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: X14KZ
Calculation Name: 1L2Y-A-MD4-39400ps
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 | -55384.520176 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47945.584817 |
| FMO2-HF: Total energy | -7438.93536 |
| FMO2-MP2: Total energy | -7461.280531 |
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. |
| 1.454 | 5.525 | 7.378 | -4.29 | -7.159 | 0.021 |
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 | 0.104 | 0.059 | 2.801 | 4.245 | 7.756 | 0.613 | -1.854 | -2.270 | 0.001 | |
| 4 | 4 | ILE | 0 | 0.017 | 0.001 | 2.082 | -3.954 | -3.640 | 6.744 | -2.374 | -4.684 | 0.019 | |
| 5 | 5 | GLN | 0 | -0.037 | -0.023 | 3.850 | 0.034 | 0.280 | 0.021 | -0.062 | -0.205 | 0.001 | |
| 6 | 6 | TRP | 0 | -0.024 | -0.026 | 6.209 | 2.480 | 2.480 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.048 | -0.030 | 6.509 | 2.332 | 2.332 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.876 | 0.946 | 8.088 | 24.653 | 24.653 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.754 | -0.860 | 10.082 | -24.305 | -24.305 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.042 | 0.005 | 12.192 | 0.976 | 0.976 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.002 | 0.012 | 10.476 | 0.808 | 0.808 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.055 | -0.039 | 11.534 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | 0.022 | 0.018 | 14.113 | 0.470 | 0.470 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.031 | 0.000 | 13.282 | 0.946 | 0.946 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.060 | 0.045 | 15.503 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.799 | 0.887 | 9.362 | 26.078 | 26.078 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.039 | 0.020 | 13.883 | -0.237 | -0.237 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.022 | 0.019 | 9.965 | -1.238 | -1.238 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.158 | -0.094 | 6.205 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.885 | -0.919 | 8.154 | -32.168 | -32.168 | 0.000 | 0.000 | 0.000 | 0.000 |