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: 3N8GL
Calculation Name: 1L2Y-A-MD58-99800ps
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-13
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 10 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -24891.430483 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20289.246458 |
| FMO2-HF: Total energy | -4602.184025 |
| FMO2-MP2: Total energy | -4615.663173 |
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(:1:GLN )
Summations of interaction energy for
fragment #1(:1:GLN )
| 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. |
| -77.903 | -80.69 | 30.077 | -12.838 | -14.449 | -0.073 |
Interaction energy analysis for fragmet #1(:1:GLN )
| 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 | 3 | GLN | 0 | 0.049 | 0.057 | 1.884 | -20.447 | -19.906 | 8.046 | -4.456 | -4.130 | -0.042 | |
| 4 | 4 | GLN | 0 | 0.031 | 0.009 | 4.455 | -2.262 | -2.171 | -0.001 | -0.012 | -0.078 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.028 | 0.001 | 7.492 | 1.108 | 1.108 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.055 | -0.020 | 1.824 | -3.618 | -7.836 | 12.980 | -4.465 | -4.297 | 0.017 | |
| 7 | 7 | GLN | 0 | -0.009 | -0.023 | 3.682 | 2.257 | 2.772 | 0.004 | -0.107 | -0.412 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.024 | -0.017 | 4.703 | 2.589 | 2.755 | -0.001 | -0.011 | -0.153 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.075 | -0.039 | 4.468 | 2.368 | 2.499 | -0.001 | -0.013 | -0.116 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.925 | -0.922 | 1.932 | -59.898 | -59.911 | 9.050 | -3.774 | -5.263 | -0.048 |