******************************************************************************* ** Site#: 9872 For non-commercial use only Version 17.239W 64BITS ** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 17.239W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web: HTTP://OpenMOPAC.net. Days left: 364** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Mon Aug 28 22:51:05 2017 * * PM6 - The PM6 Hamiltonian to be used * COMPARE - Compare two geometries * GEO_DAT - DATA SET GEOMETRY IS IN FILE "EMETAS OPT PM6 1SCF.ARC" * GEO_REF - REFERENCE GEOMETRY IS IN FILE "EMETAS OPT-H 1SCF.ARC" * T= - A TIME OF 172800.0 SECONDS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * OUTPUT - MINIMIZE OUTPUT ******************************************************************************* geo_ref="EMETAS Opt-H 1SCF.arc" geo_dat="EMETAS Opt PM6 1SCF.arc" compare geo-ok output THE SYSTEM IS A SOLID UNIT CELL TRANSLATION VECTORS X Y Z T1 = 0.3382018 0.0210501 31.0559865 T2 = -0.0300460 22.4920750 0.0676887 T3 = 9.7141270 0.0494211 0.0251776 After docking Atoms that move a lot Atom Label GEO_REF Coordinates Movement Integral (HETATM 620 O HOH Y 50) -2.366 4.381 -1.245 1.84 1.84 (HETATM 559 2H HOH Y 29) -1.544 2.231 0.021 1.80 3.65 (HETATM 550 2H HOH Y 26) 1.612 2.189 0.052 1.71 5.35 (HETATM 621 1H HOH Y 50) -2.420 4.639 -2.177 1.69 7.04 (HETATM 657 1H HOH Y 62) 3.202 4.348 0.745 1.55 8.59 (HETATM 684 1H HOH Y 71) -4.157 5.144 -3.810 1.49 10.08 (HETATM 656 O HOH Y 62) 2.366 4.381 1.245 1.46 11.54 (HETATM 647 O HOH Y 59) -2.668 -6.901 1.245 1.46 12.99 (HETATM 622 2H HOH Y 50) -3.307 4.249 -0.983 1.44 14.43 (HETATM 211 1H3 ATP E 5) -3.234 -20.089 2.395 1.41 15.84 (HETATM 120 1H1 ATP C 3) -4.758 1.606 -17.973 1.37 17.21 (HETATM 617 O HOH Y 49) 2.366 -7.533 -16.659 1.33 18.53 (HETATM 121 2H1 ATP C 3) -5.761 2.100 -16.544 1.32 19.86 (HETATM 586 2H HOH Y 38) -3.495 -9.014 -0.132 1.30 21.16 (HETATM 618 1H HOH Y 49) 3.226 -7.509 -16.200 1.29 22.45 (HETATM 296 1H1 ATP G 7) 0.277 -9.676 -17.963 1.27 23.73 (HETATM 638 O HOH Y 56) -5.034 4.220 0.000 1.27 24.99 (HETATM 619 2H HOH Y 49) 2.152 -6.622 -16.880 1.26 26.25 (HETATM 259 2H8 ATP F 6) 0.735 -9.173 -14.286 1.26 27.51 (HETATM 644 O HOH Y 58) 2.668 3.749 -14.169 1.22 28.72 (HETATM 639 1H HOH Y 56) -4.921 3.366 0.473 1.21 29.93 (HETATM 645 1H HOH Y 58) 2.905 4.664 -13.996 1.20 31.13 (HETATM 685 2H HOH Y 71) -3.669 6.613 -3.687 1.17 32.30 (HETATM 258 1H8 ATP F 6) -0.276 -9.675 -12.861 1.16 33.45 (HETATM 646 2H HOH Y 58) 2.996 3.520 -15.027 1.13 34.58 (HETATM 658 2H HOH Y 62) 2.609 4.610 2.153 1.13 35.71 (HETATM 218 1H10 ATP E 5) 0.277 -16.040 2.551 1.12 36.83 (HETATM 297 2H1 ATP G 7) -0.742 -9.171 -16.541 1.11 37.93 (HETATM 683 O HOH Y 71) -3.353 5.705 -3.776 1.09 39.02 (HETATM 661 2H HOH Y 63) -2.969 4.661 -16.601 1.07 40.10 Difference between GEO_DAT and GEO_REF: 335.578 = total, 0.4713 = Average, 0.5451 = 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 0.146 N(HETATM 228 N4 ATP F 6) H(HETATM 32 H6 ATP A 1) 1.127 1.273 2 0.138 N(HETATM 391 N2 BIS R 18) C(HETATM 392 C6 BIS R 18) 1.422 1.283 3 0.137 N(HETATM 528 N2 BIS X 24) C(HETATM 529 C6 BIS X 24) 1.422 1.284 4 0.134 O(HETATM 145 O10 ATP D 4) H(HETATM 163 1H10 ATP D 4) 1.061 1.195 5 0.132 N(HETATM 286 N4 ATP G 7) H(HETATM 308 H4 ATP G 7) 1.155 1.287 6 0.125 N(HETATM 189 N4 ATP E 5) H(HETATM 220 H4 ATP E 5) 1.139 1.264 7 0.117 N(HETATM 363 N1 BIS Q 17) H(HETATM 384 H1 BIS Q 17) 1.086 1.203 8 0.116 N(HETATM 156 N3 ATP D 4) H(HETATM 176 H3 ATP D 4) 1.141 1.257 9 0.115 N(HETATM 456 N2 BIS U 21) H(HETATM 475 H2 BIS U 21) 1.089 1.204 10 0.106 N(HETATM 363 N1 BIS Q 17) C(HETATM 364 C2 BIS Q 17) 1.390 1.283 11 0.104 N(HETATM 26 N4 ATP A 1) H(HETATM 257 H8 ATP F 6) 1.147 1.251 12 0.102 N(HETATM 391 N2 BIS R 18) H(HETATM 340 H6 ATP H 8) 1.096 1.198 13 0.100 N(HETATM 456 N2 BIS U 21) C(HETATM 455 C2 BIS U 21) 1.384 1.284 14 0.096 N(HETATM 528 N2 BIS X 24) H(HETATM 540 2H2 BIS X 24) 1.090 1.186 15 0.094 P(HETATM 142 P3 ATP D 4) O(HETATM 145 O10 ATP D 4) 1.639 1.545 16 0.083 C(HETATM 387 C2 BIS R 18) C(HETATM 388 C3 BIS R 18) 1.433 1.350 17 0.081 C(HETATM 522 C1 BIS X 24) C(HETATM 527 C5 BIS X 24) 1.431 1.350 18 0.078 C(HETATM 436 C5 BIS T 20) C(HETATM 441 C9 BIS T 20) 1.429 1.351 19 0.075 P(HETATM 7 P3 ATP A 1) O(HETATM 6 O3 ATP A 1) 1.718 1.642 20 0.075 P(HETATM 59 P1 ATP B 2) O(HETATM 58 O3 ATP B 2) 1.653 1.578 21 0.073 P(HETATM 134 P1 ATP D 4) O(HETATM 133 O1 ATP D 4) 1.651 1.578 22 0.072 C(HETATM 455 C2 BIS U 21) C(HETATM 463 C8 BIS U 21) 1.434 1.362 23 0.071 C(HETATM 503 C4 BIS W 23) C(HETATM 504 C5 BIS W 23) 1.401 1.330 24 0.071 P(HETATM 202 P3 ATP E 5) O(HETATM 201 O8 ATP E 5) 1.713 1.642 25 0.070 C(HETATM 417 C9 BIS S 19) C(HETATM 418 C10 BIS S 19) 1.399 1.329 GEO_DAT: 'EMETAS Opt PM6 1SCF.arc' GEO_REF: 'EMETAS Opt-H 1SCF.arc' Heat of formation of GEO_DAT system: -9704.938 Kcal/mol Heat of formation of GEO_REF system: -8926.926 Kcal/mol Diff.: -778.013 Kcal/mol Analysis of Non-Covalent Interactions Total non-covalent energy of GEO_DAT system: -767.96 Kcal/mol Total non-covalent energy of GEO_REF system: -712.96 Kcal/mol Difference: -55.00 Kcal/mol Number of hydrogen bonds common to both systems: 107 Hydrogen bonds in GEO_DAT but not in GEO_REF Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "HETATM 67 O9 ATP B 2" "HETATM 79 1H9 ATP B 2" 1.409 -3.345 -3.345 2 "HETATM 641 O HOH Y 57" "HETATM 709 2H HOH Y 79" 1.769 -3.140 -6.486 3 "HETATM 140 O6 ATP D 4" "HETATM 667 2H HOH Y 65" 1.814 -2.694 -9.180 4 "HETATM 560 O HOH Y 30" "HETATM 699 1H HOH Y 76" 1.886 -2.220 -11.400 5 "HETATM 10 O6 ATP A 1" "HETATM 32 H6 ATP A 1" 1.551 -2.151 -13.551 6 "HETATM 118 O12 ATP C 3" "HETATM 571 2H HOH Y 33" 1.705 -2.086 -15.637 7 "HETATM 12 O8 ATP A 1" "HETATM 675 1H HOH Y 68" 1.911 -1.905 -17.542 8 "HETATM 647 O HOH Y 59" "HETATM 700 2H HOH Y 76" 1.766 -1.793 -19.335 9 "HETATM 322 O10 ATP H 8" "HETATM 622 2H HOH Y 50" 1.931 -1.610 -20.945 10 "HETATM 322 O10 ATP H 8" "HETATM 684 1H HOH Y 71" 2.127 -1.562 -22.507 11 "HETATM 240 O5 ATP F 6" "HETATM 672 1H HOH Y 67" 2.162 -1.541 -24.047 12 "HETATM 205 O11 ATP E 5" "HETATM 648 1H HOH Y 59" 2.095 -1.509 -25.556 13 "HETATM 339 O13 ATP H 8" "HETATM 586 2H HOH Y 38" 2.265 -1.426 -26.982 14 "HETATM 10 O6 ATP A 1" "HETATM 253 1H5 ATP F 6" 1.937 -1.040 -28.022 Hydrogen bonds in GEO_REF but not in GEO_DAT Donor atom Hydrogen atom H-bond length(A) Energy Sum 1 "HETATM 228 N4 ATP F 6" "HETATM 32 H6 ATP A 1" 1.273 -3.563 -3.563 2 "HETATM 334 N4 ATP H 8" "HETATM 79 1H9 ATP B 2" 1.232 -3.500 -7.063 3 "HETATM 638 O HOH Y 56" "HETATM 622 2H HOH Y 50" 1.987 -1.833 -8.896 4 "HETATM 683 O HOH Y 71" "HETATM 621 1H HOH Y 50" 2.136 -1.451 -10.346 5 "HETATM 656 O HOH Y 62" "HETATM 550 2H HOH Y 26" 2.607 -1.259 -11.605 6 "HETATM 620 O HOH Y 50" "HETATM 559 2H HOH Y 29" 2.627 -1.192 -12.797 7 "HETATM 647 O HOH Y 59" "HETATM 586 2H HOH Y 38" 2.654 -1.114 -13.911 The following files will be written to "M:\OpenMOPAC_NET\Manual\EMETAS\": 'Compare PM6 and CSD geometries of EMETAS.html' 'EMETAS Opt PM6 1SCF.pdb' 'EMETAS Opt-H 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 ==