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: 5361Z
Calculation Name: 2XA0-C-Xray372
Preferred Name: Apoptosis regulator BAX
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2XA0
Chain ID: C
ChEMBL ID: CHEMBL3414407
UniProt ID: Q07813
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 | 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 | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -84481.644959 |
|---|---|
| FMO2-HF: Nuclear repulsion | 73048.034263 |
| FMO2-HF: Total energy | -11433.610696 |
| FMO2-MP2: Total energy | -11464.431023 |
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:57:LYS)
Summations of interaction energy for
fragment #1(C:57: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. |
| -37.942 | -34.758 | 0.378 | -1.51 | -2.053 | 0.001 |
Interaction energy analysis for fragmet #1(C:57: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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | C | 59 | LEU | 0 | 0.090 | 0.053 | 3.883 | -3.225 | -0.941 | -0.010 | -1.193 | -1.082 | 0.003 |
| 4 | C | 60 | SER | 0 | 0.042 | 0.018 | 5.792 | -0.459 | -0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 61 | GLU | -1 | -0.797 | -0.887 | 4.924 | -27.037 | -27.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 62 | CYS | 0 | -0.094 | -0.049 | 3.179 | -5.409 | -4.509 | 0.388 | -0.317 | -0.971 | -0.002 |
| 7 | C | 63 | LEU | 0 | 0.035 | 0.003 | 5.798 | 1.224 | 1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 64 | ARG | 1 | 0.883 | 0.948 | 9.099 | 23.341 | 23.341 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 65 | ARG | 1 | 0.902 | 0.950 | 6.514 | 33.442 | 33.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 66 | ILE | 0 | 0.029 | 0.016 | 7.544 | 0.744 | 0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 67 | GLY | 0 | 0.004 | 0.010 | 10.732 | 1.718 | 1.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 68 | ASP | -1 | -0.890 | -0.958 | 13.137 | -19.817 | -19.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 69 | GLU | -1 | -0.985 | -0.978 | 10.718 | -25.240 | -25.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 70 | LEU | 0 | -0.020 | -0.013 | 14.254 | 1.200 | 1.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 71 | ASP | -1 | -0.922 | -0.968 | 16.291 | -13.902 | -13.902 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 72 | SER | 0 | 0.009 | -0.015 | 17.404 | 1.008 | 1.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 73 | ASN | 0 | -0.086 | -0.034 | 17.493 | 1.160 | 1.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 74 | MET | 0 | -0.018 | -0.009 | 19.465 | 0.829 | 0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 75 | GLU | -1 | -0.871 | -0.934 | 22.257 | -11.359 | -11.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 76 | LEU | 0 | -0.045 | -0.019 | 21.510 | 0.568 | 0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 77 | GLN | 0 | -0.024 | -0.031 | 22.717 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 78 | ARG | 1 | 0.777 | 0.871 | 25.289 | 10.686 | 10.686 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 79 | MET | 0 | 0.010 | -0.007 | 25.723 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 80 | ILE | 0 | -0.052 | -0.016 | 25.740 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 81 | ALA | 0 | -0.041 | -0.007 | 29.471 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 82 | ASP | -1 | -0.924 | -0.919 | 31.350 | -9.160 | -9.160 | 0.000 | 0.000 | 0.000 | 0.000 |