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: N251Q
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 | OptAll |
| 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 | -89291.586478 |
|---|---|
| FMO2-HF: Nuclear repulsion | 77985.034013 |
| FMO2-HF: Total energy | -11306.552465 |
| FMO2-MP2: Total energy | -11339.227692 |
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. |
| 1.601 | 3.457 | 0.101 | -0.59 | -1.368 | 0.004 |
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 | 0.086 | 0.007 | 3.900 | -2.843 | -1.014 | -0.008 | -1.093 | -0.729 | 0.006 |
| 5 | B | 98 | ASN | 0 | 0.054 | 0.022 | 6.712 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 98 | ASN | 0 | -0.042 | 0.084 | 7.137 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 99 | LEU | 0 | 0.032 | -0.119 | 4.426 | 1.141 | 1.187 | -0.001 | 0.003 | -0.046 | 0.000 |
| 8 | B | 99 | LEU | 0 | -0.032 | 0.120 | 3.479 | 0.019 | -0.182 | 0.001 | 0.349 | -0.150 | 0.000 |
| 9 | B | 100 | TRP | 0 | 0.095 | -0.091 | 5.555 | -0.024 | -0.001 | -0.002 | -0.002 | -0.020 | 0.000 |
| 10 | B | 100 | TRP | 0 | -0.101 | 0.075 | 3.516 | 1.577 | 1.975 | 0.001 | -0.167 | -0.231 | 0.000 |
| 11 | B | 101 | ALA | 0 | 0.054 | -0.105 | 6.284 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 101 | ALA | 0 | -0.046 | 0.118 | 10.011 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 102 | ALA | 0 | 0.144 | -0.086 | 8.409 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 102 | ALA | 0 | -0.071 | 0.113 | 7.707 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 103 | GLN | 0 | 0.079 | -0.088 | 6.683 | 0.501 | 0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 103 | GLN | 0 | -0.090 | 0.081 | 3.484 | -2.550 | -2.789 | 0.110 | 0.320 | -0.192 | -0.002 |
| 17 | B | 104 | ARG | 0 | 0.039 | -0.086 | 7.884 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 104 | ARG | 1 | 0.881 | 1.053 | 9.739 | 1.542 | 1.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 105 | TYR | 0 | 0.095 | -0.077 | 11.060 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 105 | TYR | 0 | -0.063 | 0.108 | 12.097 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 106 | GLY | 0 | 0.024 | -0.095 | 11.246 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 107 | ARG | 0 | 0.148 | 0.049 | 11.903 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 107 | ARG | 1 | 0.704 | 0.956 | 12.054 | 0.640 | 0.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 108 | GLU | 0 | 0.030 | -0.109 | 13.558 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 108 | GLU | -1 | -0.859 | -0.762 | 15.271 | -0.579 | -0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 109 | LEU | 0 | 0.167 | -0.080 | 15.728 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 109 | LEU | 0 | -0.093 | 0.101 | 15.634 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 110 | ARG | 0 | 0.106 | -0.064 | 16.019 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 110 | ARG | 1 | 0.766 | 1.006 | 14.630 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 111 | ARG | 0 | 0.101 | -0.047 | 17.590 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 111 | ARG | 1 | 0.781 | 0.981 | 17.370 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 112 | MET | 0 | 0.122 | -0.076 | 19.800 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 112 | MET | 0 | -0.116 | 0.067 | 20.527 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 113 | SER | 0 | 0.008 | -0.057 | 20.778 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 113 | SER | 0 | -0.083 | 0.039 | 19.837 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 114 | ASP | 0 | 0.126 | -0.080 | 21.495 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 114 | ASP | -1 | -0.951 | -0.857 | 19.943 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 115 | GLU | 0 | 0.126 | -0.086 | 23.058 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 115 | GLU | -1 | -1.040 | -0.867 | 25.007 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 116 | PHE | 0 | 0.075 | -0.071 | 25.186 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 116 | PHE | 0 | -0.124 | 0.056 | 25.476 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 117 | GLU | 0 | 0.092 | -0.100 | 25.876 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 117 | GLU | -1 | -1.003 | -0.858 | 25.642 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 118 | GLY | 0 | -0.055 | -0.132 | 27.280 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 119 | SER | 0 | -0.003 | 0.006 | 29.238 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 119 | SER | 0 | -0.071 | 0.056 | 29.624 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 120 | PHE | 0 | -0.018 | -0.109 | 31.276 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 120 | PHE | 0 | -0.105 | 0.088 | 28.099 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 121 | LYS | 0 | 0.009 | -0.104 | 32.849 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 121 | LYS | 1 | 0.957 | 0.986 | 36.617 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |