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_7248601
_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         'C10 H16 Cd N4 O4, C9 H12 N3 O8 P, 3(H2 O)'
_chemical_formula_sum            'C19 H34 Cd N7 O15 P'
_chemical_formula_weight         743.90
_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     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2g2951
_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                 106.071(4)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   9.3779(13)
_cell_length_b                   12.2117(18)
_cell_length_c                   13.6250(19)
_cell_measurement_reflns_used    9902
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      30.345
_cell_measurement_theta_min      2.260
_cell_volume                     1499.4(4)
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.915
_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  0.0221
_diffrn_reflns_av_unetI/netI     0.0374
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.915
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            20743
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.877
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         31.697
_diffrn_reflns_theta_min         1.555
_exptl_absorpt_coefficient_mu    0.861
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.648
_exptl_crystal_description       block
_exptl_crystal_F_000             760
_exptl_crystal_size_max          0.32
_exptl_crystal_size_mid          0.25
_exptl_crystal_size_min          0.17
_refine_diff_density_max         1.065
_refine_diff_density_min         -0.272
_refine_diff_density_rms         0.064
_refine_ls_abs_structure_details
;
 Flack x determined using 3455 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.003(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.014
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     417
_refine_ls_number_reflns         8886
_refine_ls_number_restraints     16
_refine_ls_restrained_S_all      1.016
_refine_ls_R_factor_all          0.0330
_refine_ls_R_factor_gt           0.0281
_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^)+(0.0348P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0632
_refine_ls_wR_factor_ref         0.0655
_reflns_Friedel_coverage         0.840
_reflns_Friedel_fraction_full    0.998
_reflns_Friedel_fraction_max     0.835
_reflns_number_gt                8136
_reflns_number_total             8886
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ce00150h2.cif
_cod_data_source_block           1_b_CCDC1
_cod_depositor_comments
'Adding full bibliography for 7248599--7248603.cif.'
_cod_database_code               7248601
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.867
_shelx_estimated_absorpt_t_min   0.770
_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
 H3B-O14_$1
 1.88 with sigma of 0.02
 H13A-H10A
 2.12 with sigma of 0.02
 H14C-O13
 2.12 with sigma of 0.02
 O11-H14D_$2
 2.12 with sigma of 0.02
 H14C-H7A_$3
 2.12 with sigma of 0.02
 H14C_$4-H7A
 2.12 with sigma of 0.02
 H2A-H2B
 1.2 with sigma of 0.02
 H10A-H13A
 2.1 with sigma of 0.02
 Cd1-H2A \\sim Cd1-H2B
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O15) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
4.a Rotating group:
 O1(H1A,H1B), O3(H3A,H3B), O4(H4A,H4B)
4.b Ternary CH refined with riding coordinates:
 C5(H5), C8(H8), C12(H12), C17(H17)
4.c Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B)
4.d Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C6(H6), C7(H7), C9(H9), C10(H10), C15(H15), C18(H18),
 C16(H16), C19(H19)
4.e X=CH2 refined with riding coordinates:
 N7(H7A,H7B)
4.f Idealised tetrahedral OH refined as rotating group:
 O10(H10A), O11(H11)
;
_shelx_res_checksum              37161
_olex2_submission_special_instructions 'No special instructions were received'