There is no limit to the number of bond types (and angle types) you want to constrained in the shake command. Just make sure the group that the fix is acting on includes both the water and the ionic liquid molecules (eg "all" does this)
Have you tried using something like this?
fix water_shake all shake 0.0001 20 0 b 1 5 6 7 a 1
I could be getting the details wrong. I'm typing this on my phone. For more details, see:
Also: You may also want to take a look at the molecule builder tools at
These tools will build a LAMMPS DATA file which allows you to have more control over the placement and composition of the molecules in your system and how they are connected together, as well as the use of several canned force fields. There are several moltemplate examples, for example that show how to build a box of SPC/E water and add ions and other molecules.