Complete Donor-Set Guidance for Frozen Diffusion Docking Models

Coordination information can guide a pretrained docking model, but its value depends on how specifically donor atoms are identified and how that information is used. We study a common Complete-Identity Contract Guidance (CICG) interface that applies a donor set during the final two denoising steps without retraining the generator or its confidence model. Historical Contract Transfer (HCT) supplies reference-mapped atom identities; trajectory-specific nearest-donor policies instead use historical donor counts, with or without elemental quotas, to select atoms from intermediate poses. No reference ligand coordinates are used as pose targets. We evaluate these policies in a pooled follow-up analysis of 86 assessable queries in 33 structural groups. Across two seeds, historical guidance raises joint pose, coordination, and validity success from 21.51% to 36.63%: +15.12 percentage points (95% group-bootstrap interval, 8.00-24.63). Composition-matched nearest-donor guidance reaches 33.14%, leaving the historical advantage unresolved at +3.49 points [-0.42, 8.87]. A retrospective audit using native donor labels finds that all 57 successes of the composition-matched policy occur on selected trajectories whose assigned sets match the native donor set, while 50 other exact assignments fail. Under the same donor-aware selector, a post-hoc comparison finds an additional 7.56-point gain [1.11, 14.04] from coordinate guidance, accompanied by lower ligand accuracy. These results support the usefulness of several donor-information policies within the evaluated scope, rather than a general advantage of fixed historical membership.