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top_opls_aam.inp
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top_opls_aam.inp
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*>>>>>>>>>>> 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 [email protected]
!
!**** 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