data_9RTL
#
_model_server_result.job_id            0kB-vnlPSgmetlsFevfPCw 
_model_server_result.datetime_utc      '2025-08-31 16:41:24' 
_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          9rtl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":201}' 
#
_entry.id    9RTL 
#
_exptl.entry_id    9RTL 
_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         120 
_cell.entry_id            9RTL 
_cell.length_a            71.81 
_cell.length_b            71.81 
_cell.length_c            146.16 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9RTL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    'P 65' 
_symmetry.space_group_name_H-M     'P 65' 
#
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,D,E,F,G,J 1 1 
B,H,I,K 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 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 B SG CYS 5 B CYS 5 1_555 B SG CYS 9 B CYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
#
_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                     9RTL 
_atom_sites.fract_transf_matrix[1][1]    0.013926 
_atom_sites.fract_transf_matrix[1][2]    0.00804 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01608 
_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]    0.006842 
_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 3 GOL A 1 202 202 GOL GOL . 
E 3 GOL A 1 203 203 GOL GOL . 
F 3 GOL A 1 204 301 GOL GOL . 
G 3 GOL A 1 205 202 GOL GOL . 
H 2 A1EI4 B 1 201 201 A1EI4 XXX . 
I 3 GOL B 1 202 203 GOL GOL . 
J 4 HOH A 1 301 67 HOH HOH . 
J 4 HOH A 2 302 62 HOH HOH . 
J 4 HOH A 3 303 77 HOH HOH . 
J 4 HOH A 4 304 51 HOH HOH . 
J 4 HOH A 5 305 82 HOH HOH . 
J 4 HOH A 6 306 68 HOH HOH . 
J 4 HOH A 7 307 111 HOH HOH . 
J 4 HOH A 8 308 63 HOH HOH . 
J 4 HOH A 9 309 114 HOH HOH . 
J 4 HOH A 10 310 21 HOH HOH . 
J 4 HOH A 11 311 116 HOH HOH . 
J 4 HOH A 12 312 30 HOH HOH . 
J 4 HOH A 13 313 6 HOH HOH . 
J 4 HOH A 14 314 80 HOH HOH . 
J 4 HOH A 15 315 72 HOH HOH . 
J 4 HOH A 16 316 20 HOH HOH . 
J 4 HOH A 17 317 49 HOH HOH . 
J 4 HOH A 18 318 50 HOH HOH . 
J 4 HOH A 19 319 128 HOH HOH . 
J 4 HOH A 20 320 52 HOH HOH . 
J 4 HOH A 21 321 104 HOH HOH . 
J 4 HOH A 22 322 88 HOH HOH . 
J 4 HOH A 23 323 36 HOH HOH . 
J 4 HOH A 24 324 54 HOH HOH . 
J 4 HOH A 25 325 79 HOH HOH . 
J 4 HOH A 26 326 57 HOH HOH . 
J 4 HOH A 27 327 55 HOH HOH . 
J 4 HOH A 28 328 87 HOH HOH . 
J 4 HOH A 29 329 41 HOH HOH . 
J 4 HOH A 30 330 14 HOH HOH . 
J 4 HOH A 31 331 46 HOH HOH . 
J 4 HOH A 32 332 127 HOH HOH . 
J 4 HOH A 33 333 48 HOH HOH . 
J 4 HOH A 34 334 66 HOH HOH . 
J 4 HOH A 35 335 9 HOH HOH . 
J 4 HOH A 36 336 95 HOH HOH . 
J 4 HOH A 37 337 10 HOH HOH . 
J 4 HOH A 38 338 118 HOH HOH . 
J 4 HOH A 39 339 93 HOH HOH . 
J 4 HOH A 40 340 12 HOH HOH . 
J 4 HOH A 41 341 34 HOH HOH . 
J 4 HOH A 42 342 38 HOH HOH . 
J 4 HOH A 43 343 122 HOH HOH . 
J 4 HOH A 44 344 117 HOH HOH . 
J 4 HOH A 45 345 59 HOH HOH . 
J 4 HOH A 46 346 101 HOH HOH . 
J 4 HOH A 47 347 18 HOH HOH . 
J 4 HOH A 48 348 26 HOH HOH . 
J 4 HOH A 49 349 81 HOH HOH . 
J 4 HOH A 50 350 123 HOH HOH . 
J 4 HOH A 51 351 92 HOH HOH . 
J 4 HOH A 52 352 39 HOH HOH . 
J 4 HOH A 53 353 22 HOH HOH . 
J 4 HOH A 54 354 100 HOH HOH . 
J 4 HOH A 55 355 125 HOH HOH . 
J 4 HOH A 56 356 83 HOH HOH . 
J 4 HOH A 57 357 98 HOH HOH . 
J 4 HOH A 58 358 97 HOH HOH . 
J 4 HOH A 59 359 102 HOH HOH . 
J 4 HOH A 60 360 103 HOH HOH . 
J 4 HOH A 61 361 85 HOH HOH . 
J 4 HOH A 62 362 84 HOH HOH . 
J 4 HOH A 63 363 73 HOH HOH . 
K 4 HOH B 1 301 74 HOH HOH . 
K 4 HOH B 2 302 40 HOH HOH . 
K 4 HOH B 3 303 90 HOH HOH . 
K 4 HOH B 4 304 94 HOH HOH . 
K 4 HOH B 5 305 75 HOH HOH . 
K 4 HOH B 6 306 28 HOH HOH . 
K 4 HOH B 7 307 37 HOH HOH . 
K 4 HOH B 8 308 24 HOH HOH . 
K 4 HOH B 9 309 4 HOH HOH . 
K 4 HOH B 10 310 33 HOH HOH . 
K 4 HOH B 11 311 3 HOH HOH . 
K 4 HOH B 12 312 5 HOH HOH . 
K 4 HOH B 13 313 78 HOH HOH . 
K 4 HOH B 14 314 25 HOH HOH . 
K 4 HOH B 15 315 17 HOH HOH . 
K 4 HOH B 16 316 56 HOH HOH . 
K 4 HOH B 17 317 120 HOH HOH . 
K 4 HOH B 18 318 45 HOH HOH . 
K 4 HOH B 19 319 44 HOH HOH . 
K 4 HOH B 20 320 53 HOH HOH . 
K 4 HOH B 21 321 7 HOH HOH . 
K 4 HOH B 22 322 11 HOH HOH . 
K 4 HOH B 23 323 65 HOH HOH . 
K 4 HOH B 24 324 113 HOH HOH . 
K 4 HOH B 25 325 121 HOH HOH . 
K 4 HOH B 26 326 70 HOH HOH . 
K 4 HOH B 27 327 89 HOH HOH . 
K 4 HOH B 28 328 76 HOH HOH . 
K 4 HOH B 29 329 23 HOH HOH . 
K 4 HOH B 30 330 64 HOH HOH . 
K 4 HOH B 31 331 15 HOH HOH . 
K 4 HOH B 32 332 71 HOH HOH . 
K 4 HOH B 33 333 8 HOH HOH . 
K 4 HOH B 34 334 107 HOH HOH . 
K 4 HOH B 35 335 106 HOH HOH . 
K 4 HOH B 36 336 109 HOH HOH . 
K 4 HOH B 37 337 19 HOH HOH . 
K 4 HOH B 38 338 29 HOH HOH . 
K 4 HOH B 39 339 110 HOH HOH . 
K 4 HOH B 40 340 61 HOH HOH . 
K 4 HOH B 41 341 32 HOH HOH . 
K 4 HOH B 42 342 69 HOH HOH . 
K 4 HOH B 43 343 42 HOH HOH . 
K 4 HOH B 44 344 13 HOH HOH . 
K 4 HOH B 45 345 31 HOH HOH . 
K 4 HOH B 46 346 105 HOH HOH . 
K 4 HOH B 47 347 27 HOH HOH . 
K 4 HOH B 48 348 35 HOH HOH . 
K 4 HOH B 49 349 115 HOH HOH . 
K 4 HOH B 50 350 119 HOH HOH . 
K 4 HOH B 51 351 108 HOH HOH . 
K 4 HOH B 52 352 47 HOH HOH . 
K 4 HOH B 53 353 58 HOH HOH . 
K 4 HOH B 54 354 126 HOH HOH . 
K 4 HOH B 55 355 43 HOH HOH . 
K 4 HOH B 56 356 99 HOH HOH . 
K 4 HOH B 57 357 124 HOH HOH . 
K 4 HOH B 58 358 112 HOH HOH . 
K 4 HOH B 59 359 86 HOH HOH . 
K 4 HOH B 60 360 96 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 . . . H 2 -45.895 -10.754 -17.402 1 28.41 ? C1 A1EI4 201 B 1 
HETATM 2 C C3 A1EI4 . . . H 2 -45.856 -13.219 -17.642 1 29.95 ? C3 A1EI4 201 B 1 
HETATM 3 C C4 A1EI4 . . . H 2 -47.8 -12.111 -16.632 1 24.83 ? C4 A1EI4 201 B 1 
HETATM 4 C C5 A1EI4 . . . H 2 -48.408 -13.354 -16.402 1 24.35 ? C5 A1EI4 201 B 1 
HETATM 5 C C6 A1EI4 . . . H 2 -49.665 -13.441 -15.837 1 28.08 ? C6 A1EI4 201 B 1 
HETATM 6 C C7 A1EI4 . . . H 2 -50.373 -12.291 -15.495 1 27.53 ? C7 A1EI4 201 B 1 
HETATM 7 C C10 A1EI4 . . . H 2 -52.469 -14.039 -13.321 1 32.22 ? C10 A1EI4 201 B 1 
HETATM 8 C C11 A1EI4 . . . H 2 -53.006 -15.284 -13.024 1 31.9 ? C11 A1EI4 201 B 1 
HETATM 9 C C12 A1EI4 . . . H 2 -53.45 -16.115 -14.033 1 32.61 ? C12 A1EI4 201 B 1 
HETATM 10 C C13 A1EI4 . . . H 2 -53.347 -15.724 -15.358 1 34.73 ? C13 A1EI4 201 B 1 
HETATM 11 C C14 A1EI4 . . . H 2 -52.789 -14.486 -15.687 1 30.39 ? C14 A1EI4 201 B 1 
HETATM 12 C C15 A1EI4 . . . H 2 -52.674 -14.181 -17.141 1 28.15 ? C15 A1EI4 201 B 1 
HETATM 13 C C18 A1EI4 . . . H 2 -52.33 -11.089 -14.636 1 28.24 ? C18 A1EI4 201 B 1 
HETATM 14 C C19 A1EI4 . . . H 2 -53.567 -11.013 -13.999 1 28.64 ? C19 A1EI4 201 B 1 
HETATM 15 C C20 A1EI4 . . . H 2 -54.16 -9.796 -13.71 1 27.51 ? C20 A1EI4 201 B 1 
HETATM 16 C C21 A1EI4 . . . H 2 -53.548 -8.599 -14.093 1 28.16 ? C21 A1EI4 201 B 1 
HETATM 17 C C23 A1EI4 . . . H 2 -55.408 -7.339 -13.109 1 34.88 ? C23 A1EI4 201 B 1 
HETATM 18 C C24 A1EI4 . . . H 2 -53.895 -6.23 -14.7 1 23.84 ? C24 A1EI4 201 B 1 
HETATM 19 C C25 A1EI4 . . . H 2 -52.293 -8.662 -14.721 1 25.77 ? C25 A1EI4 201 B 1 
HETATM 20 C C26 A1EI4 . . . H 2 -51.692 -9.887 -14.962 1 24.81 ? C26 A1EI4 201 B 1 
HETATM 21 C C28 A1EI4 . . . H 2 -49.771 -11.059 -15.744 1 26.88 ? C28 A1EI4 201 B 1 
HETATM 22 C C29 A1EI4 . . . H 2 -48.503 -10.962 -16.282 1 25.14 ? C29 A1EI4 201 B 1 
HETATM 23 C C8 A1EI4 . . . H 2 -51.708 -12.297 -14.922 1 28.26 ? C8 A1EI4 201 B 1 
HETATM 24 C C9 A1EI4 . . . H 2 -52.357 -13.622 -14.655 1 29.73 ? C9 A1EI4 201 B 1 
HETATM 25 N N2 A1EI4 . . . H 2 -46.557 -12.032 -17.184 1 26.31 ? N2 A1EI4 201 B 1 
HETATM 26 N N22 A1EI4 . . . H 2 -54.178 -7.395 -13.882 1 29.56 ? N22 A1EI4 201 B 1 
HETATM 27 O O16 A1EI4 . . . H 2 -53.331 -13.103 -17.522 1 30.24 ? O16 A1EI4 201 B 1 
HETATM 28 O O17 A1EI4 . . . H 2 -52.049 -14.901 -17.932 1 33.72 ? O17 A1EI4 201 B 1 
HETATM 29 O O27 A1EI4 . . . H 2 -50.425 -9.863 -15.506 1 26.21 ? O27 A1EI4 201 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           29 
#