data_8GMI
#
_model_server_result.job_id            SrmCl8_eTChSjJAnN34qlA 
_model_server_result.datetime_utc      '2024-11-12 21:17:48' 
_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          8gmi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":402}' 
#
_entry.id    8GMI 
#
_exptl.entry_id    8GMI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              276.193 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            N-phenyl-2-selanylbenzamide 
_entity.pdbx_number_of_molecules    8 
_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            8GMI 
_cell.length_a            122.017 
_cell.length_b            167.486 
_cell.length_c            220.997 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GMI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,V,W 1 1 
C,D,L,M,N,O,X,Y 2 1 
E,F,P,Q,R,S,Z,AA 3 1 
G,H,T,U,BA,CA 4 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 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 T N N 
? 2 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
covale ? covale1 A SG CYS 143 A CYS 143 1_555 I SE1 9JT . A 9JT 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
covale ? covale2 B SG CYS 143 B CYS 143 1_555 K SE1 9JT . B 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
covale ? covale3 C SG CYS 143 C CYS 143 1_555 M SE1 9JT . C 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
covale ? covale4 D SG CYS 143 D CYS 143 1_555 O SE1 9JT . D 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
covale ? covale5 E SG CYS 143 E CYS 143 1_555 Q SE1 9JT . E 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
covale ? covale6 F SG CYS 143 F CYS 143 1_555 S SE1 9JT . F 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
covale ? covale7 G SG CYS 143 G CYS 143 1_555 T SE1 9JT . G 9JT 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
covale ? covale8 H SG CYS 143 H CYS 143 1_555 U SE1 9JT . H 9JT 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
#
_chem_comp.formula           'C13 H11 N O Se' 
_chem_comp.formula_weight    276.193 
_chem_comp.id                9JT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-phenyl-2-selanylbenzamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '~{N}-phenyl-2-selanyl-benzamide;Ebselen, bound form' 
#
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
C05 C04 9JT doub 1 n y 
C05 C06 9JT sing 2 n y 
C04 C03 9JT sing 3 n y 
C06 C07 9JT doub 4 n y 
C03 C02 9JT doub 5 n y 
C07 C02 9JT sing 6 n y 
C07 C08 9JT sing 7 n n 
C16 C15 9JT doub 8 n y 
C16 C11 9JT sing 9 n y 
C02 SE1 9JT sing 10 n n 
N10 C08 9JT sing 11 n n 
N10 C11 9JT sing 12 n n 
C15 C14 9JT sing 13 n y 
C08 O09 9JT doub 14 n n 
C11 C12 9JT doub 15 n y 
C14 C13 9JT doub 16 n y 
C12 C13 9JT sing 17 n y 
C12 H1 9JT sing 18 n n 
C13 H2 9JT sing 19 n n 
C14 H3 9JT sing 20 n n 
C15 H4 9JT sing 21 n n 
C06 H5 9JT sing 22 n n 
C05 H6 9JT sing 23 n n 
C04 H7 9JT sing 24 n n 
C03 H8 9JT sing 25 n n 
SE1 H9 9JT sing 26 n n 
N10 H10 9JT sing 27 n n 
C16 H11 9JT sing 28 n n 
#
_atom_sites.entry_id                     8GMI 
_atom_sites.fract_transf_matrix[1][1]    0.008196 
_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]    0.005971 
_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]    0.004525 
_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 2 9JT A 1 401 143 9JT LIG . 
J 3 FLC B 1 401 401 FLC FLC . 
K 2 9JT B 1 402 143 9JT LIG . 
L 3 FLC C 1 401 401 FLC FLC . 
M 2 9JT C 1 402 143 9JT LIG . 
N 3 FLC D 1 401 401 FLC FLC . 
O 2 9JT D 1 402 143 9JT LIG . 
P 3 FLC E 1 401 401 FLC FLC . 
Q 2 9JT E 1 402 143 9JT LIG . 
R 3 FLC F 1 401 401 FLC FLC . 
S 2 9JT F 1 402 143 9JT LIG . 
T 2 9JT G 1 401 143 9JT LIG . 
U 2 9JT H 1 401 143 9JT LIG . 
V 4 HOH A 1 501 89 HOH HOH . 
V 4 HOH A 2 502 9 HOH HOH . 
V 4 HOH A 3 503 2 HOH HOH . 
V 4 HOH A 4 504 54 HOH HOH . 
V 4 HOH A 5 505 48 HOH HOH . 
V 4 HOH A 6 506 42 HOH HOH . 
V 4 HOH A 7 507 119 HOH HOH . 
V 4 HOH A 8 508 95 HOH HOH . 
V 4 HOH A 9 509 51 HOH HOH . 
V 4 HOH A 10 510 83 HOH HOH . 
V 4 HOH A 11 511 25 HOH HOH . 
V 4 HOH A 12 512 39 HOH HOH . 
V 4 HOH A 13 513 116 HOH HOH . 
V 4 HOH A 14 514 66 HOH HOH . 
W 4 HOH B 1 501 78 HOH HOH . 
W 4 HOH B 2 502 5 HOH HOH . 
W 4 HOH B 3 503 27 HOH HOH . 
W 4 HOH B 4 504 52 HOH HOH . 
W 4 HOH B 5 505 17 HOH HOH . 
W 4 HOH B 6 506 34 HOH HOH . 
W 4 HOH B 7 507 63 HOH HOH . 
W 4 HOH B 8 508 90 HOH HOH . 
W 4 HOH B 9 509 38 HOH HOH . 
W 4 HOH B 10 510 15 HOH HOH . 
W 4 HOH B 11 511 59 HOH HOH . 
W 4 HOH B 12 512 18 HOH HOH . 
W 4 HOH B 13 513 96 HOH HOH . 
W 4 HOH B 14 514 84 HOH HOH . 
W 4 HOH B 15 515 86 HOH HOH . 
W 4 HOH B 16 516 58 HOH HOH . 
W 4 HOH B 17 517 109 HOH HOH . 
W 4 HOH B 18 518 102 HOH HOH . 
W 4 HOH B 19 519 80 HOH HOH . 
W 4 HOH B 20 520 99 HOH HOH . 
X 4 HOH C 1 501 41 HOH HOH . 
X 4 HOH C 2 502 23 HOH HOH . 
X 4 HOH C 3 503 65 HOH HOH . 
X 4 HOH C 4 504 106 HOH HOH . 
X 4 HOH C 5 505 4 HOH HOH . 
X 4 HOH C 6 506 75 HOH HOH . 
X 4 HOH C 7 507 53 HOH HOH . 
X 4 HOH C 8 508 91 HOH HOH . 
X 4 HOH C 9 509 121 HOH HOH . 
X 4 HOH C 10 510 98 HOH HOH . 
X 4 HOH C 11 511 60 HOH HOH . 
X 4 HOH C 12 512 20 HOH HOH . 
X 4 HOH C 13 513 104 HOH HOH . 
X 4 HOH C 14 514 43 HOH HOH . 
X 4 HOH C 15 515 112 HOH HOH . 
X 4 HOH C 16 516 111 HOH HOH . 
X 4 HOH C 17 517 14 HOH HOH . 
X 4 HOH C 18 518 92 HOH HOH . 
X 4 HOH C 19 519 81 HOH HOH . 
X 4 HOH C 20 520 122 HOH HOH . 
Y 4 HOH D 1 501 76 HOH HOH . 
Y 4 HOH D 2 502 87 HOH HOH . 
Y 4 HOH D 3 503 19 HOH HOH . 
Y 4 HOH D 4 504 107 HOH HOH . 
Y 4 HOH D 5 505 72 HOH HOH . 
Y 4 HOH D 6 506 69 HOH HOH . 
Y 4 HOH D 7 507 37 HOH HOH . 
Y 4 HOH D 8 508 32 HOH HOH . 
Y 4 HOH D 9 509 61 HOH HOH . 
Y 4 HOH D 10 510 28 HOH HOH . 
Y 4 HOH D 11 511 22 HOH HOH . 
Y 4 HOH D 12 512 46 HOH HOH . 
Y 4 HOH D 13 513 45 HOH HOH . 
Y 4 HOH D 14 514 24 HOH HOH . 
Y 4 HOH D 15 515 77 HOH HOH . 
Y 4 HOH D 16 516 31 HOH HOH . 
Y 4 HOH D 17 517 73 HOH HOH . 
Y 4 HOH D 18 518 57 HOH HOH . 
Z 4 HOH E 1 501 94 HOH HOH . 
Z 4 HOH E 2 502 6 HOH HOH . 
Z 4 HOH E 3 503 29 HOH HOH . 
Z 4 HOH E 4 504 10 HOH HOH . 
Z 4 HOH E 5 505 21 HOH HOH . 
Z 4 HOH E 6 506 105 HOH HOH . 
Z 4 HOH E 7 507 120 HOH HOH . 
Z 4 HOH E 8 508 30 HOH HOH . 
Z 4 HOH E 9 509 56 HOH HOH . 
Z 4 HOH E 10 510 47 HOH HOH . 
Z 4 HOH E 11 511 11 HOH HOH . 
Z 4 HOH E 12 512 35 HOH HOH . 
Z 4 HOH E 13 513 117 HOH HOH . 
Z 4 HOH E 14 514 85 HOH HOH . 
Z 4 HOH E 15 515 36 HOH HOH . 
Z 4 HOH E 16 516 64 HOH HOH . 
Z 4 HOH E 17 517 40 HOH HOH . 
Z 4 HOH E 18 518 101 HOH HOH . 
Z 4 HOH E 19 519 55 HOH HOH . 
Z 4 HOH E 20 520 44 HOH HOH . 
Z 4 HOH E 21 521 49 HOH HOH . 
Z 4 HOH E 22 522 115 HOH HOH . 
Z 4 HOH E 23 523 3 HOH HOH . 
Z 4 HOH E 24 524 100 HOH HOH . 
Z 4 HOH E 25 525 108 HOH HOH . 
Z 4 HOH E 26 526 79 HOH HOH . 
Z 4 HOH E 27 527 1 HOH HOH . 
Z 4 HOH E 28 528 12 HOH HOH . 
Z 4 HOH E 29 529 114 HOH HOH . 
Z 4 HOH E 30 530 82 HOH HOH . 
Z 4 HOH E 31 531 88 HOH HOH . 
AA 4 HOH F 1 501 118 HOH HOH . 
AA 4 HOH F 2 502 93 HOH HOH . 
AA 4 HOH F 3 503 26 HOH HOH . 
AA 4 HOH F 4 504 71 HOH HOH . 
AA 4 HOH F 5 505 62 HOH HOH . 
AA 4 HOH F 6 506 8 HOH HOH . 
AA 4 HOH F 7 507 103 HOH HOH . 
AA 4 HOH F 8 508 16 HOH HOH . 
AA 4 HOH F 9 509 67 HOH HOH . 
AA 4 HOH F 10 510 110 HOH HOH . 
AA 4 HOH F 11 511 33 HOH HOH . 
AA 4 HOH F 12 512 50 HOH HOH . 
BA 4 HOH G 1 501 13 HOH HOH . 
BA 4 HOH G 2 502 74 HOH HOH . 
CA 4 HOH H 1 501 113 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 C11 9JT . . . O 2 -0.989 -28.651 -15.192 0.87 72.59 ? C11 9JT 402 D 1 
HETATM 2 C C12 9JT . . . O 2 -1.212 -29.563 -14.211 0.87 70.1 ? C12 9JT 402 D 1 
HETATM 3 C C13 9JT . . . O 2 -0.704 -30.821 -14.223 0.87 73.27 ? C13 9JT 402 D 1 
HETATM 4 C C14 9JT . . . O 2 0.092 -31.222 -15.284 0.87 75.4 ? C14 9JT 402 D 1 
HETATM 5 C C15 9JT . . . O 2 0.357 -30.308 -16.329 0.87 68.9 ? C15 9JT 402 D 1 
HETATM 6 O O09 9JT . . . O 2 -2.189 -27.09 -17.292 0.87 77.13 ? O09 9JT 402 D 1 
HETATM 7 C C08 9JT . . . O 2 -2.166 -26.613 -16.207 0.87 85.02 ? C08 9JT 402 D 1 
HETATM 8 C C07 9JT . . . O 2 -2.766 -25.224 -15.981 0.87 82.3 ? C07 9JT 402 D 1 
HETATM 9 C C06 9JT . . . O 2 -1.96 -24.193 -15.524 0.87 84.03 ? C06 9JT 402 D 1 
HETATM 10 C C05 9JT . . . O 2 -2.496 -22.933 -15.317 0.87 82.3 ? C05 9JT 402 D 1 
HETATM 11 C C04 9JT . . . O 2 -3.839 -22.704 -15.567 0.87 86.02 ? C04 9JT 402 D 1 
HETATM 12 C C03 9JT . . . O 2 -4.646 -23.734 -16.024 0.87 76.37 ? C03 9JT 402 D 1 
HETATM 13 C C02 9JT . . . O 2 -4.11 -24.994 -16.233 0.87 77.44 ? C02 9JT 402 D 1 
HETATM 14 SE SE1 9JT . . . O 2 -5.255 -26.439 -16.874 0.87 115.64 ? SE1 9JT 402 D 1 
HETATM 15 N N10 9JT . . . O 2 -1.579 -27.325 -15.081 0.87 79.43 ? N10 9JT 402 D 1 
HETATM 16 C C16 9JT . . . O 2 -0.193 -29.008 -16.27 0.87 68.03 ? C16 9JT 402 D 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#