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: XR528
Calculation Name: 1L2Y-A-MD4-38100ps
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 | -54559.725784 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47120.75862 |
| FMO2-HF: Total energy | -7438.967164 |
| FMO2-MP2: Total energy | -7461.316018 |
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. |
| 1.394 | 5.6 | 7.526 | -3.799 | -7.931 | 0.022 |
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 | 0.065 | 0.036 | 2.914 | 5.006 | 7.725 | 0.836 | -1.281 | -2.274 | 0.006 | |
| 4 | 4 | ILE | 0 | -0.010 | -0.020 | 2.142 | -5.157 | -4.302 | 6.678 | -2.360 | -5.172 | 0.016 | |
| 5 | 5 | GLN | 0 | -0.057 | -0.015 | 3.909 | 0.257 | 0.742 | 0.013 | -0.146 | -0.352 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.078 | 0.057 | 5.208 | 3.736 | 3.883 | -0.001 | -0.012 | -0.133 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.001 | -0.018 | 6.338 | 3.076 | 3.076 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.889 | 0.953 | 7.845 | 32.212 | 32.212 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.886 | -0.962 | 8.974 | -28.723 | -28.723 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.046 | -0.028 | 11.168 | 1.948 | 1.948 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.019 | 0.026 | 11.096 | 1.203 | 1.203 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.052 | -0.051 | 12.098 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | 0.010 | 0.035 | 14.983 | 0.793 | 0.793 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.098 | -0.045 | 13.904 | 0.598 | 0.598 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.051 | 0.021 | 16.339 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.910 | 0.943 | 13.010 | 19.563 | 19.563 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.053 | 0.027 | 13.684 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.022 | -0.003 | 10.979 | -1.473 | -1.473 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.104 | -0.020 | 6.813 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.918 | -0.963 | 7.309 | -32.767 | -32.767 | 0.000 | 0.000 | 0.000 | 0.000 |