# # file: oplsaa.define # author: Pieter J. in 't Veld # date: November 16, 25, 2012, March 17, 24, 2013, December 30, 2014, # January 15, 2016, February 3, 2017, November 9, 2020, # November 20-30, December 1-20, 2024. # purpose: OPLS-AA force field definitions and typing rules # version: 2.0beta # # Copyright (c) 2004-2025 Pieter J. in 't Veld # Distributed under GNU Public License as stated in LICENSE file in EMCroot # directory # # rule keys: # ~ any bond # - single bond # : partial bond # = double bond # # triple bond # * wildcard, specified number of bonds # ^ followed by a number indicates the number of ring members # # type conventions (by character): # 1[-2] lower case letters indicating element (mandatory) # 2 number of connections (mandatory) # 3 chemical indicator, e.g. e: ether, a: aromatic # or connected to element # 4 can indicate number of ring members in case of aromatic # # Empty lines are skipped # Specified types represent numerical OPLS assignments # # notes: # 20121116 - Creation date, v0.1beta # 20121125 - Addition of keywords DEFINE, MASS, REFERENCES, EXTRA, # and PRECEDENCE # 20130317 - Addition of keywords EQUIVALENCE, BOND, ANGLE, TORSION, # IMPROPER # 20130324 - Redefinition of EXTRA to include management of double # torsions # - Addition of REDEFINE # 20141230 - Switch to v0.2beta # - Refinement of mass comments # - Refinement of existing rules to phase out ? as connectivity # - Additional rules for halogenides and acids # - Testing with simple compounds: alkanes, benzenes (see # examples) # 20160115 - Corrected typing of acid side groups # - Corrected typing of alpha hydrogen for acid side groups # 20170203 - Switch to 0.3beta # - Corrected typing of alkenes # - Corrected dicarboxylic acid entries # - Added isocyanate entries # 20201109 - Added sulfone and ionic liquid entries # 20230814 - Added carbonate entries (DLV, Vigil/Sandia) # 20241120 - New inception # - Needs emc_opls.pl v2.0 and higher # - Complete redesign # - New type definitions # - Inclusion of bond increments and streams # - General rules based on stream derived rules # - Dropped ITEM keywords EXTRA, PRECEDENCE, and REDEFINE # - Added ITEM keyword STREAM and RULES # - Zero increment contribution is assumed between two GROUP # blocks # - Use /* */ or (* *) for commenting out blocks in STREAM # - Latter only works at beginning of line # # Definitions ITEM DEFINE FFMODE OPLS FFTYPE ATOMISTIC FFINDEX ELEMENTS FFCHARGE ALL FFDEPTH 10 ITEM END # Literature references ITEM REFERENCES # year volume page journal 1954 ?? ?? Wiley (Hirschfelder) 1972 24 1013 Mol. Phys. 1988 63 547 Mol. Phys. 1984 106 6638 J. Am. Chem. Soc. 1991 113 8262 J. Am. Chem. Soc. 1996 118 11225 J. Am. Chem. Soc. 1999 121 4827 J. Am. Chem. Soc. 1983 79 926 J. Chem. Phys. 1990 11 958 J. Comput. Chem. 1997 18 1955 J. Comput. Chem. 1986 90 1276 J. Phys. Chem. 1986 90 2174 J. Phys. Chem. 1986 90 6379 J. Phys. Chem. 1990 94 1683 J. Phys. Chem. 1991 95 3315 J. Phys. Chem. 2001 105 4118 J. Phys. Chem. A 1998 102 8049 J. Phys. Chem. B 2004 18 16264 J. Phys. Chem. B 1998 424 145 Theochem. 2007 806 23 J. Mol. Struct. THEOCHEM 2006 2 1499 J. Chem. Theory Comput. 2009 5 1038 J. Chem. Theory Comput. ITEM END # Masses ITEM MASS # WARNING: # - ordered by importance => alter with care # - general rules below assume order as given # - do not change the first entry of each source group unless # absolute certainty exists # - first per each source group appears as bonded type in equivalence table # - sorting used in wildcard types for bonded interactions (auto types), e.g. # - c4* stands for all types starting with c4 # dest src mass element ncons index charge sigma epsilon comment # # Actinide # # Ac ac+3 Ac 227.027 Ac 0 697 3 3.473 0.054 Actinide 3+ ion # # Americum # # Am am+3 Am 243.061 Am 0 699 3 3.3 0.05 Americium 3+ ion # # Argon # # Ar ar Ar 39.948 Ar 0 103 0 3.401 0.2339 Argon # # Barium # # Ba #ba+2 Ba 137.327 Ba 0 414 0 3.81661 0.047096 Barium 2+ ion (old) ba+2 Ba 137.327 Ba 0 1114 2 4.18 0.047096 Barium 2+ ion # # Bromide # # Br br1 Br 79.904 Br 1 722 0 3.47 0.47 Bromide in alkanes (UA) br- Br 79.904 Br 0 1102 -1 4.51 0.09 Bromide 1- anion # # Carbon # # C c3o C 12.011 C 3 231 0 3.75 0.105 C=O in ketones c3oa C 12.011 C 3 231 0 3.75 0.105 C=O in deprotonated acids c3oh C 12.011 C 3 231 0 3.75 0.105 C=O in protonated acids c3oe C 12.011 C 3 231 0 3.75 0.105 C=O in esters c3ou C 12.011 C 3 231 0 3.75 0.105 C=O in urea c3oan C 12.011 C 3 231 0 3.75 0.105 C=O in maleic anhydride c3oam C 12.011 C 3 231 0 3.75 0.105 C=O in amides c3oim C 12.011 C 3 231 0 3.75 0.105 C=O in imides # C! c3ab C! 12.011 C 3 519 0 3.55 0.07 Bridging aromatic carbon in biphenyl # C$ c3o4 C$ 12.011 C 3 685 0 3.75 0.105 C=O in beta-lactam # C* c3a5 C* 12.011 C 3 500 0 3.55 0.07 Aromatic carbon (CG in tryptophan 5-ring) # C+ c3+ C+ 12.011 C 3 700 0 3.55 0.076 SP2 carbon (C+ in t-butyl+) # C2 #c4h2 C2 12.011 C 2 723 0 3.905 0.118 CH2 alkyl bromide (UA) # C3 c4ai C3 12.011 C 4 415 0 4.2 0.3 SP3 carbon in thiolate and alkoxide anions # C: c2 C: 12.011 C 2 1157 0 3.3 0.086 Middle carbon in allenes # C= c3an C= 12.011 C 3 2532 0 3.55 0.07 SP2 carbon in maleic anhydride c3u C= 12.011 C 3 2532 0 3.55 0.07 SP2 carbon in uracil c3d C= 12.011 C 3 150 0 3.55 0.076 Diene =CH-CH= # CA c3a CA 12.011 C 3 145 0 3.55 0.07 Aromatic carbon c3as CA 12.011 C 3 145 0 3.55 0.07 Aromatic carbon in sulfates c3aso CA 12.011 C 3 145 0 3.55 0.07 Aromatic ortho carbon in sulfates c3ai CA 12.011 C 3 2686 0 3.55 0.076 Aromatic carbon (1-phenylbenzimidazole shared 5- and 6-ring) c3ap CA 12.011 C 3 312 0 3.5 0.08 Aromatic carbon (diaminepyridine) c3a+ CA 12.011 C 3 302 0 3.55 0.05 C: guanidinium C+ # CB c3aa CB 12.011 C 3 349 0 3.5 0.08 Adenine C4 (bridge C between 2 N in 5- and 6-ring) c3a6 CB 12.011 C 3 501 0 3.55 0.07 CD in tryptophan shared 5- and 6-ring # CK c3a5a CK 12.011 C 3 353 0 3.5 0.08 Aromatic carbon between 2 N in 5-ring (adenine C8) c3a5m CK 12.011 C 3 627 0 3.55 0.07 Aromatic carbon between 2 N in 5-ring (purine C8) # CM c3= CM 12.011 C 3 141 0 3.55 0.076 SP2 carbon in alkene c3ao CM 12.011 C 3 323 0 3.5 0.08 SP2 carbon C=O in 6-ring (uracil C5) c3ao1 CM 12.011 C 3 2906 0 3.55 0.07 SP2 carbon C=O in 6-ring (3-phenyl-4-pyridone) c31= CM 12.011 C 3 1154 0 3.3 0.086 SP2 carbon in allene (outer C) # CN c3at CN 12.011 C 3 502 0 3.55 0.07 CE C in TRP (aromatic carbon in 5- and 6-ring next to N) # CO c4o2 CO 12.011 C 3 189 0 3.5 0.066 C(H2O2): acetal OCH2O (SP3 carbon connected to 2 O and 1 H) # CQ c3a6n CQ 12.011 C 3 531 0 3.55 0.07 Aromatic carbon between 2 N in 6-ring c3a6a CQ 12.011 C 3 347 0 3.5 0.08 Aromatic carbon between 2 N in 6-ring (adenine C2) # CR c3a53 CR 12.011 C 3 506 0 3.55 0.07 Aromatic carbon between 2 N in 5-ring (histidine CE1) # CS c3a5n CS 12.011 C 3 544 0 3.55 0.07 Aromatic carbon in 5-ring with 1 N (pyrrole C3) C3a5o CS 12.011 C 3 568 0 3.55 0.076 Aromatic carbon in 5-ring with 1 O (furan C3) # CT c4 CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon c4n CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in amines c4nn CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in nitriles c4ns CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in sulfonamides c4o CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in benzyl alcohols c4s CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in sulfides c4p CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in phosphates c4pm CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in phosphates c4sa CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in sulfonamides c4oe CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in ethers and esters c4br CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in bromo-alkanes c4cl CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in chloro-alkanes c4i CT 12.011 C 4 135 0 3.5 0.066 SP3 carbon in iodo-alkanes c4an CT 12.011 C 4 755 0 3.3 0.066 C of methyl group in acetonitrile c4t CT 12.011 C 3 331 0 3.5 0.08 SP3 carbon in thymine C-C5 c4f CT 12.011 C 4 161 0 3.25 0.062 SP3 carbon in R-CF3 c4ac CT 12.011 C 4 421 0 4.2 0.3 SP3 carbon in acetonitrile ion (C1 in CH2CN-) c4f4 CT 12.011 C 4 964 0 3.5 0.097 SP3 carbon in CF4 c4h3 CT 12.011 C 4 396 0 3.55 0.066 SP3 carbon C in methyl group # CU c3a55 CU 12.011 C 3 550 0 3.55 0.07 Aromatic carbon next to 2 N in 5-ring (pyrazole C3) # CV c3a52 CV 12.011 C 3 507 0 3.55 0.07 Aromatic carbon in 5-ring (histidine CD2 in HID, CG in HIE) # CW c3a51 CW 12.011 C 3 508 0 3.55 0.07 Aromatic carbon in 5-ring (histidine CG in HID, CD2 in HIE) c3a5f CW 12.011 C 3 567 0 3.55 0.076 Aromatic carbon (furan C2) c3a5s CW 12.011 C 3 2013 0 3.55 0.076 Aromatic carbon (3-phenylthiophene) # CX c3a54 CX 12.011 C 3 510 0 3.55 0.07 Aromatic carbon in 5-ring (histidine CG, CD2 in HIP) # CY c44 CY 12.011 C 4 3354 0 3.55 0.07 SP3 carbon in 4-ring (2-phenylazetidine) c441 CY 12.011 C 4 687 0 3.5 0.066 SP3 carbon in 4-ring (penicillin CH(N)) # CZ c2n CZ 12.011 C 2 754 0 3.3 0.066 SP carbon in cyano group c2na CZ 12.011 C 2 261 0 3.65 0.15 SP carbon in benzonitrile c2ct CZ 12.011 C 2 925 0 3.3 0.086 Terminal SP carbon in acetylene c2c2 CZ 12.011 C 2 927 0 3.3 0.21 SP carbon in alkyne (RC#CH C2 R-with 2 or 3 H) c2c1 CZ 12.011 C 2 928 0 3.3 0.135 SP carbon in alkyne (RC#CH C2 R-with 1 H) c2ca CZ 12.011 C 2 929 0 3.3 0.1 SP carbon in alkyne (RC#CH C2 R-with no H or R=phenyl) # # Calcium # # Ca #ca+2 Ca 40.078 Ca 0 412 0 2.412031 0.449657 Calcium 2+ ion (old) ca+2 Ca 40.078 Ca 0 1112 0 3.47 0.449657 Calcium 2+ ion # # Chlorine # # Cl cl1 Cl 35.4527 Cl 1 151 0 3.4 0.3 Cl in alkyl chlorides #cl- Cl 35.4527 Cl 0 401 -1 4.02 0.71 Chlorine 1- anion (old) cl- Cl 35.4527 Cl 0 1101 -1 4.18 0.11779 Chlorine 1- anion # # Cesium # # Cs #cs+ Cs 132.905 Cs 0 410 1 6.2 0.0005 Cesium 1+ ion (old) cs+ Cs 132.905 Cs 0 1110 1 4.82 8.1e-05 Cesium 1+ ion # # Europium # # Eu eu+3 Eu 151.964 Eu 0 705 3 3.3 0.05 Europium 3+ ion # # Fluorine # # F f1 F 18.998 F 1 164 0 2.94 0.061 Fluor in trifluoroethanol f1a F 18.998 F 1 719 0 2.85 0.061 Fluor in fluorobenzene f1ao F 18.998 F 1 986 0 2.9 0.06 Fluor in trifluoroanisole f1c F 18.998 F 1 965 0 2.95 0.053 Fluor in perfluoroalkanes #f- F 18.998 F 0 400 -1 3.05 0.71 Fluor 1- anion (old) f- F 18.998 F 0 1100 -1 3.08 0.72 Fluor 1- anion f1p F 18.998 F 1 786 0 3.1181 0.061 Fluor in hexafluorophosphate (PF6-) # # Gadolinium # # Gd gd+3 Gd 157.25 Gd 0 706 3 3.3 0.05 Gadolinium 3+ ion # # Helium # # He he He 4.0026 He 0 101 0 2.556 0.02 Helium # # Hydrogen # # H h1n H 1.0079 H 1 240 0 1 0 Hydrogen on nitrogen in primary amide h1n1 H 1.0079 H 1 2967 0 2.42 0.03 4-phenyl-1,2,3-triazole h1si H 1.0079 H 1 1064 0 2.5 0.03 Hydrogen on Si in silane h1n2 H 1.0079 H 1 428 0 2.5 0.05 Hydrogen on N in CH3NH- # H3 h1n3 H3 1.0079 H 1 289 0 1 0 Hydrogen in guanidinium h1n4 H3 1.0079 H 1 289 0 1 0 Hydrogen in ammonium derivatives # H4 h1a2 H4 1.0079 H 1 345 0 2.5 0.05 Aromatic hydrogen (cytosine H-C6) # H5 h1a3 H5 1.0079 H 1 355 0 2.5 0.05 Aromatic hydrogen (adenine H-C2 nucleoside) # HA h1a HA 1.0079 H 1 146 0 2.42 0.03 Aromatic hydrogen (benzene H - 12 site) h1a1 HA 1.0079 H 1 316 0 2.5 0.05 Aromatic hydrogen (diaminepyridine) # HC h1 HC 1.0079 H 1 140 0 2.5 0.03 Hydrogen in alkanes h1cl HC 1.0079 H 1 140 0 2.5 0.03 Hydrogen in halocarbons h1oh HC 1.0079 H 1 140 0 2.5 0.03 Hydrogen on SP3 carbon with alcohol OH h1a4 HC 1.0079 H 1 329 0 2.5 0.05 Aromatic hydrogen (uracil H-C5) h1= HC 1.0079 H 1 144 0 2.42 0.03 Hydrogen in alkenes h1co HC 1.0079 H 1 279 0 2.42 0.015 Hydrogen in aldehyde and formamide h1cn HC 1.0079 H 1 759 0 2.5 0.015 Hydrogen on SP3 carbon next to cyanocarbon in nitriles h1cs HC 1.0079 H 1 759 0 2.5 0.015 Hydrogen on SP3 methyl carbon in sulfonamides h1co2 HC 1.0079 H 1 255 0 2.5 0.02 Hydrogen in formimide h1cp HC 1.0079 H 1 759 0 2.5 0.015 Hydrogen on SP3 methyl carbon in phosphonates h1r HC 1.0079 H 1 255 0 2.5 0.02 Hydrogen in RMIM+ # HO h1o HO 1.0079 H 1 155 0 2.5 0 Hydrogen in mono alcohols # HS h1s HS 1.0079 H 1 204 0 2.5 0 Hydrogen in thiols # HW h1w HW 1.0079 H 1 98 0 2.5 0 Hydrogen in water # # Iodine # # I i1 I 126.904 I 1 732 0 3.75 0.6 Iodine in iodobenzene #i- I 126.904 I 0 403 -1 4.81 0.71 I- 400-410 new OPLS: i- I 126.904 I 0 1103 -1 5.15 0.07 Iodine 1- anion # # Krypton # # Kr kr Kr 83.8 Kr 0 104 0 3.624 0.317 Krypton # # Lanthanum # # La la+3 La 138.905 La 0 703 3 3.75 0.06 Lanthanum 3+ ion # # Lithium # # Li #li+ Li 6.941 Li 0 406 1 2.87 0.0005 Lithium 1+ ion (old) li+ Li 6.941 Li 0 1106 1 2.7 0.018279 Lithium 1+ ion # # Lone pair # # LP lp LP 1 Lp 1 99 0 1 0 Lone pair # # Magnesium # # Mg #mg+2 Mg 24.305 Mg 0 411 2 1.644471 0.875044 Magnesium 2+ ion (old) mg+2 Mg 24.305 Mg 0 1111 2 2.91 0.875044 Magnesium 2+ ion # # Neon # # Ne ne Ne 20.18 Ne 0 102 0 2.78 0.069 Neon # # Nitrogen # # N n3am0 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in tertiary amides n3am1 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in secondary amides n3am2 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in primary amides n3sa0 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in tertiary sulfonamides n3sa1 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in secondary sulfonamides n3sa2 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in primary sulfonamides n3ur2 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in primary amides n3ah N 14.0067 N 3 2910 0 3.3 0.17 Nitrogen in pyridone n3im1 N 14.0067 N 3 237 0 3.25 0.17 Nitrogen in secondary imides n3+ N 14.0067 N 3 787 0 3.15 0.17 Nitrogen in nitrate #nh4+ N 14.0067 N 0 405 1 5.34 0.0005 Ammonium 1+ ion (UA) # N$ n34 N$ 14.0067 N 3 686 0 3.25 0.17 Nitrogen in beta-lactam # N* n3a5h N* 14.0067 N 3 936 0 3.25 0.17 Protonated nitrogen in 5-ring (adenine N9) # N2 n3ch N2 14.0067 N 3 300 0 3.25 0.17 Nitrogen in methylguanidinium n3ch2 N2 14.0067 N 3 300 0 3.25 0.17 Nitrogen in guanidinium # N3 n4 N3 14.0067 N 4 286 0 3.25 0.17 Nitrogen in ammonium ion with no protons n4h N3 14.0067 N 4 286 0 3.25 0.17 Nitrogen in ammonium ion with one proton n4h2 N3 14.0067 N 4 286 0 3.25 0.17 Nitrogen in ammonium ion with two protons n4h3 N3 14.0067 N 4 286 0 3.25 0.17 Nitrogen in ammonium ion with three protons n4h4 N3 14.0067 N 4 286 0 3.25 0.17 Nitrogen in ammonium ion with four protons n2c N3 14.0067 N 2 427 0 3.4 0.25 Nitrogen in deprotonated amine (methylamine) # NA n3a NA 14.0067 N 3 319 0 3.25 0.17 Nitrogen in aromatic ring n3ah1 NA 14.0067 N 3 319 0 3.25 0.17 Protonated nitrogen in 6-ring (uracil N1) # NB n2a5 NB 14.0067 N 2 352 0 3.25 0.17 Nitrogen in 5-ring (adenine N7) # NC n2a6 NC 14.0067 N 2 311 0 3.25 0.17 Nitrogen in 6-ring (diaminopyridine N1) # NM n3c3 NM 14.0067 N 3 1037 0 3.25 0.17 Nitrogen in tertiary amide # NO n3o2 NO 14.0067 N 3 760 0 3.25 0.12 Nitrogen in nitro R-NO2 # NT n3 NT 14.0067 N 3 900 0 3.3 0.17 Nitrogen in tertiary amines n3h NT 14.0067 N 3 900 0 3.3 0.17 Nitrogen in secondary amines n3h2 NT 14.0067 N 3 900 0 3.3 0.17 Nitrogen in primary amines # NY n3y NY 14.0067 N 3 749 0 3.25 0.17 Nitrogen in arginine next to amine group # NZ n1 NZ 14.0067 N 1 262 0 3.2 0.17 Nitrogen in benzonitrile n1- NZ 14.0067 N 1 424 0 3.4 0.25 Nitrogen in acetonitrile (CH3CN-) # # Neodynium # # Nd nd+3 Nd 144.242 Nd 0 704 3 3.473 0.054 Neodymium 3+ ion # # Oxygen # # O o1= O 15.9994 O 1 236 0 2.96 0.21 Oxygen in amides and ketones o1n O 15.9994 O 1 788 0 2.86 0.21 Oxygen in nitrate ion (NO3-) # O2 o1a O2 15.9994 O 1 272 0 2.96 0.21 Oxygen in deprotonated acids o1p O2 15.9994 O 1 441 0 3.15 0.2 Oxygen in phosphate (O= in Me2PO4-) o1p= O2 15.9994 O 1 441 0 3.15 0.2 Oxygen in phosphate (O= in Me2PO4-) # OH o2h OH 15.9994 O 2 154 0 3.12 0.17 Oxygen in alcohols o2ha OH 15.9994 O 2 268 0 3 0.17 Oxygen in protonated acids o2hh OH 15.9994 O 2 162 0 3.07 0.17 Oxygen in diols and phenols o2ht OH 15.9994 O 2 162 0 3.07 0.17 Oxygen in diols and phenols o2hi OH 15.9994 O 1 420 0 3.15 0.25 Oxygen in alkoxide (CH3O-) o1h- OH 15.9994 O 1 434 0 3.2 0.25 Oxygen in hydroxide (OH-, d(O-H) = 0.953 A) # ON o1n1 ON 15.9994 O 1 761 0 2.96 0.17 Oxygen in nitro R-NO2 # OS o2 OS 15.9994 O 2 177 0 2.9 0.14 Oxygen in ethers o2e OS 15.9994 O 2 177 0 2.9 0.14 Oxygen in ethers o2p OS 15.9994 O 1 395 0 3 0.17 Oxygen in phosphate (O- in Me2PO4-) o2s OS 15.9994 O 1 395 0 3 0.17 Oxygen in esters # OU o2u OU 15.9994 O 2 437 0 3.11815 0.2 Oxygen in uranium oxide (UO2+, d(U-O) = 1.80 A) # OW o2w OW 15.9994 O 2 133 0 3.16557 0.1554 Oxygen in SPC/E water o2w3 OW 15.9994 O 2 111 0 3.15061 0.1521 Oxygen in TIP3P water o2w3f OW 15.9994 O 2 116 0 3.176 0.15 Oxygen in TIP3F water (flexible model) o2w4f OW 15.9994 O 2 795 0 3.27 0.1 Oxygen in TIP4F water (flexible model) o2w4 OW 15.9994 O 2 113 0 3.15365 0.155 Oxygen in TIP4P water o2w5 OW 15.9994 O 2 97 0 3.12 0.16 Oxygen in TIP5P water # OY o1s OY 15.9994 O 1 497 0 2.93 0.28 Oxygen in sulfoxide o1s= OY 15.9994 O 1 475 0 2.96 0.17 Oxygen in sulfonamide # # Phosphorus # # P p4 P 30.974 P 4 393 0 3.74 0.2 Phosphorus in phosphates p41 P 30.974 P 4 393 0 3.74 0.2 Phosphorus in methylphosphate anion p42 P 30.974 P 4 393 0 3.74 0.2 Phosphorus in dimethylphosphate anion p43 P 30.974 P 4 393 0 3.74 0.2 Phosphorus in dimethyl methylphosphonate # P+ p4+ P+ 30.974 P 4 781 0 3.74 0.2 Phosphorus in phosphonium R4P+ # # Potassium # # K #k+ K 39.098 K 0 408 1 5.17 0.0005 Potassium 1+ ion (old) k+ K 39.098 K 0 1108 1 4.06 0.000328 Potassium 1+ ion # # Rubidium # # Rb #rb+ Rb 85.468 Rb 0 409 1 5.6 0.0005 Rubidium 1+ ion (old) rb+ Rb 85.468 Rb 0 1109 1 4.32 0.000171 Rubidium 1+ ion # # Sodium # # Na #na+ Na 22.99 Na 0 407 1 4.07 0.0005 Sodium 1+ ion (old) na+ Na 22.99 Na 0 1107 1 3.35 0.002772 Sodium 1+ ion # # Sulfur # # S s2 S 32.066 S 2 202 0 3.55 0.25 Sulfur in organic sulfides # SH s2h SH 32.066 S 2 200 0 3.55 0.25 Sulfur in thiols s2h2 SH 32.066 S 2 201 0 3.7 0.25 Sulfur in hydrogen sulfide s2- SH 32.066 S 2 417 0 4.25 0.5 Sulfur in CH3S- # SY s4 SY 32.066 S 4 474 0 3.55 0.25 Sulfur in sulfone s4c SY 32.066 S 4 474 0 3.55 0.25 Sulfur in sulfonate anion s4am SY 32.066 S 4 474 0 3.55 0.25 Sulfur in sulfonamide # SZ s3 SZ 32.066 S 3 495 0 3.56 0.395 Sulfur in alkyl aryl sulfoxide # # Silicon # # Si si4 Si 28.085 Si 4 1060 0 4 0.1 Silicon in tetraalkylsilane R4Si # # Strontium # # Sr #sr+2 Sr 87.62 Sr 0 413 2 3.102688 0.118226 Strontium 2+ ion (old) sr+2 Sr 87.62 Sr 0 1113 2 3.82 0.118226 Strontium 2+ ion # # Thorium # # Th th+4 Th 232.038 Th 0 698 4 3.3 0.05 Thorium 4+ ion # # Uranium # # U u2 U 238.029 U 2 436 0 2.81524 0.4 Uranium in UO2+ # # Xenon # # Xe xe Xe 131.29 Xe 0 105 0 3.935 0.433 Xenon # # Ytterbium # # Yb yb+3 Yb 173.04 Yb 0 707 3 2.95 0.04 Ytterbium 3+ ion # # Zinc # # Zn zn4 Zn 65.39 Zn 4 1005 0 1.96 0.0125 Zinc in metalloproteins (JACS 1991, 113, 8262) ITEM END # MASS # Equivalence ITEM EQUIVALENCE # type pair incr bond angle torsion improper #h1n3 h1n3 h1n3 h1n h1n h1n h1n #h1n4 h1n4 h1n4 h1n h1n h1n h1n ITEM END # EQUIVALENCE ######################################################################### # # # Noble gases # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule ar Ar - - 0 [Ar] he He - - 0 [He] kr Kr - - 0 [Kr] ne Ne - - 0 [Ne] xe Xe - - 0 [Xe] ITEM END # RULES ######################################################################### # # # Ions and water # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule #o2w O - - 0 O(H)(H) br- Br - - -1 [Br-] cl- Cl - - -1 [Cl-] cs+ Cs - - 1 [Cs+] eu+3 Eu - - 3 [Eu+3] f- F - - -1 [F-] i- I - - -1 [I-] k+ K - - 1 [K+] la+3 La - - 3 [La+3] li+ Li - - 1 [Li+] mg+2 Mg - - 2 [Mg+2] na+ Na - - 1 [Na+] #nh4+ N - - 1 [N+](H)(H)(H)(H) nd+3 Nd - - 3 [Nd+3] sr+2 Sr - - 2 [Sr+2] th+4 Th - - 4 [Th+4] yb+3 Yb - - 3 [Yb+3] ITEM END # RULES # Stream ITEM STREAM # 133-134 RESI SPCE 0 ! H2O, water (SPC/E) GROUP ! ATOM O o2w -0.8476 ! H1--O--H2 ATOM H1 h1w 0.4238 ! ATOM H2 h1w 0.4238 ! CONECT O H1 H2 RESI HYDR -1 ! HO, hydroxide GROUP ! ATOM O o1h- -1.3 ! H--O(-) ATOM H h1o 0.3 ! CONECT O H UNLINK o1h- h1o ITEM END # STREAM ######################################################################### # # # Alkanes # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4 C - - 0 C(C)(C)(C)(C) c4 C - - 0 C(C)(C)(C)(H) c4 C - - 0 C(C)(C)(H)(H) c4 C - - 0 C(C)(H)(H)(H) c4 C - - 0 C(H)(H)(H)(H) c4 C - - 0 C(~*)(~*)(~*)(~*) h1 H - - 0 H(C) h1 H - - 0 H(~C) ITEM END # RULES # Increment section ITEM INCREMENT # type1 type2 delta12 delta21 c4* c4* 0 0 ITEM END # INCREMENT # Stream ITEM STREAM # 138, 140 RESI METH 0 ! CH4, methane GROUP ! ATOM C1 c4 -0.24 ! H11 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H12--C1--H14 ATOM H13 h1 0.06 ! | ATOM H14 h1 0.06 ! H13 CONECT C1 H11 H12 H13 H14 # 135, 140 RESI ETHA 0 ! C2H6, ethane GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4 -0.18 ! | ATOM H21 h1 0.06 ! H23 ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 C2 H11 H12 H13 CONECT C2 H21 H22 H23 # RESI CPRO 0 ! C3H6, cyclopropane GROUP ! ATOM C1 c4 -0.12 ! ATOM H11 h1 0.06 ! ATOM H12 h1 0.06 ! GROUP ! ATOM C2 c4 -0.12 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! GROUP ! ATOM C3 c4 -0.12 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! CONECT C1 ^3C2 H11 H12 CONECT C2 ^3C3 H21 H22 CONECT C3 ^3C1 H31 H32 ITEM END # STREAM ######################################################################### # # # Alkenes # # # ######################################################################### # Stream ITEM STREAM # 142-143 RESI ETHE 0 ! C2H4, ethylene GROUP ! ATOM C1 c3= -0.23 ! H11 H12 ATOM H11 h1= 0.115 ! \ / ATOM H12 h1= 0.115 ! C1 GROUP ! || ATOM C2 c3= -0.23 ! C2 ATOM H21 h1= 0.115 ! / \ ATOM H22 h1= 0.115 ! H21 H22 CONECT C1 =C2 H11 H12 CONECT C2 H21 H22 # 142, 144 RESI PROE 0 ! C3H6, propylene GROUP ! ATOM C1 c3= -0.23 ! H11 H12 ATOM H11 h1= 0.115 ! \ / ATOM H12 h1= 0.115 ! C1 GROUP ! || ATOM C2 c3= -0.115 ! H21--C2 ATOM H21 h1= 0.115 ! | GROUP ! H31--C3--H33 ATOM C3 c4 -0.18 ! | ATOM H31 h1 0.06 ! H32 ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 =C2 H11 H12 CONECT C2 C3 H21 CONECT C3 H31 H32 H33 ITEM END # STREAM ######################################################################### # # # Aromatics # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c3a C - - 0 ^6c(^6:c)(^6:c)(~C) c3a C - - 0 ^6c(^6:c)(^6:c)(H) c4 C - - 0 C(^6c)(C)(C)(C) c4 C - - 0 C(^6c)(C)(C)(H) c4 C - - 0 C(^6c)(C)(H)(H) ITEM END # RULES # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* c4 c4 c4 1.3 1 0 -0.05 2 0 0.2 3 0 ITEM END # TORSION # Stream ITEM STREAM # 145-146 RESI BENZ 0 ! C6H6, benzene GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 ATOM C2 c3a -0.115 ! / \\ ATOM H2 h1a 0.115 ! H2--C2 C6--H6 GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM H6 h1a 0.115 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 H6 # 148 RESI TOLU 0 ! C7H8, toluene GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6--------C7--H73 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c4 -0.065 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM H73 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 H71 H72 H73 # 260-262 RESI DIPH 0 ! C12H10, diphenyl, biphenyl, phenylbenzene GROUP ! ATOM C1 c3a -0.115 ! H1 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C1 C12 ATOM C2 c3a -0.115 ! / \\ / \\ ATOM H2 h1a 0.115 ! H2--C2 C6--------C7 C11--H11 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C4 H5 H8 C9 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H9 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3ab 0 ! GROUP ! ATOM C7 c3ab 0 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 ^6:C8 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^6:C7 H12 # 147 RESI NAPH 0 ! C10H8, naphtalene GROUP ! ATOM C1 c3a -0.115 ! H1 H7 ATOM H1 h1a 0.115 ! | | GROUP ! C1 C7 ATOM C2 c3a -0.115 ! / \\ / \\ ATOM H2 h1a 0.115 ! H2--C2 C6 C8--H8 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5 C9--H9 ATOM H3 h1a 0.115 ! \ // \ // GROUP ! C4 C10 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H10 GROUP ! ATOM C5 c3a 0 ! GROUP ! ATOM C6 c3a 0 ! GROUP ! ATOM C7 c3a -0.115 ! ATOM H7 h1a 0.115 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 ^6:C10 CONECT C6 ^6:C7 ^6:C1 CONECT C7 ^6:C8 H7 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C5 H10 RESI FLUO 0 ! C13H10, fluorene GROUP ! ATOM C1 c3a -0.115 ! H4 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C4 C12 ATOM C2 c3a -0.115 ! / \\ / \\ ATOM H2 h1a 0.115 ! H3--C3 C5----C13 C11--H11 GROUP ! || | || | ATOM C3 c3a -0.115 ! H2--C2 C6 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C1 C7 C9 ATOM C4 c3a -0.115 ! | / \ | ATOM H4 h1a 0.115 ! H1 H81 H82 H9 GROUP ! ATOM C5 c3a 0 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c4 0.11 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM C8 c3a -0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! ATOM C13 c3a 0 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^5:C5 H4 CONECT C5 ^5:C6 CONECT C6 ^5:C1 ^5C7 CONECT C7 ^5C8 H71 H72 CONECT C8 ^6:C9 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^5:C13 H12 CONECT C13 ^5:C5 ^5:C8 ITEM END # STREAM ######################################################################### # # # Alcohols # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4 C - - 0 C(C)(C)(C)(O) c4 C - - 0 C(C)(C)(O)(H) c4 C - - 0 C(C)(O)(H)(H) c4 C - - 0 C(O)(H)(H)(H) c4o C - - 0 C(^6c)(O(H))(C)(C) c4o C - - 0 C(^6c)(O(H))(C)(H) o2h O - - 0 O(C)(H) h1o H - - 0 H(O(C)) ITEM END # RULES # Stream ITEM STREAM # 154-157 RESI MEOH 0 ! CH4O, methanol GROUP ATOM C1 c4 0.145 ! H11 ATOM H11 h1oh 0.04 ! | ATOM H12 h1oh 0.04 ! H12--C1--O--H ATOM H13 h1oh 0.04 ! | ATOM O o2h -0.683 ! H13 ATOM H h1o 0.418 ! CONECT C1 O H11 H12 H13 CONECT O H # 154-155, 157 RESI ETOH 0 ! C2H6O, ethanol GROUP ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--O--H ATOM C2 c4 0.145 ! | ATOM H21 h1 0.06 ! H22 ATOM H22 h1 0.06 ! ATOM O o2h -0.683 ! ATOM H h1o 0.418 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O H21 H22 CONECT O H # 169-170 RESI ETDO 0 ! C2H6O2, ethanediol GROUP ATOM C1 c4 0.145 ! H12 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--O1--H1 ATOM O1 o2hh -0.7 ! | ATOM H1 h1o 0.435 ! H21--C2--O2--H2 GROUP ! | ATOM C2 c4 0.145 ! H22 ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM O2 o2hh -0.7 ! ATOM H2 h1o 0.435 ! CONECT C1 C2 O1 H11 H12 CONECT O1 H1 CONECT C2 O2 H21 H22 CONECT O2 H2 # 169-170 RESI PRDO 0 ! C3H8O2, 1,2-propanediol GROUP ATOM C1 c4 0.145 ! H12 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--O1--H1 ATOM O1 o2hh -0.7 ! | ATOM H1 h1o 0.435 ! H21--C2--O2--H2 GROUP ! | ATOM C2 c4 0.205 ! H31--C3--H32 ATOM H21 h1 0.06 ! | ATOM O2 o2hh -0.7 ! H33 ATOM H2 h1o 0.435 ! GROUP ! ATOM C3 c4 -0.18 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 C2 O1 H11 H12 CONECT O1 H1 CONECT C2 C3 O2 H21 CONECT O2 H2 CONECT C3 H31 H32 H33 # 169-170 RESI BUDO 0 ! C4H10O2, 2,3-butanediol GROUP ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--O2--H2 ATOM C2 c4 0.205 ! | ATOM H21 h1 0.06 ! H31--C3--O3--H3 ATOM O2 o2hh -0.7 ! | ATOM H2 h1o 0.435 ! H41--C4--H42 GROUP ! | ATOM C3 c4 0.205 ! H43 ATOM H31 h1 0.06 ! ATOM O3 o2hh -0.7 ! ATOM H3 h1o 0.435 ! GROUP ! ATOM C4 c4 -0.18 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! CONECT C1 C2 H11 H12 H13 CONECT C2 C3 O2 H21 CONECT O2 H2 CONECT C3 C4 O3 H31 CONECT O3 H3 CONECT C4 H41 H42 H43 # 171-172 RESI PRTO 0 ! C3H8O2, 1,2,3-propanetriol GROUP ATOM C1 c4 0.145 ! H12 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--O1--H1 ATOM O1 o2ht -0.73 ! | ATOM H1 h1o 0.465 ! H21--C2--O2--H2 GROUP ! | ATOM C2 c4 0.205 ! H31--C3--O3--H3 ATOM H21 h1 0.06 ! | ATOM O2 o2ht -0.73 ! H32 ATOM H2 h1o 0.465 ! GROUP ! ATOM C3 c4 0.145 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM O3 o2ht -0.73 ! ATOM H3 h1o 0.465 ! CONECT C1 C2 O1 H11 H12 CONECT O1 H1 CONECT C2 C3 O2 H21 CONECT O2 H2 CONECT C3 O3 H31 H32 CONECT O3 H3 # 171-172 RESI BUTO 0 ! C4H10O3, 1,2,3-butanetriol GROUP ATOM C1 c4 0.145 ! H12 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--O1--H1 ATOM O1 o2ht -0.73 ! | ATOM H1 h1o 0.465 ! H21--C2--O2--H2 GROUP ! | ATOM C2 c4 0.205 ! H31--C3--O3--H3 ATOM H21 h1 0.06 ! | ATOM O2 o2ht -0.73 ! H41--C4--H42 ATOM H2 h1o 0.465 ! | GROUP ! H43 ATOM C3 c4 0.205 ! ATOM H31 h1 0.06 ! ATOM O3 o2ht -0.73 ! ATOM H3 h1o 0.465 ! GROUP ! ATOM C4 c4 -0.18 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! CONECT C1 C2 O1 H11 H12 CONECT O1 H1 CONECT C2 C3 O2 H21 CONECT O2 H2 CONECT C3 C4 O3 H31 CONECT O3 H3 CONECT C4 H41 H42 H43 # 166-168 RESI PHEN 0 ! C6H6O, phenol GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 ATOM C2 c3a -0.115 ! / \\ ATOM H2 h1a 0.115 ! H2--C2 C6--O--H GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.15 ! ATOM O o2hh -0.585 ! ATOM H h1o 0.435 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O CONECT O H # 218, 221 RESI BNMA 0 ! C7H8O, benzyl methanol, benzyl alcohol GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--O--H GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.055 ! ATOM C7 c4o 0.2 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM O o2h -0.683 ! ATOM H h1o 0.418 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 O H71 H72 CONECT O H # 219, 221 RESI BNEA 0 ! C8H8O, benzyl ethanol GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 H81 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--C8--H83 GROUP ! || | | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O H82 ATOM H3 h1a 0.115 ! \ // | GROUP ! C4 H ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.055 ! ATOM C7 c4o 0.26 ! ATOM H71 h1 0.06 ! ATOM O o2h -0.683 ! ATOM H h1o 0.418 ! GROUP ! ATOM C8 c4 -0.18 ! ATOM H81 h1 0.06 ! ATOM H82 h1 0.06 ! ATOM H83 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 C8 O H71 CONECT C8 H81 H82 H83 CONECT O H ITEM END # STREAM ######################################################################### # # # Ketones # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c3o C - - 0 C(C)(C)(=O) ITEM END # RULES # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3a c3a c4 c* 0 1 0 c* c3o c4 c* 1.454 1 0 -0.144 2 0 -0.775 3 0 ITEM END # TORSION # Stream ITEM STREAM # 280-281 RESI ACHY 0 ! C2H4O, acetaldehyde GROUP ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! C2 ATOM C2 c3o 0.47 ! / \\ ATOM H21 h1co 0 ! H21 O ATOM O o1= -0.47 ! CONECT C1 C2 H11 H12 H13 CONECT C2 =O H21 # 232 RESI BZHY 0 ! C8H8O, benzaldehyde GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7==O GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c3o 0.585 ! ATOM H71 h1co 0 ! ATOM O o1= -0.47 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 =O H71 # 233 RESI ACPH 0 ! C8H8O, acetophenone GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H81 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--C8--H83 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c3o 0.585 ! ATOM O o1= -0.47 ! GROUP ! ATOM C8 c4 -0.18 ! ATOM H81 h1 0.06 ! ATOM H82 h1 0.06 ! ATOM H83 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 C8 =O CONECT C8 H81 H82 H83 # 231 RESI BZPH 0 ! C13H10O, benzophenone GROUP ! ATOM C1 c3a -0.115 ! H1 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C1 O C12 ATOM C2 c3a -0.115 ! / \\ || / \\ ATOM H2 h1a 0.115 ! H2--C2 C6----C---C7 C11--H11 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C4 H5 H8 C9 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H9 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C c3o 0.7 ! ATOM O o1= -0.47 ! ATOM C7 c3a -0.115 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C CONECT C C7 =O CONECT C7 ^6:C8 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^6:C7 H12 ITEM END # STREAM ######################################################################### # # # Acids # # # ######################################################################### # Stream ITEM STREAM # 267-270 RESI FOAH 0 ! CH2O2, formic acid GROUP ! ATOM C1 c3oh 0.52 ! H1--O1 ATOM H11 h1 0 ! \ ATOM O1 o2ha -0.53 ! C1--H11 ATOM H1 h1o 0.45 ! // ATOM O2 o1= -0.44 ! O2 CONECT C1 O1 =O2 H11 CONECT O1 H1 # 267-270 RESI ACAH 0 ! C2H5O2, acetic acid GROUP ! ATOM C1 c3oh 0.52 ! H1--O1 H21 ATOM O1 o2ha -0.53 ! \ | ATOM H1 h1o 0.45 ! C1--C2--H23 ATOM O2 o1= -0.44 ! // | GROUP ! O2 H22 ATOM C2 c4 -0.18 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 C2 O1 =O2 CONECT O1 H1 CONECT C2 H21 H22 H23 # 470 RESI BNAH 0 ! C7H6O2, benzoic acid GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O6--H6 ATOM C2 c3a -0.115 ! / \\ / ATOM H2 h1a 0.115 ! H2--C2 C6----C7 GROUP ! || | \\ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O7 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c3oh 0.635 ! ATOM O7 o1= -0.44 ! ATOM O6 o2ha -0.53 ! ATOM H6 h1o 0.45 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 O6 =O7 CONECT O6 H6 # 271-276 RESI FOAC 0 ! CH2O2, formic acid GROUP ! ATOM C1 c3oa 0.7 ! O1 ATOM O1 o1a -0.8 ! \ ATOM O2 o1a -0.8 ! (-) C1--H11 ATOM H11 h1 -0.1 ! // ! O2 CONECT C1 :O1 :O2 H11 UNLINK c3oa o1a # 271-276 RESI ACAC -1 ! C2H5O2, acetic acid GROUP ! ATOM C1 c3oa 0.7 ! O1 H21 ATOM O1 o1a -0.8 ! \ | ATOM O2 o1a -0.8 ! (-) C1--C2--H23 ATOM C2 c4 -0.28 ! // | ATOM H21 h1 0.06 ! O2 H22 ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 C2 :O1 :O2 CONECT C2 H21 H22 H23 UNLINK c3oa o1a # 470 RESI BNAC -1 ! C7H6O2, benzoic acid GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O6 ATOM C2 c3a -0.115 ! / \\ / ATOM H2 h1a 0.115 ! H2--C2 C6----C7 (-) GROUP ! || | \\ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O7 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c3oa 0.715 ! ATOM O7 o1a -0.8 ! ATOM O6 o1a -0.8 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 :O6 :O7 UNLINK c3oa o1a ITEM END # STREAM ######################################################################### # # # Esters # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule o2s O - - 0 O(C(=O)(~C))(~C) h1co H BZUR H81 0 H(C(O(C(=O)(*)))(H)(H)) h1co H EACE H31 0 H(C(C)(O(C(=O)(*)))(H)) ITEM END # RULES # Angles ITEM ANGLE # type1 type2 type3 k theta0 c3a* c4 c4 63 114 c3o* o2* c3o* 70 106.5 c3o* c3a* c4 70 119.7 c3a* c3a* c3o* 85 120 c3o* c3an h1 35 126.8 ITEM END # ANGLE # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3a* c3a* c4 c4 0 1 0 c3a* c3a* c4 h1 -0.372 3 0 c3a* c3o* o2* c3o* 7.25 2 0 c3a* c4 c4 h1 0.462 3 0 c3o* c3a* c3a* c4 0.2 2 0 c3o* c3a* c3a* h1 0.2 2 0 c3o* c3a* c4 c4 0 1 0 c3o* c3a* c4 h1 -0.372 3 0 c3o* o2* c3o* c4 1.5 1 0 5 2 0 c3o* o2* c3o* o1= 5 2 0 h1 c3a* c3o* o1= 0 1 0 h1 c3a* c3o* o2* 2.1 2 0 ITEM END # TORSION # Stream ITEM STREAM # 465-469 RESI MACE 0 ! C3H6O2, methyl acetate GROUP ! ATOM C1 c4 -0.18 ! H11 O2 H31 ATOM H11 h1 0.06 ! | || | ATOM H12 h1 0.06 ! H13--C1--C2--O1--C3--H33 ATOM H13 h1 0.06 ! | | GROUP ! H12 H32 ATOM C2 c3oe 0.51 ! ATOM O2 o1= -0.43 ! ATOM O1 o2s -0.33 ! ATOM C3 c4oe 0.16 ! ATOM H31 h1co 0.03 ! ATOM H32 h1co 0.03 ! ATOM H33 h1co 0.03 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O1 =O2 CONECT O1 C3 CONECT C3 H31 H32 H33 # 465-469 RESI EACE 0 ! C4H8O2, ethyl acetate GROUP ! ATOM C1 c4 -0.18 ! H11 O2 H31 H41 ATOM H11 h1 0.06 ! | || | | ATOM H12 h1 0.06 ! H13--C1--C2--O1--C3--C4--H43 ATOM H13 h1 0.06 ! | | | GROUP ! H12 H32 H42 ATOM C2 c3oe 0.51 ! ATOM O2 o1= -0.43 ! ATOM O1 o2s -0.33 ! ATOM C3 c4oe 0.19 ! ATOM H31 h1co 0.03 ! ATOM H32 h1co 0.03 ! GROUP ! ATOM C4 c4 -0.18 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O1 =O2 CONECT O1 C3 CONECT C3 C4 H31 H32 CONECT C4 H41 H42 H43 # 465-466, 472-473 RESI PACE 0 ! C8H8O2, phenyl acetate GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O7 H81 ATOM C2 c3a -0.115 ! / \\ || | ATOM H2 h1a 0.115 ! H2--C2 C6--O6--C7--C8--H83 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.135 ! ATOM O6 o2s -0.215 ! ATOM C7 c3oe 0.51 ! ATOM O7 o1= -0.43 ! GROUP ! ATOM C8 c4 -0.18 ! ATOM H81 h1 0.06 ! ATOM H82 h1 0.06 ! ATOM H83 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O6 CONECT O6 C7 CONECT C7 C8 =O7 CONECT C8 H81 H82 H83 # 466, 467, 471-472 RESI MBEN 0 ! C8H8O2, methyl benzoate GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O7 H81 ATOM C2 c3a -0.115 ! / \\ || | ATOM H2 h1a 0.115 ! H2--C2 C6--C7--O6--C8--H83 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C7 c3oe 0.625 ! ATOM O7 o1= -0.43 ! ATOM O6 o2s -0.33 ! ATOM C8 c4oe 0.16 ! ATOM H81 h1co 0.03 ! ATOM H82 h1co 0.03 ! ATOM H83 h1co 0.03 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 O6 =O7 CONECT O6 C8 CONECT C8 H81 H82 H83 # 465-469 RESI HMAN 0 ! C4H4O3, hydrogenated maleic anhydride GROUP ! ATOM O1 o2e -0.16 ! O1 ATOM C2 c3oe 0.51 ! / \ ATOM O2 o1= -0.43 ! O2==C2 C5==O5 ATOM C5 c3oe 0.51 ! | | ATOM O5 o1= -0.43 ! H31--C3--C4--H41 GROUP ! | | ATOM C3 c4 -0.12 ! H32 H42 ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! GROUP ! ATOM C4 c4 -0.12 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5C4 H31 H32 CONECT C4 ^5C5 H41 H42 CONECT C5 ^5O1 =O5 # 135-140, 465-469 RESI HMMA 0 ! C5H5O3, hydrogenated 3-methyl maleic anhydride GROUP ! ATOM O1 o2e -0.16 ! O1 ATOM C2 c3oe 0.51 ! / \ ATOM O2 o1= -0.43 ! O2==C2 C5==O5 ATOM C5 c3oe 0.51 ! | | ATOM O5 o1= -0.43 ! H3--C3--C4--H41 GROUP ! | | ATOM C3 c4 -0.06 ! | H42 ATOM H3 h1 0.06 ! | GROUP ! H61--C6--H63 ATOM C4 c4 -0.12 ! | ATOM H41 h1 0.06 ! H62 ATOM H42 h1 0.06 ! GROUP ! ATOM C6 c4 -0.18 ! ATOM H61 h1 0.06 ! ATOM H62 h1 0.06 ! ATOM H63 h1 0.06 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5C4 C6 H3 CONECT C4 ^5C5 H41 H42 CONECT C5 ^5O1 =O5 CONECT C6 H61 H62 H63 # 145-146, 465-469 RESI HPMA 0 ! C10H8O3, hydrogenated 3-phenyl maleic anhydride GROUP ! ATOM O1 o2e -0.16 ! O1 ATOM C2 c3oe 0.51 ! / \ ATOM O2 o1= -0.43 ! O2==C2 C5==O5 ATOM C5 c3oe 0.51 ! | | ATOM O5 o1= -0.43 ! H3--C3--C4--H42 GROUP ! | | ATOM C3 c4 0.055 ! C6 H41 ATOM H3 h1 0.06 ! / \\ ATOM C6 c3a -0.115 ! H7--C7 C11--H11 GROUP ! || | ATOM C4 c4 -0.12 ! H8--C8 C10--H10 ATOM H41 h1 0.06 ! \ // ATOM H42 h1 0.06 ! C9 GROUP ! | ATOM C7 c3a -0.115 ! H9 ATOM H7 h1a 0.115 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5C4 C6 H3 CONECT C4 ^5C5 H41 H42 CONECT C5 ^5O1 =O5 CONECT C6 ^6:C7 CONECT C7 ^6:C8 H7 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C6 H11 # 2593-2601 RESI MAAN 0 ! C4H2O3, maleic anhydride GROUP ! ATOM O1 o2e -0.28 ! O1 ATOM C2 c3oan 0.465 ! / \ ATOM O2 o1= -0.325 ! O2==C2 C5==O5 ATOM C5 c3oan 0.465 ! | | ATOM O5 o1= -0.325 ! H3--C3==C4--H4 GROUP ! ATOM C3 c3an -0.2 ! ATOM H3 h1= 0.2 ! GROUP ! ATOM C4 c3an -0.2 ! ATOM H4 h1= 0.2 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5=C4 H3 CONECT C4 ^5C5 H4 CONECT C5 ^5O1 =O5 # 2593-2601 RESI MMAN 0 ! C5H4O3, 3-methyl maleic anhydride GROUP ! ATOM O1 o2e -0.28 ! O1 ATOM C2 c3oan 0.465 ! / \ ATOM O2 o1= -0.325 ! O2==C2 C5==O5 ATOM C5 c3oan 0.465 ! | | ATOM O5 o1= -0.325 ! C3==C4--H4 GROUP ! | ATOM C3 c3an -0.1 ! H61--C6--H63 ATOM C6 c4 -0.08 ! | ATOM H61 h1 0.06 ! H62 ATOM H62 h1 0.06 ! ATOM H63 h1 0.06 ! GROUP ! ATOM C4 c3an -0.2 ! ATOM H4 h1= 0.2 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5=C4 C6 CONECT C4 ^5C5 H4 CONECT C5 ^5O1 =O5 CONECT C6 H61 H62 H63 # 2593-2601 RESI PMAN 0 ! C10H6O3, 3-phenyl maleic anhydride GROUP ! ATOM O1 o2e -0.28 ! O1 ATOM C2 c3oan 0.465 ! / \ ATOM O2 o1= -0.325 ! O2==C2 C5==O5 ATOM C5 c3oan 0.465 ! | | ATOM O5 o1= -0.325 ! C3==C4--H4 GROUP ! | ATOM C3 c3an -0.1 ! C6 ATOM C6 c3ab 0.1 ! / \\ GROUP ! H7--C7 C11--H11 ATOM C4 c3an -0.2 ! || | ATOM H4 h1= 0.2 ! H8--C8 C10--H10 GROUP ! \ // ATOM C7 c3a -0.115 ! C9 ATOM H7 h1a 0.115 ! | GROUP ! H9 ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! CONECT O1 ^5C2 CONECT C2 ^5C3 =O2 CONECT C3 ^5=C4 C6 CONECT C4 ^5C5 H4 CONECT C5 ^5O1 =O5 CONECT C6 ^6:C7 CONECT C7 ^6:C8 H7 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C6 H11 ITEM END # STREAM ######################################################################### # # # Ethers # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4oe C - - 0 C(O(C))(~C)(~C)(~C) c4oe C - - 0 C(O(C))(~C)(~C)(H) c4oe C - - 0 C(O(C))(~C)(O)(H) c4oe C - - 0 C(O(C))(~C)(H)(H) c4oe C - - 0 C(O(C))(H)(H)(H) o2e O - - 0 O(~C)(~C) ITEM END # RULES # Angles ITEM ANGLE # type1 type2 type3 k theta0 c3a* o2* c3a* 70 106.5 c4* c3a5n c3a5n 70 125 # furan c3a* c3o h1 35 115 c3a* c3o o2 81 111.4 c3* c3a* o2 70 121.6 ITEM END # ANGLE # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* c4 o2* c4 0.65 1 0 -0.25 2 0 0.67 3 0 c3a* c3a* o2* c3a* 7.25 2 0 c3a51 o2* c3a51 * 7.25 2 0 * c3a51 c3a5n * 7.25 2 0 * c3a5n c3a5n * 2.17 2 0 # furan c3a* c3a* c3o h1 0.2 2 0 c3a* c3a* c3o o2 2.1 2 0 c3a* c3a* c3o o1= 2.1 2 0 o2 c3a* c3o o1= 2.1 2 0 o2 c3a* c3o h1 2.1 2 0 ITEM END # TORSION # Stream ITEM STREAM # 180-181 RESI DMET 0 ! C2H6O, dimethyl ether GROUP ATOM C1 c4oe 0.11 ! H11 H21 ATOM H11 h1 0.03 ! | | ATOM H12 h1 0.03 ! H12--C1--O--C2--H22 ATOM H13 h1 0.03 ! | | ATOM O o2e -0.4 ! H13 H23 ATOM C2 c4oe 0.11 ! ATOM H21 h1 0.03 ! ATOM H22 h1 0.03 ! ATOM H23 h1 0.03 ! CONECT C1 O H11 H12 H13 CONECT O C2 CONECT C2 H21 H22 H23 # 180-182 RESI EMET 0 ! C2H6O, ethyl-methyl ether GROUP ATOM C1 c4oe 0.11 ! H11 H21 H31 ATOM H11 h1 0.03 ! | | | ATOM H12 h1 0.03 ! H12--C1--O--C2--C3--H33 ATOM H13 h1 0.03 ! | | | ATOM O o2e -0.4 ! H13 H23 H32 ATOM C2 c4oe 0.14 ! ATOM H21 h1 0.03 ! ATOM H22 h1 0.03 ! GROUP ! ATOM C3 c4 -0.18 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 O H11 H12 H13 CONECT O C2 CONECT C2 C3 H21 H22 CONECT C3 H31 H32 H33 # 179 RESI ANIS 0 ! C7H8O, anisole GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6-----O--C7--H73 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.085 ! ATOM O o2e -0.285 ! ATOM C7 c4oe 0.11 ! ATOM H71 h1 0.03 ! ATOM H72 h1 0.03 ! ATOM H73 h1 0.03 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O CONECT O C7 CONECT C7 H71 H72 H73 # 221, 922 RESI BNME 0 ! C7H8O, benzyl methyl ether GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 H81 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--O--C8--H83 GROUP ! || | | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.055 ! ATOM C7 c4oe 0.195 ! ATOM H71 h1 0.03 ! ATOM H72 h1 0.03 ! ATOM O o2e -0.4 ! ATOM C8 c4oe 0.11 ! ATOM H81 h1 0.03 ! ATOM H82 h1 0.03 ! ATOM H83 h1 0.03 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 O H71 H72 CONECT O C8 CONECT C8 H81 H82 H83 # 177 RESI DPHE 0 ! C12H10O, diphenyl ether GROUP ! ATOM C1 c3a -0.115 ! H1 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C1 C12 ATOM C2 c3a -0.115 ! / \\ / \\ ATOM H2 h1a 0.115 ! H2--C2 C6----O---C7 C11--H11 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C4 H5 H8 C9 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H9 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.085 ! ATOM O o2e -0.17 ! ATOM C7 c3a 0.085 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O CONECT O C7 CONECT C7 ^6:C8 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^6:C7 H12 # Epoxy addition RESI EOXI 0 ! C3H6, cyclopropane GROUP ! ATOM O1 o2e -0.4 ! H12 H22 ATOM C1 c4oe 0.14 ! \ / ATOM H11 h1 0.03 ! H11--C1--C2--H12 ATOM H12 h1 0.03 ! \ / ATOM C2 c4oe 0.14 ! O1 ATOM H21 h1 0.03 ! ATOM H22 h1 0.03 ! CONECT O1 ^3C1 CONECT C1 ^3C2 H11 H12 CONECT C2 ^3O1 H21 H22 # 566-570 RESI FURA 0 ! C4H4O, furan GROUP ! ATOM O1 o2e -0.19 ! O1 ATOM C2 c3a5f -0.019 ! / \ ATOM H2 h1a 0.142 ! H2--C2 C5--H5 ATOM C3 c3a5o -0.154 ! || || ATOM H3 h1a 0.126 ! H3--C3----C4--H4 ATOM C4 c3a5o -0.154 ! ATOM H4 h1a 0.126 ! ATOM C5 c3a5f -0.019 ! ATOM H5 h1a 0.142 ! CONECT O1 ^5:C2 CONECT C2 ^5:C3 H2 CONECT C3 ^5:C4 H3 CONECT C4 ^5:C5 H4 CONECT C5 ^5:O1 H5 # 566-570 RESI 2MFU 0 ! C4H4O, 2-methyl-furan GROUP ! ATOM O1 o2e -0.19 ! O1 H61 ATOM C2 c3a5f -0.019 ! / \ | ATOM H2 h1a 0.142 ! H2--C2 C5------C6--H62 ATOM C3 c3a5o -0.154 ! || || | ATOM H3 h1a 0.126 ! H3--C3----C4--H4 H63 ATOM C4 c3a5o -0.154 ! ATOM H4 h1a 0.126 ! ATOM C5 c3a5f -0.019 ! ATOM C6 c4 -0.038 ! ATOM H61 h1 0.06 ! ATOM H62 h1 0.06 ! ATOM H63 h1 0.06 ! CONECT O1 ^5:C2 CONECT C2 ^5:C3 H2 CONECT C3 ^5:C4 H3 CONECT C4 ^5:C5 H4 CONECT C5 ^5:O1 C6 CONECT C6 H61 H62 H63 # 566-570 RESI 3MFU 0 ! C4H4O, 3-methyl-furan GROUP ! ATOM O1 o2e -0.19 ! O1 ATOM C2 c3a5f -0.019 ! / \ ATOM H2 h1a 0.142 ! H2--C2 C5--H5 ATOM C3 c3a5o -0.154 ! || || ATOM C4 c3a5o -0.154 ! C3----C4--H4 ATOM H4 h1a 0.126 ! | ATOM C5 c3a5f -0.019 ! H61--C6--H63 ATOM H5 h1a 0.142 ! | ATOM C6 c4 -0.054 ! H62 ATOM H61 h1 0.06 ! ATOM H62 h1 0.06 ! ATOM H63 h1 0.06 ! CONECT O1 ^5:C2 CONECT C2 ^5:C3 H2 CONECT C3 ^5:C4 C6 CONECT C4 ^5:C5 H4 CONECT C5 ^5:O1 H5 CONECT C6 H61 H62 H63 # 566-570 RESI FU2O 0 ! C4H4O, furan-2-carbaldehyde, furfural GROUP ! ATOM O1 o2e -0.19 ! O1 H6 ATOM C2 c3a5f -0.019 ! / \ | ATOM H2 h1a 0.142 ! H2--C2 C5------C6==O6 ATOM C3 c3a5o -0.154 ! || || ATOM H3 h1a 0.126 ! H3--C3----C4--H4 ATOM C4 c3a5o -0.154 ! ATOM H4 h1a 0.126 ! ATOM C5 c3a5f -0.019 ! ATOM C6 c3o 0.612 ! ATOM H6 h1co 0 ! ATOM O6 o1= -0.47 ! CONECT O1 ^5:C2 CONECT C2 ^5:C3 H2 CONECT C3 ^5:C4 H3 CONECT C4 ^5:C5 H4 CONECT C5 ^5:O1 C6 CONECT C6 =O6 H6 # 566-570 RESI FU3O 0 ! C4H4O, furan-3-carbaldehyde GROUP ! ATOM O1 o2e -0.19 ! O1 ATOM C2 c3a5f -0.019 ! / \ ATOM H2 h1a 0.142 ! H2--C2 C5--H5 ATOM C3 c3a5o -0.154 ! || || ATOM C4 c3a5o -0.154 ! C3----C4--H4 ATOM H4 h1a 0.126 ! | ATOM C5 c3a5f -0.019 ! H6--C6 ATOM H5 h1a 0.142 ! || ATOM C6 c3o 0.596 ! O6 ATOM H6 h1co 0 ! ATOM O6 o1= -0.47 ! CONECT O1 ^5:C2 CONECT C2 ^5:C3 H2 CONECT C3 ^5:C4 C6 CONECT C4 ^5:C5 H4 CONECT C5 ^5:O1 H5 CONECT C6 =O6 H6 ITEM END # STREAM ######################################################################### # # # Hemiacetal ethers # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4o2 C - - 0 C(C)(O)(O)(H) c4o2 C - - 0 C(C)(O)(O)(C) ITEM END # RULES # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c4 c4* o2e c4* 0.65 1 0 -0.25 2 0 0.67 3 0 c4 c4* o2h h1o -0.356 1 0 -0.174 2 0 0.492 3 0 h1 c4* c4* h1 0.3 3 0 h1 c4 c4* o2h 0.468 3 0 h1 c4* o2h h1o 0.3524 3 0 ITEM END # TORSION # Stream ITEM STREAM # 191-192 RESI MMAE 0 ! C2H6O2, methyl-methanol ether GROUP ATOM C1 c4oe 0.11 ! H11 H21 ATOM H11 h1 0.03 ! | | ATOM H12 h1 0.03 ! H12--C1--O--C2--H22 ATOM H13 h1 0.03 ! | | ATOM O o2e -0.4 ! H13 O2 ATOM C2 c4o2 0.265 ! | ATOM H21 h1 0.1 ! H2 ATOM H22 h1 0.1 ! ATOM O2 o2hh -0.7 ! ATOM H2 h1o 0.435 ! CONECT C1 O H11 H12 H13 CONECT O C2 CONECT C2 O2 H21 H22 CONECT O2 H2 # 195-196 RESI MEAO 0 ! C3H8O2, methyl-ethanol ether GROUP ATOM C1 c4oe 0.11 ! H11 H21 H31 ATOM H11 h1 0.03 ! | | | ATOM H12 h1 0.03 ! H12--C1--O--C2--C3--H33 ATOM H13 h1 0.03 ! | | | ATOM O o2e -0.4 ! H13 O2 H32 ATOM C2 c4o2 0.365 ! | ATOM H21 h1 0.1 ! H2 ATOM O2 o2hh -0.7 ! ATOM H2 h1o 0.435 ! GROUP ! ATOM C3 c4 -0.18 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 O H11 H12 H13 CONECT O C2 CONECT C2 O2 C3 H21 CONECT O2 H2 CONECT C3 H31 H32 H33 ITEM END # STREAM ######################################################################### # # # Acetal ethers # # # ######################################################################### # Stream ITEM STREAM # 189-190 RESI DMME 0 ! C3H8O2, dimethoxymethane GROUP ATOM C1 c4oe 0.11 ! H11 H21 ATOM H11 h1 0.03 ! | | ATOM H12 h1 0.03 ! H12--C1--O1--C2--H22 ATOM H13 h1 0.03 ! | | ATOM O1 o2e -0.4 ! H13 O2 ATOM C2 c4o2 0.2 ! | ATOM H21 h1 0.1 ! H31--C3--H33 ATOM H22 h1 0.1 ! | ATOM O2 o2e -0.4 ! H32 ATOM C3 c4oe 0.11 ! ATOM H31 h1 0.03 ! ATOM H32 h1 0.03 ! ATOM H33 h1 0.03 ! CONECT C1 O1 H11 H12 H13 CONECT O1 C2 CONECT C2 O2 H21 H22 CONECT O2 C3 CONECT C3 H31 H32 H33 # 193-194 RESI DMEE 0 ! C4H10O2, 1,1-dimethoxyethane GROUP ATOM C1 c4oe 0.11 ! H11 H21 H41 ATOM H11 h1 0.03 ! | | | ATOM H12 h1 0.03 ! H12--C1--O1--C2--C4--H43 ATOM H13 h1 0.03 ! | | | ATOM O1 o2e -0.4 ! H13 O2 H42 ATOM C2 c4o2 0.3 ! | ATOM H21 h1 0.1 ! H31--C3--H33 ATOM O2 o2e -0.4 ! | ATOM C3 c4oe 0.11 ! H32 ATOM H31 h1 0.03 ! ATOM H32 h1 0.03 ! ATOM H33 h1 0.03 ! GROUP ! ATOM C4 c4 -0.18 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! GROUP ! CONECT C1 O1 H11 H12 H13 CONECT O1 C2 CONECT C2 O2 C4 H21 CONECT O2 C3 CONECT C3 H31 H32 H33 CONECT C4 H41 H42 H43 ITEM END # STREAM ######################################################################### # # # Nitriles # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4nn C - - 0 C(C(#N))(~C)(~C)(~C) c4nn C - - 0 C(C(#N))(~C)(~C)(H) c4nn C - - 0 C(C(#N))(~C)(H)(H) h1cn H - - 0 H(C(C(#N))(~C)(~C)) h1cn H - - 0 H(C(C(#N))(~C)(H)) ITEM END # RULES # Stream ITEM STREAM # 753-759 RESI ACNI 0 ! C2H3N, acetonitrile GROUP ATOM C1 c4nn -0.08 ! H13 ATOM H11 h1cn 0.06 ! | ATOM H12 h1cn 0.06 ! H11--C1--H12 ATOM H13 h1cn 0.06 ! | GROUP ! C2 ATOM C2 c2n 0.46 ! # ATOM N n1 -0.56 ! N CONECT C1 C2 H11 H12 H13 CONECT C2 #N UNLINK c2n n1 UNLINK c2n c4nn UNLINK c4nn h1cn # 260-262 RESI BZNI 0 ! C7H5N, benzonitrile GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 ATOM C2 c3a -0.115 ! / \\ ATOM H2 h1a 0.115 ! H2--C2 C6--C##N GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.035 ! ATOM C c2na 0.395 ! ATOM N n1 -0.43 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C CONECT C #N # 753-759 ITEM END # STREAM ######################################################################### # # # Amines # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4n C - - 0 C(N)(~C)(C)(C) c4n C - - 0 C(N)(~C)(C)(H) c4n C - - 0 C(N)(~C)(H)(H) h1n H - - 0 H(N(C(~C)(C)(C))(C)) h1n H - - 0 H(N(C(~C)(C)(H))(C)) h1n H - - 0 H(N(C(~C)(H)(H))(C)) h1n H - - 0 H(N(C(~C)(C)(C))(^6c)) h1n H - - 0 H(N(C(~C)(C)(H))(^6c)) h1n H - - 0 H(N(C(~C)(H)(H))(^6c)) h1n H - - 0 H(N(C(~C)(C)(C))(H)) h1n H - - 0 H(N(C(~C)(C)(H))(H)) h1n H - - 0 H(N(C(~C)(H)(H))(H)) n3 N - - 0 N(~C)(C)(C) n3h N - - 0 N(~C)(C)(H) n3h2 N - - 0 N(~C)(H)(H) ITEM END # RULES # Angle ITEM ANGLE # type1 type2 type3 k theta0 n3* c4 n3* 70 109.5 ITEM END # ANGLE # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* c4 n3 c* 0.416 1 0 -0.128 2 0 0.695 3 0 c* c4 n3 h1n -0.19 1 0 -0.417 2 0 0.418 3 0 c3* n3* c4 n3* 0.462 2 0 h1n* n3ch c3a n3ch 3.9 2 0 h1n* n3ch c4 h1 0 1 0 ITEM END # TORSION # Stream ITEM STREAM # 900, 903, 909 RESI MEAN 0 ! CH5N, methylamine GROUP ! ATOM N n3h2 -0.9 ! HN1 H11 ATOM HN1 h1n 0.36 ! \ | ATOM HN2 h1n 0.36 ! N--C1--H13 ATOM C1 c4n 0 ! / | ATOM H11 h1cn 0.06 ! HN2 H12 ATOM H12 h1cn 0.06 ! ATOM H13 h1cn 0.06 ! CONECT N C1 HN1 HN2 CONECT C1 H11 H12 H13 # 901, 906, 909 RESI ETAN 0 ! C2H7N, ethylamine GROUP ! ATOM N n3h2 -0.9 ! HN1 H11 H21 ATOM HN1 h1n 0.36 ! \ | | ATOM HN2 h1n 0.36 ! N--C1--C2--H23 ATOM C1 c4 0.06 ! / | | ATOM H11 h1cn 0.06 ! HN2 H12 H22 ATOM H12 h1cn 0.06 ! ATOM C2 c4 -0.18 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT N C1 HN1 HN2 CONECT C1 C2 H11 H12 CONECT C2 H21 H22 H23 # 901, 904, 910 RESI DMAN 0 ! C2H7N, dimethylamine GROUP ! ATOM N n3h -0.78 ! H11 HN H21 ATOM HN h1n 0.38 ! | | | ATOM C1 c4n 0.02 ! H13--C1--N--C2--H23 ATOM H11 h1cn 0.06 ! | | ATOM H12 h1cn 0.06 ! H12 H22 ATOM H13 h1cn 0.06 ! ATOM C2 c4n 0.02 ! ATOM H21 h1cn 0.06 ! ATOM H22 h1cn 0.06 ! ATOM H23 h1cn 0.06 ! CONECT N C1 C2 HN CONECT C1 H11 H12 H13 CONECT C2 H21 H22 H23 # 901, 904, 910 RESI TMAN 0 ! CH5N, trimethylamine GROUP ! ATOM N n3 -0.63 ! H11 H21 ATOM C1 c4n 0.03 ! | | ATOM H11 h1cn 0.06 ! H13--C1--N--C2--H23 ATOM H12 h1cn 0.06 ! | | | ATOM H13 h1cn 0.06 ! H12 | H22 ATOM C2 c4n 0.03 ! | ATOM H21 h1cn 0.06 ! H31--C3--H32 ATOM H22 h1cn 0.06 ! | ATOM H23 h1cn 0.06 ! H33 ATOM C3 c4n 0.03 ! ATOM H31 h1cn 0.06 ! ATOM H32 h1cn 0.06 ! ATOM H33 h1cn 0.06 ! CONECT N C1 C2 C3 CONECT C1 H11 H12 H13 CONECT C2 H21 H22 H23 CONECT C3 H31 H32 H33 # 900, 916 RESI ANIL 0 ! C6H7N, aniline GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 HN1 ATOM C2 c3a -0.115 ! / \\ / ATOM H2 h1a 0.115 ! H2--C2 C6----N GROUP ! || | \ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 HN2 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.18 ! ATOM N n3h2 -0.9 ! ATOM HN1 h1n 0.36 ! ATOM HN2 h1n 0.36 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 N CONECT N HN1 HN2 # 901, 917 RESI MEAL 0 ! C7H9N, methylaniline GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 HN H71 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6--N---C7--H73 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.2 ! ATOM N n3h -0.78 ! ATOM HN h1n 0.38 ! ATOM C7 c4n 0.02 ! ATOM H71 h1cn 0.06 ! ATOM H72 h1cn 0.06 ! ATOM H73 h1cn 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 N CONECT N C7 HN CONECT C7 H71 H72 H73 # 902, 918 RESI DMAL 0 ! C7H9N, methylaniline GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6------N---C7--H73 GROUP ! || | | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 | H72 ATOM H3 h1a 0.115 ! \ // | GROUP ! C4 H81--C8--H82 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H83 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.21 ! ATOM N n3 -0.63 ! ATOM C7 c4n 0.03 ! ATOM H71 h1cn 0.06 ! ATOM H72 h1cn 0.06 ! ATOM H73 h1cn 0.06 ! ATOM C8 c4n 0.03 ! ATOM H81 h1cn 0.06 ! ATOM H82 h1cn 0.06 ! ATOM H83 h1cn 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 N CONECT N C7 C8 CONECT C7 H71 H72 H73 CONECT C8 H81 H82 H83 # 221, 903, 919 RESI BNAM 0 ! C7H9N, benzylamine GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 HN1 ATOM C2 c3a -0.115 ! / \\ | / ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--N GROUP ! || | | \ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 HN2 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.055 ! ATOM C7 c4n 0.115 ! ATOM H71 h1cn 0.06 ! ATOM H72 h1cn 0.06 ! ATOM N n3h2 -0.9 ! ATOM HN1 h1n 0.36 ! ATOM HN2 h1n 0.36 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 N H71 H72 CONECT N HN1 HN2 # 300-302 RESI GUAN 1 ! CH6N3, guanidinium GROUP ! ATOM C1 c3a+ 0.64 ! H11 H21 ATOM N1 n3ch2 -0.8 ! \ / ATOM H11 h1n3 0.46 ! N1 N2 ATOM H12 h1n3 0.46 ! / \ / \ ATOM N2 n3ch2 -0.8 ! H12 C1 H22 ATOM H21 h1n3 0.46 ! (+)| ATOM H22 h1n3 0.46 ! N3 ATOM N3 n3ch2 -0.8 ! / \ ATOM H31 h1n3 0.46 ! H31 H32 ATOM H32 h1n3 0.46 ! CONECT C1 :N1 :N2 :N3 CONECT N1 H11 H12 CONECT N2 H21 H22 CONECT N3 H31 H32 UNLINK c3a+ n3ch2 # 302-306 RESI TMGU 1 ! C3H12N3, trimethylguanidinium GROUP ! ATOM C c3a+ 0.64 ! H11 HN1 HN2 H21 ATOM N1 n3ch -0.7 ! | | (+) | | ATOM HN1 h1n3 0.44 ! H13--C1--N1==C--N2--C2--H23 ATOM C1 c4n 0.2 ! | | | ATOM H11 h1 0.06 ! H12 HN3--N3 H22 ATOM H12 h1 0.06 ! | ATOM H13 h1 0.06 ! H31--C3--H32 ATOM N2 n3ch -0.7 ! | ATOM HN2 h1n3 0.44 ! H33 ATOM C2 c4n 0.2 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! ATOM N3 n3ch -0.7 ! ATOM HN3 h1n3 0.44 ! ATOM C3 c4n 0.2 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C :N1 :N2 :N3 CONECT N1 C1 HN1 CONECT C1 H11 H12 H13 CONECT N2 C2 HN2 CONECT C2 H21 H22 H23 CONECT N3 C3 HN3 CONECT C3 H31 H32 H33 UNLINK c3a+ n3ch ITEM END # STREAM ######################################################################### # # # Ammonium # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4n C - - 0 C(^5n)(~C)(C)(C) c4n C - - 0 C(^5n)(~C)(C)(H) c4n C - - 0 C(^5n)(~C)(H)(H) c4 C - - 0 C([N+])(C)(C)(C) c4 C - - 0 C([N+])(C)(C)(H) c4 C - - 0 C([N+])(C)(H)(H) h1r C - - 0 H(C(^5n)(C)(C)) h1r C - - 0 H(C(^5n)(C)(H)) n3a N - - 0 ^5n(^5:c)(^5:c)(H) n4 N - - 0 N(~*)(~*)(~*)(~*) ITEM END # RULES # Angles ITEM ANGLE # type1 type2 type3 k theta0 c4 c4 n3a* 50 109.5 # RMIM c3a* n3a* c4* 70 125.8 # RMIM c3a5* c3a5* h1a* 35 120 # RMIM ITEM END # ANGLE # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c4* c4 n4 h1n 0.3 3 0 n4 c4 c4 o* 1.711 1 0 -0.5 2 0 0.663 3 0 h1 c4 c4 n3a* 0.2 3 0 # RMIM c4 c4 c4 n3a -0.788 1 0 -0.8 2 0 0.4 3 0 # RMIM ITEM END # TORSION # Stream ITEM STREAM # 286, 289 RESI AMMO 1 ! NH4, ammonium GROUP ! ATOM N n4h4 -0.4 ! HN1 ATOM HN1 h1n4 0.35 ! (+)| ATOM HN2 h1n4 0.35 ! HN3--N--HN4 ATOM HN3 h1n4 0.35 ! | ATOM HN4 h1n4 0.35 ! HN2 CONECT N HN1 HN2 HN3 HN4 UNLINK n4h4 h1n4 # 287, 290 RESI MAMM 1 ! CH6N, methylammonium GROUP ! ATOM N n4h3 -0.3 ! HN1 H11 ATOM HN1 h1n4 0.33 ! (+)| | ATOM HN2 h1n4 0.33 ! HN3--N---C1--H13 ATOM HN3 h1n4 0.33 ! | | ATOM C1 c4 0.13 ! HN2 H12 ATOM H11 h1 0.06 ! ATOM H12 h1 0.06 ! ATOM H13 h1 0.06 ! CONECT N C1 HN1 HN2 HN3 CONECT C1 H11 H12 H13 UNLINK n4h3 h1n4 UNLINK n4h3 c4 # 297, 309, 310 RESI DAMM 1 ! C2H8N, dimethylammonium GROUP ! ATOM N n4h2 -0.2 ! H21 HN1 H11 ATOM HN1 h1n4 0.31 ! | (+)| | ATOM HN2 h1n4 0.31 ! H23--C2---N---C1--H13 ATOM C1 c4 0.11 ! | | | ATOM H11 h1 0.06 ! H22 HN2 H12 ATOM H12 h1 0.06 ! ATOM H13 h1 0.06 ! ATOM C2 c4 0.11 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT N C1 C2 HN1 HN2 CONECT C1 H11 H12 H13 CONECT C2 H21 H22 H23 UNLINK n4h2 h1n4 UNLINK n4h2 c4 # 940 RESI TAMM 1 ! C3H10N, trimethylammonium GROUP ! ATOM N n4h -0.1 ! H21 HN1 H11 ATOM HN1 h1n4 0.29 ! | (+)| | ATOM C1 c4 0.09 ! H23--C2---N---C1--H13 ATOM H11 h1 0.06 ! | | | ATOM H12 h1 0.06 ! H22 | H12 ATOM H13 h1 0.06 ! | ATOM C2 c4 0.09 ! H31--C3--H32 ATOM H21 h1 0.06 ! | ATOM H22 h1 0.06 ! H33 ATOM H23 h1 0.06 ! ATOM C3 c4 0.09 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT N C1 C2 C3 HN1 CONECT C1 H11 H12 H13 CONECT C2 H21 H22 H23 CONECT C3 H31 H32 H33 UNLINK n4h h1n4 UNLINK n4h c4 # RESI FAMM 1 ! C4H12N, tetramethylammonium GROUP ! ATOM N n4 0 ! H43 ATOM C1 c4 0.07 ! | ATOM H11 h1 0.06 ! H41--C4--H42 ATOM H12 h1 0.06 ! | ATOM H13 h1 0.06 ! H21 | H11 ATOM C2 c4 0.07 ! | (+)| | ATOM H21 h1 0.06 ! H23--C2---N---C1--H13 ATOM H22 h1 0.06 ! | | | ATOM H23 h1 0.06 ! H22 | H12 ATOM C3 c4 0.07 ! | ATOM H31 h1 0.06 ! H31--C3--H32 ATOM H32 h1 0.06 ! | ATOM H33 h1 0.06 ! H33 ATOM C4 c4 0.07 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! CONECT N C1 C2 C3 C4 CONECT C1 H11 H12 H13 CONECT C2 H21 H22 H23 CONECT C3 H31 H32 H33 CONECT C4 H41 H42 H43 UNLINK n4 c4 # J. Chem. Theory Comput. 2009, 5, 1038 RESI RMIM 1 ! C6H11N2, 1-ethyl-3-methylimidazolium GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4n -0.17 ! | ATOM H21 h1r 0.18 ! N1 ATOM H22 h1r 0.18 ! // \ ATOM N1 n3a 0.22 ! H3--C3 C6--H6 ATOM C3 c3a53 -0.09 ! | | ATOM H3 h1a 0.21 ! N2===C5--H5 ATOM N2 n3a 0.22 ! | ATOM C4 c4n -0.35 ! H41--C4--H42 ATOM H41 h1r 0.18 ! | ATOM H42 h1r 0.18 ! H43 ATOM H43 h1r 0.18 ! ATOM C5 c3a51 -0.24 ! ATOM H5 h1a 0.27 ! ATOM C6 c3a51 -0.24 ! ATOM H6 h1a 0.27 ! CONECT C1 C2 H11 H12 H13 CONECT C2 ^5N1 H21 H22 CONECT N1 ^5:C3 CONECT C3 ^5:N2 H3 CONECT N2 ^5:C5 C4 CONECT C4 H41 H42 H43 CONECT C5 ^5:C6 H5 CONECT C6 ^5:N1 H6 UNLINK c4n n3a ITEM END # STREAM ######################################################################### # # # Aromatics containing nitrogen in ring # # # ######################################################################### # stream ITEM STREAM /* # COMMENT START # needs type duplication mechanism for increments # 311-318 RESI DAP 0 ! C5H7N3, 2,6-diaminopyridine GROUP ! ATOM N1 n2a6 -0.46 ! H22 ATOM C2 c3ap 0.36 ! | ATOM N2 n3ch -0.85 ! H21--N2 H3 ATOM H21 h1n 0.37 ! \ / ATOM H22 h1n 0.37 ! C2==C3 ATOM C6 c3ap 0.36 ! / \ ATOM N6 n3ch -0.85 ! N1 C4--H4 ATOM H61 h1n 0.37 ! \\ // ATOM H62 h1n 0.37 ! C6--C5 ATOM C3 c3ap -0.15 ! / \ ATOM H3 h1a1 0.1 ! H61--N6 H5 ATOM C4 c3ap -0.04 ! | ATOM H4 h1a 0.1 ! H62 ATOM C5 c3ap -0.15 ! ATOM H5 h1a 0.1 ! CONECT N1 ^6:C2 CONECT C2 ^6:C3 N2 CONECT N2 H21 H22 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:N1 N6 CONECT N6 H61 H62 */ # COMMENT END ITEM END # STREAM ######################################################################### # # # Nucleotides # # # ######################################################################### # Stream ITEM STREAM /* # COMMENT START # needs type duplication mechanism for increments # 320-330 RESI URAC 0 ! C4H4N2O2, uracil GROUP ! ATOM N1 n3ah1 -0.6 ! O2 H3 ATOM H1 h1n 0.41 ! \\ / ATOM C2 c3o 0.5 ! C2--N3 ATOM O2 o1= -0.4 ! / \ ATOM N3 n3ah1 -0.51 ! H1--N1 C4==O4 ATOM H3 h1n 0.36 ! \ / ATOM C4 c3o 0.45 ! C6==C5 ATOM O4 o1= -0.42 ! / \ ATOM C5 c3ao -0.07 ! H6 H5 ATOM H5 h1a4 0.1 ! ATOM C6 c3ao 0.08 ! ATOM H6 h1a4 0.1 ! CONECT N1 ^6C2 H1 CONECT C2 ^6N3 =O2 CONECT N3 ^6C4 H3 CONECT C4 ^6C5 =O4 CONECT C5 ^6=C6 H5 CONECT C6 ^6N1 H6 # 320-332 RESI THYM 0 ! C5H6N2O2, thymine GROUP ! ATOM N1 n3ah1 -0.6 ! O2 H3 ATOM H1 h1n 0.41 ! \\ / ATOM C2 c3o 0.5 ! C2--N3 ATOM O2 o1= -0.4 ! / \ ATOM N3 n3ah1 -0.51 ! H1--N1 C4==O4 ATOM H3 h1n 0.36 ! \ / ATOM C4 c3o 0.45 ! C6==C5 ATOM O4 o1= -0.42 ! / \ ATOM C5 c3ao -0.07 ! H6 \ ATOM C6 c3ao 0.08 ! H71--C7--H72 ATOM H6 h1a4 0.1 ! | ATOM C7 c4t -0.14 ! H73 ATOM H71 h1a4 0.08 ! ATOM H72 h1a4 0.08 ! ATOM H73 h1a4 0.08 ! CONECT N1 ^6C2 H1 CONECT C2 ^6N3 =O2 CONECT N3 ^6C4 H3 CONECT C4 ^6C5 =O4 CONECT C5 ^6=C6 C7 CONECT C6 ^6N1 H6 CONECT C7 H71 H72 H73 # 333-345 RESI CYTO 0 ! C4H5N3O, cytosine GROUP ! ATOM N1 n3ah1 -0.56 ! O2 ATOM H1 h1n 0.38 ! \\ ATOM C2 c3o 0.55 ! C2--N3 H41 ATOM O2 o1= -0.48 ! / \\ / ATOM N3 n2a6 -0.54 ! H1--N1 C4--N4 ATOM C4 c3ap 0.46 ! \ / \ ATOM N4 n3ch -0.79 ! C6==C5 H42 ATOM H41 h1n 0.385 ! / \ ATOM H42 h1n 0.355 ! H6 H5 ATOM C5 c3ao -0.06 ! ATOM H5 h1a4 0.1 ! ATOM C6 c3ao 0.1 ! ATOM H6 h1a4 0.1 ! CONECT N1 ^6C2 H1 CONECT C2 ^6N3 =O2 CONECT N3 ^6=C4 CONECT C4 ^6C5 N4 CONECT N4 H41 H42 CONECT C5 ^6=C6 H5 CONECT C6 ^6N1 H6 # 346-360 RESI ADEN 0 ! C5H5N5, adenine GROUP ! ATOM N1 n2a6 -0.53 ! H2 ATOM C2 c3a6a 0.22 ! \ ATOM H2 h1a3 0.2 ! C2--N1 H61 ATOM N3 n2a6 -0.55 ! // \\ / ATOM C4 c3aa 0.38 ! N3 C6--N6 ATOM C5 c3aa 0.15 ! \ / \ ATOM C6 c3ap 0.44 ! C4==C5 H62 ATOM N6 n3ch -0.81 ! | | ATOM H61 h1n 0.385 ! H9--N9 N7 ATOM H62 h1n 0.355 ! \\ / ATOM N7 n2a5 -0.49 ! C8 ATOM C8 c3a5a 0.2 ! | ATOM H8 h1a3 0.2 ! H8 ATOM N9 n3ah1 -0.5 ! ATOM H9 h1n 0.35 ! CONECT N1 ^6:C2 CONECT C2 ^6:N3 H2 CONECT N3 ^6:C4 CONECT C4 ^6:C5 CONECT C5 ^6:C6 ^5N7 CONECT C6 ^6:N1 N6 CONECT N6 H61 H62 CONECT N7 ^5C8 CONECT C8 ^5=N9 H8 CONECT N9 ^6C4 H9 # 359-370 RESI GUAN 0 ! C5H5N4O, guanine GROUP ! ATOM N1 n3ah1 -0.56 ! H22 ATOM H1 h1n 0.38 ! | ATOM C2 c3ap 0.46 ! H21--N2 H1 ATOM N2 n3ch -0.8 ! \ / ATOM H21 h1n 0.4 ! C2--N1 ATOM H22 h1n 0.4 ! // \ ATOM N3 n2a6 -0.51 ! N3 C6==O6 ATOM C4 c3aa 0.34 ! \ / ATOM C5 c3aa 0.12 ! C4==C5 ATOM C6 c3o 0.52 ! | | ATOM O6 o1= -0.51 ! H9--N9 N7 ATOM N7 n2a5 -0.49 ! \\ / ATOM C8 c3a5a 0.2 ! C8 ATOM H8 h1a3 0.2 ! | ATOM N9 n3ah1 -0.5 ! H8 ATOM H9 h1n 0.35 ! CONECT N1 ^6C2 H1 CONECT C2 ^6=N3 N2 CONECT N2 H21 H22 CONECT N3 ^6C4 CONECT C4 ^6=C5 CONECT C5 ^6C6 ^5N7 CONECT C6 ^6N1 =O6 CONECT N7 ^5C8 CONECT C8 ^5=N9 H8 CONECT N9 ^6C4 H9 */ # COMMENT END ITEM END # STREAM ######################################################################### # # # Amides # # # ######################################################################### ITEM RULES # type element residue atom charge rule c3oam C - - 0 C(C)(N)(=O) n3am0 N - - 0 N(C(=O)(~C))(~C)(C) n3am0 N - - 0 N(C(=O)(H))(~C)(C) n3am1 N - - 0 N(C(=O)(~C))(~C)(H) n3am1 N - - 0 N(C(=O)(H))(~C)(H) n3am2 N - - 0 N(C(=O)(~C))(H)(H) n3am2 N - - 0 N(C(=O)(H))(H)(H) ITEM END # RULES # Stream ITEM STREAM # 235-237, 240, 255 RESI FORM 0 ! CH3NO, formamide GROUP ! ATOM C c3oam 0.5 ! HC O ATOM HC h1co 0 ! \ // ATOM O o1= -0.5 ! C GROUP ! | ATOM N n3am2 -0.76 ! N ATOM HN1 h1n 0.38 ! / \ ATOM HN2 h1n 0.38 ! HN1 HN2 CONECT C N =O HC CONECT N HN1 HN2 # 235-237, 240 RESI ACAM 0 ! C2H5NO, acetamide GROUP ! ATOM C1 c4 -0.18 ! H11 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H12--C1--H13 ATOM H13 h1 0.06 ! | GROUP ! C==O ATOM C c3oam 0.5 ! | ATOM O o1= -0.5 ! N GROUP ! / \ ATOM N n3am2 -0.76 ! HN1 HN2 ATOM HN1 h1n 0.38 ! ATOM HN2 h1n 0.38 ! CONECT C1 C H11 H12 H13 CONECT C N =O CONECT N HN1 HN2 # 235-236, 238, 241 RESI NMAM 0 ! C3H7NO, n-methylacetamide GROUP ! ATOM C1 c4 -0.18 ! H11 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H12--C1--H13 ATOM H13 h1 0.06 ! | GROUP ! C==O ATOM C c3oam 0.5 ! | ATOM O o1= -0.5 ! HN--N GROUP ! | ATOM N n3am1 -0.5 ! H21--C2--H22 ATOM HN h1n 0.3 ! | ATOM C2 c4 0.02 ! H23 ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 C H11 H12 H13 CONECT C N =O CONECT N C2 HN CONECT C2 H21 H22 H23 # 235-236, 239 RESI DMAM 0 ! C3H7NO, dimethylacetamide, 243 (not 1035-1041) GROUP ! ATOM C1 c4 -0.18 ! H11 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H12--C1--H13 ATOM H13 h1 0.06 ! | GROUP ! C==O H31 ATOM C c3oam 0.5 ! | | ATOM O o1= -0.5 ! N---------C3--H33 GROUP ! | | ATOM N n3am0 -0.14 ! H21--C2--H22 H32 ATOM C2 c4 -0.11 ! | ATOM H21 h1 0.06 ! H23 ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! ATOM C3 c4 -0.11 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 C H11 H12 H13 CONECT C N =O CONECT N C2 C3 CONECT C2 H21 H22 H23 CONECT C3 H31 H32 H33 # 234 RESI BZAM 0 ! C7H7NO, benzamide GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O HN1 ATOM C2 c3a -0.115 ! / \\ || / ATOM H2 h1a 0.115 ! H2--C2 C6-----C--N GROUP ! || | \ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 HN2 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.115 ! ATOM C c3oam 0.615 ! ATOM O o1= -0.5 ! ATOM N n3am2 -0.76 ! ATOM HN1 h1n 0.38 ! ATOM HN2 h1n 0.38 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C CONECT C =O N CONECT N HN1 HN2 # 265-266 RESI ACAN 0 ! C7H7NO, acetanilide GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 HN H71 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6-----N--C--C7--H73 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.085 ! ATOM N n3am1 -0.385 ! ATOM HN h1n 0.3 ! GROUP ! ATOM C c3oam 0.5 ! ATOM O o1= -0.5 ! GROUP ! ATOM C7 c4 -0.18 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM H73 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 N CONECT N C HN CONECT C C7 =O CONECT C7 H71 H72 H73 ITEM END # STREAM ######################################################################### # # # Carbamates # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4 C - - 0 C(N(C(=O)(O))(H))(~C)(C)(C) c4 C - - 0 C(N(C(=O)(O))(H))(~C)(C)(H) c4 C - - 0 C(N(C(=O)(O))(H))(~C)(H)(H) n3am0 N - - 0 N(C(=O)(O))(~C)(C) n3am1 N - - 0 N(C(=O)(O))(~C)(H) n3am2 N - - 0 N(C(=O)(O))(H)(H) ITEM END # RULES # Increments ITEM INCREMENT c3* c4* 0 0 ITEM END # INCREMENT # Angles ITEM ANGLE # type1 type2 type3 k theta0 c3a c4 n3* 80 111.2 c3* c4 o2h 50 109.5 ITEM END # ANGLE # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3a c4 n3* c3* 0 1 0 n3* c3* c4* o2* 0 1 0 c3a n3* c3o o2* 2.1 2 0 c3* c4 o2h h1o -0.9 1 0 c* c4 c4 o2 1.711 1 0 -0.5 2 0 0.663 3 0 c* c4 o2* c* 0.65 1 0 -0.25 2 0 0.67 3 0 ITEM END # TORSION # Stream ITEM STREAM RESI ETCA 0 ! C3H7NO2, ethyl carbamate GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4oe 0.19 ! | ATOM H21 h1co 0.03 ! O2 ATOM H22 h1co 0.03 ! | ATOM O3 o2s -0.33 ! C3==O3 ATOM C3 c3oe 0.51 ! | ATOM O4 o1= -0.43 ! N4 GROUP ! / \ ATOM N4 n3am2 -0.76 ! H41 H42 ATOM H41 h1n 0.38 ! ATOM H42 h1n 0.38 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O3 H21 H22 CONECT O3 C3 CONECT C3 N4 =O4 CONECT N4 H41 H42 RESI MECA 0 ! C4H9NO2, methyl ethyl carbamate GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4oe 0.19 ! | ATOM H21 h1co 0.03 ! O2 ATOM H22 h1co 0.03 ! | ATOM O2 o2s -0.33 ! C3==O3 ATOM C3 c3oe 0.51 ! | ATOM O3 o1= -0.43 ! HN4--N4 GROUP ! | ATOM N4 n3am1 -0.5 ! H51--C5--H52 ATOM HN4 h1n 0.3 ! | ATOM C5 c4 0.02 ! H53 ATOM H51 h1 0.06 ! ATOM H52 h1 0.06 ! ATOM H53 h1 0.06 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O2 H21 H22 CONECT O2 C3 CONECT C3 N4 =O3 CONECT N4 C5 HN4 CONECT C5 H51 H52 H53 RESI PMCA 0 ! C8H9NO2, phenyl methyl carbamate GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 HN H81 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6-----N--C7--O8--C8--H83 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O7 H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.085 ! ATOM N n3am1 -0.385 ! ATOM HN h1n 0.3 ! GROUP ! ATOM C7 c3oe 0.51 ! ATOM O7 o1= -0.43 ! ATOM O8 o2s -0.33 ! ATOM C8 c4oe 0.16 ! ATOM H81 h1co 0.03 ! ATOM H82 h1co 0.03 ! ATOM H83 h1co 0.03 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 N CONECT N C7 HN CONECT C7 O8 =O7 CONECT O8 C8 CONECT C8 H81 H82 H83 ITEM END # STREAM ######################################################################### # # # Imides # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c3oim C IMID C2 0 C(C)(N(C(C)(=O))(H))(=O) ITEM END # RULES # Torsion ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3* n3am* c3o c4 2.3 1 0 6.089 2 0 c3* n3am* c3o o1= 6.089 2 0 ITEM END # TORSION # Stream ITEM STREAM RESI IMID 0 ! C4H7NO2 GROUP ! ATOM C1 c4 -0.12 ! H11 O2 O3 H41 ATOM H11 h1 0.06 ! | || || | ATOM H12 h1 0.06 ! H13--C1--C2--N--C3--C4--H43 ATOM H13 h1 0.06 ! | | | ATOM C2 c3oim 0.42 ! H12 HN H42 ATOM O2 o1= -0.42 ! ATOM N n3im1 -0.49 ! ATOM HN h1n 0.37 ! ATOM C3 c3oim 0.42 ! ATOM O3 o1= -0.42 ! ATOM C4 c4 -0.12 ! ATOM H41 h1 0.06 ! ATOM H42 h1 0.06 ! ATOM H43 h1 0.06 ! CONECT C1 C2 H11 H12 H13 CONECT C2 N =O2 CONECT N C3 HN CONECT C3 C4 =O3 CONECT C4 H41 H42 H43 ITEM END # STREAM ######################################################################### # # # Ureas # # # ######################################################################### # Stream # 247-250 ITEM STREAM RESI UREA 0 ! CH4N2O, urea GROUP ! ATOM N1 n3ur2 -0.542 ! H11 O1 H21 ATOM H11 h1n 0.333 ! \ || / ATOM H12 h1n 0.333 ! N1--C1--N2 ATOM C1 c3ou 0.142 ! / \ ATOM O1 o1= -0.39 ! H12 H22 ATOM N2 n3ur2 -0.542 ! ATOM H21 h1n 0.333 ! ATOM H22 h1n 0.333 ! CONECT N1 C1 H11 H12 CONECT C1 N2 =O1 CONECT N2 H21 H22 ITEM END # STREAM ######################################################################### # # # Thiols # # # ######################################################################### ITEM RULES # type element residue atom charge rule c4s C - - 0 C(S(H))(~C)(C)(C) c4s C - - 0 C(S(H))(~C)(C)(H) c4s C - - 0 C(S(H))(~C)(H)(H) ITEM END # RULES # Stream ITEM STREAM # 201, 205 RESI H2S 0 ! H2S, hydrogen sulfide GROUP ! ATOM S s2h2 -0.47 ! H1--S--H2 ATOM H1 h1s 0.235 ! ATOM H2 h1s 0.235 | CONECT S H1 H2 # 200, 204, 217 RESI MESH 0 ! CH4S, methanethiol ATOM C1 c4s 0 ! ATOM H1 h1 0.06 ! H11 ATOM H2 h1 0.06 ! | ATOM H3 h1 0.06 ! H12--C1--S--H ATOM S s2h -0.335 ! | ATOM H h1s 0.155 ! H13 CONECT C1 S H1 H2 H3 CONECT S H # 204, 734-735 RESI THPH 0 ! C7H8S, thiophenol GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 ATOM C2 c3a -0.115 ! / \\ ATOM H2 h1a 0.115 ! H2--C2 C6-----S7--H7 GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.065 ! ATOM S7 s2h -0.22 ! ATOM H7 h1s 0.155 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S7 CONECT S7 H7 ITEM END # STREAM ######################################################################### # # # Sulfides # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4s C - - 0 C(S)(~C)(C)(C) c4s C - - 0 C(S)(~C)(C)(H) c4s C - - 0 C(S)(~C)(H)(H) ITEM END # RULES # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* c4 s2 c4 0.925 1 0 -0.576 2 0 0.677 3 0 c3a c3a c4 s* 0 1 0 ITEM END # TORSION # Stream ITEM STREAM # 202, 209 RESI DMES 0 ! C2H6S, dimethyl sulfide ATOM C1 c4s 0.0375 ! ATOM H11 h1 0.06 ! H11 H21 ATOM H12 h1 0.06 ! | | ATOM H13 h1 0.06 ! H12--C1--S--C2--H22 ATOM S s2 -0.435 ! | | ATOM C2 c4s 0.0375 ! H13 H23 ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 S H11 H12 H13 CONECT S C2 CONECT C2 H21 H22 H23 # 202, 209 RESI EMES 0 ! C2H6S, ethyl methyl sulfide ATOM C1 c4s 0.0375 ! ATOM H11 h1 0.06 ! H11 H21 H31 ATOM H12 h1 0.06 ! | | | ATOM H13 h1 0.06 ! H13--C1--S--C2--C3--H33 ATOM S s2 -0.435 ! | | | ATOM C2 c4s 0.0975 ! H12 H22 H32 ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM C3 c4 -0.18 ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 S H11 H12 H13 CONECT S C2 CONECT C2 C3 H21 H22 CONECT C3 H31 H32 H33 # 203, 209 RESI DMDS 0 ! C2H6S, dimethyl disulfide ATOM C1 c4s 0.0375 ! ATOM H11 h1 0.06 ! H11 H21 ATOM H12 h1 0.06 ! | | ATOM H13 h1 0.06 ! H12--C1--S1--S2--C2--H22 ATOM S1 s2 -0.2175 ! | | ATOM S2 s2 -0.2175 ! H13 H23 ATOM C2 c4s 0.0375 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 S1 H11 H12 H13 CONECT S1 S2 CONECT S2 C2 CONECT C2 H21 H22 H23 # 222 RESI THAN 0 ! C7H8S, thioanisole GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6-----S--C7--H73 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.1025 ! ATOM S s2 -0.32 ! ATOM C7 c4s 0.0375 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM H73 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S CONECT S C7 CONECT C7 H71 H72 H73 # 221, 922 RESI BNMS 0 ! C7H8O, benzyl methyl sulfide GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 H81 ATOM C2 c3a -0.115 ! / \\ | | ATOM H2 h1a 0.115 ! H2--C2 C6-------C7--S--C8--H83 GROUP ! || | | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 H82 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a -0.055 ! ATOM C7 c4s 0.1525 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM S s2 -0.435 ! ATOM C8 c4s 0.0375 ! ATOM H81 h1 0.06 ! ATOM H82 h1 0.06 ! ATOM H83 h1 0.06 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 S H71 H72 CONECT S C8 CONECT C8 H81 H82 H83 ITEM END # STREAM ######################################################################### # # # Sulfoxides # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule o1s O - - 0 O(=S(~C)(~C)) s3 S - - 0 S(~C)(~C)(=O) ITEM END # RULES # Bonds ITEM BOND # type1 type2 k l0 c3a s3 340 1.79 ITEM END # BOND # Angles ITEM ANGLE # type1 type2 type3 k theta0 c3* s3 c3* 62 96 c3* c3* s3 85 119.4 c3* s3 o1s 74 107 ITEM END # ANGLE # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3* c3* s3 c* -0.9 2 0 c* c* s3 o1s 0 1 0 ITEM END # TORSION # Stream ITEM STREAM # 496-498 RESI DMSO 0 ! C2H6O2S, dimethylsulfoxide GROUP ! ATOM C1 c4s -0.035 ! H11 O1 H21 ATOM H11 h1 0.06 ! | || | ATOM H12 h1 0.06 ! H13--C1--S1--C2--H23 ATOM H13 h1 0.06 ! | | ATOM S1 s3 0.13 ! H12 H22 ATOM O1 o1s -0.42 ! ATOM C2 c4s -0.035 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 S1 H11 H12 H13 CONECT S1 C2 =O1 CONECT C2 H21 H22 H23 # 495-497 RESI DPSO 0 ! C12H10O, diphenyl sulfoxide GROUP ! ATOM C1 c3a -0.115 ! H1 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C1 O1 C12 ATOM C2 c3a -0.115 ! / \\ || / \\ ATOM H2 h1a 0.115 ! H2--C2 C6---S1---C7 C11--H11 GROUP ! || | || | ATOM C3 c3a -0.115 ! H3--C3 C5 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C4 H5 H8 C9 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H9 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.0875 ! ATOM S1 s3 0.245 ! ATOM O1 o1s -0.42 ! ATOM C7 c3a 0.0875 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S1 CONECT S1 C7 =O1 CONECT C7 ^6:C8 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^6:C7 H12 ITEM END # STREAM ######################################################################### # # # Sulfones # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule o1s= O - - 0 O(=S(~C)(~C)(=O)) s4 S - - 0 S(~C)(~C)(=O)(=O) ITEM END # RULES # Angles ITEM ANGLE # type1 type2 type3 k theta0 c3a* s4 c3a* 78.7 104.4 ITEM END # ANGLE # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3a* c3a* s4 c3a* -0.45 2 180 c3a* s4 c4* c4* 0 1 0 ITEM END # TORSION # Stream ITEM STREAM # 493-494 RESI MSME 0 ! C2H6O2S, methylsulfonylmethane GROUP ! ATOM C1 c4s -0.18 ! H11 O1 H21 ATOM H11 h1 0.06 ! | || | ATOM H12 h1 0.06 ! H13--C1--S1--C2--H23 ATOM H13 h1 0.06 ! | || | GROUP ! H12 O2 H22 ATOM S1 s4 1.374 ! ATOM O1 o1s= -0.687 ! ATOM O2 o1s= -0.687 ! GROUP ! ATOM C2 c4s -0.18 ! ATOM H21 h1 0.06 ! ATOM H22 h1 0.06 ! ATOM H23 h1 0.06 ! CONECT C1 S1 H11 H12 H13 CONECT S1 C2 =O1 =O2 CONECT C2 H21 H22 H23 # 493-494 RESI DPHS 0 ! C12H10O, diphenyl sulfone GROUP ! ATOM C1 c3a -0.115 ! H1 H12 ATOM H1 h1a 0.115 ! | | GROUP ! C1 O1 C12 ATOM C2 c3a -0.115 ! / \\ || / \\ ATOM H2 h1a 0.115 ! H2--C2 C6---S1---C7 C11--H11 GROUP ! || | || || | ATOM C3 c3a -0.115 ! H3--C3 C5 O2 C8 C10--H10 ATOM H3 h1a 0.115 ! \ // \ / \ // GROUP ! C4 H5 H8 C9 ATOM C4 c3a -0.115 ! | | ATOM H4 h1a 0.115 ! H4 H9 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0 ! ATOM S1 s4 1.374 ! ATOM O1 o1s= -0.687 ! ATOM O2 o1s= -0.687 ! ATOM C7 c3a 0 ! GROUP ! ATOM C8 c3a -0.115 ! ATOM H8 h1a 0.115 ! GROUP ! ATOM C9 c3a -0.115 ! ATOM H9 h1a 0.115 ! GROUP ! ATOM C10 c3a -0.115 ! ATOM H10 h1a 0.115 ! GROUP ! ATOM C11 c3a -0.115 ! ATOM H11 h1a 0.115 ! GROUP ! ATOM C12 c3a -0.115 ! ATOM H12 h1a 0.115 ! GROUP ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S1 CONECT S1 C7 =O1 =O2 CONECT C7 ^6:C8 CONECT C8 ^6:C9 H8 CONECT C9 ^6:C10 H9 CONECT C10 ^6:C11 H10 CONECT C11 ^6:C12 H11 CONECT C12 ^6:C7 H12 ITEM END # STREAM ######################################################################### # # # Sulfonates # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule ITEM END # RULES # Streams ITEM STREAM # Using ESNA from CHARMM CGENFF RESI ESNA -1 ! C2H5O3S, ethyl sulfonate anion GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4s -0.2 ! | ATOM H21 h1 0.06 ! O3==S1==O4 ATOM H22 h1 0.06 ! | ATOM S1 s4c 0.73 ! O2 (-) ATOM O2 o1s -0.55 ! ATOM O3 o1s -0.55 ! ATOM O4 o1s -0.55 ! CONECT C1 C2 H11 H12 H13 CONECT C2 S1 H21 H22 CONECT S1 :O2 :O3 :O4 UNLINK s4c o1s # Using BSAT from CHARMM CGENFF RESI BSAT -1 ! C6H5O3S, benzenesulfonate anion GROUP ! ATOM C1 c3aso -0.21 ! H1 ATOM H1 h1a 0.21 ! | GROUP ! C1 O1 ATOM C2 c3a -0.115 ! / \\ || ATOM H2 h1a 0.115 ! H2--C2 C6------S1--O3 (-) GROUP ! || | || ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O2 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3aso -0.21 ! ATOM H5 h1a 0.21 ! GROUP ! ATOM C6 c3as -0.4 ! ATOM S1 s4 1.35 ! ATOM O1 o1s -0.65 ! ATOM O2 o1s -0.65 ! ATOM O3 o1s -0.65 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S1 CONECT S1 :O1 :O2 :O3 UNLINK s4 o1s ITEM END ######################################################################### # # # Sulfates # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4s C - - 0 C(O(:S))(C)(C)(C) c4s C - - 0 C(O(:S))(C)(C)(H) c4s C - - 0 C(O(:S))(C)(H)(H) c4s C - - 0 C(O(:S))(~C)(C)(C) c4s C - - 0 C(O(:S))(~C)(C)(H) c4s C - - 0 C(O(:S))(~C)(H)(H) h1 H - - 0 H(C(O(:S))(C)(C)) h1 H - - 0 H(C(O(:S))(C)(H)) h1 H - - 0 H(C(O(:S))(H)(H)) h1 H - - 0 H(C(O(:S))(~C)(C)) h1 H - - 0 H(C(O(:S))(~C)(H)) ITEM END # RULES # Bonds ITEM BOND # type1 type2 k l0 o2s s4 230 1.61 ITEM END # BOND # Angles ITEM ANGLE # type1 type2 type3 k theta0 c* o2* s4* 100 120.5 o1* s4* o2* 100 108.23 ITEM END # ANGLE # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c3a c3a o2* s4* 2.99 2 0 c3* o2 c4 c4 -1.22 1 0 -0.126 2 0 0.422 3 0 c* c4 o2* s4* -1.42 1 0 -0.62 2 0 0.1 3 0 h1 c4 o2* s4* 0.3 3 0 ITEM END # TORSION # Stream ITEM STREAM # Using -SO4(-) from CHARMM CGENFF RESI MSUL -1 ! CH3O4S, methylsulfate anion GROUP ! ATOM C1 c4s -0.28 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | ATOM O1 o2s -0.28 ! O1 ATOM S1 s4 1.33 ! | ATOM O2 o1s -0.65 ! O3==S1==O4 ATOM O3 o1s -0.65 ! | ATOM O4 o1s -0.65 ! O2 (-) CONECT C1 O1 H11 H12 H13 CONECT O1 :S1 CONECT S1 :O2 :O3 :O4 UNLINK s4 o1s # Using -SO4(-) from CHARMM CGENFF RESI ESUL -1 ! C2H5O4S, ethylsulfate anion GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4s -0.22 ! | ATOM H21 h1 0.06 ! O1 ATOM H22 h1 0.06 ! | ATOM O1 o2s -0.28 ! O3==S1==O4 ATOM S1 s4 1.33 ! | ATOM O2 o1s -0.65 ! O2 (-) ATOM O3 o1s -0.65 ! ATOM O4 o1s -0.65 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O1 H21 H22 CONECT O1 :S1 CONECT S1 :O2 :O3 :O4 UNLINK s4 o1s # 463-464 RESI BNSU -1 ! C6H5O4S, benzenesulfate anion GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O2 ATOM C2 c3a -0.115 ! / \\ || ATOM H2 h1a 0.115 ! H2--C2 C6--O1--S1--O4 (-) GROUP ! || | || ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O3 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3as -0.1 ! ATOM O1 o2s -0.28 ! ATOM S1 s4 1.33 ! ATOM O2 o1s -0.65 ! ATOM O3 o1s -0.65 ! ATOM O4 o1s -0.65 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O1 CONECT O1 :S1 CONECT S1 :O2 :O3 :O4 UNLINK s4 o1s # 463-464 RESI BZSU -1 ! C7H7O4S, benzenesulfate anion GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 H71 O2 ATOM C2 c3a -0.115 ! / \\ | || ATOM H2 h1a 0.115 ! H2--C2 C6------C7--O1--S1--O4 (-) GROUP ! || | | || ATOM C3 c3a -0.115 ! H3--C3 C5--H5 H72 O3 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3as -0.115 ! ATOM C7 c4s -0.105 ! ATOM H71 h1 0.06 ! ATOM H72 h1 0.06 ! ATOM O1 o2s -0.28 ! ATOM S1 s4 1.33 ! ATOM O2 o1s -0.65 ! ATOM O3 o1s -0.65 ! ATOM O4 o1s -0.65 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 O1 H71 H72 CONECT O1 :S1 CONECT S1 :O2 :O3 :O4 UNLINK s4 o1s ITEM END # STREAM ######################################################################### # # # Sulfonamides # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4ns C - - 0 C(N(S)(H))(C)(C)(C) c4ns C - - 0 C(N(S)(H))(C)(C)(H) c4ns C - - 0 C(N(S)(H))(C)(H)(H) c4sa C - - 0 C(S(N)(=O)(=O))(~C)(C)(C) c4sa C - - 0 C(S(N)(=O)(=O))(~C)(C)(H) c4sa C - - 0 C(S(N)(=O)(=O))(~C)(H)(H) h1cs H - - 0 H(C(N(S)(H))(C)(C)) h1cs H - - 0 H(C(N(S)(H))(C)(H)) o1s= O - - 0 O(=S(~C)(N)(=O)) s4am S - - 0 S(~C)(N)(=O)(=O) ITEM END # RULES # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* s4 n3* c4* 2.074 1 0 -2.966 2 0 2.473 3 0 c* s4 n3* h1n 1.671 1 0 -4.901 2 0 0.669 3 0 ITEM END # TORSION # Stream ITEM STREAM # 474-479 RESI MSAM 0 ! CH5NO2S, methanesulfonamide GROUP ! ATOM C1 c4sa -0.54 ! H13 ATOM H11 h1 0.18 ! | ATOM H12 h1 0.18 ! H11--C1--H12 ATOM H13 h1 0.18 ! | GROUP ! O1==S==O2 ATOM S s4am 1.48 ! | ATOM O1 o1s= -0.68 ! N ATOM O2 o1s= -0.68 ! / \ ATOM N n3sa2 -1 ! HN1 HN2 ATOM HN1 h1n 0.44 ! ATOM HN2 h1n 0.44 ! CONECT C1 S H11 H12 H13 CONECT S N =O1 =O2 CONECT N HN1 HN2 # 474-479 RESI ESAM 0 ! C2H7NO2S, ethanesulfonamide GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H22--C2--H22 ATOM C2 c4sa -0.36 ! | ATOM H21 h1 0.18 ! O1==S==O2 ATOM H22 h1 0.18 ! | GROUP ! N ATOM S s4am 1.48 ! / \ ATOM O1 o1s= -0.68 ! HN1 HN2 ATOM O2 o1s= -0.68 ! ATOM N n3sa2 -1 ! ATOM HN1 h1n 0.44 ! ATOM HN2 h1n 0.44 ! CONECT C1 C2 H11 H12 H13 CONECT C2 S H21 H22 CONECT S N =O1 =O2 CONECT N HN1 HN2 # 474-477, 480-481 RESI NMSA 0 ! C2H7NO2S, n-methyl methanesulfonamide GROUP ! ATOM C1 c4sa -0.54 ! H13 ATOM H11 h1 0.18 ! | ATOM H12 h1 0.18 ! H11--C1--H12 ATOM H13 h1 0.18 ! | GROUP ! O1==S==O2 ATOM S s4am 1.48 ! | ATOM O1 o1s= -0.68 ! HN--N ATOM O2 o1s= -0.68 ! | ATOM N n3sa1 -0.8 ! H21--C2--H22 ATOM HN h1n 0.41 ! | ATOM C2 c4ns 0.18 ! H23 ATOM H21 h1cs 0.03 ! ATOM H22 h1cs 0.03 ! ATOM H23 h1cs 0.03 ! CONECT C1 S H11 H12 H13 CONECT S N =O1 =O2 CONECT N C2 HN CONECT C2 H21 H22 H23 # 474-477, 484-487 RESI NESA 0 ! C3H9NO2S, n-ethyl methanesulfonamide GROUP ! ATOM C1 c4sa -0.54 ! H13 ATOM H11 h1 0.18 ! | ATOM H12 h1 0.18 ! H11--C1--H12 ATOM H13 h1 0.18 ! | GROUP ! O1==S==O2 ATOM S s4am 1.48 ! | ATOM O1 o1s= -0.68 ! HN--N ATOM O2 o1s= -0.68 ! | ATOM N n3sa1 -0.8 ! H21--C2--H22 ATOM HN h1n 0.41 ! | ATOM C2 c4ns 0.21 ! H31--C3--H32 ATOM H21 h1cs 0.03 ! | ATOM H22 h1cs 0.03 ! H33 GROUP ! ATOM C3 c4 -0.18 ! ATOM H31 h1 0.06 ! ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 S H11 H12 H13 CONECT S N =O1 =O2 CONECT N C2 HN CONECT C2 C3 H21 H22 CONECT C3 H31 H32 H33 # RESI BZSA 0 ! C6H7NO2S, benzylsulfonamide GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O1 HN1 ATOM C2 c3a -0.115 ! / \\ || / ATOM H2 h1a 0.115 ! H2--C2 C6-----S1--N GROUP ! || | || \ ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O2 HN2 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0 ! ATOM S1 s4am 1.48 ! ATOM O1 o1s= -0.68 ! ATOM O2 o1s= -0.68 ! ATOM N n3sa2 -1 ! ATOM HN1 h1n 0.44 ! ATOM HN2 h1n 0.44 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 S1 CONECT S1 N =O1 =O2 CONECT N HN1 HN2 ITEM END # STREAM ######################################################################### # # # Phosphates # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4p C - - 0 C(O(P))(C)(C)(C) c4p C - - 0 C(O(P))(C)(C)(H) c4p C - - 0 C(O(P))(C)(H)(H) h1 H - - 0 H(C(O(P))(C)(C)) h1 H - - 0 H(C(O(P))(C)(H)) h1 H - - 0 H(C(O(P))(H)(H)) ITEM END # Torsions ITEM TORSION # type1 type2 type3 type4 k n delta [...] c* o2 p4 o2 -0.375 1 0 -1.358 2 0 0.004 3 0 ITEM END # TORSION # Stream ITEM STREAM # 445-449 RESI MPHO -2 ! CH3O4P, methylphosphate anion GROUP ! ATOM C1 c4pm 0.44 ! H13 ATOM H11 h1 -0.1 ! | ATOM H12 h1 -0.1 ! H11--C1--H12 ATOM H13 h1 -0.1 ! | ATOM O1 o2p -0.7 ! O1 ATOM P1 p41 1.92 ! | ATOM O2 o1p -1.12 ! O3==P1--O4 (-) ATOM O3 o1p -1.12 ! | ATOM O4 o1p -1.12 ! O2 (-) CONECT C1 O1 H11 H12 H13 CONECT O1 P1 CONECT P1 :O2 :O3 :O4 UNLINK p41 o1p # 445-449 RESI EPHO -2 ! C2H5O4P, ethylphosphate anion GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4pm 0.34 ! | ATOM H21 h1 -0.1 ! O1 ATOM H22 h1 -0.1 ! | ATOM O1 o2p -0.7 ! O3==P1--O4 (-) ATOM P1 p41 1.92 ! | ATOM O2 o1p -1.12 ! O2 (-) ATOM O3 o1p -1.12 ! ATOM O4 o1p -1.12 ! CONECT C1 C2 H11 H12 H13 CONECT C2 O1 H21 H22 CONECT O1 P1 CONECT P1 :O2 :O3 :O4 UNLINK p41 o1p # 440-444 RESI DMPO -1 ! C2H6O4P, dimethylphosphate anion GROUP ! ATOM C1 c4p 0.3 ! H13 ATOM H11 h1 -0.03 ! | ATOM H12 h1 -0.03 ! H11--C1--H12 ATOM H13 h1 -0.03 ! | ATOM O1 o2p -0.6 ! O1 ATOM P1 p42 1.62 ! | ATOM O2 o2p -0.6 ! O3==P1==O4 (-) ATOM O3 o1p -0.92 ! | ATOM O4 o1p -0.92 ! O2 ATOM C2 c4p 0.3 ! | ATOM H21 h1 -0.03 ! H21--C2--H22 ATOM H22 h1 -0.03 ! | ATOM H23 h1 -0.03 ! H23 CONECT C1 O1 H11 H12 H13 CONECT O1 P1 CONECT P1 O2 :O3 :O4 CONECT O2 C2 CONECT C2 H21 H22 H23 UNLINK p42 o1p # 440-444 RESI EMPO -1 ! C2H6O4P, ethyl methylphosphate anion GROUP ! ATOM C1 c4p 0.3 ! H13 ATOM H11 h1 -0.03 ! | ATOM H12 h1 -0.03 ! H11--C1--H12 ATOM H13 h1 -0.03 ! | ATOM O1 o2p -0.6 ! O1 ATOM P1 p42 1.62 ! | ATOM O2 o2p -0.6 ! O3==P1==O4 (-) ATOM O3 o1p -0.92 ! | ATOM O4 o1p -0.92 ! O2 ATOM C2 c4p 0.27 ! | ATOM H21 h1 -0.03 ! H21--C2--H22 ATOM H22 h1 -0.03 ! | GROUP ! H31--C3--H32 ATOM C3 c4 -0.18 ! | ATOM H31 h1 0.06 ! H33 ATOM H32 h1 0.06 ! ATOM H33 h1 0.06 ! CONECT C1 O1 H11 H12 H13 CONECT O1 P1 CONECT P1 O2 :O3 :O4 CONECT O2 C2 CONECT C2 C3 H21 H22 CONECT C3 H31 H32 H33 UNLINK p42 o1p # 463-464 RESI BZPO -2 ! C6H5O4P, benzylphosphate anion GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 O2 (-) ATOM C2 c3a -0.115 ! / \\ || ATOM H2 h1a 0.115 ! H2--C2 C6--O1--P1--O4 (-) GROUP ! || | || ATOM C3 c3a -0.115 ! H3--C3 C5--H5 O3 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.14 ! ATOM O1 o2p -0.7 ! ATOM P1 p41 1.92 ! ATOM O2 o1p -1.12 ! ATOM O3 o1p -1.12 ! ATOM O4 o1p -1.12 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 O1 CONECT O1 P1 CONECT P1 :O2 :O3 :O4 UNLINK p41 o1p # 450-456 RESI DMMP -1 ! C3H9O3P, dimethyl methylphosphonate GROUP ! ATOM C1 c4p 0.3 ! H13 ATOM H11 h1 -0.03 ! | ATOM H12 h1 -0.03 ! H11--C1--H12 ATOM H13 h1 -0.03 ! | ATOM O1 o2p -0.63 ! O1 H21 ATOM P1 p43 1.62 ! | | ATOM O2 o2p -0.63 ! O3==P1------C2--H23 ATOM O3 o1p= -0.97 ! | | ATOM C2 c4p -0.51 ! O2 H22 ATOM H21 h1cp -0.1 ! | ATOM H22 h1cp -0.1 ! H31--C3--H32 ATOM H23 h1cp -0.1 ! | ATOM C3 c4p 0.3 ! H33 ATOM H31 h1 -0.03 ! ATOM H32 h1 -0.03 ! ATOM H33 h1 -0.03 ! CONECT C1 O1 H11 H12 H13 CONECT O1 P1 CONECT P1 C2 O2 =O3 CONECT C2 H21 H22 H23 CONECT O2 C3 CONECT C3 H31 H32 H33 UNLINK p43 o1p= ITEM END # STREAM ######################################################################### # # # Halocarbons # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule c4 C - - 0 C(C)(C)([Cl])(H) c4 C - - 0 C(C)(C)(C)([Cl]) c4 C - - 0 C(C)(F)(H)(H) c4 C - - 0 C(C)(F)(F)(H) c4 C - - 0 C(C)(C)(F)(F) c4 C - - 0 C(C)(C)(F)(H) c4 C - - 0 C(C)(C)(C)(F) ITEM END # RULES # Stream ITEM STREAM # 975-976, 982 RESI ETBR 0 ! C2[Cl]H5, bromo-ethane GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4br -0.006 ! | ATOM H21 h1 0.103 ! BR ATOM H22 h1 0.103 ! ATOM BR br1 -0.2 ! CONECT C1 C2 H11 H12 H13 CONECT C2 BR H21 H22 # 151-153 RESI ETCL 0 ! C2[Cl]H5, chloro-ethane GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4cl -0.006 ! | ATOM H21 h1 0.103 ! CL ATOM H22 h1 0.103 ! ATOM CL cl1 -0.2 ! CONECT C1 C2 H11 H12 H13 CONECT C2 CL H21 H22 # 975-976, 982 RESI ETIO 0 ! C2[Cl]H5, iodo-ethane GROUP ! ATOM C1 c4 -0.18 ! H13 ATOM H11 h1 0.06 ! | ATOM H12 h1 0.06 ! H11--C1--H12 ATOM H13 h1 0.06 ! | GROUP ! H21--C2--H22 ATOM C2 c4i -0.07 ! | ATOM H21 h1 0.1 ! I ATOM H22 h1 0.1 ! ATOM I i1 -0.13 ! CONECT C1 C2 H11 H12 H13 CONECT C2 I H21 H22 # 226-227 RESI EECL 0 ! C2[Cl]H3, chloro-ethene GROUP ! ATOM C1 c3= -0.23 ! H11 H12 ATOM H11 h1= 0.115 ! \ / ATOM H12 h1= 0.115 ! C1 GROUP ! || ATOM C2 c3= 0.005 ! C2 ATOM H21 h1= 0.115 ! / \ ATOM CL cl1 -0.12 ! CL H21 CONECT C1 =C2 H11 H12 CONECT C2 CL H21 # 160-165 RESI ETOF 0 ! C2F3H3O, tri-fluoro-ethanol GROUP ! ATOM C1 c4 0.615 ! F13 ATOM F11 f1 -0.205 ! | ATOM F12 f1 -0.205 ! F11--C1--F12 ATOM F13 f1 -0.205 ! | GROUP ! H21--C2--H22 ATOM C2 c4 0.145 ! | ATOM H21 h1 0.06 ! O ATOM H22 h1 0.06 ! | ATOM O o2h -0.683 ! H ATOM H h1o 0.418 ! CONECT C1 C2 F11 F12 F13 CONECT C2 O H21 H22 CONECT O H # 263-264 RESI BZCL 0 ! C6H5Cl, chlorobenzene GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 ATOM C2 c3a -0.115 ! / \\ ATOM H2 h1a 0.115 ! H2--C2 C6--CL GROUP ! || | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.18 ! ATOM CL cl1 -0.18 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 CL # 724-726 RESI BZTF 0 ! C7H5F3, trifluoromethylbenzene GROUP ! ATOM C1 c3a -0.115 ! H1 ATOM H1 h1a 0.115 ! | GROUP ! C1 F71 ATOM C2 c3a -0.115 ! / \\ | ATOM H2 h1a 0.115 ! H2--C2 C6------C7--F73 GROUP ! || | | ATOM C3 c3a -0.115 ! H3--C3 C5--H5 F72 ATOM H3 h1a 0.115 ! \ // GROUP ! C4 ATOM C4 c3a -0.115 ! | ATOM H4 h1a 0.115 ! H4 GROUP ! ATOM C5 c3a -0.115 ! ATOM H5 h1a 0.115 ! GROUP ! ATOM C6 c3a 0.15 ! ATOM C7 c4f 0.45 ! ATOM F71 f1 -0.2 ! ATOM F72 f1 -0.2 ! ATOM F73 f1 -0.2 ! CONECT C1 ^6:C2 H1 CONECT C2 ^6:C3 H2 CONECT C3 ^6:C4 H3 CONECT C4 ^6:C5 H4 CONECT C5 ^6:C6 H5 CONECT C6 ^6:C1 C7 CONECT C7 F71 F72 F73 ITEM END # STREAM ######################################################################### # # # Silicates # # # ######################################################################### # Rules ITEM RULES # type element residue atom charge rule si4 Si - - 0 [Si](~C)(C)(C)(C) si4 Si - - 0 [Si](~C)(C)(C)(H) si4 Si - - 0 [Si](~C)(C)(H)(H) si4 Si - - 0 [Si](~C)(H)(H)(H) ITEM END # RULES # Streams ITEM STREAM # 1060-1068 RESI MESI 0 ! CH6Si, methylsilane GROUP ! ATOM C1 c4 -0.43 ! H11 H21 ATOM H11 h1 0.06 ! | | ATOM H12 h1 0.06 ! H13--C1--SI2--H23 ATOM H13 h1 0.06 ! | | ATOM SI2 si4 0.55 ! H12 H22 ATOM H21 h1si -0.1 ! ATOM H22 h1si -0.1 ! ATOM H23 h1si -0.1 ! CONECT C1 SI2 H11 H12 H13 CONECT SI2 H21 H22 H23 ITEM END # STREAM