1. MMFFSYMB.PAR: This file specifies the four-character symbolic atom types used in MMFF and defines the numeric atom type to which each corresponds. * * Copyright (c) Merck and Co., Inc., 1994, 1995, 1996 * All Rights Reserved * * * SYMBOL TYPE DEFINITION * CR 1 ALKYL CARBON, SP3 C=C 2 VINYLIC CARBON, SP2 CSP2 2 GENERIC SP2 CARBON C=O 3 GENERAL CARBONYL CARBON C=N 3 SP2 CARBON IN C=N CGD 3 GUANIDINE CARBON, DOUBLY BONDED TO N C=OR 3 KETONE OR ALDEHYDE CARBONYL CARBON C=ON 3 AMIDE CARBONYL CARBON CONN 3 UREA CARBONYL CARBON COO 3 CARBOXYLIC ACID OR ESTER CARBONYL CARBON COON 3 CARBAMATE CARBONYL CARBON COOO 3 C ARBONIC ACID OR ESTER CARBONYL CARBON C=OS 3 THIOESTER CARBONYL CARBON, DOUBLE BONDED TO O C=S 3 THIOESTER CARBON, DOUBLY BONDED TO S C=SN 3 THIOAMIDE, CARBON, DOUBLY BONDED TO S CSO2 3 CARBON IN >C=SO2 CS=O 3 CARBON IN >C=S=O (SULFINYL GROUP) CSS 3 THIOCARBOXYLIC ACID OR ESTER CARBONYL CARBON C=P 3 CARBON DOUBLE BONDED TO PHOSPHOROUS CSP 4 ACETYLENIC CARBON =C= 4 ALLENIC CARBON HC 5 H ATTACHED TO C HSI 5 H ATTACHED TO SI OR 6 ALCOHOL OR ETHER OXYGEN OC=O 6 ESTER OR CARBOXYLIC ACID -O- OC=C 6 ENOLIC OR PHENOLIC OXYGEN OC=N 6 DIVALENT OXYGEN OC=S 6 THIOESTER OR THIOACID -O- ONO2 6 DIVALENT NITRATE "ETHER" OXYGEN ON=O 6 DIVALENT NITRITE "ETHER" OXYGEN OSO3 6 DIVALENT OXYGEN ATTACHED TO SULFUR OSO2 6 DIVALENT OXYGEN ATTACHED TO SULFUR OSO 6 DIVALENT OXYGEN ATTACHED TO SULFUR OS=O 6 DIVALENT OXYGEN ATTACHED TO SULFOXIDE SULFUR -OS 6 GENERAL DIVALENT OX ATTACHED TO S OPO3 6 DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS OPO2 6 DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS OPO 6 DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS -OP 6 DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS -O- 6 GENERAL DIVALENT O O=C 7 GENERAL C=O O=CN 7 CARBONYL OXYGEN, AMIDES O=CR 7 CARBONYL OXYGEN, ALDEHYDES AND KETONES O=CO 7 CARBONYL OXYGEN, CARBOXYLIC ACIDS AND ESTERS O=N 7 NITROSO OXYGEN O=S 7 O=S IN SULFOXIDES O=S= 7 O=S ON SULFUR DOUBLY BONDED TO, E.G., CARBON NR 8 NITROGEN IN ALIPHATIC AMINES N=C 9 NITROGEN IN IMINES N=N 9 NITROGEN IN AZO COMPOUNDS NC=O 10 NITROGEN IN AMIDES NC=S 10 NITROGEN IN N-C=S, THIOAMIDE NN=C 10 NITROGEN IN N-N=C NN=N 10 NITROGEN IN N-N=N F 11 FLUORINE CL 12 CHLORINE BR 13 BROMINE I 14 IODINE S 15 SULFUR IN THIOETHERS AND MERCAPTANS S=C 16 TERMINAL SULFUR DOUBLY BONDED TO CARBON S=O 17 SULFUR IN SULFOXIDES >S=N 17 SULFUR, TRICOORD, DOUBLY BONDED TO N SO2 18 SULFUR IN SULFONES SO2N 18 SULFUR IN SULFONAMIDES SO3 18 SULFONATE SULFUR SO4 18 SULFATE SULFUR =SO2 18 SULFONE SULPHER DOUBLY BONDED TO CARBON SNO 18 SULFUR IN NITROGEN ANALOG OF A SULFONE SI 19 SILICON CR4R 20 CARBON IN 4-MEMBERED RINGS HOR 21 HYDROGEN IN ALCOHOLS HO 21 GENERAL H ON OXYGEN HOM 21 HYDROGEN IN HYDROXIDE ANION CR3R 22 CARBON IN A 3-MEMBERED RING HNR 23 H-N(SP3) H3N 23 H-N(SP3), AMMONIA HPYL 23 H-N IN PYRROLE HNOX 23 H-N IN IN A N-OXIDE HNM 23 H ON DICOORD, NEGATIVELY CHARGED NITROGEN HN 23 GENERAL H ON NITROGEN HOCO 24 H-O IN CARBOXYLIC ACIDS HOP 24 HYDROGEN ON OXYGEN ATTACHED TO PHOSPHOROUS PO4 25 PHOSPHOROUS IN PHOSPHATES AND PHOSPHODIESTERS PO3 25 TETRACOORDINATE P WITH THREE ATTACHED OXYGENS PO2 25 TETRACOORDINATE P WITH TWO ATTACHED OXYGENS PO 25 TETRACOORDINATE P WITH ONE ATTACHED OXYGEN PTET 25 GENERAL TETRACOORDINATE PHOSPHORUS P 26 TRICOORDINATE P, AS IN PHOSPHINES HN=N 27 AZO HYDROGEN HN=C 27 IMINE HYDROGEN HNCO 28 AMIDE HYDROGEN HNCS 28 THIOAMIDE HYDROGEN HNCC 28 H-N IN ENAMINES HNCN 28 H-N IN H-N-C=N HNNC 28 H-N IN H-N-N=C HNNN 28 H-N IN H-N-N=N HNSO 28 H-N IN SULFONAMIDE HNPO 28 H-N IN PHOSPHONAMIDE HNC% 28 HYDROGEN ON N ATTACHED TO TRIPLY BONDED CARBON HSP2 28 GENERAL H ON SP2 NITROGEN HOCC 29 H-O IN ENOLS AND PHENOLS HOCN 29 H-O IN HO-C=N CE4R 30 OLEFINIC CARBON IN 4-MEMBERED RINGS HOH 31 HYDROGEN IN H2O O2CM 32 OXYGEN IN CARBOXYLATE ANION OXN 32 N-OXIDE OXYGEN O2N 32 NITRO OXYGEN O2NO 32 NITRO-GROUP OXYGEN IN NITRATE O3N 32 NITRATE ANION OXYGEN O-S 32 SINGLE TERMINAL OXYGEN ON TETRACOORD SULFUR O2S 32 TERMINAL O-S IN SULFONES AND SULFONAMIDES O3S 32 TERMINAL O IN SULFONATES O4S 32 TERMINAL O IN SO4(-3) OSMS 32 TERM O IN THIOSULFINATE ANION - FORMAL CHARGE=-0.5 OP 32 TERMINAL O IN PHOSPHOXIDES O2P 32 TERMINAL O IN PHOSPHINATES O3P 32 TERMINAL OXYGEN IN PHOSPHONATES O4P 32 TERMINAL OXYGEN IN PHOSPHATES AND PHOSPHODIESTERS O4CL 32 OXYGEN IN CLO4(-) ANION - FORMAL CHARGE=-0.25 HOS 33 H ON OXYGEN ATTACHED TO SULFUR NR+ 34 QUATERNARY NITROGEN, SP3, POSITIVELY CHARGED OM 35 ALKOXIDE OXYGEN, NEGATIVELY CHARGED OM2 35 OXIDE OXYGEN ON SP2 CARBON, NEGATIVELY CHARGED HNR+ 36 H ON QUATERNARY NITROGEN HIM+ 36 H ON IMIDAZOLIUM-TYPE NITROGEN HPD+ 36 H ON PROTONATED PYRIDINE NITROGEN HNN+ 36 H ON AMIDINIUM-TYPE NITROGEN HNC+ 36 H ON PROTONATED IMINE NITROGEN HGD+ 36 H ON GUANIDINIUM-TYPE NITROGEN HN5+ 36 H ON N5+, N5A+ OR N5B+ CB 37 CARBON AS IN BENZENE, PYRROLE NPYD 38 NITROGEN, AS IN PYRIDINE NPYL 39 NITROGEN, AS IN PYRROLE NC=C 40 NITROGEN ON N-C=C NC=N 40 NITROGEN IN N-C=N NC=P 40 NITROGEN IN N-C=P NC%C 40 NITROGEN ATTACHED TO C-C TRIPLE BOND CO2M 41 CARBOXYLATE ANION CARBON CS2M 41 CARBON IN THIOCARBOXYLATE ANION NSP 42 NITROGEN, TRIPLE BONDED NSO2 43 NITROGEN IN SULFONAMIDES NSO3 43 NITROGEN IN SULFONAMIDES, THREE O'S ON S NPO2 43 NITROGEN IN PHOSPHONAMIDES NPO3 43 NITROGEN IN PHOSPHONAMIDES, THREE O'S ON P NC%N 43 NITROGEN ATTACHED TO CYANO GROUP STHI 44 SULFUR AS IN THIOPHENE NO2 45 NITRO GROUP NITROGEN NO3 45 NITRATE GROUP NITROGEN N=O 46 NITROSO NITROGEN NAZT 47 TERMINAL NITROGEN IN AZIDO OR DIAZO GROUP NSO 48 DIVALENT NITROGEN REPLACING MONOVALENT O IN SO2 GROUP O+ 49 POSITIVELY CHARGED OXONIUM (TRICOORDINATE) OXYGEN HO+ 50 HYDROGEN ON O+ OXYGEN O=+ 51 POSITIVELY CHARGED OXENIUM (DICOORDINATE) OXYGEN HO=+ 52 HYDROGEN ON OXENIUM OXYGEN =N= 53 NITROGEN IN C=N=N OR -N=N=N N+=C 54 POSITIVELY CHARGED IMINIUM NITROGEN N+=N 54 POSITIVELY CHARGED NITROGEN DOUBLE-BONDED TO N NCN+ 55 N IN +N=C-N RESONANCE STRUCTURES - FORMAL CHARGE=1/2 NGD+ 56 GUANIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1/3 CGD+ 57 GUANIDINIUM CARBON CNN+ 57 C IN +N=C-N RESONANCE STRUCTURES NPD+ 58 PYRIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1 OFUR 59 AROMATIC OXYGEN AS IN FURAN C% 60 ISONITRILE CARBON NR% 61 ISONITRILE NITROGEN [FC = 0] OR DIAZO NITROGEN [FC = 1] NM 62 DEPROTONATED SULFONAMIDE N-; FORMAL CHARGE=-1 C5A 63 ALPHA CARBON IN 5-MEMBERED HETEROAROMATIC RING C5B 64 BETA CARBON IN 5-MEMBERED HETEROAROMATIC RING N5A 65 ALPHA AROM HETEROCYCLIC 5-RING NITROGEN N5B 66 BETA AROM HETEROCYCLIC 5-RING NITROGEN N2OX 67 SP2-HYDRIDIZED N-OXIDE NITROGEN N3OX 68 SP3-HYDRIDIZED N-OXIDE NITROGEN NPOX 69 PYRIDINE N-OXIDE NITROGEN OH2 70 OXYGEN ON WATER HS 71 H ATTACHED TO DIVALENT, DICOORDINATE S HS=N 71 H ATTACHED TO TETRAVALENT, TRICOODR S DBL BONDED TO N HP 71 H ATTACHED TO TRI- OR TETRACOORDINATE PHOSPHORUS S-P 72 TERMINAL SULFUR BONDED TO PHOSPHORUS S2CM 72 TERMINAL SULFUR IN THIOCARBOXYLATE ANION SM 72 TERMINAL SULFUR - FORMAL CHARGE=-1 SSMO 72 TERMINAL SULFUR IN THIOSULFINATE GROUP SO2M 73 SULFUR IN NEGATIVELY CHARGED SULFINATE GROUP SSOM 73 TRICOORD SULFUR IN THIOSULFINATE GROUP =S=O 74 SULFINYL SULFUR, EG. IN C=S=O -P=C 75 PHOSPHOROUS DOUBLY BONDED TO CARBON N5M 76 NEGATIVELY CHARGED N IN, E.G, TRI- OR TETRAZOLE ANION CLO4 77 CHLORINE IN PERCHLORATE ANION, CLO4(-) C5 78 GENERAL CARBON IN 5-MEMBERED HETEROAROMATIC RING N5 79 GENERAL NITROGEN IN 5-MEMBERED HETEROCYCLIC RING CIM+ 80 C IN N-C-N IN IMIDAZOLIUM ION NIM+ 81 IMIDAZOLIUM-TYPE NITROGEN - FORMAL CHARGE=1/2 N5A+ 81 POSITIVE N5A NITROGEN - FORMAL CHARGE=1 N5B+ 81 POSITIVE N5B NITROGEN - FORMAL CHARGE=1 N5+ 81 POSITIVE N5 NITROGEN - FORMAL CHARGE=1 N5AX 82 N-OXIDE NITROGEN IN 5-RING ALPHA POSITION N5BX 82 N-OXIDE NITROGEN IN 5-RING BETA POSITION N5OX 82 N-OXIDE NITROGEN IN GENERAL 5-RING POSITION FE+2 87 IRON +2 CATION FE+3 88 IROM +3 CATION F- 89 FLUORIDE ANION CL- 90 CHLORIDE ANION BR- 91 BROMIDE ANION LI+ 92 LITHIUM CATION NA+ 93 SODIUM CATION K+ 94 POTASSIUM CATION ZINC 95 DIPOSITIVE ZINC ZN+2 95 DIPOSITIVE ZINC CA+2 96 DIPOSITIVE CALCIUM CU+1 97 MONOPOSITIVE COPPER CU+2 98 DIPOSITIVE COPPER MG+2 99 DIPOSITIVE MAGNESIUM CATION