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_7248603
_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         'C28 H38 Cd N10 O16 P2, 2(H2 O), H O, O'
_chemical_formula_sum            'C28 H43 Cd N10 O20 P2'
_chemical_formula_weight         1014.06
_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     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2g2962
_audit_creation_date             2024-03-23
_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                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.5898(15)
_cell_length_b                   14.6787(17)
_cell_length_c                   21.008(2)
_cell_measurement_reflns_used    9865
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      28.241
_cell_measurement_theta_min      2.260
_cell_volume                     4190.7(8)
_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    'SHELXT 2014/4 (Sheldrick, 2014)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.948
_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  0.0562
_diffrn_reflns_av_unetI/netI     0.0571
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.948
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       30
_diffrn_reflns_limit_l_min       -30
_diffrn_reflns_number            58229
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.921
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         31.695
_diffrn_reflns_theta_min         1.785
_exptl_absorpt_coefficient_mu    0.687
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.607
_exptl_crystal_description       block
_exptl_crystal_F_000             2076
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.25
_exptl_crystal_size_min          0.25
_refine_diff_density_max         1.595
_refine_diff_density_min         -0.486
_refine_diff_density_rms         0.087
_refine_ls_abs_structure_details
;
 Flack x determined using 4063 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.000(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.026
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     569
_refine_ls_number_reflns         13047
_refine_ls_number_restraints     8
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0590
_refine_ls_R_factor_gt           0.0435
_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/[\s^2^(Fo^2^)+(0.0482P)^2^+1.4315P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0950
_refine_ls_wR_factor_ref         0.1006
_reflns_Friedel_coverage         0.777
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.888
_reflns_number_gt                10824
_reflns_number_total             13047
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ce00150h2.cif
_cod_data_source_block           1_a
_cod_depositor_comments
'Adding full bibliography for 7248599--7248603.cif.'
_cod_original_cell_volume        4190.8(8)
_cod_database_code               7248603
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.847
_shelx_estimated_absorpt_t_min   0.795
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H) groups
 At 1.5 times of:
  All O(H) groups, All O(H,H) groups
2. Restrained distances
 H17B-O18
 2.04 with sigma of 0.02
 H3A-H20B
 2.12 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O18) \\sim Ueq: with sigma of 0.003 and sigma for terminal atoms of 0.006
4. Others
 Fixed Z: Cd1(0.26464)
5.a Rotating group:
 O3(H3A,H3B), O4(H4A,H4B)
5.b Ternary CH refined with riding coordinates:
 C6(H6), C16(H16), C17(H17), C23(H23), C24(H24), C25(H25)
5.c Secondary CH2 refined with riding coordinates:
 C5(H5A,H5B), C15(H15A,H15B), C26(H26A,H26B), C27(H27A,H27B)
5.d Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), N6(H6A), C7(H7), C8(H8), C9(H9), C11(H11), C12(H12), C14(H14),
  C19(H19), C20(H20), C21(H21), C22(H22)
5.e X=CH2 refined with riding coordinates:
 N7(H7A,H7B), N10(H10A,H10B)
5.f Idealised tetrahedral OH refined as rotating group:
 O5(H5), O9(H9A), O15(H15)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              30822
_shelx_fab_checksum              94549
_olex2_submission_special_instructions 'No special instructions were received'