When a polymer is created HELM tries to reflect the chemistry as closely as possible, so the R groups reflect the leaving groups in reality. However in the RNA backbone we needed to decide whether the phosphate or sugar should be the source of the oxygens that remain in the polymer.
The HELM project decided that the phosphate should lose both oxygens and the ribose should keep both oxygens.
This does make the connections unequal as below:
Defining the monomers like this means you need to be careful when connecting phosphates together (e.g. ATP). The triphosphate will be chemically nonsense:
Correspondingly, connecting ribose's together creates peroxide bonds.
If you need to connect phosphates to phosphates or sugars to sugars, you need to define alternative monomers.