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: 4NJ2N
Calculation Name: 1L2Y-A-MD56-32700ps
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 | -23633.370787 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19031.184288 |
| FMO2-HF: Total energy | -4602.186499 |
| FMO2-MP2: Total energy | -4615.634104 |
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. |
| -108.291 | -97.053 | 19.04 | -12.336 | -17.94 | -0.043 |
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 | 0.088 | 0.037 | 2.822 | -0.634 | 1.541 | 0.321 | -1.113 | -1.383 | -0.006 | |
| 4 | 4 | GLN | 0 | 0.013 | 0.013 | 4.860 | -0.285 | -0.186 | -0.001 | -0.007 | -0.090 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.094 | -0.033 | 2.854 | -3.210 | -1.427 | 0.464 | -0.723 | -1.524 | 0.004 | |
| 6 | 6 | GLN | 0 | 0.035 | -0.013 | 3.114 | -0.180 | 1.104 | 1.213 | -0.759 | -1.739 | 0.002 | |
| 7 | 7 | GLN | 0 | -0.025 | -0.001 | 1.987 | -11.760 | -12.075 | 9.702 | -3.749 | -5.637 | 0.025 | |
| 8 | 8 | GLN | 0 | 0.025 | 0.007 | 2.714 | -11.604 | -10.161 | 0.227 | -0.580 | -1.089 | -0.010 | |
| 9 | 9 | GLN | 0 | -0.052 | -0.034 | 2.144 | -29.413 | -25.446 | 7.090 | -5.024 | -6.033 | -0.055 | |
| 10 | 10 | GLN | -1 | -0.902 | -0.931 | 3.461 | -51.205 | -50.403 | 0.024 | -0.381 | -0.445 | -0.003 |