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I'm looking at the tripos mol2 format. (This is the most recent mirror of the specification document that I have found so far: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf). What is the purpose of the SUBSTRUCTURE section? I notice that obabel does not include it.

It appears to specify connectivity, but that seems a duplicate of the BOND section.

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    $\begingroup$ Although I am not sure, I would say (based on a quick search), that it seems to exist for defining smaller units within a macromolecule (or other large unit), so that they can be compared against the whole molecule or other subunits. Think of atoms belonging in to chains in PDB-files. $\endgroup$ – Bdrs Apr 17 '18 at 14:01
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    $\begingroup$ Yes, it exists to define substructures smaller than the entire molecule - something that is relevant for structural manipulation. Imagine for instance that you have two complex molecules sharing a core; defining a substructure for the core allows you to align the molecules based on the core and then compare the rest of their structures. $\endgroup$ – user41033 Apr 18 '18 at 13:54

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