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: 1VK2Z
Calculation Name: 1IRQ-A-Xray549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1IRQ
Chain ID: A
UniProt ID: Q57468
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 | -214101.992372 |
|---|---|
| FMO2-HF: Nuclear repulsion | 194589.218538 |
| FMO2-HF: Total energy | -19512.773834 |
| FMO2-MP2: Total energy | -19569.207705 |
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:24:ILE)
Summations of interaction energy for
fragment #1(A:24: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. |
| -34.615 | -31.814 | 0.085 | -1.56 | -1.324 | -0.008 |
Interaction energy analysis for fragmet #1(A:24: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 | 26 | GLY | 0 | 0.007 | 0.008 | 2.993 | -13.858 | -11.097 | 0.086 | -1.556 | -1.290 | -0.008 |
| 4 | A | 27 | ASP | -1 | -0.821 | -0.904 | 5.385 | -32.750 | -32.710 | -0.001 | -0.004 | -0.034 | 0.000 |
| 5 | A | 28 | LYS | 1 | 0.909 | 0.934 | 8.857 | 27.509 | 27.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 29 | THR | 0 | 0.009 | 0.015 | 12.588 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 30 | VAL | 0 | 0.058 | 0.025 | 15.621 | 0.545 | 0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 31 | ARG | 1 | 0.905 | 0.953 | 18.436 | 13.341 | 13.341 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 32 | VAL | 0 | 0.064 | 0.039 | 20.051 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 33 | ARG | 1 | 0.862 | 0.886 | 22.789 | 10.918 | 10.918 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 34 | ALA | 0 | 0.030 | 0.009 | 25.700 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 35 | ASP | -1 | -0.748 | -0.841 | 26.932 | -10.823 | -10.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 36 | LEU | 0 | 0.008 | 0.005 | 25.606 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 37 | HIS | 0 | 0.012 | 0.004 | 20.271 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 38 | HIS | 0 | 0.000 | -0.003 | 23.927 | -0.529 | -0.529 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 39 | ILE | 0 | 0.011 | 0.004 | 26.615 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 40 | ILE | 0 | 0.047 | 0.025 | 20.599 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 41 | LYS | 1 | 0.944 | 0.994 | 22.739 | 12.503 | 12.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 42 | ILE | 0 | -0.040 | -0.023 | 23.711 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 43 | GLU | -1 | -0.842 | -0.907 | 24.851 | -11.272 | -11.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 44 | THR | 0 | -0.060 | -0.059 | 19.768 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 45 | ALA | 0 | -0.012 | -0.003 | 22.558 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 46 | LYS | 1 | 0.796 | 0.895 | 24.647 | 11.014 | 11.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 47 | ASN | 0 | -0.014 | -0.007 | 21.800 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 48 | GLY | 0 | 0.019 | 0.020 | 21.994 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 49 | GLY | 0 | 0.012 | 0.021 | 18.063 | -0.761 | -0.761 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 50 | ASN | 0 | -0.003 | -0.018 | 12.751 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 51 | VAL | 0 | 0.007 | -0.013 | 16.845 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 52 | LYS | 1 | 0.784 | 0.893 | 8.653 | 31.916 | 31.916 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 53 | GLU | -1 | -0.835 | -0.912 | 10.686 | -27.459 | -27.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 54 | VAL | 0 | 0.023 | 0.014 | 13.810 | 0.496 | 0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 55 | MET | 0 | -0.095 | -0.047 | 15.343 | 1.059 | 1.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 56 | ASP | -1 | -0.826 | -0.913 | 10.850 | -27.101 | -27.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 57 | GLN | 0 | -0.023 | -0.013 | 13.739 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 58 | ALA | 0 | -0.004 | -0.003 | 16.060 | 0.721 | 0.721 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 59 | LEU | 0 | -0.042 | -0.021 | 14.726 | 0.862 | 0.862 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 60 | GLU | -1 | -0.806 | -0.890 | 12.652 | -21.731 | -21.731 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 61 | GLU | -1 | -0.891 | -0.941 | 15.757 | -14.343 | -14.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 62 | TYR | 0 | -0.055 | -0.028 | 19.265 | 0.868 | 0.868 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 63 | ILE | 0 | -0.016 | -0.018 | 15.458 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 64 | ARG | 1 | 0.803 | 0.875 | 13.003 | 19.991 | 19.991 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 65 | LYS | 1 | 0.890 | 0.976 | 19.457 | 12.196 | 12.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 66 | TYR | 0 | -0.055 | -0.042 | 22.479 | 0.737 | 0.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 67 | LEU | 0 | -0.095 | -0.037 | 20.056 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 68 | PRO | 0 | 0.067 | 0.031 | 19.546 | -0.809 | -0.809 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 69 | ASP | -1 | -0.909 | -0.966 | 18.704 | -13.340 | -13.340 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 70 | LYS | 1 | 0.843 | 0.924 | 16.688 | 14.408 | 14.408 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 71 | LEU | -1 | -0.882 | -0.919 | 11.457 | -20.391 | -20.391 | 0.000 | 0.000 | 0.000 | 0.000 |