FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: XQ19Y
Calculation Name: 1L2Y-A-MD4-48000ps
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
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 |
| Remarks |
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 | -55036.188749 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47597.241261 |
| FMO2-HF: Total energy | -7438.947488 |
| FMO2-MP2: Total energy | -7461.283075 |
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. |
| 16.595 | 16.765 | 15.843 | -5.986 | -10.028 | 0.034 |
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 | 0.121 | 0.089 | 2.186 | 0.553 | 2.374 | 4.613 | -2.487 | -3.947 | 0.013 | |
| 4 | 4 | ILE | 0 | 0.009 | -0.022 | 1.878 | -7.998 | -10.531 | 11.209 | -3.150 | -5.527 | 0.019 | |
| 5 | 5 | GLN | 0 | -0.046 | -0.036 | 3.826 | -0.012 | 0.870 | 0.021 | -0.349 | -0.554 | 0.002 | |
| 6 | 6 | TRP | 0 | 0.067 | 0.028 | 5.530 | 3.473 | 3.473 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.038 | -0.035 | 6.411 | 2.216 | 2.216 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.880 | 0.947 | 5.382 | 44.898 | 44.898 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.808 | -0.878 | 9.531 | -21.529 | -21.529 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.025 | 0.004 | 11.213 | 1.843 | 1.843 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.061 | -0.015 | 10.259 | 1.200 | 1.200 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.020 | 0.005 | 11.306 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.023 | 0.003 | 13.761 | 0.916 | 0.916 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.067 | -0.022 | 12.893 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.030 | 0.000 | 15.097 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.840 | 0.918 | 10.215 | 24.191 | 24.191 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.037 | 0.021 | 12.950 | -0.297 | -0.297 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.030 | -0.009 | 8.993 | -1.271 | -1.271 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.070 | -0.048 | 6.028 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.932 | -0.951 | 7.175 | -32.580 | -32.580 | 0.000 | 0.000 | 0.000 | 0.000 |