{ "schema": "dia-health-one.nnc2215-b29-topology-audit.v1", "run": { "generated_at_utc": "2026-10-25T23:05:58.964864+00:00", "script": "research/audit_nnc2215_b29_topology.py", "script_sha256": "98b9679f5fb9745563302544b6842f920a8841176d89989e0ee67e219778a539", "python_version": "3.11.17", "rdkit_version": "2026.03.1", "networkx_version": "3.6.1", "gpu_used": false, "coordinate_files_modified": false }, "inputs": { "sha256_file_integrity_records": { "product_smiles": { "path": "structures/nnc2215-b29-linker-roof-product.smi", "sha256_observed": "b677316c1fced61045d2eebab4de85cdb2f1ef956280d18ab9d610df1181bd40", "sha256_expected": "b677316c1fced61045d2eebab4de85cdb2f1ef956280d18ab9d610df1181bd40", "expected_hash_source": "product map legend graph_sha256", "hash_check": "pass" }, "product_map_legend": { "path": "data/nnc2215-b29-linker-roof-product-map.json", "sha256_observed": "eb028433748cf294744ac02f381e909f029f79916484a2e05dfbf966f7faa0c5", "sha256_expected": null, "expected_hash_source": null, "hash_check": "recorded_only_no_independent_expected_hash" }, "coordinate_reconciliation_record": { "path": "data/nnc2215-carbon-reconciliation-candidate.json", "sha256_observed": "7aed13e3d8bcd13d9aa8b3e468f8831b5dec322caf3de454dd67f68087d4e133", "sha256_expected": "7aed13e3d8bcd13d9aa8b3e468f8831b5dec322caf3de454dd67f68087d4e133", "expected_hash_source": "prior roof mapping audit input hash", "hash_check": "pass" }, "prior_roof_coordinate_mapping_audit": { "path": "data/nnc2215-roof-graph-coordinate-mapping-audit.json", "sha256_observed": "7c45fc8c491307ffcd757b30761d5d3f86eb650af68ad17d9e346567ff9a33d0", "sha256_expected": null, "expected_hash_source": null, "hash_check": "recorded_only_no_independent_expected_hash" }, "linker_mapping_audit": { "path": "data/nnc2215-linker-mapping-audit.json", "sha256_observed": "1c39ec94156c7047e1316d429c31875675c6d8cf43dc9dc98c424e8efcbd0c97", "sha256_expected": "1c39ec94156c7047e1316d429c31875675c6d8cf43dc9dc98c424e8efcbd0c97", "expected_hash_source": "product map legend input hash", "hash_check": "pass" }, "source_roof_smiles": { "path": "structures/nnc2215-roof-propyl-azide.smi", "sha256_observed": "ed4340362d1436fc7518bfc577d6d23ac4b8434d3b60f40492b2bb36fd394325", "sha256_expected": "ed4340362d1436fc7518bfc577d6d23ac4b8434d3b60f40492b2bb36fd394325", "expected_hash_source": "product map legend and source graph audit", "hash_check": "pass" }, "source_roof_atom_map_legend": { "path": "data/nnc2215-roof-macrocycle-atom-map.json", "sha256_observed": "48f716a63696d01f89339d0e6da009d9794ffd03e8349dc9a3fd471248e75ec8", "sha256_expected": "48f716a63696d01f89339d0e6da009d9794ffd03e8349dc9a3fd471248e75ec8", "expected_hash_source": "product map legend input hash", "hash_check": "pass" }, "source_roof_graph_validation_audit": { "path": "data/nnc2215-roof-macrocycle-graph-audit.json", "sha256_observed": "cefc4c622c2d8d49e2c2fe072024d2b37ccdf3546b3a4e067b3f5c9f98af5810", "sha256_expected": "cefc4c622c2d8d49e2c2fe072024d2b37ccdf3546b3a4e067b3f5c9f98af5810", "expected_hash_source": "prior roof mapping audit input hash", "hash_check": "pass" }, "source_chemistry_audit": { "path": "data/nnc2215-chemistry-source-audit.json", "sha256_observed": "3e8918bfe088575cd7c6870d8e1b4ae20a32b933c97afa43e8566b5c25c4b31e", "sha256_expected": "3e8918bfe088575cd7c6870d8e1b4ae20a32b933c97afa43e8566b5c25c4b31e", "expected_hash_source": "product map legend input hash", "hash_check": "pass" }, "active_open_pre_reconciliation_pdb": { "path": "structures/nnc2215-open-model.pdb", "sha256_observed": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "sha256_expected": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "expected_hash_source": "coordinate reconciliation record and linker mapping audit", "hash_check": "pass" }, "active_open_corrected_candidate_pdb": { "path": "structures/nnc2215-open-source-corrected-candidate.pdb", "sha256_observed": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "sha256_expected": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "expected_hash_source": "coordinate reconciliation record output_sha256", "hash_check": "pass" }, "inactive_closed_pre_reconciliation_pdb": { "path": "structures/nnc2215-closed-model.pdb", "sha256_observed": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "sha256_expected": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "expected_hash_source": "coordinate reconciliation record and linker mapping audit", "hash_check": "pass" }, "inactive_closed_corrected_candidate_pdb": { "path": "structures/nnc2215-closed-source-corrected-candidate.pdb", "sha256_observed": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e", "sha256_expected": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e", "expected_hash_source": "coordinate reconciliation record output_sha256", "hash_check": "pass" } }, "hash_validation_boundary": [ "The product map legend and prior roof coordinate-mapping audit have recorded SHA-256 values but no independent expected self-checksum in the committed input set; their bytes are recorded, and their graph, legend, reconciliation, linker, and source-audit references are cross-checked against the corresponding files.", "All artifacts with an upstream expected checksum are verified against that checksum before graph matching; both pre-reconciliation source PDBs and corrected candidate PDBs are checked against reconciliation/linker records." ], "input_integrity_checks": { "product_map_ids_complete_1_to_92": true, "product_inventory_matches_legend": true, "product_node_edge_component_cycle_counts_match_legend": true, "product_graph_matches_committed_validation_counts": true, "roof_map_ids_complete_1_to_83": true, "roof_inventory_matches_source_audit": true, "roof_counts_match_source_audit": true, "roof_legend_matches_product_inherited_map_ids": true }, "corrected_candidate_pdbs": { "active_open": { "pre_reconciliation_source_file": "structures/nnc2215-open-model.pdb", "pre_reconciliation_source_sha256": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "corrected_candidate_file": "structures/nnc2215-open-source-corrected-candidate.pdb", "corrected_candidate_sha256": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "corrected_candidate_expected_by_reconciliation": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc" }, "inactive_closed": { "pre_reconciliation_source_file": "structures/nnc2215-closed-model.pdb", "pre_reconciliation_source_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "corrected_candidate_file": "structures/nnc2215-closed-source-corrected-candidate.pdb", "corrected_candidate_sha256": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e", "corrected_candidate_expected_by_reconciliation": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e" } }, "all_corrected_candidate_pdb_hashes_unchanged_after_audit": true, "candidate_hashes_after_audit": { "structures/nnc2215-open-source-corrected-candidate.pdb": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "structures/nnc2215-closed-source-corrected-candidate.pdb": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e" } }, "ambiguity_and_mapping_assumptions": [ "The six map IDs 78-83 used in the roof-only precursor search are fixed to candidate tail/azide anchors from the prior linker mapping audit; this does not authorize those anchors as source chemistry evidence.", "Complete-product exact mappings are enumerated without fixing the prior candidate labels. The graph matcher compares element labels and simple adjacency only.", "PDB CONECT resolves by atom serial. PDB LINK resolves only by a unique full chain, residue, insertion code, altloc, and atom-name identity.", "Source bond-label-preserving automorphisms define mapping equivalence classes. Distinct classes remain separate because they can transfer different source bond labels onto the unlabeled PDB adjacency.", "PDB coordinates do not choose among exact mappings or bond-label transfer classes; geometry is reported after mapping as a screen only.", "PDB atom names, including the open/closed aliases for map 79 and map 90, are candidate coordinate labels and are not source-authoritative atom names." ], "source_product_graph": { "graph_file": "structures/nnc2215-b29-linker-roof-product.smi", "graph_sha256": "b677316c1fced61045d2eebab4de85cdb2f1ef956280d18ab9d610df1181bd40", "map_legend_file": "data/nnc2215-b29-linker-roof-product-map.json", "map_legend_sha256": "eb028433748cf294744ac02f381e909f029f79916484a2e05dfbf966f7faa0c5", "source_product_drawing_regiochemistry": "source-supported 1,4-disubstituted 1,2,3-triazole", "source_assignment_basis": "Nature Fig. 2a directly draws the product with the roof propyl substituent bonded to triazole N1 and the B29 linker substituent bonded to C4. This assigns source azide N attached to C23 as N1, internal alkyne carbon C7 as C4, and terminal alkyne carbon C8 as C5. The atom assignment follows the primary product drawing, not PDB adjacency or distances.", "product_map_id_legend": { "inherited_roof_map_ids_1_to_83": { "floor_aromatic_ring": [ 1, 2, 3, 4, 5, 6 ], "roof_aromatic_ring": [ 7, 8, 9, 10, 11, 12 ], "three_spacer_aromatic_rings_in_graph_order": [ [ 13, 14, 15, 16, 17, 18 ], [ 19, 20, 21, 22, 23, 24 ], [ 25, 26, 27, 28, 29, 30 ] ], "three_floor_ethyl_substituents": [ [ 31, 32 ], [ 33, 34 ], [ 35, 36 ] ], "floor_to_spacer_urea_bridges": [ 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 ], "three_carboxyl_groups": [ [ 52, 53, 54 ], [ 60, 61, 62 ], [ 68, 69, 70 ] ], "spacer_to_roof_urea_bridges": [ [ 55, 56, 57, 58, 59 ], [ 63, 64, 65, 66, 67 ], [ 71, 72, 73, 74, 75 ] ], "roof_methyl_substituents": [ 76, 77 ], "roof_tail_source_C21_C22_C23": { "C21": 78, "C22": 79, "C23": 80 }, "azide_precursor_nitrogens_now_triazole_N1_N2_N3": [ 81, 82, 83 ] }, "added_product_atoms_84_to_92": { "84": "source linker C3, carbamate carbonyl carbon", "85": "source linker C4, oxygen-linked methylene", "86": "source linker C5 methylene", "87": "source linker C6 methylene adjacent to C7", "88": "source linker C7 internal alkyne carbon; product triazole C4", "89": "source linker C8 terminal alkyne carbon; product triazole C5", "90": "linker carbamate carbonyl oxygen", "91": "linker carbamate ether oxygen", "92": "LysB29 NZ attachment endpoint" } }, "formula_with_nz_nh2_cap": "C62H72N16O14", "formula_is_actual_conjugate_formula": false, "heavy_atom_count": 92, "heavy_element_counts": { "C": 62, "N": 16, "O": 14 }, "adjacency_edge_count": 99, "connected_component_count": 1, "cycle_rank_E_minus_V_plus_components": 8, "graph_integrity_checks": { "product_map_ids_complete_1_to_92": true, "product_inventory_matches_legend": true, "product_node_edge_component_cycle_counts_match_legend": true, "product_graph_matches_committed_validation_counts": true, "roof_map_ids_complete_1_to_83": true, "roof_inventory_matches_source_audit": true, "roof_counts_match_source_audit": true, "roof_legend_matches_product_inherited_map_ids": true }, "bond_order_representation": { "smiles_bond_form": "Explicit Kekul\u00e9 single/double bonds are written for the new linker and click ring; RDKit sanitization perceives the triazole ring as aromatic.", "carbamate_connectivity": [ { "atoms": [ 92, 84 ], "bond": "single", "description": "LysB29 NZ\u2013C3" }, { "atoms": [ 84, 90 ], "bond": "double", "description": "C3=carbonyl O" }, { "atoms": [ 84, 91 ], "bond": "single", "description": "C3\u2013ether O" }, { "atoms": [ 91, 85 ], "bond": "single", "description": "ether O\u2013C4" } ], "linker_chain_connectivity": [ { "atoms": [ 85, 86 ], "bond": "single" }, { "atoms": [ 86, 87 ], "bond": "single" }, { "atoms": [ 87, 88 ], "bond": "single" } ], "click_ring_kekule_connectivity": [ { "atoms": [ 80, 81 ], "bond": "single", "description": "roof C23\u2013azide-derived triazole N1" }, { "atoms": [ 81, 82 ], "bond": "single" }, { "atoms": [ 82, 83 ], "bond": "double" }, { "atoms": [ 83, 88 ], "bond": "single" }, { "atoms": [ 88, 89 ], "bond": "double" }, { "atoms": [ 89, 81 ], "bond": "single" } ], "consumed_terminal_alkyne": "The precursor C7\u2261C8 triple bond is consumed; C7 map 88 and C8 map 89 are triazole ring atoms in the product." }, "representation_boundaries": { "roof_carboxyl_groups": "All three macrocycle carboxyl groups retain the neutral COOH form drawn in the source: map groups [52,53,54], [60,61,62], and [68,69,70]. This is a graph representation choice, not a physiological protonation assignment.", "lys_b29_cut": "Map 92 is the NZ endpoint, represented as NH2 to cap the isolated graph and satisfy valence. The LysB29 CE continuation and all other insulin atoms are outside this graph. The computed total-hydrogen formula therefore describes this capped graph and is not the hydrogen formula of the actual conjugate.", "stereochemistry": "No stereochemistry is introduced beyond the source graph; the product drawing does not define additional stereocentres at the B29 linker or triazole." } }, "conditional_carboxylate_state_scenario": { "declared_pH": 7.4, "protonation_assumption": "All three declared macrocycle carboxyl groups are fully deprotonated in this pH 7.4 modeling scenario; site-specific pKa evidence is not available in the source record.", "carboxylate_map_groups": [ { "carbon_map_id": 52, "oxygen_map_ids": [ 53, 54 ], "equivalent_edge_map_ids": [ [ 52, 53 ], [ 52, 54 ] ] }, { "carbon_map_id": 60, "oxygen_map_ids": [ 61, 62 ], "equivalent_edge_map_ids": [ [ 60, 61 ], [ 60, 62 ] ] }, { "carbon_map_id": 68, "oxygen_map_ids": [ 69, 70 ], "equivalent_edge_map_ids": [ [ 68, 69 ], [ 68, 70 ] ] } ], "neutral_reference": { "formula_with_lys_b29_nz_nh2_boundary_cap": "C62H72N16O14", "formal_charge_delta_reference": "neutral source fragment before the assumed three deprotonations" }, "conditional_fragment_delta": { "assumed_removed_protons": 3, "assumed_local_charge_delta": -3, "formula_with_lys_b29_nz_nh2_boundary_cap": "C62H69N16O14", "formula_derivation": "C62H72N16O14 minus three assumed acid protons gives C62H69N16O14.", "charge_scope": "The -3 value applies to the isolated NZ-NH2-capped B29 fragment; it is not the full conjugate charge." }, "graph_equivalence_rule": "For mapping equivalence only, the two C\u2013O edges in each declared carboxylate group share bond class carboxylate_resonance and numeric order 1.5. All other source bond labels are preserved.", "state_class_counts": { "active_open": 1, "inactive_closed": 1 }, "assumptions_and_limits": [ "pH 7.4 and full deprotonation are modeling assumptions, not measured site-specific pKa evidence.", "The normalization is a graph-equivalence representation, not a validated protonation calculation.", "No PDB oxygen atom names are assigned, and coordinates or distances do not select among mappings.", "No partial charges or force-field parameters are created or validated; complete-conjugate protonation and charge remain open." ] }, "source_roof_graph_precursor": { "graph_file": "structures/nnc2215-roof-propyl-azide.smi", "graph_sha256": "ed4340362d1436fc7518bfc577d6d23ac4b8434d3b60f40492b2bb36fd394325", "map_legend_file": "data/nnc2215-roof-macrocycle-atom-map.json", "map_legend_sha256": "48f716a63696d01f89339d0e6da009d9794ffd03e8349dc9a3fd471248e75ec8", "formula": "C56H63N15O12", "heavy_atom_count": 83, "heavy_element_counts": { "C": 56, "N": 15, "O": 12 }, "adjacency_edge_count": 89, "connected_component_count": 1, "cycle_rank_E_minus_V_plus_components": 7, "bond_label_preserving_automorphism_count": 2, "bond_label_preserving_automorphisms": [ { "1": 1, "2": 2, "3": 3, "4": 4, "5": 5, "6": 6, "7": 7, "8": 8, "9": 9, "10": 10, "11": 11, "12": 12, "13": 13, "14": 14, "15": 15, "16": 16, "17": 17, "18": 18, "19": 19, "20": 20, "21": 21, "22": 22, "23": 23, "24": 24, "25": 25, "26": 26, "27": 27, "28": 28, "29": 29, "30": 30, "31": 31, "32": 32, "33": 33, "34": 34, "35": 35, "36": 36, "37": 37, "38": 38, "39": 39, "40": 40, "41": 41, "42": 42, "43": 43, "44": 44, "45": 45, "46": 46, "47": 47, "48": 48, "49": 49, "50": 50, "51": 51, "52": 52, "53": 53, "54": 54, "55": 55, "56": 56, "57": 57, "58": 58, "59": 59, "60": 60, "61": 61, "62": 62, "63": 63, "64": 64, "65": 65, "66": 66, "67": 67, "68": 68, "69": 69, "70": 70, "71": 71, "72": 72, "73": 73, "74": 74, "75": 75, "76": 76, "77": 77, "78": 78, "79": 79, "80": 80, "81": 81, "82": 82, "83": 83 }, { "1": 1, "2": 6, "3": 5, "4": 4, "5": 3, "6": 2, "7": 7, "8": 12, "9": 11, "10": 10, "11": 9, "12": 8, "13": 25, "14": 26, "15": 27, "16": 28, "17": 29, "18": 30, "19": 19, "20": 20, "21": 21, "22": 22, "23": 23, "24": 24, "25": 13, "26": 14, "27": 15, "28": 16, "29": 17, "30": 18, "31": 31, "32": 32, "33": 35, "34": 36, "35": 33, "36": 34, "37": 47, "38": 48, "39": 49, "40": 50, "41": 51, "42": 42, "43": 43, "44": 44, "45": 45, "46": 46, "47": 37, "48": 38, "49": 39, "50": 40, "51": 41, "52": 68, "53": 69, "54": 70, "55": 71, "56": 72, "57": 73, "58": 74, "59": 75, "60": 60, "61": 61, "62": 62, "63": 63, "64": 64, "65": 65, "66": 66, "67": 67, "68": 52, "69": 53, "70": 54, "71": 55, "72": 56, "73": 57, "74": 58, "75": 59, "76": 77, "77": 76, "78": 78, "79": 79, "80": 80, "81": 81, "82": 82, "83": 83 } ], "interpretation": "The two source roof automorphisms are a precursor symmetry result; the complete clicked product is audited separately." }, "geometry_screen_method": { "purpose": "Conservative broad plausibility screen for mapped heavy-heavy coordinate distances.", "basis": { "citation": "B. Cordero et al., Covalent radii revisited, Dalton Trans. 2008, 2832-2838, DOI: 10.1039/B801115J.", "doi_url": "https://doi.org/10.1039/B801115J", "reported_covalent_radii_angstrom_used": { "C": 0.76, "N": 0.71, "O": 0.66 }, "values_are_rounded_from_reported_reference_radii": true }, "heuristic_bond_class_offsets_from_radii_sum_angstrom": { "single": [ -0.18, 0.25 ], "double": [ -0.35, -0.06 ], "triple": [ -0.45, -0.18 ], "aromatic": [ -0.2, 0.05 ] }, "interval_definition": "For each source bond class, add the tabulated low and high heuristic offsets to the sum of the two element covalent radii.", "custom_offsets_are_heuristic_not_supplied_by_cordero_paper": true, "interpretation_limits": [ "These numeric intervals are a conservative geometry screen, not bond-order evidence.", "Distances are not used to select, rank, or reject graph mappings.", "All mapped edges are retained, including those outside the screen.", "The PDB adjacency records do not encode bond order, charge, or stereochemistry." ] }, "states": [ { "state": "active_open", "coordinate_candidate_file": "structures/nnc2215-open-source-corrected-candidate.pdb", "coordinate_candidate_sha256_expected_by_reconciliation": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "coordinate_candidate_sha256_before_audit": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "coordinate_candidate_sha256_after_audit": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "coordinate_candidate_unchanged_during_audit": true, "source_pdb_file_before_reconciliation": "structures/nnc2215-open-model.pdb", "source_pdb_sha256_before_reconciliation": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "selected_target_scope": { "heavy_atoms": "all heavy atoms from LYX B30 and MC C1 plus exactly LYS B29 NZ", "lys_b29_nz_selection": "chain B, residue 29, insertion code blank, residue LYS, atom NZ; exactly one match required", "excluded_atoms": "LYS B29 CE and every other atom outside LYX B30, MC C1, and the single selected NZ are excluded", "hydrogen_and_deuterium_excluded_from_graph": true, "selected_node_induction": "Only CONECT/LINK edges whose two endpoints are selected nodes enter the target graph." }, "target_inventory": { "selected_atom_count": 92, "selected_heavy_element_counts": { "C": 62, "N": 16, "O": 14 }, "selected_residue_element_inventory": { "B:29:LYS:N": 1, "B:30:LYX:C": 8, "B:30:LYX:N": 3, "B:30:LYX:O": 2, "C:1:MC:C": 54, "C:1:MC:N": 12, "C:1:MC:O": 12 }, "selected_connected_component_count": 1, "selected_adjacency_edge_count": 99, "selected_cycle_rank_E_minus_V_plus_components": 8, "excluded_b29_nz_boundary_edges": [ { "selected_atom": { "serial": 480, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue": "LYS", "altloc": "", "name": "NZ", "element": "N" }, "outside_scope_atom": { "serial": 479, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue": "LYS", "altloc": "", "name": "CE", "element": "C" }, "adjacency_sources": [ "CONECT" ] }, { "selected_atom": { "serial": 480, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue": "LYS", "altloc": "", "name": "NZ", "element": "N" }, "outside_scope_atom": { "serial": 492, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue": "LYS", "altloc": "", "name": "HZ2", "element": "H" }, "adjacency_sources": [ "CONECT" ] } ] }, "roof_only_preliminary_result": { "source_roof_graph": { "heavy_atom_count": 83, "heavy_element_counts": { "C": 56, "N": 15, "O": 12 }, "adjacency_edge_count": 89, "connected_component_count": 1, "cycle_rank_E_minus_V_plus_components": 7 }, "candidate_anchor_embedding": { "fixed_candidate_anchors_by_map_id": { "78": { "map_id": 78, "source_anchor_key": "source_macrocycle_c21_candidate", "candidate_source_model_serial": 861, "candidate_coordinate_atom": { "serial": 862, "record_type": 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"60": 869, "61": 907, "62": 871, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 870, "69": 872, "70": 908, "71": 835, "72": 879, "73": 885, "74": 882, "75": 876, "76": 859, "77": 861, "78": 862, "79": 502, "80": 501, "81": 496, "82": 495, "83": 494 } }, { "embedding_id": "roof_embedding_16", "map_id_to_pdb_serial": { "1": 896, "2": 897, "3": 898, "4": 899, "5": 900, "6": 895, "7": 902, "8": 903, "9": 904, "10": 905, "11": 906, "12": 901, "13": 846, "14": 848, "15": 838, "16": 840, "17": 842, "18": 844, "19": 856, "20": 857, "21": 852, "22": 853, "23": 854, "24": 855, "25": 847, "26": 849, "27": 839, "28": 841, "29": 843, "30": 845, "31": 865, "32": 866, "33": 863, "34": 864, "35": 867, "36": 868, "37": 873, "38": 889, "39": 886, "40": 892, "41": 836, "42": 832, "43": 890, "44": 887, "45": 893, "46": 851, "47": 874, "48": 891, "49": 888, "50": 894, "51": 837, "52": 909, "53": 911, "54": 910, "55": 834, "56": 877, "57": 883, "58": 880, "59": 875, "60": 869, "61": 907, "62": 871, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 870, "69": 908, "70": 872, "71": 835, "72": 879, "73": 885, "74": 882, "75": 876, "76": 859, "77": 861, "78": 862, "79": 502, "80": 501, "81": 496, "82": 495, "83": 494 } } ], "search_scope": "Element-labeled, edge-preserving subgraph monomorphism; extra target edges are allowed. This is a precursor check, not a complete-product assignment." }, "expected_anchored_embeddings": 16, "prior_roof_audit_anchored_embedding_count": 16, "matches_prior_roof_audit_count": true, "preliminary_only": true, "interpretation": "The anchored roof-only embeddings reproduce the precursor search. They are not complete-product assignments." }, "resolved_pdb_link_records": [ { "record": "LINK C31 MC C 1 CD6 LYX B 30 1555 1555 1.56", "first_endpoint": { "name": "C31", "altloc": "", "residue": "MC", "chain": "C", "residue_number": "1", "insertion_code": "" }, "second_endpoint": { "name": "CD6", "altloc": "", "residue": "LYX", "chain": "B", "residue_number": "30", "insertion_code": "" }, "resolved_serials": [ 862, 502 ], "edge_pair": [ 502, 862 ] }, { "record": "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.38", "first_endpoint": { "name": "CD1", "altloc": "", "residue": "LYX", "chain": "B", "residue_number": "30", "insertion_code": "" }, "second_endpoint": { "name": "NZ", "altloc": "", "residue": "LYS", "chain": "B", "residue_number": "29", "insertion_code": "" }, "resolved_serials": [ 497, 480 ], "edge_pair": [ 480, 497 ] }, { "record": "LINK N PHE B 1 C2 PHX B 0 1555 1555 1.34", "first_endpoint": { "name": "N", "altloc": "", "residue": "PHE", "chain": "B", "residue_number": "1", "insertion_code": "" }, "second_endpoint": { "name": "C2", "altloc": "", "residue": "PHX", "chain": "B", "residue_number": "0", "insertion_code": "" }, "resolved_serials": [ 37, 3 ], "edge_pair": [ 3, 37 ] } ], "pdb_adjacency_record_statistics": { "raw_directed_conect_reference_count": 546, "unique_directed_conect_reference_count": 546, "directional_or_reciprocal_conect_reference_duplicates_collapsed": 0, "unique_undirected_conect_edge_count": 273, "conect_link_overlapping_undirected_edge_count_deduplicated": 3, "resolved_link_record_count": 3, "link_endpoints_require_unique_full_identity_match": true, "full_link_identity_fields": [ "chain", "residue_number", "insertion_code", "residue", "altloc", "atom_name" ], "reciprocal_conect_and_conect_link_overlap_deduplicated": true, "selected_graph_edges_include_link_only_edges": true }, "complete_product_exact_graph_comparison": { "comparison_type": "Exact element-labeled graph isomorphism; no extra target nodes or edges and no monomorphism.", "source_node_count": 92, "source_edge_count": 99, "source_connected_component_count": 1, "source_cycle_rank_E_minus_V_plus_components": 8, "target_node_count": 92, "target_edge_count": 99, "target_connected_component_count": 1, "target_cycle_rank_E_minus_V_plus_components": 8, "source_and_target_node_counts_equal": true, "source_and_target_edge_counts_equal": true, "source_and_target_component_counts_equal": true, "source_and_target_cycle_ranks_equal": true, "source_and_target_element_counts_equal": true, "exact_element_labeled_graph_isomorphism_found": true, "exact_mapping_count": 16, "expected_feasibility_review_mapping_count": 16, "matches_independent_feasibility_review_count": true, "every_exact_mapping_uses_all_target_nodes": true, "unmatched_target_atoms": [], "unmatched_target_edges_after_representative_mapping": [], "unmapped_source_map_ids_when_no_exact_isomorphism": [], "unmapped_source_edges_when_no_exact_isomorphism": [], "full_source_bond_label_preserving_automorphism_count": 2, "full_source_bond_label_preserving_automorphisms": [ { "1": 1, "2": 2, "3": 3, "4": 4, "5": 5, "6": 6, "7": 7, "8": 8, "9": 9, "10": 10, "11": 11, "12": 12, "13": 13, "14": 14, "15": 15, "16": 16, "17": 17, "18": 18, "19": 19, "20": 20, "21": 21, "22": 22, "23": 23, "24": 24, "25": 25, "26": 26, "27": 27, "28": 28, "29": 29, "30": 30, "31": 31, "32": 32, "33": 33, "34": 34, "35": 35, "36": 36, "37": 37, "38": 38, "39": 39, "40": 40, "41": 41, "42": 42, "43": 43, "44": 44, "45": 45, "46": 46, "47": 47, "48": 48, "49": 49, "50": 50, "51": 51, "52": 52, "53": 53, "54": 54, "55": 55, "56": 56, "57": 57, "58": 58, "59": 59, "60": 60, "61": 61, "62": 62, "63": 63, "64": 64, "65": 65, "66": 66, "67": 67, "68": 68, "69": 69, "70": 70, "71": 71, "72": 72, "73": 73, "74": 74, "75": 75, "76": 76, "77": 77, "78": 78, "79": 79, "80": 80, "81": 81, "82": 82, "83": 83, "84": 84, "85": 85, "86": 86, "87": 87, "88": 88, "89": 89, "90": 90, "91": 91, "92": 92 }, { "1": 1, "2": 6, "3": 5, "4": 4, "5": 3, "6": 2, "7": 7, "8": 12, "9": 11, "10": 10, "11": 9, "12": 8, "13": 25, "14": 26, "15": 27, "16": 28, "17": 29, "18": 30, "19": 19, "20": 20, "21": 21, "22": 22, "23": 23, "24": 24, "25": 13, "26": 14, "27": 15, "28": 16, "29": 17, "30": 18, "31": 31, "32": 32, "33": 35, "34": 36, "35": 33, "36": 34, "37": 47, "38": 48, "39": 49, "40": 50, "41": 51, "42": 42, "43": 43, "44": 44, "45": 45, "46": 46, "47": 37, "48": 38, "49": 39, "50": 40, "51": 41, "52": 68, "53": 69, "54": 70, "55": 71, "56": 72, "57": 73, "58": 74, "59": 75, "60": 60, "61": 61, "62": 62, "63": 63, "64": 64, "65": 65, "66": 66, "67": 67, "68": 52, "69": 53, "70": 54, "71": 55, "72": 56, "73": 57, "74": 58, "75": 59, "76": 77, "77": 76, "78": 78, "79": 79, "80": 80, "81": 81, "82": 82, "83": 83, "84": 84, "85": 85, "86": 86, "87": 87, "88": 88, "89": 89, "90": 90, "91": 91, "92": 92 } ], "symmetry_equivalence_rule": "Two exact source-to-PDB mappings share a class when composing one with an element- and source bond-label-preserving automorphism of the complete source graph yields the other.", "symmetry_classes": [ { "symmetry_class_id": "source_bond_label_class_01", "embedding_ids": [ "exact_mapping_01", "exact_mapping_09" ], "embedding_count": 2, "representative_embedding_id": "exact_mapping_01", "representative_map_id_to_pdb_serial": { "1": 896, "2": 895, "3": 900, "4": 899, "5": 898, "6": 897, "7": 902, "8": 901, "9": 906, "10": 905, "11": 904, "12": 903, "13": 847, "14": 849, "15": 839, "16": 841, "17": 843, "18": 845, "19": 856, "20": 857, "21": 852, "22": 853, "23": 854, "24": 855, "25": 846, "26": 848, "27": 838, "28": 840, "29": 842, "30": 844, "31": 865, "32": 866, "33": 867, "34": 868, "35": 863, "36": 864, "37": 874, "38": 891, "39": 888, "40": 894, "41": 837, "42": 832, "43": 890, "44": 887, "45": 893, "46": 851, "47": 873, "48": 889, "49": 886, "50": 892, "51": 836, "52": 870, "53": 872, "54": 908, "55": 835, "56": 879, "57": 885, "58": 882, "59": 876, "60": 869, "61": 871, "62": 907, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 909, "69": 910, "70": 911, "71": 834, "72": 877, "73": 883, "74": 880, "75": 875, "76": 861, "77": 859, "78": 862, "79": 502, "80": 501, "81": 496, "82": 495, "83": 494, "84": 497, "85": 498, "86": 505, "87": 506, "88": 499, "89": 500, "90": 503, "91": 504, "92": 480 }, "class_signature_serials": [ 896, 895, 900, 899, 898, 897, 902, 901, 906, 905, 904, 903, 847, 849, 839, 841, 843, 845, 856, 857, 852, 853, 854, 855, 846, 848, 838, 840, 842, 844, 865, 866, 867, 868, 863, 864, 874, 891, 888, 894, 837, 832, 890, 887, 893, 851, 873, 889, 886, 892, 836, 870, 872, 908, 835, 879, 885, 882, 876, 869, 871, 907, 850, 878, 884, 881, 833, 909, 910, 911, 834, 877, 883, 880, 875, 861, 859, 862, 502, 501, 496, 495, 494, 497, 498, 505, 506, 499, 500, 503, 504, 480 ] }, { "symmetry_class_id": "source_bond_label_class_02", "embedding_ids": [ "exact_mapping_02", "exact_mapping_13" ], "embedding_count": 2, "representative_embedding_id": "exact_mapping_02", "representative_map_id_to_pdb_serial": { "1": 896, "2": 895, "3": 900, "4": 899, "5": 898, "6": 897, "7": 902, "8": 901, "9": 906, "10": 905, "11": 904, "12": 903, "13": 847, "14": 849, "15": 839, "16": 841, "17": 843, "18": 845, "19": 856, "20": 857, "21": 852, "22": 853, "23": 854, "24": 855, "25": 846, "26": 848, "27": 838, "28": 840, "29": 842, "30": 844, "31": 865, "32": 866, "33": 867, "34": 868, "35": 863, "36": 864, "37": 874, "38": 891, "39": 888, "40": 894, "41": 837, "42": 832, "43": 890, "44": 887, "45": 893, "46": 851, "47": 873, "48": 889, "49": 886, "50": 892, "51": 836, "52": 870, "53": 872, "54": 908, "55": 835, "56": 879, "57": 885, "58": 882, "59": 876, "60": 869, "61": 871, "62": 907, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 909, "69": 911, "70": 910, "71": 834, "72": 877, "73": 883, "74": 880, "75": 875, "76": 861, "77": 859, "78": 862, "79": 502, "80": 501, "81": 496, 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exact graph mapping has been enumerated. PDB adjacency does not carry bond order, charge, or stereochemistry." }, "conditional_carboxylate_resonance_normalized_comparison": { "comparison_type": "Separate graph-equivalence analysis for the declared fully deprotonated tri-carboxylate scenario.", "normalized_graph": { "heavy_atom_count": 92, "adjacency_edge_count": 99, "normalized_carboxylate_groups": [ { "carbon_map_id": 52, "oxygen_map_ids": [ 53, 54 ], "equivalent_edge_map_ids": [ [ 52, 53 ], [ 52, 54 ] ] }, { "carbon_map_id": 60, "oxygen_map_ids": [ 61, 62 ], "equivalent_edge_map_ids": [ [ 60, 61 ], [ 60, 62 ] ] }, { "carbon_map_id": 68, "oxygen_map_ids": [ 69, 70 ], "equivalent_edge_map_ids": [ [ 68, 69 ], [ 68, 70 ] ] } ], "normalization_rule": "Only the six declared C\u2013O edges are assigned shared carboxylate_resonance labels with numeric bond order 1.5; every other source edge label remains unchanged." }, "exact_mapping_count": 16, "exact_mappings": [ { "mapping_id": "exact_mapping_01", "map_id_to_pdb_serial": { "1": 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{ "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 505 ] }, "87": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 506 ] }, "88": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 499 ] }, "89": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 500 ] }, "90": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 503 ] }, "91": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 504 ] }, "92": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 480 ] } }, "interpretation_limits": [ "This graph normalization represents equivalence of the two C\u2013O edges in each assumed carboxylate; it does not assign PDB oxygen names.", "The exact coordinate mappings are reused without ranking or selection by coordinates or distances.", "The normalized graph is not a pKa or protonation validation and does not establish partial charges or force-field parameters." ] }, "candidate_linker_tail_anchor_consistency": { "all_tail_azide_anchor_maps_consistent": true, "by_map_id": { "78": { "candidate_coordinate_serial": 862, "exact_mapping_candidate_serials": [ 862 ], "unique_and_consistent": true }, "79": { "candidate_coordinate_serial": 502, "exact_mapping_candidate_serials": [ 502 ], "unique_and_consistent": true }, "80": { "candidate_coordinate_serial": 501, "exact_mapping_candidate_serials": [ 501 ], "unique_and_consistent": true }, "81": { "candidate_coordinate_serial": 496, "exact_mapping_candidate_serials": [ 496 ], "unique_and_consistent": true }, "82": { "candidate_coordinate_serial": 495, "exact_mapping_candidate_serials": [ 495 ], "unique_and_consistent": true }, "83": { "candidate_coordinate_serial": 494, "exact_mapping_candidate_serials": [ 494 ], "unique_and_consistent": true } } }, "candidate_coordinate_aliases_and_name_collisions": { "state_specific_map_id_aliases": { "79": { "source_label": "roof tail C22", "expected_state_specific_pdb_name": "CD6", "observed_target_atom": { "serial": 502, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "CD6", "element": "C" }, "unique_and_as_expected": true }, "90": { "source_label": "linker carbonyl oxygen", "expected_state_specific_pdb_name": "OD", "observed_target_atom": { "serial": 503, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "OD", "element": "O" }, "unique_and_as_expected": true } }, "same_name_collisions_in_selected_graph_resolved_by_full_identity_and_serial": { "C1": [ { "serial": 505, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C1", "element": "C" }, { "serial": 832, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C1", "element": "C" } ], "C2": [ { "serial": 506, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C2", "element": "C" }, { "serial": 833, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C2", "element": "C" } ] }, "lyx_c1_and_mc_c1_are_distinguished_by_chain_and_residue": [ { "serial": 505, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C1", "element": "C" }, { "serial": 832, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C1", "element": "C" } ] }, "hydrogen_neighbor_connectivity_from_conect": { "data_location": 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"cycle_rank_E_minus_V_plus_components": 7 }, "candidate_anchor_embedding": { "fixed_candidate_anchors_by_map_id": { "78": { "map_id": 78, "source_anchor_key": "source_macrocycle_c21_candidate", "candidate_source_model_serial": 862, "candidate_coordinate_atom": { "serial": 862, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C31", "element": "C" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "roof tail C21" }, "79": { "map_id": 79, "source_anchor_key": "source_macrocycle_c22_candidate", "candidate_source_model_serial": 817, "candidate_coordinate_atom": { "serial": 817, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C", "element": "C" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "roof tail C22" }, "80": { "map_id": 80, "source_anchor_key": "source_macrocycle_c23_candidate", "candidate_source_model_serial": 816, "candidate_coordinate_atom": { "serial": 816, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "CD5", "element": "C" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "roof tail C23" }, "81": { "map_id": 81, "source_anchor_key": "source_azide_n_attached_to_c23_candidate", "candidate_source_model_serial": 811, "candidate_coordinate_atom": { "serial": 811, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "ND3", "element": "N" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "azide-derived triazole N1 attached to C23" }, "82": { "map_id": 82, "source_anchor_key": "source_triazole_n2_candidate", "candidate_source_model_serial": 810, "candidate_coordinate_atom": { "serial": 810, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "ND2", "element": "N" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "triazole N2" }, "83": { "map_id": 83, "source_anchor_key": "source_triazole_n1_candidate", "candidate_source_model_serial": 809, "candidate_coordinate_atom": { "serial": 809, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "ND1", "element": "N" }, "resolution_rule": "Full chain/residue/insertion/altloc/atom-name/element identity; unique match required.", "source_graph_label": "triazole N3" } }, "anchored_embedding_count": 16, "embeddings": [ { "embedding_id": 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"31": 865, "32": 866, "33": 863, "34": 864, "35": 867, "36": 868, "37": 873, "38": 889, "39": 886, "40": 892, "41": 836, "42": 832, "43": 890, "44": 887, "45": 893, "46": 851, "47": 874, "48": 891, "49": 888, "50": 894, "51": 837, "52": 909, "53": 911, "54": 910, "55": 834, "56": 877, "57": 883, "58": 880, "59": 875, "60": 869, "61": 907, "62": 871, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 870, "69": 872, "70": 908, "71": 835, "72": 879, "73": 885, "74": 882, "75": 876, "76": 859, "77": 861, "78": 862, "79": 817, "80": 816, "81": 811, "82": 810, "83": 809 } }, { "embedding_id": "roof_embedding_16", "map_id_to_pdb_serial": { "1": 896, "2": 897, "3": 898, "4": 899, "5": 900, "6": 895, "7": 902, "8": 903, "9": 904, "10": 905, "11": 906, "12": 901, "13": 846, "14": 848, "15": 838, "16": 840, "17": 842, "18": 844, "19": 856, "20": 857, "21": 852, "22": 853, "23": 854, "24": 855, "25": 847, "26": 849, "27": 839, "28": 841, "29": 843, "30": 845, "31": 865, "32": 866, "33": 863, "34": 864, "35": 867, "36": 868, "37": 873, "38": 889, "39": 886, "40": 892, "41": 836, "42": 832, "43": 890, "44": 887, "45": 893, "46": 851, "47": 874, "48": 891, "49": 888, "50": 894, "51": 837, "52": 909, "53": 911, "54": 910, "55": 834, "56": 877, "57": 883, "58": 880, "59": 875, "60": 869, "61": 907, "62": 871, "63": 850, "64": 878, "65": 884, "66": 881, "67": 833, "68": 870, "69": 908, "70": 872, "71": 835, "72": 879, "73": 885, "74": 882, "75": 876, "76": 859, "77": 861, "78": 862, "79": 817, "80": 816, "81": 811, "82": 810, "83": 809 } } ], "search_scope": "Element-labeled, edge-preserving subgraph monomorphism; extra target edges are allowed. This is a precursor check, not a complete-product assignment." }, "expected_anchored_embeddings": 16, "prior_roof_audit_anchored_embedding_count": 16, "matches_prior_roof_audit_count": true, "preliminary_only": true, "interpretation": "The anchored roof-only embeddings reproduce the precursor search. They are not complete-product assignments." }, "resolved_pdb_link_records": [ { "record": "LINK C31 MC C 1 C LYX B 30 1555 1555 1.55", "first_endpoint": { "name": "C31", "altloc": "", "residue": "MC", "chain": "C", "residue_number": "1", "insertion_code": "" }, "second_endpoint": { "name": "C", "altloc": "", "residue": "LYX", "chain": "B", "residue_number": "30", "insertion_code": "" }, "resolved_serials": [ 862, 817 ], "edge_pair": [ 817, 862 ] }, { "record": "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.37", "first_endpoint": { "name": "CD1", "altloc": "", "residue": "LYX", "chain": "B", "residue_number": "30", "insertion_code": "" }, "second_endpoint": { "name": "NZ", "altloc": "", "residue": "LYS", "chain": "B", "residue_number": "29", "insertion_code": "" }, "resolved_serials": [ 812, 794 ], "edge_pair": [ 794, 812 ] }, { "record": "LINK N PHE B 1 C2 PHX B 0 1555 1555 1.35", "first_endpoint": { "name": "N", "altloc": "", "residue": "PHE", "chain": "B", "residue_number": "1", "insertion_code": "" }, "second_endpoint": { "name": "C2", "altloc": "", "residue": "PHX", "chain": "B", "residue_number": "0", "insertion_code": "" }, "resolved_serials": [ 351, 316 ], "edge_pair": [ 316, 351 ] } ], "pdb_adjacency_record_statistics": { "raw_directed_conect_reference_count": 464, "unique_directed_conect_reference_count": 464, "directional_or_reciprocal_conect_reference_duplicates_collapsed": 0, "unique_undirected_conect_edge_count": 232, "conect_link_overlapping_undirected_edge_count_deduplicated": 3, "resolved_link_record_count": 3, "link_endpoints_require_unique_full_identity_match": true, "full_link_identity_fields": [ "chain", "residue_number", "insertion_code", "residue", "altloc", "atom_name" ], "reciprocal_conect_and_conect_link_overlap_deduplicated": true, "selected_graph_edges_include_link_only_edges": true }, "complete_product_exact_graph_comparison": { "comparison_type": "Exact element-labeled graph isomorphism; no extra target nodes or edges and no monomorphism.", "source_node_count": 92, "source_edge_count": 99, "source_connected_component_count": 1, "source_cycle_rank_E_minus_V_plus_components": 8, "target_node_count": 92, "target_edge_count": 99, "target_connected_component_count": 1, "target_cycle_rank_E_minus_V_plus_components": 8, "source_and_target_node_counts_equal": true, "source_and_target_edge_counts_equal": true, "source_and_target_component_counts_equal": true, "source_and_target_cycle_ranks_equal": true, "source_and_target_element_counts_equal": true, "exact_element_labeled_graph_isomorphism_found": true, "exact_mapping_count": 16, "expected_feasibility_review_mapping_count": 16, "matches_independent_feasibility_review_count": true, "every_exact_mapping_uses_all_target_nodes": true, "unmatched_target_atoms": [], "unmatched_target_edges_after_representative_mapping": [], "unmapped_source_map_ids_when_no_exact_isomorphism": [], "unmapped_source_edges_when_no_exact_isomorphism": [], "full_source_bond_label_preserving_automorphism_count": 2, "full_source_bond_label_preserving_automorphisms": [ { "1": 1, "2": 2, "3": 3, "4": 4, "5": 5, "6": 6, "7": 7, "8": 8, "9": 9, "10": 10, "11": 11, "12": 12, "13": 13, "14": 14, "15": 15, "16": 16, "17": 17, "18": 18, "19": 19, "20": 20, "21": 21, "22": 22, "23": 23, "24": 24, "25": 25, "26": 26, "27": 27, "28": 28, "29": 29, "30": 30, "31": 31, "32": 32, "33": 33, "34": 34, "35": 35, "36": 36, "37": 37, "38": 38, "39": 39, "40": 40, "41": 41, "42": 42, "43": 43, "44": 44, "45": 45, "46": 46, "47": 47, "48": 48, "49": 49, "50": 50, "51": 51, "52": 52, "53": 53, "54": 54, "55": 55, "56": 56, "57": 57, "58": 58, "59": 59, "60": 60, "61": 61, "62": 62, "63": 63, "64": 64, "65": 65, "66": 66, "67": 67, "68": 68, "69": 69, "70": 70, "71": 71, "72": 72, "73": 73, "74": 74, "75": 75, "76": 76, "77": 77, "78": 78, "79": 79, "80": 80, "81": 81, "82": 82, "83": 83, "84": 84, "85": 85, "86": 86, "87": 87, "88": 88, "89": 89, "90": 90, 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PDB adjacency does not carry bond order, charge, or stereochemistry." }, "conditional_carboxylate_resonance_normalized_comparison": { "comparison_type": "Separate graph-equivalence analysis for the declared fully deprotonated tri-carboxylate scenario.", "normalized_graph": { "heavy_atom_count": 92, "adjacency_edge_count": 99, "normalized_carboxylate_groups": [ { "carbon_map_id": 52, "oxygen_map_ids": [ 53, 54 ], "equivalent_edge_map_ids": [ [ 52, 53 ], [ 52, 54 ] ] }, { "carbon_map_id": 60, "oxygen_map_ids": [ 61, 62 ], "equivalent_edge_map_ids": [ [ 60, 61 ], [ 60, 62 ] ] }, { "carbon_map_id": 68, "oxygen_map_ids": [ 69, 70 ], "equivalent_edge_map_ids": [ [ 68, 69 ], [ 68, 70 ] ] } ], "normalization_rule": "Only the six declared C\u2013O edges are assigned shared carboxylate_resonance labels with numeric bond order 1.5; every other source edge label remains unchanged." }, "exact_mapping_count": 16, "exact_mappings": [ { "mapping_id": "exact_mapping_01", "map_id_to_pdb_serial": { "1": 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{ "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 820 ] }, "87": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 821 ] }, "88": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 814 ] }, "89": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 815 ] }, "90": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 818 ] }, "91": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 819 ] }, "92": { "candidate_count": 1, "unique_across_all_exact_mappings": true, "candidate_pdb_serials": [ 794 ] } }, "interpretation_limits": [ "This graph normalization represents equivalence of the two C\u2013O edges in each assumed carboxylate; it does not assign PDB oxygen names.", "The exact coordinate mappings are reused without ranking or selection by coordinates or distances.", "The normalized graph is not a pKa or protonation validation and does not establish partial charges or force-field parameters." ] }, "candidate_linker_tail_anchor_consistency": { "all_tail_azide_anchor_maps_consistent": true, "by_map_id": { "78": { "candidate_coordinate_serial": 862, "exact_mapping_candidate_serials": [ 862 ], "unique_and_consistent": true }, "79": { "candidate_coordinate_serial": 817, "exact_mapping_candidate_serials": [ 817 ], "unique_and_consistent": true }, "80": { "candidate_coordinate_serial": 816, "exact_mapping_candidate_serials": [ 816 ], "unique_and_consistent": true }, "81": { "candidate_coordinate_serial": 811, "exact_mapping_candidate_serials": [ 811 ], "unique_and_consistent": true }, "82": { "candidate_coordinate_serial": 810, "exact_mapping_candidate_serials": [ 810 ], "unique_and_consistent": true }, "83": { "candidate_coordinate_serial": 809, "exact_mapping_candidate_serials": [ 809 ], "unique_and_consistent": true } } }, "candidate_coordinate_aliases_and_name_collisions": { "state_specific_map_id_aliases": { "79": { "source_label": "roof tail C22", "expected_state_specific_pdb_name": "C", "observed_target_atom": { "serial": 817, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C", "element": "C" }, "unique_and_as_expected": true }, "90": { "source_label": "linker carbonyl oxygen", "expected_state_specific_pdb_name": "O", "observed_target_atom": { "serial": 818, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "O", "element": "O" }, "unique_and_as_expected": true } }, "same_name_collisions_in_selected_graph_resolved_by_full_identity_and_serial": { "C1": [ { "serial": 820, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C1", "element": "C" }, { "serial": 832, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C1", "element": "C" } ], "C2": [ { "serial": 821, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C2", "element": "C" }, { "serial": 833, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C2", "element": "C" } ] }, "lyx_c1_and_mc_c1_are_distinguished_by_chain_and_residue": [ { "serial": 820, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue": "LYX", "altloc": "", "name": "C1", "element": "C" }, { "serial": 832, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue": "MC", "altloc": "", "name": "C1", "element": "C" } ] }, "hydrogen_neighbor_connectivity_from_conect": { "data_location": "complete_product_exact_graph_comparison.target_atom_inventory_by_pdb_serial[*].hydrogen_neighbors_from_conect", "hydrogen_edges_source": "CONECT records only", "hydrogen_names_are_model_records_not_validated_chemistry": true }, "input_pdb_bytes_unchanged": true } ], "open_closed_hydrogen_neighbor_comparison": { "source": "PDB CONECT records only; hydrogen names/counts are not treated as chemically validated.", "by_map_id": { "78": { "source_map_id": 78, "source_label": "roof C21", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 862, "parent_pdb_atom": { "chain": "C", "residue_number": "1", "residue": "MC", "altloc": "", "name": "C31" }, "hydrogen_neighbor": { "serial": 912, "name": "H1", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 862, "parent_pdb_atom": { "chain": "C", "residue_number": "1", "residue": "MC", "altloc": "", "name": "C31" }, "hydrogen_neighbor": { "serial": 913, "name": "H2", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 862, "parent_pdb_atom": { "chain": "C", "residue_number": "1", "residue": "MC", "altloc": "", "name": "C31" }, "hydrogen_neighbor": { "serial": 912, "name": "H1", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 862, "parent_pdb_atom": { "chain": "C", "residue_number": "1", "residue": "MC", "altloc": "", "name": "C31" }, "hydrogen_neighbor": { "serial": 913, "name": "H2", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "H1", "H2" ], "inactive_closed": [ "H1", "H2" ] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "79": { "source_map_id": 79, "source_label": "roof C22", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 502, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD6" }, "hydrogen_neighbor": { "serial": 517, "name": "HX22", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 502, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD6" }, "hydrogen_neighbor": { "serial": 516, "name": "HX31", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 817, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C" }, "hydrogen_neighbor": { "serial": 823, "name": "HCB", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 817, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C" }, "hydrogen_neighbor": { "serial": 824, "name": "HCC", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "HX22", "HX31" ], "inactive_closed": [ "HCB", "HCC" ] }, "observed_relation": "different", "expected_relation": "different", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "80": { "source_map_id": 80, "source_label": "roof C23", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 501, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD5" }, "hydrogen_neighbor": { "serial": 508, "name": "HC2", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 501, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD5" }, "hydrogen_neighbor": { "serial": 509, "name": "HC3", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 816, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD5" }, "hydrogen_neighbor": { "serial": 822, "name": "HCA", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 816, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD5" }, "hydrogen_neighbor": { "serial": 825, "name": "HCD", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "HC2", "HC3" ], "inactive_closed": [ "HCA", "HCD" ] }, "observed_relation": "different", "expected_relation": "different", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "81": { "source_map_id": 81, "source_label": "triazole N1", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [], "inactive_closed": [] }, "hydrogen_neighbor_names_by_state": { "active_open": [], "inactive_closed": [] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "82": { "source_map_id": 82, "source_label": "triazole N2", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [], "inactive_closed": [] }, "hydrogen_neighbor_names_by_state": { "active_open": [], "inactive_closed": [] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "83": { "source_map_id": 83, "source_label": "triazole N3", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [], "inactive_closed": [] }, "hydrogen_neighbor_names_by_state": { "active_open": [], "inactive_closed": [] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "85": { "source_map_id": 85, "source_label": "linker C4", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 498, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD2" }, "hydrogen_neighbor": { "serial": 507, "name": "HC1", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 498, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD2" }, "hydrogen_neighbor": { "serial": 510, "name": "HXTA", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 813, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD2" }, "hydrogen_neighbor": { "serial": 826, "name": "HXTA", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "HC1", "HXTA" ], "inactive_closed": [ "HXTA" ] }, "observed_relation": "different", "expected_relation": "different", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "86": { "source_map_id": 86, "source_label": "linker C5", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 505, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C1" }, "hydrogen_neighbor": { "serial": 511, "name": "H1", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 505, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C1" }, "hydrogen_neighbor": { "serial": 512, "name": "H2A", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 820, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C1" }, "hydrogen_neighbor": { "serial": 827, "name": "H1", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 820, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C1" }, "hydrogen_neighbor": { "serial": 828, "name": "H2", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "H1", "H2A" ], "inactive_closed": [ "H1", "H2" ] }, "observed_relation": "different", "expected_relation": "different", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "87": { "source_map_id": 87, "source_label": "linker C6", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 506, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C2" }, "hydrogen_neighbor": { "serial": 514, "name": "H2B", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 506, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C2" }, "hydrogen_neighbor": { "serial": 513, "name": "H3", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 821, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C2" }, "hydrogen_neighbor": { "serial": 829, "name": "HD3", "element": "H", "connectivity_source": "CONECT" } }, { "parent_pdb_serial": 821, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "C2" }, "hydrogen_neighbor": { "serial": 830, "name": "HD4", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "H2B", "H3" ], "inactive_closed": [ "HD3", "HD4" ] }, "observed_relation": "different", "expected_relation": "different", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "88": { "source_map_id": 88, "source_label": "linker C7 / triazole C4", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [], "inactive_closed": [] }, "hydrogen_neighbor_names_by_state": { "active_open": [], "inactive_closed": [] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "89": { "source_map_id": 89, "source_label": "linker C8 / triazole C5", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 500, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD4" }, "hydrogen_neighbor": { "serial": 515, "name": "HXTB", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 815, "parent_pdb_atom": { "chain": "B", "residue_number": "30", "residue": "LYX", "altloc": "", "name": "CD4" }, "hydrogen_neighbor": { "serial": 831, "name": "HXTB", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "HXTB" ], "inactive_closed": [ "HXTB" ] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true }, "92": { "source_map_id": 92, "source_label": "LysB29 NZ", "candidate_map_is_unique_in_each_state": { "active_open": true, "inactive_closed": true }, "hydrogen_neighbors_by_state": { "active_open": [ { "parent_pdb_serial": 480, "parent_pdb_atom": { "chain": "B", "residue_number": "29", "residue": "LYS", "altloc": "", "name": "NZ" }, "hydrogen_neighbor": { "serial": 492, "name": "HZ2", "element": "H", "connectivity_source": "CONECT" } } ], "inactive_closed": [ { "parent_pdb_serial": 794, "parent_pdb_atom": { "chain": "B", "residue_number": "29", "residue": "LYS", "altloc": "", "name": "NZ" }, "hydrogen_neighbor": { "serial": 807, "name": "HZ2", "element": "H", "connectivity_source": "CONECT" } } ] }, "hydrogen_neighbor_names_by_state": { "active_open": [ "HZ2" ], "inactive_closed": [ "HZ2" ] }, "observed_relation": "same", "expected_relation": "same", "observed_open_names_match_expected": true, "observed_closed_names_match_expected": true, "observed_as_expected": true, "hydrogen_labels_and_counts_are_model_records_not_validated_chemistry": true } }, "all_required_observations_surface_as_expected": true, "known_differences": [ { "map_id": 79, "source_label": "roof C22", "open_names": [ "HX22", "HX31" ], "closed_names": [ "HCB", "HCC" ], "open_count": 2, "closed_count": 2, "open_minus_closed_names": [ "HX22", "HX31" ], "closed_minus_open_names": [ "HCB", "HCC" ], "open_count_minus_closed_count": 0, "closed_has_one_fewer_recorded_hydrogen": false }, { "map_id": 80, "source_label": "roof C23", "open_names": [ "HC2", "HC3" ], "closed_names": [ "HCA", "HCD" ], "open_count": 2, "closed_count": 2, "open_minus_closed_names": [ "HC2", "HC3" ], "closed_minus_open_names": [ "HCA", "HCD" ], "open_count_minus_closed_count": 0, "closed_has_one_fewer_recorded_hydrogen": false }, { "map_id": 85, "source_label": "linker C4", "open_names": [ "HC1", "HXTA" ], "closed_names": [ "HXTA" ], "open_count": 2, "closed_count": 1, "open_minus_closed_names": [ "HC1" ], "closed_minus_open_names": [], "open_count_minus_closed_count": 1, "closed_has_one_fewer_recorded_hydrogen": true }, { "map_id": 86, "source_label": "linker C5", "open_names": [ "H1", "H2A" ], "closed_names": [ "H1", "H2" ], "open_count": 2, "closed_count": 2, "open_minus_closed_names": [ "H2A" ], "closed_minus_open_names": [ "H2" ], "open_count_minus_closed_count": 0, "closed_has_one_fewer_recorded_hydrogen": false }, { "map_id": 87, "source_label": "linker C6", "open_names": [ "H2B", "H3" ], "closed_names": [ "HD3", "HD4" ], "open_count": 2, "closed_count": 2, "open_minus_closed_names": [ "H2B", "H3" ], "closed_minus_open_names": [ "HD3", "HD4" ], "open_count_minus_closed_count": 0, "closed_has_one_fewer_recorded_hydrogen": false } ] }, "assessment": { "both_states_have_exact_full_element_labeled_adjacency_isomorphism": true, "both_states_match_92_nodes_99_edges_and_inventory": true, "exact_mappings_per_state_match_feasibility_review_16": true, "map_ids_78_to_92_unique_across_exact_mappings_in_both_states": true, "multiple_bond_label_transfer_classes_remain_in_both_states": true, "bond_label_transfer_class_count_by_state": { "active_open": 8, "inactive_closed": 8 }, "carboxylate_normalized_class_count_by_state": { "active_open": 1, "inactive_closed": 1 }, "all_states_have_one_carboxylate_normalized_class": true, "state_specific_tail_and_carbonyl_aliases_resolved_as_expected": true, "all_mapped_source_bonds_have_coordinate_screen_records": true, "required_hydrogen_neighbor_observations_match": true, "corrected_candidate_pdbs_unchanged": true, "complete_source_to_pdb_atom_map_unique": false, "unique_topology_claimed": false, "interpretation": "The complete 92-node, 99-edge source product graph has an exact element-labeled adjacency isomorphism to each selected corrected PDB target. Each state has 16 exact map-to-coordinate assignments; map IDs 78-92 are consistent and unique across them, while roof/scaffold map IDs retain ambiguity. The two bond-label-preserving source roof automorphisms are reported as a precursor result. Source bond labels are transferred only after mapping and the PDB records remain adjacency-only. Coordinates are screened against disclosed broad heuristic intervals and do not validate bond order or mapping. The source drawing supports 1,4-disubstituted click regiochemistry. In the neutral graph, the 8 bond-label symmetry classes per state arise from the three independent carboxyl carbonyl-O/OH label swaps; they are not alternative click regioisomer claims. Under the separate conditional tri-carboxylate graph, those paired C\u2013O edges are resonance-equivalent and yield one chemistry-equivalent label class per state. The 16 exact coordinate mappings and source-to-PDB atom-label ambiguity remain unresolved.", "mismatch_handling": "If any exact isomorphism is absent, or unmatched target atoms/edges remain, the corresponding state reports the unmatched inventory and cannot support a unique topology assignment. Here, multiple source bond-label mapping classes are reported as unresolved scaffold-to-coordinate mapping and bond-label transfer; they do not challenge the source-drawing 1,4 click regiochemistry.", "bond_order_or_regiochemistry_validated_from_pdb_coordinates": false, "pdb_hydrogen_records_validated_as_chemistry": false, "simulation_readiness_established": false, "limitations": [ "Corrected candidate PDBs are model-coordinate derivatives, not experimentally resolved NNC2215 structures.", "PDB CONECT and LINK records are adjacency-only; bond orders, formal charges, stereochemistry, and protonation are not validated here.", "The source product graph represents the source-supported click product connectivity and does not establish simulation-pH protonation or force-field parameters.", "The geometry intervals are intentionally broad heuristic screens and do not establish chemical bonds, mapping, or click regiochemistry.", "Hydrogen neighbor labels and counts reproduce model CONECT records and are not validated chemistry." ] } }