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: KV4M3
Calculation Name: 4S1Z-F-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4S1Z
Chain ID: F
UniProt ID: P62987
Base Structure: X-ray
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 | -103887.579393 |
|---|---|
| FMO2-HF: Nuclear repulsion | 91353.513034 |
| FMO2-HF: Total energy | -12534.066358 |
| FMO2-MP2: Total energy | -12566.42747 |
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:6:ILE)
Summations of interaction energy for
fragment #1(A:6: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. |
| -23.292 | -24.88 | 11.863 | -1.115 | -9.162 | -0.057 |
Interaction energy analysis for fragmet #1(A:6: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 | 8 | TRP | 0 | 0.032 | -0.002 | 2.174 | -8.446 | -10.491 | 11.301 | -1.600 | -7.657 | -0.056 |
| 4 | A | 9 | ALA | 0 | 0.033 | 0.021 | 3.094 | 5.400 | 4.667 | 0.198 | 0.775 | -0.240 | -0.001 |
| 13 | A | 18 | TRP | 0 | 0.054 | 0.018 | 4.435 | -10.445 | -10.331 | -0.001 | -0.027 | -0.087 | 0.000 |
| 14 | A | 19 | PRO | 0 | 0.026 | 0.003 | 2.462 | 2.208 | 3.095 | 0.366 | -0.242 | -1.011 | 0.000 |
| 15 | A | 20 | SER | 0 | 0.004 | -0.006 | 4.412 | 1.668 | 1.857 | -0.001 | -0.021 | -0.167 | 0.000 |
| 5 | A | 10 | CYS | 0 | -0.030 | -0.011 | 6.479 | 1.412 | 1.412 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 11 | GLU | -1 | -0.797 | -0.904 | 9.087 | -20.589 | -20.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 12 | TYR | 0 | -0.041 | -0.007 | 11.613 | 0.832 | 0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 13 | CYS | 0 | -0.112 | -0.049 | 12.014 | 0.634 | 0.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 14 | THR | 0 | 0.033 | 0.028 | 11.204 | 1.224 | 1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 15 | TYR | 0 | 0.016 | -0.021 | 10.527 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 16 | GLU | -1 | -0.831 | -0.902 | 5.848 | -44.840 | -44.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 17 | ASN | 0 | 0.039 | 0.020 | 5.806 | 5.130 | 5.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 21 | ALA | 0 | -0.042 | 0.008 | 7.343 | 3.118 | 3.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 22 | ILE | 0 | 0.025 | -0.004 | 8.085 | -1.404 | -1.404 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 23 | LYS | 1 | 0.956 | 0.980 | 10.589 | 18.464 | 18.464 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 24 | CYS | 0 | -0.038 | 0.010 | 10.113 | -1.598 | -1.598 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 25 | THR | 0 | -0.034 | -0.025 | 10.734 | 1.829 | 1.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 26 | MET | 0 | 0.002 | 0.004 | 13.049 | 1.736 | 1.736 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 27 | CYS | 0 | 0.018 | -0.001 | 14.372 | 0.922 | 0.922 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 28 | ARG | 1 | 0.864 | 0.941 | 14.723 | 14.884 | 14.884 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 29 | ALA | 0 | 0.046 | -0.008 | 14.180 | 0.667 | 0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 30 | GLN | 0 | -0.052 | -0.016 | 11.198 | 2.023 | 2.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 31 | ARG | 1 | 0.880 | 0.943 | 6.381 | 27.865 | 27.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 32 | PRO | -1 | -0.822 | -0.886 | 6.730 | -25.561 | -25.561 | 0.000 | 0.000 | 0.000 | 0.000 |