1-Deoxy-1-[(5-nitro-2,6-dioxo-1,2,3,6-tetrahydro-4-pyrimidinyl)amino]-D-ribitol | C9H14N4O8 | MD Topology | NMR | X-Ray

Visualize with JSmol

Show Structure

Molecule Information
Molecule Typeheteromolecule
Residue Name (RNME)INI
FormulaC9H14N4O8
IUPAC InChI Key
KSKGHNZSCSCHEQ-RPDRRWSUSA-N
IUPAC InChI
InChI=1S/C9H14N4O8/c14-2-4(16)6(17)3(15)1-10-7-5(13(20)21)8(18)12-9(19)11-7/h3-4,6,14-17H,1-2H2,(H3,10,11,12,18,19)/t3-,4+,6-/m0/s1
IUPAC Name
5-nitro-6-[[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino]-1H-pyrimidine-2,4-dione
Common Name1-Deoxy-1-[(5-nitro-2,6-dioxo-1,2,3,6-tetrahydro-4-pyrimidinyl)amino]-D-ribitol
Canonical SMILES (Daylight)
OC[C@H]([C@H]([C@H](CNc1[nH]c(=O)[nH]c(=O)c1N(=O)=O)O)O)O
Number of atoms35
Net Charge0
Forcefieldmultiple
Molecule ID10477
ChemSpider ID394088
PDB hetId INI
Visibility Public
Molecule Tags

Format

Molecular Dynamics (MD) Files

Generating ...

X-Ray - Docking Files

Generating ...

NMR Parameters

1H NMR Spectrum

Generating ...

Fragment-Based Charges

No charge assignments available. Use the button above to use OFraMP fragment-based charge assignment.

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) 2000 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 Time2 days, 15:49:09 (hh:mm:ss)

ATB Pipeline Setting

Calculated Solvation Free Energy

Access to this feature is currently restricted

Submit New Solvation Free Energy Computation

Conditions of Use