#------------------------------------------------------------------------------
#$Date: 2025-08-19 13:52:15 +0200 (Tue 19 de Aug de 2025) $
#$Revision: 301804 $
#$URL: svn://www.crystallography.net/cod/cif/2/21/55/2215590.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_2215590
loop_
_publ_author_name
'Pawel Sledz'
'Maksymilian Chruszcz'
'Wladek Minor'
_publ_section_title
;Absolute configuration from a redetermination of
 (+)-5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
 at 118(2) K
;
_journal_coeditor_code           LH2504
_journal_issue                   10
_journal_name_full               'Acta Crystallographica Section E'
_journal_page_first              o4159
_journal_page_last               o4160
_journal_paper_doi               10.1107/S1600536807046077
_journal_volume                  63
_journal_year                    2007
_chemical_formula_iupac          'C9 H11 Br N2 O5'
_chemical_formula_moiety         'C9 H11 Br N2 O5'
_chemical_formula_sum            'C9 H11 Br N2 O5'
_chemical_formula_weight         307.10
_chemical_name_common            (+)-5-bromo-2'-deoxyuridine
_chemical_name_systematic
;
(+)-5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-
pyrimidine-2,4-dione
;
_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'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-97
_cell_angle_alpha                90.00
_cell_angle_beta                 108.27(2)
_cell_angle_gamma                90.00
_cell_formula_units_Z            2
_cell_length_a                   9.1590(10)
_cell_length_b                   5.0670(10)
_cell_length_c                   12.0410(10)
_cell_measurement_reflns_used    50017
_cell_measurement_temperature    118(2)
_cell_measurement_theta_max      36.3
_cell_measurement_theta_min      3.4
_cell_volume                     530.64(14)
_computing_cell_refinement       'HKL-2000 (Otwinowski & Minor, 1997)'
_computing_data_collection       'HKL-2000 (Otwinowski & Minor, 1997)'
_computing_data_reduction        'HKL-2000 (Otwinowski & Minor, 1997)'
_computing_molecular_graphics
;
HKL-3000SM (Minor et al.,  2006),
Mercury (Macrae et al.,  2006),
ORTEPIII (Burnett & Johnson, 1996) and
ORTEP-3 (Farrugia, 1997)
;
_computing_publication_material  'HKL-3000SM (Minor et al.,  2006)'
_computing_structure_refinement
'SHELXL97 (Sheldrick, 1997) and HKL-3000SM (Minor et al.,  2006)'
_computing_structure_solution
'SHELXS97 (Sheldrick, 1990) and HKL-3000SM (Minor et al.,  2006)'
_diffrn_ambient_temperature      118(2)
_diffrn_detector_area_resol_mean 10
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device_type  'Rigaku R-AXIS RAPID'
_diffrn_measurement_method       'ω scans with χ offset'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_source         'fine-focus sealed tube'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71074
_diffrn_reflns_av_R_equivalents  0.040
_diffrn_reflns_av_sigmaI/netI    0.0142
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            50017
_diffrn_reflns_theta_full        36.32
_diffrn_reflns_theta_max         36.3
_diffrn_reflns_theta_min         3.4
_diffrn_standards_decay_%        0
_exptl_absorpt_coefficient_mu    3.887
_exptl_absorpt_correction_T_max  0.34
_exptl_absorpt_correction_T_min  0.20
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   '(Otwinowski et al.,  2003)'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.922
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             308
_exptl_crystal_size_max          0.48
_exptl_crystal_size_mid          0.36
_exptl_crystal_size_min          0.28
_refine_diff_density_max         0.493
_refine_diff_density_min         -0.713
_refine_ls_abs_structure_details 'Flack (1983), 2325 Friedel pairs'
_refine_ls_abs_structure_Flack   0.003(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.039
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     154
_refine_ls_number_reflns         5127
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.039
_refine_ls_R_factor_all          0.0209
_refine_ls_R_factor_gt           0.0206
_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/[σ²(Fo²)+(0.0319P)²+0.2794P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0547
_refine_ls_wR_factor_ref         0.0549
_reflns_number_gt                5084
_reflns_number_total             5127
_reflns_observed_criterion       I>-3\s(I)
_reflns_threshold_expression     I>2σ(I)
_cod_data_source_file            lh2504.cif
_cod_data_source_block           I
_cod_original_cell_volume        530.64(13)
_cod_database_code               2215590
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, y+1/2, -z'
loop_
_atom_site_type_symbol
_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
Br Br1 0.473749(11) 1.16469(3) 0.095388(8) 0.01312(3) Uani d . 1
N N3 0.66121(10) 0.6900(3) 0.37944(8) 0.01119(16) Uani d . 1
H H3 0.7508 0.6643 0.4291 0.013 Uiso calc R 1
N N1 0.40144(11) 0.5755(2) 0.30904(9) 0.00981(14) Uani d . 1
O O1' 0.17705(10) 0.3420(2) 0.21144(8) 0.01273(15) Uani d . 1
C C3' 0.02368(12) 0.4037(2) 0.33875(10) 0.01077(16) Uani d . 1
H H3' -0.0702 0.5045 0.3315 0.013 Uiso calc R 1
O O3' 0.04776(10) 0.2022(2) 0.42633(8) 0.01338(17) Uani d . 1
H H3" -0.0255 0.1003 0.4087 0.016 Uiso calc R 1
C C1' 0.27203(12) 0.4251(2) 0.32355(9) 0.00976(16) Uani d . 1
H H1' 0.3110 0.2701 0.3725 0.012 Uiso calc R 1
C C4' 0.02472(12) 0.2945(2) 0.21923(10) 0.00998(16) Uani d . 1
H H4' 0.0046 0.1042 0.2159 0.012 Uiso calc R 1
C C4 0.65106(13) 0.8828(3) 0.29697(10) 0.01201(17) Uani d . 1
C C6 0.38024(12) 0.7642(2) 0.22349(10) 0.01052(16) Uani d . 1
H H6 0.2825 0.7900 0.1708 0.013 Uiso calc R 1
C C2 0.54369(12) 0.5328(2) 0.39153(10) 0.01011(16) Uani d . 1
O O2 0.56615(11) 0.3696(2) 0.46919(9) 0.01548(16) Uani d . 1
C C5 0.49829(13) 0.9133(2) 0.21428(9) 0.01099(16) Uani d . 1
O O5' -0.06987(12) 0.3682(2) 0.00909(8) 0.01670(16) Uani d . 1
H H5"' -0.0772 0.2083 -0.0017 0.025 Uiso calc R 1
C C2' 0.16485(13) 0.5801(2) 0.37371(10) 0.01131(16) Uani d . 1
H H2' 0.2069 0.5978 0.4580 0.014 Uiso calc R 1
H H2" 0.1426 0.7538 0.3386 0.014 Uiso calc R 1
O O4 0.76514(12) 1.0107(2) 0.29704(10) 0.01909(19) Uani d . 1
C C5' -0.09319(14) 0.4298(3) 0.11780(10) 0.01425(19) Uani d . 1
H H5' -0.1955 0.3745 0.1154 0.017 Uiso calc R 1
H H5" -0.0862 0.6193 0.1297 0.017 Uiso calc R 1
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'
O O 0.0106 0.0060 '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'
Br Br -0.2901 2.4595 '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'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
C4 N3 C2 127.34(9)
C4 N3 H3 116.3
C2 N3 H3 116.3
C6 N1 C2 121.76(10)
C6 N1 C1' 121.46(9)
C2 N1 C1' 116.58(10)
C1' O1' C4' 107.65(8)
O3' C3' C2' 107.09(9)
O3' C3' C4' 112.66(10)
C2' C3' C4' 102.46(9)
O3' C3' H3' 111.4
C2' C3' H3' 111.4
C4' C3' H3' 111.4
C3' O3' H3" 109.5
O1' C1' N1 108.55(9)
O1' C1' C2' 104.53(9)
N1 C1' C2' 115.19(10)
O1' C1' H1' 109.5
N1 C1' H1' 109.5
C2' C1' H1' 109.5
O1' C4' C5' 109.27(9)
O1' C4' C3' 106.75(8)
C5' C4' C3' 112.17(10)
O1' C4' H4' 109.5
C5' C4' H4' 109.5
C3' C4' H4' 109.5
O4 C4 N3 120.59(11)
O4 C4 C5 125.57(12)
N3 C4 C5 113.83(10)
C5 C6 N1 121.45(10)
C5 C6 H6 119.3
N1 C6 H6 119.3
O2 C2 N3 121.51(10)
O2 C2 N1 123.49(11)
N3 C2 N1 115.00(10)
C6 C5 C4 120.61(10)
C6 C5 Br1 122.30(8)
C4 C5 Br1 117.10(8)
C5' O5' H5"' 109.5
C3' C2' C1' 100.68(9)
C3' C2' H2' 111.6
C1' C2' H2' 111.6
C3' C2' H2" 111.6
C1' C2' H2" 111.6
H2' C2' H2" 109.4
O5' C5' C4' 111.51(10)
O5' C5' H5' 109.3
C4' C5' H5' 109.3
O5' C5' H5" 109.3
C4' C5' H5" 109.3
H5' C5' H5" 108.0
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
Br1 C5 1.8765(11)
N3 C4 1.3752(17)
N3 C2 1.3830(15)
N3 H3 0.8600
N1 C6 1.3742(15)
N1 C2 1.3855(14)
N1 C1' 1.4647(14)
O1' C1' 1.4213(14)
O1' C4' 1.4476(14)
C3' O3' 1.4345(15)
C3' C2' 1.5188(16)
C3' C4' 1.5448(16)
C3' H3' 0.9800
O3' H3" 0.8200
C1' C2' 1.5221(16)
C1' H1' 0.9800
C4' C5' 1.5169(17)
C4' H4' 0.9800
C4 O4 1.2293(14)
C4 C5 1.4490(16)
C6 C5 1.3515(16)
C6 H6 0.9300
C2 O2 1.2163(15)
O5' C5' 1.4252(16)
O5' H5"' 0.8200
C2' H2' 0.9700
C2' H2" 0.9700
C5' H5' 0.9700
C5' H5" 0.9700
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
N3 H3 O3' 2_656 0.86 2.11 2.9440(10) 162.9
O3' H3" O4 1_445 0.82 2.02 2.7450(10) 147.5
O5' H5"' O5' 2_545 0.82 2.21 2.8770(10) 139.3
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
C4' O1' C1' N1 -156.77(9)
C4' O1' C1' C2' -33.36(12)
C6 N1 C1' O1' 44.95(14)
C2 N1 C1' O1' -140.08(11)
C6 N1 C1' C2' -71.81(14)
C2 N1 C1' C2' 103.16(12)
C1' O1' C4' C5' 131.84(10)
C1' O1' C4' C3' 10.32(12)
O3' C3' C4' O1' -98.19(10)
C2' C3' C4' O1' 16.54(12)
O3' C3' C4' C5' 142.16(10)
C2' C3' C4' C5' -103.11(11)
C2 N3 C4 O4 179.17(13)
C2 N3 C4 C5 -1.25(18)
C2 N1 C6 C5 1.51(18)
C1' N1 C6 C5 176.22(11)
C4 N3 C2 O2 -179.14(13)
C4 N3 C2 N1 1.11(18)
C6 N1 C2 O2 179.12(12)
C1' N1 C2 O2 4.17(18)
C6 N1 C2 N3 -1.13(17)
C1' N1 C2 N3 -176.09(10)
N1 C6 C5 C4 -1.67(18)
N1 C6 C5 Br1 177.99(9)
O4 C4 C5 C6 -178.98(13)
N3 C4 C5 C6 1.47(17)
O4 C4 C5 Br1 1.34(18)
N3 C4 C5 Br1 -178.21(9)
O3' C3' C2' C1' 83.90(10)
C4' C3' C2' C1' -34.83(11)
O1' C1' C2' C3' 42.75(11)
N1 C1' C2' C3' 161.76(9)
O1' C4' C5' O5' 49.61(13)
C3' C4' C5' O5' 167.79(10)
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 ChemSpider 5813
2 PubChem 6035
