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: 3NM9L
Calculation Name: 1L2Y-A-MD57-67800ps
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 | -24829.585084 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20227.426874 |
| FMO2-HF: Total energy | -4602.15821 |
| FMO2-MP2: Total energy | -4615.617546 |
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. |
| -83.185 | -74.375 | 9.281 | -7.457 | -10.633 | -0.066 |
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 | 0.034 | 0.026 | 2.844 | -3.527 | -1.496 | 0.250 | -1.017 | -1.264 | -0.007 | |
| 4 | 4 | GLN | 0 | -0.003 | -0.008 | 5.371 | 5.014 | 5.170 | -0.001 | -0.004 | -0.151 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.025 | -0.021 | 6.513 | -3.622 | -3.622 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.076 | -0.019 | 3.204 | -1.059 | 0.008 | 0.132 | -0.344 | -0.855 | 0.003 | |
| 7 | 7 | GLN | 0 | 0.022 | 0.033 | 2.747 | -11.222 | -8.664 | 0.469 | -1.306 | -1.721 | -0.013 | |
| 8 | 8 | GLN | 0 | 0.013 | -0.042 | 2.239 | -40.839 | -37.910 | 8.429 | -4.807 | -6.550 | -0.049 | |
| 9 | 9 | GLN | 0 | -0.053 | -0.022 | 3.571 | -1.337 | -1.268 | 0.002 | 0.021 | -0.092 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.893 | -0.928 | 6.826 | -26.593 | -26.593 | 0.000 | 0.000 | 0.000 | 0.000 |