Solving this puzzle was easier than expected.
Saving instructions was harder than expected.

The left side of my solution deconstructs all reagents by spinning them around the debonder. It then sends the atoms through the conduit in a pattern where they are reconstructed by the right sight.

Left Bond Missing = 2nd, 3rd, 5th atom
Right Bond Missing = 1st, 3rd, 4th atom
Top Bond Missing = 3rd, 4th, 5th atom