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: K3543
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 | 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 | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -84628.719184 |
|---|---|
| FMO2-HF: Nuclear repulsion | 73195.601738 |
| FMO2-HF: Total energy | -11433.117446 |
| FMO2-MP2: Total energy | -11464.000114 |
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. |
| -31.854 | -28.392 | 0.375 | -1.606 | -2.231 | 0.002 |
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 | 0.074 | 0.049 | 3.809 | -2.590 | -0.069 | -0.021 | -1.283 | -1.217 | 0.004 |
| 4 | C | 60 | SER | 0 | 0.057 | 0.022 | 5.901 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 61 | GLU | -1 | -0.864 | -0.931 | 4.754 | -26.060 | -25.946 | -0.001 | -0.004 | -0.109 | 0.000 |
| 6 | C | 62 | CYS | 0 | -0.111 | -0.057 | 3.137 | -4.694 | -3.867 | 0.397 | -0.319 | -0.905 | -0.002 |
| 7 | C | 63 | LEU | 0 | 0.033 | -0.005 | 5.473 | 1.280 | 1.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 64 | ARG | 1 | 0.907 | 0.970 | 8.726 | 23.127 | 23.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 65 | ARG | 1 | 0.984 | 1.002 | 6.043 | 36.299 | 36.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 66 | ILE | 0 | 0.017 | 0.018 | 7.388 | 0.757 | 0.757 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 67 | GLY | 0 | -0.007 | -0.005 | 10.571 | 1.763 | 1.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 68 | ASP | -1 | -0.904 | -0.961 | 12.804 | -19.110 | -19.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 69 | GLU | -1 | -1.005 | -0.994 | 10.923 | -24.859 | -24.859 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 70 | LEU | 0 | -0.025 | -0.039 | 14.133 | 1.202 | 1.202 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 71 | ASP | -1 | -0.895 | -0.953 | 16.302 | -13.853 | -13.853 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 72 | SER | 0 | 0.028 | -0.003 | 17.368 | 0.911 | 0.911 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 73 | ASN | 0 | -0.076 | -0.042 | 17.517 | 1.167 | 1.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 74 | MET | 0 | -0.019 | 0.008 | 19.367 | 0.837 | 0.837 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 75 | GLU | -1 | -0.908 | -0.942 | 22.168 | -11.777 | -11.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 76 | LEU | 0 | -0.026 | -0.014 | 21.901 | 0.604 | 0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 77 | GLN | 0 | -0.054 | -0.045 | 22.479 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 78 | ARG | 1 | 0.893 | 0.956 | 25.131 | 10.755 | 10.755 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 79 | MET | 0 | 0.016 | 0.014 | 25.460 | 0.445 | 0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 80 | ILE | 0 | -0.024 | -0.012 | 26.009 | 0.401 | 0.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 81 | ALA | 0 | -0.134 | -0.052 | 29.563 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 82 | ASP | -1 | -0.974 | -0.973 | 31.491 | -9.341 | -9.341 | 0.000 | 0.000 | 0.000 | 0.000 |