A measurement of jet substructure variables is presented using data collected in 2016 by the ATLAS experiment at the LHC with proton-proton collisions at $s=13$ TeV. Large-radius jets groomed with the trimming and soft-drop algorithms are studied. Dedicated event selections are used to study jets produced by light quarks or gluons, and hadronically decaying top quarks and $W$ bosons. The variables measured are sensitive to pronged substructure, and therefore are typically used for tagging jets from boosted massive particles. These include the energy correlation functions and the $N$-subjettiness variables. The number of subjets and the Les Houches angularity are also considered. The distributions of the substructure variables, corrected for detector effects, are compared to the predictions of various Monte Carlo event generators. They are also compared between the large-radius jets originating from light quarks or gluons, and hadronically decaying top quarks and $W$ bosons.