I think Marvin Beans could be a goot option. MarvinSketch allows users to quickly draw molecules through basic functions on the GUI and advanced functionalities such as sprout drawing, customisable shortcuts, abbreviated groups, default and user-defined templates and context-sensitive popup menus.

It's free for Academics.

All the best,

Miguel

Hi,

Try OpenBabel to convert 2D (sdf, smiles, ...) to 3D molecules (sdf, pdb or mol2).

http://openbabel.org/wiki/Main_Page

http://openbabel.org/docs/dev/GUI/GUI.html

http://openbabel.org/docs/dev/Command-line_tools/babel.html

http://openbabel.org/docs/2.3.0/FileFormats/Overview.html

https://www.youtube.com/watch?v=I6xf2itreeQ

http://openbabel.org/docs/2.3.0/FileFormats/Overview.html

LigandScout should handle 3D sdf, pdb and mol2 files.

You can use Ligandscout's idbgen to prepare you ligand database.  idbgen will help you to generate ldb file from 2D smiles file, mol2 or sdf file.