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: 3N8ML
Calculation Name: 1L2Y-A-MD58-97800ps
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 | -24719.395875 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20117.177667 |
| FMO2-HF: Total energy | -4602.218208 |
| FMO2-MP2: Total energy | -4615.6675 |
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. |
| -62.763 | -56.103 | 7.749 | -6.593 | -7.818 | -0.059 |
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 | 0.024 | 0.031 | 2.281 | -17.417 | -14.370 | 3.578 | -3.166 | -3.460 | -0.025 | |
| 4 | 4 | GLN | 0 | 0.109 | 0.056 | 5.208 | 0.564 | 0.620 | -0.001 | -0.009 | -0.046 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.024 | -0.002 | 7.295 | -2.088 | -2.088 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.058 | -0.034 | 2.363 | -23.323 | -21.080 | 3.601 | -2.882 | -2.962 | -0.032 | |
| 7 | 7 | GLN | 0 | -0.007 | -0.014 | 6.090 | 2.912 | 2.912 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.027 | -0.005 | 7.496 | 1.744 | 1.744 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.064 | -0.036 | 8.917 | 3.780 | 3.780 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.953 | -0.948 | 3.175 | -28.935 | -27.621 | 0.571 | -0.536 | -1.350 | -0.002 |