FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: J2J39
Calculation Name: 2BZW-B-Xray540
Preferred Name: Bcl-2-like protein 1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2BZW
Chain ID: B
ChEMBL ID: CHEMBL3309112
UniProt ID: Q64373
Base Structure: X-ray
Registration Date: 2025-07-10
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 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -89344.19473 |
|---|---|
| FMO2-HF: Nuclear repulsion | 78038.271949 |
| FMO2-HF: Total energy | -11305.922781 |
| FMO2-MP2: Total energy | -11338.631069 |
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(B:95:ALA)
Summations of interaction energy for
fragment #1(B:95:ALA)
| 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. |
| 1.735 | 4.148 | 0.028 | -0.938 | -1.505 | 0.006 |
Interaction energy analysis for fragmet #1(B:95:ALA)
| 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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | B | 97 | PRO | 0 | 0.126 | 0.020 | 3.834 | -3.282 | -1.208 | -0.012 | -1.227 | -0.836 | 0.007 |
| 5 | B | 98 | ASN | 0 | 0.037 | 0.013 | 6.680 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 98 | ASN | 0 | -0.013 | 0.092 | 6.776 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 99 | LEU | 0 | -0.006 | -0.141 | 4.270 | 1.319 | 1.370 | -0.001 | 0.010 | -0.059 | 0.000 |
| 8 | B | 99 | LEU | 0 | -0.011 | 0.132 | 3.401 | 0.039 | -0.364 | 0.004 | 0.554 | -0.156 | 0.000 |
| 9 | B | 100 | TRP | 0 | 0.099 | -0.110 | 5.393 | -0.391 | -0.371 | -0.002 | -0.001 | -0.017 | 0.000 |
| 10 | B | 100 | TRP | 0 | -0.091 | 0.102 | 3.108 | 1.492 | 2.060 | 0.006 | -0.218 | -0.356 | 0.000 |
| 11 | B | 101 | ALA | 0 | 0.045 | -0.138 | 6.259 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 101 | ALA | 0 | -0.036 | 0.137 | 10.077 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 102 | ALA | 0 | 0.098 | -0.097 | 8.193 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 102 | ALA | 0 | -0.038 | 0.122 | 7.339 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 103 | GLN | 0 | 0.089 | -0.085 | 6.910 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 103 | GLN | 0 | -0.134 | 0.086 | 3.751 | -1.990 | -1.887 | 0.033 | -0.056 | -0.081 | -0.001 |
| 17 | B | 104 | ARG | 0 | 0.032 | -0.102 | 7.947 | 0.376 | 0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 104 | ARG | 1 | 0.899 | 1.056 | 10.049 | 1.521 | 1.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 105 | TYR | 0 | 0.119 | -0.097 | 11.144 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 105 | TYR | 0 | -0.068 | 0.125 | 11.972 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 106 | GLY | 0 | 0.013 | -0.080 | 11.180 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 107 | ARG | 0 | 0.152 | 0.031 | 11.955 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 107 | ARG | 1 | 0.803 | 1.031 | 12.189 | 0.682 | 0.682 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 108 | GLU | 0 | 0.058 | -0.126 | 13.615 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 108 | GLU | -1 | -0.973 | -0.830 | 15.666 | -0.534 | -0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 109 | LEU | 0 | 0.154 | -0.103 | 15.648 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 109 | LEU | 0 | -0.103 | 0.115 | 15.801 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 110 | ARG | 0 | 0.110 | -0.059 | 16.169 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 110 | ARG | 1 | 0.857 | 1.050 | 13.402 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 111 | ARG | 0 | 0.077 | -0.073 | 17.748 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 111 | ARG | 1 | 0.820 | 1.029 | 17.668 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 112 | MET | 0 | 0.122 | -0.075 | 20.063 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 112 | MET | 0 | -0.110 | 0.082 | 20.424 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 113 | SER | 0 | 0.004 | -0.063 | 20.899 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 113 | SER | 0 | -0.074 | 0.036 | 19.919 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 114 | ASP | 0 | 0.212 | -0.073 | 21.936 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 114 | ASP | -1 | -1.068 | -0.869 | 21.222 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 115 | GLU | 0 | 0.089 | -0.113 | 23.541 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 115 | GLU | -1 | -1.060 | -0.864 | 25.144 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 116 | PHE | 0 | 0.090 | -0.089 | 25.392 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 116 | PHE | 0 | -0.129 | 0.060 | 25.569 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 117 | GLU | 0 | 0.054 | -0.102 | 25.902 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 117 | GLU | -1 | -0.989 | -0.848 | 25.595 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 118 | GLY | 0 | -0.075 | -0.135 | 27.418 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 119 | SER | 0 | 0.020 | -0.017 | 29.649 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 119 | SER | 0 | -0.066 | 0.061 | 29.914 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 120 | PHE | 0 | -0.051 | -0.134 | 31.446 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 120 | PHE | 0 | -0.089 | 0.113 | 28.393 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 121 | LYS | 0 | 0.010 | -0.086 | 33.135 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 121 | LYS | 1 | 0.940 | 0.975 | 36.877 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |