******************************************************************************* ** Site#: 28262 E-mail support: MrMOPAC@ATT.net Version 17.275W 64BITS ** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 17.275W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web-site: HTTP://OpenMOPAC.net. ** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Mon Oct 02 14:37:23 2017 * * COMPARE - Compare two geometries * GEO_DAT - DATA SET GEOMETRY IS IN FILE "../STARTING MODEL (NEW)/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 5 - OLD MTH1 CHAIN A + 8OG OPTIMIZED WITH BIAS=3, NOW OPTIMIZE 5 ANGSTROMS AROUND 8OG WITHOUT BIAS 1SCF.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 5 - Old MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc" geo_dat="../Starting model (new)/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 old and new Step 5 After docking Atoms that move a lot Atom Label GEO_REF Coordinates Movement Integral (ATOM 2936 HE2 GLU A 55) -16.370 -11.602 -13.537 2.45 2.45 (ATOM 2935 HE2 GLU A 52) -11.624 -10.360 -15.045 2.28 4.74 (HETATM 2556 2H HOH A2008) 3.875 -18.520 2.222 2.08 6.81 (HETATM 2777 1H HOH A2082) -13.052 -25.939 -5.489 2.06 8.87 (HETATM 2591 1H HOH A2020) -9.248 -21.185 -23.482 1.95 10.82 (HETATM 2676 2H HOH A2048) -7.558 -8.565 2.941 1.90 12.72 (HETATM 2654 1H HOH A2041) -13.593 3.491 -15.783 1.86 14.57 (HETATM 2735 1H HOH A2068) 0.291 -4.668 1.729 1.83 16.40 (HETATM 2579 1H HOH A2016) -15.739 -14.811 -1.406 1.80 18.21 (HETATM 2828 1H HOH A2099) 8.243 -24.855 -13.854 1.80 20.00 (HETATM 2688 2H HOH A2052) -12.151 -14.700 -3.750 1.78 21.78 (HETATM 2640 2H HOH A2036) -11.849 -7.886 -16.761 1.76 23.54 (HETATM 2525 H4 SO4 A1158) -1.097 -4.067 3.619 1.73 25.27 (HETATM 2690 1H HOH A2053) -12.274 -13.809 -1.553 1.71 26.98 (HETATM 2820 2H HOH A2096) 6.613 -28.196 -8.545 1.67 28.65 (HETATM 2643 2H HOH A2037) -13.400 -7.387 -14.873 1.67 30.31 (HETATM 2628 2H HOH A2032) 4.276 -12.875 2.352 1.66 31.98 (ATOM 1868 HG SER A 121) 13.416 -14.610 -14.171 1.65 33.62 (HETATM 2561 1H HOH A2010) 1.598 -25.567 1.409 1.64 35.27 (HETATM 2558 1H HOH A2009) 6.986 -18.335 0.381 1.64 36.91 (HETATM 2681 1H HOH A2050) 11.092 -18.483 -1.698 1.64 38.54 (HETATM 2696 1H HOH A2055) -14.264 -11.493 -15.144 1.62 40.16 (HETATM 2567 1H HOH A2012) 9.463 -24.627 -1.705 1.60 41.77 (HETATM 2552 1H HOH A2007) -0.921 -19.635 -26.103 1.59 43.36 (HETATM 2858 1H HOH A2109) 13.413 -12.654 2.983 1.59 44.95 (HETATM 2700 2H HOH A2056) -11.533 -9.864 -17.053 1.52 46.47 (HETATM 2706 2H HOH A2058) 18.033 -1.401 -20.311 1.51 47.99 (HETATM 2909 1H HOH A2126) 17.240 0.429 -19.467 1.50 49.48 (HETATM 2907 2H HOH A2125) 13.324 -8.485 -21.403 1.49 50.98 (HETATM 2582 1H HOH A2017) -1.820 -21.043 -24.220 1.47 52.44 Difference between GEO_DAT and GEO_REF: 217.138 = total, 0.0740 = Average, 0.2400 = 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 0.144 O(ATOM 836 OE2 GLU A 55) C(ATOM 834 CD GLU A 55) 1.223 1.367 2 0.121 O(ATOM 835 OE1 GLU A 55) C(ATOM 834 CD GLU A 55) 1.324 1.204 3 0.113 O(ATOM 785 OE2 GLU A 52) C(ATOM 783 CD GLU A 52) 1.227 1.340 4 0.106 O(ATOM 784 OE1 GLU A 52) C(ATOM 783 CD GLU A 52) 1.319 1.213 5 0.054 N(HETATM 2491 N9 8OG A1157) C(HETATM 2495 C8 8OG A1157) 1.445 1.391 6 0.053 N(HETATM 2494 N7 8OG A1157) C(HETATM 2495 C8 8OG A1157) 1.392 1.445 7 0.052 O(ATOM 1493 OD2 ASP A 99) H(ATOM 1498 HD2 ASP A 99) 1.010 1.062 8 0.042 N(ATOM 974 ND1 HIS A 65) C(ATOM 977 CE1 HIS A 65) 1.388 1.346 9 0.042 N(ATOM 976 NE2 HIS A 65) C(ATOM 977 CE1 HIS A 65) 1.347 1.388 10 0.034 O(ATOM 784 OE1 GLU A 52) H(ATOM 2935 HE2 GLU A 52) 1.057 1.023 11 0.034 C(ATOM 1902 CZ3 TRP A 123) C(ATOM 1903 CH2 TRP A 123) 1.414 1.380 12 0.034 C(ATOM 1901 CZ2 TRP A 123) C(ATOM 1903 CH2 TRP A 123) 1.379 1.414 13 0.033 O(ATOM 835 OE1 GLU A 55) H(ATOM 2936 HE2 GLU A 55) 1.033 1.000 14 0.032 C(ATOM 491 CZ2 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.381 1.413 15 0.032 C(ATOM 492 CZ3 TRP A 32) C(ATOM 493 CH2 TRP A 32) 1.413 1.381 16 0.032 C(ATOM 1591 CZ2 TRP A 105) C(ATOM 1593 CH2 TRP A 105) 1.381 1.412 17 0.032 C(ATOM 1592 CZ3 TRP A 105) C(ATOM 1593 CH2 TRP A 105) 1.413 1.381 18 0.030 O(HETATM 2635 O HOH A2035) H(HETATM 2636 1H HOH A2035) 1.038 1.007 19 0.030 O(ATOM 1507 OE2 GLU A 100) H(ATOM 1514 HE2 GLU A 100) 1.073 1.042 20 0.029 C(ATOM 1806 CZ3 TRP A 117) C(ATOM 1807 CH2 TRP A 117) 1.411 1.382 21 0.029 C(ATOM 1805 CZ2 TRP A 117) C(ATOM 1807 CH2 TRP A 117) 1.382 1.411 22 0.029 O(HETATM 2701 O HOH A2057) H(HETATM 2702 1H HOH A2057) 0.985 0.956 23 0.027 N(HETATM 2502 N3 8OG A1157) C(HETATM 2492 C4 8OG A1157) 1.345 1.372 24 0.027 O(HETATM 2854 O HOH A2108) H(HETATM 2856 2H HOH A2108) 0.956 0.983 25 0.026 N(HETATM 2502 N3 8OG A1157) C(HETATM 2500 C2 8OG A1157) 1.371 1.345 GEO_DAT: '../Starting model (new)/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 5 - Old MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 1SCF.arc' Heat of formation of GEO_DAT system: -24492.049 Kcal/mol Heat of formation of GEO_REF system: -24446.180 Kcal/mol Diff.: -45.869 Kcal/mol Analysis of Non-Covalent Interactions Total non-covalent energy of GEO_DAT system: -4186.62 Kcal/mol Total non-covalent energy of GEO_REF system: -4176.47 Kcal/mol Difference: -10.15 Kcal/mol Number of hydrogen bonds common to both systems: 576 Hydrogen bonds in GEO_DAT but not in GEO_REF Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "HETATM 2701 O HOH A2057" "ATOM 2935 HE2 GLU A 52" 1.515 -5.050 -5.050 2 "HETATM 2704 O HOH A2058" "HETATM 2909 1H HOH A2126" 1.715 -4.864 -9.915 3 "HETATM 2791 O HOH A2087" "HETATM 2789 1H HOH A2086" 1.709 -4.839 -14.754 4 "HETATM 2842 O HOH A2104" "ATOM 1868 HG SER A 121" 1.663 -4.816 -19.570 5 "ATOM 785 OE2 GLU A 52" "HETATM 2700 2H HOH A2056" 1.644 -4.800 -24.370 6 "HETATM 2695 O HOH A2055" "ATOM 2936 HE2 GLU A 55" 1.644 -4.800 -29.170 7 "HETATM 2569 O HOH A2013" "HETATM 2546 1H HOH A2005" 1.704 -4.769 -33.939 8 "HETATM 2665 O HOH A2045" "HETATM 2906 1H HOH A2125" 1.714 -4.737 -38.675 9 "HETATM 2560 O HOH A2010" "HETATM 2564 1H HOH A2011" 1.713 -4.720 -43.395 10 "HETATM 2686 O HOH A2052" "HETATM 2690 1H HOH A2053" 1.724 -4.719 -48.114 11 "HETATM 2698 O HOH A2056" "HETATM 2640 2H HOH A2036" 1.724 -4.658 -52.772 12 "HETATM 2833 O HOH A2101" "HETATM 2843 1H HOH A2104" 1.724 -4.538 -57.309 13 "ATOM 1726 O PHE A 113" "HETATM 2834 1H HOH A2101" 1.741 -4.450 -61.759 14 "HETATM 2557 O HOH A2009" "HETATM 2855 1H HOH A2108" 1.752 -4.289 -66.048 15 "HETATM 2521 O4 SO4 A1158" "HETATM 2735 1H HOH A2068" 1.812 -3.500 -69.548 16 "ATOM 392 NH2 ARG A 25" "HETATM 2591 1H HOH A2020" 1.915 -2.367 -71.915 17 "ATOM 880 O LEU A 59" "HETATM 2688 2H HOH A2052" 1.992 -1.897 -73.812 18 "HETATM 2818 O HOH A2096" "HETATM 2817 2H HOH A2095" 2.128 -1.774 -75.586 19 "ATOM 449 N GLY A 30" "HETATM 2553 2H HOH A2007" 2.534 -1.724 -77.310 20 "ATOM 2257 O ASP A 143" "HETATM 2907 2H HOH A2125" 2.225 -1.572 -78.882 21 "ATOM 209 O PRO A 15" "HETATM 2558 1H HOH A2009" 2.330 -1.261 -80.144 Hydrogen bonds in GEO_REF but not in GEO_DAT Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "HETATM 2908 O HOH A2126" "HETATM 2706 2H HOH A2058" 1.705 -4.869 -4.869 2 "ATOM 988 O LYS A 66" "HETATM 2735 1H HOH A2068" 1.715 -4.856 -9.725 3 "ATOM 835 OE1 GLU A 55" "HETATM 2696 1H HOH A2055" 1.718 -4.825 -14.551 4 "HETATM 2638 O HOH A2036" "HETATM 2700 2H HOH A2056" 1.695 -4.761 -19.312 5 "HETATM 2788 O HOH A2086" "HETATM 2792 1H HOH A2087" 1.709 -4.710 -24.023 6 "HETATM 2563 O HOH A2011" "HETATM 2561 1H HOH A2010" 1.735 -4.603 -28.625 7 "HETATM 2761 O HOH A2077" "HETATM 2765 1H HOH A2078" 1.728 -4.538 -33.164 8 "HETATM 2734 O HOH A2068" "HETATM 2525 H4 SO4 A1158" 1.667 -4.514 -37.677 9 "HETATM 2698 O HOH A2056" "ATOM 2935 HE2 GLU A 52" 1.670 -4.476 -42.153 10 "HETATM 2641 O HOH A2037" "HETATM 2640 2H HOH A2036" 1.720 -4.471 -46.624 11 "HETATM 2689 O HOH A2053" "HETATM 2688 2H HOH A2052" 1.759 -4.393 -51.017 12 "HETATM 2569 O HOH A2013" "HETATM 2547 2H HOH A2005" 1.737 -4.157 -55.175 13 "HETATM 2842 O HOH A2104" "HETATM 2834 1H HOH A2101" 1.762 -4.041 -59.216 14 "HETATM 2791 O HOH A2087" "ATOM 1498 HD2 ASP A 99" 1.525 -3.978 -63.194 15 "ATOM 784 OE1 GLU A 52" "HETATM 2703 2H HOH A2057" 1.767 -3.974 -67.168 16 "HETATM 2854 O HOH A2108" "HETATM 2558 1H HOH A2009" 1.787 -3.721 -70.888 17 "HETATM 2551 O HOH A2007" "HETATM 2582 1H HOH A2017" 1.777 -3.643 -74.531 18 "ATOM 1863 OG SER A 121" "HETATM 2843 1H HOH A2104" 1.780 -3.262 -77.793 19 "HETATM 2665 O HOH A2045" "HETATM 2907 2H HOH A2125" 1.805 -3.046 -80.839 20 "HETATM 2815 O HOH A2095" "HETATM 2820 2H HOH A2096" 2.100 -1.460 -82.299 21 "HETATM 2857 O HOH A2109" "HETATM 2852 1H HOH A2107" 2.489 -1.405 -83.703 22 "ATOM 2426 O VAL A 153" "HETATM 2877 2H HOH A2115" 1.992 -1.343 -85.046 23 "ATOM 1167 OE1 GLU A 77" "HETATM 2762 1H HOH A2077" 2.428 -1.326 -86.372 24 "ATOM 1583 O TRP A 105" "HETATM 2817 2H HOH A2095" 2.118 -1.312 -87.684 25 "ATOM 736 NE ARG A 50" "HETATM 2690 1H HOH A2053" 2.506 -1.236 -88.920 26 "ATOM 459 O ARG A 31" "HETATM 2609 1H HOH A2026" 2.129 -1.213 -90.133 27 "HETATM 2557 O HOH A2009" "HETATM 2556 2H HOH A2008" 2.743 -1.136 -91.269 28 "ATOM 1937 O PRO A 125" "HETATM 2868 2H HOH A2112" 2.985 -0.971 -92.240 The following files will be written to "M:\OpenMOPAC_NET\Manual\Lab_notebook_for_Enzyme_Binding_and_Specificity\Compare New 5 and Old 5\": 'Compare New 5 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 5 - Old MTH1 Chain A + 8OG Optimized with Bias=3, now optimize 5 Angstroms around 8OG without bias 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 ==