Does there exist any data repository of chemical compound that gives the structure of the compounds with the help of coordinate geometry. It would be like each atom has a coordinate and the list of bonds it has with other atoms so that the 3D structure of the compound can be created from this very theoretical description?
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.
A pretty good database of experimental data compiled into one place has a geometry section. Check out http://cccbdb.nist.gov/
Go to the experimental data section, then click on summary of geometry data for one molecule. The database is fairly large, but not all molecules have a full geometric data set.