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: 3NJRL
Calculation Name: 1L2Y-A-MD56-29800ps
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 | -23292.064919 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18689.819541 |
| FMO2-HF: Total energy | -4602.245378 |
| FMO2-MP2: Total energy | -4615.687144 |
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. |
| -53.521 | -43.808 | 6.07 | -5.192 | -10.59 | -0.006 |
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 | 0.039 | 0.012 | 3.568 | 0.720 | 2.390 | 0.005 | -0.735 | -0.939 | 0.000 | |
| 4 | 4 | GLN | 0 | 0.034 | 0.033 | 5.460 | -0.727 | -0.727 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.069 | -0.040 | 2.254 | 3.424 | 4.770 | 2.033 | -1.161 | -2.217 | 0.001 | |
| 6 | 6 | GLN | 0 | 0.031 | 0.004 | 2.075 | -3.889 | -2.067 | 2.561 | -1.843 | -2.540 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.070 | -0.017 | 2.604 | -2.910 | 1.520 | 1.470 | -1.368 | -4.533 | -0.007 | |
| 8 | 8 | GLN | 0 | -0.014 | -0.029 | 4.275 | -1.209 | -1.138 | 0.000 | -0.026 | -0.045 | 0.000 | |
| 9 | 9 | GLN | 0 | 0.003 | 0.005 | 6.543 | 2.121 | 2.121 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.911 | -0.934 | 3.901 | -51.051 | -50.677 | 0.001 | -0.059 | -0.316 | 0.000 |