Ibuprofen and sila-ibuprofen: polarization effects in the crystal and enzyme environments
Kleemiss, Florian; Puylaert, Pim; Duvinage, Daniel; Fugel, Malte; Sugimoto, Kunihisa; Beckmann, Jens; Grabowsky, Simon; Acta Crystallographica Section B 77 (2021) 892–905; doi:10.1107/S2052520621009379

data_2108899
_publ_section_title
;
 Ibuprofen and sila-ibuprofen: polarization effects in the crystal and
 enzyme environments
;
_journal_issue                   6
_journal_name_full               'Acta Crystallographica Section B'
_journal_page_first              892
_journal_page_last               905
_journal_paper_doi               10.1107/S2052520621009379
_journal_volume                  77
_journal_year                    2021
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C6 H15 N4 O2, C13 H17 O2'
_chemical_formula_sum            'C19 H32 N4 O4'
_chemical_formula_weight         380.490
_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'
_symmetry_Int_Tables_number      19
_audit_creation_date             2020-09-22
_audit_creation_method
;
Olex2 1.3-dev
(compiled 2020.07.16 svn.rf55b3278 for OlexSys, GUI svn.r6014)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   9.3033(6)
_cell_length_b                   14.8134(10)
_cell_length_c                   29.664(2)
_cell_measurement_reflns_used    9688
_cell_measurement_temperature    100.01
_cell_measurement_theta_max      26.45
_cell_measurement_theta_min      2.58
_cell_volume                     4088.1(5)
_computing_molecular_graphics    'Olex2 1.3-dev (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3-dev (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.3-dev (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100.01
_diffrn_measured_fraction_theta_full 0.9959
_diffrn_measured_fraction_theta_max 0.9959
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0887
_diffrn_reflns_av_unetI/netI     0.0799
_diffrn_reflns_Laue_measured_fraction_full 0.9959
_diffrn_reflns_Laue_measured_fraction_max 0.9959
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            51814
_diffrn_reflns_point_group_measured_fraction_full 0.9967
_diffrn_reflns_point_group_measured_fraction_max 0.9967
_diffrn_reflns_theta_full        20.8125
_diffrn_reflns_theta_max         20.81
_diffrn_reflns_theta_min         2.29
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.087
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.236
_exptl_crystal_description       block
_exptl_crystal_F_000             1648.774
_exptl_crystal_size_max          0.162
_exptl_crystal_size_mid          0.158
_exptl_crystal_size_min          0.106
_refine_diff_density_max         0.5813
_refine_diff_density_min         -0.4758
_refine_diff_density_rms         0.1162
_refine_ls_abs_structure_details
'Flack, H. D. (1983). Acta Cryst. A39, 876-881.'
_refine_ls_abs_structure_Flack   -0(3)
_refine_ls_d_res_high            1.0002
_refine_ls_d_res_low             8.8770
_refine_ls_goodness_of_fit_ref   1.0522
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    116
_refine_ls_number_parameters     511
_refine_ls_number_reflns         4263
_refine_ls_number_restraints     770
_refine_ls_restrained_S_all      0.9585
_refine_ls_R_factor_all          0.1039
_refine_ls_R_factor_gt           0.1009
_refine_ls_shift/su_max          0.0002
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0000P)^2^+50.3900P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2093
_refine_ls_wR_factor_ref         0.2110
_reflns_Friedel_coverage         0.998
_reflns_limit_h_max              9
_reflns_limit_h_min              -9
_reflns_limit_k_max              14
_reflns_limit_k_min              -14
_reflns_limit_l_max              29
_reflns_limit_l_min              -29
_reflns_number_gt                4097
_reflns_number_total             4263
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            px5037sup1.cif
_cod_data_source_block           ibu_arg
_cod_original_sg_symbol_Hall     ' P 2ac 2ab'
_cod_database_code               2108899
_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, All
  N(H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C01H-C01I \\sim C2-C01J
 with sigma of 0.02
 C01J-C3 \\sim C01K-C3
 with sigma of 0.04
 C2-C3 \\sim C2A-C3
 with sigma of 0.02
 C2-C01J \\sim C2A-C01K
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C00S) \\sim Ueq, Uanis(O001) \\sim Ueq, Uanis(C00F) \\sim Ueq,
Uanis(O002) \\sim Ueq, Uanis(C00O) \\sim Ueq, Uanis(N00E) \\sim Ueq,
Uanis(C00R) \\sim Ueq, Uanis(C00L) \\sim Ueq, Uanis(N00H) \\sim Ueq,
Uanis(C00J) \\sim Ueq, Uanis(N00D) \\sim Ueq, Uanis(N00G) \\sim Ueq,
Uanis(C00Q) \\sim Ueq, Uanis(O003) \\sim Ueq, Uanis(C00I) \\sim Ueq,
Uanis(O005) \\sim Ueq, Uanis(C00M) \\sim Ueq, Uanis(N008) \\sim Ueq,
Uanis(C00U) \\sim Ueq, Uanis(C00P) \\sim Ueq, Uanis(N00B) \\sim Ueq,
Uanis(C00K) \\sim Ueq, Uanis(N00A) \\sim Ueq, Uanis(N00C) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(C0) \\sim Ueq, Uanis(O0) \\sim Ueq, Uanis(C20) \\sim Ueq, Uanis(C2) \\sim
Ueq, Uanis(O1) \\sim Ueq, Uanis(C2A) \\sim Ueq, Uanis(C01J) \\sim Ueq,
Uanis(C3) \\sim Ueq, Uanis(C01K) \\sim Ueq, Uanis(C4) \\sim Ueq, Uanis(C5)
\\sim Ueq, Uanis(C6) \\sim Ueq, Uanis(C7) \\sim Ueq, Uanis(C8) \\sim Ueq,
Uanis(C9) \\sim Ueq, Uanis(C10) \\sim Ueq, Uanis(C11) \\sim Ueq, Uanis(C14)
\\sim Ueq, Uanis(C01H) \\sim Ueq, Uanis(C01I) \\sim Ueq, Uanis(C12) \\sim Ueq,
Uanis(C13A) \\sim Ueq, Uanis(C16) \\sim Ueq, Uanis(C17) \\sim Ueq, Uanis(O2)
\\sim Ueq, Uanis(O3) \\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C18) \\sim Ueq,
Uanis(C19) \\sim Ueq, Uanis(C1A) \\sim Ueq, Uanis(C1B) \\sim Ueq, Uanis(C1C)
\\sim Ueq, Uanis(C00{) \\sim Ueq, Uanis(C1D) \\sim Ueq: with sigma of 0.025 and
sigma for terminal atoms of 0.05
4. Rigid body (RIGU) restrains
 C00U, O003, C00I, O005, C00M, N008, C00P, C00Q, N00B, C00K, N00A, N00C
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C00S, O001, C00F, O002, C00O, N00E, C00R, C00L, N00H, C00J, N00D, N00G
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C12, C01H, C01I, C13A, C14, C16, C17, O2, O3, C15, C18, C19, C1A, C1B, C1C,
 C00{, C1D
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C3, O0, C20, C2A, C2, O1, C01K, C01J, C4, C5, C6, C7, C0, C8, C9, C10, C11
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(C14)=Sof(H14)=Sof(C15)=Sof(H15a)=Sof(H15b)=Sof(H15c)=1-FVAR(1)
 Sof(C01H)=Sof(H01H)=Sof(C01I)=Sof(H01a)=Sof(H01b)=Sof(H01c)=FVAR(1)
 Sof(C01K)=Sof(H01g)=Sof(H01i)=Sof(H01j)=Sof(C2A)=Sof(H2A)=1-FVAR(2)
 Sof(C2)=Sof(H2)=Sof(C01J)=Sof(H01d)=Sof(H01e)=Sof(H01f)=FVAR(2)
6.a Ternary CH refined with riding coordinates:
 C00M(H00z), C00O(H00O), C01H(H01H), C2(H2), C9(H9), C14(H14), C1C(H1C),
 C2A(H2A)
6.b Secondary CH2 refined with riding coordinates:
 C00L(H00l,H00m), C00P(H00,H), C00Q(H1,Hb), C00R(H00n,H00p), C00S(H00q,H00r),
 C00U(H3,Ha), C8(H8a,H8b), C1B(H1Ba,H1Bb)
6.c Aromatic/amide H refined with riding coordinates:
 N00B(H00x), N00H(H00k), C7(H7), C6(H6), C4(H4), C5(H5), C18(H18), C16(H16),
 C17(H17), C19(H19)
6.d Fitted hexagon refined as free rotating group:
 C7(C0,C6,C4,C3,C5), C18(C16,C12,C17,C19,C1A)
6.e X=CH2 refined with riding coordinates:
 N00A(H00v,H00w), N00C(H00y,Hc), N00D(H00d,H00e), N00G(H00i,H00j)
6.f Idealised Me refined as rotating group:
 N008(H00s,H00t,H00u), N00E(H00f,H00g,H00h), C01I(H01a,H01b,H01c), C01J(H01d,
 H01e,H01f), C10(H10a,H10b,H10c), C11(H11a,H11b,H11c), C15(H15a,H15b,H15c),
 C00{(H00a,H00b,H00c), C1D(H1Da,H1Db,H1Dc), C01K(H01g,H01i,H01j)
;
_olex2_submission_special_instructions 'No special instructions were received'
_cod_database_fobs_code 2108899