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: KQ4J3
Calculation Name: 1OQE-K-Xray549
Preferred Name: Tumor necrosis factor ligand superfamily member 13B
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1OQE
Chain ID: K
ChEMBL ID: CHEMBL2364158
UniProt ID: Q9Y275
Base Structure: X-ray
Registration Date: 2025-10-11
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -100055.549074 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87534.799642 |
| FMO2-HF: Total energy | -12520.749432 |
| FMO2-MP2: Total energy | -12554.23047 |
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. |
| -0.406 | 6.752 | 0.178 | -3.558 | -3.775 | -0.024 |
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 | 0.021 | 0.016 | 3.405 | -0.143 | 5.130 | 0.017 | -2.643 | -2.647 | -0.015 |
| 10 | K | 10 | PHE | 0 | 0.036 | 0.006 | 2.927 | -5.927 | -4.271 | 0.163 | -0.902 | -0.916 | -0.009 |
| 15 | K | 15 | ARG | 1 | 0.873 | 0.946 | 4.782 | 32.645 | 32.733 | -0.001 | -0.003 | -0.083 | 0.000 |
| 16 | K | 16 | HIS | 0 | -0.003 | -0.018 | 4.718 | -4.958 | -4.817 | -0.001 | -0.010 | -0.129 | 0.000 |
| 4 | K | 4 | CYS | 0 | -0.015 | 0.031 | 6.049 | -1.959 | -1.959 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | K | 5 | VAL | 0 | 0.062 | 0.036 | 8.302 | 1.240 | 1.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | K | 6 | PRO | 0 | 0.030 | 0.004 | 12.001 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 7 | ALA | 0 | 0.005 | 0.003 | 14.617 | 0.719 | 0.719 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 8 | GLU | -1 | -0.952 | -0.969 | 10.930 | -22.788 | -22.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 9 | CYS | 0 | -0.066 | -0.062 | 10.464 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | K | 11 | ASP | -1 | -0.818 | -0.898 | 7.503 | -24.704 | -24.704 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 12 | LEU | 0 | -0.013 | -0.026 | 6.236 | -3.447 | -3.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 13 | LEU | 0 | -0.072 | -0.022 | 8.477 | -0.389 | -0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 14 | VAL | 0 | -0.006 | -0.017 | 9.913 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | K | 18 | VAL | 0 | 0.061 | 0.040 | 7.987 | 2.013 | 2.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | K | 19 | ALA | 0 | 0.073 | 0.042 | 11.713 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 21 | GLY | 0 | -0.012 | 0.000 | 15.304 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 22 | LEU | 0 | -0.003 | 0.009 | 15.988 | 0.786 | 0.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 23 | LEU | 0 | -0.043 | -0.004 | 12.758 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 24 | ARG | 1 | 0.925 | 0.951 | 17.299 | 16.105 | 16.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 25 | THR | 0 | 0.028 | 0.015 | 17.827 | -0.712 | -0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 26 | PRO | 0 | 0.021 | 0.007 | 15.150 | 0.594 | 0.594 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 27 | ARG | 1 | 0.943 | 0.971 | 17.372 | 14.231 | 14.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 28 | PRO | 0 | 0.018 | -0.004 | 18.744 | -0.621 | -0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 29 | LYS | 1 | 0.921 | 0.956 | 18.809 | 14.800 | 14.800 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 30 | PRO | 0 | -0.039 | -0.013 | 14.645 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 31 | ALA | -1 | -0.882 | -0.915 | 16.874 | -18.120 | -18.120 | 0.000 | 0.000 | 0.000 | 0.000 |