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

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

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

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

See also:

• Which Chemical Database Software Are Available?
• Program that simulates basic reactions in organic chemistry

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

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

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

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

See also:

• Which Chemical Database Software Are Available?
• Program that simulates basic reactions in organic chemistry

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

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

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

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

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

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

See also:

• Which Chemical Database Software Are Available?
• Program that simulates basic reactions in organic chemistry

You may try to download Structures, Sequences and Ligand for free from Protein Data Bank (RCSB) by specifying PDB IDs which you looking for (e.g. 2bg9). Alternatively (as suggested by Joe) from PubChem (BioAssays, Compounds and Substances).

Or eventually you can extract the data from Wikipedia (Chemical_substances) by downloading the whole database or specific category (e.g. Chemical substances, Chemical compounds, etc.) by using Special:Export into XML format.

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

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