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: Q58JY
Calculation Name: 5EPM-C-Xray547
Preferred Name:
Target Type:
Ligand Name: pyroglutamic acid
Ligand 3-letter code: PCA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5EPM
Chain ID: C
UniProt ID: P84507
Base Structure: X-ray
Registration Date: 2025-10-06
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 | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -143908.046413 |
|---|---|
| FMO2-HF: Nuclear repulsion | 128334.341678 |
| FMO2-HF: Total energy | -15573.704735 |
| FMO2-MP2: Total energy | -15613.123201 |
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(C:1:ASP)
Summations of interaction energy for
fragment #1(C:1:ASP)
| 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. |
| -2.811 | -0.455 | 0.021 | -1.137 | -1.24 | 0.002 |
Interaction energy analysis for fragmet #1(C:1:ASP)
| 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 | C | 3 | LEU | 0 | 0.007 | 0.005 | 3.404 | 1.491 | 3.847 | 0.021 | -1.137 | -1.240 | 0.002 |
| 4 | C | 4 | GLY | 0 | 0.076 | 0.019 | 5.937 | 1.591 | 1.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 5 | MET | 0 | 0.002 | -0.007 | 7.768 | -1.439 | -1.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 6 | PHE | 0 | -0.025 | -0.019 | 11.353 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 7 | LYS | 1 | 0.938 | 0.989 | 7.367 | -1.171 | -1.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 8 | SER | 0 | 0.041 | 0.006 | 10.411 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 9 | CYS | 0 | -0.053 | -0.006 | 10.433 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 10 | ASP | -1 | -0.738 | -0.863 | 12.006 | -2.446 | -2.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 11 | PRO | 0 | -0.078 | -0.065 | 13.844 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 12 | GLU | -1 | -0.951 | -0.960 | 16.421 | -1.473 | -1.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 13 | ASN | 0 | -0.079 | -0.041 | 12.062 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 14 | ASP | -1 | -0.788 | -0.905 | 11.064 | -2.410 | -2.410 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 15 | LYS | 1 | 0.974 | 0.983 | 6.485 | 9.218 | 9.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 16 | CYS | 0 | -0.103 | -0.023 | 6.953 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 18 | LYS | 1 | 1.020 | 0.992 | 7.432 | -4.730 | -4.730 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 19 | ARG | 1 | 0.942 | 0.974 | 10.023 | -1.890 | -1.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 20 | LEU | 0 | -0.027 | 0.004 | 9.280 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 21 | VAL | 0 | -0.028 | -0.014 | 12.593 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 23 | SER | 0 | -0.052 | -0.015 | 14.814 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 24 | ARG | 1 | 0.934 | 0.950 | 16.927 | 0.759 | 0.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 25 | SER | 0 | -0.017 | -0.005 | 20.793 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 26 | HIS | 0 | 0.011 | -0.002 | 18.874 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 27 | ARG | 1 | 0.954 | 0.992 | 16.586 | 1.023 | 1.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 28 | TRP | 0 | 0.084 | 0.035 | 13.475 | -0.319 | -0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 30 | LYS | 1 | 0.965 | 0.981 | 12.737 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 31 | TRP | 0 | 0.079 | 0.016 | 13.837 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 32 | LYS | 1 | 0.802 | 0.898 | 15.712 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 33 | LEU | -1 | -0.832 | -0.900 | 17.297 | 0.606 | 0.606 | 0.000 | 0.000 | 0.000 | 0.000 |