A combined crystallographic and theoretical investigation of noncovalent interactions in 1,3,4-oxadiazole-2-thione-N-Mannich derivatives: in vitro bioactivity and molecular docking
Al-Wahaibi, Lamya H.; Alagappan, Kowsalya; Gomila, Rosa M.; Blacque, Olivier; Frontera, Antonio; Percino, M. Judith; El-Emam, Ali A.; Thamotharan, Subbiah; RSC Advances 13 (2023) 34064–34077; doi:10.1039/D3RA07169C

data_7247761
_publ_section_title
;
 A combined crystallographic and theoretical investigation of noncovalent
 interactions in 1,3,4-oxadiazole-2-thione-N-Mannich derivatives: in vitro
 bioactivity and molecular docking
;
_journal_issue                   48
_journal_name_full               'RSC Advances'
_journal_page_first              34064
_journal_page_last               34077
_journal_paper_doi               10.1039/D3RA07169C
_journal_volume                  13
_journal_year                    2023
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C15 H10 Cl F2 N3 O S'
_chemical_formula_sum            'C15 H10 Cl F2 N3 O S'
_chemical_formula_weight         353.77
_space_group_crystal_system      orthorhombic
_space_group_IT_number           45
_space_group_name_Hall           'I 2 -2c'
_space_group_name_H-M_alt        'I b a 2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2021-01-07
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6226)
;
_audit_update_record
;
2023-10-18 deposited with the CCDC.	2023-11-15 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   28.8781(9)
_cell_length_b                   13.8936(4)
_cell_length_c                   7.7325(3)
_cell_measurement_reflns_used    5035
_cell_measurement_temperature    160(1)
_cell_measurement_theta_max      76.0830
_cell_measurement_theta_min      3.0520
_cell_volume                     3102.44(18)
_computing_cell_refinement       'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL (Sheldrick, 2015b)'
_computing_structure_solution    'SHELXT (Sheldrick, 2015a)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      160(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.3801
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w   -107.00 -13.00   1.00    7.00    --  -38.50 -57.00   0.00   94
  2  \w    -27.00  64.00   1.00    7.00    --   43.74 -37.00 150.00   91
  3  \w     24.00  95.00   1.00    7.00    --   43.74-121.00 113.00   71
  4  \w     40.00 110.00   1.00   28.00    --  111.00-121.00 113.00   70
  5  \w     61.00 146.00   1.00   28.00    --  111.00 178.00 -90.00   85
  6  \w     43.00 137.00   1.00   28.00    --  111.00 -61.00   0.00   94
  7  \w     90.00 178.00   1.00   28.00    --  111.00  30.00 -60.00   88
  8  \w     38.00 109.00   1.00   28.00    --  111.00-111.00 -60.00   71
  9  \w    104.00 178.00   1.00   28.00    --  111.00 111.00-150.00   74
 10  \w     31.00 107.00   1.00   28.00    --  111.00 -94.00 150.00   76
 11  \w     89.00 178.00   1.00   28.00    --  111.00  45.00-180.00   89
 12  \w     31.00 107.00   1.00   28.00    --  111.00 -94.00-150.00   76
 13  \w     19.00 112.00   1.00    7.00    --   43.74  57.00 150.00   93
 14  \w     19.00 112.00   1.00    7.00    --   43.74  57.00 -90.00   93
 15  \w     71.00 178.00   1.00   28.00    --  111.00  15.00  90.00  107
 16  \w     85.00 178.00   1.00   28.00    --  111.00  61.00   0.00   93
 17  \w     89.00 178.00   1.00   28.00    --  111.00  45.00-120.00   89
 18  \w     31.00  73.00   1.00   28.00    --  111.00 -94.00 -30.00   42
 19  \w    103.00 178.00   1.00   28.00    --  111.00  77.00 120.00   75
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0220707000
_diffrn_orient_matrix_UB_12      -0.0170183000
_diffrn_orient_matrix_UB_13      -0.1788621000
_diffrn_orient_matrix_UB_21      -0.0479490000
_diffrn_orient_matrix_UB_22      -0.0099004000
_diffrn_orient_matrix_UB_23      0.0856730000
_diffrn_orient_matrix_UB_31      -0.0077831000
_diffrn_orient_matrix_UB_32      0.1090439000
_diffrn_orient_matrix_UB_33      -0.0202224000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0466
_diffrn_reflns_av_unetI/netI     0.0326
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       36
_diffrn_reflns_limit_h_min       -36
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       9
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            15474
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.430
_diffrn_reflns_theta_min         3.061
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.709
_exptl_absorpt_correction_T_max  0.941
_exptl_absorpt_correction_T_min  0.745
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.68a (Rigaku Oxford Diffraction, 2019)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.515
_exptl_crystal_description       needle
_exptl_crystal_F_000             1440
_exptl_crystal_size_max          0.11
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.179
_refine_diff_density_min         -0.157
_refine_diff_density_rms         0.036
_refine_ls_abs_structure_details
;
 Flack x determined using 1217 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.004(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.061
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     212
_refine_ls_number_reflns         3163
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.061
_refine_ls_R_factor_all          0.0334
_refine_ls_R_factor_gt           0.0270
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0258P)^2^+0.3772P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0581
_refine_ls_wR_factor_ref         0.0607
_reflns_Friedel_coverage         0.845
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.997
_reflns_number_gt                2856
_reflns_number_total             3163
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3ra07169c2.cif
_cod_data_source_block           emam-52
_cod_original_cell_volume        3102.43(17)
_cod_database_code               7247761
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.930
_shelx_estimated_absorpt_t_min   0.686
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2.a Secondary CH2 refined with riding coordinates:
 C9(H9A,H9B)
2.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5), C6(H6), C12(H12), C13(H13), C15(H15)
;
_shelx_res_checksum              53652