{ "formula_comparison": { "interpretation": "The CXS snapshot preserves the same model atom inventory. Its computed IDATM types are metadata derived by ChimeraX; they are not an atom-mapped source chemical definition. The two-carbon excess in LYX+MC versus the published formula-derived B29 component remains unresolved.", "model_target_residue_heavy_atoms": { "active_open": { "C": 74, "N": 15, "O": 22 }, "inactive_closed": { "C": 74, "N": 15, "O": 22 } }, "published_expected_attachment_heavy_atoms": { "C": 72, "N": 15, "O": 22 } }, "models": { "active_open": { "atom_count": 990, "bond_edge_count": 1010, "chimerax_structure_session_version": 19, "compared_pdb": "nnc2215-open-model.pdb", "computed_idatm_type_counts_all_atoms": { "C2": 64, "C3": 181, "Cac": 8, "Car": 80, "H": 100, "HC": 370, "N2": 2, "N3+": 1, "Ng+": 3, "Npl": 73, "O2": 63, "O2-": 16, "O3": 23, "S3": 6 }, "computed_idatm_type_counts_by_target_residue": { "LYX": { "C2": 1, "C3": 5, "Car": 2, "HC": 11, "N2": 2, "Npl": 1, "O2": 1, "O3": 1 }, "MC": { "C2": 6, "C3": 17, "Cac": 3, "Car": 30, "H": 12, "HC": 48, "Npl": 12, "O2": 6, "O2-": 6 }, "PHX": { "C2": 1, "C3": 9, "H": 4, "HC": 13, "O2": 1, "O3": 7 } }, "element_counts_by_target_residue": { "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 } }, "explicit_idatm_type_counts_all_atoms": {}, "explicit_idatm_type_counts_by_target_residue": { "LYX": {}, "MC": {}, "PHX": {} }, "model_name": "2215_active-alt_glucose_rec_correctaminopacids.pdb", "pdb_atom_identity_name_aliases_applied": { "BGLC": "BGL" }, "pdb_atom_identity_sequence_match": true, "pdb_atom_identity_sequence_match_before_alias": false, "pdb_coordinate_atom_count": 990, "pdb_link_records": [ "LINK C31 MC C 1 CD6 LYX B 30 1555 1555 1.56", "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.38" ], "residue_count": 54, "source_title_records": [ "TITLE 2215_active_glucose_rec " ], "state": "active_open", "target_attachment_heavy_atom_counts": { "C": 74, "N": 15, "O": 22 } }, "inactive_closed": { "atom_count": 968, "bond_edge_count": 986, "chimerax_structure_session_version": 19, "compared_pdb": "nnc2215-closed-model.pdb", "computed_idatm_type_counts_all_atoms": { "C2": 63, "C3": 175, "Cac": 9, "Car": 80, "H": 98, "HC": 361, "N2": 2, "N3+": 1, "Ng+": 3, "Npl": 73, "O2": 62, "O2-": 18, "O3": 17, "S3": 6 }, "computed_idatm_type_counts_by_target_residue": { "LYX": { "C2": 1, "C3": 5, "Car": 2, "HC": 10, "N2": 2, "Npl": 1, "O2": 1, "O3": 1 }, "MC": { "C2": 6, "C3": 17, "Cac": 3, "Car": 30, "H": 12, "HC": 48, "Npl": 12, "O2": 6, "O2-": 6 }, "PHX": { "C2": 1, "C3": 9, "H": 5, "HC": 13, "O2": 1, "O3": 7 } }, "element_counts_by_target_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 } }, "explicit_idatm_type_counts_all_atoms": {}, "explicit_idatm_type_counts_by_target_residue": { "LYX": {}, "MC": {}, "PHX": {} }, "model_name": "2215_inactive_correctaminoacids.pdb", "pdb_atom_identity_name_aliases_applied": { "BGLC": "BGL" }, "pdb_atom_identity_sequence_match": true, "pdb_atom_identity_sequence_match_before_alias": true, "pdb_coordinate_atom_count": 968, "pdb_link_records": [ "LINK C31 MC C 1 C LYX B 30 1555 1555 1.55", "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.38" ], "residue_count": 53, "source_title_records": [ "TITLE 2215_from2205moe " ], "state": "inactive_closed", "target_attachment_heavy_atom_counts": { "C": 74, "N": 15, "O": 22 } } }, "readiness": { "bond_orders_authoritatively_resolved": false, "clinical_use": false, "explicit_idatm_types_present_for_target_residues": false, "force_field_parameters_validated": false, "model_coordinates_match_pdb_atom_identity_order": true, "production_md_ready": false, "target_binding_md_started": false, "two_carbon_discrepancy_resolved": false }, "run": { "created_at_utc": "2026-10-18T04:42:00.181924+00:00", "msgpack_version": "1.2.3", "nvidia_gpu_used": false, "run_id": "DHO-NNC2215-CXS-20261018T044200Z", "runtime_python": "3.14.4", "script": "research/audit_nnc2215_chimerax_session.py", "script_sha256": "3a95ec99ca3b49f8ab19e93e0402819de9d24add1c7b35630cb34f78dd3d1b85" }, "schema": "dia-health-one.nnc2215-chimerax-session-audit.v1", "serialization_findings": { "basis": "At the pinned ChimeraX source commit, Structure::session_info serializes the number of bonds followed by endpoint atom-index pairs and then Bond session state; Bond has no bond-order property. Atom session state stores computed and explicit IDATM type strings separately.", "bond_edges_saved_as_atom_index_pairs": true, "bond_order_field_saved": false, "source_files": [ "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.cpp", "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Bond.h", "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Atom.cpp" ] }, "source": { "chimerax_atom_source": "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Atom.cpp", "chimerax_bond_source": "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Bond.h", "chimerax_residue_source": "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Residue.h", "chimerax_source_commit": "b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f", "chimerax_structure_source": "https://github.com/RBVI/ChimeraX/blob/b18ee9afe9a1536d0044139dcdc4c0ea539d2f7f/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.cpp", "dataset_doi": "10.6084/m9.figshare.26526460.v1", "dataset_license": "CC BY 4.0", "dataset_url": "https://springernature.figshare.com/articles/dataset/3D_models_of_NNC2215/26526460", "decompressed_session_bytes": 111053522, "decompressed_session_sha256": "c660b040ca4383ed6b51b752b6668f48cf9773b018bcb2595367ae62111934a3", "local_cxs_digest": { "bytes": 79145092, "md5": "33143f4fad4e80bf4accd09718339aa7", "sha256": "bcfd37935142cec08a84271f12b172b84911c7e6e4adb3411801e37ea4d65fb3" }, "local_cxs_md5_matches_published": true, "published_file_bytes": 79145092, "published_file_md5": "33143f4fad4e80bf4accd09718339aa7", "session_download_url": "https://ndownloader.figshare.com/files/48308389", "session_file_id": 48308389, "session_filename": "NNC2215 in open and closed forms docked into insulin receptor.cxs" } }