******************************************************************************* ** Site#: 28262 E-mail support: MrMOPAC@ATT.net Version 17.279W 64BITS ** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 17.279W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web-site: HTTP://OpenMOPAC.net. ** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Fri Oct 06 10:04:22 2017 * * COMPARE - Compare two geometries * GEO_DAT - DATA SET GEOMETRY IS IN FILE "../STARTING MODEL (NEW)/STEP 5 - MTH1 CHAIN A PLUS 8OG OPTIMIZED WITH BIAS=3, NOW OPTIMIZE 5 ANGSTROMS AROUND 8OG WITHOUT BIAS 1SCF.ARC.TXT" * GEO_REF - REFERENCE GEOMETRY IS IN FILE "../STARTING MODEL (NEW)/STEP 4 - OPTIMIZE MTH1 CHAIN A PLUS 8OG GEOMETRY USING A BIAS OF 3 1SCF.ARC.TXT" * T= - A TIME OF 172800.0 SECONDS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * OUTPUT - MINIMIZE OUTPUT ******************************************************************************* geo_ref="../Starting model (new)/Step 4 - Optimize MTH1 Chain A plus 8OG geometry using a bias of 3 1SCF.arc.txt" geo_dat="../Starting model (new)/Step 5 - MTH1 Chain A plus 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc.txt" compare output Compare the geometries of Step 4 and Step 5, new method After docking Atoms that move a lot Atom Label GEO_REF Coordinates Movement Integral (HETATM 2800 1H HOH A2089) -10.905 -11.734 -19.015 0.92 0.92 (HETATM 2799 O HOH A2089) -11.863 -11.753 -19.031 0.73 1.65 (ATOM 115 3HD1 LEU A 9) -0.697 -12.435 -12.030 0.51 2.15 (ATOM 113 1HD1 LEU A 9) -2.249 -12.227 -11.194 0.37 2.52 (HETATM 2801 2H HOH A2089) -12.107 -11.286 -18.220 0.35 2.87 (ATOM 114 2HD1 LEU A 9) -1.755 -11.109 -12.468 0.34 3.22 (HETATM 2591 2H HOH A2019) -8.002 -10.619 -22.039 0.34 3.56 (ATOM 106 CD1 LEU A 9) -1.392 -11.694 -11.614 0.33 3.88 (HETATM 2606 2H HOH A2024) -1.424 -10.721 -17.893 0.32 4.20 (HETATM 2587 1H HOH A2018) -8.141 -12.477 -21.086 0.31 4.51 (HETATM 2589 O HOH A2019) -7.286 -11.057 -21.549 0.31 4.82 (ATOM 112 HG LEU A 9) -0.616 -11.375 -9.612 0.30 5.12 (ATOM 558 2HA GLY A 37) -7.317 -8.921 -15.425 0.30 5.41 (HETATM 2936 2H HOH A2134) 3.306 -6.025 -18.682 0.29 5.71 (HETATM 2934 O HOH A2134) 2.906 -6.846 -18.972 0.28 5.99 (ATOM 557 1HA GLY A 37) -8.947 -9.399 -14.879 0.27 6.26 (HETATM 2935 1H HOH A2134) 3.362 -7.542 -18.466 0.26 6.53 (HETATM 2590 1H HOH A2019) -7.025 -10.405 -20.864 0.26 6.79 (ATOM 358 2HZ LYS A 23) -6.029 -12.410 -19.805 0.26 7.04 (HETATM 2625 O HOH A2031) -2.858 -13.439 -17.140 0.25 7.29 (HETATM 2520 HP2 8OG A1157) -6.711 -8.576 -19.720 0.24 7.54 (HETATM 2586 O HOH A2018) -8.681 -13.257 -20.899 0.24 7.78 (HETATM 2588 2H HOH A2018) -8.917 -13.212 -19.985 0.24 8.02 (ATOM 515 2HB ASN A 33) 0.192 -15.313 -16.036 0.23 8.25 (ATOM 1242 2HE MET A 81) -2.909 -4.442 -17.748 0.22 8.47 (ATOM 357 1HZ LYS A 23) -4.884 -13.235 -20.703 0.22 8.70 (ATOM 110 1HB LEU A 9) -0.980 -8.875 -9.609 0.22 8.91 (ATOM 359 3HZ LYS A 23) -4.634 -12.985 -19.063 0.22 9.13 (ATOM 516 1HD2 ASN A 33) 0.184 -11.739 -15.365 0.21 9.34 (HETATM 2626 1H HOH A2031) -2.329 -12.659 -17.289 0.20 9.54 Difference between GEO_DAT and GEO_REF: 29.798 = total, 0.0101 = Average, 0.0426 = 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 0.054 N(HETATM 2493 N9 8OG A1157) C(HETATM 2497 C8 8OG A1157) 1.446 1.391 2 0.052 N(HETATM 2496 N7 8OG A1157) C(HETATM 2497 C8 8OG A1157) 1.392 1.444 3 0.041 N(ATOM 976 ND1 HIS A 65) C(ATOM 979 CE1 HIS A 65) 1.388 1.347 4 0.041 N(ATOM 978 NE2 HIS A 65) C(ATOM 979 CE1 HIS A 65) 1.347 1.388 5 0.035 C(ATOM 1904 CZ3 TRP A 123) C(ATOM 1905 CH2 TRP A 123) 1.414 1.379 6 0.035 C(ATOM 1903 CZ2 TRP A 123) C(ATOM 1905 CH2 TRP A 123) 1.380 1.414 7 0.032 C(ATOM 1594 CZ3 TRP A 105) C(ATOM 1595 CH2 TRP A 105) 1.413 1.380 8 0.032 C(ATOM 1593 CZ2 TRP A 105) C(ATOM 1595 CH2 TRP A 105) 1.380 1.413 9 0.032 C(ATOM 492 CZ3 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.413 1.381 10 0.032 C(ATOM 491 CZ2 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.381 1.413 11 0.029 C(ATOM 1807 CZ2 TRP A 117) C(ATOM 1809 CH2 TRP A 117) 1.383 1.412 12 0.029 C(ATOM 1808 CZ3 TRP A 117) C(ATOM 1809 CH2 TRP A 117) 1.411 1.382 13 0.026 N(HETATM 2504 N3 8OG A1157) C(HETATM 2494 C4 8OG A1157) 1.345 1.371 14 0.024 N(HETATM 2504 N3 8OG A1157) C(HETATM 2502 C2 8OG A1157) 1.371 1.347 15 0.012 N(ATOM 2113 ND1 HIS A 134) C(ATOM 2116 CE1 HIS A 134) 1.372 1.360 16 0.012 N(ATOM 2115 NE2 HIS A 134) C(ATOM 2116 CE1 HIS A 134) 1.360 1.372 GEO_DAT: '../Starting model (new)/Step 5 - MTH1 Chain A plus 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc.txt' GEO_REF: '../Starting model (new)/Step 4 - Optimize MTH1 Chain A plus 8OG geometry using a bias of 3 1SCF.arc.txt' Heat of formation of GEO_DAT system: -24500.463 Kcal/mol Heat of formation of GEO_REF system: -24491.919 Kcal/mol Diff.: -8.544 Kcal/mol Analysis of Non-Covalent Interactions Total non-covalent energy of GEO_DAT system: -4189.38 Kcal/mol Total non-covalent energy of GEO_REF system: -4182.50 Kcal/mol Difference: -6.88 Kcal/mol Number of hydrogen bonds common to both systems: 648 The following files will be written to "M:\OpenMOPAC_NET\Manual\Lab_notebook_for_Enzyme_Binding_and_Specificity\Compare New 4 and New 5\": 'Compare New 4 and New 5.html' 'Step 5 - MTH1 Chain A plus 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.pdb' 'Step 4 - Optimize MTH1 Chain A plus 8OG geometry using a bias of 3 1SCF.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 ==