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: 1J8YZ
Calculation Name: 1L2Y-A-MD58-96300ps
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:
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 | -24653.977335 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20051.806452 |
| FMO2-HF: Total energy | -4602.170883 |
| FMO2-MP2: Total energy | -4615.604944 |
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. |
| -86.719 | -85.402 | 27.694 | -14.459 | -14.552 | -0.115 |
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 | 0.011 | 0.011 | 2.275 | -16.584 | -13.771 | 3.396 | -2.957 | -3.253 | -0.026 | |
| 4 | 4 | GLN | 0 | 0.055 | 0.025 | 4.737 | -0.633 | -0.577 | -0.001 | -0.010 | -0.045 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.033 | 0.017 | 7.934 | 2.108 | 2.108 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.025 | 0.008 | 1.933 | -26.045 | -27.468 | 14.315 | -6.805 | -6.087 | -0.053 | |
| 7 | 7 | GLN | 0 | -0.038 | -0.011 | 4.312 | -0.146 | 0.281 | -0.001 | -0.044 | -0.382 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.015 | -0.014 | 5.244 | 2.977 | 3.057 | -0.001 | -0.002 | -0.076 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.077 | -0.031 | 7.750 | 3.443 | 3.443 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.898 | -0.918 | 1.887 | -51.839 | -52.475 | 9.986 | -4.641 | -4.709 | -0.036 |