FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-06
All entries: 70436
Number of unique PDB entries: 28101
FMODB ID: KVVM3
Calculation Name: 2Q1K-C-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
PDB ID: 2Q1K
Chain ID: C
UniProt ID: Q1EHA4
Base Structure: X-ray
Registration Date: 2025-10-05
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 52 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -249160.957983 |
|---|---|
| FMO2-HF: Nuclear repulsion | 228433.316326 |
| FMO2-HF: Total energy | -20727.641658 |
| FMO2-MP2: Total energy | -20788.758704 |
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:14:PRO)
Summations of interaction energy for
fragment #1(A:14: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. |
| -22.884 | -18.042 | 0.979 | -1.995 | -3.828 | -0.017 |
Interaction energy analysis for fragmet #1(A:14: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 | A | 16 | PHE | 0 | 0.087 | 0.036 | 3.836 | 1.482 | 2.947 | -0.004 | -0.574 | -0.887 | -0.001 |
| 4 | A | 17 | ALA | 0 | 0.036 | 0.028 | 2.246 | 3.394 | 4.602 | 0.918 | -0.786 | -1.340 | -0.010 |
| 5 | A | 18 | ARG | 1 | 0.917 | 0.962 | 3.971 | 36.024 | 36.301 | -0.001 | -0.060 | -0.217 | 0.000 |
| 51 | A | 64 | ILE | 0 | -0.075 | -0.029 | 3.936 | -0.108 | 0.051 | -0.001 | -0.027 | -0.132 | 0.000 |
| 52 | A | 65 | LYS | 0 | -0.084 | -0.022 | 2.853 | -22.069 | -20.336 | 0.067 | -0.548 | -1.252 | -0.006 |
| 6 | A | 19 | GLU | -1 | -0.853 | -0.933 | 6.539 | -28.357 | -28.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 20 | LEU | 0 | 0.008 | -0.002 | 7.634 | 3.209 | 3.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 21 | HIS | 0 | 0.016 | 0.011 | 8.096 | 2.331 | 2.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 22 | ALA | 0 | 0.033 | 0.018 | 9.800 | 2.611 | 2.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 23 | GLN | 0 | -0.041 | -0.022 | 11.878 | 3.179 | 3.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 24 | LEU | 0 | 0.004 | 0.010 | 11.347 | 1.559 | 1.559 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 25 | VAL | 0 | 0.008 | 0.000 | 13.639 | 1.487 | 1.487 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 26 | GLN | 0 | -0.041 | -0.019 | 15.881 | 1.933 | 1.933 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 27 | ALA | 0 | 0.049 | 0.040 | 17.502 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 28 | LEU | 0 | 0.049 | 0.015 | 17.886 | 1.044 | 1.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 29 | GLY | 0 | -0.020 | -0.008 | 20.029 | 0.854 | 0.854 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 30 | ASP | -1 | -0.846 | -0.912 | 21.932 | -12.851 | -12.851 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 31 | VAL | 0 | 0.002 | 0.008 | 22.722 | 0.763 | 0.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 32 | LYS | 1 | 0.925 | 0.958 | 21.440 | 14.639 | 14.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 33 | ARG | 1 | 0.849 | 0.903 | 23.121 | 13.306 | 13.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 34 | ARG | 1 | 0.837 | 0.919 | 27.576 | 10.227 | 10.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 35 | LEU | 0 | 0.017 | 0.008 | 27.123 | 0.495 | 0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 36 | LEU | 0 | -0.014 | 0.000 | 30.437 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 37 | ARG | 1 | 0.868 | 0.937 | 32.704 | 9.095 | 9.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 38 | GLY | 0 | 0.034 | 0.041 | 34.781 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 39 | GLY | 0 | 0.040 | 0.014 | 35.402 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 40 | THR | 0 | 0.007 | 0.002 | 37.178 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 41 | GLN | 0 | 0.058 | 0.012 | 36.434 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 42 | GLN | 0 | 0.037 | 0.030 | 35.132 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 43 | GLN | 0 | 0.001 | -0.004 | 33.463 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 44 | TYR | 0 | 0.024 | 0.017 | 31.743 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 45 | GLN | 0 | 0.028 | 0.018 | 30.426 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 46 | GLN | 0 | -0.012 | -0.012 | 29.359 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 47 | TRP | 0 | -0.005 | -0.018 | 25.885 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 48 | GLN | 0 | -0.021 | -0.013 | 25.965 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 49 | GLN | 0 | 0.015 | 0.014 | 24.809 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 50 | GLU | -1 | -0.930 | -0.957 | 22.593 | -14.295 | -14.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 51 | ALA | 0 | -0.064 | -0.025 | 21.189 | -0.781 | -0.781 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 52 | ASP | -1 | -0.834 | -0.922 | 20.107 | -13.613 | -13.613 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 53 | ALA | 0 | -0.024 | -0.010 | 19.535 | -0.804 | -0.804 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 54 | ILE | 0 | -0.034 | -0.022 | 16.338 | -1.336 | -1.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 55 | GLU | -1 | -0.927 | -0.978 | 15.347 | -16.685 | -16.685 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 56 | ALA | 0 | 0.023 | 0.018 | 15.295 | -1.282 | -1.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 57 | GLY | 0 | 0.002 | -0.001 | 13.264 | -1.289 | -1.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 58 | MET | 0 | -0.073 | -0.042 | 11.192 | -2.396 | -2.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 59 | ASN | 0 | 0.010 | 0.006 | 10.824 | -1.480 | -1.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 60 | ILE | 0 | -0.075 | -0.035 | 9.956 | -1.308 | -1.308 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 61 | ILE | 0 | -0.031 | -0.026 | 5.895 | -3.579 | -3.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 62 | GLU | -1 | -0.929 | -0.964 | 6.457 | -29.350 | -29.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 63 | LYS | 1 | 0.929 | 0.964 | 8.003 | 21.951 | 21.951 | 0.000 | 0.000 | 0.000 | 0.000 |