  Recent developments in machine-learning based molecular fragment linking have
demonstrated the importance of informing the generation process with structural
information specifying the relative orientation of the fragments to be linked.
However, such structural information has not yet been provided in the form of a
complete relative coordinate system. Mathematical details for a decoupled set
of bond lengths, bond angles and torsion angles are elaborated and the
coordinate system is demonstrated to be complete. Significant impact on the
quality of the generated linkers is demonstrated numerically. The amount of
reliable information within the different types of degrees of freedom is
investigated. Ablation studies and an information-theoretical analysis are
performed. The presented benefits suggest the application of a complete and
decoupled relative coordinate system as a standard good practice in linker
design.
