Sugar–nucleobase hydrogen bonding in cytidine 5′-monophosphate nucleotide-cadmium coordination complexes
Khan, Yaqoot; Ismail, Ismail; Ma, Hongwei; Li, Zhongkui; Li, Hui; CrystEngComm 26 (2024) 2775–2783; doi:10.1039/D4CE00150H

data_7248602
_publ_section_title
;
 Sugar--nucleobase hydrogen bonding in cytidine 5&#x2032;-monophosphate
 nucleotide-cadmium coordination complexes
;
_journal_issue                   21
_journal_name_full               CrystEngComm
_journal_page_first              2775
_journal_page_last               2783
_journal_paper_doi               10.1039/D4CE00150H
_journal_volume                  26
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C21 H28 Cd N5 O11 P, 2(H2 O)'
_chemical_formula_sum            'C21 H32 Cd N5 O13 P'
_chemical_formula_weight         705.88
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_block_doi                 10.5517/ccdc.csd.cc2h2r5j
_audit_creation_date             2024-03-22
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2024-04-01 deposited with the CCDC.	2024-04-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 92.58(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   8.310(5)
_cell_length_b                   11.901(7)
_cell_length_c                   14.109(8)
_cell_measurement_reflns_used    6838
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      30.95
_cell_measurement_theta_min      2.24
_cell_volume                     1393.9(14)
_computing_cell_refinement       'SAINT v8.34A (Bruker, 2013)'
_computing_data_reduction        'SAINT v8.34A (Bruker, 2013)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.918
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0194
_diffrn_reflns_av_unetI/netI     0.0288
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.918
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            18764
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.876
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         31.411
_diffrn_reflns_theta_min         1.445
_diffrn_source_current           35.0
_diffrn_source_power             1.575
_diffrn_source_voltage           45.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.914
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            'clear whiteish colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   whiteish
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.682
_exptl_crystal_description       block
_exptl_crystal_F_000             720
_exptl_crystal_size_max          0.27
_exptl_crystal_size_mid          0.25
_exptl_crystal_size_min          0.21
_refine_diff_density_max         0.387
_refine_diff_density_min         -0.341
_refine_diff_density_rms         0.050
_refine_ls_abs_structure_details
;
 Flack x determined using 3466 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.003(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.040
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     381
_refine_ls_number_reflns         8061
_refine_ls_number_restraints     17
_refine_ls_restrained_S_all      1.064
_refine_ls_R_factor_all          0.0194
_refine_ls_R_factor_gt           0.0183
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0173P)^2^+0.1362P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0437
_refine_ls_wR_factor_ref         0.0443
_reflns_Friedel_coverage         0.829
_reflns_Friedel_fraction_full    0.995
_reflns_Friedel_fraction_max     0.830
_reflns_number_gt                7822
_reflns_number_total             8061
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ce00150h2.cif
_cod_data_source_block           2_sq
_cod_depositor_comments
'Adding full bibliography for 7248599--7248603.cif.'
_cod_database_code               7248602
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.831
_shelx_estimated_absorpt_t_min   0.790
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All O(H) groups, All O(H,H) groups
2. Restrained distances
 H13B-O14
 2 with sigma of 0.02
 H1B_$1-H13A
 2.15 with sigma of 0.02
 H14A-O12_$2
 2.1 with sigma of 0.02
 H14B-H14A
 1.2 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O13) \\sim Ueq, Uanis(O14) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(O14) \\sim Ueq, Uanis(O13) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(O14) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(O13) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
4. Others
 Fixed Z: Cd1(1.02709)
5.a Riding coordinates:
 O1(H1A,H1B), O2(H2A,H2B), O3(H3A,H3B), O9(H9), O11(H11), N5(H5A,H5B)
5.b Ternary CH refined with riding coordinates:
 C5(H5), C7(H7), C11(H11A), C17(H17)
5.c Secondary CH2 refined with riding coordinates:
 C18(H18A,H18B)
5.d Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C6(H6), C8(H8), C10(H10), C12(H12), C13(H13), C14(H14),
 C15(H15), C16(H16), C19(H19), C20(H20)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              71384
_shelx_fab_checksum              63650
_olex2_submission_special_instructions 'No special instructions were received'