#------------------------------------------------------------------------------
#$Date: 2021-06-06 19:15:44 +0300 (Sun, 06 Jun 2021) $
#$Revision: 266207 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/02/23/2022349.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_2022349
loop_
_publ_author_name
'Budow-Busse, Simone'
'Chai, Yingying'
'Müller, Sebastian Lars'
'Daniliuc, Constantin'
'Seela, Frank'
_publ_section_title
;
 The α-<small>D</small>-anomer of 2'-deoxycytidine: crystal structure,
 nucleoside conformation and Hirshfeld surface analysis
;
_journal_coeditor_code           VP3014
_journal_issue                   5
_journal_name_full               'Acta Crystallographica Section C'
_journal_page_first              202
_journal_page_last               208
_journal_paper_doi               10.1107/S2053229621003430
_journal_volume                  77
_journal_year                    2021
_chemical_absolute_configuration ad
_chemical_formula_iupac          'C9 H13 N3 O4'
_chemical_formula_moiety         'C9 H13 N3 O4'
_chemical_formula_sum            'C9 H13 N3 O4'
_chemical_formula_weight         227.22
_chemical_name_systematic
;
2'-Deoxycytidine
;
_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
_atom_sites_solution_primary     direct
_audit_creation_method           'APEX3 v2016.1-0'
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.8378(4)
_cell_length_b                   11.4334(7)
_cell_length_c                   12.7595(8)
_cell_measurement_reflns_used    9144
_cell_measurement_temperature    100.(2)
_cell_measurement_theta_max      66.8644
_cell_measurement_theta_min      5.1945
_cell_volume                     997.53(11)
_computing_cell_refinement
;
SAINT (Bruker, 2015)
;
_computing_data_collection
;
APEX3 (Bruker, 2016)
;
_computing_data_reduction
;
SAINT (Bruker, 2015)
;
_computing_molecular_graphics
;
APEX3 (Bruker, 2016)
;
_computing_publication_material
;
APEX3 (Bruker, 2016) and
XP (Bruker, 1998)
;
_computing_structure_refinement
;
SHELXL2014 (Sheldrick, 2015b)
;
_computing_structure_solution
;
SHELXS2014 (Sheldrick, 2015a)
;
_diffrn_ambient_temperature      100.(2)
_diffrn_detector_area_resol_mean 8.3333
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device_type  'Bruker APEXII Kappa CCD'
_diffrn_measurement_method       'φ and ω scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0365
_diffrn_reflns_av_unetI/netI     0.0210
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            11824
_diffrn_reflns_theta_full        66.86
_diffrn_reflns_theta_max         66.86
_diffrn_reflns_theta_min         5.19
_diffrn_source                   'fine-focus sealed tube'
_exptl_absorpt_coefficient_mu    1.024
_exptl_absorpt_correction_T_max  0.85
_exptl_absorpt_correction_T_min  0.75
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(SADABS; Bruker, 2014)
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.513
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             480
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.18
_exptl_crystal_size_min          0.16
_refine_diff_density_max         0.119
_refine_diff_density_min         -0.180
_refine_ls_abs_structure_details
;
Flack x determined using 684 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al.,  2013)
;
_refine_ls_abs_structure_Flack   0.04(9)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.124
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     161
_refine_ls_number_reflns         1768
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.124
_refine_ls_R_factor_all          0.0257
_refine_ls_R_factor_gt           0.0248
_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)+(0.0234P)²+0.3118P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0601
_refine_ls_wR_factor_ref         0.0609
_reflns_number_gt                1719
_reflns_number_total             1768
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            vp3014sup1.cif
_cod_data_source_block           I
_cod_depositor_comments          'Adding full bibliography for 2022349.cif.'
_cod_database_code               2022349
_cod_database_fobs_code          2022349
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x+1/2, -y, z+1/2'
'-x, y+1/2, -z+1/2'
'x+1/2, -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_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
N N1 0.8363(2) 0.56682(14) 0.36354(13) 0.0141(4) Uani d 1 . .
N N3 0.9151(2) 0.75960(14) 0.30990(13) 0.0150(4) Uani d 1 . .
N N4 0.8602(3) 0.91354(15) 0.42076(14) 0.0179(4) Uani d 1 . .
H H4A 0.851(4) 0.941(2) 0.484(2) 0.025(7) Uiso d 1 . .
H H4B 0.912(4) 0.960(2) 0.368(2) 0.041(8) Uiso d 1 . .
O O2 0.9632(2) 0.60359(12) 0.20186(11) 0.0168(3) Uani d 1 . .
C C2 0.9078(3) 0.64392(17) 0.28828(15) 0.0139(4) Uani d 1 . .
C C4 0.8596(3) 0.79804(17) 0.40431(15) 0.0143(4) Uani d 1 . .
C C5 0.8004(3) 0.72036(16) 0.48517(15) 0.0159(4) Uani d 1 . .
H H5A 0.7702 0.748 0.5535 0.019 Uiso calc 1 . .
C C6 0.7887(3) 0.60552(17) 0.46094(16) 0.0154(4) Uani d 1 . .
H H6 0.7467 0.5512 0.5126 0.018 Uiso calc 1 . .
C C1' 0.8145(3) 0.44122(16) 0.33182(15) 0.0150(4) Uani d 1 . .
H H1 0.9404 0.4117 0.3019 0.018 Uiso calc 1 . .
C C2' 0.6507(3) 0.42608(17) 0.25202(15) 0.0154(4) Uani d 1 . .
H H2A 0.6779 0.3599 0.2042 0.018 Uiso calc 1 . .
H H2B 0.632 0.4981 0.2101 0.018 Uiso calc 1 . .
C C3' 0.4725(3) 0.40127(17) 0.32044(16) 0.0155(4) Uani d 1 . .
H H3A 0.3738 0.3528 0.2823 0.019 Uiso calc 1 . .
C C4' 0.5609(3) 0.33435(17) 0.41243(15) 0.0143(4) Uani d 1 . .
H H4 0.4897 0.3557 0.4781 0.017 Uiso calc 1 . .
C C5' 0.5584(3) 0.20248(17) 0.39946(15) 0.0170(4) Uani d 1 . .
H H5B 0.6242 0.166 0.4603 0.02 Uiso calc 1 . .
H H5C 0.4211 0.175 0.3985 0.02 Uiso calc 1 . .
O O3' 0.3873(2) 0.50722(12) 0.35979(11) 0.0179(3) Uani d 1 . .
H H3 0.381(5) 0.559(3) 0.303(3) 0.054(9) Uiso d 1 . .
O O4' 0.7623(2) 0.37426(11) 0.42000(11) 0.0155(3) Uani d 1 . .
O O5' 0.6537(2) 0.16570(12) 0.30536(11) 0.0187(3) Uani d 1 . .
H H5 0.786(5) 0.167(3) 0.316(3) 0.050(9) Uiso d 1 . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0181 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'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
C6 N1 C2 . . 120.59(16) ?
C6 N1 C1' . . 122.33(16) y
C2 N1 C1' . . 117.08(15) y
C4 N3 C2 . . 119.66(17) ?
C4 N4 H4A . . 120.2(16) ?
C4 N4 H4B . . 116.9(17) ?
H4A N4 H4B . . 120.(2) ?
O2 C2 N3 . . 121.88(17) ?
O2 C2 N1 . . 118.67(17) ?
N3 C2 N1 . . 119.45(17) ?
N4 C4 N3 . . 117.71(18) ?
N4 C4 C5 . . 120.30(18) ?
N3 C4 C5 . . 121.99(18) ?
C6 C5 C4 . . 117.28(18) ?
C6 C5 H5A . . 121.4 ?
C4 C5 H5A . . 121.4 ?
C5 C6 N1 . . 120.77(18) ?
C5 C6 H6 . . 119.6 ?
N1 C6 H6 . . 119.6 ?
O4' C1' N1 . . 109.30(15) ?
O4' C1' C2' . . 106.64(16) ?
N1 C1' C2' . . 111.26(16) ?
O4' C1' H1 . . 109.9 ?
N1 C1' H1 . . 109.9 ?
C2' C1' H1 . . 109.9 ?
C1' C2' C3' . . 103.04(15) ?
C1' C2' H2A . . 111.2 ?
C3' C2' H2A . . 111.2 ?
C1' C2' H2B . . 111.2 ?
C3' C2' H2B . . 111.2 ?
H2A C2' H2B . . 109.1 ?
O3' C3' C2' . . 111.57(16) ?
O3' C3' C4' . . 108.37(16) ?
C2' C3' C4' . . 102.54(16) ?
O3' C3' H3A . . 111.3 ?
C2' C3' H3A . . 111.3 ?
C4' C3' H3A . . 111.3 ?
O4' C4' C5' . . 109.27(16) ?
O4' C4' C3' . . 105.60(15) ?
C5' C4' C3' . . 114.21(16) ?
O4' C4' H4 . . 109.2 ?
C5' C4' H4 . . 109.2 ?
C3' C4' H4 . . 109.2 ?
O5' C5' C4' . . 112.26(16) y
O5' C5' H5B . . 109.2 ?
C4' C5' H5B . . 109.2 ?
O5' C5' H5C . . 109.2 ?
C4' C5' H5C . . 109.2 ?
H5B C5' H5C . . 107.9 ?
C3' O3' H3 . . 106.4(19) ?
C1' O4' C4' . . 110.96(15) y
C5' O5' H5 . . 109.(2) ?
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 . 1.359(3) ?
N1 C2 . 1.392(3) ?
N1 C1' . 1.499(2) y
N3 C4 . 1.337(3) ?
N3 C2 . 1.352(3) ?
N4 C4 . 1.337(3) y
N4 H4A . 0.86(3) ?
N4 H4B . 0.93(3) ?
O2 C2 . 1.254(2) ?
C4 C5 . 1.420(3) ?
C5 C6 . 1.351(3) ?
C5 H5A . 0.95 ?
C6 H6 . 0.95 ?
C1' O4' . 1.407(2) ?
C1' C2' . 1.524(3) ?
C1' H1 . 1.0 ?
C2' C3' . 1.525(3) ?
C2' H2A . 0.99 ?
C2' H2B . 0.99 ?
C3' O3' . 1.435(2) ?
C3' C4' . 1.526(3) ?
C3' H3A . 1.0 ?
C4' O4' . 1.454(2) ?
C4' C5' . 1.517(3) ?
C4' H4 . 1.0 ?
C5' O5' . 1.429(2) ?
C5' H5B . 0.99 ?
C5' H5C . 0.99 ?
O3' H3 . 0.94(3) ?
O5' H5 . 0.91(4) ?
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
_geom_hbond_publ_flag
N4 H4A O3' 4_566 0.86(3) 2.10(3) 2.949(2) 168.(2) yes
N4 H4B O2 3_755 0.93(3) 2.05(3) 2.937(2) 159.(2) yes
C1' H1 N3 3_745 1.0 2.46 3.317(3) 143.7 yes
C3' H3A N3 3_645 1.0 2.53 3.524(3) 170.2 yes
O3' H3 O5' 3_655 0.94(3) 1.86(4) 2.793(2) 175.(3) yes
O5' H5 O2 3_745 0.91(4) 1.88(3) 2.716(2) 152.(3) yes
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_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion
_geom_torsion_publ_flag
C4 N3 C2 O2 . . . . -178.13(18) y
C4 N3 C2 N1 . . . . 2.1(3) ?
C6 N1 C2 O2 . . . . 175.01(18) ?
C1' N1 C2 O2 . . . . -5.2(3) ?
C6 N1 C2 N3 . . . . -5.2(3) ?
C1' N1 C2 N3 . . . . 174.55(18) ?
C2 N3 C4 N4 . . . . -176.89(18) ?
C2 N3 C4 C5 . . . . 2.8(3) ?
N4 C4 C5 C6 . . . . 175.05(18) y
N3 C4 C5 C6 . . . . -4.6(3) ?
C4 C5 C6 N1 . . . . 1.4(3) ?
C2 N1 C6 C5 . . . . 3.3(3) ?
C1' N1 C6 C5 . . . . -176.44(19) ?
C6 N1 C1' O4' . . . . -6.8(3) ?
C2 N1 C1' O4' . . . . 173.39(16) y
C6 N1 C1' C2' . . . . 110.68(19) ?
C2 N1 C1' C2' . . . . -69.1(2) ?
O4' C1' C2' C3' . . . . 27.75(19) ?
N1 C1' C2' C3' . . . . -91.35(18) ?
C1' C2' C3' O3' . . . . 82.77(18) ?
C1' C2' C3' C4' . . . . -33.03(18) y
O3' C3' C4' O4' . . . . -90.74(17) ?
C2' C3' C4' O4' . . . . 27.35(18) ?
O3' C3' C4' C5' . . . . 149.18(16) ?
C2' C3' C4' C5' . . . . -92.73(19) ?
O4' C4' C5' O5' . . . . -62.1(2) ?
C3' C4' C5' O5' . . . . 55.9(2) y
N1 C1' O4' C4' . . . . 109.54(17) ?
C2' C1' O4' C4' . . . . -10.83(19) ?
C5' C4' O4' C1' . . . . 112.58(17) ?
C3' C4' O4' C1' . . . . -10.69(19) ?
