# Version: August 13, 1993 # # LIBRARY OF RESIDUE DIHEDRAL ANGLES # # MODELLER 1.1, Copyright Andrej Sali # # # This file contains residue dihedral angle definitions for a lot of residue # types. Each residue has one definition for each existing dihedral angle # type. There can only be up to one dihedral angle of a certain type per # residue. The currently existing dihedral angle types are: phi, psi, omega, # chi1, chi2, chi3, chi4, and chi5 (disulfide). These angles can then be used # in a number of MODELLER commands for restraining, changing, and evaluating # the geometry of a protein model. # # IUPAC atom names are used to define dihedral angles. They are exactly # the same as the atom types in the CHARMM 22 topology library. As a # consequence, there are two small differences with the IUPAC atom names as # used in the PDB files: CHARMM ILE CD --> PDB ILE CD1 and LEU CD1 <--> CD2 # (with identical changes for the hydrogen atoms; the differences in the # carboxy terminus oxygen atoms are irrelevant here). MODELLER works internally # with CHARMM 22 conventions. The PDB format is dealt with only during input or # output. Be sure you take these conventions into account in all programs # that are using this library file (dih.f). The order of residues in this # file should not be important. Another potential difficuly is that it # appears that in CHARMM 19, LEU CD1 and CD2 are labelled as in the PDB and # no conversion is necessary; this can be seen from the fact that LEU CB # pseudo-chirality IMPR entry is such that no CD1/CD2 swap is neccessary # to calculate chi2 correctly (files param19.inp and toph19.inp). # # For MODELLER 7v0 the CHARMM topology library was changed to conform to PDB, # so the considerations above do not apply. # # The preferred geometries of the dihedral angle types are also specified # as pdf's which are the weighted sums of Gaussians. The weights, means, # and standard deviations were obtained with ALBASE_1 high resolution # structures, mdt2, plot2, and asgl1 (fitting and plotting); the data # and results are in the ~/constr2/mnch and ~/constr2/chi1234 directories. # # Means and standard deviations are from fitting Gaussians to the histograms, # but weights come from the class frequencies. For each type of a sidechain # dihedral angle class for each residue, the classes are ordered according to # their decreasing weights. The ordering for mainchain dihedral angle # classes is the same for all residue types. # # Cys sidehchain means and standard deviations are from the half-cystines # in disulfide bridges; weights are from all Cys residues. Except for the # small differences in weights of different classes, half-cystine and # cysteines can be considered the same as far as the dihedral angle data # in this file are concerned. # # It should be noted that for some mainchain dihedral angle classes Gaussians # do not have the same means and standard deviations here as the mainchain # conformation classes defined in MNCH.LIB file (eg Gly Psi). MODELLER should # use MAINCHAIN_CLASS (MNCH.LIB) for restraining mainchain, and CHIi_CLASS # (RESDIH.LIB) for restraining sidechains (SIDECHAIN_CLASS [SDCH.LIB] and # PHI/PSI_CLASS [RESDIH.LIB] should be ignored when restraining sidechain # and mainchain, respectively). # # CHARMM conventions with some extensions are used to indicate atoms from # other residues: # # Previous residue: '-'; # Next residue: '+'; # Nextnext residue: '#'; # Do not find it : '_'; # # # RES ATOMS N WEIGHTS MEANS DEVIATIONS RANGES # Alpha Phi Psi Omega chi1 chi2 chi3 chi4 chi5 22 ALA 4 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.552 0.064 0.382 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 CYS 9 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.380 0.035 0.583 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.301 0.088 0.610 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB SG 3 0.516 0.300 0.182 -65.2 181.4 63.6 12.1 10.9 13.1 -120 0 120 240 0 120 CA CB SG _SG 3 0.453 0.244 0.303 -75.9 75.2 188.7 21.0 19.6 27.2 -130 5 5 125 125 230 CB SG _SG _CB 2 0.500 0.500 -85.3 95.0 7.6 12.2 -180 0 0 180 _CA _CB _SG SG 3 0.453 0.244 0.303 -75.9 75.2 188.7 21.0 19.6 27.2 -130 5 5 125 125 230 _N _CA _CB _SG 3 0.516 0.300 0.182 -65.2 181.4 63.6 12.1 10.9 13.1 -120 0 120 240 0 120 ASP 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.533 0.061 0.405 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.405 0.178 0.415 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.502 0.323 0.171 -69.9 185.9 63.3 9.9 11.9 8.3 -120 0 120 240 0 120 CA CB CG OD1 2 0.500 0.500 -14.2 160.5 32.6 38.6 -105 75 75 255 GLU 7 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.632 0.030 0.337 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.544 0.074 0.381 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.541 0.336 0.122 -68.0 184.9 61.6 10.7 13.0 11.5 -120 0 120 240 0 120 CA CB CG CD 3 0.629 0.212 0.159 179.0 -69.6 73.2 14.2 19.0 16.0 125 230 -130 10 10 125 CB CG CD OE1 2 0.469 0.531 0.0 180.0 73.3 29.7 -120 120 120 240 PHE 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.427 0.019 0.552 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.366 0.079 0.554 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.540 0.320 0.139 -66.5 181.7 63.1 9.7 10.3 8.9 -120 0 120 240 0 120 CA CB CG CD1 2 0.500 0.500 -84.0 84.0 13.0 13.0 -180 0 0 180 GLY 4 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.308 0.457 0.234 -68.8 82.8 180.0 12.0 15.5 50.0 -105 0 0 127 127 255 N CA C +N 3 0.154 0.390 0.455 -42.1 3.2 180.0 5.9 23.2 27.2 -85 -29 -29 87 87 275 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 HIS 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.440 0.054 0.504 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.364 0.155 0.479 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.535 0.330 0.132 -65.0 185.7 62.1 12.1 10.2 15.8 -120 0 120 240 0 120 CA CB CG ND1 3 0.483 0.406 0.111 -82.7 83.2 170.5 21.3 23.9 20.0 -145 0 0 137 137 215 HSE 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.440 0.054 0.504 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.364 0.155 0.479 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.535 0.330 0.132 -65.0 185.7 62.1 12.1 10.2 15.8 -120 0 120 240 0 120 CA CB CG ND1 3 0.483 0.406 0.111 -82.7 83.2 170.5 21.3 23.9 20.0 -145 0 0 137 137 215 HSP 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.440 0.054 0.504 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.364 0.155 0.479 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.535 0.330 0.132 -65.0 185.7 62.1 12.1 10.2 15.8 -120 0 120 240 0 120 CA CB CG ND1 3 0.483 0.406 0.111 -82.7 83.2 170.5 21.3 23.9 20.0 -145 0 0 137 137 215 ILE 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.418 0.009 0.571 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.376 0.030 0.593 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG1 3 0.710 0.152 0.135 -63.1 62.7 190.8 9.0 6.9 9.6 -120 0 0 120 120 240 CA CB CG1 CD1 3 0.752 0.146 0.100 168.9 -60.8 68.0 10.0 10.3 10.0 110 240 -120 10 10 110 LYS 8 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.539 0.045 0.415 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.472 0.101 0.426 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.531 0.363 0.106 -67.0 185.4 63.5 12.5 12.1 14.1 -120 0 120 240 0 120 CA CB CG CD 3 0.689 0.168 0.139 168.9 -60.8 68.0 10.0 10.3 10.0 132 240 -120 0 0 132 CB CG CD CE 3 0.134 0.715 0.151 179.3 -72.0 73.0 16.4 26.9 31.7 130 230 -130 0 0 130 CG CD CE NZ 3 0.609 0.198 0.193 178.7 -66.8 72.6 20.0 22.0 28.6 120 240 -120 0 0 120 LEU 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.549 0.016 0.434 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.442 0.058 0.499 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.620 0.349 0.030 -64.2 180.7 62.0 9.9 8.7 15.2 -120 0 120 240 0 120 CA CB CG CD1 3 0.543 0.407 0.048 184.7 64.8 -65.0 9.7 10.1 10.0 120 250 -10 120 -110 10 MET 7 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.529 0.027 0.443 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.451 0.064 0.484 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.574 0.349 0.075 -66.7 184.9 66.6 10.6 12.4 14.7 -120 0 120 240 0 120 CA CB CG SD 3 0.618 0.243 0.136 178.4 -66.7 70.4 13.8 12.7 9.1 120 240 -120 0 0 120 CB CG SD CE 3 0.362 0.336 0.298 -73.5 69.6 182.6 19.7 14.1 20.0 -127 0 0 120 120 233 ASN 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.391 0.125 0.482 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.316 0.273 0.409 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.517 0.313 0.165 -68.9 187.4 63.5 11.2 11.7 9.1 -120 0 120 240 0 120 CA CB CG OD1 2 0.427 0.571 -36.1 123.5 37.2 72.6 -127 50 50 233 PRO 7 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 1 1.000 -62.9 11.0 -180 180 N CA C +N 2 0.377 0.622 -28.8 146.4 11.9 13.1 -120 60 60 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.310 0.419 0.268 -26.7 29.8 -0.3 6.5 7.7 16.1 -180 -12 12 180 -12 12 CA CB CG CD 2 0.600 0.400 -34.6 34.6 8.0 8.0 -180 0 0 180 CB CG CD N 2 0.400 0.600 -30.0 30.0 10.5 7.9 -180 0 0 180 GLN 7 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.508 0.037 0.453 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.429 0.092 0.478 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.538 0.358 0.104 -65.6 182.7 64.1 11.0 11.4 7.8 -120 0 120 240 0 120 CA CB CG CD 3 0.647 0.189 0.164 179.7 -68.4 70.1 12.5 17.1 17.3 120 240 -120 0 0 120 CB CG CD OE1 2 0.743 0.257 0.0 180.0 70.0 40.0 -120 120 120 240 ARG 8 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.525 0.031 0.442 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.459 0.081 0.458 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.532 0.329 0.133 -66.8 182.7 60.1 12.5 12.8 7.1 -120 0 120 240 0 120 CA CB CG CD 3 0.741 0.148 0.103 181.5 -80.0 68.0 16.0 27.6 12.0 115 230 -130 0 0 115 CB CG CD NE 3 0.415 0.302 0.275 180.0 -65.0 70.0 13.9 15.0 25.5 135 230 -130 -15 -15 135 CG CD NE CZ 3 0.554 0.254 0.183 170.9 -88.5 85.7 43.1 15.9 10.9 110 235 -125 0 0 110 SER 5 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.472 0.036 0.490 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.373 0.101 0.524 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB OG 3 0.398 0.342 0.255 65.2 -64.5 179.9 12.3 12.4 11.2 0 120 -120 0 120 240 THR 5 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.379 0.013 0.607 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.328 0.078 0.592 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB OG1 3 0.485 0.397 0.115 -58.8 62.9 189.4 7.0 8.8 9.9 -120 0 0 120 120 240 VAL 5 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.390 0.008 0.600 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.328 0.032 0.638 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG1 3 0.665 0.216 0.116 175.1 -62.7 65.9 7.8 8.8 12.5 120 240 -120 0 0 120 TRP 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.481 0.025 0.492 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.409 0.078 0.511 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.537 0.297 0.164 -68.1 180.8 60.6 9.0 9.1 10.0 -120 0 120 240 0 120 CA CB CG CD1 3 0.596 0.287 0.115 91.0 -93.1 0.0 17.2 11.5 23.3 40 180 -180 -55 -55 40 TYR 6 -CA CA +CA #CA 3 0.661 0.025 0.312 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 -C N CA C 3 0.377 0.028 0.593 -64.5 58.0 -115.0 7.9 10.3 28.0 -87 0 0 120 -240 -87 N CA C +N 3 0.293 0.096 0.609 -39.6 35.0 138.7 10.5 15.0 20.8 -120 -3 -3 75 75 240 CA C +N +CA 2 0.999 0.001 180.0 0.0 5.0 5.0 90 270 -90 90 N CA CB CG 3 0.561 0.312 0.125 -65.2 179.3 62.9 9.3 10.0 10.2 -120 0 120 240 0 120 CA CB CG CD1 2 0.500 0.500 -83.0 83.0 13.0 13.0 -180 0 0 180