FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: Z788N
Calculation Name: 1V7F-A-Other547
Preferred Name:
Target Type:
Ligand Name: amino group
Ligand 3-letter code: NH2
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1V7F
Chain ID: A
UniProt ID: P61230
Base Structure: SolutionNMR
Registration Date: 2025-10-03
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -121261.5769 |
|---|---|
| FMO2-HF: Nuclear repulsion | 107244.814423 |
| FMO2-HF: Total energy | -14016.762476 |
| FMO2-MP2: Total energy | -14051.735432 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:1:TYR)
Summations of interaction energy for
fragment #1(A:1:TYR)
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| 83.051 | 87.385 | 1.038 | -1.961 | -3.41 | -0.003 |
Interaction energy analysis for fragmet #1(A:1:TYR)
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | A | 3 | GLN | 0 | 0.019 | 0.014 | 2.747 | -2.164 | 0.548 | 0.579 | -1.428 | -1.863 | -0.008 |
| 4 | A | 4 | LYS | 1 | 1.017 | 1.005 | 2.530 | 44.495 | 45.927 | 0.460 | -0.518 | -1.374 | 0.005 |
| 7 | A | 7 | TRP | 0 | 0.007 | 0.009 | 4.797 | -3.289 | -3.099 | -0.001 | -0.015 | -0.173 | 0.000 |
| 5 | A | 5 | TRP | 0 | 0.063 | 0.012 | 5.404 | 2.014 | 2.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | MET | 0 | -0.031 | -0.012 | 8.705 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | THR | 0 | 0.063 | 0.020 | 9.826 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | CYS | 0 | -0.143 | -0.074 | 10.547 | -3.677 | -3.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ASP | -1 | -0.783 | -0.904 | 12.615 | -21.675 | -21.675 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | -0.012 | -0.012 | 15.423 | -0.821 | -0.821 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ALA | 0 | 0.056 | 0.034 | 15.721 | 0.579 | 0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.859 | 0.956 | 7.502 | 31.015 | 31.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LYS | 1 | 0.888 | 0.928 | 7.491 | 26.851 | 26.851 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | CYS | 0 | -0.040 | -0.008 | 7.030 | -5.889 | -5.889 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | GLU | -1 | -0.873 | -0.939 | 5.162 | -22.168 | -22.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | GLY | 0 | 0.068 | 0.036 | 6.887 | -1.295 | -1.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | -0.083 | -0.042 | 6.245 | 0.711 | 0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | VAL | 0 | 0.025 | 0.013 | 10.185 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | ARG | 1 | 0.961 | 0.967 | 13.406 | 16.610 | 16.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | LEU | 0 | 0.040 | 0.045 | 16.604 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | TRP | 0 | 0.036 | -0.002 | 13.218 | -0.969 | -0.969 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 26 | LYS | 1 | 0.946 | 0.979 | 11.312 | 15.886 | 15.886 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 27 | LYS | 1 | 0.995 | 0.998 | 10.211 | 20.357 | 20.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | ILE | 0 | -0.088 | -0.045 | 12.418 | 0.788 | 0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | ILE | -1 | -0.853 | -0.914 | 15.007 | -14.999 | -14.999 | 0.000 | 0.000 | 0.000 | 0.000 |