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: 59YKZ
Calculation Name: 1L2Y-A-MD57-56600ps
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 | -25053.732198 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20451.440598 |
| FMO2-HF: Total energy | -4602.2916 |
| FMO2-MP2: Total energy | -4615.787194 |
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. |
| -173.382 | -170.517 | 37.653 | -19.15 | -21.367 | -0.177 |
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 | 0.075 | 0.041 | 1.988 | -10.155 | -10.770 | 10.983 | -4.028 | -6.339 | -0.005 | |
| 4 | 4 | GLN | 0 | -0.010 | -0.003 | 3.643 | 1.368 | 1.199 | 0.039 | 0.432 | -0.301 | 0.001 | |
| 5 | 5 | GLN | 0 | -0.023 | -0.046 | 6.205 | -3.170 | -3.170 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.005 | 0.000 | 1.787 | -15.838 | -20.502 | 11.904 | -3.904 | -3.337 | -0.040 | |
| 7 | 7 | GLN | 0 | -0.002 | 0.037 | 3.537 | 2.166 | 3.062 | 0.038 | -0.242 | -0.692 | -0.001 | |
| 8 | 8 | GLN | 0 | 0.027 | 0.005 | 2.283 | -22.436 | -20.262 | 4.545 | -3.419 | -3.300 | -0.031 | |
| 9 | 9 | GLN | 0 | 0.008 | -0.017 | 2.240 | -33.710 | -32.483 | 6.772 | -4.019 | -3.980 | -0.045 | |
| 10 | 10 | GLN | -1 | -0.833 | -0.904 | 2.201 | -91.607 | -87.591 | 3.372 | -3.970 | -3.418 | -0.056 |