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"coordinates_angstrom": [ 2.153, 14.246, -3.746 ] } ], "phe_b1_n_conect_hydrogen_neighbors": [ { "serial": 48, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "H2", "element": "H", "coordinates_angstrom": [ -0.933, 11.316, -10.828 ] } ], "nearest_phx_owned_hydrogens_to_phe_b1_n": [ { "record_owner": "PHX B 0", "atom": { "serial": 20, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue": "PHX", "altloc": "", "name": "H222", "element": "H", "coordinates_angstrom": [ 0.13, 9.912, -12.312 ] }, "distance_to_phe_b1_n_angstrom": 2.5644330757498817, "explicit_conect_neighbor_of_phe_b1_n": false }, { "record_owner": "PHX B 0", "atom": { "serial": 19, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue": "PHX", "altloc": "", "name": "H221", "element": "H", "coordinates_angstrom": [ 1.682, 9.232, -11.903 ] }, "distance_to_phe_b1_n_angstrom": 3.264568271609587, "explicit_conect_neighbor_of_phe_b1_n": false }, { "record_owner": "PHX B 0", "atom": { "serial": 34, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue": "PHX", "altloc": "", "name": "H34", "element": "H", "coordinates_angstrom": [ 0.455, 7.806, -9.182 ] }, "distance_to_phe_b1_n_angstrom": 3.69939643725838, "explicit_conect_neighbor_of_phe_b1_n": false } ], "ownership_and_connectivity_interpretation": "Hydrogen ownership is the ATOM/HETATM residue record owner; explicit adjacency is reported only from CONECT. 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"element": "H", "coordinates_angstrom": [ -1.632, 4.498, -9.644 ] }, { "serial": 365, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "HD2", "element": "H", "coordinates_angstrom": [ -1.245, 6.264, -11.215 ] }, { "serial": 366, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "HD1", "element": "H", "coordinates_angstrom": [ 2.039, 4.737, -8.854 ] }, { "serial": 367, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "HE2", "element": "H", "coordinates_angstrom": [ 0.344, 7.645, -12.522 ] }, { "serial": 368, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "HE1", "element": "H", "coordinates_angstrom": [ 3.621, 6.126, -10.166 ] }, { "serial": 369, "record_type": "ATOM", "chain": "B", "residue_number": "1", "insertion_code": "", "residue": "PHE", "altloc": "", "name": "HZ", "element": "H", "coordinates_angstrom": [ 2.779, 7.586, -11.999 ] } ], "phe_b1_n_conect_hydrogen_neighbors": [], "nearest_phx_owned_hydrogens_to_phe_b1_n": [ { "record_owner": "PHX B 0", "atom": { "serial": 332, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue": "PHX", "altloc": "", "name": "H2A", "element": "H", "coordinates_angstrom": [ -1.281, 3.195, -7.01 ] }, "distance_to_phe_b1_n_angstrom": 1.0063756753817135, "explicit_conect_neighbor_of_phe_b1_n": false }, { "record_owner": "PHX B 0", "atom": { "serial": 333, "record_type": "HETATM", "chain": "B", "residue_number": "0", "insertion_code": "", "residue": "PHX", "altloc": "", "name": "H221", "element": "H", "coordinates_angstrom": [ -1.793, 2.528, -4.584 ] }, "distance_to_phe_b1_n_angstrom": 2.760809482742335, "explicit_conect_neighbor_of_phe_b1_n": false }, { "record_owner": "PHX B 0", "atom": { "serial": 334, 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true, "screen_result": "in_range" }, { "source_map_ids": [ 17, 18 ], "target_serials": [ 324, 329 ], "target_atom_names": [ "C236", "C241" ], "element_pair": [ "C", "C" ], "source_bond_class_annotation": "single", "source_bond_order_numeric_annotation": 1.0, "target_pdb_adjacency_sources": [ "CONECT" ], "raw_distance_angstrom": 1.5384293938949556, "broad_heuristic_screen_interval_angstrom": [ 1.34, 1.77 ], "geometry_screen_only": true, "screen_result": "in_range" }, { "source_map_ids": [ 18, 19 ], "target_serials": [ 329, 330 ], "target_atom_names": [ "C241", "O242" ], "element_pair": [ "C", "O" ], "source_bond_class_annotation": "single", "source_bond_order_numeric_annotation": 1.0, "target_pdb_adjacency_sources": [ "CONECT" ], "raw_distance_angstrom": 1.430080766949895, "broad_heuristic_screen_interval_angstrom": [ 1.24, 1.67 ], "geometry_screen_only": true, "screen_result": "in_range" } ], "geometry_screen_summary": { "edge_count": 19, "in_range_count": 19, "out_of_range_count": 0, "minimum_distance_angstrom": 1.2091211684525247, "maximum_distance_angstrom": 1.550199019481047, "interpretation": "Distances are observed after graph mapping; no mapping was selected or rejected by geometry." } } ], "source_graph_symmetry": { "automorphism_count_element_and_adjacency_preserving": 1, "source_node_orbits": [ [ 1 ], [ 2 ], [ 3 ], [ 4 ], [ 5 ], [ 6 ], [ 7 ], [ 8 ], [ 9 ], [ 10 ], [ 11 ], [ 12 ], [ 13 ], [ 14 ], [ 15 ], [ 16 ], [ 17 ], [ 18 ], [ 19 ] ], "mapping_groups_by_source_graph_symmetry": [ { "symmetry_group_id": "symmetry_01", "mapping_ids": [ "mapping_001" ], "representative_target_serial_vector_by_sorted_source_map": [ 351, 316, 319, 317, 318, 331, 314, 315, 320, 325, 321, 326, 322, 327, 323, 328, 324, 329, 330 ] } ], "bond_orders_and_coordinates_not_used_for_symmetry_or_mapping": true }, "source_model_context": { "source_model_path": "structures/nnc2215-closed-model.pdb", "source_model_sha256": "a8287b859e73b274e8403ee56cd83564bc30fd0503d852829fa805fdc777e12d", "coordinate_status": "Publisher-supplied model coordinates; not an experimentally resolved NNC2215 structure." } } ], "overall_correspondence_status": "both_candidates_exact", "candidate_pdbs_modified_by_audit": false, "limits": [ "The corrected candidate coordinates are derivatives of publisher-supplied author models, not experimentally resolved NNC2215 structures.", "PDB LINK and CONECT records establish adjacency only; this audit does not infer their bond order, formal charge, or stereochemistry.", "Source bond classes are annotations transferred after exact graph mapping. Heuristic distance intervals are a geometry screen only and do not choose mappings.", "PheB1 backbone atoms beyond the N boundary endpoint are outside the B1 attachment component graph.", "The B1\u2013B22 mass check is a fragment-composition benchmark under stated cleavage/reduction assumptions; it does not prove atom-by-atom coordinates.", "Physiological protonation, full-conjugate graph, formal charges, custom force-field parameters, and simulation stability remain unvalidated.", "No target-binding molecular dynamics readiness is established by this B1 topology audit." ] }