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Unverified Commit 6e073b48 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2317 from jing-huang/master 

Support CHARMM psf that contains colinear type of lonepair.
parents 325fead1 75bedabe
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wrappers/python/CMakeLists.txt
View file @ 6e073b48
......@@ -59,6 +59,7 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.cif"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rtf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.crd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.gro"
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 6e073b48
......@@ -366,25 +366,30 @@ class CharmmPsfFile(object):
holder = psfsections['NUMLP NUMLPH'][1]
lonepair_list = TrackedList()
if numlp != 0 or numlph != 0:
lp_hostnum_list=[]
lp_distance_list=[]
lp_angle_list=[]
lp_dihe_list=[]
for i in range(numlp):
lpline = holder[i].split()
if len(lpline)!=6 or lpline[0] != '3' or lpline[2] != 'F' or int(lpline[1]) != 4*i+1 :
if len(lpline)!=6 or lpline[2] != 'F' :
raise CharmmPSFError('Lonepair format error')
else:
lp_hostnum_list.append(int(lpline[0]))
lp_distance_list.append(float(lpline[3]))
lp_angle_list.append(float(lpline[4]))
lp_dihe_list.append(float(lpline[5]))
lp_atom_counter=0
for i in range(numlp):
lpline = holder[int(i/2)+numlp].split()
icolumn = (i%2) * 4
id1=int(lpline[icolumn]) -1
id2=int(lpline[icolumn+1])-1
id3=int(lpline[icolumn+2])-1
id4=int(lpline[icolumn+3])-1
lonepair_list.append([id1, id2, id3, id4, lp_distance_list[i], lp_angle_list[i], lp_dihe_list[i]])
idall=[]
for j in range(lp_hostnum_list[i]+1):
iline = int((lp_atom_counter+j)/8)+numlp
icolumn = (lp_atom_counter+j)%8
idall.append(int(holder[iline].split()[icolumn])-1)
if len(idall)==3:
idall.append(-1) # use id4=-1 to mark colinear
lonepair_list.append([idall[0], idall[1], idall[2], idall[3], lp_distance_list[i], lp_angle_list[i], lp_dihe_list[i]])
lp_atom_counter += lp_hostnum_list[i]+1
# In Drude psf, here comes anisotropic section
if IsDrudePSF:
numaniso = psfsections['NUMANISO'][0]
......@@ -709,6 +714,7 @@ class CharmmPsfFile(object):
if atom.type is not None:
# This is the most reliable way of determining the element
atomic_num = atom.type.atomic_number
if atomic_num != 0:
elem = element.Element.getByAtomicNumber(atomic_num)
else:
# Figure it out from the mass
......@@ -906,16 +912,18 @@ class CharmmPsfFile(object):
bond.bond_type.req*length_conv)
# Add virtual sites
if hasattr(self, 'lonepair_list'):
if verbose: print('Adding lonepairs...')
for lpsite in self.lonepair_list:
index=lpsite[0]
atom1=lpsite[1]
atom2=lpsite[2]
atom3=lpsite[3]
if lpsite[4] > 0 : #relative
if atom3 > 0:
if lpsite[4] > 0 : # relative lonepair type
r = lpsite[4] /10.0 # in nanometer
xweights = [-1.0, 0.0, 1.0]
elif lpsite[4] < 0: # bisector
elif lpsite[4] < 0: # bisector lonepair type
r = lpsite[4] / (-10.0)
xweights = [-1.0, 0.5, 0.5]
theta = lpsite[5] * pi / 180.0
......@@ -923,6 +931,15 @@ class CharmmPsfFile(object):
p = [r*cos(theta), r*sin(theta)*cos(phi), r*sin(theta)*sin(phi)]
p = [x if abs(x) > 1e-10 else 0 for x in p] # Avoid tiny numbers caused by roundoff error
system.setVirtualSite(index, mm.LocalCoordinatesSite(atom1, atom3, atom2, mm.Vec3(1.0, 0.0, 0.0), mm.Vec3(xweights[0],xweights[1],xweights[2]), mm.Vec3(0.0, -1.0, 1.0), mm.Vec3(p[0],p[1],p[2])))
else: # colinear lonepair type
# find a real atom to be the third one for LocalCoordinatesSite
for bond in self.bond_list:
if (bond.atom1.idx == atom2 and bond.atom2.idx != atom1):
a3=bond.atom2.idx
elif (bond.atom2.idx == atom2 and bond.atom1.idx != atom1):
a3=bond.atom1.idx
r = lpsite[4] / 10.0 # in nanometer
system.setVirtualSite(index, mm.LocalCoordinatesSite(atom1, atom2, a3, mm.Vec3(1.0, 0.0, 0.0), mm.Vec3(1.0,-1.0, 0.0), mm.Vec3(0.0, -1.0, 1.0), mm.Vec3(r,0.0,0.0)))
# Add Bond forces
if verbose: print('Adding bonds...')
force = mm.HarmonicBondForce()
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 6e073b48
......@@ -116,8 +116,8 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_drude(self):
"""Tests CHARMM systems with Drude force field"""
def test_Drude(self):
"""Test CHARMM systems with Drude force field"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
......@@ -136,6 +136,29 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, -1831.54, delta=0.5)
def test_Lonepair(self):
"""Test the lonepair facilities, in particular the colinear type of lonepairs"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/chlb_cgenff.psf')
crd = CharmmCrdFile('systems/chlb_cgenff.crd')
params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
'systems/par_all36_cgenff.prm')
plat = Platform.getPlatformByName('Reference')
system = psf.createSystem(params)
con = Context(system, VerletIntegrator(2*femtoseconds), plat)
con.setPositions(crd.positions)
init_coor = con.getState(getPositions=True).getPositions()
# move the position of the lonepair and recompute its coordinates
plp=12
crd.positions[plp] = Vec3(0.5, 1.0, 1.5) * angstrom
con.setPositions(crd.positions)
con.computeVirtualSites()
new_coor = con.getState(getPositions=True).getPositions()
self.assertAlmostEqual(init_coor[plp][0]/nanometers, new_coor[plp][0]/nanometers)
self.assertAlmostEqual(init_coor[plp][1]/nanometers, new_coor[plp][1]/nanometers)
self.assertAlmostEqual(init_coor[plp][2]/nanometers, new_coor[plp][2]/nanometers)
def test_InsCode(self):
""" Test the parsing of PSF files that contain insertion codes in their residue numbers """
psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
......
wrappers/python/tests/systems/chlb_cgenff.crd 0 → 100644
View file @ 6e073b48
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
*
13 EXT
1 1 CHLB C1 1.3878616207 -0.0212925645 0.0000000000 CHLB 1 -0.1000000000
2 1 CHLB H1 1.9158187876 -0.9626017904 0.0000000000 CHLB 1 0.1500000000
3 1 CHLB C2 2.0909297432 1.1920897951 -0.0000000000 CHLB 1 -0.1150000000
4 1 CHLB H2 3.1713458379 1.1910776735 -0.0000000000 CHLB 1 0.1150000000
5 1 CHLB C3 1.3891041046 2.4061558141 -0.0000000000 CHLB 1 -0.1150000000
6 1 CHLB H3 1.9293927824 3.3420080347 -0.0000000000 CHLB 1 0.1150000000
7 1 CHLB C4 -0.0132207406 2.4068634907 -0.0000000000 CHLB 1 -0.1150000000
8 1 CHLB H4 -0.5543440865 3.3420028049 -0.0000000000 CHLB 1 0.1150000000
9 1 CHLB C5 -0.7124562630 1.1912684987 0.0000000000 CHLB 1 -0.1000000000
10 1 CHLB H5 -1.7916319741 1.1777934579 0.0000000000 CHLB 1 0.1500000000
11 1 CHLB C6 -0.0118030037 -0.0204026447 0.0000000000 CHLB 1 0.0600000000
12 1 CHLB CL -0.8809968380 -1.5259625634 0.0000000000 CHLB 1 -0.2100000000
13 1 CHLB LP -1.7009674118 -2.9462612145 0.0000000000 CHLB 1 0.0500000000
wrappers/python/tests/systems/chlb_cgenff.psf 0 → 100644
View file @ 6e073b48
PSF EXT CMAP CHEQ XPLOR
3 !NTITLE
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
13 !NATOM
1 CHLB 1 CHLB C1 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
2 CHLB 1 CHLB H1 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
3 CHLB 1 CHLB C2 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
4 CHLB 1 CHLB H2 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
5 CHLB 1 CHLB C3 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
6 CHLB 1 CHLB H3 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
7 CHLB 1 CHLB C4 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
8 CHLB 1 CHLB H4 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
9 CHLB 1 CHLB C5 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
10 CHLB 1 CHLB H5 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
11 CHLB 1 CHLB C6 CG2R61 0.600000E-01 12.0110 0 0.00000 -0.301140E-02
12 CHLB 1 CHLB CL CLGR1 -0.210000 35.4530 0 0.00000 -0.301140E-02
13 CHLB 1 CHLB LP LPH 0.500000E-01 0.00000 -1 0.00000 -0.301140E-02
13 !NBOND: bonds
1 2 1 3 3 4 3 5
5 6 5 7 7 8 7 9
9 10 9 11 11 1 11 12
12 13
18 !NTHETA: angles
2 1 3 2 1 11 3 1 11
1 3 4 1 3 5 4 3 5
3 5 6 3 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 10 9 11
1 11 9 1 11 12 9 11 12
24 !NPHI: dihedrals
1 3 5 6 1 3 5 7
1 11 9 7 1 11 9 10
2 1 3 4 2 1 3 5
2 1 11 9 2 1 11 12
3 1 11 9 3 1 11 12
3 5 7 8 3 5 7 9
4 3 1 11 4 3 5 6
4 3 5 7 5 3 1 11
5 7 9 10 5 7 9 11
6 5 7 8 6 5 7 9
7 9 11 12 8 7 9 10
8 7 9 11 10 9 11 12
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0
1 0 !NGRP NST2
0 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1
1 3 !NUMLP NUMLPH
2 1 F 1.64000 0.00000 0.00000
13 12 11
0 !NCRTERM: cross-terms
wrappers/python/tests/systems/par_all36_cgenff.prm
View file @ 6e073b48
* -------------------------------------------------------------------------- *
* CGenFF: Parameters for the Charmm General Force Field v. 3.1 *
* CGenFF: Parameters for the Charmm General Force Field v. 4.1 *
* for Small Molecule Drug Design *
* -------------------------------------------------------------------------- *
* 2017/8: If protein, nucleic acid and carbohydrate topology and parameter files
* are NOT read prior to the CGenFF files "WARNING: ATOMS IN NBFIX ' errors will
* be encountered. These can be passed by setting BOMLEV ( -2) prior to reading
* this file. In addition, when generating aromatic halogens (Cl, Br, I) with
* pre c41b/c42a versions of CHARMM "MISSING PARAMETER" errors will be
* encountered that also require setting BOMLEV ( -2).
*
 
! -------------------------------------------------------------------------- !
......@@ -11,6 +17,17 @@
! - 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! !
......@@ -27,9 +44,11 @@
! 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 !
......@@ -91,181 +110,180 @@
 
ATOMS
!hydrogens
MASS 256 HGA1 1.00800 ! alphatic proton, CH
MASS 257 HGA2 1.00800 ! alphatic proton, CH2
MASS 258 HGA3 1.00800 ! alphatic proton, CH3
MASS 259 HGA4 1.00800 ! alkene proton; RHC=
MASS 260 HGA5 1.00800 ! alkene proton; H2C=CR
MASS 261 HGA6 1.00800 ! aliphatic H on fluorinated C, monofluoro
MASS 262 HGA7 1.00800 ! aliphatic H on fluorinated C, difluoro
MASS 263 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#)
MASS 264 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#)
MASS 265 HGAAM2 1.00800 ! aliphatic H, NEUTRAL methylamine (#)
MASS -1 HGA1 1.00800 ! alphatic proton, CH
MASS -1 HGA2 1.00800 ! alphatic proton, CH2
MASS -1 HGA3 1.00800 ! alphatic proton, CH3
MASS -1 HGA4 1.00800 ! alkene proton; RHC=
MASS -1 HGA5 1.00800 ! alkene proton; H2C=CR
MASS -1 HGA6 1.00800 ! aliphatic H on fluorinated C, monofluoro
MASS -1 HGA7 1.00800 ! aliphatic H on fluorinated C, difluoro
MASS -1 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#)
MASS -1 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#)
MASS -1 HGAAM2 1.00800 ! 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 266 HGP1 1.00800 ! polar H
MASS 267 HGP2 1.00800 ! polar H, +ve charge
MASS 268 HGP3 1.00800 ! polar H, thiol
MASS 269 HGP4 1.00800 ! polar H, neutral conjugated -NH2 group (NA bases)
MASS 270 HGP5 1.00800 ! polar H on quarternary ammonium salt (choline)
MASS 271 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H
MASS 272 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#)
MASS 273 HGPAM3 1.00800 ! polar H, NEUTRAL ammonia (#)
MASS -1 HGP1 1.00800 ! polar H
MASS -1 HGP2 1.00800 ! polar H, +ve charge
MASS -1 HGP3 1.00800 ! polar H, thiol
MASS -1 HGP4 1.00800 ! polar H, neutral conjugated -NH2 group (NA bases)
MASS -1 HGP5 1.00800 ! polar H on quarternary ammonium salt (choline)
MASS -1 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H
MASS -1 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#)
MASS -1 HGPAM3 1.00800 ! 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 274 HGR51 1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene
MASS 275 HGR52 1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge
MASS 276 HGR53 1.00800 ! nonpolar H, +ve charge HIS he1(+1)
MASS 277 HGR61 1.00800 ! aromatic H
MASS 278 HGR62 1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom
MASS 279 HGR63 1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens
MASS 280 HGR71 1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo
MASS -1 HGR51 1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene
MASS -1 HGR52 1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge
MASS -1 HGR53 1.00800 ! nonpolar H, +ve charge HIS he1(+1)
MASS -1 HGR61 1.00800 ! aromatic H
MASS -1 HGR62 1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom
MASS -1 HGR63 1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens
MASS -1 HGR71 1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo
!carbons
MASS 281 CG1T1 12.01100 ! internal alkyne R-C#C
MASS 282 CG1T2 12.01100 ! terminal alkyne H-C#C
MASS 283 CG1N1 12.01100 ! C for cyano group
MASS 284 CG2D1 12.01100 ! alkene; RHC= ; imine C
MASS 285 CG2D2 12.01100 ! alkene; H2C=
MASS 286 CG2D1O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1.
MASS 287 CG2D2O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2.
MASS 288 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2
MASS 289 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2
MASS 290 CG2DC3 12.01100 ! conjugated alkenes, H2C=
MASS 291 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium
MASS 292 CG2N2 12.01100 ! conjugated C in amidinium cation
MASS 293 CG2O1 12.01100 ! carbonyl C: amides
MASS 294 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids
MASS 295 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates
MASS 296 CG2O4 12.01100 ! carbonyl C: aldehydes
MASS 297 CG2O5 12.01100 ! carbonyl C: ketones
MASS 298 CG2O6 12.01100 ! carbonyl C: urea, carbonate
MASS 299 CG2O7 12.01100 ! CO2 carbon
MASS 300 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp
MASS 301 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole
MASS 302 CG2R53 12.01100 ! 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO, kevo
MASS 303 CG2R57 12.01100 ! 5-mem ring, bipyrroles
MASS 304 CG25C1 12.01100 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond
MASS 305 CG25C2 12.01100 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond
MASS 306 CG251O 12.01100 ! same as CG2D1O but in 5-membered ring with exocyclic double bond
MASS 307 CG252O 12.01100 ! same as CG2D2O but in 5-membered ring with exocyclic double bond
MASS 308 CG2R61 12.01100 ! 6-mem aromatic C
MASS 309 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA)
MASS 310 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?)
MASS 311 CG2R64 12.01100 ! 6-mem aromatic amidine and guanidine carbon (between 2 or 3 Ns and double-bound to one of them), NA, PYRM
MASS 312 CG2R66 12.01100 ! 6-mem aromatic carbon bound to F
MASS 313 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl
MASS 314 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp
MASS 315 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene, kevo
MASS 316 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, azulene, kevo
MASS 317 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane
MASS 318 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl
MASS 319 CG311 12.01100 ! aliphatic C with 1 H, CH
MASS 320 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl
MASS 321 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+)
MASS 322 CG321 12.01100 ! aliphatic C for CH2
MASS 323 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl
MASS 324 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon
MASS 325 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (piperidine) (+)
MASS 326 CG331 12.01100 ! aliphatic C for methyl group (-CH3)
MASS 327 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+)
MASS 328 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#)
MASS 329 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#)
MASS 330 CG3AM2 12.01100 ! aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#)
MASS -1 CG1T1 12.01100 ! internal alkyne R-C#C
MASS -1 CG1T2 12.01100 ! terminal alkyne H-C#C
MASS -1 CG1N1 12.01100 ! C for cyano group
MASS -1 CG2D1 12.01100 ! alkene; RHC= ; imine C
MASS -1 CG2D2 12.01100 ! alkene; H2C=
MASS -1 CG2D1O 12.01100 ! double bond C adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1.
MASS -1 CG2D2O 12.01100 ! double bond C adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2.
MASS -1 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2
MASS -1 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2
MASS -1 CG2DC3 12.01100 ! conjugated alkenes, H2C=
MASS -1 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium
MASS -1 CG2N2 12.01100 ! conjugated C in amidinium cation
MASS -1 CG2O1 12.01100 ! carbonyl C: amides
MASS -1 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids
MASS -1 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates
MASS -1 CG2O4 12.01100 ! carbonyl C: aldehydes
MASS -1 CG2O5 12.01100 ! carbonyl C: ketones
MASS -1 CG2O6 12.01100 ! carbonyl C: urea, carbonate
MASS -1 CG2O7 12.01100 ! CO2 carbon
MASS -1 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp
MASS -1 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole
MASS -1 CG2R53 12.01100 ! 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 ! 5-mem ring, bipyrroles
MASS -1 CG25C1 12.01100 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond
MASS -1 CG25C2 12.01100 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond
MASS -1 CG251O 12.01100 ! same as CG2D1O but in 5-membered ring with exocyclic double bond
MASS -1 CG252O 12.01100 ! same as CG2D2O but in 5-membered ring with exocyclic double bond
MASS -1 CG2R61 12.01100 ! 6-mem aromatic C
MASS -1 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA)
MASS -1 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?)
MASS -1 CG2R64 12.01100 ! 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 ! 6-mem aromatic carbon bound to F
MASS -1 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl
MASS -1 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp
MASS -1 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene, kevo
MASS -1 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, azulene, kevo
MASS -1 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane
MASS -1 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl
MASS -1 CG311 12.01100 ! aliphatic C with 1 H, CH
MASS -1 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl
MASS -1 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+)
MASS -1 CG321 12.01100 ! aliphatic C for CH2
MASS -1 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl
MASS -1 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon
MASS -1 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (piperidine) (+)
MASS -1 CG331 12.01100 ! aliphatic C for methyl group (-CH3)
MASS -1 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+)
MASS -1 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#)
MASS -1 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#)
MASS -1 CG3AM2 12.01100 ! 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 331 CG3C31 12.01100 ! cyclopropyl carbon
MASS 332 CG3C41 12.01100 ! cyclobutyl carbon
MASS 333 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids)
MASS 334 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses)
MASS 335 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose)
MASS 336 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+)
MASS 337 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+)
MASS 338 CG3RC1 12.01100 ! bridgehead in bicyclic systems containing at least one 5-membered or smaller ring
MASS -1 CG3C31 12.01100 ! cyclopropyl carbon
MASS -1 CG3C41 12.01100 ! cyclobutyl carbon
MASS -1 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids)
MASS -1 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses)
MASS -1 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose)
MASS -1 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+)
MASS -1 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+)
MASS -1 CG3RC1 12.01100 ! 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 339 NG1T1 14.00700 ! N for cyano group
!MASS 340 NG1D1 14.00700 ! terminal N in azides, lsk
MASS 341 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine)
MASS 342 NG2S0 14.00700 ! N,N-disubstituted amide, proline N (CO=NRR')
MASS 343 NG2S1 14.00700 ! peptide nitrogen (CO=NHR)
MASS 344 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2)
MASS 345 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), phosphoramidate
!MASS 346 NG2S4 14.00700 ! neutral hydroxamic acid
MASS 347 NG2O1 14.00700 ! NITB, nitrobenzene
MASS 348 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium)
MASS 349 NG2R43 14.00700 ! amide in 4-memebered ring (planar), AZDO, lsk
MASS 350 NG2R50 14.00700 ! double bound neutral 5-mem planar ring, purine N7
MASS 351 NG2R51 14.00700 ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
MASS 352 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo
MASS 353 NG2R53 14.00700 ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo
MASS 354 NG2R57 14.00700 ! 5-mem ring, bipyrroles
MASS 355 NG2R60 14.00700 ! double bound neutral 6-mem planar ring, pyr1, pyzn
MASS 356 NG2R61 14.00700 ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage
MASS 357 NG2R62 14.00700 ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm
MASS 358 NG2R67 14.00700 ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.)
MASS 359 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo
MASS 360 NG301 14.00700 ! neutral trimethylamine nitrogen
MASS 361 NG311 14.00700 ! neutral dimethylamine nitrogen
MASS 362 NG321 14.00700 ! neutral methylamine nitrogen
MASS 363 NG331 14.00700 ! neutral ammonia nitrogen
MASS 364 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring
MASS 365 NG3N1 14.00700 ! N in hydrazine, HDZN
MASS 366 NG3P0 14.00700 ! quarternary N+, choline
MASS 367 NG3P1 14.00700 ! tertiary NH+ (PIP)
MASS 368 NG3P2 14.00700 ! secondary NH2+ (proline)
MASS 369 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine
MASS -1 NG1T1 14.00700 ! N for cyano group
!MASS -1 NG1D1 14.00700 ! 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-disubstituted amide, proline N (CO=NRR')
MASS -1 NG2S1 14.00700 ! peptide nitrogen (CO=NHR)
MASS -1 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2)
MASS -1 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), phosphoramidate
!MASS -1 NG2S4 14.00700 ! neutral hydroxamic acid
MASS -1 NG2O1 14.00700 ! NITB, nitrobenzene
MASS -1 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium)
MASS -1 NG2R43 14.00700 ! amide in 4-memebered ring (planar), AZDO, lsk
MASS -1 NG2R50 14.00700 ! double bound neutral 5-mem planar ring, purine N7
MASS -1 NG2R51 14.00700 ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
MASS -1 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo
MASS -1 NG2R53 14.00700 ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo
MASS -1 NG2R57 14.00700 ! 5-mem ring, bipyrroles
MASS -1 NG2R60 14.00700 ! double bound neutral 6-mem planar ring, pyr1, pyzn
MASS -1 NG2R61 14.00700 ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage
MASS -1 NG2R62 14.00700 ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm
MASS -1 NG2R67 14.00700 ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.)
MASS -1 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo
MASS -1 NG301 14.00700 ! neutral trimethylamine nitrogen
MASS -1 NG311 14.00700 ! neutral dimethylamine nitrogen
MASS -1 NG321 14.00700 ! neutral methylamine nitrogen
MASS -1 NG331 14.00700 ! neutral ammonia nitrogen
MASS -1 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring
MASS -1 NG3N1 14.00700 ! N in hydrazine, HDZN
MASS -1 NG3P0 14.00700 ! quarternary N+, choline
MASS -1 NG3P1 14.00700 ! tertiary NH+ (PIP)
MASS -1 NG3P2 14.00700 ! secondary NH2+ (proline)
MASS -1 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine
!oxygens
MASS 370 OG2D1 15.99940 ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
MASS 371 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate
MASS 372 OG2D3 15.99940 ! carbonyl O: ketones
MASS 373 OG2D4 15.99940 ! 6-mem aromatic carbonyl oxygen (nucleic bases)
MASS 374 OG2D5 15.99940 ! CO2 oxygen
MASS 375 OG2N1 15.99940 ! NITB, nitrobenzene
MASS 376 OG2P1 15.99940 ! =O in phosphate or sulfate
MASS 377 OG2R50 15.99940 ! FURA, furan
MASS 378 OG3R60 15.99940 ! O in 6-mem cyclic enol ether (PY01, PY02) or ester
MASS 379 OG301 15.99940 ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60???
MASS 380 OG302 15.99940 ! ester -O-
MASS 381 OG303 15.99940 ! phosphate/sulfate ester oxygen
MASS 382 OG304 15.99940 ! linkage oxygen in pyrophosphate/pyrosulphate
MASS 383 OG311 15.99940 ! hydroxyl oxygen
MASS 384 OG312 15.99940 ! ionized alcohol oxygen
MASS 385 OG3C31 15.99940 ! epoxide oxygen, 1EOX, 1BOX, sc
MASS 386 OG3C51 15.99940 ! 5-mem furanose ring oxygen (ether)
MASS 387 OG3C61 15.99940 ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60???
MASS -1 OG2D1 15.99940 ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
MASS -1 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate
MASS -1 OG2D3 15.99940 ! carbonyl O: ketones
MASS -1 OG2D4 15.99940 ! 6-mem aromatic carbonyl oxygen (nucleic bases)
MASS -1 OG2D5 15.99940 ! CO2 oxygen
MASS -1 OG2N1 15.99940 ! NITB, nitrobenzene
MASS -1 OG2P1 15.99940 ! =O in phosphate or sulfate
MASS -1 OG2R50 15.99940 ! FURA, furan
MASS -1 OG3R60 15.99940 ! O in 6-mem cyclic enol ether (PY01, PY02) or ester
MASS -1 OG301 15.99940 ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60???
MASS -1 OG302 15.99940 ! ester -O-
MASS -1 OG303 15.99940 ! phosphate/sulfate ester oxygen
MASS -1 OG304 15.99940 ! linkage oxygen in pyrophosphate/pyrosulphate
MASS -1 OG311 15.99940 ! hydroxyl oxygen
MASS -1 OG312 15.99940 ! ionized alcohol oxygen
MASS -1 OG3C31 15.99940 ! epoxide oxygen, 1EOX, 1BOX, sc
MASS -1 OG3C51 15.99940 ! 5-mem furanose ring oxygen (ether)
MASS -1 OG3C61 15.99940 ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60???
!sulphurs
MASS 388 SG2D1 32.06000 ! thiocarbonyl S
MASS 389 SG2R50 32.06000 ! THIP, thiophene
MASS 390 SG311 32.06000 ! sulphur, SH, -S-
MASS 391 SG301 32.06000 ! sulfur C-S-S-C type
MASS 392 SG302 32.06000 ! thiolate sulfur (-1)
MASS 393 SG3O1 32.06000 ! sulfate -1 sulfur
MASS 394 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur
MASS 395 SG3O3 32.06000 ! neutral sulfoxide sulfur
MASS -1 SG2D1 32.06000 ! thiocarbonyl S
MASS -1 SG2R50 32.06000 ! THIP, thiophene
MASS -1 SG311 32.06000 ! sulphur, SH, -S-
MASS -1 SG301 32.06000 ! sulfur C-S-S-C type
MASS -1 SG302 32.06000 ! thiolate sulfur (-1)
MASS -1 SG3O1 32.06000 ! sulfate -1 sulfur
MASS -1 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur
MASS -1 SG3O3 32.06000 ! neutral sulfoxide sulfur
!halogens
MASS 396 CLGA1 35.45300 ! CLET, DCLE, chloroethane, 1,1-dichloroethane
MASS 397 CLGA3 35.45300 ! TCLE, 1,1,1-trichloroethane
MASS 398 CLGR1 35.45300 ! CHLB, chlorobenzene
MASS 399 BRGA1 79.90400 ! BRET, bromoethane
MASS 400 BRGA2 79.90400 ! DBRE, 1,1-dibromoethane
MASS 401 BRGA3 79.90400 ! TBRE, 1,1,1-dibromoethane
MASS 402 BRGR1 79.90400 ! BROB, bromobenzene
MASS 403 IGR1 126.90447 ! IODB, iodobenzene
MASS 404 FGA1 18.99800 ! aliphatic fluorine, monofluoro
MASS 405 FGA2 18.99800 ! aliphatic fluorine, difluoro
MASS 406 FGA3 18.99800 ! aliphatic fluorine, trifluoro
MASS 407 FGP1 18.99800 ! anionic F, for ALF4 AlF4-
MASS 408 FGR1 18.99800 ! aromatic flourine
MASS -1 CLGA1 35.45300 ! CLET, DCLE, chloroethane, 1,1-dichloroethane
MASS -1 CLGA3 35.45300 ! TCLE, 1,1,1-trichloroethane
MASS -1 CLGR1 35.45300 ! CHLB, chlorobenzene
MASS -1 BRGA1 79.90400 ! BRET, bromoethane
MASS -1 BRGA2 79.90400 ! DBRE, 1,1-dibromoethane
MASS -1 BRGA3 79.90400 ! TBRE, 1,1,1-dibromoethane
MASS -1 BRGR1 79.90400 ! BROB, bromobenzene
MASS -1 IGR1 126.90447 ! IODB, iodobenzene
MASS -1 FGA1 18.99800 ! aliphatic fluorine, monofluoro
MASS -1 FGA2 18.99800 ! aliphatic fluorine, difluoro
MASS -1 FGA3 18.99800 ! aliphatic fluorine, trifluoro
MASS -1 FGP1 18.99800 ! anionic F, for ALF4 AlF4-
MASS -1 FGR1 18.99800 ! aromatic flourine
!miscellaneous
MASS 409 PG0 30.97380 ! neutral phosphate
MASS 410 PG1 30.97380 ! phosphate -1
MASS 411 PG2 30.97380 ! phosphate -2
MASS 412 ALG1 26.98154 ! Aluminum, for ALF4, AlF4-
!MASS 414 HGTIP3 1.00800 ! polar H, TIPS3P WATER HYDROGEN
!MASS 415 OGTIP3 15.99940 ! TIPS3P WATER OXYGEN
!MASS 416 DUM 0.00000 ! dummy atom
!MASS 417 HE 4.00260 ! helium
!MASS 418 NE 20.17970 ! neon
MASS -1 PG0 30.97380 ! neutral phosphate
MASS -1 PG1 30.97380 ! phosphate -1
MASS -1 PG2 30.97380 ! phosphate -2
MASS -1 ALG1 26.98154 ! Aluminum, for ALF4, AlF4-
MASS -1 LPH 0.00000 ! Lone pair for halogens
MASS -1 SG2P1 32.06000 ! mono-thio S-P bond; lsk
MASS -1 OG2S1 15.99940 ! mono-thio S-P bond modulated oxygen; lsk
MASS -1 SG2P2 32.06000 ! di-thio S-P bond; lsk
 
BONDS
CG1N1 CG2R61 345.00 1.4350 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) (MP2 by kevo)
......@@ -360,6 +378,7 @@ CG2N2 NG2D1 621.00 1.2900 ! MT2A, DH3T, fylin
CG2N2 NG2P1 475.00 1.3200 ! AMDN, amidinium; BAMI, benzamidinium; mp2 geom & molvib; pram
CG2N2 NG321 365.00 1.4200 ! MT2A, DH3T, fylin
CG2N2 SG311 187.00 1.7900 ! MT2R(+), HH3R, MT2A, DH3T, fylin
CG2O1 CG2R51 280.00 1.4750 ! INCA model for D3R, xxwy
CG2O1 CG2R61 300.00 1.4750 ! 3NAP, nicotamide. kevo: 1.45 -> 1.475
CG2O1 CG2R62 302.00 1.4800 ! NA nad/ppi, jjp1/adm jr. 7/95
CG2O1 CG311 250.00 1.4900 ! PROT Ala Dipeptide (5/91)
......@@ -404,6 +423,7 @@ CG2O5 CG311 330.00 1.5000 ! COMPDS peml re-initialized by kevo from ACO a
CG2O5 CG321 330.00 1.5000 ! BTON, butanone; from ACO, acetone; yapol
CG2O5 CG331 330.00 1.5000 ! ACO, acetone adm 11/08
CG2O5 OG2D3 700.00 1.2300 ! ACO, acetone adm 11/08
CG2O6 NG2R51 300.00 1.4000 ! TICA model for D3R, xxwy
CG2O6 NG2S1 510.00 1.3700 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo
CG2O6 NG2S2 430.00 1.3600 ! UREA, Urea. Uses a slack parameter from PROT from NG2S2 CT3, neutral glycine, adm jr. ==> re-optimize
CG2O6 OG2D1 650.00 1.2300 ! UREA, Urea. Uses a slack parameter from PROT adm jr. 4/10/91, acetamide ==> re-optimize
......@@ -434,15 +454,19 @@ CG2R51 NG3P2 330.00 1.4800 ! 2PRP, 2-pyrroline.H+, kevo
CG2R51 OG2R50 450.00 1.3710 ! FURA, furan
CG2R51 OG3C51 360.00 1.3700 ! 2DHF, 2,3-dihydrofuran, kevo
CG2R51 SG2R50 300.00 1.7300 ! THIP, thiophene
CG2R51 SG3O2 210.00 1.7300 ! TSPD model for D3R, xxwy
CG2R51 HGR51 350.00 1.0800 ! INDO/TRP
CG2R51 HGR52 375.00 1.0830 ! PROT his, adm jr., 6/27/90
CG2R52 CG2R52 400.00 1.3800 ! TRZ2, 2H-1,2,3-triazole, lf
CG2R52 CG2RC0 360.00 1.4200 ! INDA, 1H-indazole, kevo
CG2R52 CG321 295.00 1.5000 ! INCA model for D3R, xxwy
CG2R52 CG3C52 350.00 1.5050 ! 2PRZ, 2-pyrazoline, kevo
CG2R52 NG2R50 400.00 1.3150 ! PYRZ, pyrazole; 2PRZ, 2-pyrazoline, kevo
CG2R52 NG2R52 490.00 1.3000 ! 2HPP, 2H-pyrrole.H+, kevo
CG2R52 HGR52 375.00 1.0830 ! PYRZ, pyrazole
CG2R53 CG2R61 300.00 1.4400 ! 2PTZ model for D3R, xxwy
CG2R53 CG3C41 200.00 1.5600 ! AZDO, 2-azetidinone, kevo
CG2R53 CG3C50 185.00 1.5100 ! MSCH model for D3R, xxwy
CG2R53 CG3C52 300.00 1.5300 !300 350 2PDO, 2-pyrrolidinone, kevo
CG2R53 NG2R43 370.00 1.3800 ! AZDO, 2-azetidinone, kevo
CG2R53 NG2R50 400.00 1.3200 ! PROT his, ADM JR., 7/20/89
......@@ -473,6 +497,7 @@ CG2R61 CG321 230.00 1.4900 ! PROT phe,tyr, JES 8/25/89
CG2R61 CG324 230.00 1.4900 ! BPIP, N-Benzyl PIP, cacha
CG2R61 CG331 230.00 1.4900 ! PROT toluene, adm jr. 3/7/92
CG2R61 NG2O1 230.00 1.4020 ! NITB, nitrobenzene
CG2R61 NG2R51 400.00 1.4200 ! D3R set1 scaffold 1, xxwy
CG2R61 NG2R60 450.00 1.3050 ! PYR1, pyridine
CG2R61 NG2R61 380.00 1.3790 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
CG2R61 NG2R62 450.00 1.3050 ! PYRD, pyridazine
......@@ -514,6 +539,7 @@ CG2R63 OG2D4 660.00 1.2340 ! NA U,A,G par_a4 adm jr. 10/2/91
CG2R63 OG3R60 235.00 1.4000 ! RIN, coumarin, isg
CG2R63 SG2D1 373.00 1.6550 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
CG2R64 CG2RC0 360.00 1.3580 ! NA A, adm jr. 11/97
CG2R64 NG2R51 320.00 1.3700 ! PIPA model for D3R, xxwy
CG2R64 NG2R60 450.00 1.3050 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
CG2R64 NG2R61 400.00 1.3920 ! NA G
CG2R64 NG2R62 400.00 1.3420 ! NA A, adm jr. 11/97
......@@ -533,9 +559,11 @@ CG2R71 CG2R71 360.00 1.3850 ! AZUL, Azulene, kevo
CG2R71 CG2RC7 400.00 1.3800 ! AZUL, Azulene, kevo
CG2R71 HGR71 355.00 1.0900 ! AZUL, Azulene, kevo
CG2RC0 CG2RC0 360.00 1.3850 ! INDO/TRP
CG2RC0 CG3C50 240.00 1.4900 ! MSCH model for D3R, xxwy
CG2RC0 CG3C52 305.00 1.5200 ! 3HIN, 3H-indole, kevo
CG2RC0 NG2R50 310.00 1.3650 ! NA G, adm jr. 11/97
CG2RC0 NG2R51 300.00 1.3750 ! NA A, adm jr. 11/97
CG2RC0 NG2R53 360.00 1.3900 ! MSCH model for D3R, xxwy
CG2RC0 NG2R62 350.00 1.3150 ! NA G, adm jr. 11/97
CG2RC0 NG2RC0 245.00 1.4170 ! INDZ, indolizine, kevo
CG2RC0 NG3C51 330.00 1.4000 ! INDI, indoline, kevo
......@@ -585,12 +613,14 @@ CG321 CG321 222.50 1.5300 ! PROT alkane update, adm jr., 3/2/92
CG321 CG324 222.50 1.5300 ! FLAVOP PIP1,2,3
CG321 CG331 222.50 1.5280 ! PROT alkane update, adm jr., 3/2/92
CG321 CG3C31 275.00 1.5000 ! 1BOX, 1-butene oxide, sc
CG321 CG3C50 205.00 1.5200 ! MSCH model for D3R, xxwy
CG321 CG3C51 222.50 1.5280 ! TF2M, viv
CG321 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars
CG321 NG2D1 293.00 1.4400 ! EEPI, fylin
CG321 NG2R51 400.00 1.4580 ! ETRZ, 1-Ethyl-1,2,3-triazole, from CG331 NG2R51, kevo
CG321 NG2S1 320.00 1.4300 ! PROT NMA Gas & Liquid Phase IR Spectra (LK)
CG321 NG2S3 322.00 1.4400 ! NESM, N-ethyl-sulfamate, my & kevo
CG321 NG301 200.00 1.4500 ! TSPD model for D3R, xxwy
CG321 NG311 263.00 1.4740 ! AMINE aliphatic amines
CG321 NG321 263.00 1.4740 ! AMINE aliphatic amines
CG321 OG301 360.00 1.4150 ! diethylether, alex
......@@ -632,6 +662,7 @@ CG331 CG3C51 222.50 1.5280 ! TF2M, viv
CG331 CG3RC1 222.50 1.5380 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08
CG331 NG2D1 310.00 1.4400 ! RETINOL SCH1, Schiff's base, deprotonated
CG331 NG2R51 400.00 1.4580 ! NA 9-M-G/T/U, adm jr.
CG331 NG2R53 320.00 1.4300 ! MSCH model for D3R, xxwy
CG331 NG2R61 400.00 1.4560 ! NA 9-M-A/C, adm jr.
CG331 NG2S0 315.00 1.4340 ! DMA, Dimethylacetamide, xxwy
CG331 NG2S1 320.00 1.4300 ! PROT NMA Gas & Liquid Phase IR Spectra (LK)
......@@ -669,6 +700,7 @@ CG3C31 HGA1 340.00 1.0830 ! PROTMOD cyclopropane
CG3C31 HGA2 340.00 1.0830 ! PROTMOD cyclopropane
CG3C41 CG3C41 270.00 1.5400 ! CBU, cyclobutane, AZDO, 2-azetidinone, lsk
CG3C41 NG2R43 245.00 1.4500 ! AZDO, 2-azetidinone, kevo
CG3C41 OG3C51 350.00 1.4223 ! OXTN, oxetane, gmu
CG3C41 HGA2 348.00 1.0930 ! CBU, cyclobutane, AZDO, 2-azetidinone, lsk
CG3C51 CG3C51 195.00 1.5180 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
CG3C51 CG3C52 195.00 1.5180 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
......@@ -708,6 +740,7 @@ CG3C54 NG3P2 320.00 1.5150 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93
CG3C54 HGA2 309.00 1.1110 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93
CG3RC1 CG3RC1 222.50 1.5230 ! CARBOCY carbocyclic sugars
CG3RC1 NG2R51 220.00 1.4580 ! CARBOCY carbocyclic sugars
CG3RC1 NG2R53 370.00 1.4500 ! CBHH, glycoluril, (CG3C52 NG2R53), jing
CG3RC1 NG2R61 220.00 1.4560 ! CARBOCY carbocyclic sugars
CG3RC1 OG3C51 260.00 1.4200 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy
CG3RC1 HGA1 309.00 1.1110 ! CARBOCY carbocyclic sugars
......@@ -734,6 +767,7 @@ NG2S3 PG1 180.00 1.7920 ! NABAKB phosphoramidates
NG2S3 SG3O1 224.00 1.7000 ! NMSM, N-methyl-sulfamate, my (QM: 1.74; Crystal: 1.637 1.665 1.656 1.672, aver: 1.658)
NG2S3 HGP1 432.50 1.0250 ! NABAKB phosphoramidates
NG2S3 HGP4 488.00 1.0000 ! NA A,C,G, JWK, adm jr. 7/24/91
NG301 SG3O2 215.00 1.6300 ! TSPD model for D3R, xxwy
NG311 SG3O2 235.00 1.6500 ! MMSM, N-methylmethanesulfonamide and other sulfonamides,(org 1.6950) compromise between crystal and mp2, xxwy
NG311 HGP1 442.00 1.0210 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy
NG311 HGPAM1 447.80 1.0190 ! AMINE aliphatic amines
......@@ -756,21 +790,28 @@ OG2P1 PG2 400.00 1.5200 ! MP_2 reorganization, kevo
OG2P1 SG3O1 540.00 1.4480 ! LIPID methylsulfate
OG2P1 SG3O2 630.00 1.4400 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; compromise between crystal and mp2; xxwy & xhe
OG2P1 SG3O3 540.00 1.5300 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz
OG2S1 PG2 578.00 1.4770 ! mono-thio S-P bond modulated oxygen
OG303 PG0 230.00 1.6100 ! MP_0 reorganization, kevo
OG303 PG1 190.00 1.6500 ! MP_1 reorganization, kevo
OG303 PG2 150.00 1.6550 ! MP_2 reorganization, kevo
OG303 SG3O1 250.00 1.5750 ! LIPID methylsulfate
OG303 SG3O2 235.00 1.6000 ! MMST, methyl methanesulfonate, (org 1.640) compromise between crystal and mp2, xxwy
OG304 PG0 330.00 1.6750 ! mono-thio S-P bond
OG304 PG1 330.00 1.6750 ! PPI1, PPI2, METP reorganization, kevo ! pulls against attraction
OG304 PG2 300.00 1.7150 ! PPI1, METP reorganization, kevo ! pulls against very strong attraction
OG311 PG0 237.00 1.5800 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE!
OG311 PG1 237.00 1.6100 ! MP_1 reorganization, kevo
OG311 HGP1 545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,...
!OGTIP3 HGTIP3 450.00 0.9572 ! PROT FROM TIPS3P GEOM
PG0 SG2P1 260.40 1.9953 ! mono-thio S-P bond
PG0 SG2P2 260.40 1.9953 ! di-thio S-P bond
PG2 SG2P1 260.40 1.9953 ! mono-thio S-P bond
PG2 SG2P2 258.90 1.9953 ! di-thio S-P bond
SG301 SG301 173.00 2.0290 ! PROT improved CSSC torsion in DMDS 5/15/92 (FL)
SG311 HGP3 275.00 1.3250 ! PROT methanethiol pure solvent, adm jr., 6/22/92
FGP1 ALG1 205.00 1.7260 ! aluminum tetrafluoride, ALF4, w/UB
!HGTIP3 HGTIP3 0.00 1.5139 ! PROT FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
LPH CLGR1 0.00 0.0000 ! aromatic halogen to lone pair
LPH BRGR1 0.00 0.0000 ! aromatic halogen to lone pair
LPH IGR1 0.00 0.0000 ! aromatic halogen to lone pair
 
ANGLES
CG2R61 CG1N1 NG1T1 40.00 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN), yin
......@@ -962,6 +1003,8 @@ CG2DC1 CG2O1 OG2D1 80.00 122.50 ! RETINOL CROT
CG2DC2 CG2O1 NG2S1 80.00 116.50 ! RETINOL CROT
CG2DC2 CG2O1 NG2S2 85.00 113.00 80.0 2.46 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95
CG2DC2 CG2O1 OG2D1 80.00 122.50 ! RETINOL CROT
CG2R51 CG2O1 NG2S1 52.00 115.50 ! INCA model for D3R, xxwy
CG2R51 CG2O1 OG2D1 45.00 122.00 ! INCA model for D3R, xxwy
CG2R61 CG2O1 NG2S1 80.00 116.50 ! HDZ2, hydrazone model cmpd 2
CG2R61 CG2O1 NG2S2 50.00 110.23 ! 3NAP, nicotamide (PYRIDINE pyr-CONH2), yin
CG2R61 CG2O1 OG2D1 30.00 121.00 ! reverted to 3NAP, nicotamide. Kenno: compromise with NMA and HDZ2 ==> 124.5 --> 121.00
......@@ -1000,7 +1043,7 @@ NG2S0 CG2O1 HGR52 43.00 115.00 ! DMF, Dimethylformamide, xxwy
NG2S1 CG2O1 OG2D1 80.00 122.50 ! PROT NMA Vib Modes (LK)
NG2S2 CG2O1 OG2D1 75.00 122.50 50.00 2.37000 ! PROT adm jr. 4/10/91, acetamide update
NG2S2 CG2O1 HGR52 44.00 111.00 50.00 1.98000 ! PROT, formamide
OG2D1 CG2O1 HGR52 44.000 122.00 ! kevo reverted to adm jr., 5/13/91, formamide geometry and vibrations
OG2D1 CG2O1 HGR52 44.00 122.00 ! kevo reverted to adm jr., 5/13/91, formamide geometry and vibrations
CG2R61 CG2O2 OG2D1 70.00 123.10 20.00 2.4420 ! ZOIC, benzoic acid, MBOA, methylbenzoate, jal
CG2R61 CG2O2 OG302 50.00 111.00 20.00 2.3600 ! MBOA, methylbenzoate (UB term has been adjusted), jal
CG2R61 CG2O2 OG311 40.00 113.90 30.00 2.3700 ! ZOIC, benzoic acid (UB term has been adjusted), jal
......@@ -1058,6 +1101,8 @@ CG321 CG2O5 CG331 35.00 115.60 ! BTON, butanone; from ACO, acetone; yapo
CG321 CG2O5 OG2D3 75.00 122.20 ! BTON, butanone; from ACO, acetone; yapol
CG331 CG2O5 CG331 35.00 115.60 ! ACO, acetone adm 11/08
CG331 CG2O5 OG2D3 75.00 122.20 ! ACO, acetone adm 11/08
NG2R51 CG2O6 NG2S1 50.00 112.30 ! TICA model for D3R, xxwy
NG2R51 CG2O6 OG2D1 70.00 122.00 ! TICA model for D3R, xxwy
NG2S1 CG2O6 OG2D1 60.00 125.70 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo
NG2S1 CG2O6 OG302 90.00 110.30 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo
NG2S2 CG2O6 NG2S2 70.00 115.00 ! UREA, Urea
......@@ -1070,6 +1115,8 @@ SG2D1 CG2O6 SG311 70.00 124.00 ! DMTT, dimethyl trithiocarbonate, kevo
SG311 CG2O6 SG311 40.00 112.00 ! DMTT, dimethyl trithiocarbonate, kevo
NG2D1 CG2O7 OG2D5 42.00 172.00 ! MICY, EICY: isocyanates, xxwy
OG2D5 CG2O7 OG2D5 45.00 180.00 ! PROT CO2, JES; re-optimized by kevo
CG2O1 CG2R51 CG2R51 35.00 130.00 ! INCA model for D3R, xxwy
CG2O1 CG2R51 NG2R51 35.00 124.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 CG2R51 90.00 107.20 ! PYRL, pyrrole
CG2R51 CG2R51 CG2R52 90.00 106.00 ! PYRZ, pyrazole
CG2R51 CG2R51 CG2R53 100.00 116.50 ! B2FO, 5H-furan-2-one, ctsai
......@@ -1090,8 +1137,10 @@ CG2R51 CG2R51 NG3P2 120.00 111.00 ! 2PRP, 2-pyrroline.H+, kevo
CG2R51 CG2R51 OG2R50 130.00 111.70 ! FURA, furan @@@@@ Kenno: 108-->112 @@@@@
CG2R51 CG2R51 OG3C51 135.00 113.20 ! 2DHF, 2,3-dihydrofuran, kevo
CG2R51 CG2R51 SG2R50 105.00 109.00 ! THIP, thiophene
CG2R51 CG2R51 SG3O2 27.00 129.00 ! TSPD model for D3R, xxwy
CG2R51 CG2R51 HGR51 32.00 126.40 25.00 2.17300 ! INDO/TRP
CG2R51 CG2R51 HGR52 22.00 130.00 15.00 2.21500 ! PROT adm jr., 6/27/90, his
CG2R52 CG2R51 CG321 20.00 130.00 ! INCA model for D3R, xxwy
CG2R52 CG2R51 HGR51 15.00 127.60 !x 2HPR, 2H-pyrrole; 2HPP, 2H-pyrrole.H+, kevo
CG2R53 CG2R51 HGR51 10.00 117.10 ! B2FO, 5H-furan-2-one, ctsai
CG2R57 CG2R51 NG2R51 130.00 106.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51; lf
......@@ -1118,7 +1167,9 @@ NG3C51 CG2R51 HGR52 35.00 118.20 ! 2PRL, 2-pyrroline, kevo
NG3P2 CG2R51 HGR52 35.00 119.00 ! 2PRP, 2-pyrroline.H+, kevo
OG2R50 CG2R51 HGR52 50.00 118.30 ! FURA, furan @@@@@ Kenno: 122 --> 118 @@@@@
OG3C51 CG2R51 HGR52 39.00 116.80 ! 2DHF, 2,3-dihydrofuran, kevo
SG2R50 CG2R51 SG3O2 27.00 122.00 ! TSPD model for D3R, xxwy
SG2R50 CG2R51 HGR52 45.00 121.00 ! THIP, thiophene
CG2R51 CG2R52 CG321 32.00 130.00 ! INCA model for D3R, xxwy
CG2R51 CG2R52 NG2R50 110.00 110.50 ! PYRZ, pyrazole
CG2R51 CG2R52 NG2R52 121.00 110.00 ! 2HPP, 2H-pyrrole.H+ C4-C5-N1, kevo
CG2R51 CG2R52 HGR52 32.00 126.50 ! PYRZ, pyrazole
......@@ -1126,6 +1177,7 @@ CG2R52 CG2R52 NG2R50 70.00 106.00 ! TRZ2, 2H-1,2,3-triazole, lf
CG2R52 CG2R52 HGR52 30.00 131.00 ! TRZ2, 2H-1,2,3-triazole, lf
CG2RC0 CG2R52 NG2R50 150.00 110.40 ! INDA, 1H-indazole, kevo
CG2RC0 CG2R52 HGR52 32.00 126.60 ! INDA, 1H-indazole, kevo
CG321 CG2R52 NG2R50 45.00 120.00 ! INCA model for D3R, xxwy
CG3C52 CG2R52 NG2R50 170.00 112.00 !x 2PRZ, 2-pyrazoline; 3HPR, 3H-pyrrole N2-C3-C4, kevo
CG3C52 CG2R52 HGR52 47.00 125.00 !x 2PRZ, 2-pyrazoline; 3HPR, 3H-pyrrole H3-C3-C4, kevo
NG2R50 CG2R52 HGR52 32.00 123.00 ! PYRZ, pyrazole
......@@ -1140,8 +1192,12 @@ CG25C2 CG2R53 NG2R51 50.00 107.00 ! MEOI, methyleneoxindole, kevo & xxwy
CG25C2 CG2R53 OG2D1 55.00 125.50 ! MEOI, methyleneoxindole, kevo & xxwy
CG2R51 CG2R53 OG2D1 60.80 127.50 ! B2FO, 5H-furan-2-one, ctsai
CG2R51 CG2R53 OG3C51 65.50 105.00 ! B2FO, 5H-furan-2-one, ctsai
CG2R61 CG2R53 NG2R50 35.00 123.00 ! 2PTZ model for D3R, xxwy
CG2R61 CG2R53 SG2R50 25.00 119.80 ! 2PTZ model for D3R, xxwy
CG3C41 CG2R53 NG2R43 120.00 104.50 ! AZDO, 2-azetidinone, kevo
CG3C41 CG2R53 OG2D1 60.00 135.70 ! AZDO, 2-azetidinone, lsk & kevo
CG3C50 CG2R53 NG2R53 80.00 106.00 ! MSCH model for D3R, xxwy
CG3C50 CG2R53 OG2D1 55.00 126.20 ! MSCH model for D3R, xxwy
CG3C52 CG2R53 NG2R53 120.00 105.50 ! 2PDO, 2-pyrrolidinone N1-C2-C3 v, kevo
CG3C52 CG2R53 OG2D1 65.00 126.70 ! 2PDO, 2-pyrrolidinone, kevo
CG3C52 CG2R53 OG3C51 90.00 105.80 ! GBL, Gamma-butyrolactone, ctsai & kevo
......@@ -1179,6 +1235,7 @@ CG2O2 CG2R61 CG2R61 45.00 120.00 ! ZOIC, benzoic acid, MBOA, methylbenzoat
CG2O3 CG2R61 CG2R61 45.00 119.00 ! 3CB, Benzoate. Based on a slack parameter from 3ACP, 3-acetylpyridine ==> re-optimize
CG2O4 CG2R61 CG2R61 45.00 119.80 ! ALDEHYDE benzaldehyde unmodified
CG2O5 CG2R61 CG2R61 45.00 120.00 ! PHMK, PHEK, sum of equilibrium angles, kevo
CG2R53 CG2R61 CG2R61 32.00 120.00 ! 2PTZ model for D3R, xxwy
CG2R61 CG2R61 CG2R61 40.00 120.00 35.00 2.41620 ! PROT JES 8/25/89
CG2R61 CG2R61 CG2R62 40.00 119.00 35.00 2.41620 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg
CG2R61 CG2R61 CG2R63 40.00 120.00 35.00 2.41620 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
......@@ -1192,6 +1249,7 @@ CG2R61 CG2R61 CG321 45.80 120.00 ! EBEN, ethylbenzene, modified by kevo fo
CG2R61 CG2R61 CG324 45.80 120.00 ! BPIP, N-Benzyl PIP, modified by kevo for improved transferability
CG2R61 CG2R61 CG331 45.80 120.00 ! TOLU, toluene, modified by kevo for improved transferability
CG2R61 CG2R61 NG2O1 20.00 120.00 ! NITB, nitrobenzene
CG2R61 CG2R61 NG2R51 60.00 121.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 NG2R60 20.00 124.00 ! PYRIDINE pyridine, yin
CG2R61 CG2R61 NG2R61 125.00 120.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
CG2R61 CG2R61 NG2R62 20.00 124.00 ! PYRD, pyridazine
......@@ -1207,7 +1265,7 @@ CG2R61 CG2R61 OG311 45.20 120.00 ! PYRIDINE phenol, yin
CG2R61 CG2R61 OG312 40.00 120.00 ! PROT adm jr. 8/27/91, phenoxide
CG2R61 CG2R61 OG3R60 40.00 120.00 ! FEOZ, phenoxazine, erh
CG2R61 CG2R61 SG311 40.00 120.00 ! FETZ, phenothiazine, erh
CG2R61 CG2R61 SG3O1 10.0 122.3000 ! benzene sulfonic acid anion, og
CG2R61 CG2R61 SG3O1 10.00 122.30 ! benzene sulfonic acid anion, og
CG2R61 CG2R61 SG3O2 35.00 119.00 ! BSAM, benzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy
CG2R61 CG2R61 CLGR1 60.00 120.00 ! CHLB, chlorobenzene
CG2R61 CG2R61 BRGR1 45.00 120.00 ! BROB, bromobenzene
......@@ -1288,6 +1346,7 @@ NG2R62 CG2R63 OG2D4 130.00 123.80 ! NA C
NG2R67 CG2R63 OG2D4 130.00 119.70 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from NG2R61 CG2R63 OG2D4; isg
NG2R67 CG2R63 SG2D1 56.00 123.00 ! 3PH2SR, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone; from YTS2; isg
OG2D4 CG2R63 OG3R60 20.00 113.90 ! RIN, coumarin, isg
CG2R61 CG2R64 NG2R51 40.00 120.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R64 NG2R60 20.00 124.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
CG2R61 CG2R64 NG2R62 20.00 128.00 ! 18NFD, 1,8-naphthyridine, erh
CG2R61 CG2R64 NG2S1 40.00 120.00 35.00 2.4162 ! 2AMP, 2-Amino pyridine, from PACP, p-acetamide-phenol, kevo
......@@ -1297,6 +1356,7 @@ CG2R62 CG2R64 NG301 67.00 120.70 ! TMC, yxu
CG2RC0 CG2R64 NG2R62 60.00 110.70 ! NA Ade 6R)
CG2RC0 CG2R64 NG2S3 50.00 118.60 ! NA Ade
CG2RC0 CG2R64 NG301 40.00 120.00 ! M6A, yxu
NG2R51 CG2R64 NG2R60 40.00 116.00 ! PIPA model for D3R, xxwy
NG2R60 CG2R64 NG2S1 40.00 120.00 35.00 2.4162 ! 2AMP, 2-Amino pyridine, from PACP, p-acetamide-phenol, cacha (verified by kevo)
NG2R61 CG2R64 NG2R62 70.00 122.20 ! NA Gua 6R)
NG2R61 CG2R64 NG2S3 95.00 115.40 ! NA Gua n2
......@@ -1339,9 +1399,11 @@ CG2R52 CG2RC0 CG2R61 60.00 134.10 ! INDA, 1H-indazole, kevo
CG2R52 CG2RC0 CG2RC0 90.00 105.90 ! INDA, 1H-indazole, kevo
CG2R61 CG2RC0 CG2R67 50.00 120.00 ! CRBZ, carbazole, erh
CG2R61 CG2RC0 CG2RC0 50.00 120.00 !adm,dec06 110.00 ! INDO/TRP
CG2R61 CG2RC0 CG3C50 50.00 130.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 CG3C52 60.00 130.00 ! 3HIN, 3H-indole, kevo
CG2R61 CG2RC0 NG2R50 130.00 130.00 ! ZIMI, benzimidazole, kevo
CG2R61 CG2RC0 NG2R51 130.00 132.60 !adm,dec06 129.50 ! INDO/TRP
CG2R61 CG2RC0 NG2R53 50.00 130.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 NG2RC0 80.00 118.80 ! INDZ, indolizine, kevo
CG2R61 CG2RC0 NG3C51 35.00 130.70 ! INDI, indoline, kevo
CG2R61 CG2RC0 OG2R50 100.00 129.40 ! ZFUR, benzofuran, kevo
......@@ -1353,9 +1415,11 @@ CG2R64 CG2RC0 CG2RC0 60.00 121.00 ! NA Ade 6R) bridgeC5
CG2R64 CG2RC0 NG2R50 100.00 129.00 ! NA Ade bridgeC5
CG2R67 CG2RC0 CG3C52 110.00 110.00 ! FLRN, Fluorene, erh
CG2R67 CG2RC0 NG2R51 100.00 105.70 ! CRBZ, carbazole, erh
CG2RC0 CG2RC0 CG3C50 70.00 110.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 CG3C52 110.00 110.00 ! 3HIN, 3H-indole, kevo
CG2RC0 CG2RC0 NG2R50 100.00 110.00 ! NA Ade 5R) bridgeC5
CG2RC0 CG2RC0 NG2R51 100.00 105.70 ! NA Ade 5R) bridgeC4
CG2RC0 CG2RC0 NG2R53 70.00 110.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 NG2R62 60.00 127.40 ! NA Ade 6R) bridgeC4
CG2RC0 CG2RC0 NG3C51 100.00 109.30 ! INDI, indoline, kevo
CG2RC0 CG2RC0 OG2R50 110.00 110.60 ! ZFUR, benzofuran, kevo
......@@ -1412,7 +1476,7 @@ CG2O3 CG311 NG2R53 50.00 107.00 ! drug design project, xxwy
CG2O3 CG311 NG2S1 50.00 107.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters
CG2O3 CG311 OG301 45.00 109.00 ! CC321 CC3163 OC3C61 optimize on PROA, gk (not affected by mistake)
CG2O3 CG311 HGA1 50.00 109.50 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters
CG2O5 CG311 OG311 112.00 111.00 ! BIPHENYL ANALOGS unmodified, peml ! reset by kevo to value from CG2O5 CG311 OG312 (see discussion with Dan Arlow) ==> RE-OPTIMIZE !!!
CG2O5 CG311 OG311 112.00 111.00 ! BIPHENYL ANALOGS unmodified, peml ! reset by kevo to value from CG2O5 CG311 OG312 ==> RE-OPTIMIZE !!!
CG2O5 CG311 OG312 130.00 111.00 ! BIPHENYL ANALOGS unmodified, peml
CG2O5 CG311 HGA1 50.00 109.50 ! BIPHENYL ANALOGS from PROT Alanine Dipeptide ab initio calc's (LK) consistent with adm 11/08
CG2R61 CG311 CG321 51.80 107.50 ! Slack parameter from difluorotoluene picked up by FBIC ==> RE-OPTIMIZE !!!
......@@ -1536,14 +1600,19 @@ CG2O3 CG321 HGA1 50.00 109.50 ! PROT adm jr. 4/05/91, for asn,asp,gln,g
CG2O3 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters
CG2O4 CG321 CG331 60.00 113.80 ! ALDEHYDE propionaldehyde unmodified
CG2O4 CG321 CLGA1 65.00 111.82 ! ALDEHYDE chloroacetaldehyde unmodified
CG2O4 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PALD, propionaldehyde from PROT adm jr. 5/02/91, acetic acid pure solvent. Consistent with adm 11/08
CG2O4 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PALD, propionaldehyde from PROT adm jr. 5/02/91, Consistent with adm 11/08
CG2O5 CG321 CG321 60.00 113.80 ! CHON, cyclohexanone; from PALD, propionaldehyde; yapol
CG2O5 CG321 CG331 60.00 111.50 ! PHEK, phenyl ethyl ketone; from BTON, butanone; mcs
CG2O5 CG321 HGA2 50.00 109.50 ! BTON, butanone; from ACO, acetone; yapol
CG2R51 CG321 CG311 58.35 114.00 ! INDO/TRP
CG2R51 CG321 CG314 58.35 114.00 ! PROT N-terminal AA - standard parameter collided with INDO/TRP
!CG2R51 CG321 CG321 58.00 111.00 ! INCA model for D3R, xxwy
CG2R51 CG321 CG321 58.35 114.00 ! WBG, from CG2R51 CG321 CG311, yxu
CG2R51 CG321 CG331 58.35 114.00 ! INDO/TRP
CG2R51 CG321 NG301 57.00 107.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 HGA2 55.00 109.50 ! INDO/TRP
CG2R52 CG321 CG321 58.00 111.00 ! INCA model for D3R, xxwy
CG2R52 CG321 HGA2 50.00 109.50 ! INCA model for D3R, xxwy
CG2R61 CG321 CG2R61 51.80 107.50 ! PYRIDINE pyr_CH2C6H5, yin
CG2R61 CG321 CG311 51.80 107.50 ! PROT PARALLH19 (JES)
CG2R61 CG321 CG314 51.80 107.50 ! PROT PARALLH19 (JES)
......@@ -1579,9 +1648,11 @@ CG314 CG321 HGA2 33.43 110.10 22.53 2.17900 ! PROT alkanes
CG321 CG321 CG321 58.35 113.60 11.16 2.56100 ! PROT alkane update, adm jr., 3/2/92
CG321 CG321 CG324 58.35 110.50 11.16 2.56100 ! FLAVOP PIP1,2,3
CG321 CG321 CG331 58.00 115.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92
CG321 CG321 CG3C50 53.00 112.00 8.00 2.56100 ! MSCH model for D3R, xxwy
CG321 CG321 CG3RC1 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars
CG321 CG321 NG2D1 103.00 112.00 ! EEPI, from CG321 CG321 NG2S1, fylin
CG321 CG321 NG2S1 70.00 113.50 ! slack parameter picked up by 3CPD ==> re-optimize?
CG321 CG321 NG301 57.00 107.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG311 43.70 110.00 ! K2Cn, cgenff_compromise, kevo
CG321 CG321 OG301 45.00 111.50 ! diethylether, alex
CG321 CG321 OG302 75.70 110.10 ! LIPID acetic acid
......@@ -1619,6 +1690,7 @@ CG331 CG321 CLGA1 71.00 112.20 ! CLET
CG331 CG321 BRGA1 71.00 111.00 ! BRET
CG331 CG321 HGA2 34.60 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92
CG3C31 CG321 HGA2 42.00 109.00 ! 1BOX, 1-butene oxide, sc
CG3C50 CG321 HGA2 32.00 109.00 22.53 2.17900 ! MSCH model for D3R, xxwy
CG3C51 CG321 OG301 75.70 110.10 ! 3POMP, 3-phenoxymethylpyrrolidine; standard parameter; kevo
CG3C51 CG321 OG303 75.70 110.10 ! LIPID acetic acid
CG3C51 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89
......@@ -1630,6 +1702,7 @@ NG2D1 CG321 HGA2 45.00 107.50 ! EEPI, from NG2D1 CG331 HGA3, fylin
NG2R51 CG321 HGA2 33.43 110.10 ! ETRZ, 1-Ethyl-1,2,3-triazole, from NG2R51 CG331 HGA3, kevo
NG2S1 CG321 HGA2 51.50 109.50 ! PROT from NG2S1 CG331 HA, for lactams, adm jr.
NG2S3 CG321 HGA2 38.30 105.20 ! NESM, N-ethyl-sulfamate, my & kevo
NG301 CG321 HGA2 32.40 109.00 ! TSPD model for D3R, xxwy
NG311 CG321 NG311 90.00 113.00 ! OBTZ, 1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine, xxwy
NG311 CG321 HGA2 32.40 109.50 50.00 2.1300 ! PEI polymers, kevo
NG321 CG321 HGA2 32.40 109.50 50.00 2.1400 ! AMINE aliphatic amines
......@@ -1721,6 +1794,7 @@ CG3C51 CG331 HGA3 34.60 110.10 22.53 2.179 ! TF2M viv
CG3RC1 CG331 HGA3 33.43 110.10 22.53 2.179 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08
NG2D1 CG331 HGA3 42.00 113.50 ! RETINOL SCH1, Schiff's base, deprotonated
NG2R51 CG331 HGA3 33.43 110.10 ! NA FOR 9-M-G(C), adm jr.
NG2R53 CG331 HGA3 39.00 109.00 ! MSCH model for D3R, xxwy
NG2R61 CG331 HGA3 33.43 110.10 22.53 2.179 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm
NG2S0 CG331 HGA3 50.00 105.00 ! DMF, Dimethylformamide, xxwy
NG2S1 CG331 HGA3 51.50 109.50 ! PROT NMA crystal (JCS)
......@@ -1769,9 +1843,15 @@ CG2R53 CG3C41 CG3C41 90.00 106.00 ! AZDO, 2-azetidinone, lsk & kevo
CG2R53 CG3C41 HGA2 46.00 112.30 ! AZDO, 2-azetidinone, lsk & kevo
CG3C41 CG3C41 CG3C41 70.00 106.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk
CG3C41 CG3C41 NG2R43 90.00 104.50 ! AZDO, 2-azetidinone, lsk & kevo
CG3C41 CG3C41 OG3C51 89.00 99.49 ! OXTN, oxetane, gmu
CG3C41 CG3C41 HGA2 46.00 110.50 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk
NG2R43 CG3C41 HGA2 51.00 110.80 ! AZDO, 2-azetidinone, lsk & kevo
OG3C51 CG3C41 HGA2 55.00 112.00 ! OXTN, oxetane, gmu
HGA2 CG3C41 HGA2 28.00 105.00 5.40 1.8067 ! CBU, cyclobutane; AZDO, 2-azetidinone; QM by Nikolay Simakov; lsk & kevo
CG2R53 CG3C50 CG2RC0 45.00 103.00 ! MSCH model for D3R, xxwy
CG2R53 CG3C50 CG321 45.00 103.00 ! MSCH model for D3R, xxwy
CG2RC0 CG3C50 CG321 45.00 105.00 ! MSCH model for D3R, xxwy
CG321 CG3C50 CG321 58.00 110.00 11.16 2.56100 ! MSCH model for D3R, xxwy
CG2O1 CG3C51 CG3C52 52.00 112.30 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93
CG2O1 CG3C51 NG2S0 50.00 108.20 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93
CG2O1 CG3C51 HGA1 50.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93
......@@ -1942,9 +2022,12 @@ CG3C52 CG3RC1 NG2R51 70.00 113.70 ! CARBOCY carbocyclic sugars
CG3C52 CG3RC1 NG2R61 70.00 113.70 ! CARBOCY carbocyclic sugars
CG3C52 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 NG2R51 70.00 113.70 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 NG2R53 70.00 113.70 ! CBHH, glycoluril, (CG3RC1 CG3RC1 NG2R51), jing
CG3RC1 CG3RC1 NG2R61 70.00 113.70 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 OG3C51 50.00 109.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy
CG3RC1 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars
NG2R53 CG3RC1 NG2R53 70.00 117.00 ! CBHH, glycoluril, jing
NG2R53 CG3RC1 HGA1 59.00 111.00 ! CBHH, glycoluril, (NG2R53 CG3C52 HGA2), jing
OG3C51 CG3RC1 OG3C51 70.00 105.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy
OG3C51 CG3RC1 HGA1 55.00 106.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy
CG2D1 NG2D1 CG321 74.50 111.00 ! EEPI, from CG2D1 NG2D1 CG331, fylin
......@@ -1992,10 +2075,15 @@ CG2R53 NG2R50 NG2R51 100.00 101.00 ! TRZ4, triazole124, xxwy
CG2R53 NG2R50 OG2R50 50.00 103.00 ! OXD4, oxadiazole124, xxwy
NG2R50 NG2R50 NG2R51 160.00 102.20 ! TRZ3, triazole123 @@@@@ Kenno: 101.9 --> 102.2 @@@@@
NG2R50 NG2R50 OG2R50 110.00 103.00 ! OXAD, oxadiazole123 @@@@@ Kenno: 105.5 --> 103.0 @@@@@
CG2O6 NG2R51 CG2R51 30.00 125.50 ! TICA model for D3R, xxwy
CG2R51 NG2R51 CG2R51 100.00 109.00 ! PYRL, pyrrole
CG2R51 NG2R51 CG2R53 130.00 107.50 ! PROT his, adm jr., 6/27/90
CG2R51 NG2R51 CG2R61 40.00 127.00 ! D3R set1 scaffold 1, xxwy
CG2R51 NG2R51 CG2R64 35.00 128.00 ! PIPA model for D3R, xxwy
CG2R51 NG2R51 CG2RC0 85.00 110.00 ! adm,dec06(112.0)INDO/TRP
CG2R51 NG2R51 CG321 70.00 127.10 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo
!CG2R51 NG2R51 CG331 40.00 127.00 ! INCA model for D3R, xxwy
CG2R51 NG2R51 CG331 70.00 127.80 ! RCG, from G, cgenff_xyu, yxu
CG2R51 NG2R51 CG3C51 130.00 126.00 ! NA
CG2R51 NG2R51 NG2R50 160.00 115.00 ! PYRZ, pyrazole
CG2R51 NG2R51 HGP1 30.00 125.50 20.00 2.15000 ! PROT his, adm jr., 6/27/90
......@@ -2005,6 +2093,8 @@ CG2R53 NG2R51 CG3C51 45.00 126.30 ! NA G
CG2R53 NG2R51 CG3RC1 45.00 127.60 ! CARBOCY carbocyclic sugars
CG2R53 NG2R51 NG2R50 130.00 114.00 ! TRZ4, triazole124, xxwy
CG2R53 NG2R51 HGP1 30.00 127.00 20.00 2.14000 ! PROT his, adm jr., 6/27/90
CG2R61 NG2R51 NG2R50 40.00 118.00 ! D3R set1 scaffold 1, xxwy
CG2R64 NG2R51 NG2R50 35.00 117.00 ! PIPA model for D3R, xxwy
CG2RC0 NG2R51 CG2RC0 85.00 110.00 ! CRBZ, carbazole, erh
CG2RC0 NG2R51 CG331 70.00 125.90 ! NA 9-M-G, adm jr.
CG2RC0 NG2R51 CG3C51 45.00 126.50 ! NA G
......@@ -2012,6 +2102,7 @@ CG2RC0 NG2R51 CG3RC1 45.00 126.50 ! CARBOCY carbocyclic sugars
CG2RC0 NG2R51 NG2R50 190.00 114.50 ! INDA, 1H-indazole, kevo
CG2RC0 NG2R51 HGP1 28.00 126.00 ! INDO/TRP
CG321 NG2R51 NG2R50 70.00 117.90 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo
CG331 NG2R51 NG2R50 40.00 118.00 ! INCA model for D3R, xxwy
NG2R50 NG2R51 NG2R50 90.00 121.00 ! TRZ2, 2H-1,2,3-triazole, lf
NG2R50 NG2R51 HGP1 32.00 119.50 ! PYRZ, pyrazole
CG2R51 NG2R52 CG2R53 145.00 108.00 ! PROT his, ADM JR., 7/20/89
......@@ -2026,10 +2117,15 @@ CG251O NG2R53 HGP1 38.00 123.00 ! MHYO, 5-methylenehydantoin, xxwy
CG252O NG2R53 CG2R53 116.00 117.50 ! MHYO, 5-methylenehydantoin, xxwy
CG252O NG2R53 HGP1 38.00 123.00 ! MHYO, 5-methylenehydantoin, xxwy
CG2R53 NG2R53 CG2R53 55.00 120.50 ! MRDN, methylidene rhodanine, kevo & xxwy
CG2R53 NG2R53 CG2RC0 35.00 111.00 ! MSCH model for D3R, xxwy
CG2R53 NG2R53 CG311 50.00 120.00 ! drug design project, xxwy
CG2R53 NG2R53 CG331 30.00 124.00 ! MSCH model for D3R, xxwy
CG2R53 NG2R53 CG3C52 75.00 111.00 ! 2PDO, 2-pyrrolidinone C5-N1-C2 v, kevo
CG2R53 NG2R53 CG3RC1 75.00 112.00 ! CBHH, glycoluril, jing
CG2R53 NG2R53 HGP1 38.00 119.50 ! 2PDO, 2-pyrrolidinone (H1-N1-C2), kevo
CG2RC0 NG2R53 CG331 30.00 125.00 ! MSCH model for D3R, xxwy
CG3C52 NG2R53 HGP1 38.00 116.00 ! 2PDO, 2-pyrrolidinone (C5-N1-H1), kevo
CG3RC1 NG2R53 HGP1 38.00 116.00 ! CBHH, glycoluril, (CG3C52 NG2R53 HGP1), jing
CG2R51 NG2R57 CG2R51 100.00 109.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 NG2R51 CG2R51; lf
CG2R51 NG2R57 CG2R57 42.00 125.50 ! 13BPO, 1,3-bipyrrole, lf
CG2R51 NG2R57 NG2R57 54.00 125.50 ! 11BPO, 1,1-bipyrrole, lf
......@@ -2113,6 +2209,8 @@ CG2D2O NG301 CG2D2O 20.00 114.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi
CG2D2O NG301 CG3C51 70.00 121.70 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95
CG2R61 NG301 CG331 48.00 113.50 ! TMC, trimethylcytosine, yxu; DMAN, N,N-dimethylaniline, kevo
CG2R64 NG301 CG331 48.00 113.50 ! TMC, trimethylcytosine, yxu
CG321 NG301 CG321 70.00 112.00 ! TSPD model for D3R, xxwy
CG321 NG301 SG3O2 35.00 111.00 ! TSPD model for D3R, xxwy
CG331 NG301 CG331 42.50 116.00 ! TMC, trimethylcytosine, yxu; DMAN, N,N-dimethylaniline, kevo
CG3AM0 NG301 CG3AM0 53.00 110.90 ! AMINE aliphatic amines
CG2D1O NG311 CG2D1O 20.00 114.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95
......@@ -2216,6 +2314,7 @@ CG2O6 OG302 CG331 40.00 111.00 ! DMCB & DMCA, dimethyl carbamate & carbo
CG2R61 OG303 PG1 90.00 120.00 20.00 2.30 ! PROTNA phenol phosphate, 6/94, adm jr.
CG2R61 OG303 SG3O2 33.00 108.00 ! PMST, phenyl methanesulfonate, PSMT, phenyl sulfamate, xxwy
CG311 OG303 PG2 20.00 120.00 35.00 2.33 ! NA IP_2
CG321 OG303 PG0 20.00 120.00 35.00 2.33000 ! mono-thio S-P bond
CG321 OG303 PG1 20.00 120.00 35.00 2.33 ! NA !Reorganization: PC and others
CG321 OG303 PG2 20.00 120.00 35.00 2.33 ! NA !Reorganization: TH5P and others
CG321 OG303 SG3O1 15.00 109.00 27.00 1.90 ! LIPID methylsulfate
......@@ -2226,6 +2325,7 @@ CG331 OG303 SG3O1 15.00 109.00 27.00 1.90 ! LIPID methylsulfate
CG331 OG303 SG3O2 48.00 113.00 ! MMST, methyl methanesulfonate, xxwy
CG3C51 OG303 PG1 20.00 120.00 35.0 2.33 ! BPNP and others
CG3C51 OG303 PG2 20.00 120.00 35.0 2.33 ! TH3P and others
PG0 OG304 PG0 45.00 143.00 40.00 3.25000 ! mono-thio S-P bond
PG1 OG304 PG1 45.00 143.00 40.0 3.25 ! PPI2, METP reorganization, kevo
PG1 OG304 PG2 45.00 139.50 40.0 3.05 ! PPI1, METP reorganization, kevo
CG2O2 OG311 HGP1 55.00 115.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent
......@@ -2244,6 +2344,7 @@ CG2R51 OG3C51 CG2R53 85.00 104.00 ! A2FO, 3H-furan-2-one, ctsai
CG2R51 OG3C51 CG3C52 125.00 104.40 ! 2DHF, 2,3-dihydrofuran, kevo
CG2R53 OG3C51 CG3C52 90.00 107.10 ! GBL, Gamma-butyrolactone, ctsai
CG2RC0 OG3C51 CG3C52 76.00 108.05 !107.15 ZDOL, 1,3-benzodioxole, kevo
CG3C41 OG3C51 CG3C41 55.00 89.12 ! OXTN, oxetane, gmu (CG3C52 OG3C51 CG3C52)
CG3C51 OG3C51 CG3C51 95.00 111.00 ! THF 10/21/05, viv
CG3C51 OG3C51 CG3C52 95.00 111.00 ! THF 10/21/05, viv
CG3C51 OG3C51 CG3C53 110.00 108.00 ! NA
......@@ -2256,11 +2357,23 @@ CG2D2O OG3R60 CG2D2O 40.00 99.00 ! PY01, 4h-pyran, maintain 720 in ring
CG2D2O OG3R60 CG321 20.00 99.00 ! PY02, 2h-pyran
CG2R61 OG3R60 CG2R61 40.00 115.00 ! FEOZ, phenoxazine, erh
CG2R62 OG3R60 CG2R63 102.00 126.50 ! RIN, coumarin, isg
!HGTIP3 OGTIP3 HGTIP3 55.00 104.52 ! PROT TIP3P GEOMETRY, ADM JR.
OG2P1 PG0 OG303 98.90 111.60 ! LIPID phosphate !Reorganization:MP_0 RE-OPTIMIZE!
OG2P1 PG0 OG304 98.90 111.60 ! mono-thio S-P bond
OG2P1 PG0 OG311 98.90 108.23 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE!
OG2P1 PG0 SG2P1 75.00 131.03 ! mono-thio S-P bond
OG303 PG0 OG303 48.10 108.00 ! GTP neutral
OG303 PG0 OG304 48.10 108.00 ! mono-thio S-P bond
OG303 PG0 OG311 48.10 108.00 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE!
OG303 PG0 SG2P1 98.90 111.60 ! mono-thio S-P bond
OG303 PG0 SG2P2 98.90 111.60 ! di-thio S-P bond
OG304 PG0 OG304 48.10 108.00 ! mono-thio S-P bond
OG304 PG0 OG311 48.10 108.00 ! mono-thio S-P bond
OG304 PG0 SG2P1 96.80 112.84 ! mono-thio S-P bond
OG304 PG0 SG2P2 96.80 112.84 ! di-thio S-P bond
OG311 PG0 OG311 98.90 104.00 ! NA MP_0, ADM Jr.
OG311 PG0 SG2P1 75.00 131.03 ! mono-thio S-P bond
OG311 PG0 SG2P2 75.00 131.03 ! di-thio S-P bond
SG2P2 PG0 SG2P2 92.40 128.47 ! di-thio S-P bond
CG312 PG1 OG2P1 98.90 94.00 ! BDFP, Difuorobenzylphosphonate \ re-optimize?
CG312 PG1 OG311 90.10 90.00 ! BDFP, BDFD, Difuorobenzylphosphonate
CG321 PG1 OG2P1 98.90 103.00 ! BDFP, Benzylphosphonate \ re-optimize?
......@@ -2281,6 +2394,17 @@ CG321 PG2 OG2P1 98.90 103.00 ! BDFD, Benzylphosphonate / re-optimize?
OG2P1 PG2 OG2P1 104.00 121.00 ! MP_2 reorganization, kevo
OG2P1 PG2 OG303 88.90 111.00 ! MP_2 reorganization, kevo
OG2P1 PG2 OG304 88.90 111.60 ! NA nad/ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1, PPI2
OG2P1 PG2 SG2P1 75.00 131.03 ! mono-thio S-P bond
OG2S1 PG2 OG2S1 104.00 121.00 ! mono-thio S-P bond
OG2S1 PG2 OG303 88.90 111.00 ! mono-thio S-P bond
OG2S1 PG2 OG304 88.90 111.60 ! mono-thio S-P bond
OG2S1 PG2 SG2P1 75.00 131.03 ! mono-thio S-P bond
OG2S1 PG2 SG2P2 75.00 131.03 ! di-thio S-P bond
OG303 PG2 SG2P1 88.90 111.00 ! mono-thio S-P bond
OG303 PG2 SG2P2 88.90 111.00 ! di-thio S-P bond
OG304 PG2 SG2P1 96.80 112.84 ! mono-thio S-P bond
OG304 PG2 SG2P2 96.80 112.84 ! di-thio S-P bond
SG2P2 PG2 SG2P2 92.40 128.47 ! di-thio S-P bond
CG2R51 SG2R50 CG2R51 105.00 95.00 ! THIP, thiophene
CG2R51 SG2R50 CG2R53 110.00 97.00 ! THAZ, thiazole @@@@@ Kenno: 95 --> 97 @@@@@
CG2R51 SG2R50 CG2RC0 70.00 99.50 ! ZTHP, benzothiophene, kevo
......@@ -2305,6 +2429,9 @@ CG331 SG3O1 OG2P1 85.00 100.00 ! MSNA, methyl sulfonate, xhe
NG2S3 SG3O1 OG2P1 33.20 94.20 ! NMSM, N-methyl-sulfamate, my
OG2P1 SG3O1 OG2P1 130.00 109.47 35.0 2.45 ! LIPID methylsulfate
OG2P1 SG3O1 OG303 85.00 98.00 ! LIPID methylsulfate
CG2R51 SG3O2 NG301 50.00 97.00 ! TSPD model for D3R, xxwy
CG2R51 SG3O2 OG2P1 70.00 106.50 ! TSPD model for D3R, xxwy
CG2R61 SG3O2 NG301 50.00 97.00 ! D3R set1 scaffold 2, xxwy
CG2R61 SG3O2 NG311 70.00 97.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy
CG2R61 SG3O2 NG321 60.00 98.00 ! BSAM, benzenesulfonamide, xxwy
CG2R61 SG3O2 OG2P1 60.00 101.00 ! BSAM, benzenesulfonamide, xxwy
......@@ -2316,6 +2443,7 @@ CG331 SG3O2 NG311 73.00 103.00 ! MMSM, N-methylmethanesulfonamide; PMSM,
CG331 SG3O2 NG321 83.00 101.00 ! MSAM, methanesulfonamide, xxwy
CG331 SG3O2 OG2P1 79.00 108.50 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; xxwy & xhe
CG331 SG3O2 OG303 93.00 96.00 ! MMST, methyl methanesulfonate, xxwy
NG301 SG3O2 OG2P1 70.00 108.50 ! TSPD model for D3R, xxwy
NG311 SG3O2 NG311 83.10 102.30 ! MESI, N-methyl,N'-ethylsulfamide, rting
NG311 SG3O2 OG2P1 75.00 110.50 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy
NG321 SG3O2 OG2P1 80.00 111.00 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy
......@@ -2329,7 +2457,6 @@ CG331 SG3O3 OG2P1 79.00 106.75 ! DMSO, dimethylsulfoxide (ML Strader, et
FGP1 ALG1 FGP1 23.00 109.47 15.0 2.81855 ! aluminum tetrafluoride, ALF4, tetrahedral
 
DIHEDRALS
!HGA3 CG1T1 CG1T1 HGA3 0.0005 3 180.00 !!Just a test! 2BTY, 2-butyne, kevo
CG2R53 CG251O CG25C1 CG2R53 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy
CG2R53 CG251O CG25C1 CG2RC0 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy
NG2R53 CG251O CG25C1 CG2R53 3.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy
......@@ -2930,6 +3057,14 @@ NG321 CG2N2 SG311 CG321 0.3300 4 0.00 ! DH3T, fylin
NG321 CG2N2 SG311 CG331 0.6400 1 180.00 ! MT2A, fylin
NG321 CG2N2 SG311 CG331 1.1200 2 180.00 ! MT2A, fylin
NG321 CG2N2 SG311 CG331 0.3300 4 0.00 ! MT2A, fylin
NG2S1 CG2O1 CG2R51 CG2R51 1.7000 2 180.00 ! INCA model for D3R, xxwy
NG2S1 CG2O1 CG2R51 CG2R51 0.3600 4 0.00 ! INCA model for D3R, xxwy
NG2S1 CG2O1 CG2R51 NG2R51 1.7000 2 180.00 ! INCA model for D3R, xxwy
NG2S1 CG2O1 CG2R51 NG2R51 0.3600 4 0.00 ! INCA model for D3R, xxwy
OG2D1 CG2O1 CG2R51 CG2R51 1.7000 2 180.00 ! INCA model for D3R, xxwy
OG2D1 CG2O1 CG2R51 CG2R51 0.3600 4 0.00 ! INCA model for D3R, xxwy
OG2D1 CG2O1 CG2R51 NG2R51 1.7000 2 180.00 ! INCA model for D3R, xxwy
OG2D1 CG2O1 CG2R51 NG2R51 0.3600 4 0.00 ! INCA model for D3R, xxwy
NG2S1 CG2O1 CG2R61 CG2R61 1.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2
NG2S1 CG2O1 CG2R61 CG2RC0 1.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2
NG2S2 CG2O1 CG2R61 CG2R61 1.0000 2 180.00 ! 3NAP, nicotinamide (PYRIDINE pyr-CONH2), yin
......@@ -3106,6 +3241,9 @@ CG2DC2 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! RETINOL FRET
CG2DC2 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! RETINOL CROT
CG2DC2 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! RETINOL CROT
CG2DC2 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! RETINOL CROT
CG2R51 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2O1 NG2S1 CG331 4.0000 2 180.00 ! INCA model for D3R, xxwy
CG2R51 CG2O1 NG2S1 HGP1 1.0000 2 180.00 ! INCA model for D3R, xxwy
CG2R61 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! 3CPD, Gamma-3-Amide Pyridine Lysine CDCA Amide; from HDZ2, hydrazone model cmpd 2; cacha
CG2R61 CG2O1 NG2S1 CG321 4.0000 2 180.00 ! 3CPD, Gamma-3-Amide Pyridine Lysine CDCA Amide; from HDZ2, hydrazone model cmpd 2; cacha
CG2R61 CG2O1 NG2S1 NG2D1 1.6000 1 0.00 ! HDZ2, hydrazone model cmpd 2
......@@ -3340,6 +3478,13 @@ CG2R61 CG2O5 CG331 HGA3 0.1000 3 0.00 ! 3ACP, 3-acetylpyridine; res
CG321 CG2O5 CG331 HGA3 0.1000 3 0.00 ! BTON, butanone; from ACO, acetone; yapol
CG331 CG2O5 CG331 HGA3 0.1000 3 0.00 ! ketone, RIMP2/cc-pVTZ//MP2/6-31G(d), adm 11/08
OG2D3 CG2O5 CG331 HGA3 0.0000 3 0.00 ! 3ACP, ACO; ketone, RIMP2/cc-pVTZ//MP2/6-31G(d), adm 11/08
NG2S1 CG2O6 NG2R51 CG2R51 1.4300 2 180.00 ! TICA model for D3R, xxwy
NG2S1 CG2O6 NG2R51 CG2R51 0.1800 4 0.00 ! TICA model for D3R, xxwy
OG2D1 CG2O6 NG2R51 CG2R51 1.4300 2 180.00 ! TICA model for D3R, xxwy
OG2D1 CG2O6 NG2R51 CG2R51 0.1800 4 0.00 ! TICA model for D3R, xxwy
NG2R51 CG2O6 NG2S1 CG331 8.0000 2 180.00 ! TICA model for D3R, xxwy
NG2R51 CG2O6 NG2S1 CG331 0.9500 4 0.00 ! TICA model for D3R, xxwy
NG2R51 CG2O6 NG2S1 HGP1 4.0000 2 180.00 ! TICA model for D3R, xxwy
NG2S1 CG2O6 NG2S1 CG331 1.6000 1 0.00 ! S132R, from NMTU, pram
NG2S1 CG2O6 NG2S1 CG331 2.5000 2 180.00 ! S132R, from NMTU, pram
OG2D1 CG2O6 NG2S1 CG321 4.0000 2 180.00 ! DECB, diethyl carbamate, from DMCB, cacha & xxwy
......@@ -3376,15 +3521,20 @@ SG2D1 CG2O6 SG311 CG331 2.1300 2 180.00 ! DMTT, dimethyl trithiocarbo
SG311 CG2O6 SG311 CG331 0.1000 1 0.00 ! DMTT, dimethyl trithiocarbonate, kevo
SG311 CG2O6 SG311 CG331 2.1300 2 180.00 ! DMTT, dimethyl trithiocarbonate, kevo
OG2D5 CG2O7 NG2D1 CG331 0.4000 2 180.00 ! MICY, methyl isocyanate, xxwy
CG2O1 CG2R51 CG2R51 CG2R52 0.0000 2 180.00 ! INCA model for D3R, xxwy
CG2O1 CG2R51 CG2R51 CG321 0.0000 2 180.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 CG2R51 CG2R51 15.0000 2 180.00 ! PYRL, pyrrole
CG2R51 CG2R51 CG2R51 CG2RC0 2.0000 2 180.00 ! INDZ, indolizine, kevo
CG2R51 CG2R51 CG2R51 CG2RC7 9.0000 2 180.00 ! AZUL, Azulene, kevo
!CG2R51 CG2R51 CG2R51 CG321 3.0000 2 180.00 ! TICA model for D3R, xxwy
CG2R51 CG2R51 CG2R51 CG321 4.3000 2 180.00 ! hpiz, from DWG, yxu
CG2R51 CG2R51 CG2R51 CG3C52 4.0000 2 180.00 ! CPDE, cyclopentadiene, kevo
CG2R51 CG2R51 CG2R51 NG2R51 4.0000 2 180.00 ! PYRL, pyrrole
CG2R51 CG2R51 CG2R51 NG2R57 4.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 NG2R51; lf
CG2R51 CG2R51 CG2R51 NG2RC0 16.0000 2 180.00 ! INDZ, indolizine, kevo
CG2R51 CG2R51 CG2R51 OG2R50 8.5000 2 180.00 ! FURA, furan
CG2R51 CG2R51 CG2R51 SG2R50 8.5000 2 180.00 ! THIP, thiophene
CG2R51 CG2R51 CG2R51 SG3O2 1.6000 2 180.00 ! TSPD model for D3R, xxwy
CG2R51 CG2R51 CG2R51 HGR51 1.0000 2 180.00 ! PYRL, pyrrole
CG2R51 CG2R51 CG2R51 HGR52 1.5000 2 180.00 ! PYRL, pyrrole
CG2R52 CG2R51 CG2R51 CG3C52 6.6000 2 180.00 ! 2HPR, 2H-pyrrole !1,(1a), kevo
......@@ -3405,9 +3555,11 @@ CG2RC0 CG2R51 CG2R51 SG2R50 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo
CG2RC0 CG2R51 CG2R51 HGR51 2.8000 2 180.00 ! INDO/TRP
CG2RC0 CG2R51 CG2R51 HGR52 2.8000 2 180.00 ! INDO/TRP
CG2RC7 CG2R51 CG2R51 HGR51 2.7000 2 180.00 ! AZUL, Azulene, kevo
CG321 CG2R51 CG2R51 CG321 2.0000 2 180.00 ! TICA model for D3R, xxwy
CG321 CG2R51 CG2R51 NG2R50 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89
CG321 CG2R51 CG2R51 NG2R51 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89
CG321 CG2R51 CG2R51 NG2R52 2.5000 2 180.00 ! PROT his, adm jr., 6/27/90
CG321 CG2R51 CG2R51 HGR51 1.0000 2 180.00 ! TICA model for D3R, xxwy
CG321 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90
CG331 CG2R51 CG2R51 NG2R50 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89
CG331 CG2R51 CG2R51 NG2R51 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89
......@@ -3439,12 +3591,16 @@ OG2R50 CG2R51 CG2R51 HGR52 3.0000 2 180.00 ! OXAZ, oxazole
OG3C51 CG2R51 CG2R51 HGR51 3.7000 2 180.00 ! 2DHF, 2,3-dihydrofuran, kevo
SG2R50 CG2R51 CG2R51 HGR51 4.0000 2 180.00 ! THIP, thiophene
SG2R50 CG2R51 CG2R51 HGR52 5.5000 2 180.00 ! THAZ, thiazole
SG3O2 CG2R51 CG2R51 HGR51 0.1000 2 180.00 ! TSPD model for D3R, xxwy
HGR51 CG2R51 CG2R51 HGR51 1.0000 2 180.00 ! INDO/TRP
HGR51 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PYRL, pyrrole
HGR52 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90, his
CG2R51 CG2R51 CG2R52 CG321 3.0000 2 180.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 CG2R52 NG2R50 8.5000 2 180.00 ! PYRZ, pyrazole
CG2R51 CG2R51 CG2R52 NG2R52 4.1500 2 180.00 ! 4.1 2HPP, 2H-pyrrole.H+ 1, kevo
CG2R51 CG2R51 CG2R52 HGR52 3.8000 2 180.00 ! PYRZ, pyrazole
CG321 CG2R51 CG2R52 CG321 2.5000 2 180.00 ! INCA model for D3R, xxwy
CG321 CG2R51 CG2R52 NG2R50 3.0000 2 180.00 ! INCA model for D3R, xxwy
HGR51 CG2R51 CG2R52 NG2R50 4.5000 2 180.00 !v 4.25 2HPR, 2H-pyrrole !wC4H !coupled with pyrz, pyrazole, kevo
HGR51 CG2R51 CG2R52 NG2R52 4.5000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo
HGR51 CG2R51 CG2R52 HGR52 0.1000 2 180.00 ! 2HPR, 2H-pyrrole; 2HPP, 2H-pyrrole.H+, kevo
......@@ -3455,7 +3611,6 @@ HGR51 CG2R51 CG2R53 OG3C51 3.7000 2 180.00 ! B2FO, from OG3C51 CG2R51 CG
CG2R51 CG2R51 CG2R57 CG2R51 15.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 CG2R51; lf
CG2R51 CG2R51 CG2R57 CG2R57 2.1000 2 180.00 ! 33BPO, 3,3-bipyrrole, lf
CG2R51 CG2R51 CG2R57 NG2R57 1.9000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf
CG2R51 CG2R51 CG2R57 HGR52 1.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 HGR52; lf
NG2R51 CG2R51 CG2R57 CG2R51 4.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 NG2R51; lf
NG2R51 CG2R51 CG2R57 CG2R57 2.1000 2 180.00 ! 33BPO, 3,3-bipyrrole, lf
NG2R51 CG2R51 CG2R57 NG2R57 1.9000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf
......@@ -3489,10 +3644,19 @@ CG2R51 CG2R51 CG321 CG311 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G
CG2R51 CG2R51 CG321 CG314 0.2000 1 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 CG314 0.2700 2 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 CG314 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 CG321 0.2000 1 0.00 ! INCA model for D3R, xxwy, from WBG, from CG2R51 CG2R51 CG321 CG311, yxu
!!CG2R51 CG2R51 CG321 CG321 0.2700 2 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 CG321 CG331 0.2000 1 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 CG331 0.2700 2 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 CG331 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CG2R51 CG2R51 CG321 NG301 0.2000 1 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG2R51 CG321 NG301 0.2700 2 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG2R51 CG321 HGA2 0.0000 3 0.00 ! PROT 4-methylimidazole 4-21G//rot bar. adm jr., 9/4/89
CG2R52 CG2R51 CG321 CG321 0.2000 1 0.00 ! INCA model for D3R, xxwy
CG2R52 CG2R51 CG321 CG321 0.2700 2 0.00 ! INCA model for D3R, xxwy
CG2R52 CG2R51 CG321 NG301 0.2000 1 0.00 ! D3R set1 scaffold 1, xxwy
CG2R52 CG2R51 CG321 NG301 0.2700 2 0.00 ! D3R set1 scaffold 1, xxwy
CG2R52 CG2R51 CG321 HGA2 0.0000 3 0.00 ! INCA model for D3R, xxwy
CG2RC0 CG2R51 CG321 CG311 0.0900 2 180.00 ! INDO/TRP
CG2RC0 CG2R51 CG321 CG311 0.5700 3 0.00 ! INDO/TRP
CG2RC0 CG2R51 CG321 CG314 0.0900 2 180.00 ! INDO/TRP
......@@ -3504,7 +3668,9 @@ NG2R50 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT HIS CB-CG TORSION,
NG2R50 CG2R51 CG321 HGA2 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R51 CG2R51 CG321 CG311 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R51 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R51 CG2R51 CG321 CG321 0.1900 3 0.00 ! TICA model for D3R, xxwy
NG2R51 CG2R51 CG321 CG331 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R51 CG2R51 CG321 NG301 0.1900 3 0.00 ! D3R set1 scaffold 2, xxwy
NG2R51 CG2R51 CG321 HGA2 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R52 CG2R51 CG321 CG311 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
NG2R52 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89
......@@ -3548,10 +3714,18 @@ CG321 CG2R51 NG2R50 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89,
HGR52 CG2R51 NG2R50 CG2R52 2.0000 2 180.00 ! 3HPR, 3H-pyrrole, kevo
HGR52 CG2R51 NG2R50 CG2R53 3.0000 2 180.00 ! PROT adm jr., 3/24/92
HGR52 CG2R51 NG2R50 NG2R50 5.5000 2 180.00 ! OXAD, oxadiazole123
CG2O1 CG2R51 NG2R51 CG2R61 3.0000 2 180.00 ! D3R set1 scaffold 1, xxwy
CG2O1 CG2R51 NG2R51 CG331 3.0000 2 180.00 ! INCA model for D3R, xxwy
CG2O1 CG2R51 NG2R51 NG2R50 0.0000 2 180.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 NG2R51 CG2O6 0.0000 2 180.00 ! TICA model for D3R, xxwy
CG2R51 CG2R51 NG2R51 CG2R51 10.0000 2 180.00 ! PYRL, pyrrole
CG2R51 CG2R51 NG2R51 CG2R53 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89
CG2R51 CG2R51 NG2R51 CG2R61 0.0000 1 0.00 ! D3R set1 scaffold 1, xxwy
CG2R51 CG2R51 NG2R51 CG2R64 0.2000 2 180.00 ! PIPA model for D3R, xxwy
CG2R51 CG2R51 NG2R51 CG2RC0 5.0000 2 180.00 ! PROT JWK 05/14/91 fit to indole
CG2R51 CG2R51 NG2R51 CG321 0.0000 1 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from CG2R51 CG2R51 NG2R51 CG3C51, kevo
!CG2R51 CG2R51 NG2R51 CG331 0.0000 1 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2R51 NG2R51 CG331 11.0000 2 180.00 ! DCG, yxu
CG2R51 CG2R51 NG2R51 CG3C51 0.0000 1 0.00 ! NA, glycosyl linkage
CG2R51 CG2R51 NG2R51 NG2R50 10.0000 2 180.00 ! PYRZ, pyrazole
CG2R51 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/20/89
......@@ -3559,12 +3733,16 @@ CG2R57 CG2R51 NG2R51 CG2R51 10.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from
CG2R57 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51 HGP1; lf
CG2RC0 CG2R51 NG2R51 CG2R51 6.0000 2 180.00 ! ISOI, isoindole, kevo
CG2RC0 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! ISOI, isoindole, kevo
CG321 CG2R51 NG2R51 CG2O6 0.0000 2 180.00 ! TICA model for D3R, xxwy
CG321 CG2R51 NG2R51 CG2R51 3.0000 2 180.00 ! TICA model for D3R, xxwy
CG321 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89, FROM HGR52 CG2R51 NG2R51CPH2
CG321 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/22/89, FROM HGR52 CG2R51 NG2R51H
CG331 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89, FROM HGR52 CG2R51 NG2R51CPH2
CG331 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/22/89, FROM HGR52 CG2R51 NG2R51H
HGR52 CG2R51 NG2R51 CG2O6 0.0000 2 180.00 ! TICA model for D3R, xxwy
HGR52 CG2R51 NG2R51 CG2R51 2.6000 2 180.00 ! PYRL, pyrrole
HGR52 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT adm jr., 3/24/92
HGR52 CG2R51 NG2R51 CG2R64 0.0000 2 180.00 ! PIPA model for D3R, xxwy
HGR52 CG2R51 NG2R51 CG2RC0 2.6000 2 180.00 ! INDO/TRP
HGR52 CG2R51 NG2R51 CG321 0.0000 2 180.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from HGR52 CG2R53 NG2R51 CG331, kevo
HGR52 CG2R51 NG2R51 CG3C51 0.0000 2 180.00 ! NA, glycosyl linkage
......@@ -3611,10 +3789,17 @@ CG2R51 CG2R51 SG2R50 CG2R51 8.5000 2 180.00 ! THIP, thiophene
CG2R51 CG2R51 SG2R50 CG2R53 8.5000 2 180.00 ! THAZ, thiazole @@@@@ Kenno: 8.0 --> 8.5 @@@@@
CG2R51 CG2R51 SG2R50 CG2RC0 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo
CG2R51 CG2R51 SG2R50 NG2R50 9.0000 2 180.00 ! ISOT, isothiazole
SG3O2 CG2R51 SG2R50 CG2R51 1.6000 2 180.00 ! TSPD model for D3R, xxwy
HGR52 CG2R51 SG2R50 CG2R51 4.0000 2 180.00 ! THIP, thiophene
HGR52 CG2R51 SG2R50 CG2R53 5.5000 2 180.00 ! THAZ, thiazole
HGR52 CG2R51 SG2R50 CG2RC0 3.9000 2 180.00 ! ZTHP, benzothiophene, kevo
HGR52 CG2R51 SG2R50 NG2R50 4.5000 2 180.00 ! ISOT, isothiazole
CG2R51 CG2R51 SG3O2 NG301 3.2600 1 180.00 ! TSPD model for D3R, xxwy
CG2R51 CG2R51 SG3O2 NG301 0.2400 2 180.00 ! TSPD model for D3R, xxwy
CG2R51 CG2R51 SG3O2 OG2P1 0.0000 6 0.00 ! TSPD model for D3R, xxwy
SG2R50 CG2R51 SG3O2 NG301 3.2600 1 180.00 ! TSPD model for D3R, xxwy
SG2R50 CG2R51 SG3O2 NG301 0.2400 2 180.00 ! TSPD model for D3R, xxwy
SG2R50 CG2R51 SG3O2 OG2P1 0.0000 6 0.00 ! TSPD model for D3R, xxwy
NG2R50 CG2R52 CG2R52 NG2R50 9.5000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf
NG2R50 CG2R52 CG2R52 HGR52 3.9000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf
HGR52 CG2R52 CG2R52 HGR52 0.1700 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf
......@@ -3622,6 +3807,12 @@ NG2R50 CG2R52 CG2RC0 CG2R61 2.0000 2 180.00 ! INDA, 1H-indazole, kevo
NG2R50 CG2R52 CG2RC0 CG2RC0 8.0000 2 180.00 ! INDA, 1H-indazole, kevo
HGR52 CG2R52 CG2RC0 CG2R61 2.4000 2 180.00 ! INDA, 1H-indazole, kevo
HGR52 CG2R52 CG2RC0 CG2RC0 2.4000 2 180.00 ! INDA, 1H-indazole, kevo
CG2R51 CG2R52 CG321 CG321 0.2000 1 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2R52 CG321 CG321 0.2700 2 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2R52 CG321 CG321 0.0000 3 0.00 ! INCA model for D3R, xxwy
CG2R51 CG2R52 CG321 HGA2 0.0000 3 0.00 ! INCA model for D3R, xxwy
NG2R50 CG2R52 CG321 CG321 0.1900 3 0.00 ! INCA model for D3R, xxwy
NG2R50 CG2R52 CG321 HGA2 0.1900 3 0.00 ! INCA model for D3R, xxwy
NG2R50 CG2R52 CG3C52 CG2R51 3.5000 3 180.00 ! 3HPR, 3H-pyrrole, kevo
NG2R50 CG2R52 CG3C52 CG2RC0 3.5000 3 180.00 ! 3HIN, 3H-indole, kevo
NG2R50 CG2R52 CG3C52 CG3C52 2.8000 3 180.00 ! 2.85 2PRZ, 2-pyrazoline, kevo
......@@ -3636,6 +3827,7 @@ CG2R51 CG2R52 NG2R50 OG2R50 12.0000 2 180.00 ! ISOX, isoxazole
CG2R51 CG2R52 NG2R50 SG2R50 8.5000 2 180.00 ! ISOT, isothiazole
CG2R52 CG2R52 NG2R50 NG2R51 12.0000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf
CG2RC0 CG2R52 NG2R50 NG2R51 13.5000 2 180.00 ! INDA, 1H-indazole, kevo
CG321 CG2R52 NG2R50 NG2R51 3.8000 2 180.00 ! INCA model for D3R, xxwy
CG3C52 CG2R52 NG2R50 CG2R51 6.5000 2 180.00 ! 3HPR, 3H-pyrrole, kevo
CG3C52 CG2R52 NG2R50 CG2RC0 13.0000 2 180.00 ! 3HIN, 3H-indole, kevo
CG3C52 CG2R52 NG2R50 NG3C51 17.0000 2 180.00 ! 2PRZ, 2-pyrazoline, kevo
......@@ -3650,10 +3842,18 @@ CG2R51 CG2R52 NG2R52 CG3C54 6.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+ 1a, kev
CG2R51 CG2R52 NG2R52 HGP2 2.7000 2 180.00 ! 2.5 2HPP, 2H-pyrrole.H+, kevo
HGR52 CG2R52 NG2R52 CG3C54 9.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo
HGR52 CG2R52 NG2R52 HGP2 0.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo
NG2R50 CG2R53 CG2R61 CG2R61 0.8900 2 180.00 ! 2PTZ model for D3R, xxwy
NG2R50 CG2R53 CG2R61 CG2R61 0.1000 4 0.00 ! 2PTZ model for D3R, xxwy
SG2R50 CG2R53 CG2R61 CG2R61 0.8900 2 180.00 ! 2PTZ model for D3R, xxwy
SG2R50 CG2R53 CG2R61 CG2R61 0.1000 4 0.00 ! 2PTZ model for D3R, xxwy
NG2R43 CG2R53 CG3C41 CG3C41 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo
NG2R43 CG2R53 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo
OG2D1 CG2R53 CG3C41 CG3C41 0.5700 3 0.00 ! AZDO, 2-azetidinone, kevo
OG2D1 CG2R53 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone, kevo
NG2R53 CG2R53 CG3C50 CG2RC0 1.0000 3 180.00 ! MSCH model for D3R, xxwy
NG2R53 CG2R53 CG3C50 CG321 1.0000 3 180.00 ! MSCH model for D3R, xxwy
OG2D1 CG2R53 CG3C50 CG2RC0 0.0800 3 0.00 ! MSCH model for D3R, xxwy
OG2D1 CG2R53 CG3C50 CG321 0.0800 3 0.00 ! MSCH model for D3R, xxwy
NG2R53 CG2R53 CG3C52 CG3C52 1.0500 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo
NG2R53 CG2R53 CG3C52 HGA2 0.0000 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo
OG2D1 CG2R53 CG3C52 CG2R51 0.0800 3 0.00 ! A2FO, from OG2D1 CG2R53 CG3C52 CG3C52, ctsai
......@@ -3667,6 +3867,7 @@ CG3C41 CG2R53 NG2R43 CG3C41 1.5000 2 180.00 ! AZDO, 2-azetidinone, kevo
CG3C41 CG2R53 NG2R43 HGP1 0.0000 1 0.00 ! AZDO, 2-azetidinone, kevo
OG2D1 CG2R53 NG2R43 CG3C41 2.5000 2 180.00 ! AZDO, 2-azetidinone, kevo
OG2D1 CG2R53 NG2R43 HGP1 2.5000 2 180.00 ! AZDO, 2-azetidinone, kevo
CG2R61 CG2R53 NG2R50 CG2R51 4.0000 2 180.00 ! 2PTZ model for D3R, xxwy
NG2R50 CG2R53 NG2R50 CG2R53 10.0000 2 180.00 ! TRZ4, triazole124, xxwy
NG2R50 CG2R53 NG2R50 NG2R51 12.0000 2 180.00 ! TRZ4, triazole124, xxwy
NG2R50 CG2R53 NG2R50 OG2R50 12.0000 2 180.00 ! OXD4, oxadiazole124, xxwy
......@@ -3718,18 +3919,24 @@ CG252O CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine
CG252O CG2R53 NG2R53 CG311 1.6000 1 0.00 ! drug design project, xxwy
CG252O CG2R53 NG2R53 CG311 2.5000 2 180.00 ! drug design project, xxwy
CG252O CG2R53 NG2R53 HGP1 1.7000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy
CG3C50 CG2R53 NG2R53 CG2RC0 0.2000 2 180.00 ! MSCH model for D3R, xxwy
CG3C50 CG2R53 NG2R53 CG331 0.2000 2 180.00 ! MSCH model for D3R, xxwy
CG3C52 CG2R53 NG2R53 CG3C52 0.4000 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo
CG3C52 CG2R53 NG2R53 HGP1 1.2700 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo
NG2R53 CG2R53 NG2R53 CG251O 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
NG2R53 CG2R53 NG2R53 CG252O 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
NG2R53 CG2R53 NG2R53 CG2R53 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
NG2R53 CG2R53 NG2R53 CG311 0.5000 2 180.00 ! drug design project, xxwy
NG2R53 CG2R53 NG2R53 CG3RC1 0.5000 2 180.00 ! CBHH, glycoluril, (NG2R53 CG2R53 NG2R53 CG311), jing
NG2R53 CG2R53 NG2R53 HGP1 0.8000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
OG2D1 CG2R53 NG2R53 CG251O 6.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
OG2D1 CG2R53 NG2R53 CG252O 6.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy
OG2D1 CG2R53 NG2R53 CG2R53 1.1000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy
OG2D1 CG2R53 NG2R53 CG2RC0 0.2000 2 180.00 ! MSCH model for D3R, xxwy
OG2D1 CG2R53 NG2R53 CG311 2.5000 2 180.00 ! drug design project, xxwy
OG2D1 CG2R53 NG2R53 CG331 0.2000 2 180.00 ! MSCH model for D3R, xxwy
OG2D1 CG2R53 NG2R53 CG3C52 2.5900 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo
OG2D1 CG2R53 NG2R53 CG3RC1 2.5900 2 180.00 ! CBHH, glycoluril, (OG2D1 CG2R53 NG2R53 CG3C52), jing
OG2D1 CG2R53 NG2R53 HGP1 0.8600 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo
SG2D1 CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy
SG2D1 CG2R53 NG2R53 CG311 1.5000 2 180.00 ! drug design project, xxwy
......@@ -3752,6 +3959,7 @@ CG3C52 CG2R53 OG3C51 CG2R51 0.5120 3 180.00 ! A2FO, 3H-furan-2-one, ctsai
CG3C52 CG2R53 OG3C51 CG3C52 3.8000 2 180.00 ! GBL, Gamma-butyrolactone, ctsai
OG2D1 CG2R53 OG3C51 CG2R51 4.3400 2 180.00 ! A2FO, from CG2R51 CG2R51 OG3C51 CG3C52, ctsai
OG2D1 CG2R53 OG3C51 CG3C52 4.3400 2 180.00 ! GBL, from CG2R51 CG2R51 OG3C51 CG3C52, ctsai
CG2R61 CG2R53 SG2R50 CG2R51 4.0000 2 180.00 ! 2PTZ model for D3R, xxwy
NG2R50 CG2R53 SG2R50 CG2R51 8.5000 2 180.00 ! THAZ, thiazole @@@@@ Kenno: 8.0 --> 8.5 @@@@@
NG2R50 CG2R53 SG2R50 CG2RC0 3.0000 2 180.00 ! ZTHZ, benzothiazole, kevo
HGR52 CG2R53 SG2R50 CG2R51 5.5000 2 180.00 ! THAZ, thiazole
......@@ -3803,6 +4011,8 @@ CG2O5 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS unmodified
CG2O5 CG2R61 CG2R61 NG2R60 5.0000 2 180.00 ! 3ACP, 3-acetylpyridine unmodified
CG2O5 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! 3ACP, 3-acetylpyridine reset to default by kevo; verified by mcs
CG2O5 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3ACP, 3-acetylpyridine reset to default by kevo; verified by mcs
CG2R53 CG2R61 CG2R61 CG2R61 3.0000 2 180.00 ! 2PTZ model for D3R, xxwy
CG2R53 CG2R61 CG2R61 HGR61 2.0000 2 180.00 ! 2PTZ model for D3R, xxwy
CG2R61 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! PROT JES 8/25/89
CG2R61 CG2R61 CG2R61 CG2R62 0.5000 2 180.00 ! RIN, coumarin, isg
CG2R61 CG2R61 CG2R61 CG2R63 3.2000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
......@@ -3816,6 +4026,7 @@ CG2R61 CG2R61 CG2R61 CG321 3.1000 2 180.00 ! PROT JES 8/25/89 toluene an
CG2R61 CG2R61 CG2R61 CG324 3.1000 2 180.00 ! BPIP, N-Benzyl PIP, cacha
CG2R61 CG2R61 CG2R61 CG331 3.1000 2 180.00 ! PROT toluene, adm jr., 3/7/92
CG2R61 CG2R61 CG2R61 NG2O1 2.0000 2 180.00 ! NITB, nitrobenzene
CG2R61 CG2R61 CG2R61 NG2R51 5.0000 2 180.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 CG2R61 NG2R60 1.2000 2 180.00 ! PYR1, pyridine, yin
CG2R61 CG2R61 CG2R61 NG2R61 3.7000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg
CG2R61 CG2R61 CG2R61 NG2R62 1.2000 2 180.00 ! PYRD, pyridazine (also applies to PYRM, pyrimidine); from PYR1, pyridine, yin; adm
......@@ -3868,6 +4079,7 @@ CG331 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! FBIA, Fatty Binding Inhibit
CG331 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4
CG331 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PROT toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4
NG2O1 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! NITB, nitrobenzene
NG2R51 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! D3R set1 scaffold 1, xxwy
NG2R60 CG2R61 CG2R61 NG2R60 0.9000 2 180.00 ! PYZN, pyrazine
NG2R60 CG2R61 CG2R61 NG2R62 3.0000 2 180.00 ! PTID, pteridine, erh
NG2R60 CG2R61 CG2R61 NG2S1 5.0000 2 180.00 ! 3AMP, 3-Amino pyridine, cacha
......@@ -3904,8 +4116,11 @@ OG3R60 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! FEOZ, phenoxazine, erh
SG311 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! FETZ, phenothiazine, erh based on toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4
SG3O1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! based on toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4
SG3O2 CG2R61 CG2R61 HGR61 2.1000 2 180.00 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy
CLGR1 CG2R61 CG2R61 CLGR1 2.4000 2 180.00 ! 12DCB, 1,2,dichlorobenzene, (CG331 CG2R61 CG2R61 CG311), isg/fylin
CLGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! CHLB, chlorobenzene
BRGR1 CG2R61 CG2R61 BRGR1 2.4000 2 180.00 ! 12DBB, 1,2,dibromobenzene, (CG331 CG2R61 CG2R61 CG311), isg/fylin
BRGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! BROB, bromobenzene
IGR1 CG2R61 CG2R61 IGR1 2.4000 2 180.00 ! 12DIB, 1,2,diiodobenzene, (CG331 CG2R61 CG2R61 CG311), isg/fylin
IGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! IODB, iodobenzene
HGR61 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT JES 8/25/89 benzene
HGR61 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! BROB, bromobenzene
......@@ -3926,16 +4141,18 @@ CG2R61 CG2R61 CG2R63 SG2D1 4.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolin
HGR62 CG2R61 CG2R63 NG2R61 1.0000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from HGR62 CG2R62 CG2R63 NG2R61; isg
HGR62 CG2R61 CG2R63 NG2R67 1.0000 2 180.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from HGR62 CG2R62 CG2R63 NG2R61, NA; isg
HGR62 CG2R61 CG2R63 SG2D1 2.4000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from SG311 CG2R61 CG2R61 HGR61; isg
CG2R61 CG2R61 CG2R64 NG2R51 4.0000 2 180.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R61 CG2R64 NG2R60 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
CG2R61 CG2R61 CG2R64 NG2R62 1.2000 2 180.00 ! 18NFD, 1,8-naphthyridine, from PYR1, pyridine, erh
CG2R61 CG2R61 CG2R64 NG2S1 3.1000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo
NG2R60 CG2R61 CG2R64 NG2R62 1.5000 2 0.00 ! PTID, pteridine, erh
OG311 CG2R61 CG2R64 NG2R60 3.1000 2 180.00 ! 2A3HPD, cacha
OG311 CG2R61 CG2R64 NG2S1 2.4000 2 180.00 ! 2A3HPD, cacha
HGR61 CG2R61 CG2R64 NG2R51 1.5000 2 180.00 ! PIPA model for D3R, xxwy
HGR61 CG2R61 CG2R64 NG2R60 2.8000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
HGR61 CG2R61 CG2R64 NG2S1 2.4000 2 180.00 ! 2AMP, 2-amino pyridine, default parameter by analogy to PACP, kevo
CG2R61 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! NAMODEL difluorotoluene
CG2R61 CG2R61 CG2R66 CG2R67 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 CG2R61, penalty= 0.5
CG2R61 CG2R61 CG2R66 CG2R67 3.1000 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 CG2R61, penalty= 0.5
CG2R61 CG2R61 CG2R66 FGR1 4.5000 2 180.00 ! NAMODEL difluorotoluene
CG2R66 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! NAMODEL difluorotoluene
CG2R66 CG2R61 CG2R66 FGR1 4.5000 2 180.00 ! NAMODEL difluorotoluene
......@@ -3946,10 +4163,10 @@ NG2R60 CG2R61 CG2R66 FGR1 3.1000 2 180.00 ! PYRIDINE fluoropyridine, yi
NG2S1 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize
NG2S1 CG2R61 CG2R66 FGR1 2.4000 2 180.00 ! 2FBD, Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha Kenno: 3.1 -> 2.4
HGR62 CG2R61 CG2R66 CG2R61 4.2000 2 180.00 ! NAMODEL difluorotoluene
HGR62 CG2R61 CG2R66 CG2R67 4.20 2 180.00 ! PYO2F , from HGR62 CG2R61 CG2R66 CG2R61, penalty= 0.5
HGR62 CG2R61 CG2R66 CG2R67 4.2000 2 180.00 ! PYO2F , from HGR62 CG2R61 CG2R66 CG2R61, penalty= 0.5
HGR62 CG2R61 CG2R66 FGR1 2.4000 2 180.00 ! NAMODEL difluorotoluene
CG2R61 CG2R61 CG2R67 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml
CG2R61 CG2R61 CG2R67 CG2R66 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 1.5
CG2R61 CG2R61 CG2R67 CG2R66 3.1000 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 1.5
CG2R61 CG2R61 CG2R67 CG2R67 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml
CG2R61 CG2R61 CG2R67 CG2RC0 0.2500 2 180.00 ! CRBZ, carbazole, erh
CG2R61 CG2R61 CG2R67 NG2R60 1.2000 2 180.00 ! 22BPY, 2,2'-bipyridine, from CG2R61 CG2R61 CG2R61 NG2R60, kevo
......@@ -3957,7 +4174,7 @@ CG2R61 CG2R61 CG2R67 NG2R67 3.1000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyri
NG2R60 CG2R61 CG2R67 CG2R61 1.2000 2 180.00 ! 3PHP, 3-phenyl-pyridine; Kenno: 3.1 -> 1.2 from PYRIDINE pyridine, yin
NG2R60 CG2R61 CG2R67 CG2R67 1.0000 2 180.00 ! 3PHP, 3-phenyl-pyridine, Kenno: 3.1 -> 1.0 from 3-methylpyridine, yin
HGR61 CG2R61 CG2R67 CG2R61 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml
HGR61 CG2R61 CG2R67 CG2R66 4.20 2 180.00 ! PYO2F , from HGR61 CG2R61 CG2R67 CG2R61, penalty= 1.5
HGR61 CG2R61 CG2R67 CG2R66 4.2000 2 180.00 ! PYO2F , from HGR61 CG2R61 CG2R67 CG2R61, penalty= 1.5
HGR61 CG2R61 CG2R67 CG2R67 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml
HGR61 CG2R61 CG2R67 CG2RC0 3.0000 2 180.00 ! CRBZ, carbazole, erh
HGR61 CG2R61 CG2R67 NG2R60 2.8000 2 180.00 ! 22BPY, 2,2'-bipyridine, from NG2R60 CG2R61 CG2R61 HGR61, kevo
......@@ -3972,9 +4189,11 @@ CG2R61 CG2R61 CG2RC0 CG2R51 4.0000 2 180.00 ! INDO/TRP
CG2R61 CG2R61 CG2RC0 CG2R52 1.5000 2 180.00 ! INDA, 1H-indazole, kevo
CG2R61 CG2R61 CG2RC0 CG2R67 0.2500 2 180.00 ! CRBZ, carbazole, erh
CG2R61 CG2R61 CG2RC0 CG2RC0 3.0000 2 180.00 ! INDO/TRP
CG2R61 CG2R61 CG2RC0 CG3C50 0.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2R61 CG2RC0 CG3C52 0.0000 2 180.00 ! 3HIN, 3H-indole, kevo
CG2R61 CG2R61 CG2RC0 NG2R50 1.5000 2 180.00 ! ZIMI, benzimidazole, kevo
CG2R61 CG2R61 CG2RC0 NG2R51 3.0000 2 180.00 ! INDO/TRP
CG2R61 CG2R61 CG2RC0 NG2R53 3.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2R61 CG2RC0 NG2RC0 3.5000 2 180.00 ! INDZ, indolizine, kevo
CG2R61 CG2R61 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo
CG2R61 CG2R61 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo
......@@ -3989,9 +4208,11 @@ HGR61 CG2R61 CG2RC0 CG2R51 4.0000 2 180.00 ! INDO/TRP
HGR61 CG2R61 CG2RC0 CG2R52 0.0000 2 180.00 ! INDA, 1H-indazole, kevo
HGR61 CG2R61 CG2RC0 CG2R67 3.0000 2 180.00 ! CRBZ, carbazole, erh
HGR61 CG2R61 CG2RC0 CG2RC0 3.0000 2 180.00 ! INDO/TRP
HGR61 CG2R61 CG2RC0 CG3C50 0.0000 2 180.00 ! MSCH model for D3R, xxwy
HGR61 CG2R61 CG2RC0 CG3C52 0.0000 2 180.00 ! 3HIN, 3H-indole, kevo
HGR61 CG2R61 CG2RC0 NG2R50 0.8000 2 180.00 ! ZIMI, benzimidazole, kevo
HGR61 CG2R61 CG2RC0 NG2R51 3.0000 2 180.00 ! INDO/TRP
HGR61 CG2R61 CG2RC0 NG2R53 0.0000 2 180.00 ! MSCH model for D3R, xxwy
HGR61 CG2R61 CG2RC0 NG2RC0 0.0000 2 180.00 ! INDZ, indolizine, kevo
HGR61 CG2R61 CG2RC0 NG3C51 0.0000 2 180.00 ! INDI, indoline, kevo
HGR61 CG2R61 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo
......@@ -4031,6 +4252,10 @@ CG2R61 CG2R61 CG331 HGA3 0.0020 6 0.00 ! PYRIDINE toluene Kenno: 180
CG2R66 CG2R61 CG331 HGA3 0.0020 6 0.00 ! PYRIDINE toluene Kenno: 180 -> 0
NG2R60 CG2R61 CG331 HGA3 0.0030 6 180.00 ! 3A2MPD, 3-amino-2-methyl-pyridine CDCA conjugate, cacha
CG2R61 CG2R61 NG2O1 OG2N1 0.9000 2 180.00 ! NITB, nitrobenzene
CG2R61 CG2R61 NG2R51 CG2R51 0.2000 1 0.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 NG2R51 CG2R51 1.1000 2 180.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 NG2R51 CG2R51 0.6000 3 0.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 NG2R51 NG2R50 1.0000 2 180.00 ! D3R set1 scaffold 1, xxwy
CG2R61 CG2R61 NG2R60 CG2R61 1.2000 2 180.00 ! PYRIDINE pyridine, yin
CG2R61 CG2R61 NG2R60 CG2R64 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
CG2R61 CG2R61 NG2R60 CG2R67 1.2000 2 180.00 ! 22BPY, 2,2'-bipyridine, from CG2R61 CG2R61 NG2R60 CG2R61, kevo
......@@ -4087,6 +4312,7 @@ CG2R64 CG2R61 OG311 HGP1 0.9900 2 180.00 ! 2A3HPD, from PROT phenol, c
CG2R61 CG2R61 OG3R60 CG2R61 0.7600 2 0.00 ! FEOZ, phenoxazine fit_dihedral, erh
CG2R61 CG2R61 SG311 CG2R61 1.7500 2 0.00 ! FETZ, phenothiazine fit_dihedral, erh
CG2R61 CG2R61 SG3O1 OG2P1 0.0040 6 0.00 ! benzene sulfonic acid anion, og
CG2R61 CG2R61 SG3O2 NG301 0.2200 2 0.00 ! D3R set1 scaffold 2, xxwy
CG2R61 CG2R61 SG3O2 NG311 0.2200 2 0.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy
CG2R61 CG2R61 SG3O2 NG321 0.3500 2 0.00 ! BSAM, benzenesulfonamide, xxwy
CG2R61 CG2R61 SG3O2 OG2P1 0.0000 6 0.00 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy
......@@ -4108,22 +4334,22 @@ CG2R62 CG2R62 CG2R62 NG2R67 3.5000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyri
CG2R62 CG2R62 CG2R62 OG3R60 0.4000 2 180.00 ! RIN, coumarin, isg
CG2R62 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! 2PYO, 2-Pyridone, xxwy
CG2R62 CG2R62 CG2R62 HGR63 1.0000 2 180.00 ! NA bases
CG2R63 CG2R62 CG2R62 CG2R67 3.70 2 180.00 ! pyo3b , from CG2R61 CG2R62 CG2R62 CG2R63, penalty= 0.5
CG2R63 CG2R62 CG2R62 CG2R67 3.7000 2 180.00 ! pyo3b , from CG2R61 CG2R62 CG2R62 CG2R63, penalty= 0.5
CG2R63 CG2R62 CG2R62 NG2R61 3.0000 2 180.00 ! NA T
CG2R63 CG2R62 CG2R62 NG2R62 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg
CG2R63 CG2R62 CG2R62 NG2R67 3.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R63 CG2R62 CG2R62 NG2R61; isg
CG2R63 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! NA bases
CG2R64 CG2R62 CG2R62 NG2R61 6.0000 2 180.00 ! NA C
CG2R64 CG2R62 CG2R62 HGR62 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93
CG2R67 CG2R62 CG2R62 NG2R61 3.50 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 NG2R61, penalty= 0.5
CG2R67 CG2R62 CG2R62 HGR62 1.00 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 0.5
CG2R67 CG2R62 CG2R62 HGR63 1.00 2 180.00 ! PIUB , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 1.5
CG2R67 CG2R62 CG2R62 NG2R61 3.5000 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 NG2R61, penalty= 0.5
CG2R67 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 0.5
CG2R67 CG2R62 CG2R62 HGR63 1.0000 2 180.00 ! PIUB , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 1.5
CG331 CG2R62 CG2R62 NG2R61 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93
CG331 CG2R62 CG2R62 HGR62 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93
NG2R61 CG2R62 CG2R62 HGR62 3.4000 2 180.00 ! NA C
NG2R61 CG2R62 CG2R62 HGR63 7.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95
NG2R62 CG2R62 CG2R62 HGR62 6.0000 2 180.00 ! 43HPY, 4(3H)-pyrimidinone; from NG2R62 CG2R61 CG2R61 HGR62; isg
NG2R62 CG2R62 CG2R62 HGR63 1.10 2 180.00 ! PYRH ,6.0000 2 180.00 ! from NG2R62 CG2R62 CG2R62 HGR62, penalty= 1
NG2R62 CG2R62 CG2R62 HGR63 1.1000 2 180.00 ! PYRH ,6.0000 2 180.00 ! from NG2R62 CG2R62 CG2R62 HGR62, penalty= 1
NG2R67 CG2R62 CG2R62 HGR62 3.4000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R61 CG2R62 CG2R62 HGR62; isg
HGR62 CG2R62 CG2R62 HGR62 3.0000 2 180.00 ! NA U
HGR63 CG2R62 CG2R62 HGR63 2.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95
......@@ -4136,8 +4362,8 @@ CG2R62 CG2R62 CG2R63 NG2R67 1.8000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyri
CG2R62 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! NA bases
CG2R62 CG2R62 CG2R63 OG3R60 0.4000 2 180.00 ! RIN, coumarin, isg
CG2R62 CG2R62 CG2R63 SG2D1 4.5000 2 180.00 ! YT2S, 3,4-dihydro-4-thioxo-2(1H)-quinazolinone; from CG2R61 CG2R61 CG2R61 SG311, FETZ; isg
CG2R67 CG2R62 CG2R63 NG2R61 1.80 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 NG2R61, penalty= 0.5
CG2R67 CG2R62 CG2R63 OG2D4 1.00 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 OG2D4, penalty= 0.5
CG2R67 CG2R62 CG2R63 NG2R61 1.8000 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 NG2R61, penalty= 0.5
CG2R67 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 OG2D4, penalty= 0.5
CG331 CG2R62 CG2R63 NG2R61 5.6000 2 180.00 ! NA T
CG331 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! NA bases
HGR62 CG2R62 CG2R63 CG2R62 0.5000 2 180.00 ! 4PYO, 4(1H)-pyridinone, isg
......@@ -4152,18 +4378,18 @@ CG2R62 CG2R62 CG2R64 NG301 3.1000 2 180.00 ! TMC, from 4MC, yxu
HGR62 CG2R62 CG2R64 NG2R62 3.4000 2 180.00 ! NA C
HGR62 CG2R62 CG2R64 NG2S3 2.0000 2 180.00 ! NA C
HGR62 CG2R62 CG2R64 NG301 0.0000 2 180.00 ! TMC, from 4MC, yxu
CG2R62 CG2R62 CG2R67 CG2R62 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 6
CG2R62 CG2R62 CG2R67 CG2R67 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5.5
CG2R63 CG2R62 CG2R67 CG2R62 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 8.5
CG2R63 CG2R62 CG2R67 CG2R67 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 8
NG2R61 CG2R62 CG2R67 CG2R62 1.20 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 27.5
NG2R61 CG2R62 CG2R67 CG2R67 1.00 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 27
NG2R62 CG2R62 CG2R67 CG2R62 1.20 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 6.5
NG2R62 CG2R62 CG2R67 CG2R67 1.00 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 6
HGR62 CG2R62 CG2R67 CG2R62 4.20 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 5.5
HGR62 CG2R62 CG2R67 CG2R67 4.20 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 5
HGR63 CG2R62 CG2R67 CG2R62 4.20 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 6.5
HGR63 CG2R62 CG2R67 CG2R67 4.20 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 6
CG2R62 CG2R62 CG2R67 CG2R62 3.1000 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 6
CG2R62 CG2R62 CG2R67 CG2R67 3.1000 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5.5
CG2R63 CG2R62 CG2R67 CG2R62 3.1000 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 8.5
CG2R63 CG2R62 CG2R67 CG2R67 3.1000 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 8
NG2R61 CG2R62 CG2R67 CG2R62 1.2000 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 27.5
NG2R61 CG2R62 CG2R67 CG2R67 1.0000 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 27
NG2R62 CG2R62 CG2R67 CG2R62 1.2000 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 6.5
NG2R62 CG2R62 CG2R67 CG2R67 1.0000 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 6
HGR62 CG2R62 CG2R67 CG2R62 4.2000 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 5.5
HGR62 CG2R62 CG2R67 CG2R67 4.2000 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 5
HGR63 CG2R62 CG2R67 CG2R62 4.2000 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 6.5
HGR63 CG2R62 CG2R67 CG2R67 4.2000 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 6
CG2R62 CG2R62 CG331 HGA3 0.4600 3 0.00 ! NA T
CG2R63 CG2R62 CG331 HGA3 0.4600 3 0.00 ! NA T
CG2R61 CG2R62 NG2R61 CG2R63 0.6000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg
......@@ -4176,12 +4402,12 @@ CG2R62 CG2R62 NG2R61 CG3C53 11.0000 2 180.00 ! NA, glycosyl linkage
CG2R62 CG2R62 NG2R61 CG3RC1 1.0000 2 180.00 ! NA bases
CG2R62 CG2R62 NG2R61 HGP1 1.0000 2 180.00 ! NA base
CG2R62 CG2R62 NG2R61 HGP2 1.0000 2 180.00 ! NA base
CG2R67 CG2R62 NG2R61 CG2R62 4.00 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 CG2R62, penalty= 1.5
CG2R67 CG2R62 NG2R61 CG2R63 0.60 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 CG2R63, penalty= 0.5
CG2R67 CG2R62 NG2R61 HGP1 1.00 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 HGP1, penalty= 0.5
CG2R67 CG2R62 NG2R61 HGP2 1.00 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 HGP2, penalty= 1.5
NG2R62 CG2R62 NG2R61 CG2R62 0.15 2 180.00 ! PYRH ,0.2000 2 180.00 ! from NG2R62 CG2R64 NG2R61 CG2R63, penalty= 17
NG2R62 CG2R62 NG2R61 HGP2 3.20 2 180.00 ! PYRH ,3.6000 2 180.00 ! from NG2R62 CG2R64 NG2R61 HGP1, penalty= 18
CG2R67 CG2R62 NG2R61 CG2R62 4.0000 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 CG2R62, penalty= 1.5
CG2R67 CG2R62 NG2R61 CG2R63 0.6000 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 CG2R63, penalty= 0.5
CG2R67 CG2R62 NG2R61 HGP1 1.0000 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 HGP1, penalty= 0.5
CG2R67 CG2R62 NG2R61 HGP2 1.0000 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 HGP2, penalty= 1.5
NG2R62 CG2R62 NG2R61 CG2R62 0.1500 2 180.00 ! PYRH ,0.2000 2 180.00 ! from NG2R62 CG2R64 NG2R61 CG2R63, penalty= 17
NG2R62 CG2R62 NG2R61 HGP2 3.2000 2 180.00 ! PYRH ,3.6000 2 180.00 ! from NG2R62 CG2R64 NG2R61 HGP1, penalty= 18
HGR62 CG2R62 NG2R61 CG2R62 5.6000 2 180.00 ! 4PYO, 4(1H)-pyridinone, isg
HGR62 CG2R62 NG2R61 CG2R63 4.6000 2 180.00 ! NA C
HGR62 CG2R62 NG2R61 CG331 0.3000 2 180.00 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm
......@@ -4192,12 +4418,12 @@ HGR63 CG2R62 NG2R61 CG2R62 7.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/
HGR63 CG2R62 NG2R61 CG3C53 1.0000 2 180.00 ! NA base
HGR63 CG2R62 NG2R61 HGP2 3.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95
CG2R61 CG2R62 NG2R62 CG2R64 2.0000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg
CG2R62 CG2R62 NG2R62 CG2R62 2.70 2 180.00 ! PYRH ,0.5000 2 180.00 ! from CG2R62 CG2R62 NG2R62 CG2R64, penalty= 2.5
CG2R62 CG2R62 NG2R62 CG2R62 2.7000 2 180.00 ! PYRH ,0.5000 2 180.00 ! from CG2R62 CG2R62 NG2R62 CG2R64, penalty= 2.5
CG2R62 CG2R62 NG2R62 CG2R64 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg
CG2R67 CG2R62 NG2R62 CG2R62 2.00 2 180.00 ! PYRF , from CG2R61 CG2R62 NG2R62 CG2R64, penalty= 3
NG2R61 CG2R62 NG2R62 CG2R62 3.00 2 180.00 ! PYRH ,4.0000 2 180.00 ! from NG2R61 CG2R64 NG2R62 CG2R62, penalty= 15
CG2R67 CG2R62 NG2R62 CG2R62 2.0000 2 180.00 ! PYRF , from CG2R61 CG2R62 NG2R62 CG2R64, penalty= 3
NG2R61 CG2R62 NG2R62 CG2R62 3.0000 2 180.00 ! PYRH ,4.0000 2 180.00 ! from NG2R61 CG2R64 NG2R62 CG2R62, penalty= 15
HGR62 CG2R62 NG2R62 CG2R64 7.3000 2 180.00 ! 43HPY, 4(3H)-pyrimidinone; from HGR62 CG2R61 NG2R62 CG2R64; isg
HGR63 CG2R62 NG2R62 CG2R62 7.40 2 180.00 ! PYRH ,7.3000 2 180.00 ! from HGR62 CG2R62 NG2R62 CG2R64, penalty= 3.5
HGR63 CG2R62 NG2R62 CG2R62 7.4000 2 180.00 ! PYRH ,7.3000 2 180.00 ! from HGR62 CG2R62 NG2R62 CG2R64, penalty= 3.5
CG2R62 CG2R62 NG2R67 CG2R62 4.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R62; isg
CG2R62 CG2R62 NG2R67 CG2R63 0.6000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R63, NA; isg
CG2R62 CG2R62 NG2R67 CG2R67 4.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R62; isg
......@@ -4271,7 +4497,16 @@ NG2S3 CG2R64 CG2RC0 CG2RC0 4.0000 2 180.00 ! NA A
NG2S3 CG2R64 CG2RC0 NG2R50 0.0000 2 180.00 ! NA A
NG301 CG2R64 CG2RC0 CG2RC0 4.0000 2 180.00 ! M6A, yxu
NG301 CG2R64 CG2RC0 NG2R50 4.7000 2 180.00 ! M6A, yxu
CG2R61 CG2R64 NG2R51 CG2R51 0.2000 1 0.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R64 NG2R51 CG2R51 1.1000 2 180.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R64 NG2R51 CG2R51 0.6000 3 0.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R64 NG2R51 NG2R50 1.0000 2 180.00 ! PIPA model for D3R, xxwy
NG2R60 CG2R64 NG2R51 CG2R51 1.0000 2 180.00 ! PIPA model for D3R, xxwy
NG2R60 CG2R64 NG2R51 NG2R50 0.2000 1 0.00 ! PIPA model for D3R, xxwy
NG2R60 CG2R64 NG2R51 NG2R50 1.1000 2 180.00 ! PIPA model for D3R, xxwy
NG2R60 CG2R64 NG2R51 NG2R50 0.6000 3 0.00 ! PIPA model for D3R, xxwy
CG2R61 CG2R64 NG2R60 CG2R61 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo
NG2R51 CG2R64 NG2R60 CG2R61 4.0000 2 180.00 ! PIPA model for D3R, xxwy
NG2S1 CG2R64 NG2R60 CG2R61 3.1000 2 180.00 ! 2AMP, 2-Amino pyridine, cacha (verified by kevo)
NG2R62 CG2R64 NG2R61 CG2R63 0.2000 2 180.00 ! NA G
NG2R62 CG2R64 NG2R61 HGP1 3.6000 2 180.00 ! NA G
......@@ -4327,21 +4562,21 @@ NG2R62 CG2R64 NG301 CG331 1.9800 2 180.00 ! TMC, yxu
NG2R61 CG2R64 SG311 CG331 1.4500 1 0.00 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone, isg
NG2R62 CG2R64 SG311 CG331 2.1200 2 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine, isg
NG2R62 CG2R64 SG311 CG331 0.1900 4 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine, isg
CG2R61 CG2R66 CG2R67 CG2R61 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 5
CG2R61 CG2R66 CG2R67 CG2R67 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5
FGR1 CG2R66 CG2R67 CG2R61 4.50 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 FGR1, penalty= 30
FGR1 CG2R66 CG2R67 CG2R67 1.00 2 180.00 ! PYO2F , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 89
CG2R61 CG2R66 CG2R67 CG2R61 3.1000 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 5
CG2R61 CG2R66 CG2R67 CG2R67 3.1000 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5
FGR1 CG2R66 CG2R67 CG2R61 4.5000 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 FGR1, penalty= 30
FGR1 CG2R66 CG2R67 CG2R67 1.0000 2 180.00 ! PYO2F , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 89
CG2R61 CG2R67 CG2R67 CG2R61 0.8900 2 180.00 ! BIPHENYL ANALOGS, peml
CG2R61 CG2R67 CG2R67 CG2R62 0.46 2 180.00 ! pyo2b ,tune the middle 180 from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5
CG2R61 CG2R67 CG2R67 CG2R62 0.23 4 0.00 ! low will down the two peaks;phs 4, 0 pyo2b , from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5
CG2R61 CG2R67 CG2R67 CG2R62 0.4600 2 180.00 ! pyo2b ,tune the middle 180 from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5
CG2R61 CG2R67 CG2R67 CG2R62 0.2300 4 0.00 ! low will down the two peaks;phs 4, 0 pyo2b , from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5
CG2R61 CG2R67 CG2R67 CG2RC0 2.0000 2 180.00 ! CRBZ, carbazole, erh
CG2R61 CG2R67 CG2R67 NG2R60 0.3750 1 0.00 ! 22BPY, 2,2'-bipyridine, kevo
CG2R61 CG2R67 CG2R67 NG2R60 0.9400 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo
CG2R61 CG2R67 CG2R67 NG2R60 0.1900 3 180.00 ! 22BPY, 2,2'-bipyridine, kevo
CG2R61 CG2R67 CG2R67 NG2R60 0.1600 4 0.00 ! 22BPY, 2,2'-bipyridine, kevo
CG2R62 CG2R67 CG2R67 CG2R66 0.43 2 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2R62 CG2R67 CG2R67 CG2R66 0.12 4 0.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2R62 CG2R67 CG2R67 CG2R66 0.02 6 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2R62 CG2R67 CG2R67 CG2R66 0.4300 2 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2R62 CG2R67 CG2R67 CG2R66 0.1200 4 0.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2R62 CG2R67 CG2R67 CG2R66 0.0200 6 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin
CG2RC0 CG2R67 CG2R67 CG2RC0 1.5000 2 180.00 ! CRBZ, carbazole, erh
NG2R60 CG2R67 CG2R67 NG2R60 0.3750 1 180.00 ! 22BPY, 2,2'-bipyridine, kevo
NG2R60 CG2R67 CG2R67 NG2R60 0.9400 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo
......@@ -4384,9 +4619,11 @@ CG2R51 CG2RC0 CG2RC0 SG2R50 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo
CG2R52 CG2RC0 CG2RC0 CG2R61 1.5000 2 180.00 ! INDA, 1H-indazole, kevo
CG2R52 CG2RC0 CG2RC0 NG2R51 12.0000 2 180.00 ! INDA, 1H-indazole, kevo
CG2R61 CG2RC0 CG2RC0 CG2R61 3.0000 2 180.00 ! INDO/TRP
CG2R61 CG2RC0 CG2RC0 CG3C50 3.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 CG2RC0 CG3C52 6.5000 2 180.00 ! 3HIN, 3H-indole, kevo
CG2R61 CG2RC0 CG2RC0 NG2R50 1.5000 2 180.00 ! ZIMI, benzimidazole, kevo
CG2R61 CG2RC0 CG2RC0 NG2R51 1.5000 2 180.00 ! INDO/TRP (Kenno: 4.0 --> 1.5)
CG2R61 CG2RC0 CG2RC0 NG2R53 15.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 CG2RC0 NG2R62 0.0000 2 180.00 ! PUR9, purine(N9H), kevo
CG2R61 CG2RC0 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo
CG2R61 CG2RC0 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo
......@@ -4396,6 +4633,7 @@ CG2R63 CG2RC0 CG2RC0 NG2R51 10.0000 2 180.00 ! NA G
CG2R63 CG2RC0 CG2RC0 NG2R62 2.0000 2 180.00 ! NA G
CG2R64 CG2RC0 CG2RC0 NG2R51 7.0000 2 180.00 ! NA A
CG2R64 CG2RC0 CG2RC0 NG2R62 2.0000 2 180.00 ! NA A
CG3C50 CG2RC0 CG2RC0 NG2R53 3.0000 2 180.00 ! MSCH model for D3R, xxwy
CG3C52 CG2RC0 CG2RC0 NG2R50 6.5000 2 180.00 ! 3HIN, 3H-indole, kevo
CG3C52 CG2RC0 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo
NG2R50 CG2RC0 CG2RC0 NG2R51 10.0000 2 180.00 ! NA G
......@@ -4403,6 +4641,10 @@ NG2R50 CG2RC0 CG2RC0 NG2R62 7.0000 2 180.00 ! NA A
NG2R50 CG2RC0 CG2RC0 SG2R50 4.0000 2 180.00 ! ZTHZ, benzothiazole, kevo
NG2R51 CG2RC0 CG2RC0 NG2R62 8.5000 2 180.00 ! PUR7, purine(N7H), kevo
OG3C51 CG2RC0 CG2RC0 OG3C51 7.7000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi
CG2R61 CG2RC0 CG3C50 CG2R53 2.0000 3 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 CG3C50 CG321 2.0000 3 180.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 CG3C50 CG2R53 2.0000 3 180.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 CG3C50 CG321 2.0000 3 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 CG3C52 CG2R51 0.9000 3 0.00 ! INDE, indene, kevo
CG2R61 CG2RC0 CG3C52 CG2R52 3.5000 3 0.00 ! 3HIN, 3H-indole, kevo
CG2R61 CG2RC0 CG3C52 CG2RC0 0.9000 3 0.00 ! FLRN, Fluorene, erh
......@@ -4440,6 +4682,10 @@ NG2R62 CG2RC0 NG2R51 CG331 11.0000 2 180.00 ! 9MAD, 9-Methyl-Adenine, kev
NG2R62 CG2RC0 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage
NG2R62 CG2RC0 NG2R51 CG3RC1 1.2000 2 180.00 ! PYRIDINE pyridine, yin
NG2R62 CG2RC0 NG2R51 HGP1 1.2000 2 180.00 ! NA G
CG2R61 CG2RC0 NG2R53 CG2R53 3.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2R61 CG2RC0 NG2R53 CG331 1.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 NG2R53 CG2R53 6.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 NG2R53 CG331 1.0000 2 180.00 ! MSCH model for D3R, xxwy
CG2RC0 CG2RC0 NG2R62 CG2R64 0.2000 2 180.00 ! NA G
NG2R50 CG2RC0 NG2R62 CG2R64 2.0000 2 180.00 ! PUR7, purine(N7H), kevo
NG2R51 CG2RC0 NG2R62 CG2R64 2.0000 2 180.00 ! NA G
......@@ -4883,6 +5129,12 @@ CG2O5 CG321 CG321 CG321 0.3500 3 180.00 ! CHON, cyclohexanone; from L
CG2O5 CG321 CG321 CG321 0.1100 4 0.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol
CG2O5 CG321 CG321 CG321 0.0900 6 180.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol
CG2O5 CG321 CG321 HGA2 0.1950 3 0.00 ! CHON, cyclohexanone; from CG2O2 CG321 CG321 HGA2; yapol
CG2R51 CG321 CG321 CG321 0.0400 3 0.00 ! INCA model for D3R, xxwy
CG2R51 CG321 CG321 NG301 0.0400 3 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 CG321 HGA2 0.2000 3 0.00 ! INCA model for D3R, xxwy
CG2R52 CG321 CG321 CG321 0.0400 3 0.00 ! INCA model for D3R, xxwy
CG2R52 CG321 CG321 NG301 0.0400 3 0.00 ! D3R set1 scaffold 1, xxwy
CG2R52 CG321 CG321 HGA2 0.2000 3 0.00 ! INCA model for D3R, xxwy
CG2R61 CG321 CG321 CG321 0.0400 3 0.00 ! PROT ethylbenzene
CG2R61 CG321 CG321 NG2S1 0.1900 3 0.00 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, corrected by kevo
CG2R61 CG321 CG321 HGA2 0.0400 3 0.00 ! PROT ethylbenzene
......@@ -4910,6 +5162,7 @@ CG321 CG321 CG321 CG331 0.15051 2 0.00 ! LIPID alkane, 4/04, jbk (Je
CG321 CG321 CG321 CG331 0.08133 3 180.00 ! LIPID alkane, 4/04, jbk
CG321 CG321 CG321 CG331 0.10824 4 0.00 ! LIPID alkane, 4/04, jbk
CG321 CG321 CG321 CG331 0.20391 5 0.00 ! LIPID alkane, 4/04, jbk
CG321 CG321 CG321 CG3C50 0.4000 3 0.00 ! MSCH model for D3R, xxwy
CG321 CG321 CG321 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
CG321 CG321 CG321 NG2D1 0.7900 1 180.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin
CG321 CG321 CG321 NG2D1 0.2000 2 0.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin
......@@ -4917,6 +5170,8 @@ CG321 CG321 CG321 NG2D1 0.1200 3 0.00 ! from EEPI's CG331 CG321 CG3
CG321 CG321 CG321 NG2D1 0.1500 4 0.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin
CG321 CG321 CG321 NG2D1 0.0500 6 180.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin
CG321 CG321 CG321 NG2S1 0.2000 3 0.00 ! ALBE, Alpha Lysine Benzyl Ester CDCA Amide, cacha
CG321 CG321 CG321 NG301 0.1600 1 180.00 ! TSPD model for D3R, xxwy
CG321 CG321 CG321 NG301 0.3900 2 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 CG321 OG301 0.1600 1 180.00 ! methylpropylether, 2/12/05, ATM
CG321 CG321 CG321 OG301 0.3900 2 0.00 ! methylpropylether
CG321 CG321 CG321 OG302 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92
......@@ -4944,12 +5199,16 @@ CG331 CG321 CG321 SG3O1 0.9400 1 180.00 ! PSNA, propyl sulfonate, xhe
CG331 CG321 CG321 SG3O1 0.3800 2 0.00 ! PSNA, propyl sulfonate, xhe
CG331 CG321 CG321 SG3O1 0.1100 3 0.00 ! PSNA, propyl sulfonate, xhe
CG331 CG321 CG321 HGA2 0.1800 3 0.00 ! LIPID alkane
CG3C50 CG321 CG321 NG301 0.1600 1 180.00 ! D3R set2 scaffold, xxwy
CG3C50 CG321 CG321 NG301 0.3900 2 0.00 ! D3R set2 scaffold, xxwy
CG3C50 CG321 CG321 HGA2 0.5000 3 0.00 ! MSCH model for D3R, xxwy
CG3RC1 CG321 CG321 HGA2 0.1950 3 0.00 ! LIPID alkanes
NG2D1 CG321 CG321 HGA2 0.2000 3 0.00 ! EEPI, from NG2S1 CG321 CG321 HGA2, fylin
NG2S1 CG321 CG321 SG3O1 0.9500 1 180.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo
NG2S1 CG321 CG321 SG3O1 1.3300 2 0.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo
NG2S1 CG321 CG321 SG3O1 0.0800 3 180.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo
NG2S1 CG321 CG321 HGA2 0.1950 3 0.00 ! TCA, Taurocholic Acid, cacha, 03/06 OK
NG301 CG321 CG321 HGA2 0.1600 3 0.00 ! TSPD model for D3R, xxwy
NG311 CG321 CG321 HGA2 0.1950 3 0.00 ! K2Cn, cgenff_compromise, kevo
OG301 CG321 CG321 OG301 0.2500 1 180.00 ! 1,2 dimethoxyethane, 2/12/05, ATM
OG301 CG321 CG321 OG301 1.2400 2 0.00 ! 1,2 dimethoxyethane
......@@ -5043,6 +5302,12 @@ HGA2 CG321 CG3C31 CG3C31 0.0200 3 0.00 ! 1BOX, 1-butene oxide, kevo
HGA2 CG321 CG3C31 OG3C31 0.5000 1 0.00 ! 1BOX, 1-butene oxide, kevo
HGA2 CG321 CG3C31 OG3C31 0.2700 3 0.00 ! 1BOX, 1-butene oxide, kevo
HGA2 CG321 CG3C31 HGA1 0.0000 3 0.00 ! 1BOX, 1-butene oxide; kept at 0; sc
CG321 CG321 CG3C50 CG2R53 0.8000 4 180.00 ! MSCH model for D3R, xxwy
CG321 CG321 CG3C50 CG2RC0 0.8000 4 180.00 ! MSCH model for D3R, xxwy
CG321 CG321 CG3C50 CG321 0.4000 3 0.00 ! MSCH model for D3R, xxwy
HGA2 CG321 CG3C50 CG2R53 0.0000 3 0.00 ! MSCH model for D3R, xxwy
HGA2 CG321 CG3C50 CG2RC0 0.0000 3 0.00 ! MSCH model for D3R, xxwy
HGA2 CG321 CG3C50 CG321 0.0000 3 0.00 ! MSCH model for D3R, xxwy
OG301 CG321 CG3C51 CG3C52 0.2000 3 180.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from NA, sugar; kevo
OG301 CG321 CG3C51 HGA1 0.1950 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from NA, sugar; kevo
OG303 CG321 CG3C51 CG3C51 2.5000 1 180.00 ! NA, sugar
......@@ -5151,6 +5416,20 @@ CG331 CG321 NG2S3 HGP1 0.3210 2 0.00 ! NESM, N-ethyl-sulfamate, my
CG331 CG321 NG2S3 HGP1 0.2350 3 180.00 ! NESM, N-ethyl-sulfamate, my & kevo
HGA2 CG321 NG2S3 SG3O1 0.1500 3 0.00 ! NESM, N-ethyl-sulfamate; from HGA3 CG331 NG2S3 PG1; my
HGA2 CG321 NG2S3 HGP1 0.0100 3 0.00 ! NESM, N-ethyl-sulfamate; from HGA3 CG331 NG2S3 HGP1; my
CG2R51 CG321 NG301 CG321 1.4200 1 180.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 NG301 CG321 0.8200 2 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 NG301 CG321 1.0200 3 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 NG301 SG3O2 0.1000 1 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 NG301 SG3O2 0.7000 2 0.00 ! D3R set1 scaffold 2, xxwy
CG2R51 CG321 NG301 SG3O2 0.1000 3 0.00 ! D3R set1 scaffold 2, xxwy
CG321 CG321 NG301 CG321 1.4200 1 180.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG301 CG321 0.8200 2 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG301 CG321 1.0200 3 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG301 SG3O2 0.1000 1 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG301 SG3O2 0.7000 2 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG301 SG3O2 0.1000 3 0.00 ! TSPD model for D3R, xxwy
HGA2 CG321 NG301 CG321 0.1000 3 0.00 ! TSPD model for D3R, xxwy
HGA2 CG321 NG301 SG3O2 0.1000 3 0.00 ! TSPD model for D3R, xxwy
CG321 CG321 NG311 HGPAM1 0.3000 3 0.00 ! K2Cn, cgenff_compromise, kevo
CG331 CG321 NG311 SG3O2 0.1000 1 0.00 ! EESM, N-ethylethanesulfonamide, xxwy
CG331 CG321 NG311 SG3O2 0.7000 2 0.00 ! EESM, N-ethylethanesulfonamide, xxwy
......@@ -5217,6 +5496,9 @@ CG324 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorg
CG331 CG321 OG303 PG2 0.6000 1 180.00 ! EP_2 phospho-ser/thr
CG331 CG321 OG303 PG2 0.6500 2 0.00 ! EP_2 phospho-ser/thr
CG331 CG321 OG303 PG2 0.0500 3 0.00 ! EP_2 phospho-ser/thr
CG3C51 CG321 OG303 PG0 0.6000 1 180.00 ! mono-thio S-P bond
CG3C51 CG321 OG303 PG0 0.6500 2 0.00 ! mono-thio S-P bond
CG3C51 CG321 OG303 PG0 0.0500 3 0.00 ! mono-thio S-P bond
CG3C51 CG321 OG303 PG1 0.6000 1 180.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
CG3C51 CG321 OG303 PG1 0.6500 2 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
CG3C51 CG321 OG303 PG1 0.0500 3 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
......@@ -5226,6 +5508,7 @@ CG3C51 CG321 OG303 PG2 0.0500 3 0.00 ! TH5P carbocyclic sugars res
CG3RC1 CG321 OG303 PG1 0.6000 1 180.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr
CG3RC1 CG321 OG303 PG1 0.6500 2 0.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr
CG3RC1 CG321 OG303 PG1 0.0500 3 0.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr
HGA2 CG321 OG303 PG0 0.0000 3 0.00 ! mono-thio S-P bond
HGA2 CG321 OG303 PG1 0.0000 3 0.00 ! NA dmp !Reorganization: PC and others
HGA2 CG321 OG303 PG2 0.0000 3 0.00 ! NA dmp !Reorganization: TH5P and others
HGA2 CG321 OG303 SG3O1 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr.
......@@ -5290,8 +5573,8 @@ CG311 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT methanethiol pure solv
CG314 CG321 SG311 HGP3 0.2400 1 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92
CG314 CG321 SG311 HGP3 0.1500 2 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92
CG314 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92
CG321 CG321 SG311 CG2N2 0.24 1 180.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt.
CG321 CG321 SG311 CG2N2 0.37 3 0.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt.
CG321 CG321 SG311 CG2N2 0.2400 1 180.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt.
CG321 CG321 SG311 CG2N2 0.3700 3 0.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt.
CG321 CG321 SG311 CG321 0.2400 1 180.00 ! PROT expt. MeEtS, 3/26/92 (FL)
CG321 CG321 SG311 CG321 0.3700 3 0.00 ! PROT expt. MeEtS, 3/26/92 (FL)
CG321 CG321 SG311 CG331 0.2400 1 180.00 ! PROT expt. MeEtS, 3/26/92 (FL)
......@@ -5308,7 +5591,7 @@ CG331 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT ethanethiol C-C-S-H su
CG3C51 CG321 SG311 CG321 0.2400 1 180.00 ! PROT MeEtS reset by kevo
CG3C51 CG321 SG311 CG321 0.3700 3 0.00 ! PROT MeEtS reset by kevo
SG311 CG321 SG311 CG321 1.3000 3 0.00 ! TRIT, trithiane
HGA2 CG321 SG311 CG2N2 0.36 3 0.00 ! DH3T , from HGA3 CG331 SG311 CG2O6, penalty= 19.5 no opt.
HGA2 CG321 SG311 CG2N2 0.3600 3 0.00 ! DH3T , from HGA3 CG331 SG311 CG2O6, penalty= 19.5 no opt.
HGA2 CG321 SG311 CG321 0.2800 3 0.00 ! PROT DTN 8/24/90
HGA2 CG321 SG311 CG331 0.2800 3 0.00 ! PROT DTN 8/24/90
HGA2 CG321 SG311 HGP3 0.2000 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92
......@@ -5403,8 +5686,12 @@ HGA3 CG331 CG3RC1 CG3RC1 0.1500 3 180.00 ! BAM1, bile acid steroidal C
HGA3 CG331 NG2D1 CG2D1 0.1000 3 0.00 ! RETINOL SCH1, Schiff's base, deprotonated
HGA3 CG331 NG2D1 CG2N1 0.1100 3 180.00 ! MGU1, methylguanidine
HGA3 CG331 NG2D1 CG2O7 0.0300 3 0.00 ! MICY, methyl isocyanate, xxwy
HGA3 CG331 NG2R51 CG2R51 0.0000 3 0.00 ! INCA model for D3R, xxwy
HGA3 CG331 NG2R51 CG2R53 0.0000 3 0.00 ! NA 9-M-A
HGA3 CG331 NG2R51 CG2RC0 0.1900 3 0.00 ! NA 9-M-G
HGA3 CG331 NG2R51 NG2R50 0.0000 3 0.00 ! INCA model for D3R, xxwy
HGA3 CG331 NG2R53 CG2R53 0.1000 3 0.00 ! MSCH model for D3R, xxwy
HGA3 CG331 NG2R53 CG2RC0 0.1000 3 0.00 ! MSCH model for D3R, xxwy
HGA3 CG331 NG2R61 CG2R62 0.0000 3 0.00 ! NA 1-M-C
HGA3 CG331 NG2R61 CG2R63 0.1900 3 0.00 ! NA 1-M-C
HGA3 CG331 NG2S0 CG2O1 0.0000 3 0.00 ! DMA, dimethylacetamide; from PROT, sp2-methyl, no torsion potential; xxwy & jhs
......@@ -5440,7 +5727,7 @@ HGA3 CG331 OG303 SG3O1 0.0000 3 0.00 ! LIPID methylsulfate
HGA3 CG331 OG303 SG3O2 0.0000 3 0.00 ! MMST, methyl methanesulfonate, xxwy
HGA3 CG331 OG311 HGP1 0.1800 3 0.00 ! og methanol
HGA3 CG331 SG301 SG301 0.1580 3 0.00 ! PROT expt. dimethyldisulfide, 3/26/92 (FL)
HGA3 CG331 SG311 CG2N2 0.36 3 0.00 ! MT2A , from HGA3 CG331 SG311 CG2O6
HGA3 CG331 SG311 CG2N2 0.3600 3 0.00 ! MT2A , from HGA3 CG331 SG311 CG2O6
HGA3 CG331 SG311 CG2O6 0.3600 3 0.00 ! DMTT, dimethyl trithiocarbonate, kevo
HGA3 CG331 SG311 CG2R64 0.1500 3 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine; from HGA3 CG331 SG311 CG2O6; isg
HGA3 CG331 SG311 CG321 0.2800 3 0.00 ! PROT DTN 8/24/90
......@@ -5504,13 +5791,17 @@ HGA2 CG3C31 OG3C31 CG3C31 0.8100 6 180.00 ! 1EOX, 1-ethylene oxide, kev
CG2R53 CG3C41 CG3C41 NG2R43 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo
CG2R53 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo
CG3C41 CG3C41 CG3C41 CG3C41 1.4300 3 0.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk
CG3C41 CG3C41 CG3C41 OG3C51 0.0000 3 0.00 ! OXTN, oxetane, gmu
CG3C41 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk
NG2R43 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo
OG3C51 CG3C41 CG3C41 HGA2 0.1900 3 0.00 ! OXTN, oxetane, gmu
HGA2 CG3C41 CG3C41 HGA2 0.0000 3 0.00 ! CBU, cyclobutane, kevo
CG3C41 CG3C41 NG2R43 CG2R53 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo
CG3C41 CG3C41 NG2R43 HGP1 0.2000 3 180.00 ! AZDO, 2-azetidinone, kevo
HGA2 CG3C41 NG2R43 CG2R53 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo
HGA2 CG3C41 NG2R43 HGP1 0.0000 3 0.00 ! AZDO, 2-azetidinone, lsk & kevo
CG3C41 CG3C41 OG3C51 CG3C41 0.5000 3 0.00 ! OXTN, oxetane, gmu (CG3C52 CG3C52 OG3C51 CG3C52)
HGA2 CG3C41 OG3C51 CG3C41 0.3000 3 0.00 ! OXTN, oxetane, gmu
CG321 CG3C51 CG3C51 CG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
CG321 CG3C51 CG3C51 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
CG321 CG3C51 CG3C51 NG2S3 0.5000 2 180.00 ! NABAKB phosphoramidates
......@@ -6044,6 +6335,8 @@ CG3C52 CG3RC1 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
CG3C52 CG3RC1 CG3RC1 OG3C51 1.2000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy
CG3C52 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
NG2R51 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
NG2R53 CG3RC1 CG3RC1 NG2R53 0.1500 3 0.00 ! CBHH, glycoluril, (CG3C52 CG3RC1 CG3RC1 NG2R51), jing
NG2R53 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CBHH, glycoluril, (NG2R51 CG3RC1 CG3RC1 HGA1), jing
NG2R61 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
OG3C51 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from CARBOCY; xxwy
HGA1 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars
......@@ -6053,6 +6346,12 @@ CG3C52 CG3RC1 NG2R51 CG2R53 0.1000 3 0.00 ! CARBOCY carbocyclic sugars
CG3C52 CG3RC1 NG2R51 CG2RC0 0.3000 3 0.00 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 NG2R51 CG2R53 1.1000 1 180.00 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 NG2R51 CG2RC0 1.1000 1 180.00 ! CARBOCY carbocyclic sugars
CG3RC1 CG3RC1 NG2R53 CG2R53 1.1000 1 180.00 ! CBHH, glycoluril, (CG3RC1 CG3RC1 NG2R51 CG2R53), jing
CG3RC1 CG3RC1 NG2R53 HGP1 0.7600 3 0.00 ! CBHH, glycoluril, (CG3C52 CG3C52 NG2R53 HGP1), jing
NG2R53 CG3RC1 NG2R53 CG2R53 2.3100 3 180.00 ! CBHH, glycoluril, (CG3C52 CG3C52 NG2R53 CG2R53), jing
NG2R53 CG3RC1 NG2R53 HGP1 0.7600 3 0.00 ! CBHH, glycoluril, (CG3C52 CG3C52 NG2R53 HGP1), jing
HGA1 CG3RC1 NG2R53 CG2R53 0.0000 3 0.00 ! CBHH, glycoluril, (HGA2 CG3C52 NG2R53 CG2R53), jing
HGA1 CG3RC1 NG2R53 HGP1 0.0000 3 180.00 ! CBHH, glycoluril, (HGA2 CG3C52 NG2R53 HGP1), jing
CG3C31 CG3RC1 NG2R61 CG2R62 0.0000 3 180.00 ! CARBOCY carbocyclic sugars
CG3C31 CG3RC1 NG2R61 CG2R63 0.3000 3 0.00 ! CARBOCY carbocyclic sugars
CG3C52 CG3RC1 NG2R61 CG2R62 0.0000 3 180.00 ! CARBOCY carbocyclic sugars
......@@ -6074,7 +6373,10 @@ CG2DC2 NG2D1 NG2S1 HGP1 2.5000 2 180.00 ! HDZ2, hydrazone model cmpd
CG2R51 NG2R50 NG2R50 NG2R51 14.0000 2 180.00 ! TRZ3, triazole123
CG2R51 NG2R50 NG2R50 OG2R50 14.0000 2 180.00 ! OXAD, oxadiazole123
CG2R52 NG2R50 NG2R51 CG2R51 12.0000 2 180.00 ! PYRZ, pyrazole
CG2R52 NG2R50 NG2R51 CG2R61 1.4000 2 180.00 ! D3R set1 scaffold 1, xxwy
CG2R52 NG2R50 NG2R51 CG2R64 0.2000 2 180.00 ! PIPA model for D3R, xxwy
CG2R52 NG2R50 NG2R51 CG2RC0 8.5000 2 180.00 ! INDA, 1H-indazole, kevo
CG2R52 NG2R50 NG2R51 CG331 1.4000 2 180.00 ! INCA model for D3R, xxwy
CG2R52 NG2R50 NG2R51 NG2R50 9.5000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf
CG2R52 NG2R50 NG2R51 HGP1 1.4000 2 180.00 ! PYRZ, pyrazole
CG2R53 NG2R50 NG2R51 CG2R53 10.0000 2 180.00 ! TRZ4, triazole124, xxwy
......@@ -6102,6 +6404,13 @@ HGP1 NG2S3 PG1 OG303 0.0500 3 0.00 ! NABAKB phosphoramidates
CG321 NG2S3 SG3O1 OG2P1 0.5520 3 0.00 ! NESM, N-ethyl-sulfamate, my & kevo
CG331 NG2S3 SG3O1 OG2P1 0.5370 3 0.00 ! NMSM, N-methyl-sulfamate, my
HGP1 NG2S3 SG3O1 OG2P1 0.0500 3 0.00 ! NMSM, N-methyl-sulfamate; from HGP1 NG2S3 PG1 OG2P1; my
CG321 NG301 SG3O2 CG2R51 1.1700 1 180.00 ! TSPD model for D3R, xxwy
CG321 NG301 SG3O2 CG2R51 1.1600 2 0.00 ! TSPD model for D3R, xxwy
CG321 NG301 SG3O2 CG2R51 1.0200 3 0.00 ! TSPD model for D3R, xxwy
CG321 NG301 SG3O2 CG2R61 1.1700 1 180.00 ! D3R set1 scaffold 2, xxwy
CG321 NG301 SG3O2 CG2R61 1.1600 2 0.00 ! D3R set1 scaffold 2, xxwy
CG321 NG301 SG3O2 CG2R61 1.0200 3 0.00 ! D3R set1 scaffold 2, xxwy
CG321 NG301 SG3O2 OG2P1 0.2000 3 0.00 ! TSPD model for D3R, xxwy
CG2R61 NG311 SG3O2 CG2R61 1.2000 1 180.00 ! PBSM, N-phenylbenzenesulfonamide, xxwy
CG2R61 NG311 SG3O2 CG2R61 1.4000 2 0.00 ! PBSM, N-phenylbenzenesulfonamide, xxwy
CG2R61 NG311 SG3O2 CG331 2.2000 2 0.00 ! PMSM, N-phenylmethanesulfonamide, xxwy
......@@ -6161,6 +6470,13 @@ HGP1 NG3N1 NG3N1 HGP1 1.1000 1 180.00 ! HDZN, hydrazine, ed
HGP1 NG3N1 NG3N1 HGP1 4.5000 2 0.00 ! HDZN, hydrazine, ed
HGP1 NG3N1 NG3N1 HGP1 0.0500 3 0.00 ! HDZN, hydrazine, ed
CG334 NG3P0 OG311 HGP1 0.2770 3 0.00 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy
CG321 OG303 PG0 OG2P1 0.1000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 OG304 0.9500 2 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 OG304 0.5000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 OG311 0.9500 2 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 OG311 0.5000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 SG2P1 0.1000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG0 SG2P2 0.1000 3 0.00 ! di-thio S-P bond
CG331 OG303 PG0 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization:MP_0 RE-OPTIMIZE!
CG331 OG303 PG0 OG311 0.9500 2 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE!
CG331 OG303 PG0 OG311 0.5000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE!
......@@ -6196,7 +6512,15 @@ CG3C51 OG303 PG1 OG311 0.9500 2 0.00 ! NA T3PH, adm jr.
CG3C51 OG303 PG1 OG311 0.5000 3 0.00 ! NA T3PH, adm jr.
CG311 OG303 PG2 OG2P1 0.1000 3 0.00 ! IP_2 NA dmp,eps, O1P-P-O3'-C3'
CG321 OG303 PG2 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization: TH5P and others
CG321 OG303 PG2 OG2S1 0.1000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG2 SG2P1 0.1000 3 0.00 ! mono-thio S-P bond
CG321 OG303 PG2 SG2P2 0.1000 3 0.00 ! di-thio S-P bond
CG331 OG303 PG2 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization:MP_2
CG331 OG303 PG2 SG2P1 0.4000 1 0.00 ! mono-thio S-P bond
CG331 OG303 PG2 SG2P1 0.1000 3 0.00 ! mono-thio S-P bond
CG331 OG303 PG2 SG2P2 0.4500 1 180.00 ! di-thio S-P bond
CG331 OG303 PG2 SG2P2 0.2000 2 0.00 ! di-thio S-P bond
CG331 OG303 PG2 SG2P2 0.1000 3 0.00 ! di-thio S-P bond
CG3C51 OG303 PG2 OG2P1 0.1000 3 0.00 ! TH3P and others dmp,eps, O1P-P-O3'-C3'
CG321 OG303 SG3O1 OG2P1 0.0000 3 0.00 ! LIPID methylsulfate
CG331 OG303 SG3O1 OG2P1 0.0000 3 0.00 ! LIPID methylsulfate
......@@ -6214,6 +6538,16 @@ CG331 OG303 SG3O2 NG321 1.8000 1 180.00 ! MSMT, methyl sulfamate, xxw
CG331 OG303 SG3O2 NG321 0.5000 2 0.00 ! MSMT, methyl sulfamate, xxwy
CG331 OG303 SG3O2 NG321 0.4000 3 0.00 ! MSMT, methyl sulfamate, xxwy
CG331 OG303 SG3O2 OG2P1 0.3000 3 0.00 ! MMST, methyl methanesulfonate, xxwy
PG0 OG304 PG0 OG2P1 0.1000 2 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG2P1 0.0300 3 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG303 0.0300 2 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG303 0.0300 3 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG304 0.0300 2 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG304 0.0300 3 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG311 0.1000 2 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 OG311 0.0300 3 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 SG2P1 0.0300 3 0.00 ! mono-thio S-P bond
PG0 OG304 PG0 SG2P2 0.0300 3 0.00 ! di-thio S-P bond
PG1 OG304 PG1 OG2P1 0.1000 2 0.00 ! NA ppi2 !Reorganization:PPI2
PG1 OG304 PG1 OG2P1 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2
PG1 OG304 PG1 OG303 0.0300 2 0.00 ! NA ppi2 !Reorganization:PPI2
......@@ -6229,10 +6563,17 @@ PG2 OG304 PG1 OG303 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !
PG2 OG304 PG1 OG304 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
PG2 OG304 PG1 OG304 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
PG1 OG304 PG2 OG2P1 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1
PG1 OG304 PG2 OG2S1 0.0300 3 0.00 ! mono-thio S-P bond
PG1 OG304 PG2 SG2P1 0.0300 3 0.00 ! mono-thio S-P bond
PG1 OG304 PG2 SG2P2 0.0300 3 0.00 ! di-thio S-P bond
HGP1 OG311 PG0 OG2P1 0.3000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE!
HGP1 OG311 PG0 OG303 1.6000 1 180.00 ! PROTNA phenol phosphate !Reorganization:MP_0 RE-OPTIMIZE!
HGP1 OG311 PG0 OG303 0.9000 2 0.00 ! PROTNA phenol phosphate !Reorganization:MP_0 RE-OPTIMIZE!
HGP1 OG311 PG0 OG304 1.6000 1 180.00 ! mono-thio S-P bond
HGP1 OG311 PG0 OG304 0.9000 2 0.00 ! mono-thio S-P bond
HGP1 OG311 PG0 OG311 0.3000 3 0.00 ! NA MP_0, adm jr.
HGP1 OG311 PG0 SG2P1 0.3000 3 0.00 ! mono-thio S-P bond
HGP1 OG311 PG0 SG2P2 0.3000 3 0.00 ! mono-thio S-P bond
HGP1 OG311 PG1 CG312 0.2000 1 180.00 ! BDFP, BDFD, Difuorobenzylphosphonate
HGP1 OG311 PG1 CG312 1.6000 2 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate
HGP1 OG311 PG1 CG321 0.6000 1 180.00 ! BDFP, BDFD, Benzylphosphonate
......@@ -6293,6 +6634,7 @@ CG2O1 CG2DC1 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes
CG2O1 CG2DC1 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
CG2O1 CG2DC2 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
CG2O1 CG2DC2 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
CG2O1 CG2R51 NG2S1 OG2D1 70.0000 0 0.00 ! INCA model for D3R, xxwy
CG2O1 CG2R61 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
CG2O1 CG2R61 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
CG2O1 CG2R62 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD
......@@ -6347,6 +6689,7 @@ CG2O5 CG2R61 CG331 OG2D3 60.0000 0 0.00 ! 3ACP, 3-acetylpyridine; PHM
CG2O5 CG321 CG321 OG2D3 70.0000 0 0.00 ! CHON, cyclohexanone; from ACO, acetone; yapol
CG2O5 CG321 CG331 OG2D3 70.0000 0 0.00 ! BTON, butanone; from ACO, acetone; yapol
CG2O5 CG331 CG331 OG2D3 70.0000 0 0.00 ! ketone, acetone adm 11/08
CG2O6 NG2R51 NG2S1 OG2D1 60.0000 0 0.00 ! TICA model for D3R, xxwy
CG2O6 NG2S2 NG2S2 OG2D1 80.0000 0 0.00 ! UREA, Urea
CG2O6 OG302 OG302 OG2D1 145.0000 0 0.00 ! DMCA, dimethyl carbonate, xxwy
CG2O6 OG2D2 OG2D2 OG2D2 107.0000 0 0.00 ! PROTMOD carbonate
......@@ -6358,6 +6701,7 @@ CG2R53 CG252O NG2R53 OG2D1 90.0000 0 0.00 ! MRDN, methylidene rhodanine
CG2R53 CG25C1 NG2R51 OG2D1 90.0000 0 0.00 ! MEOI, methyleneoxindole, kevo & xxwy from 2PDO WILDCARD
CG2R53 CG25C2 NG2R51 OG2D1 90.0000 0 0.00 ! MEOI, methyleneoxindole, kevo & xxwy from 2PDO WILDCARD
CG2R53 CG3C41 NG2R43 OG2D1 120.0000 0 0.00 ! AZDO, 2-azetidinone, kevo
CG2R53 CG3C50 NG2R53 OG2D1 110.000 0 0.00 ! MSCH model for D3R, xxwy
CG2R53 CG3C52 NG2R53 OG2D1 90.0000 0 0.00 !90 120 2PDO, 2-pyrrolidinone, kevo
CG2R53 NG2R53 NG2R53 OG2D1 90.0000 0 0.00 ! MHYO, 5-methylenehydantoin, xxwy from 2PDO WILDCARD
CG2R53 CG2R51 OG2D1 OG3C51 28.6000 0 0.00 ! B2FO, 5H-furan-2-one, ctsai
......@@ -6548,12 +6892,9 @@ FGP1 0.0 -0.0970 1.6000 ! Aluminum tetraflouride, ALF4
FGR1 0.0 -0.1200 1.7000 ! aromatic F, 1,3-difluorobenzene pure solvent
CLGA1 0.0 -0.3430 1.9100 ! CLET, DCLE, chloroethane, 1,1-dichloroethane
CLGA3 0.0 -0.3100 1.9100 ! TCLE
CLGR1 0.0 -0.3200 1.9300 ! CHLB, chlorobenzene
BRGA1 0.0 -0.4800 1.9700 ! BRET
BRGA2 0.0 -0.5300 2.0500 ! DBRE
BRGA3 0.0 -0.5400 2.0000 ! TBRE
BRGR1 0.0 -0.4200 2.0700 ! BROM, bromobenzene
IGR1 0.0 -0.5500 2.1900 ! IODB, iodobenzene
!miscellaneous
!DUM 0.0 -0.0000 0.0000 ! dummy atom
!HE 0.0 -0.02127 1.4800 ! helium
......@@ -6562,6 +6903,31 @@ PG0 0.0 -0.5850 2.1500 ! neutral phosphate
PG1 0.0 -0.5850 2.1500 ! phosphate -1
PG2 0.0 -0.5850 2.1500 ! phosphate -2
ALG1 0.0 -0.6500 2.0000 ! Aluminum tetraflouride, ALF4
!Halogens with lone-pairs
LPH 0.0 0.0000 0.0000 ! lone-pair on chlorine attached to aromatic, isg/fylin
CLGR1 0.0 -0.2300 1.8600 ! CHLB, chlorobenzene, adjusted for lone-pair, fylin
BRGR1 0.0 -0.3200 1.9800 ! BROB, bromobenzene, adjusted for lone-pair, fylin
IGR1 0.0 -0.5200 2.2400 ! IODB, iodobenzene, adjusted for lone-pair, fylin
SG2P1 0.0 -0.6308 2.0937 ! mono-thio S-P bond
OG2S1 0.0 -0.1423 1.6796 ! mono-thio S-P bond
SG2P2 0.0 -0.6199 2.0546 ! di-thio S-P bond
NBFIX
!!! IMPORTANT!!!
!!! The following topology & parameter files should be read before reading top_all36_cgenff.rtf/par_all36_cgenff.prm
!!! for correctly implementing the NBFIX between the chlorine with the lone-pair and the carbonyl oxygen in amides
!!! 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
!!! IMPORTANT!!!
OG2D1 CLGR1 -0.2000 3.4000 ! NBFIX based on NMA (carbonyl oxygen in amide) and CL of CGenFF
O CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in amide of protein
ON1 CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
ON1C CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
OC2D1 CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in carbohydrate amides
S CLGR1 -0.3800 3.8300 ! NBFIX for cysteine sulphur
HS CLGR1 -0.2000 2.8200 ! NBFIX for cysteine sulphur
 
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
! READ PARAM APPEND CARD
......
wrappers/python/tests/systems/top_all36_cgenff.rtf
View file @ 6e073b48
* -------------------------------------------------------------------------- *
* CGenFF: Topology for the Charmm General Force Field v. 3.1 *
* CGenFF: Topology for the Charmm General Force Field v. 4.1 *
* for Small Molecule Drug Design *
* -------------------------------------------------------------------------- *
*
......@@ -12,6 +12,17 @@
! - 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! !
......@@ -28,9 +39,11 @@
! 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 !
......@@ -59,184 +72,183 @@
! -------------------------------------------------------------------------- !
 
!hydrogens
MASS 256 HGA1 1.00800 ! alphatic proton, CH
MASS 257 HGA2 1.00800 ! alphatic proton, CH2
MASS 258 HGA3 1.00800 ! alphatic proton, CH3
MASS 259 HGA4 1.00800 ! alkene proton; RHC=
MASS 260 HGA5 1.00800 ! alkene proton; H2C=CR
MASS 261 HGA6 1.00800 ! aliphatic H on fluorinated C, monofluoro
MASS 262 HGA7 1.00800 ! aliphatic H on fluorinated C, difluoro
MASS 263 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#)
MASS 264 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#)
MASS 265 HGAAM2 1.00800 ! aliphatic H, NEUTRAL methylamine (#)
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 266 HGP1 1.00800 ! polar H
MASS 267 HGP2 1.00800 ! polar H, +ve charge
MASS 268 HGP3 1.00800 ! polar H, thiol
MASS 269 HGP4 1.00800 ! polar H, neutral conjugated -NH2 group (NA bases)
MASS 270 HGP5 1.00800 ! polar H on quarternary ammonium salt (choline)
MASS 271 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H
MASS 272 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#)
MASS 273 HGPAM3 1.00800 ! polar H, NEUTRAL ammonia (#)
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 274 HGR51 1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene
MASS 275 HGR52 1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge
MASS 276 HGR53 1.00800 ! nonpolar H, +ve charge HIS he1(+1)
MASS 277 HGR61 1.00800 ! aromatic H
MASS 278 HGR62 1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom
MASS 279 HGR63 1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens
MASS 280 HGR71 1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo
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 281 CG1T1 12.01100 ! internal alkyne R-C#C
MASS 282 CG1T2 12.01100 ! terminal alkyne H-C#C
MASS 283 CG1N1 12.01100 ! C for cyano group
MASS 284 CG2D1 12.01100 ! alkene; RHC= ; imine C
MASS 285 CG2D2 12.01100 ! alkene; H2C=
MASS 286 CG2D1O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1.
MASS 287 CG2D2O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2.
MASS 288 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2
MASS 289 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2
MASS 290 CG2DC3 12.01100 ! conjugated alkenes, H2C=
MASS 291 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium
MASS 292 CG2N2 12.01100 ! conjugated C in amidinium cation
MASS 293 CG2O1 12.01100 ! carbonyl C: amides
MASS 294 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids
MASS 295 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates
MASS 296 CG2O4 12.01100 ! carbonyl C: aldehydes
MASS 297 CG2O5 12.01100 ! carbonyl C: ketones
MASS 298 CG2O6 12.01100 ! carbonyl C: urea, carbonate
MASS 299 CG2O7 12.01100 ! CO2 carbon
MASS 300 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp
MASS 301 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole
MASS 302 CG2R53 12.01100 ! 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO, kevo
MASS 303 CG2R57 12.01100 ! 5-mem ring, bipyrroles
MASS 304 CG25C1 12.01100 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond
MASS 305 CG25C2 12.01100 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond
MASS 306 CG251O 12.01100 ! same as CG2D1O but in 5-membered ring with exocyclic double bond
MASS 307 CG252O 12.01100 ! same as CG2D2O but in 5-membered ring with exocyclic double bond
MASS 308 CG2R61 12.01100 ! 6-mem aromatic C
MASS 309 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA)
MASS 310 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?)
MASS 311 CG2R64 12.01100 ! 6-mem aromatic amidine and guanidine carbon (between 2 or 3 Ns and double-bound to one of them), NA, PYRM
MASS 312 CG2R66 12.01100 ! 6-mem aromatic carbon bound to F
MASS 313 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl
MASS 314 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp
MASS 315 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene, kevo
MASS 316 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, azulene, kevo
MASS 317 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane
MASS 318 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl
MASS 319 CG311 12.01100 ! aliphatic C with 1 H, CH
MASS 320 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl
MASS 321 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+)
MASS 322 CG321 12.01100 ! aliphatic C for CH2
MASS 323 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl
MASS 324 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon
MASS 325 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (piperidine) (+)
MASS 326 CG331 12.01100 ! aliphatic C for methyl group (-CH3)
MASS 327 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+)
MASS 328 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#)
MASS 329 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#)
MASS 330 CG3AM2 12.01100 ! aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#)
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 331 CG3C31 12.01100 ! cyclopropyl carbon
MASS 332 CG3C41 12.01100 ! cyclobutyl carbon
MASS 333 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids)
MASS 334 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses)
MASS 335 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose)
MASS 336 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+)
MASS 337 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+)
MASS 338 CG3RC1 12.01100 ! bridgehead in bicyclic systems containing at least one 5-membered or smaller ring
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 339 NG1T1 14.00700 ! N for cyano group
!MASS 340 NG1D1 14.00700 ! terminal N in azides, lsk
MASS 341 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine)
MASS 342 NG2S0 14.00700 ! N,N-disubstituted amide, proline N (CO=NRR')
MASS 343 NG2S1 14.00700 ! peptide nitrogen (CO=NHR)
MASS 344 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2)
MASS 345 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), phosphoramidate
!MASS 346 NG2S4 14.00700 ! neutral hydroxamic acid
MASS 347 NG2O1 14.00700 ! NITB, nitrobenzene
MASS 348 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium)
MASS 349 NG2R43 14.00700 ! amide in 4-memebered ring (planar), AZDO, lsk
MASS 350 NG2R50 14.00700 ! double bound neutral 5-mem planar ring, purine N7
MASS 351 NG2R51 14.00700 ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
MASS 352 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo
MASS 353 NG2R53 14.00700 ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo
MASS 354 NG2R57 14.00700 ! 5-mem ring, bipyrroles
MASS 355 NG2R60 14.00700 ! double bound neutral 6-mem planar ring, pyr1, pyzn
MASS 356 NG2R61 14.00700 ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage
MASS 357 NG2R62 14.00700 ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm
MASS 358 NG2R67 14.00700 ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.)
MASS 359 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo
MASS 360 NG301 14.00700 ! neutral trimethylamine nitrogen
MASS 361 NG311 14.00700 ! neutral dimethylamine nitrogen
MASS 362 NG321 14.00700 ! neutral methylamine nitrogen
MASS 363 NG331 14.00700 ! neutral ammonia nitrogen
MASS 364 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring
MASS 365 NG3N1 14.00700 ! N in hydrazine, HDZN
MASS 366 NG3P0 14.00700 ! quarternary N+, choline
MASS 367 NG3P1 14.00700 ! tertiary NH+ (PIP)
MASS 368 NG3P2 14.00700 ! secondary NH2+ (proline)
MASS 369 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine
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 370 OG2D1 15.99940 ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
MASS 371 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate
MASS 372 OG2D3 15.99940 ! carbonyl O: ketones
MASS 373 OG2D4 15.99940 ! 6-mem aromatic carbonyl oxygen (nucleic bases)
MASS 374 OG2D5 15.99940 ! CO2 oxygen
MASS 375 OG2N1 15.99940 ! NITB, nitrobenzene
MASS 376 OG2P1 15.99940 ! =O in phosphate or sulfate
MASS 377 OG2R50 15.99940 ! FURA, furan
MASS 378 OG3R60 15.99940 ! O in 6-mem cyclic enol ether (PY01, PY02) or ester
MASS 379 OG301 15.99940 ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60???
MASS 380 OG302 15.99940 ! ester -O-
MASS 381 OG303 15.99940 ! phosphate/sulfate ester oxygen
MASS 382 OG304 15.99940 ! linkage oxygen in pyrophosphate/pyrosulphate
MASS 383 OG311 15.99940 ! hydroxyl oxygen
MASS 384 OG312 15.99940 ! ionized alcohol oxygen
MASS 385 OG3C31 15.99940 ! epoxide oxygen, 1EOX, 1BOX, sc
MASS 386 OG3C51 15.99940 ! 5-mem furanose ring oxygen (ether)
MASS 387 OG3C61 15.99940 ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60???
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 388 SG2D1 32.06000 ! thiocarbonyl S
MASS 389 SG2R50 32.06000 ! THIP, thiophene
MASS 390 SG311 32.06000 ! sulphur, SH, -S-
MASS 391 SG301 32.06000 ! sulfur C-S-S-C type
MASS 392 SG302 32.06000 ! thiolate sulfur (-1)
MASS 393 SG3O1 32.06000 ! sulfate -1 sulfur
MASS 394 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur
MASS 395 SG3O3 32.06000 ! neutral sulfoxide sulfur
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 396 CLGA1 35.45300 ! CLET, DCLE, chloroethane, 1,1-dichloroethane
MASS 397 CLGA3 35.45300 ! TCLE, 1,1,1-trichloroethane
MASS 398 CLGR1 35.45300 ! CHLB, chlorobenzene
MASS 399 BRGA1 79.90400 ! BRET, bromoethane
MASS 400 BRGA2 79.90400 ! DBRE, 1,1-dibromoethane
MASS 401 BRGA3 79.90400 ! TBRE, 1,1,1-dibromoethane
MASS 402 BRGR1 79.90400 ! BROB, bromobenzene
MASS 403 IGR1 126.90447 ! IODB, iodobenzene
MASS 404 FGA1 18.99800 ! aliphatic fluorine, monofluoro
MASS 405 FGA2 18.99800 ! aliphatic fluorine, difluoro
MASS 406 FGA3 18.99800 ! aliphatic fluorine, trifluoro
MASS 407 FGP1 18.99800 ! anionic F, for ALF4 AlF4-
MASS 408 FGR1 18.99800 ! aromatic flourine
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 409 PG0 30.97380 ! neutral phosphate
MASS 410 PG1 30.97380 ! phosphate -1
MASS 411 PG2 30.97380 ! phosphate -2
MASS 412 ALG1 26.98154 ! Aluminum, for ALF4, AlF4-
!MASS 414 HGTIP3 1.00800 ! polar H, TIPS3P WATER HYDROGEN
!MASS 415 OGTIP3 15.99940 ! TIPS3P WATER OXYGEN
!MASS 416 DUM 0.00000 ! dummy atom
!MASS 417 HE 4.00260 ! helium
!MASS 418 NE 20.17970 ! neon
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
AUTO ANGLES DIHE PATCH DRUDE
 
!RESI TIP3 0.00 ! tip3p water model, generate using noangle nodihedral
!GROUP
......@@ -13246,86 +13258,6 @@ 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 BROB 0.000 ! C6H5Br bromobenzene
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 ! 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 -0.08
ATOM BR BRGR1 -0.10
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 BR
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 CHLB 0.000 ! C6H5Cl compound # : chlorobenzene
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 ! 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 0.03
ATOM CL CLGR1 -0.13
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 CL
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 IODB 0.000 ! C6H5I iodobenzene
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 ! I--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 -0.08
ATOM I6 IGR1 -0.08
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 I6
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 UREA 0.00 ! CH4N2O Urea, adm
GROUP
......@@ -23354,42 +23286,6 @@ 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 PCLT 0.00 ! C7H7Cl p-chlorotoluene, kevo for gsk/ibm
GROUP
ATOM CG CG2R61 0.03
ATOM CL CLGR1 -0.13
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 ! 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
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 34MP 0.00 ! C7H9N 3,4-dimethylpyridine, kevo for gsk/ibm
GROUP
ATOM NZ NG2R60 -0.600
......@@ -23595,128 +23491,6 @@ 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.
 
RESI PMHA 0.00 ! C25H20ClN3O2 3-(N-(3-chloroPhenyl)carnoMoyl)propionyl
GROUP ! Anthracene-9-carbaldehyde Hydrazone, sz
ATOM C1 CG2R61 0.10
ATOM C2 CG2R61 -0.14 ! H49 H47
ATOM H3 HGR62 0.22 ! \ /
ATOM C4 CG2R61 0.10 ! H9 C48--C46
ATOM CL5 CLGR1 -0.18 ! | // \\
ATOM C6 CG2R61 -0.16 ! C8 H11 H51-C50 C44-H45
ATOM H7 HGR62 0.19 ! / \\ / \ /
ATOM C8 CG2R61 -0.12 ! H7--C6 C10 O15 H20 H21 H25 H28 C30--C31
ATOM H9 HGR61 0.12 ! || | || \ / | | // \\
ATOM C10 CG2R61 -0.16 ! Cl5-C4 C1 C14 C19 N24 C27--C29 C32-H33
ATOM H11 HGR61 0.19 ! \ // \ / \ / \ / \ // \ /
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
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
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
!End drug-like molecules, S. Zhong, jun2008
!Hydrazine, E. Darian, jun2008
RESI HDZN 0.00 ! N2H4 Hydrazine neutral, ed
GROUP
......@@ -25640,153 +25414,53 @@ 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 3A6BPD 0.00 ! C7H6BrN2O Gamma-3-Amino-6-bromo Pyridine GA CDCA Amide (alpha deprotected), cacha
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 ! 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--BR
ATOM NG NG2S1 -0.47 ! / \ | / || \ __ /
ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1
ATOM CZ CG2R61 0.14 ! Me19 | | |
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 CD2 CG2R61 0.120 ! / \|/ \ / \ /
ATOM HD2 HGR62 0.270 ! C2 C10 C8 C15
ATOM CC CG2O1 0.52 ! / \|/ \ / \ /
ATOM OC OG2D1 -0.52 ! C2 C10 C8 C15
GROUP ! | | |
ATOM NZ NG2R60 -0.600 ! C3 C5 C7
ATOM CZ CG2R61 0.00 ! C3 C5 C7
GROUP ! / \ / \ / \
ATOM CP CG2R61 -0.080 ! HO C4 C6 OH
ATOM BR BRGR1 -0.100
GROUP ! 3A6BPD
ATOM CE1 CG2R61 0.120
ATOM HE1 HGR62 0.270
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 CG OG CG NG NG HG NG CZ
BOND CZ CD2 CD2 HD2
BOND CD2 NZ NZ CP CP BR
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 CG CC3 NG OG
IC CC2 CC3 CG NG 1.5540 115.24 -45.81 117.72 1.3410
IC CG CZ *NG HG 1.3410 128.42 -179.30 113.55 1.0153
IC NG CC3 *CG OG 1.3410 117.72 -179.06 119.68 1.2286
IC CC3 CG NG CZ 1.5034 117.72 -178.25 128.42 1.4176
IC CG NG CZ CD2 1.3410 128.42 -3.63 126.12 1.4068
IC NG CZ CD2 NZ 1.4176 126.12 179.74 123.57 1.3372
IC CZ CD2 NZ CP 1.4068 123.57 -0.57 119.25 1.3290
IC CD2 NZ CP CE1 1.3372 119.25 0.00 122.25 1.4059
IC NZ CP CE1 CD1 1.3290 122.25 0.26 118.39 1.4018
IC CZ NZ *CD2 HD2 1.4068 123.57 -179.82 116.18 1.0787
IC CZ CE1 *CD1 HD1 1.4032 119.66 -179.83 120.65 1.0797
IC CP CD1 *CE1 HE1 1.4059 118.39 -179.97 121.47 1.0746
IC NZ CE1 *CP BR 1.3290 122.25 179.86 118.80 1.9014
PRES 3A5BPD 0.00 ! C7H6BrN2O Gamma-3-Amino-5-bromo 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 Br
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 0.120 ! HO C4 C6 OH
ATOM HP HGR62 0.270
GROUP ! 3A5BPD
ATOM CE1 CG2R61 -0.080
ATOM BR BRGR1 -0.100
GROUP
ATOM CD1 CG2R61 -0.060
ATOM HD1 HGR62 0.150
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 BR CE1 CD1 CD1 HD1 CD1 CZ
IMPR CG CC3 NG OG
IC CC2 CC3 CG NG 1.5539 114.93 -46.89 117.47 1.3414
IC CG CZ *NG HG 1.3414 128.73 -179.59 113.40 1.0162
IC NG CC3 *CG OG 1.3414 117.47 -179.17 119.56 1.2281
IC CC3 CG NG CZ 1.5032 117.47 -179.42 128.73 1.4192
IC CG NG CZ CD2 1.3414 128.73 -1.78 126.47 1.4101
IC NG CZ CD2 NZ 1.4192 126.47 -179.99 124.16 1.3390
IC CZ CD2 NZ CP 1.4101 124.16 -0.27 118.04 1.3323
IC CD2 NZ CP CE1 1.3390 118.04 0.09 123.58 1.4040
IC NZ CP CE1 CD1 1.3323 123.58 0.00 117.68 1.4046
IC CZ NZ *CD2 HD2 1.4101 124.16 -179.81 114.91 1.0791
IC CZ CE1 *CD1 HD1 1.4055 119.88 -179.96 120.93 1.0813
IC CP CD1 *CE1 BR 1.4040 117.68 180.00 121.49 1.9030
IC NZ CE1 *CP HP 1.3323 123.58 179.98 120.99 1.0802
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
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
......@@ -26320,30 +25994,6 @@ 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 3CBD 0.00 ! C3H2Cl Gamma 3-Chloro amino benzene glutamic acid CDCA amide, cacha
!To be patched with residue GABD
DELETE ATOM HE1
ATOM CD1 CG2R61 -0.100 ! CD1--CE1--CL
ATOM HD1 HGR62 0.150 ! // \
ATOM CE1 CG2R61 0.030 ! --CG--NG--CZ CP
ATOM CL CLGR1 -0.130 ! || \ __ //
ATOM CP CG2R61 -0.100 ! OG CD2--CE2
ATOM HP HGR62 0.150
BOND CE1 CL
IC CP CD1 *CE1 CL 1.4002 119.96 179.97 120.18 1.7396
PRES 4CBD 0.00 ! C3H2Cl Gamma 4-Chloro amino benzene glutamic acid CDCA amide, cacha
!To be patched with residue GABD
DELETE ATOM HP
ATOM CE1 CG2R61 -0.100 ! CD1--CE1
ATOM HE1 HGR62 0.150 ! // \
ATOM CP CG2R61 0.030 ! --CG--NG--CZ CP--CL
ATOM CL CLGR1 -0.130 ! || \ __ //
ATOM CE2 CG2R61 -0.100 ! OG CD2--CE2
ATOM HE2 HGR62 0.150
BOND CP CL
IC CE1 CE2 *CP CL 1.3996 119.90 -179.82 120.09 1.7397
PRES 24MFD 0.00 ! C4H6O2 Gamma-2,4 Dimethoxy amino benzene GA CDCA Amide, cacha
! patch core residue GABD
DELETE ATOM HD1
......@@ -30723,4 +30373,2603 @@ 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
 
END
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
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