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

Abstract: 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.