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"all_expected_hashes_match": true }, { "state": "inactive_closed", "path": "research/structures/nnc2215-closed-model.pdb", "observed_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "formula_audit_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "reconciliation_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "all_expected_hashes_match": true } ], "assembly": { "source_components": [ { "component": "insulin chain A", "method": "RDKit MolFromFASTA", "sequence": "GIVEQCCTSICSLYQLENYCN" }, { "component": "insulin chain B desB30", "method": "RDKit MolFromFASTA", "sequence": "FVNQHLCGSHLVEALYLVCGERGFFYTPK" }, { "component": "B1 glucoside", "source_graph": "research/structures/nnc2215-b1-glucoside-attachment.smi", "map_legend": "research/data/nnc2215-b1-glucoside-atom-map.json", "source_maps_preserved": true }, { "component": "B29 linker-roof", "source_graph": 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84 carbamate bond" } ], "disulfides": [ { "atom_identities": [ { "chain": "A", "residue_number": 6, "atom_name": "SG" }, { "chain": "A", "residue_number": 11, "atom_name": "SG" } ], "bond_order": "single", "provenance": "declared insulin disulfide connectivity" }, { "atom_identities": [ { "chain": "A", "residue_number": 7, "atom_name": "SG" }, { "chain": "B", "residue_number": 7, "atom_name": "SG" } ], "bond_order": "single", "provenance": "declared insulin disulfide connectivity" }, { "atom_identities": [ { "chain": "A", "residue_number": 20, "atom_name": "SG" }, { "chain": "B", "residue_number": 19, "atom_name": "SG" } ], "bond_order": "single", "provenance": "declared insulin disulfide connectivity" } ], "only_declared_disulfides_added": true }, "formula": { "rdkit_formula": "C325H461N79O97S6", "atom_ledger_formula": "C325H461N79O97S6", "element_counts": { "C": 325, "H": 461, "N": 79, "O": 97, "S": 6 }, "heavy_element_counts": { "C": 325, "N": 79, "O": 97, "S": 6 }, 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16, "b29_full_ambiguity_preserved": true, "coordinate_mappings_used_to_assemble_graph": false } ], "b29_coordinate_map_selected": false, "coordinate_values_used_to_select_or_rank_mappings": false }, "pdb_cross_checks": [ { "state": "active_open", "candidate_pdb": "research/structures/nnc2215-open-source-corrected-candidate.pdb", "candidate_pdb_sha256_before_parse": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "candidate_pdb_sha256_after_parse": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "candidate_pdb_unchanged": true, "sequence_by_chain": { "A": "GIVEQCCTSICSLYQLENYCN", "B": "FVNQHLCGSHLVEALYLVCGERGFFYTPK" }, "sequence_matches_formula_audit_and_required_sequences": true, "ssbond_record_count": 3, "ssbond_pairs": [ { "first": { "residue_name": "CYS", "chain": "A", "residue_number": 6, "insertion_code": "" }, "second": { "residue_name": "CYS", "chain": "A", "residue_number": 11, "insertion_code": "" } }, { "first": { "residue_name": "CYS", 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1.5, "is_aromatic": true, "is_conjugated": true, "provenance": "Mapped B29 source SMILES edge map 89\u201381" }, { "edge_id": "bond_0524", "atom_node_ids": [ "atom_0397", "atom_0461" ], "atom_indices_zero_based": [ 396, 460 ], "bond_type": "SINGLE", "bond_order": 1.0, "is_aromatic": false, "is_conjugated": true, "provenance": "B29 protein attachment boundary; source cap replaced at map 84" }, { "edge_id": "bond_0525", "atom_node_ids": [ "atom_0043", "atom_0076" ], "atom_indices_zero_based": [ 42, 75 ], "bond_type": "SINGLE", "bond_order": 1.0, "is_aromatic": false, "is_conjugated": false, "provenance": "Declared insulin disulfide source: A6 SG\u2013A11 SG" }, { "edge_id": "bond_0526", "atom_node_ids": [ "atom_0049", "atom_0222" ], "atom_indices_zero_based": [ 48, 221 ], "bond_type": "SINGLE", "bond_order": 1.0, "is_aromatic": false, "is_conjugated": false, "provenance": "Declared insulin disulfide source: A7 SG\u2013B7 SG" }, { "edge_id": "bond_0527", "atom_node_ids": [ "atom_0154", "atom_0312" ], "atom_indices_zero_based": [ 153, 311 ], "bond_type": "SINGLE", "bond_order": 1.0, "is_aromatic": false, "is_conjugated": false, "provenance": "Declared insulin disulfide source: A20 SG\u2013B19 SG" } ], "checks": { "source_sequences_match_expected": true, "one_connected_full_graph": true, "neutral_formula_matches_reported_formula": true, "per_atom_provenance_complete": true, "implicit_hydrogen_ledger_matches_formula": true, "three_declared_disulfides_present": true, "b1_and_b29_boundary_caps_removed_and_replaced": true, "candidate_pdb_sequences_links_and_disulfides_match": true, "b1_one_and_b29_sixteen_exact_mappings_per_state_retained": true, "source_and_corrected_candidate_hashes_match_upstream_records": true, "conditional_tri_carboxylate_remains_separate": true, "full_system_protonation_force_field_or_md_resolved": false }, "assessment": { "status": "source-derived neutral constitutional graph assembled and internally audited", "formula_and_connectivity": "The graph is connected, valence-sanitized, and formula-consistent with the reported C325H461N79O97S6 composition.", "scope": "The corrected model-built PDBs were used only for named sequence, SSBOND, LINK, and hash cross-checks.", "not_established": [ "a unique B29 coordinate atom map; sixteen exact mappings per state remain", "PheB1 hydrogen ownership; the H2/H2A discrepancy remains open", "neutral macrocycle oxygen-label assignment or a physiological-pH full-system microstate", "histidine tautomer choice beyond the pinned RDKit neutral template", "roof stereochemistry beyond the source graph", "whole-system charge, force-field parameters, structural relaxation, or molecular dynamics", "drug efficacy or clinical readiness" ] } }