Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration

Classical molecular docking is fundamentally constrained by the combinatorial growth of ligand translational and rotational degrees of freedom, rendering exhaustive pose enumeration infeasible on classical hardware. This work introduces a quantum-native formulation that encodes ligand occupancy on discretized three-dimensional grids and coherently generates the full ensemble of spatial configurations within a single quantum state. Multi-step translations and rotational transformations are controlled by ancillary qubits, enabling all symmetry-related configurations to be activated simultaneously. This framework provides a scalable foundation for quantum-accelerated virtual screening and is amenable to integration with quantum scoring approaches as quantum hardware continues to advance.