data_4I54
#
_model_server_result.job_id            w7mo6L_YzfdfOFVY3nUXJg 
_model_server_result.datetime_utc      '2024-11-28 07:54:39' 
_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":"C","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 . . . C 2 1.274 -15.243 -10.449 1 64.24 ? N01 1C1 501 A 1 
HETATM 2 C C02 1C1 . . . C 2 0.6 -15 -11.522 1 59.63 ? C02 1C1 501 A 1 
HETATM 3 N N03 1C1 . . . C 2 -0.225 -13.791 -11.597 1 58.13 ? N03 1C1 501 A 1 
HETATM 4 C C04 1C1 . . . C 2 -1.011 -13.535 -12.807 1 53.12 ? C04 1C1 501 A 1 
HETATM 5 C C05 1C1 . . . C 2 -2.508 -13.552 -12.531 1 44.42 ? C05 1C1 501 A 1 
HETATM 6 C C06 1C1 . . . C 2 -3.222 -13.097 -13.763 1 39.62 ? C06 1C1 501 A 1 
HETATM 7 C C07 1C1 . . . C 2 -4.083 -14.277 -14.17 1 49.66 ? C07 1C1 501 A 1 
HETATM 8 C C08 1C1 . . . C 2 -4.971 -14.414 -15.367 1 54 ? C08 1C1 501 A 1 
HETATM 9 C C09 1C1 . . . C 2 -5.685 -15.625 -15.513 1 59.68 ? C09 1C1 501 A 1 
HETATM 10 C C10 1C1 . . . C 2 -5.594 -16.68 -14.597 1 52.5 ? C10 1C1 501 A 1 
HETATM 11 C C11 1C1 . . . C 2 -4.751 -16.572 -13.454 1 49.84 ? C11 1C1 501 A 1 
HETATM 12 C C12 1C1 . . . C 2 -3.969 -15.3 -13.27 1 48.23 ? C12 1C1 501 A 1 
HETATM 13 C C13 1C1 . . . C 2 -3.027 -14.877 -12.163 1 42.76 ? C13 1C1 501 A 1 
HETATM 14 N N14 1C1 . . . C 2 -3.844 -14.736 -10.962 1 44.54 ? N14 1C1 501 A 1 
HETATM 15 C C15 1C1 . . . C 2 -3.423 -15.306 -9.69 1 41.02 ? C15 1C1 501 A 1 
HETATM 16 O O16 1C1 . . . C 2 -2.24 -15.529 -9.503 1 41.29 ? O16 1C1 501 A 1 
HETATM 17 C C17 1C1 . . . C 2 -4.404 -15.21 -8.558 1 36.27 ? C17 1C1 501 A 1 
HETATM 18 O O18 1C1 . . . C 2 -5.494 -14.672 -8.798 1 29.27 ? O18 1C1 501 A 1 
HETATM 19 N N19 1C1 . . . C 2 -3.941 -15.504 -7.204 1 30.1 ? N19 1C1 501 A 1 
HETATM 20 C C20 1C1 . . . C 2 -4.528 -14.947 -6.009 1 40.99 ? C20 1C1 501 A 1 
HETATM 21 C C21 1C1 . . . C 2 -5.844 -14.814 -5.938 1 28.98 ? C21 1C1 501 A 1 
HETATM 22 C C22 1C1 . . . C 2 -6.538 -14.591 -4.764 1 28.65 ? C22 1C1 501 A 1 
HETATM 23 F F23 1C1 . . . C 2 -7.858 -14.448 -4.65 1 28.15 ? F23 1C1 501 A 1 
HETATM 24 C C24 1C1 . . . C 2 -5.698 -14.52 -3.588 1 29.01 ? C24 1C1 501 A 1 
HETATM 25 CL CL1 1C1 . . . C 2 -6.553 -14.221 -2.119 1 34.85 ? CL1 1C1 501 A 1 
HETATM 26 C C26 1C1 . . . C 2 -4.297 -14.655 -3.681 1 29.65 ? C26 1C1 501 A 1 
HETATM 27 C C27 1C1 . . . C 2 -3.747 -14.868 -4.932 1 35.95 ? C27 1C1 501 A 1 
HETATM 28 N N28 1C1 . . . C 2 0.648 -15.838 -12.558 1 53.25 ? N28 1C1 501 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#