FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: GNMJ1
Calculation Name: 2H4M-D-Xray372
Preferred Name: Heterogeneous nuclear ribonucleoprotein A1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2H4M
Chain ID: D
ChEMBL ID: CHEMBL1955709
UniProt ID: P09651
Base Structure: X-ray
Registration Date: 2023-06-21
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
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 | 27 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -58186.147065 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48019.75435 |
| FMO2-HF: Total energy | -10166.392715 |
| FMO2-MP2: Total energy | -10195.322917 |
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(D:263:PHE)
Summations of interaction energy for
fragment #1(D:263:PHE)
| 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. |
| -2.782 | 1.042 | 0.146 | -1.803 | -2.166 | -0.003 |
Interaction energy analysis for fragmet #1(D:263:PHE)
| 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 | D | 265 | ASN | 0 | -0.019 | -0.013 | 3.630 | -0.425 | 1.976 | -0.008 | -1.240 | -1.152 | 0.000 |
| 4 | D | 266 | TYR | 0 | 0.003 | -0.007 | 3.028 | -2.767 | -1.344 | 0.154 | -0.563 | -1.014 | -0.003 |
| 5 | D | 267 | ASN | 0 | -0.013 | -0.011 | 6.140 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 268 | ASN | 0 | -0.002 | 0.003 | 8.499 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 269 | GLN | 0 | 0.025 | 0.012 | 11.545 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 270 | SER | 0 | 0.009 | 0.016 | 14.528 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 271 | SER | 0 | 0.010 | 0.001 | 17.549 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 272 | ASN | 0 | -0.017 | -0.003 | 18.415 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 273 | PHE | 0 | -0.008 | -0.004 | 20.368 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 274 | GLY | 0 | 0.033 | 0.009 | 21.905 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 275 | PRO | 0 | -0.025 | -0.002 | 25.182 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 276 | MET | 0 | 0.028 | -0.002 | 23.362 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 277 | LYS | 1 | 0.926 | 0.967 | 28.223 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 278 | GLY | 0 | 0.054 | 0.035 | 31.258 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 279 | GLY | 0 | -0.007 | -0.003 | 33.860 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 280 | ASN | 0 | -0.007 | -0.004 | 34.909 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 281 | PHE | 0 | 0.035 | 0.006 | 38.102 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 282 | GLY | 0 | 0.012 | 0.012 | 40.316 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 283 | GLY | 0 | -0.020 | 0.005 | 37.879 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 284 | ARG | 1 | 0.921 | 0.941 | 32.694 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 285 | SER | 0 | 0.036 | 0.017 | 38.937 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 286 | SER | 0 | 0.019 | 0.011 | 38.263 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 287 | GLY | 0 | -0.006 | 0.013 | 37.985 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 288 | PRO | 0 | -0.011 | -0.029 | 39.213 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 289 | TYR | 0 | 0.008 | 0.027 | 34.805 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |