******************************************************************************* ** 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: 361** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Thu Aug 31 21:51:47 2017 * * GEO-OK - OVERRIDE INTERATOMIC DISTANCE AND OTHER SAFETY CHECKS * INVERT - REVERSE ALL OPTIMIZATION FLAGS * GEO_DAT - DATA SET GEOMETRY IS IN FILE "../TS/STEP 5-6.ARC" * MOZYME - USE LOCALIZED M.O.s IN SOLVING THE SCF EQUATIONS * * * * CHARGE ON SYSTEM = -1 * * * * EPS= 78.40 - USE ANDREAS KLAMT'S COSMO IMPLICIT SOLVATION MODEL * XYZ - CARTESIAN COORDINATE SYSTEM TO BE USED * FORCETS - VERIFY THAT TRANSITION STATE IS GENUINE * T= - A TIME OF 1.0 WEEKS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * OUTPUT - REDUCE OUTPUT, BUT PRINT: * N - NORMAL COORDINATES) * ISOTOPE - FORCE MATRIX WRITTEN TO DISK (CHAN. 9 ) ******************************************************************************* invert output xyz EPS=78.4 geo-ok GEO_DAT="../TS/Step 5-6.arc" T=1W CHARGE=-1 MOZYME FORCETS output(N) isotope Verify that the Chymotrypsin Step 5-6 transition state is valid General Reference for PM7: "Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximations and Re-optimization of Parameters", J. J. P. Stewart, J. Mol. Mod., 1:32, 19 (2013) http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s00894-012-1667-x Empirical Formula: C1115 H2449 N302 O704 S16 = 4586 atoms Ion Atom No. Label Charge (Distances are between charged sites predicted by Lewis structure theory) 1 N 144 (ATOM 144 N SER E 11) +1 (2.5 Angstroms from anion O 214, Label: ATOM 215 OE2 GLU F 20) 2 N 148 (ATOM 149 N ILE F 16) +1 (2.6 Angstroms from anion O 2727, Label: ATOM 2729 OD2 ASP G 194) 3 C 2141 (ATOM 2143 CZ ARG G 154) +1 (4.4 Angstroms from anion O 229, Label: ATOM 230 OE2 GLU F 21) 1 O 214 (ATOM 215 OE2 GLU F 20) -1 (2.5 Angstroms from cation N 144, Label: ATOM 144 N SER E 11) 2 O 229 (ATOM 230 OE2 GLU F 21) -1 (4.4 Angstroms from cation C 2141, Label: ATOM 2143 CZ ARG G 154) 3 O 1445 (ATOM 1446 OD2 ASP F 102) -1 4 O 2727 (ATOM 2729 OD2 ASP G 194) -1 (2.6 Angstroms from cation N 148, Label: ATOM 149 N ILE F 16) COMPUTED CHARGE ON SYSTEM: -1, THIS AGREES WITH THE CHARGE DEFINED BY KEYWORD "CHARGE" HEAT OF FORMATION = -47879.385845 KCALS/MOLE GRADIENT NORM = 23.74045 TIME FOR SCF CALCULATION = 1737.83 TIME FOR DERIVATIVES = 645.35 FIRST DERIVATIVES WILL BE USED IN THE CALCULATION OF SECOND DERIVATIVES ESTIMATED TIME TO COMPLETE CALCULATION = 100093.55 SECONDS STEP: 1 TIME = 3118.32 SECS, INTEGRAL = 3118.32 TIME LEFT: 599298.50 STEP: 2 TIME = 2084.55 SECS, INTEGRAL = 5202.88 TIME LEFT: 597213.95 STEP: 3 RESTART FILE WRITTEN, INTEGRAL = 11576.00 TIME LEFT: 590840.82 STEP: 4 TIME = 1283.74 SECS, INTEGRAL = 12859.74 TIME LEFT: 589557.08 STEP: 5 RESTART FILE WRITTEN, INTEGRAL = 14835.81 TIME LEFT: 587581.01 STEP: 6 TIME = 1164.00 SECS, INTEGRAL = 15999.81 TIME LEFT: 586417.01 STEP: 7 TIME = 1263.63 SECS, INTEGRAL = 17263.45 TIME LEFT: 585153.38 STEP: 8 TIME = 1810.59 SECS, INTEGRAL = 19074.03 TIME LEFT: 583342.79 STEP: 9 TIME = 2204.50 SECS, INTEGRAL = 21278.53 TIME LEFT: 581138.29 STEP: 10 RESTART FILE WRITTEN, INTEGRAL = 22421.38 TIME LEFT: 579995.45 STEP: 11 TIME = 1524.62 SECS, INTEGRAL = 23946.00 TIME LEFT: 578470.82 STEP: 12 TIME = 1446.27 SECS, INTEGRAL = 25392.27 TIME LEFT: 577024.55 STEP: 13 TIME = 2787.16 SECS, INTEGRAL = 28179.44 TIME LEFT: 574237.38 STEP: 14 TIME = 1439.45 SECS, INTEGRAL = 29618.88 TIME LEFT: 572797.94 STEP: 15 RESTART FILE WRITTEN, INTEGRAL = 30684.23 TIME LEFT: 571732.59 STEP: 16 TIME = 1032.28 SECS, INTEGRAL = 31716.51 TIME LEFT: 570700.31 STEP: 17 TIME = 888.80 SECS, INTEGRAL = 32605.30 TIME LEFT: 569811.52 STEP: 18 TIME = 1038.08 SECS, INTEGRAL = 33643.38 TIME LEFT: 568773.44 STEP: 19 TIME = 1274.01 SECS, INTEGRAL = 34917.39 TIME LEFT: 567499.43 STEP: 20 TIME = 985.48 SECS, INTEGRAL = 35902.87 TIME LEFT: 566513.95 STEP: 21 TIME = 1272.40 SECS, INTEGRAL = 37175.27 TIME LEFT: 565241.55 MOLECULAR WEIGHT =31867.17 ROTATIONAL CONSTANTS IN CM(-1) A = 0.00000350 B = 0.00000292 C = 0.00000256 PRINCIPAL MOMENTS OF INERTIA IN UNITS OF 10**(-40)*GRAM-CM**2 A = 7990779.4233 B = 9599932.8101 C = 10922087.8900 HEAT OF FORMATION = -47879.343354 KCALS/MOLE ZERO POINT ENERGY 22.209 KCAL/MOL NOTE: SYSTEM IS NOT A GROUND STATE, THEREFORE ZERO POINT ENERGY IS NOT MEANINGFULL. ZERO POINT ENERGY PRINTED DOES NOT INCLUDE THE 1 IMAGINARY FREQUENCIES Atoms used in the FORCETS calculation 1 N(ATOM 761 NE2 HIS F 57) 29.34892668 +1 3.21466932 +1 34.40750543 +1 2 O(ATOM 2739 OG SER G 195) 27.05679188 +1 2.85659549 +1 35.43982218 +1 3 C(ATOM 3487 C TRP C 252) 26.39470920 +1 1.74046394 +1 36.59948022 +1 4 N(ATOM 3509 N THR C 253) 28.35324833 +1 -0.27173847 +1 34.24632825 +1 5 O(HETATM 4596 O HOH C 647) 26.92744724 +1 0.57498935 +1 36.15211433 +1 6 H(ATOM 4597 1H HOH C 647) 26.65814282 +1 0.31903377 +1 35.21234060 +1 7 H(ATOM 4598 2H HOH C 647) 28.27170120 +1 2.73530310 +1 35.08247621 +1 NORMAL COORDINATE ANALYSIS (Total motion = 1 Angstrom) Root No. 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 -851.1 99.3 174.2 281.8 313.8 410.5 465.4 512.2 1 -0.0157 0.0005 -0.0000 0.0027 -0.0016 0.1865 -0.0457 -0.0165 2 -0.0006 0.0011 -0.0010 -0.0002 0.0022 0.0960 -0.0169 0.0021 3 0.0209 -0.0001 -0.0041 -0.0089 0.0195 0.4999 -0.0412 -0.0241 4 -0.0234 0.0008 0.0185 0.0483 -0.0771 -0.0689 -0.1699 -0.0455 5 -0.0480 0.0646 -0.0999 -0.0789 0.1519 0.0064 -0.1009 0.3282 6 -0.0017 -0.0111 -0.0074 -0.0410 0.0663 0.0564 0.1800 -0.0041 7 0.0305 -0.0020 -0.0157 -0.0366 0.0307 -0.0030 0.0323 -0.0255 8 0.0670 0.0312 -0.0633 -0.0409 0.1567 -0.0027 0.1018 0.0534 9 -0.0666 0.0065 0.0396 0.1382 -0.0531 -0.0012 -0.1024 0.0175 10 0.0054 0.0115 0.0063 -0.0214 0.0057 -0.0024 -0.0188 -0.0459 11 -0.0012 -0.0043 -0.0000 0.0135 -0.0053 0.0019 0.0125 0.0273 12 -0.0017 -0.0016 0.0018 0.0046 -0.0020 0.0015 -0.0037 -0.0065 13 -0.0010 0.0817 -0.0128 -0.1197 0.1953 -0.0510 -0.1037 -0.2092 14 -0.0091 0.1155 -0.1532 -0.1243 0.2173 -0.0403 -0.0500 -0.0332 15 0.0001 -0.0924 0.2532 0.2444 -0.0538 0.0232 0.0313 0.0608 16 0.0008 0.4276 0.3903 -0.0726 0.0154 -0.0003 0.0011 0.0111 17 0.0036 0.4373 -0.2022 0.2508 0.0322 0.0022 0.0123 -0.0163 18 0.0043 -0.2915 0.2047 0.2029 0.1477 -0.0112 -0.0106 -0.0128 19 0.6749 0.0118 0.0019 0.0476 -0.0983 -0.0140 -0.2452 0.1454 20 0.0642 0.0407 -0.0281 -0.0241 0.0608 0.0769 0.0050 0.2100 21 -0.4256 0.0016 -0.0105 -0.0664 0.1275 0.2695 0.2670 -0.1144 Root No. 9 10 11 12 13 14 15 16 9 10 11 12 13 14 15 16 542.3 641.6 816.0 864.0 912.8 933.5 965.7 1081.2 1 -0.0157 0.0425 -0.0393 -0.0027 -0.0020 0.0044 0.0078 -0.0200 2 -0.0022 -0.0012 0.0052 -0.0015 -0.0062 -0.0057 -0.0128 0.2947 3 -0.0135 0.0080 0.0086 0.0008 0.0007 0.0005 -0.0056 -0.0576 4 -0.0553 0.1847 -0.1844 -0.0142 0.0278 0.0214 0.1938 0.0362 5 0.0736 -0.0758 -0.1010 -0.0074 -0.0107 -0.0035 0.0180 -0.0312 6 0.0350 -0.0799 -0.0353 -0.0046 0.0416 0.0400 0.3395 0.0031 7 -0.0130 -0.0011 -0.1152 0.0164 0.0248 0.0015 -0.0067 0.0105 8 -0.0005 0.1844 -0.0254 0.0349 0.1867 0.0689 -0.0525 0.0036 9 0.0128 -0.0546 0.2322 0.0318 0.1718 0.0915 0.1275 -0.0083 10 0.5634 0.0113 -0.0098 -0.0212 -0.0442 0.3150 -0.0144 0.0019 11 -0.2887 -0.0051 -0.0040 0.3319 -0.1296 0.4457 -0.0064 0.0051 12 0.1804 0.0148 0.0032 0.6258 -0.0239 -0.2561 0.0189 -0.0010 13 -0.0767 -0.1831 -0.1118 0.0729 0.1327 0.0371 -0.0330 -0.0008 14 -0.0471 0.1258 0.1880 0.0395 0.0797 0.0348 0.0263 0.0127 15 0.0119 -0.0277 -0.0759 0.1129 0.3461 0.1074 -0.0804 0.0051 16 -0.0065 0.0141 0.0121 -0.0091 -0.0300 -0.0114 0.0075 -0.0009 17 0.0086 -0.0082 -0.0188 -0.0133 -0.0344 -0.0129 -0.0031 -0.0008 18 0.0058 0.0122 0.0082 -0.0368 -0.1035 -0.0336 0.0120 -0.0006 19 -0.0063 -0.1610 0.1011 0.0176 0.0363 0.0088 0.3186 0.0518 20 0.0940 -0.2115 0.0981 -0.0294 -0.0303 -0.0712 -0.0567 0.5871 21 0.0371 0.1051 -0.1682 -0.0232 0.0302 -0.0148 -0.0267 0.1815 Root No. 17 18 19 20 21 17 18 19 20 21 1102.5 1208.6 1277.6 1423.9 1508.4 1 0.4972 -0.0155 -0.0001 -0.0100 -0.0182 2 -0.0348 -0.1111 -0.0126 -0.0235 -0.0426 3 -0.1881 0.0087 0.0002 0.0179 0.0296 4 -0.0854 0.0283 -0.0231 0.0003 0.0366 5 -0.0230 -0.0204 -0.0011 -0.0068 -0.0185 6 0.0289 -0.0276 -0.0719 0.0163 0.0214 7 -0.0028 -0.0048 0.3428 0.2664 -0.0491 8 0.0023 -0.0136 0.1690 -0.1722 0.0444 9 0.0039 -0.0081 0.2544 -0.0528 -0.0017 10 -0.0007 0.0009 -0.0076 0.0066 -0.0005 11 -0.0017 0.0053 0.0026 -0.0033 0.0013 12 0.0008 -0.0012 0.0087 -0.0077 0.0019 13 -0.0007 -0.0031 0.0072 -0.0791 0.0176 14 0.0073 0.0188 -0.1835 0.1714 -0.0315 15 0.0025 0.0068 -0.1762 0.0907 -0.0150 16 -0.0002 -0.0009 0.0118 -0.0011 -0.0002 17 -0.0006 -0.0008 -0.0032 0.0010 -0.0001 18 -0.0010 -0.0002 0.0160 -0.0020 0.0000 19 0.0587 0.2604 -0.0754 -0.2016 -0.3991 20 0.3123 0.5627 0.1083 0.1816 0.4883 21 -0.1648 0.5046 0.1011 -0.3035 -0.4772 MASS-WEIGHTED COORDINATE ANALYSIS (NORMAL COORDINATES) Root No. 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 -851.1 99.3 174.2 281.8 313.8 410.5 465.4 512.2 1 -0.0653 0.0005 -0.0000 0.0046 -0.0037 0.3345 -0.1397 -0.0427 2 -0.0025 0.0010 -0.0012 -0.0004 0.0052 0.1722 -0.0517 0.0054 3 0.0868 -0.0001 -0.0052 -0.0148 0.0454 0.8967 -0.1259 -0.0622 4 -0.0902 0.0007 0.0216 0.0749 -0.1665 -0.1145 -0.4810 -0.1088 5 -0.1847 0.0576 -0.1168 -0.1225 0.3279 0.0106 -0.2856 0.7843 6 -0.0065 -0.0099 -0.0086 -0.0637 0.1432 0.0937 0.5096 -0.0097 7 0.1173 -0.0018 -0.0183 -0.0567 0.0662 -0.0049 0.0915 -0.0609 8 0.2578 0.0278 -0.0740 -0.0635 0.3381 -0.0045 0.2881 0.1276 9 -0.2564 0.0058 0.0463 0.2145 -0.1145 -0.0020 -0.2900 0.0418 10 0.0242 0.0118 0.0084 -0.0383 0.0142 -0.0046 -0.0613 -0.1266 11 -0.0055 -0.0044 -0.0000 0.0241 -0.0132 0.0037 0.0410 0.0754 12 -0.0077 -0.0016 0.0025 0.0083 -0.0050 0.0029 -0.0120 -0.0179 13 -0.0039 0.0728 -0.0150 -0.1858 0.4216 -0.0848 -0.2936 -0.4999 14 -0.0350 0.1029 -0.1791 -0.1929 0.4691 -0.0669 -0.1416 -0.0794 15 0.0002 -0.0823 0.2960 0.3792 -0.1162 0.0385 0.0886 0.1454 16 0.0051 0.6225 0.7455 -0.1840 0.0542 -0.0008 0.0052 0.0432 17 0.0225 0.6366 -0.3863 0.6359 0.1136 0.0060 0.0571 -0.0638 18 0.0273 -0.4244 0.3909 0.5143 0.5209 -0.0303 -0.0490 -0.0500 19 0.7526 0.0030 0.0006 0.0214 -0.0615 -0.0068 -0.2011 0.1006 20 0.0716 0.0105 -0.0095 -0.0109 0.0380 0.0370 0.0041 0.1454 21 -0.4746 0.0004 -0.0036 -0.0298 0.0797 0.1297 0.2190 -0.0792 Root No. 9 10 11 12 13 14 15 16 9 10 11 12 13 14 15 16 542.3 641.6 816.0 864.0 912.8 933.5 965.7 1081.2 1 -0.0219 0.1209 -0.1017 -0.0034 -0.0042 0.0066 0.0192 -0.0576 2 -0.0031 -0.0033 0.0135 -0.0019 -0.0128 -0.0086 -0.0316 0.8498 3 -0.0188 0.0227 0.0222 0.0010 0.0015 0.0008 -0.0139 -0.1662 4 -0.0715 0.4867 -0.4414 -0.0170 0.0534 0.0297 0.4435 0.0967 5 0.0952 -0.1998 -0.2417 -0.0089 -0.0206 -0.0048 0.0413 -0.0832 6 0.0452 -0.2105 -0.0845 -0.0055 0.0798 0.0556 0.7769 0.0083 7 -0.0169 -0.0029 -0.2759 0.0197 0.0475 0.0021 -0.0154 0.0282 8 -0.0007 0.4860 -0.0609 0.0419 0.3583 0.0958 -0.1201 0.0096 9 0.0165 -0.1440 0.5559 0.0381 0.3296 0.1272 0.2918 -0.0221 10 0.8414 0.0343 -0.0272 -0.0294 -0.0980 0.5052 -0.0381 0.0060 11 -0.4311 -0.0154 -0.0109 0.4592 -0.2871 0.7149 -0.0169 0.0158 12 0.2695 0.0451 0.0090 0.8658 -0.0529 -0.4108 0.0500 -0.0032 13 -0.0993 -0.4826 -0.2676 0.0874 0.2547 0.0516 -0.0754 -0.0020 14 -0.0609 0.3315 0.4500 0.0474 0.1528 0.0484 0.0603 0.0340 15 0.0154 -0.0730 -0.1816 0.1353 0.6641 0.1492 -0.1840 0.0136 16 -0.0137 0.0605 0.0472 -0.0177 -0.0941 -0.0258 0.0280 -0.0038 17 0.0182 -0.0351 -0.0735 -0.0261 -0.1079 -0.0292 -0.0118 -0.0033 18 0.0122 0.0525 0.0320 -0.0720 -0.3245 -0.0764 0.0448 -0.0025 19 -0.0024 -0.1229 0.0701 0.0061 0.0202 0.0036 0.2112 0.0400 20 0.0352 -0.1614 0.0680 -0.0102 -0.0169 -0.0287 -0.0376 0.4542 21 0.0139 0.0802 -0.1167 -0.0080 0.0168 -0.0060 -0.0177 0.1404 Root No. 17 18 19 20 21 17 18 19 20 21 1102.5 1208.6 1277.6 1423.9 1508.4 1 0.9070 -0.0628 -0.0002 -0.0267 -0.0775 2 -0.0634 -0.4499 -0.0255 -0.0630 -0.1816 3 -0.3431 0.0353 0.0004 0.0478 0.1264 4 -0.1442 0.1061 -0.0432 0.0007 0.1447 5 -0.0388 -0.0766 -0.0020 -0.0167 -0.0731 6 0.0488 -0.1036 -0.1347 0.0404 0.0844 7 -0.0047 -0.0181 0.6421 0.6602 -0.1941 8 0.0039 -0.0511 0.3166 -0.4269 0.1756 9 0.0067 -0.0305 0.4765 -0.1308 -0.0067 10 -0.0014 0.0037 -0.0164 0.0188 -0.0024 11 -0.0033 0.0228 0.0055 -0.0094 0.0060 12 0.0016 -0.0052 0.0189 -0.0219 0.0085 13 -0.0012 -0.0116 0.0136 -0.1961 0.0697 14 0.0124 0.0705 -0.3437 0.4249 -0.1243 15 0.0043 0.0256 -0.3299 0.2248 -0.0594 16 -0.0005 -0.0058 0.0360 -0.0043 -0.0014 17 -0.0016 -0.0051 -0.0099 0.0039 -0.0006 18 -0.0028 -0.0010 0.0490 -0.0080 0.0003 19 0.0287 0.2829 -0.0409 -0.1448 -0.4567 20 0.1528 0.6113 0.0587 0.1304 0.5588 21 -0.0807 0.5482 0.0548 -0.2179 -0.5462 ********************** * * * JOB ENDED NORMALLY * * * ********************** TOTAL JOB TIME: 39561.51 SECONDS == MOPAC DONE ==