data_9RTM
#
_model_server_result.job_id            HynXtQoWXz8p8U6PyOxgSA 
_model_server_result.datetime_utc      '2025-09-16 03:20:14' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          9rtm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    9RTM 
#
_exptl.entry_id    9RTM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              387.451 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            9RTM 
_cell.length_a            62.09 
_cell.length_b            62.35 
_cell.length_c            96.79 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9RTM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 A SG CYS 5 A CYS 5 1_555 A SG CYS 9 A CYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf2 B SG CYS 5 B CYS 5 1_555 B SG CYS 9 B CYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_chem_comp.formula           'C24 H23 N2 O3 1' 
_chem_comp.formula_weight    387.451 
_chem_comp.id                A1EI4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     9-(2-carboxyphenyl)-3,6-bis(dimethylamino)xanthylium 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C11 C12 A1EI4 doub 1 n y 
C11 C10 A1EI4 sing 2 n y 
C12 C13 A1EI4 sing 3 n y 
C10 C9 A1EI4 doub 4 n y 
C13 C14 A1EI4 doub 5 n y 
C6 C5 A1EI4 doub 6 n n 
C6 C7 A1EI4 sing 7 n n 
C9 C14 A1EI4 sing 8 n y 
C9 C8 A1EI4 sing 9 n n 
C5 C4 A1EI4 sing 10 n n 
C1 N2 A1EI4 sing 11 n n 
C14 C15 A1EI4 sing 12 n n 
C7 C8 A1EI4 doub 13 n n 
C7 C28 A1EI4 sing 14 n n 
C8 C18 A1EI4 sing 15 n n 
C4 N2 A1EI4 doub 16 n n 
C4 C29 A1EI4 sing 17 n n 
N2 C3 A1EI4 sing 18 n n 
C28 C29 A1EI4 doub 19 n n 
C28 O27 A1EI4 sing 20 n n 
C15 O17 A1EI4 doub 21 n n 
C15 O16 A1EI4 sing 22 n n 
C18 C19 A1EI4 doub 23 n y 
C18 C26 A1EI4 sing 24 n y 
C19 C20 A1EI4 sing 25 n y 
O27 C26 A1EI4 sing 26 n n 
C26 C25 A1EI4 doub 27 n y 
C20 C21 A1EI4 doub 28 n y 
C25 C21 A1EI4 sing 29 n y 
C21 N22 A1EI4 sing 30 n n 
N22 C24 A1EI4 sing 31 n n 
N22 C23 A1EI4 sing 32 n n 
C1 H1 A1EI4 sing 33 n n 
C1 H2 A1EI4 sing 34 n n 
C1 H3 A1EI4 sing 35 n n 
C3 H4 A1EI4 sing 36 n n 
C3 H5 A1EI4 sing 37 n n 
C3 H6 A1EI4 sing 38 n n 
C5 H7 A1EI4 sing 39 n n 
C6 H8 A1EI4 sing 40 n n 
C10 H9 A1EI4 sing 41 n n 
C11 H10 A1EI4 sing 42 n n 
C12 H11 A1EI4 sing 43 n n 
C13 H12 A1EI4 sing 44 n n 
C19 H13 A1EI4 sing 45 n n 
C20 H14 A1EI4 sing 46 n n 
C23 H15 A1EI4 sing 47 n n 
C23 H16 A1EI4 sing 48 n n 
C23 H17 A1EI4 sing 49 n n 
C24 H18 A1EI4 sing 50 n n 
C24 H19 A1EI4 sing 51 n n 
C24 H20 A1EI4 sing 52 n n 
C25 H21 A1EI4 sing 53 n n 
C29 H22 A1EI4 sing 54 n n 
O16 H23 A1EI4 sing 55 n n 
#
_atom_sites.entry_id                     9RTM 
_atom_sites.fract_transf_matrix[1][1]    0.016106 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016038 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010332 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 A1EI4 A 1 201 201 A1EI4 XXX . 
D 2 A1EI4 B 1 201 201 A1EI4 XXX . 
E 3 HOH A 1 301 9 HOH HOH . 
E 3 HOH A 2 302 13 HOH HOH . 
E 3 HOH A 3 303 18 HOH HOH . 
E 3 HOH A 4 304 31 HOH HOH . 
E 3 HOH A 5 305 30 HOH HOH . 
E 3 HOH A 6 306 17 HOH HOH . 
E 3 HOH A 7 307 11 HOH HOH . 
E 3 HOH A 8 308 20 HOH HOH . 
E 3 HOH A 9 309 21 HOH HOH . 
E 3 HOH A 10 310 5 HOH HOH . 
E 3 HOH A 11 311 25 HOH HOH . 
F 3 HOH B 1 301 7 HOH HOH . 
F 3 HOH B 2 302 4 HOH HOH . 
F 3 HOH B 3 303 22 HOH HOH . 
F 3 HOH B 4 304 15 HOH HOH . 
F 3 HOH B 5 305 16 HOH HOH . 
F 3 HOH B 6 306 8 HOH HOH . 
F 3 HOH B 7 307 23 HOH HOH . 
F 3 HOH B 8 308 29 HOH HOH . 
F 3 HOH B 9 309 6 HOH HOH . 
F 3 HOH B 10 310 27 HOH HOH . 
F 3 HOH B 11 311 28 HOH HOH . 
F 3 HOH B 12 312 14 HOH HOH . 
F 3 HOH B 13 313 24 HOH HOH . 
F 3 HOH B 14 314 3 HOH HOH . 
F 3 HOH B 15 315 26 HOH HOH . 
F 3 HOH B 16 316 19 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 A1EI4 . . . C 2 1.317 5.945 29.125 1 42.47 ? C1 A1EI4 201 A 1 
HETATM 2 C C3 A1EI4 . . . C 2 0.316 5.384 31.281 1 38.35 ? C3 A1EI4 201 A 1 
HETATM 3 C C4 A1EI4 . . . C 2 2.703 5.922 31.143 1 35.8 ? C4 A1EI4 201 A 1 
HETATM 4 C C5 A1EI4 . . . C 2 2.943 5.242 32.33 1 30.61 ? C5 A1EI4 201 A 1 
HETATM 5 C C6 A1EI4 . . . C 2 4.19 5.264 32.927 1 29.95 ? C6 A1EI4 201 A 1 
HETATM 6 C C7 A1EI4 . . . C 2 5.245 5.966 32.356 1 29.67 ? C7 A1EI4 201 A 1 
HETATM 7 C C10 A1EI4 . . . C 2 7.559 4.202 34.287 1 34.83 ? C10 A1EI4 201 A 1 
HETATM 8 C C11 A1EI4 . . . C 2 7.733 3.526 35.484 1 33.07 ? C11 A1EI4 201 A 1 
HETATM 9 C C12 A1EI4 . . . C 2 7.195 4.024 36.645 1 32.42 ? C12 A1EI4 201 A 1 
HETATM 10 C C13 A1EI4 . . . C 2 6.48 5.208 36.632 1 39.54 ? C13 A1EI4 201 A 1 
HETATM 11 C C14 A1EI4 . . . C 2 6.296 5.908 35.438 1 34.02 ? C14 A1EI4 201 A 1 
HETATM 12 C C15 A1EI4 . . . C 2 5.52 7.172 35.488 1 27.87 ? C15 A1EI4 201 A 1 
HETATM 13 C C18 A1EI4 . . . C 2 7.594 6.712 32.222 1 33.29 ? C18 A1EI4 201 A 1 
HETATM 14 C C19 A1EI4 . . . C 2 8.933 6.737 32.614 1 29.93 ? C19 A1EI4 201 A 1 
HETATM 15 C C20 A1EI4 . . . C 2 9.884 7.446 31.899 1 30.09 ? C20 A1EI4 201 A 1 
HETATM 16 C C21 A1EI4 . . . C 2 9.517 8.176 30.765 1 39.45 ? C21 A1EI4 201 A 1 
HETATM 17 C C23 A1EI4 . . . C 2 11.802 9.022 30.551 1 31.24 ? C23 A1EI4 201 A 1 
HETATM 18 C C24 A1EI4 . . . C 2 9.961 10.081 29.296 1 30.94 ? C24 A1EI4 201 A 1 
HETATM 19 C C25 A1EI4 . . . C 2 8.193 8.099 30.331 1 40.09 ? C25 A1EI4 201 A 1 
HETATM 20 C C26 A1EI4 . . . C 2 7.261 7.37 31.035 1 33.74 ? C26 A1EI4 201 A 1 
HETATM 21 C C28 A1EI4 . . . C 2 5.001 6.632 31.163 1 30.99 ? C28 A1EI4 201 A 1 
HETATM 22 C C29 A1EI4 . . . C 2 3.762 6.621 30.557 1 30.61 ? C29 A1EI4 201 A 1 
HETATM 23 C C8 A1EI4 . . . C 2 6.596 6.024 32.915 1 28.91 ? C8 A1EI4 201 A 1 
HETATM 24 C C9 A1EI4 . . . C 2 6.834 5.39 34.245 1 41.51 ? C9 A1EI4 201 A 1 
HETATM 25 N N2 A1EI4 . . . C 2 1.46 5.93 30.566 1 47.6 ? N2 A1EI4 201 A 1 
HETATM 26 N N22 A1EI4 . . . C 2 10.42 8.972 30.118 1 32.51 ? N22 A1EI4 201 A 1 
HETATM 27 O O16 A1EI4 . . . C 2 6.189 8.25 35.266 1 31.61 ? O16 A1EI4 201 A 1 
HETATM 28 O O17 A1EI4 . . . C 2 4.337 7.177 35.724 1 33.79 ? O17 A1EI4 201 A 1 
HETATM 29 O O27 A1EI4 . . . C 2 5.985 7.338 30.506 1 31.39 ? O27 A1EI4 201 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           29 
#