data_4I54
#
_model_server_result.job_id            mqfGF-w_n_xBpvx0Em-xHg 
_model_server_result.datetime_utc      '2024-12-01 01:11:01' 
_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          4i54 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
#
_entry.id    4I54 
#
_exptl.entry_id    4I54 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.846 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium' 
_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          90.89 
_cell.angle_gamma         90 
_cell.entry_id            4I54 
_cell.length_a            65.324 
_cell.length_b            68.775 
_cell.length_c            94.443 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4I54 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,E,F,G,H,I,J,K,L,W 1 1 
B,M,N,O,P,Q,R,S,T,U,V,X 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 M 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 11 A CYS 54 1_555 A SG CYS 31 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 A SG CYS 76 A CYS 119 1_555 A SG CYS 89 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf3 A SG CYS 102 A CYS 218 1_555 A SG CYS 131 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 A SG CYS 112 A CYS 228 1_555 A SG CYS 123 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf5 A SG CYS 180 A CYS 296 1_555 A SG CYS 199 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 A SG CYS 245 A CYS 378 1_555 A SG CYS 306 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf7 A SG CYS 252 A CYS 385 1_555 A SG CYS 279 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf8 B SG CYS 11 B CYS 54 1_555 B SG CYS 31 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf9 B SG CYS 76 B CYS 119 1_555 B SG CYS 89 B CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf10 B SG CYS 102 B CYS 218 1_555 B SG CYS 131 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf11 B SG CYS 112 B CYS 228 1_555 B SG CYS 123 B CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf12 B SG CYS 180 B CYS 296 1_555 B SG CYS 199 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf13 B SG CYS 245 B CYS 378 1_555 B SG CYS 306 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 B SG CYS 252 B CYS 385 1_555 B SG CYS 279 B CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 118 A ASN 234 1_555 E C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale2 A ND2 ASN 146 A ASN 262 1_555 F C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale3 A ND2 ASN 160 A ASN 276 1_555 G C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale4 A ND2 ASN 173 A ASN 289 1_555 H C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? 
covale ? covale5 A ND2 ASN 179 A ASN 295 1_555 I C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale6 A ND2 ASN 202 A ASN 334 1_555 J C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale7 A ND2 ASN 223 A ASN 355 1_555 K C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.557 ? 
covale ? covale8 A ND2 ASN 253 A ASN 386 1_555 L C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale9 B ND2 ASN 118 B ASN 234 1_555 N C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
covale ? covale10 B ND2 ASN 125 B ASN 241 1_555 T C1 NAG . B NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale11 B ND2 ASN 146 B ASN 262 1_555 O C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale12 B ND2 ASN 160 B ASN 276 1_555 P C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale13 B ND2 ASN 173 B ASN 289 1_555 Q C1 NAG . B NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale14 B ND2 ASN 179 B ASN 295 1_555 R C1 NAG . B NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale15 B ND2 ASN 253 B ASN 386 1_555 S C1 NAG . B NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale16 B ND2 ASN 309 B ASN 448 1_555 U C1 NAG . B NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
#
_chem_comp.formula           'C19 H20 Cl F N5 O2 1' 
_chem_comp.formula_weight    404.846 
_chem_comp.id                1C1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '[amino({[(1R,2R)-1-{[(4-chloro-3- fluorophenyl)carbamoyl]formamido}-2,3-dihydro-1H- inden-2-yl]methyl}amino)methylidene]azanium' 
#
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
N28 C02 1C1 doub 1 n n 
C02 N03 1C1 sing 2 n n 
C02 N01 1C1 sing 3 n n 
N03 C04 1C1 sing 4 n n 
C04 C05 1C1 sing 5 n n 
C27 C26 1C1 doub 6 n y 
C27 C20 1C1 sing 7 n y 
C26 C24 1C1 sing 8 n y 
C05 C06 1C1 sing 9 n n 
C05 C13 1C1 sing 10 n n 
O16 C15 1C1 doub 11 n n 
C20 N19 1C1 sing 12 n n 
C20 C21 1C1 doub 13 n y 
N19 C17 1C1 sing 14 n n 
C24 CL1 1C1 sing 15 n n 
C24 C22 1C1 doub 16 n y 
C15 C17 1C1 sing 17 n n 
C15 N14 1C1 sing 18 n n 
C06 C07 1C1 sing 19 n n 
C13 N14 1C1 sing 20 n n 
C13 C12 1C1 sing 21 n n 
C17 O18 1C1 doub 22 n n 
C21 C22 1C1 sing 23 n y 
C22 F23 1C1 sing 24 n n 
C07 C12 1C1 doub 25 n y 
C07 C08 1C1 sing 26 n y 
C12 C11 1C1 sing 27 n y 
C08 C09 1C1 doub 28 n y 
C11 C10 1C1 doub 29 n y 
C09 C10 1C1 sing 30 n y 
N01 H1 1C1 sing 31 n n 
N01 H2 1C1 sing 32 n n 
N03 H3 1C1 sing 33 n n 
C04 H4 1C1 sing 34 n n 
C04 H5 1C1 sing 35 n n 
C05 H6 1C1 sing 36 n n 
C06 H7 1C1 sing 37 n n 
C06 H8 1C1 sing 38 n n 
C08 H9 1C1 sing 39 n n 
C09 H10 1C1 sing 40 n n 
C10 H11 1C1 sing 41 n n 
C11 H12 1C1 sing 42 n n 
C13 H13 1C1 sing 43 n n 
N14 H14 1C1 sing 44 n n 
N19 H15 1C1 sing 45 n n 
C21 H16 1C1 sing 46 n n 
C26 H17 1C1 sing 47 n n 
C27 H18 1C1 sing 48 n n 
N28 H19 1C1 sing 49 n n 
N28 H20 1C1 sing 50 n n 
#
_atom_sites.entry_id                     4I54 
_atom_sites.fract_transf_matrix[1][1]    0.015308 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000238 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01454 
_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]    0.01059 
_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 1C1 A 1 501 1 1C1 D1C . 
D 3 EPE A 1 502 500 EPE EPE . 
E 4 NAG A 1 503 501 NAG NAG . 
F 4 NAG A 1 504 502 NAG NAG . 
G 4 NAG A 1 505 503 NAG NAG . 
H 4 NAG A 1 506 506 NAG NAG . 
I 4 NAG A 1 507 505 NAG NAG . 
J 4 NAG A 1 508 506 NAG NAG . 
K 4 NAG A 1 509 509 NAG NAG . 
L 4 NAG A 1 510 508 NAG NAG . 
M 2 1C1 B 1 501 1 1C1 D1C . 
N 4 NAG B 1 502 502 NAG NAG . 
O 4 NAG B 1 503 502 NAG NAG . 
P 4 NAG B 1 504 503 NAG NAG . 
Q 4 NAG B 1 505 504 NAG NAG . 
R 4 NAG B 1 506 505 NAG NAG . 
S 4 NAG B 1 507 506 NAG NAG . 
T 4 NAG B 1 508 507 NAG NAG . 
U 4 NAG B 1 509 508 NAG NAG . 
V 3 EPE B 1 510 509 EPE EPE . 
W 5 HOH A 1 601 1 HOH HOH . 
W 5 HOH A 2 602 2 HOH HOH . 
W 5 HOH A 3 603 3 HOH HOH . 
W 5 HOH A 4 604 5 HOH HOH . 
W 5 HOH A 5 605 6 HOH HOH . 
W 5 HOH A 6 606 7 HOH HOH . 
W 5 HOH A 7 607 14 HOH HOH . 
W 5 HOH A 8 608 15 HOH HOH . 
W 5 HOH A 9 609 16 HOH HOH . 
W 5 HOH A 10 610 17 HOH HOH . 
W 5 HOH A 11 611 18 HOH HOH . 
W 5 HOH A 12 612 19 HOH HOH . 
W 5 HOH A 13 613 20 HOH HOH . 
W 5 HOH A 14 614 23 HOH HOH . 
W 5 HOH A 15 615 24 HOH HOH . 
W 5 HOH A 16 616 25 HOH HOH . 
W 5 HOH A 17 617 26 HOH HOH . 
X 5 HOH B 1 601 4 HOH HOH . 
X 5 HOH B 2 602 8 HOH HOH . 
X 5 HOH B 3 603 9 HOH HOH . 
X 5 HOH B 4 604 10 HOH HOH . 
X 5 HOH B 5 605 11 HOH HOH . 
X 5 HOH B 6 606 12 HOH HOH . 
X 5 HOH B 7 607 13 HOH HOH . 
X 5 HOH B 8 608 21 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 N N01 1C1 . . . M 2 -41.786 -34.022 -53.106 1 93.01 ? N01 1C1 501 B 1 
HETATM 2 C C02 1C1 . . . M 2 -40.914 -33.042 -52.871 1 91.88 ? C02 1C1 501 B 1 
HETATM 3 N N03 1C1 . . . M 2 -41.308 -31.835 -52.121 1 80.21 ? N03 1C1 501 B 1 
HETATM 4 C C04 1C1 . . . M 2 -42.724 -31.563 -51.802 1 73.33 ? C04 1C1 501 B 1 
HETATM 5 C C05 1C1 . . . M 2 -42.982 -31.502 -50.301 1 68.48 ? C05 1C1 501 B 1 
HETATM 6 C C06 1C1 . . . M 2 -44.313 -30.85 -50.118 1 56.27 ? C06 1C1 501 B 1 
HETATM 7 C C07 1C1 . . . M 2 -45.18 -31.939 -49.494 1 67.85 ? C07 1C1 501 B 1 
HETATM 8 C C08 1C1 . . . M 2 -46.639 -31.897 -49.166 1 70.75 ? C08 1C1 501 B 1 
HETATM 9 C C09 1C1 . . . M 2 -47.234 -33.037 -48.598 1 71.4 ? C09 1C1 501 B 1 
HETATM 10 C C10 1C1 . . . M 2 -46.506 -34.2 -48.324 1 69.74 ? C10 1C1 501 B 1 
HETATM 11 C C11 1C1 . . . M 2 -45.119 -34.265 -48.623 1 66.13 ? C11 1C1 501 B 1 
HETATM 12 C C12 1C1 . . . M 2 -44.458 -33.065 -49.241 1 58.24 ? C12 1C1 501 B 1 
HETATM 13 C C13 1C1 . . . M 2 -43.011 -32.841 -49.66 1 56.8 ? C13 1C1 501 B 1 
HETATM 14 N N14 1C1 . . . M 2 -42.173 -32.964 -48.46 1 55.05 ? N14 1C1 501 B 1 
HETATM 15 C C15 1C1 . . . M 2 -40.707 -33.052 -48.431 1 54.46 ? C15 1C1 501 B 1 
HETATM 16 O O16 1C1 . . . M 2 -40.089 -33.564 -49.337 1 55.33 ? O16 1C1 501 B 1 
HETATM 17 C C17 1C1 . . . M 2 -40.039 -32.898 -47.097 1 58.49 ? C17 1C1 501 B 1 
HETATM 18 O O18 1C1 . . . M 2 -40.774 -32.644 -46.125 1 55.32 ? O18 1C1 501 B 1 
HETATM 19 N N19 1C1 . . . M 2 -38.613 -32.57 -47.116 1 60.43 ? N19 1C1 501 B 1 
HETATM 20 C C20 1C1 . . . M 2 -37.717 -32.54 -45.978 1 62.83 ? C20 1C1 501 B 1 
HETATM 21 C C21 1C1 . . . M 2 -38.188 -32.483 -44.746 1 50.22 ? C21 1C1 501 B 1 
HETATM 22 C C22 1C1 . . . M 2 -37.386 -32.24 -43.636 1 48.97 ? C22 1C1 501 B 1 
HETATM 23 F F23 1C1 . . . M 2 -37.886 -32.196 -42.415 1 48.23 ? F23 1C1 501 B 1 
HETATM 24 C C24 1C1 . . . M 2 -35.959 -32.045 -43.9 1 51.66 ? C24 1C1 501 B 1 
HETATM 25 CL CL1 1C1 . . . M 2 -34.854 -31.74 -42.574 1 55.6 ? CL1 1C1 501 B 1 
HETATM 26 C C26 1C1 . . . M 2 -35.502 -32.112 -45.232 1 49.59 ? C26 1C1 501 B 1 
HETATM 27 C C27 1C1 . . . M 2 -36.421 -32.365 -46.234 1 66.28 ? C27 1C1 501 B 1 
HETATM 28 N N28 1C1 . . . M 2 -39.71 -33.158 -53.312 1 97.2 ? N28 1C1 501 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#