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: XYM82
Calculation Name: 1L2Y-A-MD50-70500ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-09
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 | -23274.354223 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18672.125076 |
| FMO2-HF: Total energy | -4602.229147 |
| FMO2-MP2: Total energy | -4615.659104 |
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. |
| -102.569 | -97.833 | 24.176 | -12.901 | -16.011 | -0.06 |
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 | -0.012 | 0.006 | 1.799 | -2.268 | -5.538 | 13.356 | -5.219 | -4.867 | 0.039 | |
| 4 | 4 | GLN | 0 | -0.003 | -0.019 | 2.925 | -9.059 | -7.575 | 0.188 | -0.344 | -1.328 | -0.006 | |
| 5 | 5 | GLN | 0 | 0.054 | 0.061 | 3.192 | 1.642 | 3.188 | 0.213 | -0.487 | -1.272 | 0.004 | |
| 6 | 6 | GLN | 0 | -0.005 | -0.032 | 2.573 | -16.434 | -13.224 | 0.835 | -1.940 | -2.105 | -0.025 | |
| 7 | 7 | GLN | 0 | -0.023 | -0.014 | 1.841 | -45.706 | -43.969 | 9.537 | -5.123 | -6.151 | -0.071 | |
| 8 | 8 | GLN | 0 | -0.017 | -0.020 | 3.498 | 7.146 | 7.175 | 0.047 | 0.212 | -0.288 | -0.001 | |
| 9 | 9 | GLN | 0 | -0.021 | -0.018 | 6.190 | -3.769 | -3.769 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.883 | -0.912 | 5.770 | -34.121 | -34.121 | 0.000 | 0.000 | 0.000 | 0.000 |