*>>>>>>>>>>> OPLS-AA/M All-atom Toplogy File for Proteins <<<< *>>>>>>>>>>>>>>>>>>>>>>>> Jun 2015 <<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>> Generated automatically from pepz database files <<<<< *>>>>>>>>>> script in perl, available from D. Price <<<<<<<<<< *>>>>>>>>>>> Edited by M.J. Robertson to OPLS-AA/M <<<<<<<<<<<<< *>>>>>>>>>>>>>>>> email: michael.robertson at yale.edu <<<<<<< * 27 1 !README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) !** reference for OPLS-AA for proteins: !** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) !** reference for OPLS-AA/M: !** Robertson, M.J. et al., J. Chem. Theory Comput., (2015) !and see additional reference below ! !PLEASE ENSURE USE OF PROPER LJ COMBINING RULES AND 1-4 SCALING TO ENSURE !PROPER IMPLEMENTATION OF THE OPLS-AA/M FORCE FIELD ! ! !Proper usage of these files requires CHARMM software version c28b1 or greater. !If you are presently using c28b1, please check that you have the latest release, !as not all of the pertinant code was included in the initial release, but was !included in a later bugfix. Compilation of CHARMM requires that the OPLS !keyword be included in pref.dat at compile time. The relevant code has added !the ability to combine Lennard-Jones radii with a geometric average, and use !V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the !OPLS option in pref.dat can still use all other previously released topology and !parameter files (CHARMM22, CHARMM19, etc.). ! !Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. !Consequently, any CHARMM script that reads CHARMM22 topology and parameter files !can be converted to using OPLS-AA by adjusting the appropriate file OPEN !statements. The atom types have the OPLS atom type embedded within them for !easy cross-reference. For example, type H140 in opls.rtf and opls.prm is !type 140 the OPLS-AA parameter files available from Prof. Jorgensen. ! !The topology and parameter files here include only the protein portion of the !OPLS-AA force field. User-defined topology and parameter files are required for !other functionalities. ! !While the OPLS-AA topology and parameter files are compatible with all !functionality within CHARMM that is also compatible with CHARMM22, minimizations !and simulations with a distance-dependent dielectric (RDIE) is not recommended !as collapse of atoms with hydrogens on heteroatoms is possible, causing !unreasonable structures and energies. Also, there is no current !optimzied parameter set for the linearized form of the Generalized Born equation !as currently implemented in CHARMM. ! !Any questions, email priced@scripps.edu ! !**** These files were created in the laboratory of: !**** Prof. C.L. Brooks III !**** Dept. of Mol. Biol. !**** The Scripps Research Institute ! !**** OPLS-AA is developed in the laboratory of: !**** Prof. W.L. Jorgensen !**** Dept. of Chemistry !**** Yale University !Additional References ! !OPLS All-Atom Model for Amines: Resolution of the Amine Hydration !Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, !4827-4836 (1999). ! !Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro !Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, !and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). ! !Evaluation and Reparameterization of the OPLS-AA Force Field for !Proteins via Comparison with Accurate Quantum Chemical Calculations on !Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. !Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). ! !Perfluoroalkanes: Conformational Analysis and Liquid-State Properties !from Ab Initio and Monte Carlo Calculations. E. K. Watkins and !W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). ! !Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic !Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, !0000-0000. Submitted. ! !A five-site model for liquid water and the reproduction of the density !anomaly by rigid, non-polarizable models. M. W. Mahoney and !W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). ! !Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney !and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). ! !Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo !Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and !W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). ! !Quantum, intramolecular flexibility, and polarizability effects on the !reproduction of the density anomaly of liquid water by simple !potential functions. M. W. Mahoney and W. L. Jorgensen, !J. Chem. Phys., 115, 10758-10768 (2001). ! !Improved Peptide and Protein Torsional Energetics with the OPLS-AA !Force Field M. J. Robertson, J. Tirado-Rives and W. L. Jorgensen, !J. Chem. Theory. Comput. (2015) MASS 1 C135 12.01100 C ! CH3 all-atom C: alkanes ALL-ATOM MASS 2 C136 12.01100 C ! CH2 all-atom C: alkanes PARAMETERS MASS 3 C137 12.01100 C ! CH all-atom C: alkanes FROM HERE ON MASS 4 C145 12.01100 C ! Benzene C - 12 site JACS,112,4768-90 MASS 5 C149 12.01100 C ! all-atom C: CH2, ethyl benzene MASS 6 C157 12.01100 C ! all-atom C: CH3 & CH2, alcohols MASS 7 C158 12.01100 C ! all-atom C: CH, alcohols MASS 8 C166 12.01100 C ! C(OH) phenol Use with all MASS 9 C206 12.01100 C ! all-atom C: CH2, thiols MASS 10 C209 12.01100 C ! all-atom C: CH3, sulfides MASS 11 C210 12.01100 C ! all-atom C: CH2, sulfides MASS 12 C214 12.01100 C ! all-atom C: CH2, disulfides MASS 13 C223 12.01100 C ! C in RCH2NH2 and Gly CA (See 900 for amines) MASS 14 C224 12.01100 C ! C in R2CHNH2 and Ala CA MASS 15 C235 12.01100 C ! C: C=O in amide. Acyl R in amides MASS 16 C242 12.01100 C ! C on N: secondary N-Me amide MASS 17 C245 12.01100 C ! C on N: tertiary N-CH2R amide (Pro Cdelta) MASS 18 C246 12.01100 C ! C on N: tertiary N-CHR2 amide (Pro Calpha) MASS 19 C267 12.01100 C ! Co in CCOOH carboxylic acid MASS 20 C271 12.01100 C ! C in COO- carboxylate MASS 21 C274 12.01100 C ! C: CH2, carboxylate ion MASS 22 C283 12.01100 C ! AA C-alpha on C-terminal ALA MASS 23 C284 12.01100 C ! AA C-alpha on C-terminal GLY MASS 24 C285 12.01100 C ! AA C-alpha on C-terminal PRO MASS 25 C292 12.01100 C ! C in RCH2NH3+ & CA in N-term Gly MASS 26 C293 12.01100 C ! C in R2CHNH3+ & CA in N-term Ala, etc. MASS 27 C295 12.01100 C ! AA:C-alpha in N-term PRO MASS 28 C296 12.01100 C ! AA:C-delta in N-term PRO MASS 29 C302 12.01100 C ! C: guanidinium C+ MASS 30 C307 12.01100 C ! C: CH2(D), ARG, ethylguanidinium MASS 31 C308 12.01100 C ! C: CH2(G), ARG MASS 32 C500 12.01100 C ! CG in TRP MASS 33 C501 12.01100 C ! CD C in TRP MASS 34 C502 12.01100 C ! CE C in TRP MASS 35 C505 12.01100 C ! CB in HIS MASS 36 C506 12.01100 C ! CE1 in HID, HIE MASS 37 C507 12.01100 C ! CD2 in HID, CG in HIE MASS 38 C508 12.01100 C ! CG in HID, CD2 in HIE MASS 39 C509 12.01100 C ! CE1 in HIP MASS 40 C510 12.01100 C ! CG, CD2 in HIP MASS 41 C514 12.01100 C ! CD1 in TRP !MASS 42 C748 12.01100 C ! CD of neutral ARG, adm jr. !MASS 43 C752 12.01100 C ! CZ " " ", adm jr. !MASS 44 C906 12.01100 C ! CH2(N) primary aliphatic amines, H(C) type 911 MASS 45 H140 1.00800 H ! H all-atom H: alkanes MASS 46 H146 1.00800 H ! Benzene H - 12 site " MASS 47 H155 1.00800 H ! all-atom H(O): mono alcohols MASS 48 H168 1.00800 H ! H phenol 145 & 146 MASS 49 H204 1.00800 H ! all-atom H(S): thiols (mod 11/99) MASS 50 H240 1.00800 H ! H on N: primary amide MASS 51 H241 1.00800 H ! H on N: secondary amide MASS 52 H270 1.00800 H ! H in CCOOH MASS 53 H290 1.00800 H ! H (RNH3+) " MASS 54 H301 1.00800 H ! H: guanidinium NH2 MASS 55 H304 1.00800 H ! H: guanidinium NHR MASS 56 H310 1.00800 H ! H (R2NH2+) MASS 57 H504 1.00800 H ! H on NE in TRP MASS 58 H513 1.00800 H ! H on N in HIP !MASS 59 H909 1.00800 H ! H(N) primary amines, adm jr. !MASS 60 H910 1.00800 H ! H(N) secondary amines, adm jr. !MASS 61 H911 1.00800 H ! H(C) for Carbons directly bonded to N in amines, diamines, adm jr. MASS 62 N237 14.00700 N ! N: primary amide. alkane parameters. MASS 63 N238 14.00700 N ! N: secondary amide 279 for formyl H. MASS 64 N239 14.00700 N ! N: tertiary amide MASS 65 N287 14.00700 N ! N (RNH3+) " MASS 66 N300 14.00700 N ! N: guanidinium NH2 MASS 67 N303 14.00700 N ! N: guanidinium NHR MASS 68 N309 14.00700 N ! N (R2NH2+) MASS 69 N503 14.00700 N ! NE in TRP MASS 70 N511 14.00700 N ! NE in HID, ND in HIE MASS 71 N512 14.00700 N ! N in HIP !MASS 72 N749 14.00700 N ! NE ", adm jr. !MASS 73 N750 14.00700 N ! N1 " " " (HN=CZ), adm jr. !MASS 74 N751 14.00700 N ! N2 " " " (H2N-CZ), adm jr. !MASS 75 N900 14.00700 N ! N primary amines, adm jr. MASS 76 O154 15.99940 O ! all-atom O: mono alcohols MASS 77 O167 15.99940 O ! O phenol atom C, H MASS 78 O236 15.99940 O ! O: C=O in amide. is neutral - use MASS 79 O268 15.99940 O ! Oh in CCOOH R in RCOOH is MASS 80 O269 15.99940 O ! Oc in CCOOH neutral; use 135-140 MASS 81 O272 15.99940 O ! O: O in COO- carboxylate MASS 82 S200 32.06000 S ! all-atom S: thiols (mod 11/99) MASS 83 S202 32.06000 S ! all-atom S: sulfides MASS 84 S203 32.06000 S ! all-atom S: disulfides MASS 85 OT 15.99940 O MASS 86 HT 1.00800 H MASS 90 SOD 22.98977 NA ! Sodium Ion, adm jr. MASS 91 CLA 35.45000 CL ! Chloride Ion, adm jr. 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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 ATOM HA H140 0.060 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB C135 -0.180 ! | \ ATOM HB1 H140 0.060 ! | HB3 ATOM HB2 H140 0.060 ! O=C ATOM HB3 H140 0.060 ! | GROUP ! ATOM C C235 0.500 ! ATOM O O236 -0.500 ! BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR HN N -C CA O C CA +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 N238 -0.500 ! | HH11 ATOM HN H241 0.300 ! HN-N | ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA H140 0.060 ! | | | | | //(+) GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB C136 -0.120 ! | | | | \ ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 NH2-HH22 ATOM HB2 H140 0.060 ! O=C | GROUP ! | HH21 ATOM CG C308 -0.050 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! ATOM CD C307 0.190 ! ATOM HD1 H140 0.060 ! ATOM HD2 H140 0.060 ! ATOM NE N303 -0.700 ! ATOM HE H304 0.440 ! ATOM CZ C302 0.640 ! ATOM NH1 N300 -0.800 ! ATOM HH11 H301 0.460 ! ATOM HH12 H301 0.460 ! ATOM NH2 N300 -0.800 ! ATOM HH21 H301 0.460 ! ATOM HH22 H301 0.460 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR NH2 CZ NE NH1 HE NE CD CZ IMPR HH12 NH1 CZ HH11 HH22 NH2 CZ HH21 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 ASN 0.00 GROUP ATOM N N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 OD1 HD21 (cis to OD1) ATOM HA H140 0.060 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB C136 -0.120 ! | | \ ATOM HB1 H140 0.060 ! | HB2 HD22 (trans to OD1) ATOM HB2 H140 0.060 ! O=C GROUP ! | ATOM CG C235 0.500 ! ATOM OD1 O236 -0.500 ! GROUP ATOM ND2 N237 -0.760 ! ATOM HD21 H240 0.380 ! ATOM HD22 H240 0.380 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR OD1 CG CB ND2 IMPR HD22 ND2 CG HD21 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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 OD1 ATOM HA H140 0.060 ! | | // GROUP ! HA-CA--CB--CG ATOM CB C274 -0.220 ! | | \ ATOM HB1 H140 0.060 ! | HB2 OD2(-) ATOM HB2 H140 0.060 ! O=C ATOM CG C271 0.700 ! | ATOM OD1 O272 -0.800 ! ATOM OD2 O272 -0.800 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR OD2 CG CB OD1 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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 ATOM HA H140 0.060 ! | | GROUP ! HA-CA--CB--SG ATOM CB C206 0.060 ! | | \ ATOM HB1 H140 0.060 ! | HB2 HG1 ATOM HB2 H140 0.060 ! O=C ATOM SG S200 -0.335 ! | ATOM HG1 H204 0.155 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA H140 0.060 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB C136 -0.120 ! | | | \ ATOM HB1 H140 0.060 ! | HB2 HG2 HE22 (trans to OE1) ATOM HB2 H140 0.060 ! O=C GROUP ! | ATOM CG C136 -0.120 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! GROUP ATOM CD C235 0.500 ! ATOM OE1 O236 -0.500 ! GROUP ATOM NE2 N237 -0.760 ! ATOM HE21 H240 0.380 ! ATOM HE22 H240 0.380 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR OE1 CD CG NE2 IMPR HE22 NE2 CD HE21 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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 HG1 OE1 ATOM HA H140 0.060 ! | | | // GROUP ! HA-CA--CB--CG--CD ATOM CB C136 -0.120 ! | | | \ ATOM HB1 H140 0.060 ! | HB2 HG2 OE2(-) ATOM HB2 H140 0.060 ! O=C GROUP ! | ATOM CG C274 -0.220 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! ATOM CD C271 0.700 ! ATOM OE1 O272 -0.800 ! ATOM OE2 O272 -0.800 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR OE2 CD CG OE1 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 N238 -0.500 ! | ATOM HN H241 0.300 ! N-H ATOM CA C223 0.080 ! | ATOM HA1 H140 0.060 ! | ATOM HA2 H140 0.060 ! HA1-CA-HA2 GROUP ! | ATOM C C235 0.500 ! | ATOM O O236 -0.500 ! C=O ! | BOND N HN N CA C CA BOND C +N CA HA1 CA HA2 DOUBLE O C IMPR HN N -C CA O C CA +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 LAST GLYC RESI HSD 0.00 ! neutral HIS, proton on ND1 GROUP ATOM N N238 -0.500 ! | HD1 HE1 ATOM HN H241 0.300 ! HN-N | / ATOM CA C224 0.140 ! | HB1 ND1--CE1 ATOM HA H140 0.060 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB C505 -0.005 ! | | \\ || ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 ATOM HB2 H140 0.060 ! O=C | ATOM ND1 N503 -0.570 ! | HD2 ATOM HD1 H504 0.420 ! ATOM CG C508 0.015 ! ATOM CE1 C506 0.295 ! ATOM HE1 H146 0.115 ! ATOM NE2 N511 -0.490 ! ATOM CD2 C507 -0.015 ! ATOM HD2 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HD1 ND1 CG CE1 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 IMPR CB CG ND1 CD2 IMPR HN N -C CA O C CA +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 N238 -0.500 ! | HE1 ATOM HN H241 0.300 ! HN-N __ / ATOM CA C224 0.140 ! | HB1 ND1--CE1 ATOM HA H140 0.060 ! | | / | GROUP ! HA-CA--CB--CG | ATOM CB C505 -0.005 ! | | \\ | ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 ATOM HB2 H140 0.060 ! O=C | \ ATOM ND1 N511 -0.490 ! | HD2 HE2 ATOM CG C507 -0.015 ! ATOM CE1 C506 0.295 ! ATOM HE1 H146 0.115 ! ATOM NE2 N503 -0.570 ! ATOM HE2 H504 0.420 ! ATOM CD2 C508 0.015 ! ATOM HD2 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 IMPR CB CG ND1 CD2 IMPR HN N -C CA O C CA +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 N238 -0.500 ! | HD1 HE1 ATOM HN H241 0.300 ! HN-N | / ATOM CA C224 0.140 ! | HB1 ND1--CE1 ATOM HA H140 0.060 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB C505 -0.005 ! | | \\ || ATOM HB1 H140 0.060 ! | HB2 CD2--NE2(+) ATOM HB2 H140 0.060 ! O=C | \ ATOM CD2 C510 0.215 ! | HD2 HE2 ATOM HD2 H146 0.115 ! ATOM CG C510 0.215 ! ATOM NE2 N512 -0.540 ! ATOM HE2 H513 0.460 ! ATOM ND1 N512 -0.540 ! ATOM HD1 H513 0.460 ! ATOM CE1 C509 0.385 ! ATOM HE1 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HD1 ND1 CG CE1 HE1 CE1 ND1 NE2 IMPR HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG IMPR CB CG ND1 CD2 IMPR HN N -C CA O C CA +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 N238 -0.500 ! | HG21 HG22 ATOM HN H241 0.300 ! HN-N | / ATOM CA C224 0.140 ! | CG2--HG23 ATOM HA H140 0.060 ! | / GROUP ! HA-CA--CB-HB HD1 ATOM CB C137 -0.060 ! | \ / ATOM HB H140 0.060 ! | CG1--CD--HD2 GROUP ! O=C / \ \ ATOM CG2 C135 -0.180 ! | HG11 HG12 HD3 ATOM HG21 H140 0.060 ! ATOM HG22 H140 0.060 ! ATOM HG23 H140 0.060 ! GROUP ATOM CG1 C136 -0.120 ! ATOM HG11 H140 0.060 ! ATOM HG12 H140 0.060 ! GROUP ATOM CD C135 -0.180 ! ATOM HD1 H140 0.060 ! ATOM HD2 H140 0.060 ! ATOM HD3 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 N238 -0.500 ! | HD11 HD12 ATOM HN H241 0.300 ! HN-N | / ATOM CA C224 0.140 ! | HB1 CD1--HD13 ATOM HA H140 0.060 ! | | / GROUP ! HA-CA--CB--CG-HG ATOM CB C136 -0.120 ! | | \ ATOM HB1 H140 0.060 ! | HB2 CD2--HD23 ATOM HB2 H140 0.060 ! O=C | \ GROUP ! | HD21 HD22 ATOM CG C137 -0.060 ! ATOM HG H140 0.060 ! GROUP ATOM CD1 C135 -0.180 ! ATOM HD11 H140 0.060 ! ATOM HD12 H140 0.060 ! ATOM HD13 H140 0.060 ! GROUP ATOM CD2 C135 -0.180 ! ATOM HD21 H140 0.060 ! ATOM HD22 H140 0.060 ! ATOM HD23 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA H140 0.060 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB C136 -0.120 ! | | | | | \ ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 HE2 HZ3 ATOM HB2 H140 0.060 ! O=C GROUP ! | ATOM CG C136 -0.120 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! GROUP ATOM CD C136 -0.120 ! ATOM HD1 H140 0.060 ! ATOM HD2 H140 0.060 ! GROUP ATOM CE C292 0.190 ! ATOM HE1 H140 0.060 ! ATOM HE2 H140 0.060 ! ATOM NZ N287 -0.300 ! ATOM HZ1 H290 0.330 ! ATOM HZ2 H290 0.330 ! ATOM HZ3 H290 0.330 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 MET 0.00 GROUP ATOM N N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 HG1 HE1 ATOM HA H140 0.060 ! | | | | GROUP ! HA-CA--CB--CG--SD--CE--HE3 ATOM CB C136 -0.120 ! | | | | ATOM HB1 H140 0.060 ! | HB2 HG2 HE2 ATOM HB2 H140 0.060 ! O=C GROUP ! | ATOM CG C210 0.0475 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! ATOM SD S202 -0.335 ! ATOM CE C209 -0.0125 ! ATOM HE1 H140 0.060 ! ATOM HE2 H140 0.060 ! ATOM HE3 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 N238 -0.500 ! | HD1 HE1 ATOM HN H241 0.300 ! HN-N | | ATOM CA C224 0.140 ! | HB1 CD1--CE1 ATOM HA H140 0.060 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--HZ ATOM CB C149 -0.005 ! | | \ __ / ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 ATOM HB2 H140 0.060 ! O=C | | ATOM CG C145 -0.115 ! | HD2 HE2 GROUP ATOM CD1 C145 -0.115 ! ATOM HD1 H146 0.115 ! GROUP ATOM CE1 C145 -0.115 ! ATOM HE1 H146 0.115 ! GROUP ATOM CZ C145 -0.115 ! ATOM HZ H146 0.115 ! GROUP ATOM CD2 C145 -0.115 ! ATOM HD2 H146 0.115 ! GROUP ATOM CE2 C145 -0.115 ! ATOM HE2 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ HZ CZ CE1 CE2 IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 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 N239 -0.140 ! | \ / ATOM CD C245 -0.050 ! N---CD HG1 ATOM CA CP1 0.02 ATOM HD1 H140 0.060 ! | \ / ATOM HD2 H140 0.060 ! | CG ATOM CA C246 0.010 ! | / \ ATOM HA H140 0.060 ! HA-CA--CB HG2 GROUP ! | / \ ATOM CB C136 -0.120 ! | HB1 HB2 ATOM HB1 H140 0.060 ! O=C ATOM HB2 H140 0.060 ! | GROUP ATOM CG C136 -0.120 ! ATOM HG1 H140 0.060 ! ATOM HG2 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 CD N -C CA IMPR O C CA +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 LAST PROC RESI SER 0.00 GROUP ATOM N N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | HB1 ATOM HA H140 0.060 ! | | GROUP ! HA-CA--CB--OG ATOM CB C157 0.145 ! | | \ ATOM HB1 H140 0.060 ! | HB2 HG1 ATOM HB2 H140 0.060 ! O=C ATOM OG O154 -0.683 ! | ATOM HG1 H155 0.418 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 N238 -0.500 ! | ATOM HN H241 0.300 ! HN-N ATOM CA C224 0.140 ! | OG1--HG1 ATOM HA H140 0.060 ! | / GROUP ! HA-CA--CB-HB ATOM CB C158 0.205 ! | \ ATOM HB H140 0.060 ! | CG2--HG21 ATOM OG1 O154 -0.683 ! O=C / \ ATOM HG1 H155 0.418 ! | HG21 HG22 GROUP ATOM CG2 C135 -0.180 ! ATOM HG21 H140 0.060 ! ATOM HG22 H140 0.060 ! ATOM HG23 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 N238 -0.500 ! | HE3 ATOM HN H241 0.300 ! HN-N | ATOM CA C224 0.140 ! | HB1 CE3 ATOM HA H140 0.060 ! | | / \\ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM CB C136 -0.120 ! | | || || | ATOM HB1 H140 0.060 ! | HB2 CD1 CE2 CH2-HH2 ATOM HB2 H140 0.060 ! O=C / \ / \ // GROUP ! | HD1 NE1 CZ2 ATOM CG C500 0.075 ! | | ATOM CD1 C514 -0.115 ! HE1 HZ2 ATOM HD1 H146 0.115 ! ATOM NE1 N503 -0.570 ! ATOM HE1 H504 0.420 ! ATOM CE2 C502 0.130 ! ATOM CD2 C501 -0.055 ! GROUP ATOM CE3 C145 -0.115 ! ATOM HE3 H146 0.115 ! GROUP ATOM CZ3 C145 -0.115 ! ATOM HZ3 H146 0.115 ! GROUP ATOM CZ2 C145 -0.115 ! ATOM HZ2 H146 0.115 ! GROUP ATOM CH2 C145 -0.115 ! ATOM HH2 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR CB CG CD1 CD2 HD1 CD1 CG NE1 HE1 NE1 CD1 CE2 IMPR HZ2 CZ2 CE2 CH2 HH2 CH2 CZ2 CZ3 HZ3 CZ3 CH2 CE3 IMPR HE3 CE3 CZ3 CD2 CE2 CD2 CE3 CG CZ2 CE2 CD2 NE1 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 N238 -0.500 ! | HD1 HE1 ATOM HN H241 0.300 ! HN-N | | ATOM CA C224 0.140 ! | HB1 CD1--CE1 ATOM HA H140 0.060 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--OH ATOM CB C149 -0.005 ! | | \ __ / \ ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 HH ATOM HB2 H140 0.060 ! O=C | | ATOM CG C145 -0.115 ! | HD2 HE2 GROUP ATOM CD1 C145 -0.115 ! ATOM HD1 H146 0.115 ! GROUP ATOM CE1 C145 -0.115 ! ATOM HE1 H146 0.115 ! GROUP ATOM CZ C166 0.150 ! ATOM OH O167 -0.585 ! ATOM HH H168 0.435 ! GROUP ATOM CD2 C145 -0.115 ! ATOM HD2 H146 0.115 ! GROUP ATOM CE2 C145 -0.115 ! ATOM HE2 H146 0.115 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +N IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ OH CZ CE1 CE2 IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 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 N238 -0.500 ! | HG11 HG12 ATOM HN H241 0.300 ! HN-N | / ATOM CA C224 0.140 ! | CG1--HG13 ATOM HA H140 0.060 ! | / GROUP ! HA-CA--CB-HB ATOM CB C137 -0.060 ! | \ ATOM HB H140 0.060 ! | CG2--HG21 GROUP ! O=C / \ ATOM CG1 C135 -0.180 ! | HG21 HG22 ATOM HG11 H140 0.060 ! ATOM HG12 H140 0.060 ! ATOM HG13 H140 0.060 ! GROUP ATOM CG2 C135 -0.180 ! ATOM HG21 H140 0.060 ! ATOM HG22 H140 0.060 ! ATOM HG23 H140 0.060 ! GROUP ATOM C C235 0.500 ! ATOM O O236 -0.500 ! 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 HN N -C CA O C CA +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 PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N N287 -0.300 ! ATOM HT1 H290 0.330 ! HT1 ATOM HT2 H290 0.330 ! (+)/ ATOM HT3 H290 0.330 ! --CA--N--HT2 ATOM CA C293 0.250 ! | \ ATOM HA H140 0.060 ! 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 N287 -0.300 ! ATOM HT1 H290 0.330 ! HA1 HT1 ATOM HT2 H290 0.330 ! | (+)/ ATOM HT3 H290 0.330 ! --CA--N--HT2 ATOM CA C292 0.190 ! | \ ATOM HA1 H140 0.060 ! HA2 HT3 ATOM HA2 H140 0.060 ! 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 N309 -0.200 ! HA ATOM HN1 H310 0.310 ! | ATOM HN2 H310 0.310 ! -CA HN1 ATOM CD C296 0.170 ! / \ / ATOM HD1 H140 0.060 ! N(+) ATOM HD2 H140 0.060 ! / \ ATOM CA C295 0.230 ! -CD HN2 ATOM HA H140 0.060 ! | \ 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 ACE 0.00 ! acetylated N-terminus GROUP ! use in generate statement ATOM CAY C135 -0.180 ! ATOM HY1 H140 0.060 ! HY1 HY2 HY3 ATOM HY2 H140 0.060 ! \ | / ATOM HY3 H140 0.060 ! CAY GROUP ! | ATOM CY C235 0.500 ! CY=OY ATOM OY O236 -0.500 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR OY CY CAY N IMPR HN N CY CA 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 C135 -0.180 ! ATOM HY1 H140 0.060 ! HY1 HY2 HY3 ATOM HY2 H140 0.060 ! \ | / ATOM HY3 H140 0.060 ! CAY GROUP ! | ATOM CY C235 0.500 ! CY=OY ATOM OY O236 -0.500 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR OY CY CAY N IMPR CD N CY CA 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 -0.86 ! standard C-terminus GROUP ! use in generate statement ATOM CA C283 0.040 ! line added in template for script pepz2rtf ATOM C C271 0.700 ! OT2(-) ATOM OT1 O272 -0.800 ! / ATOM OT2 O272 -0.800 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 IMPR OT2 C CA 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 CTP 0.14 ! protonated C-terminus, corrected adm jr. GROUP ! use in generate statement ATOM CA C224 0.14 ! line added in template for script pepz2rtf ATOM C C267 0.52 ! OT2--HT2 ATOM OT1 O269 -0.44 ! / ATOM OT2 O268 -0.53 ! -C ATOM HT2 H270 0.45 ! \\ DELETE ATOM O ! OT1 BOND C OT2 OT2 HT2 ! DOUBLE C OT1 IMPR OT2 C CA OT1 ACCEPTOR OT1 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 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 ! protonated C-terminal Gly, adm jr. PRES CTPG 0.08 ! protonated C-terminal Gly GROUP ! use in generate statement ATOM CA C223 0.08 ! line added in template for script pepz2rtf ATOM C C267 0.52 ! OT2--HT2 ATOM OT1 O269 -0.44 ! / ATOM OT2 O268 -0.53 ! -C ATOM HT2 H270 0.45 ! \\ DELETE ATOM O ! OT1 BOND C OT2 OT2 HT2 ! DOUBLE C OT1 IMPR OT2 C CA OT1 ACCEPTOR OT1 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 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT3 0.00 ! N-Methylamide C-terminus use in generate statement GROUP ! C=O ATOM NT N238 -0.500 ! | ATOM HNT H241 0.300 ! NT-HNT ATOM CAT C242 0.020 ! | ATOM HT1 H140 0.060 ! HT1-CAT-HT3 ATOM HT2 H140 0.060 ! | ATOM HT3 H140 0.060 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 !DIHE CA C NT CAT IMPR HNT NT C CAT O C CA NT 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 GLYC -0.92 ! standard C-terminus GROUP ! use in generate statement ATOM CA C284 -0.020 ! line added in template for script pepz2rtf ATOM C C271 0.700 ! OT2(-) ATOM OT1 O272 -0.800 ! / ATOM OT2 O272 -0.800 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 IMPR OT1 C CA OT2 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 PROC -0.99 ! standard C-terminus GROUP ! use in generate statement ATOM CA C285 -0.090 ! line added in template for script pepz2rtf ATOM C C271 0.700 ! OT2(-) ATOM OT1 O272 -0.800 ! / ATOM OT2 O272 -0.800 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 IMPR OT1 C CA OT2 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 ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 GROUP ! via acetic acid, use in a patch statement ATOM CB C136 -0.120 ! ATOM HB1 H140 0.060 ! HB1 OD1 ATOM HB2 H140 0.060 ! | // ATOM CG C267 0.520 ! -CB--CG ATOM OD1 O269 -0.440 ! | \ ATOM OD2 O268 -0.530 ! HB2 OD2-HD2 ATOM HD2 H270 0.450 ! 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 C136 -0.120 ! ATOM HG1 H140 0.060 ! HG1 OE1 ATOM HG2 H140 0.060 ! | // ATOM CD C267 0.520 ! -CG--CD ATOM OE1 O269 -0.440 ! | \ ATOM OE2 O268 -0.530 ! HG2 OE2-HE2 ATOM HE2 H270 0.450 ! 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 2HN 2N 1C 2CA 1O 1C 1CA 2N 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 -0.24 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. GROUP ! use in a patch statement ATOM 1CB C214 0.0975! ATOM 1SG S203 -0.2175 ! 2SG--2CB-- ATOM 2SG S203 -0.2175 ! / ATOM 2CB C214 0.0975! -1CB--1SG 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 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 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 2HN 2N 1C 2CA 1O 1C 1CA 2N 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 2HN 2N 1C 2CA 1O 1C 1CA 2N 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 2HN 2N 1C 2CA 1O 1C 1CA 2N 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 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 SOD 1.00 ! Sodium Ion, adm jr. GROUP ATOM SOD SOD 1.00 PATCHING FIRST NONE LAST NONE RESI CLA -1.00 ! Chloride Ion, adm jr. GROUP ATOM CLA CLA -1.00 PATCHING FIRST NONE LAST NONE END