#------------------------------------------------------------------------------
#$Date: 2021-06-29 00:35:01 +0300 (Tue, 29 Jun 2021) $
#$Revision: 266741 $
#$URL: file:///home/coder/svn-repositories/cod/cif/4/51/88/4518844.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_4518844
loop_
_publ_author_name
'Iwaoka, Michio'
'Hiyoshi, Yuta'
'Arai, Shota'
'Ito, Takeru'
_publ_section_title
;
 Synthesis of 4-Selenothreofuranose Derivatives via Pummerer-Type
 Reactions of trans-3,4-Dioxygenated Tetrahydroselenophenes Mediated by a
 Selenonium Intermediate
;
_journal_name_full               'ACS Omega'
_journal_paper_doi               10.1021/acsomega.1c02160
_journal_year                    2021
_chemical_formula_moiety         'C25 H20 O6 Se'
_chemical_formula_sum            'C25 H20 O6 Se'
_chemical_formula_weight         495.39
_chemical_name_common            4b'
_chemical_name_systematic
'(3R,4R/3S,4S)-Tetrahydroselenophene-2,3,4-triyl tribenzoate'
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_update_record
;
2020-11-24 deposited with the CCDC.	2021-04-24 downloaded from the CCDC.
;
_cell_angle_alpha                90.0000
_cell_angle_beta                 96.632(4)
_cell_angle_gamma                90.0000
_cell_formula_units_Z            4
_cell_length_a                   9.7088(11)
_cell_length_b                   10.2175(9)
_cell_length_c                   21.667(2)
_cell_measurement_reflns_used    3636
_cell_measurement_temperature    100
_cell_measurement_theta_max      27.50
_cell_measurement_theta_min      3.10
_cell_volume                     2135.0(4)
_computing_cell_refinement       'CrystalClear-SM Expert 2.1 b45'
_computing_data_collection
'CrystalClear-SM Expert 2.1 b45 (Rigaku, 2015)'
_computing_data_reduction        'CrystalClear-SM Expert 2.1 b45'
_computing_molecular_graphics    'CrystalStructure 4.3'
_computing_publication_material  'CrystalStructure 4.3 (Rigaku, 2019)'
_computing_structure_refinement  'SHELXL Version 2018/3 (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT Version 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100
_diffrn_detector_area_resol_mean 5.814
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.949
_diffrn_measurement_device_type  'Rigaku XtaLAB P200'
_diffrn_measurement_method       ω
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71075
_diffrn_reflns_av_R_equivalents  0.0955
_diffrn_reflns_av_unetI/netI     0.0621
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.949
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -27
_diffrn_reflns_number            20133
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.949
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.530
_diffrn_reflns_theta_min         3.130
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.800
_exptl_absorpt_correction_T_max  0.698
_exptl_absorpt_correction_T_min  0.477
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'REQAB (Rigaku, 1998)'
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.541
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             1008.00
_exptl_crystal_size_max          0.200
_exptl_crystal_size_mid          0.200
_exptl_crystal_size_min          0.200
_refine_diff_density_max         0.50
_refine_diff_density_min         -0.53
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.042
_refine_ls_hydrogen_treatment    constr
_refine_ls_number_parameters     289
_refine_ls_number_reflns         4677
_refine_ls_number_restraints     0
_refine_ls_R_factor_all          0.0592
_refine_ls_R_factor_gt           0.0372
_refine_ls_shift/su_max          0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w = 1/[σ²(Fo²)+(0.0469P)²+0.5395P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0873
_refine_ls_wR_factor_ref         0.0982
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3584
_reflns_number_total             4677
_reflns_threshold_expression     F²>2.0σ(F²)
_cod_data_source_file            2046027.cif
_cod_data_source_block           20170802_yuta_c
_cod_database_code               4518844
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 +X,+Y,+Z
2 -X,1/2+Y,1/2-Z
3 -X,-Y,-Z
4 +X,-1/2-Y,-1/2+Z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
Se1 Se 0.34421(2) 0.45533(2) 0.58180(2) 0.02374(10) Uani 1 1 d . . . . .
O1 O 0.62380(16) 0.59490(17) 0.65000(8) 0.0214(4) Uani 1 1 d . . . . .
O2 O 0.67432(17) 0.77420(19) 0.70939(9) 0.0277(4) Uani 1 1 d . . . . .
O3 O 0.28480(17) 0.65380(16) 0.70342(8) 0.0214(4) Uani 1 1 d . . . . .
O4 O 0.30848(17) 0.86674(17) 0.73058(9) 0.0262(4) Uani 1 1 d . . . . .
O5 O 0.41117(17) 0.71942(17) 0.55764(8) 0.0215(4) Uani 1 1 d . . . . .
O6 O 0.25002(18) 0.6716(2) 0.47737(9) 0.0297(4) Uani 1 1 d . . . . .
C1 C 0.4527(2) 0.4311(2) 0.66339(12) 0.0217(5) Uani 1 1 d . . . . .
H1A H 0.393830 0.394723 0.693639 0.026 Uiso 1 1 calc R U . . .
H1B H 0.531298 0.370708 0.660176 0.026 Uiso 1 1 calc R U . . .
C2 C 0.5057(2) 0.5686(2) 0.68365(12) 0.0213(5) Uani 1 1 d . . . . .
H2 H 0.532955 0.572308 0.729554 0.026 Uiso 1 1 calc R U . . .
C3 C 0.3938(2) 0.6693(2) 0.66337(12) 0.0198(5) Uani 1 1 d . . . . .
H3 H 0.433114 0.759814 0.667302 0.024 Uiso 1 1 calc R U . . .
C4 C 0.3317(2) 0.6432(2) 0.59645(12) 0.0196(5) Uani 1 1 d . . . . .
H4 H 0.232474 0.671580 0.590438 0.023 Uiso 1 1 calc R U . . .
C5 C 0.6973(2) 0.7051(3) 0.66642(12) 0.0220(5) Uani 1 1 d . . . . .
C6 C 0.8044(2) 0.7311(3) 0.62380(12) 0.0228(5) Uani 1 1 d . . . . .
C7 C 0.8328(2) 0.6436(3) 0.57766(13) 0.0249(5) Uani 1 1 d . . . . .
H7 H 0.787492 0.561104 0.573858 0.030 Uiso 1 1 calc R U . . .
C8 C 0.9282(3) 0.6781(3) 0.53704(14) 0.0294(6) Uani 1 1 d . . . . .
H8 H 0.949146 0.618279 0.505854 0.035 Uiso 1 1 calc R U . . .
C9 C 0.9928(3) 0.7995(3) 0.54205(15) 0.0317(6) Uani 1 1 d . . . . .
H9 H 1.055748 0.823519 0.513541 0.038 Uiso 1 1 calc R U . . .
C10 C 0.9657(3) 0.8856(3) 0.58844(16) 0.0361(7) Uani 1 1 d . . . . .
H10 H 1.010810 0.968222 0.591966 0.043 Uiso 1 1 calc R U . . .
C11 C 0.8727(3) 0.8515(3) 0.62987(15) 0.0311(6) Uani 1 1 d . . . . .
H11 H 0.855564 0.909930 0.662231 0.037 Uiso 1 1 calc R U . . .
C12 C 0.2499(2) 0.7634(2) 0.73335(11) 0.0188(5) Uani 1 1 d . . . . .
C13 C 0.1310(2) 0.7422(2) 0.76994(12) 0.0182(5) Uani 1 1 d . . . . .
C14 C 0.0442(2) 0.6334(3) 0.76071(13) 0.0232(5) Uani 1 1 d . . . . .
H14 H 0.062743 0.566874 0.732167 0.028 Uiso 1 1 calc R U . . .
C15 C -0.0700(3) 0.6235(3) 0.79387(14) 0.0268(6) Uani 1 1 d . . . . .
H15 H -0.130420 0.550361 0.787502 0.032 Uiso 1 1 calc R U . . .
C16 C -0.0958(3) 0.7195(3) 0.83605(13) 0.0260(6) Uani 1 1 d . . . . .
H16 H -0.174613 0.712231 0.858044 0.031 Uiso 1 1 calc R U . . .
C17 C -0.0082(3) 0.8261(3) 0.84660(13) 0.0258(6) Uani 1 1 d . . . . .
H17 H -0.025191 0.890510 0.876425 0.031 Uiso 1 1 calc R U . . .
C18 C 0.1056(2) 0.8379(2) 0.81287(13) 0.0229(5) Uani 1 1 d . . . . .
H18 H 0.165597 0.911347 0.819279 0.028 Uiso 1 1 calc R U . . .
C19 C 0.3563(3) 0.7277(3) 0.49732(12) 0.0231(5) Uani 1 1 d . . . . .
C20 C 0.4394(3) 0.8128(3) 0.46067(13) 0.0236(5) Uani 1 1 d . . . . .
C21 C 0.5756(3) 0.8460(3) 0.48174(14) 0.0292(6) Uani 1 1 d . . . . .
H21 H 0.616567 0.816880 0.521281 0.035 Uiso 1 1 calc R U . . .
C22 C 0.6515(3) 0.9224(3) 0.44448(16) 0.0370(7) Uani 1 1 d . . . . .
H22 H 0.745227 0.944015 0.458161 0.044 Uiso 1 1 calc R U . . .
C23 C 0.5895(4) 0.9670(3) 0.38694(16) 0.0399(8) Uani 1 1 d . . . . .
H23 H 0.641688 1.017961 0.361275 0.048 Uiso 1 1 calc R U . . .
C24 C 0.4521(4) 0.9374(3) 0.36706(15) 0.0388(7) Uani 1 1 d . . . . .
H24 H 0.409478 0.970663 0.328566 0.047 Uiso 1 1 calc R U . . .
C25 C 0.3771(3) 0.8592(3) 0.40349(14) 0.0317(6) Uani 1 1 d . . . . .
H25 H 0.283512 0.837305 0.389593 0.038 Uiso 1 1 calc R U . . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0033 0.0016
;
International Tables for Crystallography
(Vol. C, Tables 4.2.6.8 and 6.1.1.4)
;
H H 0.0000 0.0000
;
International Tables for Crystallography
(Vol. C, Table 6.1.1.4)
;
O O 0.0106 0.0060
;
International Tables for Crystallography
(Vol. C, Tables 4.2.6.8 and 6.1.1.4)
;
Se Se -0.0929 2.2259
;
International Tables for Crystallography
(Vol. C, Tables 4.2.6.8 and 6.1.1.4)
;
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C4 Se1 C1 90.85(10) . . ?
C5 O1 C2 116.31(19) . . ?
C12 O3 C3 115.77(18) . . ?
C19 O5 C4 114.89(19) . . ?
C2 C1 Se1 105.51(16) . . ?
C2 C1 H1A 110.6 . . ?
Se1 C1 H1A 110.6 . . ?
C2 C1 H1B 110.6 . . ?
Se1 C1 H1B 110.6 . . ?
H1A C1 H1B 108.8 . . ?
O1 C2 C3 107.93(19) . . ?
O1 C2 C1 106.42(19) . . ?
C3 C2 C1 109.2(2) . . ?
O1 C2 H2 111.0 . . ?
C3 C2 H2 111.0 . . ?
C1 C2 H2 111.0 . . ?
O3 C3 C2 107.36(19) . . ?
O3 C3 C4 108.23(18) . . ?
C2 C3 C4 110.2(2) . . ?
O3 C3 H3 110.3 . . ?
C2 C3 H3 110.3 . . ?
C4 C3 H3 110.3 . . ?
O5 C4 C3 106.33(19) . . ?
O5 C4 Se1 113.00(16) . . ?
C3 C4 Se1 107.52(16) . . ?
O5 C4 H4 110.0 . . ?
C3 C4 H4 110.0 . . ?
Se1 C4 H4 110.0 . . ?
O2 C5 O1 123.2(2) . . ?
O2 C5 C6 125.2(2) . . ?
O1 C5 C6 111.6(2) . . ?
C7 C6 C11 120.1(2) . . ?
C7 C6 C5 122.7(2) . . ?
C11 C6 C5 117.1(2) . . ?
C6 C7 C8 119.5(2) . . ?
C6 C7 H7 120.3 . . ?
C8 C7 H7 120.3 . . ?
C9 C8 C7 120.2(3) . . ?
C9 C8 H8 119.9 . . ?
C7 C8 H8 119.9 . . ?
C10 C9 C8 120.2(3) . . ?
C10 C9 H9 119.9 . . ?
C8 C9 H9 119.9 . . ?
C9 C10 C11 120.1(3) . . ?
C9 C10 H10 119.9 . . ?
C11 C10 H10 119.9 . . ?
C10 C11 C6 119.8(3) . . ?
C10 C11 H11 120.1 . . ?
C6 C11 H11 120.1 . . ?
O4 C12 O3 123.7(2) . . ?
O4 C12 C13 123.6(2) . . ?
O3 C12 C13 112.7(2) . . ?
C18 C13 C14 120.4(2) . . ?
C18 C13 C12 117.5(2) . . ?
C14 C13 C12 122.1(2) . . ?
C15 C14 C13 119.2(2) . . ?
C15 C14 H14 120.4 . . ?
C13 C14 H14 120.4 . . ?
C16 C15 C14 120.3(2) . . ?
C16 C15 H15 119.8 . . ?
C14 C15 H15 119.8 . . ?
C15 C16 C17 120.8(2) . . ?
C15 C16 H16 119.6 . . ?
C17 C16 H16 119.6 . . ?
C16 C17 C18 119.3(2) . . ?
C16 C17 H17 120.4 . . ?
C18 C17 H17 120.4 . . ?
C13 C18 C17 120.0(2) . . ?
C13 C18 H18 120.0 . . ?
C17 C18 H18 120.0 . . ?
O6 C19 O5 122.4(2) . . ?
O6 C19 C20 125.5(2) . . ?
O5 C19 C20 112.1(2) . . ?
C21 C20 C25 120.4(3) . . ?
C21 C20 C19 121.6(2) . . ?
C25 C20 C19 117.9(2) . . ?
C20 C21 C22 119.6(3) . . ?
C20 C21 H21 120.2 . . ?
C22 C21 H21 120.2 . . ?
C21 C22 C23 119.8(3) . . ?
C21 C22 H22 120.1 . . ?
C23 C22 H22 120.1 . . ?
C24 C23 C22 120.4(3) . . ?
C24 C23 H23 119.8 . . ?
C22 C23 H23 119.8 . . ?
C23 C24 C25 119.9(3) . . ?
C23 C24 H24 120.1 . . ?
C25 C24 H24 120.1 . . ?
C24 C25 C20 119.8(3) . . ?
C24 C25 H25 120.1 . . ?
C20 C25 H25 120.1 . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Se1 C4 1.952(2) . ?
Se1 C1 1.966(3) . ?
O1 C5 1.358(3) . ?
O1 C2 1.453(3) . ?
O2 C5 1.210(3) . ?
O3 C12 1.356(3) . ?
O3 C3 1.453(3) . ?
O4 C12 1.204(3) . ?
O5 C19 1.356(3) . ?
O5 C4 1.435(3) . ?
O6 C19 1.216(3) . ?
C1 C2 1.543(3) . ?
C1 H1A 0.9900 . ?
C1 H1B 0.9900 . ?
C2 C3 1.524(3) . ?
C2 H2 1.0000 . ?
C3 C4 1.528(4) . ?
C3 H3 1.0000 . ?
C4 H4 1.0000 . ?
C5 C6 1.492(4) . ?
C6 C7 1.392(4) . ?
C6 C11 1.396(4) . ?
C7 C8 1.395(4) . ?
C7 H7 0.9500 . ?
C8 C9 1.389(4) . ?
C8 H8 0.9500 . ?
C9 C10 1.384(4) . ?
C9 H9 0.9500 . ?
C10 C11 1.389(4) . ?
C10 H10 0.9500 . ?
C11 H11 0.9500 . ?
C12 C13 1.490(3) . ?
C13 C18 1.391(4) . ?
C13 C14 1.396(3) . ?
C14 C15 1.392(3) . ?
C14 H14 0.9500 . ?
C15 C16 1.384(4) . ?
C15 H15 0.9500 . ?
C16 C17 1.385(4) . ?
C16 H16 0.9500 . ?
C17 C18 1.398(3) . ?
C17 H17 0.9500 . ?
C18 H18 0.9500 . ?
C19 C20 1.478(4) . ?
C20 C21 1.390(4) . ?
C20 C25 1.398(4) . ?
C21 C22 1.393(4) . ?
C21 H21 0.9500 . ?
C22 C23 1.397(5) . ?
C22 H22 0.9500 . ?
C23 C24 1.386(5) . ?
C23 H23 0.9500 . ?
C24 C25 1.388(4) . ?
C24 H24 0.9500 . ?
C25 H25 0.9500 . ?
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
C5 O1 C2 C3 70.5(3) . . . . ?
C5 O1 C2 C1 -172.4(2) . . . . ?
Se1 C1 C2 O1 -78.87(19) . . . . ?
Se1 C1 C2 C3 37.4(2) . . . . ?
C12 O3 C3 C2 125.5(2) . . . . ?
C12 O3 C3 C4 -115.6(2) . . . . ?
O1 C2 C3 O3 -172.13(19) . . . . ?
C1 C2 C3 O3 72.5(2) . . . . ?
O1 C2 C3 C4 70.2(2) . . . . ?
C1 C2 C3 C4 -45.1(3) . . . . ?
C19 O5 C4 C3 -168.59(19) . . . . ?
C19 O5 C4 Se1 73.7(2) . . . . ?
O3 C3 C4 O5 151.31(18) . . . . ?
C2 C3 C4 O5 -91.6(2) . . . . ?
O3 C3 C4 Se1 -87.40(18) . . . . ?
C2 C3 C4 Se1 29.7(2) . . . . ?
C2 O1 C5 O2 5.2(3) . . . . ?
C2 O1 C5 C6 -172.8(2) . . . . ?
O2 C5 C6 C7 175.5(2) . . . . ?
O1 C5 C6 C7 -6.5(3) . . . . ?
O2 C5 C6 C11 -7.4(4) . . . . ?
O1 C5 C6 C11 170.6(2) . . . . ?
C11 C6 C7 C8 -1.0(4) . . . . ?
C5 C6 C7 C8 176.0(2) . . . . ?
C6 C7 C8 C9 -1.0(4) . . . . ?
C7 C8 C9 C10 1.8(4) . . . . ?
C8 C9 C10 C11 -0.6(4) . . . . ?
C9 C10 C11 C6 -1.3(4) . . . . ?
C7 C6 C11 C10 2.1(4) . . . . ?
C5 C6 C11 C10 -175.1(3) . . . . ?
C3 O3 C12 O4 -3.9(3) . . . . ?
C3 O3 C12 C13 175.93(19) . . . . ?
O4 C12 C13 C18 -13.8(4) . . . . ?
O3 C12 C13 C18 166.3(2) . . . . ?
O4 C12 C13 C14 164.0(3) . . . . ?
O3 C12 C13 C14 -15.8(3) . . . . ?
C18 C13 C14 C15 1.6(4) . . . . ?
C12 C13 C14 C15 -176.2(2) . . . . ?
C13 C14 C15 C16 -0.9(4) . . . . ?
C14 C15 C16 C17 -0.8(4) . . . . ?
C15 C16 C17 C18 1.7(4) . . . . ?
C14 C13 C18 C17 -0.7(4) . . . . ?
C12 C13 C18 C17 177.2(2) . . . . ?
C16 C17 C18 C13 -0.9(4) . . . . ?
C4 O5 C19 O6 -2.1(3) . . . . ?
C4 O5 C19 C20 177.17(19) . . . . ?
O6 C19 C20 C21 -163.2(3) . . . . ?
O5 C19 C20 C21 17.6(3) . . . . ?
O6 C19 C20 C25 16.6(4) . . . . ?
O5 C19 C20 C25 -162.6(2) . . . . ?
C25 C20 C21 C22 -2.2(4) . . . . ?
C19 C20 C21 C22 177.5(2) . . . . ?
C20 C21 C22 C23 1.3(4) . . . . ?
C21 C22 C23 C24 0.9(5) . . . . ?
C22 C23 C24 C25 -2.3(4) . . . . ?
C23 C24 C25 C20 1.3(4) . . . . ?
C21 C20 C25 C24 1.0(4) . . . . ?
C19 C20 C25 C24 -178.9(2) . . . . ?
