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: ZNG6N
Calculation Name: 1OQE-K-Xray540
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: 2025-07-08
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 | 53 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -100441.678181 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87926.061462 |
| FMO2-HF: Total energy | -12515.616719 |
| FMO2-MP2: Total energy | -12549.055765 |
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. |
| -3.702 | 2.333 | 0.223 | -3.114 | -3.144 | -0.005 |
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 | 2 | THR | 0 | -0.024 | 0.047 | 3.766 | 0.291 | 1.444 | 0.004 | -0.663 | -0.494 | 0.001 |
| 4 | K | 3 | PRO | 0 | 0.025 | -0.093 | 3.141 | -2.989 | 1.086 | 0.125 | -2.114 | -2.086 | -0.003 |
| 5 | K | 4 | CYS | 0 | 0.004 | -0.007 | 5.909 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | K | 4 | CYS | 0 | -0.114 | 0.234 | 6.745 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 5 | VAL | 0 | 0.113 | -0.082 | 8.233 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 5 | VAL | 0 | -0.023 | 0.124 | 10.901 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 6 | PRO | 0 | 0.017 | -0.101 | 11.742 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | K | 7 | ALA | 0 | 0.126 | 0.017 | 14.303 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | K | 7 | ALA | 0 | -0.074 | 0.111 | 16.603 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 8 | GLU | 0 | -0.005 | -0.191 | 11.848 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 8 | GLU | -1 | -1.014 | -0.838 | 11.131 | -0.633 | -0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 9 | CYS | 0 | 0.059 | -0.103 | 10.747 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | K | 9 | CYS | 0 | -0.213 | 0.179 | 12.004 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | K | 10 | PHE | 0 | 0.210 | -0.054 | 6.994 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | K | 10 | PHE | 0 | -0.089 | 0.112 | 3.056 | -1.444 | -0.637 | 0.094 | -0.337 | -0.564 | -0.003 |
| 18 | K | 11 | ASP | 0 | 0.045 | -0.129 | 8.120 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 11 | ASP | -1 | -0.862 | -0.786 | 9.680 | -0.911 | -0.911 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 12 | LEU | 0 | 0.028 | -0.121 | 7.568 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 12 | LEU | 0 | -0.082 | 0.087 | 6.662 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 13 | LEU | 0 | 0.091 | -0.077 | 8.645 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 13 | LEU | 0 | -0.119 | 0.077 | 12.472 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 14 | VAL | 0 | -0.002 | -0.159 | 10.245 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 14 | VAL | 0 | -0.058 | 0.128 | 10.456 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 15 | ARG | 0 | -0.021 | -0.085 | 6.085 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 15 | ARG | 1 | 0.842 | 1.039 | 5.168 | 1.077 | 1.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 16 | HIS | 0 | 0.152 | -0.094 | 5.323 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 16 | HIS | 0 | -0.091 | 0.052 | 7.055 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | K | 17 | CYS | 0 | 0.038 | -0.122 | 6.613 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | K | 18 | VAL | 0 | 0.103 | -0.048 | 8.361 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | K | 18 | VAL | 0 | -0.075 | 0.097 | 10.868 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | K | 19 | ALA | 0 | 0.250 | -0.029 | 12.111 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | K | 19 | ALA | 0 | -0.080 | 0.103 | 16.304 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | K | 20 | CYS | 0 | -0.028 | -0.166 | 14.902 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | K | 21 | GLY | 0 | -0.003 | -0.091 | 15.634 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | K | 22 | LEU | 0 | 0.033 | -0.020 | 17.193 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | K | 22 | LEU | 0 | -0.077 | 0.104 | 16.246 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | K | 23 | LEU | 0 | 0.084 | -0.091 | 15.772 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | K | 23 | LEU | 0 | -0.088 | 0.109 | 12.582 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | K | 24 | ARG | 0 | 0.084 | -0.088 | 17.177 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | K | 24 | ARG | 1 | 0.855 | 1.050 | 19.758 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | K | 25 | THR | 0 | 0.062 | -0.099 | 18.105 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | K | 25 | THR | 0 | -0.047 | 0.095 | 21.099 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | K | 26 | PRO | 0 | 0.034 | -0.078 | 15.229 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | K | 27 | ARG | 0 | 0.137 | 0.028 | 17.442 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | K | 27 | ARG | 1 | 0.831 | 1.056 | 19.507 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | K | 28 | PRO | 0 | 0.016 | -0.100 | 18.722 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | K | 29 | LYS | 0 | 0.006 | 0.002 | 18.664 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | K | 29 | LYS | 1 | 0.897 | 1.053 | 18.749 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | K | 30 | PRO | 0 | 0.060 | -0.068 | 14.511 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | K | 31 | ALA | 0 | -0.091 | -0.035 | 16.501 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | K | 31 | ALA | 0 | 0.083 | 0.058 | 19.642 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |