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: G4QK1
Calculation Name: 2WPV-H-Xray549
Preferred Name:
Target Type:
Ligand Name: mercury (ii) ion
Ligand 3-letter code: HG
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2WPV
Chain ID: H
UniProt ID: Q12125
Base Structure: X-ray
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 | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -169217.083868 |
|---|---|
| FMO2-HF: Nuclear repulsion | 150737.357785 |
| FMO2-HF: Total energy | -18479.726082 |
| FMO2-MP2: Total energy | -18535.325386 |
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(H:7:GLY)
Summations of interaction energy for
fragment #1(H:7: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. |
| 21.414 | 24.107 | 0.115 | -0.991 | -1.816 | -0.007 |
Interaction energy analysis for fragmet #1(H:7: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 | H | 9 | GLU | -1 | -0.895 | -0.939 | 3.672 | -37.928 | -36.658 | -0.005 | -0.453 | -0.811 | -0.002 |
| 4 | H | 10 | HIS | 0 | -0.029 | -0.008 | 2.660 | 2.458 | 3.605 | 0.121 | -0.488 | -0.779 | -0.005 |
| 5 | H | 11 | GLU | -1 | -0.897 | -0.948 | 4.360 | -29.245 | -28.969 | -0.001 | -0.050 | -0.226 | 0.000 |
| 6 | H | 12 | PHE | 0 | 0.007 | 0.001 | 6.479 | 6.775 | 6.775 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | H | 13 | VAL | 0 | 0.040 | 0.010 | 7.752 | 4.352 | 4.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | H | 14 | SER | 0 | 0.004 | 0.014 | 8.333 | 4.817 | 4.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | H | 15 | LYS | 1 | 0.933 | 0.961 | 9.970 | 27.336 | 27.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | H | 16 | PHE | 0 | 0.003 | 0.009 | 11.833 | 2.414 | 2.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | H | 17 | LEU | 0 | 0.020 | 0.009 | 12.963 | 1.835 | 1.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | H | 18 | THR | 0 | -0.026 | -0.015 | 13.723 | 1.688 | 1.688 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | H | 19 | LEU | 0 | -0.025 | -0.009 | 16.072 | 1.202 | 1.202 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | H | 20 | ALA | 0 | -0.045 | -0.030 | 17.526 | 1.087 | 1.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | H | 21 | THR | 0 | -0.083 | -0.056 | 18.045 | 0.750 | 0.750 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | H | 22 | LEU | 0 | -0.011 | 0.018 | 20.543 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | H | 23 | THR | 0 | -0.047 | -0.024 | 21.841 | 0.804 | 0.804 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | H | 24 | GLU | -1 | -0.916 | -0.960 | 24.162 | -11.537 | -11.537 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | H | 25 | PRO | 0 | -0.002 | 0.007 | 23.824 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | H | 26 | LYS | 1 | 0.947 | 0.958 | 25.954 | 10.092 | 10.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | H | 27 | LEU | 0 | -0.039 | -0.007 | 28.087 | 0.484 | 0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | H | 28 | PRO | 0 | 0.072 | 0.042 | 27.393 | -0.465 | -0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | H | 29 | LYS | 1 | 0.979 | 0.960 | 23.330 | 12.737 | 12.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | H | 30 | SER | 0 | 0.020 | 0.024 | 27.040 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | H | 31 | TYR | 0 | -0.025 | -0.011 | 30.133 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | H | 32 | THR | 0 | 0.023 | 0.013 | 31.431 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | H | 33 | LYS | 1 | 0.868 | 0.936 | 34.186 | 8.686 | 8.686 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | H | 34 | PRO | 0 | 0.033 | 0.008 | 36.343 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | H | 35 | LEU | 0 | 0.064 | 0.025 | 37.847 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | H | 36 | LYS | 1 | 0.850 | 0.913 | 39.977 | 7.224 | 7.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | H | 37 | ASP | -1 | -0.812 | -0.891 | 40.912 | -7.355 | -7.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | H | 38 | VAL | 0 | -0.051 | -0.019 | 37.284 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | H | 39 | THR | 0 | 0.015 | 0.007 | 39.750 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | H | 40 | ASN | 0 | 0.006 | -0.004 | 37.126 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | H | 41 | LEU | 0 | 0.026 | 0.014 | 35.632 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | H | 42 | GLY | 0 | -0.030 | 0.004 | 32.665 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | H | 43 | VAL | 0 | -0.008 | -0.010 | 30.362 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | H | 44 | PRO | 0 | -0.002 | -0.009 | 32.345 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | H | 45 | LEU | 0 | 0.013 | 0.017 | 27.624 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | H | 46 | PRO | 0 | -0.004 | 0.004 | 26.932 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | H | 47 | THR | 0 | 0.019 | 0.007 | 29.647 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | H | 48 | LEU | 0 | 0.019 | 0.006 | 26.733 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | H | 49 | LYS | 1 | 0.925 | 0.967 | 23.449 | 13.337 | 13.337 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | H | 50 | TYR | 0 | 0.006 | -0.012 | 25.538 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | H | 51 | LYS | 1 | 0.942 | 0.990 | 31.021 | 8.363 | 8.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | H | 52 | TYR | 0 | 0.023 | 0.017 | 33.340 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | H | 53 | LYS | 0 | -0.076 | -0.052 | 35.003 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | H | 54 | GLN | -1 | -0.870 | -0.926 | 36.939 | -8.203 | -8.203 | 0.000 | 0.000 | 0.000 | 0.000 |