I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules that contain silicon. Where can I find these atomic coordinates?
There are a few sites where you can find geometries, for example
- PubChem https://pubchem.ncbi.nlm.nih.gov/
- CCCBDB: Computational Chemistry Comparison and Benchmark Database https://cccbdb.nist.gov/geom1x.asp
- ChemSpider http://www.chemspider.com/
- NIST Chemistry WebBook https://webbook.nist.gov/chemistry/
- Public Computational Chemistry Database http://pccdb.org/
The problem with the database structures is that they are often of poor quality: the coordinates are typically optimized at B3LYP/6-31G* level of theory, and I'm not sure whether they correspond to the lowest-lying conformation.
You didn't say what purpose you have in mind for the geometries, and how large molecules you are interested in. My general advice is to try to find a general database, and extract the kinds of molecules you are interested in. For instance, the tmQM transition metal dataset J. Chem. Inf. Model. 2020, 60, 12, 6135 appears to have also molecules with silicon atoms in it.