*>> All-hydrogen topology for small model compounds used in the << *>> development of the CHARMM22 protein all-hydrogen parameters << *>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< *>>>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<< * 27 1 !May00; additions for PSC workshop from standard protein topology file ! references ! !PROTEINS ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HE1 1.00800 H ! for alkene; RHC=CR MASS 12 HE2 1.00800 H ! for alkene; H2C=CR !MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params !MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params !MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params MASS 20 C 12.01100 C ! polar C MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu MASS 33 CD 12.01100 C ! carbonyl C for none amides, asp,glu,cter MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR !MASS 41 CT 12.01100 C ! aliphatic sp3 C for CH, new LJ params, no hydrogens !MASS 42 CT1n 12.01100 C ! aliphatic sp3 C for CH, new LJ params !MASS 43 CT2n 12.01100 C ! aliphatic sp3 C for CH2, new LJ params !MASS 44 CT3n 12.01100 C ! aliphatic sp3 C for CH3, new LJ params MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 90 CAL 40.08000 CA ! calcium 2+ MASS 91 ZN 65.37000 ZN ! zinc (II) cation MASS 92 FE 55.84700 FE ! heme iron 56 MASS 99 DUM 0.00000 H ! dummy atom DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA DEFA FIRS NONE LAST NONE AUTO ANGLES DIHE RESI ACET -1.00 ! acetate, K. Kuczera GROUP ATOM C1 CT3 -0.37 ! ATOM C2 CC 0.62 ! H1 O1 (-) ATOM H1 HA 0.09 ! | / ATOM H2 HA 0.09 ! H2--C1--C2 ATOM H3 HA 0.09 ! | \\ ATOM O1 OC -0.76 ! H3 O2 ATOM O2 OC -0.76 ! Bond c1 h1 c1 h2 c1 h3 Bond c1 c2 c2 o1 Double c2 o2 impr c2 c1 o2 o1 ic h1 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 ic h2 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 ic h3 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 ic h1 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 ic h2 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 ic h3 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 ic h1 c1 h2 h3 0.00 0.00 0.0 0.00 0.00 ic h2 c1 h3 h1 0.00 0.00 0.0 0.00 0.00 ic h3 c1 h1 h2 0.00 0.00 0.0 0.00 0.00 ic o1 o2 *c2 c1 0.00 0.00 0.0 0.00 0.00 patc firs none last none RESI GUAN 1.00 ! guandinium, K. Kuczera GROUP ATOM C C 0.64 ! H11 H12 ATOM N1 NC2 -0.80 ! \ / ATOM H11 HC 0.46 ! N1 (+) ATOM H12 HC 0.46 ! || ATOM N2 NC2 -0.80 ! C ATOM H21 HC 0.46 ! / \ ATOM H22 HC 0.46 ! H21-N2 N3-H31 ATOM N3 NC2 -0.80 ! | | ATOM H31 HC 0.46 ! H22 H32 ATOM H32 HC 0.46 ! BOND C N2 C N3 DOUBLE C N1 BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 H32 IMPH C N2 N1 N3 IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 IC H32 N3 C N2 0.00 0.00 0.0 0.00 0.00 patc firs none last none RESI MGUA 1.00 ! methyl-guanidinium GROUP ATOM C C 0.64 ! H11 H12 ATOM N1 NC2 -0.80 ! \ / ATOM H11 HC 0.46 ! N1 (+) ATOM H12 HC 0.46 ! || ATOM N2 NC2 -0.80 ! C HC1 ATOM H21 HC 0.46 ! / \ / ATOM H22 HC 0.46 ! H21-N2 N3--C2-HC2 ATOM N3 NC2 -0.70 ! | | \ ATOM H31 HC 0.44 ! H22 H31 HC3 ATOM C2 CT3 0.11 ! ATOM HC1 HA 0.09 ATOM HC2 HA 0.09 ATOM HC3 HA 0.09 BOND C N2 C N3 DOUBLE C N1 BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2 BOND C2 HC1 C2 HC2 C2 HC3 IMPH C N2 N1 N3 IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 IC C2 N3 C N1 0.00 0.00 180.0 0.00 0.00 IC C N3 C2 HC1 0.00 0.00 0.0 0.00 0.00 IC C N3 C2 HC2 0.00 0.00 120.0 0.00 0.00 IC C N3 C2 HC3 0.00 0.00 240.0 0.00 0.00 patc firs none last none RESI GLYN 0.00 ! neutral glycine GROUP ! ATOM N NH2 -0.96 ! ATOM HT1 HC 0.34 ! HT1 HT2 ATOM HT2 HC 0.34 ! \ / ATOM CA CT2 0.18 ! N ATOM HA1 HB 0.05 ! | ATOM HA2 HB 0.05 ! HA1-CA-HA2 GROUP ! | ATOM C CD 0.75 ! C ATOM OT1 OB -0.55 ! // \ ATOM OT2 OH1 -0.64 ! OT1 OT2 ATOM HO2 H 0.44 ! | ! HO2 ! BOND N CA CA C C OT2 OT2 HO2 BOND N HT1 N HT2 CA HA1 CA HA2 DOUBLE OT1 C DONO HT1 N DONO HT2 N DONO HO2 OT2 IC N CA C OT1 1.5010 119.00 88.76 126.10 1.2218 IC N CA C OT2 1.5010 119.00 -111.57 113.44 1.3958 IC OT1 OT2 *C CA 1.2218 117.44 -161.57 113.44 1.5780 IC CA C OT2 HO2 1.5780 113.44 -168.97 107.16 0.9565 IC C CA N HT1 1.5780 119.00 164.86 110.99 1.0023 IC C CA N HT2 1.5780 119.00 -77.98 111.22 1.0030 IC N C *CA HA1 1.5010 119.00 120.0 110.0 1.1 IC N C *CA HA2 1.5010 119.00 -120.0 110.0 1.1 PATCHING FIRS NONE LAST NONE RESI MAMM 1.00 ! methylammonium, K. Kuczera GROUP Atom ce ct3 0.16 ! Atom nz nh3 -0.30 ! HE1 HZ1 Atom he1 ha 0.05 ! \ (+) | Atom he2 ha 0.05 !HE2-CE---NZ--HZ2 Atom he3 ha 0.05 ! / | Atom hz1 hc 0.33 ! HE3 HZ3 Atom hz2 hc 0.33 ! Atom hz3 hc 0.33 ! Bond ce he1 ce he2 ce he3 Bond ce nz nz hz1 nz hz2 nz hz3 ic he1 ce nz hz1 0.00 0.00 0.0 0.0 0.0 ic he1 ce nz hz2 0.00 0.00 120.0 0.0 0.0 ic he1 ce nz hz3 0.00 0.00 240.0 0.0 0.0 ic he2 ce nz hz1 0.00 0.00 120.0 0.0 0.0 ic he2 ce nz hz2 0.00 0.00 0.0 0.0 0.0 ic he2 ce nz hz3 0.00 0.00 240.0 0.0 0.0 ic he3 ce nz hz1 0.00 0.00 240.0 0.0 0.0 ic he3 ce nz hz2 0.00 0.00 120.0 0.0 0.0 ic he3 ce nz hz3 0.00 0.00 0.0 0.0 0.0 ic ce nz hz1 hz3 0.00 0.00 0.0 0.0 0.0 patc firs none last none RESI MAMI 0.00 ! methylamine, adm jr. GROUP ATOM N1 NH2 -0.96 ! ATOM C1 CT3 0.13 ! HC1 HN1 ATOM HN1 HC 0.34 ! \ / ATOM HC1 HA 0.05 ! HC2-C1---NZ ATOM HC2 HA 0.05 ! / \ ATOM HC3 HA 0.05 ! HC3 HN2 ATOM HN2 HC 0.34 ! BOND N1 C1 N1 HN1 N1 HN2 BOND C1 HC1 C1 HC2 C1 HC3 IC BLNK HN1 N1 C1 0.0 0.0 180. 0.0 0.0 IC HN1 N1 C1 HC1 0.0 0.0 180. 0.0 0.0 IC HN1 N1 C1 HC2 0.0 0.0 60. 0.0 0.0 IC HN1 N1 C1 HC3 0.0 0.0 300. 0.0 0.0 IC HC1 C1 N1 HN2 0.0 0.0 0. 0.0 0.0 RESI ACEH 0.00 ! acetic acid, ADM jr. GROUP ATOM C2 CT3 -0.30 ! ATOM C1 CD 0.75 ! H21 O2 ATOM H21 HA 0.09 ! \ // ATOM H22 HA 0.09 ! H22-C2--C1 ATOM H23 HA 0.09 ! / \ ATOM O2 OB -0.55 ! H23 O1-HO1 ATOM O1 OH1 -0.61 ! ATOM HO1 H 0.44 ! BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 DOUBLE C1 O2 IMPR C1 C2 O1 O2 DONO BLNK HO1 ! O1 ACCE O1 ACCE O2 IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 RESI MAS 0.00 ! methylacetate GROUP ! ATOM C1 CT3 -0.17 ! H22 ATOM C CD 0.63 ! | ATOM OM OS -0.34 ! H21-C2-H23 ATOM C2 CT3 -0.14 ! \ ATOM O OB -0.52 ! OM ATOM H11 HA 0.09 ! / ATOM H12 HA 0.09 ! O=C ATOM H13 HA 0.09 ! | ATOM H21 HA 0.09 ! H11-C1-H13 ATOM H22 HA 0.09 ! | ATOM H23 HA 0.09 ! H12 BOND C1 C C OM OM C2 DOUBLE C O BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IMPR C C1 OM O ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 RESI MEOH 0.00 ! methanol, adm jr. GROUP ! order of atoms to match that used in ab initio ATOM CB CT3 -0.04 ! H11 ATOM OG OH1 -0.66 ! \ ATOM HG1 H 0.43 ! H12--C1--O1 ATOM HB1 HA 0.09 ! / \ ATOM HB2 HA 0.09 ! H13 HO1 ATOM HB3 HA 0.09 ! BOND CB OG OG HG1 BOND CB HB1 CB HB2 CB HB3 DONO HG1 OG ACCE OG ! only for analysis IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HG1 OG CB HB2 0.0000 0.0000 180.0000 0.0000 0.0000 IC HG1 OG CB HB3 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 RESI METO -1.00 ! methoxide, adm jr. GROUP ! order of atoms to match that used in ab initio ATOM CB CT3 -0.41 ! HB1 ATOM OG OC -0.92 ! \ ! HB2--CB--OG (-) ATOM HB1 HA 0.11 ! / ATOM HB2 HA 0.11 ! HB3 ATOM HB3 HA 0.11 ! BOND CB OG BOND CB HB1 CB HB2 CB HB3 ACCE OG ! only for analysis IC HB2 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG HB2 *CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 RESI ETOH 0.00 ! Ethanol, adm jr. GROUP ATOM C1 CT2 0.05 ! H21 H11 H12 ATOM O1 OH1 -0.66 ! \ \ / ATOM HO1 H 0.43 ! H22--C2--C1 ATOM H11 HA 0.09 ! / \ ATOM H12 HA 0.09 ! H23 O1--HO1 GROUP ATOM C2 CT3 -0.27 ATOM H21 HA 0.09 ATOM H22 HA 0.09 ATOM H23 HA 0.09 BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 BOND C2 H21 C2 H22 C2 H23 DONO HO1 O1 ACCE O1 ! for ic build IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 IC O1 C1 C2 H23 0.0000 0.0000 300.0000 0.0000 0.0000 IC H21 C2 C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 IC H21 C2 C1 H12 0.0000 0.0000 240.0000 0.0000 0.0000 IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000 ! only for analysis !IC HO1 O1 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 !IC HO1 O1 C1 H12 0.0000 0.0000 180.0000 0.0000 0.0000 !IC HO1 O1 C1 H13 0.0000 0.0000 180.0000 0.0000 0.0000 !IC O1 C1 H11 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI ETO -1.00 ! Ethoxide, adm jr. GROUP ATOM OG OC -0.92 ! HA1 HB1 HB2 ATOM CB CT2 -0.30 ! \ \ / ATOM CA CT3 -0.27 ! HA2--CA--CB ATOM HB1 HA 0.11 ! / \ ATOM HB2 HA 0.11 ! HA3 OG (-) !GROUP ATOM HA1 HA 0.09 ATOM HA2 HA 0.09 ATOM HA3 HA 0.09 BOND CA CB CB OG CB HB1 CB HB2 BOND CA HA1 CA HA2 CA HA3 ACCE OG ! for ic build ic cb ca Ha1 ha2 0.0000 0.0000 180.0000 0.0000 0.0000 ic ca og cb hb1 0.0000 0.0000 180.0000 0.0000 0.0000 ic ca og cb hb2 0.0000 0.0000 180.0000 0.0000 0.0000 ic ca og cb hb3 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 IC HA1 CA CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HA1 CA CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 RESI PRO2 0.00 ! 2-propanol, adm jr. GROUP ATOM C2 CT1 0.14 ! H12 H13 H33 H32 ATOM O2 OH1 -0.66 ! \ / \ / ATOM HO2 H 0.43 ! H11--C1 C3--H31 ATOM H21 HA 0.09 ! \ / GROUP ! C2 ATOM C1 CT3 -0.27 ! / \ ATOM H11 HA 0.09 ! O2 H21 ATOM H12 HA 0.09 ! | ATOM H13 HA 0.09 ! HO2 GROUP ! ATOM C3 CT3 -0.27 ! ATOM H31 HA 0.09 ATOM H32 HA 0.09 ATOM H33 HA 0.09 BOND C1 C2 C2 C3 C2 O2 C2 H21 O2 HO2 BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 DONO HO2 O2 ACCE O2 ! for ic build IC C1 C2 C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 IC C1 C2 C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1 C2 C3 H33 0.0000 0.0000 240.0000 0.0000 0.0000 IC C3 C2 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3 C2 C1 H12 0.0000 0.0000 60.0000 0.0000 0.0000 IC C3 C2 C1 H13 0.0000 0.0000 300.0000 0.0000 0.0000 IC H31 C3 C2 O2 0.0000 0.0000 120.0000 0.0000 0.0000 IC H31 C3 C2 H21 0.0000 0.0000 240.0000 0.0000 0.0000 IC C3 C2 O2 HO2 0.0000 0.0000 180.0000 0.0000 0.0000 ! only for analysis !IC HO1 O1 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 !IC HO1 O1 C1 H12 0.0000 0.0000 180.0000 0.0000 0.0000 !IC HO1 O1 C1 H13 0.0000 0.0000 180.0000 0.0000 0.0000 !IC O1 C1 H11 H12 0.0000 0.0000 180.0000 0.0000 0.0000 RESI FORM 0.00 ! formamide, adm jr. ATOM HA HA 0.08 ! ATOM C CC 0.42 ! O Hc ATOM N NH2 -0.69 ! \\ / ATOM Hc H 0.35 ! C--N ATOM Ht H 0.35 ! / \ ATOM O O -0.51 ! HA Ht ! BOND C HA C N N Hc N Ht DOUBLE C O !BOND O DUM IMPR C HA N O c n ha o ! GAS PHASE GEOMETRY !IC DUM O C N 1.00 90.0 0. 124.70 1.352 IC O C N HC 1.2190 124.70 0. 118.50 1.0016 ! variable 1 IC HC N C HA 1.0016 118.50 180. 112.70 1.0980 ! variable 2 IC O C N HT 1.2190 124.70 180. 120.00 1.0015 ! variable 3 RESI ACEM 0.00 ! acetamide, adm jr. ! the amide charges listed below are used in asparagine and glutamine ! if Hc and Ht are made equivalent use N = -0.64, Hc = Ht = 0.32 GROUP ATOM CC CT3 -0.27 ! ATOM C CC 0.55 ! HC1 Ht ATOM N NH2 -0.62 ! \ / ATOM Hc H 0.32 ! HC2--CC--C---N ATOM Ht H 0.30 ! / || \ ATOM O O -0.55 ! HC3 O Hc ATOM HC1 HA 0.09 ! ATOM HC2 HA 0.09 ! ATOM HC3 HA 0.09 ! !atom dum dum 0.0 ! dummy for ic build BOND C N N Hc N Ht DOUBLE C O BOND C CC CC HC1 CC HC2 CC HC3 !BOND O DUM IMPR C CC N O C N CC O IMPR N C HC HT N C HT HC ! GAS PHASE GEOMETRY IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 IC O C CC HC1 1.2012 123.27 0. 113.80 1.0832 IC O C CC HC2 1.2012 123.27 120. 108.52 1.0836 IC O C CC HC3 1.2012 123.27 300. 108.52 1.0836 RESI NMA 0.00 ! N-methylacetamide, Louis Kuchnir GROUP ATOM CL CT3 -0.27 ATOM HL1 HA 0.09 ATOM HL2 HA 0.09 ATOM HL3 HA 0.09 ATOM C C 0.51 ATOM O O -0.51 ATOM N NH1 -0.47 ATOM H H 0.31 ATOM CR CT3 -0.11 ATOM HR1 HA 0.09 ATOM HR2 HA 0.09 ATOM HR3 HA 0.09 BOND HL1 CL HL2 CL HL3 CL ! N-Methylacetamide: BOND CL C C N N CR ! HL1\ O /HR1 BOND N H ! HL2-- CL -- C -- N -- CR --HR2 BOND HR1 CR HR2 CR HR3 CR ! HL3/ H \HR3 DOUBLE C O ! multiple dihedrals (check) DIHE CL C N CR IMPR N C CR H IMPR C CL N O ic o c n h 1.2233 122.84 180. 119.23 0.9933 ! variable 1 ic h n c cl 0.9933 119.23 0. 116.25 1.5118 ! variable 8 ic o c n cr 1.2233 122.84 0. 122.57 1.4488 ! variable 8 ic n c cl hl1 1.3418 116.25 180. 109.3 1.109 ! variable 2 ic n c cl hl2 1.3418 116.25 60. 109.3 1.109 ! variable 3 ic n c cl hl3 1.3418 116.25 300. 109.3 1.109 ! variable 4 ic c n cr hr1 1.3418 122.57 180. 110.7 1.113 ! variable 5 ic c n cr hr2 1.3418 122.57 60. 110.7 1.113 ! variable 6 ic c n cr hr3 1.3418 122.57 300. 110.7 1.113 ! variable 7 RESI ALAD 0.00 ! Alanine dipeptide, Louis Kuchnir GROUP ATOM CL CT3 -0.27 ATOM HL1 HA 0.09 ATOM HL2 HA 0.09 ATOM HL3 HA 0.09 GROUP ATOM CLP C 0.51 ATOM OL O -0.51 GROUP ATOM NL NH1 -0.47 ATOM HL H 0.31 ATOM CA CT1 0.07 ATOM HA HB 0.09 GROUP ATOM CB CT3 -0.27 ! HL1 OL OR HR1 ATOM HB1 HA 0.09 ! \ || HL HA || HR / ATOM HB2 HA 0.09 ! \ || | | || | / ATOM HB3 HA 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 GROUP ! / | \ ATOM CRP C 0.51 ! / HB1--CB--HB3 \ ATOM OR O -0.51 ! HL3 | HR3 GROUP ! HB2 ATOM NR NH1 -0.47 ATOM HR H 0.31 ATOM CR CT3 -0.11 ATOM HR1 HA 0.09 ATOM HR2 HA 0.09 ATOM HR3 HA 0.09 BOND CL CLP CLP NL NL CA BOND CA CRP CRP NR NR CR DOUBLE CLP OL CRP OR BOND NL HL NR HR BOND CA HA CA CB BOND CL HL1 CL HL2 CL HL3 BOND CB HB1 CB HB2 CB HB3 BOND CR HR1 CR HR2 CR HR3 IMPR CLP CL NL OL NL CLP CA HL IMPR CRP CA NR OR NR CRP CR HR ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 RESI MESH 0.00 ! methanethiol, DZUNG NGUYEN GROUP ATOM H1 HA 0.09 ! H1 ATOM H2 HA 0.09 ! \ ATOM H3 HA 0.09 ! H2--CM--S ATOM CM CT3 -0.20 ! / \ ATOM S S -0.23 ! H3 H4 ATOM H4 HS 0.16 ! Bond cm h1 cm h2 cm h3 Bond cm s s h4 ic h1 cm s h4 0.00 0.00 0.0 0.00 0.00 ic h2 cm s h4 0.00 0.00 120.0 0.00 0.00 ic h3 cm s h4 0.00 0.00 240.0 0.00 0.00 ic cm s h4 h1 0.00 0.00 0.0 0.00 0.00 patc firs none last none RESI MES1 -1.00 ! methylthiolate, adm jr. GROUP ATOM S SS -0.80 ! H11 ATOM C1 CS -0.47 ! \ ATOM H11 HA 0.09 ! H12--C1--S (-) ATOM H12 HA 0.09 ! / ATOM H13 HA 0.09 ! H13 ! BOND S C1 C1 H11 C1 H12 C1 H13 IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC S H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 patch first none last none RESI ETSH 0.00 ! ethanethiol, Dzung Nguyen GROUP Atom h1 ha 0.09 ! H1 H4 H5 Atom h2 ha 0.09 ! \ \ / Atom h3 ha 0.09 ! H2-CM1--CM2 Atom cm1 ct3 -0.27 ! / \ GROUP ! H3 S3--H6 Atom h4 ha 0.09 Atom h5 ha 0.09 Atom cm2 ct2 -0.11 Atom s3 s -0.23 Atom h6 hs 0.16 Bond cm1 h1 cm1 h2 cm1 h3 Bond cm1 cm2 cm2 h4 cm2 h5 bond cm2 s3 s3 h6 ic h1 cm1 cm2 s3 0.00 0.00 60.0 0.0 0.0 ic h2 cm1 cm2 s3 0.00 0.00 180.0 0.0 0.0 ic h3 cm1 cm2 s3 0.00 0.00 300.0 0.0 0.0 ic h1 cm1 cm2 h4 0.00 0.00 180.0 0.0 0.0 ic h2 cm1 cm2 h4 0.00 0.00 300.0 0.0 0.0 ic h3 cm1 cm2 h4 0.00 0.00 60.0 0.0 0.0 ic h1 cm1 cm2 h5 0.00 0.00 300.0 0.0 0.0 ic h2 cm1 cm2 h5 0.00 0.00 60.0 0.0 0.0 ic h3 cm1 cm2 h5 0.00 0.00 180.0 0.0 0.0 ic cm1 cm2 s3 h6 0.00 0.00 60.0 0.0 0.0 ic h4 cm2 s3 h6 0.00 0.00 180.0 0.0 0.0 ic h5 cm2 s3 h6 0.00 0.00 300.0 0.0 0.0 RESI ES1 -1.00 ! ethylthiolate, adm jr. GROUP ATOM S SS -0.80 ! H21 H11 H12 ATOM C1 CS -0.38 ! \ \ / ATOM C2 CT3 -0.27 ! H22--C2--C1 ATOM H21 HA 0.09 ! / \ ATOM H22 HA 0.09 ! H23 S (-) ATOM H23 HA 0.09 ATOM H11 HA 0.09 ATOM H12 HA 0.09 BOND S C1 C1 H11 C1 H12 C1 C2 BOND C2 H21 C2 H22 C2 H23 IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC S H11 *C1 C2 0.0000 0.0000 -120.0000 0.0000 0.0000 IC H12 C2 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 IC S C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC S C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 IC S C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 patch first none last none RESI DMDS 0.00 ! dimethyldisulfide, Dzung Nguyen GROUP atom h1 ha 0.09 ! atom h2 ha 0.09 ! H1 atom h3 ha 0.09 ! \ atom cm1 ct3 -0.19 ! H2-CM1 atom s2 sm -0.08 ! / \ GROUP ! H3 S2--S3 H4 atom s3 sm -0.08 ! \ / atom cm4 ct3 -0.19 ! CM4-H5 atom h4 ha 0.09 ! \ atom h5 ha 0.09 ! H6 atom h6 ha 0.09 ! bond h1 cm1 h2 cm1 h3 cm1 cm1 s2 bond s2 s3 s3 cm4 cm4 h4 cm4 h5 bond cm4 h6 ic h1 cm1 s2 s3 0.00 0.00 60.0 0.0 0.0 ic h2 cm1 s2 s3 0.00 0.00 180.0 0.0 0.0 ic h3 cm1 s2 s3 0.00 0.00 300.0 0.0 0.0 ic cm1 s2 s3 cm4 0.00 0.00 90.0 0.0 0.0 ic s2 s3 cm4 h4 0.00 0.00 60.0 0.0 0.0 ic s2 s3 cm4 h5 0.00 0.00 180.0 0.0 0.0 ic s2 s3 cm4 h6 0.00 0.00 300.0 0.0 0.0 patc firs none last none RESI EMS 0.00 ! ethylmethylsulfide, Dzung Nguyen group Atom h1 ha 0.09 ! Atom h2 ha 0.09 ! H1 H4 H5 Atom h3 ha 0.09 ! \ \ / Atom cm1 ct3 -0.27 ! H2-CM1--CM2 H6 group ! \ / Atom h4 ha 0.09 ! S3--CM4-H7 Atom h5 ha 0.09 ! \ Atom cm2 ct2 -0.14 ! H8 Atom s3 s -0.09 ! atom cm4 ct3 -0.22 ! atom h6 ha 0.09 ! atom h7 ha 0.09 ! atom h8 ha 0.09 ! Bond cm1 h1 cm1 h2 cm1 h3 Bond cm1 cm2 cm2 h4 cm2 h5 bond cm2 s3 s3 cm4 bond cm4 h6 cm4 h7 cm4 h8 ic h1 cm1 cm2 s3 0.00 0.00 60.0 0.0 0.0 ic h2 cm1 cm2 s3 0.00 0.00 180.0 0.0 0.0 ic h3 cm1 cm2 s3 0.00 0.00 300.0 0.0 0.0 ic h1 cm1 cm2 h4 0.00 0.00 180.0 0.0 0.0 ic h2 cm1 cm2 h4 0.00 0.00 300.0 0.0 0.0 ic h3 cm1 cm2 h4 0.00 0.00 60.0 0.0 0.0 ic h1 cm1 cm2 h5 0.00 0.00 300.0 0.0 0.0 ic h2 cm1 cm2 h5 0.00 0.00 60.0 0.0 0.0 ic h3 cm1 cm2 h5 0.00 0.00 180.0 0.0 0.0 ic cm1 cm2 s3 cm4 0.00 0.00 60.0 0.0 0.0 ic h4 cm2 s3 cm4 0.00 0.00 180.0 0.0 0.0 ic h5 cm2 s3 cm4 0.00 0.00 300.0 0.0 0.0 ic cm2 s3 cm4 h6 0.00 0.00 60.0 0.0 0.0 ic cm2 s3 cm4 h7 0.00 0.00 180.0 0.0 0.0 ic cm2 s3 cm4 h8 0.00 0.00 300.0 0.0 0.0 patch first none last none RESI IMIA 0.00 ! Imidazole, adm jr. GROUP ATOM CG CPH1 -0.05 ! HD1 HE1 ATOM HG HR3 0.09 ! | / ATOM CD2 CPH1 0.22 ! ND1--CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.36 ! HG-CG || ATOM HD1 H 0.32 ! \\ || ATOM CE1 CPH2 0.25 ! CD2--NE2 ATOM HE1 HR1 0.13 ! | ATOM NE2 NR2 -0.70 ! HD2 ! BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG HG DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 ! KEEPS HYDROGENS IN RING PLANE IMPH ND1 CG CE1 HD1 ND1 CE1 CG HD1 IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPH CG CD2 ND1 HG CG ND1 CD2 HG DONO HD1 ND1 ACCE NE2 ! for analysis dono he1 ce1 dono hg cg acce ce1 acce nd1 acce cd2 IC ND1 CG CD2 NE2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 ND1 *CG HG 0.0000 0.00 180.00 0.00 0.0000 IC NE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC HG CG ND1 CE1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC NE2 ND1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 RESI MIMI 0.00 ! 4-methylimidazole, adm jr. GROUP ATOM ND1 NR1 -0.36 ! HD1 HE1 ATOM HD1 H 0.32 ! | / ATOM CG CPH1 -0.05 ! HB1 ND1--CE1 ATOM CB CT2 -0.18 ! | / || ATOM HB1 HA 0.09 ! HB2-CB-CG || ATOM HB2 HA 0.09 ! | \\ || ATOM HB3 HA 0.09 ! HB3 CD2--NE2 GROUP ! | ATOM NE2 NR2 -0.70 ! HD2 ATOM CD2 CPH1 0.22 ! ATOM HD2 HR3 0.10 ! ATOM CE1 CPH2 0.25 ! ATOM HE1 HR1 0.13 ! BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB HB3 ! KEEPS HYDROGENS IN RING PLANE IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 DONO HD1 ND1 ACCE NE2 IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 IC CD2 CG CB HB3 0.0 0.0 240.0 0.0 0.0 RESI EIMI 0.00 ! 4-ethylimidazole, adm jr. GROUP ATOM CA CT3 -0.27 ! Optimized charges to minimize group size ATOM HA1 HA 0.09 ATOM HA2 HA 0.09 ATOM HA3 HA 0.09 GROUP ATOM ND1 NR1 -0.36 ! HD1 HE1 ATOM HD1 H 0.32 ! | / ATOM CG CPH1 -0.05 ! HA1 HB1 ND1--CE1 ATOM CB CT2 -0.09 ! \ | / || ATOM HB1 HA 0.09 ! HA2-CA--CB-CG || ATOM HB2 HA 0.09 ! / | \\ || GROUP ! HA3 HB2 CD2--NE2 ATOM NE2 NR2 -0.70 ! | ATOM CD2 CPH1 0.22 ! HD2 ATOM HD2 HR3 0.10 ! ATOM CE1 CPH2 0.25 ! ATOM HE1 HR1 0.13 ! BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 ! KEEPS HYDROGENS IN RING PLANE IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 DONO HD1 ND1 ACCE NE2 IC HA1 CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC HA1 CB *CA HA2 0.0000 0.00 120.00 0.00 0.0000 IC HA1 CB *CA HA3 0.0000 0.00 -120.00 0.00 0.0000 IC CG CA *CB HB1 0.0000 0.00 120.00 0.00 0.0000 IC CG CA *CB HB2 0.0000 0.00 -120.00 0.00 0.0000 IC CA CB CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC ND1 CB *CG CD2 0.0000 0.00 180.00 0.00 0.0000 IC CB CG ND1 CE1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD2 NE2 0.0000 0.00 180.00 0.00 0.0000 IC NE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 IC NE2 ND1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 RESI IMIM 1.00 ! Imidazolium, adm jr. GROUP ATOM CG CPH1 0.19 ! HD1 HE1 ATOM HG HR1 0.13 ! | / ATOM CD2 CPH1 0.19 ! ND1--CE1 ATOM HD2 HR1 0.13 ! / || GROUP ! HG-CG || ATOM ND1 NR3 -0.51 ! \\ || ATOM HD1 H 0.44 ! CD2--NE2 (+) ATOM NE2 NR3 -0.51 ! | \ ATOM HE2 H 0.44 ! HD2 HE2 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG HG DOUBLE NE2 CE1 CD2 CG BOND ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 ! KEEPS HYDROGENS IN RING PLANE IMPH ND1 CG CE1 HD1 NE2 CD2 CE1 HE2 IMPH ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 DONO HD1 ND1 DONO HE2 NE2 IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 IC HE1 CE1 NE2 HE2 1.0879 125.00 0.00 125.00 1.0000 RESI EIMM 1.00 ! Ethyl-Imidazolium, adm jr. GROUP ATOM CA CT3 -0.27 ATOM HA1 HA 0.09 ATOM HA2 HA 0.09 ATOM HA3 HA 0.09 GROUP ! ATOM CB CT2 -0.05 ! HD1 HE1 ATOM HB1 HA 0.09 ! | / ATOM HB2 HA 0.09 ! HA1 HB1 ND1--CE1 ATOM CG CPH1 0.19 ! \ | / || ATOM CD2 CPH1 0.19 ! HA2-CA--CB-CG || ATOM HD2 HR1 0.13 ! / | \\ || GROUP ! HA3 HB2 CD2--NE2(+) ATOM ND1 NR3 -0.51 ! | \ ATOM HD1 H 0.44 ! HD2 HE2 ATOM NE2 NR3 -0.51 ! ATOM HE2 H 0.44 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 BOND NE2 CD2 ND1 CG CE1 ND1 BOND CG CB NE2 HE2 DOUBLE CD2 CG NE2 CE1 BOND ND1 HD1 CD2 HD2 CE1 HE1 BOND CB HB1 CB HB2 CB CA BOND CA HA1 CA HA2 CA HA3 ! KEEPS HYDROGENS IN RING PLANE IMPH ND1 CG CE1 HD1 NE2 CD2 CE1 HE2 IMPH ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 DONO HD1 ND1 ACCE NE2 IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 IC CD2 CG CB CA 0.0 0.0 240.0 0.0 0.0 IC CG CB CA HA1 0.0 0.0 -180.0 0.0 0.0 IC CG CB CA HA2 0.0 0.0 -60.0 0.0 0.0 IC CG CB CA HA3 0.0 0.0 60.0 0.0 0.0 RESI HSE 0.00 ! neutral His, proton on NE2 GROUP ATOM N NH1 -0.47 ! | HE1 ATOM HN H 0.31 ! HN-N __ / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM CB CT2 -0.08 ! | | \\ | ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | \ ATOM ND1 NR2 -0.70 ! | HD2 HE2 ATOM CG CPH1 0.22 ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 GROUP ATOM NE2 NR1 -0.36 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG BOND NE2 CD2 N HN N CA BOND C CA C +N NE2 CE1 CA HA CB HB1 BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG CE1 ND1 IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HE2 NE2 ACCEPTOR ND1 ACCEPTOR O C IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2(-) ATOM OT1 OC -0.67 ! / ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 !IMPR OT1 CA OT2 C IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 RESI HSP 1.00 ! Protonated His GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB CT2 -0.05 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+) ATOM HB2 HA 0.09 ! O=C | \ ATOM CD2 CPH1 0.19 ! | HD2 HE2 ATOM HD2 HR1 0.13 ATOM CG CPH1 0.19 GROUP ATOM NE2 NR3 -0.51 ATOM HE2 H 0.44 ATOM ND1 NR3 -0.51 ATOM HD1 H 0.44 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG NE2 CE1 IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HD1 ND1 DONOR HE2 NE2 ACCEPTOR O C IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 PRES ACE 0.00 ! acetylated N-terminus GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA HN ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 RESI BENZ 0.00 ! benzene, adm jr. GROUP ATOM CG CA -0.115 ! ATOM HG HP 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CA -0.115 ! CD1--CE1 ATOM HD1 HP 0.115 ! / \ GROUP ! HG--CG CZ--HZ ATOM CD2 CA -0.115 ! \ / ATOM HD2 HP 0.115 ! CD2--CE2 GROUP ! | | ATOM CE1 CA -0.115 ! HD2 HE2 ATOM HE1 HP 0.115 ! GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM CZ CA -0.115 ATOM HZ HP 0.115 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ HZ IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 RESI PHEN 0.00 ! phenol, adm jr. GROUP ATOM CG CA -0.115 ! ATOM HG HP 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CA -0.115 ! CD1--CE1 ATOM HD1 HP 0.115 ! // \\ GROUP ! HG--CG CZ--OH ATOM CD2 CA -0.115 ! \ / \ ATOM HD2 HP 0.115 ! CD2==CE2 HH GROUP ! | | ATOM CE1 CA -0.115 ! HD2 HE2 ATOM HE1 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 BOND CD2 CG CE1 CD1 BOND CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OH OH HH DOUBLE CD1 CG CE2 CD2 CZ CE1 IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 RESI PHEO -1.00 ! phenoxide, adm jr. GROUP ATOM CG CA -0.115 ! ATOM HG HP 0.115 ! HD1 HE1 GROUP ! | | ATOM CD1 CA -0.115 ! CD1--CE1 ATOM HD1 HP 0.115 ! / \ GROUP ! HG--CG CZ--OH ATOM CD2 CA -0.115 ! \ / ATOM HD2 HP 0.115 ! CD2--CE2 GROUP ! | | ATOM CE1 CA -0.60 ! HD2 HE2 ATOM HE1 HP 0.28 ATOM CE2 CA -0.60 ATOM HE2 HP 0.28 ATOM CZ CA 0.40 ATOM OH OC -0.76 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ OH IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 RESI INDO 0.00 ! indole, adm jr. GROUP ATOM HG HP 0.115 ! HE3 ATOM CG CY -0.145 ! | ATOM CD2 CPT -0.020 ! HG CE3 ATOM CD1 CA 0.035 ! \ / \\ ATOM HD1 HP 0.115 ! CG-----CD2 CZ3-HZ3 ATOM NE1 NY -0.610 ! || || | ATOM HE1 H 0.380 ! CD1 CE2 CH2-HH2 ATOM CE2 CPT 0.130 ! / \ / \ // GROUP ! HD1 NE1 CZ2 ATOM CE3 CA -0.115 ! | | ATOM HE3 HP 0.115 ! HE1 HZ2 GROUP ATOM CZ2 CA -0.115 ATOM HZ2 HP 0.115 GROUP ATOM CZ3 CA -0.115 ATOM HZ3 HP 0.115 GROUP ATOM CH2 CA -0.115 ATOM HH2 HP 0.115 BOND CG HG CD2 CG NE1 CD1 BOND CZ2 CE2 BOND CZ3 CH2 CD2 CE3 NE1 CE2 BOND CD1 HD1 NE1 HE1 CE3 HE3 BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 DONOR HE1 NE1 IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE2 CG *CD2 CE3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CD2 CE3 CZ3 0.0000 0.0000 0.0000 0.0000 0.0000 IC CD2 CE3 CZ3 CH2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CE3 CZ3 CH2 CZ2 0.0000 0.0000 0.0000 0.0000 0.0000 IC CZ3 CD2 *CE3 HE3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CH2 CE3 *CZ3 HZ3 0.0000 0.0000 180.0000 0.0000 0.0000 IC CZ2 CZ3 *CH2 HH2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE2 CH2 *CZ2 HZ2 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CE2 *NE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CG NE1 *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 RESI AP2 0.00 ! acetyl-prolineamide, R. Dunbrack ! !HY1 HY2 HY3 ATOM N N -0.29 ! \ | / ATOM CA CP1 0.02 ! CAY ATOM CB CP2 -0.18 ! | ATOM CG CP2 -0.18 ! OY=CY HD1 HD2 ATOM CD CP3 0.00 ! \ \ / ATOM CY C 0.51 ! N---CD HG1 ATOM OY O -0.51 ! | \ / ATOM C CC 0.51 ! | CG ATOM HA HB 0.09 ! | / \ ATOM HB1 HA 0.09 ! HA-CA--CB HG2 ATOM HB2 HA 0.09 ! | / \ ATOM HG1 HA 0.09 ! | HB1 HB2 ATOM HG2 HA 0.09 ! O=C ATOM HD1 HA 0.09 ! | ATOM HD2 HA 0.09 ! NT ATOM CAY CT3 -0.27 ! / \ ATOM HY1 HA 0.09 ! HT1 HT2 ATOM HY2 HA 0.09 ATOM HY3 HA 0.09 ATOM O O -0.51 ATOM NT NH2 -0.62 ATOM HT1 H 0.31 ATOM HT2 H 0.31 BOND CY N CAY HY1 CAY HY2 CAY HY3 BOND CY CAY N CA CA CB CB CG CG CD CD N BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND C CA C NT NT HT1 NT HT2 DOUBLE C O CY OY IMPR CY CAY N OY IMPR C CA NT O IMPR C NT CA O IMPR N CY CA CD IMPR NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT ACCEPTOR OY CY ACCEPTOR O C ! Improper ICs IC CY CA *N CD 0.00 0.00 180.00 0.00 0.00 IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 IC N CAY *CY OY 0.00 0.00 180.00 0.00 0.00 ! Backbone + Peptide bond IC's IC OY CY N CA 0.00 0.00 0.00 0.00 0.00 !Omega IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !Omega IC CY N CA C 0.00 120.64 -60.00 0.00 0.00 !Psi IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi IC CAY CY N CD 0.00 0.00 0.00 120.64 0.00 IC CY N CD CG 0.00 0.00 168.60 103.28 0.00 IC CY N CA CB 0.00 0.00 168.64 103.34 0.00 ! Ring IC's IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 ! Carbonyl IC's IC CD N CA C 0.00 112.90 120.00 108.00 0.00 ! Hydrogen IC's IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 RESI TP2 1.00 ! prolineamide, R. Dunbrack ATOM N NP -0.07 ! ATOM HN1 HC 0.24 ! ATOM HN2 HC 0.24 ! ATOM CD CP3 0.16 ! ATOM CB CP2 -0.18 ! HN1 HD1 HD2 ATOM CG CP2 -0.18 ! \ \ / ATOM CA CP1 0.16 ! HN2--N---CD HG1 ATOM C CC 0.51 ! | \ / ATOM O O -0.51 ! | CG ATOM HA HB 0.09 ! | / \ ATOM HB1 HA 0.09 ! HA-CA--CB HG2 ATOM HB2 HA 0.09 ! | / \ ATOM HG1 HA 0.09 ! | HB1 HB2 ATOM HG2 HA 0.09 ! O=C ATOM HD1 HA 0.09 ! | ATOM HD2 HA 0.09 ! NT ATOM NT NH2 -0.62 ! / \ ATOM HT1 H 0.31 ! HT1 HT2 ATOM HT2 H 0.31 ! BOND HN1 N HN2 N N CA CA CB CB CG CG CD CD N BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND C CA C NT NT HT1 NT HT2 DOUBLE C O IMPR C CA NT O IMPR C NT CA O IMPR NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT DONOR HN1 N DONOR HN2 N ACCEPTOR O C ! Improper ICs IC HN1 CA *N CD 0.00 0.00 120.00 0.00 0.00 IC HN2 CA *N HN1 0.00 0.00 120.00 0.00 0.00 IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 ! Backbone + Peptide bond IC's IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi ! Ring IC's IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 ! Carbonyl IC's IC CD N CA C 0.00 112.90 120.00 108.00 0.00 ! Hydrogen IC's IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 Resi ETHA 0.00 ! ethane, S. Fischer Group Atom h1 ha 0.09 ! H1 H4 Atom h2 ha 0.09 ! \ / Atom h3 ha 0.09 ! H2-C1--C2-H5 Atom c1 ct3 -0.27 ! / \ Group ! H3 H6 Atom h4 ha 0.09 Atom h5 ha 0.09 Atom h6 ha 0.09 Atom c2 ct3 -0.27 Bond c1 h1 c1 h2 c1 h3 Bond c1 c2 c2 h4 c2 h5 c2 h6 ic h1 c1 c2 h4 0.00 0.00 0.0 0.0 0.0 ic h1 c1 c2 h5 0.00 0.00 120.0 0.0 0.0 ic h1 c1 c2 h6 0.00 0.00 240.0 0.0 0.0 ic h2 c1 c2 h6 0.00 0.00 120.0 0.0 0.0 ic h3 c1 c2 h6 0.00 0.00 240.0 0.0 0.0 Resi PROP 0.00 ! propane, adm jr. Group ! Atom h11 ha 0.09 ! H11 H21 H31 Atom h12 ha 0.09 ! \ | / Atom h13 ha 0.09 ! H12-C1--C2--C3-H32 Atom c1 ct3 -0.27 ! / | \ Group ! H13 H22 H33 Atom c2 ct2 -0.18 ! Atom h21 ha 0.09 ! Atom H22 ha 0.09 Group Atom h31 ha 0.09 Atom h32 ha 0.09 Atom h33 ha 0.09 Atom c3 ct3 -0.27 Bond c1 h11 c1 h12 c1 h13 Bond c1 c2 c2 h21 c2 h22 bond c2 c3 c3 h31 c3 h32 c3 h33 ic h11 c1 c2 c3 0.00 0.00 0.0 0.0 0.0 ic h11 c1 c2 h21 0.00 0.00 120.0 0.0 0.0 ic h11 c1 c2 h22 0.00 0.00 240.0 0.0 0.0 ic c1 c2 c3 h31 0.00 0.00 0.0 0.0 0.0 ic c1 c2 c3 h32 0.00 0.00 120.0 0.0 0.0 ic c1 c2 c3 h33 0.00 0.00 240.0 0.0 0.0 ic c3 c2 c1 h12 0.00 0.00 120.0 0.0 0.0 ic c3 c2 c1 h13 0.00 0.00 120.0 0.0 0.0 Resi BUTA 0.00 ! butane, S. Fischer Group Atom h11 ha 0.09 ! H11 H21 H31 H41 Atom h12 ha 0.09 ! \ | | / Atom h13 ha 0.09 ! H12-C1--C2--C3--C4-H42 Atom c1 ct3 -0.27 ! / | | \ Group ! H13 H22 H33 H43 Atom h21 ha 0.09 Atom h22 ha 0.09 Atom c2 ct2 -0.18 Group Atom h31 ha 0.09 Atom h32 ha 0.09 atom c3 ct2 -0.18 Group atom h41 ha 0.09 atom h42 ha 0.09 atom h43 ha 0.09 atom c4 ct3 -0.27 Bond h11 c1 h12 c1 h13 c1 c1 c2 Bond h21 c2 h22 c2 c2 c3 Bond h31 c3 h32 c3 c3 c4 Bond h41 c4 h42 c4 h43 c4 ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h11 c1 c2 h21 0.00 0.00 120.0 0.00 0.00 ic h11 c1 c2 h22 0.00 0.00 240.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 ic h13 c1 c2 c3 0.00 0.00 240.0 0.00 0.00 ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 ic c1 c2 c3 h31 0.00 0.00 120.0 0.00 0.00 ic c1 c2 c3 h32 0.00 0.00 240.0 0.00 0.00 ic h21 c2 c3 c4 0.00 0.00 120.0 0.00 0.00 ic h22 c2 c3 c4 0.00 0.00 240.0 0.00 0.00 ic c2 c3 c4 h41 0.00 0.00 0.0 0.00 0.00 ic c2 c3 c4 h42 0.00 0.00 120.0 0.00 0.00 ic c2 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 ic h31 c3 c4 h43 0.00 0.00 120.0 0.00 0.00 ic h32 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 Resi IBUT 0.00 ! Iso-butane, S. Fischer Group atom ct ct1 -0.09 ! H12 atom ht ha 0.09 ! | Group ! H11-C1-H13 Atom c1 ct3 -0.27 ! | Atom h11 ha 0.09 ! CT-HT Atom h12 ha 0.09 ! / \ Atom h13 ha 0.09 ! / \ Group ! H21-C2 C3-H31 Atom c2 ct3 -0.27 ! / | | \ Atom h21 ha 0.09 ! H22 H23 H33 H32 Atom h22 ha 0.09 ! Atom h23 ha 0.09 ! Group atom c3 ct3 -0.27 Atom h31 ha 0.09 atom h32 ha 0.09 atom h33 ha 0.09 Bond ct c1 ct c2 ct c3 ct ht Bond c1 h11 c1 h12 c1 h13 Bond c2 h21 c2 h22 c2 h23 Bond c3 h31 c3 h32 c3 h33 ic ht ct c1 h11 0.00 0.00 60.0 0.00 0.00 ic ct c1 h11 h12 0.00 0.00 0.0 0.00 0.00 ic ht ct c1 h12 0.00 0.00 180.0 0.00 0.00 ic ht ct c1 h13 0.00 0.00 300.0 0.00 0.00 ic h12 c1 ct c2 0.00 0.00 60.0 0.00 0.00 ic h12 c1 ct c3 0.00 0.00 -60.0 0.00 0.00 ic ht ct c2 h21 0.00 0.00 60.0 0.00 0.00 ic ht ct c2 h22 0.00 0.00 180.0 0.00 0.00 ic ht ct c2 h23 0.00 0.00 300.0 0.00 0.00 ic ht ct c3 h31 0.00 0.00 60.0 0.00 0.00 ic ht ct c3 h32 0.00 0.00 180.0 0.00 0.00 ic ht ct c3 h33 0.00 0.00 300.0 0.00 0.00 Resi PENT 0.00 ! pentane, adm jr. Group Atom C1 CT3 -0.27 ! H11 H21 H31 H41 H51 Atom H11 HA 0.09 ! \ | | | / Atom H12 HA 0.09 ! H12-C1--C2--C3--C4--C5-H52 Atom H13 HA 0.09 ! / | | | \ Group ! H13 H22 H33 H42 H53 Atom C2 CT2 -0.18 Atom H21 HA 0.09 Atom H22 HA 0.09 Group Atom C3 CT2 -0.18 Atom H31 HA 0.09 Atom H32 HA 0.09 Group Atom C4 CT2 -0.18 Atom H41 HA 0.09 Atom H42 HA 0.09 Group Atom C5 CT3 -0.27 Atom H51 HA 0.09 Atom H52 HA 0.09 Atom H53 HA 0.09 Bond C1 C2 C2 C3 C3 C4 C4 C5 Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 Bond C5 H52 C5 H53 Ic H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 Ic C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 Ic C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 Ic C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 Ic H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 Ic H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 Ic C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 Ic C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 Ic C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 Ic C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 Ic C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 Ic C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 Ic C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 Ic C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 patc firs none last none RESI HEME -2.00 ! 6-liganded planar heme GROUP ATOM FE FE 0.24 ! O2A O1A O2D O1D ATOM NA NPH -0.18 ! \\ // \\ // ATOM NB NPH -0.18 ! CGA CGD ATOM NC NPH -0.18 ! | | ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 ATOM C1A CPA 0.12 ! | | | ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 ATOM C3A CPB -0.06 ! | / \ | ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D ATOM C1B CPA 0.12 ! | | | | ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 ATOM C1C CPA 0.12 ! C4A \ / C1D ATOM C2C CPB -0.06 ! / \ / \ ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD ATOM C4C CPA 0.12 ! \ / \ / ATOM C1D CPA 0.12 ! C1B / \ C4C HAC ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 GROUP ! | | | | CBC ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 ATOM HA HA 0.10 ! | \_CHC_/ | GROUP ! CAB | CMC--HMC3 ATOM CHB CPM -0.10 ! // \ HC / | ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2 GROUP ! / \ ATOM CHC CPM -0.10 ! HBB1 HBB2 ATOM HC HA 0.10 ! GROUP ATOM CHD CPM -0.10 ATOM HD HA 0.10 GROUP ATOM CMA CT3 -0.27 ATOM HMA1 HA 0.09 ATOM HMA2 HA 0.09 ATOM HMA3 HA 0.09 GROUP ATOM CAA CT2 -0.18 ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 GROUP ATOM CBA CT2 -0.28 ATOM HBA1 HA 0.09 ATOM HBA2 HA 0.09 ATOM CGA CC 0.62 ATOM O1A OC -0.76 ATOM O2A OC -0.76 GROUP ATOM CMB CT3 -0.27 ATOM HMB1 HA 0.09 ATOM HMB2 HA 0.09 ATOM HMB3 HA 0.09 GROUP ATOM CAB C -0.20 ATOM HAB HA 0.20 GROUP ATOM CBB C -0.20 ATOM HBB1 HA 0.10 ATOM HBB2 HA 0.10 GROUP ATOM CMC CT3 -0.27 ATOM HMC1 HA 0.09 ATOM HMC2 HA 0.09 ATOM HMC3 HA 0.09 GROUP ATOM CAC C -0.20 ATOM HAC HA 0.20 GROUP ATOM CBC C -0.20 ATOM HBC1 HA 0.10 ATOM HBC2 HA 0.10 GROUP ATOM CMD CT3 -0.27 ATOM HMD1 HA 0.09 ATOM HMD2 HA 0.09 ATOM HMD3 HA 0.09 GROUP ATOM CAD CT2 -0.18 ATOM HAD1 HA 0.09 ATOM HAD2 HA 0.09 GROUP ATOM CBD CT2 -0.28 ATOM HBD1 HA 0.09 ATOM HBD2 HA 0.09 ATOM CGD CC 0.62 ATOM O1D OC -0.76 ATOM O2D OC -0.76 BOND FE NA FE NB FE NC FE ND NA C1A BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A BOND CHA HA CHB HB CHC HC CHD HD BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 BOND CMA HMA1 CMA HMA2 CMA HMA3 BOND CMB HMB1 CMB HMB2 CMB HMB3 BOND CAB HAB CBB HBB1 CBB HBB2 BOND CMC HMC1 CMC HMC2 CMC HMC3 BOND CAC HAC CBC HBC1 CBC HBC2 BOND CMD HMD1 CMD HMD2 CMD HMD3 BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPR C2D C1D C3D CMD C3D C2D C4D CAD IMPR CGA O2A CBA O1A CGD O2D CBD O1D IMPR C4A NA C1A C2A C1A NA C4A C3A IMPR C4B NB C1B C2B C1B NB C4B C3B IMPR C4C NC C1C C2C C1C NC C4C C3C IMPR C4D ND C1D C2D C1D ND C4D C3D IMPR NA C1A C2A C3A NA C4A C3A C2A IMPR NB C1B C2B C3B NB C4B C3B C2B IMPR NC C1C C2C C3C NC C4C C3C C2C IMPR ND C1D C2D C3D ND C4D C3D C2D IMPR NA C1A CHA C4D NA C4A CHB C1B IMPR NB C1B CHB C4A NB C4B CHC C1C IMPR NC C1C CHC C4B NC C4C CHD C1D IMPR ND C1D CHD C4C ND C4D CHA C1A IMPR CHA C1A C4D HA IMPR CHB C1B C4A HB IMPR CHC C1C C4B HC IMPR CHD C1D C4C HD IMPR C1A C2A CHA NA C4A C3A CHB NA IMPR C1B C2B CHB NB C4B C3B CHC NB IMPR C1C C2C CHC NC C4C C3C CHD NC IMPR C1D C2D CHD ND C4D C3D CHA ND IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 ACCEPTOR NA ACCEPTOR O1A ! CGA ACCEPTOR O2A ! CGA ACCEPTOR NB ACCEPTOR NC ACCEPTOR ND ACCEPTOR O1D ! CGD ACCEPTOR O2D ! CGD IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 PATCHING FIRS NONE LAST NONE PRES FHEM 0.00000 ! fix up the heme by deleting unwanted autogenerated angles ! unliganded heme patch, K. Kuczera DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND RESI TIP3 0.00 ! TIPS3P WATER MODEL, adm jr. GROUP ! Generate noangle nodihedral ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ACCE OH2 RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p GROUP ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI OCOH 0.0 ! OCTANOL GROUP ATOM C1 CT2 0.05 ATOM H11 HA 0.09 ATOM H12 HA 0.09 ATOM O1 OH1 -0.66 ATOM HO1 H 0.43 GROUP ATOM C2 CT2 -0.180 ATOM H21 HA 0.090 ATOM H22 HA 0.090 GROUP ATOM C3 CT2 -0.180 ATOM H31 HA 0.090 ATOM H32 HA 0.090 GROUP ATOM C4 CT2 -0.180 ATOM H41 HA 0.090 ATOM H42 HA 0.090 GROUP ATOM C5 CT2 -0.180 ATOM H51 HA 0.090 ATOM H52 HA 0.090 GROUP ATOM C6 CT2 -0.180 ATOM H61 HA 0.090 ATOM H62 HA 0.090 GROUP ATOM C7 CT2 -0.180 ATOM H71 HA 0.090 ATOM H72 HA 0.090 GROUP ATOM C8 CT3 -0.270 ATOM H81 HA 0.090 ATOM H82 HA 0.090 ATOM H83 HA 0.090 BOND C1 C2 C2 C3 C3 C4 C4 C5 BOND C5 C6 C6 C7 C7 C8 C1 O1 O1 HO1 BOND C1 H11 C1 H12 C2 H21 C2 H22 BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 BOND C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 BOND C8 H81 C8 H82 C8 H83 IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C6 C7 C8 H83 0.0000 0.00 180.00 0.00 0.0000 IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 IC H11 C2 *C1 O1 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 IC C4 C6 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 IC C6 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 IC C7 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 IC C7 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 PATC FIRS NONE LAST NONE Resi ETHE 0.00 ! ethylene, yin/adm jr. Group Atom c1 ce2 -0.42 Atom h11 HE2 0.21 Atom h12 HE2 0.21 Group Atom c2 ce2 -0.42 Atom h21 HE2 0.21 Atom h22 HE2 0.21 Bond c1 h11 c1 h12 Double c1 c2 Bond c2 h21 c2 h22 IMPR c1 c2 h12 h11 IMPR c1 c2 h11 h12 IMPR c2 c1 h22 h21 IMPR c2 c1 h21 h22 ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 ic h22 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 ic c1 c2 h21 h22 0.00 0.00 180.0 0.0 0.0 patc firs none last none Resi PRPE 0.00 ! propene, yin/adm jr. Group Atom c1 ce2 -0.42 Atom h11 HE2 0.21 Atom h12 HE2 0.21 Group Atom c2 ce1 -0.15 Atom h21 HE1 0.15 Group Atom c3 ct3 -0.27 Atom h31 ha 0.09 Atom h32 ha 0.09 Atom h33 ha 0.09 Bond c1 h11 c1 h12 Double c1 c2 Bond c2 h21 Bond c2 c3 bond c3 h31 c3 h32 c3 h33 ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 ic c3 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 ic h31 c3 c2 c1 0.00 0.00 0.0 0.0 0.0 ic h32 c3 c2 c1 0.00 0.00 120.0 0.0 0.0 ic h33 c3 c2 c1 0.00 0.00 -120.0 0.0 0.0 patc firs none last none Resi BTE1 0.00 ! 1-Butene, yin/adm jr. Group Atom c1 ce2 -0.42 Atom h11 HE2 0.21 Atom h12 HE2 0.21 Group Atom c2 ce1 -0.15 Atom h21 HE1 0.15 Group Atom c3 ct2 -0.18 Atom h31 ha 0.09 Atom h32 ha 0.09 Group Atom c4 ct3 -0.27 Atom h41 ha 0.09 Atom h42 ha 0.09 Atom h43 ha 0.09 BOND c1 h11 c1 h12 DOUBLE c1 c2 BOND c2 h21 BOND c2 c3 BOND c3 h31 c3 h32 BOND c3 c4 BOND c4 h41 c4 h42 c4 h43 ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 ic h11 c1 c2 c3 0.00 0.00 180.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 ic h31 c2 *c3 c4 0.00 0.00 120.0 0.00 0.00 ic h32 c2 *c3 c4 0.00 0.00 -120.0 0.00 0.00 ic h41 c4 c3 c2 0.00 0.00 180.0 0.00 0.00 ic h42 c4 c3 c2 0.00 0.00 60.0 0.00 0.00 ic h43 c4 c3 c2 0.00 0.00 -60.0 0.00 0.00 patc firs none last none Resi BTE2 0.00 ! 2-Butene, yin/adm jr. Group Atom c1 ct3 -0.27 Atom h11 ha 0.09 Atom h12 ha 0.09 Atom h13 ha 0.09 Group Atom c2 ce1 -0.15 Atom h21 HE1 0.15 Group Atom c3 ce1 -0.15 Atom h31 HE1 0.15 Group Atom c4 ct3 -0.27 Atom h41 ha 0.09 Atom h42 ha 0.09 Atom h43 ha 0.09 BOND c1 h11 c1 h12 c1 h13 BOND c1 c2 BOND c2 h21 DOUBLE c2 c3 BOND c3 h31 BOND c3 c4 BOND c4 h41 c4 h42 c4 h43 ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00 ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 ic h31 c4 *c3 c2 0.00 0.00 180.0 0.00 0.00 ic h41 c4 c3 c2 0.00 0.00 0.0 0.00 0.00 ic h42 c4 c3 c2 0.00 0.00 120.0 0.00 0.00 ic h43 c4 c3 c2 0.00 0.00 -120.0 0.00 0.00 patc firs none last none RESI HE1 0.00 ! helium GROUP ATOM HE01 HE 0.00 PATCHING FIRST NONE LAST NONE RESI NE1 0.00 ! neon GROUP ATOM NE01 NE 0.00 PATCHING FIRST NONE LAST NONE RESI DUM 0.00 ! DUMMY ATOM GROUP ATOM DUM DUM 0.00 PATCHING FIRST NONE LAST NONE END