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############################################################################## |
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# # |
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# Open Babel file: phmodel.txt # |
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# # |
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# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # |
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# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison # |
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# Part of the Open Babel package, under the GNU General Public License (GPL)# |
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# # |
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# pH model data (used by phmodel.cpp:OBPhModel) # |
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# # |
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# TRANSFORM: chemical transforms can be used to modify formal charges, bond # |
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# orders, and to delete atoms (i.e hydrogens). Changes are applied# |
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# to vector bound atoms (use the [:#] SMARTS notation) and bonds # |
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# between vector bound atoms. # |
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# SEEDCHARGE: used to seed partial charges. Seed partial charges # |
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# are used as initial values in Gasteiger charge calculation # |
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# # |
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############################################################################## |
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|
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#carboxylic acid |
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TRANSFORM O=CO[#1:1] >> O=CO |
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TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] |
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|
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#charged amine |
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TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] |
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|
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#imidazole: note pKa=7.0, histidine pKa=6.0 |
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#if you uncomment this, also uncomment the seedcharge statement below |
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#TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 |
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|
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#imine |
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TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] |
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|
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#tetrazole |
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TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 |
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TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 |
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TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 |
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|
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#azide |
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TRANSFORM [ND2:1]=[ND2:2]=A >> [N:1]=[N+:2]=A |
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TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A |
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|
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#hydroxamic acid |
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TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] |
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TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] |
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|
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#sulfinic acid |
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TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] |
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TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] |
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|
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#sulfonic acid |
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TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] |
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TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] |
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|
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#sulfuric acid |
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TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] |
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TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] |
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|
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#guanidine or amidine |
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TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* |
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|
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# histidine |
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TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1 |
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# uncomment for tryptophan |
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# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1 |
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|
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#phosphate ester |
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TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] |
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TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] |
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|
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#phosphoric acid |
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TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] |
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TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O |
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TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] |
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|
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#phosphate |
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|
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# |
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# Seeding partial charges for gasteiger calculation |
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# |
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#default charges |
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SEEDCHARGE [#6+] 1.0 |
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SEEDCHARGE [#6-] -1.0 |
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SEEDCHARGE [#7+] 1.0 |
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SEEDCHARGE [#7-] -1.0 |
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SEEDCHARGE [#8+] 1.0 |
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SEEDCHARGE [#8-] -1.0 |
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SEEDCHARGE [#15+] 1.0 |
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SEEDCHARGE [#15-] -1.0 |
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SEEDCHARGE [#16+] 1.0 |
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SEEDCHARGE [#16-] -1.0 |
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|
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#charges spread over multiple atoms |
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#carboxylic acid |
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SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5 |
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|
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#amines |
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SEEDCHARGE [N+] 1.0 |
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#tetrazole |
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SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2 |
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|
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#sulfinic |
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SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5 |
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#sulfuric acid |
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SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0 |
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#sulfonic acid |
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SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 |
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|
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#guanidine |
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SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33 |
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|
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#amidine |
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SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5 |
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|
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#phosphoate ester |
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SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5 |
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#phosphoric acid |
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SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66 |
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|
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|
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#phosphuric acid |
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SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5 |
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#phosphonic acid |
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SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 |
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|
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#hydroxamic acid |
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SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5 |
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SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 -0.33 |
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|
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#imidazole: note pKa=7.0, histidine pKa=6.0 |
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#if you uncomment this, also uncomment the transform statement above |
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#SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0 |
