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: P2Y3R
Calculation Name: 1L2Y-A-MD53-7300ps
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 | -22334.184944 |
|---|---|
| FMO2-HF: Nuclear repulsion | 17732.053697 |
| FMO2-HF: Total energy | -4602.131247 |
| FMO2-MP2: Total energy | -4615.548148 |
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. |
| -39.544 | -30.18 | 3.822 | -5.305 | -7.88 | -0.026 |
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 | 0.047 | 0.022 | 2.458 | 3.259 | 7.592 | 0.566 | -2.035 | -2.863 | -0.011 | |
| 4 | 4 | GLN | 0 | -0.019 | -0.007 | 3.163 | -7.062 | -5.001 | 0.765 | -1.334 | -1.492 | -0.011 | |
| 5 | 5 | GLN | 0 | 0.007 | 0.008 | 2.544 | -8.354 | -5.386 | 2.469 | -2.208 | -3.230 | -0.005 | |
| 6 | 6 | GLN | 0 | -0.037 | -0.007 | 3.583 | -0.320 | -0.341 | 0.023 | 0.272 | -0.273 | 0.001 | |
| 7 | 7 | GLN | 0 | 0.044 | -0.006 | 5.163 | 1.422 | 1.445 | -0.001 | 0.000 | -0.022 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.060 | -0.030 | 8.850 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.054 | -0.010 | 6.300 | -1.232 | -1.232 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.861 | -0.918 | 8.699 | -27.148 | -27.148 | 0.000 | 0.000 | 0.000 | 0.000 |