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: 4J84N
Calculation Name: 4C0H-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
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 | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
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 | -83713.262761 |
|---|---|
| FMO2-HF: Nuclear repulsion | 72182.762297 |
| FMO2-HF: Total energy | -11530.500464 |
| FMO2-MP2: Total energy | -11564.45719 |
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. |
| -2.082 | -0.655 | -0.016 | -0.677 | -0.734 | 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 | 0.063 | 0.021 | 3.778 | -2.295 | -0.868 | -0.016 | -0.677 | -0.734 | 0.001 |
| 4 | C | 467 | ASN | 0 | -0.032 | -0.021 | 5.801 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 476 | ASN | 0 | 0.000 | -0.013 | 19.556 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 477 | ILE | 0 | -0.008 | 0.004 | 15.121 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 478 | GLN | 0 | 0.022 | 0.009 | 17.856 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 479 | SER | 0 | -0.029 | -0.024 | 15.756 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 480 | ARG | 1 | 0.948 | 0.988 | 17.036 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 481 | ASN | 0 | 0.032 | 0.017 | 18.921 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 482 | TRP | 0 | 0.000 | -0.009 | 16.779 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 483 | TYR | 0 | -0.005 | -0.003 | 22.407 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 484 | LEU | 0 | 0.016 | 0.020 | 25.818 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 485 | SER | 0 | 0.005 | 0.003 | 29.171 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 486 | ASP | -1 | -0.846 | -0.933 | 30.831 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 487 | SER | 0 | -0.036 | -0.025 | 34.120 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 488 | GLN | 0 | -0.007 | -0.015 | 30.633 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 489 | TRP | 0 | 0.015 | 0.007 | 32.270 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 490 | ALA | 0 | 0.011 | 0.014 | 34.198 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 491 | ALA | 0 | -0.039 | -0.026 | 37.581 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 492 | PHE | 0 | -0.010 | 0.016 | 32.440 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 493 | LYS | 1 | 0.800 | 0.900 | 36.570 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 494 | ASP | -1 | -0.832 | -0.932 | 34.126 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 495 | ASP | -1 | -0.949 | -0.971 | 35.804 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 496 | GLU | -1 | -0.927 | -0.966 | 34.656 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 497 | ILE | 0 | -0.067 | -0.020 | 30.619 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 498 | THR | 0 | -0.060 | -0.024 | 33.175 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 499 | SER | 0 | -0.035 | -0.014 | 35.270 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |