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: J2NJ9
Calculation Name: 2RF9-C-Xray540
Preferred Name: Epidermal growth factor receptor erbB1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2RF9
Chain ID: C
ChEMBL ID: CHEMBL203
UniProt ID: P00533
Base Structure: X-ray
Registration Date: 2025-07-09
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 | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -72036.823963 |
|---|---|
| FMO2-HF: Nuclear repulsion | 61710.627271 |
| FMO2-HF: Total energy | -10326.196692 |
| FMO2-MP2: Total energy | -10355.940573 |
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:336:LYS)
Summations of interaction energy for
fragment #1(C:336:LYS)
| 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. |
| -4.156 | -0.474 | -0.036 | -2.123 | -1.523 | -0.003 |
Interaction energy analysis for fragmet #1(C:336:LYS)
| 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 | C | 337 | SER | 0 | -0.074 | 0.098 | 4.294 | -0.680 | -0.383 | -0.001 | -0.168 | -0.128 | 0.000 |
| 5 | C | 338 | LEU | 0 | 0.122 | -0.129 | 3.819 | -2.738 | 0.402 | -0.039 | -1.871 | -1.230 | -0.003 |
| 6 | C | 338 | LEU | 0 | -0.020 | 0.138 | 3.691 | -0.237 | 0.008 | 0.004 | -0.084 | -0.165 | 0.000 |
| 7 | C | 339 | PRO | 0 | 0.021 | -0.079 | 5.906 | -0.522 | -0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 340 | SER | 0 | 0.031 | 0.025 | 9.346 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 340 | SER | 0 | -0.012 | 0.089 | 8.736 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 341 | TYR | 0 | 0.115 | -0.104 | 10.526 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 341 | TYR | 0 | -0.093 | 0.102 | 13.394 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 342 | LEU | 0 | 0.007 | -0.106 | 13.778 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 342 | LEU | 0 | -0.038 | 0.121 | 15.752 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 343 | ASN | 0 | 0.157 | -0.053 | 15.397 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 343 | ASN | 0 | -0.105 | 0.076 | 18.412 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 344 | GLY | 0 | -0.026 | -0.132 | 14.187 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 345 | VAL | 0 | 0.038 | -0.018 | 15.217 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 345 | VAL | 0 | -0.077 | 0.112 | 17.339 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 346 | MET | 0 | 0.188 | -0.104 | 16.406 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 346 | MET | 0 | -0.109 | 0.118 | 15.644 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 347 | PRO | 0 | -0.095 | -0.115 | 16.667 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 348 | PRO | 0 | 0.021 | -0.005 | 19.889 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 349 | THR | 0 | 0.012 | -0.005 | 21.648 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 349 | THR | 0 | -0.041 | 0.064 | 23.199 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 350 | GLN | 0 | 0.154 | -0.038 | 18.425 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 350 | GLN | 0 | -0.087 | 0.108 | 15.591 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 351 | SER | 0 | 0.020 | -0.103 | 19.734 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 351 | SER | 0 | -0.015 | 0.094 | 21.046 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 352 | PHE | 0 | 0.007 | -0.118 | 20.135 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 352 | PHE | 0 | -0.085 | 0.108 | 16.605 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 353 | ALA | 0 | 0.175 | -0.073 | 21.662 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 353 | ALA | 0 | -0.057 | 0.098 | 25.757 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 354 | PRO | 0 | -0.065 | -0.145 | 23.398 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 355 | ASP | 0 | 0.070 | -0.004 | 23.543 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 355 | ASP | -1 | -0.888 | -0.794 | 22.578 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 356 | PRO | 0 | -0.007 | -0.112 | 24.868 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 357 | LYS | 0 | 0.119 | 0.012 | 24.836 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 357 | LYS | 1 | 0.803 | 1.023 | 21.360 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 358 | TYR | 0 | -0.014 | -0.094 | 24.428 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 358 | TYR | 0 | -0.040 | 0.087 | 20.022 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 359 | VAL | 0 | 0.066 | -0.118 | 25.814 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 359 | VAL | 0 | -0.079 | 0.131 | 26.372 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 360 | SER | 0 | 0.013 | -0.084 | 28.570 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 360 | SER | 0 | -0.025 | 0.073 | 31.889 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 361 | SER | 0 | 0.044 | -0.091 | 32.069 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | C | 361 | SER | 0 | -0.025 | 0.105 | 35.418 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | C | 362 | LYS | 0 | -0.049 | -0.096 | 35.287 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | C | 362 | LYS | 1 | 1.001 | 0.994 | 35.287 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |