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: 43Z1N
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 | 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 | -84471.891863 |
|---|---|
| FMO2-HF: Nuclear repulsion | 73038.433691 |
| FMO2-HF: Total energy | -11433.458172 |
| FMO2-MP2: Total energy | -11464.297887 |
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. |
| -32.67 | -29.268 | 0.693 | -1.67 | -2.424 | 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 | 0.087 | 0.052 | 3.809 | -2.504 | -0.004 | -0.021 | -1.269 | -1.210 | 0.004 |
| 4 | C | 60 | SER | 0 | 0.060 | 0.028 | 5.937 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 61 | GLU | -1 | -0.870 | -0.924 | 4.675 | -25.595 | -25.479 | -0.001 | -0.004 | -0.110 | 0.000 |
| 6 | C | 62 | CYS | 0 | -0.114 | -0.064 | 3.081 | -4.916 | -4.130 | 0.715 | -0.397 | -1.104 | -0.003 |
| 7 | C | 63 | LEU | 0 | 0.036 | -0.002 | 5.493 | 1.246 | 1.246 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 64 | ARG | 1 | 0.892 | 0.957 | 8.762 | 23.089 | 23.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 65 | ARG | 1 | 0.998 | 1.005 | 5.986 | 34.938 | 34.938 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 66 | ILE | 0 | 0.022 | 0.020 | 7.764 | 0.868 | 0.868 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 67 | GLY | 0 | 0.002 | 0.000 | 10.681 | 1.754 | 1.754 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 68 | ASP | -1 | -0.914 | -0.968 | 12.943 | -19.297 | -19.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 69 | GLU | -1 | -1.007 | -0.995 | 10.935 | -24.789 | -24.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 70 | LEU | 0 | -0.034 | -0.034 | 14.351 | 1.185 | 1.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 71 | ASP | -1 | -0.886 | -0.941 | 16.519 | -13.798 | -13.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 72 | SER | 0 | 0.006 | -0.015 | 17.328 | 0.923 | 0.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 73 | ASN | 0 | -0.078 | -0.041 | 17.736 | 1.063 | 1.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 74 | MET | 0 | -0.015 | -0.003 | 19.711 | 0.753 | 0.753 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 75 | GLU | -1 | -0.881 | -0.929 | 22.397 | -11.457 | -11.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 76 | LEU | 0 | -0.041 | -0.025 | 21.818 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 77 | GLN | 0 | -0.043 | -0.039 | 22.788 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 78 | ARG | 1 | 0.823 | 0.912 | 25.366 | 10.589 | 10.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 79 | MET | 0 | -0.007 | -0.006 | 25.816 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 80 | ILE | 0 | -0.013 | -0.005 | 26.184 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 81 | ALA | 0 | -0.102 | -0.033 | 29.778 | 0.387 | 0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 82 | ASP | -1 | -0.924 | -0.934 | 31.725 | -9.160 | -9.160 | 0.000 | 0.000 | 0.000 | 0.000 |