FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: 6685Z
Calculation Name: 1OQE-K-Xray372
Preferred Name: Tumor necrosis factor ligand superfamily member 13B
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1OQE
Chain ID: K
ChEMBL ID: CHEMBL2364158
UniProt ID: Q9Y275
Base Structure: X-ray
Registration Date: 2023-06-19
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
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 | 29 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -100446.751581 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87926.061462 |
| FMO2-HF: Total energy | -12520.690119 |
| FMO2-MP2: Total energy | -12554.243156 |
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(K:1:PRO)
Summations of interaction energy for
fragment #1(K:1:PRO)
| 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. |
| -4.31 | 0.853 | 0.218 | -2.601 | -2.781 | -0.007 |
Interaction energy analysis for fragmet #1(K:1:PRO)
| 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 | K | 3 | PRO | 0 | 0.004 | -0.007 | 3.141 | -3.351 | 0.963 | 0.124 | -2.261 | -2.178 | -0.004 |
| 4 | K | 4 | CYS | 0 | -0.067 | 0.016 | 5.909 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | K | 5 | VAL | 0 | 0.046 | 0.031 | 8.233 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | K | 6 | PRO | 0 | 0.045 | 0.012 | 11.742 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 7 | ALA | 0 | -0.026 | -0.018 | 14.303 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 8 | GLU | -1 | -0.949 | -0.976 | 11.131 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 9 | CYS | 0 | -0.092 | -0.059 | 10.747 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | K | 10 | PHE | 0 | 0.068 | 0.022 | 3.056 | -1.312 | -0.463 | 0.094 | -0.340 | -0.603 | -0.003 |
| 11 | K | 11 | ASP | -1 | -0.823 | -0.894 | 8.120 | -0.795 | -0.795 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 12 | LEU | 0 | -0.015 | -0.030 | 6.662 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 13 | LEU | 0 | -0.074 | -0.020 | 8.645 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 14 | VAL | 0 | -0.021 | -0.022 | 10.245 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | K | 15 | ARG | 1 | 0.869 | 0.942 | 5.168 | 1.114 | 1.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | K | 16 | HIS | 0 | 0.019 | -0.008 | 5.323 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | K | 18 | VAL | 0 | 0.056 | 0.036 | 8.361 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | K | 19 | ALA | 0 | 0.095 | 0.048 | 12.111 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 21 | GLY | 0 | -0.008 | 0.008 | 15.634 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 22 | LEU | 0 | -0.018 | -0.011 | 16.246 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 23 | LEU | 0 | -0.041 | 0.002 | 12.582 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 24 | ARG | 1 | 0.956 | 0.965 | 17.177 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 25 | THR | 0 | 0.017 | 0.006 | 18.105 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 26 | PRO | 0 | 0.025 | 0.006 | 15.229 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 27 | ARG | 1 | 0.948 | 0.979 | 17.442 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 28 | PRO | 0 | 0.029 | 0.004 | 18.722 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 29 | LYS | 1 | 0.942 | 0.968 | 18.664 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 30 | PRO | 0 | 0.035 | 0.026 | 14.511 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 31 | ALA | 0 | -0.010 | 0.015 | 16.501 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |