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 ?
$\begingroup$
$\endgroup$
2
asked Dec 6, 2011 at 10:29
-
1$\begingroup$ 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/… $\endgroup$– YannCommented Dec 6, 2011 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. $\endgroup$– XuMuKCommented Sep 16, 2016 at 8:32
Add a comment
|
5 Answers
$\begingroup$
$\endgroup$
3
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).
-
2$\begingroup$ 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.Commented Dec 6, 2011 at 17:33
-
3$\begingroup$ It would help to know why format conversion is not an acceptable solution. $\endgroup$– khinsenCommented Dec 8, 2011 at 17:38
-
$\begingroup$ ChemSpider is useful, but not ideal. I just found the structure of dimethyl disulfide on ChemSpider. The conformation seems wrong and it doesn't have hydrogen. This means that one has to add hydrogen and do geometric relaxation before doing any other meaningful calculation. cccbdb.nist.gov is a better website that gives geometrically relaxed structures (from @Dr_bitz comment) $\endgroup$– Bohan XuCommented Oct 4 at 17:07
1
-
$\begingroup$ N.B. The files here are in *.mol format. $\endgroup$– J. M.Commented Dec 8, 2011 at 7:55
$\begingroup$
$\endgroup$
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.
$\begingroup$
$\endgroup$
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.
$\begingroup$
$\endgroup$
1
Try the TABS database here: it's less than 2000 structures but still very useful. https://www2.unb.ca/~ajit/download.htm
