Inser smiles gives wrong stereo isomer

Bugs item #2824269, was opened at 2009-07-20 15:43
Message generated for change (Tracker Item Submitted) made by jhjensen2
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Category: Commands / Extensions
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jan Jensen (jhjensen2)
Assigned to: Nobody/Anonymous (nobody)
Summary: inser smiles gives wrong stereo isomer

Initial Comment:

  1. I generates this SMILES string for cis decalin: C1[C@H]2C@@HCCCC2 using

  2. When pasting it into Avogadro via “Build > Insert > SMILES”, I get the trans-isomer

  3. Pasting C1[C@H]2C@@HCCCC2 into Chemdraw gives the cis isomer, so SMILES is correct

  4. Other observation: [H][C@@]12C@@([H])CCCC1 (found at gives the right isomer in BOTH Avogadro and ChemDraw

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