FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: YQJV2
Calculation Name: 1L2Y-A-MD58-90500ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
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 |
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 | -25029.642183 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20427.483803 |
| FMO2-HF: Total energy | -4602.158379 |
| FMO2-MP2: Total energy | -4615.625673 |
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. |
| -57.554 | -46.635 | 15 | -12.868 | -13.052 | -0.121 |
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 | 0.003 | 0.037 | 3.256 | 10.549 | 17.180 | -0.047 | -3.000 | -3.585 | -0.011 | |
| 4 | 4 | GLN | 0 | 0.036 | -0.001 | 5.082 | -1.703 | -1.646 | -0.001 | -0.011 | -0.045 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.079 | 0.049 | 7.918 | 3.181 | 3.181 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.038 | 0.041 | 2.225 | -25.660 | -21.746 | 5.979 | -4.980 | -4.914 | -0.048 | |
| 7 | 7 | GLN | 0 | -0.032 | -0.033 | 3.580 | -2.565 | -1.804 | 0.020 | -0.197 | -0.583 | 0.001 | |
| 8 | 8 | GLN | 0 | -0.123 | -0.069 | 4.629 | 4.276 | 4.404 | -0.001 | -0.009 | -0.118 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.005 | -0.031 | 7.281 | 1.853 | 1.853 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.906 | -0.894 | 1.813 | -47.485 | -48.057 | 9.050 | -4.671 | -3.807 | -0.063 |