b-Sophorose | C12H22O11 | MD Topology | NMR | X-Ray

Visualize with JSmol

Molecule Information

Molecule Typesugar
Residue Name (RNME)_IDW
FormulaC12H22O11
IUPAC InChI Key
HIWPGCMGAMJNRG-BTLHAWITSA-N
IUPAC InChI
InChI=1S/C12H22O11/c13-1-3-6(16)8(18)10(11(20)21-3)23-12-9(19)7(17)5(15)4(2-14)22-12/h3-20H,1-2H2/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12+/m1/s1
IUPAC Name
(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[(2R,3R,4S,5S,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]oxyoxane-3,4,5-triol
Common Nameb-Sophorose
Canonical SMILES (Daylight)
OC[C@H]1O[C@@H](O)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
Number of atoms45
Net Charge0
Forcefieldmultiple
Molecule ID500
ChemSpider ID390165
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 Time2:40:30 (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.

Calculated Solvation Free Energy

Access to this feature is currently restricted

Submit New Solvation Free Energy Computation