1-[2,3-Dideoxy-3-(methylamino)pentofuranosyl]-5-methyl-2,4(1H,3H)-pyrimidinedione | C11H17N3O4 | MD Topology | NMR | X-Ray

Visualize with JSmol

Molecule Information

Molecule Typeheteromolecule
Residue Name (RNME)AU6W
FormulaC11H17N3O4
IUPAC InChI Key
LDZKBUFNIZADPS-HRDYMLBCSA-N
IUPAC InChI
InChI=1S/C11H17N3O4/c1-6-4-14(11(17)13-10(6)16)9-3-7(12-2)8(5-15)18-9/h4,7-9,12,15H,3,5H2,1-2H3,(H,13,16,17)/t7-,8+,9-/m1/s1
IUPAC Name
Common Name1-[2,3-Dideoxy-3-(methylamino)pentofuranosyl]-5-methyl-2,4(1H,3H)-pyrimidinedione
Canonical SMILES (Daylight)
CN[C@@H]1C[C@@H](O[C@H]1CO)n1cc(C)c(=O)[nH]c1=O
Number of atoms35
Net Charge0
Forcefieldmultiple
Molecule ID335408
ChemSpider ID330739
ChEMBL ID 1971796
Visibility Public
Molecule Tags

Force Field Parameters

Molecular Dynamics (MD) Files

Generating ...

X-Ray - Docking Files

Generating ...

NMR Parameters

1H NMR Spectrum

Generating ...

Topology History

Processing Information

QM Processing Stage

Click table to toggle details.

Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 1000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing Time22:30:06 (hh:mm:ss)

ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)

Calculated Solvation Free Energy

Access to this feature is currently restricted

Submit New Solvation Free Energy Computation