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: 2GN7R
Calculation Name: 4V6W-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4V6W
Chain ID: A
UniProt ID: P13060
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
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 | 52 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -263653.299106 |
|---|---|
| FMO2-HF: Nuclear repulsion | 241023.805617 |
| FMO2-HF: Total energy | -22629.493489 |
| FMO2-MP2: Total energy | -22691.429383 |
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:77:ILE)
Summations of interaction energy for
fragment #1(A:77:ILE)
| 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. |
| 172.632 | 173.748 | 0.006 | -0.35 | -0.772 | 0.001 |
Interaction energy analysis for fragmet #1(A:77:ILE)
| 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 | 79 | GLU | -1 | -0.829 | -0.905 | 3.647 | -39.769 | -38.746 | 0.007 | -0.333 | -0.697 | 0.001 |
| 7 | A | 83 | ARG | 1 | 0.880 | 0.955 | 4.051 | 50.825 | 50.918 | -0.001 | -0.017 | -0.075 | 0.000 |
| 4 | A | 80 | PRO | 0 | 0.016 | -0.011 | 6.038 | 1.910 | 1.910 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 81 | SER | 0 | 0.073 | 0.035 | 9.032 | 1.283 | 1.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 82 | LEU | 0 | 0.062 | 0.017 | 5.899 | 1.703 | 1.703 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 84 | ILE | 0 | 0.045 | 0.023 | 9.561 | 2.218 | 2.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 85 | LEU | 0 | -0.021 | -0.006 | 11.581 | 1.793 | 1.793 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 86 | ALA | 0 | 0.043 | 0.025 | 9.897 | 1.488 | 1.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 87 | GLN | 0 | -0.035 | -0.046 | 11.851 | 0.497 | 0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 88 | LYS | 1 | 1.010 | 1.021 | 14.183 | 18.038 | 18.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 89 | TYR | 0 | 0.041 | 0.026 | 15.624 | 1.065 | 1.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 90 | ASN | 0 | -0.063 | -0.025 | 13.573 | 1.941 | 1.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 91 | CYS | 0 | 0.004 | 0.007 | 15.627 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 92 | ASP | -1 | -0.873 | -0.929 | 17.812 | -15.661 | -15.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 93 | LYS | 1 | 0.841 | 0.912 | 19.721 | 15.060 | 15.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 94 | MET | 0 | 0.002 | 0.017 | 23.141 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 95 | ILE | 0 | -0.012 | -0.012 | 23.960 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 96 | CYS | 0 | -0.082 | -0.022 | 28.053 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 97 | ARG | 1 | 0.893 | 0.922 | 31.566 | 8.975 | 8.975 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 98 | LYS | 1 | 0.996 | 1.014 | 33.691 | 7.925 | 7.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 99 | CYS | 0 | 0.037 | -0.002 | 32.596 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 100 | TYR | 0 | 0.061 | 0.032 | 28.715 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 101 | ALA | 0 | -0.043 | -0.020 | 27.629 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 102 | ARG | 1 | 0.978 | 0.980 | 19.492 | 14.107 | 14.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 103 | LEU | 0 | -0.009 | -0.001 | 25.251 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 104 | HIS | 0 | 0.089 | 0.029 | 24.977 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 105 | PRO | 0 | 0.006 | -0.001 | 22.898 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 106 | ARG | 1 | 0.991 | 0.998 | 25.648 | 11.291 | 11.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 107 | ALA | 0 | -0.055 | -0.013 | 29.000 | 0.376 | 0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 108 | THR | 0 | 0.090 | 0.036 | 30.899 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 109 | ASN | 0 | 0.021 | 0.015 | 34.460 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 110 | CYS | 0 | -0.035 | -0.022 | 33.440 | -0.379 | -0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 111 | ARG | 1 | 0.934 | 0.952 | 30.827 | 9.676 | 9.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 112 | LYS | 1 | 0.937 | 0.982 | 29.467 | 10.235 | 10.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 113 | LYS | 1 | 1.046 | 1.029 | 35.243 | 7.511 | 7.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 114 | LYS | 1 | 1.024 | 0.996 | 37.626 | 7.694 | 7.694 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 115 | CYS | 0 | 0.003 | 0.006 | 36.202 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 116 | GLY | 0 | 0.016 | 0.008 | 38.342 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 117 | HIS | 0 | 0.001 | 0.000 | 37.533 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 118 | THR | 0 | 0.035 | 0.025 | 38.061 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 119 | ASN | 0 | 0.049 | 0.019 | 36.578 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 120 | ASN | 0 | 0.019 | 0.025 | 36.322 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 121 | LEU | 0 | -0.006 | -0.001 | 31.188 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 122 | ARG | 1 | 0.962 | 0.974 | 29.351 | 9.860 | 9.860 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 123 | PRO | 0 | 0.116 | 0.055 | 25.078 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 124 | LYS | 1 | 0.809 | 0.892 | 18.948 | 15.907 | 15.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 125 | LYS | 1 | 0.906 | 0.949 | 22.487 | 11.406 | 11.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 126 | LYS | 1 | 0.942 | 0.981 | 18.668 | 15.213 | 15.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 127 | LEU | 0 | -0.024 | -0.008 | 12.579 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 128 | LYS | 0 | 0.130 | 0.090 | 16.250 | 0.436 | 0.436 | 0.000 | 0.000 | 0.000 | 0.000 |