0.0 IC C2 N C C3 0.0 0.00 180.00 0.0 0.0 IC C3 N *C O 0.0 0.00 180.00 0.0 0.0 IC N C C3 H31 0.0 0.00 180.00 0.0 0.0 IC C H31 *C3 H32 0.0 0.00 120.00 0.0 0.0 IC C H31 *C3 H33 0.0 0.00 -120.00 0.0 0.0 PRES TAUR -1.00 ! C3H5NO4S taurine patch for bile acid, cacha & kevo ! patch combination: ! core residue cholic acid (CA) >> taurocholic acid (TCA) ! core residue deoxycholic acid (DCA) >> taurodeoxycholic acid (TDCA) ! core residue lithocholic acid (LCA) >> taurolithocholic acid (TLCA) ! core residue chenodeoxycholic acid (CDCA) >> taurochenodeoxycholic acid (TCDCA) ! core residue ursodeoxycholic acid (UDCA) >> tauroursodeoxycholic acid (TUDCA) DELETE ATOM OE2 ATOM CD CG2O1 0.51 ! OE1 O1S ATOM OE1 OG2D1 -0.51 ! || || ATOM N NG2S1 -0.47 ! OH Me21 C22 CD C1G S--O2S(-1) ATOM HN HGP1 0.31 ! | \ / \ / \ / \ / \\ ATOM C1G CG321 -0.02 ! C12 Me18 C20 C23 NH C2G O3S ATOM H1GA HGA2 0.09 ! / \ | / ATOM H1GB HGA2 0.09 ! C11 C13---C17 ATOM C2G CG321 -0.26 ! Me19 | | | ATOM H2GA HGA2 0.09 ! C1 | C9 C14 C16 ATOM H2GB HGA2 0.09 ! / \|/ \ / \ / ATOM S SG3O1 0.73 ! C2 C10 C8 C15 Taurocholic acid (TCA) ATOM O1S OG2P1 -0.55 ! | | | ATOM O2S OG2P1 -0.55 ! C3 C5 C7 ATOM O3S OG2P1 -0.55 ! / \ / \ / \ ! HO C4 C6 OH BOND CD N N HN BOND N C1G C1G H1GA C1G H1GB BOND C1G C2G C2G H2GA C2G H2GB BOND C2G S S O1S S O2S S O3S IMPR CD C23 N OE1 IC OE1 C23 *CD N 1.2243 119.69 -179.68 116.74 1.3409 IC C23 CD N C1G 1.5017 116.74 -179.30 126.20 1.4354 IC C1G CD *N HN 1.4354 126.20 179.36 118.75 0.9870 IC CD N C1G C2G 1.3409 126.20 178.33 109.02 1.5463 IC C2G N *C1G H1GA 1.5463 109.02 120.57 110.50 1.1164 IC H1GA N *C1G H1GB 1.1164 110.50 118.98 110.47 1.1166 IC N C1G C2G S 1.4354 109.02 -179.35 119.43 1.8188 IC S C1G *C2G H2GA 1.8188 119.43 121.46 108.45 1.1077 IC H2GA C1G *C2G H2GB 1.1077 108.45 116.91 108.50 1.1077 IC C1G C2G S O1S 1.5463 119.43 179.97 107.05 1.5726 IC O1S C2G *S O2S 1.5726 107.05 118.76 109.79 1.5714 IC O1S C2G *S O3S 1.5726 107.05 -118.67 109.74 1.5715 RESI MICY 0.00 ! C2H3NO methyl isocyanate, xxwy GROUP ATOM O OG2D5 -0.43 ATOM C CG2O7 0.68 ! H11 ATOM N NG2D1 -0.52 ! | ATOM C1 CG331 -0.00 ! H12--C1--N==C==O ATOM H11 HGA3 0.09 ! | ATOM H12 HGA3 0.09 ! H13 ATOM H13 HGA3 0.09 DOUBLE O C C N BOND C1 N BOND C1 H11 C1 H12 C1 H13 IC O C N C1 0.0000 0.00 180.00 0.00 0.0000 IC C N C1 H11 0.0000 0.00 180.00 0.00 0.0000 IC H11 N *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 N *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 ! Added to address gap in coverage - still eligible for future improvement RESI CO31 -1.00 ! CHO3 bicarbonate, xxwy & kevo ATOM C CG2O6 0.69 ! H3 O1 ATOM H3 HGP1 0.43 ! | / ATOM O1 OG2D2 -0.76 ! O3--C (-) ATOM O2 OG2D2 -0.76 ! \ ATOM O3 OG311 -0.60 ! O2 BOND C O1 C O2 C O3 O3 H3 IMPR C O1 O2 O3 ! seed = O1 C O2 IC O2 O1 *C O3 0.0000 0.00 180.00 0.00 0.0000 IC O1 C O3 H3 0.0000 0.00 0.00 0.00 0.0000 RESI GBL 0.00 ! C4H6O2 Gamma-butyrolactone (aka. oxolan-2-one which provided atom numbering), ctsai GROUP ATOM O1 OG3C51 -0.27 ATOM C2 CG2R53 0.15 ATOM O2 OG2D1 -0.39 ATOM C3 CG3C52 0.07 ! H41 H32 ATOM H31 HGA2 0.09 ! | | ATOM H32 HGA2 0.09 ! H42--C4--C3--H31 ATOM C4 CG3C52 -0.19 ! / \ ATOM H41 HGA2 0.09 ! H51--C5 C2 ATOM H42 HGA2 0.09 ! / \ / \\ ATOM C5 CG3C52 0.09 ! H52 O1 O2 ATOM H51 HGA2 0.09 ATOM H52 HGA2 0.09 BOND O1 C5 O1 C2 C2 C3 C2 O2 C3 C4 BOND C3 H31 C3 H32 C4 C5 C4 H41 C4 H42 BOND C5 H51 C5 H52 IMPR C2 C3 O2 O1 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 IC O1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 O1 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 O1 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 RESI B2FO 0.00 ! C4H4O2 5H-furan-2-one, ctsai GROUP ATOM O1 OG3C51 -0.31 ATOM C2 CG2R53 0.29 ATOM C3 CG2R51 -0.14 ! H3 H4 ATOM H3 HGR51 0.22 ! | | ATOM C4 CG2R51 -0.22 ! C3==C4 H51 ATOM H4 HGR51 0.22 ! / \ / ATOM C5 CG3C52 0.19 ! O6==C2 C5 ATOM H51 HGA2 0.09 ! \ / \ ATOM H52 HGA2 0.09 ! O1 H52 ATOM O6 OG2D1 -0.43 BOND O1 C2 O1 C5 C2 C3 C2 O6 C3 C4 BOND C3 H3 C4 C5 C4 H4 C5 H51 C5 H52 IMPR C2 C3 O6 O1 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 O1 *C2 O6 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 IC C4 O1 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 O1 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 RESI A2FO 0.00 ! C4H4O2 3H-furan-2-one, ctsai GROUP ATOM O1 OG3C51 -0.23 ATOM C2 CG2R53 0.30 ATOM C3 CG3C52 0.06 ! H31 H4 ATOM H31 HGA2 0.09 ! | / ATOM H32 HGA2 0.09 ! H32--C3--C4 ATOM C4 CG2R51 -0.28 ! / \\ ATOM H4 HGR51 0.21 ! C2 C5 ATOM C5 CG2R51 -0.05 ! // \ / \ ATOM H5 HGR52 0.21 ! O6 O1 H5 ATOM O6 OG2D1 -0.40 BOND O1 C2 O1 C5 C2 O6 C2 C3 C3 C4 BOND C3 H31 C3 H32 C4 C5 C4 H4 C5 H5 IMPR C2 C3 O6 O1 IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 O1 *C2 O6 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 120.00 0.00 0.0000 IC C4 O1 *C5 H5 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 ! 3.1 additions, Jul 15 RESI MT2A 0.00 ! C4H10N2S (Z)-N'-ethyl(methylsulfanyl)methanimidamide, fylin GROUP ATOM C1 CG331 -0.04 ATOM H11 HGA3 0.09 ATOM H12 HGA3 0.09 ! H13 ATOM H13 HGA3 0.09 ! | ATOM S2 SG311 -0.29 ! H11- C1 -S2 H41 ATOM C3 CG2N2 0.56 ! | \ / ATOM N4 NG321 -0.96 ! H12 C3 - N4 ATOM H41 HGPAM2 0.43 ! || \ ATOM H42 HGPAM2 0.43 ! N5 H42 ATOM N5 NG2D1 -0.60 ! / ATOM C6 CG321 0.02 ! H61 - C6 - H62 ATOM H61 HGA2 0.09 ! | ATOM H62 HGA2 0.09 ! H71 - C7 - H72 ATOM C7 CG331 -0.27 ! | ATOM H71 HGA3 0.09 ! H73 ATOM H72 HGA3 0.09 ATOM H73 HGA3 0.09 BOND C1 H11 C1 H12 C1 H13 C1 S2 S2 C3 BOND C3 N4 N4 H41 N4 H42 C3 N5 BOND N5 C6 C6 H61 C6 H62 BOND C6 C7 C7 H71 C7 H72 C7 H73 IMPR C3 N5 N4 S2 IC C1 S2 C3 N5 0.0000 0.00 0.00 0.00 0.0000 IC C3 S2 C1 H13 0.0000 0.00 150.00 0.00 0.0000 IC S2 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 IC S2 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 IC S2 N5 *C3 N4 0.0000 0.00 180.00 0.00 0.0000 IC S2 C3 N4 H41 0.0000 0.00 120.00 0.00 0.0000 IC S2 C3 N4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC S2 C3 N5 C6 0.0000 0.00 165.00 0.00 0.0000 IC C3 N5 C6 C7 0.0000 0.00 155.00 0.00 0.0000 IC N5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC N5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC N5 C6 C7 H73 0.0000 0.00 -120.00 0.00 0.0000 IC C6 H73 *C7 H71 0.0000 0.00 55.00 0.00 0.0000 IC C6 H73 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 RESI DH3T 0.00 ! C4H8N2S 5,6-dihydro-4H-1,3-thiazin-2-amine, fylin GROUP ATOM S1 SG311 -0.29 ATOM C2 CG2N2 0.56 ATOM N3 NG321 -0.96 ! H31 ATOM H31 HGPAM2 0.43 ! | ATOM H32 HGPAM2 0.43 ! H71 S1 N3-H32 ATOM N4 NG2D1 -0.60 ! \ / \ / ATOM C5 CG321 0.02 ! H72-C7 C2 ATOM H51 HGA2 0.09 ! | || ATOM H52 HGA2 0.09 ! H61-C6 N4 ATOM C6 CG321 -0.18 ! / \ / ATOM H61 HGA2 0.09 ! H62 C5 ATOM H62 HGA2 0.09 ! / \ ATOM C7 CG321 0.05 ! H51 H52 ATOM H71 HGA2 0.09 ATOM H72 HGA2 0.09 BOND S1 C2 S1 C7 C2 N3 C2 N4 N3 H31 N3 H32 BOND N4 C5 C5 H51 C5 H52 C5 C6 C6 H61 C6 H62 BOND C6 C7 C7 H71 C7 H72 IMPR C2 N4 N3 S1 IC S1 C2 N4 C5 0.0000 0.00 65.00 0.00 0.0000 IC C2 N4 C5 C6 0.0000 0.00 -10.00 0.00 0.0000 IC N4 C2 S1 C7 0.0000 0.00 -30.00 0.00 0.0000 IC S1 N4 *C2 N3 0.0000 0.00 180.00 0.00 0.0000 IC S1 C2 N3 H31 0.0000 0.00 0.00 0.00 0.0000 IC C2 H31 *N3 H32 0.0000 0.00 180.00 0.00 0.0000 IC N4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC N4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C6 S1 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC C6 S1 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 RESI EEPI 0.00 ! C5H11N (E)-ethylidene(propyl)amine, fylin GROUP ATOM C1 CG331 -0.27 ATOM C2 CG321 -0.18 ATOM C3 CG321 0.04 ATOM N4 NG2D1 -0.60 ATOM C5 CG2D1 0.23 ATOM C6 CG331 -0.27 ATOM H11 HGA3 0.09 ! H13 H21 H32 H51 H61 ATOM H12 HGA3 0.09 ! | | | | | ATOM H13 HGA3 0.09 ! H12-C1--C2--C3--N4=C5--C6--H63 (trans) ATOM H21 HGA2 0.09 ! | | | | ATOM H22 HGA2 0.09 ! H11 H22 H31 H62 ATOM H31 HGA2 0.09 ATOM H32 HGA2 0.09 ATOM H51 HGA4 0.15 ATOM H61 HGA3 0.09 ATOM H62 HGA3 0.09 ATOM H63 HGA3 0.09 BOND C1 C2 C2 C3 C3 N4 N4 C5 BOND C5 C6 C5 H51 C1 H11 C1 H12 BOND C1 H13 C2 H21 C2 H22 C3 H31 BOND C3 H32 C6 H61 C6 H62 C6 H63 IMPR C5 C6 N4 H51 IC C1 C2 C3 N4 0.0000 0.00 165.00 0.00 0.0000 IC H11 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC H12 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 IC H13 C1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 IC H21 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 IC H22 C2 C3 N4 0.0000 0.00 -60.00 0.00 0.0000 IC C2 C3 N4 C5 0.0000 0.00 155.00 0.00 0.0000 IC H31 C3 N4 C5 0.0000 0.00 60.00 0.00 0.0000 IC H32 C3 N4 C5 0.0000 0.00 -60.00 0.00 0.0000 IC C3 N4 C5 H51 0.0000 0.00 0.00 0.00 0.0000 IC C3 N4 C5 C6 0.0000 0.00 170.00 0.00 0.0000 IC N4 C5 C6 H61 0.0000 0.00 160.00 0.00 0.0000 IC N4 C5 C6 H62 0.0000 0.00 60.00 0.00 0.0000 IC N4 C5 C6 H63 0.0000 0.00 -60.00 0.00 0.0000 RESI PYRH 1.00 ! C4H5N2 pyrimidin-1-ium, fylin GROUP ATOM N1 NG2R62 -0.49 ATOM C2 CG2R62 0.38 ! H5 H6 ATOM N3 NG2R61 -0.53 ! \ ___ / ATOM C4 CG2R62 0.24 ! C5---C6 ATOM C5 CG2R62 0.08 ! / \ ATOM C6 CG2R62 0.11 ! H4--C4 N1 ATOM H3 HGP2 0.46 ! \\ // ATOM H2 HGR63 0.23 ! N3---C2 ATOM H4 HGR63 0.19 ! /(+1) \ ATOM H6 HGR63 0.22 ! H3 H2 ATOM H5 HGR63 0.11 BOND N1 C2 N1 C6 C2 N3 N3 C4 C4 C5 C5 C6 BOND N3 H3 C2 H2 C4 H4 C6 H6 C5 H5 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 RESI PIUM 1.00 ! C5H6N pyridin-1-ium, fylin GROUP ATOM C1 CG2R62 0.15 ATOM C5 CG2R62 0.15 ! H3 ATOM H1 HGR63 0.20 ! | ATOM H5 HGR63 0.20 ! C3 ATOM C2 CG2R62 -0.09 ! / \\ ATOM C4 CG2R62 -0.09 ! H4--C4 C2--H2 ATOM H2 HGR63 0.18 ! || | ATOM H4 HGR63 0.18 ! H5--C5 C1--H1 ATOM C3 CG2R62 -0.19 ! \+// ATOM H3 HGR63 0.25 ! N6 ATOM N6 NG2R61 -0.35 ! | ATOM H6 HGP2 0.41 ! H6 BOND C1 C2 C1 N6 C1 H1 C2 C3 C2 H2 C3 C4 BOND C3 H3 C4 C5 C4 H4 C5 N6 C5 H5 N6 H6 IC N6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.000 IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.000 IC N6 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.000 IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.000 RESI PYO2B 0.000 ! C11H9NO 4-phenyl-1,2-dihydropyridin-2-one, fylin GROUP ATOM C1 CG2R63 0.16 ! H5 H4 H13 H12 ATOM C2 CG2R62 -0.26 ! \ / \ / ATOM C3 CG2R67 0.00 ! C5 = C4 C13-C12 ATOM C4 CG2R62 -0.22 ! / \ // \\ ATOM C5 CG2R62 0.15 ! H6-N6 C3---C8 C11-H11 ATOM N6 NG2R61 -0.13 ! \ // \ / ATOM C9 CG2R61 -0.115 ! C1--C2 C9=C10 ATOM C10 CG2R61 -0.115 ! // \ / \ ATOM C11 CG2R61 -0.115 ! O7 H2 H9 H10 ATOM C12 CG2R61 -0.115 ATOM C13 CG2R61 -0.115 ATOM C8 CG2R67 0.00 ATOM O7 OG2D4 -0.48 ATOM H2 HGR62 0.22 ATOM H4 HGR62 0.15 ATOM H5 HGR62 0.13 ATOM H6 HGP1 0.28 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 ATOM H13 HGR61 0.115 BOND C1 C2 C1 N6 C2 C3 C3 C4 C4 C5 C5 N6 BOND C9 C10 C9 C8 C10 C11 C11 C12 C12 C13 C13 C8 BOND C3 C8 C1 O7 C2 H2 C4 H4 C5 H5 N6 H6 BOND C9 H9 C10 H10 C11 H11 C12 H12 C13 H13 IMPR C1 C2 N6 O7 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N6 C2 *C1 O7 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C8 C9 0.0000 0.00 -40.00 0.00 0.0000 IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 RESI PYO3B 0.000 ! C11H9NO 5-phenyl-1,2-dihydropyridin-2-one, fylin GROUP ATOM N1 NG2R61 -0.13 ! H5 H4 H13 H12 ATOM C2 CG2R62 0.15 ! \ / \ / ATOM C3 CG2R67 -0.07 ! C5 = C4 C13-C12 ATOM C4 CG2R62 -0.22 ! / \ // \\ ATOM C5 CG2R62 -0.26 ! O7=C6 C3---C8 C11-H11 ATOM C6 CG2R63 0.16 ! \ // \ / ATOM C9 CG2R61 -0.115 ! N1--C2 C9=C10 ATOM C10 CG2R61 -0.115 ! // \ / \ ATOM C11 CG2R61 -0.115 ! H1 H2 H9 H10 ATOM C12 CG2R61 -0.115 ATOM C13 CG2R61 -0.115 ATOM C8 CG2R67 0.00 ATOM H2 HGR62 0.13 ATOM H4 HGR62 0.22 ATOM H5 HGR62 0.22 ATOM O7 OG2D4 -0.48 ATOM H9 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 ATOM H13 HGR61 0.115 ATOM H1 HGP1 0.28 BOND N1 C2 N1 C6 C2 C3 C3 C4 C4 C5 C5 C6 BOND C9 C10 C9 C8 C10 C11 C11 C12 C12 C13 C13 C8 BOND C3 C8 C2 H2 C4 H4 C5 H5 C6 O7 C9 H9 BOND C10 H10 C11 H11 C12 H12 C13 H13 N1 H1 IMPR C6 C5 N1 O7 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 O7 0.0000 0.00 180.00 0.00 0.0000 IC C6 C2 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 RESI PIUB 1.000 ! C11H10N 4-phenylpyridine, fylin GROUP ! transfr ATOM C1 CG2R62 0.15 ATOM N2 NG2R61 -0.35 ! H1 H6 H12 H11 ATOM C3 CG2R62 0.15 ! \ / \ / ATOM C4 CG2R62 -0.09 ! C1--C6 C12-C11 ATOM C5 CG2R67 0.06 ! // \\ // \\ ATOM C6 CG2R62 -0.09 ! H2-N2+ C5 ---C7 C10-H10 ATOM C7 CG2R67 0.00 ! \ / \ / ATOM C8 CG2R61 -0.115 ! C3=C4 C8=C9 ATOM C12 CG2R61 -0.115 ! / \ / \ ATOM C11 CG2R61 -0.115 ! H3 H4 H8 H9 ATOM C10 CG2R61 -0.115 ATOM C9 CG2R61 -0.115 ATOM H2 HGP2 0.41 ATOM H1 HGR63 0.20 ATOM H3 HGR63 0.20 ATOM H4 HGR63 0.18 ATOM H6 HGR63 0.18 ATOM H8 HGR61 0.115 ATOM H12 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H10 HGR61 0.115 ATOM H9 HGR61 0.115 BOND C1 N2 C1 C6 N2 C3 C3 C4 C4 C5 C5 C6 BOND C5 C7 C12 C11 C11 C10 C10 C9 C8 C9 C8 C7 BOND C7 C12 N2 H2 C1 H1 C3 H3 C4 H4 C6 H6 BOND C8 H8 C12 H12 C11 H11 C10 H10 C9 H9 IC C1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.000 IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.000 IC C5 C6 C1 N2 0.0000 0.00 0.00 0.00 0.000 IC C6 C1 N2 C3 0.0000 0.00 0.00 0.00 0.000 IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.000 IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.000 IC C6 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 IC C1 C3 *N2 H2 0.0000 0.00 180.00 0.00 0.000 IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 RESI PYO2F 0.000 ! C11H8FNO 4-(2-fluorophenyl)-1,2-dihydropyridin-2-one, fylin GROUP ! CHARGE ATOM C1 CG2R63 0.16 ATOM C2 CG2R62 -0.26 ! H5 H4 H13 H12 ATOM C3 CG2R67 0.00 ! \ / \ / ATOM C4 CG2R62 -0.22 ! C5 = C4 C13-C12 ATOM C5 CG2R62 0.15 ! / \ // \\ ATOM N6 NG2R61 -0.13 ! H6-N6 C3---C8 C11-H11 ATOM O7 OG2D4 -0.48 ! \ // \ / ATOM C8 CG2R67 0.185 ! C1--C2 C9=C10 ATOM C9 CG2R66 0.10 ! // \ / \ ATOM C10 CG2R61 -0.13 ! O7 H2 F9 H10 ATOM C11 CG2R61 -0.18 ATOM C12 CG2R61 -0.10 ATOM C13 CG2R61 -0.18 ATOM H2 HGR62 0.22 ATOM H4 HGR62 0.15 ATOM H5 HGR62 0.13 ATOM H6 HGP1 0.28 ATOM F9 FGR1 -0.23 ATOM H10 HGR62 0.19 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 ATOM H13 HGR61 0.115 BOND C1 C2 C1 N6 C1 O7 C2 C3 C2 H2 C3 C4 BOND C3 C8 C4 C5 C4 H4 C5 N6 C5 H5 N6 H6 BOND C8 C9 C8 C13 C9 C10 C9 F9 C10 C11 C10 H10 BOND C11 C12 C11 H11 C12 C13 C12 H12 C13 H13 IMPR C1 C2 N6 O7 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 IC N6 C2 *C1 O7 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C8 C9 0.0000 0.00 -40.00 0.00 0.0000 IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 *C9 F9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 RESI PYO3F 0.000 ! C11H8FNO 5-(2-fluorophenyl)-1,2-dihydropyridin-2-one, fylin GROUP ! CHARGE ATOM N1 NG2R61 -0.13 ATOM C2 CG2R62 0.15 ! H5 H4 H13 H12 ATOM C3 CG2R67 -0.07 ! \ / \ / ATOM C4 CG2R62 -0.22 ! C5 = C4 C13-C12 ATOM C5 CG2R62 -0.26 ! / \ // \\ ATOM C6 CG2R63 0.16 ! O7=C6 C3---C8 C11-H11 ATOM O7 OG2D4 -0.48 ! \ // \ / ATOM C8 CG2R67 0.185 ! N1--C2 C9=C10 ATOM C9 CG2R66 0.10 ! // \ / \ ATOM C10 CG2R61 -0.13 ! H1 H2 F9 H10 ATOM C11 CG2R61 -0.18 ATOM C12 CG2R61 -0.10 ATOM C13 CG2R61 -0.18 ATOM H1 HGP1 0.28 ATOM H2 HGR62 0.13 ATOM H4 HGR62 0.22 ATOM H5 HGR62 0.22 ATOM F9 FGR1 -0.23 ATOM H10 HGR62 0.19 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 ATOM H13 HGR61 0.115 BOND N1 C2 N1 C6 N1 H1 C2 C3 C2 H2 C3 C4 BOND C3 C8 C4 C5 C4 H4 C5 C6 C5 H5 C6 O7 BOND C8 C13 C8 C9 C9 C10 C9 F9 C10 C11 C10 H10 BOND C11 C12 C11 H11 C12 C13 C12 H12 C13 H13 IMPR C6 C5 N1 O7 IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 O7 0.0000 0.00 180.00 0.00 0.0000 IC C6 C2 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C8 C9 0.0000 0.00 0.00 0.00 0.0000 IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 *C9 F9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 RESI PIUF 1.000 ! C11H9FN 4-(2-fluorophenyl)pyridine, fylin GROUP ! CHARGE ATOM C1 CG2R62 0.15 ATOM N2 NG2R61 -0.35 ! H1 H6 H12 H11 ATOM C3 CG2R62 0.15 ! \ / \ / ATOM C4 CG2R62 -0.09 ! C1--C6 C12-C11 ATOM C5 CG2R67 0.06 ! // \\ // \\ ATOM C6 CG2R62 -0.09 ! H2-N2+ C5 ---C7 C10-H10 ATOM C7 CG2R67 0.185 ! \ / \ / ATOM C8 CG2R66 0.10 ! C3=C4 C8=C9 ATOM C9 CG2R61 -0.13 ! / \ / \ ATOM C10 CG2R61 -0.18 ! H3 H4 F8 H9 ATOM C11 CG2R61 -0.10 ATOM C12 CG2R61 -0.18 ATOM H1 HGR63 0.20 ATOM H2 HGP2 0.41 ATOM H3 HGR63 0.20 ATOM H4 HGR63 0.18 ATOM H6 HGR63 0.18 ATOM F8 FGR1 -0.23 ATOM H9 HGR62 0.19 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND C1 N2 C1 C6 C1 H1 N2 C3 N2 H2 C3 C4 BOND C3 H3 C4 C5 C4 H4 C5 C6 C5 C7 C6 H6 BOND C7 C12 C7 C8 C8 C9 C8 F8 C9 C10 C9 H9 BOND C10 C11 C10 H10 C11 C12 C11 H11 C12 H12 IC C1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.000 IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.000 IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.000 IC C5 C6 C1 N2 0.0000 0.00 0.00 0.00 0.000 IC C6 C1 N2 C3 0.0000 0.00 0.00 0.00 0.000 IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.000 IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.000 IC C6 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 IC C1 C3 *N2 H2 0.0000 0.00 180.00 0.00 0.000 IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 IC C7 C9 *C8 F8 0.0000 0.00 180.00 0.00 0.000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 RESI PYRF 1.000 ! C10H8FN2 5-(2-fluorophenyl)pyrimidin-2-yl, fylin GROUP ! CHARGE ATOM N1 NG2R62 -0.49 ATOM C2 CG2R62 0.38 ! H6 H12 H11 ATOM N3 NG2R61 -0.53 ! / \ / ATOM C4 CG2R62 0.24 ! N1 == C6 C12--C11 ATOM C5 CG2R67 0.19 ! / \ // \\ ATOM C6 CG2R62 0.11 ! H2-C2 C5 ---C7 C10-H10 ATOM C7 CG2R67 0.185 ! \\ // \ / ATOM C8 CG2R66 0.10 ! (+1)N3--C4 C8=C9 ATOM C9 CG2R61 -0.13 ! / \ / \ ATOM C10 CG2R61 -0.18 ! H3 H4 F8 H9 ATOM C11 CG2R61 -0.10 ATOM C12 CG2R61 -0.18 ATOM H2 HGR63 0.23 ATOM H3 HGP2 0.46 ATOM H4 HGR63 0.19 ATOM H6 HGR63 0.22 ATOM F8 FGR1 -0.23 ATOM H9 HGR62 0.19 ATOM H10 HGR61 0.115 ATOM H11 HGR61 0.115 ATOM H12 HGR61 0.115 BOND N1 C2 N1 C6 C2 N3 C2 H2 N3 C4 N3 H3 BOND C4 C5 C4 H4 C5 C6 C5 C7 C6 H6 C7 C8 BOND C7 C12 C8 C9 C8 F8 C9 C10 C9 H9 C10 C11 BOND C10 H10 C11 C12 C11 H11 C12 H12 IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 IC C7 C9 *C8 F8 0.0000 0.00 180.00 0.00 0.000 IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 RESI BTMC 0.00 ! C7H11N3O N4,N4,-O-trimethylcytosine, yxu GROUP ATOM N1 NG2R61 -0.03 ATOM C2 CG2R63 0.57 ATOM O2 OG2D4 -0.52 ! H73 H83 ATOM N3 NG2R62 -0.74 ! \ / ATOM C4 CG2R64 0.60 ! H72-C7 C8-H82 ATOM N4 NG301 -0.37 ! / \ / \ ATOM C5 CG2R62 -0.18 ! H71 N4 H81 ATOM H5 HGR62 0.03 ! | ATOM C6 CG2R62 0.11 ! C4 ATOM H6 HGR62 0.13 ! / \\ ATOM C7 CG331 -0.07 ! H5-C5 N3 ATOM H71 HGA3 0.09 ! || | ATOM H72 HGA3 0.09 ! H6-C6 C2 ATOM H73 HGA3 0.09 ! \ / \\ ATOM C8 CG331 -0.07 ! N1 O2 ATOM H81 HGA3 0.09 ! \ ATOM H82 HGA3 0.09 ! \ ATOM H83 HGA3 0.09 ! \ GROUP ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CM HM1 CM HM2 CM HM3 BOND N1 C2 N1 C6 C2 O2 C2 N3 BOND N3 C4 C4 C5 C4 N4 N4 C7 BOND N4 C8 C7 H71 C7 H72 C7 H73 BOND C8 H81 C8 H82 C8 H83 C5 C6 BOND C5 H5 C6 H6 BOND CM N1 IMPR C2 N1 N3 O2 C4 C5 N3 N4 ACCE O2 C2 ACCE N3 IC C2 C6 *N1 CM 1.4228 119.21 179.94 121.44 1.4761 IC C6 N1 C2 N3 1.3609 119.21 -0.05 119.30 1.3580 IC N3 N1 *C2 O2 1.3580 119.30 -179.92 118.95 1.2300 IC N1 C2 N3 C4 1.4228 119.30 0.02 121.89 1.3575 IC C2 N3 C4 N4 1.3580 121.89 179.99 119.16 1.3747 IC N4 N3 *C4 C5 1.3747 119.16 -179.98 119.18 1.4365 IC C6 C4 *C5 H5 1.3659 118.58 179.99 122.05 1.0892 IC C5 N1 *C6 H6 1.3659 121.84 -179.99 116.76 1.0899 IC N3 C4 N4 C7 1.3575 119.16 170.00 121.80 1.4600 IC C7 C4 *N4 C8 1.4600 121.80 -160.00 120.54 1.4628 IC C4 N4 C7 H71 1.3747 121.80 -179.87 111.57 1.1122 IC H71 N4 *C7 H72 1.1122 111.57 119.71 111.21 1.1131 IC H71 N4 *C7 H73 1.1122 111.57 -119.64 111.21 1.1146 IC C4 N4 C8 H81 1.3747 120.54 -179.93 112.02 1.1111 IC H81 N4 *C8 H82 1.1111 112.02 120.29 111.11 1.1140 IC H81 N4 *C8 H83 1.1111 112.02 -120.18 111.05 1.1147 IC C6 N1 CM HM1 1.3609 121.44 120.78 110.62 1.1145 IC HM1 N1 *CM HM2 1.1145 110.62 118.50 110.67 1.1148 IC HM1 N1 *CM HM3 1.1145 110.62 -120.76 112.73 1.1124 RESI BM6A 0.00 ! C8H11N5 N6,N6-dimethyladenosine, MA6, DMA, yxu GROUP ATOM N9 NG2R51 -0.01 ATOM C8 CG2R53 0.31 ATOM H8 HGR52 0.09 ATOM N7 NG2R50 -0.67 ATOM C5 CG2RC0 0.41 ATOM C6 CG2R64 0.52 ! H91 H101 ATOM N6 NG301 -0.53 ! \ / ATOM N1 NG2R62 -0.69 ! H92 -C9 C10-H102 ATOM C2 CG2R64 0.57 ! / \ / \ ATOM H2 HGR62 0.08 ! H93 N6 H103 ATOM N3 NG2R62 -0.87 ! | ATOM C4 CG2RC0 0.43 ! C6 ATOM C9 CG331 -0.09 ! // \ ATOM H91 HGA3 0.09 ! N1 C5--N7\\ ATOM H92 HGA3 0.09 ! | || C8-H8 ATOM H93 HGA3 0.09 ! C2 C4--N9/ ATOM C10 CG331 -0.09 ! / \\ / \ ATOM H101 HGA3 0.09 ! H2 N3 \ ATOM H102 HGA3 0.09 ! \ ATOM H103 HGA3 0.09 ! \ GROUP ATOM CM CG331 -0.27 ATOM HM1 HGA3 0.09 ATOM HM2 HGA3 0.09 ATOM HM3 HGA3 0.09 BOND CM HM1 CM HM2 CM HM3 BOND N9 C8 N9 C4 C8 N7 C8 H8 BOND N7 C5 C5 C6 C5 C4 C6 N6 BOND C6 N1 N6 C10 N6 C9 N1 C2 BOND C2 N3 C2 H2 N3 C4 C10 H101 BOND C10 H102 C10 H103 C9 H91 C9 H92 BOND C9 H93 BOND CM N9 IMPR C6 C5 N1 N6 ACCE N3 ACCE N7 ACCE N1 IC C8 C4 *N9 CM 1.3791 106.12 -179.87 126.32 1.4712 IC C4 N9 C8 N7 1.3828 106.12 0.04 113.88 1.3241 IC N7 N9 *C8 H8 1.3241 113.88 -179.96 121.51 1.0919 IC N9 C8 N7 C5 1.3791 113.88 0.03 103.97 1.4048 IC C4 N7 *C5 C6 1.4035 110.12 -179.72 133.42 1.4200 IC N7 C5 C6 N6 1.4048 133.42 0.69 126.34 1.3855 IC N6 C5 *C6 N1 1.3855 126.34 177.74 117.19 1.3810 IC C5 C6 N1 C2 1.4200 117.19 1.71 121.05 1.3551 IC C6 N1 C2 N3 1.3810 121.05 -1.00 124.74 1.3537 IC N3 N1 *C2 H2 1.3537 124.74 -179.63 117.62 1.0920 IC C5 C6 N6 C10 1.4200 126.34 166.31 121.38 1.4628 IC C10 C6 *N6 C9 1.4628 121.38 177.05 122.46 1.4607 IC C6 N6 C9 H91 1.3855 122.46 -165.22 111.64 1.1121 IC H91 N6 *C9 H92 1.1121 111.64 119.65 111.59 1.1136 IC H91 N6 *C9 H93 1.1121 111.64 -120.01 111.04 1.1137 IC C6 N6 C10 H101 1.3855 121.38 -169.68 111.73 1.1118 IC H101 N6 *C10 H102 1.1118 111.73 119.69 111.45 1.1139 IC H101 N6 *C10 H103 1.1118 111.73 -120.15 110.95 1.1142 IC C4 N9 CM HM1 1.3828 126.32 58.88 110.04 1.1126 IC HM1 N9 *CM HM2 1.1126 110.04 120.79 112.49 1.1119 IC HM1 N9 *CM HM3 1.1126 110.04 -118.33 110.07 1.1124 RESI DMAN 0.00 ! C8H11N N,N-dimethylaniline, sc & kevo GROUP ATOM C1 CG2R61 -0.115 ATOM H1 HGR61 0.115 ATOM C2 CG2R61 -0.115 ! H3 ATOM H2 HGR61 0.115 ! | ATOM C3 CG2R61 -0.115 ! C3 ATOM H3 HGR61 0.115 ! / \\ ATOM C4 CG2R61 -0.115 ! H2--C2 C4--H4 ATOM H4 HGR61 0.115 ! || | ATOM C5 CG2R61 -0.115 ! || | ATOM H5 HGR61 0.115 ! H1--C1 C5--H5 ATOM C6 CG2R61 0.13 ! \ // ATOM N1 NG301 -0.49 ! C6 ATOM C7 CG331 -0.09 ! | ATOM H71 HGA3 0.09 ! N1 ATOM H72 HGA3 0.09 ! / \ ATOM H73 HGA3 0.09 ! H71--C7 C8--H83 ATOM C8 CG331 -0.09 ! / \ / \ ATOM H81 HGA3 0.09 ! / \ / \ ATOM H82 HGA3 0.09 ! H72 H73 H81 H82 ATOM H83 HGA3 0.09 BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 BOND C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 BOND C7 H71 C7 H72 C7 H73 C8 H81 C8 H82 C8 H83 BOND C6 N1 C7 N1 C8 N1 IC C6 N1 C7 H71 0.0000 0.00 180.00 0.00 0.0000 IC N1 H71 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 IC N1 H71 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C7 *N1 C8 0.0000 0.00 -140.00 0.00 0.0000 IC C6 N1 C8 H81 0.0000 0.00 180.00 0.00 0.0000 IC N1 H81 *C8 H82 0.0000 0.00 120.00 0.00 0.0000 IC N1 H81 *C8 H83 0.0000 0.00 -120.00 0.00 0.0000 IC C7 N1 C6 C1 0.0000 0.00 170.00 0.00 0.0000 IC N1 C1 *C6 C5 0.0000 0.00 180.00 0.00 0.0000 IC C1 C6 C5 C4 0.0000 0.00 0.00 0.00 0.0000 IC C5 C6 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C6 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 RESI OXTN 0.00 ! C3H6O oxetane, gmu GROUP ATOM C1 CG3C41 -0.035 ATOM H4 HGA2 0.090 ! H4 H8 ATOM H5 HGA2 0.090 ! | | ATOM C2 CG3C41 -0.035 ! H5--C1--C3--H9 ATOM H6 HGA2 0.090 ! | | ATOM H7 HGA2 0.090 ! O1--C2--H6 ATOM C3 CG3C41 -0.087 ! | ATOM H8 HGA2 0.090 ! H7 ATOM H9 HGA2 0.090 ATOM O1 OG3C51 -0.383 BOND C1 C3 C2 C3 C2 O1 O1 C1 BOND C1 H4 C1 H5 BOND C3 H8 C3 H9 BOND C2 H6 C2 H7 IC C3 O1 *C1 H4 0.0000 0.00 120.00 0.00 0.0000 IC C3 O1 *C1 H5 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C1 C3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C2 C1 *C3 H8 0.0000 0.00 120.00 0.00 0.0000 IC C2 C1 *C3 H9 0.0000 0.00 -120.00 0.00 0.0000 IC O1 C3 *C2 H6 0.0000 0.00 120.00 0.00 0.0000 IC O1 C3 *C2 H7 0.0000 0.00 -120.00 0.00 0.0000 RESI CBHH 0.000 ! C4H6N4O2 glycoluril, jing GROUP ATOM C1 CG3RC1 0.290 ! O10 ATOM H1 HGA1 0.090 ! || ATOM C2 CG3RC1 0.290 ! C8 ATOM H2 HGA1 0.090 ! / \ ATOM N3 NG2R53 -0.480 ! H5-N5 N6-H6 ATOM H3 HGP1 0.340 ! \ / ATOM N4 NG2R53 -0.480 ! H1-C1--C2-H2 ATOM H4 HGP1 0.340 ! / \ ATOM N5 NG2R53 -0.480 ! H3-N3 N4-H4 ATOM H5 HGP1 0.340 ! \ / ATOM N6 NG2R53 -0.480 ! C7 ATOM H6 HGP1 0.340 ! || ATOM C7 CG2R53 0.360 ! O9 ATOM C8 CG2R53 0.360 ! ATOM O9 OG2D1 -0.460 ! ATOM O10 OG2D1 -0.460 ! BOND C1 H1 BOND C1 C2 BOND C1 N3 BOND C1 N5 BOND C2 H2 BOND C2 N4 BOND C2 N6 BOND N3 H3 BOND N3 C7 BOND N4 H4 BOND N4 C7 BOND N5 H5 BOND N5 C8 BOND N6 H6 BOND N6 C8 BOND C7 O9 BOND C8 O10 IMPR C7 N3 N4 O9 IMPR C8 N5 N6 O10 IC C1 C2 N4 C7 1.5230 113.70 0.00 112.00 1.3800 IC C2 N4 C7 N3 1.4500 112.00 0.00 104.40 1.3800 IC C7 N3 C1 C2 1.3800 112.00 0.00 113.70 1.5230 IC C2 C1 N5 C8 1.5230 113.70 0.00 112.00 1.3800 IC C1 N5 C8 N6 1.4500 112.00 0.00 104.40 1.3800 IC N5 C8 N6 C2 1.3800 104.40 0.00 112.00 1.4500 IC N3 C1 C2 N6 1.4500 113.70 -180.00 113.70 1.4500 IC N4 C2 C1 N5 1.4500 113.70 -180.00 113.70 1.4500 IC H1 C1 N3 C7 1.1110 111.00 -120.00 112.00 1.3800 IC H2 C2 N4 C7 1.1110 111.00 120.00 112.00 1.3800 IC C7 C1 *N3 H3 1.3800 112.00 180.00 116.00 1.0150 IC C7 C2 *N4 H4 1.3800 112.00 180.00 116.00 1.0150 IC C8 C1 *N5 H5 1.3800 112.00 180.00 116.00 1.0150 IC C8 C2 *N6 H6 1.3800 112.00 180.00 116.00 1.0150 IC N4 N3 *C7 O9 1.3800 104.40 180.00 127.80 1.2350 IC N6 N5 *C8 O10 1.3800 104.40 180.00 127.80 1.2350 IC N3 C2 *C1 N5 1.4500 113.70 120.00 113.70 1.4500 IC N3 C2 *C1 H1 1.4500 113.70 120.00 110.10 1.1110 IC H1 C1 C2 N4 1.1110 110.10 180.00 113.70 1.4500 IC N4 C1 *C2 N6 1.4500 113.70 120.00 113.70 1.4500 IC N4 C1 *C2 H2 1.4500 113.70 -120.00 110.10 1.1110 RESI CHLB 0.000 ! C6H5Cl chlorobenzene + lonepair, isg/fylin ! with Virtual atom on Cl GROUP ! ATOM C1 CG2R61 -0.10 ! ATOM H1 HGR62 0.15 ! H5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP-CL--C6 C3--H3 ATOM C4 CG2R61 -0.115 ! \\ // ATOM H4 HGR61 0.115 ! C1---C2 ATOM C5 CG2R61 -0.10 ! / \ ATOM H5 HGR62 0.15 ! H1 H2 ATOM C6 CG2R61 0.06 ! ATOM CL CLGR1 -0.21 ! ATOM LP LPH 0.05 ! BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 C5 BOND C5 H5 C5 C6 C6 C1 C6 CL BOND CL LP LONEPAIR COLINEAR LP CL C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL 0.0000 0.00 180.00 0.00 0.0000 RESI PCLT 0.00 ! C7H7Cl p-chlorotoluene, kevo (lsk added a lone-pair; transferred from CHLB) GROUP ATOM CG CG2R61 0.06 ATOM CL CLGR1 -0.21 ATOM LP LPH 0.050 ATOM CD1 CG2R61 -0.10 ! HD1 HE1 ATOM HD1 HGR62 0.15 ! | | ATOM CD2 CG2R61 -0.10 ! CD1--CE1 H11 ATOM HD2 HGR62 0.15 ! / \ / ATOM CE1 CG2R61 -0.115 !LP-CL--CG CZ--CT--H12 ATOM HE1 HGR61 0.115 ! \ / \ ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 ATOM HE2 HGR61 0.115 ! | | ATOM CZ CG2R61 0.000 ! HD2 HE2 ATOM CT CG331 -0.270 ATOM H11 HGA3 0.090 ATOM H12 HGA3 0.090 ATOM H13 HGA3 0.090 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG CL CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ CT BOND CT H11 CT H12 CT H13 LONEPAIR COLINEAR LP CL CG DIST 1.640 IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 IC CD1 CD2 *CG CL 1.4000 120.00 180.00 120.00 1.7400 IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 RESI PMHA 0.00 ! C25H20ClN3O2 3-(N-(3-chloroPhenyl)carnoMoyl)propionyl GROUP ! Anthracene-9-carbaldehyde Hydrazone, sz, (lsk added a lone-pair; transferred from CHLB) ATOM C1 CG2R61 0.16 ATOM C2 CG2R61 -0.10 ! H49 H47 ATOM H3 HGR62 0.15 ! \ / ATOM C4 CG2R61 0.06 ! H9 C48--C46 ATOM CL5 CLGR1 -0.21 ! | // \\ ATOM C6 CG2R61 -0.10 ! C8 H11 H51-C50 C44-H45 ATOM H7 HGR62 0.15 ! / \\ / \ / ATOM C8 CG2R61 -0.115! H7--C6 C10 O15 H20 H21 H25 H28 C30--C31 ATOM H9 HGR61 0.115! || | || \ / | | // \\ ATOM C10 CG2R61 -0.115!LP--Cl5-C4 C1 C14 C19 N24 C27--C29 C32-H33 ATOM H11 HGR61 0.115! \ // \ / \ / \ / \ // \ / ATOM N12 NG2S1 -0.47 ! C2 N12 C16 C22 N26 C35==C34 ATOM H13 HGP1 0.31 ! | | / \ || / \ ATOM C14 CG2O1 0.51 ! H3 H13 H17 H18 O23 H37-C36 C42-H43 ATOM O15 OG2D1 -0.51 ! \\ // ATOM C16 CG321 -0.18 ! Group 2 C38--C40 ATOM H17 HGA2 0.09 ! / \ ATOM H18 HGA2 0.09 ! H39 H41 ATOM C19 CG321 -0.18 ATOM H20 HGA2 0.09 ATOM H21 HGA2 0.09 ATOM C22 CG2O1 0.58 ! Group 3 ATOM O23 OG2D1 -0.49 ATOM N24 NG2S1 -0.34 ATOM H25 HGP1 0.31 ATOM N26 NG2D1 -0.31 ATOM C27 CG2DC1 -0.24 ATOM H28 HGA4 0.24 ATOM C29 CG2R61 0.25 ATOM C30 CG2R61 0.00 ! Group 4 ATOM C31 CG2R61 0.00 ATOM C32 CG2R61 -0.115 ATOM H33 HGR61 0.115 ATOM C34 CG2R61 0.00 ATOM C35 CG2R61 0.00 ATOM C36 CG2R61 -0.115 ATOM H37 HGR61 0.115 ATOM C38 CG2R61 -0.115 ATOM H39 HGR61 0.115 ATOM C40 CG2R61 -0.115 ATOM H41 HGR61 0.115 ATOM C42 CG2R61 -0.115 ATOM H43 HGR61 0.115 ATOM C44 CG2R61 -0.115 ATOM H45 HGR61 0.115 ATOM C46 CG2R61 -0.115 ATOM H47 HGR61 0.115 ATOM C48 CG2R61 -0.115 ATOM H49 HGR61 0.115 ATOM C50 CG2R61 -0.115 ATOM H51 HGR61 0.115 ATOM LP LPH 0.050 BOND C1 C2 C2 H3 C2 C4 C4 CL5 BOND C4 C6 C6 H7 C6 C8 C8 H9 BOND C8 C10 C10 H11 C10 C1 C1 N12 BOND N12 H13 N12 C14 C14 O15 C14 C16 BOND C16 H17 C16 H18 C16 C19 C19 H20 C19 H21 C19 C22 BOND C22 O23 C22 N24 N24 H25 N24 N26 N26 C27 C27 H28 BOND C27 C29 BOND C29 C30 C30 C31 C31 C32 C32 H33 C32 C34 C34 C35 C35 C29 BOND C30 C50 C50 H51 C50 C48 C48 H49 C48 C46 BOND C31 C44 C44 H45 C44 C46 C46 H47 BOND C34 C42 C42 H43 C42 C40 C40 H41 C40 C38 BOND C35 C36 C36 H37 C36 C38 C38 H39 IMPR C14 C16 N12 O15 IMPR C22 C19 N24 O23 IMPR C27 C29 N26 H28 BOND CL5 LP LONEPAIR COLINEAR LP CL5 C4 DIST 1.640 IC C1 C2 C4 C6 0.0000 0.00 0.00 0.00 0.0000 IC C2 C4 C6 C8 0.0000 0.00 0.00 0.00 0.0000 IC C4 C6 C8 C10 0.0000 0.00 0.00 0.00 0.0000 IC C6 C8 C10 C1 0.0000 0.00 0.00 0.00 0.0000 IC C8 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 IC C10 C1 C2 C4 0.0000 0.00 0.00 0.00 0.0000 IC C1 C4 *C2 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C6 *C4 CL5 0.0000 0.00 180.00 0.00 0.0000 IC C4 C8 *C6 H7 0.0000 0.00 180.00 0.00 0.0000 IC C6 C10 *C8 H9 0.0000 0.00 180.00 0.00 0.0000 IC C8 C1 *C10 H11 0.0000 0.00 180.00 0.00 0.0000 IC C10 C2 *C1 N12 0.0000 0.00 180.00 0.00 0.0000 IC C14 N12 C1 C10 0.0000 0.00 90.00 0.00 0.0000 IC C14 C1 *N12 H13 0.0000 0.00 180.00 0.00 0.0000 IC O15 C14 N12 H13 0.0000 0.00 180.00 0.00 0.0000 IC O15 N12 *C14 C16 0.0000 0.00 180.00 0.00 0.0000 IC C19 C16 C14 O15 0.0000 0.00 0.00 0.00 0.0000 IC C19 C14 *C16 H17 0.0000 0.00 120.00 0.00 0.0000 IC C19 C14 *C16 H18 0.0000 0.00 -120.00 0.00 0.0000 IC C22 C19 C16 C14 0.0000 0.00 180.00 0.00 0.0000 IC C16 C22 *C19 H20 0.0000 0.00 -120.00 0.00 0.0000 IC C16 C22 *C19 H21 0.0000 0.00 120.00 0.00 0.0000 IC O23 C22 C19 C16 0.0000 0.00 0.00 0.00 0.0000 IC N24 O23 *C22 C19 0.0000 0.00 180.00 0.00 0.0000 IC N26 C22 *N24 H25 0.0000 0.00 180.00 0.00 0.0000 IC N26 N24 C22 O23 0.0000 0.00 0.00 0.00 0.0000 IC C27 N26 N24 C22 0.0000 0.00 180.00 0.00 0.0000 IC C29 N26 *C27 H28 0.0000 0.00 180.00 0.00 0.0000 IC C29 C27 N26 N24 0.0000 0.00 180.00 0.00 0.0000 IC C30 C29 C27 N26 0.0000 0.00 90.00 0.00 0.0000 IC C31 C30 C29 C27 0.0000 0.00 180.00 0.00 0.0000 IC C32 C31 C30 C29 0.0000 0.00 0.00 0.00 0.0000 IC C34 C32 C31 C30 0.0000 0.00 0.00 0.00 0.0000 IC C31 C34 *C32 H33 0.0000 0.00 180.00 0.00 0.0000 IC C35 C34 C32 C31 0.0000 0.00 0.00 0.00 0.0000 IC C31 C29 *C30 C50 0.0000 0.00 180.00 0.00 0.0000 IC C32 C30 *C31 C44 0.0000 0.00 180.00 0.00 0.0000 IC C48 C50 C30 C31 0.0000 0.00 0.00 0.00 0.0000 IC C46 C44 C31 C30 0.0000 0.00 0.00 0.00 0.0000 IC C48 C30 *C50 H51 0.0000 0.00 180.00 0.00 0.0000 IC C46 C50 *C48 H49 0.0000 0.00 180.00 0.00 0.0000 IC C44 C48 *C46 H47 0.0000 0.00 180.00 0.00 0.0000 IC C31 C46 *C44 H45 0.0000 0.00 180.00 0.00 0.0000 IC C34 C29 *C35 C36 0.0000 0.00 180.00 0.00 0.0000 IC C32 C35 *C34 C42 0.0000 0.00 180.00 0.00 0.0000 IC C38 C36 C35 C34 0.0000 0.00 0.00 0.00 0.0000 IC C40 C42 C34 C35 0.0000 0.00 0.00 0.00 0.0000 IC C38 C35 *C36 H37 0.0000 0.00 180.00 0.00 0.0000 IC C40 C36 *C38 H39 0.0000 0.00 180.00 0.00 0.0000 IC C42 C38 *C40 H41 0.0000 0.00 180.00 0.00 0.0000 IC C34 C40 *C42 H43 0.0000 0.00 180.00 0.00 0.0000 RESI 12DCB 0.000 ! C6H4Cl2 1,2-dichlorobenzene, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.10 ! \ ATOM H1 HGR62 0.15 ! CL5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP6-CL6--C6 C3--H3 ATOM C4 CG2R61 -0.10 ! \\ // ATOM H4 HGR62 0.15 ! C1---C2 ATOM C5 CG2R61 0.06 ! / \ ATOM CL5 CLGR1 -0.16 ! H1 H2 ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.06 ! ATOM CL6 CLGR1 -0.16 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 C5 C5 CL5 C5 C6 C6 CL6 BOND CL5 LP5 BOND CL6 LP6 LONEPAIR COLINEAR LP5 CL5 C5 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 CL5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI 13DCB 0.000 ! C6H4Cl2 1,3-dichlorobenzene, isg/fylin GROUP ! LP4 ATOM C1 CG2R61 -0.10 ! / ATOM H1 HGR62 0.15 ! H5 CL4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.10 ! / \ ATOM H3 HGR62 0.15 ! LP6-CL6--C6 C3--H3 ATOM C4 CG2R61 0.05 ! \\ // ATOM CL4 CLGR1 -0.19 ! C1---C2 ATOM C5 CG2R61 -0.05 ! / \ ATOM H5 HGR62 0.13 ! H1 H2 ATOM LP4 LPH 0.05 ! ATOM C6 CG2R61 0.05 ! ATOM CL6 CLGR1 -0.19 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 CL4 BOND C4 C5 C5 H5 C5 C6 C6 CL6 BOND CL6 LP6 CL4 LP4 LONEPAIR COLINEAR LP4 CL4 C4 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 CL4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI 14DCB 0.000 ! C6H4Cl2 1,4-dichlorobenzene, isg/fylin ! with Virtual atom on Cl GROUP ! ATOM C1 CG2R61 -0.03 ! ATOM H1 HGR62 0.07 ! H5 H4 ATOM C2 CG2R61 -0.03 ! \ ___ / ATOM H2 HGR62 0.07 ! C5---C4 ATOM C3 CG2R61 0.03 ! / \ ATOM CL3 CLGR1 -0.16 ! LP6-CL6--C6 C3--CL3-LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 -0.03 ! C1---C2 ATOM H4 HGR62 0.07 ! / \ ATOM C5 CG2R61 -0.03 ! H1 H2 ATOM H5 HGR62 0.07 ! ATOM C6 CG2R61 0.03 ! ATOM CL6 CLGR1 -0.16 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 CL3 C3 C4 C4 H4 BOND C4 C5 C5 H5 C5 C6 C6 CL6 BOND CL6 LP6 CL3 LP3 LONEPAIR COLINEAR LP3 CL3 C3 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 CL3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI 123TCB 0.000 ! C6H3Cl3 1,2,3-trichlorobenzene, isg/fylin ! with Virtual atom on Cl GROUP ! LP5 LP4 ATOM C1 CG2R61 -0.10 ! \ / ATOM H1 HGR62 0.15 ! CL5 CL4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.10 ! / \ ATOM H3 HGR62 0.15 ! LP6-CL6--C6 C3--H3 ATOM C4 CG2R61 0.01 ! \\ // ATOM CL4 CLGR1 -0.17 ! C1---C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 0.23 ! H1 H2 ATOM CL5 CLGR1 -0.16 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.01 ! ATOM CL6 CLGR1 -0.17 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 CL4 BOND C4 C5 C5 CL5 C5 C6 C6 CL6 BOND CL6 LP6 CL4 LP4 CL5 LP5 LONEPAIR COLINEAR LP4 CL4 C4 DIST 1.640 LONEPAIR COLINEAR LP5 CL5 C5 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 CL4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 CL5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI 124TCB 0.000 ! C6H3Cl3 1,2,4-trichlorobenzene, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.08 ! \ ATOM H1 HGR62 0.13 ! CL5 H4 ATOM C2 CG2R61 -0.08 ! \ ___ / ATOM H2 HGR62 0.13 ! C5---C4 ATOM C3 CG2R61 0.06 ! / \ ATOM CL3 CLGR1 -0.18 !LP6-CL6--C6 C3--CL3-LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 -0.06 ! C1---C2 ATOM H4 HGR62 0.12 ! / \ ATOM C5 CG2R61 0.07 ! H1 H2 ATOM CL5 CLGR1 -0.17 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.07 ! ATOM CL6 CLGR1 -0.16 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 H2 BOND C2 C3 C3 CL3 C3 C4 BOND C4 H4 C4 C5 C5 CL5 C5 C6 BOND C6 CL6 BOND CL3 LP3 CL6 LP6 CL5 LP5 LONEPAIR COLINEAR LP3 CL3 C3 DIST 1.640 LONEPAIR COLINEAR LP5 CL5 C5 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 CL3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 CL5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI 135TCB 0.000 ! C6H3Cl3 1,3,5-trichlorobenzene, isg/fylin GROUP ! LP4 ATOM C1 CG2R61 -0.05 ! / ATOM H1 HGR62 0.13 ! H5 CL4 ATOM C2 CG2R61 0.04 ! \ ___ / ATOM CL2 CLGR1 -0.17 ! C5---C4 ATOM LP2 LPH 0.05 ! / \ ATOM C3 CG2R61 -0.05 ! LP6-CL6--C6 C3--H3 ATOM H3 HGR62 0.13 ! \\ // ATOM C4 CG2R61 0.04 ! C1---C2 ATOM CL4 CLGR1 -0.17 ! / \ ATOM LP4 LPH 0.05 ! H1 CL2 ATOM C5 CG2R61 -0.05 ! \ ATOM H5 HGR62 0.13 ! LP2 ATOM C6 CG2R61 0.04 ! ATOM CL6 CLGR1 -0.17 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 CL2 BOND C2 C3 C3 H3 C3 C4 C4 CL4 BOND C4 C5 C5 H5 C5 C6 C6 CL6 BOND CL6 LP6 CL4 LP4 CL2 LP2 LONEPAIR COLINEAR LP2 CL2 C2 DIST 1.640 LONEPAIR COLINEAR LP4 CL4 C4 DIST 1.640 LONEPAIR COLINEAR LP6 CL6 C6 DIST 1.640 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 CL2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 CL4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 CL6 0.0000 0.00 180.00 0.00 0.0000 RESI BROB 0.000 ! C6H5Br Bromobenzene + lone pair , isg/fylin GROUP ! ATOM C1 CG2R61 -0.06 ! ATOM H1 HGR62 0.15 ! H5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP-BR--C6 C3--H3 ATOM C4 CG2R61 -0.115 ! \\ // ATOM H4 HGR61 0.115 ! C1---C2 ATOM C5 CG2R61 -0.06 ! / \ ATOM H5 HGR62 0.15 ! H1 H2 ATOM C6 CG2R61 -0.05 ! ATOM BR BRGR1 -0.18 ! ATOM LP LPH 0.05 ! BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 C5 BOND C5 H5 C5 C6 C6 C1 C6 BR BOND BR LP LONEPAIR COLINEAR LP BR C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR 0.0000 0.00 180.00 0.00 0.0000 RESI 12DBB 0.000 ! C6H4Br2 1,2 dibromobenzene + lone pair, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.06 ! \ ATOM H1 HGR62 0.15 ! BR5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP6-BR6--C6 C3--H3 ATOM C4 CG2R61 -0.06 ! \\ // ATOM H4 HGR62 0.15 ! C1---C2 ATOM C5 CG2R61 0.01 ! / \ ATOM BR5 BRGR1 -0.15 ! H1 H2 ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.01 ! ATOM LP6 LPH 0.05 ! ATOM BR6 BRGR1 -0.15 ! BOND C6 C1 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 C5 C5 BR5 C5 C6 C6 BR6 BOND BR5 LP5 BR6 LP6 LONEPAIR COLINEAR LP5 BR5 C5 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 BR5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI 13DBB 0.000 ! C6H4Br2 1,3-dibromobenzene + lonepair, isg/fylin GROUP ! LP4 ATOM C1 CG2R61 -0.06 ! / ATOM H1 HGR62 0.15 ! H5 BR4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.06 ! / \ ATOM H3 HGR62 0.15 ! LP6-BR6--C6 C3--H3 ATOM C4 CG2R61 -0.07 ! \\ // ATOM BR4 BRGR1 -0.17 ! C1---C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 0.11 ! H1 H2 ATOM H5 HGR62 0.09 ! ATOM C6 CG2R61 -0.07 ! ATOM LP6 LPH 0.05 ! ATOM BR6 BRGR1 -0.17 ! BOND C6 C1 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 BR4 BOND C4 C5 C5 H5 C5 C6 C6 BR6 BOND BR4 LP4 BR6 LP6 LONEPAIR COLINEAR LP4 BR4 C4 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 BR4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI 14DBB 0.000 ! C6H4Br2 1,4-dibromobenzene + lonepair, isg/fylin GROUP ! ATOM C1 CG2R61 -0.06 ! ATOM H1 HGR62 0.15 ! H5 H4 ATOM C2 CG2R61 -0.06 ! \ ___ / ATOM H2 HGR62 0.15 ! C5---C4 ATOM C3 CG2R61 -0.06 ! / \ ATOM BR3 BRGR1 -0.17 ! LP6-BR6--C6 C3-- BR3-LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 -0.06 ! C1---C2 ATOM H4 HGR62 0.15 ! / \ ATOM C5 CG2R61 -0.06 ! H1 H2 ATOM H5 HGR62 0.15 ! ATOM C6 CG2R61 -0.06 ! ATOM LP6 LPH 0.05 ! ATOM BR6 BRGR1 -0.17 ! BOND C6 C1 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 BR3 C3 C4 C4 H4 BOND C4 C5 C5 H5 C5 C6 C6 BR6 BOND BR3 LP3 BR6 LP6 LONEPAIR COLINEAR LP3 BR3 C3 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 BR3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI 123TBB 0.000 ! C6H3Br3 1,2,3-tribromobenzene + lonepair, isg/fylin GROUP ! LP5 LP4 ATOM C1 CG2R61 -0.07 ! \ / ATOM H1 HGR62 0.11 ! BR5 BR4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.07 ! / \ ATOM H3 HGR62 0.11 ! LP6-BR6--C6 C3--H3 ATOM C4 CG2R61 0.08 ! \\ // ATOM BR4 BRGR1 -0.15 ! C1---C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 0.05 ! H1 H2 ATOM BR5 BRGR1 -0.14 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.08 ! ATOM BR6 BRGR1 -0.15 ! ATOM LP6 LPH 0.05 ! BOND C6 C1 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 BR4 BOND C4 C5 C5 BR5 C5 C6 C6 BR6 BOND BR4 LP4 BR5 LP5 BR6 LP6 LONEPAIR COLINEAR LP4 BR4 C4 DIST 1.890 LONEPAIR COLINEAR LP5 BR5 C5 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 BR4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 BR5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI 124TBB 0.000 ! C6H3Br3 1,2,4-tribromobenzene + lonepair, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.06 ! \ ATOM H1 HGR62 0.11 ! BR5 H4 ATOM C2 CG2R61 -0.06 ! \ ___ / ATOM H2 HGR62 0.11 ! C5---C4 ATOM C3 CG2R61 0.06 ! / \ ATOM BR3 BRGR1 -0.17 ! LP6-BR6--C6 C3--BR3-LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 -0.04 ! C1---C2 ATOM H4 HGR62 0.11 ! / \ ATOM C5 CG2R61 0.01 ! H1 H2 ATOM BR5 BRGR1 -0.12 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.02 ! ATOM BR6 BRGR1 -0.12 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 H2 BOND C2 C3 C3 BR3 C3 C4 C4 H4 BOND C4 C5 C5 BR5 C5 C6 C6 BR6 BOND BR3 LP3 BR5 LP5 BR6 LP6 LONEPAIR COLINEAR LP3 BR3 C3 DIST 1.890 LONEPAIR COLINEAR LP5 BR5 C5 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 BR3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 BR5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI 135TBB 0.00 ! C6H3Br3 1,3,5-tribromobenzene + lonepair, isg/fylin GROUP ! LP4 ATOM C1 CG2R61 -0.02 ! / ATOM H1 HGR62 0.11 ! H5 BR4 ATOM C2 CG2R61 0.01 ! \ ___ / ATOM BR2 BRGR1 -0.15 ! C5---C4 ATOM LP2 LPH 0.05 ! / \ ATOM C3 CG2R61 -0.02 !LP6-BR6--C6 C3-- H3 ATOM H3 HGR62 0.11 ! \\ // ATOM C4 CG2R61 0.01 ! C1---C2 ATOM BR4 BRGR1 -0.15 ! / \ ATOM LP4 LPH 0.05 ! H1 BR2 ATOM C5 CG2R61 -0.02 ! \ ATOM H5 HGR62 0.11 ! LP2 ATOM C6 CG2R61 0.01 ! ATOM BR6 BRGR1 -0.15 ! ATOM LP6 LPH 0.05 ! BOND C1 H1 C1 C2 C1 C6 C2 BR2 BOND C2 C3 C3 H3 C3 C4 C4 BR4 BOND C4 C5 C5 H5 C5 C6 C6 BR6 BOND BR2 LP2 BR4 LP4 BR6 LP6 LONEPAIR COLINEAR LP2 BR2 C2 DIST 1.890 LONEPAIR COLINEAR LP4 BR4 C4 DIST 1.890 LONEPAIR COLINEAR LP6 BR6 C6 DIST 1.890 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 BR2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 BR4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 BR6 0.0000 0.00 180.00 0.00 0.0000 RESI IODB 0.000 ! C6H5I Iodobenzene + lonepair, isg/fylin GROUP ! ATOM C1 CG2R61 -0.06 ! ATOM H1 HGR62 0.14 ! H5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP-I6--C6 C3--H3 ATOM C4 CG2R61 -0.115 ! \\ // ATOM H4 HGR61 0.115 ! C1---C2 ATOM C5 CG2R61 -0.06 ! / \ ATOM H5 HGR62 0.14 ! H1 H2 ATOM C6 CG2R61 -0.04 ! ATOM I6 IGR1 -0.17 ! ATOM LP LPH 0.05 ! BOND C1 H1 C1 C2 C2 H2 C2 C3 BOND C3 H3 C3 C4 C4 H4 C4 C5 BOND C5 H5 C5 C6 C6 C1 C6 I6 BOND I6 LP LONEPAIR COLINEAR LP I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 12DIB 0.000 ! C6H4I2 1,2-diiodobenzene + lonepair, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.06 ! \ ATOM H1 HGR62 0.14 ! I5 H4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.115 ! / \ ATOM H3 HGR61 0.115 ! LP6-I6--C6 C3--H3 ATOM C4 CG2R61 -0.06 ! \\ // ATOM H4 HGR62 0.14 ! C1---C2 ATOM C5 CG2R61 0.02 ! / \ ATOM I5 IGR1 -0.15 ! H1 H2 ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 0.02 ! ATOM I6 IGR1 -0.15 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 H4 BOND C4 C5 C5 I5 C5 C6 C6 I6 BOND I5 LP5 I6 LP6 LONEPAIR COLINEAR LP5 I5 C5 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 I5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 13DIB 0.000 ! C6H4I2 1,3-diiodobenzene + lonepair, isg/fylin GROUP ! LP4 ATOM C1 CG2R61 -0.06 ! / ATOM H1 HGR62 0.14 ! H5 I4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.06 ! / \ ATOM H3 HGR62 0.14 ! LP6-I6--C6 C3--H3 ATOM C4 CG2R61 -0.02 ! \\ // ATOM I4 IGR1 -0.14 ! C1---C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 -0.06 ! H1 H2 ATOM H5 HGR62 0.12 ! ATOM C6 CG2R61 -0.02 ! ATOM I6 IGR1 -0.14 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 I4 BOND C4 C5 C5 H5 C5 C6 C6 I6 BOND I4 LP4 I6 LP6 LONEPAIR COLINEAR LP4 I4 C4 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 I4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 14DIB 0.000 ! C6H4I2 1,4-diodobenzene + lonepair, isg/fylin GROUP ! ATOM C1 CG2R61 -0.02 ! ATOM H1 HGR62 0.10 ! H5 H4 ATOM C2 CG2R61 -0.02 ! \ ___ / ATOM H2 HGR62 0.10 ! C5---C4 ATOM C3 CG2R61 -0.08 ! / \ ATOM I3 IGR1 -0.13 ! LP6-I6--C6 C3--I3--LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 -0.02 ! C1---C2 ATOM H4 HGR62 0.10 ! / \ ATOM C5 CG2R61 -0.02 ! H1 H2 ATOM H5 HGR62 0.10 ! ATOM C6 CG2R61 -0.08 ! ATOM I6 IGR1 -0.13 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 I3 C3 C4 C4 H4 BOND C4 C5 C5 H5 C5 C6 C6 I6 BOND I3 LP3 I6 LP6 LONEPAIR COLINEAR LP3 I3 C3 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 I3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 123TIB 0.000 ! C6H3I3 1,2,3-Triiodobenzene + lonepair, isg/fylin GROUP ! LP5 LP4 ATOM C1 CG2R61 -0.06 ! \ / ATOM H1 HGR62 0.14 ! I5 I4 ATOM C2 CG2R61 -0.115 ! \ ___ / ATOM H2 HGR61 0.115 ! C5---C4 ATOM C3 CG2R61 -0.06 ! / \ ATOM H3 HGR62 0.14 ! LP6-I6--C6 C3--H3 ATOM C4 CG2R61 -0.05 ! \\ // ATOM I4 IGR1 -0.11 ! C1--C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 0.10 ! H1 H2 ATOM I5 IGR1 -0.09 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 -0.05 ! ATOM I6 IGR1 -0.11 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 H3 C3 C4 C4 I4 BOND C4 C5 C5 I5 C5 C6 C6 I6 BOND I4 LP4 I5 LP5 I6 LP6 LONEPAIR COLINEAR LP4 I4 C4 DIST 2.200 LONEPAIR COLINEAR LP5 I5 C5 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 I4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 I5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 124TIB 0.000 ! C6H3I3 1,2,4-Triiodobenzene + lonepair, isg/fylin GROUP ! LP5 ATOM C1 CG2R61 -0.08 ! \ ATOM H1 HGR62 0.14 ! I5 H4 ATOM C2 CG2R61 -0.08 ! \ ___ / ATOM H2 HGR62 0.14 ! C5---C4 ATOM C3 CG2R61 -0.04 ! / \ ATOM I3 IGR1 -0.12 ! LP6-I6--C6 C3--I3-LP3 ATOM LP3 LPH 0.05 ! \\ // ATOM C4 CG2R61 0.02 ! C1---C2 ATOM H4 HGR62 0.10 ! / \ ATOM C5 CG2R61 -0.03 ! H1 H2 ATOM I5 IGR1 -0.08 ! ATOM LP5 LPH 0.05 ! ATOM C6 CG2R61 -0.03 ! ATOM I6 IGR1 -0.09 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 H2 BOND C2 C3 C3 I3 C3 C4 C4 H4 BOND C4 C5 C5 I5 C5 C6 C6 I6 BOND I3 LP3 I5 LP5 I6 LP6 LONEPAIR COLINEAR LP3 I3 C3 DIST 2.200 LONEPAIR COLINEAR LP5 I5 C5 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 I3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 I5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI 135TIB 0.000 ! C6H3I3 1,3,5-Triiodobenzene + lonepair, isg/fylin GROUP ! ATOM C1 CG2R61 -0.08 ! LP4 ATOM H1 HGR62 0.13 ! / ATOM C2 CG2R61 0.03 ! H5 I4 ATOM I2 IGR1 -0.13 ! \ ___ / ATOM LP2 LPH 0.05 ! C5---C4 ATOM C3 CG2R61 -0.08 ! / \ ATOM H3 HGR62 0.13 ! LP6-I6--C6 C3--H3 ATOM C4 CG2R61 0.03 ! \\ // ATOM I4 IGR1 -0.13 ! C1---C2 ATOM LP4 LPH 0.05 ! / \ ATOM C5 CG2R61 -0.08 ! H1 I2 ATOM H5 HGR62 0.13 ! \ ATOM C6 CG2R61 0.03 ! LP2 ATOM I6 IGR1 -0.13 ! ATOM LP6 LPH 0.05 ! BOND C1 C6 C1 H1 C1 C2 C2 I2 BOND C2 C3 C3 H3 C3 C4 C4 I4 BOND C4 C5 C5 H5 C5 C6 C6 I6 BOND I2 LP2 I4 LP4 I6 LP6 LONEPAIR COLINEAR LP2 I2 C2 DIST 2.200 LONEPAIR COLINEAR LP4 I4 C4 DIST 2.200 LONEPAIR COLINEAR LP6 I6 C6 DIST 2.200 IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 IC C3 C1 *C2 I2 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 IC C5 C3 *C4 I4 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 RESI OIRD 0.000 ! oxindol-3-ylidene rhodanine, kevo & xxwy !RING 5 S1 C2 N3 C4 C5 !RING 5 C6 C7 N8 C9 C14 !RING 6 C9 C10 C11 C12 C13 C14 ATOM S1 SG311 -0.14 ATOM C2 CG2R53 0.26 ATOM S2 SG2D1 -0.27 ATOM N3 NG2R53 -0.24 ! H3 S2 ATOM H3 HGP1 0.31 ! \ // ATOM C4 CG2R53 0.29 ! N3----C2 ATOM O4 OG2D1 -0.39 ! | | ATOM C5 CG252O 0.18 !or CG251O O4==C4 S1 ATOM C6 CG25C2 -0.09 !or CG25C1 \ / ATOM C7 CG2R53 0.67 ! H13 C5 ATOM O7 OG2D1 -0.57 ! | || ATOM N8 NG2R51 -0.45 ! C13 C6 O7 ATOM H8 HGP1 0.32 ! // \ / \ // ATOM C9 CG2RC0 0.25 ! H12--C12 C14 C7 ATOM C10 CG2R61 -0.34 ! | || | ATOM H10 HGR61 0.24 ! H11--C11 C9----N8 ATOM C11 CG2R61 -0.20 ! \\ / \ ATOM H11 HGR61 0.22 ! C10 H8 ATOM C12 CG2R61 -0.23 ! | ATOM H12 HGR61 0.21 ! H10 ATOM C13 CG2R61 -0.32 ATOM H13 HGR61 0.28 ATOM C14 CG2RC0 0.01 BOND S1 C2 C2 N3 N3 C4 C4 C5 BOND C5 S1 C2 S2 N3 H3 C4 O4 BOND C5 C6 BOND C6 C7 C7 N8 N8 C9 C9 C10 C10 C11 BOND C11 C12 C12 C13 C13 C14 C14 C6 C9 C14 BOND C7 O7 N8 H8 C10 H10 C11 H11 C12 H12 BOND C13 H13 IMPR C2 N3 S2 S1 IMPR C4 C5 N3 O4 IMPR C7 C6 N8 O7 IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 IC C4 N3 C2 S1 0.0000 0.00 0.00 0.00 0.0000 IC N3 S1 *C2 S2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 IC S1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC S1 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 IC C5 C7 *C6 C14 0.0000 0.00 180.00 0.00 0.0000 IC C7 C6 C14 C9 0.0000 0.00 0.00 0.00 0.0000 IC C6 C14 C9 N8 0.0000 0.00 0.00 0.00 0.0000 IC C6 C9 *C14 C13 0.0000 0.00 180.00 0.00 0.0000 IC C14 N8 *C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C14 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 IC C9 C14 C13 C12 0.0000 0.00 0.00 0.00 0.0000 IC N8 C6 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *N8 H8 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 !! Note, use charmm c40b1 or higher to avoid seg-fault PRES 3CBD 0.00 ! C3H2Cl Gamma 3-Chloro amino benzene glutamic acid CDCA amide, cacha (lsk added lone-pair on chlorine) !To be patched with residue GABD DELETE ATOM HE1 ATOM CD1 CG2R61 -0.100 ! CD1--CE1--CL-LP ATOM HD1 HGR62 0.150 ! // \ ATOM CE1 CG2R61 0.060 ! --CG--NG--CZ CP ATOM CL CLGR1 -0.210 ! || \ __ // ATOM CP CG2R61 -0.100 ! OG CD2--CE2 ATOM HP HGR62 0.150 ATOM LP LPH 0.050 BOND CE1 CL BOND CL LP LONEPAIR COLINEAR LP CL CE1 DIST 1.640 IC CP CD1 *CE1 CL 1.4002 119.96 179.97 120.18 1.7396 !! Note, use charmm c40b1 or higher to avoid seg-fault PRES 4CBD 0.00 ! C3H2Cl Gamma 4-Chloro amino benzene glutamic acid CDCA amide, cacha (lsk added a lone-pair on chlorine) !To be patched with residue GABD DELETE ATOM HP ATOM CE1 CG2R61 -0.100 ! CD1--CE1 ATOM HE1 HGR62 0.150 ! // \ ATOM CP CG2R61 0.060 ! --CG--NG--CZ CP--CL-LP ATOM CL CLGR1 -0.210 ! || \ __ // ATOM CE2 CG2R61 -0.100 ! OG CD2--CE2 ATOM HE2 HGR62 0.150 ATOM LP LPH 0.050 BOND CP CL BOND CL LP LONEPAIR COLINEAR LP CL CP DIST 1.640 IC CE1 CE2 *CP CL 1.3996 119.90 -179.82 120.09 1.7397 PRES B576 -1.97 ! BCL6 inhibitor 57-6, Chirality ~ L-Asp, kevo & xxwy (lsk added a lone-pair on bromine) DELETE ATOM H12 ! O33A (-) DELETE ATOM H3 ! | !GROUP ! (-) O34A H32A C33--O33B ATOM C11 CG2R61 -0.06 ! | \ / ATOM H11 HGR62 0.15 ! O34B--C34 C32 ATOM C12 CG2R61 -0.05 ! \ / \ ATOM BR2 BRGR1 -0.18 ! C31 H32B S2 ATOM C13 CG2R61 -0.06 ! / \ // ATOM H13 HGR62 0.11 ! H31 N3----C2 !GROUP ! | | ATOM N3 NG2R53 -0.09 ! O4==C4 S1 ATOM C31 CG311 -0.03 ! \ / ATOM H31 HGA1 0.09 ! H13 C5 ATOM C32 CG321 -0.28 ! | || ATOM H32A HGA2 0.09 ! C13 C6 O7 ATOM H32B HGA2 0.09 ! // \ / \ // ATOM C33 CG2O3 0.62 !LP-Br2--C12 C14 C7 ATOM O33A OG2D2 -0.76 ! | || | ATOM O33B OG2D2 -0.76 ! H11--C11 C9----N8 ATOM C34 CG2O3 0.62 ! \\ / \ ATOM O34A OG2D2 -0.76 ! C10 H8 ATOM O34B OG2D2 -0.76 ! | ATOM LP LPH 0.05 ! H10 BOND C12 BR2 BOND N3 C31 C31 C32 C32 C33 C31 C34 BOND C33 O33A C33 O33B C34 O34A C34 O34B BOND C31 H31 C32 H32A C32 H32B BOND BR2 LP IMPR C34 O34A O34B C31 IMPR C33 O33A O33B C32 LONEPAIR COLINEAR LP BR2 C12 DIST 1.890 IC C13 C11 *C12 BR2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 C31 0.0000 0.00 180.00 0.00 0.0000 IC C2 N3 C31 C32 0.0000 0.00 -120.00 0.00 0.0000 !-120 IC N3 C31 C32 C33 0.0000 0.00 180.00 0.00 0.0000 IC N3 C32 *C31 C34 0.0000 0.00 -120.00 0.00 0.0000 !Chirality ~ L-Asp IC N3 C32 *C31 H31 0.0000 0.00 120.00 0.00 0.0000 !Chirality ~ L-Asp IC C31 C33 *C32 H32A 0.0000 0.00 120.00 0.00 0.0000 IC C31 C33 *C32 H32B 0.0000 0.00 -120.00 0.00 0.0000 IC C31 C32 C33 O33A 0.0000 0.00 150.00 0.00 0.0000 IC C32 O33A *C33 O33B 0.0000 0.00 180.00 0.00 0.0000 IC N3 C31 C34 O34A 0.0000 0.00 90.00 0.00 0.0000 IC C31 O34A *C34 O34B 0.0000 0.00 180.00 0.00 0.0000 PRES 576P 0.03 ! Protonated BCL6 inhibitor 57-6, Chirality ~ L-Asp, kevo & xxwy (lsk added a lone-pair on bromine) DELETE ATOM H12 ! O33A--H33A DELETE ATOM H3 ! | !GROUP !H34A-O34A H32A C33--O33B ATOM C11 CG2R61 -0.06 ! | \ / ATOM H11 HGR62 0.15 ! O34B--C34 C32 ATOM C12 CG2R61 -0.05 ! \ / \ ATOM BR2 BRGR1 -0.18 ! C31 H32B S2 ATOM C13 CG2R61 -0.06 ! / \ // ATOM H13 HGR62 0.11 ! H31 N3----C2 !GROUP ! | | ATOM N3 NG2R53 -0.09 ! O4==C4 S1 ATOM C31 CG311 0.07 ! \ / ATOM H31 HGA1 0.09 ! H13 C5 ATOM C32 CG321 -0.18 ! | || ATOM H32A HGA2 0.09 ! C13 C6 O7 ATOM H32B HGA2 0.09 ! // \ / \ // ATOM C33 CG2O2 0.75 !LP-Br2--C12 C14 C7 ATOM O33A OG311 -0.63 ! | || | ATOM O33B OG2D1 -0.55 ! H11--C11 C9----N8 ATOM C34 CG2O2 0.75 ! \\ / \ ATOM O34A OG311 -0.63 ! C10 H8 ATOM O34B OG2D1 -0.55 ! | ATOM H33A HGP1 0.43 ! H10 ATOM H34A HGP1 0.43 ! ATOM LP LPH 0.05 ! BOND C12 BR2 BOND N3 C31 C31 C32 C32 C33 C31 C34 BOND C33 O33A C33 O33B C34 O34A C34 O34B BOND C31 H31 C32 H32A C32 H32B BOND O33A H33A O34A H34A BOND BR2 LP IMPR C34 C31 O34B O34A IMPR C33 C32 O33B O33A LONEPAIR COLINEAR LP BR2 C12 DIST 1.890 IC C13 C11 *C12 BR2 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *N3 C31 0.0000 0.00 180.00 0.00 0.0000 IC C2 N3 C31 C32 0.0000 0.00 -120.00 0.00 0.0000 !-120 IC N3 C31 C32 C33 0.0000 0.00 180.00 0.00 0.0000 IC N3 C32 *C31 C34 0.0000 0.00 -120.00 0.00 0.0000 !Chirality ~ L-Asp IC N3 C32 *C31 H31 0.0000 0.00 120.00 0.00 0.0000 !Chirality ~ L-Asp IC C31 C33 *C32 H32A 0.0000 0.00 120.00 0.00 0.0000 IC C31 C33 *C32 H32B 0.0000 0.00 -120.00 0.00 0.0000 IC C31 C32 C33 O33A 0.0000 0.00 150.00 0.00 0.0000 IC C32 O33A *C33 O33B 0.0000 0.00 180.00 0.00 0.0000 IC N3 C31 C34 O34A 0.0000 0.00 90.00 0.00 0.0000 IC C31 O34A *C34 O34B 0.0000 0.00 180.00 0.00 0.0000 IC H33A O33A C33 O33B 0.0000 0.00 0.00 0.00 0.0000 IC H34A O34A C34 O34B 0.0000 0.00 0.00 0.00 0.0000 RESI TSPD 0.000 ! 1-(2-Thienylsulfonyl)piperidine, xxwy !RING * 5 C6 C7 C8 S2 C9 !RING * 6 C1 N C2 C3 C4 C5 GROUP ! CHARGE ATOM C1 CG321 0.09 ATOM H1 HGA2 0.09 ATOM H2 HGA2 0.09 ATOM N NG301 -0.48 ATOM C2 CG321 0.09 ATOM H3 HGA2 0.09 ATOM H4 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H5 HGA2 0.09 ATOM H6 HGA2 0.09 ATOM C4 CG321 -0.18 ATOM H7 HGA2 0.09 ATOM H8 HGA2 0.09 ATOM C5 CG321 -0.18 ATOM H9 HGA2 0.09 ATOM H10 HGA2 0.09 ATOM S1 SG3O2 0.54 ATOM O1 OG2P1 -0.36 ATOM O2 OG2P1 -0.36 ATOM C6 CG2R51 -0.16 ATOM H11 HGR51 0.20 ATOM C7 CG2R51 -0.21 ATOM H12 HGR51 0.26 ATOM C8 CG2R51 -0.06 ATOM S2 SG2R50 0.02 ATOM C9 CG2R51 -0.11 ATOM H13 HGR52 0.18 BOND C1 H1 C1 H2 C1 N C1 C5 BOND N C2 N S1 C2 H3 C2 H4 BOND C2 C3 C3 H5 C3 H6 C3 C4 BOND C4 H7 C4 H8 C4 C5 C5 H9 BOND C5 H10 S1 O1 S1 O2 S1 C8 BOND C6 H11 C6 C7 C6 C9 C7 H12 BOND C7 C8 C8 S2 S2 C9 C9 H13 IC C1 N C2 C3 1.4749 113.45 58.37 109.91 1.5401 IC N C2 C3 C4 1.4786 109.91 -53.03 112.84 1.5333 IC C2 C3 C4 C5 1.5401 112.84 50.92 109.85 1.5331 IC C5 N *C1 H1 1.5372 108.79 118.88 108.63 1.1122 IC H1 N *C1 H2 1.1122 108.63 118.72 112.40 1.1133 IC H1 C1 N S1 1.1122 108.63 -157.31 116.10 1.6550 IC S1 C1 *N C2 1.6550 116.10 -144.06 113.45 1.4786 IC C1 N C2 C3 1.4749 113.45 58.37 109.91 1.5401 IC C3 N *C2 H3 1.5401 109.91 -118.81 108.05 1.1123 IC H3 N *C2 H4 1.1123 108.05 -118.44 112.46 1.1118 IC N C2 C3 C4 1.4786 109.91 -53.03 112.84 1.5333 IC C4 C2 *C3 H5 1.5333 112.84 120.60 108.77 1.1129 IC H5 C2 *C3 H6 1.1129 108.77 116.87 109.43 1.1112 IC C5 C3 *C4 H7 1.5331 109.85 -119.45 109.11 1.1134 IC H7 C3 *C4 H8 1.1134 109.11 -118.66 110.32 1.1121 IC C4 C1 *C5 H9 1.5331 112.20 122.14 109.47 1.1113 IC C4 C1 *C5 H10 1.5331 112.20 -120.62 108.70 1.1142 IC C1 N S1 C8 1.4749 116.10 155.34 101.17 1.7550 IC C8 N *S1 O1 1.7550 101.17 115.36 109.66 1.4390 IC O1 N *S1 O2 1.4390 109.66 133.43 107.74 1.4394 IC N S1 C8 S2 1.6550 101.17 107.94 121.66 1.7163 IC S2 S1 *C8 C7 1.7163 121.66 -168.69 127.80 1.3747 IC S1 C8 C7 C6 1.7550 127.80 170.92 113.94 1.3782 IC C6 C8 *C7 H12 1.3782 113.94 178.46 121.70 1.0840 IC C8 C7 C6 C9 1.3747 113.94 -0.60 113.25 1.3677 IC C9 C7 *C6 H11 1.3677 113.25 179.44 123.47 1.0834 IC S2 C6 *C9 H13 1.7119 110.57 180.00 129.60 1.0830 RESI WEI1 0.000 ! scaffold 1 for D3R, xxwy !RING * 6 C15 C16 C17 C18 C19 C20 !RING * 6 C7 C8 C9 C10 C11 C12 !RING * 6 C1 N1 C2 C3 C4 C5 !RING * 5 C3 C4 N2 C6 N3 GROUP ! CHARGE ATOM C1 CG321 0.09 ATOM H4 HGA2 0.09 ATOM H5 HGA2 0.09 ATOM N1 NG301 -0.48 ATOM C2 CG321 0.09 ATOM H6 HGA2 0.09 ATOM H7 HGA2 0.09 ATOM C3 CG2R51 -0.02 ATOM C4 CG2R52 0.39 ATOM C5 CG321 -0.18 ATOM H8 HGA2 0.09 ATOM H9 HGA2 0.09 ATOM S SG3O2 0.54 ATOM O1 OG2P1 -0.36 ATOM O2 OG2P1 -0.36 ATOM N2 NG2R51 0.39 ATOM C6 CG2R51 -0.45 ATOM N3 NG2R50 -0.56 ATOM C7 CG2R61 -0.115 ATOM H10 HGR61 0.115 ATOM C8 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C9 CG2R61 -0.115 ATOM H12 HGR61 0.115 ATOM C10 CG2R61 0.08 ATOM C11 CG2R61 -0.115 ATOM H13 HGR61 0.115 ATOM C12 CG2R61 -0.115 ATOM H14 HGR61 0.115 ATOM C13 CG2O1 0.63 ATOM O3 OG2D1 -0.49 ATOM N4 NG2S1 -0.47 ATOM C14 CG331 -0.08 ATOM H1 HGA3 0.09 ATOM H2 HGA3 0.09 ATOM H3 HGA3 0.09 ATOM H20 HGP1 0.31 ATOM C15 CG2R61 -0.115 ATOM H15 HGR61 0.115 ATOM C16 CG2R61 -0.115 ATOM H16 HGR61 0.115 ATOM C17 CG2R61 -0.115 ATOM H17 HGR61 0.115 ATOM C18 CG2R61 0.12 ATOM C19 CG2R61 -0.115 ATOM H18 HGR61 0.115 ATOM C20 CG2R61 -0.115 ATOM H19 HGR61 0.115 BOND C1 H4 BOND C1 H5 BOND C1 N1 BOND C1 C5 BOND N1 C2 BOND N1 S BOND C2 H6 BOND C2 H7 BOND C2 C3 BOND C3 C4 BOND C3 C6 BOND C4 C5 BOND C4 N3 BOND C5 H8 BOND C5 H9 BOND S O1 BOND S O2 BOND S C18 BOND N2 C6 BOND N2 N3 BOND N2 C10 BOND C6 C13 BOND C7 H10 BOND C7 C8 BOND C7 C12 BOND C8 H11 BOND C8 C9 BOND C9 H12 BOND C9 C10 BOND C10 C11 BOND C11 H13 BOND C11 C12 BOND C12 H14 BOND C13 O3 BOND C13 N4 BOND N4 C14 BOND N4 H20 BOND C14 H1 BOND C14 H2 BOND C14 H3 BOND C15 H15 BOND C15 C16 BOND C15 C20 BOND C16 H16 BOND C16 C17 BOND C17 H17 BOND C17 C18 BOND C18 C19 BOND C19 H18 BOND C19 C20 BOND C20 H19 IMPR C13 C6 N4 O3 IC C1 N1 C2 C3 1.4825 113.77 52.06 109.45 1.5236 IC N1 C2 C3 C4 1.4955 109.45 -19.50 120.65 1.4001 IC C2 C3 C4 C5 1.5236 120.65 -0.25 124.62 1.4972 IC C2 N1 C1 H4 1.4955 113.77 171.29 112.39 1.1130 IC H4 N1 *C1 H5 1.1130 112.39 -116.89 106.95 1.1139 IC C5 C1 N1 C2 1.5447 110.67 -64.39 113.77 1.4955 IC C2 C1 *N1 S 1.4955 113.77 149.32 119.56 1.6605 IC C1 N1 C2 C3 1.4825 113.77 52.06 109.45 1.5236 IC C3 N1 *C2 H6 1.5236 109.45 -119.47 109.32 1.1119 IC H6 N1 *C2 H7 1.1119 109.32 -118.59 111.75 1.1145 IC N1 C2 C3 C6 1.4955 109.45 158.17 132.99 1.3666 IC C6 C2 *C3 C4 1.3666 132.99 -177.66 120.65 1.4001 IC C4 C1 *C5 H8 1.4972 111.26 -120.26 109.89 1.1073 IC C4 C1 *C5 H9 1.4972 111.26 121.23 109.68 1.1098 IC C1 N1 S C18 1.4825 119.56 -90.71 105.06 1.7806 IC C18 N1 *S O1 1.7806 105.06 112.75 108.92 1.4408 IC O1 N1 *S O2 1.4408 108.92 134.69 108.76 1.4394 IC C2 C3 C6 N2 1.5236 132.99 -174.12 104.45 1.3859 IC N2 C3 *C6 C13 1.3859 104.45 -166.30 125.92 1.4733 IC C5 C3 *C4 N3 1.4972 124.62 175.69 112.39 1.3137 IC N3 C6 *N2 C10 1.3617 112.71 175.26 129.93 1.4520 IC C6 N2 C10 C11 1.3859 129.93 140.44 121.57 1.4154 IC C11 N2 *C10 C9 1.4154 121.57 178.58 120.61 1.4158 IC N2 C10 C9 C8 1.4520 120.61 179.30 121.16 1.4001 IC C8 C10 *C9 H12 1.4001 121.16 179.77 120.03 1.0817 IC C10 C9 C8 C7 1.4158 121.16 0.74 119.92 1.3990 IC C7 C9 *C8 H11 1.3990 119.92 179.76 120.12 1.0821 IC C9 C8 C7 C12 1.4001 119.92 0.61 119.98 1.3995 IC C12 C8 *C7 H10 1.3995 119.98 179.51 119.94 1.0818 IC C12 C10 *C11 H13 1.3993 120.97 179.67 119.76 1.0824 IC C11 C7 *C12 H14 1.3993 120.14 179.81 120.10 1.0810 IC C3 C6 C13 N4 1.3666 125.92 144.64 116.32 1.3392 IC N4 C6 *C13 O3 1.3392 116.32 -175.98 121.72 1.2240 IC C6 C13 N4 C14 1.4733 116.32 -173.45 123.26 1.4455 IC C14 C13 *N4 H20 1.4455 123.26 179.05 118.46 0.9932 IC C13 N4 C14 H1 1.3392 123.26 153.56 110.12 1.1127 IC H1 N4 *C14 H2 1.1127 110.12 119.91 110.61 1.1127 IC H1 N4 *C14 H3 1.1127 110.12 -119.40 111.48 1.1158 IC N1 S C18 C19 1.6605 105.06 -83.31 119.56 1.4125 IC C19 S *C18 C17 1.4125 119.56 176.43 122.04 1.4115 IC S C18 C17 C16 1.7806 122.04 -173.78 120.63 1.4017 IC C16 C18 *C17 H17 1.4017 120.63 178.60 119.87 1.0811 IC C18 C17 C16 C15 1.4115 120.63 -0.91 120.17 1.4004 IC C15 C17 *C16 H16 1.4004 120.17 179.43 119.99 1.0803 IC C17 C16 C15 C20 1.4017 120.17 -1.02 119.87 1.3984 IC C20 C16 *C15 H15 1.3984 119.87 -179.83 120.35 1.0817 IC C20 C18 *C19 H18 1.3990 120.90 -178.30 119.89 1.0814 IC C19 C15 *C20 H19 1.3990 120.05 179.51 120.06 1.0803 RESI WEI2 0.000 ! D3R set1 scaffold 2, xxwy !RING * 6 C6 C7 C8 C9 C10 C11 !RING * 6 C1 N1 C2 C3 C4 C5 !RING * 5 C3 C4 C12 C13 N2 GROUP ! CHARGE ATOM C1 CG321 0.09 ATOM H4 HGA2 0.09 ATOM H5 HGA2 0.09 ATOM N1 NG301 -0.48 ATOM C2 CG321 0.09 ATOM H6 HGA2 0.09 ATOM H7 HGA2 0.09 ATOM C3 CG2R51 0.08 ATOM C4 CG2R51 -0.06 ATOM C5 CG321 -0.18 ATOM H8 HGA2 0.09 ATOM H9 HGA2 0.09 ATOM S SG3O2 0.54 ATOM O1 OG2P1 -0.36 ATOM O2 OG2P1 -0.36 ATOM C6 CG2R61 -0.115 ATOM H10 HGR61 0.115 ATOM C7 CG2R61 -0.115 ATOM H11 HGR61 0.115 ATOM C8 CG2R61 -0.115 ATOM H12 HGR61 0.115 ATOM C9 CG2R61 0.12 ATOM C10 CG2R61 -0.115 ATOM H13 HGR61 0.115 ATOM C11 CG2R61 -0.115 ATOM H14 HGR61 0.115 ATOM C12 CG2R51 -0.18 ATOM H15 HGR51 0.18 ATOM C13 CG2R51 -0.20 ATOM H16 HGR52 0.22 ATOM N2 NG2R51 -0.20 ATOM C14 CG2O6 0.52 ATOM O3 OG2D1 -0.46 ATOM N3 NG2S1 -0.40 ATOM C15 CG331 -0.03 ATOM H1 HGA3 0.09 ATOM H2 HGA3 0.09 ATOM H3 HGA3 0.09 ATOM H17 HGP1 0.26 BOND C1 H4 BOND C1 H5 BOND C1 N1 BOND C1 C5 BOND N1 C2 BOND N1 S BOND C2 H6 BOND C2 H7 BOND C2 C3 BOND C3 C4 BOND C3 N2 BOND C4 C5 BOND C4 C12 BOND C5 H8 BOND C5 H9 BOND S O1 BOND S O2 BOND S C9 BOND C6 H10 BOND C6 C7 BOND C6 C11 BOND C7 H11 BOND C7 C8 BOND C8 H12 BOND C8 C9 BOND C9 C10 BOND C10 H13 BOND C10 C11 BOND C11 H14 BOND C12 H15 BOND C12 C13 BOND C13 H16 BOND C13 N2 BOND N2 C14 BOND C14 O3 BOND C14 N3 BOND N3 C15 BOND N3 H17 BOND C15 H1 BOND C15 H2 BOND C15 H3 IMPR C14 N2 N3 O3 IC C1 N1 C2 C3 1.4875 112.76 47.44 110.81 1.5203 IC N1 C2 C3 C4 1.4989 110.81 -19.22 124.42 1.3571 IC C2 C3 C4 C5 1.5203 124.42 5.18 120.25 1.5051 IC C5 N1 *C1 H4 1.5523 110.05 118.87 107.93 1.1122 IC H4 N1 *C1 H5 1.1122 107.93 118.03 112.18 1.1130 IC H4 C1 N1 S 1.1122 107.93 -164.38 114.66 1.6551 IC S C1 *N1 C2 1.6551 114.66 -138.15 112.76 1.4989 IC C1 N1 C2 C3 1.4875 112.76 47.44 110.81 1.5203 IC C3 N1 *C2 H6 1.5203 110.81 -119.33 109.04 1.1115 IC H6 N1 *C2 H7 1.1115 109.04 -118.44 111.74 1.1104 IC N1 C2 C3 N2 1.4989 110.81 163.44 128.38 1.3844 IC N2 C2 *C3 C4 1.3844 128.38 177.34 124.42 1.3571 IC C4 C1 *C5 H8 1.5051 113.44 -120.04 108.23 1.1125 IC C4 C1 *C5 H9 1.5051 113.44 122.75 109.22 1.1105 IC C1 N1 S C9 1.4875 114.66 163.61 102.84 1.7754 IC C9 N1 *S O1 1.7754 102.84 -110.83 109.05 1.4392 IC O1 N1 *S O2 1.4392 109.05 -136.10 110.14 1.4412 IC N1 S C9 C10 1.6551 102.84 106.26 121.38 1.4115 IC C10 S *C9 C8 1.4115 121.38 -178.13 120.10 1.4102 IC S C9 C8 C7 1.7754 120.10 178.67 120.76 1.4006 IC C7 C9 *C8 H12 1.4006 120.76 179.80 119.63 1.0801 IC C9 C8 C7 C6 1.4102 120.76 -0.43 119.96 1.3996 IC C6 C8 *C7 H11 1.3996 119.96 -179.85 120.04 1.0807 IC C8 C7 C6 C11 1.4006 119.96 0.03 120.05 1.3993 IC C11 C7 *C6 H10 1.3993 120.05 -179.74 119.99 1.0806 IC C11 C9 *C10 H13 1.3996 120.73 179.75 120.01 1.0801 IC C10 C6 *C11 H14 1.3996 120.01 -179.98 120.12 1.0804 IC C5 C3 *C4 C12 1.5051 120.25 176.83 109.04 1.3608 IC C3 C4 C12 C13 1.3571 109.04 0.29 108.86 1.3616 IC C13 C4 *C12 H15 1.3616 108.86 -179.54 125.01 1.0809 IC N2 C12 *C13 H16 1.3884 106.92 176.93 129.12 1.0828 IC C13 C3 *N2 C14 1.3884 108.02 174.70 123.84 1.4165 IC C3 N2 C14 N3 1.3844 123.84 -147.31 113.96 1.3691 IC N3 N2 *C14 O3 1.3691 113.96 177.18 123.18 1.2282 IC N2 C14 N3 C15 1.4165 113.96 177.10 120.81 1.4409 IC C15 C14 *N3 H17 1.4409 120.81 -170.91 119.06 0.9937 IC C14 N3 C15 H1 1.3691 120.81 -175.60 110.79 1.1119 IC H1 N3 *C15 H2 1.1119 110.79 119.92 110.54 1.1137 IC H1 N3 *C15 H3 1.1119 110.79 -120.38 110.41 1.1134 RESI MSCH 0.000 ! 1'-Methylspiro[cyclohexane-1,3'-indol]-2'(1'H)-one, xxwy !RING * 6 C9 C10 C11 C12 C13 C14 !RING * 6 C1 C3 C4 C5 C6 C7 !RING * 5 C5 C6 N C8 C9 GROUP ! CHARGE ATOM C1 CG2R61 -0.219 ATOM H3 HGR61 0.196 ATOM C3 CG2R61 -0.219 ATOM H4 HGR61 0.196 ATOM C4 CG2R61 -0.334 ATOM H5 HGR61 0.196 ATOM C5 CG2RC0 0.368 ATOM C6 CG2RC0 0.250 ATOM C7 CG2R61 -0.334 ATOM H6 HGR61 0.196 ATOM N NG2R53 -0.200 ATOM C2 CG331 -0.110 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 ATOM C8 CG2R53 0.066 ATOM C9 CG3C50 0.028 ATOM O OG2D1 -0.350 ATOM C10 CG321 -0.180 ATOM H1 HGA2 0.090 ATOM H2 HGA2 0.090 ATOM C11 CG321 -0.180 ATOM H7 HGA2 0.090 ATOM H11 HGA2 0.090 ATOM C12 CG321 -0.180 ATOM H8 HGA2 0.090 ATOM H12 HGA2 0.090 ATOM C13 CG321 -0.180 ATOM H9 HGA2 0.090 ATOM H13 HGA2 0.090 ATOM C14 CG321 -0.180 ATOM H10 HGA2 0.090 ATOM H14 HGA2 0.090 BOND C1 H3 BOND C1 C3 BOND C1 C7 BOND C3 H4 BOND C3 C4 BOND C4 H5 BOND C4 C5 BOND C5 C6 BOND C5 C9 BOND C6 C7 BOND C6 N BOND C7 H6 BOND N C2 BOND N C8 BOND C2 H21 BOND C2 H22 BOND C2 H23 BOND C8 C9 BOND C8 O BOND C9 C10 BOND C9 C14 BOND C10 H1 BOND C10 H2 BOND C10 C11 BOND C11 H7 BOND C11 H11 BOND C11 C12 BOND C12 H8 BOND C12 H12 BOND C12 C13 BOND C13 H9 BOND C13 H13 BOND C13 C14 BOND C14 H10 BOND C14 H14 IMPR C8 C9 N O IC C1 C3 C4 C5 1.3984 120.04 -0.81 119.75 1.3959 IC C3 C4 C5 C6 1.3999 119.75 3.61 119.91 1.4070 IC C4 C5 C6 C7 1.3959 119.91 -4.66 120.28 1.3919 IC C3 C7 *C1 H3 1.3984 120.33 179.31 120.04 1.0844 IC C7 C1 C3 C4 1.4006 120.33 -0.99 120.04 1.3999 IC C4 C1 *C3 H4 1.3999 120.04 -179.66 119.68 1.0845 IC C1 C3 C4 C5 1.3984 120.04 -0.81 119.75 1.3959 IC C5 C3 *C4 H5 1.3959 119.75 -177.97 120.86 1.0797 IC C3 C4 C5 C9 1.3999 119.75 173.93 130.66 1.4996 IC C9 C4 *C5 C6 1.4996 130.66 -170.33 119.91 1.4070 IC C6 C1 *C7 H6 1.3919 119.54 -178.99 120.39 1.0802 IC C7 C5 *C6 N 1.3919 120.28 179.12 109.73 1.3945 IC C5 C6 N C8 1.4070 109.73 -4.01 111.06 1.3849 IC C8 C6 *N C2 1.3849 111.06 177.37 126.09 1.4414 IC C6 N C2 H21 1.3945 126.09 158.90 111.09 1.1134 IC H21 N *C2 H22 1.1134 111.09 119.84 109.75 1.1113 IC H21 N *C2 H23 1.1134 111.09 -119.80 110.61 1.1109 IC C9 N *C8 O 1.5404 107.81 179.77 125.53 1.2334 IC C8 C5 *C9 C14 1.5404 102.38 119.28 110.17 1.5472 IC C8 C5 *C9 C10 1.5404 102.38 -116.31 109.11 1.5477 IC C5 C9 C10 C11 1.4996 109.11 -170.75 112.89 1.5386 IC C11 C9 *C10 H1 1.5386 112.89 119.39 108.58 1.1134 IC H1 C9 *C10 H2 1.1134 108.58 117.93 110.31 1.1129 IC C9 C10 C11 C12 1.5477 112.89 52.43 111.95 1.5335 IC C12 C10 *C11 H7 1.5335 111.95 -119.66 108.87 1.1145 IC H7 C10 *C11 H11 1.1145 108.87 -117.60 109.90 1.1117 IC C10 C11 C12 C13 1.5386 111.95 -56.46 110.89 1.5335 IC C13 C11 *C12 H8 1.5335 110.89 120.41 109.21 1.1127 IC H8 C11 *C12 H12 1.1127 109.21 118.26 109.71 1.1125 IC C14 C12 *C13 H9 1.5384 111.92 122.56 110.16 1.1118 IC H9 C12 *C13 H13 1.1118 110.16 117.43 108.31 1.1144 IC C13 C9 *C14 H10 1.5384 112.90 122.47 109.87 1.1128 IC C13 C9 *C14 H14 1.5384 112.90 -119.47 108.95 1.1127 RESI WEI3 ! D3R set2 scaffold, xxwy !RING * 6 C14 C15 C16 C17 C18 C19 !RING * 6 C9 C10 C11 N2 C12 C13 !RING * 6 C1 C3 C4 C5 C6 C7 !RING * 5 C5 C6 N1 C8 C9 GROUP ! CHARGE ATOM C1 CG2R61 -0.219 ATOM H3 HGR61 0.196 ATOM C3 CG2R61 -0.219 ATOM H4 HGR61 0.196 ATOM C4 CG2R61 -0.334 ATOM H5 HGR61 0.196 ATOM C5 CG2RC0 0.368 ATOM C6 CG2RC0 0.250 ATOM C7 CG2R61 -0.334 ATOM H6 HGR61 0.196 ATOM N1 NG2R53 -0.200 ATOM C2 CG331 -0.110 ATOM H21 HGA3 0.090 ATOM H22 HGA3 0.090 ATOM H23 HGA3 0.090 ATOM C8 CG2R53 0.066 ATOM C9 CG3C50 0.028 ATOM O1 OG2D1 -0.350 ATOM C10 CG321 -0.180 ATOM H1 HGA2 0.090 ATOM H2 HGA2 0.090 ATOM C11 CG321 0.090 ATOM H12 HGA2 0.090 ATOM H15 HGA2 0.090 ATOM N2 NG301 -0.480 ATOM C12 CG321 0.090 ATOM H13 HGA2 0.090 ATOM H16 HGA2 0.090 ATOM C13 CG321 -0.180 ATOM H14 HGA2 0.090 ATOM H17 HGA2 0.090 ATOM S SG3O2 0.540 ATOM O2 OG2P1 -0.360 ATOM O3 OG2P1 -0.360 ATOM C14 CG2R61 -0.115 ATOM H7 HGR61 0.115 ATOM C15 CG2R61 -0.115 ATOM H8 HGR61 0.115 ATOM C16 CG2R61 -0.115 ATOM H9 HGR61 0.115 ATOM C17 CG2R61 0.120 ATOM C18 CG2R61 -0.115 ATOM H10 HGR61 0.115 ATOM C19 CG2R61 -0.115 ATOM H11 HGR61 0.115 BOND C1 H3 BOND C1 C3 BOND C1 C7 BOND C3 H4 BOND C3 C4 BOND C4 H5 BOND C4 C5 BOND C5 C6 BOND C5 C9 BOND C6 C7 BOND C6 N1 BOND C7 H6 BOND N1 C2 BOND N1 C8 BOND C2 H21 BOND C2 H22 BOND C2 H23 BOND C8 C9 BOND C8 O1 BOND C9 C10 BOND C9 C13 BOND C10 H1 BOND C10 H2 BOND C10 C11 BOND C11 H12 BOND C11 H15 BOND C11 N2 BOND N2 C12 BOND N2 S BOND C12 H13 BOND C12 H16 BOND C12 C13 BOND C13 H14 BOND C13 H17 BOND S O2 BOND S O3 BOND S C17 BOND C14 H7 BOND C14 C15 BOND C14 C19 BOND C15 H8 BOND C15 C16 BOND C16 H9 BOND C16 C17 BOND C17 C18 BOND C18 H10 BOND C18 C19 BOND C19 H11 IMPR C8 C9 N1 O1 IC C1 C3 C4 C5 1.3979 120.06 -1.81 120.07 1.3979 IC C3 C4 C5 C6 1.4000 120.07 7.00 118.93 1.4115 IC C4 C5 C6 C7 1.3979 118.93 -8.84 120.76 1.3894 IC C3 C7 *C1 H3 1.3979 120.26 178.76 119.94 1.0841 IC C7 C1 C3 C4 1.3997 120.26 -1.76 120.06 1.4000 IC C4 C1 *C3 H4 1.4000 120.06 -179.50 119.61 1.0852 IC C1 C3 C4 C5 1.3979 120.06 -1.81 120.07 1.3979 IC C5 C3 *C4 H5 1.3979 120.07 -176.21 120.26 1.0791 IC C3 C4 C5 C9 1.4000 120.07 168.32 131.16 1.5014 IC C9 C4 *C5 C6 1.5014 131.16 -161.32 118.93 1.4115 IC C6 C1 *C7 H6 1.3894 119.40 -177.72 120.35 1.0806 IC C7 C5 *C6 N1 1.3894 120.76 179.16 109.88 1.3966 IC C5 C6 N1 C8 1.4115 109.88 -10.00 110.69 1.3834 IC C8 C6 *N1 C2 1.3834 110.69 173.41 127.25 1.4397 IC C6 N1 C2 H21 1.3966 127.25 147.49 110.49 1.1129 IC H21 N1 *C2 H22 1.1129 110.49 119.27 109.67 1.1120 IC H21 N1 *C2 H23 1.1129 110.49 -120.04 111.44 1.1101 IC C9 N1 *C8 O1 1.5321 107.42 179.10 126.25 1.2308 IC C8 C5 *C9 C13 1.5321 103.15 121.03 113.64 1.5454 IC C8 C5 *C9 C10 1.5321 103.15 -114.44 110.16 1.5457 IC C5 C9 C10 C11 1.5014 110.16 -162.48 110.44 1.5365 IC C11 C9 *C10 H1 1.5365 110.44 121.24 110.28 1.1116 IC H1 C9 *C10 H2 1.1116 110.28 118.30 110.64 1.1140 IC C9 C10 C11 N2 1.5457 110.44 63.21 108.81 1.4803 IC N2 C10 *C11 H12 1.4803 108.81 -119.81 110.70 1.1132 IC H12 C10 *C11 H15 1.1132 110.70 -117.81 109.26 1.1132 IC C10 C11 N2 S 1.5365 108.81 135.50 120.22 1.6513 IC S C11 *N2 C12 1.6513 120.22 -158.73 117.53 1.4735 IC C13 N2 *C12 H13 1.5363 107.10 122.44 111.22 1.1116 IC H13 N2 *C12 H16 1.1116 111.22 119.73 109.70 1.1147 IC C12 C9 *C13 H14 1.5363 111.03 120.80 110.73 1.1145 IC C12 C9 *C13 H17 1.5363 111.03 -121.05 109.88 1.1120 IC C11 N2 S C17 1.4803 120.22 -89.39 105.75 1.7776 IC C17 N2 *S O2 1.7776 105.75 111.20 109.58 1.4370 IC O2 N2 *S O3 1.4370 109.58 135.40 108.21 1.4405 IC N2 S C17 C18 1.6513 105.75 -133.09 120.25 1.4114 IC C18 S *C17 C16 1.4114 120.25 -177.67 121.38 1.4111 IC S C17 C16 C15 1.7776 121.38 179.23 120.67 1.4010 IC C15 C17 *C16 H9 1.4010 120.67 -179.37 120.09 1.0781 IC C17 C16 C15 C14 1.4111 120.67 -1.12 120.11 1.3997 IC C14 C16 *C15 H8 1.3997 120.11 -179.57 120.03 1.0812 IC C16 C15 C14 C19 1.4010 120.11 0.03 120.03 1.3997 IC C19 C15 *C14 H7 1.3997 120.03 -179.54 120.08 1.0809 IC C19 C17 *C18 H10 1.3997 121.02 179.16 119.85 1.0807 IC C18 C14 *C19 H11 1.3997 119.81 -179.69 120.22 1.0818 RESI PIPA 0.000 ! pyridyl-pyrazole, xxwy !RING * 6 C4 C5 N3 C6 C7 C8 !RING * 5 C1 C2 N1 N2 C3 GROUP ! CHARGE ATOM C1 CG2R51 -0.38 ATOM H1 HGR51 0.26 ATOM C2 CG2R52 -0.04 ATOM H2 HGR52 0.18 ATOM N1 NG2R50 -0.38 ATOM N2 NG2R51 0.17 ATOM C3 CG2R51 -0.16 ATOM H3 HGR52 0.16 ATOM C4 CG2R61 -0.115 ATOM H4 HGR61 0.115 ATOM C5 CG2R61 0.18 ATOM H5 HGR62 0.11 ATOM N3 NG2R60 -0.45 ATOM C6 CG2R64 0.35 ATOM C7 CG2R61 -0.115 ATOM H6 HGR61 0.115 ATOM C8 CG2R61 -0.115 ATOM H7 HGR61 0.115 BOND C1 H1 BOND C1 C2 BOND C1 C3 BOND C2 H2 BOND C2 N1 BOND N1 N2 BOND N2 C3 BOND N2 C6 BOND C3 H3 BOND C4 H4 BOND C4 C5 BOND C4 C8 BOND C5 H5 BOND C5 N3 BOND N3 C6 BOND C6 C7 BOND C7 H6 BOND C7 C8 BOND C8 H7 IC C1 C2 N1 N2 1.4063 111.61 -0.08 104.29 1.3616 IC N1 C2 C1 C3 1.3197 111.61 0.10 106.46 1.3593 IC C1 C3 N2 C6 1.3593 105.11 -170.14 127.46 1.4030 IC C2 C3 *C1 H1 1.4063 106.46 -179.43 126.74 1.0811 IC C3 C1 C2 N1 1.3593 106.46 0.10 111.61 1.3197 IC N1 C1 *C2 H2 1.3197 111.61 -179.82 126.63 1.0858 IC C1 C2 N1 N2 1.4063 111.61 -0.08 104.29 1.3616 IC N2 C1 *C3 H3 1.3786 105.11 178.50 131.45 1.0813 IC C3 N1 *N2 C6 1.3786 112.53 171.05 119.30 1.4030 IC N1 N2 C6 C7 1.3616 119.30 -122.71 120.79 1.4102 IC C7 N2 *C6 N3 1.4102 120.79 -178.06 118.85 1.3402 IC N2 C6 N3 C5 1.4030 118.85 179.65 122.06 1.3285 IC C6 N3 C5 C4 1.3402 122.06 -1.07 121.37 1.4010 IC C4 N3 *C5 H5 1.4010 121.37 -179.51 117.89 1.0831 IC N3 C5 C4 C8 1.3285 121.37 0.31 118.20 1.4018 IC C8 C5 *C4 H4 1.4018 118.20 179.77 120.60 1.0786 IC C8 C6 *C7 H6 1.4062 118.37 -178.46 120.92 1.0784 IC C7 C4 *C8 H7 1.4062 119.65 179.72 120.22 1.0810 RESI 2PTZ 0.000 ! 2-PHENYLTHIAZOLE, xxwy !RING * 6 C4 C5 C6 C7 C8 C9 !RING * 5 C1 C2 N C3 S GROUP ! CHARGE ATOM C1 CG2R51 -0.08 ATOM H1 HGR52 0.15 ATOM C2 CG2R51 0.08 ATOM H2 HGR52 0.13 ATOM N NG2R50 -0.60 ATOM C3 CG2R53 0.40 ATOM S SG2R50 -0.15 ATOM C4 CG2R61 -0.115 ATOM H3 HGR61 0.115 ATOM C5 CG2R61 -0.115 ATOM H4 HGR61 0.115 ATOM C6 CG2R61 -0.115 ATOM H5 HGR61 0.115 ATOM C7 CG2R61 0.07 ATOM C8 CG2R61 -0.115 ATOM H6 HGR61 0.115 ATOM C9 CG2R61 -0.115 ATOM H7 HGR61 0.115 BOND C1 H1 BOND C1 C2 BOND C1 S BOND C2 H2 BOND C2 N BOND N C3 BOND C3 S BOND C3 C7 BOND C4 H3 BOND C4 C5 BOND C4 C9 BOND C5 H4 BOND C5 C6 BOND C6 H5 BOND C6 C7 BOND C7 C8 BOND C8 H6 BOND C8 C9 BOND C9 H7 IC C1 C2 N C3 1.3712 115.35 0.15 109.59 1.3366 IC C2 N C3 C4 1.4058 109.59 -179.05 123.28 4.3098 IC N C3 C4 C5 1.3366 123.28 26.09 59.79 1.3982 IC C2 S *C1 H1 1.3712 109.67 -179.90 120.92 1.0822 IC S C1 C2 N 1.7076 109.67 0.03 115.35 1.4058 IC N C1 *C2 H2 1.4058 115.35 -179.99 127.20 1.0856 IC C1 C2 N C3 1.3712 115.35 0.15 109.59 1.3366 IC S N *C3 C7 1.7128 114.32 -179.11 123.61 1.4779 IC N C3 C7 C8 1.3366 123.61 -153.63 121.77 1.4162 IC C8 C3 *C7 C6 1.4162 121.77 179.97 120.57 1.4159 IC C3 C7 C6 C5 1.4779 120.57 179.79 121.20 1.3995 IC C5 C7 *C6 H5 1.3995 121.20 179.94 119.90 1.0818 IC C7 C6 C5 C4 1.4159 121.20 0.08 120.00 1.3982 IC C4 C6 *C5 H4 1.3982 120.00 179.91 119.96 1.0810 IC C6 C5 C4 C9 1.3995 120.00 0.10 120.00 1.3983 IC C9 C5 *C4 H3 1.3983 120.00 179.83 119.98 1.0809 IC C9 C7 *C8 H6 1.4002 121.10 -179.56 120.51 1.0806 IC C8 C4 *C9 H7 1.4002 120.06 179.91 119.93 1.0810 RESI INCA 0.000 ! N,2-Dimethyl-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide, xxwy !RING * 6 C1 C2 C3 C4 C5 C6 !RING * 5 C4 C5 N2 N1 C8 GROUP ! CHARGE ATOM C1 CG321 -0.18 ATOM H4 HGA2 0.09 ATOM H5 HGA2 0.09 ATOM C2 CG321 -0.18 ATOM H6 HGA2 0.09 ATOM H1 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H7 HGA2 0.09 ATOM H8 HGA2 0.09 ATOM C4 CG2R51 -0.02 ATOM C5 CG2R52 0.39 ATOM C6 CG321 -0.18 ATOM H9 HGA2 0.09 ATOM H10 HGA2 0.09 ATOM N1 NG2R51 0.39 ATOM C7 CG331 -0.19 ATOM H11 HGA3 0.09 ATOM H2 HGA3 0.09 ATOM H3 HGA3 0.09 ATOM C8 CG2R51 -0.45 ATOM N2 NG2R50 -0.56 ATOM C9 CG2O1 0.63 ATOM O OG2D1 -0.49 ATOM N3 NG2S1 -0.47 ATOM C10 CG331 -0.08 ATOM H12 HGA3 0.09 ATOM H14 HGA3 0.09 ATOM H15 HGA3 0.09 ATOM H13 HGP1 0.31 BOND C1 H4 BOND C1 H5 BOND C1 C2 BOND C1 C6 BOND C2 H6 BOND C2 H1 BOND C2 C3 BOND C3 H7 BOND C3 H8 BOND C3 C4 BOND C4 C5 BOND C4 C8 BOND C5 C6 BOND C5 N2 BOND C6 H9 BOND C6 H10 BOND N1 C7 BOND N1 C8 BOND N1 N2 BOND C7 H11 BOND C7 H2 BOND C7 H3 BOND C8 C9 BOND C9 O BOND C9 N3 BOND N3 C10 BOND N3 H13 BOND C10 H12 BOND C10 H14 BOND C10 H15 IMPR C9 C8 N3 O IC C1 C2 C3 C4 1.5415 112.12 -45.31 112.38 1.5056 IC C2 C3 C4 C5 1.5444 112.38 17.52 120.97 1.4039 IC C3 C4 C5 C6 1.5056 120.97 -2.62 125.67 1.5028 IC C2 C6 *C1 H4 1.5415 112.11 119.51 109.07 1.1145 IC H4 C6 *C1 H5 1.1145 109.07 117.67 109.66 1.1118 IC C6 C1 C2 C3 1.5470 112.11 59.56 112.12 1.5444 IC C3 C1 *C2 H6 1.5444 112.12 122.17 110.24 1.1119 IC H6 C1 *C2 H1 1.1119 110.24 117.54 108.37 1.1143 IC C1 C2 C3 C4 1.5415 112.12 -45.31 112.38 1.5056 IC C4 C2 *C3 H7 1.5056 112.38 -122.07 109.60 1.1128 IC H7 C2 *C3 H8 1.1128 109.60 -117.87 109.22 1.1118 IC C2 C3 C4 C8 1.5444 112.38 -162.58 132.37 1.3616 IC C8 C3 *C4 C5 1.3616 132.37 -179.90 120.97 1.4039 IC C5 C1 *C6 H9 1.5028 110.88 118.67 109.62 1.1101 IC C5 C1 *C6 H10 1.5028 110.88 -121.78 110.33 1.1100 IC C3 C4 C8 C9 1.5056 132.37 0.09 127.80 1.4721 IC C9 C4 *C8 N1 1.4721 127.80 178.75 103.95 1.3754 IC C4 C8 N1 C7 1.3616 103.95 -177.60 130.45 1.4585 IC C7 C8 *N1 N2 1.4585 130.45 178.67 113.94 1.3500 IC C8 N1 C7 H11 1.3754 130.45 156.81 111.48 1.1122 IC H11 N1 *C7 H2 1.1122 111.48 119.83 109.83 1.1089 IC H11 N1 *C7 H3 1.1122 111.48 -119.35 110.48 1.1099 IC C4 C8 C9 N3 1.3616 127.80 -150.94 116.66 1.3388 IC N3 C8 *C9 O 1.3388 116.66 178.51 122.50 1.2241 IC C8 C9 N3 C10 1.4721 116.66 179.45 122.36 1.4440 IC C10 C9 *N3 H13 1.4440 122.36 -174.73 118.15 0.9917 IC C9 N3 C10 H12 1.3388 122.36 172.40 110.67 1.1117 IC H12 N3 *C10 H14 1.1117 110.67 120.18 110.63 1.1138 IC H12 N3 *C10 H15 1.1117 110.67 -120.01 110.87 1.1148 RESI TICA 0.000 ! 4,5,6,7-Tetrahydro-1H-indole-carboxy-amide, xxwy !RING * 6 C1 C2 C3 C4 C5 C6 !RING * 5 C4 C5 C7 C8 N1 GROUP ! CHARGE ATOM C1 CG321 -0.18 ATOM H4 HGA2 0.09 ATOM H5 HGA2 0.09 ATOM C2 CG321 -0.18 ATOM H6 HGA2 0.09 ATOM H1 HGA2 0.09 ATOM C3 CG321 -0.18 ATOM H7 HGA2 0.09 ATOM H8 HGA2 0.09 ATOM C4 CG2R51 0.08 ATOM C5 CG2R51 -0.06 ATOM C6 CG321 -0.18 ATOM H9 HGA2 0.09 ATOM H10 HGA2 0.09 ATOM C7 CG2R51 -0.18 ATOM H11 HGR51 0.18 ATOM C8 CG2R51 -0.20 ATOM H12 HGR52 0.22 ATOM N1 NG2R51 -0.20 ATOM C9 CG2O6 0.52 ATOM O OG2D1 -0.46 ATOM N2 NG2S1 -0.40 ATOM C10 CG331 -0.03 ATOM H13 HGA3 0.09 ATOM H2 HGA3 0.09 ATOM H3 HGA3 0.09 ATOM H14 HGP1 0.26 BOND C1 H4 BOND C1 H5 BOND C1 C2 BOND C1 C6 BOND C2 H6 BOND C2 H1 BOND C2 C3 BOND C3 H7 BOND C3 H8 BOND C3 C4 BOND C4 C5 BOND C4 N1 BOND C5 C6 BOND C5 C7 BOND C6 H9 BOND C6 H10 BOND C7 H11 BOND C7 C8 BOND C8 H12 BOND C8 N1 BOND N1 C9 BOND C9 O BOND C9 N2 BOND N2 C10 BOND N2 H14 BOND C10 H13 BOND C10 H2 BOND C10 H3 IMPR C9 N1 N2 O IC C1 C2 C3 C4 1.5405 111.89 -40.30 112.78 1.5092 IC C2 C3 C4 C5 1.5450 112.78 13.29 123.89 1.3608 IC C3 C4 C5 C6 1.5092 123.89 -2.58 122.81 1.5071 IC C2 C6 *C1 H4 1.5405 111.51 119.43 108.99 1.1141 IC H4 C6 *C1 H5 1.1141 108.99 117.98 109.85 1.1111 IC C6 C1 C2 C3 1.5438 111.51 57.77 111.89 1.5450 IC C3 C1 *C2 H6 1.5450 111.89 122.78 110.62 1.1109 IC H6 C1 *C2 H1 1.1109 110.62 117.78 107.96 1.1142 IC C1 C2 C3 C4 1.5405 111.89 -40.30 112.78 1.5092 IC C4 C2 *C3 H7 1.5092 112.78 -122.32 109.40 1.1112 IC H7 C2 *C3 H8 1.1112 109.40 -117.98 109.18 1.1112 IC C2 C3 C4 N1 1.5450 112.78 -170.76 128.63 1.3870 IC N1 C3 *C4 C5 1.3870 128.63 -175.94 123.89 1.3608 IC C5 C1 *C6 H9 1.5071 112.18 119.46 108.78 1.1122 IC C5 C1 *C6 H10 1.5071 112.18 -122.46 109.62 1.1117 IC C6 C4 *C5 C7 1.5071 122.81 -179.43 108.71 1.3604 IC C4 C5 C7 C8 1.3608 108.71 -0.69 109.12 1.3607 IC C8 C5 *C7 H11 1.3607 109.12 179.94 124.81 1.0805 IC N1 C7 *C8 H12 1.3899 107.05 -179.31 128.48 1.0814 IC C8 C4 *N1 C9 1.3899 107.72 176.30 124.94 1.4244 IC C4 N1 C9 N2 1.3870 124.94 178.58 114.27 1.3704 IC N2 N1 *C9 O 1.3704 114.27 179.91 124.10 1.2277 IC N1 C9 N2 C10 1.4244 114.27 -179.70 121.20 1.4403 IC C10 C9 *N2 H14 1.4403 121.20 179.37 119.44 0.9913 IC C9 N2 C10 H13 1.3704 121.20 -178.00 110.53 1.1118 IC H13 N2 *C10 H2 1.1118 110.53 120.09 110.58 1.1137 IC H13 N2 *C10 H3 1.1118 110.53 -120.11 110.45 1.1134 RESI GTPG -4.00 ! guanine-triphosphate-gamma-sulphur; GTP is based on ATP; !RING 5 C4 C5 N7 C8 N9 ! S-P bond is from mono-thio phosphate sulphur in DMPR (nucleic acid patch) !RING 6 N1 C2 N3 C4 C5 C6 GROUP ! ATOM C4' CG3C51 0.16 ! ATOM H4' HGA1 0.09 ! ATOM O4' OG3C51 -0.50 ! ATOM C1' CG3C51 0.16 ! ATOM H1' HGA1 0.09 ! GROUP ! ATOM N9 NG2R51 -0.02 ! ATOM C4 CG2RC0 0.26 ! ATOM N2 NG2S3 -0.68 ! ATOM H21 HGP4 0.32 ! ATOM H22 HGP4 0.35 ! ATOM N3 NG2R62 -0.74 ! ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.62 ATOM PA PG1 1.50 ATOM O1A OG2P1 -0.82 ATOM O2A OG2P1 -0.82 ATOM O3A OG304 -0.74 ATOM PB PG1 1.50 ATOM O1B OG2P1 -0.82 ATOM O2B OG2P1 -0.82 ATOM O3B OG304 -0.86 ! charge adjusted to yield total triP of -4.0 ATOM PG PG2 1.10 ATOM O1G OG2S1 -0.90 ATOM S2G SG2P1 -0.90 ATOM O3G OG2S1 -0.90 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG S2G PG O3G BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' H3T BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR N2 H22 H21 C2 IMPR C2 N1 N3 N2 IMPR C6 C5 N1 O6 IC C4' O4' C1' N9 1.4420 105.78 -163.37 108.13 1.4764 IC O4' C1' N9 C4 1.4305 108.13 -136.89 127.39 1.3710 IC C1' N9 C4 N2 1.4764 127.39 6.13 150.02 3.4860 IC O4' C5' *C4' C3' 1.4420 114.67 125.03 118.35 1.5503 IC O4' C5' *C4' H4' 1.4420 114.67 -115.16 104.97 1.1055 IC C5' C4' O4' C1' 1.5423 114.67 171.97 105.78 1.4305 IC C4' O4' C1' N9 1.4420 105.78 -163.37 108.13 1.4764 IC N9 O4' *C1' C2' 1.4764 108.13 121.17 104.13 1.5534 IC N9 O4' *C1' H1' 1.4764 108.13 -121.94 107.09 1.1036 IC O4' C1' N9 C4 1.4305 108.13 -136.89 127.39 1.3710 IC C4 C1' *N9 C8 1.3710 127.39 177.72 126.48 1.3754 IC C1' N9 C4 C5 1.4764 127.39 179.76 106.31 1.4128 IC C5 N9 *C4 N3 1.4128 106.31 -178.46 128.31 1.3430 IC N9 C4 N3 C2 1.3710 128.31 175.57 115.52 1.3277 IC C4 N3 C2 N1 1.3430 115.52 3.70 122.28 1.3768 IC N1 N3 *C2 N2 1.3768 122.28 178.61 119.94 1.3237 IC N3 C2 N2 H21 1.3277 119.94 -175.39 124.93 0.9902 IC H21 C2 *N2 H22 0.9902 124.93 178.82 113.58 0.9982 IC N3 C2 N1 C6 1.3277 122.28 -2.22 125.11 1.3855 IC C6 C2 *N1 H1 1.3855 125.11 -175.20 118.69 1.0001 IC C5 N1 *C6 O6 1.4245 112.69 -179.39 116.95 1.2360 IC C6 C4 *C5 N7 1.4245 118.93 177.46 109.77 1.3895 IC N7 N9 *C8 H8 1.3349 113.61 177.95 120.51 1.0923 IC C3' C1' *C2' O2' 1.5545 103.87 123.34 112.69 1.4394 IC C3' C1' *C2' H2'' 1.5545 103.87 -117.06 109.79 1.1029 IC C1' C2' O2' H2' 1.5534 112.69 -125.29 108.62 0.9713 IC C2' C4' *C3' O3' 1.5545 103.51 119.24 113.14 1.4329 IC C2' C4' *C3' H3' 1.5545 103.51 -120.69 108.56 1.1024 IC C4' C3' O3' H3T 1.5503 113.14 74.05 103.43 0.9969 IC O4' C4' C5' O5' 1.4420 114.67 150.02 111.04 1.4327 IC O5' C4' *C5' H5' 1.4327 111.04 127.20 111.54 1.1095 IC O5' C4' *C5' H5'' 1.4327 111.04 -116.54 107.76 1.1081 IC C4' C5' O5' PA 1.5423 111.04 99.23 122.36 1.6318 IC C5' O5' PA O3A 1.4327 122.36 -143.19 100.14 1.6231 IC O3A O5' *PA O1A 1.6231 100.14 -119.86 102.44 1.5085 IC O1A O5' *PA O2A 1.5085 102.44 -122.24 103.62 1.5182 IC O5' PA O3A PB 1.6318 100.14 -170.74 131.13 1.6350 IC PA O3A PB O3B 1.6231 131.13 -176.00 100.40 1.6278 IC O3B O3A *PB O1B 1.6278 100.40 -116.88 105.14 1.5118 IC O1B O3A *PB O2B 1.5118 105.14 -125.57 105.14 1.5139 IC O3A PB O3B PG 1.6350 100.40 179.64 132.89 1.6667 IC PB O3B PG S2G 1.6278 132.89 130.51 104.93 1.9993 IC S2G O3B *PG O1G 1.9993 104.93 -123.51 106.86 1.4738 IC O1G O3B *PG O3G 1.4738 106.86 -116.42 103.29 1.4768 RESI GTGN 0.00 ! neutral form of guanine-triphosphate-gamma-sulphur; GTP is based on ATP; !RING 5 C4 C5 N7 C8 N9 ! S-P bond is from mono-thio phosphate sulphur in DMPR (nucleic acid patch) !RING 6 N1 C2 N3 C4 C5 C6 GROUP ! ATOM C4' CG3C51 0.16 ! ATOM H4' HGA1 0.09 ! ATOM O4' OG3C51 -0.50 ! ATOM C1' CG3C51 0.16 ! ATOM H1' HGA1 0.09 ! GROUP ! ATOM N9 NG2R51 -0.02 ! ATOM C4 CG2RC0 0.26 ! ATOM N2 NG2S3 -0.68 ! ATOM H21 HGP4 0.32 ! ATOM H22 HGP4 0.35 ! ATOM N3 NG2R62 -0.74 ! ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.68 ATOM PA PG0 1.40 ATOM O1A OG311 -0.62 ATOM H1A HGP1 0.42 ATOM O2A OG2P1 -0.62 ATOM O3A OG304 -0.68 ATOM PB PG0 1.50 ATOM O1B OG311 -0.62 ATOM H1B HGP1 0.42 ATOM O2B OG2P1 -0.62 ATOM O3B OG304 -0.53 ATOM PG PG0 1.55 ATOM O1G OG311 -0.62 ATOM H1G HGP1 0.42 ATOM S2G SG2P1 -0.62 ATOM O3G OG311 -0.62 ATOM H3G HGP1 0.42 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG S2G PG O3G BOND O3G H3G O1G H1G O1A H1A O1B H1B BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' H3T BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR N2 H22 H21 C2 IMPR C2 N1 N3 N2 IMPR C6 C5 N1 O6 IC C4' O4' C1' N9 1.4316 106.41 -164.81 108.54 1.4684 IC O4' C1' N9 C4 1.4304 108.54 -133.29 126.95 1.3717 IC C1' N9 C4 N2 1.4684 126.95 0.20 151.04 3.4961 IC O4' C5' *C4' C3' 1.4316 111.51 122.41 118.72 1.5528 IC O4' C5' *C4' H4' 1.4316 111.51 -114.48 107.06 1.1040 IC C5' C4' O4' C1' 1.5454 111.51 168.73 106.41 1.4304 IC C4' O4' C1' N9 1.4316 106.41 -164.81 108.54 1.4684 IC N9 O4' *C1' C2' 1.4684 108.54 120.95 103.07 1.5452 IC N9 O4' *C1' H1' 1.4684 108.54 -121.74 107.52 1.1023 IC O4' C1' N9 C4 1.4304 108.54 -133.29 126.95 1.3717 IC C4 C1' *N9 C8 1.3717 126.95 179.62 126.66 1.3749 IC C1' N9 C4 C5 1.4684 126.95 -179.83 105.86 1.4101 IC C5 N9 *C4 N3 1.4101 105.86 179.98 128.47 1.3462 IC N9 C4 N3 C2 1.3717 128.47 179.97 115.06 1.3347 IC C4 N3 C2 N1 1.3462 115.06 -0.01 122.07 1.3723 IC N1 N3 *C2 N2 1.3723 122.07 -179.94 120.82 1.3235 IC N3 C2 N2 H21 1.3347 120.82 179.66 123.54 0.9920 IC H21 C2 *N2 H22 0.9920 123.54 179.99 115.46 0.9951 IC N3 C2 N1 C6 1.3347 122.07 0.04 125.66 1.3816 IC C6 C2 *N1 H1 1.3816 125.66 -179.98 118.63 0.9990 IC C5 N1 *C6 O6 1.4204 112.61 179.96 117.18 1.2312 IC C6 C4 *C5 N7 1.4204 118.93 179.68 109.96 1.3886 IC N7 N9 *C8 H8 1.3271 113.44 179.23 121.32 1.0916 IC C3' C1' *C2' O2' 1.5534 103.82 122.40 112.43 1.4340 IC C3' C1' *C2' H2'' 1.5534 103.82 -116.99 109.57 1.1035 IC C1' C2' O2' H2' 1.5452 112.43 154.56 109.03 0.9624 IC C2' C4' *C3' O3' 1.5534 103.39 119.39 113.56 1.4350 IC C2' C4' *C3' H3' 1.5534 103.39 -118.91 109.50 1.1005 IC C4' C3' O3' H3T 1.5528 113.56 78.28 107.91 0.9750 IC O4' C4' C5' O5' 1.4316 111.51 149.87 111.53 1.4408 IC O5' C4' *C5' H5' 1.4408 111.53 127.94 110.79 1.1149 IC O5' C4' *C5' H5'' 1.4408 111.53 -117.21 106.65 1.1154 IC C4' C5' O5' PA 1.5454 111.53 91.98 123.49 1.5472 IC C5' O5' PA O3A 1.4408 123.49 -161.14 111.64 1.6155 IC O3A O5' *PA O1A 1.6155 111.64 -108.55 94.40 1.5475 IC O1A O5' *PA O2A 1.5475 94.40 -115.15 116.70 1.4678 IC O5' PA O1A H1A 1.5472 94.40 1.58 103.42 0.9725 IC O5' PA O3A PB 1.5472 111.64 -160.73 133.35 1.6079 IC PA O3A PB O3B 1.6155 133.35 149.84 104.67 1.6208 IC O3B O3A *PB O1B 1.6208 104.67 -115.41 109.67 1.5527 IC O1B O3A *PB O2B 1.5527 109.67 -125.05 114.37 1.4674 IC O3A PB O1B H1B 1.6079 109.67 24.46 113.04 0.9655 IC O3A PB O3B PG 1.6079 104.67 87.99 128.59 1.6262 IC PB O3B PG S2G 1.6208 128.59 -61.13 110.35 1.9687 IC S2G O3B *PG O1G 1.9687 110.35 131.51 96.59 1.5600 IC O1G O3B *PG O3G 1.5600 96.59 95.89 95.77 1.5501 IC O3B PG O1G H1G 1.6262 96.59 -65.17 112.99 0.9703 IC O3B PG O3G H3G 1.6262 95.77 -66.60 110.77 0.9640 RESI GTSS -4.00 ! guanine-triphosphate-gamma-di-sulphur; GTP is based on ATP; !RING 5 C4 C5 N7 C8 N9 ! S-P bond is from di-thio phosphate sulphur in DMPA (nucleic acid patch) !RING 6 N1 C2 N3 C4 C5 C6 GROUP ! ATOM C4' CG3C51 0.16 ! ATOM H4' HGA1 0.09 ! ATOM O4' OG3C51 -0.50 ! ATOM C1' CG3C51 0.16 ! ATOM H1' HGA1 0.09 ! GROUP ! ATOM N9 NG2R51 -0.02 ! ATOM C4 CG2RC0 0.26 ! ATOM N2 NG2S3 -0.68 ! ATOM H21 HGP4 0.32 ! ATOM H22 HGP4 0.35 ! ATOM N3 NG2R62 -0.74 ! ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.62 ATOM PA PG1 1.50 ATOM O1A OG2P1 -0.82 ATOM O2A OG2P1 -0.82 ATOM O3A OG304 -0.74 ATOM PB PG1 1.50 ATOM O1B OG2P1 -0.82 ATOM O2B OG2P1 -0.82 ATOM O3B OG304 -0.86 ATOM PG PG2 1.10 ATOM O1G OG2S1 -0.90 ATOM S2G SG2P2 -0.90 ATOM S3G SG2P2 -0.90 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG S2G PG S3G BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' H3T BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR N2 H22 H21 C2 IMPR C2 N1 N3 N2 IMPR C6 C5 N1 O6 IC C4' O4' C1' N9 1.4446 108.05 -134.67 108.63 1.4838 IC O4' C1' N9 C4 1.4315 108.63 -119.11 124.00 1.3676 IC C1' N9 C4 N2 1.4838 124.00 -1.24 149.30 3.4793 IC O4' C5' *C4' C3' 1.4446 111.04 121.60 117.93 1.5378 IC O4' C5' *C4' H4' 1.4446 111.04 -116.10 107.45 1.1068 IC C5' C4' O4' C1' 1.5360 111.04 158.96 108.05 1.4315 IC C4' O4' C1' N9 1.4446 108.05 -134.67 108.63 1.4838 IC N9 O4' *C1' C2' 1.4838 108.63 123.73 108.32 1.5527 IC N9 O4' *C1' H1' 1.4838 108.63 -118.61 105.10 1.1016 IC O4' C1' N9 C4 1.4315 108.63 -119.11 124.00 1.3676 IC C4 C1' *N9 C8 1.3676 124.00 -179.38 129.91 1.3810 IC C1' N9 C4 C5 1.4838 124.00 179.08 106.82 1.4093 IC C5 N9 *C4 N3 1.4093 106.82 179.50 127.73 1.3433 IC N9 C4 N3 C2 1.3676 127.73 178.90 115.83 1.3162 IC C4 N3 C2 N1 1.3433 115.83 0.09 122.27 1.3718 IC N1 N3 *C2 N2 1.3718 122.27 178.96 119.91 1.3224 IC N3 C2 N2 H21 1.3162 119.91 178.73 124.31 0.9856 IC H21 C2 *N2 H22 0.9856 124.31 176.83 113.48 1.0002 IC N3 C2 N1 C6 1.3162 122.27 1.33 125.43 1.3886 IC C6 C2 *N1 H1 1.3886 125.43 -179.97 118.18 0.9953 IC C5 N1 *C6 O6 1.4305 112.30 -179.64 116.50 1.2293 IC C6 C4 *C5 N7 1.4305 118.69 179.86 109.69 1.3914 IC N7 N9 *C8 H8 1.3436 113.16 -179.81 121.49 1.0971 IC C3' C1' *C2' O2' 1.5316 103.00 115.32 111.01 1.4301 IC C3' C1' *C2' H2'' 1.5316 103.00 -122.09 113.26 1.0978 IC C1' C2' O2' H2' 1.5527 111.01 -142.13 109.49 0.9696 IC C2' C4' *C3' O3' 1.5316 101.97 120.72 112.01 1.4338 IC C2' C4' *C3' H3' 1.5316 101.97 -119.25 111.24 1.1031 IC C4' C3' O3' H3T 1.5378 112.01 78.13 102.20 0.9899 IC O4' C4' C5' O5' 1.4446 111.04 157.27 112.65 1.4336 IC O5' C4' *C5' H5' 1.4336 112.65 127.06 110.67 1.1110 IC O5' C4' *C5' H5'' 1.4336 112.65 -117.61 107.19 1.1103 IC C4' C5' O5' PA 1.5360 112.65 79.47 121.40 1.6316 IC C5' O5' PA O3A 1.4336 121.40 -97.48 100.79 1.6182 IC O3A O5' *PA O1A 1.6182 100.79 -120.06 103.23 1.5080 IC O1A O5' *PA O2A 1.5080 103.23 -124.58 103.44 1.5189 IC O5' PA O3A PB 1.6316 100.79 -144.52 131.85 1.6318 IC PA O3A PB O3B 1.6182 131.85 -152.11 98.23 1.6241 IC O3B O3A *PB O1B 1.6241 98.23 -115.64 105.57 1.5099 IC O1B O3A *PB O2B 1.5099 105.57 -127.10 106.73 1.5078 IC O3A PB O3B PG 1.6318 98.23 175.38 132.34 1.6625 IC PB O3B PG S2G 1.6241 132.34 109.42 104.64 1.9911 IC S2G O3B *PG S3G 1.9911 104.64 118.90 102.66 1.9917 IC S2G O3B *PG O1G 1.9911 104.64 -120.71 105.90 1.4704 RESI GTNS 0.00 ! neutral form of guanine-triphosphate-gamma-di-sulphur; GTP is based on ATP; !RING 5 C4 C5 N7 C8 N9 ! S-P bond is from di-thio phosphate sulphur in DMPA (nucleic acid patch) !RING 6 N1 C2 N3 C4 C5 C6 GROUP ! ATOM C4' CG3C51 0.16 ! ATOM H4' HGA1 0.09 ! ATOM O4' OG3C51 -0.50 ! ATOM C1' CG3C51 0.16 ! ATOM H1' HGA1 0.09 ! GROUP ! ATOM N9 NG2R51 -0.02 ! ATOM C4 CG2RC0 0.26 ! ATOM N2 NG2S3 -0.68 ! ATOM H21 HGP4 0.32 ! ATOM H22 HGP4 0.35 ! ATOM N3 NG2R62 -0.74 ! ATOM C2 CG2R64 0.75 ATOM N1 NG2R61 -0.34 ATOM H1 HGP1 0.26 ATOM C6 CG2R63 0.54 ATOM O6 OG2D4 -0.51 ATOM C5 CG2RC0 0.00 ATOM N7 NG2R50 -0.60 ATOM C8 CG2R53 0.25 ATOM H8 HGR52 0.16 GROUP ATOM C2' CG3C51 0.14 ATOM H2'' HGA1 0.09 ATOM O2' OG311 -0.65 ATOM H2' HGP1 0.42 GROUP ATOM C3' CG3C51 0.14 ATOM H3' HGA1 0.09 ATOM O3' OG311 -0.65 ATOM H3T HGP1 0.42 GROUP ATOM C5' CG321 -0.08 ATOM H5' HGA2 0.09 ATOM H5'' HGA2 0.09 ATOM O5' OG303 -0.68 ATOM PA PG0 1.40 ATOM O1A OG311 -0.62 ATOM H1A HGP1 0.42 ATOM O2A OG2P1 -0.62 ATOM O3A OG304 -0.68 ATOM PB PG0 1.50 ATOM O1B OG311 -0.62 ATOM H1B HGP1 0.42 ATOM O2B OG2P1 -0.62 ATOM O3B OG304 -0.53 ATOM PG PG0 1.55 ATOM O1G OG311 -0.62 ATOM H1G HGP1 0.42 ATOM S2G SG2P2 -0.41 ATOM S3G SG2P2 -0.41 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG S2G PG S3G BOND O1G H1G O1A H1A O1B H1B BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' H3T BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR N2 H22 H21 C2 IMPR C2 N1 N3 N2 IMPR C6 C5 N1 O6 IC C4' O4' C1' N9 1.4307 106.53 -164.56 108.41 1.4679 IC O4' C1' N9 C4 1.4302 108.41 -135.42 126.85 1.3708 IC C1' N9 C4 N2 1.4679 126.85 -0.10 150.98 3.4956 IC O4' C5' *C4' C3' 1.4307 111.00 122.18 118.96 1.5530 IC O4' C5' *C4' H4' 1.4307 111.00 -114.34 107.22 1.1036 IC C5' C4' O4' C1' 1.5454 111.00 168.51 106.53 1.4302 IC C4' O4' C1' N9 1.4307 106.53 -164.56 108.41 1.4679 IC N9 O4' *C1' C2' 1.4679 108.41 121.12 103.28 1.5450 IC N9 O4' *C1' H1' 1.4679 108.41 -121.56 107.56 1.1023 IC O4' C1' N9 C4 1.4302 108.41 -135.42 126.85 1.3708 IC C4 C1' *N9 C8 1.3708 126.85 179.36 126.75 1.3752 IC C1' N9 C4 C5 1.4679 126.85 179.69 105.90 1.4105 IC C5 N9 *C4 N3 1.4105 105.90 -179.78 128.42 1.3460 IC N9 C4 N3 C2 1.3708 128.42 179.71 115.06 1.3339 IC C4 N3 C2 N1 1.3460 115.06 -0.22 122.07 1.3734 IC N1 N3 *C2 N2 1.3734 122.07 179.86 120.81 1.3238 IC N3 C2 N2 H21 1.3339 120.81 -179.12 123.57 0.9918 IC H21 C2 *N2 H22 0.9918 123.57 178.90 115.54 0.9954 IC N3 C2 N1 C6 1.3339 122.07 0.15 125.65 1.3819 IC C6 C2 *N1 H1 1.3819 125.65 -179.49 118.57 0.9980 IC C5 N1 *C6 O6 1.4200 112.58 179.89 117.14 1.2322 IC C6 C4 *C5 N7 1.4200 118.95 179.47 109.91 1.3886 IC N7 N9 *C8 H8 1.3268 113.42 178.87 121.40 1.0917 IC C3' C1' *C2' O2' 1.5552 103.77 122.46 112.24 1.4352 IC C3' C1' *C2' H2'' 1.5552 103.77 -117.03 109.60 1.1029 IC C1' C2' O2' H2' 1.5450 112.24 148.20 109.27 0.9618 IC C2' C4' *C3' O3' 1.5552 103.44 119.83 113.44 1.4352 IC C2' C4' *C3' H3' 1.5552 103.44 -118.77 109.48 1.1002 IC C4' C3' O3' H3T 1.5530 113.44 80.95 107.61 0.9741 IC O4' C4' C5' O5' 1.4307 111.00 149.13 111.73 1.4414 IC O5' C4' *C5' H5' 1.4414 111.73 128.28 110.77 1.1149 IC O5' C4' *C5' H5'' 1.4414 111.73 -117.20 106.57 1.1151 IC C4' C5' O5' PA 1.5454 111.73 91.76 123.07 1.5468 IC C5' O5' PA O3A 1.4414 123.07 -164.26 110.64 1.6164 IC O3A O5' *PA O1A 1.6164 110.64 -108.50 99.18 1.5497 IC O1A O5' *PA O2A 1.5497 99.18 -117.41 116.72 1.4681 IC O5' PA O1A H1A 1.5468 99.18 5.93 105.46 0.9702 IC O5' PA O3A PB 1.5468 110.64 -172.35 132.10 1.6102 IC PA O3A PB O3B 1.6164 132.10 162.80 103.89 1.6265 IC O3B O3A *PB O1B 1.6265 103.89 -114.25 107.18 1.5520 IC O1B O3A *PB O2B 1.5520 107.18 -122.71 114.08 1.4619 IC O3A PB O1B H1B 1.6102 107.18 -16.21 112.35 0.9669 IC O3A PB O3B PG 1.6102 103.89 129.67 130.51 1.6339 IC PB O3B PG S2G 1.6265 130.51 -63.88 108.32 1.9855 IC S2G O3B *PG S3G 1.9855 108.32 129.74 108.01 1.9865 IC S2G O3B *PG O1G 1.9855 108.32 -114.91 76.05 1.5620 IC O3B PG O1G H1G 1.6339 76.05 4.79 107.59 0.9693 END