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As from Title. Where can I find a database of simple chemical structures in XYZ format, possibly with a simple CAS -> XYZ or InChi -> XYZ REST service ?

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    $\begingroup$ What kind of searches have you done so far? If you did not find what you wanted, what's wrong with the first few hits on the google search: google.com/… $\endgroup$ – Yann Dec 6 '11 at 14:20
  • $\begingroup$ What kind of database are you looking for? Please specify what exactly are you searching! there are a lot free databases with crystal data, biological activity, just simple calculated structures. for example: 1. ZINC 2. COD 3. Super Natural II 4. I can't post more than 2 links yet... And for working with geometries and databases it is better to use something like Maestro academics. $\endgroup$ – XuMuK Sep 16 '16 at 8:32
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ChemSpider (http://www.chemspider.com/) provides structures in mol format, which is simple enough to convert to XYZ, e.g. using OpenBabel (http://openbabel.org/wiki/Main_Page).

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    $\begingroup$ If we're going to answer that way: there's a ton of places to download molecule files from, and OpenBabel can convert them all into most of the usual suspects... $\endgroup$ – J. M. Dec 6 '11 at 17:33
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    $\begingroup$ It would help to know why format conversion is not an acceptable solution. $\endgroup$ – khinsen Dec 8 '11 at 17:38
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This site has some nice enough data: http://cccbdb.nist.gov/

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  • $\begingroup$ N.B. The files here are in *.mol format. $\endgroup$ – J. M. Dec 8 '11 at 7:55
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Finding reliable sites for this kind of thing can be kind of tricky, actually. I recently had to search for small molecule structures and found that half the top sites on the Google search were down. Therefore this kind of answer may be quite helpful.

My preferred source of small ligand structures is the Binding DB. It's in .mol file format, but how to convert easily has been mentioned in previous answers. For a finite number of small molecules converting this by-hand is almost simpler than automating it.

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I like the Pubchem database for this purpose. Although it contains large molecules too, one can easily specify filters to get a list of small molecules. The website also provides a batch download service, which is convenient for large datasets. One can use InChI identifiers to search for a specific compound.

CAS to XYZ conversion does not really exist. The CAS (Chemical Abstract Service) is just a number for each molecule in the CAS database. It is not possible to derive somehow the structure from the CAS number. You can use the CAS number to look up the molecular structure, but is not free as far as I know. See www.cas.org for more information.

InChI to XYZ conversion is possible with the OpenBabel software. I'm not aware of a web service for this type of conversion.

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