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: RK8L8
Calculation Name: 4A8X-B-Xray549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4A8X
Chain ID: B
UniProt ID: Q15287
Base Structure: X-ray
Registration Date: 2025-10-12
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
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 | -85501.925492 |
|---|---|
| FMO2-HF: Nuclear repulsion | 74690.560085 |
| FMO2-HF: Total energy | -10811.365407 |
| FMO2-MP2: Total energy | -10842.889141 |
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(B:656:LEU)
Summations of interaction energy for
fragment #1(B:656:LEU)
| 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. |
| -118.687 | -112.017 | 14.988 | -11.174 | -10.484 | -0.124 |
Interaction energy analysis for fragmet #1(B:656:LEU)
| 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 | B | 658 | ASP | -1 | -0.826 | -0.912 | 3.424 | -48.350 | -46.712 | 0.000 | -0.584 | -1.053 | 0.000 |
| 4 | B | 659 | ASP | -1 | -0.861 | -0.910 | 1.903 | -117.864 | -114.140 | 14.240 | -10.260 | -7.705 | -0.121 |
| 5 | B | 660 | LEU | 0 | -0.055 | -0.015 | 2.605 | 7.421 | 8.729 | 0.748 | -0.330 | -1.726 | -0.003 |
| 6 | B | 661 | PHE | 0 | -0.023 | -0.008 | 5.225 | 6.450 | 6.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 662 | ARG | 1 | 0.935 | 0.987 | 8.147 | 19.752 | 19.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 663 | LYS | 1 | 0.929 | 0.962 | 8.262 | 32.591 | 32.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 664 | THR | 0 | -0.036 | -0.010 | 11.512 | 0.810 | 0.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 665 | LYS | 1 | 0.995 | 0.981 | 14.256 | 19.057 | 19.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 666 | GLY | 0 | 0.014 | 0.022 | 16.277 | 0.690 | 0.690 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 667 | THR | 0 | 0.002 | 0.004 | 17.409 | -0.831 | -0.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 668 | PRO | 0 | 0.051 | 0.018 | 17.681 | 0.694 | 0.694 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 669 | CYS | 0 | -0.076 | -0.041 | 12.936 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 670 | ILE | 0 | 0.023 | 0.022 | 13.782 | -0.796 | -0.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 671 | TYR | 0 | -0.029 | -0.053 | 6.425 | 0.756 | 0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 672 | TRP | 0 | 0.017 | -0.004 | 11.942 | 1.932 | 1.932 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 673 | LEU | 0 | 0.014 | -0.006 | 10.439 | -2.320 | -2.320 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 674 | PRO | 0 | -0.060 | -0.012 | 13.583 | 1.074 | 1.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 675 | LEU | 0 | 0.047 | 0.022 | 15.564 | -0.845 | -0.845 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 676 | THR | 0 | -0.057 | -0.065 | 13.312 | -0.530 | -0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 677 | PRO | 0 | -0.019 | -0.019 | 15.463 | 0.726 | 0.726 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 678 | GLU | -1 | -0.794 | -0.863 | 16.500 | -16.674 | -16.674 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 679 | ALA | 0 | 0.050 | 0.013 | 18.579 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 680 | ILE | 0 | -0.113 | -0.052 | 19.918 | 0.419 | 0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 681 | ALA | 0 | -0.096 | -0.053 | 22.482 | 0.540 | 0.540 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 682 | GLU | -2 | -1.928 | -1.934 | 22.495 | -24.107 | -24.107 | 0.000 | 0.000 | 0.000 | 0.000 |