FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-04-23
All entries: 37539
Number of unique PDB entries: 7791
FMODB ID: P52NZ
Calculation Name: 1L2Y-A-MD4-59800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: MD
Registration Date: 2018-03-06
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20171117 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 20 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -55591.623406 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48152.624945 |
| FMO2-HF: Total energy | -7438.998461 |
| FMO2-MP2: Total energy | -7461.349167 |
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:ASN)
Summations of interaction energy for
fragment #1(:1:ASN)
| 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. |
| 30.022 | 26.95 | 21.231 | -6.81 | -11.349 | 0.027 |
Interaction energy analysis for fragmet #1(:1:ASN)
| 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 | TYR | 0 | 0.117 | 0.066 | 1.890 | 1.529 | -1.389 | 10.512 | -3.409 | -4.185 | 0.020 | |
| 4 | 4 | ILE | 0 | -0.014 | -0.017 | 2.026 | -11.903 | -13.786 | 10.500 | -2.799 | -5.818 | 0.010 | |
| 5 | 5 | GLN | 0 | -0.031 | -0.036 | 2.501 | 5.297 | 6.732 | 0.221 | -0.582 | -1.074 | -0.003 | |
| 6 | 6 | TRP | 0 | 0.040 | 0.033 | 4.868 | 3.789 | 3.990 | -0.001 | -0.014 | -0.186 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.035 | 0.025 | 6.274 | 2.833 | 2.833 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.859 | 0.932 | 3.815 | 54.056 | 54.149 | -0.001 | -0.006 | -0.086 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.831 | -0.915 | 8.750 | -28.254 | -28.254 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.045 | 0.025 | 10.762 | 1.905 | 1.905 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.034 | -0.012 | 10.794 | 1.361 | 1.361 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.039 | -0.013 | 11.762 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | 0.027 | 0.012 | 14.993 | 0.852 | 0.852 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.078 | -0.024 | 12.651 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.003 | -0.009 | 14.802 | 0.702 | 0.702 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.798 | 0.898 | 8.476 | 28.075 | 28.075 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.065 | 0.031 | 13.256 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.015 | -0.011 | 9.145 | -1.277 | -1.277 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.093 | -0.047 | 5.611 | 0.619 | 0.619 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.910 | -0.937 | 7.346 | -29.884 | -29.884 | 0.000 | 0.000 | 0.000 | 0.000 |