Less common ligand coordination of transition-metal centers is often associated with peculiar valence-shell electron configurations and outstanding physical properties. One example is the Fe$^+$ ion with linear coordination, actively investigated in the research area of single-molecule magnetism. Here we address the nature of 3$d^9$ states for Cu$^{2+}$ ions sitting in the center of trigonal bipyramidal ligand cages in the quasi-two-dimensional honeycomb compound InCu$_{2/3}$V$_{1/3}$O$_3$, whose unusual magnetic properties were intensively studied in the recent past. In particular, we discuss the interplay of structural effects, electron correlations, and spin-orbit couplings in this material. A relevant computational finding is a different sequence of the Cu ($xz$, $yz$) and ($xy$, $x^2!-!y^2$) levels as compared to existing electronic-structure models, which has implications for the interpretation of various excitation spectra. Spin-orbit interactions, both first- and second-order, turn out to be stronger than previously assumed, suggesting that rather rich single-ion magnetic properties can be in principle achieved also for the 3$d^9$ configuration by properly adjusting the sequence of crystal-field states for such less usual ligand coordination.
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