Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide.
Yamane, Daiki; Onitsuka, Satsuki; Re, Suyong; Isogai, Hikaru; Hamada, Rui; Hiramoto, Tadanari; Kawanishi, Eiji; Mizuguchi, Kenji; Shindo, Naoya; Ojida, Akio; Chemical science 13 (2022) 3027–3034; doi:10.1039/d1sc06596c

data_1566407
_publ_section_title
;
 Selective covalent targeting of SARS-CoV-2 main protease by enantiopure
 chlorofluoroacetamide.
;
_journal_issue                   10
_journal_name_full               'Chemical science'
_journal_page_first              3027
_journal_page_last               3034
_journal_paper_doi               10.1039/d1sc06596c
_journal_volume                  13
_journal_year                    2022
_chemical_formula_moiety         'C22 H18 Cl F7 N4 O2 S'
_chemical_formula_sum            'C22 H18 Cl F7 N4 O2 S'
_chemical_formula_weight         570.921
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_symmetry_Int_Tables_number      14
_atom_sites_solution_primary     dual
_audit_creation_date             2021-08-23
_audit_creation_method
;
Olex2 1.5
(compiled 2021.07.19 svn.r715e62df for OlexSys, GUI svn.r6383)
;
_audit_update_record
;
2021-11-26 deposited with the CCDC.	2022-02-15 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 93.634(4)
_cell_angle_gamma                90
_cell_formula_units_Z            16
_cell_length_a                   9.4276(3)
_cell_length_b                   19.5575(5)
_cell_length_c                   50.822(2)
_cell_measurement_reflns_used    8328
_cell_measurement_temperature    100
_cell_measurement_theta_max      27.4960
_cell_measurement_theta_min      2.2120
_cell_volume                     9351.7(5)
_computing_cell_refinement       'CrysAlisPro 1.171.40.67a (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.40.67a (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.40.67a (Rigaku OD, 2019)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5 (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100
_diffrn_detector                 'Rigaku HyPix-6000 area detector'
_diffrn_detector_area_resol_mean 10.0
_diffrn_detector_type            'HPC area detector'
_diffrn_measured_fraction_theta_full 0.9943
_diffrn_measured_fraction_theta_max 0.9130
_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   -117.00  61.00   0.20   24.00    --  -27.60  45.00 158.05  890
  2  \w   -117.00  61.00   0.20   24.00    --  -27.60  45.00 -19.57  890
  3  \w   -117.00  37.00   0.20   24.00    --  -27.60  45.00 120.00  770
  4  \w   -117.00 -91.00   0.20   24.00    --  -27.60  45.00 179.54  130
  5  \w     28.00  60.00   0.20   24.00    --  -27.60  45.00 179.54  160
;
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku AFC HyPix-6000'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0007984000
_diffrn_orient_matrix_UB_12      -0.0013861000
_diffrn_orient_matrix_UB_13      -0.0139641000
_diffrn_orient_matrix_UB_21      0.0031633000
_diffrn_orient_matrix_UB_22      0.0361984000
_diffrn_orient_matrix_UB_23      -0.0004781000
_diffrn_orient_matrix_UB_31      0.0752981000
_diffrn_orient_matrix_UB_32      -0.0014915000
_diffrn_orient_matrix_UB_33      0.0007534000
_diffrn_radiation_monochromator  'multi-layer mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0717
_diffrn_reflns_av_unetI/netI     0.0736
_diffrn_reflns_Laue_measured_fraction_full 0.9943
_diffrn_reflns_Laue_measured_fraction_max 0.9130
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -26
_diffrn_reflns_limit_l_max       69
_diffrn_reflns_limit_l_min       -69
_diffrn_reflns_number            93272
_diffrn_reflns_point_group_measured_fraction_full 0.9943
_diffrn_reflns_point_group_measured_fraction_max 0.9130
_diffrn_reflns_theta_full        25.2417
_diffrn_reflns_theta_max         29.76
_diffrn_reflns_theta_min         1.91
_diffrn_source                   'rotating anode X-ray generator'
_diffrn_source_type              FR-E+
_exptl_absorpt_coefficient_mu    0.338
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.887
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.67a (Rigaku Oxford Diffraction, 2019)
Numerical absorption correction based on gaussian integration over
			a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.622
_exptl_crystal_description       plate
_exptl_crystal_F_000             4647.665
_exptl_crystal_size_max          0.333
_exptl_crystal_size_mid          0.086
_exptl_crystal_size_min          0.026
_refine_diff_density_max         2.8205
_refine_diff_density_min         -1.1778
_refine_diff_density_rms         0.2580
_refine_ls_d_res_high            0.7159
_refine_ls_d_res_low             10.6394
_refine_ls_goodness_of_fit_ref   1.1828
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    141
_refine_ls_number_parameters     1361
_refine_ls_number_reflns         24343
_refine_ls_number_restraints     48
_refine_ls_restrained_S_all      1.1815
_refine_ls_R_factor_all          0.1739
_refine_ls_R_factor_gt           0.1375
_refine_ls_shift/su_max          0.0010
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1131P)^2^+76.7149P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3251
_refine_ls_wR_factor_ref         0.3445
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              12
_reflns_limit_h_min              -12
_reflns_limit_k_max              27
_reflns_limit_k_min              0
_reflns_limit_l_max              69
_reflns_limit_l_min              -11
_reflns_number_gt                17675
_reflns_number_total             24343
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d1sc06596c2.cif
_cod_data_source_block           NS-15-060B-5
_cod_depositor_comments
'Adding full bibliography for 1566406--1566407.cif.'
_cod_original_cell_volume        9351.7(6)
_cod_original_sg_symbol_Hall     '-P 2ybc (x-z,y,z)'
_cod_database_code               1566407
_chemical_oxdiff_formula         'C11 H10 N O'
_chemical_oxdiff_usercomment     100K
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
2. Restrained distances
 F117-C115 \\sim C115-F1
 with sigma of 0.02
 F43-C41 \\sim C41-F43B
 with sigma of 0.02
 F1-C113 \\sim C113-F117
 with sigma of 0.02
 Cl11-C113 \\sim C113-Cl1
 with sigma of 0.02
 F1-C115 \\sim C115-F117
 with sigma of 0.02
 Cl11-C115 \\sim C115-Cl1
 with sigma of 0.02
3. Rigid body (RIGU) restrains
 Cl1, C115, F1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 Cl11, C71, C115, F117
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F43, C41, Cl42
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C41, F43B, Cl42
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4. Others
 Sof(H41a)=Sof(H11a)=Sof(Cl1)=Sof(F1)=Sof(F43B)=1-FVAR(1)
 Sof(Cl11)=Sof(F43)=Sof(F117)=Sof(H41)=Sof(H115)=FVAR(1)
5.a Ternary CH refined with riding coordinates:
 C93(H93), C130(H130), C78(H78), C56(H56), C19(H19), C41(H41), C41(H41a),
 C4(H4), C115(H115), C115(H11a)
5.b Secondary CH2 refined with riding coordinates:
 C103(H10a,H10b), C140(H14a,H14b), C66(H66a,H66b), C29(H29a,H29b), C104(H10c,
 H10d), C30(H30a,H30b), C141(H14c,H14d), C67(H67a,H67b)
5.c Aromatic/amide H refined with riding coordinates:
 N102(H102), N139(H139), N28(H28), N65(H65), C95(H95), C136(H136), C119(H119),
 C134(H134), C120(H120), C83(H83), C122(H122), C97(H97), C82(H82), C99(H99),
 C86(H86), C132(H132), C123(H123), C106(H106), C85(H85), C58(H58), C143(H143),
 C48(H48), C11(H11), C46(H46), C9(H9), C62(H62), C72(H72), C21(H21), C49(H49),
 C12(H12), C45(H45), C25(H25), C8(H8), C69(H69), C23(H23), C60(H60), C71(H71),
 C34(H34), C35(H35), C32(H32), C147(H147), C73(H73), C110(H110), C145(H145),
 C36(H36), C108(H108), C146(H146), C109(H109)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.506
_oxdiff_exptl_absorpt_empirical_full_min 0.777