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If I do, for example,

Export["~/Downloads/tnt.xyz", Molecule["TNT"]]

I get a nice set of coordinates for atoms within a molecule of the explosive TNT.

I don't know where these coordinates actually come from.

They could just be simple guesses based on the typical bond lengths and angles of these elements.

Or, it could be the actual coordinates determined in some experiment.

I'm especially curious to know, if I want to run further analysis on this molecule, do I need to do a geometry optimization, or are the atoms already in their equilibrium positions?

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  • $\begingroup$ Most likely the coordinates would have been calculated from an electronic structure calculation with DFT codes. In these calculations the structure of the molecule is relaxed by minimising the total energy. $\endgroup$
    – Ferca
    Sep 10, 2020 at 7:40
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    $\begingroup$ You can use pubchem.ncbi.nlm.nih.gov. They not only provide the data, but also quote sources. $\endgroup$
    – yarchik
    Sep 10, 2020 at 8:46
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    $\begingroup$ The Molecule[] framework internally uses RDKit and its various algorithms like ETKDG for generating coordinates for a molecule, after which the MMFF energy of the initially generated coordinates is accordingly minimized. $\endgroup$ Sep 10, 2020 at 11:26
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    $\begingroup$ Possible duplicate of this question. In general, if you don't provide coordinates (via mol = Molecule[atoms, bonds, AtomCoordinates -> listOfCoordinates] or mol = Import["myfile.xyz"]) then they are generated as needed using heuristic methods. $\endgroup$
    – Jason B.
    Sep 10, 2020 at 12:04

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