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: XYLK2
Calculation Name: 1L2Y-A-MD53-58500ps
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 | -24448.440026 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19846.270646 |
| FMO2-HF: Total energy | -4602.16938 |
| FMO2-MP2: Total energy | -4615.597722 |
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. |
| -49.824 | -43.113 | 3.093 | -3.919 | -5.884 | -0.023 |
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 | 0.014 | 0.024 | 2.970 | 0.987 | 5.019 | 0.524 | -1.809 | -2.746 | -0.001 | |
| 4 | 4 | GLN | 0 | 0.043 | 0.016 | 2.922 | -11.601 | -9.854 | 0.196 | -0.980 | -0.963 | -0.011 | |
| 5 | 5 | GLN | 0 | 0.037 | -0.002 | 4.453 | -3.682 | -3.575 | -0.001 | -0.016 | -0.089 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.034 | 0.028 | 5.624 | -0.578 | -0.578 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | GLN | 0 | 0.002 | 0.010 | 6.929 | 1.685 | 1.685 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.015 | 0.003 | 5.355 | -7.136 | -7.136 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.082 | -0.041 | 2.171 | -7.834 | -7.009 | 2.374 | -1.114 | -2.086 | -0.011 | |
| 10 | 10 | GLN | -1 | -0.918 | -0.940 | 6.009 | -21.665 | -21.665 | 0.000 | 0.000 | 0.000 | 0.000 |