#------------------------------------------------------------------------------ #$Date: 2025-08-18 23:52:38 +0100 (Mon, 18 Aug 2025) $ #$Revision: 301791 $ #$URL: svn://www.crystallography.net/cod/cif/2/00/89/2008930.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided by IUCr Journals, http://journals.iucr.org/. # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_2008930 loop_ _publ_author_name 'Seela, Frank' 'Zulauf, Matthias' 'Reuter, Hans' 'Kastner, Guido' _publ_section_title ; 9-(2-Deoxy-\a-D-ribofuranosyl)-7-iodo-7-deazaadenine ; _journal_issue 9 _journal_name_full 'Acta Crystallographica Section C' _journal_page_first 1560 _journal_page_last 1562 _journal_paper_doi 10.1107/S0108270199006538 _journal_volume 55 _journal_year 1999 _chemical_formula_sum 'C11 H13 I N4 O3' _chemical_formula_weight 376.15 _chemical_melting_point .469E-305 _chemical_name_common 9-(2'-Deoxy-\a-D-ribofuranosyl)-7-iodo-7-deazaadenine _space_group_IT_number 4 _symmetry_cell_setting monoclinic _symmetry_space_group_name_Hall 'P 2yb' _symmetry_space_group_name_H-M 'P 1 21 1' _audit_creation_method SHELXL-97 _cell_angle_alpha 90.00 _cell_angle_beta 97.375(12) _cell_angle_gamma 90.00 _cell_formula_units_Z 2 _cell_length_a 8.5158(8) _cell_length_b 7.0115(6) _cell_length_c 10.9335(13) _cell_measurement_reflns_used 23 _cell_measurement_temperature 293(2) _cell_measurement_theta_max 12.51 _cell_measurement_theta_min 4.72 _cell_volume 647.42(11) _computing_cell_refinement XSCANS _computing_data_collection 'XSCANS (Siemens, 1994)' _computing_data_reduction 'SHELXTL (Sheldrick, 1997)' _computing_molecular_graphics SHELXTL _computing_publication_material SHELXTL _computing_structure_refinement 'SHELXL97 (Sheldrick, 1997)' _computing_structure_solution 'SHELXS97 (Sheldrick, 1997)' _diffrn_ambient_temperature 293(2) _diffrn_measured_fraction_theta_full 0.999 _diffrn_measured_fraction_theta_max 0.999 _diffrn_measurement_device_type 'Siemens P4' _diffrn_measurement_method '2\q/\w scans' _diffrn_radiation_monochromator graphite _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_type MoK\a _diffrn_radiation_wavelength 0.71073 _diffrn_reflns_av_R_equivalents 0.0000 _diffrn_reflns_av_sigmaI/netI 0.0302 _diffrn_reflns_limit_h_max 10 _diffrn_reflns_limit_h_min -10 _diffrn_reflns_limit_k_max 8 _diffrn_reflns_limit_k_min -7 _diffrn_reflns_limit_l_max 12 _diffrn_reflns_limit_l_min 0 _diffrn_reflns_number 2004 _diffrn_reflns_theta_full 25.00 _diffrn_reflns_theta_max 25.00 _diffrn_reflns_theta_min 2.41 _diffrn_standards_decay_% 6.02 _diffrn_standards_interval_count 97 _diffrn_standards_number 3 _exptl_absorpt_coefficient_mu 2.484 _exptl_absorpt_correction_T_max 0.656 _exptl_absorpt_correction_T_min 0.557 _exptl_absorpt_correction_type empirical _exptl_absorpt_process_details '(SHELXTL; Sheldrick, 1997)' _exptl_crystal_colour 'pale yellow' _exptl_crystal_density_diffrn 1.930 _exptl_crystal_density_method 'not measured' _exptl_crystal_description 'transparent prism' _exptl_crystal_F_000 368 _exptl_crystal_size_max 0.45 _exptl_crystal_size_mid 0.23 _exptl_crystal_size_min 0.17 _refine_diff_density_max 0.706 _refine_diff_density_min -0.493 _refine_ls_abs_structure_details 'Flack (1983)' _refine_ls_abs_structure_Flack -0.03(3) _refine_ls_extinction_coef 0.0221(11) _refine_ls_extinction_method 'SHELXL97 (Sheldrick, 1997)' _refine_ls_goodness_of_fit_ref 1.051 _refine_ls_hydrogen_treatment mixed _refine_ls_matrix_type full _refine_ls_number_parameters 178 _refine_ls_number_reflns 2004 _refine_ls_number_restraints 3 _refine_ls_restrained_S_all 1.050 _refine_ls_R_factor_all 0.0232 _refine_ls_R_factor_gt 0.0226 _refine_ls_shift/su_max 0.001 _refine_ls_shift/su_mean 0.000 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'calc w = 1/[\s^2^(Fo^2^)+(0.0281P)^2^+0.5354P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_ref 0.0569 _reflns_number_gt 1965 _reflns_number_total 2004 _reflns_threshold_expression I>2\s(I) _cod_data_source_file ka1326.cif _cod_data_source_block neulin21 _cod_depositor_comments ; The following automatic conversions were performed: '_symmetry_cell_setting' value 'Monoclinic' changed to 'monoclinic' according to '/home/saulius/struct/CIF-dictionaries/cif_core.dic' dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29. Automatic conversion script Id: cif_fix_enum 1527 2010-12-29 10:47:43Z saulius The following automatic conversions were performed: '_symmetry_cell_setting' value 'Monoclinic' changed to 'monoclinic' according to /home/saulius/struct/CIF-dictionaries/cif_core.dic dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29. Automatic conversion script Id: cif_fix_values 1715 2011-07-08 13:25:40Z adriana ; _cod_original_sg_symbol_H-M 'P 21' _cod_database_code 2008930 _cod_database_fobs_code 2008930 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y+1/2, -z' loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_type_symbol N1 0.2853(4) 0.1848(9) 0.7422(3) 0.0286(12) Uani d . 1 . . N C2 0.4050(5) 0.1768(13) 0.6730(4) 0.0270(13) Uani d . 1 . . C H2 0.5064 0.1893 0.7154 0.040(4) Uiso calc R 1 . . H N3 0.3967(3) 0.1533(13) 0.5520(2) 0.0244(6) Uani d . 1 . . N C4 0.2464(4) 0.153(3) 0.4973(3) 0.0214(7) Uani d . 1 . . C C5 0.1091(4) 0.1611(13) 0.5557(3) 0.0225(7) Uani d . 1 . . C C6 0.1357(5) 0.1749(12) 0.6855(4) 0.0257(11) Uani d . 1 . . C N6 0.0170(4) 0.1794(11) 0.7565(3) 0.0380(12) Uani d D 1 . . N H61 0.0297 0.1291 0.8311 0.040(4) Uiso d RD 1 . . H H62 -0.0751 0.2223 0.7216 0.040(4) Uiso d RD 1 . . H C7 -0.0223(4) 0.1502(13) 0.4598(3) 0.0255(7) Uani d . 1 . . C I7 -0.26236(2) 0.15377(5) 0.48074(2) 0.03015(12) Uani d . 1 . . I C8 0.0368(5) 0.1371(13) 0.3519(4) 0.0282(12) Uani d . 1 . . C H8 -0.0233 0.1302 0.2747 0.040(4) Uiso calc R 1 . . H N9 0.2007(4) 0.1354(11) 0.3731(3) 0.0251(10) Uani d . 1 . . N C1' 0.3094(5) 0.1046(7) 0.2813(4) 0.0291(14) Uani d . 1 . . C H1' 0.4154 0.0776 0.3242 0.040(4) Uiso calc R 1 . . H C2' 0.3189(7) 0.2736(8) 0.1966(5) 0.0392(13) Uani d . 1 . . C H2'1 0.4116 0.3508 0.2231 0.040(4) Uiso calc R 1 . . H H2'2 0.2250 0.3527 0.1936 0.040(4) Uiso calc R 1 . . H C3' 0.3305(5) 0.1815(11) 0.0722(3) 0.0291(13) Uani d . 1 . . C H3' 0.4401 0.1425 0.0679 0.040(4) Uiso calc R 1 . . H O3' 0.2806(5) 0.3090(6) -0.0258(3) 0.0402(9) Uani d . 1 . . O H3'O 0.2497 0.4086 0.0023 0.040(4) Uiso calc R 1 . . H C4' 0.2267(5) 0.0040(7) 0.0789(4) 0.0242(9) Uani d . 1 . . C H4' 0.1148 0.0375 0.0581 0.040(4) Uiso calc R 1 . . H O4' 0.2577(4) -0.0536(5) 0.2057(3) 0.0312(8) Uani d . 1 . . O C5' 0.2687(6) -0.1648(8) -0.0001(4) 0.0337(12) Uani d . 1 . . C H5'1 0.2702 -0.1236 -0.0846 0.040(4) Uiso calc R 1 . . H H5'2 0.3730 -0.2127 0.0310 0.040(4) Uiso calc R 1 . . H O5' 0.1555(4) -0.3098(6) 0.0041(3) 0.0466(11) Uani d . 1 . . O H5'O 0.1993 -0.4141 0.0057 0.040(4) Uiso calc R 1 . . H loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 N1 0.0374(18) 0.031(3) 0.0175(13) 0.005(2) 0.0045(12) -0.0008(17) C2 0.0285(18) 0.029(4) 0.0235(16) 0.006(3) 0.0017(14) 0.002(3) N3 0.0251(14) 0.0269(16) 0.0215(13) -0.002(4) 0.0041(11) -0.002(4) C4 0.0285(17) 0.0200(17) 0.0159(14) -0.001(4) 0.0041(13) -0.004(5) C5 0.0252(16) 0.0200(17) 0.0232(15) 0.001(4) 0.0065(13) 0.004(4) C6 0.0309(18) 0.023(3) 0.0247(16) 0.003(3) 0.0078(14) 0.002(3) N6 0.0367(18) 0.056(4) 0.0236(15) 0.005(3) 0.0122(13) 0.006(2) C7 0.0217(16) 0.0250(19) 0.0301(16) -0.001(4) 0.0042(13) -0.002(5) I7 0.02179(15) 0.02782(16) 0.04109(17) -0.0003(2) 0.00502(10) -0.0060(3) C8 0.0282(18) 0.032(3) 0.0222(16) 0.001(3) -0.0036(14) -0.006(3) N9 0.0238(14) 0.035(3) 0.0176(13) 0.000(3) 0.0057(11) 0.000(2) C1' 0.028(2) 0.043(4) 0.0180(18) -0.008(2) 0.0083(15) -0.0045(19) C2' 0.057(4) 0.038(3) 0.024(3) -0.021(3) 0.011(2) -0.004(2) C3' 0.037(2) 0.033(4) 0.0185(16) -0.005(3) 0.0078(14) 0.002(2) O3' 0.068(2) 0.0321(19) 0.0238(16) -0.001(2) 0.0168(16) -0.0012(15) C4' 0.028(2) 0.028(2) 0.018(2) 0.001(2) 0.0066(16) -0.0052(18) O4' 0.042(2) 0.0309(19) 0.0229(17) -0.0044(17) 0.0118(15) -0.0040(15) C5' 0.047(3) 0.035(3) 0.022(2) 0.002(2) 0.013(2) -0.006(2) O5' 0.050(2) 0.024(3) 0.068(2) -0.0103(18) 0.0185(17) -0.0155(18) loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' I I -0.4742 1.8119 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_publ_flag C6 N1 C2 118.6(3) ? N3 C2 N1 128.2(4) ? N3 C2 H2 115.9 ? N1 C2 H2 115.9 ? C2 N3 C4 111.8(3) ? N3 C4 N9 125.1(3) ? N3 C4 C5 126.8(3) ? N9 C4 C5 107.9(3) ? C4 C5 C6 115.2(3) ? C4 C5 C7 106.4(3) ? C6 C5 C7 138.4(3) ? N1 C6 N6 117.9(4) ? N1 C6 C5 119.2(3) ? N6 C6 C5 122.9(4) ? C6 N6 H61 120.6 ? C6 N6 H62 116.7 ? H61 N6 H62 122.3 ? C8 C7 C5 107.5(3) ? C8 C7 I7 125.4(3) ? C5 C7 I7 127.1(3) ? C7 C8 N9 109.7(3) ? C7 C8 H8 125.2 ? N9 C8 H8 125.2 ? C4 N9 C8 108.5(3) ? C4 N9 C1' 124.6(3) yes C8 N9 C1' 126.8(3) yes O4' C1' N9 109.7(4) ? O4' C1' C2' 107.0(4) ? N9 C1' C2' 113.1(5) ? O4' C1' H1' 109.0 ? N9 C1' H1' 109.0 ? C2' C1' H1' 109.0 ? C1' C2' C3' 103.3(5) ? C1' C2' H2'1 111.1 ? C3' C2' H2'1 111.1 ? C1' C2' H2'2 111.1 ? C3' C2' H2'2 111.1 ? H2'1 C2' H2'2 109.1 ? O3' C3' C2' 111.2(5) ? O3' C3' C4' 115.4(4) ? C2' C3' C4' 101.4(3) ? O3' C3' H3' 109.5 ? C2' C3' H3' 109.5 ? C4' C3' H3' 109.5 ? C3' O3' H3'O 109.5 ? O4' C4' C3' 103.8(3) ? O4' C4' C5' 107.4(4) ? C3' C4' C5' 115.0(4) ? O4' C4' H4' 110.1 ? C3' C4' H4' 110.1 ? C5' C4' H4' 110.1 ? C1' O4' C4' 110.4(3) ? O5' C5' C4' 109.3(4) ? O5' C5' H5'1 109.8 ? C4' C5' H5'1 109.8 ? O5' C5' H5'2 109.8 ? C4' C5' H5'2 109.8 ? H5'1 C5' H5'2 108.3 ? C5' O5' H5'O 109.5 ? loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag N1 C6 . 1.345(5) ? N1 C2 . 1.347(5) ? C2 N3 . 1.326(5) ? C2 H2 . 0.9300 ? N3 C4 . 1.342(4) ? C4 N9 . 1.369(5) ? C4 C5 . 1.404(4) ? C5 C6 . 1.411(5) ? C5 C7 . 1.434(5) ? C6 N6 . 1.351(5) yes N6 H61 . 0.8826 ? N6 H62 . 0.8797 ? C7 C8 . 1.344(5) ? C7 I7 . 2.086(3) ? C8 N9 . 1.385(5) ? C8 H8 . 0.9300 ? N9 C1' . 1.466(5) ? C1' O4' . 1.419(5) yes C1' C2' . 1.512(7) ? C1' H1' . 0.9800 ? C2' C3' . 1.520(7) ? C2' H2'1 . 0.9700 ? C2' H2'2 . 0.9700 ? C3' O3' . 1.418(7) ? C3' C4' . 1.534(8) ? C3' H3' . 0.9800 ? O3' H3'O . 0.8200 ? C4' O4' . 1.436(5) yes C4' C5' . 1.534(7) ? C4' H4' . 0.9800 ? C5' O5' . 1.406(7) ? C5' H5'1 . 0.9700 ? C5' H5'2 . 0.9700 ? O5' H5'O . 0.8200 ? loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_site_symmetry_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA N6 H61 O3' 1_556 0.88 2.78 3.188(6) 109.4 N6 H62 O4' 2_556 0.88 2.42 3.066(7) 130.9 N6 H61 O5' 2_556 0.88 2.58 3.163(5) 124.5 O3' H3'O O5' 1_565 0.82 2.13 2.911(6) 158.7 O5' H5'O O3' 1_545 0.82 2.10 2.911(6) 167.8 loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_publ_flag C6 N1 C2 N3 -2.5(14) ? N1 C2 N3 C4 5.4(16) ? C2 N3 C4 N9 178.7(15) ? C2 N3 C4 C5 -5(2) ? N3 C4 C5 C6 2(2) ? N9 C4 C5 C6 178.5(10) ? N3 C4 C5 C7 -177.9(15) ? N9 C4 C5 C7 -0.9(15) ? C2 N1 C6 N6 178.8(8) ? C2 N1 C6 C5 -1.5(12) ? C4 C5 C6 N1 1.8(15) ? C7 C5 C6 N1 -179.0(10) ? C4 C5 C6 N6 -178.4(11) ? C7 C5 C6 N6 0.8(19) ? C4 C5 C7 C8 -0.1(12) ? C6 C5 C7 C8 -179.3(12) ? C4 C5 C7 I7 179.9(9) ? C6 C5 C7 I7 0.7(19) ? C5 C7 C8 N9 1.1(10) ? I7 C7 C8 N9 -178.9(7) ? N3 C4 N9 C8 178.6(14) ? C5 C4 N9 C8 1.6(16) ? N3 C4 N9 C1' 3(2) ? C5 C4 N9 C1' -174.0(7) ? C7 C8 N9 C4 -1.7(13) ? C7 C8 N9 C1' 173.8(7) ? C4 N9 C1' O4' 128.7(12) yes C8 N9 C1' O4' -46.0(10) ? C4 N9 C1' C2' -111.9(12) ? C8 N9 C1' C2' 73.3(9) ? O4' C1' C2' C3' -20.9(5) ? N9 C1' C2' C3' -141.8(4) ? C1' C2' C3' O3' 157.6(4) ? C1' C2' C3' C4' 34.4(5) ? O3' C3' C4' O4' -156.6(4) ? C2' C3' C4' O4' -36.3(5) ? O3' C3' C4' C5' 86.4(5) ? C2' C3' C4' C5' -153.3(4) ? N9 C1' O4' C4' 120.5(4) ? C2' C1' O4' C4' -2.5(5) ? C3' C4' O4' C1' 24.7(5) ? C5' C4' O4' C1' 146.9(4) ? O4' C4' C5' O5' 71.1(5) ? C3' C4' C5' O5' -173.9(4) yes loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 ChemSpider 21182876 2 PubChem 54035051