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: QLG4Y
Calculation Name: 4C7N-A-Xray547
Preferred Name: Microphthalmia-associated transcription factor
Target Type: SINGLE PROTEIN
Ligand Name: mercury (ii) ion
Ligand 3-letter code: HG
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4C7N
Chain ID: A
ChEMBL ID: CHEMBL1741165
UniProt ID: O75030
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 |
| 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 | 47 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -203573.553181 |
|---|---|
| FMO2-HF: Nuclear repulsion | 183429.388091 |
| FMO2-HF: Total energy | -20144.16509 |
| FMO2-MP2: Total energy | -20203.435915 |
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:2:SER)
Summations of interaction energy for
fragment #1(A:2:SER)
| 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. |
| 27.5 | 31.138 | 16.584 | -11.015 | -9.206 | -0.11 |
Interaction energy analysis for fragmet #1(A:2:SER)
| 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 | 4 | VAL | 0 | 0.057 | 0.011 | 2.763 | 0.110 | 3.426 | 0.393 | -1.546 | -2.163 | 0.005 |
| 4 | A | 5 | ASP | -1 | -0.803 | -0.882 | 1.720 | -112.998 | -113.575 | 16.185 | -9.184 | -6.423 | -0.113 |
| 5 | A | 6 | TYR | 0 | 0.017 | 0.011 | 3.254 | 6.356 | 7.167 | 0.007 | -0.282 | -0.536 | -0.002 |
| 7 | A | 8 | ARG | 1 | 0.977 | 0.971 | 4.702 | 48.070 | 48.158 | -0.001 | -0.003 | -0.084 | 0.000 |
| 6 | A | 7 | ILE | 0 | 0.014 | 0.026 | 6.546 | 5.632 | 5.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | LYS | 1 | 0.852 | 0.937 | 8.229 | 29.703 | 29.703 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | LEU | 0 | 0.015 | 0.007 | 10.025 | 2.664 | 2.664 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | GLN | 0 | 0.054 | 0.014 | 11.558 | 0.762 | 0.762 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ARG | 1 | 0.924 | 0.971 | 9.331 | 29.291 | 29.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLU | -1 | -0.836 | -0.932 | 14.182 | -18.495 | -18.495 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | GLN | 0 | -0.002 | -0.001 | 16.186 | 0.818 | 0.818 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | GLN | 0 | 0.009 | 0.014 | 17.778 | 0.687 | 0.687 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | ARG | 1 | 0.883 | 0.949 | 18.374 | 17.065 | 17.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ALA | 0 | 0.019 | 0.003 | 20.433 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | LYS | 1 | 0.887 | 0.938 | 22.139 | 13.418 | 13.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | GLU | -1 | -0.826 | -0.908 | 23.576 | -11.955 | -11.955 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | LEU | 0 | -0.048 | -0.025 | 23.708 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | GLU | -1 | -0.845 | -0.913 | 26.535 | -11.138 | -11.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ASN | 0 | -0.037 | -0.023 | 27.270 | 0.667 | 0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | ARG | 1 | 0.904 | 0.940 | 29.245 | 10.378 | 10.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | GLN | 0 | -0.035 | -0.007 | 30.792 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | LYS | 1 | 0.979 | 0.984 | 32.478 | 9.514 | 9.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | LYS | 1 | 0.914 | 0.960 | 33.957 | 9.305 | 9.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LEU | 0 | -0.019 | -0.013 | 34.157 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | GLU | -1 | -0.848 | -0.919 | 35.268 | -8.924 | -8.924 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | HIS | 0 | 0.009 | -0.003 | 37.511 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ALA | 0 | -0.005 | 0.010 | 39.795 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ASN | 0 | 0.042 | 0.005 | 40.144 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ARG | 1 | 0.971 | 1.000 | 42.859 | 7.123 | 7.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | HIS | 0 | -0.020 | -0.028 | 43.753 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | LEU | 0 | -0.038 | -0.014 | 43.822 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | LEU | 0 | 0.017 | 0.014 | 46.994 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | LEU | 0 | -0.017 | -0.008 | 48.609 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ARG | 1 | 1.009 | 1.004 | 48.348 | 6.619 | 6.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | ILE | 0 | -0.021 | -0.004 | 49.324 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | GLN | 0 | 0.018 | 0.006 | 52.734 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | GLU | -1 | -0.927 | -0.965 | 54.249 | -5.917 | -5.917 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | LEU | 0 | -0.019 | -0.015 | 53.918 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | GLU | -1 | -0.917 | -0.963 | 55.675 | -5.730 | -5.730 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | MET | 0 | -0.082 | -0.045 | 58.845 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | GLN | 0 | -0.033 | -0.018 | 59.415 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ALA | 0 | -0.020 | -0.011 | 60.890 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | ARG | 1 | 0.872 | 0.931 | 58.984 | 5.457 | 5.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | ALA | 0 | -0.058 | -0.018 | 64.717 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | HIS | -1 | -0.954 | -0.950 | 66.776 | -4.673 | -4.673 | 0.000 | 0.000 | 0.000 | 0.000 |