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: ZZ68N
Calculation Name: 1VB8-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1VB8
Chain ID: A
UniProt ID: P83937
Base Structure: SolutionNMR
Registration Date: 2025-10-05
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 | 27 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -98625.579666 |
|---|---|
| FMO2-HF: Nuclear repulsion | 86163.61653 |
| FMO2-HF: Total energy | -12461.963135 |
| FMO2-MP2: Total energy | -12492.911206 |
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:CYS)
Summations of interaction energy for
fragment #1(A:1:CYS)
| 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. |
| -275.537 | -269.707 | 78.727 | -39.871 | -44.687 | -0.292 |
Interaction energy analysis for fragmet #1(A:1:CYS)
| 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 | GLU | -1 | -0.736 | -0.841 | 3.462 | -30.937 | -28.282 | -0.001 | -1.225 | -1.429 | 0.000 |
| 4 | A | 4 | SER | 0 | 0.053 | 0.015 | 4.550 | -3.699 | -3.648 | -0.002 | -0.018 | -0.031 | 0.000 |
| 5 | A | 5 | CYS | 0 | -0.041 | -0.005 | 3.840 | -2.430 | 0.677 | -0.025 | -1.618 | -1.464 | 0.009 |
| 10 | A | 10 | CYS | 0 | -0.062 | -0.020 | 2.036 | 4.637 | 6.422 | 3.228 | -1.817 | -3.197 | 0.001 |
| 13 | A | 13 | THR | 0 | 0.007 | -0.044 | 2.178 | -3.559 | -2.788 | 5.223 | -1.896 | -4.098 | -0.001 |
| 14 | A | 14 | ALA | 0 | -0.013 | 0.007 | 2.383 | -11.658 | -9.264 | 4.179 | -2.596 | -3.977 | -0.032 |
| 15 | A | 15 | LEU | 0 | -0.011 | -0.009 | 2.636 | -7.466 | -5.834 | 0.430 | -0.678 | -1.385 | -0.016 |
| 16 | A | 16 | LEU | 0 | -0.031 | -0.013 | 3.629 | 1.435 | 3.544 | -0.007 | -0.879 | -1.222 | -0.002 |
| 22 | A | 24 | VAL | 0 | 0.007 | 0.011 | 3.555 | 1.000 | 1.209 | -0.001 | -0.047 | -0.161 | 0.000 |
| 23 | A | 26 | TYR | -1 | -0.874 | -0.947 | 1.784 | -104.702 | -106.006 | 14.596 | -7.055 | -6.237 | -0.075 |
| 24 | A | 27 | ASN | 0 | -0.019 | -0.016 | 1.799 | -1.019 | -3.706 | 11.798 | -4.240 | -4.870 | 0.037 |
| 25 | A | 28 | GLY | 0 | 0.000 | 0.015 | 4.251 | 1.529 | 2.207 | 0.009 | -0.135 | -0.552 | -0.001 |
| 26 | A | 29 | ILE | 0 | -0.025 | -0.016 | 2.737 | 2.299 | 3.082 | 2.891 | -1.265 | -2.409 | -0.007 |
| 27 | A | 30 | PRO | -1 | -0.775 | -0.856 | 1.795 | -157.007 | -163.360 | 36.409 | -16.402 | -13.655 | -0.205 |
| 6 | A | 6 | VAL | 0 | 0.007 | 0.002 | 8.906 | 2.285 | 2.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | TRP | 0 | -0.030 | -0.028 | 12.197 | 1.632 | 1.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ILE | 0 | 0.033 | 0.018 | 11.881 | 0.980 | 0.980 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | PRO | 0 | 0.010 | -0.002 | 9.740 | -2.125 | -2.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | THR | 0 | -0.058 | -0.035 | 6.494 | 2.646 | 2.646 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | VAL | 0 | -0.027 | -0.022 | 6.814 | 1.088 | 1.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 21 | SER | 0 | -0.012 | 0.007 | 6.073 | 3.544 | 3.544 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | ASN | 0 | -0.008 | -0.020 | 7.866 | 3.941 | 3.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | LYS | 1 | 0.851 | 0.922 | 9.060 | 22.049 | 22.049 | 0.000 | 0.000 | 0.000 | 0.000 |