{ "schema": "dia-health-one.nnc2215-coordinate-reconciliation-candidate.v4", "created_at_utc": "2026-10-25T15:59:26.154926+00:00", "source_chemistry": { "paper_doi": "10.1038/s41586-024-08042-3", "figure": "Extended Data Fig. 8i", "supplementary_formula": "C56H63N15O12", "nmr_assignment": "6H, H-18, corresponding to the two aryl methyl substituents", "source_formula_and_synthesis": "C325H461N79O97S6 for NNC2215; B29 linker C6H6O2; macrocycle roof propyl azide C56H63N15O12", "coordinate_source": { "authors": "Eva Johansson; Daniele Granata", "title": "3D models of NNC2215", "doi": "10.6084/m9.figshare.26526460", "license": "CC BY 4.0", "modification_note": "Candidate PDBs are modified derivatives of the author-supplied model coordinates, not original or experimentally solved structures." }, "sources": [ "https://www.nature.com/articles/s41586-024-08042-3", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-024-08042-3/MediaObjects/41586_2024_8042_MOESM1_ESM.pdf", "https://springernature.figshare.com/articles/dataset/3D_models_of_NNC2215/26526460" ] }, "mapping_inference": { "pdb_extra_atoms": [ "MC C27", "MC C29" ], "source_methyl_atoms": [ "MC C28", "MC C30" ], "source_aryl_atoms": [ "MC C73", "MC C75" ], "candidate_correction": "Delete C27/C29 and their four hydrogens; connect C28/C30 directly to C73/C75; retain C28/C30 as methyl carbons and rebuild their hydrogen coordinates.", "basis": "The source 2D chemical structure depicts two direct ring methyls, the SI assigns a six-proton H-18 signal to the two methyl groups, and this correction brings the B29 linked heavy-atom pool to the source-derived C62N15O14 in both models.", "status": "source-supported mapping inference; requires independent chemistry review before production parameterization" }, "models": [ { "state": "active_open", "source_file": "structures/nnc2215-open-model.pdb", "source_sha256": "44c29d45b28ace4ede73a75a8e076dbca62e14b34bd3938a4b495ebd1270267a", "output_file": "structures/nnc2215-open-source-corrected-candidate.pdb", "output_sha256": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "source_heavy_inventory_excluding_free_glucose": { "C": 327, "N": 79, "O": 96, "S": 6 }, "corrected_heavy_inventory_excluding_free_glucose": { "C": 325, "N": 79, "O": 97, "S": 6 }, "corrected_b29_linked_pool": { "C": 62, "N": 15, "O": 14 }, "corrections": [ { "removed_extra_atom": { "name": "C27", "element": "C", "removed_hydrogens": [ "H23", "H24" ], "source_serial": 857, "removed_hydrogen_atoms": [ { "name": "H23", "source_serial": 932 }, { "name": "H24", "source_serial": 933 } ] }, "source_methyl_atom": { "name": "C28", "source_serial": 858, "output_serial": 859 }, "aryl_atom": { "name": "C73", "source_serial": 903, "output_serial": 904 }, "new_bond": [ "C73", "C28" ], "methyl_hydrogens_retained": [ "H25", "H26", "H27" ], "new_aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "methyl_hydrogen_phase_degrees": 48.0, "closest_local_contacts_below_screening_cutoffs": [], "methyl_hydrogens": [ { "source_atom_name": "H25", "candidate_atom_name": "H25", "source_serial": 934, "output_serial": 935 }, { "source_atom_name": "H26", "candidate_atom_name": "H26B", "source_serial": 935, "output_serial": 936 }, { "source_atom_name": "H27", "candidate_atom_name": "H27", "source_serial": 936, "output_serial": 937 } ], "new_bond_source_serials": [ 903, 858 ], "new_bond_output_serials": [ 904, 859 ] }, { "removed_extra_atom": { "name": "C29", "element": "C", "removed_hydrogens": [ "H28", "H29" ], "source_serial": 859, "removed_hydrogen_atoms": [ { "name": "H28", "source_serial": 937 }, { "name": "H29", "source_serial": 938 } ] }, "source_methyl_atom": { "name": "C30", "source_serial": 860, "output_serial": 861 }, "aryl_atom": { "name": "C75", "source_serial": 905, "output_serial": 906 }, "new_bond": [ "C75", "C30" ], "methyl_hydrogens_retained": [ "H30", "H31", "H32" ], "new_aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "methyl_hydrogen_phase_degrees": 67.0, "closest_local_contacts_below_screening_cutoffs": [], "methyl_hydrogens": [ { "source_atom_name": "H30", "candidate_atom_name": "H30", "source_serial": 939, "output_serial": 940 }, { "source_atom_name": "H31", "candidate_atom_name": "H31", "source_serial": 940, "output_serial": 941 }, { "source_atom_name": "H32", "candidate_atom_name": "H32", "source_serial": 941, "output_serial": 942 } ], "new_bond_source_serials": [ 905, 860 ], "new_bond_output_serials": [ 906, 861 ] } ], "duplicate_atom_name_mapping": [ { "source_serial": 512, "output_serial": 512, "residue": [ "B", "LYX", "30" ], "source_atom_name": "H2", "candidate_atom_name": "H2A" }, { "source_serial": 514, "output_serial": 514, "residue": [ "B", "LYX", "30" ], "source_atom_name": "H2", "candidate_atom_name": "H2B" }, { "source_serial": 510, "output_serial": 510, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HXT", "candidate_atom_name": "HXTA" }, { "source_serial": 515, "output_serial": 515, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HXT", "candidate_atom_name": "HXTB" }, { "source_serial": 920, "output_serial": 921, "residue": [ "C", "MC", "1" ], "source_atom_name": "H11", "candidate_atom_name": "H11A" }, { "source_serial": 923, "output_serial": 924, "residue": [ "C", "MC", "1" ], "source_atom_name": "H11", "candidate_atom_name": "H11B" }, { "source_serial": 921, "output_serial": 922, "residue": [ "C", "MC", "1" ], "source_atom_name": "H12", "candidate_atom_name": "H12A" }, { "source_serial": 924, "output_serial": 925, "residue": [ "C", "MC", "1" ], "source_atom_name": "H12", "candidate_atom_name": "H12B" }, { "source_serial": 927, "output_serial": 928, "residue": [ "C", "MC", "1" ], "source_atom_name": "H19", "candidate_atom_name": "H19A" }, { "source_serial": 928, "output_serial": 929, "residue": [ "C", "MC", "1" ], "source_atom_name": "H19", "candidate_atom_name": "H19B" }, { "source_serial": 931, "output_serial": 932, "residue": [ "C", "MC", "1" ], "source_atom_name": "H26", "candidate_atom_name": "H26A" }, { "source_serial": 935, "output_serial": 936, "residue": [ "C", "MC", "1" ], "source_atom_name": "H26", "candidate_atom_name": "H26B" }, { "source_serial": 913, "output_serial": 914, "residue": [ "C", "MC", "1" ], "source_atom_name": "H4", "candidate_atom_name": "H4A" }, { "source_serial": 918, "output_serial": 919, "residue": [ "C", "MC", "1" ], "source_atom_name": "H4", "candidate_atom_name": "H4B" }, { "source_serial": 959, "output_serial": 960, "residue": [ "C", "MC", "1" ], "source_atom_name": "H50", "candidate_atom_name": "H50A" }, { "source_serial": 966, "output_serial": 967, "residue": [ "C", "MC", "1" ], "source_atom_name": "H50", "candidate_atom_name": "H50B" }, { "source_serial": 960, "output_serial": 961, "residue": [ "C", "MC", "1" ], "source_atom_name": "H51", "candidate_atom_name": "H51A" }, { "source_serial": 967, "output_serial": 968, "residue": [ "C", "MC", "1" ], "source_atom_name": "H51", "candidate_atom_name": "H51B" }, { "source_serial": 969, "output_serial": 970, "residue": [ "C", "MC", "1" ], "source_atom_name": "H60", "candidate_atom_name": "H60A" }, { "source_serial": 970, "output_serial": 971, "residue": [ "C", "MC", "1" ], "source_atom_name": "H60", "candidate_atom_name": "H60B" } ], "terminal_oxygen_reconstruction": { "removed_source_atom": "ASN A21 HXT", "removed_source_serial": 825, "removed_source_element": "H", "source_C_HXT_distance_angstrom": 1.08, "added_atom": "ASN A21 OXT", "added_element": "O", "reconstruction": "placed in the CA-C-O plane opposite the CA and O vectors, at a 1.25 \u00c5 C-OXT distance", "new_C_OXT_distance_angstrom": 1.25, "O_C_OXT_angle_degrees": 119.66, "protonation_assumption": "terminal carboxylate; no terminal OXT hydrogen", "candidate_serial": 830, "output_serial": 830 }, "coordinate_candidate_checks": { "serialized_pdb_reopened": true, "atom_count": 984, "atom_serials_strictly_increasing": true, "pdb_records_at_most_80_columns": true, "output_serial_name_map_matches_candidate": true, "audit_output_serial_name_references_verified": true, "conect_link_ssbond_references_valid": true, "heavy_inventory_matches_reported_formula": true, "duplicate_atom_names_within_residue": 0, "aryl_methyl_geometry": [ { "aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.089 ], "bond_record_present": true, "methyl_hydrogen_overlap_screen_passed": true }, { "aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "bond_record_present": true, "methyl_hydrogen_overlap_screen_passed": true } ], "asn_a21_terminal_oxygen": { "C_OXT_distance_angstrom": 1.25, "O_C_OXT_angle_degrees": 119.66, "OXT_bond_record_present": true, "source_HXT_removed": true } }, "full_conjugate_heavy_inventory_difference": { "source_formula_expected": { "C": 325, "N": 79, "O": 97, "S": 6 }, "coordinate_model_excluding_free_glucose": { "C": 325, "N": 79, "O": 97, "S": 6 }, "difference": { "C": 0, "N": 0, "O": 0, "S": 0 } } }, { "state": "inactive_closed", "source_file": "structures/nnc2215-closed-model.pdb", "source_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "output_file": "structures/nnc2215-closed-source-corrected-candidate.pdb", "output_sha256": "2da23e028fef992f097ad06d5899caba30826fbf7cfde22d2fd2862cd790f07e", "source_heavy_inventory_excluding_free_glucose": { "C": 327, "N": 79, "O": 97, "S": 6 }, "corrected_heavy_inventory_excluding_free_glucose": { "C": 325, "N": 79, "O": 97, "S": 6 }, "corrected_b29_linked_pool": { "C": 62, "N": 15, "O": 14 }, "corrections": [ { "removed_extra_atom": { "name": "C27", "element": "C", "removed_hydrogens": [ "H23", "H24" ], "source_serial": 858, "removed_hydrogen_atoms": [ { "name": "H23", "source_serial": 933 }, { "name": "H24", "source_serial": 934 } ] }, "source_methyl_atom": { "name": "C28", "source_serial": 859, "output_serial": 859 }, "aryl_atom": { "name": "C73", "source_serial": 904, "output_serial": 904 }, "new_bond": [ "C73", "C28" ], "methyl_hydrogens_retained": [ "H25", "H26", "H27" ], "new_aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "methyl_hydrogen_phase_degrees": 0.0, "closest_local_contacts_below_screening_cutoffs": [], "methyl_hydrogens": [ { "source_atom_name": "H25", "candidate_atom_name": "H25", "source_serial": 935, "output_serial": 935 }, { "source_atom_name": "H26", "candidate_atom_name": "H26B", "source_serial": 936, "output_serial": 936 }, { "source_atom_name": "H27", "candidate_atom_name": "H27", "source_serial": 937, "output_serial": 937 } ], "new_bond_source_serials": [ 904, 859 ], "new_bond_output_serials": [ 904, 859 ] }, { "removed_extra_atom": { "name": "C29", "element": "C", "removed_hydrogens": [ "H28", "H29" ], "source_serial": 860, "removed_hydrogen_atoms": [ { "name": "H28", "source_serial": 938 }, { "name": "H29", "source_serial": 939 } ] }, "source_methyl_atom": { "name": "C30", "source_serial": 861, "output_serial": 861 }, "aryl_atom": { "name": "C75", "source_serial": 906, "output_serial": 906 }, "new_bond": [ "C75", "C30" ], "methyl_hydrogens_retained": [ "H30", "H31", "H32" ], "new_aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "methyl_hydrogen_phase_degrees": 40.0, "closest_local_contacts_below_screening_cutoffs": [], "methyl_hydrogens": [ { "source_atom_name": "H30", "candidate_atom_name": "H30", "source_serial": 940, "output_serial": 940 }, { "source_atom_name": "H31", "candidate_atom_name": "H31", "source_serial": 941, "output_serial": 941 }, { "source_atom_name": "H32", "candidate_atom_name": "H32", "source_serial": 942, "output_serial": 942 } ], "new_bond_source_serials": [ 906, 861 ], "new_bond_output_serials": [ 906, 861 ] } ], "duplicate_atom_name_mapping": [ { "source_serial": 332, "output_serial": 332, "residue": [ "B", "PHX", "0" ], "source_atom_name": "H2", "candidate_atom_name": "H2A" }, { "source_serial": 336, "output_serial": 336, "residue": [ "B", "PHX", "0" ], "source_atom_name": "H2", "candidate_atom_name": "H2B" }, { "source_serial": 822, "output_serial": 822, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HC", "candidate_atom_name": "HCA" }, { "source_serial": 823, "output_serial": 823, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HC", "candidate_atom_name": "HCB" }, { "source_serial": 824, "output_serial": 824, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HC", "candidate_atom_name": "HCC" }, { "source_serial": 825, "output_serial": 825, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HC", "candidate_atom_name": "HCD" }, { "source_serial": 826, "output_serial": 826, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HXT", "candidate_atom_name": "HXTA" }, { "source_serial": 831, "output_serial": 831, "residue": [ "B", "LYX", "30" ], "source_atom_name": "HXT", "candidate_atom_name": "HXTB" }, { "source_serial": 921, "output_serial": 921, "residue": [ "C", "MC", "1" ], "source_atom_name": "H11", "candidate_atom_name": "H11A" }, { "source_serial": 924, "output_serial": 924, "residue": [ "C", "MC", "1" ], "source_atom_name": "H11", "candidate_atom_name": "H11B" }, { "source_serial": 922, "output_serial": 922, "residue": [ "C", "MC", "1" ], "source_atom_name": "H12", "candidate_atom_name": "H12A" }, { "source_serial": 925, "output_serial": 925, "residue": [ "C", "MC", "1" ], "source_atom_name": "H12", "candidate_atom_name": "H12B" }, { "source_serial": 928, "output_serial": 928, "residue": [ "C", "MC", "1" ], "source_atom_name": "H19", "candidate_atom_name": "H19A" }, { "source_serial": 929, "output_serial": 929, "residue": [ "C", "MC", "1" ], "source_atom_name": "H19", "candidate_atom_name": "H19B" }, { "source_serial": 932, "output_serial": 932, "residue": [ "C", "MC", "1" ], "source_atom_name": "H26", "candidate_atom_name": "H26A" }, { "source_serial": 936, "output_serial": 936, "residue": [ "C", "MC", "1" ], "source_atom_name": "H26", "candidate_atom_name": "H26B" }, { "source_serial": 914, "output_serial": 914, "residue": [ "C", "MC", "1" ], "source_atom_name": "H4", "candidate_atom_name": "H4A" }, { "source_serial": 919, "output_serial": 919, "residue": [ "C", "MC", "1" ], "source_atom_name": "H4", "candidate_atom_name": "H4B" }, { "source_serial": 960, "output_serial": 960, "residue": [ "C", "MC", "1" ], "source_atom_name": "H50", "candidate_atom_name": "H50A" }, { "source_serial": 967, "output_serial": 967, "residue": [ "C", "MC", "1" ], "source_atom_name": "H50", "candidate_atom_name": "H50B" }, { "source_serial": 961, "output_serial": 961, "residue": [ "C", "MC", "1" ], "source_atom_name": "H51", "candidate_atom_name": "H51A" }, { "source_serial": 968, "output_serial": 968, "residue": [ "C", "MC", "1" ], "source_atom_name": "H51", "candidate_atom_name": "H51B" }, { "source_serial": 970, "output_serial": 970, "residue": [ "C", "MC", "1" ], "source_atom_name": "H60", "candidate_atom_name": "H60A" }, { "source_serial": 971, "output_serial": 971, "residue": [ "C", "MC", "1" ], "source_atom_name": "H60", "candidate_atom_name": "H60B" } ], "terminal_oxygen_reconstruction": null, "coordinate_candidate_checks": { "serialized_pdb_reopened": true, "atom_count": 962, "atom_serials_strictly_increasing": true, "pdb_records_at_most_80_columns": true, "output_serial_name_map_matches_candidate": true, "audit_output_serial_name_references_verified": true, "conect_link_ssbond_references_valid": true, "heavy_inventory_matches_reported_formula": true, "duplicate_atom_names_within_residue": 0, "aryl_methyl_geometry": [ { "aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "bond_record_present": true, "methyl_hydrogen_overlap_screen_passed": true }, { "aryl_methyl_distance_angstrom": 1.5, "methyl_c_h_distances_angstrom": [ 1.09, 1.09, 1.09 ], "bond_record_present": true, "methyl_hydrogen_overlap_screen_passed": true } ], "asn_a21_terminal_oxygen": null }, "full_conjugate_heavy_inventory_difference": { "source_formula_expected": { "C": 325, "N": 79, "O": 97, "S": 6 }, "coordinate_model_excluding_free_glucose": { "C": 325, "N": 79, "O": 97, "S": 6 }, "difference": { "C": 0, "N": 0, "O": 0, "S": 0 } } } ], "readiness": { "coordinate_candidate_checks_passed": true, "two_carbon_discrepancy_resolved_as_candidate_mapping": true, "reported_full_conjugate_heavy_inventory_matched": true, "full_molecular_graph_validated": false, "bond_orders_assigned": false, "formal_charges_assigned": false, "protonation_inventory_validated": false, "force_field_parameters_generated": false, "target_md_ready": false }, "limitations": [ "PDB CONECT records provide adjacency only and do not encode bond order or formal charge.", "Coordinates for the methyl hydrogens are rebuilt geometrically; heavy atom ring coordinates are retained.", "The open-model ASN A21 terminal OXT was reconstructed from the CA-C-O plane after removing a misplaced HXT record at the OXT position; this geometry and the terminal carboxylate microstate are model assumptions.", "Hydrogen coordinates and the full protonation inventory remain unvalidated and should be rebuilt from the resolved molecular graph.", "This is a source-reconciled coordinate candidate, not a parameterized simulation system." ], "clinical_use": false }