1 |
tim |
2459 |
############################################################################## |
2 |
|
|
# # |
3 |
|
|
# Open Babel file: phmodel.txt # |
4 |
|
|
# # |
5 |
|
|
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # |
6 |
|
|
# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison # |
7 |
|
|
# Part of the Open Babel package, under the GNU General Public License (GPL)# |
8 |
|
|
# # |
9 |
|
|
# pH model data (used by phmodel.cpp:OBPhModel) # |
10 |
|
|
# # |
11 |
|
|
# TRANSFORM: chemical transforms can be used to modify formal charges, bond # |
12 |
|
|
# orders, and to delete atoms (i.e hydrogens). Changes are applied# |
13 |
|
|
# to vector bound atoms (use the [:#] SMARTS notation) and bonds # |
14 |
|
|
# between vector bound atoms. # |
15 |
|
|
# SEEDCHARGE: used to seed partial charges. Seed partial charges # |
16 |
|
|
# are used as initial values in Gasteiger charge calculation # |
17 |
|
|
# # |
18 |
|
|
############################################################################## |
19 |
|
|
|
20 |
|
|
#carboxylic acid |
21 |
|
|
TRANSFORM O=CO[#1:1] >> O=CO |
22 |
|
|
TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] |
23 |
|
|
|
24 |
|
|
#charged amine |
25 |
|
|
TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] |
26 |
|
|
|
27 |
|
|
#imidazole: note pKa=7.0, histidine pKa=6.0 |
28 |
|
|
#if you uncomment this, also uncomment the seedcharge statement below |
29 |
|
|
#TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 |
30 |
|
|
|
31 |
|
|
#imine |
32 |
|
|
TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] |
33 |
|
|
|
34 |
|
|
#tetrazole |
35 |
|
|
TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 |
36 |
|
|
TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 |
37 |
|
|
TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 |
38 |
|
|
|
39 |
|
|
#azide |
40 |
|
|
TRANSFORM [ND2:1]=[ND2:2]=A >> [N:1]=[N+:2]=A |
41 |
|
|
TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A |
42 |
|
|
|
43 |
|
|
#hydroxamic acid |
44 |
|
|
TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] |
45 |
|
|
TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] |
46 |
|
|
|
47 |
|
|
#sulfinic acid |
48 |
|
|
TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] |
49 |
|
|
TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] |
50 |
|
|
|
51 |
|
|
#sulfonic acid |
52 |
|
|
TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] |
53 |
|
|
TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] |
54 |
|
|
|
55 |
|
|
#sulfuric acid |
56 |
|
|
TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] |
57 |
|
|
TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] |
58 |
|
|
|
59 |
|
|
#guanidine or amidine |
60 |
|
|
TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* |
61 |
|
|
|
62 |
|
|
# histidine |
63 |
|
|
TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1 |
64 |
|
|
# uncomment for tryptophan |
65 |
|
|
# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1 |
66 |
|
|
|
67 |
|
|
#phosphate ester |
68 |
|
|
TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] |
69 |
|
|
TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] |
70 |
|
|
|
71 |
|
|
#phosphoric acid |
72 |
|
|
TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] |
73 |
|
|
TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O |
74 |
|
|
TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] |
75 |
|
|
|
76 |
|
|
#phosphate |
77 |
|
|
|
78 |
|
|
# |
79 |
|
|
# Seeding partial charges for gasteiger calculation |
80 |
|
|
# |
81 |
|
|
#default charges |
82 |
|
|
SEEDCHARGE [#6+] 1.0 |
83 |
|
|
SEEDCHARGE [#6-] -1.0 |
84 |
|
|
SEEDCHARGE [#7+] 1.0 |
85 |
|
|
SEEDCHARGE [#7-] -1.0 |
86 |
|
|
SEEDCHARGE [#8+] 1.0 |
87 |
|
|
SEEDCHARGE [#8-] -1.0 |
88 |
|
|
SEEDCHARGE [#15+] 1.0 |
89 |
|
|
SEEDCHARGE [#15-] -1.0 |
90 |
|
|
SEEDCHARGE [#16+] 1.0 |
91 |
|
|
SEEDCHARGE [#16-] -1.0 |
92 |
|
|
|
93 |
|
|
#charges spread over multiple atoms |
94 |
|
|
#carboxylic acid |
95 |
|
|
SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5 |
96 |
|
|
|
97 |
|
|
#amines |
98 |
|
|
SEEDCHARGE [N+] 1.0 |
99 |
|
|
#tetrazole |
100 |
|
|
SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2 |
101 |
|
|
|
102 |
|
|
#sulfinic |
103 |
|
|
SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5 |
104 |
|
|
#sulfuric acid |
105 |
|
|
SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0 |
106 |
|
|
#sulfonic acid |
107 |
|
|
SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 |
108 |
|
|
|
109 |
|
|
#guanidine |
110 |
|
|
SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33 |
111 |
|
|
|
112 |
|
|
#amidine |
113 |
|
|
SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5 |
114 |
|
|
|
115 |
|
|
#phosphoate ester |
116 |
|
|
SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5 |
117 |
|
|
#phosphoric acid |
118 |
|
|
SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66 |
119 |
|
|
|
120 |
|
|
|
121 |
|
|
#phosphuric acid |
122 |
|
|
SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5 |
123 |
|
|
#phosphonic acid |
124 |
|
|
SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 |
125 |
|
|
|
126 |
|
|
#hydroxamic acid |
127 |
|
|
SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5 |
128 |
|
|
SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 -0.33 |
129 |
|
|
|
130 |
|
|
#imidazole: note pKa=7.0, histidine pKa=6.0 |
131 |
|
|
#if you uncomment this, also uncomment the transform statement above |
132 |
|
|
#SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0 |