FMODB ID: KQLR3
Calculation Name: 1EF4-A-Other549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1EF4
Chain ID: A
UniProt ID: O26147
Base Structure: SolutionNMR
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 | 55 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -304075.690356 |
|---|---|
| FMO2-HF: Nuclear repulsion | 280354.233779 |
| FMO2-HF: Total energy | -23721.456578 |
| FMO2-MP2: Total energy | -23786.358994 |
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. |
| -37.854 | -29.822 | 16.943 | -9.826 | -15.151 | -0.089 |
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 | PRO | 0 | 0.070 | 0.032 | 2.571 | -3.042 | -0.884 | 1.593 | -1.427 | -2.324 | -0.014 |
| 4 | A | 4 | VAL | 0 | 0.024 | 0.014 | 4.273 | 2.903 | 3.029 | -0.001 | 0.005 | -0.130 | 0.000 |
| 6 | A | 6 | CYS | 0 | -0.002 | 0.000 | 4.058 | -4.341 | -4.190 | 0.002 | -0.035 | -0.117 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.030 | 0.015 | 2.165 | 1.989 | 3.094 | 1.873 | -0.802 | -2.176 | 0.001 |
| 8 | A | 8 | SER | 0 | 0.046 | -0.026 | 2.481 | -13.793 | -11.160 | 0.732 | -1.213 | -2.153 | -0.009 |
| 9 | A | 9 | CYS | 0 | -0.105 | -0.045 | 4.214 | 4.715 | 4.820 | 0.000 | -0.014 | -0.091 | 0.000 |
| 12 | A | 12 | PRO | 0 | 0.022 | 0.028 | 4.117 | -3.948 | -3.790 | -0.001 | -0.010 | -0.147 | 0.000 |
| 13 | A | 13 | VAL | 0 | 0.087 | 0.046 | 2.368 | 0.976 | 1.371 | 2.229 | -0.637 | -1.987 | -0.005 |
| 14 | A | 14 | SER | 0 | -0.025 | -0.007 | 1.852 | -25.039 | -26.242 | 10.310 | -4.412 | -4.696 | -0.051 |
| 15 | A | 15 | ALA | 0 | 0.039 | 0.025 | 4.025 | 3.253 | 3.820 | 0.003 | -0.359 | -0.211 | -0.002 |
| 17 | A | 17 | PHE | 0 | 0.005 | -0.010 | 2.934 | -3.103 | -1.340 | 0.204 | -0.919 | -1.049 | -0.009 |
| 48 | A | 48 | LEU | 0 | -0.012 | -0.006 | 4.753 | -0.829 | -0.755 | -0.001 | -0.003 | -0.070 | 0.000 |
| 5 | A | 5 | ARG | 1 | 0.946 | 0.968 | 5.692 | 28.503 | 28.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.025 | 0.031 | 5.837 | 2.515 | 2.515 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | LYS | 1 | 0.924 | 0.958 | 6.826 | 25.282 | 25.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | TYR | 0 | 0.085 | 0.043 | 7.312 | 1.680 | 1.680 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ASN | 0 | -0.028 | -0.008 | 7.249 | 3.335 | 3.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLU | -1 | -0.875 | -0.925 | 10.566 | -18.628 | -18.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | TYR | 0 | -0.015 | -0.020 | 9.538 | 1.402 | 1.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLN | 0 | 0.014 | 0.003 | 10.668 | 1.173 | 1.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ARG | 1 | 0.968 | 0.984 | 12.480 | 17.647 | 17.647 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ARG | 1 | 0.825 | 0.907 | 14.936 | 17.890 | 17.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | VAL | 0 | -0.029 | -0.020 | 14.211 | 1.004 | 1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ALA | 0 | -0.058 | -0.015 | 16.457 | 0.637 | 0.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ASP | -1 | -0.926 | -0.960 | 18.024 | -13.832 | -13.832 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | GLY | 0 | -0.039 | -0.011 | 19.778 | 0.779 | 0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.870 | -0.936 | 18.705 | -14.767 | -14.767 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ASP | -1 | -0.887 | -0.948 | 18.483 | -15.059 | -15.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | PRO | 0 | 0.035 | 0.009 | 14.345 | -0.732 | -0.732 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LYS | 1 | 0.872 | 0.912 | 14.493 | 14.008 | 14.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ASP | -1 | -0.855 | -0.906 | 16.265 | -14.915 | -14.915 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | 0.055 | 0.039 | 12.017 | -0.639 | -0.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | LEU | 0 | -0.098 | -0.071 | 9.880 | -1.765 | -1.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ASP | -1 | -0.964 | -0.973 | 12.536 | -17.392 | -17.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ASP | -1 | -0.827 | -0.915 | 13.874 | -18.327 | -18.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | LEU | 0 | -0.100 | -0.056 | 7.242 | -1.627 | -1.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | GLY | 0 | 0.006 | 0.026 | 9.155 | -2.337 | -2.337 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | -0.055 | -0.030 | 6.547 | -1.170 | -1.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LYS | 1 | 0.947 | 0.974 | 8.926 | 20.146 | 20.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ARG | 1 | 1.002 | 0.973 | 9.638 | 16.808 | 16.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | TYR | 0 | 0.073 | 0.034 | 11.254 | -1.443 | -1.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | CYS | 0 | -0.036 | -0.016 | 9.615 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | CYS | 0 | 0.019 | 0.007 | 6.969 | -0.900 | -0.900 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | ARG | 1 | 0.923 | 0.963 | 8.537 | 19.414 | 19.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | ARG | 1 | 0.972 | 0.987 | 10.736 | 18.531 | 18.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | MET | 0 | -0.043 | -0.010 | 7.261 | 1.319 | 1.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ILE | 0 | 0.011 | -0.013 | 8.912 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | SER | 0 | -0.058 | -0.021 | 12.337 | 1.509 | 1.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | HIS | 0 | -0.054 | -0.018 | 9.634 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | VAL | 0 | -0.027 | -0.021 | 5.845 | -0.973 | -0.973 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | GLU | -1 | -0.918 | -0.952 | 7.009 | -28.187 | -28.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | THR | 0 | -0.088 | -0.049 | 5.645 | -6.199 | -6.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | TRP | -1 | -0.940 | -0.945 | 7.305 | -32.542 | -32.542 | 0.000 | 0.000 | 0.000 | 0.000 |