{ "schema": "dia-health-one.nnc2215-connectivity-audit.v1", "run": { "run_id": "DHO-NNC2215-CONNECTIVITY-20261018T033024Z", "created_at_utc": "2026-10-18T03:30:24.351899+00:00", "script": "research/audit_nnc2215_connectivity.py", "script_sha256": "9cf37220d46e72a4719ab3aa4ccab2c83376151e78ea10f8597a9cf1ff69912e", "runtime_python": "3.14.4", "nvidia_gpu_used": false }, "source": { "manifest": "research/data/structure-manifest.json", "dataset_doi": "10.6084/m9.figshare.26526460.v1", "dataset_url": "https://springernature.figshare.com/articles/dataset/3D_models_of_NNC2215/26526460", "wwpdb_pdb_connectivity_spec": "https://www.wwpdb.org/documentation/file-format-content/format23/sect10.html" }, "bond_order_and_charge_evidence": { "conect_encodes_bond_order": false, "conect_encodes_formal_charge": false, "source_basis": "The wwPDB PDB v2.3 connectivity specification defines CONECT as atom-serial adjacency and states that it does not distinguish atoms with excess positive or negative charge.", "production_bond_order_inference_performed": false }, "open_closed_link_comparison": { "open_links": [ [ "MC", "C31", "LYX", "CD6" ], [ "LYX", "CD1", "LYS", "NZ" ], [ "PHE", "N", "PHX", "C2" ] ], "closed_links": [ [ "MC", "C31", "LYX", "C" ], [ "LYX", "CD1", "LYS", "NZ" ], [ "PHE", "N", "PHX", "C2" ] ], "macrocycle_to_lyx_link_differs": true, "interpretation": "The PDB LINK records identify endpoints within each file. The macrocycle-to-LYX atom label differs, but the selected heavy-atom CONECT/LINK adjacency graphs match after the documented local LYX label aliases. This does not establish bond orders or a force-field-ready chemical graph." }, "cross_state_atom_record_comparison": { "macrocycle_roof_local_neighborhood": { "open": { "atom": { "serial": 502, "name": "CD6", "element": "C" }, "neighbors_including_link_records": [ { "serial": 501, "atom_name": "CD5", "residue": "LYX", "element": "C" }, { "serial": 517, "atom_name": "HX22", "residue": "LYX", "element": "H" }, { "serial": 516, "atom_name": "HX31", "residue": "LYX", "element": "H" }, { "serial": 861, "atom_name": "C31", "residue": "MC", "element": "C" } ] }, "closed": { "atom": { "serial": 817, "name": "C", "element": "C" }, "neighbors_including_link_records": [ { "serial": 816, "atom_name": "CD5", "residue": "LYX", "element": "C" }, { "serial": 823, "atom_name": "HC", "residue": "LYX", "element": "H" }, { "serial": 824, "atom_name": "HC", "residue": "LYX", "element": "H" }, { "serial": 862, "atom_name": "C31", "residue": "MC", "element": "C" } ] }, "neighbor_element_multisets_match": true, "interpretation": "The open CD6 and closed C endpoint labels have the same local element-neighbor pattern, including the MC C31 LINK. This supports a local atom-label correspondence but does not prove full conjugate graph equivalence." }, "phenyl_b1_n_terminal_hydrogen_record": { "open": { "nitrogen": { "serial": 37, "residue": "PHE", "atom_name": "N" }, "nearest_hydrogen": { "serial": 48, "record": "ATOM", "residue": "PHE", "residue_number": "1", "atom_name": "H2" }, "distance_angstrom": 1.012, "covalent_adjacency_recorded_in_conect": true }, "closed": { "nitrogen": { "serial": 351, "residue": "PHE", "atom_name": "N" }, "nearest_hydrogen": { "serial": 332, "record": "HETATM", "residue": "PHX", "residue_number": "0", "atom_name": "H2" }, "distance_angstrom": 1.006, "covalent_adjacency_recorded_in_conect": false }, "interpretation": "The nearest H to PheB1 N occupies the corresponding local position in both models, but the closed PDB assigns it to PHX and omits a CONECT edge while the open PDB records it as PHE B1 H2 with an N-H CONECT edge. Treat this as a model-record discrepancy pending source-level reconciliation, not as validated topology." }, "lyx_cd2_hydrogen_neighbors": { "open": [ { "serial": 507, "atom_name": "HC1" }, { "serial": 510, "atom_name": "HXT" } ], "closed": [ { "serial": 826, "atom_name": "HXT" } ], "counts_match": false, "interpretation": "The open model records two CONECT hydrogen neighbors for LYX CD2; the closed model records one. The source coordinates do not establish whether the missing neighbor was omitted or assigned elsewhere." }, "full_model_topology_equivalence_established": false }, "selected_heavy_atom_adjacency_comparison": { "scope": "PHX, LYX, and MC heavy atoms plus PheB1 N and LysB29 NZ; excludes all hydrogens, free glucose, and the remainder of the insulin protein.", "explicit_atom_name_aliases": [ { "open": "LYX B30 CD6", "closed": "LYX B30 C", "basis": "same element-neighbor pattern and MC C31 LINK" }, { "open": "LYX B30 OD", "closed": "LYX B30 O", "basis": "same element and sole heavy-atom neighbor LYX CD1" } ], "open_node_count": 113, "closed_node_count": 113, "open_adjacency_edge_count": 120, "closed_adjacency_edge_count": 120, "normalized_node_sets_match": true, "normalized_adjacency_edge_sets_match": true, "selected_heavy_atom_adjacency_matches": true, "interpretation": "The selected 113-node heavy-atom CONECT/LINK adjacency graph matches after the two explicit LYX atom-name aliases. This is an adjacency comparison only; it does not validate bond orders, stereochemistry, protonation, formal charges, or force-field parameters." }, "models": [ { "state": "active_open", "file": "structures/nnc2215-open-model.pdb", "sha256": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "atom_serials_unique": true, "coordinate_atom_count": 990, "hetero_atom_count": 223, "hetero_elements_by_residue": { "BGL": { "C": 6, "H": 12, "O": 6 }, "LYX": { "C": 8, "H": 11, "N": 3, "O": 2 }, "MC": { "C": 56, "H": 60, "N": 12, "O": 12 }, "PHX": { "C": 10, "H": 17, "O": 8 } }, "conect": { "directed_reference_count": 548, "unique_undirected_pair_count": 279, "hetero_atoms_with_at_least_one_conect_neighbor": 223, "hetero_atoms_with_no_conect_neighbor": [], "interpretation": "CONECT identifies bonded atom serials. Repeated atom labels do not erase this serial-level adjacency, but CONECT does not supply bond orders or formal charges." }, "duplicate_atom_labels": { "duplicate_name_group_count": 11, "instances_in_duplicate_groups": 22, "all_instances_have_serial_connectivity": true, "groups": [ { "residue_key": [ "B", "30", "", "LYX" ], "atom_name": "H2", "serial_instances": [ { "serial": 512, "neighbors": [ { "serial": 505, "atom_name": "C1", "residue": "LYX" } ] }, { "serial": 514, "neighbors": [ { "serial": 506, "atom_name": "C2", "residue": "LYX" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "B", "30", "", "LYX" ], "atom_name": "HXT", "serial_instances": [ { "serial": 510, "neighbors": [ { "serial": 498, "atom_name": "CD2", "residue": "LYX" } ] }, { "serial": 515, "neighbors": [ { "serial": 500, "atom_name": "CD4", "residue": "LYX" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H11", "serial_instances": [ { "serial": 920, "neighbors": [ { "serial": 836, "atom_name": "N6", "residue": "MC" } ] }, { "serial": 923, "neighbors": [ { "serial": 841, "atom_name": "C11", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H12", "serial_instances": [ { "serial": 921, "neighbors": [ { "serial": 837, "atom_name": "C7", "residue": "MC" } ] }, { "serial": 924, "neighbors": [ { "serial": 842, "atom_name": "C12", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H19", "serial_instances": [ { "serial": 927, "neighbors": [ { "serial": 849, "atom_name": "N19", "residue": "MC" } ] }, { "serial": 928, "neighbors": [ { "serial": 850, "atom_name": "N20", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H23", "serial_instances": [ { "serial": 930, "neighbors": [ { "serial": 853, "atom_name": "C23", "residue": "MC" } ] }, { "serial": 932, "neighbors": [ { "serial": 857, "atom_name": "C27", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H26", "serial_instances": [ { "serial": 931, "neighbors": [ { "serial": 856, "atom_name": "C26", "residue": "MC" } ] }, { "serial": 935, "neighbors": [ { "serial": 858, "atom_name": "C28", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H4", "serial_instances": [ { "serial": 913, "neighbors": [ { "serial": 831, "atom_name": "C1", "residue": "MC" } ] }, { "serial": 918, "neighbors": [ { "serial": 834, "atom_name": "N4", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H50", "serial_instances": [ { "serial": 959, "neighbors": [ { "serial": 873, "atom_name": "C43", "residue": "MC" } ] }, { "serial": 966, "neighbors": [ { "serial": 880, "atom_name": "N50", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H51", "serial_instances": [ { "serial": 960, "neighbors": [ { "serial": 873, "atom_name": "C43", "residue": "MC" } ] }, { "serial": 967, "neighbors": [ { "serial": 881, "atom_name": "N51", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H60", "serial_instances": [ { "serial": 969, "neighbors": [ { "serial": 889, "atom_name": "N59", "residue": "MC" } ] }, { "serial": 970, "neighbors": [ { "serial": 890, "atom_name": "N60", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true } ] }, "link_records": { "count": 3, "resolved_unique_endpoint_count": 3, "ambiguous_or_missing_endpoint_count": 0, "resolved": [ { "record": "LINK C31 MC C 1 CD6 LYX B 30 1555 1555 1.56", "first_endpoint": [ "C", "1", "", "MC", "C31", "" ], "second_endpoint": [ "B", "30", "", "LYX", "CD6", "" ], "first_serial_matches": [ 861 ], "second_serial_matches": [ 502 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.561, "pdb_annotated_distance_angstrom": 1.56, "both_endpoints_nonstandard": true }, { "record": "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.38", "first_endpoint": [ "B", "30", "", "LYX", "CD1", "" ], "second_endpoint": [ "B", "29", "", "LYS", "NZ", "" ], "first_serial_matches": [ 497 ], "second_serial_matches": [ 480 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.377, "pdb_annotated_distance_angstrom": 1.38, "both_endpoints_nonstandard": false }, { "record": "LINK N PHE B 1 C2 PHX B 0 1555 1555 1.34", "first_endpoint": [ "B", "1", "", "PHE", "N", "" ], "second_endpoint": [ "B", "0", "", "PHX", "C2", "" ], "first_serial_matches": [ 37 ], "second_serial_matches": [ 3 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.336, "pdb_annotated_distance_angstrom": 1.34, "both_endpoints_nonstandard": false } ], "ambiguous_or_missing": [] } }, { "state": "inactive_closed", "file": "structures/nnc2215-closed-model.pdb", "sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "atom_serials_unique": true, "coordinate_atom_count": 968, "hetero_atom_count": 199, "hetero_elements_by_residue": { "LYX": { "C": 8, "H": 10, "N": 3, "O": 2 }, "MC": { "C": 56, "H": 60, "N": 12, "O": 12 }, "PHX": { "C": 10, "H": 18, "O": 8 } }, "conect": { "directed_reference_count": 468, "unique_undirected_pair_count": 238, "hetero_atoms_with_at_least_one_conect_neighbor": 198, "hetero_atoms_with_no_conect_neighbor": [ { "serial": 332, "atom_name": "H2", "residue": "PHX", "chain": "B", "residue_number": "0", "element": "H" } ], "interpretation": "CONECT identifies bonded atom serials. Repeated atom labels do not erase this serial-level adjacency, but CONECT does not supply bond orders or formal charges." }, "duplicate_atom_labels": { "duplicate_name_group_count": 12, "instances_in_duplicate_groups": 26, "all_instances_have_serial_connectivity": false, "groups": [ { "residue_key": [ "B", "0", "", "PHX" ], "atom_name": "H2", "serial_instances": [ { "serial": 332, "neighbors": [] }, { "serial": 336, "neighbors": [ { "serial": 321, "atom_name": "C233", "residue": "PHX" } ] } ], "serial_connectivity_disambiguates_instances": false }, { "residue_key": [ "B", "30", "", "LYX" ], "atom_name": "HC", "serial_instances": [ { "serial": 822, "neighbors": [ { "serial": 816, "atom_name": "CD5", "residue": "LYX" } ] }, { "serial": 823, "neighbors": [ { "serial": 817, "atom_name": "C", "residue": "LYX" } ] }, { "serial": 824, "neighbors": [ { "serial": 817, "atom_name": "C", "residue": "LYX" } ] }, { "serial": 825, "neighbors": [ { "serial": 816, "atom_name": "CD5", "residue": "LYX" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "B", "30", "", "LYX" ], "atom_name": "HXT", "serial_instances": [ { "serial": 826, "neighbors": [ { "serial": 813, "atom_name": "CD2", "residue": "LYX" } ] }, { "serial": 831, "neighbors": [ { "serial": 815, "atom_name": "CD4", "residue": "LYX" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H11", "serial_instances": [ { "serial": 921, "neighbors": [ { "serial": 837, "atom_name": "N6", "residue": "MC" } ] }, { "serial": 924, "neighbors": [ { "serial": 842, "atom_name": "C11", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H12", "serial_instances": [ { "serial": 922, "neighbors": [ { "serial": 838, "atom_name": "C7", "residue": "MC" } ] }, { "serial": 925, "neighbors": [ { "serial": 843, "atom_name": "C12", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H19", "serial_instances": [ { "serial": 928, "neighbors": [ { "serial": 850, "atom_name": "N19", "residue": "MC" } ] }, { "serial": 929, "neighbors": [ { "serial": 851, "atom_name": "N20", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H23", "serial_instances": [ { "serial": 931, "neighbors": [ { "serial": 854, "atom_name": "C23", "residue": "MC" } ] }, { "serial": 933, "neighbors": [ { "serial": 858, "atom_name": "C27", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H26", "serial_instances": [ { "serial": 932, "neighbors": [ { "serial": 857, "atom_name": "C26", "residue": "MC" } ] }, { "serial": 936, "neighbors": [ { "serial": 859, "atom_name": "C28", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H4", "serial_instances": [ { "serial": 914, "neighbors": [ { "serial": 832, "atom_name": "C1", "residue": "MC" } ] }, { "serial": 919, "neighbors": [ { "serial": 835, "atom_name": "N4", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H50", "serial_instances": [ { "serial": 960, "neighbors": [ { "serial": 874, "atom_name": "C43", "residue": "MC" } ] }, { "serial": 967, "neighbors": [ { "serial": 881, "atom_name": "N50", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H51", "serial_instances": [ { "serial": 961, "neighbors": [ { "serial": 874, "atom_name": "C43", "residue": "MC" } ] }, { "serial": 968, "neighbors": [ { "serial": 882, "atom_name": "N51", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true }, { "residue_key": [ "C", "1", "", "MC" ], "atom_name": "H60", "serial_instances": [ { "serial": 970, "neighbors": [ { "serial": 890, "atom_name": "N59", "residue": "MC" } ] }, { "serial": 971, "neighbors": [ { "serial": 891, "atom_name": "N60", "residue": "MC" } ] } ], "serial_connectivity_disambiguates_instances": true } ] }, "link_records": { "count": 3, "resolved_unique_endpoint_count": 3, "ambiguous_or_missing_endpoint_count": 0, "resolved": [ { "record": "LINK C31 MC C 1 C LYX B 30 1555 1555 1.55", "first_endpoint": [ "C", "1", "", "MC", "C31", "" ], "second_endpoint": [ "B", "30", "", "LYX", "C", "" ], "first_serial_matches": [ 862 ], "second_serial_matches": [ 817 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.555, "pdb_annotated_distance_angstrom": 1.55, "both_endpoints_nonstandard": true }, { "record": "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.37", "first_endpoint": [ "B", "30", "", "LYX", "CD1", "" ], "second_endpoint": [ "B", "29", "", "LYS", "NZ", "" ], "first_serial_matches": [ 812 ], "second_serial_matches": [ 794 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.374, "pdb_annotated_distance_angstrom": 1.37, "both_endpoints_nonstandard": false }, { "record": "LINK N PHE B 1 C2 PHX B 0 1555 1555 1.35", "first_endpoint": [ "B", "1", "", "PHE", "N", "" ], "second_endpoint": [ "B", "0", "", "PHX", "C2", "" ], "first_serial_matches": [ 351 ], "second_serial_matches": [ 316 ], "endpoint_resolution": "unique", "actual_coordinate_distance_angstrom": 1.346, "pdb_annotated_distance_angstrom": 1.35, "both_endpoints_nonstandard": false } ], "ambiguous_or_missing": [] } } ], "assessment": "Atom-serial CONECT records and LINK endpoints recover a traceable selected heavy-atom adjacency graph for the modified components despite repeated atom labels. After explicit normalization of two LYX atom-name differences, the open and closed selected heavy-atom node and edge sets match. Hydrogen-level correspondence remains unresolved: the closed model assigns the PheB1 N-terminal H to PHX without a CONECT edge and records one fewer hydrogen neighbor on LYX CD2. Full topology equivalence is not established. Bond orders, protonation, formal charges, stereochemical validation, and force-field parameters remain unresolved; the models are not production-MD-ready.", "target_binding_md_started": false, "clinical_use": false }