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: ZY19N
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 | OptAll |
| 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 | -99859.447161 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87338.557375 |
| FMO2-HF: Total energy | -12520.889787 |
| FMO2-MP2: Total energy | -12554.365826 |
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. |
| -4.912 | 0.202 | 0.55 | -2.598 | -3.064 | -0.012 |
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 | -0.020 | -0.009 | 3.091 | -2.781 | 0.729 | 0.087 | -1.859 | -1.737 | -0.004 |
| 4 | K | 4 | CYS | 0 | -0.024 | 0.018 | 5.921 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | K | 5 | VAL | 0 | 0.048 | 0.028 | 8.507 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | K | 6 | PRO | 0 | 0.006 | -0.008 | 12.239 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 7 | ALA | 0 | 0.032 | 0.021 | 14.614 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 8 | GLU | -1 | -0.945 | -0.973 | 10.962 | -0.513 | -0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 9 | CYS | 0 | -0.068 | -0.063 | 10.398 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | K | 10 | PHE | 0 | 0.060 | 0.018 | 2.729 | -2.098 | -0.621 | 0.464 | -0.732 | -1.209 | -0.008 |
| 11 | K | 11 | ASP | -1 | -0.822 | -0.894 | 7.302 | -0.832 | -0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 12 | LEU | 0 | -0.004 | -0.021 | 6.919 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 13 | LEU | 0 | -0.084 | -0.032 | 8.560 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 14 | VAL | 0 | -0.008 | -0.023 | 10.046 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | K | 15 | ARG | 1 | 0.863 | 0.945 | 4.805 | 1.242 | 1.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | K | 16 | HIS | 0 | 0.008 | -0.010 | 5.067 | -0.387 | -0.260 | -0.001 | -0.007 | -0.118 | 0.000 |
| 17 | K | 18 | VAL | 0 | 0.061 | 0.039 | 7.974 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | K | 19 | ALA | 0 | 0.050 | 0.034 | 11.665 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 21 | GLY | 0 | -0.015 | 0.000 | 15.295 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 22 | LEU | 0 | -0.008 | 0.004 | 15.858 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 23 | LEU | 0 | -0.051 | -0.008 | 12.755 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 24 | ARG | 1 | 0.934 | 0.957 | 17.336 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 25 | THR | 0 | 0.023 | 0.009 | 18.176 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 26 | PRO | 0 | 0.035 | 0.013 | 15.273 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 27 | ARG | 1 | 0.948 | 0.977 | 17.527 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 28 | PRO | 0 | 0.025 | -0.003 | 19.115 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 29 | LYS | 1 | 0.960 | 0.982 | 19.125 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 30 | PRO | 0 | 0.025 | 0.025 | 14.586 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 31 | ALA | 0 | -0.011 | 0.009 | 16.768 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |