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: JVYM9
Calculation Name: 2I32-E-Xray547
Preferred Name: Histone chaperone ASF1A
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2I32
Chain ID: E
ChEMBL ID: CHEMBL3392950
UniProt ID: Q9Y294
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 | 21 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -60677.57225 |
|---|---|
| FMO2-HF: Nuclear repulsion | 52024.697143 |
| FMO2-HF: Total energy | -8652.875107 |
| FMO2-MP2: Total energy | -8677.69128 |
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:446:LEU)
Summations of interaction energy for
fragment #1(A:446: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. |
| 42.828 | 48.628 | 1.355 | -2.281 | -4.873 | -0.011 |
Interaction energy analysis for fragmet #1(A:446: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 | A | 448 | LYS | 1 | 1.023 | 1.021 | 3.339 | 43.390 | 46.086 | -0.003 | -1.252 | -1.440 | -0.001 |
| 4 | A | 449 | GLN | 0 | -0.077 | -0.039 | 2.910 | -5.871 | -4.359 | 0.146 | -0.423 | -1.235 | -0.002 |
| 5 | A | 450 | VAL | 0 | 0.076 | 0.040 | 4.464 | 3.323 | 3.383 | -0.001 | -0.021 | -0.038 | 0.000 |
| 18 | A | 463 | PRO | 0 | -0.033 | -0.015 | 4.654 | -3.616 | -3.520 | -0.001 | -0.004 | -0.090 | 0.000 |
| 19 | A | 464 | LEU | 0 | -0.042 | -0.026 | 2.669 | -2.368 | -1.008 | 1.215 | -0.567 | -2.009 | -0.008 |
| 20 | A | 465 | CYS | 0 | -0.040 | -0.024 | 4.340 | 0.923 | 0.999 | -0.001 | -0.014 | -0.061 | 0.000 |
| 6 | A | 451 | GLU | -1 | -0.826 | -0.888 | 7.869 | -29.166 | -29.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 452 | THR | 0 | -0.006 | -0.001 | 9.809 | 1.354 | 1.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 453 | ARG | 1 | 0.886 | 0.924 | 13.595 | 16.339 | 16.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 454 | THR | 0 | -0.029 | -0.042 | 16.898 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 455 | ALA | 0 | 0.034 | 0.011 | 18.743 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 456 | ASP | -1 | -0.812 | -0.869 | 21.531 | -12.705 | -12.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 457 | GLY | 0 | 0.026 | 0.020 | 20.918 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 458 | ARG | 1 | 0.945 | 0.976 | 17.965 | 13.643 | 13.643 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 459 | ARG | 1 | 0.830 | 0.890 | 8.996 | 24.841 | 24.841 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 460 | ARG | 1 | 0.990 | 0.994 | 12.226 | 18.173 | 18.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 461 | ILE | 0 | -0.005 | -0.006 | 5.564 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 462 | THR | 0 | -0.015 | 0.002 | 7.804 | 2.469 | 2.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 466 | ILE | -1 | -0.882 | -0.928 | 5.090 | -27.649 | -27.649 | 0.000 | 0.000 | 0.000 | 0.000 |