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: Z2YRN
Calculation Name: 1L2Y-A-MD55-21100ps
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 | -23341.067849 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18738.813976 |
| FMO2-HF: Total energy | -4602.253873 |
| FMO2-MP2: Total energy | -4615.662013 |
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. |
| -124.24 | -117.343 | 32.002 | -17.56 | -21.339 | -0.112 |
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 | 0.025 | 0.013 | 2.628 | -8.031 | -4.915 | 1.028 | -1.980 | -2.164 | -0.009 | |
| 4 | 4 | GLN | 0 | 0.003 | 0.005 | 4.557 | -0.267 | -0.035 | -0.001 | -0.013 | -0.218 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.003 | -0.010 | 5.018 | -2.789 | -2.737 | -0.001 | -0.003 | -0.048 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.060 | 0.059 | 2.267 | -16.264 | -13.313 | 3.720 | -3.008 | -3.663 | -0.012 | |
| 7 | 7 | GLN | 0 | 0.004 | 0.029 | 1.708 | -16.732 | -23.195 | 19.255 | -7.707 | -5.086 | -0.028 | |
| 8 | 8 | GLN | 0 | 0.020 | 0.009 | 2.113 | -30.881 | -27.446 | 6.009 | -2.803 | -6.641 | -0.036 | |
| 9 | 9 | GLN | 0 | -0.001 | -0.010 | 4.268 | 1.482 | 1.514 | 0.000 | -0.021 | -0.011 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.912 | -0.939 | 2.548 | -50.758 | -47.216 | 1.992 | -2.025 | -3.508 | -0.027 |