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: 9GYZ2
Calculation Name: 5FCG-C-Xray323
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: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
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. 1.20200129 |
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. 15 / 20190524 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -85211.526526 |
|---|---|
| FMO2-HF: Nuclear repulsion | 74177.748321 |
| FMO2-HF: Total energy | -11033.778205 |
| FMO2-MP2: Total energy | -11065.877184 |
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. |
| 43.716 | 22.313 | 0.718 | 21.404 | -0.719 | 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 | -0.064 | -0.017 | 2.396 | 13.923 | -7.480 | 0.718 | 21.404 | -0.719 | 0.000 |
| 4 | C | 113 | LYS | 1 | 0.925 | 0.958 | 5.792 | -27.287 | -27.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 114 | ASP | -1 | -0.816 | -0.897 | 8.117 | 24.396 | 24.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 115 | CYS | 0 | -0.036 | -0.039 | 10.537 | -1.107 | -1.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 116 | VAL | 0 | 0.005 | 0.013 | 10.219 | -0.702 | -0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 117 | PHE | 0 | 0.003 | 0.003 | 10.081 | -0.691 | -0.691 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 118 | LYS | 1 | 0.885 | 0.937 | 11.948 | -15.864 | -15.864 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 119 | ASP | -1 | -0.874 | -0.942 | 15.210 | 15.564 | 15.564 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 120 | TRP | 0 | -0.048 | -0.025 | 9.190 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 121 | GLU | -1 | -0.937 | -0.966 | 15.574 | 14.962 | 14.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 122 | GLU | -1 | -0.921 | -0.960 | 17.849 | 13.211 | 13.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 123 | LEU | 0 | 0.034 | 0.024 | 18.598 | -0.577 | -0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 124 | GLY | 0 | -0.009 | -0.010 | 19.966 | -0.630 | -0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 125 | GLU | -1 | -0.916 | -0.971 | 21.376 | 10.875 | 10.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 126 | GLU | -1 | -0.930 | -0.969 | 23.448 | 11.634 | 11.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 127 | ILE | 0 | -0.047 | -0.030 | 22.292 | -0.550 | -0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 128 | ARG | 1 | 0.892 | 0.944 | 24.293 | -11.550 | -11.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 129 | LEU | 0 | -0.050 | -0.017 | 27.458 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 130 | LYS | 1 | 0.873 | 0.927 | 29.450 | -9.492 | -9.492 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 131 | VAL | 0 | 0.009 | 0.038 | 29.076 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 132 | PHE | 0 | -0.039 | -0.009 | 31.820 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 133 | VAL | 0 | 0.008 | -0.009 | 34.754 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 134 | LEU | 0 | -0.096 | -0.057 | 35.660 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 135 | GLY | -1 | -0.922 | -0.942 | 34.850 | 8.273 | 8.273 | 0.000 | 0.000 | 0.000 | 0.000 |