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: 7N27K
Calculation Name: 3F62-A-Xray547
Preferred Name: Interleukin-18
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3F62
Chain ID: A
ChEMBL ID: CHEMBL1741305
UniProt ID: Q14116
Base Structure: X-ray
Registration Date: 2025-10-04
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 | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 107 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -820765.563895 |
|---|---|
| FMO2-HF: Nuclear repulsion | 776439.219203 |
| FMO2-HF: Total energy | -44326.344692 |
| FMO2-MP2: Total energy | -44450.62627 |
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(A:18:GLY)
Summations of interaction energy for
fragment #1(A:18:GLY)
| 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. |
| -63.509 | -62.461 | -0.009 | -0.356 | -0.683 | 0 |
Interaction energy analysis for fragmet #1(A:18:GLY)
| 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 | A | 20 | MET | 0 | -0.001 | -0.006 | 3.812 | 2.594 | 3.642 | -0.009 | -0.356 | -0.683 | 0.000 |
| 4 | A | 21 | VAL | 0 | 0.002 | 0.000 | 6.255 | 5.142 | 5.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 22 | GLU | -1 | -0.897 | -0.940 | 7.619 | -22.832 | -22.832 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 23 | THR | 0 | -0.036 | -0.022 | 8.072 | -2.110 | -2.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 24 | LYS | 1 | 0.904 | 0.952 | 10.117 | 21.466 | 21.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 25 | CYS | 0 | 0.013 | 0.013 | 13.450 | -0.941 | -0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 26 | PRO | 0 | 0.031 | 0.014 | 15.676 | 0.594 | 0.594 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 27 | ASN | 0 | -0.037 | -0.039 | 13.269 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 28 | LEU | 0 | 0.027 | 0.024 | 16.893 | -0.376 | -0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 29 | ASP | -1 | -0.881 | -0.943 | 17.702 | -16.223 | -16.223 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 30 | ILE | 0 | -0.045 | -0.035 | 19.609 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 31 | VAL | 0 | 0.028 | 0.038 | 18.590 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 32 | THR | 0 | 0.021 | 0.008 | 21.890 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 33 | SER | 0 | -0.010 | -0.012 | 24.638 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 34 | SER | 0 | -0.016 | -0.013 | 26.706 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 35 | GLY | 0 | 0.060 | 0.040 | 30.398 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 36 | GLU | -1 | -0.876 | -0.935 | 27.164 | -11.371 | -11.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 37 | PHE | 0 | 0.046 | 0.024 | 26.314 | -0.415 | -0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 38 | HIS | 1 | 0.835 | 0.916 | 21.716 | 13.077 | 13.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 39 | CYS | 0 | -0.013 | 0.030 | 21.732 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 40 | SER | 0 | -0.029 | -0.022 | 16.983 | -0.673 | -0.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 41 | GLY | 0 | 0.040 | 0.013 | 17.569 | 0.299 | 0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 42 | CYS | 0 | -0.064 | -0.007 | 14.034 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 43 | VAL | 0 | 0.033 | -0.001 | 15.873 | 0.870 | 0.870 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 44 | GLU | -1 | -0.914 | -0.966 | 13.444 | -19.494 | -19.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 45 | HIS | 0 | 0.064 | 0.039 | 15.905 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 46 | MET | 0 | -0.046 | -0.018 | 19.223 | 0.438 | 0.438 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 47 | PRO | 0 | 0.055 | 0.051 | 18.233 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 48 | GLU | -1 | -0.865 | -0.925 | 20.386 | -13.550 | -13.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 49 | PHE | 0 | -0.031 | -0.008 | 23.571 | 0.584 | 0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 50 | SER | 0 | -0.023 | -0.038 | 21.865 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 51 | TYR | 0 | -0.018 | -0.014 | 24.188 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 52 | MET | 0 | -0.033 | -0.010 | 20.622 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 53 | TYR | 0 | -0.003 | -0.011 | 25.475 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 54 | TRP | 0 | -0.007 | -0.013 | 25.803 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 55 | LEU | 0 | -0.014 | 0.001 | 30.169 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 56 | ALA | 0 | 0.008 | 0.000 | 32.818 | -0.242 | -0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 57 | LYS | 1 | 0.828 | 0.902 | 35.568 | 7.881 | 7.881 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 58 | ASP | -1 | -0.769 | -0.852 | 38.325 | -7.536 | -7.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 59 | MET | 0 | -0.081 | -0.042 | 37.997 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 60 | LYS | 1 | 0.845 | 0.927 | 41.298 | 7.082 | 7.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 61 | SER | 0 | -0.046 | -0.040 | 44.378 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 62 | ASP | -1 | -0.956 | -0.986 | 44.627 | -6.778 | -6.778 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 63 | GLU | -1 | -0.805 | -0.872 | 44.201 | -7.001 | -7.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 64 | ASP | -1 | -0.894 | -0.939 | 42.513 | -7.484 | -7.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 65 | THR | 0 | -0.118 | -0.073 | 36.024 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 66 | LYS | 1 | 0.845 | 0.915 | 38.337 | 7.477 | 7.477 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 67 | PHE | 0 | 0.037 | 0.016 | 34.487 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 68 | ILE | 0 | 0.019 | 0.002 | 32.672 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 69 | GLU | -1 | -0.853 | -0.939 | 36.032 | -8.551 | -8.551 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 70 | HIS | 0 | -0.073 | -0.034 | 38.618 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 71 | LEU | 0 | -0.015 | 0.007 | 36.836 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 72 | GLY | 0 | 0.016 | 0.016 | 41.082 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 73 | ASP | -1 | -0.888 | -0.948 | 40.918 | -7.439 | -7.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 74 | GLY | 0 | 0.038 | 0.017 | 40.062 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 75 | ILE | 0 | -0.044 | -0.005 | 34.434 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 76 | ASN | 0 | 0.010 | 0.008 | 32.730 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 77 | GLU | -1 | -0.805 | -0.912 | 29.735 | -10.697 | -10.697 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 78 | ASP | -1 | -0.830 | -0.884 | 27.680 | -10.612 | -10.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 79 | GLU | -1 | -0.863 | -0.951 | 28.443 | -10.575 | -10.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 80 | THR | 0 | -0.096 | -0.034 | 23.233 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 81 | VAL | 0 | 0.001 | 0.010 | 19.976 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 82 | ARG | 1 | 0.874 | 0.922 | 20.040 | 13.718 | 13.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 83 | THR | 0 | -0.061 | -0.039 | 15.222 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 84 | THR | 0 | 0.018 | -0.009 | 13.735 | 0.406 | 0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 85 | ASP | -1 | -0.896 | -0.942 | 7.644 | -35.936 | -35.936 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 86 | GLY | 0 | -0.016 | 0.002 | 7.745 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 87 | GLY | 0 | -0.022 | -0.005 | 8.627 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 88 | ILE | 0 | -0.011 | 0.002 | 9.470 | 1.840 | 1.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 89 | THR | 0 | 0.014 | 0.006 | 12.149 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 90 | THR | 0 | -0.063 | -0.044 | 13.303 | -0.532 | -0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 91 | LEU | 0 | 0.001 | 0.009 | 15.813 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 92 | ARG | 1 | 0.957 | 0.958 | 13.388 | 19.633 | 19.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 93 | LYS | 1 | 0.852 | 0.929 | 20.634 | 11.660 | 11.660 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 94 | VAL | 0 | -0.023 | 0.002 | 24.102 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 95 | LEU | 0 | 0.028 | 0.021 | 26.168 | 0.336 | 0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 96 | HIS | 1 | 0.806 | 0.881 | 29.225 | 10.454 | 10.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 97 | VAL | 0 | -0.001 | -0.007 | 31.726 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 98 | THR | 0 | -0.062 | -0.041 | 34.362 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 99 | ASP | -1 | -0.831 | -0.912 | 36.796 | -7.456 | -7.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 100 | THR | 0 | -0.013 | -0.028 | 35.671 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 101 | ASN | 0 | -0.050 | -0.015 | 38.339 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 102 | LYS | 1 | 0.848 | 0.917 | 41.927 | 7.620 | 7.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 103 | PHE | 0 | 0.001 | -0.022 | 37.441 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 104 | ALA | 0 | 0.009 | 0.016 | 38.243 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 105 | HIS | 0 | 0.002 | -0.003 | 39.197 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 106 | TYR | 0 | 0.029 | 0.016 | 37.043 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 107 | ARG | 1 | 0.889 | 0.979 | 33.186 | 8.929 | 8.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 108 | PHE | 0 | 0.043 | 0.010 | 31.134 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 109 | THR | 0 | -0.039 | -0.051 | 29.577 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 111 | VAL | 0 | -0.022 | -0.017 | 26.928 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 112 | LEU | 0 | 0.007 | 0.006 | 19.949 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 113 | THR | 0 | -0.031 | -0.019 | 24.569 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 114 | THR | 0 | 0.005 | -0.010 | 21.319 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 115 | LEU | 0 | 0.030 | 0.003 | 24.534 | 0.448 | 0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 116 | ASP | -1 | -0.873 | -0.916 | 21.829 | -13.240 | -13.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 117 | GLY | 0 | -0.027 | -0.005 | 24.988 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 118 | VAL | 0 | -0.037 | -0.019 | 25.752 | -0.317 | -0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 119 | SER | 0 | -0.031 | -0.014 | 23.147 | -0.253 | -0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 120 | LYS | 1 | 0.968 | 0.973 | 25.118 | 10.402 | 10.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 121 | LYS | 1 | 0.893 | 0.947 | 21.198 | 14.137 | 14.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 122 | ASN | 0 | -0.016 | 0.000 | 25.890 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 123 | ILE | 0 | -0.025 | -0.007 | 26.059 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 124 | TRP | 0 | 0.019 | -0.005 | 29.452 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 125 | LEU | -1 | -0.902 | -0.930 | 31.391 | -9.750 | -9.750 | 0.000 | 0.000 | 0.000 | 0.000 |