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: 3NM5L
Calculation Name: 1L2Y-A-MD57-97800ps
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 | -24124.280032 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19522.03219 |
| FMO2-HF: Total energy | -4602.247842 |
| FMO2-MP2: Total energy | -4615.6898 |
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. |
| -90.944 | -79.781 | 7.032 | -8.043 | -10.154 | -0.074 |
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 | 0.029 | 2.733 | -7.105 | -4.541 | 0.511 | -1.438 | -1.637 | -0.011 | |
| 4 | 4 | GLN | 0 | -0.010 | -0.014 | 5.513 | 1.089 | 1.089 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.020 | -0.021 | 5.661 | -5.138 | -5.138 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.033 | 0.039 | 2.901 | 0.561 | 1.352 | 0.130 | -0.190 | -0.731 | -0.001 | |
| 7 | 7 | GLN | 0 | -0.004 | -0.009 | 2.654 | -12.973 | -10.328 | 1.064 | -1.502 | -2.207 | -0.018 | |
| 8 | 8 | GLN | 0 | 0.011 | 0.015 | 2.864 | -23.317 | -20.189 | 0.979 | -1.831 | -2.277 | -0.020 | |
| 9 | 9 | GLN | 0 | -0.050 | -0.039 | 2.256 | -11.599 | -9.679 | 4.348 | -3.062 | -3.207 | -0.024 | |
| 10 | 10 | GLN | -1 | -0.858 | -0.911 | 4.573 | -32.462 | -32.347 | 0.000 | -0.020 | -0.095 | 0.000 |