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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
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* 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
*******************************************************************************
geo_dat="Neutral.mop" OUTPUT site=(salt)
Test that salt bridges are generated correctly
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
Salt Bridges Found (Up to 4.0 Angstroms)
No. Cationic site Anionic site Dist. (Angstroms)
1 (ATOM 305 NZ LYS B 24) B24(+) (ATOM 1405 OE2 GLU B 97) B97(-) 2.64
2 (ATOM 675 NH1 ARG B 50) B50(+) (ATOM 628 OE2 GLU B 46) B46(-) 2.70
3 (ATOM 2051 NE2 HIS B 134) B134(+) (ATOM 2407 O VAL B 156) B156(-) 2.74
4 (ATOM 1989 NZ LYS B 131) B131(+) (ATOM 2352 OE1 GLU B 152) B152(-) 2.75
5 (ATOM 699 NH2 ARG B 51) B51(+) (ATOM 579 OE2 GLU B 43) B43(-) 2.82
6 (ATOM 402 NH2 ARG B 31) B31(+) (ATOM 2196 OD1 ASP B 143) B143(-) 3.18
7 (ATOM 1689 NZ LYS B 114) B114(+) (ATOM 1709 OD2 ASP B 115) B115(-) 3.26
8 (ATOM 1214 ND1 HIS B 84) B84(+) (ATOM 1185 OD1 ASP B 82) B82(-) 3.51
Changes in Ionization caused by keyword SITE
Keyword: "SITE=(SALT)" => SITE=(B24(+),B97(-),B50(+),B46(-),B134(+),B156(-),B131(+),
B152(-),B51(+),B43(-),B31(+),B143(-),B114(+),B115(-),B84(+),B82(-))
Hydrogen atoms added to Hydrogen atoms deleted from
1 NZ LYS B 24 OE2 GLU B 43
2 NH2 ARG B 31 OE2 GLU B 46
3 NH2 ARG B 50 OD1 ASP B 82
4 NH2 ARG B 51 OE1 GLU B 97
5 NE2 HIS B 84 OD1 ASP B 115
6 NZ LYS B 114 OD2 ASP B 143
7 NZ LYS B 131 OE2 GLU B 152
8 NE2 HIS B 134 OXT VAL B 156
Change in net ionization: +0
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: 0.30 SECONDS
== MOPAC DONE ==
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