FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-04-23
All entries: 37539
Number of unique PDB entries: 7791
FMODB ID: 5J8KZ
Calculation Name: 4C0H-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4C0H
Chain ID: C
UniProt ID: Q08685
Base Structure: X-ray
Registration Date: 2023-09-23
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
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. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -83913.88107 |
|---|---|
| FMO2-HF: Nuclear repulsion | 72383.225217 |
| FMO2-HF: Total energy | -11530.655853 |
| FMO2-MP2: Total energy | -11564.605824 |
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(C:464:SER)
Summations of interaction energy for
fragment #1(C:464:SER)
| 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. |
| -2.188 | -0.878 | -0.005 | -0.653 | -0.652 | 0.001 |
Interaction energy analysis for fragmet #1(C:464:SER)
| 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 | C | 466 | SER | 0 | 0.037 | 0.012 | 3.879 | -2.553 | -1.243 | -0.005 | -0.653 | -0.652 | 0.001 |
| 4 | C | 467 | ASN | 0 | -0.039 | -0.017 | 6.189 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 476 | ASN | 0 | 0.000 | -0.011 | 18.856 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 477 | ILE | 0 | -0.011 | -0.002 | 14.838 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 478 | GLN | 0 | 0.033 | 0.018 | 17.580 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 479 | SER | 0 | -0.027 | -0.029 | 15.354 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 480 | ARG | 1 | 0.935 | 0.976 | 16.952 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 481 | ASN | 0 | 0.033 | 0.021 | 18.922 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 482 | TRP | 0 | 0.002 | -0.006 | 17.155 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 483 | TYR | 0 | -0.016 | -0.008 | 22.564 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 484 | LEU | 0 | 0.015 | 0.023 | 26.069 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 485 | SER | 0 | 0.013 | 0.003 | 29.515 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 486 | ASP | -1 | -0.849 | -0.931 | 31.399 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 487 | SER | 0 | -0.027 | -0.020 | 34.542 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 488 | GLN | 0 | 0.006 | 0.001 | 30.901 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 489 | TRP | 0 | 0.004 | 0.004 | 32.889 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 490 | ALA | 0 | 0.021 | 0.013 | 34.661 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 491 | ALA | 0 | -0.048 | -0.027 | 37.622 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 492 | PHE | 0 | -0.019 | 0.006 | 32.355 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 493 | LYS | 1 | 0.792 | 0.890 | 36.574 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 494 | ASP | -1 | -0.843 | -0.926 | 34.134 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 495 | ASP | -1 | -0.895 | -0.948 | 35.710 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 496 | GLU | -1 | -0.921 | -0.974 | 34.342 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 497 | ILE | 0 | -0.106 | -0.041 | 30.532 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 498 | THR | 0 | -0.037 | -0.023 | 33.113 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 499 | SER | 0 | -0.057 | -0.010 | 35.471 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |