#
# $RCSfile: MMFF94AtomTypes.csv,v $
# $Date: 2015/02/28 20:48:22 $
# $Revision: 1.12 $
#
# Author: Manish Sud <msud@san.rr.com>
#
# Copyright (C) 2015 Manish Sud. All rights reserved.
#
# This file is part of MayaChemTools.
#
# MayaChemTools is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at your option) any
# later version.
#
# MayaChemTools is distributed in the hope that it will be useful, but without
# any warranty; without even the implied warranty of merchantability of fitness
# for a particular purpose.  See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
# Boston, MA, 02111-1307, USA.
#
#
# Original data sources:
#     o Halgren, T. A. [ Ref 83-87 ]
#     o Data derived from MMFFSYMB.PAR and  MMFFDEF.PAR tables in
#       MMFF-I_AppendixB.ascii [ Ref 83 ]
#
# Notes:
#     o 212 MMFF94 atom type symbols are listed
#     o 95 MMFF94 atom type numbers are listed
#     o Atom type numbers from 83 to 86 are not used
#     o AtomTypes::MMFF94Atomypes.pm module is used to assign MMFF94 atom types
#     o Number of atom type symbols for:
#         o C: 34
#         o N: 47
#         o O: 45
#         o P: 7
#         o S: 18
#         o F, Br: 2
#         o Cl: 3
#         o I: 1
#         o H: 41
#         o Fe,Cu, Zn: 2
#         o Li, Na, L, K, Mg, Si, : 1
#
#
"AtomType","AtomTypeNum","ElementSymbol","AtomTypeDefinition"
"CR","1","C","ALKYL CARBON, SP3"
"C=C","2","C","VINYLIC CARBON, SP2"
"CSP2","2","C","GENERIC SP2 CARBON"
"C=O","3","C","GENERAL CARBONYL CARBON"
"C=N","3","C","SP2 CARBON IN C=N"
"CGD","3","C","GUANIDINE CARBON, DOUBLY BONDED TO N"
"C=OR","3","C","KETONE OR ALDEHYDE CARBONYL CARBON"
"C=ON","3","C","AMIDE CARBONYL CARBON"
"CONN","3","C","UREA CARBONYL CARBON"
"COO","3","C","CARBOXYLIC ACID OR ESTER CARBONYL CARBON"
"COON","3","C","CARBAMATE CARBONYL CARBON"
"COOO","3","C","C ARBONIC ACID OR ESTER CARBONYL CARBON"
"C=OS","3","C","THIOESTER CARBONYL CARBON, DOUBLE BONDED TO O"
"C=S","3","C","THIOESTER CARBON, DOUBLY BONDED TO S"
"C=SN","3","C","THIOAMIDE, CARBON, DOUBLY BONDED TO S"
"CSO2","3","C","CARBON IN >C=SO2"
"CS=O","3","C","CARBON IN >C=S=O (SULFINYL GROUP)"
"CSS","3","C","THIOCARBOXYLIC ACID OR ESTER CARBONYL CARBON"
"C=P","3","C","CARBON DOUBLE BONDED TO PHOSPHOROUS"
"CSP","4","C","ACETYLENIC CARBON"
"=C=","4","C","ALLENIC CARBON"
"HC","5","H","H  ATTACHED TO C"
"HSI","5","H","H ATTACHED TO SI"
"OR","6","O","ALCOHOL OR ETHER OXYGEN"
"OC=O","6","O","ESTER OR CARBOXYLIC ACID -O-"
"OC=C","6","O","ENOLIC OR PHENOLIC OXYGEN"
"OC=N","6","O","DIVALENT OXYGEN"
"OC=S","6","O","THIOESTER OR THIOACID -O-"
"ONO2","6","O","DIVALENT NITRATE ETHER OXYGEN"
"ON=O","6","O","DIVALENT NITRITE ETHER OXYGEN"
"OSO3","6","O","DIVALENT OXYGEN ATTACHED TO SULFUR"
"OSO2","6","O","DIVALENT OXYGEN ATTACHED TO SULFUR"
"OSO","6","O","DIVALENT OXYGEN ATTACHED TO SULFUR"
"OS=O","6","O","DIVALENT OXYGEN ATTACHED TO SULFOXIDE SULFUR"
"-OS","6","O","GENERAL DIVALENT OX ATTACHED TO S"
"OPO3","6","O","DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS"
"OPO2","6","O","DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS"
"OPO","6","O","DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS"
"-OP","6","O","DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS"
"-O-","6","O","GENERAL DIVALENT O"
"O=C","7","O","GENERAL C=O"
"O=CN","7","O","CARBONYL OXYGEN, AMIDES"
"O=CR","7","O","CARBONYL OXYGEN, ALDEHYDES AND KETONES"
"O=CO","7","O","CARBONYL OXYGEN, CARBOXYLIC ACIDS AND ESTERS"
"O=N","7","O","NITROSO OXYGEN"
"O=S","7","O","O=S IN SULFOXIDES"
"O=S=","7","O","O=S ON SULFUR DOUBLY BONDED TO, E.G., CARBON"
"NR","8","N","NITROGEN IN ALIPHATIC AMINES"
"N=C","9","N","NITROGEN IN IMINES"
"N=N","9","N","NITROGEN IN AZO COMPOUNDS"
"NC=O","10","N","NITROGEN IN AMIDES"
"NC=S","10","N","NITROGEN IN N-C=S, THIOAMIDE"
"NN=C","10","N","NITROGEN IN N-N=C"
"NN=N","10","N","NITROGEN IN N-N=N"
"F","11","F","FLUORINE"
"CL","12","Cl","CHLORINE"
"BR","13","Br","BROMINE"
"I","14","I","IODINE"
"S","15","S","SULFUR IN THIOETHERS AND MERCAPTANS"
"S=C","16","S","TERMINAL SULFUR DOUBLY BONDED TO CARBON"
"S=O","17","S","SULFUR IN SULFOXIDES"
">S=N","17","S","SULFUR, TRICOORD, DOUBLY BONDED TO N"
"SO2","18","S","SULFUR IN SULFONES"
"SO2N","18","S","SULFUR IN SULFONAMIDES"
"SO3","18","S","SULFONATE SULFUR"
"SO4","18","S","SULFATE SULFUR"
"=SO2","18","S","SULFONE SULPHER DOUBLY BONDED TO CARBON"
"SNO","18","S","SULFUR IN NITROGEN ANALOG OF A SULFONE"
"SI","19","Si","SILICON"
"CR4R","20","C","CARBON IN 4-MEMBERED RINGS"
"HOR","21","H","HYDROGEN IN ALCOHOLS"
"HO","21","H","GENERAL H ON OXYGEN"
"HOM","21","H","HYDROGEN IN HYDROXIDE ANION"
"CR3R","22","C","CARBON IN A 3-MEMBERED RING"
"HNR","23","H","H-N(SP3)"
"H3N","23","H","H-N(SP3), AMMONIA"
"HPYL","23","H","H-N IN PYRROLE"
"HNOX","23","H","H-N IN IN A N-OXIDE"
"HNM","23","H","H ON DICOORD, NEGATIVELY CHARGED NITROGEN"
"HN","23","H","GENERAL H ON NITROGEN"
"HOCO","24","H","H-O IN CARBOXYLIC ACIDS"
"HOP","24","H","HYDROGEN ON OXYGEN ATTACHED TO PHOSPHOROUS"
"PO4","25","P","PHOSPHOROUS IN PHOSPHATES AND PHOSPHODIESTERS"
"PO3","25","P","TETRACOORDINATE P WITH THREE ATTACHED OXYGENS"
"PO2","25","P","TETRACOORDINATE P WITH TWO ATTACHED OXYGENS"
"PO","25","P","TETRACOORDINATE P WITH ONE ATTACHED OXYGEN"
"PTET","25","P","GENERAL TETRACOORDINATE PHOSPHORUS"
"P","26","P","TRICOORDINATE P, AS IN PHOSPHINES"
"HN=N","27","H","AZO HYDROGEN"
"HN=C","27","H","IMINE HYDROGEN"
"HNCO","28","H","AMIDE HYDROGEN"
"HNCS","28","H","THIOAMIDE HYDROGEN"
"HNCC","28","H","H-N IN ENAMINES"
"HNCN","28","H","H-N IN H-N-C=N"
"HNNC","28","H","H-N IN H-N-N=C"
"HNNN","28","H","H-N IN H-N-N=N"
"HNSO","28","H","H-N IN SULFONAMIDE"
"HNPO","28","H","H-N IN PHOSPHONAMIDE"
"HNC%","28","H","HYDROGEN ON N ATTACHED TO TRIPLY BONDED CARBON"
"HSP2","28","H","GENERAL H ON SP2 NITROGEN"
"HOCC","29","H","H-O IN ENOLS AND PHENOLS"
"HOCN","29","H","H-O IN HO-C=N"
"CE4R","30","C","OLEFINIC CARBON IN 4-MEMBERED RINGS"
"HOH","31","H","HYDROGEN IN H2O"
"O2CM","32","O","OXYGEN IN CARBOXYLATE ANION"
"OXN","32","O","N-OXIDE OXYGEN"
"O2N","32","O","NITRO OXYGEN"
"O2NO","32","O","NITRO-GROUP OXYGEN IN NITRATE"
"O3N","32","O","NITRATE ANION OXYGEN"
"O-S","32","O","SINGLE TERMINAL OXYGEN ON TETRACOORD SULFUR"
"O2S","32","O","TERMINAL O-S IN SULFONES AND SULFONAMIDES"
"O3S","32","O","TERMINAL O IN SULFONATES"
"O4S","32","O","TERMINAL O IN SO4(-3)"
"OSMS","32","O","TERM O IN THIOSULFINATE ANION - FORMAL CHARGE=-0.5"
"OP","32","O","TERMINAL O IN PHOSPHOXIDES"
"O2P","32","O","TERMINAL O IN PHOSPHINATES"
"O3P","32","O","TERMINAL OXYGEN IN PHOSPHONATES"
"O4P","32","O","TERMINAL OXYGEN IN PHOSPHATES AND PHOSPHODIESTERS"
"O4CL","32","O","OXYGEN IN CLO4(-) ANION - FORMAL CHARGE=-0.25"
"HOS","33","H","H ON OXYGEN ATTACHED TO SULFUR"
"NR+","34","N","QUATERNARY NITROGEN, SP3, POSITIVELY CHARGED"
"OM","35","O","ALKOXIDE OXYGEN, NEGATIVELY CHARGED"
"OM2","35","O","OXIDE OXYGEN ON SP2 CARBON, NEGATIVELY CHARGED"
"HNR+","36","H","H ON QUATERNARY NITROGEN"
"HIM+","36","H","H ON IMIDAZOLIUM-TYPE NITROGEN"
"HPD+","36","H","H ON PROTONATED PYRIDINE NITROGEN"
"HNN+","36","H","H ON AMIDINIUM-TYPE NITROGEN"
"HNC+","36","H","H ON PROTONATED IMINE NITROGEN"
"HGD+","36","H","H ON GUANIDINIUM-TYPE NITROGEN"
"HN5+","36","H","H ON N5+, N5A+ OR N5B+"
"CB","37","C","CARBON AS IN BENZENE, PYRROLE"
"NPYD","38","N","NITROGEN, AS IN PYRIDINE"
"NPYL","39","N","NITROGEN, AS IN PYRROLE"
"NC=C","40","N","NITROGEN ON N-C=C"
"NC=N","40","N","NITROGEN IN N-C=N"
"NC=P","40","N","NITROGEN IN N-C=P"
"NC%C","40","N","NITROGEN ATTACHED TO C-C TRIPLE BOND"
"CO2M","41","C","CARBOXYLATE ANION CARBON"
"CS2M","41","C","CARBON IN THIOCARBOXYLATE ANION"
"NSP","42","N","NITROGEN, TRIPLE BONDED"
"NSO2","43","N","NITROGEN IN SULFONAMIDES"
"NSO3","43","N","NITROGEN IN SULFONAMIDES, THREE Os ON S"
"NPO2","43","N","NITROGEN IN PHOSPHONAMIDES"
"NPO3","43","N","NITROGEN IN PHOSPHONAMIDES, THREE Os ON P"
"NC%N","43","N","NITROGEN ATTACHED TO CYANO GROUP"
"STHI","44","S","SULFUR AS IN THIOPHENE"
"NO2","45","N","NITRO GROUP NITROGEN"
"NO3","45","N","NITRATE GROUP NITROGEN"
"N=O","46","N","NITROSO NITROGEN"
"NAZT","47","N","TERMINAL NITROGEN IN AZIDO OR DIAZO GROUP"
"NSO","48","N","DIVALENT NITROGEN REPLACING MONOVALENT O IN SO2 GROUP"
"O+","49","O","POSITIVELY CHARGED OXONIUM (TRICOORDINATE) OXYGEN"
"HO+","50","H","HYDROGEN ON O+ OXYGEN"
"O=+","51","O","POSITIVELY CHARGED OXENIUM (DICOORDINATE) OXYGEN"
"HO=+","52","H","HYDROGEN ON OXENIUM OXYGEN"
"=N=","53","N","NITROGEN IN C=N=N OR -N=N=N"
"N+=C","54","N","POSITIVELY CHARGED IMINIUM NITROGEN"
"N+=N","54","N","POSITIVELY CHARGED NITROGEN DOUBLE-BONDED TO N"
"NCN+","55","N","N IN +N=C-N RESONANCE STRUCTURES - FORMAL CHARGE=1/2"
"NGD+","56","N","GUANIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1/3"
"CGD+","57","C","GUANIDINIUM CARBON"
"CNN+","57","C","C IN +N=C-N RESONANCE STRUCTURES"
"NPD+","58","N","PYRIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1"
"OFUR","59","O","AROMATIC OXYGEN AS IN FURAN"
"C%","60","C","ISONITRILE CARBON"
"NR%","61","N","ISONITRILE NITROGEN [FC = 0] OR DIAZO NITROGEN [FC = 1]"
"NM","62","N","DEPROTONATED SULFONAMIDE N-; FORMAL CHARGE=-1"
"C5A","63","C","ALPHA CARBON IN 5-MEMBERED HETEROAROMATIC RING"
"C5B","64","C","BETA CARBON IN 5-MEMBERED HETEROAROMATIC RING"
"N5A","65","N","ALPHA AROM HETEROCYCLIC 5-RING  NITROGEN"
"N5B","66","N","BETA AROM HETEROCYCLIC 5-RING  NITROGEN"
"N2OX","67","N","SP2-HYDRIDIZED N-OXIDE NITROGEN"
"N3OX","68","N","SP3-HYDRIDIZED N-OXIDE NITROGEN"
"NPOX","69","N","PYRIDINE N-OXIDE NITROGEN"
"OH2","70","O","OXYGEN ON WATER"
"HS","71","H","H ATTACHED TO DIVALENT, DICOORDINATE S"
"HS=N","71","H","H ATTACHED TO TETRAVALENT, TRICOODR S DBL BONDED TO N"
"HP","71","H","H ATTACHED TO TRI- OR TETRACOORDINATE PHOSPHORUS"
"S-P","72","S","TERMINAL SULFUR BONDED TO PHOSPHORUS"
"S2CM","72","S","TERMINAL SULFUR IN THIOCARBOXYLATE ANION"
"SM","72","S","TERMINAL SULFUR - FORMAL CHARGE=-1"
"SSMO","72","S","TERMINAL SULFUR IN THIOSULFINATE GROUP"
"SO2M","73","S","SULFUR IN NEGATIVELY CHARGED SULFINATE GROUP"
"SSOM","73","S","TRICOORD SULFUR IN THIOSULFINATE GROUP"
"=S=O","74","S","SULFINYL SULFUR, EG. IN C=S=O"
"-P=C","75","P","PHOSPHOROUS DOUBLY BONDED TO CARBON"
"N5M","76","N","NEGATIVELY CHARGED N IN, E.G, TRI- OR TETRAZOLE ANION"
"CLO4","77","Cl","CHLORINE IN PERCHLORATE ANION, CLO4(-)"
"C5","78","C","GENERAL CARBON IN 5-MEMBERED HETEROAROMATIC RING"
"N5","79","N","GENERAL NITROGEN IN 5-MEMBERED HETEROCYCLIC RING"
"CIM+","80","C","C IN N-C-N IN IMIDAZOLIUM ION"
"NIM+","81","N","IMIDAZOLIUM-TYPE NITROGEN - FORMAL CHARGE=1/2"
"N5A+","81","N","POSITIVE N5A NITROGEN - FORMAL CHARGE=1"
"N5B+","81","N","POSITIVE N5B NITROGEN - FORMAL CHARGE=1"
"N5+","81","N","POSITIVE N5 NITROGEN - FORMAL CHARGE=1"
"N5AX","82","N","N-OXIDE NITROGEN IN 5-RING ALPHA POSITION"
"N5BX","82","N","N-OXIDE NITROGEN IN 5-RING BETA POSITION"
"N5OX","82","N","N-OXIDE NITROGEN IN GENERAL 5-RING POSITION"
"FE+2","87","Fe","IRON +2 CATION"
"FE+3","88","Fe","IROM +3 CATION"
"F-","89","F","FLUORIDE ANION"
"CL-","90","Cl","CHLORIDE ANION"
"BR-","91","Br","BROMIDE ANION"
"LI+","92","Li","LITHIUM CATION"
"NA+","93","Na","SODIUM CATION"
"K+","94","K","POTASSIUM CATION"
"ZINC","95","Zn","DIPOSITIVE ZINC"
"ZN+2","95","Zn","DIPOSITIVE ZINC"
"CA+2","96","Ca","DIPOSITIVE CALCIUM"
"CU+1","97","Cu","MONOPOSITIVE COPPER"
"CU+2","98","Cu","DIPOSITIVE COPPER"
"MG+2","99","Mg","DIPOSITIVE MAGNESIUM CATION"
