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: 8JNVY
Calculation Name: 1L2Y-A-MD56-68100ps
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 | -23329.731452 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18727.596406 |
| FMO2-HF: Total energy | -4602.135047 |
| FMO2-MP2: Total energy | -4615.597408 |
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. |
| -57.615 | -50.504 | 13.438 | -8.463 | -12.085 | -0.022 |
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 | 0.050 | 0.021 | 2.062 | 1.216 | 3.202 | 6.957 | -3.853 | -5.090 | 0.030 | |
| 4 | 4 | GLN | 0 | -0.028 | 0.002 | 2.458 | 1.430 | 3.469 | 0.832 | -0.334 | -2.536 | 0.004 | |
| 5 | 5 | GLN | 0 | 0.011 | -0.014 | 2.001 | -34.151 | -31.217 | 5.649 | -4.139 | -4.444 | -0.055 | |
| 6 | 6 | GLN | 0 | -0.044 | -0.026 | 3.988 | -12.050 | -11.898 | 0.000 | -0.137 | -0.015 | -0.001 | |
| 7 | 7 | GLN | 0 | 0.021 | 0.037 | 5.940 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | GLN | 0 | 0.019 | -0.002 | 7.590 | 3.053 | 3.053 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.057 | -0.031 | 10.900 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.950 | -0.949 | 13.950 | -17.002 | -17.002 | 0.000 | 0.000 | 0.000 | 0.000 |