Avoiding Unwanted Bonds between Atoms in a Substructure

•	Select Bonds from the top-level menu and Exclude... from the pull-down menu.

•	Select Direct Links.

•	Click on the atoms which must not be directly linked (i.e. the atoms you want to prevent being bonded to one another).

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Hit OK.

•	In the example below, atoms 3 and 6 have been specified to form no direct links:

 

•	This query would find:

(because the specified atoms are not directly bonded to each other) but would not find: