data_5F4L
#
_model_server_result.job_id            YAkRldxVFtJe6mCZ15Drpw 
_model_server_result.datetime_utc      '2024-10-18 02:30:55' 
_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          5f4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5F4L 
#
_exptl.entry_id    5F4L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              446.906 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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         90 
_cell.entry_id            5F4L 
_cell.length_a            67.159 
_cell.length_b            127.806 
_cell.length_c            192.47 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5F4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 D 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 54 1_555 A SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 71 A CYS 119 1_555 A SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 A SG CYS 97 A CYS 218 1_555 A SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 A SG CYS 107 A CYS 228 1_555 A SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 175 A CYS 296 1_555 A SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 A SG CYS 240 A CYS 378 1_555 A SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 A SG CYS 247 A CYS 385 1_555 A SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 B SG CYS 6 B CYS 54 1_555 B SG CYS 26 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 B SG CYS 71 B CYS 119 1_555 B SG CYS 84 B CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf10 B SG CYS 97 B CYS 218 1_555 B SG CYS 126 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf11 B SG CYS 107 B CYS 228 1_555 B SG CYS 118 B CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf12 B SG CYS 175 B CYS 296 1_555 B SG CYS 194 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf13 B SG CYS 240 B CYS 378 1_555 B SG CYS 304 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf14 B SG CYS 247 B CYS 385 1_555 B SG CYS 277 B CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C21 H24 Cl F N6 O2' 
_chem_comp.formula_weight    446.906 
_chem_comp.id                5VE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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
C26 C27 5VE doub 1 n y 
C26 C24 5VE sing 2 n y 
C27 C20 5VE sing 3 n y 
N03 C04 5VE sing 4 n n 
N03 C02 5VE sing 5 n n 
CL25 C24 5VE sing 6 n n 
N28 C02 5VE doub 7 n n 
C24 C22 5VE doub 8 n y 
C04 C05 5VE sing 9 n n 
C02 N01 5VE sing 10 n n 
C06 C05 5VE sing 11 n n 
C06 C07 5VE sing 12 n n 
C05 C13 5VE sing 13 n n 
C20 N19 5VE sing 14 n n 
C20 C21 5VE doub 15 n y 
N19 C17 5VE sing 16 n n 
C17 O18 5VE doub 17 n n 
C17 C15 5VE sing 18 n n 
O16 C15 5VE doub 19 n n 
C22 C21 5VE sing 20 n y 
C22 F23 5VE sing 21 n n 
C15 N14 5VE sing 22 n n 
N14 C13 5VE sing 23 n n 
C13 C12 5VE sing 24 n n 
C07 C08 5VE doub 25 n y 
C07 C12 5VE sing 26 n y 
C08 C09 5VE sing 27 n y 
C12 C11 5VE doub 28 n y 
C09 C10 5VE doub 29 n y 
C11 C10 5VE sing 30 n y 
C10 C00 5VE sing 31 n n 
C00 N 5VE sing 32 n n 
N C 5VE sing 33 n n 
C13 H1 5VE sing 34 n n 
C21 H2 5VE sing 35 n n 
C26 H3 5VE sing 36 n n 
N H4 5VE sing 37 n n 
C H6 5VE sing 38 n n 
C H7 5VE sing 39 n n 
C H8 5VE sing 40 n n 
C00 H9 5VE sing 41 n n 
C00 H10 5VE sing 42 n n 
N01 H11 5VE sing 43 n n 
N01 H12 5VE sing 44 n n 
N03 H13 5VE sing 45 n n 
C04 H14 5VE sing 46 n n 
C04 H15 5VE sing 47 n n 
C05 H16 5VE sing 48 n n 
C06 H17 5VE sing 49 n n 
C06 H18 5VE sing 50 n n 
C08 H19 5VE sing 51 n n 
C09 H20 5VE sing 52 n n 
C11 H21 5VE sing 53 n n 
N14 H22 5VE sing 54 n n 
N19 H23 5VE sing 55 n n 
C27 H24 5VE sing 56 n n 
N28 H25 5VE sing 57 n n 
#
_atom_sites.entry_id                     5F4L 
_atom_sites.fract_transf_matrix[1][1]    0.01489 
_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]    0.007824 
_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]    0.005196 
_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 5VE A 1 501 1 5VE LIG . 
D 2 5VE B 1 501 2 5VE LIG . 
E 3 HOH A 1 601 49 HOH HOH . 
E 3 HOH A 2 602 27 HOH HOH . 
E 3 HOH A 3 603 15 HOH HOH . 
E 3 HOH A 4 604 29 HOH HOH . 
E 3 HOH A 5 605 19 HOH HOH . 
E 3 HOH A 6 606 39 HOH HOH . 
E 3 HOH A 7 607 5 HOH HOH . 
E 3 HOH A 8 608 28 HOH HOH . 
E 3 HOH A 9 609 61 HOH HOH . 
E 3 HOH A 10 610 3 HOH HOH . 
E 3 HOH A 11 611 51 HOH HOH . 
E 3 HOH A 12 612 24 HOH HOH . 
E 3 HOH A 13 613 8 HOH HOH . 
E 3 HOH A 14 614 40 HOH HOH . 
E 3 HOH A 15 615 1 HOH HOH . 
E 3 HOH A 16 616 37 HOH HOH . 
E 3 HOH A 17 617 4 HOH HOH . 
E 3 HOH A 18 618 6 HOH HOH . 
E 3 HOH A 19 619 36 HOH HOH . 
E 3 HOH A 20 620 26 HOH HOH . 
E 3 HOH A 21 621 12 HOH HOH . 
E 3 HOH A 22 622 32 HOH HOH . 
E 3 HOH A 23 623 53 HOH HOH . 
E 3 HOH A 24 624 14 HOH HOH . 
E 3 HOH A 25 625 47 HOH HOH . 
E 3 HOH A 26 626 9 HOH HOH . 
E 3 HOH A 27 627 30 HOH HOH . 
E 3 HOH A 28 628 59 HOH HOH . 
E 3 HOH A 29 629 55 HOH HOH . 
E 3 HOH A 30 630 18 HOH HOH . 
E 3 HOH A 31 631 57 HOH HOH . 
E 3 HOH A 32 632 41 HOH HOH . 
E 3 HOH A 33 633 7 HOH HOH . 
E 3 HOH A 34 634 21 HOH HOH . 
E 3 HOH A 35 635 48 HOH HOH . 
E 3 HOH A 36 636 54 HOH HOH . 
E 3 HOH A 37 637 34 HOH HOH . 
E 3 HOH A 38 638 22 HOH HOH . 
E 3 HOH A 39 639 33 HOH HOH . 
F 3 HOH B 1 601 63 HOH HOH . 
F 3 HOH B 2 602 46 HOH HOH . 
F 3 HOH B 3 603 16 HOH HOH . 
F 3 HOH B 4 604 44 HOH HOH . 
F 3 HOH B 5 605 42 HOH HOH . 
F 3 HOH B 6 606 20 HOH HOH . 
F 3 HOH B 7 607 23 HOH HOH . 
F 3 HOH B 8 608 11 HOH HOH . 
F 3 HOH B 9 609 38 HOH HOH . 
F 3 HOH B 10 610 56 HOH HOH . 
F 3 HOH B 11 611 45 HOH HOH . 
F 3 HOH B 12 612 17 HOH HOH . 
F 3 HOH B 13 613 60 HOH HOH . 
F 3 HOH B 14 614 58 HOH HOH . 
F 3 HOH B 15 615 50 HOH HOH . 
F 3 HOH B 16 616 35 HOH HOH . 
F 3 HOH B 17 617 10 HOH HOH . 
F 3 HOH B 18 618 25 HOH HOH . 
F 3 HOH B 19 619 13 HOH HOH . 
F 3 HOH B 20 620 2 HOH HOH . 
F 3 HOH B 21 621 52 HOH HOH . 
F 3 HOH B 22 622 43 HOH HOH . 
F 3 HOH B 23 623 62 HOH HOH . 
F 3 HOH B 24 624 31 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 C10 5VE . . . D 2 -17.859 -59.596 21.281 1 62.66 ? C10 5VE 501 B 1 
HETATM 2 C C13 5VE . . . D 2 -15.35 -59.395 18.351 1 59.28 ? C13 5VE 501 B 1 
HETATM 3 C C15 5VE . . . D 2 -13.583 -57.758 17.874 1 47.48 ? C15 5VE 501 B 1 
HETATM 4 C C17 5VE . . . D 2 -13.146 -56.309 17.682 1 42.78 ? C17 5VE 501 B 1 
HETATM 5 C C20 5VE . . . D 2 -11.274 -54.725 17.156 1 49.86 ? C20 5VE 501 B 1 
HETATM 6 C C21 5VE . . . D 2 -11.636 -53.639 17.948 1 53.25 ? C21 5VE 501 B 1 
HETATM 7 C C22 5VE . . . D 2 -11.121 -52.351 17.647 1 55.57 ? C22 5VE 501 B 1 
HETATM 8 C C24 5VE . . . D 2 -10.244 -52.17 16.542 1 46.81 ? C24 5VE 501 B 1 
HETATM 9 C C26 5VE . . . D 2 -9.886 -53.256 15.745 1 54.01 ? C26 5VE 501 B 1 
HETATM 10 N N 5VE . . . D 2 -18.878 -58.635 23.3 1 73.46 ? N 5VE 501 B 1 
HETATM 11 C C 5VE . . . D 2 -19.062 -58.755 24.723 1 74.92 ? C 5VE 501 B 1 
HETATM 12 C C00 5VE . . . D 2 -17.95 -59.567 22.882 1 60.26 ? C00 5VE 501 B 1 
HETATM 13 CL CL25 5VE . . . D 2 -9.606 -50.597 16.165 1 58.88 ? CL25 5VE 501 B 1 
HETATM 14 N N01 5VE . . . D 2 -13.39 -62.893 17.922 1 73.35 ? N01 5VE 501 B 1 
HETATM 15 C C02 5VE . . . D 2 -13.198 -62.367 16.793 1 53.62 ? C02 5VE 501 B 1 
HETATM 16 N N03 5VE . . . D 2 -14.26 -61.585 16.156 1 50.44 ? N03 5VE 501 B 1 
HETATM 17 C C04 5VE . . . D 2 -15.582 -61.391 16.823 1 54.89 ? C04 5VE 501 B 1 
HETATM 18 C C05 5VE . . . D 2 -15.868 -59.892 17.003 1 58.74 ? C05 5VE 501 B 1 
HETATM 19 C C06 5VE . . . D 2 -17.305 -59.646 17.016 1 53.23 ? C06 5VE 501 B 1 
HETATM 20 C C07 5VE . . . D 2 -17.712 -59.653 18.476 1 61.08 ? C07 5VE 501 B 1 
HETATM 21 C C08 5VE . . . D 2 -18.939 -59.773 19.093 1 62.63 ? C08 5VE 501 B 1 
HETATM 22 C C09 5VE . . . D 2 -19.018 -59.745 20.513 1 53.38 ? C09 5VE 501 B 1 
HETATM 23 C C11 5VE . . . D 2 -16.614 -59.474 20.658 1 57.39 ? C11 5VE 501 B 1 
HETATM 24 C C12 5VE . . . D 2 -16.545 -59.498 19.262 1 50.37 ? C12 5VE 501 B 1 
HETATM 25 N N14 5VE . . . D 2 -14.962 -58.059 18.191 1 57.82 ? N14 5VE 501 B 1 
HETATM 26 O O16 5VE . . . D 2 -12.766 -58.666 17.763 1 52.47 ? O16 5VE 501 B 1 
HETATM 27 O O18 5VE . . . D 2 -13.968 -55.414 17.795 1 49.84 ? O18 5VE 501 B 1 
HETATM 28 N N19 5VE . . . D 2 -11.751 -56.019 17.377 1 52.94 ? N19 5VE 501 B 1 
HETATM 29 C C27 5VE . . . D 2 -10.4 -54.537 16.044 1 47.11 ? C27 5VE 501 B 1 
HETATM 30 N N28 5VE . . . D 2 -12.007 -62.527 16.167 1 51.55 ? N28 5VE 501 B 1 
HETATM 31 F F23 5VE . . . D 2 -11.455 -51.316 18.399 1 63.99 ? F23 5VE 501 B 1 
#
_model_server_stats.io_time_ms              106 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           31 
#