data_9LVC
#
_model_server_result.job_id            KhUZ3myGjf05IiYX7Fodxg 
_model_server_result.datetime_utc      '2025-03-04 08:29:40' 
_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          9lvc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":101}' 
#
_entry.id    9LVC 
#
_exptl.entry_id    9LVC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              94.111 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PHENOL 
_entity.pdbx_number_of_molecules    4 
_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            9LVC 
_cell.length_a            79.064 
_cell.length_b            79.064 
_cell.length_c            79.496 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9LVC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dodecameric 12 author_and_software_defined_assembly 1 
PISA dodecameric 12 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,I,J,K,L,M,N,O,P,Y,Z,AA,BA 1 1,2,3 
E,F,G,H,Q,R,S,T,U,V,W,X,CA,DA,EA,FA 2 1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 39.532 68.471433 0 
3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -39.532 68.471433 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 I N N 
? 3 M N N 
? 3 Q N N 
? 3 U 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 6 A CYS 6 1_555 A SG CYS 11 A CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 A SG CYS 7 A CYS 7 1_555 B SG CYS 7 B CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 A SG CYS 20 A CYS 20 1_555 B SG CYS 19 B CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 C SG CYS 6 C CYS 6 1_555 C SG CYS 11 C CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 C SG CYS 7 C CYS 7 1_555 D SG CYS 7 D CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 C SG CYS 20 C CYS 20 1_555 D SG CYS 19 D CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 E SG CYS 6 E CYS 6 1_555 E SG CYS 11 E CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf8 E SG CYS 7 E CYS 7 1_555 F SG CYS 7 F CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 E SG CYS 20 E CYS 20 1_555 F SG CYS 19 F CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 G SG CYS 6 G CYS 6 1_555 G SG CYS 11 G CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf11 G SG CYS 7 G CYS 7 1_555 H SG CYS 7 H CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf12 G SG CYS 20 G CYS 20 1_555 H SG CYS 19 H CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 B NZ LYS 29 B LYS 29 1_555 L C1 MYR . B MYR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale2 D NZ LYS 29 D LYS 29 1_555 P C1 MYR . D MYR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale3 P C13 MYR . D MYR 104 1_555 T C14 MYR . F MYR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? 
covale ? covale4 F NZ LYS 29 F LYS 29 1_555 T C1 MYR . F MYR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale5 H NZ LYS 29 H LYS 29 1_555 X C1 MYR . H MYR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
metalc ? metalc1 B NE2 HIS 10 B HIS 10 1_555 J ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc2 B NE2 HIS 10 B HIS 10 1_555 J ZN ZN . B ZN 102 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc3 D NE2 HIS 10 D HIS 10 1_555 N ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc4 D NE2 HIS 10 D HIS 10 1_555 N ZN ZN . D ZN 102 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc5 F NE2 HIS 10 F HIS 10 1_555 R ZN ZN . F ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc6 F NE2 HIS 10 F HIS 10 1_555 R ZN ZN . F ZN 102 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc7 H NE2 HIS 10 H HIS 10 1_555 V ZN ZN . H ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc8 H NE2 HIS 10 H HIS 10 1_555 V ZN ZN . H ZN 102 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
#
_chem_comp.formula           'C6 H6 O' 
_chem_comp.formula_weight    94.111 
_chem_comp.id                IPH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              PHENOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C1 C2 IPH doub 158 n y 
C1 C6 IPH sing 159 n y 
C1 O1 IPH sing 160 n n 
C2 C3 IPH sing 161 n y 
C2 H2 IPH sing 162 n n 
C3 C4 IPH doub 163 n y 
C3 H3 IPH sing 164 n n 
C4 C5 IPH sing 165 n y 
C4 H4 IPH sing 166 n n 
C5 C6 IPH doub 167 n y 
C5 H5 IPH sing 168 n n 
C6 H6 IPH sing 169 n n 
O1 HO1 IPH sing 170 n n 
#
_atom_sites.entry_id                     9LVC 
_atom_sites.fract_transf_matrix[1][1]    0.012648 
_atom_sites.fract_transf_matrix[1][2]    0.007302 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014605 
_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]    0.012579 
_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
I 3 IPH B 1 101 22 IPH IPH . 
J 4 ZN B 1 102 30 ZN ZN . 
K 5 CL B 1 103 31 CL CL . 
L 6 MYR B 1 104 39 MYR MYR . 
M 3 IPH D 1 101 22 IPH IPH . 
N 4 ZN D 1 102 30 ZN ZN . 
O 5 CL D 1 103 31 CL CL . 
P 6 MYR D 1 104 39 MYR MYR . 
Q 3 IPH F 1 101 22 IPH IPH . 
R 4 ZN F 1 102 30 ZN ZN . 
S 5 CL F 1 103 31 CL CL . 
T 6 MYR F 1 104 39 MYR MYR . 
U 3 IPH H 1 101 22 IPH IPH . 
V 4 ZN H 1 102 30 ZN ZN . 
W 5 CL H 1 103 31 CL CL . 
X 6 MYR H 1 104 39 MYR MYR . 
Y 7 HOH A 1 101 41 HOH HOH . 
Y 7 HOH A 2 102 12 HOH HOH . 
Y 7 HOH A 3 103 23 HOH HOH . 
Y 7 HOH A 4 104 8 HOH HOH . 
Y 7 HOH A 5 105 25 HOH HOH . 
Y 7 HOH A 6 106 27 HOH HOH . 
Y 7 HOH A 7 107 10 HOH HOH . 
Y 7 HOH A 8 108 17 HOH HOH . 
Y 7 HOH A 9 109 26 HOH HOH . 
Z 7 HOH B 1 201 44 HOH HOH . 
Z 7 HOH B 2 202 29 HOH HOH . 
Z 7 HOH B 3 203 13 HOH HOH . 
Z 7 HOH B 4 204 2 HOH HOH . 
Z 7 HOH B 5 205 37 HOH HOH . 
Z 7 HOH B 6 206 6 HOH HOH . 
Z 7 HOH B 7 207 21 HOH HOH . 
Z 7 HOH B 8 208 5 HOH HOH . 
AA 7 HOH C 1 101 32 HOH HOH . 
AA 7 HOH C 2 102 33 HOH HOH . 
AA 7 HOH C 3 103 48 HOH HOH . 
AA 7 HOH C 4 104 20 HOH HOH . 
AA 7 HOH C 5 105 39 HOH HOH . 
AA 7 HOH C 6 106 19 HOH HOH . 
BA 7 HOH D 1 201 35 HOH HOH . 
BA 7 HOH D 2 202 11 HOH HOH . 
BA 7 HOH D 3 203 46 HOH HOH . 
CA 7 HOH E 1 101 22 HOH HOH . 
CA 7 HOH E 2 102 15 HOH HOH . 
CA 7 HOH E 3 103 40 HOH HOH . 
CA 7 HOH E 4 104 54 HOH HOH . 
CA 7 HOH E 5 105 38 HOH HOH . 
DA 7 HOH F 1 201 53 HOH HOH . 
DA 7 HOH F 2 202 16 HOH HOH . 
DA 7 HOH F 3 203 36 HOH HOH . 
DA 7 HOH F 4 204 50 HOH HOH . 
DA 7 HOH F 5 205 7 HOH HOH . 
DA 7 HOH F 6 206 18 HOH HOH . 
DA 7 HOH F 7 207 1 HOH HOH . 
DA 7 HOH F 8 208 43 HOH HOH . 
DA 7 HOH F 9 209 49 HOH HOH . 
DA 7 HOH F 10 210 42 HOH HOH . 
EA 7 HOH G 1 101 24 HOH HOH . 
EA 7 HOH G 2 102 34 HOH HOH . 
EA 7 HOH G 3 103 4 HOH HOH . 
EA 7 HOH G 4 104 47 HOH HOH . 
EA 7 HOH G 5 105 52 HOH HOH . 
EA 7 HOH G 6 106 14 HOH HOH . 
EA 7 HOH G 7 107 3 HOH HOH . 
EA 7 HOH G 8 108 31 HOH HOH . 
EA 7 HOH G 9 109 45 HOH HOH . 
FA 7 HOH H 1 201 28 HOH HOH . 
FA 7 HOH H 2 202 30 HOH HOH . 
FA 7 HOH H 3 203 9 HOH HOH . 
FA 7 HOH H 4 204 51 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 IPH . . . Q 3 -4.319 36.29 -9.376 1 29.93 ? C1 IPH 101 F 1 
HETATM 2 C C2 IPH . . . Q 3 -4.52 35.743 -10.638 1 26.92 ? C2 IPH 101 F 1 
HETATM 3 C C3 IPH . . . Q 3 -4.102 36.434 -11.769 1 26.9 ? C3 IPH 101 F 1 
HETATM 4 C C4 IPH . . . Q 3 -3.481 37.671 -11.637 1 23.91 ? C4 IPH 101 F 1 
HETATM 5 C C5 IPH . . . Q 3 -3.279 38.217 -10.375 1 23.43 ? C5 IPH 101 F 1 
HETATM 6 C C6 IPH . . . Q 3 -3.697 37.526 -9.244 1 23.41 ? C6 IPH 101 F 1 
HETATM 7 O O1 IPH . . . Q 3 -4.731 35.607 -8.262 1 29.94 ? O1 IPH 101 F 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           7 
#