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: 8J7MY
Calculation Name: 1L2Y-A-MD57-50100ps
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 | -24575.935257 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19973.681896 |
| FMO2-HF: Total energy | -4602.253362 |
| FMO2-MP2: Total energy | -4615.720314 |
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. |
| -170.038 | -166.229 | 35.011 | -19.161 | -19.659 | -0.182 |
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 | 0.050 | 0.020 | 2.847 | 0.353 | 2.936 | 0.742 | -1.179 | -2.146 | -0.005 | |
| 4 | 4 | GLN | 0 | -0.043 | -0.009 | 3.980 | 4.922 | 5.115 | -0.001 | -0.009 | -0.183 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.011 | -0.017 | 6.197 | -4.387 | -4.387 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.048 | 0.038 | 2.728 | -7.904 | -6.278 | 0.281 | -0.768 | -1.139 | -0.009 | |
| 7 | 7 | GLN | 0 | -0.031 | -0.014 | 3.642 | 0.978 | 1.881 | 0.039 | -0.236 | -0.705 | -0.001 | |
| 8 | 8 | GLN | 0 | 0.071 | 0.031 | 2.168 | -24.435 | -21.979 | 6.311 | -3.992 | -4.775 | -0.036 | |
| 9 | 9 | GLN | 0 | -0.033 | -0.025 | 2.296 | -23.136 | -22.739 | 7.119 | -3.496 | -4.020 | -0.036 | |
| 10 | 10 | GLN | -1 | -0.889 | -0.918 | 1.675 | -116.429 | -120.778 | 20.520 | -9.481 | -6.691 | -0.095 |