Data repository of organic compounds
I'm not entirely clear on what you want - I guess a database of a bunch of 3D coordinates for many organic compounds?

By far the largest such database is NIH PubChem with over 30 million compounds - mostly organic. You can search by structure or name or identifier. Most of these have 2D and 3D geometries you can visualize or download and many computed properties.

A similar database is the RSC ChemSpider with over 34 million compounds. Much like PubChem, names, 2D and 3D geometries and other properties are available.

I'll put in a plug for the Pitt Quantum Repository which contains ~64,000 molecules and growing, all with geometries computed using quantum chemical methods. One benefit of PQR is that you can easily access the site using smartphones and tablets and use a QR code or DOI to link to the compound.