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: 672YZ
Calculation Name: 5Y2E-D-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5Y2E
Chain ID: D
UniProt ID: P08434
Base Structure: X-ray
Registration Date: 2025-10-04
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 | -196189.653645 |
|---|---|
| FMO2-HF: Nuclear repulsion | 175667.531595 |
| FMO2-HF: Total energy | -20522.122049 |
| FMO2-MP2: Total energy | -20578.564151 |
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:94:MET)
Summations of interaction energy for
fragment #1(A:94:MET)
| 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. |
| 54.217 | 58.177 | 0.049 | -1.367 | -2.642 | -0.004 |
Interaction energy analysis for fragmet #1(A:94:MET)
| 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 | 96 | GLU | -1 | -0.874 | -0.921 | 3.700 | -42.077 | -39.971 | 0.001 | -0.761 | -1.346 | -0.002 |
| 4 | A | 97 | LYS | 1 | 1.016 | 1.002 | 3.504 | 46.720 | 47.308 | 0.010 | -0.141 | -0.457 | 0.000 |
| 5 | A | 98 | GLN | 0 | -0.022 | -0.006 | 3.404 | 0.936 | 2.085 | 0.039 | -0.458 | -0.730 | -0.002 |
| 6 | A | 99 | MET | 0 | 0.045 | 0.019 | 5.392 | 5.067 | 5.184 | -0.001 | -0.007 | -0.109 | 0.000 |
| 7 | A | 100 | ASP | -1 | -0.789 | -0.876 | 8.107 | -24.124 | -24.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 101 | ARG | 1 | 0.765 | 0.848 | 8.402 | 26.822 | 26.822 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 102 | VAL | 0 | 0.039 | 0.026 | 9.082 | 2.596 | 2.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 103 | VAL | 0 | 0.009 | 0.005 | 11.619 | 2.427 | 2.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 104 | LYS | 1 | 0.829 | 0.875 | 11.793 | 26.502 | 26.502 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 105 | GLU | -1 | -0.879 | -0.905 | 13.233 | -18.863 | -18.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 106 | MET | 0 | 0.025 | 0.004 | 15.567 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 107 | ARG | 1 | 0.929 | 0.977 | 17.295 | 18.685 | 18.685 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 108 | ARG | 1 | 1.023 | 1.017 | 15.055 | 18.407 | 18.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 109 | GLN | 0 | -0.033 | -0.014 | 16.836 | 0.802 | 0.802 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 110 | LEU | 0 | 0.007 | 0.001 | 21.288 | 0.622 | 0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 111 | GLU | -1 | -0.906 | -0.955 | 23.165 | -13.379 | -13.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 112 | MET | 0 | -0.037 | -0.014 | 24.687 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 113 | ILE | 0 | -0.001 | -0.008 | 24.252 | 0.468 | 0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 114 | ASP | -1 | -0.909 | -0.931 | 27.590 | -9.992 | -9.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 115 | LYS | 0 | 0.027 | 0.006 | 29.512 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 116 | LEU | 0 | -0.036 | -0.020 | 28.489 | 0.422 | 0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 117 | THR | 0 | -0.020 | -0.015 | 31.027 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 118 | THR | 0 | -0.008 | 0.003 | 33.494 | 0.410 | 0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 119 | ARG | 1 | 0.812 | 0.890 | 35.092 | 8.470 | 8.470 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 120 | GLY | 0 | 0.039 | 0.009 | 35.909 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 121 | ILE | 0 | 0.001 | -0.007 | 37.542 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 122 | GLU | -1 | -0.825 | -0.898 | 39.110 | -7.983 | -7.983 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 123 | GLN | 0 | -0.016 | -0.015 | 39.752 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 124 | VAL | 0 | -0.006 | 0.008 | 41.267 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 125 | GLU | -1 | -0.792 | -0.876 | 43.701 | -6.630 | -6.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 126 | LEU | 0 | -0.055 | -0.028 | 44.034 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 127 | LEU | 0 | -0.008 | -0.009 | 44.094 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 128 | LYS | 1 | 0.849 | 0.922 | 47.700 | 6.762 | 6.762 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 129 | ARG | 1 | 0.980 | 0.995 | 49.819 | 6.281 | 6.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 130 | ILE | 0 | -0.065 | -0.037 | 48.608 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 131 | HIS | 0 | 0.016 | -0.009 | 51.782 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 132 | ASP | -1 | -0.828 | -0.912 | 53.621 | -5.822 | -5.822 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 133 | LYS | 1 | 0.836 | 0.917 | 53.210 | 5.998 | 5.998 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 134 | LEU | 0 | -0.030 | -0.021 | 54.259 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 135 | MET | 0 | 0.008 | 0.007 | 57.415 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 136 | ILE | 0 | -0.046 | -0.028 | 59.183 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 137 | ARG | 1 | 0.896 | 0.946 | 59.959 | 5.297 | 5.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 138 | ALA | 0 | -0.025 | 0.003 | 61.581 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 139 | VAL | -1 | -0.970 | -0.962 | 63.483 | -4.709 | -4.709 | 0.000 | 0.000 | 0.000 | 0.000 |