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: 64ZGZ
Calculation Name: 2EOZ-A-Other547
Preferred Name:
Target Type:
Ligand Name: zinc ion
Ligand 3-letter code: ZN
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2EOZ
Chain ID: A
UniProt ID: Q8WTR7
Base Structure: SolutionNMR
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -161403.817093 |
|---|---|
| FMO2-HF: Nuclear repulsion | 144592.900677 |
| FMO2-HF: Total energy | -16810.916416 |
| FMO2-MP2: Total energy | -16858.671889 |
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:GLY)
Summations of interaction energy for
fragment #1(A:1: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. |
| 2.947 | 4.941 | -0.016 | -0.916 | -1.061 | -0.005 |
Interaction energy analysis for fragmet #1(A:1: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 | A | 3 | SER | 0 | 0.083 | 0.052 | 3.837 | 7.899 | 9.557 | -0.019 | -0.788 | -0.850 | -0.004 |
| 4 | A | 4 | GLY | 0 | 0.034 | 0.014 | 3.873 | -9.939 | -9.603 | 0.003 | -0.128 | -0.211 | -0.001 |
| 5 | A | 5 | SER | 0 | -0.029 | -0.022 | 6.550 | -0.735 | -0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | 0.018 | 0.005 | 8.772 | 1.137 | 1.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.029 | 0.015 | 10.531 | 0.752 | 0.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | THR | 0 | -0.047 | -0.033 | 14.361 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | 0.029 | 0.027 | 17.804 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLU | -1 | -0.950 | -0.970 | 17.756 | -16.778 | -16.778 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | LYS | 1 | 0.877 | 0.943 | 18.190 | 16.363 | 16.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | 0.030 | 0.019 | 22.252 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | TYR | 0 | 0.019 | 0.018 | 24.993 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.047 | 0.001 | 21.270 | -0.712 | -0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | CYS | -1 | -0.807 | -0.783 | 21.782 | -12.784 | -12.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ASN | 0 | -0.020 | -0.014 | 21.490 | -0.533 | -0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | 0.013 | -0.009 | 23.259 | 0.221 | 0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | CYS | 0 | -0.116 | -0.122 | 20.563 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.068 | 0.055 | 17.443 | -0.846 | -0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LYS | 1 | 0.902 | 0.952 | 17.624 | 14.359 | 14.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ALA | 0 | 0.039 | 0.019 | 19.179 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PHE | 0 | -0.033 | -0.024 | 20.833 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | VAL | 0 | 0.041 | 0.005 | 24.026 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LEU | 0 | -0.004 | 0.000 | 26.080 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | SER | 0 | 0.064 | 0.029 | 28.676 | -0.259 | -0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ALA | 0 | 0.011 | 0.007 | 30.902 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | HIS | 0 | 0.007 | -0.005 | 27.257 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | LEU | 0 | 0.025 | 0.028 | 25.321 | -0.204 | -0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ASN | 0 | 0.021 | 0.001 | 27.643 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLN | 0 | 0.012 | -0.003 | 30.474 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | HIS | 0 | -0.034 | -0.036 | 22.848 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LEU | 0 | 0.013 | -0.009 | 26.670 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | ARG | 1 | 0.930 | 0.966 | 28.750 | 9.028 | 9.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | VAL | 0 | -0.036 | -0.012 | 26.003 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | HIS | 1 | 0.869 | 0.922 | 24.240 | 11.810 | 11.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | THR | 0 | -0.006 | 0.013 | 29.438 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | GLN | 0 | -0.046 | -0.030 | 32.951 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | GLU | -1 | -0.884 | -0.931 | 34.062 | -8.394 | -8.394 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | THR | 0 | -0.037 | -0.031 | 31.721 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LEU | 0 | 0.005 | 0.016 | 33.972 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | SER | 0 | -0.049 | -0.028 | 28.766 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | GLY | 0 | 0.016 | -0.001 | 28.787 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PRO | 0 | -0.050 | -0.010 | 27.851 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | SER | 0 | 0.013 | -0.004 | 29.639 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | SER | 0 | -0.059 | -0.052 | 30.282 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | -1 | -0.907 | -0.917 | 31.758 | -8.647 | -8.647 | 0.000 | 0.000 | 0.000 | 0.000 |