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: YQVG2
Calculation Name: 1L2Y-A-MD56-28500ps
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 | -23101.080587 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18498.88733 |
| FMO2-HF: Total energy | -4602.193257 |
| FMO2-MP2: Total energy | -4615.64493 |
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. |
| -60.414 | -51.829 | 8.976 | -7.393 | -10.168 | -0.069 |
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 | 0.062 | 0.005 | 3.010 | -5.418 | -2.872 | 0.154 | -1.129 | -1.571 | -0.005 | |
| 4 | 4 | GLN | 0 | 0.011 | 0.018 | 5.202 | -1.812 | -1.627 | -0.001 | -0.007 | -0.177 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.039 | -0.022 | 2.288 | -11.752 | -8.639 | 4.584 | -2.963 | -4.733 | -0.025 | |
| 6 | 6 | GLN | 0 | 0.086 | 0.062 | 3.117 | -6.909 | -5.541 | 0.124 | -0.737 | -0.755 | -0.006 | |
| 7 | 7 | GLN | 0 | -0.002 | -0.005 | 2.119 | -15.583 | -14.328 | 4.108 | -2.592 | -2.771 | -0.033 | |
| 8 | 8 | GLN | 0 | 0.004 | 0.000 | 3.447 | 3.355 | 3.473 | 0.007 | 0.035 | -0.161 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.063 | -0.037 | 6.260 | 2.589 | 2.589 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.917 | -0.941 | 6.427 | -24.884 | -24.884 | 0.000 | 0.000 | 0.000 | 0.000 |