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: 3MZ6L
Calculation Name: 2M1J-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2M1J
Chain ID: A
UniProt ID: Q9GJY2
Base Structure: SolutionNMR
Registration Date: 2025-10-05
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 | -94670.70823 |
|---|---|
| FMO2-HF: Nuclear repulsion | 82687.137439 |
| FMO2-HF: Total energy | -11983.570792 |
| FMO2-MP2: Total energy | -12016.740505 |
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:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| 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. |
| 66.617 | 68.072 | 0.017 | -0.666 | -0.806 | 0 |
Interaction energy analysis for fragmet #1(A:1:MET)
| 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 | LYS | 1 | 1.027 | 1.011 | 3.451 | 41.380 | 42.835 | 0.017 | -0.666 | -0.806 | 0.000 |
| 4 | A | 4 | HIS | 0 | -0.031 | 0.010 | 6.285 | 2.592 | 2.592 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | LEU | 0 | 0.011 | -0.004 | 7.742 | -1.724 | -1.724 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLY | 0 | 0.053 | 0.030 | 9.871 | 1.236 | 1.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.058 | 0.018 | 13.147 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | CYS | 0 | 0.034 | 0.003 | 14.942 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | TRP | 0 | 0.056 | 0.028 | 12.523 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LEU | 0 | 0.026 | 0.006 | 14.507 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ALA | 0 | 0.031 | 0.025 | 16.979 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | -0.003 | 0.000 | 15.796 | 0.525 | 0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | VAL | 0 | -0.006 | -0.003 | 16.192 | 0.429 | 0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | CYS | 0 | -0.027 | -0.025 | 19.184 | 0.781 | 0.781 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | VAL | 0 | 0.036 | 0.020 | 22.111 | 0.535 | 0.535 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | 0.019 | 0.034 | 20.493 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | -0.018 | -0.008 | 21.989 | 0.574 | 0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PHE | 0 | 0.022 | 0.002 | 24.770 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | SER | 0 | -0.021 | -0.021 | 27.028 | 0.606 | 0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLN | 0 | 0.007 | -0.016 | 25.511 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LEU | 0 | -0.021 | 0.005 | 28.707 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | SER | 0 | -0.034 | -0.019 | 30.888 | 0.523 | 0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | SER | 0 | -0.008 | -0.022 | 31.511 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | VAL | 0 | -0.002 | 0.013 | 33.272 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LYS | 1 | 0.906 | 0.966 | 35.422 | 9.187 | 9.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ALA | 0 | -0.011 | 0.000 | 36.684 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ARG | 1 | 0.959 | 0.980 | 35.527 | 8.164 | 8.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLY | 0 | 0.005 | 0.004 | 32.561 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | 0.010 | 0.001 | 27.954 | -0.299 | -0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | LYS | 0 | 0.008 | 0.022 | 28.568 | -0.712 | -0.712 | 0.000 | 0.000 | 0.000 | 0.000 |