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: XY212
Calculation Name: 1L2Y-A-MD54-16500ps
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 | -23661.416923 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19059.29839 |
| FMO2-HF: Total energy | -4602.118533 |
| FMO2-MP2: Total energy | -4615.564717 |
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. |
| -30.199 | -25.379 | 7.103 | -4.167 | -7.754 | -0.017 |
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 | 0.032 | 0.014 | 2.664 | -8.385 | -6.083 | 0.717 | -1.307 | -1.712 | -0.013 | |
| 4 | 4 | GLN | 0 | -0.033 | -0.016 | 2.322 | -6.915 | -5.579 | 3.577 | -1.626 | -3.286 | -0.001 | |
| 5 | 5 | GLN | 0 | 0.051 | 0.024 | 2.144 | 4.674 | 5.573 | 2.811 | -1.211 | -2.499 | -0.003 | |
| 6 | 6 | GLN | 0 | 0.088 | 0.030 | 4.402 | -0.732 | -0.694 | 0.000 | -0.011 | -0.027 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.063 | -0.008 | 4.380 | -1.626 | -1.500 | -0.001 | -0.009 | -0.116 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.051 | -0.018 | 4.267 | 1.706 | 1.825 | -0.001 | -0.003 | -0.114 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.072 | -0.035 | 7.229 | 1.281 | 1.281 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.902 | -0.943 | 9.234 | -20.202 | -20.202 | 0.000 | 0.000 | 0.000 | 0.000 |