I'd like to do chemical structure prediction using a known molecule formula then change it to optimize interactions with proteins. I'm familiar with de novo protein structure prediction are there any programs which will go from formula to structure with optimal geometry of random small chemicals say 30 atoms ? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a program which computes mols from formulas. 
thank you