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: J2J89
Calculation Name: 4BXT-B-Xray540
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4BXT
Chain ID: B
UniProt ID: Q91KZ5
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 | OptHSide |
| 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 | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -75757.531762 |
|---|---|
| FMO2-HF: Nuclear repulsion | 65786.602611 |
| FMO2-HF: Total energy | -9970.929151 |
| FMO2-MP2: Total energy | -9999.621748 |
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:170:LEU)
Summations of interaction energy for
fragment #1(B:170:LEU)
| 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. |
| 2.431 | 3.714 | -0.007 | -0.349 | -0.929 | 0.004 |
Interaction energy analysis for fragmet #1(B:170:LEU)
| 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 | 171 | SER | 0 | -0.031 | 0.083 | 4.372 | -0.008 | 0.227 | 0.000 | -0.105 | -0.130 | 0.000 |
| 5 | B | 172 | ILE | 0 | 0.084 | -0.098 | 3.850 | -2.778 | -1.886 | -0.005 | -0.493 | -0.395 | 0.003 |
| 6 | B | 172 | ILE | 0 | -0.059 | 0.103 | 7.659 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 173 | GLU | 0 | 0.016 | -0.149 | 6.528 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 173 | GLU | -1 | -0.832 | -0.768 | 7.426 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 174 | ALA | 0 | 0.231 | -0.018 | 4.877 | 0.211 | 0.265 | -0.002 | -0.006 | -0.046 | 0.000 |
| 10 | B | 174 | ALA | 0 | -0.111 | 0.090 | 3.994 | -0.032 | 0.029 | 0.000 | -0.020 | -0.041 | 0.000 |
| 11 | B | 175 | ARG | 0 | 0.067 | -0.086 | 5.276 | -0.170 | -0.133 | -0.002 | -0.005 | -0.030 | 0.000 |
| 12 | B | 175 | ARG | 1 | 0.801 | 1.024 | 3.407 | 4.965 | 4.924 | 0.004 | 0.280 | -0.243 | 0.001 |
| 13 | B | 176 | LEU | 0 | 0.021 | -0.112 | 5.975 | 0.249 | 0.294 | -0.002 | 0.000 | -0.044 | 0.000 |
| 14 | B | 176 | LEU | 0 | -0.065 | 0.086 | 9.626 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 177 | GLU | 0 | 0.142 | -0.102 | 8.967 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 177 | GLU | -1 | -1.017 | -0.827 | 8.703 | -0.882 | -0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 178 | SER | 0 | 0.053 | -0.069 | 8.375 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 178 | SER | 0 | -0.105 | 0.028 | 7.607 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 179 | ILE | 0 | 0.084 | -0.098 | 9.586 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 179 | ILE | 0 | -0.127 | 0.079 | 9.758 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 180 | GLU | 0 | 0.069 | -0.150 | 11.717 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 180 | GLU | -1 | -0.980 | -0.824 | 14.028 | -0.570 | -0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 181 | GLU | 0 | 0.105 | -0.101 | 13.225 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 181 | GLU | -1 | -0.913 | -0.786 | 12.855 | -0.959 | -0.959 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 182 | LYS | 0 | -0.004 | -0.135 | 13.721 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 182 | LYS | 1 | 0.821 | 1.006 | 11.079 | 1.151 | 1.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 183 | LEU | 0 | 0.032 | -0.101 | 15.214 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 183 | LEU | 0 | -0.061 | 0.113 | 16.023 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 184 | SER | 0 | 0.053 | -0.102 | 17.766 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 184 | SER | 0 | -0.021 | 0.109 | 18.185 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 185 | MET | 0 | 0.065 | -0.091 | 18.432 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 185 | MET | 0 | -0.093 | 0.087 | 17.195 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 186 | ILE | 0 | 0.101 | -0.079 | 19.470 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 186 | ILE | 0 | -0.094 | 0.101 | 17.923 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 187 | LEU | 0 | 0.063 | -0.123 | 21.278 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 187 | LEU | 0 | -0.100 | 0.105 | 22.123 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 188 | GLY | 0 | -0.018 | -0.117 | 23.112 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 189 | LEU | 0 | 0.083 | -0.003 | 23.830 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 189 | LEU | 0 | -0.075 | 0.108 | 22.089 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 190 | LEU | 0 | 0.110 | -0.086 | 25.306 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 190 | LEU | 0 | -0.088 | 0.099 | 24.773 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 191 | ARG | 0 | 0.058 | -0.096 | 27.196 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 191 | ARG | 1 | 0.848 | 1.056 | 26.884 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 192 | THR | 0 | -0.004 | -0.082 | 28.901 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 192 | THR | 0 | -0.070 | 0.045 | 28.183 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 193 | LEU | 0 | 0.013 | -0.103 | 30.499 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 193 | LEU | 0 | -0.045 | 0.113 | 28.716 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 194 | ASN | 0 | -0.101 | -0.140 | 32.304 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 194 | ASN | 0 | 0.023 | 0.007 | 32.422 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |