Here's the instruction on how to align the axis on your Ultimaker after you have a loos pulley or had to replace a belt. Instruction is UM2 based but is the same for all machines.
https://ultimaker.com/en/resources/19953-aligning-the-axles
For the S5 you need a different size tools as it has thicker X/Y axis vs the other amchines (for wich multiple tools are available already)
As the S5 has a 10mm X axis and a 8mm Y axis you need 2 sets of tools, so print both tools 2x