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: 3KG4L
Calculation Name: 1F3K-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1F3K
Chain ID: A
UniProt ID: P56714
Base Structure: SolutionNMR
Registration Date: 2025-09-02
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 | 23 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -87009.841714 |
|---|---|
| FMO2-HF: Nuclear repulsion | 75233.433915 |
| FMO2-HF: Total energy | -11776.407799 |
| FMO2-MP2: Total energy | -11804.204867 |
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. |
| -184.301 | -171.903 | 5.882 | -7.634 | -10.646 | -0.028 |
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 | GLN | 0 | 0.076 | 0.022 | 2.000 | -19.344 | -17.926 | 5.489 | -2.023 | -4.885 | -0.034 |
| 4 | A | 4 | ALA | 0 | 0.075 | 0.010 | 4.510 | -0.732 | -0.668 | -0.002 | -0.004 | -0.058 | 0.000 |
| 8 | A | 8 | CYS | 0 | -0.108 | -0.046 | 4.696 | -10.035 | -10.037 | -0.002 | -0.030 | 0.034 | 0.000 |
| 13 | A | 13 | LEU | 0 | -0.033 | -0.008 | 3.687 | -1.876 | -1.481 | 0.002 | -0.063 | -0.333 | 0.000 |
| 14 | A | 14 | ASP | -1 | -0.759 | -0.886 | 3.845 | -43.033 | -39.982 | -0.011 | -1.447 | -1.594 | -0.009 |
| 17 | A | 18 | GLY | 0 | -0.013 | 0.002 | 2.635 | -6.368 | 0.420 | 0.410 | -4.018 | -3.180 | 0.015 |
| 18 | A | 19 | ILE | 0 | 0.033 | 0.033 | 4.403 | 1.207 | 1.627 | -0.001 | -0.033 | -0.386 | 0.000 |
| 22 | A | 25 | MET | 0 | -0.039 | -0.020 | 5.408 | 2.962 | 3.037 | -0.002 | -0.001 | -0.071 | 0.000 |
| 23 | A | 26 | TRP | -1 | -0.894 | -0.957 | 4.485 | -29.159 | -28.970 | -0.001 | -0.015 | -0.173 | 0.000 |
| 5 | A | 5 | ASP | -1 | -0.925 | -0.966 | 6.642 | -22.521 | -22.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLU | -1 | -0.902 | -0.931 | 5.866 | -36.881 | -36.881 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.015 | 0.015 | 6.874 | -1.409 | -1.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.859 | -0.925 | 7.664 | -22.098 | -22.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | VAL | 0 | -0.043 | -0.015 | 7.789 | -2.511 | -2.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | PHE | 0 | 0.009 | 0.003 | 9.748 | 2.199 | 2.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | SER | 0 | -0.046 | -0.037 | 8.851 | 1.888 | 1.888 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 21 | LEU | 0 | -0.005 | -0.007 | 6.529 | 3.050 | 3.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | GLY | 0 | -0.015 | 0.004 | 9.894 | 1.351 | 1.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | VAL | 0 | 0.014 | -0.013 | 7.888 | -0.991 | -0.991 | 0.000 | 0.000 | 0.000 | 0.000 |