You may try to download Structures, Sequences and Ligand free of charge from:

 - [Protein Data Bank (RCSB)][1] by specifying PDB IDs which you looking for (e.g. 2bg9),
 - [PubChem][2] by [NCBI][3] (BioAssays, Compounds and Substances),
 - [ChemSpider][4] (free chemical structure database providing fast access to over 28 million structures, properties and associated information),
 - Wikipedia ([Chemical_substances][5]) by downloading the whole [database][6] or specific category (e.g. [Chemical substances][7], [Chemical compounds][8], etc.) by using [Special:Export][9] into XML format.

Also check out few free chemistry softwares which could potentially contain some databases:

 - [Yenka Chemistry][10] (before Crocodile Chemistry) - complete virtual laboratory which offer free home licenses for personal, non-commercial, non-academic use only.
 - [Gamess and Quantum ESPRESSO][11] - Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale

See also:

 - [Which Chemical Database Software Are Available?][12]
 - [Program that simulates basic reactions in organic chemistry][13]


  [1]: http://www.rcsb.org/pdb/download/download.do
  [2]: https://pubchem.ncbi.nlm.nih.gov/
  [3]: http://www.ncbi.nlm.nih.gov/
  [4]: http://www.chemspider.com/
  [5]: https://en.wikipedia.org/wiki/Category:Chemical_substances
  [6]: https://en.wikipedia.org/wiki/Wikipedia:Database_download
  [7]: https://en.wikipedia.org/w/index.php?title=Special:Export&addcat&catname=Chemical_substances&pages=XXXX
  [8]: https://en.wikipedia.org/w/index.php?title=Special:Export&addcat&catname=Chemical_compounds&pages=XXXX
  [9]: https://en.wikipedia.org/wiki/Special:Export
  [10]: http://www.yenka.com/en/Free_home_licences/
  [11]: http://www.quantum-espresso.org/
  [12]: http://chemistry.stackexchange.com/questions/4040/which-chemical-database-software-are-available
  [13]: http://chemistry.stackexchange.com/questions/7765/program-that-simulates-basic-reactions-in-organic-chemistry