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: 1JYZZ
Calculation Name: 1L2Y-A-MD57-56300ps
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 | -25584.489861 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20982.164869 |
| FMO2-HF: Total energy | -4602.324992 |
| FMO2-MP2: Total energy | -4615.817767 |
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. |
| -150.208 | -145.754 | 32.992 | -16.036 | -21.409 | -0.173 |
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 | 0.058 | 0.024 | 1.973 | -14.276 | -13.016 | 6.016 | -3.180 | -4.096 | -0.034 | |
| 4 | 4 | GLN | 0 | -0.036 | -0.005 | 3.916 | 6.981 | 7.212 | -0.001 | 0.003 | -0.232 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.037 | -0.054 | 5.081 | -3.887 | -3.789 | -0.001 | -0.004 | -0.093 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.028 | -0.018 | 2.145 | -4.035 | -2.786 | 4.836 | -2.652 | -3.432 | -0.012 | |
| 7 | 7 | GLN | 0 | 0.026 | 0.042 | 3.024 | 4.713 | 4.945 | 0.868 | 1.077 | -2.178 | -0.011 | |
| 8 | 8 | GLN | 0 | 0.038 | -0.001 | 2.277 | -27.797 | -26.373 | 7.257 | -4.050 | -4.632 | -0.046 | |
| 9 | 9 | GLN | 0 | -0.023 | -0.020 | 3.283 | -6.615 | -5.639 | 0.101 | -0.314 | -0.762 | -0.003 | |
| 10 | 10 | GLN | -1 | -0.819 | -0.896 | 2.039 | -105.292 | -106.308 | 13.916 | -6.916 | -5.984 | -0.067 |