data_1IBS
#
_model_server_result.job_id            PojJK5crhR7dxI0gp5NmCA 
_model_server_result.datetime_utc      '2025-02-18 19:55:50' 
_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          1ibs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1009}' 
#
_entry.id    1IBS 
#
_exptl.entry_id    1IBS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              345.248 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'METHYL PHOSPHONIC ACID ADENOSINE ESTER' 
_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         120 
_cell.entry_id            1IBS 
_cell.length_a            115.6 
_cell.length_b            115.6 
_cell.length_c            107.67 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1IBS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 57.8 100.112537 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 -57.8 100.112537 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 G N N 
? 4 L 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
metalc ? metalc1 A NE2 HIS 136 A HIS 135 1_555 E CD CD . A CD 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc2 A OD2 ASP 175 A ASP 174 1_555 F CD CD . A CD 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc3 A OD1 ASP 224 A ASP 223 1_555 F CD CD . A CD 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? 
metalc ? metalc4 A OD2 ASP 224 A ASP 223 1_555 F CD CD . A CD 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? 
metalc ? metalc5 E CD CD . A CD 1005 1_555 G O3P ABM . A ABM 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
metalc ? metalc6 B NE2 HIS 136 B HIS 135 1_555 J CD CD . B CD 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc7 B OD2 ASP 175 B ASP 174 1_555 K CD CD . B CD 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc8 B OD2 ASP 224 B ASP 223 1_555 K CD CD . B CD 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? 
metalc ? metalc9 B OD1 ASP 224 B ASP 223 1_555 K CD CD . B CD 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
metalc ? metalc10 J CD CD . B CD 1007 1_555 L O3P ABM . B ABM 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc11 K CD CD . B CD 1008 1_555 N O HOH . B HOH 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? 
#
_chem_comp.formula           'C11 H16 N5 O6 P' 
_chem_comp.formula_weight    345.248 
_chem_comp.id                ABM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'METHYL PHOSPHONIC ACID ADENOSINE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE' 
#
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
P CM ABM sing 1 n n 
P O2P ABM doub 2 n n 
P O3P ABM sing 3 n n 
P O5' ABM sing 4 n n 
CM HM1 ABM sing 5 n n 
CM HM2 ABM sing 6 n n 
CM HM3 ABM sing 7 n n 
O3P HOP3 ABM sing 8 n n 
O5' C5' ABM sing 9 n n 
C5' C4' ABM sing 10 n n 
C5' "H5'1" ABM sing 11 n n 
C5' "H5'2" ABM sing 12 n n 
C4' O4' ABM sing 13 n n 
C4' C3' ABM sing 14 n n 
C4' H4' ABM sing 15 n n 
O4' C1' ABM sing 16 n n 
C3' O3' ABM sing 17 n n 
C3' C2' ABM sing 18 n n 
C3' H3' ABM sing 19 n n 
O3' HO3' ABM sing 20 n n 
C2' O2' ABM sing 21 n n 
C2' C1' ABM sing 22 n n 
C2' H2' ABM sing 23 n n 
O2' HO2' ABM sing 24 n n 
C1' N9 ABM sing 25 n n 
C1' H1' ABM sing 26 n n 
N9 C8 ABM sing 27 n y 
N9 C4 ABM sing 28 n y 
C8 N7 ABM doub 29 n y 
C8 H8 ABM sing 30 n n 
N7 C5 ABM sing 31 n y 
C5 C6 ABM sing 32 n y 
C5 C4 ABM doub 33 n y 
C6 N6 ABM sing 34 n n 
C6 N1 ABM doub 35 n y 
N6 HN61 ABM sing 36 n n 
N6 HN62 ABM sing 37 n n 
N1 C2 ABM sing 38 n y 
C2 N3 ABM doub 39 n y 
C2 H2 ABM sing 40 n n 
N3 C4 ABM sing 41 n y 
#
_atom_sites.entry_id                     1IBS 
_atom_sites.fract_transf_matrix[1][1]    0.00865 
_atom_sites.fract_transf_matrix[1][2]    0.00499 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00999 
_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]    0.00929 
_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 SO4 A 1 1002 1002 SO4 SO4 . 
D 2 SO4 A 1 1004 1004 SO4 SO4 . 
E 3 CD A 1 1005 1005 CD CD . 
F 3 CD A 1 1006 1006 CD CD . 
G 4 ABM A 1 1009 1009 ABM AMP . 
H 2 SO4 B 1 1001 1001 SO4 SO4 . 
I 2 SO4 B 1 1003 1003 SO4 SO4 . 
J 3 CD B 1 1007 1007 CD CD . 
K 3 CD B 1 1008 1008 CD CD . 
L 4 ABM B 1 1010 1010 ABM AMP . 
M 5 HOH A 1 1010 1 HOH HOH . 
M 5 HOH A 2 1011 2 HOH HOH . 
M 5 HOH A 3 1012 3 HOH HOH . 
M 5 HOH A 4 1013 8 HOH HOH . 
M 5 HOH A 5 1014 9 HOH HOH . 
M 5 HOH A 6 1015 10 HOH HOH . 
M 5 HOH A 7 1016 11 HOH HOH . 
M 5 HOH A 8 1017 14 HOH HOH . 
M 5 HOH A 9 1018 16 HOH HOH . 
M 5 HOH A 10 1019 17 HOH HOH . 
M 5 HOH A 11 1020 18 HOH HOH . 
M 5 HOH A 12 1021 19 HOH HOH . 
M 5 HOH A 13 1022 29 HOH HOH . 
M 5 HOH A 14 1023 30 HOH HOH . 
M 5 HOH A 15 1024 31 HOH HOH . 
M 5 HOH A 16 1025 32 HOH HOH . 
M 5 HOH A 17 1026 36 HOH HOH . 
M 5 HOH A 18 1027 37 HOH HOH . 
M 5 HOH A 19 1028 38 HOH HOH . 
M 5 HOH A 20 1029 39 HOH HOH . 
M 5 HOH A 21 1030 41 HOH HOH . 
M 5 HOH A 22 1031 46 HOH HOH . 
N 5 HOH B 1 1011 4 HOH HOH . 
N 5 HOH B 2 1012 5 HOH HOH . 
N 5 HOH B 3 1013 6 HOH HOH . 
N 5 HOH B 4 1014 7 HOH HOH . 
N 5 HOH B 5 1015 12 HOH HOH . 
N 5 HOH B 6 1016 13 HOH HOH . 
N 5 HOH B 7 1017 15 HOH HOH . 
N 5 HOH B 8 1018 20 HOH HOH . 
N 5 HOH B 9 1019 21 HOH HOH . 
N 5 HOH B 10 1020 22 HOH HOH . 
N 5 HOH B 11 1021 23 HOH HOH . 
N 5 HOH B 12 1022 24 HOH HOH . 
N 5 HOH B 13 1023 25 HOH HOH . 
N 5 HOH B 14 1024 26 HOH HOH . 
N 5 HOH B 15 1025 27 HOH HOH . 
N 5 HOH B 16 1026 28 HOH HOH . 
N 5 HOH B 17 1027 33 HOH HOH . 
N 5 HOH B 18 1028 34 HOH HOH . 
N 5 HOH B 19 1029 35 HOH HOH . 
N 5 HOH B 20 1030 40 HOH HOH . 
N 5 HOH B 21 1031 42 HOH HOH . 
N 5 HOH B 22 1032 43 HOH HOH . 
N 5 HOH B 23 1033 44 HOH HOH . 
N 5 HOH B 24 1034 45 HOH HOH . 
N 5 HOH B 25 1035 47 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 P P ABM . . . G 4 32.036 64.831 57.428 1 59.88 ? P ABM 1009 A 1 
HETATM 2 C CM ABM . . . G 4 33.716 65.545 57.513 1 56.94 ? CM ABM 1009 A 1 
HETATM 3 O O2P ABM . . . G 4 32.229 63.346 57.779 1 59.39 ? O2P ABM 1009 A 1 
HETATM 4 O O3P ABM . . . G 4 31.492 65.279 56.063 1 57.97 ? O3P ABM 1009 A 1 
HETATM 5 O O5' ABM . . . G 4 31.231 65.542 58.636 1 59.33 ? O5' ABM 1009 A 1 
HETATM 6 C C5' ABM . . . G 4 30.261 66.607 58.385 1 57.6 ? C5' ABM 1009 A 1 
HETATM 7 C C4' ABM . . . G 4 30.267 67.702 59.496 1 53.84 ? C4' ABM 1009 A 1 
HETATM 8 O O4' ABM . . . G 4 30.855 68.989 59.06 1 51.75 ? O4' ABM 1009 A 1 
HETATM 9 C C3' ABM . . . G 4 28.858 67.998 59.994 1 51.95 ? C3' ABM 1009 A 1 
HETATM 10 O O3' ABM . . . G 4 28.554 67.159 61.114 1 52.26 ? O3' ABM 1009 A 1 
HETATM 11 C C2' ABM . . . G 4 28.856 69.517 60.331 1 49.76 ? C2' ABM 1009 A 1 
HETATM 12 O O2' ABM . . . G 4 28.869 69.798 61.745 1 50.65 ? O2' ABM 1009 A 1 
HETATM 13 C C1' ABM . . . G 4 30.109 70.101 59.674 1 47.88 ? C1' ABM 1009 A 1 
HETATM 14 N N9 ABM . . . G 4 29.704 71.093 58.663 1 45.69 ? N9 ABM 1009 A 1 
HETATM 15 C C8 ABM . . . G 4 28.445 71.331 58.15 1 44.83 ? C8 ABM 1009 A 1 
HETATM 16 N N7 ABM . . . G 4 28.365 72.471 57.5 1 43.49 ? N7 ABM 1009 A 1 
HETATM 17 C C5 ABM . . . G 4 29.698 72.863 57.334 1 42.59 ? C5 ABM 1009 A 1 
HETATM 18 C C6 ABM . . . G 4 30.274 74.1 56.963 1 42.22 ? C6 ABM 1009 A 1 
HETATM 19 N N6 ABM . . . G 4 29.691 74.986 56.125 1 42.08 ? N6 ABM 1009 A 1 
HETATM 20 N N1 ABM . . . G 4 31.435 74.421 57.571 1 43.43 ? N1 ABM 1009 A 1 
HETATM 21 C C2 ABM . . . G 4 32.197 73.404 58.034 1 44.18 ? C2 ABM 1009 A 1 
HETATM 22 N N3 ABM . . . G 4 31.873 72.111 58.171 1 42.64 ? N3 ABM 1009 A 1 
HETATM 23 C C4 ABM . . . G 4 30.535 71.969 57.981 1 44.04 ? C4 ABM 1009 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           23 
#