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: 1JY8Z
Calculation Name: 1L2Y-A-MD57-44300ps
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 | -24531.608845 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19929.412148 |
| FMO2-HF: Total energy | -4602.196697 |
| FMO2-MP2: Total energy | -4615.639259 |
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. |
| -91.374 | -79.298 | 9.375 | -8.115 | -13.335 | -0.083 |
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 | 0.055 | 0.011 | 2.601 | -8.145 | -5.183 | 0.932 | -1.549 | -2.345 | -0.009 | |
| 4 | 4 | GLN | 0 | 0.000 | 0.027 | 5.309 | 2.848 | 2.980 | -0.001 | -0.004 | -0.126 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.036 | -0.031 | 6.965 | -1.316 | -1.316 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.083 | 0.046 | 7.386 | -0.725 | -0.725 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.092 | -0.044 | 2.816 | -2.022 | -0.919 | 0.602 | -0.476 | -1.229 | 0.003 | |
| 8 | 8 | GLN | 0 | 0.012 | 0.000 | 3.485 | 2.580 | 3.193 | 0.009 | -0.165 | -0.458 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.027 | -0.018 | 2.293 | -41.580 | -36.761 | 6.412 | -5.084 | -6.146 | -0.063 | |
| 10 | 10 | GLN | -1 | -0.912 | -0.949 | 2.742 | -43.014 | -40.567 | 1.421 | -0.837 | -3.031 | -0.014 |