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: N6KRQ
Calculation Name: 1E4R-A-Other549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1E4R
Chain ID: A
UniProt ID: Q91V82
Base Structure: SolutionNMR
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 | 32 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -131132.180426 |
|---|---|
| FMO2-HF: Nuclear repulsion | 116296.673853 |
| FMO2-HF: Total energy | -14835.506573 |
| FMO2-MP2: Total energy | -14873.653847 |
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. |
| 122.213 | 125.467 | 0.447 | -0.984 | -2.718 | -0.005 |
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 | PRO | 0 | 0.012 | 0.007 | 2.782 | 6.848 | 8.638 | 0.275 | -0.443 | -1.622 | -0.003 |
| 4 | A | 4 | VAL | 0 | -0.005 | 0.000 | 2.941 | 7.358 | 8.293 | 0.165 | -0.419 | -0.681 | -0.001 |
| 5 | A | 5 | SER | 0 | 0.016 | 0.010 | 3.693 | -1.194 | -0.673 | 0.009 | -0.122 | -0.408 | -0.001 |
| 6 | A | 6 | CYS | 0 | -0.025 | -0.028 | 5.274 | 3.655 | 3.663 | -0.002 | 0.000 | -0.007 | 0.000 |
| 7 | A | 7 | ILE | 0 | 0.046 | 0.021 | 8.380 | 2.189 | 2.189 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ARG | 1 | 0.880 | 0.945 | 6.773 | 38.966 | 38.966 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASN | 0 | -0.032 | -0.018 | 10.145 | 0.853 | 0.853 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.034 | 0.030 | 12.502 | 1.591 | 1.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | -0.082 | -0.033 | 13.713 | 1.352 | 1.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | 0.034 | 0.012 | 14.310 | -0.641 | -0.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | CYS | 0 | -0.054 | -0.016 | 7.529 | -3.927 | -3.927 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLN | 0 | 0.076 | 0.041 | 14.321 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | TYR | 0 | 0.047 | 0.037 | 16.003 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.860 | 0.912 | 17.398 | 14.433 | 14.433 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | CYS | 0 | -0.060 | -0.041 | 12.757 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ILE | 0 | 0.065 | 0.038 | 20.188 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.041 | 0.010 | 22.895 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LEU | 0 | 0.015 | 0.022 | 24.416 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ARG | 1 | 0.844 | 0.909 | 19.872 | 13.976 | 13.976 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | HIS | 0 | 0.041 | 0.029 | 19.891 | -0.480 | -0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LYS | 1 | 0.865 | 0.931 | 12.426 | 19.161 | 19.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ILE | 0 | 0.040 | 0.019 | 12.758 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLY | 0 | 0.058 | 0.028 | 10.387 | -1.169 | -1.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | THR | 0 | -0.060 | -0.036 | 8.499 | 2.639 | 2.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | GLY | 0 | 0.074 | 0.020 | 7.249 | -3.525 | -3.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | SER | 0 | 0.006 | 0.005 | 8.340 | 1.099 | 1.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | PRO | 0 | -0.002 | 0.011 | 10.568 | 1.212 | 1.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | PHE | 0 | 0.021 | -0.004 | 11.888 | 1.330 | 1.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | LYS | 1 | 0.910 | 0.956 | 11.272 | 14.150 | 14.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 35 | LYS | 0 | 0.223 | 0.135 | 16.443 | 2.139 | 2.139 | 0.000 | 0.000 | 0.000 | 0.000 |