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Commit d7ac083f authored by Evan Pretti's avatar Evan Pretti
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Add new CHARMM and Amber force fields

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wrappers/python/openmm/app/data/amber14/GLYCAM_06j-1.xml
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<ForceField>
<Info>
<DateGenerated>2021-10-29</DateGenerated>
<Source Source="glycam/leaprc.GLYCAM_06j-1" md5hash="a7359f8d717f92dba02d57d6e0c8f3f7" sourcePackage="AmberTools" sourcePackageVersion="20.15">glycam/leaprc.GLYCAM_06j-1</Source>
<DateGenerated>2025-04-30</DateGenerated>
<Source Source="glycam/leaprc.GLYCAM_06j-1" md5hash="a7359f8d717f92dba02d57d6e0c8f3f7" sourcePackage="AmberTools" sourcePackageVersion="24.8">glycam/leaprc.GLYCAM_06j-1</Source>
<Reference>R. Kadirvelraj; O. C. Grant; I. J. Goldstein; H. C. Winter; H. Tateno; E. Fadda; R. J. Woods. Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac&#945;2-6Gal&#946;1-4GlcNAc human- type influenza receptor. Glycobiology, 2011, 21, 973&#8211;984. M. L. DeMarco; R. J. Woods. From agonist to antagonist: Structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol. Immunol., 2011, 49, 124&#8211;133. B. L. Foley; M. B. Tessier; R. J. Woods. Carbohydrate force fields. WIREs Comput. Mol. Sci., 2012, 2, 652&#8211;697. E. Ficko-Blean; C. P. Stuart; M. D. Suits; M. Cid; M. Tessier; R. J. Woods; A. B. Boraston. Carbohy- drate Recognition by an Architecturally Complex &#945;-N-Acetylglucosaminidase from Clostridium perfrin- gens. PLoS ONE, 2012, 7, e33524.</Reference>
</Info>
<AtomTypes>
......@@ -342,8 +342,6 @@
<Bond atomName1="C2M" atomName2="H22" />
<Bond atomName1="C2M" atomName2="H21" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue>
<Residue name="0BD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" />
......@@ -1139,11 +1137,6 @@
<Bond atomName1="OHG" atomName2="HOG" />
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="0HA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" />
......@@ -1841,9 +1834,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="0OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -1887,9 +1877,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -2401,11 +2388,6 @@
<Bond atomName1="CME" atomName2="H1M" />
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="0SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -2483,11 +2465,6 @@
<Bond atomName1="C1" atomName2="O1B" />
<Bond atomName1="C1" atomName2="O1A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
</Residue>
<Residue name="0TA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" />
......@@ -2711,9 +2688,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="0UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -2757,9 +2731,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -3313,9 +3284,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="0ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -3359,9 +3327,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -3681,8 +3646,6 @@
<Bond atomName1="C2M" atomName2="H22" />
<Bond atomName1="C2M" atomName2="H23" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue>
<Residue name="0bD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" />
......@@ -4478,11 +4441,6 @@
<Bond atomName1="C1" atomName2="O1B" />
<Bond atomName1="C1" atomName2="O1A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
</Residue>
<Residue name="0hA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" />
......@@ -5180,9 +5138,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -5226,9 +5181,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="0pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -5740,11 +5692,6 @@
<Bond atomName1="C1" atomName2="O1B" />
<Bond atomName1="C1" atomName2="O1A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
</Residue>
<Residue name="0sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -5822,11 +5769,6 @@
<Bond atomName1="CME" atomName2="H3M" />
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="0tA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" />
......@@ -6050,9 +5992,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -6096,9 +6035,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="0vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -6652,9 +6588,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="0zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -6698,9 +6631,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1AA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -8402,9 +8332,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1OB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -8450,9 +8377,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -9128,9 +9052,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1UB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -9176,9 +9097,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1VA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -9754,9 +9672,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1ZB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -9802,9 +9717,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1aA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -11506,9 +11418,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1oB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -11554,9 +11463,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -12232,9 +12138,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1uB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -12280,9 +12183,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="1vA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -12858,9 +12758,6 @@
<Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="1zB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" />
......@@ -12906,9 +12803,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -14571,9 +14465,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -14616,9 +14507,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2PA" override="1">
<Atom name="O2" type="glycam-Os" charge="-0.388" />
......@@ -15273,9 +15161,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -15318,9 +15203,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2XA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.482" />
......@@ -15515,9 +15397,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -15560,9 +15439,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -17225,9 +17101,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -17270,9 +17143,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2pA" override="1">
<Atom name="O2" type="glycam-Os" charge="-0.388" />
......@@ -17927,9 +17797,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -17972,9 +17839,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="2xA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.482" />
......@@ -18169,9 +18033,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="2zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -18214,9 +18075,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -18529,8 +18387,6 @@
<Bond atomName1="C4M" atomName2="H41" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue>
<Residue name="3BD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" />
......@@ -19913,9 +19769,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -19958,9 +19811,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -20519,9 +20369,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -20564,9 +20411,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -21109,9 +20953,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -21154,9 +20995,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -21469,8 +21307,6 @@
<Bond atomName1="C2M" atomName2="H23" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue>
<Residue name="3bD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" />
......@@ -22853,9 +22689,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -22898,9 +22731,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -23459,9 +23289,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -23504,9 +23331,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="3vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -24049,9 +23873,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="3zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -24094,9 +23915,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -24967,11 +24785,6 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4HA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" />
......@@ -25654,9 +25467,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -25699,9 +25509,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -26126,11 +25933,6 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -26207,11 +26009,6 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4TA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" />
......@@ -26430,9 +26227,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -26475,9 +26269,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -26944,9 +26735,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -26989,9 +26777,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" />
......@@ -27862,11 +27647,6 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4hA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" />
......@@ -28549,9 +28329,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" />
......@@ -28594,9 +28371,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" />
......@@ -29021,11 +28795,6 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -29102,11 +28871,6 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="4tA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" />
......@@ -29325,9 +29089,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" />
......@@ -29370,9 +29131,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="4vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" />
......@@ -29839,9 +29597,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue>
<Residue name="4zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" />
......@@ -29884,9 +29639,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue>
<Residue name="5AD" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.368" />
......@@ -34029,11 +33781,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="7SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -34110,11 +33857,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="7SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -34191,11 +33933,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="7gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -34274,11 +34011,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="7sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -34355,11 +34087,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="7sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -34436,11 +34163,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8GL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -34519,11 +34241,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -34600,11 +34317,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -34681,11 +34393,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -34764,11 +34471,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -34845,11 +34547,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="8sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -34926,11 +34623,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9GL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -35009,11 +34701,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -35090,11 +34777,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -35171,11 +34853,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -35254,11 +34931,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -35335,11 +35007,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="9sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -35416,11 +35083,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ACX" override="1">
<Atom name="C1A" type="protein-C" charge="0.763" />
......@@ -35435,7 +35097,6 @@
<Bond atomName1="C2A" atomName2="H2A" />
<Bond atomName1="C2A" atomName2="H3A" />
<ExternalBond atomName="C1A" />
<ExternalBond atomName="O1A" />
</Residue>
<Residue name="AGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -35508,14 +35169,9 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ASA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -35586,14 +35242,9 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ASB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -35664,14 +35315,9 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="AgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -35744,14 +35390,9 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="AsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -35822,14 +35463,9 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="AsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -35900,14 +35536,9 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="BGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -35982,11 +35613,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
</Residue>
......@@ -36061,11 +35687,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
</Residue>
......@@ -36140,11 +35761,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
</Residue>
......@@ -36221,11 +35837,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
</Residue>
......@@ -36300,11 +35911,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
</Residue>
......@@ -36379,11 +35985,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
</Residue>
......@@ -36460,13 +36061,8 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="CSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -36539,13 +36135,8 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="CSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -36618,13 +36209,8 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="CgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -36699,13 +36285,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="CsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -36778,13 +36359,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="CsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -36857,13 +36433,8 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -36938,13 +36509,8 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -37017,13 +36583,8 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -37096,13 +36657,8 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -37177,13 +36733,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -37256,13 +36807,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="DsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -37335,13 +36881,8 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="EGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -37416,13 +36957,8 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ESA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -37495,13 +37031,8 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ESB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -37574,13 +37105,8 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="EgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -37655,13 +37181,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="EsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -37734,13 +37255,8 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="EsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -37813,13 +37329,8 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="FGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -37896,11 +37407,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="FSA" override="1">
......@@ -37976,11 +37482,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="FSB" override="1">
......@@ -38056,11 +37557,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="FgL" override="1">
......@@ -38138,11 +37634,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="FsA" override="1">
......@@ -38218,11 +37709,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="FsB" override="1">
......@@ -38298,11 +37784,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GGL" override="1">
......@@ -38380,11 +37861,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GSA" override="1">
......@@ -38460,11 +37936,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GSB" override="1">
......@@ -38540,11 +38011,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GgL" override="1">
......@@ -38622,11 +38088,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GsA" override="1">
......@@ -38702,11 +38163,6 @@
<Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="GsB" override="1">
......@@ -38782,11 +38238,6 @@
<Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" />
</Residue>
<Residue name="HGL" override="1">
......@@ -38864,11 +38315,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="HSA" override="1">
......@@ -38944,11 +38390,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="HSB" override="1">
......@@ -39024,11 +38465,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="HgL" override="1">
......@@ -39106,11 +38542,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="HsA" override="1">
......@@ -39186,11 +38617,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="HsB" override="1">
......@@ -39266,11 +38692,6 @@
<Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" />
</Residue>
<Residue name="IGL" override="1">
......@@ -39348,12 +38769,7 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ISA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -39428,12 +38844,7 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="ISB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -39508,12 +38919,7 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="IgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -39590,12 +38996,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="IsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -39670,12 +39071,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="IsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -39750,12 +39146,7 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -39832,12 +39223,7 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -39912,12 +39298,7 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -39992,12 +39373,7 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -40074,12 +39450,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -40154,12 +39525,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="JsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -40234,12 +39600,7 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -40316,12 +39677,7 @@
<Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -40396,12 +39752,7 @@
<Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -40476,12 +39827,7 @@
<Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" />
......@@ -40558,12 +39904,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" />
......@@ -40638,12 +39979,7 @@
<Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="KsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" />
......@@ -40718,12 +40054,7 @@
<Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue>
<Residue name="MEX" override="1">
<Atom name="CH3" type="glycam-Cg" charge="0.233" />
......@@ -48030,9 +47361,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -48073,9 +47401,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -48360,9 +47685,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -48403,9 +47725,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -48518,9 +47837,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -48561,9 +47877,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49444,9 +48757,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49487,9 +48797,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49774,9 +49081,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49817,9 +49121,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49932,9 +49233,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -49975,9 +49273,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
<ExternalBond atomName="O3" />
</Residue>
......@@ -56748,9 +56043,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WOB" override="1">
......@@ -56792,9 +56084,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WPA" override="1">
......@@ -57266,9 +56555,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WUB" override="1">
......@@ -57310,9 +56596,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WVA" override="1">
......@@ -57770,9 +57053,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WZB" override="1">
......@@ -57814,9 +57094,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WaA" override="1">
......@@ -59258,9 +58535,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WoB" override="1">
......@@ -59302,9 +58576,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WpA" override="1">
......@@ -59776,9 +59047,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WuB" override="1">
......@@ -59820,9 +59088,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WvA" override="1">
......@@ -60280,9 +59545,6 @@
<Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="WzB" override="1">
......@@ -60324,9 +59586,6 @@
<Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="XEA" override="1">
......@@ -62488,9 +61747,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YOB" override="1">
......@@ -62532,9 +61788,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YQA" override="1">
......@@ -62908,9 +62161,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YUB" override="1">
......@@ -62952,9 +62202,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YXA" override="1">
......@@ -63070,9 +62317,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YZB" override="1">
......@@ -63114,9 +62358,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YaA" override="1">
......@@ -64018,9 +63259,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YoB" override="1">
......@@ -64062,9 +63300,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YqA" override="1">
......@@ -64438,9 +63673,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YuB" override="1">
......@@ -64482,9 +63714,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YxA" override="1">
......@@ -64600,9 +63829,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="YzB" override="1">
......@@ -64644,9 +63870,6 @@
<Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" />
</Residue>
<Residue name="ZAA" override="1">
......@@ -65696,9 +64919,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" />
</Residue>
<Residue name="ZOB" override="1">
......@@ -65740,9 +64960,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O3" />
</Residue>
<Residue name="ZQA" override="1">
......@@ -66108,9 +65325,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" />
</Residue>
<Residue name="ZUB" override="1">
......@@ -66152,9 +65366,6 @@
<Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O3" />
</Residue>
<Residue name="ZXA" override="1">
......@@ -66344,9 +65555,6 @@
<Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" />
</Residue>
<Residue name="HYP" override="1">
......@@ -66639,8 +65847,8 @@
<Bond atomName1="CG" atomName2="ND2" />
<Bond atomName1="ND2" atomName2="HD21" />
<Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="ND2" />
<ExternalBond atomName="C" />
<ExternalBond atomName="ND2" />
</Residue>
<Residue name="NOLP" override="1">
<Atom name="N" type="protein-N3" charge="-0.202" />
......@@ -66675,8 +65883,8 @@
<Bond atomName1="CA" atomName2="HA" />
<Bond atomName1="CA" atomName2="C" />
<Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OD1" />
<ExternalBond atomName="C" />
<ExternalBond atomName="OD1" />
</Residue>
<Residue name="NOLS" override="1">
<Atom name="N" type="protein-N3" charge="0.1849" />
......@@ -66702,8 +65910,8 @@
<Bond atomName1="CB" atomName2="HB3" />
<Bond atomName1="CB" atomName2="OG" />
<Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OG" />
<ExternalBond atomName="C" />
<ExternalBond atomName="OG" />
</Residue>
<Residue name="NOLT" override="1">
<Atom name="N" type="protein-N3" charge="0.1812" />
......@@ -66735,8 +65943,8 @@
<Bond atomName1="CG2" atomName2="HG22" />
<Bond atomName1="CG2" atomName2="HG23" />
<Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OG1" />
<ExternalBond atomName="C" />
<ExternalBond atomName="OG1" />
</Residue>
</Residues>
<HarmonicBondForce>
......@@ -67895,7 +67103,6 @@ for force in sys.getForces():
from openmm.app.internal import compiled
 
class GlycamTemplateMatcher(object):
def __init__(self, glycam_residues):
self.glycam_residues = glycam_residues
 
......@@ -67907,19 +67114,18 @@ class GlycamTemplateMatcher(object):
 
# The residue doesn't actually match the template with the same name. Try the terminal variants.
 
if 'N'+residue.name in self.glycam_residues:
template = ff._templates['N'+residue.name]
if "N" + residue.name in self.glycam_residues:
template = ff._templates["N" + residue.name]
if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
return template
if 'C'+residue.name in self.glycam_residues:
template = ff._templates['C'+residue.name]
if "C" + residue.name in self.glycam_residues:
template = ff._templates["C" + residue.name]
if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
return template
return None
 
glycam_residues = set()
for residue in tree.getroot().find('Residues').findall('Residue'):
glycam_residues.add(residue.get('name'))
for residue in tree.getroot().find("Residues").findall("Residue"):
glycam_residues.add(residue.get("name"))
self.registerTemplateMatcher(GlycamTemplateMatcher(glycam_residues))
</InitializationScript>
</ForceField>
</InitializationScript></ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/amber19/DNA.OL21.xml 0 → 100644
View file @ d7ac083f
<ForceField>
<Info>
<DateGenerated>2025-04-30</DateGenerated>
<Source Source="./files/DNA.OL21/leaprc.DNA.OL21" md5hash="0d0c0ad847034aa80e4dacd33830b168" sourcePackage="AmberTools" sourcePackageVersion="24.8">./files/DNA.OL21/leaprc.DNA.OL21</Source>
<Reference>Zgarbova, M.; Sponer, J.; Jurecka, P. Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER. J. Chem. Theory Comput., 2021, 17, 6292-6301.</Reference>
</Info>
<AtomTypes>
<Type element="C" name="DNA-C" class="DNA-C" mass="12.01"/>
<Type element="C" name="DNA-CA" class="DNA-CA" mass="12.01"/>
<Type element="C" name="DNA-CB" class="DNA-CB" mass="12.01"/>
<Type element="C" name="DNA-CK" class="DNA-CK" mass="12.01"/>
<Type element="C" name="DNA-CM" class="DNA-CM" mass="12.01"/>
<Type element="C" name="DNA-CQ" class="DNA-CQ" mass="12.01"/>
<Type element="C" name="DNA-CT" class="DNA-CT" mass="12.01"/>
<Type element="H" name="DNA-H" class="DNA-H" mass="1.008"/>
<Type element="H" name="DNA-HC" class="DNA-HC" mass="1.008"/>
<Type element="H" name="DNA-H1" class="DNA-H1" mass="1.008"/>
<Type element="H" name="DNA-H2" class="DNA-H2" mass="1.008"/>
<Type element="H" name="DNA-HA" class="DNA-HA" mass="1.008"/>
<Type element="H" name="DNA-H4" class="DNA-H4" mass="1.008"/>
<Type element="H" name="DNA-H5" class="DNA-H5" mass="1.008"/>
<Type element="H" name="DNA-HO" class="DNA-HO" mass="1.008"/>
<Type element="N" name="DNA-NA" class="DNA-NA" mass="14.01"/>
<Type element="N" name="DNA-NB" class="DNA-NB" mass="14.01"/>
<Type element="N" name="DNA-NC" class="DNA-NC" mass="14.01"/>
<Type element="N" name="DNA-N2" class="DNA-N2" mass="14.01"/>
<Type element="N" name="DNA-N*" class="DNA-N*" mass="14.01"/>
<Type element="O" name="DNA-O" class="DNA-O" mass="16.0"/>
<Type element="O" name="DNA-O2" class="DNA-O2" mass="16.0"/>
<Type element="O" name="DNA-OH" class="DNA-OH" mass="16.0"/>
<Type element="O" name="DNA-OS" class="DNA-OS" mass="16.0"/>
<Type element="P" name="DNA-P" class="DNA-P" mass="30.97"/>
<Type element="C" name="DNA-C7" class="DNA-C7" mass="12.01"/>
<Type element="C" name="DNA-C2" class="DNA-C2" mass="12.01"/>
<Type element="C" name="DNA-C1" class="DNA-C1" mass="12.01"/>
<Type element="C" name="DNA-CJ" class="DNA-CJ" mass="12.01"/>
</AtomTypes>
<Residues>
<Residue name="DA">
<Atom name="P" type="DNA-P" charge="1.1659"/>
<Atom name="OP1" type="DNA-O2" charge="-0.7761"/>
<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
<Atom name="O5'" type="DNA-OS" charge="-0.4954"/>
<Atom name="C5'" type="DNA-CJ" charge="-0.0069"/>
<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
<Atom name="H1'" type="DNA-H2" charge="0.1838"/>
<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
<Atom name="C8" type="DNA-C2" charge="0.1607"/>
<Atom name="H8" type="DNA-H5" charge="0.1877"/>
<Atom name="N7" type="DNA-NB" charge="-0.6175"/>
<Atom name="C5" type="DNA-CB" charge="0.0725"/>
<Atom name="C6" type="DNA-CA" charge="0.6897"/>
<Atom name="N6" type="DNA-N2" charge="-0.9123"/>
<Atom name="H61" type="DNA-H" charge="0.4167"/>
<Atom name="H62" type="DNA-H" charge="0.4167"/>
<Atom name="N1" type="DNA-NC" charge="-0.7624"/>
<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
<Atom name="H2" type="DNA-H5" charge="0.0598"/>
<Atom name="N3" type="DNA-NC" charge="-0.7417"/>
<Atom name="C4" type="DNA-CB" charge="0.38"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OS" charge="-0.5232"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DA3">
<Atom name="P" type="DNA-P" charge="1.1659"/>
<Atom name="OP1" type="DNA-O2" charge="-0.7761"/>
<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
<Atom name="O5'" type="DNA-OS" charge="-0.4954"/>
<Atom name="C5'" type="DNA-CJ" charge="-0.0069"/>
<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
<Atom name="H1'" type="DNA-H2" charge="0.1838"/>
<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
<Atom name="C8" type="DNA-C2" charge="0.1607"/>
<Atom name="H8" type="DNA-H5" charge="0.1877"/>
<Atom name="N7" type="DNA-NB" charge="-0.6175"/>
<Atom name="C5" type="DNA-CB" charge="0.0725"/>
<Atom name="C6" type="DNA-CA" charge="0.6897"/>
<Atom name="N6" type="DNA-N2" charge="-0.9123"/>
<Atom name="H61" type="DNA-H" charge="0.4167"/>
<Atom name="H62" type="DNA-H" charge="0.4167"/>
<Atom name="N1" type="DNA-NC" charge="-0.7624"/>
<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
<Atom name="H2" type="DNA-H5" charge="0.0598"/>
<Atom name="N3" type="DNA-NC" charge="-0.7417"/>
<Atom name="C4" type="DNA-CB" charge="0.38"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OH" charge="-0.6549"/>
<Atom name="HO3'" type="DNA-HO" charge="0.4396"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DA5">
<Atom name="HO5'" type="DNA-HO" charge="0.4422"/>
<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
<Atom name="C5'" type="DNA-CJ" charge="-0.0069"/>
<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
<Atom name="H1'" type="DNA-H2" charge="0.1838"/>
<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
<Atom name="C8" type="DNA-C2" charge="0.1607"/>
<Atom name="H8" type="DNA-H5" charge="0.1877"/>
<Atom name="N7" type="DNA-NB" charge="-0.6175"/>
<Atom name="C5" type="DNA-CB" charge="0.0725"/>
<Atom name="C6" type="DNA-CA" charge="0.6897"/>
<Atom name="N6" type="DNA-N2" charge="-0.9123"/>
<Atom name="H61" type="DNA-H" charge="0.4167"/>
<Atom name="H62" type="DNA-H" charge="0.4167"/>
<Atom name="N1" type="DNA-NC" charge="-0.7624"/>
<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
<Atom name="H2" type="DNA-H5" charge="0.0598"/>
<Atom name="N3" type="DNA-NC" charge="-0.7417"/>
<Atom name="C4" type="DNA-CB" charge="0.38"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OS" charge="-0.5232"/>
<Bond atomName1="HO5'" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DAN">
<Atom name="HO5'" type="DNA-HO" charge="0.4422"/>
<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
<Atom name="C5'" type="DNA-CJ" charge="-0.0069"/>
<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
<Atom name="H1'" type="DNA-H2" charge="0.1838"/>
<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
<Atom name="C8" type="DNA-C2" charge="0.1607"/>
<Atom name="H8" type="DNA-H5" charge="0.1877"/>
<Atom name="N7" type="DNA-NB" charge="-0.6175"/>
<Atom name="C5" type="DNA-CB" charge="0.0725"/>
<Atom name="C6" type="DNA-CA" charge="0.6897"/>
<Atom name="N6" type="DNA-N2" charge="-0.9123"/>
<Atom name="H61" type="DNA-H" charge="0.4167"/>
<Atom name="H62" type="DNA-H" charge="0.4167"/>
<Atom name="N1" type="DNA-NC" charge="-0.7624"/>
<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
<Atom name="H2" type="DNA-H5" charge="0.0598"/>
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<Bond atomName1="N6" atomName2="H62"/>
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</Residue>
<Residue name="DC">
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</Residue>
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</Residue>
<Residue name="DG3">
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<Atom name="N2" type="DNA-N2" charge="-0.923"/>
<Atom name="H21" type="DNA-H" charge="0.4235"/>
<Atom name="H22" type="DNA-H" charge="0.4235"/>
<Atom name="N3" type="DNA-NC" charge="-0.6636"/>
<Atom name="C4" type="DNA-CB" charge="0.1814"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OH" charge="-0.6549"/>
<Atom name="HO3'" type="DNA-HO" charge="0.4396"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="O6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N1" atomName2="H1"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="N2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N2" atomName2="H21"/>
<Bond atomName1="N2" atomName2="H22"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DG5">
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<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
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<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0358"/>
<Atom name="H1'" type="DNA-H2" charge="0.1746"/>
<Atom name="N9" type="DNA-N*" charge="0.0577"/>
<Atom name="C8" type="DNA-CK" charge="0.0736"/>
<Atom name="H8" type="DNA-H5" charge="0.1997"/>
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<Atom name="C5" type="DNA-CB" charge="0.1991"/>
<Atom name="C6" type="DNA-C" charge="0.4918"/>
<Atom name="O6" type="DNA-O" charge="-0.5699"/>
<Atom name="N1" type="DNA-NA" charge="-0.5053"/>
<Atom name="H1" type="DNA-H" charge="0.352"/>
<Atom name="C2" type="DNA-CA" charge="0.7432"/>
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<Atom name="H21" type="DNA-H" charge="0.4235"/>
<Atom name="H22" type="DNA-H" charge="0.4235"/>
<Atom name="N3" type="DNA-NC" charge="-0.6636"/>
<Atom name="C4" type="DNA-CB" charge="0.1814"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
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<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OS" charge="-0.5232"/>
<Bond atomName1="HO5'" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="O6"/>
<Bond atomName1="C6" atomName2="N1"/>
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<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="N2" atomName2="H22"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DGN">
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<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
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<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
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<Atom name="C1'" type="DNA-CT" charge="0.0358"/>
<Atom name="H1'" type="DNA-H2" charge="0.1746"/>
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<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OH" charge="-0.6549"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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</Residue>
<Residue name="DT">
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<ExternalBond atomName="P"/>
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</Residue>
<Residue name="DT3">
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<Bond atomName1="P" atomName2="OP1"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
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<ExternalBond atomName="P"/>
</Residue>
<Residue name="DT5">
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<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
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<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OS" charge="-0.5232"/>
<Bond atomName1="HO5'" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N1"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C6" atomName2="H6"/>
<Bond atomName1="C6" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C7"/>
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<Bond atomName1="C7" atomName2="H71"/>
<Bond atomName1="C7" atomName2="H72"/>
<Bond atomName1="C7" atomName2="H73"/>
<Bond atomName1="C4" atomName2="O4"/>
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<Bond atomName1="N3" atomName2="H3"/>
<Bond atomName1="N3" atomName2="C2"/>
<Bond atomName1="C2" atomName2="O2"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DTN">
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<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
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<Improper class1="DNA-CJ" class2="DNA-H1" class3="DNA-H1" class4="DNA-OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
<Improper class1="DNA-CJ" class2="DNA-CT" class3="DNA-H1" class4="DNA-OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
<Improper class1="DNA-C2" class2="" class3="" class4="DNA-H5" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
<Improper class1="DNA-N*" class2="DNA-C2" class3="DNA-CB" class4="DNA-CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
<Improper class1="DNA-C1" class2="" class3="" class4="DNA-H4" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
<Improper class1="DNA-C1" class2="" class3="" class4="DNA-HA" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
<Improper class1="DNA-N*" class2="DNA-C" class3="DNA-C1" class4="DNA-CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
<Improper class1="DNA-C1" class2="DNA-C" class3="DNA-C1" class4="DNA-CT" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
<Improper class1="DNA-CA" class2="DNA-C1" class3="DNA-N2" class4="DNA-NC" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom class="DNA-C" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CA" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CB" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CK" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CM" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CQ" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CT" sigma="0.3399669508423535" epsilon="0.4577296"/>
<Atom class="DNA-H" sigma="0.10690784617684071" epsilon="0.06568879999999999"/>
<Atom class="DNA-HC" sigma="0.2649532787749369" epsilon="0.06568879999999999"/>
<Atom class="DNA-H1" sigma="0.2471353044121301" epsilon="0.06568879999999999"/>
<Atom class="DNA-H2" sigma="0.22931733004932334" epsilon="0.06568879999999999"/>
<Atom class="DNA-HA" sigma="0.25996424595335105" epsilon="0.06276"/>
<Atom class="DNA-H4" sigma="0.2510552587719476" epsilon="0.06276"/>
<Atom class="DNA-H5" sigma="0.24214627159054422" epsilon="0.06276"/>
<Atom class="DNA-HO" sigma="1.0" epsilon="0.0"/>
<Atom class="DNA-NA" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-NB" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-NC" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-N2" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-N*" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-O" sigma="0.2959921901149463" epsilon="0.87864"/>
<Atom class="DNA-O2" sigma="0.2959921901149463" epsilon="0.87864"/>
<Atom class="DNA-OH" sigma="0.3066473387839048" epsilon="0.8803136"/>
<Atom class="DNA-OS" sigma="0.3000012343465779" epsilon="0.7112800000000001"/>
<Atom class="DNA-P" sigma="0.37417746161894255" epsilon="0.8368000000000001"/>
<Atom class="DNA-C7" sigma="0.3399669508423535" epsilon="0.4577296"/>
<Atom class="DNA-C2" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-C1" sigma="0.3399669508423535" epsilon="0.359824"/>
<Atom class="DNA-CJ" sigma="0.3399669508423535" epsilon="0.4577296"/>
</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/amber19/protein.ff19SB.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/protein.ff19ipq.xml 0 → 100644
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wrappers/python/openmm/app/data/charmm36_2024.xml 0 → 100644
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wrappers/python/openmm/app/data/charmm_polar_2023.xml 0 → 100644
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