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{ "expected_heavy_neighbors": [ { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "CE", "altloc": "", "element": "C", "serial": 479, "coordinates_angstrom": [ -28.145, -8.424, -6.81 ] }, { "state": "active_open", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 497, "coordinates_angstrom": [ -28.183, -10.829, -7.5 ] } ], "expected_conect_hydrogen_neighbor_count": 1, "observed_conect_hydrogen_neighbors": [ { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "HZ2", "altloc": "", "element": "H", "serial": 492, "coordinates_angstrom": [ -27.305, -9.33, -8.559 ] } ], "record_pattern_status": "matches_expected_record_count", 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"exact_mapping_count": 16, "full_ambiguity_preserved": true, "source_map_serials_invariant_across_all_mappings": { "78": 862, "79": 817, "84": 812, "92": 794 }, "source_graph_summary": { "node_count": 92, "edge_count": 99, "connected_component_count": 1, "cycle_rank_E_minus_V_plus_components": 8 } } }, "attachment_boundary_joins": [ { "join_id": "b1_glucoside_attachment", "join_type": "b1_component_boundary", "state": "inactive_closed", "atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] } ], "adjacency_record_sources": [ "CONECT", "LINK" ], "distance_angstrom": 1.345537, "distance_interpretation": "coordinate observation only; not used for identity, mapping, bond-order, or hydrogen assignment", "source_graph_edge": { "map_ids": [ 1, 2 ], "source_bond_class": "single", "source_graph_adjacency": true, "provenance": "mapped source SMILES plus map legend" }, "link_record_count_for_resolved_pair": 1, "link_records": [ { "line_number": 27, "record": "LINK N PHE B 1 C2 PHX B 0 1555 1555 1.35" } ] }, { "join_id": "b29_lys_attachment", "join_type": "b29_component_boundary", "state": "inactive_closed", "atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 812, "coordinates_angstrom": [ -13.371, -3.749, 5.111 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "NZ", "altloc": "", "element": "N", "serial": 794, "coordinates_angstrom": [ -14.403, -3.56, 4.224 ] } ], "adjacency_record_sources": [ "CONECT", "LINK" ], "distance_angstrom": 1.373868, "distance_interpretation": "coordinate observation only; not used for identity, mapping, bond-order, or hydrogen assignment", "source_graph_edge": { "map_ids": [ 84, 92 ], "source_bond_class": "single", "source_graph_adjacency": true, "provenance": "mapped source SMILES plus map legend" }, "link_record_count_for_resolved_pair": 1, "link_records": [ { "line_number": 26, "record": "LINK CD1 LYX B 30 NZ LYS B 29 1555 1555 1.37" } ] }, { "join_id": "roof_tail_attachment", "join_type": "roof_tail_inter_residue_boundary", "state": "inactive_closed", "atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "C", "residue_number": "1", "insertion_code": "", "residue_name": "MC", "atom_name": "C31", "altloc": "", "element": "C", "serial": 862, "coordinates_angstrom": [ -4.808, 1.041, 1.536 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "C", "altloc": "", "element": "C", "serial": 817, "coordinates_angstrom": [ -6.329, 0.89, 1.821 ] } ], "adjacency_record_sources": [ "CONECT", "LINK" ], "distance_angstrom": 1.554821, "distance_interpretation": "coordinate observation only; not used for identity, mapping, bond-order, or hydrogen assignment", "source_graph_edge": { "map_ids": [ 78, 79 ], "source_bond_class": "single", "source_graph_adjacency": true, "provenance": "mapped source SMILES plus map legend" }, "link_record_count_for_resolved_pair": 1, "link_records": [ { "line_number": 25, "record": "LINK C31 MC C 1 C LYX B 30 1555 1555 1.55" } ] } ], "native_context_joins": [ { "join_id": "pheb1_n_ca_context", "join_type": "native_residue_context", "state": "inactive_closed", "atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] } ], "adjacency_record_sources": [ "CONECT" ], "distance_angstrom": 1.488534, "distance_interpretation": "coordinate observation only; not used for identity, mapping, bond-order, or hydrogen assignment" }, { "join_id": "lysb29_ce_nz_context", "join_type": "native_residue_context", "state": "inactive_closed", "atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "CE", "altloc": "", "element": "C", "serial": 793, "coordinates_angstrom": [ -14.855, -4.579, 3.292 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "NZ", "altloc": "", "element": "N", "serial": 794, "coordinates_angstrom": [ -14.403, -3.56, 4.224 ] } ], "adjacency_record_sources": [ "CONECT" ], "distance_angstrom": 1.453028, "distance_interpretation": "coordinate observation only; not used for identity, mapping, bond-order, or hydrogen assignment" } ], "local_attachment_neighborhoods": { "pheB1_N": { "center_atom": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, "conect_neighbors": { "heavy_atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] } ], "hydrogen_atom_identities": [] }, "link_neighbors": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] } ], "adjacent_heavy_atom_identities_from_conect_or_link": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] } ], "adjacency_sources_by_neighbor_serial": { "316": [ "CONECT", "LINK" ], "352": [ "CONECT" ] } }, "lysB29_NZ": { "center_atom": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "NZ", "altloc": "", "element": "N", "serial": 794, "coordinates_angstrom": [ -14.403, -3.56, 4.224 ] }, "conect_neighbors": { "heavy_atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "CE", "altloc": "", "element": "C", "serial": 793, "coordinates_angstrom": [ -14.855, -4.579, 3.292 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 812, "coordinates_angstrom": [ -13.371, -3.749, 5.111 ] } ], "hydrogen_atom_identities": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "HZ2", "altloc": "", "element": "H", "serial": 807, "coordinates_angstrom": [ -14.713, -2.583, 4.112 ] } ] }, "link_neighbors": [ { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 812, "coordinates_angstrom": [ -13.371, -3.749, 5.111 ] } ], "adjacent_heavy_atom_identities_from_conect_or_link": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "CE", "altloc": "", "element": "C", "serial": 793, "coordinates_angstrom": [ -14.855, -4.579, 3.292 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 812, "coordinates_angstrom": [ -13.371, -3.749, 5.111 ] } ], "adjacency_sources_by_neighbor_serial": { "793": [ "CONECT" ], "807": [ "CONECT" ], "812": [ "CONECT", "LINK" ] } } }, "pheB1_N_hydrogen_geometry": { "state": "inactive_closed", "coordinate_atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "H2A", "altloc": "", "element": "H", "serial": 332, "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_to_pheB1_N_angstrom": 1.006376, "PheB1_N_hydrogen_conect_edge_present": false, "hydrogen_conect_neighbor_identities": [], "local_angles_degrees": { "CA_N_H": 116.916, "B1_carbonyl_C_N_H": 115.369, "CA_N_B1_carbonyl_C": 127.66 }, "nearest_heavy_atoms_by_distance": [ { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, "distance_angstrom": 1.006376 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] }, "distance_angstrom": 1.995892 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] }, "distance_angstrom": 2.141206 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C22", "altloc": "", "element": "C", "serial": 317, "coordinates_angstrom": [ -2.645, 3.121, -4.819 ] }, "distance_angstrom": 2.581948 } ], "interpretation": "Coordinate geometry is descriptive only; it does not create a CONECT edge or assign hydrogen ownership." }, "expected_neutral_local_boundary_record_patterns": { "pheB1_N": { "expected_heavy_neighbors": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] } ], "expected_conect_hydrogen_neighbor_count": 1, "observed_conect_hydrogen_neighbors": [], "record_pattern_status": "hydrogen_record_discrepancy", "chemistry_validation": "not_established by coordinate-file connectivity" }, "lysB29_NZ": { "expected_heavy_neighbors": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "CE", "altloc": "", "element": "C", "serial": 793, "coordinates_angstrom": [ -14.855, -4.579, 3.292 ] }, { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "30", "insertion_code": "", "residue_name": "LYX", "atom_name": "CD1", "altloc": "", "element": "C", "serial": 812, "coordinates_angstrom": [ -13.371, -3.749, 5.111 ] } ], "expected_conect_hydrogen_neighbor_count": 1, "observed_conect_hydrogen_neighbors": [ { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "29", "insertion_code": "", "residue_name": "LYS", "atom_name": "HZ2", "altloc": "", "element": "H", "serial": 807, "coordinates_angstrom": [ -14.713, -2.583, 4.112 ] } ], "record_pattern_status": "matches_expected_record_count", "chemistry_validation": "not_established by coordinate-file connectivity" } }, "pheB1_H2A_proximity_observation": { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "H2A", "altloc": "", "element": "H", "serial": 332, "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_from_pheB1_N_angstrom": 1.006376, "has_pheB1_N_conect_edge": false, "interpretation": "distance observation only; no hydrogen ownership is assigned" } } ], "pheB1_N_hydrogen_geometry_comparison": { "open_reference": { "state": "active_open", "coordinate_atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "H2", "altloc": "", "element": "H", "serial": 48, "coordinates_angstrom": [ -0.933, 11.316, -10.828 ] }, "distance_to_pheB1_N_angstrom": 1.012274, "PheB1_N_hydrogen_conect_edge_present": true, "hydrogen_conect_neighbor_identities": [ { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 37, "coordinates_angstrom": [ -0.152, 11.315, -10.184 ] } ], "local_angles_degrees": { "CA_N_H": 113.869, "B1_carbonyl_C_N_H": 118.805, "CA_N_B1_carbonyl_C": 125.914 }, "nearest_heavy_atoms_by_distance": [ { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 37, "coordinates_angstrom": [ -0.152, 11.315, -10.184 ] }, "distance_angstrom": 1.012274 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 3, "coordinates_angstrom": [ 0.775, 10.36, -10.298 ] }, "distance_angstrom": 2.027831 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 38, "coordinates_angstrom": [ -0.328, 12.205, -9.041 ] }, "distance_angstrom": 2.085597 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "O", "altloc": "", "element": "O", "serial": 40, "coordinates_angstrom": [ -2.591, 12.274, -9.84 ] }, "distance_angstrom": 2.154732 } ], "interpretation": "Coordinate geometry is descriptive only; it does not create a CONECT edge or assign hydrogen ownership." }, "closed_unlinked_coordinate_candidate": { "state": "inactive_closed", "coordinate_atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "H2A", "altloc": "", "element": "H", "serial": 332, "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_to_pheB1_N_angstrom": 1.006376, "PheB1_N_hydrogen_conect_edge_present": false, "hydrogen_conect_neighbor_identities": [], "local_angles_degrees": { "CA_N_H": 116.916, "B1_carbonyl_C_N_H": 115.369, "CA_N_B1_carbonyl_C": 127.66 }, "nearest_heavy_atoms_by_distance": [ { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, "distance_angstrom": 1.006376 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] }, "distance_angstrom": 1.995892 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] }, "distance_angstrom": 2.141206 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C22", "altloc": "", "element": "C", "serial": 317, "coordinates_angstrom": [ -2.645, 3.121, -4.819 ] }, "distance_angstrom": 2.581948 } ], "interpretation": "Coordinate geometry is descriptive only; it does not create a CONECT edge or assign hydrogen ownership." }, "closed_minus_open_deltas": { "distance_to_pheB1_N_angstrom": -0.006, "CA_N_H": 3.047, "B1_carbonyl_C_N_H": -3.436, "CA_N_B1_carbonyl_C": 1.746 }, "interpretation": "The closed PHX H2A coordinate is geometrically similar to the open-state PheB1 N H2 record, including its N-H distance and local angles. H2A has no PheB1 N CONECT edge, so this is compatibility evidence only; no hydrogen owner is assigned and no coordinate or record is repaired." }, "discrepancies": [ { "id": "pheB1_N_hydrogen_connectivity_open_closed_difference", "state": "inactive_closed", "expected_neutral_local_pattern": "PheB1 N has one hydrogen neighbor in addition to CA and the B1 carbonyl carbon", "observed_pdb_connectivity": "PheB1 N has no CONECT hydrogen neighbor in the closed candidate; the open candidate records H2 as a CONECT neighbor", "nearby_observation": { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "H2A", "altloc": "", "element": "H", "serial": 332, "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_from_pheB1_N_angstrom": 1.006376, "has_pheB1_N_conect_edge": false, "interpretation": "distance observation only; no hydrogen ownership is assigned" }, "geometry_comparison": { "open_reference": { "state": "active_open", "coordinate_atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "H2", "altloc": "", "element": "H", "serial": 48, "coordinates_angstrom": [ -0.933, 11.316, -10.828 ] }, "distance_to_pheB1_N_angstrom": 1.012274, "PheB1_N_hydrogen_conect_edge_present": true, "hydrogen_conect_neighbor_identities": [ { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 37, "coordinates_angstrom": [ -0.152, 11.315, -10.184 ] } ], "local_angles_degrees": { "CA_N_H": 113.869, "B1_carbonyl_C_N_H": 118.805, "CA_N_B1_carbonyl_C": 125.914 }, "nearest_heavy_atoms_by_distance": [ { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 37, "coordinates_angstrom": [ -0.152, 11.315, -10.184 ] }, "distance_angstrom": 1.012274 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 3, "coordinates_angstrom": [ 0.775, 10.36, -10.298 ] }, "distance_angstrom": 2.027831 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 38, "coordinates_angstrom": [ -0.328, 12.205, -9.041 ] }, "distance_angstrom": 2.085597 }, { "atom_identity": { "state": "active_open", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "O", "altloc": "", "element": "O", "serial": 40, "coordinates_angstrom": [ -2.591, 12.274, -9.84 ] }, "distance_angstrom": 2.154732 } ], "interpretation": "Coordinate geometry is descriptive only; it does not create a CONECT edge or assign hydrogen ownership." }, "closed_unlinked_coordinate_candidate": { "state": "inactive_closed", "coordinate_atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "H2A", "altloc": "", "element": "H", "serial": 332, "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_to_pheB1_N_angstrom": 1.006376, "PheB1_N_hydrogen_conect_edge_present": false, "hydrogen_conect_neighbor_identities": [], "local_angles_degrees": { "CA_N_H": 116.916, "B1_carbonyl_C_N_H": 115.369, "CA_N_B1_carbonyl_C": 127.66 }, "nearest_heavy_atoms_by_distance": [ { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "N", "altloc": "", "element": "N", "serial": 351, "coordinates_angstrom": [ -1.515, 4.151, -6.8 ] }, "distance_angstrom": 1.006376 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C2", "altloc": "", "element": "C", "serial": 316, "coordinates_angstrom": [ -2.228, 4.336, -5.674 ] }, "distance_angstrom": 1.995892 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue_name": "PHE", "atom_name": "CA", "altloc": "", "element": "C", "serial": 352, "coordinates_angstrom": [ -0.991, 5.192, -7.726 ] }, "distance_angstrom": 2.141206 }, { "atom_identity": { "state": "inactive_closed", "model_number": 1, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue_name": "PHX", "atom_name": "C22", "altloc": "", "element": "C", "serial": 317, "coordinates_angstrom": [ -2.645, 3.121, -4.819 ] }, "distance_angstrom": 2.581948 } ], "interpretation": "Coordinate geometry is descriptive only; it does not create a CONECT edge or assign hydrogen ownership." }, "closed_minus_open_deltas": { "distance_to_pheB1_N_angstrom": -0.006, "CA_N_H": 3.047, "B1_carbonyl_C_N_H": -3.436, "CA_N_B1_carbonyl_C": 1.746 }, "interpretation": "The closed PHX H2A coordinate is geometrically similar to the open-state PheB1 N H2 record, including its N-H distance and local angles. H2A has no PheB1 N CONECT edge, so this is compatibility evidence only; no hydrogen owner is assigned and no coordinate or record is repaired." }, "interpretation": "Closed PHX H2A has local coordinates similar to the open-state H2 record at PheB1 N, but it has no CONECT edge to that N. This is compatibility evidence only; the coordinate file does not establish hydrogen ownership, and no reassignment or repair was made.", "heavy_atom_boundary_closure_affected": false } ], "assessment": { "heavy_atom_boundary_closure": "pass", "unique_attachment_LINK_count": 6, "unique_native_context_join_count": 4, "all_source_boundary_edges_cross_checked": true, "b1_exact_mappings_per_state_preserved": 1, "b29_exact_mappings_per_state_preserved": 16, "b29_ambiguity_resolved_by_coordinates": false, "hydrogen_record_chemistry_resolved": false, "full_conjugate_graph_bond_orders_stereochemistry_resolved": false, "whole_insulin_protonation_or_charge_resolved": false, "force_field_validated": false, "target_binding_md_run": false, "clinical_readiness_established": false, "interpretation": "The three named heavy-atom attachment boundaries and two native residue context joins per state resolve by source-map and PDB record evidence in corrected model-built candidates. Distances are observations only. The PheB1 hydrogen-record discrepancy and broader chemistry/model gates remain open." }, "limits": [ "Corrected candidate PDBs are model-built derivatives, not experimentally solved NNC2215 structures.", "PDB LINK and CONECT records provide adjacency evidence only; they do not validate bond order, formal charge, stereochemistry, protonation, or hydrogen ownership.", "The 16 exact B29 source-to-candidate mappings per state are preserved; this audit does not choose a unique full B29 map or resolve carboxyl oxygen-label ambiguity.", "This local boundary audit does not establish the complete conjugate graph, full insulin charge/protonation, force-field parameters, target-binding MD readiness, or clinical readiness." ] }