In gentoo portage, there are several programs to draw structures of organic molecules. The best one is gchempaint. Not in portage, but also very interesting is bkchem. A Gentoo ebuild is available, but needs to be installed from a portage overlay. To install it, just use the commands below (where I assume you have a portage overlay correctly set up in /usr/local/portage).
# mkdir -p /usr/local/portage/sci-chemistry/bkchem # cd /usr/local/portage/sci-chemistry/bkchem # wget http://bkchem.zirael.org/download/bkchem-0.12.5.ebuild # ebuild bkchem-0.12.5.ebuild digest # emerge -va bkchem
If you want to make some final adjustments to the structure of the molecule, I suggest saving the molecule as an svg image, and making the adjustments with inkscape.