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: 9YRZ2
Calculation Name: 1L2Y-A-MD57-85600ps
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 | -23478.570144 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18876.347313 |
| FMO2-HF: Total energy | -4602.222831 |
| FMO2-MP2: Total energy | -4615.672399 |
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. |
| -96.637 | -82.101 | 9.722 | -10.417 | -13.838 | -0.112 |
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 | 0.086 | 0.038 | 3.199 | -3.695 | -1.413 | 0.283 | -0.954 | -1.611 | -0.004 | |
| 4 | 4 | GLN | 0 | -0.021 | -0.007 | 4.178 | 3.776 | 3.964 | -0.001 | -0.002 | -0.185 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.000 | -0.017 | 5.953 | -3.029 | -3.029 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.014 | 0.009 | 2.839 | 1.530 | 3.460 | 0.556 | -0.648 | -1.836 | 0.004 | |
| 7 | 7 | GLN | 0 | 0.000 | 0.009 | 2.930 | -6.025 | -4.262 | 0.547 | -0.745 | -1.565 | -0.010 | |
| 8 | 8 | GLN | 0 | 0.088 | 0.013 | 2.002 | -68.144 | -59.918 | 8.334 | -8.012 | -8.547 | -0.102 | |
| 9 | 9 | GLN | 0 | -0.062 | -0.022 | 3.959 | 8.624 | 8.771 | 0.003 | -0.056 | -0.094 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.905 | -0.934 | 6.815 | -29.674 | -29.674 | 0.000 | 0.000 | 0.000 | 0.000 |