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A straightforward solution is to "bind" the submolecules, i.e., replace your code: \chemfig{ !{Val1} !{ala2} !{Phe1} !{Phe2} !{gly1} } by for example (some tweaking would be probably necessary): \chemfig{ !{Val1}-[,0.3,,,draw=none] !{ala2}-[,0.3,,,draw=none] !{Phe1}-[,0.3,,,draw=none] !{Phe2}-[,0.3,,,draw=none] !{gly1} }



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