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: XVRN1
Calculation Name: 1L2Y-A-MD4-25500ps
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 | -55494.789046 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48055.817449 |
| FMO2-HF: Total energy | -7438.971597 |
| FMO2-MP2: Total energy | -7461.336782 |
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. |
| 21.809 | 23.014 | 14.283 | -6.406 | -9.081 | 0.029 |
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 | 0.100 | 0.075 | 2.591 | 1.381 | 5.148 | 1.010 | -2.063 | -2.714 | 0.004 | |
| 4 | 4 | ILE | 0 | 0.027 | 0.009 | 1.836 | -6.601 | -10.024 | 13.243 | -4.141 | -5.678 | 0.024 | |
| 5 | 5 | GLN | 0 | -0.015 | -0.016 | 3.273 | 0.214 | 0.915 | 0.031 | -0.191 | -0.542 | 0.001 | |
| 6 | 6 | TRP | 0 | -0.017 | -0.037 | 4.957 | 3.929 | 4.089 | -0.001 | -0.011 | -0.147 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.014 | -0.011 | 6.644 | 2.551 | 2.551 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.913 | 0.961 | 5.470 | 40.216 | 40.216 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.844 | -0.912 | 8.702 | -25.497 | -25.497 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.023 | 0.019 | 10.936 | 1.792 | 1.792 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.026 | 0.017 | 10.853 | 0.934 | 0.934 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.054 | -0.041 | 11.811 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.012 | 0.015 | 15.235 | 0.843 | 0.843 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.020 | 0.014 | 12.975 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.006 | -0.006 | 15.139 | 0.752 | 0.752 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.794 | 0.898 | 8.475 | 28.378 | 28.378 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.095 | 0.056 | 14.317 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.012 | -0.028 | 10.619 | -1.289 | -1.289 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.114 | -0.062 | 6.725 | 0.653 | 0.653 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.928 | -0.942 | 9.382 | -26.734 | -26.734 | 0.000 | 0.000 | 0.000 | 0.000 |