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: PKZJ3
Calculation Name: 1L2Y-A-MD50-64800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-09
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 | -23603.568298 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19001.333917 |
| FMO2-HF: Total energy | -4602.234381 |
| FMO2-MP2: Total energy | -4615.675042 |
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. |
| -127.97 | -115.689 | 19.039 | -14.341 | -16.977 | -0.11 |
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 | 0.044 | 0.023 | 2.902 | -2.519 | 0.479 | 0.150 | -1.146 | -2.001 | -0.004 | |
| 4 | 4 | GLN | 0 | 0.010 | 0.001 | 3.184 | -3.311 | -2.284 | 0.069 | -0.532 | -0.564 | -0.005 | |
| 5 | 5 | GLN | 0 | -0.001 | 0.002 | 6.051 | 1.687 | 1.687 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.033 | 0.027 | 2.527 | -1.336 | 0.088 | 1.253 | -1.091 | -1.585 | 0.011 | |
| 7 | 7 | GLN | 0 | -0.014 | -0.011 | 2.632 | -2.717 | -0.616 | 2.108 | -1.062 | -3.147 | 0.018 | |
| 8 | 8 | GLN | 0 | 0.001 | -0.021 | 2.413 | -12.365 | -10.999 | 1.313 | -1.066 | -1.613 | -0.016 | |
| 9 | 9 | GLN | 0 | -0.066 | -0.039 | 4.626 | 0.630 | 0.798 | -0.001 | -0.018 | -0.149 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.835 | -0.878 | 1.784 | -108.039 | -104.842 | 14.147 | -9.426 | -7.918 | -0.114 |