******************************************************************************* ** Site#: 28262 E-mail support: MrMOPAC@ATT.net Version 17.273W 64BITS ** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 17.273W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web-site: HTTP://OpenMOPAC.net. ** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Mon Oct 02 08:41:04 2017 * * COMPARE - Compare two geometries * GEO_DAT - DATA SET GEOMETRY IS IN FILE "../STARTING MODEL (OLD)/STEP 5 - MTH1 CHAIN A + 8OG OPTIMIZED WITH BIAS=3, NOW OPTIMIZE 5 ANGSTROMS AROUND 8OG WITHOUT BIAS 1SCF.ARC" * GEO_REF - REFERENCE GEOMETRY IS IN FILE "../STARTING MODEL (OLD)/STEP 4 - OPTIMIZE MTH1 CHAIN A + 8OG GEOMETRY USING A BIAS OF 3.ARC" * T= - A TIME OF 172800.0 SECONDS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * OUTPUT - MINIMIZE OUTPUT ******************************************************************************* geo_ref="../Starting model (old)/Step 4 - Optimize MTH1 Chain A + 8OG geometry using a bias of 3.arc" geo_dat="../Starting model (old)/Step 5 - MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc" compare output Compare the geometries of Step 4 and Step 5, old method After docking Atoms that move a lot Atom Label GEO_REF Coordinates Movement Integral (HETATM 2642 2H HOH A2036) -10.875 -7.912 -16.704 0.97 0.97 (HETATM 2641 1H HOH A2036) -9.716 -8.525 -17.597 0.92 1.90 (HETATM 2640 O HOH A2036) -10.667 -8.479 -17.448 0.84 2.74 (ATOM 1242 2HE MET A 81) -2.901 -4.443 -17.745 0.65 3.39 (ATOM 115 3HD1 LEU A 9) -0.699 -12.436 -12.031 0.56 3.95 (ATOM 113 1HD1 LEU A 9) -2.250 -12.226 -11.192 0.51 4.45 (ATOM 558 2HA GLY A 37) -7.332 -8.929 -15.423 0.50 4.96 (ATOM 1819 HH2 TRP A 117) 1.834 -8.430 -22.590 0.45 5.41 (ATOM 112 HG LEU A 9) -0.612 -11.377 -9.613 0.45 5.86 (ATOM 358 2HZ LYS A 23) -6.019 -12.406 -19.786 0.44 6.30 (ATOM 557 1HA GLY A 37) -8.945 -9.367 -14.770 0.44 6.74 (ATOM 357 1HZ LYS A 23) -4.872 -13.227 -20.685 0.44 7.17 (HETATM 2588 2H HOH A2018) -9.006 -13.085 -20.116 0.43 7.61 (ATOM 117 2HD2 LEU A 9) 1.343 -11.319 -11.150 0.43 8.04 (ATOM 106 CD1 LEU A 9) -1.393 -11.694 -11.613 0.41 8.45 (ATOM 1817 HZ2 TRP A 117) 0.437 -10.004 -21.270 0.40 8.85 (ATOM 359 3HZ LYS A 23) -4.628 -12.988 -19.043 0.40 9.26 (ATOM 1243 3HE MET A 81) -3.546 -4.537 -19.398 0.40 9.66 (ATOM 114 2HD1 LEU A 9) -1.756 -11.107 -12.467 0.40 10.06 (HETATM 2591 2H HOH A2019) -7.983 -10.565 -22.043 0.40 10.46 (ATOM 1818 HZ3 TRP A 117) 4.215 -8.087 -22.054 0.40 10.86 (HETATM 2589 O HOH A2019) -7.267 -11.019 -21.570 0.38 11.24 (ATOM 116 1HD2 LEU A 9) 1.203 -9.745 -10.352 0.38 11.61 (HETATM 2605 1H HOH A2024) -1.397 -10.732 -17.923 0.38 11.99 (ATOM 1809 CH2 TRP A 117) 2.278 -9.005 -21.778 0.37 12.37 (HETATM 2800 1H HOH A2089) -10.904 -12.187 -18.894 0.36 12.72 (HETATM 2587 1H HOH A2018) -8.101 -12.463 -21.171 0.35 13.07 (ATOM 346 NZ LYS A 23) -5.344 -13.192 -19.769 0.34 13.42 (ATOM 1807 CZ2 TRP A 117) 1.493 -9.884 -21.056 0.34 13.76 (ATOM 1808 CZ3 TRP A 117) 3.642 -8.808 -21.472 0.33 14.09 Difference between GEO_DAT and GEO_REF: 41.197 = total, 0.0140 = Average, 0.0604 = 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) 1.445 1.391 2 0.053 N(HETATM 2496 N7 8OG A1157) C(HETATM 2497 C8 8OG A1157) 1.391 1.444 3 0.043 N(ATOM 976 ND1 HIS A 65) C(ATOM 979 CE1 HIS A 65) 1.388 1.346 4 0.043 N(ATOM 978 NE2 HIS A 65) C(ATOM 979 CE1 HIS A 65) 1.346 1.388 5 0.034 C(ATOM 1903 CZ2 TRP A 123) C(ATOM 1905 CH2 TRP A 123) 1.380 1.414 6 0.034 C(ATOM 1904 CZ3 TRP A 123) C(ATOM 1905 CH2 TRP A 123) 1.414 1.379 7 0.032 C(ATOM 492 CZ3 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.413 1.381 8 0.032 C(ATOM 491 CZ2 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.381 1.413 9 0.032 C(ATOM 1593 CZ2 TRP A 105) C(ATOM 1595 CH2 TRP A 105) 1.381 1.412 10 0.032 C(ATOM 1594 CZ3 TRP A 105) C(ATOM 1595 CH2 TRP A 105) 1.412 1.381 11 0.030 C(ATOM 1807 CZ2 TRP A 117) C(ATOM 1809 CH2 TRP A 117) 1.382 1.412 12 0.029 C(ATOM 1808 CZ3 TRP A 117) C(ATOM 1809 CH2 TRP A 117) 1.411 1.382 13 0.027 N(HETATM 2504 N3 8OG A1157) C(HETATM 2494 C4 8OG A1157) 1.345 1.372 14 0.026 N(HETATM 2504 N3 8OG A1157) C(HETATM 2502 C2 8OG A1157) 1.372 1.346 15 0.017 O(HETATM 2640 O HOH A2036) H(HETATM 2642 2H HOH A2036) 0.976 0.958 16 0.016 O(ATOM 785 OE2 GLU A 52) H(ATOM 792 HE2 GLU A 52) 1.023 1.039 17 0.011 N(ATOM 2113 ND1 HIS A 134) C(ATOM 2116 CE1 HIS A 134) 1.372 1.360 18 0.011 N(ATOM 2115 NE2 HIS A 134) C(ATOM 2116 CE1 HIS A 134) 1.360 1.372 GEO_DAT: '../Starting model (old)/Step 5 - MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc' GEO_REF: '../Starting model (old)/Step 4 - Optimize MTH1 Chain A + 8OG geometry using a bias of 3.arc' Heat of formation of GEO_DAT system: -24446.180 Kcal/mol Heat of formation of GEO_REF system: -24432.664 Kcal/mol Diff.: -13.516 Kcal/mol Analysis of Non-Covalent Interactions Total non-covalent energy of GEO_DAT system: -4176.47 Kcal/mol Total non-covalent energy of GEO_REF system: -4164.22 Kcal/mol Difference: -12.25 Kcal/mol Number of hydrogen bonds common to both systems: 646 Hydrogen bonds in GEO_DAT but not in GEO_REF Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "HETATM 2485 OP3 8OG A1157" "ATOM 358 2HZ LYS A 23" 1.797 -1.075 -1.075 The following files will be written to "M:\OpenMOPAC_NET\Manual\Lab_notebook_for_Enzyme_Binding_and_Specificity - Sandbox\Compare Old 4 and Old 5\": 'Compare Old 4 and Old 5.html' 'Step 5 - MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.pdb' 'Step 4 - Optimize MTH1 Chain A + 8OG geometry using a bias of 3.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 ==