Stage-wise Extreme Atomic Proximity in HPacker Side-chain Reconstruction

This technical note documents stage-wise extreme atomic proximity during HPacker side-chain reconstruction of 200 stored structures from a single BioEmu wild-type protein ensemble. Six sequential reconstruction stages (0–5; 1,200 archived structures) were examined using a strict distance threshold of <1.6 Å between nonadjacent interresidue heavy atoms. At stage 5, 134 of 200 structures contained at least one such contact. For the selected PHE6–PHE55 residue pair, 43 of 200 structures exhibited an ordered contact–noncontact–contact sequence, while 25 of 200 exhibited complete six-stage alternation (10 with the pattern 010101 and 15 with 101010). Exploratory, post hoc selected local-input interventions and neural-network response diagnostics documented case-specific structural and predicted side-chain responses. In a selected WT0 example, the intervention-derived stage-5 structure increased the minimum PHE6–PHE55 heavy-atom distance from 0.2773 Å to 1.8815 Å. Four selected WT0/WT1 baseline and intervention-derived structures subsequently completed a fixed minimization and short BioEmu relaxation workflow, including 0.1 ns NVT and 0.4 ns NPT, without production molecular dynamics. A separate protein heavy-atom Lennard-Jones proxy identified severe overlap contributions in selected input geometries. The observations describe one fixed reconstruction archive and selected exploratory case studies. They do not establish a general side-chain packing improvement, a unique neural-network causal pathway, higher molecular-dynamics completion rates, or thermodynamic stabilization. The record includes a Technical Note, Supplementary Information, source-linked tables, selected structures, archived intervention implementations, verification code, and provenance documentation. Funding: No external funding. Conflicts of interest: None declared. AI disclosure: Generative AI assisted with research planning, analysis scripting, verification support, figure preparation, and manuscript drafting. The human author reviewed the work and retains responsibility for scientific interpretation and final content. Licensing: Original author-written text and figures are CC BY 4.0; original author-owned code is MIT-licensed. Third-party code and data retain their respective upstream license conditions, as detailed in the included license and provenance files.