FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-06
All entries: 70436
Number of unique PDB entries: 28101
FMODB ID: N2K5Q
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):
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 | 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 | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -72064.654859 |
|---|---|
| FMO2-HF: Nuclear repulsion | 61738.079903 |
| FMO2-HF: Total energy | -10326.574956 |
| FMO2-MP2: Total energy | -10356.288082 |
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. |
| -1.514 | 0.443 | -0.01 | -0.986 | -0.959 | 0.001 |
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 | 0.062 | 4.202 | -0.652 | -0.372 | 0.000 | -0.131 | -0.149 | 0.000 |
| 5 | C | 338 | LEU | 0 | 0.049 | -0.105 | 3.865 | 0.094 | 1.484 | -0.016 | -0.749 | -0.624 | 0.000 |
| 6 | C | 338 | LEU | 0 | -0.006 | 0.136 | 3.648 | -0.366 | -0.079 | 0.006 | -0.106 | -0.186 | 0.001 |
| 7 | C | 339 | PRO | 0 | 0.016 | -0.091 | 5.876 | -0.550 | -0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 340 | SER | 0 | 0.038 | 0.042 | 9.530 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 340 | SER | 0 | -0.011 | 0.084 | 8.914 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 341 | TYR | 0 | 0.066 | -0.119 | 10.622 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 341 | TYR | 0 | -0.076 | 0.106 | 13.287 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 342 | LEU | 0 | 0.077 | -0.085 | 13.700 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 342 | LEU | 0 | -0.043 | 0.121 | 15.638 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 343 | ASN | 0 | 0.109 | -0.071 | 15.762 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 343 | ASN | 0 | -0.108 | 0.069 | 18.306 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 344 | GLY | 0 | 0.011 | -0.113 | 13.976 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 345 | VAL | 0 | 0.036 | -0.007 | 15.015 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 345 | VAL | 0 | -0.088 | 0.109 | 17.974 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 346 | MET | 0 | 0.169 | -0.101 | 16.205 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 346 | MET | 0 | -0.108 | 0.097 | 15.757 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 347 | PRO | 0 | -0.079 | -0.110 | 16.698 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 348 | PRO | 0 | 0.007 | -0.020 | 19.733 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 349 | THR | 0 | -0.002 | 0.002 | 21.590 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 349 | THR | 0 | 0.001 | 0.080 | 22.833 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 350 | GLN | 0 | 0.105 | -0.066 | 18.397 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 350 | GLN | 0 | -0.077 | 0.110 | 15.566 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 351 | SER | 0 | 0.021 | -0.113 | 19.760 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 351 | SER | 0 | -0.020 | 0.092 | 20.682 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 352 | PHE | 0 | 0.008 | -0.097 | 20.104 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 352 | PHE | 0 | -0.068 | 0.099 | 16.813 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 353 | ALA | 0 | 0.164 | -0.079 | 21.585 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 353 | ALA | 0 | -0.069 | 0.103 | 25.472 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 354 | PRO | 0 | -0.054 | -0.133 | 23.377 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 355 | ASP | 0 | 0.115 | 0.002 | 23.695 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 355 | ASP | -1 | -0.923 | -0.808 | 22.442 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 356 | PRO | 0 | 0.004 | -0.111 | 25.098 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 357 | LYS | 0 | 0.108 | 0.008 | 24.914 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 357 | LYS | 1 | 0.795 | 1.050 | 20.727 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 358 | TYR | 0 | -0.008 | -0.105 | 24.794 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 358 | TYR | 0 | -0.042 | 0.087 | 19.763 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 359 | VAL | 0 | 0.068 | -0.113 | 26.188 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 359 | VAL | 0 | -0.108 | 0.114 | 26.634 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 360 | SER | 0 | 0.074 | -0.061 | 28.799 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 360 | SER | 0 | -0.036 | 0.058 | 32.139 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 361 | SER | 0 | 0.036 | -0.070 | 32.146 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | C | 361 | SER | 0 | -0.015 | 0.108 | 34.887 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | C | 362 | LYS | 0 | -0.034 | -0.098 | 35.131 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | C | 362 | LYS | 1 | 0.951 | 0.961 | 34.632 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |