{
  "scope": "Static editorial figure. All scientific computations and structural coordinates are reused from published or author-provided sources; no new protein design, molecular simulation, experimental result or joined manufacturing route.",
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        "url": "https://raw.githubusercontent.com/RosettaCommons/foundry/d078b24d6d0e6f8607e9a0311128f4a897f83953/models/rfd3/docs/tutorials/advanced_enzyme_tutorial_files/hbond_rasa/metalloprotease_rfd3_input_hbond_rasa.json",
        "sha256": "94b6cb59f847ee28f5aa684278ab859852c3e769ee677216f33d7b96f809c9f8"
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      {
        "file": "rfd3-theozyme.pdb",
        "url": "https://raw.githubusercontent.com/RosettaCommons/foundry/d078b24d6d0e6f8607e9a0311128f4a897f83953/models/rfd3/docs/tutorials/advanced_enzyme_tutorial_files/theozyme.pdb",
        "sha256": "d9c31861ed94e141d409272e79cd94c9a6f2207eaa2620444fe6baa500977ba8"
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      {
        "file": "3i1c.pdb",
        "url": "https://files.rcsb.org/download/3I1C.pdb",
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      "name": "BSD-3-Clause",
      "copyright": "Copyright (c) 2025, Institute for Protein Design, University of Washington",
      "notice": "/figures/biology/FOUNDRY-LICENSE.txt"
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    "scope": "Official RFdiffusion3 tutorial output, not a tested active enzyme. The ligand is a phosphonamidate transition-state analog. Full model metrics are preserved in the source JSON, including unsatisfied/zero hydrogen-bond metrics; this figure does not assert that all constraints were achieved.",
    "motifMap": {
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      "A93": "A11",
      "A96": "A8",
      "A102": "A79",
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    "paper": "https://doi.org/10.1126/science.1190239",
    "scope": "Experimental protein coordinates, chain A, PDB 3I1C. No co-crystal substrates or inferred docked poses. The catalytic binding logic is a separate chemical schematic based on Figure 1 of Siegel et al.; it is not a coordinate overlay.",
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    "scope": "Idealized DNA-helical trench section and device, not a source atomistic model. 10.4 nm pitch is reported. Tube radius 0.61 nm, illustrative trench geometry, helix radius 1 nm, 0.34 nm rise/bp and 10.5 bp/turn are schematic choices. Three tubes depict a section, not a measured tube count. Identical tube world coordinates and identical camera at all stages.",
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    "scope": "Proposed research connection only. Compatible environments and attachment/joining/release remain unresolved.",
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}