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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 *
* 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
*******************************************************************************
SITE=(SALT=4.0)
Test that N-end Asp and C-end Arg form salt-bridges
ATOM CHEMICAL X Y Z
NUMBER SYMBOL (ANGSTROMS) (ANGSTROMS) (ANGSTROMS)
1 N(ATOM 1 N ASP A 1) 40.95810273 * 14.94276982 * 25.00194341 *
2 C(ATOM 2 CA ASP A 1) 41.62661392 * 14.88389701 * 23.69539119 *
3 C(ATOM 3 C ASP A 1) 40.75538668 * 14.22661571 * 22.61261850 *
4 O(ATOM 4 O ASP A 1) 40.49981955 * 14.81708621 * 21.59582962 *
5 C(ATOM 5 CB ASP A 1) 42.93297070 * 14.07105897 * 23.82328221 *
6 C(ATOM 6 CG ASP A 1) 42.78509633 * 12.80217571 * 24.59888461 *
7 O(ATOM 7 OD1 ASP A 1) 41.56353985 * 12.22869178 * 24.37187166 *
8 O(ATOM 8 OD2 ASP A 1) 43.56610453 * 12.27175565 * 25.34009673 *
9 H(ATOM 9 1H ASP A 1) 40.20574903 * 15.61297421 * 25.02945953 *
10 H(ATOM 10 2H ASP A 1) 40.63172855 * 14.03369596 * 25.30148168 *
11 H(ATOM 11 HA ASP A 1) 41.87648219 * 15.93534009 * 23.38011003 *
12 H(ATOM 12 HXT ASP A 1) 40.39129542 * 13.21123828 * 22.80464538 *
13 H(ATOM 13 1HB ASP A 1) 43.69847162 * 14.70563370 * 24.33370377 *
14 H(ATOM 14 2HB ASP A 1) 43.34150743 * 13.83861441 * 22.81502476 *
15 H(ATOM 15 HD1 ASP A 1) 41.42233677 * 11.38694064 * 24.86383923 *
16 H(ATOM 17 H ARG A 5) 34.74130831 * 17.18921890 * 23.85274498 *
17 C(ATOM 18 CA ARG A 5) 33.97529057 * 17.59928684 * 24.54333088 *
18 C(ATOM 19 CB ARG A 5) 33.22790403 * 16.47244118 * 25.26427976 *
19 C(ATOM 20 CG ARG A 5) 32.51739662 * 15.53791595 * 24.28194989 *
20 C(ATOM 21 CD ARG A 5) 31.33271529 * 16.23755486 * 23.58296709 *
21 N(ATOM 22 NE ARG A 5) 30.35459320 * 16.65721884 * 24.60785878 *
22 C(ATOM 23 CZ ARG A 5) 30.20830752 * 18.03835577 * 24.85767488 *
23 N(ATOM 24 NH1 ARG A 5) 30.82131109 * 18.92943245 * 24.14848191 *
24 N(ATOM 25 NH2 ARG A 5) 29.32794266 * 18.29745981 * 25.94010148 *
25 C(ATOM 26 C ARG A 5) 34.57438905 * 18.50522365 * 25.56764160 *
26 O(ATOM 27 O ARG A 5) 34.03744308 * 19.19309223 * 26.39580539 *
27 O(ATOM 28 O2 ARG A 5) 35.93472426 * 18.48971177 * 25.47894978 *
28 H(ATOM 29 HA ARG A 5) 33.26848228 * 18.19222355 * 23.90769726 *
29 H(ATOM 30 1HB ARG A 5) 33.92703902 * 15.90233706 * 25.90471493 *
30 H(ATOM 31 2HB ARG A 5) 32.46729347 * 16.90788545 * 25.94728270 *
31 H(ATOM 32 1HG ARG A 5) 32.14354098 * 14.65654081 * 24.83215853 *
32 H(ATOM 33 2HG ARG A 5) 33.22763071 * 15.15604693 * 23.52781583 *
33 H(ATOM 34 HE ARG A 5) 29.49987770 * 16.11473077 * 24.63170570 *
34 H(ATOM 35 HH1 ARG A 5) 30.81916374 * 19.89676023 * 24.40631338 *
35 H(ATOM 36 1HH2 ARG A 5) 29.15382428 * 17.55904210 * 26.59605073 *
36 H(ATOM 37 2HH2 ARG A 5) 29.40299987 * 19.20034407 * 26.37473760 *
37 H(ATOM 38 1HD ARG A 5) 30.84746223 * 15.54440208 * 22.86693570 *
38 H(ATOM 39 2HD ARG A 5) 31.72082263 * 17.10256325 * 22.99151446 *
39 H(ATOM 40 H2 ARG A 5) 36.38511104 * 19.07036871 * 26.13784376 *
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: C10 H20 N4 O5 = 39 atoms
MOLECULAR POINT GROUP : C1
GEOMETRY OF SYSTEM SUPPLIED
SITE=(SALT=4.0)
Test that N-end Asp and C-end Arg form salt-bridges
N(ATOM 1 N ASP A 1) 40.95810273 +1 14.94276982 +1 25.00194341 +1
C(ATOM 2 CA ASP A 1) 41.62661392 +1 14.88389701 +1 23.69539119 +1
C(ATOM 3 C ASP A 1) 40.75538668 +1 14.22661571 +1 22.61261850 +1
O(ATOM 4 O ASP A 1) 40.49981955 +1 14.81708621 +1 21.59582962 +1
C(ATOM 5 CB ASP A 1) 42.93297070 +1 14.07105897 +1 23.82328221 +1
C(ATOM 6 CG ASP A 1) 42.78509633 +1 12.80217571 +1 24.59888461 +1
O(ATOM 7 OD1 ASP A 1) 41.56353985 +1 12.22869178 +1 24.37187166 +1
O(ATOM 8 OD2 ASP A 1) 43.56610453 +1 12.27175565 +1 25.34009673 +1
H(ATOM 9 1H ASP A 1) 40.20574903 +1 15.61297421 +1 25.02945953 +1
H(ATOM 10 2H ASP A 1) 40.63172855 +1 14.03369596 +1 25.30148168 +1
H(ATOM 11 HA ASP A 1) 41.87648219 +1 15.93534009 +1 23.38011003 +1
H(ATOM 12 HXT ASP A 1) 40.39129542 +1 13.21123828 +1 22.80464538 +1
H(ATOM 13 1HB ASP A 1) 43.69847162 +1 14.70563370 +1 24.33370377 +1
H(ATOM 14 2HB ASP A 1) 43.34150743 +1 13.83861441 +1 22.81502476 +1
H(ATOM 15 HD1 ASP A 1) 41.42233677 +1 11.38694064 +1 24.86383923 +1
H(ATOM 17 H ARG A 5) 34.74130831 +1 17.18921890 +1 23.85274498 +1
C(ATOM 18 CA ARG A 5) 33.97529057 +1 17.59928684 +1 24.54333088 +1
C(ATOM 19 CB ARG A 5) 33.22790403 +1 16.47244118 +1 25.26427976 +1
C(ATOM 20 CG ARG A 5) 32.51739662 +1 15.53791595 +1 24.28194989 +1
C(ATOM 21 CD ARG A 5) 31.33271529 +1 16.23755486 +1 23.58296709 +1
N(ATOM 22 NE ARG A 5) 30.35459320 +1 16.65721884 +1 24.60785878 +1
C(ATOM 23 CZ ARG A 5) 30.20830752 +1 18.03835577 +1 24.85767488 +1
N(ATOM 24 NH1 ARG A 5) 30.82131109 +1 18.92943245 +1 24.14848191 +1
N(ATOM 25 NH2 ARG A 5) 29.32794266 +1 18.29745981 +1 25.94010148 +1
C(ATOM 26 C ARG A 5) 34.57438905 +1 18.50522365 +1 25.56764160 +1
O(ATOM 27 O ARG A 5) 34.03744308 +1 19.19309223 +1 26.39580539 +1
O(ATOM 28 O2 ARG A 5) 35.93472426 +1 18.48971177 +1 25.47894978 +1
H(ATOM 29 HA ARG A 5) 33.26848228 +1 18.19222355 +1 23.90769726 +1
H(ATOM 30 1HB ARG A 5) 33.92703902 +1 15.90233706 +1 25.90471493 +1
H(ATOM 31 2HB ARG A 5) 32.46729347 +1 16.90788545 +1 25.94728270 +1
H(ATOM 32 1HG ARG A 5) 32.14354098 +1 14.65654081 +1 24.83215853 +1
H(ATOM 33 2HG ARG A 5) 33.22763071 +1 15.15604693 +1 23.52781583 +1
H(ATOM 34 HE ARG A 5) 29.49987770 +1 16.11473077 +1 24.63170570 +1
H(ATOM 35 HH1 ARG A 5) 30.81916374 +1 19.89676023 +1 24.40631338 +1
H(ATOM 36 1HH2 ARG A 5) 29.15382428 +1 17.55904210 +1 26.59605073 +1
H(ATOM 37 2HH2 ARG A 5) 29.40299987 +1 19.20034407 +1 26.37473760 +1
H(ATOM 38 1HD ARG A 5) 30.84746223 +1 15.54440208 +1 22.86693570 +1
H(ATOM 39 2HD ARG A 5) 31.72082263 +1 17.10256325 +1 22.99151446 +1
H(ATOM 40 H2 ARG A 5) 36.38511104 +1 19.07036871 +1 26.13784376 +1
Salt Bridges Found (Up to 4.0 Angstroms)
No. Cationic site Anionic site Dist. (Angstroms)
1 (ATOM 1 N ASP A 1) A1(+) (ATOM 7 OD1 ASP A 1) A1(-) 2.85
2 (ATOM 23 NH1 ARG A 5) A5(+) (ATOM 26 O ARG A 5) A5(-) 3.93
Changes in Ionization caused by keyword SITE
Keyword: "SITE=(SALT=4.0)" => SITE=(A1(+),A1(-),A5(+),A5(-))
Hydrogen atoms added to Hydrogen atoms deleted from
1 N ASP A 1 OD1 ASP A 1
2 NH1 ARG A 5 O2 ARG A 5
Change in net ionization: +0
CHARGES MODIFIED BY SITE COMMAND
HYDROGEN ATOMS ADDED OR DELETED
Test that N-end Asp and C-end Arg form salt-bridges
N(ATOM 1 N ASP A 1) 40.95810273 +1 14.94276982 +1 25.00194341 +1
C(ATOM 2 CA ASP A 1) 41.62661392 +1 14.88389701 +1 23.69539119 +1
C(ATOM 3 C ASP A 1) 40.75538668 +1 14.22661571 +1 22.61261850 +1
O(ATOM 4 O ASP A 1) 40.49981955 +1 14.81708621 +1 21.59582962 +1
C(ATOM 5 CB ASP A 1) 42.93297070 +1 14.07105897 +1 23.82328221 +1
C(ATOM 6 CG ASP A 1) 42.78509633 +1 12.80217571 +1 24.59888461 +1
O(ATOM 7 OD1 ASP A 1) 41.56353985 +1 12.22869178 +1 24.37187166 +1
O(ATOM 8 OD2 ASP A 1) 43.56610453 +1 12.27175565 +1 25.34009673 +1
H(ATOM 9 1H ASP A 1) 40.20574903 +1 15.61297421 +1 25.02945953 +1
H(ATOM 10 2H ASP A 1) 40.63172855 +1 14.03369596 +1 25.30148168 +1
H(ATOM 11 HA ASP A 1) 41.87648219 +1 15.93534009 +1 23.38011003 +1
H(ATOM 12 HXT ASP A 1) 40.39129542 +1 13.21123828 +1 22.80464538 +1
H(ATOM 13 1HB ASP A 1) 43.69847162 +1 14.70563370 +1 24.33370377 +1
H(ATOM 14 2HB ASP A 1) 43.34150743 +1 13.83861441 +1 22.81502476 +1
H(ATOM 15 3H ASP A 1) 41.36724822 +1 15.23973460 +1 25.97888347 +1
C(ATOM 16 CA ARG A 5) 33.97529057 +1 17.59928684 +1 24.54333088 +1
C(ATOM 17 CB ARG A 5) 33.22790403 +1 16.47244118 +1 25.26427976 +1
C(ATOM 18 CG ARG A 5) 32.51739662 +1 15.53791595 +1 24.28194989 +1
C(ATOM 19 CD ARG A 5) 31.33271529 +1 16.23755486 +1 23.58296709 +1
N(ATOM 20 NE ARG A 5) 30.35459320 +1 16.65721884 +1 24.60785878 +1
C(ATOM 21 CZ ARG A 5) 30.20830752 +1 18.03835577 +1 24.85767488 +1
N(ATOM 22 NH1 ARG A 5) 30.82131109 +1 18.92943245 +1 24.14848191 +1
N(ATOM 23 NH2 ARG A 5) 29.32794266 +1 18.29745981 +1 25.94010148 +1
C(ATOM 24 C ARG A 5) 34.57438905 +1 18.50522365 +1 25.56764160 +1
O(ATOM 25 O ARG A 5) 34.03744308 +1 19.19309223 +1 26.39580539 +1
O(ATOM 26 O2 ARG A 5) 35.93472426 +1 18.48971177 +1 25.47894978 +1
H(ATOM 27 1HA ARG A 5) 34.74130831 +1 17.18921890 +1 23.85274498 +1
H(ATOM 28 2HA ARG A 5) 33.26848228 +1 18.19222355 +1 23.90769726 +1
H(ATOM 29 1HB ARG A 5) 33.92703902 +1 15.90233706 +1 25.90471493 +1
H(ATOM 30 2HB ARG A 5) 32.46729347 +1 16.90788545 +1 25.94728270 +1
H(ATOM 31 1HG ARG A 5) 32.14354098 +1 14.65654081 +1 24.83215853 +1
H(ATOM 32 2HG ARG A 5) 33.22763071 +1 15.15604693 +1 23.52781583 +1
H(ATOM 33 HE ARG A 5) 29.49987770 +1 16.11473077 +1 24.63170570 +1
H(ATOM 34 1HH1 ARG A 5) 30.81916374 +1 19.89676023 +1 24.40631338 +1
H(ATOM 35 1HH2 ARG A 5) 29.15382428 +1 17.55904210 +1 26.59605073 +1
H(ATOM 36 2HH2 ARG A 5) 29.40299987 +1 19.20034407 +1 26.37473760 +1
H(ATOM 37 1HD ARG A 5) 30.84746223 +1 15.54440208 +1 22.86693570 +1
H(ATOM 38 2HD ARG A 5) 31.72082263 +1 17.10256325 +1 22.99151446 +1
H(ATOM 39 2HH1 ARG A 5) 31.41041583 +1 18.85640991 +1 23.22240237 +1
RESIDUE SEQUENCE IN PROTEIN Chain: A
1 2 3 4 5 6 7 8 9 10
0 ASP
RESIDUE SEQUENCE IN PROTEIN FRAGMENT: 2 Chain: A
1 2 3 4 5 6 7 8 9 10
0 ARG
RESIDUE SEQUENCE IN PROTEIN Chain: A
0 D
RESIDUE SEQUENCE IN PROTEIN FRAGMENT: 2 Chain: A
0 R
******************************************************************************
* *
* 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: 0.01 SECONDS
== MOPAC DONE ==
|
