FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: VR131
Calculation Name: 5FCG-C-Xray372
Preferred Name: Apoptosis regulator Bcl-2
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 5FCG
Chain ID: C
ChEMBL ID: CHEMBL4860
UniProt ID: P10415
Base Structure: X-ray
Registration Date: 2023-06-20
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 | OptHSide |
| 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 | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -85297.343079 |
|---|---|
| FMO2-HF: Nuclear repulsion | 74262.672528 |
| FMO2-HF: Total energy | -11034.670551 |
| FMO2-MP2: Total energy | -11066.781183 |
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:110:GLU)
Summations of interaction energy for
fragment #1(C:110:GLU)
| 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. |
| 34.755 | 14.199 | 0.43 | 20.829 | -0.703 | 0 |
Interaction energy analysis for fragmet #1(C:110:GLU)
| 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 | 112 | ILE | 0 | -0.073 | -0.021 | 2.424 | 13.059 | -7.497 | 0.430 | 20.829 | -0.703 | 0.000 |
| 4 | C | 113 | LYS | 1 | 0.934 | 0.961 | 5.813 | -28.511 | -28.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 114 | ASP | -1 | -0.814 | -0.899 | 8.138 | 25.726 | 25.726 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 115 | CYS | 0 | -0.024 | -0.029 | 10.551 | -0.931 | -0.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 116 | VAL | 0 | 0.000 | 0.009 | 10.231 | -0.811 | -0.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 117 | PHE | 0 | -0.005 | -0.001 | 10.070 | -0.808 | -0.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 118 | LYS | 1 | 0.844 | 0.888 | 11.963 | -16.099 | -16.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 119 | ASP | -1 | -0.866 | -0.938 | 15.228 | 16.099 | 16.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 120 | TRP | 0 | -0.067 | -0.034 | 9.228 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 121 | GLU | -1 | -0.916 | -0.955 | 15.464 | 15.354 | 15.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 122 | GLU | -1 | -0.863 | -0.901 | 17.861 | 13.494 | 13.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 123 | LEU | 0 | 0.004 | 0.004 | 18.606 | -0.644 | -0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 124 | GLY | 0 | 0.011 | 0.001 | 19.955 | -0.642 | -0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 125 | GLU | -1 | -0.804 | -0.890 | 21.376 | 10.861 | 10.861 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 126 | GLU | -1 | -0.947 | -0.968 | 23.904 | 11.484 | 11.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 127 | ILE | 0 | -0.047 | -0.035 | 22.214 | -0.579 | -0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 128 | ARG | 1 | 0.785 | 0.863 | 24.073 | -11.811 | -11.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 129 | LEU | 0 | -0.042 | -0.012 | 27.458 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 130 | LYS | 1 | 0.875 | 0.933 | 29.450 | -9.642 | -9.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 131 | VAL | 0 | 0.010 | 0.033 | 29.009 | -0.189 | -0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 132 | PHE | 0 | -0.039 | -0.012 | 31.820 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 133 | VAL | 0 | 0.038 | 0.008 | 34.746 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 134 | LEU | 0 | -0.045 | -0.025 | 35.660 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 135 | GLY | 0 | -0.019 | 0.003 | 34.850 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |