Article ID: 393 - Last Modified: August 12, 2015
I have chirality displayed in my ChemCart dbase entry for a molecule (wedged/hashed bonds). I export the .mol file and import it into Maestro, but the molecule comes in flat. How do I import the molecule so that the chirality of the dbase entry is maintained?
Most likely when you export the structure, it is exported as a flat 2D structure with z-coordinates either non-existent or set to zero. The chirality information is recorded as a bond parity/direction property. When you import this 2D structure into Maestro, it is displayed flat, since it has no 3D information to go by. Maestro does not automatically convert from 2D to 3D. However, you can convert from 2D to 3D with LigPrep. When you run LigPrep, ensure that the "Retain specified chiralities" option under Stereoisomers is selected. You can check the chirality with "Label atoms" → "Chirality" to make sure that it is correct.
If you can copy the structure to the clipboard in your database application as a SMILES string, you can paste the structure into Maestro with Edit → Paste Special → As 3D. The molecule is converted to 3D by LigPrep using the chirality information that is stored in the SMILES string.
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