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*******************************************************************************
** **
** MOPAC v22.0.6 **
** **
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** 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 11:25:41 2023 *
* COMPARE - Compare two geometries
* START_RES - STARTING RESIDUE NUMBERS DEFINED
* Keyword: START_RES=(10B 20B 16B 30B 30B)
* GEO_DAT - DATA SET GEOMETRY IS IN FILE "Structure-1.txt"
* GEO_REF - REFERENCE GEOMETRY IS IN FILE "Structure-2.txt"
* (NO BIAS TOWARDS THE REFERENCE GEOMETRY WILL BE APPLIED)
* CHAINS - PDB CHAIN LETTERS EXPLICITLY DEFINED
* Keyword: CHAINS=(BBBBB)
* T= - A TIME OF 172800.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 7200.0 SECONDS REQUESTED
* OUTPUT - MINIMIZE OUTPUT
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START_RES=(10B 20B 16B 30B 30B) CHAINS=(BBBBB) geo_dat="Structure-1.txt" geo_ref="Structure-2.txt" compare output
Compare two very similar geometries (compare residue 10)
After docking
Atoms that move a lot
Atom Label GEO_REF Coordinates Movement Integral
(ATOM 1 N ASP B 10) 0.000 0.000 0.000 0.49 0.49
(ATOM 117 HD2 ASP B 10) 2.978 -3.861 -1.464 0.0068 0.50
(ATOM 8 OD2 ASP B 10) 2.680 -2.960 -1.781 0.0068 0.51
(ATOM 116 2HB ASP B 10) 1.255 -0.895 -1.944 0.0067 0.51
(ATOM 115 1HB ASP B 10) 2.889 -0.273 -1.585 0.0066 0.52
(ATOM 6 CG ASP B 10) 2.445 -2.159 -0.731 0.0066 0.53
(ATOM 5 CB ASP B 10) 2.024 -0.796 -1.178 0.0065 0.53
(ATOM 124 HE1 GLU B 11) -2.822 3.296 -2.683 0.0065 0.54
(ATOM 17 OE2 GLU B 11) -0.739 2.552 -2.065 0.0064 0.55
(ATOM 120 1HB GLU B 11) 1.516 4.084 -2.223 0.0064 0.55
Difference between GEO_DAT and GEO_REF: 1.150 = total, 0.0055 = Average, 0.0343 = RMS, in Angstroms
Differences between bond-lengths for the two geometries
Diff. Atom 1 Atom 2 Bond length Bond length
in GEO_DAT in GEO_REF
1 -0.500 N(ATOM 1 N ASP B 10) C(ATOM 2 CA ASP B 10) 0.963 1.463
2 +0.254 N(ATOM 1 N ASP B 10) H(ATOM 112 1H ASP B 10) 1.265 1.010
3 +0.254 N(ATOM 1 N ASP B 10) H(ATOM 113 2H ASP B 10) 1.265 1.010
GEO_DAT: 'Structure-1.txt'
GEO_REF: 'Structure-2.txt'
Analysis of Non-Covalent Interactions
Total non-covalent energy of GEO_DAT system: -66.30 Kcal/mol
Total non-covalent energy of GEO_REF system: -67.94 Kcal/mol
Difference: 1.64 Kcal/mol
Number of hydrogen bonds common to both systems: 6
The following files will be written:
'Compare_two_protein_structures.html'
From GEO_REF: 'Compare_two_protein_structures_Structure-2.pdb'
From GEO_DAT: 'Compare_two_protein_structures_Structure-1.pdb'
GEO_REF with 0SCF: Job complete
******************************************************************************
* *
* Error and normal termination messages reported in this calculation *
* *
* GEO_REF with 0SCF: Job complete *
* JOB ENDED NORMALLY *
* *
******************************************************************************
TOTAL JOB TIME: 0.00 SECONDS
== MOPAC DONE ==
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