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** Site#: 10005 For non-commercial use only Version 17.019W 64BITS **
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** Cite this program as: MOPAC2016, Version: 17.019W, James J. P. Stewart, **
** Stewart Computational Chemistry, web: HTTP://OpenMOPAC.net. Days left: 365**
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** **
** MOPAC2016 **
** **
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PM7 CALCULATION RESULTS
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* CALCULATION DONE: Thu Jan 19 10:26:12 2017 *
* GEO-OK - OVERRIDE INTERATOMIC DISTANCE AND OTHER SAFETY CHECKS
* GEO_DAT - DATA SET GEOMETRY IS IN FILE "TRANSITION STATE 1-2.ARC"
* GEO_REF - REFERENCE GEOMETRY IS IN FILE "TRANSITION STATE 2-3.ARC"
* OPT - OPTIMIZE COORDINATES OF ALL ATOMS
* LET - OVERRIDE SOME SAFETY CHECKS
* 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
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output opt geo_dat="Transition state 1-2.arc" geo_ref="Transition state 2-3.arc" 0scf HTML GEO-OK output let
Compare Transition states 1-2 and 2-3
Note that the Imidazolium ring on His 57 rotates in going from TS 1-2 to TS 2-3
After docking
Atoms that move a lot
Atom No. Atom Label GEO_REF Coordinates Movement Integral
4584 (HETATM 4588 O HOH C 647) 32.281 -0.661 34.519 3.08 3.08
4585 (HETATM 4589 1H HOH C 647) 31.471 -0.714 35.060 2.93 6.01
4586 (HETATM 4590 2H HOH C 647) 32.745 -1.491 34.673 2.82 8.82
3510 (ATOM 3513 O THR C 253) 29.893 -0.909 35.710 2.60 11.42
3522 (ATOM 3525 1H LEU C 254) 28.724 -2.366 33.149 1.98 13.40
2742 (ATOM 770 HG SER G 195) 28.716 1.778 34.495 1.00 14.40
3509 (ATOM 3512 C THR C 253) 29.035 -1.217 34.873 0.96 15.36
3514 (ATOM 3520 H THR C 253) 28.778 0.840 35.991 0.89 16.25
3521 (ATOM 3524 N LEU C 254) 29.326 -2.152 33.941 0.80 17.05
2711 (ATOM 2712 2HE MET G 192) 27.280 -1.354 39.626 0.74 17.79
2710 (ATOM 2711 1HE MET G 192) 28.853 -1.847 39.004 0.64 18.43
3507 (ATOM 3510 N THR C 253) 27.979 0.877 35.309 0.63 19.05
2703 (ATOM 2706 CE MET G 192) 27.865 -2.226 39.319 0.62 19.67
3515 (ATOM 3521 HA THR C 253) 27.132 -0.974 35.869 0.62 20.29
3508 (ATOM 3511 CA THR C 253) 27.659 -0.532 34.971 0.58 20.88
2712 (ATOM 2713 3HE MET G 192) 28.020 -2.871 40.192 0.57 21.45
2702 (ATOM 2705 SD MET G 192) 27.137 -3.117 37.915 0.55 21.99
768 (ATOM 769 HE1 HIS F 57) 28.652 4.632 34.597 0.53 22.52
2708 (ATOM 2709 1HG MET G 192) 25.375 -4.346 39.069 0.50 23.02
3520 (ATOM 3519 3HG2 THR C 253) 25.628 -2.301 34.879 0.49 23.51
3523 (ATOM 3526 2H LEU C 254) 30.257 -2.545 33.901 0.47 23.99
3485 (ATOM 3488 C TRP C 252) 26.875 1.748 35.986 0.47 24.45
4166 (HETATM 4173 2H HOH F 615) 25.973 -4.939 32.369 0.46 24.92
2737 (ATOM 2740 OG SER G 195) 27.068 2.999 35.342 0.45 25.36
3482 (ATOM 3483 3HB ALA C 251) 31.434 2.510 36.120 0.44 25.81
2701 (ATOM 2704 CG MET G 192) 25.400 -3.458 38.404 0.44 26.25
4164 (HETATM 4171 O HOH F 615) 26.883 -5.231 32.374 0.44 26.69
766 (ATOM 767 HD1 HIS F 57) 30.883 5.725 33.765 0.44 27.12
2709 (ATOM 2710 2HG MET G 192) 24.883 -3.774 37.472 0.43 27.56
767 (ATOM 768 HD2 HIS F 57) 31.328 1.481 33.595 0.43 27.99
Difference between GEO_DAT and GEO_REF: 173.684 = total, 0.0379 = Average, 0.1139 = 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 0.123 N(ATOM 3510 N THR C 253) C(ATOM 3488 C TRP C 252) 1.437 1.560
2 0.041 N(ATOM 3510 N THR C 253) H(ATOM 3520 H THR C 253) 1.010 1.051
3 0.025 O(ATOM 3489 O TRP C 252) C(ATOM 3488 C TRP C 252) 1.259 1.284
4 0.025 N(ATOM 3510 N THR C 253) C(ATOM 3511 CA THR C 253) 1.459 1.484
5 0.021 N(ATOM 3524 N LEU C 254) C(ATOM 3512 C THR C 253) 1.373 1.352
6 0.019 O(ATOM 3513 O THR C 253) C(ATOM 3512 C THR C 253) 1.219 1.238
7 0.014 N(ATOM 759 ND1 HIS F 57) H(ATOM 767 HD1 HIS F 57) 1.057 1.042
8 0.013 O(ATOM 3515 OG1 THR C 253) H(ATOM 3523 HG1 THR C 253) 0.988 1.002
9 0.013 N(ATOM 3524 N LEU C 254) H(ATOM 3525 1H LEU C 254) 1.005 1.018
10 0.011 O(ATOM 3515 OG1 THR C 253) C(ATOM 3514 CB THR C 253) 1.404 1.393
11 0.011 O(HETATM 3976 O HOH F 473) H(HETATM 3978 2H HOH F 473) 0.975 0.965
12 0.011 O(HETATM 4186 O HOH F 625) H(HETATM 4188 2H HOH F 625) 0.967 0.978
13 0.010 N(ATOM 761 NE2 HIS F 57) C(ATOM 760 CD2 HIS F 57) 1.397 1.387
GEO_DAT: 'Transition state 1-2.arc'
GEO_REF: 'Transition state 2-3.arc'
Heat of formation of GEO_DAT system: -47881.845 Kcal/mol
Heat of formation of GEO_REF system: -47882.196 Kcal/mol
Diff.: 0.351 Kcal/mol
Analysis of Non-Covalent Interactions
Total non-covalent energy of GEO_DAT system: -9349.61 Kcal/mol
Total non-covalent energy of GEO_REF system: -9349.90 Kcal/mol
Difference: 0.29 Kcal/mol
Number of hydrogen bonds common to both systems: 1621
Hydrogen bonds in GEO_DAT but not in GEO_REF
Donor atom Hydrogen atom H-bond length(A) Energy Sum
1 "ATOM 3479 O ALA C 251" "HETATM 4589 1H HOH C 647" 1.734 -4.017 -4.017
2 "ATOM 2740 OG SER G 195" "ATOM 770 HG SER G 195" 1.219 -3.055 -7.073
3 "ATOM 3524 N LEU C 254" "HETATM 4590 2H HOH C 647" 2.325 -2.140 -9.213
4 "ATOM 761 NE2 HIS F 57" "ATOM 3520 H THR C 253" 2.704 -1.378 -10.591
5 "HETATM 3976 O HOH F 473" "ATOM 3525 1H LEU C 254" 1.961 -1.317 -11.908
Hydrogen bonds in GEO_REF but not in GEO_DAT
Donor atom Hydrogen atom H-bond length(A) Energy Sum
1 "HETATM 4588 O HOH C 647" "HETATM 3977 1H HOH F 473" 1.713 -4.725 -4.725
2 "ATOM 3513 O THR C 253" "HETATM 4589 1H HOH C 647" 1.718 -4.432 -9.157
3 "HETATM 4186 O HOH F 625" "ATOM 3525 1H LEU C 254" 1.817 -2.718 -11.875
The following files will be written to "M:\OpenMOPAC_NET\Manual\Chymotrypsin_J_Mol_Mod_(2017)_files\MOPAC_files\":
'Compare TS 1-2 and TS 2-3.html'
'Transition state 1-2.pdb'
'Transition state 2-3.pdb'
GEO_REF with 0SCF: Job complete
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* *
* Error and normal termination messages reported in this calculation *
* *
* GEO_REF with 0SCF: Job complete *
* JOB ENDED NORMALLY *
* *
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TOTAL JOB TIME: 0.00 SECONDS
== MOPAC DONE ==