The term residues is generally used to refer to any component of a biomolecule. Within the '''MQ''' environment, any collection of atoms bound by chemical bonds (covalent, coordinative or ionic) is considered a residue if this fact is appropriately indicated in the input file. Specifically, all the atoms that make up a residue should have the same ''residue name'' (3-letter code) , ''residue serial number'' and ''chain identifier''.
Fragment=A fragment is a subset of atoms of the input biomolecule. It can also be understood as an arrangement of either atoms or residues. Therefore, individual atoms and residues can be considered as fragments as well.
A query is a single declarative expression of the '''MQ''' language which describes one or more structural fragments inside an input biomolecule.