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#$Date: 2025-08-21 03:34:05 +0200 (Thu 21 de Aug de 2025) $
#$Revision: 301843 $
#$URL: svn://www.crystallography.net/cod/cif/4/51/80/4518047.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_4518047
loop_
_publ_author_name
'Gissot, Arnaud'
'Massip, Stéphane'
'Barthélémy, Philippe'
_publ_section_title
;
 Intramolecular Michael Additions in Uridine Derivatives: Isolation of the
 Labile 5′O-C6 Cyclonucleoside
;
_journal_issue                   38
_journal_name_full               'ACS Omega'
_journal_page_first              24746
_journal_page_last               24753
_journal_paper_doi               10.1021/acsomega.0c03348
_journal_volume                  5
_journal_year                    2020
_chemical_absolute_configuration ad
_chemical_formula_sum            'C13 H19 Cl2 N3 O5'
_chemical_formula_weight         368.21
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_audit_creation_method           SHELXL-2014/7
_audit_update_record
;
2018-07-11 deposited with the CCDC.	2020-06-10 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.0716(3)
_cell_length_b                   14.8200(4)
_cell_length_c                   15.8935(6)
_cell_measurement_reflns_used    15929
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      73.2130
_cell_measurement_theta_min      2.7880
_cell_volume                     1665.66(10)
_computing_cell_refinement       'CrysAlisPro 1.171.38.43'
_computing_data_collection       'CrystalClear-SM Expert 2.1 (Rigaku, 2013)'
_computing_data_reduction        'CrysAlisPro 1.171.38.43'
_computing_structure_refinement  'SHELXL-2014/7 (Sheldrick, 2014)'
_computing_structure_solution    'SHELXS-2014/7 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 5.8140
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_device_type  'Rigaku PILATUS conversion'
_diffrn_measurement_method       'profile data from ω-scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0938
_diffrn_reflns_av_unetI/netI     0.0384
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            24856
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.788
_diffrn_reflns_theta_min         4.079
_diffrn_source                   'Rotating Anode'
_exptl_absorpt_coefficient_mu    3.770
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.79125
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'CrysAlisPro 1.171.38.43'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.468
_exptl_crystal_description       prism
_exptl_crystal_F_000             768
_exptl_crystal_size_max          0.080
_exptl_crystal_size_mid          0.060
_exptl_crystal_size_min          0.020
_refine_diff_density_max         0.688
_refine_diff_density_min         -0.546
_refine_diff_density_rms         0.079
_refine_ls_abs_structure_details
;
 Flack x determined using 1200 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.012(12)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.020
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     213
_refine_ls_number_reflns         3344
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.020
_refine_ls_R_factor_all          0.0609
_refine_ls_R_factor_gt           0.0585
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.0913P)²+1.4720P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1546
_refine_ls_wR_factor_ref         0.1567
_reflns_Friedel_coverage         0.722
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.982
_reflns_number_gt                3110
_reflns_number_total             3344
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            ao0c03348_si_002.cif
_cod_data_source_block           ag346
_cod_depositor_comments
'Adding full bibliography for 4518045--4518047.cif.'
_cod_database_code               4518047
_shelx_shelxl_version_number     2014/7
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
_shelx_estimated_absorpt_t_min   0.752
_shelx_estimated_absorpt_t_max   0.928
_exptl_absorpt_special_details
;
CrysAlisPro 1.171.38.43 (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x+1/2, -y, z+1/2'
'x+1/2, -y+1/2, -z'
'-x, y+1/2, -z+1/2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
N1 N 0.7334(5) 0.4878(2) 0.9366(2) 0.0260(7) Uani 1 1 d . . . . .
C2 C 0.5977(6) 0.5507(3) 0.9489(3) 0.0283(8) Uani 1 1 d . . . . .
N3 N 0.6596(5) 0.6370(2) 0.9702(3) 0.0306(8) Uani 1 1 d . . . . .
H3 H 0.5751 0.6742 0.9913 0.046 Uiso 1 1 calc R U . . .
C4 C 0.8381(7) 0.6688(3) 0.9614(3) 0.0334(10) Uani 1 1 d . . . . .
C5 C 0.9809(7) 0.6021(3) 0.9312(3) 0.0355(10) Uani 1 1 d . . . . .
H5A H 1.1055 0.6177 0.9557 0.043 Uiso 1 1 calc R U . . .
H5B H 0.9918 0.6071 0.8693 0.043 Uiso 1 1 calc R U . . .
C6 C 0.9344(6) 0.5048(3) 0.9537(3) 0.0305(9) Uani 1 1 d . . . . .
H6 H 0.9609 0.4943 1.0147 0.037 Uiso 1 1 calc R U . . .
N7 N 1.0501(6) 0.4460(2) 0.9038(3) 0.0340(8) Uani 1 1 d . . . . .
H7 H 1.157(10) 0.474(4) 0.891(4) 0.051 Uiso 1 1 d . U . . .
C8 C 1.0922(6) 0.3566(3) 0.9397(4) 0.0354(10) Uani 1 1 d . . . . .
H8A H 1.1254 0.3629 0.9999 0.043 Uiso 1 1 calc R U . . .
H8B H 1.2016 0.3296 0.9101 0.043 Uiso 1 1 calc R U . . .
C9 C 0.9208(6) 0.2960(3) 0.9305(3) 0.0369(10) Uani 1 1 d . . . . .
H9 H 0.9508 0.2342 0.9519 0.044 Uiso 1 1 calc R U . . .
O10 O 0.7648(4) 0.33380(19) 0.9776(2) 0.0322(7) Uani 1 1 d . . . . .
C11 C 0.6663(6) 0.3942(3) 0.9251(3) 0.0275(8) Uani 1 1 d . . . . .
H11 H 0.5289 0.3917 0.9398 0.033 Uiso 1 1 calc R U . . .
O12 O 0.4268(4) 0.5359(2) 0.9426(2) 0.0340(7) Uani 1 1 d . . . . .
O13 O 0.8717(5) 0.7486(2) 0.9754(3) 0.0456(9) Uani 1 1 d . . . . .
C14 C 0.8505(7) 0.2904(3) 0.8404(3) 0.0384(11) Uani 1 1 d . . . . .
H14 H 0.9533 0.3020 0.7986 0.046 Uiso 1 1 calc R U . . .
O15 O 0.7550(5) 0.2062(2) 0.8253(3) 0.0508(10) Uani 1 1 d . . . . .
C16 C 0.5905(8) 0.2269(4) 0.7778(4) 0.0464(13) Uani 1 1 d . . . . .
O17 O 0.5266(5) 0.3098(2) 0.8132(2) 0.0367(8) Uani 1 1 d . . . . .
C18 C 0.6913(6) 0.3604(3) 0.8350(3) 0.0315(9) Uani 1 1 d . . . . .
H18 H 0.7192 0.4101 0.7942 0.038 Uiso 1 1 calc R U . . .
C19 C 0.4398(9) 0.1566(4) 0.7946(5) 0.0578(16) Uani 1 1 d . . . . .
H19A H 0.4871 0.0970 0.7781 0.087 Uiso 1 1 calc R U . . .
H19B H 0.3263 0.1710 0.7619 0.087 Uiso 1 1 calc R U . . .
H19C H 0.4086 0.1563 0.8547 0.087 Uiso 1 1 calc R U . . .
C20 C 0.6342(10) 0.2395(5) 0.6845(4) 0.0629(17) Uani 1 1 d . . . . .
H20A H 0.7402 0.2816 0.6781 0.094 Uiso 1 1 calc R U . . .
H20B H 0.5226 0.2638 0.6558 0.094 Uiso 1 1 calc R U . . .
H20C H 0.6680 0.1811 0.6596 0.094 Uiso 1 1 calc R U . . .
C21 C -0.1612(10) 0.9962(5) 0.8652(4) 0.0614(16) Uani 1 1 d . . . . .
H21A H -0.2129 1.0581 0.8614 0.074 Uiso 1 1 calc R U . . .
H21B H -0.1797 0.9748 0.9236 0.074 Uiso 1 1 calc R U . . .
Cl22 Cl 0.0820(2) 0.99919(13) 0.84303(10) 0.0645(5) Uani 1 1 d . . . . .
Cl23 Cl -0.2882(2) 0.92521(10) 0.79597(10) 0.0554(4) Uani 1 1 d . . . . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0181 0.0091 '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 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Cl Cl 0.3639 0.7018 '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_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C2 N1 C6 122.7(3) . . ?
C2 N1 C11 115.9(3) . . ?
C6 N1 C11 119.7(3) . . ?
O12 C2 N1 124.2(4) . . ?
O12 C2 N3 119.4(4) . . ?
N1 C2 N3 116.4(4) . . ?
C4 N3 C2 126.0(4) . . ?
O13 C4 N3 119.8(4) . . ?
O13 C4 C5 124.4(4) . . ?
N3 C4 C5 115.7(4) . . ?
C4 C5 C6 113.9(4) . . ?
N7 C6 N1 110.2(4) . . ?
N7 C6 C5 108.8(4) . . ?
N1 C6 C5 109.2(4) . . ?
C6 N7 C8 116.6(4) . . ?
N7 C8 C9 109.5(4) . . ?
O10 C9 C8 109.3(4) . . ?
O10 C9 C14 105.1(4) . . ?
C8 C9 C14 112.7(4) . . ?
C11 O10 C9 108.5(3) . . ?
O10 C11 N1 111.4(3) . . ?
O10 C11 C18 106.8(3) . . ?
N1 C11 C18 112.7(4) . . ?
O15 C14 C9 111.0(4) . . ?
O15 C14 C18 103.5(4) . . ?
C9 C14 C18 104.8(4) . . ?
C16 O15 C14 106.6(4) . . ?
O15 C16 O17 103.7(4) . . ?
O15 C16 C19 109.5(5) . . ?
O17 C16 C19 107.5(4) . . ?
O15 C16 C20 112.1(5) . . ?
O17 C16 C20 110.0(5) . . ?
C19 C16 C20 113.4(5) . . ?
C16 O17 C18 106.9(4) . . ?
O17 C18 C11 107.8(4) . . ?
O17 C18 C14 104.8(3) . . ?
C11 C18 C14 104.7(4) . . ?
Cl22 C21 Cl23 112.8(4) . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
N1 C2 1.353(5) . ?
N1 C6 1.469(5) . ?
N1 C11 1.477(5) . ?
C2 O12 1.233(5) . ?
C2 N3 1.393(5) . ?
N3 C4 1.355(6) . ?
C4 O13 1.227(6) . ?
C4 C5 1.492(6) . ?
C5 C6 1.521(6) . ?
C6 N7 1.434(6) . ?
N7 C8 1.473(6) . ?
C8 C9 1.516(6) . ?
C9 O10 1.446(6) . ?
C9 C14 1.517(8) . ?
O10 C11 1.408(5) . ?
C11 C18 1.527(6) . ?
C14 O15 1.438(5) . ?
C14 C18 1.534(7) . ?
O15 C16 1.420(7) . ?
C16 O17 1.424(6) . ?
C16 C19 1.513(8) . ?
C16 C20 1.528(9) . ?
O17 C18 1.429(5) . ?
C21 Cl22 1.756(7) . ?
C21 Cl23 1.767(7) . ?
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_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
C6 N1 C2 O12 -173.0(4) . . . . ?
C11 N1 C2 O12 -7.6(7) . . . . ?
C6 N1 C2 N3 6.9(6) . . . . ?
C11 N1 C2 N3 172.2(4) . . . . ?
O12 C2 N3 C4 -164.3(4) . . . . ?
N1 C2 N3 C4 15.8(7) . . . . ?
C2 N3 C4 O13 173.5(5) . . . . ?
C2 N3 C4 C5 -4.2(7) . . . . ?
O13 C4 C5 C6 155.1(5) . . . . ?
N3 C4 C5 C6 -27.3(6) . . . . ?
C2 N1 C6 N7 -155.3(4) . . . . ?
C11 N1 C6 N7 39.9(5) . . . . ?
C2 N1 C6 C5 -35.9(6) . . . . ?
C11 N1 C6 C5 159.3(4) . . . . ?
C4 C5 C6 N7 164.9(4) . . . . ?
C4 C5 C6 N1 44.6(5) . . . . ?
N1 C6 N7 C8 -87.2(5) . . . . ?
C5 C6 N7 C8 153.1(4) . . . . ?
C6 N7 C8 C9 76.8(5) . . . . ?
N7 C8 C9 O10 -62.4(5) . . . . ?
N7 C8 C9 C14 54.0(5) . . . . ?
C8 C9 O10 C11 88.2(4) . . . . ?
C14 C9 O10 C11 -33.0(4) . . . . ?
C9 O10 C11 N1 -94.3(4) . . . . ?
C9 O10 C11 C18 29.2(4) . . . . ?
C2 N1 C11 O10 -130.5(4) . . . . ?
C6 N1 C11 O10 35.3(5) . . . . ?
C2 N1 C11 C18 109.4(4) . . . . ?
C6 N1 C11 C18 -84.8(5) . . . . ?
O10 C9 C14 O15 -88.2(4) . . . . ?
C8 C9 C14 O15 152.9(4) . . . . ?
O10 C9 C14 C18 23.0(5) . . . . ?
C8 C9 C14 C18 -95.9(4) . . . . ?
C9 C14 O15 C16 137.1(4) . . . . ?
C18 C14 O15 C16 25.1(5) . . . . ?
C14 O15 C16 O17 -38.1(5) . . . . ?
C14 O15 C16 C19 -152.6(4) . . . . ?
C14 O15 C16 C20 80.5(5) . . . . ?
O15 C16 O17 C18 36.0(5) . . . . ?
C19 C16 O17 C18 152.0(5) . . . . ?
C20 C16 O17 C18 -84.1(5) . . . . ?
C16 O17 C18 C11 -131.2(4) . . . . ?
C16 O17 C18 C14 -20.1(5) . . . . ?
O10 C11 C18 O17 97.9(4) . . . . ?
N1 C11 C18 O17 -139.5(3) . . . . ?
O10 C11 C18 C14 -13.4(4) . . . . ?
N1 C11 C18 C14 109.3(4) . . . . ?
O15 C14 C18 O17 -3.0(5) . . . . ?
C9 C14 C18 O17 -119.5(4) . . . . ?
O15 C14 C18 C11 110.4(4) . . . . ?
C9 C14 C18 C11 -6.1(5) . . . . ?
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 PubChem 168346786
