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*******************************************************************************
** **
** MOPAC v22.0.6 **
** **
*******************************************************************************
** Digital Object Identifier (DOI): 10.5281/zenodo.6511958 **
** Visit the DOI location for information on how to cite this program. **
*******************************************************************************
PM7 CALCULATION RESULTS
*******************************************************************************
* CALCULATION DONE: Thu Apr 13 11:25:47 2023 *
* GEO_DAT - DATA SET GEOMETRY IS IN FILE "Neutral.mop"
* SITE - SET IONIZATION LEVELS OF IONIZABLE RESIDUES
* T= - A TIME OF 172800.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 7200.0 SECONDS REQUESTED
* OUTPUT - MINIMIZE OUTPUT
* HTML - WRITE HTML SCRIPT TO READ PDB FILE USING JSMOL
*******************************************************************************
geo_dat="Neutral.mop" OUTPUT site=(ionize) HTML
Test that all ionizable sites get ionized
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)
https://link.springer.com/article/10.1007/s00894-012-1667-x
Empirical Formula: C798 H1353 N206 O314 S9 P = 2681 atoms
Changes in Ionization caused by keyword SITE
Keyword: SITE=(COO,NH3,ARG(+),SO4,PO4)
Hydrogen atoms added to Hydrogen atoms deleted from
1 N GLY B 2 OE2 GLU B 41
2 NH2 ARG B 5 OE2 GLU B 43
3 N VAL B 18 OE2 GLU B 46
4 NZ LYS B 23 OD2 ASP B 47
5 NZ LYS B 24 OE1 GLU B 52
6 NH2 ARG B 25 OE2 GLU B 55
7 NH2 ARG B 31 OE1 GLU B 56
8 NZ LYS B 38 OD2 ASP B 62
9 NH2 ARG B 50 OE1 GLU B 73
10 NH2 ARG B 51 OE2 GLU B 77
11 NZ LYS B 66 OE2 GLU B 79
12 NH2 ARG B 102 OD1 ASP B 82
13 NZ LYS B 114 OD2 ASP B 89
14 NZ LYS B 130 OE1 GLU B 97
15 NZ LYS B 131 OD2 ASP B 99
16 NZ LYS B 132 OE1 GLU B 100
17 NZ LYS B 138 OD2 ASP B 109
18 NH2 ARG B 151 OD1 ASP B 115
19 - OD1 ASP B 119
20 - OD1 ASP B 120
21 - OD2 ASP B 143
22 - OD2 ASP B 147
23 - OE2 GLU B 152
24 - OD1 ASP B 154
25 - OXT VAL B 156
26 - OP3 8OG B1157
27 - O1 SO4 B1158
28 - O4 SO4 B1158
29 - O1 SO4 B1159
30 - O4 SO4 B1159
31 - O1 SO4 B1160
32 - O4 SO4 B1160
Change in net ionization: -14
CHARGES MODIFIED BY SITE COMMAND
HYDROGEN ATOMS ADDED OR DELETED
RESIDUE SEQUENCE IN PROTEIN Chain: B
1 2 3 4 5 6 7 8 9 10
0 GLY ALA SER ARG LEU TYR THR LEU VAL
10 LEU VAL LEU
RESIDUE SEQUENCE IN PROTEIN FRAGMENT: 2 Chain: B
1 2 3 4 5 6 7 8 9 10
10 VAL LEU LEU
20 GLY MET LYS LYS ARG GLY PHE GLY ALA GLY
30 ARG TRP ASN GLY PHE GLY GLY LYS VAL GLN
40 GLU GLY GLU THR ILE GLU ASP GLY ALA ARG
50 ARG GLU LEU GLN GLU GLU SER GLY LEU THR
60 VAL ASP ALA LEU HIS LYS VAL GLY GLN ILE
70 VAL PHE GLU PHE VAL GLY GLU PRO GLU LEU
80 MET ASP VAL HIS VAL PHE CYS THR ASP SER
90 ILE GLN GLY THR PRO VAL GLU SER ASP GLU
100 MET ARG PRO CYS TRP PHE GLN LEU ASP GLN
110 ILE PRO PHE LYS ASP MET TRP PRO ASP ASP
120 SER TYR TRP PHE PRO LEU LEU LEU GLN LYS
130 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN
140 GLY GLN ASP THR ILE LEU ASP TYR THR LEU
150 ARG GLU VAL ASP THR VAL
RESIDUE SEQUENCE IN PROTEIN Chain: B
0 GASRLYTLV LVL
RESIDUE SEQUENCE IN PROTEIN FRAGMENT: 2 Chain: B
10 VLL GMKKRGFGAG RWNGFGGKVQ EGETIEDGAR RELQEESGLT
60 VDALHKVGQI VFEFVGEPEL MDVHVFCTDS IQGTPVESDE MRPCWFQLDQ
110 IPFKDMWPDD SYWFPLLLQK KKFHGYFKFQ GQDTILDYTL REVDTV
******************************************************************************
* *
* Error and normal termination messages reported in this calculation *
* *
* CHARGES MODIFIED BY SITE COMMAND *
* HYDROGEN ATOMS ADDED OR DELETED *
* JOB ENDED NORMALLY *
* *
******************************************************************************
TOTAL JOB TIME: 0.31 SECONDS
== MOPAC DONE ==
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