Superimposing fragments based on a single reference bond offers a fast and convenient alignment method. However, with only two points of reference, the relative orientation of the fragments remains undefined, potentially leading to sub-optimal conformations. BuildAMol addresses this issue by providing two options. The first approach requires defining a detailed Linkage. This linkage specifies the internal coordinates, such as bond lengths, angles, and dihedrals, for the atoms surrounding the newly formed bond.This additional geometric information allows BuildAMol to place the fragment precisely in the desired orientation. However, defining such detailed geometry might not always be feasible or necessary. Therefore, by default, BuildAMol will perform a small-scale optimization around the new bond in order to rotate the incoming fragment into an chemically sound orientation.