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: 25KZR
Calculation Name: 2X04-C-Xray549
Preferred Name: Polyadenylate-binding protein 1
Target Type: SINGLE PROTEIN
Ligand Name: sulfate ion
Ligand 3-letter code: SO4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2X04
Chain ID: C
ChEMBL ID: CHEMBL1293286
UniProt ID: P11940
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 | 15 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -37891.307017 |
|---|---|
| FMO2-HF: Nuclear repulsion | 31923.72201 |
| FMO2-HF: Total energy | -5967.585006 |
| FMO2-MP2: Total energy | -5985.77166 |
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:1385:TRP)
Summations of interaction energy for
fragment #1(C:1385:TRP)
| 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. |
| -40.855 | -47.152 | 11.272 | 1.229 | -6.204 | -0.028 |
Interaction energy analysis for fragmet #1(C:1385:TRP)
| 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 | 1387 | PRO | 0 | -0.040 | -0.014 | 2.266 | -15.254 | -21.791 | 11.270 | 1.271 | -6.003 | -0.028 |
| 4 | C | 1388 | GLU | -1 | -0.847 | -0.896 | 3.755 | -34.157 | -34.023 | 0.003 | -0.031 | -0.107 | 0.000 |
| 13 | C | 1397 | GLY | 0 | -0.061 | -0.025 | 4.499 | -2.848 | -2.742 | -0.001 | -0.011 | -0.094 | 0.000 |
| 5 | C | 1389 | PHE | 0 | -0.029 | -0.013 | 6.703 | 2.123 | 2.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 1390 | HIS | 0 | -0.003 | -0.014 | 9.447 | 1.925 | 1.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 1391 | PRO | 0 | 0.016 | -0.008 | 13.219 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 1392 | GLY | 0 | 0.009 | 0.013 | 16.735 | 0.430 | 0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 1393 | VAL | 0 | -0.032 | -0.006 | 13.066 | 0.607 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 1394 | PRO | 0 | -0.018 | -0.012 | 13.975 | -0.778 | -0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 1395 | TRP | 0 | -0.014 | -0.013 | 7.021 | -0.627 | -0.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 1396 | LYS | 1 | 0.988 | 0.980 | 6.474 | 26.702 | 26.702 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 1398 | LEU | 0 | -0.049 | -0.027 | 5.547 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 1399 | GLN | -1 | -0.916 | -0.936 | 8.229 | -19.466 | -19.466 | 0.000 | 0.000 | 0.000 | 0.000 |