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_7248600
_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         'C30 H41 Cd N8 O16 P2, H O, 3(O), H2 O'
_chemical_formula_sum            'C30 H44 Cd N8 O21 P2'
_chemical_formula_weight         1027.07
_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     iterative
_audit_block_doi                 10.5517/ccdc.csd.cc2g2940
_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                   13.813(5)
_cell_length_b                   14.472(6)
_cell_length_c                   20.721(7)
_cell_measurement_reflns_used    9754
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      25.09
_cell_measurement_theta_min      2.26
_cell_volume                     4142(3)
_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 0.951
_diffrn_measured_fraction_theta_max 0.928
_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  0.0535
_diffrn_reflns_av_unetI/netI     0.0784
_diffrn_reflns_Laue_measured_fraction_full 0.951
_diffrn_reflns_Laue_measured_fraction_max 0.928
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -7
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -21
_diffrn_reflns_number            13987
_diffrn_reflns_point_group_measured_fraction_full 0.924
_diffrn_reflns_point_group_measured_fraction_max 0.899
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         25.693
_diffrn_reflns_theta_min         1.716
_exptl_absorpt_coefficient_mu    0.696
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.647
_exptl_crystal_description       block
_exptl_crystal_F_000             2104
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.25
_exptl_crystal_size_min          0.23
_refine_diff_density_max         1.859
_refine_diff_density_min         -0.656
_refine_diff_density_rms         0.118
_refine_ls_abs_structure_details
;
 Flack x determined using 2301 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.003(17)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     580
_refine_ls_number_reflns         7089
_refine_ls_number_restraints     21
_refine_ls_restrained_S_all      1.074
_refine_ls_R_factor_all          0.0618
_refine_ls_R_factor_gt           0.0525
_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^)+(0.0727P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1270
_refine_ls_wR_factor_ref         0.1332
_reflns_Friedel_coverage         0.742
_reflns_Friedel_fraction_full    0.889
_reflns_Friedel_fraction_max     0.863
_reflns_number_gt                6239
_reflns_number_total             7089
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ce00150h2.cif
_cod_data_source_block           33_a
_cod_depositor_comments
'Adding full bibliography for 7248599--7248603.cif.'
_cod_database_code               7248600
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.856
_shelx_estimated_absorpt_t_min   0.793
_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
 C7-C13
 1.45 with sigma of 0.02
 H9B-H9A
 1.2 with sigma of 0.02
 Cd1-H11A \\sim Cd1-H11B
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C13) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O5) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C7) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
4. Others
 Fixed Y: Cd1(0.536719)
5.a Rotating group:
 O14(H14A,H14B)
5.b Ternary CH refined with riding coordinates:
 C3(H3), C8(H8), C11(H11), C18(H18), C21(H21), C22(H22)
5.c Secondary CH2 refined with riding coordinates:
 C7(H7C,H7D), C13(H13A,H13B), C14(H14C,H14D), C15(H15A,H15B), C27(H27A,H27B),
 C29(H29A,H29B)
5.d Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2A), C4(H4), C9(H9), C10(H10), C16(H16), C17(H17), C19(H19),
 C20(H20), C23(H23), C26(H26), C28(H28)
5.e X=CH2 refined with riding coordinates:
 N5(H5A,H5B), N7(H7A,H7B)
5.f Idealised tetrahedral OH refined as rotating group:
 O15(H15), O20(H20A)
;
_shelx_res_checksum              5359
_olex2_submission_special_instructions 'No special instructions were received'