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: R1N28
Calculation Name: 1L2Y-A-MD54-69000ps
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 | -24523.461298 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19921.382224 |
| FMO2-HF: Total energy | -4602.079074 |
| FMO2-MP2: Total energy | -4615.561045 |
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. |
| -18.69 | -10.08 | 9.456 | -6.829 | -11.238 | -0.036 |
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 | 0.135 | 0.078 | 3.660 | 3.338 | 8.742 | -0.024 | -2.734 | -2.647 | -0.017 | |
| 4 | 4 | GLN | 0 | -0.029 | -0.006 | 2.149 | 3.971 | 4.499 | 1.972 | -0.710 | -1.790 | -0.004 | |
| 5 | 5 | GLN | 0 | 0.045 | 0.040 | 4.273 | 1.218 | 1.298 | -0.001 | -0.020 | -0.059 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.003 | -0.013 | 2.576 | -0.310 | 1.155 | 2.167 | -0.941 | -2.691 | 0.008 | |
| 7 | 7 | GLN | 0 | 0.027 | -0.025 | 2.473 | -8.006 | -6.841 | 5.343 | -2.422 | -4.086 | -0.023 | |
| 8 | 8 | GLN | 0 | -0.025 | 0.007 | 5.439 | 0.286 | 0.254 | -0.001 | -0.002 | 0.035 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.055 | -0.010 | 8.249 | 1.980 | 1.980 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.980 | -0.986 | 7.907 | -21.167 | -21.167 | 0.000 | 0.000 | 0.000 | 0.000 |