/usr/share/openbabel/2.3.2/atomtyp.txt is in libopenbabel4v5 2.3.2+dfsg-3build1.
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# #
# Open Babel file: atomtyp.txt #
# #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
# #
# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) #
# #
# INTHYB: used to assign the internal hybridization values for atoms #
# IMPVAL: used to assign the implicit valence of an atom #
# EXTTYP: used to assign the external type of an atom for translation to #
# package specific types (i.e. Sybyl Mol2) #
# (these should correspond to INT type names in types.txt too.) #
# #
# The LAST PATTERN MATCHED is used to assign values with the corresponding #
# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
# in the EXTRA DEFINITIONS section (to separate from original patterns.) #
# #
##############################################################################
INTHYB [D4] 3 #any 4-valent atom -- tetrahedral
INTHYB [D5] 5 #any 5-valent atom -- trigbipy
INTHYB [D6] 6 #any 6-valent atom -- oct
INTHYB [C] 3 #sp3 carbon
INTHYB [c,$(C=*)] 2 #sp2 carbon
# INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597
INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon
INTHYB [N] 3 #sp3 nitrogen
INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen
INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen
INTHYB [O] 3 #sp3 oxygen
INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen
INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen
INTHYB [$(O#*)] 1 #sp oxygen
INTHYB [P] 3 #sp3 phosphorus
INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus
INTHYB [PD5] 5 #sp3d phosphorus, as in PF5
INTHYB [Pv5] 5 #sp3d phosphorus, as in H3PO4
INTHYB [S] 3 #sp3 sulfur
INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur
INTHYB [SD6] 6 #sp3d2 sulfur, as in SF6
INTHYB [B] 2 #sp2 boron
INTHYB [BD4] 3 #sp3 boron
INTHYB [Al] 2 # typical sp2 Al (and family)
INTHYB [Ga] 2
INTHYB [In] 2
INTHYB [Tl] 2
INTHYB [AlD4] 3 # sp3 Al
INTHYB [Si] 3 # sp3 Si (and family)
INTHYB [Pb] 3
INTHYB [Ge;!D5] 3
INTHYB [Sn;!D5] 3
INTHYB [AsD3] 3 # AsCl3 (AsCl5 handled by D5 above)
INTHYB [SbD3] 3 #
# SbD5, AsD5 are all trigbpy so are handled by D5 above
INTHYB [BiD3] 3 #
INTHYB [BiD5] 6 # BiF5 is square-pyr, not trigbpy
INTHYB [se] 2 # aromatic sp2 Se
INTHYB [Se] 3 # sp3 hybridization Se (and family)
INTHYB [Te] 3
INTHYB [Po] 3
INTHYB [Be] 1 # Alkaline earth, like sp hybrids
INTHYB [Mg] 1
INTHYB [Ca] 1
INTHYB [Sr] 1
INTHYB [Ba] 1
INTHYB [Ra] 1
#INTHYB [Pt] 4 # normally square planar
#INTHYB [Pd] 4
#INTHYB [Cu] 4
#INTHYB [Ag] 4
#INTHYB [Au] 4
#
#IMPLICIT VALENCE RULES
#
#IMPVAL [#3,#11,#19,#37,#55,#87] 1 # Alkali metals
#IMPVAL [#4,#12,#20,#38,#56,#88] 2 # Alkaline earth
IMPVAL [#5+] 2
IMPVAL [#5-] 4
IMPVAL [#5] 3 # Generic boron
IMPVAL [$([#6+]=*)] 2
IMPVAL [$([#6+]#*)] 1 # just for InChI C2
IMPVAL [#6^3] 4
IMPVAL [#6^2] 3
IMPVAL [#6^1] 2
IMPVAL [#6^3+] 3
IMPVAL [#6^2+] 2
IMPVAL [#6^1+] 1
IMPVAL [#6^3-] 3
IMPVAL [#6^2-] 2
IMPVAL [#6^1-] 1 # isocyanides, CO (valence=1, bond order=3)
IMPVAL [c+] 2
IMPVAL [N^3] 3
IMPVAL [N^3+] 4
IMPVAL [N^2] 3
#IMPVAL [N^2-,N^3-] 2
IMPVAL [ND1^1] 1
IMPVAL [ND2^1] 2
IMPVAL [$(N([OD1])*)] 3
IMPVAL [$(NC=O)] 3
#IMPVAL [$(n(c=O)c=O)] 3 # aromatic diimide
IMPVAL [$(N(~[OD1])~[OD1])] 3
IMPVAL [$([Nr0]C=[Nr0])] 3
IMPVAL [$(N=*)] 2
#IMPVAL [$([Nr0]=C[Nr0])] 3
IMPVAL [$([Nr0]=C[Nr0])] 2
IMPVAL [$([N+r0]=C[Nr0])] 3 # patch from Steve Constable
IMPVAL [$([#7D1-]=*)] 1
IMPVAL [N^1-] 1 # N2O [N-]=[N+]=O (valence=1, bondorder=2)
IMPVAL [N-] 2
IMPVAL [n] 2
IMPVAL [n-] 2
IMPVAL [n+] 3
IMPVAL [$([#7-]=*)] 1
IMPVAL [$([#7+]#*)] 2
IMPVAL [$([#7+]=*)] 3
IMPVAL [$([#7+](=*)=*)] 2
IMPVAL [#8] 2 # Generic O
IMPVAL [#8-] 1
IMPVAL [#8-2] 0
IMPVAL [#8+] 3
IMPVAL [$([#8]=*)] 1
IMPVAL [#8^1+] 1 # carbon monoxide
IMPVAL [$([#8]#*)] 1
IMPVAL [#9D0] 1
IMPVAL [#9D0-] 0 #[F-]
IMPVAL [#13] 3 # generic Al
IMPVAL [#14] 4 # regular sp3 Si
IMPVAL [#14^2] 2 # silylenes
IMPVAL [$([#14]=*)] 3 # e.g., Si=O
IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O
IMPVAL [$([#14+]#*)] 1 # just for InChI Si2
IMPVAL [$([#14-]#*)] 1 # just for InChI Si2
IMPVAL [#15D4] 4
IMPVAL [#15D3] 3
IMPVAL [#15D2] 3
IMPVAL [#15D1^3] 3
IMPVAL [#15D1^2] 3
IMPVAL [#15D0] 3
IMPVAL [$([#15]=[#6])] 2
IMPVAL [pD2] 2
IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence)
IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence)
IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2
IMPVAL [#16] 2 #revised CM April 2008
IMPVAL [$([#16D1]=*)] 1
IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O
IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O
IMPVAL [#16D1-] 1
IMPVAL [#17D0] 1
IMPVAL [#17D0-] 0 #[Cl-]
IMPVAL [#31] 3
IMPVAL [#32] 4
IMPVAL [#33] 3
IMPVAL [as] 3
IMPVAL [#34] 2
IMPVAL [#35D0] 1
IMPVAL [#35D0-] 0 #[Br-]
#IMPVAL [#49,#81] 3 # In, Tl, like Ga
#IMPVAL [#50,#82] 4 # Sn, Pb, like Ge
#IMPVAL [#51,#83] 3 # Sb, Bi, like As
IMPVAL [#52] 2
IMPVAL [#53D0] 1
IMPVAL [#53D0-] 0 #[I-]
#
#EXTERNAL TYPE RULES
#
# Tinker OH hydrogens for MM2
# Fixes PR# 1839274
EXTTYP [#1][#8] HO
EXTTYP [#7^3] N3
EXTTYP [#7X4] N3+
EXTTYP [#7^2] Npl
EXTTYP [#7^1] N1
EXTTYP [$(N=*)] N2
EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+
EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+
EXTTYP [$([ND1]=C[ND1])] Ng+
EXTTYP [$([ND1]C=[ND1])] Ng+
EXTTYP [$(N(O)*)] Nox
EXTTYP [$(NC=[O,S])] Nam
EXTTYP [$(N(~[OD1])~[OD1])] Ntr
EXTTYP [n] Nar
EXTTYP [#6^3] C3
EXTTYP [#6^2] C2
EXTTYP [$(C(=O)[OD1])] Cac
EXTTYP [c] Car
EXTTYP [#6^1] C1
EXTTYP [#6+] C+
EXTTYP [#6-] C-
EXTTYP [#8^3] O3
EXTTYP [#8^2] O2
EXTTYP [$(Oa)] O2
#The following 2 lines used for correct Sybyl atom typing
EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen
EXTTYP [$(Oa)] O3 #aromatic ether
EXTTYP [#8-] O-
EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2
EXTTYP [#15] P
EXTTYP [#15X4+] P3+
EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac
EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac
EXTTYP [#16] S3
EXTTYP [#16D3+,#16X3+] S3+
EXTTYP [#16;s,$([SD1]=*)] S2
EXTTYP [#16D4;$(S(=O)(=O))] So2
EXTTYP [#16D3;$(S(=O))] Sox
EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac
EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac
EXTTYP [#5] B2
EXTTYP [#5D4] B3
######################## Add Extra Definitions Here ##########################
#INTHYB [U] 3
#INTHYB [W] 3
#INTHYB [Mo] 6 # for development
#INTHYB [Cr] 5 # for development
############################# End Extra Definitions ##########################
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