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: 8N39Y
Calculation Name: 2H4M-D-Xray540
Preferred Name: Heterogeneous nuclear ribonucleoprotein A1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2H4M
Chain ID: D
ChEMBL ID: CHEMBL1955709
UniProt ID: P09651
Base Structure: X-ray
Registration Date: 2025-07-10
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 | OptH |
| 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 | 45 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -58269.637178 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48107.18009 |
| FMO2-HF: Total energy | -10162.457089 |
| FMO2-MP2: Total energy | -10191.308067 |
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. |
| -0.331 | 2.123 | -0.008 | -1.31 | -1.135 | -0.001 |
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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | D | 265 | ASN | 0 | 0.121 | 0.029 | 3.604 | -1.158 | 1.053 | -0.006 | -1.272 | -0.933 | -0.001 |
| 5 | D | 265 | ASN | 0 | -0.117 | 0.066 | 5.241 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 266 | TYR | 0 | 0.049 | -0.105 | 4.689 | 2.161 | 2.282 | -0.002 | -0.010 | -0.109 | 0.000 |
| 7 | D | 266 | TYR | 0 | -0.102 | 0.099 | 4.214 | -0.297 | -0.175 | 0.000 | -0.028 | -0.093 | 0.000 |
| 8 | D | 267 | ASN | 0 | 0.169 | -0.061 | 6.611 | -0.589 | -0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 267 | ASN | 0 | -0.162 | 0.037 | 8.360 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 268 | ASN | 0 | 0.141 | -0.070 | 9.238 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 268 | ASN | 0 | -0.130 | 0.069 | 11.685 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 269 | GLN | 0 | 0.072 | -0.121 | 11.852 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 269 | GLN | 0 | -0.059 | 0.136 | 12.827 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 270 | SER | 0 | 0.075 | -0.077 | 14.503 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 270 | SER | 0 | -0.026 | 0.102 | 19.204 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 271 | SER | 0 | -0.037 | -0.088 | 17.451 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 271 | SER | 0 | -0.011 | 0.072 | 18.013 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 272 | ASN | 0 | 0.078 | -0.076 | 18.347 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 272 | ASN | 0 | -0.101 | 0.070 | 19.210 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 273 | PHE | 0 | 0.111 | -0.088 | 20.624 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 273 | PHE | 0 | -0.068 | 0.106 | 20.665 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 274 | GLY | 0 | -0.008 | -0.092 | 21.888 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 275 | PRO | 0 | -0.024 | -0.013 | 25.442 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 276 | MET | 0 | 0.110 | -0.024 | 27.819 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 276 | MET | 0 | -0.078 | 0.138 | 24.052 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 277 | LYS | 0 | 0.074 | -0.098 | 28.424 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 277 | LYS | 1 | 0.889 | 1.057 | 30.628 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 278 | GLY | 0 | 0.016 | -0.065 | 31.443 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 279 | GLY | 0 | -0.002 | -0.007 | 33.965 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 280 | ASN | 0 | 0.102 | 0.060 | 35.255 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 280 | ASN | 0 | -0.082 | 0.046 | 36.028 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 281 | PHE | 0 | 0.043 | -0.113 | 38.187 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 281 | PHE | 0 | -0.090 | 0.107 | 39.723 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 282 | GLY | 0 | 0.034 | -0.093 | 40.575 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 283 | GLY | 0 | 0.018 | 0.012 | 38.605 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | D | 284 | ARG | 0 | 0.070 | 0.031 | 38.100 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 284 | ARG | 1 | 0.861 | 1.023 | 33.107 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 285 | SER | 0 | 0.111 | -0.049 | 39.399 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | D | 285 | SER | 0 | -0.054 | 0.062 | 40.780 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 286 | SER | 0 | 0.012 | -0.091 | 39.146 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 286 | SER | 0 | -0.002 | 0.102 | 40.966 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 287 | GLY | 0 | -0.024 | -0.089 | 39.200 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 288 | PRO | 0 | -0.024 | -0.026 | 40.023 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 289 | TYR | 0 | -0.027 | 0.013 | 39.439 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 289 | TYR | 0 | 0.045 | 0.014 | 36.502 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |