from __future__ import absolute_import, division, print_function import os from libtbx import easy_run from six.moves import range pdbs = {"linking_test_CYS_CYS_alt_loc.pdb" : """ ATOM 274 N CYS A 27 17.541 4.439 12.897 1.00 13.99 N ATOM 275 CA CYS A 27 16.566 5.527 12.862 1.00 14.57 C ATOM 276 C CYS A 27 16.236 6.026 11.467 1.00 14.53 C ATOM 277 O CYS A 27 15.254 6.760 11.351 1.00 16.95 O ATOM 278 CB CYS A 27 17.114 6.698 13.662 1.00 15.77 C ATOM 279 SG CYS A 27 17.230 6.332 15.443 1.00 17.57 S ATOM 1225 CB CYS A 123 14.607 7.591 16.260 1.00 24.16 C ATOM 1226 SG CYS A 123 15.316 5.939 15.946 1.00 20.05 S ATOM 1217 N ACYS A 123 15.023 7.279 18.624 0.58 26.40 N ATOM 1219 CA ACYS A 123 15.266 8.190 17.491 0.58 25.69 C ATOM 1221 C ACYS A 123 14.764 9.599 17.776 0.58 26.33 C ATOM 1223 O ACYS A 123 14.197 10.238 16.886 0.58 28.70 O ATOM 1227 OXTACYS A 123 14.975 10.081 18.878 0.58 28.31 O ATOM 1218 N BCYS A 123 15.023 7.288 18.685 0.42 25.68 N ATOM 1220 CA BCYS A 123 15.108 8.205 17.548 0.42 25.86 C ATOM 1222 C BCYS A 123 14.270 9.460 17.813 0.42 26.42 C ATOM 1224 O BCYS A 123 13.915 10.125 16.837 0.42 27.75 O ATOM 1228 OXTBCYS A 123 13.981 9.728 18.968 0.42 28.04 O """, "linking_test_NAG-NAG.pdb" : """ ATOM 982 N ASN A 131 59.894 31.406 61.164 1.00 8.27 N ATOM 983 CA ASN A 131 60.727 32.209 60.265 1.00 8.51 C ATOM 984 C ASN A 131 62.218 31.862 60.359 1.00 9.14 C ATOM 985 O ASN A 131 63.057 32.700 59.954 1.00 11.54 O ATOM 986 CB ASN A 131 60.527 33.684 60.538 1.00 8.67 C ATOM 987 CG ASN A 131 60.938 34.568 59.363 1.00 9.10 C ATOM 988 OD1 ASN A 131 60.572 34.301 58.221 1.00 8.69 O ATOM 989 ND2 ASN A 131 61.660 35.631 59.674 1.00 10.39 N HETATM 2693 C1 NAG A 361 61.950 36.682 58.740 1.00 10.88 C HETATM 2694 C2 NAG A 361 61.484 38.019 59.269 1.00 11.23 C HETATM 2695 C3 NAG A 361 61.917 39.166 58.345 1.00 12.36 C HETATM 2696 C4 NAG A 361 63.416 39.059 58.041 1.00 12.10 C HETATM 2697 C5 NAG A 361 63.760 37.632 57.548 1.00 12.32 C HETATM 2698 C6 NAG A 361 65.221 37.430 57.213 1.00 16.14 C HETATM 2699 C7 NAG A 361 59.438 37.677 60.568 1.00 11.18 C HETATM 2700 C8 NAG A 361 57.935 37.538 60.529 1.00 12.29 C HETATM 2701 N2 NAG A 361 60.056 37.983 59.429 1.00 11.34 N HETATM 2702 O3 NAG A 361 61.602 40.407 58.980 1.00 14.07 O HETATM 2703 O4 NAG A 361 63.792 39.965 56.971 1.00 13.40 O HETATM 2704 O5 NAG A 361 63.357 36.678 58.496 1.00 11.54 O HETATM 2705 O6 NAG A 361 65.973 37.639 58.364 1.00 17.57 O HETATM 2706 O7 NAG A 361 60.051 37.500 61.614 1.00 12.67 O HETATM 2707 C1 NAG A 362 64.268 41.214 57.404 1.00 15.39 C HETATM 2708 C2 NAG A 362 65.186 41.796 56.314 1.00 16.15 C HETATM 2709 C3 NAG A 362 65.630 43.192 56.758 1.00 19.28 C HETATM 2710 C4 NAG A 362 64.431 44.087 57.131 1.00 19.23 C HETATM 2711 C5 NAG A 362 63.526 43.362 58.126 1.00 18.32 C HETATM 2712 C6 NAG A 362 62.219 44.114 58.366 1.00 18.44 C HETATM 2713 C7 NAG A 362 66.649 40.270 55.063 1.00 15.73 C HETATM 2714 C8 NAG A 362 67.859 39.361 55.043 1.00 17.34 C HETATM 2715 N2 NAG A 362 66.303 40.872 56.196 1.00 16.94 N HETATM 2716 O3 NAG A 362 66.321 43.771 55.701 1.00 23.91 O HETATM 2717 O4 NAG A 362 64.893 45.314 57.706 1.00 22.28 O HETATM 2718 O5 NAG A 362 63.154 42.081 57.584 1.00 16.19 O HETATM 2719 O6 NAG A 362 61.496 43.532 59.419 1.00 20.18 O HETATM 2720 O7 NAG A 362 66.009 40.389 54.022 1.00 14.38 O """, "linking_test_MAN-SER.pdb" : """ HETATM 2721 C1 MAN A 364 43.704 27.933 15.645 1.00 16.07 C HETATM 2722 C2 MAN A 364 42.296 27.563 15.194 1.00 20.45 C HETATM 2723 C3 MAN A 364 42.280 26.343 14.240 1.00 21.29 C HETATM 2724 C4 MAN A 364 43.262 26.552 13.084 1.00 19.50 C HETATM 2725 C5 MAN A 364 44.616 27.026 13.597 1.00 15.55 C HETATM 2726 C6 MAN A 364 45.515 27.538 12.507 1.00 19.27 C HETATM 2727 O2 MAN A 364 41.697 28.638 14.482 1.00 21.51 O HETATM 2728 O3 MAN A 364 40.973 26.218 13.718 1.00 26.03 O HETATM 2729 O4 MAN A 364 43.352 25.365 12.310 1.00 23.56 O HETATM 2730 O5 MAN A 364 44.525 28.138 14.481 1.00 15.77 O HETATM 2731 O6 MAN A 364 46.856 27.797 12.809 1.00 32.01 O ATOM 2544 N SER A 336 46.708 25.446 16.017 1.00 10.08 N ATOM 2545 CA SER A 336 46.632 26.822 16.443 1.00 11.00 C ATOM 2546 C SER A 336 47.835 27.172 17.291 1.00 10.18 C ATOM 2547 O SER A 336 48.284 26.389 18.124 1.00 11.56 O ATOM 2548 CB SER A 336 45.335 27.061 17.256 1.00 12.96 C ATOM 2549 OG SER A 336 44.189 26.866 16.408 1.00 15.06 O """, "linking_test_ASN-NAG.pdb" : """ ATOM 1989 N ASN A 270 20.738 61.827 110.156 1.00 11.35 N ATOM 1990 CA ASN A 270 20.866 63.240 110.482 1.00 11.45 C ATOM 1991 C ASN A 270 20.238 64.075 109.377 1.00 11.25 C ATOM 1992 O ASN A 270 20.902 64.453 108.408 1.00 10.95 O ATOM 1993 CB ASN A 270 22.330 63.643 110.648 1.00 12.36 C ATOM 1994 CG ASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1 ASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2 ASN A 270 23.440 65.083 112.236 1.00 13.89 N HETATM 3221 C1 NAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 NAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 NAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 NAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 NAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 NAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 NAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 NAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 NAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 NAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 NAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 NAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 NAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 NAG A 435 22.047 63.959 114.195 1.00 19.58 O """, "linking_test_CYS-VSP.pdb" : """ ATOM 631 N CYS A 338 -12.642 13.597 13.517 1.00 7.89 N ATOM 632 CA CYS A 338 -12.754 14.691 12.554 1.00 6.21 C ATOM 633 C CYS A 338 -14.168 14.844 12.007 1.00 8.51 C ATOM 634 O CYS A 338 -15.020 13.986 12.195 1.00 13.75 O ATOM 635 CB CYS A 338 -11.756 14.486 11.426 1.00 5.09 C ATOM 636 SG CYS A 338 -9.991 14.515 11.993 1.00 18.62 S ATOM 2670 N CYS B 338 -8.615 45.421 -38.743 1.00 19.16 N ATOM 2671 CA CYS B 338 -8.357 46.490 -37.804 1.00 9.38 C ATOM 2672 C CYS B 338 -6.940 46.477 -37.283 1.00 13.38 C ATOM 2673 O CYS B 338 -6.183 45.531 -37.509 1.00 12.78 O ATOM 2674 CB CYS B 338 -9.340 46.408 -36.640 1.00 6.81 C ATOM 2675 SG CYS B 338 -11.059 46.627 -37.137 1.00 18.08 S HETATM 4105 C10 VSP A 600 -12.073 10.268 5.878 1.00 15.21 C HETATM 4106 C13 VSP A 600 -9.415 12.009 8.138 1.00 17.34 C HETATM 4107 C17 VSP A 600 -9.173 15.500 9.538 1.00 18.06 C HETATM 4108 C21 VSP A 600 -9.724 11.447 10.488 1.00 13.59 C HETATM 4109 C22 VSP A 600 -10.796 10.611 10.141 1.00 13.09 C HETATM 4110 O20 VSP A 600 -6.512 15.097 9.546 1.00 36.73 O HETATM 4111 N01 VSP A 600 -13.584 12.637 7.376 1.00 2.48 N HETATM 4112 C11 VSP A 600 -10.820 11.061 6.336 1.00 16.83 C HETATM 4113 C02 VSP A 600 -14.234 11.590 6.685 1.00 0.00 C HETATM 4114 C12 VSP A 600 -10.480 11.165 7.808 1.00 19.86 C HETATM 4115 C03 VSP A 600 -13.499 10.594 6.048 1.00 7.99 C HETATM 4116 C23 VSP A 600 -11.178 10.454 8.807 1.00 13.40 C HETATM 4117 N24 VSP A 600 -15.578 9.539 5.351 1.00 5.37 N HETATM 4118 C04 VSP A 600 -14.214 9.541 5.368 1.00 6.59 C HETATM 4119 C14 VSP A 600 -9.040 12.146 9.490 1.00 20.32 C HETATM 4120 N05 VSP A 600 -13.277 8.720 4.845 1.00 14.36 N HETATM 4121 N15 VSP A 600 -7.941 13.011 9.844 1.00 30.28 N HETATM 4122 C25 VSP A 600 -16.266 10.507 5.972 1.00 8.74 C HETATM 4123 N26 VSP A 600 -15.595 11.531 6.617 1.00 7.31 N HETATM 4124 C06 VSP A 600 -13.564 7.524 4.064 1.00 21.61 C HETATM 4125 S16 VSP A 600 -7.758 14.494 9.137 1.00 29.97 S HETATM 4126 C07 VSP A 600 -12.688 6.369 4.532 1.00 18.74 C HETATM 4127 C08 VSP A 600 -13.266 7.825 2.614 1.00 11.95 C HETATM 4128 C18 VSP A 600 -9.254 15.824 11.014 1.00 27.59 C HETATM 4129 N09 VSP A 600 -12.038 9.143 5.150 1.00 15.70 N HETATM 4130 O19 VSP A 600 -7.560 14.438 7.701 1.00 31.30 O HETATM 4131 C10 VSP B 600 -9.100 42.047 -31.076 1.00 15.42 C HETATM 4132 C13 VSP B 600 -11.662 43.913 -33.270 1.00 14.18 C HETATM 4133 C17 VSP B 600 -11.854 47.483 -34.510 1.00 33.18 C HETATM 4134 C21 VSP B 600 -11.316 43.454 -35.629 1.00 18.55 C HETATM 4135 C22 VSP B 600 -10.247 42.605 -35.296 1.00 16.17 C HETATM 4136 O20 VSP B 600 -14.506 47.137 -34.713 1.00 28.59 O HETATM 4137 N01 VSP B 600 -7.431 44.349 -32.620 1.00 3.96 N HETATM 4138 C11 VSP B 600 -10.309 42.931 -31.468 1.00 13.44 C HETATM 4139 C02 VSP B 600 -6.859 43.222 -31.970 1.00 9.31 C HETATM 4140 C12 VSP B 600 -10.611 43.066 -32.949 1.00 16.06 C HETATM 4141 C03 VSP B 600 -7.659 42.259 -31.325 1.00 10.60 C HETATM 4142 C23 VSP B 600 -9.886 42.396 -33.954 1.00 14.26 C HETATM 4143 N24 VSP B 600 -5.646 41.044 -30.732 1.00 11.16 N HETATM 4144 C04 VSP B 600 -7.014 41.143 -30.686 1.00 10.43 C HETATM 4145 C14 VSP B 600 -12.022 44.125 -34.611 1.00 21.96 C HETATM 4146 N05 VSP B 600 -8.006 40.380 -30.149 1.00 12.14 N HETATM 4147 N15 VSP B 600 -13.131 45.011 -34.903 1.00 21.91 N HETATM 4148 C25 VSP B 600 -4.907 41.964 -31.365 1.00 14.73 C HETATM 4149 N26 VSP B 600 -5.504 43.046 -31.973 1.00 6.61 N HETATM 4150 C06 VSP B 600 -7.852 39.153 -29.374 1.00 16.29 C HETATM 4151 S16 VSP B 600 -13.310 46.515 -34.202 1.00 24.65 S HETATM 4152 C07 VSP B 600 -8.917 38.154 -29.784 1.00 12.46 C HETATM 4153 C08 VSP B 600 -8.172 39.532 -27.956 1.00 15.34 C HETATM 4154 C18 VSP B 600 -11.699 47.833 -35.975 1.00 29.79 C HETATM 4155 N09 VSP B 600 -9.203 40.922 -30.367 1.00 10.22 N HETATM 4156 O19 VSP B 600 -13.564 46.514 -32.785 1.00 21.41 O """, "vsp.cif" : """data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level VSP VSP 'N-(3-{[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]methyl}phenyl)ethanesulfonamide' ligand 48 26 . # data_comp_VSP # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z VSP C10 C CR5 . -1.0980 0.5259 -1.4219 VSP C13 C CR16 . 1.7614 -0.3172 0.5726 VSP C17 C CH2 . 5.6014 -2.4120 3.1666 VSP C21 C CR16 . 1.7453 0.7693 2.7632 VSP C22 C CR16 . 0.8735 1.7367 2.2769 VSP O20 O OS . 5.2933 -0.3503 1.4516 VSP N01 N NH2 . -0.3458 2.0703 -4.1108 VSP C11 C CH2 . 0.4050 0.6157 -1.3625 VSP C02 C CR6 . -1.6892 1.7101 -3.6579 VSP C12 C CR6 . 0.8759 0.6638 0.0868 VSP C03 C CR56 . -1.9069 1.0097 -2.4216 VSP C23 C CR16 . 0.4365 1.6918 0.9409 VSP N24 N N . -4.2441 1.0766 -2.8909 VSP C04 C CR56 . -3.2296 0.7025 -2.0603 VSP C14 C CR6 . 2.1976 -0.2670 1.9141 VSP N05 N NR5 . -3.1716 0.0434 -0.8597 VSP N15 N NC1 . 3.1146 -1.2864 2.4232 VSP C25 C CR16 . -3.9926 1.7210 -4.0202 VSP N26 N N . -2.7539 2.0345 -4.4038 VSP C06 C CH1 . -4.2964 -0.4622 -0.1100 VSP S16 S S . 4.7064 -0.9300 2.6495 VSP C07 C CH3 . -5.2645 0.6852 0.2164 VSP C08 C CH3 . -5.0317 -1.5364 -0.9389 VSP C18 C CH3 . 6.7580 -2.6668 2.2013 VSP N09 N N . -1.8758 -0.0508 -0.4964 VSP O19 O OS . 4.8764 0.1446 3.5931 VSP H13 H HCR6 . 2.0684 -1.0255 -0.0103 VSP H17 H HCH2 . 5.9543 -2.2830 4.0830 VSP H17A H HCH2 . 4.9925 -3.1829 3.1559 VSP H21 H HCR6 . 2.0424 0.8054 3.6816 VSP H22 H HCR6 . 0.5656 2.4466 2.8623 VSP HN01 H HNH2 . -0.0669 2.9442 -4.0707 VSP HN0A H HNH2 . 0.2203 1.4223 -4.4341 VSP H11 H HCH2 . 0.7930 -0.1642 -1.8001 VSP H11A H HCH2 . 0.7032 1.4281 -1.8250 VSP H23 H HCR6 . -0.1657 2.3626 0.6121 VSP HN15 H HNC1 . 2.8065 -2.1149 2.6093 VSP H25 H HCR6 . -4.7360 1.9744 -4.5899 VSP H06 H HCH1 . -3.9722 -0.8645 0.7323 VSP H07 H HCH3 . -5.8747 0.4033 0.9157 VSP H07A H HCH3 . -4.7525 1.4713 0.5237 VSP H07B H HCH3 . -5.7736 0.9202 -0.5815 VSP H08 H HCH3 . -5.5202 -1.1073 -1.6737 VSP H08A H HCH3 . -4.3705 -2.1772 -1.3107 VSP H08B H HCH3 . -5.6638 -2.0152 -0.3647 VSP H18 H HCH3 . 6.4134 -2.7373 1.2907 VSP H18A H HCH3 . 7.3897 -1.9326 2.2516 VSP H18B H HCH3 . 7.2035 -3.4950 2.4420 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd VSP C10 C11 single 1.507 0.020 VSP C10 C03 aromatic 1.374 0.020 VSP C10 N09 aromatic 1.339 0.020 VSP C13 C12 aromatic 1.408 0.020 VSP C13 C14 aromatic 1.412 0.020 VSP C17 S16 single 1.807 0.020 VSP C17 C18 single 1.528 0.020 VSP C21 C22 aromatic 1.390 0.020 VSP C21 C14 aromatic 1.414 0.020 VSP C22 C23 aromatic 1.406 0.020 VSP O20 S16 double 1.454 0.020 VSP N01 C02 single 1.463 0.020 VSP C11 C12 single 1.525 0.020 VSP C02 C03 aromatic 1.437 0.020 VSP C02 N26 aromatic 1.340 0.020 VSP C12 C23 aromatic 1.407 0.020 VSP C03 C04 aromatic 1.405 0.020 VSP N24 C04 aromatic 1.363 0.020 VSP N24 C25 aromatic 1.324 0.020 VSP C04 N05 aromatic 1.371 0.020 VSP C14 N15 single 1.463 0.020 VSP N05 C06 single 1.443 0.020 VSP N05 N09 aromatic 1.349 0.020 VSP N15 S16 single 1.647 0.020 VSP C25 N26 aromatic 1.334 0.020 VSP C06 C07 single 1.536 0.020 VSP C06 C08 single 1.543 0.020 VSP S16 O19 double 1.440 0.020 VSP C13 H13 single 0.967 0.020 VSP C17 H17 single 0.990 0.020 VSP C17 H17A single 0.982 0.020 VSP C21 H21 single 0.966 0.020 VSP C22 H22 single 0.970 0.020 VSP N01 HN01 single 0.918 0.020 VSP N01 HN0A single 0.919 0.020 VSP C11 H11 single 0.975 0.020 VSP C11 H11A single 0.981 0.020 VSP C23 H23 single 0.959 0.020 VSP N15 HN15 single 0.903 0.020 VSP C25 H25 single 0.970 0.020 VSP C06 H06 single 0.988 0.020 VSP C07 H07 single 0.970 0.020 VSP C07 H07A single 0.987 0.020 VSP C07 H07B single 0.975 0.020 VSP C08 H08 single 0.981 0.020 VSP C08 H08A single 0.993 0.020 VSP C08 H08B single 0.979 0.020 VSP C18 H18 single 0.976 0.020 VSP C18 H18A single 0.970 0.020 VSP C18 H18B single 0.971 0.020 # """, "linking_test_LYS-ABA-GLU.pdb" : """ ATOM 41 N LYS S 7 -13.818 -0.993 15.491 1.00 17.94 N ATOM 42 CA LYS S 7 -13.936 -0.779 14.054 1.00 17.73 C ATOM 43 C LYS S 7 -13.883 -2.110 13.316 1.00 17.51 C ATOM 44 O LYS S 7 -14.643 -2.338 12.374 1.00 14.65 O ATOM 45 CB LYS S 7 -12.808 0.129 13.558 1.00 19.47 C ATOM 46 CG LYS S 7 -12.855 0.415 12.068 1.00 24.22 C ATOM 47 CD LYS S 7 -11.746 1.372 11.655 1.00 27.47 C ATOM 48 CE LYS S 7 -11.804 1.661 10.162 1.00 31.97 C ATOM 49 NZ LYS S 7 -10.718 2.586 9.730 1.00 34.51 N HETATM 50 N ABA S 8 -12.984 -2.991 13.745 1.00 15.85 N HETATM 51 CA ABA S 8 -12.846 -4.298 13.109 1.00 15.74 C HETATM 52 C ABA S 8 -14.142 -5.102 13.246 1.00 14.66 C HETATM 53 O ABA S 8 -14.565 -5.778 12.308 1.00 16.07 O HETATM 54 CB ABA S 8 -11.676 -5.068 13.736 1.00 17.05 C HETATM 55 CG ABA S 8 -11.423 -6.426 13.100 1.00 20.97 C ATOM 56 N GLU S 9 -14.778 -5.025 14.413 1.00 14.08 N ATOM 57 CA GLU S 9 -16.026 -5.746 14.648 1.00 15.05 C ATOM 58 C GLU S 9 -17.147 -5.199 13.765 1.00 15.55 C ATOM 59 O GLU S 9 -17.893 -5.956 13.136 1.00 15.55 O ATOM 60 CB GLU S 9 -16.441 -5.626 16.114 1.00 16.16 C ATOM 61 CG GLU S 9 -15.413 -6.165 17.096 1.00 20.84 C ATOM 62 CD GLU S 9 -15.822 -5.942 18.542 1.00 26.26 C ATOM 63 OE1 GLU S 9 -16.348 -4.851 18.850 1.00 29.12 O ATOM 64 OE2 GLU S 9 -15.608 -6.850 19.370 1.00 30.05 O """, "linking_test_ASN-NAG-altloc1.pdb" : """ ATOM 1989 N ASN A 270 20.738 61.827 110.156 1.00 11.35 N ATOM 1990 CA ASN A 270 20.866 63.240 110.482 1.00 11.45 C ATOM 1991 C ASN A 270 20.238 64.075 109.377 1.00 11.25 C ATOM 1992 O ASN A 270 20.902 64.453 108.408 1.00 10.95 O ATOM 1993 CB ASN A 270 22.330 63.643 110.648 1.00 12.36 C ATOM 1994 CG ASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1 ASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2 ASN A 270 23.440 65.083 112.236 1.00 13.89 N HETATM 3221 C1 ANAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 ANAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 ANAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 ANAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 ANAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 ANAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 ANAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 ANAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 ANAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 ANAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 ANAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 ANAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 ANAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 ANAG A 435 22.047 63.959 114.195 1.00 19.58 O HETATM 3221 C1 BNAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 BNAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 BNAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 BNAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 BNAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 BNAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 BNAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 BNAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 BNAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 BNAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 BNAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 BNAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 BNAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 BNAG A 435 22.047 63.959 114.195 1.00 19.58 O """, "linking_test_ASN-NAG-altloc2.pdb" : """ ATOM 1989 N AASN A 270 20.738 61.827 110.156 1.00 11.35 N ATOM 1990 CA AASN A 270 20.866 63.240 110.482 1.00 11.45 C ATOM 1991 C AASN A 270 20.238 64.075 109.377 1.00 11.25 C ATOM 1992 O AASN A 270 20.902 64.453 108.408 1.00 10.95 O ATOM 1993 CB AASN A 270 22.330 63.643 110.648 1.00 12.36 C ATOM 1994 CG AASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1AASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2AASN A 270 23.440 65.083 112.236 1.00 13.89 N ATOM 1989 N BASN A 270 20.738 61.827 110.156 1.00 11.35 N ATOM 1990 CA BASN A 270 20.866 63.240 110.482 1.00 11.45 C ATOM 1991 C BASN A 270 20.238 64.075 109.377 1.00 11.25 C ATOM 1992 O BASN A 270 20.902 64.453 108.408 1.00 10.95 O ATOM 1993 CB BASN A 270 22.330 63.643 110.648 1.00 12.36 C ATOM 1994 CG BASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1BASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2BASN A 270 23.440 65.083 112.236 1.00 13.89 N HETATM 3221 C1 ANAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 ANAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 ANAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 ANAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 ANAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 ANAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 ANAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 ANAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 ANAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 ANAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 ANAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 ANAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 ANAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 ANAG A 435 22.047 63.959 114.195 1.00 19.58 O HETATM 3221 C1 BNAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 BNAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 BNAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 BNAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 BNAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 BNAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 BNAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 BNAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 BNAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 BNAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 BNAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 BNAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 BNAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 BNAG A 435 22.047 63.959 114.195 1.00 19.58 O """, "linking_test_ASN-NAG-altloc3.pdb" : """ ATOM 1989 N ASN A 270 20.738 61.827 110.156 1.00 11.35 N ATOM 1990 CA ASN A 270 20.866 63.240 110.482 1.00 11.45 C ATOM 1991 C ASN A 270 20.238 64.075 109.377 1.00 11.25 C ATOM 1992 O ASN A 270 20.902 64.453 108.408 1.00 10.95 O ATOM 1993 CB ASN A 270 22.330 63.643 110.648 1.00 12.36 C ATOM 1994 CG AASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1AASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2AASN A 270 23.440 65.083 112.236 1.00 13.89 N ATOM 1994 CG BASN A 270 22.475 64.985 111.329 1.00 13.25 C ATOM 1995 OD1BASN A 270 21.731 65.920 111.033 1.00 13.36 O ATOM 1996 ND2BASN A 270 23.440 65.083 112.236 1.00 13.89 N HETATM 3221 C1 ANAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 ANAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 ANAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 ANAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 ANAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 ANAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 ANAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 ANAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 ANAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 ANAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 ANAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 ANAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 ANAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 ANAG A 435 22.047 63.959 114.195 1.00 19.58 O HETATM 3221 C1 BNAG A 435 23.764 66.364 112.833 1.00 15.11 C HETATM 3222 C2 BNAG A 435 23.381 66.347 114.325 1.00 16.09 C HETATM 3223 C3 BNAG A 435 23.832 67.642 115.011 1.00 16.01 C HETATM 3224 C4 BNAG A 435 25.317 67.871 114.758 1.00 15.48 C HETATM 3225 C5 BNAG A 435 25.583 67.877 113.254 1.00 14.91 C HETATM 3226 C6 BNAG A 435 27.059 68.022 112.960 1.00 14.68 C HETATM 3227 C7 BNAG A 435 21.392 64.986 114.378 1.00 18.41 C HETATM 3228 C8 BNAG A 435 19.882 64.903 114.521 1.00 19.12 C HETATM 3229 N2 BNAG A 435 21.944 66.193 114.461 1.00 17.50 N HETATM 3230 O3 BNAG A 435 23.601 67.552 116.408 1.00 16.86 O HETATM 3231 O4 BNAG A 435 25.725 69.107 115.324 1.00 15.49 O HETATM 3232 O5 BNAG A 435 25.166 66.624 112.676 1.00 14.58 O HETATM 3233 O6 BNAG A 435 27.784 66.911 113.470 1.00 14.35 O HETATM 3234 O7 BNAG A 435 22.047 63.959 114.195 1.00 19.58 O """, "linking_test_DT-4MF-DA.pdb" : """ ATOM 2093 P DT C 26 0.288 1.691 -25.901 1.00 51.23 P ATOM 2094 OP1 DT C 26 1.525 1.058 -26.431 1.00 51.10 O ATOM 2095 OP2 DT C 26 -0.538 2.550 -26.800 1.00 50.36 O ATOM 2096 O5' DT C 26 -0.678 0.604 -25.234 1.00 47.26 O ATOM 2097 C5' DT C 26 -0.147 -0.278 -24.258 1.00 44.30 C ATOM 2098 C4' DT C 26 -1.108 -0.531 -23.117 1.00 40.69 C ATOM 2099 O4' DT C 26 -1.860 0.647 -22.788 1.00 39.38 O ATOM 2100 C3' DT C 26 -2.247 -1.484 -23.405 1.00 40.36 C ATOM 2101 O3' DT C 26 -1.754 -2.822 -23.434 1.00 39.62 O ATOM 2102 C2' DT C 26 -3.214 -1.187 -22.243 1.00 39.03 C ATOM 2103 C1' DT C 26 -2.726 0.186 -21.778 1.00 36.96 C ATOM 2104 N1 DT C 26 -3.767 1.212 -21.523 1.00 36.37 N ATOM 2105 C2 DT C 26 -4.324 1.300 -20.260 1.00 35.70 C ATOM 2106 O2 DT C 26 -4.018 0.575 -19.325 1.00 35.41 O ATOM 2107 N3 DT C 26 -5.271 2.290 -20.125 1.00 34.72 N ATOM 2108 C4 DT C 26 -5.714 3.176 -21.081 1.00 34.88 C ATOM 2109 O4 DT C 26 -6.571 4.022 -20.842 1.00 35.55 O ATOM 2110 C5 DT C 26 -5.100 3.038 -22.379 1.00 35.49 C ATOM 2111 C7 DT C 26 -5.637 3.830 -23.539 1.00 34.73 C ATOM 2112 C6 DT C 26 -4.166 2.075 -22.536 1.00 36.24 C HETATM 2113 O2P 4MF C 27 -3.441 -4.407 -23.957 1.00 41.52 O HETATM 2114 P 4MF C 27 -2.133 -4.347 -23.209 1.00 40.92 P HETATM 2115 O1P 4MF C 27 -0.830 -4.701 -23.874 1.00 40.35 O HETATM 2116 O5' 4MF C 27 -2.273 -5.251 -21.880 1.00 43.61 O HETATM 2117 C5' 4MF C 27 -2.804 -4.709 -20.672 1.00 45.90 C HETATM 2118 C4' 4MF C 27 -4.324 -4.877 -20.528 1.00 48.09 C HETATM 2119 C3' 4MF C 27 -5.014 -5.783 -21.538 1.00 48.57 C HETATM 2120 O3' 4MF C 27 -5.183 -7.086 -20.990 1.00 49.62 O HETATM 2121 C2' 4MF C 27 -6.376 -5.166 -21.819 1.00 49.28 C HETATM 2122 C1' 4MF C 27 -6.327 -3.804 -21.133 1.00 49.96 C HETATM 2123 O4' 4MF C 27 -4.988 -3.610 -20.660 1.00 50.00 O HETATM 2124 N1 4MF C 27 -6.624 -2.783 -22.129 1.00 50.63 N HETATM 2125 C7A 4MF C 27 -7.134 -1.592 -21.893 1.00 50.94 C HETATM 2126 C7 4MF C 27 -7.511 -0.950 -20.876 1.00 50.46 C HETATM 2127 C6 4MF C 27 -7.823 0.199 -21.023 1.00 50.24 C HETATM 2128 C5 4MF C 27 -8.031 0.699 -22.101 1.00 50.59 C HETATM 2129 C4 4MF C 27 -7.681 0.140 -23.189 1.00 50.69 C HETATM 2130 C4M 4MF C 27 -7.799 0.755 -24.356 1.00 50.25 C HETATM 2131 C3A 4MF C 27 -7.199 -1.092 -23.071 1.00 50.73 C HETATM 2132 C3 4MF C 27 -6.765 -1.912 -23.925 1.00 51.26 C HETATM 2133 C2 4MF C 27 -6.425 -2.920 -23.332 1.00 50.64 C ATOM 2134 P DA C 28 -5.472 -8.466 -21.727 1.00 49.25 P ATOM 2135 OP1 DA C 28 -4.838 -9.205 -20.608 1.00 49.49 O ATOM 2136 OP2 DA C 28 -4.975 -8.640 -23.106 1.00 48.81 O ATOM 2137 O5' DA C 28 -7.046 -8.727 -21.708 1.00 49.80 O ATOM 2138 C5' DA C 28 -7.693 -9.165 -20.528 1.00 51.19 C ATOM 2139 C4' DA C 28 -9.182 -8.886 -20.616 1.00 52.05 C ATOM 2140 O4' DA C 28 -9.387 -7.491 -20.963 1.00 51.89 O ATOM 2141 C3' DA C 28 -9.926 -9.711 -21.664 1.00 52.66 C ATOM 2142 O3' DA C 28 -11.105 -10.227 -21.073 1.00 54.53 O ATOM 2143 C2' DA C 28 -10.233 -8.695 -22.768 1.00 51.97 C ATOM 2144 C1' DA C 28 -10.388 -7.412 -21.957 1.00 50.53 C ATOM 2145 N9 DA C 28 -10.194 -6.169 -22.690 1.00 49.74 N ATOM 2146 C8 DA C 28 -9.269 -5.919 -23.662 1.00 49.76 C ATOM 2147 N7 DA C 28 -9.328 -4.705 -24.145 1.00 49.73 N ATOM 2148 C5 DA C 28 -10.361 -4.112 -23.430 1.00 49.84 C ATOM 2149 C6 DA C 28 -10.936 -2.820 -23.456 1.00 49.81 C ATOM 2150 N6 DA C 28 -10.525 -1.842 -24.264 1.00 49.75 N ATOM 2151 N1 DA C 28 -11.956 -2.559 -22.614 1.00 49.98 N ATOM 2152 C2 DA C 28 -12.373 -3.529 -21.793 1.00 49.56 C ATOM 2153 N3 DA C 28 -11.917 -4.774 -21.688 1.00 49.25 N ATOM 2154 C4 DA C 28 -10.901 -5.004 -22.529 1.00 48.98 C """, "4mf.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level 4MF 4MF '1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methyl-1H-indole' ligand 38 22 . # data_comp_4MF # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z 4MF O3P O OP . 0.3880 -6.5014 -0.0977 4MF O2P O OP . 2.8128 -6.3045 0.2744 4MF P P P . 1.4780 -5.6201 0.4475 4MF O1P O O . 1.2312 -5.3632 1.9128 4MF O5' O O2 . 1.4842 -4.2849 -0.3118 4MF C5' C CH2 . 0.4523 -3.3972 -0.1241 4MF C4' C CH1 . 0.4545 -2.3849 -1.2304 4MF C3' C CH1 . 1.6882 -1.6217 -1.1949 4MF O3' O OH1 . 2.4943 -1.9836 -2.2794 4MF C2' C CH2 . 1.3646 -0.1729 -1.2778 4MF C1' C CH1 . -0.1502 -0.1860 -1.2349 4MF O4' O O2 . -0.6137 -1.5216 -1.0689 4MF N1 N NR5 . -0.5939 0.6028 -0.1623 4MF C7A C CR56 . -0.7732 1.9661 -0.2075 4MF C7 C CR16 . -0.5799 2.8750 -1.2494 4MF C6 C CR16 . -0.8345 4.2251 -1.0458 4MF C5 C CR16 . -1.2864 4.6714 0.2113 4MF C4 C CR6 . -1.4808 3.7274 1.2736 4MF C4M C CH3 . -1.9588 4.1914 2.6065 4MF C3A C CR56 . -1.2204 2.3671 1.0551 4MF C3 C CR15 . -1.3024 1.2223 1.8455 4MF C2 C CR15 . -0.9093 0.1452 1.0684 4MF H5'1 H HCH2 . -0.3941 -3.8790 -0.1265 4MF H5'2 H HCH2 . 0.5662 -2.9370 0.7439 4MF H4' H HCH1 . 0.3777 -2.8403 -2.0880 4MF H3' H HCH1 . 2.1650 -1.8026 -0.3580 4MF H3T H HOH1 . 3.2930 -2.2169 -1.9870 4MF H2'1 H HCH2 . 1.7298 0.3100 -0.5098 4MF H2'2 H HCH2 . 1.6862 0.2071 -2.1162 4MF H1' H HCH1 . -0.5001 0.1731 -2.0687 4MF H7 H HCR6 . -0.2675 2.5671 -2.1190 4MF H6 H HCR6 . -0.6998 4.8655 -1.7753 4MF H5 H HCR6 . -1.4667 5.6202 0.3592 4MF H4M1 H HCH3 . -1.2789 3.9974 3.2823 4MF H4M2 H HCH3 . -2.1218 5.1482 2.5767 4MF H4M3 H HCH3 . -2.7822 3.7299 2.8339 4MF H3 H HCR5 . -1.5857 1.1856 2.7788 4MF H2 H HCR5 . -0.8680 -0.7821 1.3604 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd 4MF O3P P deloc 1.504 0.020 4MF O2P P deloc 1.510 0.020 4MF P O1P deloc 1.508 0.020 4MF P O5' single 1.536 0.020 4MF O5' C5' single 1.374 0.020 4MF C5' C4' single 1.500 0.020 4MF C5' H5'1 single 0.974 0.020 4MF C5' H5'2 single 0.989 0.020 4MF C4' C3' single 1.451 0.020 4MF C4' O4' single 1.383 0.020 4MF C4' H4' single 0.974 0.020 4MF C3' C2' single 1.487 0.020 4MF C3' O3' single 1.399 0.020 4MF C3' H3' single 0.980 0.020 4MF O3' H3T single 0.882 0.020 4MF C2' C1' single 1.516 0.020 4MF C2' H2'1 single 0.978 0.020 4MF C2' H2'2 single 0.975 0.020 4MF C1' N1 single 1.403 0.020 4MF C1' O4' single 1.423 0.020 4MF C1' H1' single 0.973 0.020 4MF N1 C2 aromatic 1.350 0.020 4MF N1 C7A aromatic 1.376 0.020 4MF C7A C3A aromatic 1.398 0.020 4MF C7A C7 aromatic 1.396 0.020 4MF C7 C6 aromatic 1.389 0.020 4MF C7 H7 single 0.974 0.020 4MF C6 C5 aromatic 1.408 0.020 4MF C6 H6 single 0.980 0.020 4MF C5 C4 aromatic 1.434 0.020 4MF C5 H5 single 0.977 0.020 4MF C4 C4M single 1.490 0.020 4MF C4 C3A aromatic 1.402 0.020 4MF C4M H4M1 single 0.978 0.020 4MF C4M H4M2 single 0.971 0.020 4MF C4M H4M3 single 0.971 0.020 4MF C3A C3 aromatic 1.394 0.020 4MF C3 C2 aromatic 1.385 0.020 4MF C3 H3 single 0.976 0.020 4MF C2 H2 single 0.973 0.020 """, "linking_test_NAG-FU4.pdb" : """ HETATM 9423 C1 NAG D1584 6.798 -15.752 22.420 1.00 22.72 C HETATM 9424 C2 NAG D1584 5.572 -16.434 23.033 1.00 24.18 C HETATM 9425 C3 NAG D1584 4.596 -15.354 23.498 1.00 23.13 C HETATM 9426 C4 NAG D1584 5.251 -14.345 24.447 1.00 23.39 C HETATM 9427 C5 NAG D1584 6.580 -13.815 23.895 1.00 24.93 C HETATM 9428 C6 NAG D1584 7.379 -13.088 24.991 1.00 27.57 C HETATM 9429 C7 NAG D1584 5.155 -18.617 22.021 1.00 29.09 C HETATM 9430 C8 NAG D1584 4.408 -19.417 20.984 1.00 29.54 C HETATM 9431 N2 NAG D1584 4.916 -17.305 22.067 1.00 25.34 N HETATM 9432 O3 NAG D1584 3.454 -15.926 24.089 1.00 23.03 O HETATM 9433 O4 NAG D1584 4.387 -13.247 24.573 1.00 22.66 O HETATM 9434 O5 NAG D1584 7.367 -14.889 23.394 1.00 23.22 O HETATM 9435 O7 NAG D1584 5.951 -19.182 22.779 1.00 31.04 O HETATM 9436 O6 NAG D1584 7.429 -13.988 26.081 1.00 31.80 O HETATM 9462 C1 FU4 D1588 8.042 -13.514 27.304 1.00 37.58 C HETATM 9463 C2 FU4 D1588 7.470 -14.288 28.512 1.00 38.91 C HETATM 9464 C3 FU4 D1588 7.920 -15.750 28.448 1.00 41.29 C HETATM 9465 C4 FU4 D1588 9.448 -15.793 28.444 1.00 41.76 C HETATM 9466 C5 FU4 D1588 9.980 -14.949 27.275 1.00 40.83 C HETATM 9467 C6 FU4 D1588 11.507 -14.975 27.258 1.00 40.52 C HETATM 9468 O2 FU4 D1588 6.059 -14.235 28.600 1.00 39.96 O HETATM 9469 O3 FU4 D1588 7.398 -16.498 29.524 1.00 40.18 O HETATM 9470 O4 FU4 D1588 9.951 -15.298 29.675 1.00 43.17 O HETATM 9471 O5 FU4 D1588 9.470 -13.611 27.319 1.00 39.54 O """, "fu4.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level FU4 FU4 '2,6-anhydro-1-deoxy-D-galactitol' ligand 22 10 . # data_comp_FU4 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z FU4 C1 C CH2 . -0.9215 0.7090 -1.3477 FU4 C2 C CH1 . 0.5905 0.7090 -1.3477 FU4 C3 C CH1 . 1.0944 0.7090 0.0773 FU4 C4 C CH1 . 0.4272 -0.4074 0.8476 FU4 C5 C CH1 . -1.0718 -0.3124 0.6757 FU4 C6 C CH3 . -1.7403 -1.4199 1.4597 FU4 O2 O OH1 . 1.0598 1.8584 -2.0114 FU4 O3 O OH1 . 2.4889 0.5143 0.0821 FU4 O4 O OH1 . 0.8778 -1.6488 0.3597 FU4 O5 O O2 . -1.3966 -0.4405 -0.6867 FU4 H1C1 H HCH2 . -1.2461 0.7114 -2.2683 FU4 H1C2 H HCH2 . -1.2462 1.5059 -0.8870 FU4 H2 H HCH1 . 0.9159 -0.0880 -1.8079 FU4 H3 H HCH1 . 0.8839 1.5648 0.4968 FU4 H4 H HCH1 . 0.6518 -0.3289 1.7943 FU4 H5 H HCH1 . -1.3829 0.5524 1.0045 FU4 H6C1 H HCH3 . -2.7057 -1.2758 1.4678 FU4 H6C2 H HCH3 . -1.5431 -2.2795 1.0413 FU4 H6C3 H HCH3 . -1.4036 -1.4191 2.3759 FU4 HA H HOH1 . 1.3561 1.6345 -2.8176 FU4 HB H HOH1 . 2.8770 1.1651 0.5444 FU4 HC H HOH1 . 1.4344 -2.0133 0.9472 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd FU4 C1 C2 single 1.512 0.020 FU4 C1 O5 single 1.408 0.020 FU4 C1 H1C1 single 0.976 0.020 FU4 C1 H1C2 single 0.976 0.020 FU4 C2 C3 single 1.511 0.020 FU4 C2 O2 single 1.408 0.020 FU4 C2 H2 single 0.976 0.020 FU4 C3 C4 single 1.511 0.020 FU4 C3 O3 single 1.408 0.020 FU4 C3 H3 single 0.976 0.020 FU4 C4 C5 single 1.512 0.020 FU4 C4 O4 single 1.408 0.020 FU4 C4 H4 single 0.976 0.020 FU4 C5 C6 single 1.513 0.020 FU4 C5 O5 single 1.406 0.020 FU4 C5 H5 single 0.976 0.020 FU4 C6 H6C1 single 0.976 0.020 FU4 C6 H6C2 single 0.976 0.020 FU4 C6 H6C3 single 0.976 0.020 FU4 O2 HA single 0.888 0.020 FU4 O3 HB single 0.888 0.020 FU4 O4 HC single 0.888 0.020 """, "linking_test_BGC-BGC.pdb" : """ HETATM 2374 C2 BGC B 401 5.858 17.444 53.947 1.00 10.73 C HETATM 2375 C3 BGC B 401 6.199 18.564 52.974 1.00 10.02 C HETATM 2376 C4 BGC B 401 4.883 19.259 52.650 1.00 9.66 C HETATM 2377 C5 BGC B 401 4.352 19.862 53.947 1.00 9.19 C HETATM 2378 C6 BGC B 401 3.073 20.685 53.802 1.00 9.97 C HETATM 2379 C1 BGC B 401 5.210 18.029 55.193 1.00 12.05 C HETATM 2380 O1 BGC B 401 4.688 16.987 55.955 1.00 13.71 O HETATM 2381 O2 BGC B 401 7.016 16.779 54.404 1.00 12.15 O HETATM 2382 O3 BGC B 401 6.709 18.077 51.750 1.00 10.15 O HETATM 2383 O4 BGC B 401 5.090 20.298 51.721 1.00 9.48 O HETATM 2384 O5 BGC B 401 4.087 18.799 54.833 1.00 8.55 O HETATM 2385 O6 BGC B 401 2.004 19.920 53.229 1.00 8.55 O HETATM 2386 C2 BGC B 402 8.524 17.329 50.431 1.00 12.41 C HETATM 2387 C3 BGC B 402 10.050 17.335 50.257 1.00 12.69 C HETATM 2388 C4 BGC B 402 10.659 18.712 50.487 1.00 12.30 C HETATM 2389 C5 BGC B 402 10.171 19.272 51.825 1.00 10.88 C HETATM 2390 C6 BGC B 402 10.610 20.705 52.119 1.00 10.57 C HETATM 2391 C1 BGC B 402 8.143 18.001 51.734 1.00 11.41 C HETATM 2392 O2 BGC B 402 7.987 16.015 50.403 1.00 13.00 O HETATM 2393 O3 BGC B 402 10.347 17.051 48.908 1.00 15.37 O HETATM 2394 O4 BGC B 402 12.073 18.535 50.546 1.00 13.31 O HETATM 2395 O5 BGC B 402 8.743 19.283 51.808 1.00 9.88 O HETATM 2396 O6 BGC B 402 10.164 21.605 51.121 1.00 11.09 O """, "bgc.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level BGC BGC 'beta-D-glucopyranose ' ligand 24 12 . # data_comp_BGC # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z BGC C2 C CH1 . 1.0181 0.7466 -1.2014 BGC C3 C CH1 . -0.4936 0.7466 -1.2014 BGC C4 C CH1 . -0.9974 -0.4285 -0.3952 BGC C5 C CH1 . -0.4042 -0.3777 0.9944 BGC C6 C CH2 . -0.8493 -1.5929 1.7774 BGC C1 C CH1 . 1.5218 0.7466 0.2233 BGC O1 O OH1 . 2.9275 0.6794 0.2239 BGC O2 O OH1 . 1.4875 1.8963 -1.8652 BGC O3 O OH1 . -0.9629 0.6435 -2.5248 BGC O4 O OH1 . -2.4015 -0.3707 -0.3086 BGC O5 O O2 . 0.9993 -0.3659 0.9049 BGC O6 O OH1 . -0.2097 -1.6024 3.0344 BGC H2 H HCH1 . 1.3435 -0.0504 -1.6615 BGC H3 H HCH1 . -0.8190 1.5769 -0.8045 BGC H4 H HCH1 . -0.7324 -1.2603 -0.8319 BGC H5 H HCH1 . -0.7081 0.4312 1.4486 BGC H6C1 H HCH2 . -1.8166 -1.5616 1.9048 BGC H6C2 H HCH2 . -0.6121 -2.4019 1.2854 BGC H1 H HCH1 . 1.2351 1.5659 0.6699 BGC HA H HOH1 . 3.2455 1.1381 0.9141 BGC HB H HOH1 . 2.0042 1.6551 -2.5454 BGC HC H HOH1 . -1.4335 1.3679 -2.7292 BGC HD H HOH1 . -2.7570 -0.9641 -0.8647 BGC H6 H HOH1 . -0.5848 -2.2177 3.5527 # """, "linking_test_LEU-CSY-VAL.pdb" : """ ATOM 470 N LEU A 64 11.530 10.554 5.290 1.00 15.95 N ATOM 471 CA LEU A 64 12.272 9.726 6.192 1.00 21.72 C ATOM 472 CB LEU A 64 13.571 10.414 6.526 1.00 18.65 C ATOM 473 CG LEU A 64 14.569 10.566 5.400 1.00 16.06 C ATOM 474 CD1 LEU A 64 15.684 11.496 5.782 1.00 15.79 C ATOM 475 CD2 LEU A 64 15.142 9.234 5.000 1.00 19.26 C ATOM 476 C LEU A 64 11.524 9.463 7.499 1.00 47.31 C ATOM 477 O LEU A 64 11.704 8.447 8.057 1.00 19.74 O ATOM 478 O CSY A 66 7.079 6.443 8.014 1.00 20.23 O ATOM 479 C CSY A 66 7.307 7.455 8.592 1.00 42.84 C ATOM 480 CA3 CSY A 66 7.949 8.535 7.772 1.00 22.48 C ATOM 481 N3 CSY A 66 7.755 9.898 8.205 1.00 20.36 N ATOM 482 C2 CSY A 66 6.699 10.604 7.953 1.00 18.89 C ATOM 483 O2 CSY A 66 5.661 10.200 7.389 1.00 18.87 O ATOM 484 CA2 CSY A 66 6.889 11.895 8.529 1.00 17.00 C ATOM 485 N2 CSY A 66 8.098 11.934 9.059 1.00 17.35 N ATOM 486 C1 CSY A 66 8.613 10.698 8.850 1.00 23.65 C ATOM 487 CA1 CSY A 66 9.984 10.257 9.208 1.00 15.87 C ATOM 488 N CSY A 66 10.796 10.290 7.982 1.00 16.92 N ATOM 489 CB1 CSY A 66 10.657 11.187 10.190 1.00 22.76 C ATOM 490 OG1 CSY A 66 10.041 11.081 11.425 1.00 26.93 O ATOM 491 CB2 CSY A 66 5.901 12.951 8.489 1.00 21.22 C ATOM 492 CG2 CSY A 66 6.045 14.317 8.943 1.00 17.77 C ATOM 493 CD1 CSY A 66 7.186 14.821 9.489 1.00 16.75 C ATOM 494 CE1 CSY A 66 7.230 16.153 9.841 1.00 17.97 C ATOM 495 CZ CSY A 66 6.167 16.999 9.597 1.00 17.84 C ATOM 496 OH CSY A 66 6.180 18.295 9.906 1.00 18.10 O ATOM 497 CE2 CSY A 66 5.053 16.481 9.007 1.00 17.93 C ATOM 498 CD2 CSY A 66 5.000 15.167 8.689 1.00 16.52 C ATOM 499 N VAL A 68 7.337 7.591 9.827 1.00 22.68 N ATOM 500 CA VAL A 68 6.874 6.579 10.743 1.00 17.94 C ATOM 501 CB VAL A 68 8.031 5.907 11.484 1.00 18.83 C ATOM 502 CG1 VAL A 68 8.808 5.000 10.546 1.00 18.49 C ATOM 503 CG2 VAL A 68 8.940 6.946 12.060 1.00 21.81 C ATOM 504 C VAL A 68 5.837 7.169 11.692 1.00 18.71 C ATOM 505 O VAL A 68 6.046 7.339 12.840 1.00 18.66 O """, "csy.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CSY CSY 'Unknown ' ligand 36 21 . # data_comp_CSY # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CSY O O O . 6.5225 8.8391 10.1578 CSY C C C1 . 6.8040 8.0495 9.2786 CSY CA3 C CH2 . 7.7300 8.4648 8.1571 CSY N3 N NR5 . 7.7692 9.9112 8.0435 CSY C2 C CR5 . 6.8095 10.6833 7.5020 CSY O2 O OH1 . 5.5652 10.2401 6.9578 CSY CA2 C CR5 . 7.2462 12.0320 7.6413 CSY N2 N N . 8.4469 11.9889 8.2606 CSY C1 C CR5 . 8.7507 10.7094 8.4972 CSY CA1 C CH1 . 10.0456 10.2262 9.1064 CSY N N NH2 . 11.0914 10.3565 8.1586 CSY CB1 C C1 . 10.3683 11.0559 10.3320 CSY OG1 O O . 9.6909 10.9426 11.3400 CSY CB2 C CH2 . 6.5545 13.2812 7.0704 CSY CG2 C CR6 . 6.3534 14.3333 8.2072 CSY CD1 C CR16 . 7.3740 15.2590 8.4985 CSY CE1 C CR16 . 7.1903 16.2102 9.5124 CSY CZ C CR6 . 5.9969 16.2401 10.2329 CSY OH O OH1 . 5.8390 17.1584 11.3068 CSY CE2 C CR16 . 4.9783 15.3171 9.9430 CSY CD2 C CR16 . 5.1631 14.3623 8.9250 CSY HC1 H H . 6.4050 7.1514 9.2787 CSY HA31 H HCH2 . 7.4089 8.0824 7.3139 CSY HA32 H HCH2 . 8.6295 8.1304 8.3411 CSY H21 H HOH1 . 5.6829 9.9885 6.1182 CSY HA11 H HCH1 . 9.9540 9.2881 9.3635 CSY HN2 H HNH2 . 11.6123 9.6000 8.1723 CSY HN3 H HNH2 . 11.6050 11.0843 8.3689 CSY HB11 H H . 11.0974 11.7100 10.3027 CSY HB21 H HCH2 . 5.6862 13.0307 6.7011 CSY HB22 H HCH2 . 7.1096 13.6673 6.3644 CSY HD11 H HCR6 . 8.1999 15.2679 7.9588 CSY HE11 H HCR6 . 7.9314 16.8265 9.7542 CSY HH1 H HOH1 . 5.2232 17.7727 11.0875 CSY HE21 H HCR6 . 4.1503 15.3164 10.4733 CSY HD21 H HCR6 . 4.4341 13.7482 8.6900 # """, "linking_test_ALA-ALA-ALA.pdb" : """ HETATM 1 N ALA A 1 -0.424 1.960 3.877 1.00 20.00 A N+1 HETATM 2 H ALA A 1 0.452 1.694 3.861 1.00 20.00 A H HETATM 3 H2 ALA A 1 -0.472 2.843 4.121 1.00 20.00 A H HETATM 4 H3 ALA A 1 -0.888 1.448 4.484 1.00 20.00 A H HETATM 5 CA ALA A 1 -0.994 1.794 2.582 1.00 20.00 A C HETATM 6 HA ALA A 1 -0.584 2.442 1.977 1.00 20.00 A H HETATM 7 CB ALA A 1 -2.476 2.066 2.644 1.00 20.00 A C HETATM 8 HB1 ALA A 1 -2.627 2.987 2.945 1.00 20.00 A H HETATM 9 HB2 ALA A 1 -2.867 1.945 1.755 1.00 20.00 A H HETATM 10 HB3 ALA A 1 -2.896 1.444 3.272 1.00 20.00 A H HETATM 11 C ALA A 1 -0.695 0.397 2.070 1.00 20.00 A C HETATM 12 O ALA A 1 -1.218 -0.566 2.593 1.00 20.00 A O HETATM 13 N ALA A 2 0.165 0.219 0.945 1.00 20.00 A N HETATM 14 H ALA A 2 0.578 0.941 0.568 1.00 20.00 A H HETATM 15 CA ALA A 2 0.460 -1.094 0.477 1.00 20.00 A C HETATM 16 HA ALA A 2 -0.095 -1.682 1.027 1.00 20.00 A H HETATM 17 CB ALA A 2 1.882 -1.540 0.755 1.00 20.00 A C HETATM 18 HB1 ALA A 2 2.509 -0.921 0.323 1.00 20.00 A H HETATM 19 HB2 ALA A 2 2.039 -1.544 1.721 1.00 20.00 A H HETATM 20 HB3 ALA A 2 2.016 -2.441 0.399 1.00 20.00 A H HETATM 21 C ALA A 2 -0.001 -1.357 -0.949 1.00 20.00 A C HETATM 22 O ALA A 2 -1.001 -2.020 -1.152 1.00 20.00 A O HETATM 23 N ALA A 3 0.750 -0.851 -2.042 1.00 20.00 A N HETATM 24 H ALA A 3 1.494 -0.350 -1.890 1.00 20.00 A H HETATM 25 CA ALA A 3 0.361 -1.157 -3.372 1.00 20.00 A C HETATM 26 HA ALA A 3 -0.113 -2.013 -3.369 1.00 20.00 A H HETATM 27 CB ALA A 3 1.587 -1.293 -4.240 1.00 20.00 A C HETATM 28 HB1 ALA A 3 2.124 -0.477 -4.175 1.00 20.00 A H HETATM 29 HB2 ALA A 3 1.315 -1.431 -5.171 1.00 20.00 A H HETATM 30 HB3 ALA A 3 2.118 -2.058 -3.937 1.00 20.00 A H HETATM 31 C ALA A 3 -0.576 -0.091 -3.884 1.00 20.00 A C HETATM 32 O ALA A 3 -1.633 -0.418 -4.488 1.00 20.00 A O HETATM 33 OXT ALA A 3 -0.293 1.123 -3.725 1.00 20.00 A O-1 """, "linking_test_3g2j-LLP.pdb" : """ ATOM 5294 N MET A 679 23.170 19.173 20.583 1.00 27.07 N ATOM 5295 CA MET A 679 22.542 17.860 20.608 1.00 27.59 C ATOM 5296 C MET A 679 21.147 17.931 21.225 1.00 27.78 C ATOM 5297 O MET A 679 20.213 17.315 20.716 1.00 28.06 O ATOM 5298 CB MET A 679 23.413 16.867 21.380 1.00 27.20 C ATOM 5299 CG MET A 679 24.806 16.705 20.814 1.00 27.16 C ATOM 5300 SD MET A 679 25.889 15.923 22.006 1.00 27.84 S ATOM 5301 CE MET A 679 27.462 16.037 21.161 1.00 27.18 C HETATM 5302 N1 LLP A 680 24.297 25.452 30.133 1.00 26.73 N HETATM 5303 C2 LLP A 680 23.189 24.669 30.383 1.00 27.24 C HETATM 5304 C2' LLP A 680 22.258 25.076 31.486 1.00 27.21 C HETATM 5305 C3 LLP A 680 22.947 23.518 29.621 1.00 28.75 C HETATM 5306 O3 LLP A 680 21.948 22.817 29.843 1.00 28.91 O HETATM 5307 C4 LLP A 680 23.842 23.169 28.598 1.00 28.00 C HETATM 5308 C4' LLP A 680 23.628 21.946 27.737 1.00 28.32 C HETATM 5309 C5 LLP A 680 24.962 23.975 28.379 1.00 27.80 C HETATM 5310 C6 LLP A 680 25.178 25.121 29.134 1.00 27.34 C HETATM 5311 C5' LLP A 680 25.930 23.666 27.283 1.00 27.48 C HETATM 5312 OP4 LLP A 680 25.584 24.381 26.078 1.00 28.12 O HETATM 5313 P LLP A 680 26.626 24.603 24.884 1.00 30.04 P HETATM 5314 OP1 LLP A 680 25.728 25.192 23.877 1.00 30.41 O HETATM 5315 OP2 LLP A 680 27.647 25.508 25.455 1.00 29.33 O HETATM 5316 OP3 LLP A 680 27.132 23.253 24.540 1.00 28.52 O HETATM 5317 N LLP A 680 21.015 18.702 22.304 1.00 28.08 N HETATM 5318 CA LLP A 680 19.732 18.900 22.970 1.00 28.30 C HETATM 5319 CB LLP A 680 19.877 19.833 24.180 1.00 28.35 C HETATM 5320 CG LLP A 680 20.859 19.371 25.247 1.00 28.13 C HETATM 5321 CD LLP A 680 21.068 20.451 26.293 1.00 28.09 C HETATM 5322 CE LLP A 680 22.289 20.159 27.151 1.00 29.38 C HETATM 5323 NZ LLP A 680 22.551 21.255 28.114 1.00 29.67 N HETATM 5324 C LLP A 680 18.699 19.460 21.992 1.00 28.76 C HETATM 5325 O LLP A 680 17.553 18.996 21.953 1.00 28.82 O ATOM 5326 N PHE A 681 19.111 20.458 21.211 1.00 28.66 N ATOM 5327 CA PHE A 681 18.259 21.049 20.185 1.00 29.08 C ATOM 5328 C PHE A 681 17.927 20.071 19.069 1.00 29.48 C ATOM 5329 O PHE A 681 16.805 20.055 18.579 1.00 29.87 O ATOM 5330 CB PHE A 681 18.920 22.265 19.557 1.00 28.88 C ATOM 5331 CG PHE A 681 18.889 23.490 20.417 1.00 28.62 C ATOM 5332 CD1 PHE A 681 17.751 24.287 20.474 1.00 28.27 C ATOM 5333 CD2 PHE A 681 20.013 23.867 21.142 1.00 28.47 C ATOM 5334 CE1 PHE A 681 17.732 25.427 21.255 1.00 28.69 C ATOM 5335 CE2 PHE A 681 20.003 25.007 21.930 1.00 28.03 C ATOM 5336 CZ PHE A 681 18.871 25.787 21.985 1.00 28.57 C """, "linking_test_ASN-NAG-altloc4.pdb" : """ HETATM 125 C1 ANAG A 1 30.978 40.626 -25.446 0.50 98.96 E C HETATM 126 C2 ANAG A 1 30.428 41.897 -26.138 0.50100.81 E C HETATM 127 N2 ANAG A 1 29.783 41.751 -27.447 0.50 94.26 E N HETATM 128 C7 ANAG A 1 28.807 42.561 -27.924 0.50 89.45 E C HETATM 129 O7 ANAG A 1 28.325 42.377 -29.035 0.50 83.16 E O HETATM 130 C8 ANAG A 1 28.252 43.720 -27.128 0.50 87.63 E C HETATM 131 C3 ANAG A 1 31.618 42.847 -26.221 0.50102.77 E C HETATM 132 O3 ANAG A 1 31.420 43.888 -27.159 0.50102.25 E O HETATM 133 C4 ANAG A 1 31.840 43.369 -24.802 0.50103.37 E C HETATM 134 O4 ANAG A 1 32.969 44.217 -24.782 0.50104.91 E O HETATM 135 C5 ANAG A 1 32.040 42.223 -23.785 0.50 94.99 E C HETATM 136 C6 ANAG A 1 31.564 42.633 -22.381 0.50 86.60 E C HETATM 137 O6 ANAG A 1 32.632 42.591 -21.462 0.50 77.76 E O HETATM 138 O5 ANAG A 1 31.458 40.954 -24.130 0.50 99.19 E O HETATM 139 C1 BNAG A 1 30.271 40.925 -24.108 0.50 98.96 E C HETATM 140 C2 BNAG A 1 31.415 41.878 -23.684 0.50100.81 E C HETATM 141 N2 BNAG A 1 32.048 41.664 -22.378 0.50 94.26 E N HETATM 142 C7 BNAG A 1 33.331 41.981 -22.079 0.50 89.45 E C HETATM 143 O7 BNAG A 1 33.784 41.778 -20.959 0.50 83.16 E O HETATM 144 C8 BNAG A 1 34.276 42.586 -23.092 0.50 87.63 E C HETATM 145 C3 BNAG A 1 30.816 43.277 -23.775 0.50102.77 E C HETATM 146 O3 BNAG A 1 31.569 44.240 -23.061 0.50102.25 E O HETATM 147 C4 BNAG A 1 30.718 43.597 -25.266 0.50103.37 E C HETATM 148 O4 BNAG A 1 30.115 44.862 -25.440 0.50104.91 E O HETATM 149 C5 BNAG A 1 29.907 42.532 -26.038 0.50 94.99 E C HETATM 150 C6 BNAG A 1 30.373 42.426 -27.500 0.50 86.60 E C HETATM 151 O6 BNAG A 1 29.320 42.743 -28.381 0.50 77.76 E O HETATM 152 O5 BNAG A 1 29.866 41.216 -25.458 0.50 99.19 E O ATOM 745 N ASN A 116 27.207 36.475 -25.453 1.00 62.15 A N ATOM 746 CA AASN A 116 28.475 37.144 -25.135 0.50 61.77 A C ATOM 747 CB AASN A 116 28.182 38.336 -24.223 0.50 69.02 A C ATOM 748 CG AASN A 116 29.037 39.555 -24.495 0.50 79.45 A C ATOM 749 OD1AASN A 116 28.656 40.644 -24.047 0.50 83.18 A O ATOM 750 ND2AASN A 116 30.178 39.419 -25.218 0.50 87.72 A N ATOM 751 C ASN A 116 29.353 36.143 -24.389 1.00 53.28 A C ATOM 752 O ASN A 116 29.778 36.380 -23.266 1.00 48.83 A O ATOM 753 CA BASN A 116 28.575 37.144 -25.135 0.50 61.77 A C ATOM 754 CB BASN A 116 28.282 38.336 -24.223 0.50 69.02 A C ATOM 755 CG BASN A 116 29.487 39.201 -23.920 0.50 79.45 A C ATOM 756 OD1BASN A 116 30.611 38.710 -24.084 0.50 83.18 A O ATOM 757 ND2BASN A 116 29.299 40.471 -23.478 0.50 87.72 A N """, "linking_test_ASN_A-NAG_B.pdb" : """ ATOM 2279 N ASN A 303 7.500 12.479 6.505 1.00 50.55 N ATOM 2280 CA ASN A 303 8.366 11.834 7.487 1.00 48.33 C ATOM 2281 C ASN A 303 7.525 11.114 8.549 1.00 49.96 C ATOM 2282 O ASN A 303 6.418 11.545 8.868 1.00 49.99 O ATOM 2283 CB ASN A 303 9.328 12.845 8.125 1.00 49.14 C ATOM 2284 CG ASN A 303 10.450 13.261 7.184 1.00 51.22 C ATOM 2285 OD1 ASN A 303 11.016 12.431 6.474 1.00 50.95 O ATOM 2286 ND2 ASN A 303 10.787 14.549 7.186 1.00 55.18 N TER HETATM11738 C1 NAG B1349 11.771 15.301 6.383 1.00 64.93 C HETATM11739 C2 NAG B1349 11.260 16.717 6.129 1.00 71.42 C HETATM11740 C3 NAG B1349 12.340 17.588 5.490 1.00 76.60 C HETATM11741 C4 NAG B1349 13.598 17.552 6.354 1.00 85.65 C HETATM11742 C5 NAG B1349 14.040 16.100 6.541 1.00 77.74 C HETATM11743 C6 NAG B1349 15.243 16.002 7.471 1.00 78.29 C HETATM11744 C7 NAG B1349 8.880 17.098 5.780 1.00 66.42 C HETATM11745 C8 NAG B1349 8.026 16.100 6.508 1.00 39.77 C HETATM11746 N2 NAG B1349 10.056 16.673 5.317 1.00 65.92 N HETATM11747 O3 NAG B1349 11.875 18.912 5.361 1.00 77.58 O HETATM11748 O4 NAG B1349 14.644 18.346 5.809 1.00 96.99 O HETATM11749 O5 NAG B1349 12.999 15.308 7.087 1.00 74.70 O HETATM11750 O6 NAG B1349 16.436 16.098 6.729 1.00 77.54 O HETATM11751 O7 NAG B1349 8.483 18.252 5.630 1.00 80.43 O """, "linking_test_nstd_rna_dna_h_bond.pdb" : """ HETATM 100 P A44 A 5 15.790 -6.178 18.620 1.00 33.68 P HETATM 101 OP2 A44 A 5 16.475 -4.926 18.273 1.00 37.12 O HETATM 102 OP1 A44 A 5 16.553 -7.268 19.263 1.00 37.20 O HETATM 103 O5' A44 A 5 15.148 -6.673 17.251 1.00 35.19 O HETATM 104 C5' A44 A 5 14.132 -7.683 17.238 1.00 36.66 C HETATM 105 C4' A44 A 5 13.552 -7.828 15.849 1.00 38.49 C HETATM 106 O4' A44 A 5 12.637 -6.734 15.559 1.00 39.35 O HETATM 107 C3' A44 A 5 14.540 -7.792 14.691 1.00 39.06 C HETATM 108 O3' A44 A 5 15.263 -8.992 14.487 1.00 39.12 O HETATM 109 C2' A44 A 5 13.644 -7.425 13.514 1.00 40.78 C HETATM 110 O2' A44 A 5 12.914 -8.512 12.973 1.00 41.20 O HETATM 111 C1' A44 A 5 12.679 -6.437 14.168 1.00 38.59 C HETATM 112 N9 A44 A 5 13.167 -5.067 13.981 1.00 37.63 N HETATM 113 C8 A44 A 5 13.886 -4.289 14.859 1.00 38.01 C HETATM 114 N7 A44 A 5 14.200 -3.106 14.380 1.00 38.45 N HETATM 115 C5 A44 A 5 13.643 -3.103 13.107 1.00 36.06 C HETATM 116 C6 A44 A 5 13.607 -2.138 12.099 1.00 34.61 C HETATM 117 N6 A44 A 5 14.159 -0.933 12.209 1.00 36.45 N HETATM 118 N1 A44 A 5 12.967 -2.450 10.958 1.00 33.41 N HETATM 119 C2 A44 A 5 12.399 -3.647 10.845 1.00 32.30 C HETATM 120 N3 A44 A 5 12.361 -4.638 11.717 1.00 34.10 N HETATM 121 C4 A44 A 5 13.006 -4.301 12.846 1.00 36.44 C HETATM 122 CA' A44 A 5 12.063 -8.031 11.930 1.00 46.36 C HETATM 123 CD' A44 A 5 11.616 -11.212 12.261 1.00 58.12 C HETATM 124 OC' A44 A 5 10.850 -10.006 12.555 1.00 53.39 O HETATM 125 CB' A44 A 5 11.090 -9.064 11.485 1.00 49.86 C HETATM 478 P U36 B 20 11.477 3.696 3.004 1.00 42.30 P HETATM 479 OP1 U36 B 20 10.335 4.004 2.145 1.00 44.51 O HETATM 480 OP2 U36 B 20 11.842 4.626 4.093 1.00 45.81 O HETATM 481 O5' U36 B 20 11.173 2.296 3.679 1.00 42.73 O HETATM 482 C5' U36 B 20 10.757 1.210 2.877 1.00 42.45 C HETATM 483 C4' U36 B 20 10.319 0.065 3.737 1.00 42.68 C HETATM 484 O4' U36 B 20 11.457 -0.572 4.347 1.00 42.31 O HETATM 485 C3' U36 B 20 9.406 0.368 4.909 1.00 41.73 C HETATM 486 O3' U36 B 20 8.059 0.493 4.530 1.00 44.16 O HETATM 487 C2' U36 B 20 9.567 -0.885 5.739 1.00 42.76 C HETATM 488 O2' U36 B 20 8.836 -1.946 5.173 1.00 46.09 O HETATM 489 C1' U36 B 20 11.046 -1.178 5.554 1.00 41.52 C HETATM 490 N1 U36 B 20 11.789 -0.588 6.668 1.00 40.08 N HETATM 491 C2 U36 B 20 11.863 -1.336 7.813 1.00 41.61 C HETATM 492 O2 U36 B 20 11.363 -2.445 7.904 1.00 42.96 O HETATM 493 N3 U36 B 20 12.545 -0.747 8.850 1.00 43.77 N HETATM 494 C4 U36 B 20 13.154 0.495 8.855 1.00 42.08 C HETATM 495 O4 U36 B 20 13.738 0.884 9.875 1.00 37.89 O HETATM 496 C5 U36 B 20 13.040 1.208 7.617 1.00 41.51 C HETATM 497 C6 U36 B 20 12.374 0.651 6.587 1.00 39.50 C HETATM 498 CA' U36 B 20 9.181 -3.182 5.789 1.00 49.64 C HETATM 499 CB' U36 B 20 9.334 -4.295 4.806 1.00 50.46 C HETATM 500 CD' U36 B 20 10.943 -5.943 4.104 1.00 51.43 C HETATM 501 OC' U36 B 20 10.740 -4.603 4.641 1.00 52.78 O """, "a44.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level A44 A44 '2'-O-(2-methoxyethyl)adenosine 5'-(dihydrogen phosphate)' ligand 45 27 . # data_comp_A44 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z A44 P P P . 2.5224 -5.5637 0.6446 A44 OP2 O OP . 4.0244 -5.2909 0.6504 A44 OP1 O O . 2.0353 -5.7363 2.0663 A44 O5' O O2 . 1.7520 -4.3205 -0.0401 A44 C5' C CH2 . 1.7304 -3.1036 0.6336 A44 C4' C CR15 . 1.2062 -2.0228 -0.2918 A44 O4' O O . -0.0783 -1.9855 -0.2471 A44 C3' C CR15 . 1.6764 -0.6041 0.2038 A44 O3' O OH1 . 2.5794 -0.0871 -0.6532 A44 C2' C CR15 . 0.4371 0.2496 0.2212 A44 O2' O O2 . 0.6982 1.5749 -0.5050 A44 C1' C CR15 . -0.4813 -0.4608 -0.4288 A44 N9 N NR5 . -1.7808 -0.2191 0.1349 A44 C8 C CR15 . -2.0670 -0.3505 1.4454 A44 N7 N N . -3.4269 -0.2922 1.5891 A44 C5 C CR56 . -3.9797 -0.1222 0.3440 A44 C6 C CR6 . -5.3029 -0.0049 -0.0829 A44 N6 N NH2 . -6.5639 0.0390 0.5147 A44 N1 N N . -5.5783 0.1542 -1.3948 A44 C2 C CR16 . -4.5689 0.2002 -2.3007 A44 N3 N N . -3.2570 0.0844 -1.8806 A44 C4 C CR56 . -2.9767 -0.0766 -0.5532 A44 CA' C CH2 . 1.2611 2.6105 0.3430 A44 CD' C CH3 . 3.8911 5.0297 -0.3369 A44 OC' O O2 . 2.8946 4.3578 0.3441 A44 CB' C CH2 . 2.0410 3.5848 -0.4972 A44 OP3 O OP . 2.2422 -6.8280 -0.1418 """, "u36.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level U36 U36 '2'-O-(2-methoxyethyl)uridine 5'-(dihydrogen phosphate)' ligand 42 25 . # data_comp_U36 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z U36 P P P . -0.0923 3.8242 3.7169 U36 OP1 O O . -0.7464 3.7757 5.0772 U36 OP2 O OP . -1.0067 4.5301 2.7434 U36 OP3 O OP . 1.2153 4.5737 3.8136 U36 O5' O O2 . 0.1807 2.3510 3.2104 U36 C5' C CH2 . -0.1828 2.0165 1.8914 U36 C4' C CH1 . 0.1665 0.7096 1.6366 U36 O4' O O2 . -1.0654 -0.1293 1.4258 U36 C3' C CH1 . 1.0034 0.6117 0.2648 U36 O3' O OH1 . 2.4358 0.2844 0.5536 U36 C2' C CH1 . 0.4751 -0.3054 -0.3636 U36 O2' O O2 . 1.1615 -1.5865 -0.0670 U36 C1' C CH1 . -1.0908 -0.3701 0.1523 U36 N1 N NR6 . -1.8533 0.5989 -0.5044 U36 C2 C CR6 . -2.9446 1.2709 0.2003 U36 O2 O O . -3.2291 0.9400 1.3340 U36 N3 N NR16 . -3.6934 2.3410 -0.4578 U36 C4 C CR6 . -3.4325 2.6580 -1.8160 U36 O4 O O . -4.1270 3.4693 -2.3943 U36 C5 C CR16 . -2.3699 1.9506 -2.5425 U36 C6 C CR16 . -1.5867 0.9104 -1.8626 U36 CA' C CH2 . 1.3872 -2.3894 -1.2028 U36 CB' C CH2 . 2.2425 -3.5784 -0.8184 U36 CD' C CH3 . 2.9132 -5.6983 -1.6208 U36 OC' O O2 . 1.9630 -4.6568 -1.6813 """, "linking_test_nstd_rna_dna.pdb" : """ HETATM 478 P U36 B 20 11.477 3.696 3.004 1.00 42.30 P HETATM 479 OP1 U36 B 20 10.335 4.004 2.145 1.00 44.51 O HETATM 480 OP2 U36 B 20 11.842 4.626 4.093 1.00 45.81 O HETATM 481 O5' U36 B 20 11.173 2.296 3.679 1.00 42.73 O HETATM 482 C5' U36 B 20 10.757 1.210 2.877 1.00 42.45 C HETATM 483 C4' U36 B 20 10.319 0.065 3.737 1.00 42.68 C HETATM 484 O4' U36 B 20 11.457 -0.572 4.347 1.00 42.31 O HETATM 485 C3' U36 B 20 9.406 0.368 4.909 1.00 41.73 C HETATM 486 O3' U36 B 20 8.059 0.493 4.530 1.00 44.16 O HETATM 487 C2' U36 B 20 9.567 -0.885 5.739 1.00 42.76 C HETATM 488 O2' U36 B 20 8.836 -1.946 5.173 1.00 46.09 O HETATM 489 C1' U36 B 20 11.046 -1.178 5.554 1.00 41.52 C HETATM 490 N1 U36 B 20 11.789 -0.588 6.668 1.00 40.08 N HETATM 491 C2 U36 B 20 11.863 -1.336 7.813 1.00 41.61 C HETATM 492 O2 U36 B 20 11.363 -2.445 7.904 1.00 42.96 O HETATM 493 N3 U36 B 20 12.545 -0.747 8.850 1.00 43.77 N HETATM 494 C4 U36 B 20 13.154 0.495 8.855 1.00 42.08 C HETATM 495 O4 U36 B 20 13.738 0.884 9.875 1.00 37.89 O HETATM 496 C5 U36 B 20 13.040 1.208 7.617 1.00 41.51 C HETATM 497 C6 U36 B 20 12.374 0.651 6.587 1.00 39.50 C HETATM 498 CA' U36 B 20 9.181 -3.182 5.789 1.00 49.64 C HETATM 499 CB' U36 B 20 9.334 -4.295 4.806 1.00 50.46 C HETATM 500 CD' U36 B 20 10.943 -5.943 4.104 1.00 51.43 C HETATM 501 OC' U36 B 20 10.740 -4.603 4.641 1.00 52.78 O HET C43 B 21 24 LINK O3' U36 B 20 P C43 B 21 1555 1555 1.60 LINK O3' C43 B 21 P G48 B 22 1555 1555 1.61 HETATM 502 P C43 B 21 7.042 1.245 5.508 1.00 45.71 P HETATM 503 OP2 C43 B 21 7.731 2.473 5.993 1.00 47.37 O HETATM 504 OP1 C43 B 21 5.771 1.363 4.736 1.00 43.78 O HETATM 505 O5' C43 B 21 6.853 0.247 6.738 1.00 39.90 O HETATM 506 C5' C43 B 21 6.411 -1.086 6.501 1.00 38.58 C HETATM 507 C4' C43 B 21 6.481 -1.910 7.754 1.00 37.96 C HETATM 508 O4' C43 B 21 7.858 -2.119 8.141 1.00 37.13 O HETATM 509 C3' C43 B 21 5.834 -1.356 9.001 1.00 39.94 C HETATM 510 O3' C43 B 21 4.419 -1.513 9.009 1.00 38.74 O HETATM 511 C2' C43 B 21 6.517 -2.174 10.095 1.00 42.40 C HETATM 512 O2' C43 B 21 5.975 -3.463 10.290 1.00 51.49 O HETATM 513 C1' C43 B 21 7.925 -2.350 9.532 1.00 38.54 C HETATM 514 N1 C43 B 21 8.857 -1.402 10.159 1.00 36.39 N HETATM 515 C2 C43 B 21 9.294 -1.667 11.451 1.00 33.63 C HETATM 516 O2 C43 B 21 8.947 -2.703 11.998 1.00 28.79 O HETATM 517 N3 C43 B 21 10.082 -0.780 12.075 1.00 34.10 N HETATM 518 C4 C43 B 21 10.449 0.335 11.459 1.00 36.14 C HETATM 519 N4 C43 B 21 11.208 1.196 12.143 1.00 39.09 N HETATM 520 C5 C43 B 21 10.051 0.621 10.126 1.00 34.73 C HETATM 521 C6 C43 B 21 9.265 -0.271 9.515 1.00 36.40 C HETATM 522 CA' C43 B 21 6.672 -4.189 11.334 1.00 58.64 C HETATM 523 CB' C43 B 21 7.917 -4.946 10.870 1.00 64.99 C HETATM 524 CD' C43 B 21 8.788 -5.769 13.046 1.00 68.99 C HETATM 525 OC' C43 B 21 9.059 -5.026 11.816 1.00 67.88 O """, "c43.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level C43 C43 '2'-O-(2-methoxyethyl)cytidine 5'-(dihydrogen phosphate)' ligand 43 25 . # data_comp_C43 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z C43 P P P . 3.7565 3.2915 1.5876 C43 OP3 O OP . 4.2694 2.5857 2.8218 C43 OP2 O OP . 2.7755 4.3524 1.9881 C43 OP1 O O . 4.9068 3.9231 0.8595 C43 O5' O O2 . 3.0486 2.2550 0.6486 C43 C5' C CH2 . 1.8203 1.6916 1.0686 C43 C4' C CR15 . 1.6741 0.4618 0.5078 C43 O4' O O . 0.9711 -0.4760 1.4642 C43 C3' C CR15 . 0.7330 0.5479 -0.7879 C43 O3' O OH1 . 1.5421 0.3327 -2.0324 C43 C2' C CR15 . -0.0850 -0.3670 -0.6482 C43 O2' O O2 . 0.4137 -1.6016 -1.3197 C43 C1' C CR15 . -0.2173 -0.6200 0.9744 C43 N1 N NR6 . -1.0961 0.3267 1.5414 C43 C2 C CR6 . -2.2763 0.7649 0.7937 C43 O2 O O . -2.5555 0.2318 -0.2825 C43 N3 N N . -3.1751 1.7982 1.3634 C43 C4 C CR6 . -2.9944 2.2380 2.7088 C43 N4 N NH2 . -3.9728 3.1027 3.3229 C43 C5 C CR16 . -1.8514 1.7296 3.5031 C43 C6 C CR16 . -0.9017 0.7650 2.8947 C43 CA' C CH2 . -0.4824 -2.1632 -2.1831 C43 CB' C CH2 . 0.1430 -3.3861 -2.8405 C43 CD' C CH3 . -0.1994 -4.9988 -4.6237 C43 OC' O O2 . -0.7247 -3.8624 -3.9069 """, "linking_test_Mg_HOH.pdb" : """ HETATM 1 MG MG A 1 14.481 28.862 20.807 1.00 20.00 A MG+2 HETATM 2 O HOH A 2 16.505 29.075 21.158 1.00 20.00 A O HETATM 3 O HOH A 3 12.607 28.705 20.389 1.00 20.00 A O HETATM 4 O HOH A 4 15.029 27.124 19.772 1.00 20.00 A O HETATM 5 O HOH A 5 14.172 30.496 21.689 1.00 20.00 A O HETATM 6 O HOH A 6 14.474 27.674 22.398 1.00 20.00 A O HETATM 7 O HOH A 7 14.683 29.906 19.056 1.00 20.00 A O """, "linking_test_Mg_HOH_CRYST1.pdb" : """ CRYST1 13.898 13.372 13.342 90.00 90.00 90.00 P 1 SCALE1 0.071953 0.000000 0.000000 0.00000 SCALE2 0.000000 0.074783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.074951 0.00000 HETATM 1 MG MG A 1 6.874 6.738 6.751 1.00 20.00 A MG+2 HETATM 2 O HOH A 2 8.898 6.951 7.102 1.00 20.00 A O HETATM 3 O HOH A 3 5.000 6.581 6.333 1.00 20.00 A O HETATM 4 O HOH A 4 7.422 5.000 5.716 1.00 20.00 A O HETATM 5 O HOH A 5 6.565 8.372 7.633 1.00 20.00 A O HETATM 6 O HOH A 6 6.867 5.550 8.342 1.00 20.00 A O HETATM 7 O HOH A 7 7.076 7.782 5.000 1.00 20.00 A O TER """, "linking_test_Mg_EDT.pdb" : """ HETATM 1 MG MG A1501 -7.869 -0.167 32.075 0.76 19.71 Mg HETATM 2 O01 EDT A 1 -8.014 0.505 29.989 0.49 19.08 O HETATM 3 C02 EDT A 1 -8.838 -0.073 29.218 0.49 21.60 C HETATM 4 O03 EDT A 1 -9.035 0.272 28.025 0.49 21.74 O HETATM 5 C04 EDT A 1 -9.648 -1.250 29.726 0.49 20.37 C HETATM 6 N05 EDT A 1 -9.634 -1.304 31.200 0.49 22.50 N HETATM 7 C06 EDT A 1 -9.423 -2.672 31.724 0.49 20.66 C HETATM 8 C07 EDT A 1 -7.955 -3.048 31.586 0.49 23.87 C HETATM 9 O08 EDT A 1 -7.636 -4.245 31.436 0.49 23.73 O HETATM 10 O09 EDT A 1 -7.092 -2.152 31.618 0.49 25.09 O HETATM 11 C10 EDT A 1 -10.892 -0.735 31.713 0.49 21.64 C HETATM 12 C11 EDT A 1 -10.806 0.778 31.984 0.49 21.39 C HETATM 13 N12 EDT A 1 -9.522 1.212 32.554 0.49 22.50 N HETATM 14 C13 EDT A 1 -9.643 1.195 34.028 0.49 20.27 C HETATM 15 C14 EDT A 1 -8.884 0.036 34.628 0.49 21.97 C HETATM 16 O15 EDT A 1 -9.056 -0.252 35.836 0.49 20.76 O HETATM 17 O16 EDT A 1 -8.088 -0.608 33.907 0.49 19.08 O HETATM 18 C17 EDT A 1 -9.242 2.584 32.090 0.49 20.69 C HETATM 19 C18 EDT A 1 -7.769 2.967 32.220 0.49 23.96 C HETATM 20 O19 EDT A 1 -6.885 2.088 32.322 0.49 25.12 O HETATM 21 O20 EDT A 1 -7.479 4.176 32.238 0.49 23.80 O """, "edt.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level EDT EDT 'Unknown ' ligand 32 20 . # data_comp_EDT # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z EDT O01 O O . -0.9770 -5.1640 -35.4940 EDT C02 C C . -0.8990 -6.3850 -35.1670 EDT O03 O OC . -0.1220 -7.2090 -35.7080 EDT C04 C CH2 . -1.7640 -6.9100 -34.0410 EDT N05 N NT . -1.9780 -5.8560 -33.0320 EDT C06 C CH2 . -0.7560 -5.5740 -32.2430 EDT C07 C C . -0.5840 -4.0730 -32.0610 EDT O08 O O . 0.3270 -3.6420 -31.3290 EDT O09 O OC . -1.3550 -3.2970 -32.6510 EDT C10 C CH2 . -3.0920 -6.2330 -32.1430 EDT C11 C CH2 . -4.0630 -5.0930 -31.8120 EDT N12 N NT . -4.3530 -4.1550 -32.9060 EDT C13 C CH2 . -4.7520 -2.8590 -32.3240 EDT C14 C C . -4.2850 -1.7280 -33.2010 EDT O15 O O . -4.6870 -0.5650 -32.9710 EDT O16 O OC . -3.5120 -1.9950 -34.1490 EDT C17 C CH2 . -5.4790 -4.6970 -33.6920 EDT C18 C C . -5.0620 -5.2790 -35.0410 EDT O19 O O . -3.9340 -5.0370 -35.5190 EDT O20 O OC . -5.8920 -5.9720 -35.6540 EDT H041 H HCH2 . -1.3187 -7.6788 -33.6195 EDT H042 H HCH2 . -2.6312 -7.1948 -34.4028 EDT H061 H HCH2 . 0.0263 -5.9362 -32.7143 EDT H062 H HCH2 . -0.8318 -6.0020 -31.3616 EDT H101 H HCH2 . -2.7149 -6.5735 -31.3006 EDT H102 H HCH2 . -3.5994 -6.9574 -32.5721 EDT H111 H HCH2 . -3.6877 -4.5805 -31.0618 EDT H112 H HCH2 . -4.9130 -5.4915 -31.5177 EDT H131 H HCH2 . -4.3504 -2.7658 -31.4322 EDT H132 H HCH2 . -5.7312 -2.8259 -32.2447 EDT H171 H HCH2 . -6.1277 -3.9755 -33.8490 EDT H172 H HCH2 . -5.9159 -5.4037 -33.1675 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd EDT C02 O01 deloc 1.266 0.020 EDT O03 C02 deloc 1.255 0.020 EDT C04 C02 single 1.514 0.020 EDT N05 C04 single 1.475 0.020 EDT C07 C06 single 1.522 0.020 EDT O08 C07 deloc 1.246 0.020 EDT O09 C07 deloc 1.243 0.020 EDT C06 N05 single 1.482 0.020 EDT C10 N05 single 1.474 0.020 EDT C11 C10 single 1.534 0.020 EDT N12 C11 single 1.470 0.020 EDT C14 C13 single 1.505 0.020 EDT O15 C14 deloc 1.252 0.020 EDT O16 C14 deloc 1.252 0.020 EDT C13 N12 single 1.476 0.020 EDT C17 N12 single 1.476 0.020 EDT C18 C17 single 1.527 0.020 EDT O19 C18 deloc 1.249 0.020 EDT O20 C18 deloc 1.243 0.020 EDT H041 C04 single 0.983 0.020 EDT H042 C04 single 0.982 0.020 EDT H061 C06 single 0.982 0.020 EDT H062 C06 single 0.983 0.020 EDT H101 C10 single 0.984 0.020 EDT H102 C10 single 0.983 0.020 EDT H111 C11 single 0.983 0.020 EDT H112 C11 single 0.984 0.020 EDT H131 C13 single 0.983 0.020 EDT H132 C13 single 0.983 0.020 EDT H171 C17 single 0.983 0.020 EDT H172 C17 single 0.983 0.020 # """, "linking_test_1jbe_ALA-SNN-ACY-ALA.pdb" : """ ATOM 600 N ALA A 74 28.223 10.182 26.006 1.00 9.40 N ATOM 601 CA ALA A 74 28.012 10.148 27.455 1.00 11.26 C ATOM 602 C ALA A 74 29.306 10.199 28.232 1.00 13.02 C ATOM 603 O ALA A 74 29.290 10.257 29.458 1.00 16.02 O ATOM 604 CB ALA A 74 27.262 8.877 27.829 1.00 15.69 C HETATM 605 N1 SNN A 75 33.758 11.091 28.225 1.00 13.76 N HETATM 606 C2 SNN A 75 32.448 11.310 28.512 1.00 12.79 C HETATM 607 C3 SNN A 75 31.700 10.019 28.212 1.00 11.71 C HETATM 608 N3 SNN A 75 30.432 10.162 27.536 1.00 11.34 N HETATM 609 C4 SNN A 75 32.736 9.250 27.383 1.00 12.39 C HETATM 610 C5 SNN A 75 34.123 9.826 27.531 1.00 12.20 C HETATM 611 O2 SNN A 75 31.994 12.355 28.940 1.00 17.38 O HETATM 612 O5 SNN A 75 35.186 9.317 27.190 1.00 17.87 O HETATM 613 C ACY A 76 35.504 12.683 27.565 1.00 16.21 C HETATM 614 O ACY A 76 34.812 13.387 26.829 1.00 17.55 O HETATM 615 CH3 ACY A 76 34.852 11.912 28.684 1.00 16.85 C ATOM 616 N ALA A 77 36.810 12.555 27.393 1.00 17.53 N ATOM 617 CA ALA A 77 37.522 13.396 26.441 1.00 17.22 C ATOM 618 C ALA A 77 36.978 13.243 25.024 1.00 15.73 C ATOM 619 O ALA A 77 36.998 14.214 24.277 1.00 16.94 O ATOM 620 CB ALA A 77 39.018 13.091 26.481 1.00 27.39 C """, "snn.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level SNN SNN '(3S)-3-aminopyrrolidine-2,5-dione' ligand 14 8 . # data_comp_SNN # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z SNN N1 N NH1 . -1.1318 -0.2275 -1.2446 SNN C2 C C . 0.2247 -0.2275 -1.2446 SNN C3 C CH1 . 0.6936 -0.2275 0.2180 SNN N3 N NH2 . 1.6615 0.7434 0.3846 SNN C4 C CH2 . -0.6212 -0.2275 1.0200 SNN C5 C C . -1.5673 0.3826 -0.0137 SNN O2 O O . 0.9386 -0.3193 -2.2232 SNN O5 O O . -2.4854 1.1684 0.1080 SNN HN H HNH1 . -1.6677 -0.4697 -1.9417 SNN H3 H HCH1 . 1.2207 -0.9991 0.5003 SNN HN31 H HNH2 . 1.7785 0.9065 1.2742 SNN HN32 H HNH2 . 2.4472 0.4548 0.0225 SNN H41 H HCH2 . -0.5948 0.1814 1.9060 SNN H42 H HCH2 . -0.8965 -1.1391 1.2345 # """, "linking_test_3gmq_NAG-FUC.pdb" : """ HETATM 3108 C1 NAG A 294 5.929 -23.329 20.979 1.00 36.07 C HETATM 3109 C2 NAG A 294 6.923 -23.190 22.146 1.00 36.71 C HETATM 3110 C3 NAG A 294 8.360 -23.145 21.617 1.00 36.96 C HETATM 3111 C4 NAG A 294 8.692 -24.336 20.749 1.00 36.82 C HETATM 3112 C5 NAG A 294 7.591 -24.460 19.696 1.00 38.98 C HETATM 3113 C6 NAG A 294 7.798 -25.785 18.952 1.00 38.89 C HETATM 3114 C7 NAG A 294 5.795 -21.923 23.855 1.00 34.86 C HETATM 3115 C8 NAG A 294 5.669 -20.618 24.563 1.00 36.07 C HETATM 3116 N2 NAG A 294 6.712 -21.966 22.871 1.00 35.60 N HETATM 3117 O3 NAG A 294 9.221 -23.104 22.736 1.00 39.69 O HETATM 3118 O4 NAG A 294 9.926 -24.109 20.077 1.00 36.71 O HETATM 3119 O5 NAG A 294 6.288 -24.471 20.285 1.00 34.73 O HETATM 3120 O6 NAG A 294 6.889 -25.880 17.874 1.00 42.57 O HETATM 3121 O7 NAG A 294 5.008 -22.854 24.057 1.00 40.29 O HETATM 3169 C1 FUC A 299 7.292 -25.423 16.517 1.00 46.98 C HETATM 3170 C2 FUC A 299 6.227 -26.090 15.616 1.00 49.47 C HETATM 3171 C3 FUC A 299 4.835 -25.506 15.941 1.00 49.89 C HETATM 3172 C4 FUC A 299 4.818 -23.991 15.655 1.00 53.30 C HETATM 3173 C5 FUC A 299 5.984 -23.378 16.459 1.00 50.98 C HETATM 3174 C6 FUC A 299 6.038 -21.848 16.375 1.00 45.12 C HETATM 3175 O2 FUC A 299 6.203 -27.506 15.815 1.00 49.49 O HETATM 3176 O3 FUC A 299 3.810 -26.238 15.266 1.00 47.77 O HETATM 3177 O4 FUC A 299 4.964 -23.690 14.277 1.00 51.21 O HETATM 3178 O5 FUC A 299 7.240 -24.036 16.163 1.00 46.78 O """, "linking_test_CD_GHE_A_B.pdb" : """ CRYST1 154.379 108.579 120.263 90.00 138.53 90.00 C 1 2 1 20 HETATM 8577 CD CD C1205 -85.285 28.175 80.928 1.00 13.07 CD HETATM 8578 CD CD C1206 -86.132 30.445 78.070 1.00 13.45 CD HETATM 8579 N1 AGHE C1207 -87.632 33.273 82.068 0.25 15.93 N HETATM 8580 C2 AGHE C1207 -87.139 31.954 82.363 0.25 13.77 C HETATM 8581 C3 AGHE C1207 -85.848 32.181 82.970 0.25 13.59 C HETATM 8582 C4 AGHE C1207 -85.379 33.497 82.427 0.25 15.16 C HETATM 8583 C5 AGHE C1207 -86.627 34.267 82.225 0.25 18.36 C HETATM 8584 C1 AGHE C1207 -86.965 31.040 81.200 0.25 12.73 C HETATM 8585 O2 AGHE C1207 -86.877 31.463 79.997 0.25 13.10 O HETATM 8586 O1 AGHE C1207 -86.879 29.793 81.461 0.25 11.38 O HETATM 8587 C6 AGHE C1207 -88.988 33.572 81.719 0.25 20.72 C HETATM 8588 O6 AGHE C1207 -89.317 34.719 81.513 0.25 24.50 O HETATM 8589 C7 AGHE C1207 -89.928 32.396 81.589 0.25 13.71 C HETATM 8590 C8 AGHE C1207 -90.599 32.349 80.226 0.25 23.85 C HETATM 8591 C9 AGHE C1207 -89.628 32.441 79.013 0.25 23.81 C HETATM 8592 C10AGHE C1207 -90.298 32.455 77.696 0.25 13.75 C HETATM 8593 C11AGHE C1207 -91.284 33.597 77.576 0.25 20.78 C HETATM 8594 O11AGHE C1207 -90.998 34.811 77.764 0.25 24.27 O HETATM 8595 N2 AGHE C1207 -92.616 33.250 77.274 0.25 15.91 N HETATM 8596 C15AGHE C1207 -93.060 31.918 77.024 0.25 13.70 C HETATM 8597 C14AGHE C1207 -94.339 32.116 76.287 0.25 13.63 C HETATM 8598 C13AGHE C1207 -94.859 33.436 76.736 0.25 15.20 C HETATM 8599 C12AGHE C1207 -93.641 34.215 77.139 0.25 18.35 C HETATM 8600 C16AGHE C1207 -93.276 31.124 78.251 0.25 12.59 C HETATM 8601 O16AGHE C1207 -93.343 29.864 78.193 0.25 10.81 O HETATM 8602 O17AGHE C1207 -93.406 31.667 79.357 0.25 13.15 O HETATM 8579 N1 BGHE C1207 -87.762 33.127 82.051 0.25 15.93 N HETATM 8580 C2 BGHE C1207 -87.157 31.870 82.281 0.25 13.77 C HETATM 8581 C3 BGHE C1207 -85.824 32.206 82.976 0.25 13.59 C HETATM 8582 C4 BGHE C1207 -85.481 33.523 82.395 0.25 15.16 C HETATM 8583 C5 BGHE C1207 -86.817 34.170 82.230 0.25 18.36 C HETATM 8584 C1 BGHE C1207 -86.997 31.025 81.014 0.25 12.73 C HETATM 8585 O2 BGHE C1207 -86.879 31.590 79.969 0.25 13.10 O HETATM 8586 O1 BGHE C1207 -86.924 29.833 81.336 0.25 11.38 O HETATM 8587 C6 BGHE C1207 -89.137 33.243 81.727 0.25 20.72 C HETATM 8588 O6 BGHE C1207 -89.853 32.297 81.625 0.25 24.50 O HETATM 8589 C7 BGHE C1207 -89.559 34.637 81.532 0.25 13.71 C HETATM 8590 C8 BGHE C1207 -90.563 34.607 80.287 0.25 23.85 C HETATM 8591 C9 BGHE C1207 -89.667 34.602 79.002 0.25 23.81 C HETATM 8592 C10BGHE C1207 -90.628 34.667 77.787 0.25 13.75 C HETATM 8593 C11BGHE C1207 -91.092 33.238 77.563 0.25 20.78 C HETATM 8594 O11BGHE C1207 -90.376 32.288 77.659 0.25 24.27 O HETATM 8595 N2 BGHE C1207 -92.458 33.129 77.232 0.25 15.91 N HETATM 8596 C15BGHE C1207 -93.058 31.883 76.995 0.25 13.70 C HETATM 8597 C14BGHE C1207 -94.408 32.218 76.304 0.25 13.63 C HETATM 8598 C13BGHE C1207 -94.743 33.524 76.887 0.25 15.20 C HETATM 8599 C12BGHE C1207 -93.408 34.169 77.056 0.25 18.35 C HETATM 8600 C16BGHE C1207 -93.228 31.034 78.271 0.25 12.59 C HETATM 8601 O16BGHE C1207 -93.298 29.819 77.942 0.25 10.81 O HETATM 8602 O17BGHE C1207 -93.349 31.594 79.315 0.25 13.15 O """, "ghe.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level GHE GHE 'Unknown ' ligand 46 24 . # data_comp_GHE # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z GHE N1 N NT . -79.2922 87.5583 63.7529 GHE C2 C CH1 . -78.2204 88.2930 63.9823 GHE C3 C CH2 . -77.1377 87.8430 62.8003 GHE C4 C CH2 . -77.3209 86.5460 62.6252 GHE C5 C CH2 . -78.8231 86.2738 63.0451 GHE C1 C C . -77.6682 88.1432 65.4087 GHE O2 O O . -77.7245 87.0287 65.9917 GHE O1 O OC . -77.1497 89.1322 65.9901 GHE C6 C C . -80.6286 87.8903 64.0949 GHE O6 O O . -80.8690 88.9411 64.6552 GHE C7 C CH2 . -81.7587 86.9547 63.7250 GHE C8 C CH2 . -83.1158 87.5330 64.0610 GHE C9 C CH2 . -84.1621 87.1799 63.0266 GHE C10 C CH2 . -85.4675 87.9082 63.2593 GHE C11 C C . -86.3747 87.8603 62.0495 GHE O11 O O . -86.0710 87.1812 61.0892 GHE N2 N NT . -87.5618 88.6367 62.0221 GHE C15 C CH1 . -88.4134 88.7124 61.0336 GHE C14 C CH2 . -89.0906 90.1723 61.1953 GHE C13 C CH2 . -88.6543 90.6746 62.5810 GHE C12 C CH2 . -88.1072 89.5871 63.2049 GHE C16 C C . -89.4518 87.5401 61.0112 GHE O16 O O . -89.6653 86.9087 59.9431 GHE O17 O OC . -90.0884 87.2431 62.0560 GHE H21 H HCH1 . -78.4208 89.2507 63.9474 GHE H31 H HCH2 . -77.3239 88.3266 61.9687 GHE H32 H HCH2 . -76.2204 88.0184 63.0967 GHE H41 H HCH2 . -77.1829 86.3077 61.6850 GHE H42 H HCH2 . -76.7108 86.0367 63.1983 GHE H51 H HCH2 . -78.8705 85.5130 63.6581 GHE H52 H HCH2 . -79.3707 86.1051 62.2524 GHE H71 H HCH2 . -81.7199 86.7754 62.7642 GHE H72 H HCH2 . -81.6444 86.1127 64.2096 GHE H81 H HCH2 . -83.0404 88.5067 64.1157 GHE H82 H HCH2 . -83.4008 87.1876 64.9306 GHE H91 H HCH2 . -84.3269 86.2163 63.0589 GHE H92 H HCH2 . -83.8224 87.4141 62.1397 GHE H101 H HCH2 . -85.2749 88.8429 63.4740 GHE H102 H HCH2 . -85.9288 87.4971 64.0175 GHE H151 H HCH1 . -87.9759 88.6068 60.1655 GHE H141 H HCH2 . -88.7644 90.7760 60.4982 GHE H142 H HCH2 . -90.0651 90.1000 61.1528 GHE H131 H HCH2 . -87.9860 91.3852 62.4895 GHE H132 H HCH2 . -89.4297 90.9997 63.0837 GHE H121 H HCH2 . -88.7897 89.1182 63.7284 GHE H122 H HCH2 . -87.3675 89.8655 63.7838 """, "linking_test_ALY_MCM.pdb" : """ HETATM 2888 OH ALY C 5 -15.286 24.739 8.076 1.00 45.73 C O HETATM 2889 CH ALY C 5 -16.455 25.116 7.877 1.00 41.87 C C HETATM 2890 CH3 ALY C 5 -16.828 25.980 6.695 1.00 36.75 C C HETATM 2891 NZ ALY C 5 -17.470 24.749 8.740 1.00 48.84 C N HETATM 2892 CE ALY C 5 -17.263 23.930 9.901 1.00 39.21 C C HETATM 2893 CD ALY C 5 -18.562 23.629 10.640 1.00 41.37 C C HETATM 2894 CG ALY C 5 -18.329 22.814 11.892 1.00 41.99 C C HETATM 2895 CB ALY C 5 -19.662 22.656 12.590 1.00 45.24 C C HETATM 2896 CA ALY C 5 -19.524 22.011 13.974 1.00 51.20 C C HETATM 2897 N ALY C 5 -20.755 21.670 14.665 1.00 49.87 C N HETATM 2898 C ALY C 5 -18.619 22.936 14.781 1.00 47.11 C C HETATM 2899 O ALY C 5 -17.427 22.728 15.024 1.00 49.30 C O HETATM 2900 N MCM C 6 -19.324 23.360 15.960 1.00 49.19 C N HETATM 2901 CA MCM C 6 -18.698 24.321 16.695 1.00 44.46 C C HETATM 2902 C2 MCM C 6 -19.284 25.579 16.752 1.00 49.13 C C HETATM 2903 C3 MCM C 6 -18.708 26.580 17.525 1.00 48.36 C C HETATM 2904 C4 MCM C 6 -18.700 28.830 18.338 1.00 45.36 C C HETATM 2905 C5 MCM C 6 -17.544 28.627 19.099 1.00 42.82 C C HETATM 2906 C6 MCM C 6 -16.902 27.390 19.114 1.00 45.52 C C HETATM 2907 C7 MCM C 6 -17.484 26.294 18.302 1.00 46.42 C C HETATM 2908 C8 MCM C 6 -16.929 25.030 18.246 1.00 40.92 C C HETATM 2909 C9 MCM C 6 -17.552 24.060 17.457 1.00 43.70 C C HETATM 2910 C10 MCM C 6 -15.654 27.180 19.937 1.00 42.32 C C HETATM 2911 O1 MCM C 6 -19.260 27.832 17.578 1.00 46.61 C O HETATM 2912 O2 MCM C 6 -19.248 29.950 18.344 1.00 44.55 C O """, "mcm.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level MCM MCM '7-amino-4-methyl-2H-chromen-2-one' ligand 22 13 . # data_comp_MCM # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z MCM N N NH2 . -3.8313 0.0126 -0.1203 MCM CA C CR6 . -2.4124 0.0126 -0.1203 MCM C2 C CR16 . -1.7183 0.0126 1.0827 MCM C3 C CR66 . -0.3102 0.0126 1.0833 MCM C4 C CR6 . 1.7583 0.0126 2.2891 MCM C5 C CR16 . 2.4557 0.0126 1.0847 MCM C6 C CR6 . 1.7703 0.0126 -0.1062 MCM C7 C CR66 . 0.3770 0.0126 -0.1073 MCM C8 C CR16 . -0.3279 0.0126 -1.3263 MCM C9 C CR16 . -1.7167 0.0126 -1.3257 MCM C10 C CH3 . 2.5277 -0.0477 -1.4146 MCM O1 O O . 0.3860 0.0126 2.2882 MCM O2 O OC . 2.3647 0.0146 3.3417 MCM HN1 H HNH2 . -4.2873 0.8024 -0.1159 MCM HN2 H HNH2 . -4.2873 -0.7772 -0.1160 MCM H2 H HCR6 . -2.2066 0.0126 1.9279 MCM H5 H HCR6 . 3.4319 0.0126 1.0860 MCM H8 H HCR6 . 0.1597 0.0126 -2.1720 MCM H9 H HCR6 . -2.2050 0.0131 -2.1709 MCM H101 H HCH3 . 2.3139 0.7394 -1.9509 MCM H102 H HCH3 . 3.4869 -0.0680 -1.2348 MCM H103 H HCH3 . 2.2709 -0.8533 -1.9024 """, "linking_test_XYP_XYP.pdb" : """ HETATM 2826 O3B XYP E 1 -19.496 30.622 -25.625 1.00 40.53 O HETATM 2827 C3B XYP E 1 -20.078 29.454 -25.182 1.00 38.50 C HETATM 2828 C4B XYP E 1 -19.553 28.253 -25.964 1.00 42.57 C HETATM 2829 O4B XYP E 1 -20.091 28.171 -27.284 1.00 43.82 O HETATM 2830 C5B XYP E 1 -19.957 27.023 -25.162 1.00 43.75 C HETATM 2831 O5B XYP E 1 -19.354 27.144 -23.900 1.00 41.03 O HETATM 2832 C1B XYP E 1 -19.814 28.095 -22.997 1.00 48.42 C HETATM 2833 C2B XYP E 1 -19.795 29.449 -23.683 1.00 38.61 C HETATM 2834 O2B XYP E 1 -20.419 30.487 -22.970 1.00 36.77 O HETATM 2835 O3B XYP E 2 -17.702 26.306 -20.601 1.00 21.95 O HETATM 2836 C3B XYP E 2 -18.690 27.191 -20.166 1.00 22.83 C HETATM 2837 C4B XYP E 2 -19.848 27.282 -21.144 1.00 29.33 C HETATM 2838 O4B XYP E 2 -19.535 27.935 -22.359 1.00 39.74 O HETATM 2839 C5B XYP E 2 -21.016 27.978 -20.518 1.00 32.56 C HETATM 2840 O5B XYP E 2 -21.364 27.415 -19.297 1.00 36.29 O HETATM 2841 C1B XYP E 2 -20.357 27.458 -18.342 1.00 36.98 C HETATM 2842 C2B XYP E 2 -19.138 26.714 -18.808 1.00 27.91 C HETATM 2843 O2B XYP E 2 -18.170 26.657 -17.835 1.00 29.93 O """, "xyp.cif" : """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level XYP XYP 'beta-D-xylopyranose ' ligand 20 10 . # data_comp_XYP # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z XYP O4A O OH1 . -2.6653 0.5410 -0.7788 XYP C1B C CH1 . -1.2854 0.5410 -0.7788 XYP C2B C CH1 . -0.7949 0.5410 0.6557 XYP C3B C CH1 . 0.6771 0.3610 0.7492 XYP C4B C CH1 . 1.1508 -0.8250 -0.0209 XYP C5B C CH2 . 0.6485 -0.8204 -1.4579 XYP O2B O OH1 . -1.1499 1.7930 1.2682 XYP O3B O OH1 . 1.0411 0.1907 2.1434 XYP O4B O OH1 . 2.5828 -0.8283 -0.0313 XYP O5B O O2 . -0.8048 -0.6378 -1.5443 XYP HO4A H HOH1 . -2.9613 0.7962 -1.5757 XYP H1B H HCH1 . -0.9700 1.3528 -1.2196 XYP H2B H HCH1 . -1.2337 -0.1841 1.1400 XYP H3B H HCH1 . 1.1168 1.1604 0.4021 XYP H4B H HCH1 . 0.8356 -1.6360 0.4216 XYP H5B1 H HCH2 . 0.8851 -1.6694 -1.8775 XYP H5B2 H HCH2 . 1.0868 -0.0955 -1.9429 XYP HO2B H HOH1 . -1.7421 1.6494 1.9136 XYP HO3B H HOH1 . 0.7049 -0.5731 2.4459 XYP HO4B H HOH1 . 2.8778 -1.6570 0.0880 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd _chem_comp_bond.value_dist_neutron XYP O4A C1B single 1.359 0.020 1.359 XYP O4A HO4A single 0.850 0.020 0.980 XYP C1B C2B single 1.528 0.020 1.528 XYP C1B O5B single 1.500 0.020 1.500 XYP C1B H1B single 0.970 0.020 1.090 XYP C2B C3B single 1.489 0.020 1.489 XYP C2B O2B single 1.435 0.020 1.435 XYP C2B H2B single 0.970 0.020 1.090 XYP C3B C4B single 1.495 0.020 1.495 XYP C3B O3B single 1.453 0.020 1.453 XYP C3B H3B single 0.970 0.020 1.090 XYP C4B C5B single 1.536 0.020 1.536 XYP C4B O4B single 1.428 0.020 1.428 XYP C4B H4B single 0.970 0.020 1.090 XYP C5B O5B single 1.479 0.020 1.479 XYP C5B H5B1 single 0.970 0.020 1.090 XYP C5B H5B2 single 0.970 0.020 1.090 XYP O2B HO2B single 0.850 0.020 0.980 XYP O3B HO3B single 0.850 0.020 0.980 XYP O4B HO4B single 0.850 0.020 0.980 """, # CRYST1 16.302 21.238 70.013 90.07 90.04 67.31 P 1 # SCALE1 0.061342 -0.025647 0.000016 0.00000 # SCALE2 0.000000 0.051035 0.000053 0.00000 # SCALE3 0.000000 0.000000 0.014283 0.00000 'linking_test_cyclic_main_chain.pdb' : ''' ATOM 1 N SER A 1 -4.265 -4.954 -1.607 1.00 8.10 N ATOM 2 CA SER A 1 -4.144 -5.756 -2.800 1.00 12.96 C ATOM 3 C SER A 1 -4.846 -5.023 -3.931 1.00 15.20 C ATOM 4 O SER A 1 -5.852 -4.345 -3.752 1.00 13.88 O ATOM 5 CB SER A 1 -4.783 -7.118 -2.597 1.00 11.98 C ATOM 6 OG SER A 1 -6.157 -6.982 -2.308 1.00 20.63 O ATOM 7 H1 SER A 1 -3.830 -5.404 -0.877 1.00 9.73 H ATOM 8 H3 SER A 1 -5.194 -4.834 -1.375 1.00 9.73 H ATOM 9 HA SER A 1 -3.212 -5.906 -3.021 1.00 15.57 H ATOM 10 HB2 SER A 1 -4.679 -7.641 -3.407 1.00 14.39 H ATOM 11 HB3 SER A 1 -4.346 -7.566 -1.855 1.00 14.39 H ATOM 12 HG SER A 1 -6.551 -6.619 -2.955 1.00 24.78 H ATOM 13 N GLY A 2 -4.267 -5.151 -5.101 1.00 9.33 N ATOM 14 CA GLY A 2 -4.825 -4.626 -6.311 1.00 12.49 C ATOM 15 C GLY A 2 -5.008 -5.783 -7.263 1.00 9.40 C ATOM 16 O GLY A 2 -4.714 -6.935 -6.932 1.00 11.00 O ATOM 17 H GLY A 2 -3.518 -5.556 -5.222 1.00 11.21 H ATOM 18 HA2 GLY A 2 -5.683 -4.208 -6.136 1.00 15.01 H ATOM 19 HA3 GLY A 2 -4.229 -3.970 -6.704 1.00 15.01 H ATOM 20 N CYS A 33 -2.546 1.149 1.766 1.00 4.81 N ATOM 21 CA CYS A 33 -2.165 0.125 0.812 1.00 7.98 C ATOM 22 C CYS A 33 -3.153 -1.036 0.819 1.00 7.86 C ATOM 23 O CYS A 33 -3.760 -1.377 1.846 1.00 9.25 O ATOM 24 CB CYS A 33 -0.764 -0.397 1.128 1.00 8.49 C ATOM 25 SG CYS A 33 0.515 0.890 1.039 1.00 6.44 S ATOM 26 H CYS A 33 -2.063 1.185 2.476 1.00 5.78 H ATOM 27 HA CYS A 33 -2.161 0.511 -0.078 1.00 9.59 H ATOM 28 HB2 CYS A 33 -0.760 -0.760 2.027 1.00 10.20 H ATOM 29 HB3 CYS A 33 -0.536 -1.090 0.489 1.00 10.20 H ATOM 30 N GLY A 34 -3.323 -1.639 -0.350 1.00 6.42 N ATOM 31 CA GLY A 34 -4.109 -2.847 -0.461 1.00 8.51 C ATOM 32 C GLY A 34 -3.699 -3.646 -1.668 1.00 5.95 C ATOM 33 O GLY A 34 -2.828 -3.223 -2.415 1.00 5.28 O ATOM 34 H GLY A 34 -2.991 -1.363 -1.093 1.00 7.72 H ATOM 35 HA2 GLY A 34 -3.984 -3.392 0.331 1.00 10.22 H ATOM 36 HA3 GLY A 34 -5.048 -2.619 -0.543 1.00 10.22 H ''', "linking_test_cyclic_side_chain.pdb" : """ ATOM 3269 N SER P 1 18.059 15.260 -24.071 1.00 30.30 N ATOM 3270 CA SER P 1 17.744 15.799 -25.407 1.00 28.03 C ATOM 3271 C SER P 1 17.804 14.711 -26.452 1.00 26.79 C ATOM 3272 O SER P 1 17.637 14.921 -27.647 1.00 26.96 O ATOM 3273 CB SER P 1 18.762 16.955 -25.664 1.00 24.81 C ATOM 3274 OG SER P 1 20.066 16.481 -25.290 1.00 25.91 O ATOM 3275 N HIS P 2 18.186 13.483 -26.051 1.00 27.55 N ATOM 3276 CA HIS P 2 18.293 12.344 -26.970 1.00 26.35 C ATOM 3277 C HIS P 2 17.629 11.119 -26.311 1.00 28.18 C ATOM 3278 O HIS P 2 17.571 11.054 -25.068 1.00 26.85 O ATOM 3279 CB HIS P 2 19.701 11.995 -27.457 1.00 25.52 C ATOM 3280 CG HIS P 2 20.361 13.249 -28.028 1.00 28.42 C ATOM 3281 ND1 HIS P 2 20.863 14.172 -27.147 1.00 24.54 N ATOM 3282 CD2 HIS P 2 20.448 13.734 -29.305 1.00 26.62 C ATOM 3283 CE1 HIS P 2 21.328 15.194 -27.878 1.00 26.65 C ATOM 3284 NE2 HIS P 2 21.104 14.954 -29.164 1.00 26.82 N ATOM 3285 N PHE P 3 17.144 10.201 -27.143 1.00 29.14 N ATOM 3286 CA PHE P 3 16.344 9.075 -26.655 1.00 30.32 C ATOM 3287 C PHE P 3 17.184 8.115 -25.808 1.00 30.69 C ATOM 3288 O PHE P 3 16.528 7.489 -24.951 1.00 28.96 O ATOM 3289 CB PHE P 3 15.661 8.283 -27.795 1.00 30.32 C ATOM 3290 CG PHE P 3 16.571 7.318 -28.492 1.00 31.30 C ATOM 3291 CD1 PHE P 3 17.474 7.781 -29.449 1.00 31.02 C ATOM 3292 CD2 PHE P 3 16.540 5.956 -28.197 1.00 32.14 C ATOM 3293 CE1 PHE P 3 18.367 6.926 -30.034 1.00 32.25 C ATOM 3294 CE2 PHE P 3 17.438 5.082 -28.804 1.00 31.93 C ATOM 3295 CZ PHE P 3 18.354 5.566 -29.735 1.00 32.42 C ATOM 3296 N ASN P 4 18.483 8.081 -26.027 1.00 29.01 N ATOM 3297 CA ASN P 4 19.372 7.142 -25.362 1.00 30.69 C ATOM 3298 C ASN P 4 20.157 7.719 -24.189 1.00 28.07 C ATOM 3299 O ASN P 4 21.300 7.375 -23.910 1.00 30.39 O ATOM 3300 CB ASN P 4 20.314 6.536 -26.417 1.00 30.85 C ATOM 3301 CG ASN P 4 21.272 7.509 -27.112 1.00 30.81 C ATOM 3302 OD1 ASN P 4 20.921 8.699 -27.117 1.00 29.68 O ATOM 3303 ND2 ASN P 4 22.387 7.033 -27.684 1.00 24.16 N ATOM 3304 N GLU P 5 19.570 8.666 -23.470 1.00 29.50 N ATOM 3305 CA GLU P 5 20.265 9.227 -22.291 1.00 29.41 C ATOM 3306 C GLU P 5 19.129 9.685 -21.395 1.00 29.39 C ATOM 3307 O GLU P 5 18.001 9.896 -21.859 1.00 29.14 O ATOM 3308 CB GLU P 5 21.196 10.384 -22.704 1.00 26.92 C ATOM 3309 CG GLU P 5 20.427 11.613 -23.230 1.00 25.95 C ATOM 3310 CD GLU P 5 21.249 12.501 -24.174 1.00 24.67 C ATOM 3311 OE1 GLU P 5 22.366 12.144 -24.576 1.00 22.04 O ATOM 3312 OE2 GLU P 5 20.781 13.651 -24.433 1.00 24.57 O ATOM 3313 N TYR P 6 19.464 9.979 -20.145 1.00 31.01 N ATOM 3314 CA TYR P 6 18.409 10.410 -19.228 1.00 34.43 C ATOM 3315 C TYR P 6 18.354 11.920 -19.206 1.00 33.94 C ATOM 3316 O TYR P 6 19.419 12.506 -18.972 1.00 35.68 O ATOM 3317 CB TYR P 6 18.737 9.834 -17.839 1.00 34.87 C ATOM 3318 CG TYR P 6 17.785 10.332 -16.768 1.00 36.73 C ATOM 3319 CD1 TYR P 6 16.458 9.895 -16.735 1.00 36.01 C ATOM 3320 CD2 TYR P 6 18.234 11.220 -15.814 1.00 35.99 C ATOM 3321 CE1 TYR P 6 15.596 10.343 -15.743 1.00 35.81 C ATOM 3322 CE2 TYR P 6 17.367 11.686 -14.813 1.00 36.01 C ATOM 3323 CZ TYR P 6 16.070 11.225 -14.792 1.00 37.50 C ATOM 3324 OH TYR P 6 15.232 11.666 -13.801 1.00 37.68 O ATOM 3325 N GLU P 7 17.200 12.518 -19.441 1.00 33.03 N ATOM 3326 CA GLU P 7 17.093 13.964 -19.391 1.00 38.47 C ATOM 3327 C GLU P 7 16.164 14.469 -18.288 1.00 44.24 C ATOM 3328 O GLU P 7 16.286 15.663 -17.967 1.00 46.55 O ATOM 3329 CB GLU P 7 16.582 14.559 -20.709 1.00 34.66 C ATOM 3330 CG GLU P 7 17.504 14.149 -21.826 1.00 31.31 C ATOM 3331 CD GLU P 7 17.202 14.901 -23.139 1.00 32.19 C ATOM 3332 OE1 GLU P 7 15.956 14.941 -23.401 1.00 29.65 O ATOM 3333 OXT GLU P 7 15.672 13.468 -17.541 1.00 45.81 O """, "linking_test_over_valence.pdb" : """ ATOM 3451 C27 SEI L 1 65.362 58.026 53.718 1.00 20.00 C ATOM 3463 O39 SEI L 1 65.091 58.948 52.663 1.00 20.00 O ATOM 3495 H39 SEI L 1 65.115 58.519 51.936 1.00 20.00 H ATOM 2595 N GLY A 193 65.965 60.594 51.166 1.00 2.00 N ATOM 2596 CA GLY A 193 64.824 61.465 50.949 1.00 2.00 C ATOM 2597 C GLY A 193 63.671 60.712 50.330 1.00 3.58 C ATOM 2598 O GLY A 193 62.604 61.282 50.115 1.00 6.18 O ATOM 2599 H GLY A 193 65.893 60.083 51.841 1.00 2.00 H ATOM 2600 HA2 GLY A 193 64.531 61.829 51.799 1.00 2.00 H ATOM 2601 HA3 GLY A 193 65.062 62.202 50.366 1.00 2.00 H """, "sei.cif" : """ data_comp_SEI # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.charge SEI C27 C 'CH1 ' 0.000 0 SEI O39 O 'OH1 ' 0.000 0 SEI H39 H 'HCH1' 0.000 0 """, "linking_test_c2_c6.pdb" : """ HETATM15124 C1 BMA B1954 12.904 -11.942 -55.687 1.00 47.00 C HETATM15125 C2 BMA B1954 12.394 -13.167 -54.934 1.00 46.45 C HETATM15126 C3 BMA B1954 13.532 -14.149 -54.722 1.00 47.94 C HETATM15127 C4 BMA B1954 14.248 -14.423 -56.039 1.00 48.98 C HETATM15128 C5 BMA B1954 14.607 -13.131 -56.783 1.00 50.00 C HETATM15129 C6 BMA B1954 15.208 -13.371 -58.158 1.00 49.36 C HETATM15130 O2 BMA B1954 11.341 -13.818 -55.637 1.00 43.37 O HETATM15131 O3 BMA B1954 12.997 -15.377 -54.260 1.00 50.40 O HETATM15132 O4 BMA B1954 15.420 -15.170 -55.759 1.00 49.22 O HETATM15133 O5 BMA B1954 13.436 -12.314 -56.945 1.00 47.68 O HETATM15134 O6 BMA B1954 14.350 -14.201 -58.934 1.00 50.59 O HETATM15157 C1 MAN B1957 13.587 -14.646 -60.954 1.00 26.90 C HETATM15158 C2 MAN B1957 14.671 -14.846 -59.882 1.00 25.95 C HETATM15159 C3 MAN B1957 15.018 -16.290 -60.094 1.00 25.04 C HETATM15160 C4 MAN B1957 13.866 -17.159 -59.640 1.00 24.45 C HETATM15161 C5 MAN B1957 12.714 -16.962 -60.596 1.00 24.51 C HETATM15162 C6 MAN B1957 11.427 -17.605 -60.044 1.00 26.73 C HETATM15163 O3 MAN B1957 16.232 -16.635 -59.360 1.00 26.05 O HETATM15164 O4 MAN B1957 14.341 -18.518 -59.750 1.00 26.46 O HETATM15165 O5 MAN B1957 12.440 -15.560 -60.696 1.00 26.50 O HETATM15166 O6 MAN B1957 10.269 -17.445 -60.950 1.00 27.70 O """, "linking_test_ccp4_other.pdb" : """ HETATM 7642 O3G DCT I 1 28.285 -27.771 -23.129 1.00 52.29 O HETATM 7643 PG DCT I 1 27.597 -26.624 -23.822 1.00 59.65 P HETATM 7644 O1G DCT I 1 28.519 -25.410 -23.888 1.00 63.83 O HETATM 7645 O2G DCT I 1 26.360 -26.264 -23.025 1.00 63.59 O HETATM 7646 O3B DCT I 1 27.136 -27.016 -25.315 1.00 64.88 O HETATM 7647 PB DCT I 1 25.604 -26.763 -25.757 1.00 70.90 P HETATM 7648 O1B DCT I 1 25.443 -27.147 -27.205 1.00 57.04 O HETATM 7649 O2B DCT I 1 24.673 -27.588 -24.895 1.00 61.96 O HETATM 7650 O3A DCT I 1 25.433 -25.167 -25.518 1.00 78.96 O HETATM 7651 PA DCT I 1 24.084 -24.455 -24.963 1.00 91.36 P HETATM 7652 O1A DCT I 1 24.435 -23.045 -24.498 1.00 68.41 O HETATM 7653 O2A DCT I 1 23.403 -25.253 -23.850 1.00 60.82 O HETATM 7654 O5' DCT I 1 23.173 -24.412 -26.309 1.00 69.24 O HETATM 7655 C5' DCT I 1 22.624 -25.634 -26.758 1.00 56.94 C HETATM 7656 C4' DCT I 1 21.239 -25.488 -27.366 1.00 54.90 C HETATM 7657 C3' DCT I 1 21.192 -26.185 -28.716 1.00 49.77 C HETATM 7658 C2' DCT I 1 21.038 -25.070 -29.730 1.00 40.06 C HETATM 7659 O4' DCT I 1 20.924 -24.128 -27.578 1.00 65.15 O HETATM 7660 C1' DCT I 1 20.528 -23.892 -28.917 1.00 52.31 C HETATM 7661 N1 DCT I 1 21.157 -22.640 -29.382 1.00 53.66 N HETATM 7662 C6 DCT I 1 22.021 -21.959 -28.559 1.00 49.31 C HETATM 7663 C5 DCT I 1 22.612 -20.776 -28.995 1.00 41.72 C HETATM 7664 C4 DCT I 1 22.312 -20.298 -30.266 1.00 43.10 C HETATM 7665 N4 DCT I 1 22.872 -19.170 -30.699 1.00 43.04 N HETATM 7666 N3 DCT I 1 21.431 -20.987 -31.082 1.00 43.68 N HETATM 7667 C2 DCT I 1 20.850 -22.158 -30.641 1.00 44.64 C HETATM 7668 O2 DCT I 1 20.070 -22.778 -31.367 1.00 44.43 O ATOM 167 P Cd C 13 19.617 -19.479 -22.016 1.00 46.14 P ATOM 168 O1P Cd C 13 19.618 -19.829 -20.585 1.00 37.17 O ATOM 169 O2P Cd C 13 20.813 -18.844 -22.664 1.00 37.84 O ATOM 170 O5* Cd C 13 19.190 -20.751 -22.929 1.00 43.68 O ATOM 171 C1* Cd C 13 18.014 -20.805 -26.805 1.00 40.99 C ATOM 172 C2* Cd C 13 18.861 -22.059 -26.630 1.00 36.03 C ATOM 173 C3* Cd C 13 18.539 -22.506 -25.197 1.00 45.57 C ATOM 174 C4* Cd C 13 17.601 -21.426 -24.638 1.00 41.26 C ATOM 175 C5* Cd C 13 17.815 -21.006 -23.191 1.00 34.63 C ATOM 176 O4* Cd C 13 17.790 -20.288 -25.514 1.00 41.01 O ATOM 177 N1 Cd C 13 18.634 -19.740 -27.625 1.00 40.70 N ATOM 178 C2 Cd C 13 17.989 -19.394 -28.817 1.00 38.52 C ATOM 179 N3 Cd C 13 18.516 -18.420 -29.604 1.00 29.24 N ATOM 180 C4 Cd C 13 19.648 -17.820 -29.229 1.00 38.13 C ATOM 181 C5 Cd C 13 20.322 -18.161 -28.007 1.00 42.18 C ATOM 182 C6 Cd C 13 19.791 -19.126 -27.237 1.00 40.17 C ATOM 183 O2 Cd C 13 16.945 -20.000 -29.087 1.00 37.42 O ATOM 184 N4 Cd C 13 20.140 -16.868 -30.033 1.00 34.83 N ATOM 246 P Gd D 5 22.253 -15.271 -40.882 1.00 71.71 P ATOM 247 O1P Gd D 5 21.628 -14.785 -42.128 1.00 43.88 O ATOM 248 O2P Gd D 5 22.140 -14.525 -39.624 1.00 61.19 O ATOM 249 O5* Gd D 5 21.647 -16.686 -40.522 1.00 48.09 O ATOM 250 O3* Gd D 5 18.486 -19.251 -41.040 1.00 26.87 O ATOM 251 C1* Gd D 5 20.240 -18.959 -38.638 1.00 30.71 C ATOM 252 C2* Gd D 5 19.325 -17.910 -39.252 1.00 33.86 C ATOM 253 C3* Gd D 5 19.402 -18.250 -40.735 1.00 30.14 C ATOM 254 C4* Gd D 5 20.806 -18.812 -40.918 1.00 32.12 C ATOM 255 C5* Gd D 5 21.805 -17.790 -41.392 1.00 43.37 C ATOM 256 O4* Gd D 5 21.221 -19.274 -39.612 1.00 31.50 O ATOM 257 N9 Gd D 5 20.898 -18.510 -37.405 1.00 39.95 N ATOM 258 C8 Gd D 5 21.748 -17.431 -37.226 1.00 40.77 C ATOM 259 N7 Gd D 5 22.170 -17.293 -35.994 1.00 41.36 N ATOM 260 C5 Gd D 5 21.566 -18.346 -35.305 1.00 35.61 C ATOM 261 C4 Gd D 5 20.784 -19.102 -36.161 1.00 37.92 C ATOM 262 N1 Gd D 5 20.867 -19.840 -33.654 1.00 42.49 N ATOM 263 C2 Gd D 5 20.119 -20.525 -34.581 1.00 37.44 C ATOM 264 N3 Gd D 5 20.036 -20.196 -35.871 1.00 30.36 N ATOM 265 C6 Gd D 5 21.637 -18.715 -33.939 1.00 33.17 C ATOM 266 O6 Gd D 5 22.276 -18.200 -33.026 1.00 33.11 O ATOM 267 N2 Gd D 5 19.447 -21.579 -34.104 1.00 37.54 N """, "linking_test_two_ASN-NAG.pdb" : """ ATOM 10643 N ASN C 281 -19.478 10.820 35.398 1.00 81.69 UNK N ATOM 10644 CA ASN C 281 -19.872 11.829 34.423 1.00 81.69 UNK C ATOM 10645 C ASN C 281 -18.678 12.767 34.352 1.00 81.69 UNK C ATOM 10646 O ASN C 281 -17.651 12.498 34.967 1.00 81.69 UNK O ATOM 10647 CB ASN C 281 -21.101 12.584 34.900 1.00 20.00 UNK C ATOM 10648 CG ASN C 281 -20.973 12.990 36.338 1.00 20.00 UNK C ATOM 10649 OD1 ASN C 281 -19.993 13.641 36.709 1.00 20.00 UNK O ATOM 10650 ND2 ASN C 281 -21.942 12.609 37.167 1.00 20.00 UNK N ATOM 10662 N ASN C 284 -17.638 14.353 38.268 1.00 1.00 N ATOM 10663 CA ASN C 284 -17.098 13.672 39.449 1.00 1.00 C ATOM 10664 C ASN C 284 -15.831 12.857 39.226 1.00 1.00 C ATOM 10665 O ASN C 284 -15.399 12.126 40.112 1.00 1.00 O ATOM 10666 CB ASN C 284 -18.176 12.838 40.159 1.00 20.00 C ATOM 10667 CG ASN C 284 -19.570 13.376 39.919 1.00 20.00 C ATOM 10668 OD1 ASN C 284 -19.960 14.412 40.455 1.00 20.00 O ATOM 10669 ND2 ASN C 284 -20.321 12.672 39.100 1.00 20.00 N HETATM 135 C1 NAG C 751 -21.757 12.993 38.644 1.00 88.86 C HETATM 136 C2 NAG C 751 -22.945 12.574 39.656 1.00 88.86 C HETATM 137 C3 NAG C 751 -23.602 13.737 40.389 1.00 88.86 C HETATM 138 C4 NAG C 751 -24.038 14.792 39.375 1.00 88.86 C HETATM 139 C5 NAG C 751 -23.012 15.048 38.266 1.00 88.86 C HETATM 140 C6 NAG C 751 -22.855 16.548 38.038 1.00 88.86 C HETATM 141 C7 NAG C 751 -23.929 10.591 38.674 1.00 88.86 C HETATM 142 C8 NAG C 751 -22.762 10.103 37.868 1.00 88.86 C HETATM 143 N2 NAG C 751 -23.970 11.898 38.896 1.00 88.86 N HETATM 144 O3 NAG C 751 -22.675 14.320 41.308 1.00 88.86 O HETATM 145 O4 NAG C 751 -25.267 14.372 38.772 1.00 88.86 O HETATM 146 O5 NAG C 751 -21.747 14.436 38.578 1.00 88.86 O HETATM 147 O6 NAG C 751 -22.602 16.781 36.649 1.00 88.86 O HETATM 148 O7 NAG C 751 -24.791 9.842 39.102 1.00 88.86 O """, "linking_test_SER_C.pdb" : """ ATOM 1 P C 643 -75.543 -1.303 308.744 1.00 91.01 D16S P ATOM 2 C5' C 643 -77.315 -3.206 308.385 1.00 99.83 D16S C ATOM 3 O5' C 643 -75.992 -2.834 308.736 1.00 92.18 D16S O ATOM 4 C4' C 643 -77.466 -4.699 308.231 1.00 91.83 D16S C ATOM 5 O4' C 643 -76.541 -5.198 307.222 1.00 86.11 D16S O ATOM 6 C3' C 643 -77.142 -5.522 309.466 1.00 83.89 D16S C ATOM 7 O3' C 643 -78.192 -5.550 310.411 1.00 90.22 D16S O ATOM 8 C2' C 643 -76.796 -6.877 308.870 1.00 75.13 D16S C ATOM 9 O2' C 643 -77.966 -7.558 308.435 1.00 66.17 D16S O ATOM 10 C1' C 643 -76.015 -6.448 307.629 1.00 71.55 D16S C ATOM 11 N1 C 643 -74.568 -6.277 307.938 1.00 72.53 D16S N ATOM 12 C2 C 643 -73.785 -7.404 308.299 1.00 72.36 D16S C ATOM 13 O2 C 643 -74.298 -8.549 308.341 1.00 82.06 D16S O ATOM 14 N3 C 643 -72.467 -7.201 308.589 1.00 67.68 D16S N ATOM 15 C4 C 643 -71.937 -5.966 308.532 1.00 71.55 D16S C ATOM 16 N4 C 643 -70.646 -5.814 308.832 1.00 68.18 D16S N ATOM 17 C5 C 643 -72.701 -4.825 308.168 1.00 79.88 D16S C ATOM 18 C6 C 643 -73.988 -5.025 307.883 1.00 75.82 D16S C ATOM 19 OP1 C 643 -76.597 -0.455 309.339 1.00 76.88 D16S O ATOM 20 OP2 C 643 -74.175 -1.305 309.279 1.00 82.47 D16S O1- ATOM 1 N SER 115 -76.499 -0.597 309.288 1.00 76.74 DS08 N ATOM 2 CA SER 115 -75.220 0.093 309.453 1.00 83.12 DS08 C ATOM 3 C SER 115 -75.112 1.417 308.701 1.00 78.72 DS08 C ATOM 4 O SER 115 -74.545 2.372 309.209 1.00 72.36 DS08 O ATOM 5 CB SER 115 -74.096 -0.829 309.007 1.00 81.98 DS08 C ATOM 6 OG SER 115 -74.613 -2.114 308.687 1.00 93.10 DS08 O """, "linking_test_ASN-NAG-not-THR.pdb" : """ ATOM 11100 N ASN C 281 -20.823 10.632 36.650 1.00128.11 N ATOM 11101 CA ASN C 281 -21.542 11.723 36.020 1.00126.84 C ATOM 11102 C ASN C 281 -20.321 12.535 35.687 1.00133.47 C ATOM 11103 O ASN C 281 -19.289 12.313 36.291 1.00141.10 O ATOM 11104 CB ASN C 281 -22.554 12.488 36.879 1.00132.74 C ATOM 11105 CG ASN C 281 -22.348 12.326 38.361 1.00136.41 C ATOM 11106 OD1 ASN C 281 -21.585 11.488 38.806 1.00137.40 O ATOM 11107 ND2 ASN C 281 -23.058 13.149 39.138 1.00142.79 N ATOM 11108 N GLY C 282 -20.400 13.479 34.769 1.00132.24 N ATOM 11109 CA GLY C 282 -19.205 14.196 34.360 1.00136.73 C ATOM 11110 C GLY C 282 -18.431 14.831 35.495 1.00138.96 C ATOM 11111 O GLY C 282 -17.216 14.977 35.444 1.00139.29 O ATOM 11112 N THR C 283 -19.149 15.231 36.515 1.00133.75 N ATOM 11113 CA THR C 283 -18.571 15.870 37.669 1.00134.08 C ATOM 11114 C THR C 283 -17.581 15.120 38.564 1.00137.98 C ATOM 11115 O THR C 283 -16.604 15.691 39.022 1.00143.56 O ATOM 11116 CB THR C 283 -19.722 16.166 38.613 1.00144.68 C ATOM 11117 OG1 THR C 283 -20.222 14.917 39.104 1.00143.45 O ATOM 11118 CG2 THR C 283 -20.836 16.883 37.874 1.00141.28 C HETATM14227 C1 NAG C1281 -23.045 13.197 40.578 1.00155.05 C HETATM14228 C2 NAG C1281 -24.038 13.231 41.733 1.00155.85 C HETATM14229 C3 NAG C1281 -24.245 14.639 42.281 1.00159.74 C HETATM14230 C4 NAG C1281 -22.956 15.416 42.476 1.00164.53 C HETATM14231 C5 NAG C1281 -21.978 15.164 41.334 1.00162.17 C HETATM14232 C6 NAG C1281 -20.583 15.654 41.678 1.00163.10 C HETATM14233 C7 NAG C1281 -26.167 13.389 40.586 1.00151.28 C HETATM14234 C8 NAG C1281 -26.553 12.787 39.271 1.00144.48 C HETATM14235 N2 NAG C1281 -25.308 12.684 41.309 1.00153.73 N HETATM14236 O3 NAG C1281 -24.905 14.555 43.545 1.00169.63 O HETATM14237 O4 NAG C1281 -23.259 16.819 42.509 1.00164.51 O HETATM14238 O5 NAG C1281 -21.850 13.775 41.067 1.00160.58 O HETATM14239 O6 NAG C1281 -19.653 14.829 40.962 1.00160.49 O HETATM14240 O7 NAG C1281 -26.606 14.456 40.975 1.00157.16 O """, "linking_test_HEM_TYR.pdb" : """ ATOM 6 CG TYR A 140 98.997 4.611 10.805 1.00 38.35 C ATOM 7 CD1 TYR A 140 99.820 3.648 11.373 1.00 36.78 C ATOM 8 CD2 TYR A 140 98.847 5.821 11.476 1.00 37.30 C ATOM 9 CE1 TYR A 140 100.465 3.853 12.607 1.00 37.29 C ATOM 10 CE2 TYR A 140 99.502 6.047 12.739 1.00 42.05 C ATOM 11 CZ TYR A 140 100.316 5.053 13.295 1.00 39.27 C ATOM 12 OH TYR A 140 101.024 5.185 14.508 1.00 47.51 O ATOM 13 N CYS A 470 106.717 6.301 20.283 1.00 34.42 N ATOM 14 CA CYS A 470 107.171 7.557 19.724 1.00 35.14 C ATOM 15 C CYS A 470 108.672 7.540 19.477 1.00 37.62 C ATOM 16 O CYS A 470 109.451 7.026 20.285 1.00 39.29 O ATOM 17 CB CYS A 470 106.833 8.698 20.693 1.00 30.41 C ATOM 18 SG CYS A 470 107.139 10.328 20.022 1.00 34.85 S ATOM 19 CAA HEM A 601 102.373 6.235 20.462 1.00 29.04 C ATOM 20 CAB HEM A 601 105.667 15.514 22.495 1.00 32.15 C ATOM 21 CAC HEM A 601 108.356 13.649 15.330 1.00 33.91 C ATOM 22 CAD HEM A 601 105.102 6.382 15.766 1.00 29.31 C ATOM 23 NA HEM A 601 103.895 9.666 19.977 1.00 30.01 N ATOM 24 CBA HEM A 601 101.025 6.147 19.746 1.00 31.00 C ATOM 25 CBB HEM A 601 105.408 16.127 23.646 1.00 39.39 C ATOM 26 CBC HEM A 601 109.441 14.426 15.313 1.00 37.97 C ATOM 27 CBD HEM A 601 103.624 6.099 15.536 1.00 31.13 C ATOM 28 NB HEM A 601 104.842 12.376 20.622 1.00 28.66 N ATOM 29 CGA HEM A 601 100.437 4.775 19.956 1.00 31.11 C ATOM 30 CGD HEM A 601 103.294 4.677 15.216 1.00 36.63 C ATOM 31 ND HEM A 601 105.110 9.805 17.433 1.00 28.27 N ATOM 32 CHA HEM A 601 104.002 7.823 18.350 1.00 28.03 C ATOM 33 CHB HEM A 601 103.388 10.956 22.005 1.00 29.20 C ATOM 34 CHC HEM A 601 106.256 14.228 19.862 1.00 31.30 C ATOM 35 CHD HEM A 601 106.404 11.313 15.985 1.00 28.55 C ATOM 36 CMA HEM A 601 101.920 8.258 22.900 1.00 30.34 C ATOM 37 CMB HEM A 601 103.702 13.324 24.099 1.00 31.20 C ATOM 38 CMC HEM A 601 108.238 15.628 17.974 1.00 30.92 C ATOM 39 CMD HEM A 601 106.699 8.724 14.156 1.00 27.61 C ATOM 40 C1A HEM A 601 103.617 8.383 19.542 1.00 31.73 C ATOM 41 C1B HEM A 601 104.130 12.102 21.772 1.00 30.51 C ATOM 42 C1C HEM A 601 106.579 13.710 18.629 1.00 31.98 C ATOM 43 C1D HEM A 601 105.856 10.084 16.301 1.00 28.65 C ATOM 44 O1A HEM A 601 99.301 4.511 19.494 1.00 36.78 O ATOM 45 O1D HEM A 601 104.283 3.883 15.263 1.00 33.51 O ATOM 46 C2A HEM A 601 102.863 7.699 20.570 1.00 33.39 C ATOM 47 C2B HEM A 601 104.328 13.232 22.690 1.00 33.80 C ATOM 48 C2C HEM A 601 107.499 14.297 17.699 1.00 30.13 C ATOM 49 C2D HEM A 601 105.949 8.853 15.516 1.00 36.74 C ATOM 50 O2A HEM A 601 101.111 3.928 20.599 1.00 35.99 O ATOM 51 O2D HEM A 601 102.032 4.472 14.888 1.00 47.04 O ATOM 52 C3A HEM A 601 102.693 8.556 21.587 1.00 33.17 C ATOM 53 C3B HEM A 601 105.108 14.136 22.069 1.00 30.61 C ATOM 54 C3C HEM A 601 107.530 13.499 16.617 1.00 32.10 C ATOM 55 C3D HEM A 601 105.302 7.882 16.179 1.00 35.98 C ATOM 56 C4A HEM A 601 103.337 9.814 21.234 1.00 28.53 C ATOM 57 C4B HEM A 601 105.443 13.603 20.772 1.00 26.80 C ATOM 58 C4C HEM A 601 106.652 12.369 16.852 1.00 31.29 C ATOM 59 C4D HEM A 601 104.750 8.469 17.397 1.00 29.94 C ATOM 60 NC HEM A 601 106.086 12.539 18.099 1.00 32.94 N ATOM 61 FE HEM A 601 105.139 11.046 19.090 1.00 32.47 Fe """, "linking_test_HEM_TYR.params" : """ pdb_interpretation { automatic_linking { automatic_linking { link_metals = True link_residues = True inter_residue_bond_cutoff = 2.5 } } } geometry_restraints.edits { bond { atom_selection_1 = chain 'A' and resid ' 601 ' and name 'FE ' and \ altloc ' ' atom_selection_2 = chain 'A' and resid ' 470 ' and name ' SG ' and \ altloc ' ' distance_ideal = 2.33 sigma = 0.02 } } """, "linking_test_MAN-before-ASN.pdb" : """ HETATM 32 C1 MAN A 13 -23.598 63.781-180.576 1.00 20.00 C HETATM 33 O5 MAN A 13 -24.198 64.994-181.028 1.00 20.00 O HETATM 34 C5 MAN A 13 -25.269 65.301-180.140 1.00 20.00 C HETATM 35 C6 MAN A 13 -26.064 66.487-180.693 1.00 20.00 C HETATM 36 O6 MAN A 13 -26.588 66.150-181.978 1.00 20.00 O HETATM 37 C4 MAN A 13 -24.712 65.661-178.762 1.00 20.00 C HETATM 38 O4 MAN A 13 -25.786 65.996-177.882 1.00 20.00 O HETATM 39 C3 MAN A 13 -23.949 64.456-178.202 1.00 20.00 C HETATM 40 O3 MAN A 13 -23.296 64.820-176.985 1.00 20.00 O HETATM 41 C2 MAN A 13 -22.904 64.015-179.233 1.00 20.00 C HETATM 42 O2 MAN A 13 -21.915 65.035-179.378 1.00 20.00 O ATOM 43 O ASN A 210 -64.131 35.488 -16.482 1.00 77.95 O ATOM 44 N ASN A 210 -63.707 32.434 -14.675 1.00 35.76 N ATOM 45 CA ASN A 210 -64.179 33.784 -14.816 1.00 64.69 C ATOM 46 C ASN A 210 -63.605 34.499 -16.022 1.00 72.64 C ATOM 47 CB ASN A 210 -63.830 34.555 -13.567 1.00 77.34 C """, "linking_test_partial_alt_loc_glyco.pdb" : """ HETATM 3615 C1 ANDG B 401 11.587 187.498 -2.208 0.50 17.33 C HETATM 3616 C2 ANDG B 401 10.855 188.231 -1.091 0.50 17.55 C HETATM 3617 C3 ANDG B 401 10.531 189.647 -1.547 0.50 16.69 C HETATM 3618 C4 ANDG B 401 11.775 190.352 -2.092 0.50 16.31 C HETATM 3619 C5 ANDG B 401 12.356 189.491 -3.197 0.50 16.42 C HETATM 3620 C6 ANDG B 401 13.546 190.144 -3.891 0.50 17.65 C HETATM 3621 C7 ANDG B 401 9.454 186.869 0.419 0.50 17.55 C HETATM 3622 C8 ANDG B 401 8.079 186.314 0.643 0.50 16.99 C HETATM 3623 O ANDG B 401 12.733 188.238 -2.631 0.50 16.58 O HETATM 3624 O3 ANDG B 401 10.019 190.380 -0.453 0.50 17.04 O HETATM 3625 O4 ANDG B 401 11.386 191.615 -2.628 0.50 15.06 O HETATM 3626 O6 ANDG B 401 14.616 190.314 -2.961 0.50 17.54 O HETATM 3627 O7 ANDG B 401 10.336 186.702 1.248 0.50 18.38 O HETATM 3628 N2 ANDG B 401 9.620 187.548 -0.722 0.50 17.55 N HETATM 3629 O1LANDG B 401 10.701 187.349 -3.322 0.50 17.86 O HETATM 3630 C1 BNAG B 402 11.696 187.522 -2.281 0.50 19.30 C HETATM 3631 C2 BNAG B 402 10.842 188.218 -1.233 0.50 19.73 C HETATM 3632 C3 BNAG B 402 10.507 189.651 -1.615 0.50 18.14 C HETATM 3633 C4 BNAG B 402 11.754 190.377 -2.114 0.50 17.57 C HETATM 3634 C5 BNAG B 402 12.374 189.564 -3.233 0.50 17.69 C HETATM 3635 C6 BNAG B 402 13.544 190.278 -3.896 0.50 19.10 C HETATM 3636 C7 BNAG B 402 9.520 186.549 -0.070 0.50 22.13 C HETATM 3637 C8 BNAG B 402 8.215 185.818 0.005 0.50 22.97 C HETATM 3638 N2 BNAG B 402 9.630 187.444 -1.049 0.50 20.88 N HETATM 3639 O1 BNAG B 402 12.174 186.314 -1.691 0.50 19.78 O HETATM 3640 O3 BNAG B 402 10.007 190.337 -0.478 0.50 17.72 O HETATM 3641 O4 BNAG B 402 11.350 191.649 -2.605 0.50 15.73 O HETATM 3642 O5 BNAG B 402 12.803 188.319 -2.692 0.50 18.12 O HETATM 3643 O6 BNAG B 402 14.675 190.273 -3.024 0.50 18.91 O HETATM 3644 O7 BNAG B 402 10.422 186.331 0.724 0.50 24.09 O HETATM 3645 C1 AFUC B 403 8.585 190.434 -0.438 0.50 18.44 C HETATM 3646 C1 BFUC B 403 8.574 190.425 -0.442 0.50 18.71 C HETATM 3647 C2 FUC B 403 8.154 190.791 0.979 1.00 19.23 C HETATM 3648 C3 FUC B 403 8.688 192.169 1.357 1.00 19.53 C HETATM 3649 C4 FUC B 403 8.143 193.181 0.356 1.00 20.34 C HETATM 3650 C5 FUC B 403 8.484 192.740 -1.077 1.00 20.67 C HETATM 3651 C6 FUC B 403 7.889 193.667 -2.123 1.00 22.65 C HETATM 3652 O2 FUC B 403 8.618 189.805 1.908 1.00 20.29 O HETATM 3653 O3 FUC B 403 8.325 192.496 2.712 1.00 19.86 O HETATM 3654 O4 FUC B 403 6.720 193.304 0.464 1.00 20.42 O HETATM 3655 O5 FUC B 403 8.050 191.390 -1.356 1.00 18.33 O HETATM 3656 C1 AGAL B 404 12.208 192.729 -2.260 0.50 14.68 C HETATM 3657 C1 BGAL B 404 12.218 192.731 -2.262 0.50 15.08 C HETATM 3658 C2 AGAL B 404 11.977 193.809 -3.313 0.50 14.65 C HETATM 3659 C2 BGAL B 404 11.974 193.813 -3.310 0.50 14.87 C HETATM 3660 C3 GAL B 404 12.714 195.089 -2.980 1.00 14.36 C HETATM 3661 C4 AGAL B 404 12.326 195.524 -1.566 0.50 14.68 C HETATM 3662 C4 BGAL B 404 12.331 195.517 -1.566 0.50 14.89 C HETATM 3663 C5 AGAL B 404 12.545 194.397 -0.567 0.50 14.42 C HETATM 3664 C5 BGAL B 404 12.656 194.395 -0.596 0.50 14.74 C HETATM 3665 C6 AGAL B 404 12.057 194.809 0.817 0.50 14.38 C HETATM 3666 C6 BGAL B 404 12.314 194.806 0.831 0.50 14.69 C HETATM 3667 O2 AGAL B 404 12.381 193.340 -4.606 0.50 14.14 O HETATM 3668 O2 BGAL B 404 12.367 193.348 -4.608 0.50 14.30 O HETATM 3669 O3 GAL B 404 12.351 196.082 -3.971 1.00 15.47 O HETATM 3670 O4 AGAL B 404 10.951 195.945 -1.547 0.50 14.29 O HETATM 3671 O4 BGAL B 404 10.932 195.846 -1.506 0.50 14.61 O HETATM 3672 O5 AGAL B 404 11.840 193.232 -0.984 0.50 15.24 O HETATM 3673 O5 BGAL B 404 11.921 193.232 -0.964 0.50 15.68 O HETATM 3674 O6 AGAL B 404 12.320 193.790 1.794 0.50 13.65 O HETATM 3675 O6 BGAL B 404 12.433 193.702 1.739 0.50 14.16 O """, 'linking_test_CM-SO4.pdb' : ''' HETATM 5816 N26 CM C 4 11.872 46.521 11.694 1.00 15.75 A N HETATM 6475 S SO4 D 4 12.593 45.477 7.849 1.00 30.00 S HETATM 6476 O1 SO4 D 4 13.522 46.224 6.981 1.00 30.00 O HETATM 6477 O2 SO4 D 4 11.558 44.829 7.018 1.00 30.00 O HETATM 6478 O3 SO4 D 4 13.343 44.439 8.588 1.00 30.00 O HETATM 6479 O4 SO4 D 4 11.949 46.390 8.816 1.00 30.00 O ''', "CM.cif" : """ data_comp_CM # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.charge CM N26 N N 0.000 0 """, 'linking_test_exclusion_SO4.pdb' : ''' CRYST1 126.007 546.508 585.856 90.00 90.00 90.00 P 2 21 21 ATOM 5781 N ARG A 782 -68.913-438.467 717.772 1.00 96.17 N ATOM 5782 CA ARG A 782 -68.051-437.794 718.737 1.00 96.10 C ATOM 5783 C ARG A 782 -68.057-438.454 720.114 1.00 96.19 C ATOM 5784 O ARG A 782 -67.489-437.889 721.054 1.00 96.06 O ATOM 5785 CB ARG A 782 -68.457-436.323 718.866 1.00 95.82 C ATOM 5786 CG ARG A 782 -67.625-435.372 718.021 1.00 95.68 C ATOM 5787 CD ARG A 782 -66.340-434.995 718.736 1.00 95.65 C ATOM 5788 NE ARG A 782 -65.486-434.139 717.918 1.00 95.53 N ATOM 5789 CZ ARG A 782 -64.442-434.578 717.222 1.00 95.65 C ATOM 5790 NH1 ARG A 782 -64.123-435.865 717.246 1.00 95.88 N1+ ATOM 5791 NH2 ARG A 782 -63.715-433.731 716.504 1.00 95.52 N ATOM 4791 N LYS A 660 -54.507-433.397 715.702 1.00 89.00 N ATOM 4792 CA LYS A 660 -55.052-434.689 715.302 1.00 89.16 C ATOM 4793 C LYS A 660 -53.950-435.729 715.157 1.00 89.32 C ATOM 4794 O LYS A 660 -54.180-436.916 715.414 1.00 89.49 O ATOM 4795 CB LYS A 660 -55.827-434.552 713.989 1.00 89.09 C ATOM 4796 CG LYS A 660 -57.191-433.881 714.110 1.00 88.95 C ATOM 4797 CD LYS A 660 -58.164-434.700 714.947 1.00 89.07 C ATOM 4798 CE LYS A 660 -59.455-433.926 715.203 1.00 88.92 C ATOM 4799 NZ LYS A 660 -60.489-434.725 715.925 1.00 89.03 N1+ HETATM 6886 O1 SO4 A 923 -60.519-433.073 715.370 0.00 86.34 O HETATM 6887 O2 SO4 A 923 -62.688-432.381 714.671 1.00 86.19 O HETATM 6888 O3 SO4 A 923 -62.430-433.668 716.666 0.10 86.40 O HETATM 6889 O4 SO4 A 923 -61.695-431.404 716.606 1.00 86.05 O HETATM 6890 S SO4 A 923 -61.834-432.632 715.827 1.00 86.25 S ''', 'so4_exclude.phil' : ''' pdb_interpretation { exclude_from_automatic_linking { selection_1 = "resname SO4" selection_2 = all } } ''', } links = { "linking_test_ASN-NAG.pdb" : [21, 22], "linking_test_ASN-NAG-altloc1.pdb" : [35, 37], "linking_test_ASN-NAG-altloc2.pdb" : [42, 44], "linking_test_ASN-NAG-altloc3.pdb" : [38, 40], "linking_test_ASN-NAG-altloc4.pdb" : [43, 43], "linking_test_NAG-FU4.pdb" : [24, 25], "linking_test_NAG-NAG.pdb" : [35, 37], 'linking_test_BGC-BGC.pdb' : [0, 1], 'linking_test_CYS-VSP.pdb' : [66, 68], "linking_test_LEU-CSY-VAL.pdb" : [13,15], 'linking_test_DT-4MF-DA.pdb' : [69, 69], 'linking_test_LYS-ABA-GLU.pdb' : [23,23], "linking_test_ALA-ALA-ALA.pdb" : [32,32], "linking_test_MAN-SER.pdb" : [17, 17], "linking_test_3g2j-LLP.pdb" : [44, 44], "linking_test_ASN_A-NAG_B.pdb" : [21, 22], "linking_test_nstd_rna_dna_h_bond.pdb" : [0,0], "linking_test_nstd_rna_dna.pdb" : [0,1], "linking_test_Mg_HOH.pdb" : [0,6], #6], # metal coordination "linking_test_Mg_HOH_CRYST1.pdb" : [0,6], "linking_test_Mg_EDT.pdb" : [19,25], #25], "linking_test_1jbe_ALA-SNN-ACY-ALA.pdb" : [10,13], "linking_test_3gmq_NAG-FUC.pdb" : [24,25], "linking_test_CD_GHE_A_B.pdb" : [0,0], #4], "linking_test_XYP_XYP.pdb" : [18,19], "linking_test_ALY_MCM.pdb" : [11,12], # links AA with quasi-AA "linking_test_cyclic_side_chain.pdb" : [67,68], # side chain cross link "linking_test_cyclic_main_chain.pdb" : [34,35], # main chain cyclic "linking_test_over_valence.pdb" : [6,6], "linking_test_c2_c6.pdb" : [21,22], "linking_test_ccp4_other.pdb" : [71,71], "linking_test_SER_C.pdb" : [26,27], # "linking_test_two_ASN-NAG.pdb" : [28,29,29,29], # "linking_test_ASN-NAG-not-THR.pdb" : [32,33], # "linking_test_HEM_TYR.pdb" : [63,63], # "linking_test_CYS_CYS_alt_loc.pdb" : [17,17], # "linking_test_MAN-before-ASN.pdb" : [15,15], "linking_test_partial_alt_loc_glyco.pdb" : [63,67], 'linking_test_CM-SO4.pdb' : [4,4], 'linking_test_exclusion_SO4.pdb' :[24,22] } def run_and_test(cmd, pdb, i, skip_links=False): result = easy_run.fully_buffered(cmd).raise_if_errors() assert (result.return_code == 0) for line in result.stdout_lines : if ("Write PDB file" in line): break else : raise RuntimeError("Missing expected log output") print("OK") # test .geo f=open(pdb.replace(".pdb", "_minimized.geo"), "r") lines = f.read() f.close() if pdb=='linking_test_cyclic_main_chain.pdb': if i==1: assert lines.find('link_TRANS restraints: 1')>-1 bonds = 0 for line in lines.splitlines(): for bond_like in ["Bond restraints:", 'Bond-like restraints:', 'Metal coordination restraints:', # 'Disulphide bridge restraints:', 'User supplied restraints:', 'Standard Glycosidic restraints:', 'Custom Glycosidic restraints:', 'Misc. restraints:', # 'link_' ]: if line.find(bond_like)>-1: print('Adding %s for "%s"' % (int(line.split()[-1]), line)) bonds += int(line.split()[-1]) if line.find('Bond angle')>-1: break assert bonds == links[pdb][i], "found %d bonds but expected %s! File: %s" % ( bonds, links[pdb][i], pdb) new_geo = pdb.replace(".pdb", "_minimized_%d.geo" % i) if (os.path.isfile(new_geo)): os.remove(new_geo) os.rename(pdb.replace(".pdb", "_minimized.geo"), new_geo) print("OK") if skip_links: return number_of_links=0 fname = pdb.replace(".pdb", "_minimized.pdb") f=open(fname, "r") lines = f.readlines() f.close() for line in lines: if line.find("LINK")>-1: number_of_links+=1 if i==0: expected = 0 else: expected = links[pdb][i]-links[pdb][0] if pdb in ['linking_test_LEU-CSY-VAL.pdb']: expected -= 2 # peptide-like link if pdb in ["linking_test_HEM_TYR.pdb"]: # unset defined edits expected += 1 # assert number_of_links == expected, "found %d LINK but expected %s! File: %s" % ( number_of_links, expected, fname) if 0: cmd = "phenix.start_coot --no-guano --pdb %s" % pdb.replace(".pdb", "_minimized.pdb" ) os.system(cmd) def run(only_i=None): try: only_i=int(only_i) except ValueError: only_i=None except TypeError: only_i=None longer_tests = [ "linking_test_two_ASN-NAG.pdb", ] # test exclusion if only_i is not None and only_i==1: cifs = "" for pdb in pdbs: f=open(pdb, "w") f.write(pdbs[pdb]) f.close() if pdb.endswith(".phil"): cifs += " %s" % pdb for pdb in pdbs: if pdb=='linking_test_exclusion_SO4.pdb': cmd = "phenix.geometry_minimization %s write_geo_file=True" % pdb cmd += ' link_small_molecules=True' print(cmd) run_and_test(cmd, pdb, 0, True) cmd += " %s" % (cifs) print(cmd) run_and_test(cmd, pdb, 1, True) # cifs = "" for pdb in pdbs: f=open(pdb, "w") f.write(pdbs[pdb]) f.close() if pdb.endswith(".cif"): cifs += " %s" % pdb j=0 for pdb in sorted(pdbs): #break if pdb.endswith(".cif"): continue if pdb.endswith(".params"): continue if pdb.endswith(".phil"): continue if pdb in longer_tests: continue if pdb.find("CD_GHE")>-1: continue if pdb.find("partial")>-1: continue #if pdb.find('SO4')==-1: continue if pdb in ['linking_test_exclusion_SO4.pdb']: continue print('pdb '*10,pdb) j+=1 if only_i is not None and only_i!=j: continue for i in range(2): log_filename = "%s_%d.log" % (pdb, i) cmd = "phenix.geometry_minimization %s write_geo_file=True" % pdb cmd += " link_all=%d link_carbohydrate=%d %s" % (i, i, cifs) cmd += " link_ligand=%d" % i if pdb in [ "linking_test_ccp4_other.pdb", ]: if i: cmd += " secondary_structure.enabled=1" if pdb.replace(".pdb", ".params") in pdbs: cmd += " %s" % pdb.replace(".pdb", ".params") print("test number:",j) print(cmd) run_and_test(cmd, pdb,i) for pdb in sorted(pdbs): if pdb not in longer_tests: continue j+=1 if only_i is not None and only_i!=j: continue k=0 for i in range(2): for ii in range(2): log_filename = "%s_%d_%d.log" % (pdb, i, ii) cmd = "phenix.geometry_minimization %s write_geo_file=True" % pdb cmd += " link_all=%d link_carbohydrate=%d" % (i, ii) print(cmd) run_and_test(cmd, pdb,k) k+=1 if __name__=="__main__": import sys run(*tuple(sys.argv[1:]))