/usr/share/openbabel/2.3.2/phmodel.txt is in libopenbabel4v5 2.3.2+dfsg-3build1.
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# #
# Open Babel file: phmodel.txt #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
# #
# pH model data (used by phmodel.cpp:OBPhModel) #
# #
# TRANSFORM: chemical transforms can be used to modify formal charges, bond #
# orders, and to delete atoms (i.e hydrogens). Changes are applied#
# to vector bound atoms (use the [:#] SMARTS notation) and bonds #
# between vector bound atoms. #
# SEEDCHARGE: used to seed partial charges. Seed partial charges #
# are used as initial values in Gasteiger charge calculation #
# #
##############################################################################
#carboxylic acid # pKa
#TRANSFORM O=CO[#1:1] >> O=CO 4.0 # pKa from acid (AH)
TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] 4.0 # pKa from acid (AH)
#uncomment for vinylogous carboxylic acids (e.g. ascorbic acid)
TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O-:1][C:2]=[C:3][C:4]=[O:5] 4.0 # pKa from acid (AH)
#charged amine
TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] 10.0 # pKa from conjugated acid (BH+)
#imidazole: note pKa=7.0
#if you uncomment this, also uncomment the seedcharge statement below
TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0
#imine
TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] 4.0 # pKa from conjugated acid (BH+)
#tetrazole
TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH)
TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 4.89 #pKa from acid (AH)
TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH)
#azide
TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A 1E+10 # always apply transformation
TRANSFORM [ND2:1]=[ND2:2]=A >> N=[N+:2]=A 1E+10 # always apply this transformation
#hydroxamic acid
#TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] 8.0
TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] 8.0
#sulfinic acid
TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] 2.0
TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] 2.0
#sulfonic acid
TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6
TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6
#sulfuric acid (same as sulfonic acid...)
#TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]
#TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]
#guanidine or amidine
TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5
#phosphate ester
TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0
#TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0
#phosphoric acid
#TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] 2.12
TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O 2.12
TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] 2.12
#phosphate
#
# Amino acids
# pKa sidechain
# aspartic acid
#TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O 3.8
TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1] 3.8
TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1] 3.8
# glutamic acid
#TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O 4.3
TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1] 5.0
TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1] 5.0
# arginine
TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 12.0
TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0
# lysine
TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 10.5
TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 10.5
# histidine
TRANSFORM O=C(O)C(N)Cc1nc[n:1]c1 >> O=C(O)C(N)Cc1nc[n+:1]c1 6.08
TRANSFORM O=C(NCC=O)C(N)Cc1nc[n:1]c1 >> O=C(NCC=O)C(N)Cc1nc[n+:1]c1 6.08
# cysteine
TRANSFORM O=C(O)C(N)C[S:1] >> O=C(O)C(N)C[S-:1] 8.28
TRANSFORM O=C(NCC=O)C(N)C[S:1] >> O=C(NCC=O)C(N)C[S-:1] 8.28
# tyrosine
TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1 >> O=C(O)C(N)Cc1ccc([O-:1])cc1 10.1
TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1 >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1 10.1
# old:
# histidine
#TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1
# uncomment for tryptophan
# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1
#, histidine pKa=6.0
#
# Seeding partial charges for gasteiger calculation
#
#default charges
SEEDCHARGE [#6+] 1.0
SEEDCHARGE [#6-] -1.0
SEEDCHARGE [#7+] 1.0
SEEDCHARGE [#7-] -1.0
SEEDCHARGE [#8+] 1.0
SEEDCHARGE [#8-] -1.0
SEEDCHARGE [#15+] 1.0
SEEDCHARGE [#15-] -1.0
SEEDCHARGE [#16+] 1.0
SEEDCHARGE [#16-] -1.0
#charges spread over multiple atoms
#carboxylic acid
SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5
#amines
SEEDCHARGE [N+] 1.0
#tetrazole
SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2
#sulfinic
SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5
#sulfuric acid
SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0
#sulfonic acid
SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33
#guanidine
SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33
#amidine
SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5
#phosphoate ester
SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5
#phosphoric acid
SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66
#phosphuric acid
SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5
#phosphonic acid
SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33
#hydroxamic acid
SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5
SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 0.0 -0.33
#imidazole: note pKa=7.0, histidine pKa=6.0
#if you uncomment this, also uncomment the transform statement above
SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0
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