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: JKGL9
Calculation Name: 1J2X-B-Xray549
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1J2X
Chain ID: B
UniProt ID: Q9Y5B0
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 | 18 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -45489.449353 |
|---|---|
| FMO2-HF: Nuclear repulsion | 37991.684441 |
| FMO2-HF: Total energy | -7497.764913 |
| FMO2-MP2: Total energy | -7517.732348 |
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:944:SER)
Summations of interaction energy for
fragment #1(B:944:SER)
| 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. |
| -156.487 | -153.522 | 20.335 | -12.907 | -10.392 | -0.135 |
Interaction energy analysis for fragmet #1(B:944:SER)
| 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 | 946 | ALA | 0 | 0.043 | 0.011 | 3.009 | 0.664 | 3.317 | 0.154 | -1.237 | -1.569 | 0.003 |
| 4 | B | 947 | ASP | -1 | -0.795 | -0.886 | 1.732 | -126.323 | -126.784 | 20.180 | -11.419 | -8.300 | -0.137 |
| 5 | B | 948 | GLU | -1 | -0.876 | -0.923 | 3.732 | -50.578 | -49.805 | 0.001 | -0.251 | -0.523 | -0.001 |
| 6 | B | 949 | MET | 0 | -0.019 | -0.013 | 5.996 | 6.808 | 6.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 950 | ALA | 0 | -0.007 | 0.012 | 6.935 | 4.124 | 4.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 951 | LYS | 1 | 0.883 | 0.919 | 5.627 | 51.239 | 51.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 952 | ALA | 0 | -0.014 | -0.001 | 9.629 | 3.085 | 3.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 953 | LEU | 0 | -0.016 | -0.004 | 11.488 | 2.474 | 2.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 954 | GLU | -1 | -0.966 | -0.996 | 11.389 | -24.677 | -24.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 955 | ALA | 0 | 0.004 | -0.002 | 13.645 | 1.498 | 1.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 956 | GLU | 0 | -0.068 | -0.068 | 15.353 | 1.145 | 1.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 957 | LEU | 0 | -0.058 | -0.033 | 16.440 | 1.200 | 1.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 958 | ASN | 0 | -0.124 | -0.057 | 18.010 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 959 | ASP | -1 | -0.938 | -0.963 | 20.528 | -12.750 | -12.750 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 960 | LEU | 0 | -0.065 | -0.018 | 17.289 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 961 | MET | -1 | -0.923 | -0.921 | 18.366 | -14.757 | -14.757 | 0.000 | 0.000 | 0.000 | 0.000 |