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: RKN68
Calculation Name: 2K5Q-A-Other549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2K5Q
Chain ID: A
UniProt ID: Q812L6
Base Structure: SolutionNMR
Registration Date: 2025-10-12
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 | 105 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -767445.779239 |
|---|---|
| FMO2-HF: Nuclear repulsion | 724246.770828 |
| FMO2-HF: Total energy | -43199.008411 |
| FMO2-MP2: Total energy | -43326.410048 |
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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| 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. |
| 85.764 | 87.259 | -0.021 | -0.398 | -1.075 | 0 |
Interaction energy analysis for fragmet #1(A:1:MET)
| 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 | 3 | LEU | 0 | 0.035 | 0.028 | 3.654 | 6.882 | 8.313 | -0.020 | -0.394 | -1.017 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.900 | 0.966 | 4.681 | 43.442 | 43.506 | -0.001 | -0.004 | -0.058 | 0.000 |
| 4 | A | 4 | ASN | 0 | 0.021 | -0.018 | 6.425 | 2.112 | 2.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | ARG | 1 | 1.009 | 1.008 | 9.439 | 24.744 | 24.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | MET | 0 | -0.052 | -0.033 | 7.528 | 1.067 | 1.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | -0.014 | 0.005 | 9.783 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.802 | -0.872 | 11.561 | -17.373 | -17.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLU | -1 | -0.827 | -0.902 | 12.860 | -18.559 | -18.559 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | TYR | 0 | -0.029 | -0.008 | 15.132 | 0.689 | 0.689 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | TYR | 0 | -0.007 | -0.007 | 18.034 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | VAL | 0 | 0.039 | 0.020 | 19.627 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLN | 0 | 0.010 | -0.007 | 22.186 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ILE | 0 | -0.028 | 0.017 | 21.213 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | THR | 0 | 0.023 | 0.008 | 25.217 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | -0.027 | 0.001 | 25.861 | 0.339 | 0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ASP | -1 | -0.739 | -0.877 | 26.606 | -11.180 | -11.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | -0.002 | 0.009 | 27.531 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LYS | 1 | 0.847 | 0.928 | 27.019 | 10.919 | 10.919 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLU | -1 | -0.794 | -0.879 | 26.790 | -10.182 | -10.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | VAL | 0 | 0.032 | 0.023 | 24.702 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | HIS | 0 | -0.049 | -0.039 | 27.143 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | SER | 0 | 0.009 | -0.008 | 28.367 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LYS | 1 | 0.848 | 0.932 | 21.121 | 14.001 | 14.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ALA | 0 | 0.026 | 0.023 | 25.700 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ASP | -1 | -0.861 | -0.928 | 23.742 | -12.764 | -12.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ASN | 0 | -0.041 | -0.004 | 26.546 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | GLY | 0 | 0.010 | 0.014 | 28.302 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLN | 0 | -0.070 | -0.043 | 27.839 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LYS | 1 | 0.953 | 0.951 | 30.288 | 8.906 | 8.906 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | TYR | 0 | 0.007 | 0.020 | 24.077 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | LYS | 1 | 0.777 | 0.862 | 25.645 | 9.939 | 9.939 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | ASP | -1 | -0.878 | -0.923 | 20.480 | -14.537 | -14.537 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | TYR | 0 | -0.022 | -0.025 | 22.141 | 0.613 | 0.613 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | GLU | -1 | -0.862 | -0.924 | 22.075 | -11.910 | -11.910 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | TYR | 0 | 0.001 | -0.004 | 21.262 | 0.443 | 0.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | LYS | 1 | 0.820 | 0.889 | 22.376 | 11.102 | 11.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | -0.044 | -0.021 | 21.548 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | THR | 0 | 0.007 | 0.004 | 24.615 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | GLY | 0 | -0.022 | -0.009 | 21.639 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | PHE | 0 | 0.012 | 0.008 | 22.677 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ASP | -1 | -0.769 | -0.880 | 20.404 | -13.506 | -13.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | LYS | 1 | 0.840 | 0.891 | 16.657 | 16.640 | 16.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | ASP | -1 | -0.863 | -0.922 | 21.834 | -12.403 | -12.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | 0 | -0.062 | -0.023 | 24.363 | 0.591 | 0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | LYS | 1 | 0.842 | 0.922 | 24.097 | 12.427 | 12.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | GLU | -1 | -0.884 | -0.950 | 25.380 | -10.334 | -10.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | LYS | 1 | 0.882 | 0.956 | 19.236 | 14.752 | 14.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLU | -1 | -0.836 | -0.905 | 23.690 | -11.156 | -11.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | LEU | 0 | -0.038 | -0.027 | 18.188 | -0.667 | -0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | GLU | -1 | -0.829 | -0.908 | 21.206 | -12.590 | -12.590 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | PHE | 0 | -0.031 | -0.013 | 17.105 | -0.715 | -0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | THR | 0 | 0.017 | 0.011 | 18.372 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ALA | 0 | -0.019 | 0.000 | 17.691 | -0.994 | -0.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLN | 0 | 0.045 | 0.009 | 17.776 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | LYS | 1 | 0.918 | 0.958 | 19.082 | 14.649 | 14.649 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | ASN | 0 | -0.001 | -0.011 | 21.113 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | LEU | 0 | -0.059 | -0.013 | 19.131 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | ARG | 1 | 0.923 | 0.954 | 21.889 | 12.873 | 12.873 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LYS | 1 | 0.914 | 0.930 | 23.890 | 9.698 | 9.698 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | GLU | -1 | -0.982 | -0.990 | 26.561 | -9.421 | -9.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ALA | 0 | -0.047 | -0.007 | 22.689 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | PHE | 0 | 0.008 | -0.016 | 22.839 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | LEU | 0 | -0.025 | -0.006 | 16.807 | -0.399 | -0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ARG | 1 | 0.867 | 0.917 | 15.244 | 17.446 | 17.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | VAL | 0 | 0.038 | 0.009 | 14.624 | -1.098 | -1.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | TYR | 0 | -0.061 | -0.029 | 8.081 | -1.009 | -1.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | HIS | 0 | -0.017 | -0.046 | 12.196 | 0.735 | 0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | SER | 0 | -0.043 | -0.034 | 9.936 | -2.798 | -2.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | ASP | -1 | -0.827 | -0.911 | 12.080 | -21.901 | -21.901 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | LYS | 1 | 0.912 | 0.952 | 8.589 | 30.924 | 30.924 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | LYS | 1 | 0.897 | 0.957 | 9.464 | 23.727 | 23.727 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | GLY | 0 | 0.053 | 0.054 | 12.501 | 0.815 | 0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | VAL | 0 | 0.051 | 0.019 | 12.582 | -0.399 | -0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | SER | 0 | -0.108 | -0.068 | 8.596 | -2.014 | -2.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ALA | 0 | 0.013 | 0.020 | 7.720 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | TRP | 0 | 0.032 | -0.005 | 9.834 | 0.969 | 0.969 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | GLU | -1 | -0.932 | -0.951 | 12.112 | -20.642 | -20.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | GLU | -1 | -0.888 | -0.951 | 14.782 | -13.666 | -13.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | VAL | 0 | -0.024 | 0.002 | 17.826 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | LYS | 1 | 0.871 | 0.911 | 20.609 | 12.452 | 12.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | LYS | 1 | 0.843 | 0.900 | 23.772 | 9.633 | 9.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ASP | -1 | -0.842 | -0.909 | 26.208 | -10.049 | -10.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | GLU | -1 | -0.800 | -0.882 | 20.831 | -12.773 | -12.773 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | LEU | 0 | -0.029 | -0.002 | 19.838 | -0.548 | -0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | PRO | 0 | 0.020 | 0.005 | 21.114 | 0.481 | 0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ALA | 0 | 0.072 | 0.029 | 24.268 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | LYS | 1 | 0.964 | 0.983 | 25.631 | 10.794 | 10.794 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | VAL | 0 | -0.002 | -0.005 | 22.966 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | LYS | 1 | 0.975 | 0.991 | 26.197 | 8.968 | 8.968 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | GLU | -1 | -0.963 | -0.991 | 29.736 | -9.322 | -9.322 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | LYS | 1 | 0.783 | 0.905 | 26.197 | 11.224 | 11.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | LEU | 0 | 0.016 | -0.001 | 27.524 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | GLY | 0 | 0.012 | 0.007 | 30.432 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | VAL | 0 | -0.029 | -0.003 | 33.190 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.841 | 0.927 | 35.405 | 7.314 | 7.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | LEU | 0 | 0.071 | 0.030 | 39.150 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | GLU | -1 | -0.857 | -0.945 | 42.100 | -6.769 | -6.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | HIS | 0 | -0.033 | -0.020 | 35.634 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | HIS | 0 | 0.004 | 0.006 | 39.688 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | HIS | 0 | -0.011 | 0.001 | 42.309 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | HIS | 1 | 0.840 | 0.904 | 43.200 | 6.623 | 6.623 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | HIS | 0 | 0.022 | 0.014 | 45.105 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | HIS | -1 | -0.898 | -0.922 | 47.291 | -6.293 | -6.293 | 0.000 | 0.000 | 0.000 | 0.000 |