  Designer heterostructures, where the desired physics emerges from the
controlled interactions between different components, represent one of the most
powerful strategies to realize unconventional electronic states. This approach
has been particularly fruitful in combining magnetism and superconductivity to
create exotic superconducting states. In this work, we use a heterostructure
platform combining supramolecular metal complexes (SMCs) with a quasi-2D van
der Waals (vdW) superconductor NbSe$_2$. Our scanning tunneling microscopy
(STM) measurements demonstrate the emergence of Yu-Shiba-Rusinov (YSR) bands
arising from the interaction between the SMC magnetism and the NbSe$_2$
superconductivity. Using X-ray absorption spectroscopy (XAS) and X-ray magnetic
circular dichroism (XMCD) measurements, we show the presence of
antiferromagnetic coupling between the SMC units. These result in the emergence
of an unconventional $3\times3$ reconstruction in the magnetic ground state
that is directly reflected in real space modulation of the YSR bands. The
combination of flexible molecular building blocks, frustrated magnetic
textures, and superconductivity in heterostructures establishes a fertile
starting point to fabricating tunable quantum materials, including
unconventional superconductors and quantum spin liquids.
