******************************************************************************* ** Site#: 23746 For non-commercial use only Version 16.019W 64BITS** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 16.019W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web: HTTP://OpenMOPAC.net. Days left: 365** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Tue Jan 19 12:21:02 2016 * * GEO-OK - OVERRIDE INTERATOMIC DISTANCE AND OTHER SAFETY CHECKS * START_RES- STARTING RESIDUE NUMBERS DEFINED * Keyword: START_RES=(1A) * GEO_DAT - DATA SET GEOMETRY IS IN FILE "PDB1EJG.ENT" * GEO_REF - REFERENCE GEOMETRY IS IN FILE "PDB1CBN.ENT" * CHAIN - PDB CHAIN LETTERS EXPLICITLY DEFINED * Keyword: CHAINS=(A) * 0SCF - AFTER READING AND PRINTING DATA, STOP * T= - A TIME OF 172800.0 SECONDS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * OUTPUT - MINIMIZE OUTPUT * HTML - WRITE HTML SCRIPT TO READ PDB FILE USING JSMOL ******************************************************************************* START_RES=(1A) CHAINS=(A) geo_dat="PDB1EJG.ent" geo_ref="PDB1CBN.ent" 0scf html GEO-OK OUTPUT Compare the common atoms in two PDB structures of Crambin. Differences in atoms sets Atoms in data-set only Atoms in GEO_REF only ATOM 400 N PRO A 22 ATOM 352 N SER A 22 ATOM 401 CA PRO A 22 ATOM 354 CA SER A 22 ATOM 402 C PRO A 22 ATOM 356 C SER A 22 ATOM 403 O PRO A 22 ATOM 358 O SER A 22 ATOM 404 CB PRO A 22 ATOM 360 CB SER A 22 ATOM 405 CG PRO A 22 ATOM 362 OG SER A 22 ATOM 406 CD PRO A 22 ATOM 364 H SER A 22 ATOM 407 HA PRO A 22 ATOM 366 HA SER A 22 ATOM 408 HB2 PRO A 22 ATOM 368 HB2 SER A 22 ATOM 409 HB3 PRO A 22 ATOM 370 HB3 SER A 22 ATOM 410 HG2 PRO A 22 ATOM 415 N ILE A 25 ATOM 411 HG3 PRO A 22 ATOM 417 CA ILE A 25 ATOM 412 HD2 PRO A 22 ATOM 419 C ILE A 25 ATOM 413 HD3 PRO A 22 ATOM 421 O ILE A 25 ATOM 457 N LEU A 25 ATOM 423 CB ILE A 25 ATOM 458 CA LEU A 25 ATOM 425 CG1 ILE A 25 ATOM 459 C LEU A 25 ATOM 427 CG2 ILE A 25 ATOM 460 O LEU A 25 ATOM 429 CD1 ILE A 25 ATOM 461 CB LEU A 25 ATOM 431 H ILE A 25 ATOM 462 CG LEU A 25 ATOM 433 HA ILE A 25 ATOM 463 CD1 LEU A 25 ATOM 435 HB ILE A 25 ATOM 464 CD2 LEU A 25 ATOM 437 HG12 ILE A 25 ATOM 465 H LEU A 25 ATOM 439 HG13 ILE A 25 ATOM 466 HA LEU A 25 ATOM 441 HG21 ILE A 25 ATOM 467 HB2 LEU A 25 ATOM 443 HG22 ILE A 25 ATOM 468 HB3 LEU A 25 ATOM 445 HG23 ILE A 25 ATOM 469 HG LEU A 25 ATOM 447 HD11 ILE A 25 ATOM 470 HD11 LEU A 25 ATOM 449 HD12 ILE A 25 ATOM 471 HD12 LEU A 25 ATOM 451 HD13 ILE A 25 ATOM 472 HD13 LEU A 25 ATOM 675 HB THR A 39 ATOM 473 HD21 LEU A 25 ATOM 676 HG1 THR A 39 ATOM 474 HD22 LEU A 25 ATOM 677 HG21 THR A 39 ATOM 475 HD23 LEU A 25 ATOM 678 HG22 THR A 39 ATOM 587 HH TYR A 29 ATOM 679 HG23 THR A 39 HETATM 774 C1 EOH A 66 HETATM 775 C2 EOH A 66 HETATM 777 O EOH A 66 Number of atoms in dataset: 637 Number of atoms in GEO_REF: 640 Number of atoms common to both systems: 603 -------------------------------------------------------------------------------- List of atoms in GEO_REF that are swapped in order to maximize overlap Atom Label and Atom Label Difference to GEO_REF 1 (ATOM 757 HB3 ALA A 45) (ATOM 755 HB1 ALA A 45) -2.03 2 (ATOM 662 HB3 ALA A 38) (ATOM 660 HB1 ALA A 38) -2.08 3 (ATOM 630 HD12 ILE A 35) (ATOM 629 HD11 ILE A 35) -2.26 4 (ATOM 628 HG23 ILE A 35) (ATOM 627 HG22 ILE A 35) -2.19 5 (ATOM 609 HD12 ILE A 34) (ATOM 607 HD11 ILE A 34) -2.26 6 (ATOM 606 HG23 ILE A 34) (ATOM 605 HG22 ILE A 34) -0.45 7 (ATOM 606 HG23 ILE A 34) (ATOM 604 HG21 ILE A 34) -2.04 8 (ATOM 589 HD13 ILE A 33) (ATOM 587 HD11 ILE A 33) -2.03 9 (ATOM 586 HG23 ILE A 33) (ATOM 584 HG21 ILE A 33) -1.99 10 (ATOM 553 HG23 THR A 30) (ATOM 551 HG21 THR A 30) -2.16 11 (ATOM 504 HG22 THR A 28) (ATOM 503 HG21 THR A 28) -2.22 12 (ATOM 491 HB3 ALA A 27) (ATOM 490 HB2 ALA A 27) -2.22 13 (ATOM 414 HB3 ALA A 24) (ATOM 413 HB2 ALA A 24) -2.23 14 (ATOM 350 HG22 THR A 21) (ATOM 349 HG21 THR A 21) -2.11 15 (ATOM 315 HD22 LEU A 18) (ATOM 314 HD21 LEU A 18) -2.23 16 (ATOM 313 HD13 LEU A 18) (ATOM 312 HD12 LEU A 18) -2.21 17 (ATOM 263 HG23 VAL A 15) (ATOM 262 HG22 VAL A 15) -2.16 18 (ATOM 260 HG13 VAL A 15) (ATOM 258 HG11 VAL A 15) -1.99 19 (ATOM 230 HE2 PHE A 13) (ATOM 228 HE1 PHE A 13) -5.64 20 (ATOM 226 HD2 PHE A 13) (ATOM 224 HD1 PHE A 13) -5.68 21 (ATOM 214 CE2 PHE A 13) (ATOM 212 CE1 PHE A 13) -3.35 22 (ATOM 210 CD2 PHE A 13) (ATOM 208 CD1 PHE A 13) -3.35 23 (ATOM 174 HH22 ARG A 10) (ATOM 173 HH21 ARG A 10) -2.16 24 (ATOM 144 HB3 ALA A 9) (ATOM 142 HB1 ALA A 9) -2.16 25 (ATOM 133 HG23 VAL A 8) (ATOM 131 HG22 VAL A 8) -1.59 26 (ATOM 127 HG13 VAL A 8) (ATOM 123 HG11 VAL A 8) -2.09 27 (ATOM 107 HD13 ILE A 7) (ATOM 103 HD11 ILE A 7) -0.63 28 (ATOM 105 HD12 ILE A 7) (ATOM 103 HD11 ILE A 7) -0.03 29 (ATOM 102 HG23 ILE A 7) (ATOM 100 HG21 ILE A 7) -1.31 30 (ATOM 101 HG22 ILE A 7) (ATOM 100 HG21 ILE A 7) -1.41 31 (ATOM 98 HG13 ILE A 7) (ATOM 96 HG12 ILE A 7) -0.42 32 (ATOM 38 HG23 THR A 2) (ATOM 36 HG21 THR A 2) -2.17 33 (ATOM 20 HG22 THR A 1) (ATOM 19 HG21 THR A 1) -1.94 34 (ATOM 15 H3 THR A 1) (ATOM 13 H1 THR A 1) -1.87 After docking Atoms that move a lot Atom No. Atom Label GEO_REF Coordinates Movement Integral 603 (ATOM 772 HD22 ASN A 46) 11.363 5.321 15.626 3.98 3.98 93 (ATOM 105 HD12 ILE A 7) 10.621 -0.936 15.493 3.47 7.44 602 (ATOM 771 HD21 ASN A 46) 12.099 4.327 16.606 2.46 9.90 88 (ATOM 98 HG13 ILE A 7) 11.212 0.916 13.450 2.42 12.32 596 (ATOM 765 ND2 ASN A 46) 11.960 4.596 15.706 2.31 14.63 595 (ATOM 764 OD1 ASN A 46) 13.482 3.211 14.877 2.17 16.80 94 (ATOM 107 HD13 ILE A 7) 11.718 -1.089 14.277 1.69 18.50 92 (ATOM 103 HD11 ILE A 7) 12.032 -0.153 15.597 1.69 20.19 83 (ATOM 91 CD1 ILE A 7) 11.324 -0.462 14.963 1.67 21.86 27 (ATOM 35 HG1 THR A 2) 13.284 9.378 3.932 1.50 23.36 578 (ATOM 747 HH TYR A 44) 8.427 15.027 15.903 1.40 24.77 90 (ATOM 101 HG22 ILE A 7) 8.905 -1.253 13.418 0.95 25.71 553 (ATOM 721 OD2 ASP A 43) 12.320 14.890 19.218 0.94 26.66 512 (ATOM 671 CG2 THR A 39) 23.254 12.863 12.772 0.80 27.46 108 (ATOM 129 HG21 VAL A 8) 4.462 0.320 13.893 0.68 28.13 551 (ATOM 717 CG ASP A 43) 13.156 14.000 18.875 0.67 28.80 552 (ATOM 719 OD1 ASP A 43) 14.124 14.166 18.138 0.63 29.43 397 (ATOM 550 HG1 THR A 30) 5.173 9.963 6.960 0.62 30.06 511 (ATOM 669 OG1 THR A 39) 24.203 13.547 10.719 0.61 30.66 81 (ATOM 89 CG1 ILE A 7) 10.691 0.727 14.293 0.58 31.25 556 (ATOM 725 HB2 ASP A 43) 11.866 12.526 19.488 0.57 31.82 87 (ATOM 96 HG12 ILE A 7) 10.818 1.518 14.891 0.56 32.38 110 (ATOM 133 HG23 VAL A 8) 3.330 0.999 14.756 0.54 32.92 91 (ATOM 102 HG23 ILE A 7) 9.605 -0.439 12.187 0.54 33.46 169 (ATOM 199 HD22 ASN A 12) 1.634 5.006 9.979 0.52 33.98 550 (ATOM 715 CB ASP A 43) 12.848 12.639 19.429 0.48 34.46 557 (ATOM 726 HB3 ASP A 43) 13.130 12.639 20.381 0.47 34.93 168 (ATOM 198 HD21 ASN A 12) 0.923 3.620 10.286 0.47 35.40 86 (ATOM 95 HB ILE A 7) 8.648 0.641 14.635 0.47 35.86 89 (ATOM 100 HG21 ILE A 7) 8.018 -0.270 12.486 0.46 36.33 Difference between GEO_DAT and GEO_REF: 98.24 = total, 0.1629 = Average, 0.3654 = RMS, in Angstroms Differences between bond-lengths for the two geometries Diff. Atom 1 Atom 2 Bond length Bond length in GEO_DAT in GEO_REF 1 0.269 C(ATOM 695 CG PRO A 41) H(ATOM 700 HG2 PRO A 41) 1.099 0.831 2 0.260 C(ATOM 64 CG PRO A 5) H(ATOM 69 HG2 PRO A 5) 1.099 0.839 3 0.260 C(ATOM 322 CG PRO A 19) H(ATOM 327 HG2 PRO A 19) 1.099 0.839 4 0.257 C(ATOM 637 CG PRO A 36) H(ATOM 642 HG2 PRO A 36) 1.099 0.842 5 0.217 C(ATOM 694 CB PRO A 41) H(ATOM 698 HB2 PRO A 41) 1.099 0.882 6 0.207 C(ATOM 63 CB PRO A 5) H(ATOM 67 HB2 PRO A 5) 1.099 0.892 7 0.200 C(ATOM 321 CB PRO A 19) H(ATOM 325 HB2 PRO A 19) 1.099 0.899 8 0.186 C(ATOM 636 CB PRO A 36) H(ATOM 640 HB2 PRO A 36) 1.099 0.913 9 0.174 C(ATOM 214 CE2 PHE A 13) H(ATOM 230 HE2 PHE A 13) 1.098 0.924 10 0.161 C(ATOM 208 CD1 PHE A 13) H(ATOM 224 HD1 PHE A 13) 1.099 0.938 11 0.156 C(ATOM 212 CE1 PHE A 13) H(ATOM 228 HE1 PHE A 13) 1.099 0.944 12 0.153 C(ATOM 152 CD ARG A 10) H(ATOM 169 HD3 ARG A 10) 1.099 0.946 13 0.145 C(ATOM 280 CD ARG A 17) H(ATOM 292 HD3 ARG A 17) 1.099 0.954 14 0.144 C(ATOM 40 CA CYS A 3) H(ATOM 46 HA CYS A 3) 1.099 0.954 15 0.144 C(ATOM 63 CB PRO A 5) H(ATOM 68 HB3 PRO A 5) 1.098 0.954 16 0.144 C(ATOM 279 CG ARG A 17) H(ATOM 290 HG3 ARG A 17) 1.099 0.955 17 0.143 C(ATOM 694 CB PRO A 41) H(ATOM 699 HB3 PRO A 41) 1.099 0.957 18 0.140 C(ATOM 201 CA PHE A 13) H(ATOM 219 HA PHE A 13) 1.099 0.959 19 0.140 C(ATOM 115 CG1 VAL A 8) H(ATOM 123 HG11 VAL A 8) 1.106 0.966 20 0.140 C(ATOM 321 CB PRO A 19) H(ATOM 326 HB3 PRO A 19) 1.099 0.960 21 0.138 C(ATOM 150 CG ARG A 10) H(ATOM 167 HG3 ARG A 10) 1.099 0.960 22 0.137 C(ATOM 647 CA GLY A 37) H(ATOM 651 HA2 GLY A 37) 1.114 0.977 23 0.136 N(ATOM 386 N GLU A 23) H(ATOM 399 H GLU A 23) 1.029 0.894 24 0.135 C(ATOM 115 CG1 VAL A 8) H(ATOM 125 HG12 VAL A 8) 1.111 0.975 25 0.135 C(ATOM 664 CA THR A 39) H(ATOM 674 HA THR A 39) 1.099 0.964 GEO_DAT: 'PDB1EJG.ent' GEO_REF: 'PDB1CBN.ent' Analysis of Non-Covalent Interactions Total non-covalent energy of GEO_DAT system: -546.43 Kcal/mol Total non-covalent energy of GEO_REF system: -551.77 Kcal/mol Difference: 5.33 Kcal/mol Number of hydrogen bonds common to both systems: 57 Hydrogen bonds in GEO_REF but not in GEO_DAT Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "ATOM 73 N SER A 6" "ATOM 772 HD22 ASN A 46" 2.918 -1.606 -1.606 2 "ATOM 62 O PRO A 5" "ATOM 772 HD22 ASN A 46" 2.990 -0.840 -2.446 The following files will be written to "G:\path\": 'Compare 1EJG and 1CBN.html' 'PDB1EJG.pdb' 'PDB1CBN.pdb' GEO_REF with 0SCF: Job complete ****************************************************************************** * * * Error and normal termination messages reported in this calculation * * * * GEO_REF with 0SCF: Job complete * * JOB ENDED NORMALLY * * * ****************************************************************************** TOTAL JOB TIME: 0.00 SECONDS == MOPAC DONE ==