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: 8Q95Y
Calculation Name: 1WT8-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1WT8
Chain ID: A
UniProt ID: Q7Z0H4
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 | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -107537.207943 |
|---|---|
| FMO2-HF: Nuclear repulsion | 94026.582057 |
| FMO2-HF: Total energy | -13510.625886 |
| FMO2-MP2: Total energy | -13543.473031 |
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:THR)
Summations of interaction energy for
fragment #1(A:1:THR)
| 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. |
| -20.888 | -17.285 | 7.237 | -4.732 | -6.108 | -0.06 |
Interaction energy analysis for fragmet #1(A:1:THR)
| 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 | TYR | 0 | 0.110 | 0.049 | 2.239 | -18.994 | -15.391 | 7.237 | -4.732 | -6.108 | -0.060 |
| 4 | A | 4 | PRO | 0 | 0.007 | 0.031 | 5.545 | 2.363 | 2.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | VAL | 0 | 0.024 | 0.013 | 7.780 | 3.052 | 3.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ASN | 0 | 0.029 | 0.014 | 10.476 | -0.788 | -0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | CYS | 0 | -0.105 | -0.016 | 13.615 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.848 | 0.890 | 17.077 | 14.589 | 14.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | THR | 0 | -0.006 | -0.012 | 20.190 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ASP | -1 | -0.770 | -0.861 | 19.701 | -14.816 | -14.816 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ARG | 1 | 0.999 | 0.991 | 20.325 | 13.060 | 13.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ASP | -1 | -0.875 | -0.923 | 19.331 | -14.969 | -14.969 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | CYS | 0 | 0.006 | -0.013 | 12.440 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | 0.035 | 0.034 | 17.500 | -0.443 | -0.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | MET | 0 | -0.054 | -0.026 | 15.830 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | CYS | 0 | -0.092 | -0.036 | 10.700 | 0.378 | 0.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.009 | 0.012 | 16.508 | -0.502 | -0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LEU | 0 | -0.012 | -0.001 | 19.217 | 0.826 | 0.826 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.037 | 0.017 | 21.245 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ILE | 0 | -0.058 | -0.027 | 14.841 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | SER | 0 | 0.009 | -0.027 | 17.126 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 0.921 | 0.972 | 10.894 | 23.239 | 23.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ASN | 0 | -0.004 | -0.019 | 15.942 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | GLY | 0 | 0.039 | 0.027 | 15.868 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | TYR | 0 | -0.051 | -0.044 | 7.244 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 28 | GLN | 0 | -0.025 | -0.028 | 9.565 | -1.522 | -1.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 29 | GLY | 0 | -0.013 | -0.028 | 10.496 | 0.909 | 0.909 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | THR | -1 | -0.918 | -0.934 | 6.665 | -26.284 | -26.284 | 0.000 | 0.000 | 0.000 | 0.000 |