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: 5GY3Z
Calculation Name: 7QWQ-m-Other547
Preferred Name:
Target Type:
Ligand Name: magnesium ion | zinc ion
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7QWQ
Chain ID: m
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
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 | 52 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -265197.586331 |
|---|---|
| FMO2-HF: Nuclear repulsion | 242553.37214 |
| FMO2-HF: Total energy | -22644.214191 |
| FMO2-MP2: Total energy | -22706.168397 |
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:77:ILE)
Summations of interaction energy for
fragment #1(A:77:ILE)
| 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. |
| 137.93 | 140.089 | 0 | -1.013 | -1.147 | -0.001 |
Interaction energy analysis for fragmet #1(A:77:ILE)
| 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 | 79 | GLU | -1 | -0.829 | -0.910 | 3.450 | -43.672 | -41.513 | 0.000 | -1.013 | -1.147 | -0.001 |
| 4 | A | 80 | PRO | 0 | 0.022 | 0.007 | 5.888 | 2.588 | 2.588 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 81 | SER | 0 | 0.072 | 0.024 | 8.199 | 2.312 | 2.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 82 | LEU | 0 | 0.065 | 0.036 | 8.298 | 2.122 | 2.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 83 | ARG | 1 | 0.941 | 0.974 | 4.870 | 36.844 | 36.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 84 | GLN | 0 | -0.022 | -0.019 | 8.717 | 1.397 | 1.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 85 | LEU | 0 | 0.008 | 0.015 | 12.285 | 1.966 | 1.966 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 86 | ALA | 0 | 0.043 | 0.019 | 10.502 | 1.576 | 1.576 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 87 | GLN | 0 | 0.023 | 0.008 | 10.126 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 88 | LYS | 1 | 0.937 | 0.987 | 13.395 | 17.003 | 17.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 89 | TYR | 0 | -0.043 | -0.027 | 16.018 | 1.744 | 1.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 90 | ASN | 0 | -0.013 | -0.004 | 12.701 | 1.817 | 1.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 91 | CYS | -1 | -0.790 | -0.851 | 14.056 | -18.505 | -18.505 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 92 | ASP | -1 | -0.914 | -0.955 | 16.089 | -16.763 | -16.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 93 | LYS | 1 | 0.872 | 0.936 | 18.538 | 14.541 | 14.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 94 | MET | 0 | -0.006 | 0.008 | 21.616 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 95 | ILE | 0 | -0.026 | -0.009 | 22.715 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 96 | CYS | 0 | 0.026 | 0.009 | 26.419 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 97 | ARG | 1 | 0.870 | 0.915 | 29.787 | 9.713 | 9.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 98 | LYS | 1 | 1.000 | 1.017 | 31.339 | 8.035 | 8.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 99 | CYS | 0 | -0.029 | -0.031 | 32.063 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 100 | TYR | 0 | 0.030 | 0.017 | 26.615 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 101 | ALA | 0 | -0.007 | 0.004 | 26.300 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 102 | ARG | 1 | 0.986 | 0.990 | 20.387 | 13.811 | 13.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 103 | LEU | 0 | -0.032 | -0.018 | 24.967 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 104 | HIS | 0 | 0.078 | 0.031 | 24.390 | -0.781 | -0.781 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 105 | PRO | 0 | 0.035 | 0.004 | 22.245 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 106 | ARG | 1 | 0.980 | 0.984 | 24.831 | 10.415 | 10.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 107 | ALA | 0 | -0.064 | -0.014 | 28.215 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 108 | VAL | 0 | 0.085 | 0.038 | 30.194 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 109 | ASN | 0 | 0.050 | 0.026 | 32.931 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 110 | CYS | 0 | -0.038 | -0.007 | 32.202 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 111 | ARG | 1 | 0.948 | 0.974 | 27.002 | 10.693 | 10.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 112 | LYS | 1 | 0.929 | 0.948 | 30.726 | 9.748 | 9.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 113 | LYS | 1 | 1.101 | 1.035 | 34.968 | 7.211 | 7.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 114 | LYS | 1 | 0.979 | 1.000 | 33.352 | 8.885 | 8.885 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 115 | CYS | 0 | -0.054 | -0.002 | 34.538 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 116 | GLY | 0 | 0.070 | 0.047 | 37.560 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 117 | HIS | 0 | -0.024 | -0.028 | 36.696 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 118 | THR | 0 | 0.030 | -0.018 | 36.164 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 119 | ASN | 0 | 0.024 | 0.019 | 34.742 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 120 | ASN | 0 | 0.036 | 0.034 | 33.862 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 121 | LEU | 0 | -0.003 | 0.005 | 28.437 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 122 | ARG | 1 | 0.906 | 0.958 | 23.110 | 11.995 | 11.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 123 | PRO | 0 | 0.103 | 0.049 | 22.373 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 124 | LYS | 1 | 0.708 | 0.802 | 15.900 | 17.136 | 17.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 125 | LYS | 1 | 0.942 | 0.971 | 19.105 | 12.484 | 12.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 126 | LYS | 1 | 0.954 | 0.977 | 13.704 | 18.763 | 18.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 127 | VAL | 0 | -0.012 | -0.008 | 10.123 | 0.779 | 0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 128 | LYS | 0 | 0.107 | 0.068 | 11.174 | -5.897 | -5.897 | 0.000 | 0.000 | 0.000 | 0.000 |