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: 2JL5R
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 | 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 | 30 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -93480.795597 |
|---|---|
| FMO2-HF: Nuclear repulsion | 81734.829365 |
| FMO2-HF: Total energy | -11745.966233 |
| FMO2-MP2: Total energy | -11779.780925 |
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. |
| -9.066 | -2.407 | 2.822 | -3.734 | -5.746 | 0.025 |
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 | -0.003 | 0.009 | 2.737 | -1.547 | 1.295 | 0.368 | -1.426 | -1.784 | 0.008 |
| 4 | C | 79 | GLN | 0 | 0.000 | -0.012 | 2.197 | -6.998 | -3.747 | 2.452 | -2.130 | -3.572 | 0.017 |
| 5 | C | 80 | GLU | -1 | -0.809 | -0.881 | 3.838 | -2.276 | -1.710 | 0.002 | -0.178 | -0.390 | 0.000 |
| 6 | C | 81 | ASP | -1 | -0.826 | -0.901 | 5.696 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 82 | ILE | 0 | -0.073 | -0.024 | 6.172 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 83 | ILE | 0 | 0.014 | 0.010 | 6.014 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 84 | ARG | 1 | 0.822 | 0.869 | 8.284 | 1.311 | 1.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 85 | ASN | 0 | -0.052 | -0.027 | 11.131 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 86 | ILE | 0 | 0.012 | 0.010 | 11.067 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 87 | ALA | 0 | 0.006 | 0.005 | 13.483 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 88 | ARG | 1 | 0.901 | 0.943 | 15.181 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 89 | HIS | 0 | -0.014 | -0.004 | 17.006 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 90 | LEU | 0 | 0.002 | -0.010 | 16.707 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 91 | ALA | 0 | -0.001 | 0.011 | 19.509 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 92 | GLN | 0 | -0.026 | -0.004 | 21.451 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 93 | VAL | 0 | -0.025 | -0.006 | 22.604 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 94 | GLY | 0 | 0.009 | 0.005 | 23.965 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 95 | ASP | -1 | -0.876 | -0.948 | 24.982 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 96 | SER | 0 | -0.117 | -0.082 | 26.739 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 97 | MET | 0 | -0.030 | -0.007 | 28.264 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 98 | ASP | -1 | -0.854 | -0.932 | 30.657 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 99 | ARG | 1 | 0.820 | 0.922 | 30.480 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 100 | SER | 0 | -0.049 | -0.012 | 33.724 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 101 | ILE | 0 | -0.005 | 0.008 | 36.404 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 102 | PRO | 0 | -0.023 | -0.028 | 37.212 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 103 | PRO | 0 | 0.036 | 0.018 | 33.217 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 104 | GLY | 0 | -0.003 | -0.010 | 31.178 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 105 | LEU | 0 | -0.007 | 0.016 | 25.818 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |