*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< *>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< * 27 1 ! ! 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. ! !PHOSPHOTYROSINE ! !Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. !Structural Characterization of the Phosphotyrosine Binding Region of a !High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics !Simulation and Chemical Shift Calculations. Journal of the American !Chemical Society, 1996, 118: 11265-11277. ! !IONS (see lipid and nucleic acid topology and parameter files for !additional ions ! !ZINC ! !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: !Structure, Function, and Genetics 23:12-31 (1995) ! 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 20 C 12.01100 C ! carbonyl C, peptide backbone 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, asn,asp,gln,glu,cter,ct2 MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 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 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 NTER LAST CTER AUTO ANGLES DIHE RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 RESI ARG 1.00 GROUP ATOM N NH1 -0.47 ! | HH11 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA HB 0.09 ! | | | | | //(+) GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB CT2 -0.18 ! | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 ATOM HB2 HA 0.09 ! O=C | GROUP ! | HH21 ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 0.20 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM NE NC2 -0.70 ATOM HE HC 0.44 ATOM CZ C 0.64 ATOM NH1 NC2 -0.80 ATOM HH11 HC 0.46 ATOM HH12 HC 0.46 ATOM NH2 NC2 -0.80 ATOM HH21 HC 0.46 ATOM HH22 HC 0.46 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH2 CZ N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 DOUBLE O C CZ NH1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N IMPR CZ NH1 NH2 NE DONOR HN N DONOR HE NE DONOR HH11 NH1 DONOR HH12 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 RESI ARGN 0.00 ! an arbitrary "deprotonated" state GROUP ATOM N NH1 -0.47 ! | HH11 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1 ATOM HA HB 0.09 ! | | | | | // GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB CT2 -0.18 ! | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 ATOM HB2 HA 0.09 ! O=C | GROUP ! | HH21 ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 0.00 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM NE NC2 -0.70 ATOM HE HC 0.43 ATOM CZ C 0.40 ATOM NH1 NC2 -0.62 ATOM HH11 HC 0.31 ATOM NH2 NC2 -0.62 ATOM HH21 HC 0.31 ATOM HH22 HC 0.31 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH2 CZ N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 BOND NE HE NH1 HH11 NH2 HH21 NH2 HH22 DOUBLE O C CZ NH1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N IMPR CZ NH1 NH2 NE DONOR HN N DONOR HE NE DONOR HH11 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 RESI ASN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) ATOM HA HB 0.09 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CC 0.55 ATOM OD1 O -0.55 GROUP ATOM ND2 NH2 -0.62 ATOM HD21 H 0.32 ATOM HD22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 DOUBLE C O CG OD1 IMPR N -C CA HN C CA +N O IMPR CG ND2 CB OD1 CG CB ND2 OD1 IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 CMAP -C N CA C N CA C +N DONOR HN N DONOR HD21 ND2 DONOR HD22 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 RESI ASP -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 ATOM HA HB 0.09 ! | | // GROUP ! HA-CA--CB--CG ATOM CB CT2 -0.28 ! | | \ ATOM HB1 HA 0.09 ! | HB2 OD2(-) ATOM HB2 HA 0.09 ! O=C ATOM CG CC 0.62 ! | ATOM OD1 OC -0.76 ATOM OD2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 DOUBLE O C CG OD1 IMPR N -C CA HN C CA +N O !IMPR OD1 CB OD2 CG IMPR CG CB OD2 OD1 CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR OD1 CG ACCEPTOR OD2 CG ACCEPTOR O C IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 RESI CYS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--SG ATOM CB CT2 -0.11 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM SG S -0.23 ! | ATOM HG1 HS 0.16 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 SG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 SG ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 RESI GLN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA HB 0.09 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CC 0.55 ATOM OE1 O -0.55 GROUP ATOM NE2 NH2 -0.62 ATOM HE21 H 0.32 ATOM HE22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 NE2 HE21 NE2 HE22 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O IMPR CD NE2 CG OE1 CD CG NE2 OE1 IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 CMAP -C N CA C N CA C +N DONOR HN N DONOR HE21 NE2 DONOR HE22 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 RESI GLU -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 ATOM HA HB 0.09 ! | | | // GROUP ! HA-CA--CB--CG--CD ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.28 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM CD CC 0.62 ATOM OE1 OC -0.76 ATOM OE2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O !IMPR OE1 CG OE2 CD IMPR CD CG OE2 OE1 CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 RESI GLY 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! N-H ATOM CA CT2 -0.02 ! | ATOM HA1 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA1-CA-HA2 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! | BOND N HN N CA C CA BOND C +N CA HA1 CA HA2 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCHING FIRS GLYP RESI HSD 0.00 ! neutral HIS, proton on ND1 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 -0.09 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | ATOM ND1 NR1 -0.36 ! | HD2 ATOM HD1 H 0.32 ATOM CG CPH1 -0.05 GROUP ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 ATOM NE2 NR2 -0.70 ATOM CD2 CPH1 0.22 ATOM HD2 HR3 0.10 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 CD2 HD2 CE1 HE1 DOUBLE O C CG CD2 CE1 NE2 IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 !!!! copy of HSD RESI HIS 0.00 ! neutral HIS, proton on ND1 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 -0.09 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | ATOM ND1 NR1 -0.36 ! | HD2 ATOM HD1 H 0.32 ATOM CG CPH1 -0.05 GROUP ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 ATOM NE2 NR2 -0.70 ATOM CD2 CPH1 0.22 ATOM HD2 HR3 0.10 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 CD2 HD2 CE1 HE1 DOUBLE O C CG CD2 CE1 NE2 IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 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 CMAP -C N CA C N CA C +N 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 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 CMAP -C N CA C N CA C +N 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 RESI ILE 0.00 GROUP ATOM N NH1 -0.47 ! | HG21 HG22 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG2--HG23 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB HD1 ATOM CB CT1 -0.09 ! | \ / ATOM HB HA 0.09 ! | CG1--CD--HD2 GROUP ! O=C / \ \ ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM CG1 CT2 -0.18 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 GROUP ATOM CD CT3 -0.27 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM HD3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB CD CG1 BOND N HN N CA C CA C +N BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 RESI LEU 0.00 GROUP ATOM N NH1 -0.47 ! | HD11 HD12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 CD1--HD13 ATOM HA HB 0.09 ! | | / GROUP ! HA-CA--CB--CG-HG ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 CD2--HD23 ATOM HB2 HA 0.09 ! O=C | \ GROUP ! | HD21 HD22 ATOM CG CT1 -0.09 ATOM HG HA 0.09 GROUP ATOM CD1 CT3 -0.27 ATOM HD11 HA 0.09 ATOM HD12 HA 0.09 ATOM HD13 HA 0.09 GROUP ATOM CD2 CT3 -0.27 ATOM HD21 HA 0.09 ATOM HD22 HA 0.09 ATOM HD23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 !IC CD1 CB *CG HG 1.5361 110.4800 116.6300 108.6800 1.1168 old IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 RESI LYS 1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB CT2 -0.18 ! | | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP ATOM CE CT2 0.21 ATOM HE1 HA 0.05 ATOM HE2 HA 0.05 ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 DOUBLE O C BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 RESI LYN 0.00 ! neutral Lys w/ HZ3 removed GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB CT2 -0.18 ! | | | | | ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP ATOM CE CT2 0.40 ATOM HE1 HA -0.05 ATOM HE2 HA -0.05 ATOM NZ NH3 -0.98 ATOM HZ1 HC 0.34 ATOM HZ2 HC 0.34 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 DOUBLE O C BOND NZ HZ1 NZ HZ2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 RESI MET 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HE1 ATOM HA HB 0.09 ! | | | | GROUP ! HA-CA--CB--CG--SD--CE--HE3 ATOM CB CT2 -0.18 ! | | | | ATOM HB1 HA 0.09 ! | HB2 HG2 HE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.14 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM SD S -0.09 ATOM CE CT3 -0.22 ATOM HE1 HA 0.09 ATOM HE2 HA 0.09 ATOM HE3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB SD CG CE SD BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND CE HE1 CE HE2 CE HE3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 RESI PHE 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--HZ ATOM CB CT2 -0.18 ! | | \ __ / ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA -0.115 ATOM HZ HP 0.115 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 N HN BOND N CA C CA C +N CA HA BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 DOUBLE O C CD1 CG CZ CE1 CE2 CD2 BOND CE2 HE2 CZ HZ IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 RESI PRO 0.00 GROUP ! HD1 HD2 ATOM N N -0.29 ! | \ / ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 ATOM HD1 HA 0.09 ! | \ / ATOM HD2 HA 0.09 ! | CG ATOM CA CP1 0.02 ! | / \ ATOM HA HB 0.09 ! HA-CA--CB HG2 GROUP ! | / \ ATOM CB CP2 -0.18 ! | HB1 HB2 ATOM HB1 HA 0.09 ! O=C ATOM HB2 HA 0.09 ! | GROUP ATOM CG CP2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND C CA C +N BOND N CA CA CB CB CG CG CD N CD BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB DOUBLE O C IMPR N -C CA CD IMPR C CA +N O !CMAP -C N CA C N CA C +N ACCEPTOR O C IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 PATCHING FIRS PROP RESI SER 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--OG ATOM CB CT2 0.05 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM OG OH1 -0.66 ! | ATOM HG1 H 0.43 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 OG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 OG ACCEPTOR OG ACCEPTOR O C IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 RESI THR 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | OG1--HG1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 0.14 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 ATOM OG1 OH1 -0.66 ! O=C / \ ATOM HG1 H 0.43 ! | HG21 HG22 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 OG1 ACCEPTOR OG1 ACCEPTOR O C IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 RESI TRP 0.00 GROUP ATOM N NH1 -0.47 ! | HE3 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 CE3 ATOM HA HB 0.09 ! | | / \\ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM CB CT2 -0.18 ! | | || || | ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2 ATOM HB2 HA 0.09 ! O=C / \ / \ // GROUP ! | HD1 NE1 CZ2 ATOM CG CY -0.03 ! | | ATOM CD1 CA 0.035 ! HE1 HZ2 ATOM HD1 HP 0.115 ATOM NE1 NY -0.61 ATOM HE1 H 0.38 ATOM CE2 CPT 0.13 ATOM CD2 CPT -0.02 GROUP ATOM CE3 CA -0.115 ATOM HE3 HP 0.115 GROUP ATOM CZ3 CA -0.115 ATOM HZ3 HP 0.115 GROUP ATOM CZ2 CA -0.115 ATOM HZ2 HP 0.115 GROUP ATOM CH2 CA -0.115 ATOM HH2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND N HN N CA C CA C +N BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 BOND CZ3 HZ3 CH2 HH2 DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HE1 NE1 ACCEPTOR O C IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 RESI TYR 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--OH ATOM CB CT2 -0.18 ! | | \ __ / \ ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 OH CZ BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH DOUBLE O C CD1 CG CE1 CZ CE2 CD2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HH OH ACCEPTOR OH ACCEPTOR O C IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 RESI VAL 0.00 GROUP ATOM N NH1 -0.47 ! | HG11 HG12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG1--HG13 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 -0.09 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 GROUP ! O=C / \ ATOM CG1 CT3 -0.27 ! | HG21 HG22 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 ATOM HG13 HA 0.09 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 BOND CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral GROUP 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 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE 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 CAL 2.00 ! Calcium ion GROUP ATOM CAL CAL 2.00 PATCHING FIRST NONE LAST NONE RESI ZN2 2.00 ! Zinc ion GROUP ATOM ZN ZN 2.00 PATCHING FIRST 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 CBA O2A O1A CGD CBD O2D 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 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 GLYP 1.00 ! Glycine N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HA1 HT1 ATOM HT2 HC 0.33 ! | (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT2 0.13 ! | \ ATOM HA1 HB 0.09 ! HA2 HT3 ATOM HA2 HB 0.09 ! 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 PROP 1.00 ! Proline N-Terminal GROUP ! use in generate statement ATOM N NP -0.07 ! HA ATOM HN1 HC 0.24 ! | ATOM HN2 HC 0.24 ! -CA HN1 ATOM CD CP3 0.16 ! / \ / ATOM HD1 HA 0.09 ! N(+) ATOM HD2 HA 0.09 ! / \ ATOM CA CP1 0.16 ! -CD HN2 ATOM HA HB 0.09 ! | \ BOND HN1 N HN2 N ! HD1 HD2 DONOR HN1 N DONOR HN2 N IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES SIN -1.00 ! succinyl N-terminus (based on ACE and GLU) GROUP ! HGY1 OEY1 ATOM CAY CT2 -0.18 ! | // ATOM HY1 HA 0.09 ! HY1 HY2 CGY--CDY ATOM HY2 HA 0.09 ! \ | / \ \ GROUP ! CAY HGY2 OEY2(-1) ATOM CGY CT2 -0.28 ! | ATOM HGY1 HA 0.09 ! CY=OY ATOM HGY2 HA 0.09 ! ! ATOM CDY CC 0.62 ATOM OEY1 OC -0.76 ATOM OEY2 OC -0.76 GROUP ATOM CY C 0.51 ATOM OY O -0.51 BOND CY CAY CY N CAY HY1 CAY HY2 CAY CGY BOND CGY HGY1 CGY HGY2 CGY CDY CDY OEY2 DOUBLE OY CY CDY OEY1 IMPR CY CAY N OY IMPR N CY CA HN IMPR CDY CGY OEY2 OEY ACCEPTOR OY CY ACCEPTOR OEY1 CDY ACCEPTOR OEY2 CDY 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 CGY 0.0000 0.0000 -60.0000 0.0000 0.0000 !IC CGY CY *CAY HY1 1.5557 115.6900 121.2200 108.1600 1.1145 !IC CGY CY *CAY HY2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CY CAY CGY CDY 1.5516 115.6900 180.0000 115.7300 1.5307 IC CDY CAY *CGY HGY1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CDY CAY *CGY HGY2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CAY CGY CDY OEY1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OEY1 CGY *CDY OEY2 1.2590 114.9900 -179.1000 120.0800 1.2532 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 PRES ACP 0.00 ! acetylated N-terminus for proline 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 CD ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N CD 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 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 PRES CT1 0.00 ! methylated C-terminus from methyl acetate GROUP ! use in generate statement ATOM N NH1 -0.47 ! ATOM HN H 0.31 ! OT1 ATOM CA CT1 0.17 ! | // ATOM HA HB 0.09 ! -N--CA--C HT1 ATOM C CD 0.63 ! | | \ / ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 ATOM OT2 OS -0.34 ! \ ATOM CT CT3 -0.14 ! HT3 ATOM HT1 HA 0.09 ! ATOM HT2 HA 0.09 ! ATOM HT3 HA 0.09 ! DELETE ATOM O BOND C OT2 OT2 CT BOND CT HT1 CT HT2 CT HT3 DOUBLE C OT1 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 IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM C CC 0.55 ! ATOM O O -0.55 ! | GROUP ! O=C ATOM NT NH2 -0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 ! / \ BOND C NT ! HT1 HT2 BOND NT HT1 NT HT2 ! DIHE CA C NT HT2 ! (HT1 is cis to O) IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT3 0.00 ! N-Methylamide C-terminus GROUP ! use in generate statement ATOM C C 0.51 ! ATOM O O -0.51 ! | GROUP ! C=O ATOM NT NH1 -0.47 ! | ATOM HNT H 0.31 ! NT-HNT ATOM CAT CT3 -0.11 ! | ATOM HT1 HA 0.09 ! HT1-CAT-HT3 ATOM HT2 HA 0.09 ! | ATOM HT3 HA 0.09 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 !DIHE CA C NT CAT IMPR NT C CAT HNT C CA NT O DONOR HNT NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 GROUP ! via acetic acid, use in a patch statement ATOM CB CT2 -0.21 ! ATOM HB1 HA 0.09 ! HB1 OD1 ATOM HB2 HA 0.09 ! | // ATOM CG CD 0.75 ! -CB--CG ATOM OD1 OB -0.55 ! | \ ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 ATOM HD2 H 0.44 ! BOND OD2 HD2 ANGLE HD2 OD2 CG DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB DONOR HD2 OD2 IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 GROUP ! via acetic acid, use in a patch statement ATOM CG CT2 -0.21 ! ATOM HG1 HA 0.09 ! HG1 OE1 ATOM HG2 HA 0.09 ! | // ATOM CD CD 0.75 ! -CG--CD ATOM OE1 OB -0.55 ! | \ ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 ATOM HE2 H 0.44 ! BOND OE2 HE2 ANGLE HE2 OE2 CD DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG DONOR HE2 OE2 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES LINK 0.00 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal) ! 2 refers to next (C terminal) ! use in a patch statement BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. GROUP ! use in a patch statement ATOM 1CB CT2 -0.10 ! ATOM 1SG SM -0.08 ! 2SG--2CB-- GROUP ! / ATOM 2SG SM -0.08 ! -1CB--1SG ATOM 2CB CT2 -0.10 ! DELETE ATOM 1HG1 DELETE ATOM 2HG1 BOND 1SG 2SG ANGLE 1CB 1SG 2SG 1SG 2SG 2CB DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA DIHE 1CB 1SG 2SG 2CB !DIHE 1CB 1SG 2SG 2CB IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 GROUP ! use in a patch statement ATOM CE1 CPH2 0.25 ! HE1 ATOM HE1 HR1 0.13 ! / ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 ATOM CG CPH1 0.22 ! | / | ATOM CB CT2 -0.08 ! -CB--CG | ATOM HB1 HA 0.09 ! | \ | ATOM HB2 HA 0.09 ! HB2 CD2--NE2 GROUP ! | \ ATOM NE2 NR1 -0.36 ! HD2 HE2 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 DELETE ATOM HD1 DELETE ACCE NE2 BOND NE2 HE2 ANGLE CD2 NE2 HE2 CE1 NE2 HE2 DIHE HE2 NE2 CE1 HE1 HE2 NE2 CE1 ND1 HE2 NE2 CD2 HD2 DIHE HE2 NE2 CD2 CG IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 DONOR HE2 NE2 ACCEPTOR ND1 IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 RESI O2 0.00 ! O2 ligand for heme GROUP ATOM O1 OM 0.021 ATOM O2 OM -0.021 BOND O1 O2 PATCHING FIRS NONE LAST NONE RESI CO 0.00 ! CO ligand for heme GROUP ATOM C CM 0.021 ATOM O OM -0.021 TRIPLE C O PATCHING FIRS NONE LAST NONE PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES ! unliganded heme patch DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND PRES PHEM 0.00 ! Patch for HEME to His link. ! Patch residues must be 1-HIS, and 2-HEME. DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND BOND 1NE2 2FE ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND IC 1CD2 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CE1 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be ! 1-O2 , 2-HEME , and 3-HIS ! O1 of the oxygen is bonded to the iron. BOND 1O1 2FE ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB ANGLE 1O1 2FE 2NC 1O1 2FE 2ND DIHE 1O2 1O1 2FE 2NA IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1C 2FE ANGLE 1C 2FE 3NE2 ANGLE 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB ANGLE 1C 2FE 2NC 1C 2FE 2ND IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 ! patches for cyclic peptides PRES LIG1 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG2 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG3 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 RESI DUM 0.00 ! DUMMY ATOM GROUP ATOM DUM DUM 0.00 PATCHING FIRST NONE LAST NONE PRES CTRP 0.00 ! patch for protonated CTER, proton on ot2 GROUP ! use in a patch statement ATOM C CC 0.72 ! OT1 ATOM OT1 OC -0.55 ! // ATOM OT2 OC -0.61 ! -C ATOM HC2 H 0.44 ! \ BOND OT2 HC2 ! OT2-HC2 DONOR HC2 OT2 IC HC2 OT2 C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES CTRP2 0.00 ! patch for protonated CTER, proton on ot2 GROUP ! use in a patch statement, use AUTOGEN, ignore charges ATOM C CC 0.72 ! OT1-HC1 ATOM OT1 OC -0.55 ! / ATOM OT2 OC -0.61 ! -C ATOM HC1 H 0.00 HC2!\ ATOM HC2 H 0.44 HC1! OT2-HC2 BOND OT1 HC1 BOND OT2 HC2 DONOR HC1 OT1 DONOR HC2 OT2 IC HC1 OT1 C OT2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HC2 OT2 C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES CTRP1 0.00 ! patch for protonated CTER, proton on ot2 GROUP ! use in a patch statement ATOM C CC 0.72 ! OT1-HC1 ATOM OT1 OC -0.61 ! / ATOM OT2 OC -0.55 ! -C ATOM HC1 H 0.44 ! \\ BOND OT1 HC1 ! OT2 DONOR HC1 OT1 PRES ASPP2 0.00 ! patch for use in PHMD, proton on od1 GROUP ! and od1 via acetic acid, use in a patch statement ! ANGLes DIHEdrals are given ATOM CB CT2 -0.21 ! ATOM HB1 HA 0.09 ! HB1 OD1-HD1 ATOM HB2 HA 0.09 ! | / ATOM CG CC 0.75 ! -CB--CG ATOM OD1 OC -0.55 ! | \ ATOM OD2 OC -0.61 ! HB2 OD2-HD2 ATOM HD1 H 0.0 HD2! ATOM HD2 H 0.44 HD1! BOND OD1 HD1 BOND OD2 HD2 DONOR HD1 OD1 DONOR HD2 OD2 IC HD1 OD1 CG OD2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES ASPP1 0.00 ! patch for use in PHMD, proton on od1 GROUP ! and od1 via acetic acid, use in a patch statement ! ANGLes DIHEdrals are given ATOM CB CT2 -0.21 ! ATOM HB1 HA 0.09 ! HB1 OD1-HD1 ATOM HB2 HA 0.09 ! | / ATOM CG CD 0.75 ! -CB--CG ATOM OD1 OH1 -0.61 ! | \\ ATOM OD2 OB -0.55 ! HB2 OD2 ATOM HD1 H 0.44 ! BOND OD1 HD1 DONOR HD1 OD1 IC HD1 OD1 CG OD2 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP2 0.00 ! patch for use in PHMD, proton on od1 GROUP ! and od1 via acetic acid, use in a patch statement ! follow with AUTOGEN ATOM CG CT2 -0.21 ! ATOM HG1 HA 0.09 ! HG1 OE1-HE1 ATOM HG2 HA 0.09 ! | / ATOM CD CC 0.75 ! -CG--CD ATOM OE1 OC -0.55 ! | \ ATOM OE2 OC -0.61 ! HG2 OE2-HE2 ATOM HE1 H 0.0 HE2! ATOM HE2 H 0.44 HE1! BOND OE1 HE1 BOND OE2 HE2 DONOR HE1 OE1 DONOR HE2 OE2 IC HE1 OE1 CD OE2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP1 0.00 ! patch for use in PHMD, proton on od1 GROUP ! and od1 via acetic acid, use in a patch statement ! follow with AUTOGEN ATOM CG CT2 -0.21 ! ATOM HG1 HA 0.09 ! HG1 OE1-HE1 ATOM HG2 HA 0.09 ! | / ATOM CD CD 0.75 ! -CG--CD ATOM OE1 OH1 -0.61 ! | \\ ATOM OE2 OB -0.55 ! HG2 OE2 ATOM HE1 H 0.44 ! BOND OE1 HE1 DONOR HE1 OE1 IC HE1 OE1 CD OE2 0.0000 0.0000 0.0000 0.0000 0.0000 PRES CT4 0.00 ! N-Methylamide C-terminus GROUP ! use in generate statement ATOM C C 0.51 ! ATOM O O -0.51 ! | GROUP ! C=O ATOM NT NH1 -0.47 ! | ATOM HNT H 0.31 ! NT-HNT ATOM CAT CT3 -0.11 ! | ATOM HT11 HA 0.09 ! HT1-CAT-HT3 ATOM HT12 HA 0.09 ! | ATOM HT13 HA 0.09 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT11 CAT HT12 CAT HT13 DIHE CA C NT CAT IMPR NT C CAT HNT C CA NT O DONOR HNT NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT11 0.0000 0.0000 60.0000 0.0000 0.0000 IC C NT CAT HT12 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT13 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES SINP2 0.00 ! succinyl N-terminus (based on ACE and GLU) GROUP ! ATOM CGY CT2 -0.21 ! HGY1 OEY1-HEY1 ATOM HGY1 HA 0.09 ! | / ATOM HGY2 HA 0.09 ! CGY--CDY ATOM CDY CC 0.75 ! | \ ATOM OEY1 OC -0.55 ! HGY2 OEY2-HEY2 ATOM OEY2 OC -0.61 ! ATOM HEY1 H 0.0 !HEY2 ATOM HEY2 H 0.44 !HEY1 BOND OEY1 HEY1 BOND OEY2 HEY2 DONOR HEY1 OEY1 DONOR HEY2 OEY2 IC HEY1 OEY1 CDY OEY2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HEY2 OEY2 CDY OEY1 0.0000 0.0000 0.0000 0.0000 0.0000 !PRES LYSN 0.00 ! patch for neutral lys !GROUP !ATOM CE CT2 0.40 !ATOM HE1 HA -0.05 !ATOM HE2 HA -0.05 !ATOM NZ NH3 -0.98 !ATOM HZ1 HC 0.34 !ATOM HZ2 HC 0.34 !ATOM HZ3 HC 0.00 END ! The following patches for phosphotyrosine must be used with a ! parameter file containing both the protein and nucleic acid parameters. ! In addition, the commented parameters listed below must be included ! in the combined parameter file ! PRES TP1 -1.00 ! convert tyrosine to monoanionic phosphotyrosine ! use in a patch statement as follows ! ! patch to convert tyrosine to phenolphosphate !PATCH TP1 TYR 1 SETUP WARN ! ! this patch requires that the use of the following ! !1) protein topology file that contains mass list of atoms in both ! the protein and nucleic acid topology files and ! ! add to the topology file !MASS 179 ON2b 15.999400 ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) ! !2) parameter file that contains both the protein and nucleic acid ! parameters plus the parameters listed below ! ! parameters to be added to the protein/nucleic acid parameter file ! !bonds !CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. !ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. !angles !CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. !ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. !ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. !dihedrals !CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. !HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. !nonbonded !ON2b 0.0 -0.1521 1.77 ! ! end of parameters to be added DELE ATOM 1HH GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.16 ATOM OH ON2b -0.36 ! NA ATOM TYPE ATOM P1 P 1.40 ! NA ATOM TYPE ATOM O2 ON4 -0.76 ! NA ATOM TYPE ATOM H2 HN4 0.40 ! NA ATOM TYPE ATOM O3 ON3 -0.76 ! NA ATOM TYPE ATOM O4 ON3 -0.76 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND O2 H2 ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL P1 O2 H2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 PRES TP1A -1.00 ! patch to convert tyrosine to ! monoanionic phenol-phosphate model compound ! use in patch statement DELE ATOM N DELE ATOM HN DELE ATOM CA DELE ATOM HA DELE ATOM CB DELE ATOM HB1 DELE ATOM HB2 DELE ATOM C DELE ATOM O DELE ATOM 1HH GROUP ATOM CG CA -0.115 ATOM HG HP 0.115 GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.16 ATOM OH ON2B -0.36 ! NA ATOM TYPE ATOM P1 P 1.40 ! NA ATOM TYPE ATOM O2 ON4 -0.76 ! NA ATOM TYPE ATOM H2 HN4 0.40 ! NA ATOM TYPE ATOM O3 ON3 -0.76 ! NA ATOM TYPE ATOM O4 ON3 -0.76 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND O2 H2 BOND CG HG ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL P1 O2 H2 ANGL HG CG CD1 HG CG CD2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 DIHE HG CG CD1 CE1 HG CG CD1 HD1 DIHE HG CG CD2 CE2 HG CG CD2 HD2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 PRES TP2 -2.00 ! patch to convert tyrosine to ! dianionic phosphotyrosine ! use in patch statement ! ! see PRES TP1 for proper preparation of the topology and ! parameter files ! DELE ATOM 1HH GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.28 ATOM OH ON2B -0.28 ! NA ATOM TYPE ATOM P1 P 1.44 ! NA ATOM TYPE ATOM O2 ON3 -0.96 ! NA ATOM TYPE ATOM O3 ON3 -0.96 ! NA ATOM TYPE ATOM O4 ON3 -0.96 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 PRES TP2A -2.00 ! patch to convert tyrosine to ! dianionic phosphotyrosine ! use in patch statement ! ! this converts a single tyrosine to a phenol phosphate ! see PRES TP1 for proper preparation of the topology and ! parameter files DELE ATOM N DELE ATOM HN DELE ATOM CA DELE ATOM HA DELE ATOM CB DELE ATOM HB1 DELE ATOM HB2 DELE ATOM C DELE ATOM O DELE ATOM 1HH GROUP ATOM CG CA -0.115 ATOM HG HP 0.115 GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.28 ATOM OH ON2B -0.28 ! NA ATOM TYPE ATOM P1 P 1.44 ! NA ATOM TYPE ATOM O2 ON3 -0.96 ! NA ATOM TYPE ATOM O3 ON3 -0.96 ! NA ATOM TYPE ATOM O4 ON3 -0.96 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND CG HG ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL HG CG CD1 HG CG CD2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE HG CG CD1 CE1 HG CG CD1 HD1 DIHE HG CG CD2 CE2 HG CG CD2 HD2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 END