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: 1VLJZ
Calculation Name: 1EJA-B-Xray549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1EJA
Chain ID: B
UniProt ID: P82107
Base Structure: X-ray
Registration Date: 2025-10-11
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 48 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -230965.152947 |
|---|---|
| FMO2-HF: Nuclear repulsion | 208262.583329 |
| FMO2-HF: Total energy | -22702.569618 |
| FMO2-MP2: Total energy | -22758.419079 |
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(B:7:THR)
Summations of interaction energy for
fragment #1(B:7:THR)
| 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. |
| -149.762 | -144.476 | 24.878 | -15.384 | -14.781 | -0.159 |
Interaction energy analysis for fragmet #1(B:7:THR)
| 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 | B | 9 | PRO | 0 | -0.016 | -0.002 | 3.865 | 1.691 | 3.213 | -0.019 | -0.676 | -0.826 | -0.001 |
| 4 | B | 10 | CYS | 0 | -0.046 | -0.019 | 4.335 | 6.442 | 6.514 | -0.002 | -0.016 | -0.054 | 0.000 |
| 9 | B | 15 | CYS | 0 | -0.031 | 0.012 | 3.144 | 0.963 | 1.902 | 0.054 | -0.446 | -0.547 | -0.002 |
| 10 | B | 16 | SER | 0 | 0.025 | 0.002 | 2.104 | -18.806 | -17.542 | 8.668 | -5.527 | -4.406 | -0.051 |
| 11 | B | 17 | GLY | 0 | 0.039 | 0.001 | 2.936 | -3.605 | -2.528 | 1.540 | -0.713 | -1.904 | 0.001 |
| 12 | B | 18 | ALA | 0 | 0.007 | 0.000 | 1.826 | -32.171 | -33.311 | 8.537 | -3.854 | -3.543 | -0.049 |
| 13 | B | 19 | GLN | 0 | -0.010 | 0.019 | 3.634 | 3.133 | 3.660 | 0.003 | -0.178 | -0.352 | -0.001 |
| 14 | B | 20 | MET | 0 | -0.026 | 0.008 | 1.887 | -50.422 | -49.397 | 6.097 | -3.974 | -3.149 | -0.056 |
| 5 | B | 11 | GLY | 0 | 0.107 | 0.058 | 9.011 | 1.445 | 1.445 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 12 | PRO | 0 | -0.053 | -0.023 | 12.667 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 13 | VAL | 0 | -0.016 | 0.009 | 8.980 | 0.523 | 0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 14 | THR | 0 | -0.022 | -0.021 | 5.398 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 22 | GLU | -1 | -0.745 | -0.878 | 6.893 | -19.818 | -19.818 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 23 | VAL | 0 | -0.034 | -0.012 | 10.479 | 1.953 | 1.953 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 24 | ASP | -1 | -0.905 | -0.985 | 12.490 | -20.993 | -20.993 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 25 | LYS | 1 | 0.843 | 0.929 | 10.910 | 22.486 | 22.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 27 | VAL | 0 | 0.022 | -0.004 | 7.550 | 1.472 | 1.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 28 | CYS | 0 | -0.061 | -0.040 | 6.919 | -5.496 | -5.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 29 | SER | 0 | -0.043 | -0.015 | 6.896 | 0.770 | 0.770 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 30 | ASP | -1 | -0.796 | -0.903 | 7.729 | -32.518 | -32.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 31 | LEU | 0 | -0.060 | -0.029 | 9.285 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 32 | HIS | 0 | 0.003 | 0.007 | 11.191 | 0.630 | 0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 33 | CYS | 0 | -0.133 | -0.079 | 13.940 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 34 | LYS | 1 | 0.945 | 0.958 | 13.927 | 20.380 | 20.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 35 | VAL | 0 | 0.015 | 0.007 | 17.545 | 0.861 | 0.861 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 36 | LYS | 1 | 0.940 | 0.966 | 19.096 | 13.018 | 13.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 37 | CYS | 0 | 0.008 | 0.023 | 19.455 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 38 | GLU | -1 | -0.939 | -0.973 | 21.097 | -12.061 | -12.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 39 | HIS | 1 | 0.810 | 0.907 | 22.254 | 12.796 | 12.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 40 | GLY | 0 | 0.070 | 0.060 | 18.131 | -0.351 | -0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 41 | PHE | 0 | -0.030 | -0.032 | 14.888 | 1.141 | 1.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 42 | LYS | 1 | 0.849 | 0.924 | 18.167 | 12.514 | 12.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 43 | LYS | 1 | 0.989 | 0.994 | 15.475 | 18.019 | 18.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 44 | ASP | -1 | -0.928 | -0.972 | 18.528 | -13.673 | -13.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 45 | ASP | -1 | -0.899 | -0.938 | 19.962 | -13.593 | -13.593 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 46 | ASN | 0 | -0.107 | -0.066 | 16.441 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 47 | GLY | 0 | 0.013 | 0.025 | 15.603 | -0.644 | -0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 49 | GLU | -1 | -0.837 | -0.921 | 12.638 | -20.202 | -20.202 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 50 | TYR | 0 | 0.013 | 0.012 | 14.008 | -0.892 | -0.892 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 51 | ALA | 0 | -0.009 | 0.002 | 15.177 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 53 | ILE | 0 | 0.046 | 0.023 | 19.412 | 0.931 | 0.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 55 | ALA | 0 | 0.044 | 0.019 | 21.225 | 0.537 | 0.537 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 56 | ASP | -1 | -0.843 | -0.898 | 22.978 | -11.615 | -11.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 57 | ALA | 0 | -0.034 | -0.025 | 26.770 | 0.311 | 0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 58 | PRO | 0 | -0.059 | -0.062 | 23.778 | -0.461 | -0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 59 | GLN | -1 | -0.919 | -0.935 | 20.253 | -14.083 | -14.083 | 0.000 | 0.000 | 0.000 | 0.000 |