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: 1Y73Z
Calculation Name: 3EGF-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 3EGF
Chain ID: A
UniProt ID: P01132
Base Structure: SolutionNMR
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 | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -257075.255064 |
|---|---|
| FMO2-HF: Nuclear repulsion | 234153.863861 |
| FMO2-HF: Total energy | -22921.391202 |
| FMO2-MP2: Total energy | -22982.310104 |
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:ASN)
Summations of interaction energy for
fragment #1(A:1:ASN)
| 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. |
| -85.16 | -80.362 | 4.416 | -3.756 | -5.459 | -0.038 |
Interaction energy analysis for fragmet #1(A:1:ASN)
| 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 | TYR | 0 | 0.035 | 0.043 | 3.823 | 2.744 | 4.179 | -0.019 | -0.584 | -0.832 | -0.002 |
| 22 | A | 23 | ILE | 0 | 0.014 | -0.007 | 4.538 | -6.011 | -5.906 | -0.001 | -0.024 | -0.080 | 0.000 |
| 23 | A | 24 | GLU | -1 | -0.901 | -0.973 | 2.325 | -75.461 | -72.925 | 4.434 | -2.983 | -3.987 | -0.035 |
| 24 | A | 25 | SER | 0 | -0.094 | -0.047 | 3.673 | 0.052 | 0.617 | 0.003 | -0.144 | -0.424 | -0.001 |
| 25 | A | 26 | LEU | 0 | -0.016 | -0.020 | 4.372 | 5.782 | 5.939 | -0.001 | -0.021 | -0.136 | 0.000 |
| 4 | A | 4 | PRO | 0 | 0.017 | 0.014 | 6.098 | 2.352 | 2.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | GLY | 0 | 0.040 | -0.003 | 9.902 | 0.641 | 0.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | CYS | 0 | -0.020 | -0.046 | 12.024 | -2.181 | -2.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | -0.001 | 0.029 | 14.467 | 0.900 | 0.900 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | SER | 0 | 0.038 | 0.003 | 17.394 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | SER | 0 | -0.030 | -0.012 | 18.268 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | TYR | 0 | -0.056 | -0.026 | 15.047 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ASP | -1 | -0.849 | -0.932 | 21.087 | -12.916 | -12.916 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | GLY | 0 | -0.043 | -0.011 | 22.809 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | TYR | 0 | -0.041 | -0.024 | 15.337 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | CYS | 0 | -0.100 | -0.025 | 12.749 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LEU | 0 | 0.040 | 0.027 | 20.154 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ASN | 0 | -0.038 | -0.036 | 22.673 | -0.744 | -0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.017 | -0.003 | 23.098 | 0.584 | 0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLY | 0 | 0.028 | 0.015 | 19.258 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | VAL | 0 | -0.024 | -0.008 | 15.563 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | MET | 0 | -0.085 | -0.034 | 7.127 | -1.291 | -1.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | HIS | 1 | 0.857 | 0.939 | 7.216 | 34.378 | 34.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ASP | -1 | -0.863 | -0.919 | 7.276 | -28.840 | -28.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | SER | 0 | 0.028 | 0.032 | 8.809 | 3.462 | 3.462 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | TYR | 0 | -0.025 | -0.025 | 9.655 | -3.073 | -3.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | THR | 0 | 0.011 | -0.010 | 9.882 | 0.534 | 0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 32 | ASN | 0 | 0.020 | 0.029 | 13.140 | 0.562 | 0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 33 | CYS | 0 | -0.056 | -0.007 | 14.915 | 1.045 | 1.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 34 | VAL | 0 | 0.052 | 0.036 | 18.083 | -0.437 | -0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 35 | ILE | 0 | 0.006 | 0.002 | 20.819 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 36 | GLY | 0 | -0.024 | -0.006 | 23.039 | 0.518 | 0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 37 | TYR | 0 | -0.042 | -0.038 | 22.204 | 0.528 | 0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 38 | SER | 0 | 0.030 | 0.015 | 16.973 | -0.708 | -0.708 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 39 | GLY | 0 | -0.022 | -0.004 | 16.339 | 0.835 | 0.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 40 | ASP | -1 | -0.789 | -0.885 | 13.900 | -22.451 | -22.451 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 41 | ARG | 1 | 0.909 | 0.938 | 15.043 | 16.640 | 16.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 43 | GLN | 0 | 0.029 | 0.021 | 20.309 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 44 | THR | 0 | -0.029 | -0.022 | 19.361 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 45 | ARG | 1 | 0.910 | 0.959 | 21.948 | 10.611 | 10.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 46 | ASP | -1 | -0.895 | -0.952 | 23.510 | -11.461 | -11.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 47 | LEU | 0 | -0.012 | -0.010 | 24.019 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 48 | ARG | 1 | 0.931 | 0.952 | 21.091 | 12.878 | 12.878 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 49 | TRP | 0 | 0.019 | 0.014 | 20.858 | -0.570 | -0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 50 | TRP | 0 | -0.001 | 0.023 | 16.476 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 51 | GLU | -1 | -0.898 | -0.954 | 16.021 | -16.679 | -16.679 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 52 | LEU | 0 | -0.044 | -0.028 | 15.370 | 0.830 | 0.830 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 53 | ARG | 0 | 0.048 | 0.038 | 17.850 | -1.684 | -1.684 | 0.000 | 0.000 | 0.000 | 0.000 |