Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite-1.0/data/OpenBabel/mmffdef.par @ 14:55c32b55c2c2
Uploaded Version 1.1
| author | marcel |
|---|---|
| date | Thu, 12 Jan 2012 11:00:43 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.0/data/OpenBabel/mmffdef.par Thu Jan 12 11:00:43 2012 -0500 @@ -0,0 +1,192 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* PRIMARY +* MMFF MMFF +*SYMBOL TYPE DEFAULT TYPES DEFINITION +* + CR 1 1 1 1 0 ALKYL CARBON + C=C 2 2 2 1 0 VINYLIC +* CSP2 2 2 2 1 0 GENERIC CSP2 +* CGD 2 2 2 1 0 GUANIDINE CARBON + C=O 3 3 3 1 0 GENERAL CARBONYL C +* C=N 3 3 3 1 0 C=N +* C=OR 3 3 3 1 0 KETONE OR ALDEHYDE CO +* C=ON 3 3 3 1 0 AMIDE CARBONYL +* COO 3 3 3 1 0 CARBOXYLIC ACID OF EST +* COON 3 3 3 1 0 CARBAMATE CARBONYL +* COOO 3 3 3 1 0 CARBONIC ACID OR ESTER +* C=OS 3 3 3 1 0 THIOESTER, C=O +* C=S 3 3 3 1 0 THIOESTER, C=S +* C=SN 3 3 3 1 0 THIOAMIDE +* CSO2 3 3 3 1 0 CARBON IN >C=SO2 + CSP 4 4 4 1 0 ACETYLENIC C +* =C= 4 4 4 1 0 ALLENIC C + HC 5 5 5 5 0 H-C +* HSI 5 5 5 5 0 H-SI +* HP 5 5 5 5 0 H-P + OR 6 6 6 6 0 O-CSP3 +* OH2 6 6 6 6 0 OXYGEN IN H2O +* OC=O 6 6 6 6 0 ESTER OR ACID -O- +* OC=C 6 6 6 6 0 ENOL OR PHEMOLIC O +* OC=N 6 6 6 6 0 OXYGEN IN -O-C=N MOIETY +* OSO3 6 6 6 6 0 DIVALENT O IN SULFATE +* OSO2 6 6 6 6 0 DIVALENT O IN SULFITE +* OSO 6 6 6 6 0 PAIR OF DIVALENT O ON S +* -OS 6 6 6 6 0 OTHER DIVALENT O ON S +* OPO3 6 6 6 6 0 DIVALENT O IN PHOSPHATE +* OPO2 6 6 6 6 0 DIVALENT O IN PHOSPHITE +* OPO 6 6 6 6 0 PAIR OF DIVALENT O ON P +* -OP 6 6 6 6 0 OTHER DIVALENT O ON P +* -O- 6 6 6 6 0 GENERAL DIVALENT OX + O=C 7 7 7 6 0 O=C, GENERIC +* O=CN 7 7 7 6 0 O=C IN AMIDES +* O=CR 7 7 7 6 0 O=C IN KET, ALD +* O=CO 7 7 7 6 0 O=C IN ACIDS, ESTERS +* O=S 7 7 7 6 0 TERMINAL O SULFOXIDES +* O=N 7 7 7 6 0 NITROSO-GROUP OXYGEN + NR 8 8 8 8 0 AMINE N + N=C 9 9 9 8 0 N=C, IMINES +* N=N 9 9 9 8 0 N=N, AZO COMPOUNDS + NC=O 10 10 10 8 0 N-C=O, AMIDES +* NC=S 10 10 10 8 0 N-C=S (DELOC LP) +* NN=C 10 10 10 8 0 N-N=C (DELOC LP) +* NN=N 10 10 10 8 0 N-N=N (DELOC LP) + F 11 11 11 11 0 FLUORINE + CL 12 12 12 12 0 CHLORINE + BR 13 13 13 13 0 BROMINE + I 14 14 14 14 0 IODINE + S 15 15 15 15 0 THIOL, SULFIDE + S=C 16 16 16 15 0 S DOUBLY BONDED TO C + S=O 17 17 17 15 0 SULFOXIDE S + SO2 18 18 18 15 0 SULFONE S +* SO2N 18 18 18 15 0 SULFONAMIDE S +* SO3 18 18 18 15 0 SULFONATE S +* =SO2 18 18 18 15 0 OXYGENATED SULFONE S +* SNO 18 18 18 15 0 NITROGEN ANALOG OF SO2 + SI 19 19 19 19 0 SILICON + CR4R 20 20 1 1 0 C IN CYCLOBUTYL + HOR 21 21 21 5 0 H-O, ALCOHOLS +* HO 21 21 21 5 0 GENERAL H ON O + CR3R 22 22 22 1 0 C IN CYCLOPROPLY + HNR 23 23 23 5 0 H-N, AMINES +* H3N 23 23 23 5 0 H, AMMONIA +* HPYL 23 23 23 5 0 H-N IN PYRROLE +* HN 23 23 23 5 0 GENERAL H-N + HOCO 24 24 24 5 0 H-O, ACIDS +* HOP 24 21 21 5 0 H-O-P, PHOS ACIDS + PO4 25 25 25 25 0 PHOSPHODIESTER +* PO3 25 25 25 25 0 TETRACRD P, 3 OXYGENS +* PO2 25 25 25 25 0 TETRACRD P, 2 OXYGENS +* PO 25 25 25 25 0 TETRACRD P, 2 OXYGENS +* PTET 25 25 25 25 0 GENERAL TETRACRD P + P 26 26 26 25 0 TRICOORDINATE P + HN=C 27 27 28 5 0 IMINE N-H +* HN=N 27 27 28 5 0 AZO N-H + HNCO 28 28 28 5 0 H-N, AMIDES +* HNCC 28 28 28 5 0 H-N, ENAMINES +* HNCS 28 28 28 5 0 H-N, THIOAMIDES +* HNCN 28 28 28 5 0 H-N, HN-C=N +* HNNC 28 28 28 5 0 H-N, HN-N=C +* HNNN 28 28 28 5 0 H-N, HN-N=N +* HSP2 28 28 28 5 0 GENERAL H ON SP2 N + HOCC 29 29 29 5 0 H-O, ENOLS, PHENOLS +* HOCN 29 29 29 5 0 H-O IN HO-C=N + CE4R 30 30 2 1 0 C=C IN 4-RING + HOH 31 31 31 31 0 H-OH + O2CM 32 32 7 6 0 O, CARBOXYLATE ANION +* OXN 32 32 7 6 0 OXIDE ON NITROHGEN +* O2N 32 32 7 6 0 NITRO-GROUP OXYGEN +* O2NO 32 32 7 6 0 NITRO-GROUP IN NITRATE +* O3N 32 32 7 6 0 NITRATE ANION OXYGEN +* O-S 32 32 7 6 0 SINGLE TERM O ON TET S +* O2S 32 32 7 6 0 SULFONES, SULFONAMIDES +* O3S 32 32 7 6 0 SULFONATES, TERM OX +* O4S 32 32 7 6 0 SO4(3-) +* OSMS 32 32 7 6 0 THIOSULFINATE O (-1/2) +* OP 32 32 7 6 0 TERMINAL O, O-P +* O2P 32 32 7 6 0 TERMINAL O, O2P GROUP +* O3P 32 32 7 6 0 TERMINAL O, O3P GROUP +* O4P 32 32 7 6 0 TERMINAL O, PO4(-3) +* O4CL 32 32 7 6 0 TERMINAL O IN CLO4(-) + HOS 33 33 21 5 0 H-O-S, SULF ACIDS + NR+ 34 34 8 8 0 N+, QUATERNARY N + OM 35 35 6 6 0 OXIDE OXYGEN ON SP3 C +* OM2 35 35 6 6 0 OXIDE OXYGEN ON SP2 C + HNR+ 36 36 36 5 0 H-N+ +* HNN+ 36 36 36 5 0 H ON IMIDAZOLIUM N +* HNC+ 36 36 36 5 0 H ON PROTONATED N+=C-N +* HGD+ 36 36 36 5 0 H ON GUANIDINIUM N + CB 37 37 2 1 0 AROMATIC C + NPYD 38 38 9 8 0 AROMATIC N, PYRIDINE + NPYL 39 39 10 8 0 AROMATIC N, PYRROLE + NC=C 40 40 10 8 0 N-C=C (DELOC LP) +* NC=N 40 40 10 8 0 N-C=N (DELOC LP) + CO2M 41 41 3 1 0 C IN CO2- ANION +* CS2M 41 41 3 1 0 THIOCARBOXYLATE C + NSP 42 42 42 8 0 N TRIPLE BONDED + NSO2 43 43 10 8 0 N, SULFONAMIDES + STHI 44 44 16 15 0 S IN THIOPHENE + NO2 45 45 10 8 0 NITRO GROUP N +* NO3 45 45 10 8 0 NITRATE GROUP N + N=O 46 46 9 8 0 NITROSO GROUP N + NAZT 47 47 42 8 0 TERMINAL N, AZIDE + NSO 48 48 9 8 0 DIVAL. N IN S(N)(O) GP + O+ 49 49 6 6 0 OXONIUM (TRICOORD) O + HO+ 50 50 21 5 0 H ON OXONIUM OXYGEN + O=+ 51 51 7 6 0 OXENIUM OXYGEN+ + HO=+ 52 52 21 5 0 H ON OXENIUM O+ + =N= 53 53 42 8 0 N TWICE DOUBLE BONDED + N+=C 54 54 9 8 0 IMINIUM NITROGEN +* N+=N 54 54 9 8 0 AZONIUM NITROGEN + NCN+ 55 55 10 8 0 N IN +N=C-N: ; Q=1/2 + NGD+ 56 56 10 8 0 GUANIDINIUM N; Q=1/3 + CGD+ 57 57 2 1 0 GUANIDINIUM CARBON +* CNN+ 57 57 2 1 0 C IN +N=C-N RESONANCE + NPD+ 58 58 10 8 0 N PYRIDINIUM ION + OFUR 59 59 6 6 0 AROMATIC O, FURAN + C% 60 60 4 1 0 ISONITRILE CARBON + NR% 61 61 42 8 0 ISONITRILE N + NM 62 62 10 8 0 SULFONAMIDE N- + C5A 63 63 2 1 0 ALPHA AROM 5-RING C + C5B 64 64 2 1 0 BETA AROM 5-RING C + N5A 65 65 9 8 0 ALPHA AROM 5-RING N + N5B 66 66 9 8 0 ALPHA AROM 5-RING N + N2OX 67 67 9 8 0 NITROGEN IN N-OXIDE + N3OX 68 68 8 8 0 NITROGEN IN N-OXIDE + NPOX 69 69 9 8 0 NITROGEN IN N-OXIDE + OH2 70 70 70 70 70 OXYGEN IN WATER + HS 71 71 5 5 0 H-S + S2CM 72 72 16 15 0 THIOCARBOXYLATE S +* S-P 72 72 16 15 0 TERMINAL SULFUR ON P +* SM 72 72 16 15 0 TERMINAL SULFUR ON C +* SSMO 72 72 16 15 0 TERM S, THIOSULFINATE + SO2M 73 73 18 15 0 SULFUR IN SULFINATE +* SSOM 73 73 18 15 0 SULFUR, THIOSULFINATE + =S=O 74 74 17 15 0 SULFINYL SULFUR, C=S=O + -P=C 75 75 26 25 0 P DOUBLY BONDED TO C + N5M 76 76 9 8 0 NEG N IN TETRAZOLE AN + CLO4 77 77 12 12 0 CHLORINE IN CLO4(-) + C5 78 78 2 1 0 GENERAL AROM 5-RING C + N5 79 79 9 8 0 GENERAL AROM 5-RING N + CIM+ 80 80 2 1 0 C IN N-C-N, IM+ ION + NIM+ 81 81 10 8 0 N IN N-C-N, IM+ ION + N5AX 82 82 9 8 0 5R NITROGEN IN N-OXIDE +* N5BX 82 82 9 8 0 5R NITROGEN IN N-OXIDE +* N5OX 82 82 9 8 0 5R NITROGEN IN N-OXIDE + FE+2 87 87 87 87 87 IRON +2 CATION + FE+3 88 88 88 88 88 IRON +3 CATION + F- 89 89 89 89 89 FLUORIDE ANION + CL- 90 90 90 90 90 CHLORIDE ANION + BR- 91 91 91 91 91 BROMIDE ANION + LI+ 92 92 92 92 92 LITHIUM CATION + NA+ 93 93 93 93 93 SODIUM CATION + K+ 94 94 94 94 94 POTASSIUM CATION + ZN+2 95 95 95 95 95 DIPOSITIVE ZINC CATION +* ZINC 95 95 95 95 95 DIPOSITIVE ZINC CATION + CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM CATION + CU+1 97 97 97 97 97 MONOPOSITIVE COPPER CATION + CU+2 98 98 98 98 98 DIPOSITIVE COPPER CATION + MG+2 99 99 99 99 99 DIPOSITIVE MAGNESIUM CATION +$