Probably not the best option out there, but nobody else has commented, it works and it's free: MarvinSketch. If you select the structure you've drawn and hit F7 you can rotate things in 3D. The conformation calculator gives you a 3D model that you can manipulate. Not quite as easy as building the models by hand, but it's less tedious sometimes and I find it pretty useful. You can play with how the structure is displayed (wireframe, ball and stick, spacefill) and each atom/bond's colors to make different areas stand out more. Big downside is that if you don't generate a 3D conformation, all the bond lengths are the same.
I'm not explaining very well. I need to insert in the document file like this. I evalueted, in previous thread, that all chemical package are inefficent to make this type of scheme: program such as ChemDraw or Marvin Sketch are faster and also contain usefull program that I need (simulation of spetra for example).
So once I draw my scheme the question is "how integrate them in my org file"? I use org file principally to edit LaTex and, also, i convert them to Markdown and then in .doc for other people I work. So the most effective way to implement ChemDraw file in LaTex is the one i described up there, the question is how implement that code in org mode so it can be translate also in other file.
In my opinion you have 3 relatively competitive softwares for drawing molecules:
If your university doesn't have ChemDraw subscription just go for ChemSketch. Its freeware, simple to use and you can simply paste molecules straight into Word and edit them later.
The Marvin suite is free, has tons of tutorials, and even has free 3D programs as well that I use regularly for docking even though I have the chemdraw suite through my institution.