******************************************************************************* ** Site#: 28262 E-mail support: MrMOPAC@ATT.net Version 17.273W 64BITS ** ******************************************************************************* ** Cite this program as: MOPAC2016, Version: 17.273W, James J. P. Stewart, ** ** Stewart Computational Chemistry, web-site: HTTP://OpenMOPAC.net. ** ******************************************************************************* ** ** ** MOPAC2016 ** ** ** ******************************************************************************* PM7 CALCULATION RESULTS ******************************************************************************* * CALCULATION DONE: Sat Sep 30 14:50:36 2017 * * SETPI - SOME OR ALL PI BONDS EXPLICITLY SET BY USER * MOZYME - USE LOCALIZED M.O.s IN SOLVING THE SCF EQUATIONS * ADD-H - ADD HYDROGEN ATOMS TO SATISFY VALENCE * SITE - SET IONIZATION LEVELS OF IONIZABLE RESIDUES * * * * CHARGE ON SYSTEM = -1 * * * * T= - A TIME OF 2.0 WEEKS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS * GNORM= - EXIT WHEN GRADIENT NORM DROPS BELOW 5.00 * OUTPUT - MINIMIZE OUTPUT * HTML - WRITE HTML SCRIPT TO READ PDB FILE USING JSMOL ******************************************************************************* HTML OUTPUT add-H setpi t=2W GNORM=5 charge=-1 MOZYME site=(salt,"NZ LYS A 23"(+),"OP3 8OG A1157"(-),"N1 8OG A1157"(0),"[ASP]120:A.OD2"(-),"[ASP]120:A.OD1"(0)) Add hydrogen atoms to MTH1 A Keyword SETPI used, pi-bonds specified are: Bond No. Atom to Atom 1 "HETATM 2501 N1 8OG A1157" - "HETATM 2499 C6 8OG A1157" 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: C817 H1514 N214 O382 S8 P = 2936 atoms Hydrogen atom 789 bonds to "ATOM 782 OE2 GLU A 52 " and "HETATM 2701 O HOH A2056 " (Keeping bond to "ATOM 782 OE2 GLU A 52 ") RESIDUE SEQUENCE IN PROTEIN Chain: A 1 2 3 4 5 6 7 8 9 10 0 ALA SER ARG LEU TYR THR LEU VAL 10 LEU VAL LEU GLN PRO GLN ARG 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: A 0 ASRLYTLV LVLQPQRVLL GMKKRGFGAG RWNGFGGKVQ EGETIEDGAR 50 RELQEESGLT VDALHKVGQI VFEFVGEPEL MDVHVFCTDS IQGTPVESDE 100 MRPCWFQLDQ IPFKDMWPDD SYWFPLLLQK KKFHGYFKFQ GQDTILDYTL 150 REVDTV HYDROGEN ATOMS ADDED Salt Bridges Found (Up to 4.0 Angstroms) No. Cationic site Anionic site Dist. (Angstroms) 1 (ATOM 737 NH1 ARG A 50) A50(+) (ATOM 690 OE2 GLU A 46) A46(-) 2.63 2 (ATOM 2113 NE2 HIS A 134) A134(+) (ATOM 2469 O VAL A 156) A156(-) 2.67 3 (ATOM 758 NE ARG A 51) A51(+) (ATOM 640 OE1 GLU A 43) A43(-) 2.77 4 (ATOM 367 NZ LYS A 24) A24(+) (ATOM 1467 OE2 GLU A 97) A97(-) 2.79 5 (ATOM 464 NH2 ARG A 31) A31(+) (ATOM 2258 OD1 ASP A 143) A143(-) 2.80 6 (ATOM 1276 ND1 HIS A 84) A84(+) (ATOM 1247 OD1 ASP A 82) A82(-) 3.42 7 (ATOM 2178 NZ LYS A 138) A138(+) (ATOM 2324 OD2 ASP A 147) A147(-) 3.80 Changes in Ionization caused by keyword SITE Keyword: "SITE=(SALT,"NZ LYS A 23"(+),"OP3 8OG A1157"(-),"N1 8OG A1157"(0),"[ASP]120:A.OD2"(-), "[ASP]120:A.OD1"(0))" => SITE=(A50(+),A46(-),A134(+),A156(-),A51(+),A43(-),A24(+),A97(-), A31(+),A143(-),A84(+),A82(-),A138(+),A147(-),"NZ LYS A 23"(+),"OP3 8OG A1157"(-),"N1 8OG A1157"(0), "[ASP]120:A.OD2"(-),"[ASP]120:A.OD1"(0)) Hydrogen atoms added to Hydrogen atoms deleted from 1 NZ LYS A 24 OE1 GLU A 43 2 NH2 ARG A 31 OE2 GLU A 46 3 NH2 ARG A 50 OD2 ASP A 82 4 NH2 ARG A 51 OE1 GLU A 97 5 NE2 HIS A 84 OD2 ASP A 120 6 NE2 HIS A 134 OD2 ASP A 143 7 NZ LYS A 138 OD2 ASP A 147 8 NZ LYS A 23 OXT VAL A 156 9 OD1 ASP A 120 N1 8OG A1157 10 - OP3 8OG A1157 Change in net ionization: -1 CHARGES MODIFIED BY SITE COMMAND GEOMETRY RESEQUENCED ****************************************************************************** * * * Error and normal termination messages reported in this calculation * * * * HYDROGEN ATOMS ADDED * * CHARGES MODIFIED BY SITE COMMAND * * GEOMETRY RESEQUENCED * * JOB ENDED NORMALLY * * * ****************************************************************************** TOTAL JOB TIME: 0.00 SECONDS == MOPAC DONE ==