FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: MV92Z
Calculation Name: 4BD2-C-Xray372
Preferred Name: Apoptosis regulator BAX
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 4BD2
Chain ID: C
ChEMBL ID: CHEMBL5318
UniProt ID: Q07812
Base Structure: X-ray
Registration Date: 2023-06-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 30 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -93037.933867 |
|---|---|
| FMO2-HF: Nuclear repulsion | 81292.17221 |
| FMO2-HF: Total energy | -11745.761657 |
| FMO2-MP2: Total energy | -11779.583109 |
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:76:SER)
Summations of interaction energy for
fragment #1(C:76:SER)
| 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. |
| -9.749 | -2.539 | 1.088 | -3.454 | -4.846 | 0.022 |
Interaction energy analysis for fragmet #1(C:76:SER)
| 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 | 78 | SER | 0 | -0.010 | 0.007 | 2.729 | -3.159 | 0.514 | 0.431 | -1.953 | -2.151 | 0.010 |
| 4 | C | 79 | GLN | 0 | -0.010 | -0.020 | 2.589 | -5.571 | -2.418 | 0.657 | -1.418 | -2.393 | 0.012 |
| 5 | C | 80 | GLU | -1 | -0.888 | -0.941 | 4.046 | -2.738 | -2.354 | 0.000 | -0.083 | -0.302 | 0.000 |
| 6 | C | 81 | ASP | -1 | -0.901 | -0.954 | 5.833 | 0.308 | 0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 82 | ILE | 0 | -0.046 | -0.020 | 6.305 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 83 | ILE | 0 | 0.033 | 0.019 | 6.595 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 84 | ARG | 1 | 0.934 | 0.971 | 9.060 | 1.272 | 1.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 85 | ASN | 0 | -0.025 | -0.012 | 11.696 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 86 | ILE | 0 | -0.008 | 0.005 | 11.684 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 87 | ALA | 0 | 0.007 | 0.008 | 13.936 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 88 | ARG | 1 | 0.931 | 0.964 | 15.133 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 89 | HIS | 0 | -0.004 | -0.007 | 17.351 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 90 | LEU | 0 | 0.004 | -0.003 | 17.234 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 91 | ALA | 0 | 0.014 | 0.012 | 19.898 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 92 | GLN | 0 | 0.000 | 0.012 | 21.649 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 93 | VAL | 0 | -0.023 | -0.010 | 23.041 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 94 | GLY | 0 | -0.009 | -0.010 | 24.308 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 95 | ASP | -1 | -0.883 | -0.943 | 25.582 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 96 | SER | 0 | -0.120 | -0.085 | 27.266 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 97 | MET | 0 | -0.041 | -0.015 | 28.623 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 98 | ASP | -1 | -0.857 | -0.926 | 30.950 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 99 | ARG | 1 | 0.803 | 0.911 | 31.466 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 100 | SER | 0 | -0.042 | -0.003 | 34.535 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 101 | ILE | 0 | -0.014 | 0.019 | 36.784 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 102 | PRO | 0 | -0.028 | -0.034 | 37.819 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 103 | PRO | 0 | 0.055 | 0.012 | 33.511 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 104 | GLY | 0 | -0.012 | -0.002 | 31.641 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 105 | LEU | 0 | -0.007 | 0.003 | 26.254 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |