#------------------------------------------------------------------------------
#$Date: 2025-08-22 10:56:18 +0200 (Fri 22 de Aug de 2025) $
#$Revision: 301860 $
#$URL: svn://www.crystallography.net/cod/cif/7/12/20/7122067.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_7122067
loop_
_publ_author_name
'Sohtome, Yoshihiro'
'Shimazu, Tadahiro'
'Barjau, Joaquin'
'Fujishiro, Shinya'
'Akakabe, Mai'
'Terayama, Naoki'
'Dodo, Kosuke'
'Ito, Akihiro'
'Yoshida, Minoru'
'Shinkai, Yoichi'
'Sodeoka, Mikiko'
_publ_section_title
;
 Unveiling epidithiodiketopiperazine as a non-histone arginine
 methyltransferase inhibitor by chemical protein methylome analyses.
;
_journal_issue                   66
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              9202
_journal_page_last               9205
_journal_paper_doi               10.1039/c8cc03907k
_journal_volume                  54
_journal_year                    2018
_chemical_absolute_configuration adrm
_chemical_formula_moiety         'C15 H26 N2 O3 S2 Si'
_chemical_formula_sum            'C15 H26 N2 O3 S2 Si'
_chemical_formula_weight         374.59
_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_space_group_name_Hall  'P 2ac 2ab'
_symmetry_space_group_name_H-M   'P 21 21 21'
_atom_sites_solution_hydrogens   difmap
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_block_doi                 10.5517/ccdc.csd.cc1z87s8
_audit_creation_method           SHELXL-2018/1
_audit_update_record
;
2018-02-22 deposited with the CCDC.
2018-07-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.68141(14)
_cell_length_b                   10.8441(2)
_cell_length_c                   23.4756(4)
_cell_measurement_reflns_used    19684
_cell_measurement_temperature    170
_cell_measurement_theta_max      68.240
_cell_measurement_theta_min      3.765
_cell_volume                     1955.47(6)
_computing_cell_refinement       PROCESS-AUTO
_computing_data_collection       PROCESS-AUTO
_computing_data_reduction        PROCESS-AUTO
_computing_molecular_graphics    SHELXLE
_computing_publication_material  'SHELXL-97 (Sheldrick, 2008)'
_computing_structure_refinement  'SHELXL-2018/1 (Sheldrick, 2018)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 2008)'
_diffrn_ambient_temperature      170
_diffrn_detector_area_resol_mean 10
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.995
_diffrn_measurement_device_type  'Rigaku RAXIS-RAPID'
_diffrn_measurement_method       ω-scan
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_source         'fine-focus sealed tube'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54187
_diffrn_reflns_av_R_equivalents  0.0421
_diffrn_reflns_av_unetI/netI     0.0291
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       28
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            21681
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.994
_diffrn_reflns_theta_full        67.687
_diffrn_reflns_theta_max         68.241
_diffrn_reflns_theta_min         3.766
_exptl_absorpt_coefficient_mu    3.177
_exptl_absorpt_correction_T_max  0.6879
_exptl_absorpt_correction_T_min  0.2858
_exptl_absorpt_correction_type   numerical
_exptl_absorpt_process_details
;
 numabs
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.272
_exptl_crystal_description       pillar
_exptl_crystal_F_000             800
_exptl_crystal_size_max          0.83
_exptl_crystal_size_mid          0.16
_exptl_crystal_size_min          0.14
_refine_diff_density_max         0.216
_refine_diff_density_min         -0.189
_refine_diff_density_rms         0.037
_refine_ls_abs_structure_details
;
 Flack x determined using 1389 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.012(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.080
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     215
_refine_ls_number_reflns         3550
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.080
_refine_ls_R_factor_all          0.0278
_refine_ls_R_factor_gt           0.0267
_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/[σ²(Fo²)+(0.0336P)²+0.3114P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0656
_refine_ls_wR_factor_ref         0.0661
_reflns_Friedel_coverage         0.724
_reflns_Friedel_fraction_full    0.993
_reflns_Friedel_fraction_max     0.991
_reflns_number_gt                3454
_reflns_number_total             3550
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            c8cc03907k2.cif
_cod_data_source_block           FP488-1
_cod_depositor_comments          'Adding full bibliography for 7122067.cif.'
_cod_original_cell_volume        1955.48(6)
_cod_database_code               7122067
_shelx_shelxl_version_number     2018/1
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
_shelx_estimated_absorpt_t_min   0.178
_shelx_estimated_absorpt_t_max   0.665
loop_
_space_group_symop_operation_xyz
'x, y, z'
'x+1/2, -y+1/2, -z'
'-x, y+1/2, -z+1/2'
'-x+1/2, -y, z+1/2'
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
S1 S 0.55559(8) 0.62131(5) 0.55550(2) 0.03037(15) Uani 1 1 d . .
S2 S 0.58762(8) 0.74325(5) 0.48813(2) 0.02832(14) Uani 1 1 d . .
Si1 Si 0.24127(9) 0.75919(7) 0.26437(3) 0.03285(17) Uani 1 1 d . .
O1 O 0.3610(2) 0.37555(16) 0.48195(8) 0.0361(4) Uani 1 1 d . .
O2 O 0.9243(2) 0.59519(15) 0.41666(7) 0.0301(4) Uani 1 1 d . .
O3 O 0.3728(3) 0.66839(19) 0.30041(7) 0.0449(5) Uani 1 1 d . .
N1 N 0.4811(2) 0.53356(18) 0.43205(7) 0.0251(4) Uani 1 1 d . .
N2 N 0.7879(2) 0.48960(17) 0.48855(8) 0.0240(4) Uani 1 1 d . .
C1 C 0.4741(3) 0.4535(2) 0.47568(9) 0.0260(5) Uani 1 1 d . .
C2 C 0.6233(3) 0.4746(2) 0.51804(10) 0.0256(5) Uani 1 1 d . .
C3 C 0.7938(3) 0.5690(2) 0.44342(9) 0.0236(5) Uani 1 1 d . .
C4 C 0.6169(3) 0.6251(2) 0.43074(9) 0.0243(5) Uani 1 1 d . .
C5 C 0.5967(3) 0.6863(2) 0.37303(10) 0.0317(6) Uani 1 1 d . .
H5A H 0.667730 0.643798 0.343809 0.038 Uiso 1 1 calc R U
H5B H 0.631401 0.774119 0.374650 0.038 Uiso 1 1 calc R U
C6 C 0.4014(3) 0.6732(2) 0.36020(10) 0.0334(6) Uani 1 1 d . .
H6 H 0.335602 0.743683 0.377233 0.040 Uiso 1 1 calc R U
C7 C 0.3470(3) 0.5522(3) 0.38851(10) 0.0339(6) Uani 1 1 d . .
H7A H 0.230076 0.559330 0.405941 0.041 Uiso 1 1 calc R U
H7B H 0.346302 0.483522 0.360705 0.041 Uiso 1 1 calc R U
C8 C 0.6262(3) 0.3749(2) 0.56322(11) 0.0350(6) Uani 1 1 d . .
H8A H 0.656571 0.295789 0.545625 0.052 Uiso 1 1 calc R U
H8B H 0.511055 0.368624 0.580953 0.052 Uiso 1 1 calc R U
H8C H 0.712907 0.395678 0.592297 0.052 Uiso 1 1 calc R U
C9 C 0.9503(3) 0.4422(2) 0.51289(12) 0.0349(6) Uani 1 1 d . .
H9A H 0.971668 0.481736 0.549763 0.052 Uiso 1 1 calc R U
H9B H 1.047014 0.460229 0.486989 0.052 Uiso 1 1 calc R U
H9C H 0.940757 0.352772 0.518204 0.052 Uiso 1 1 calc R U
C10 C 0.0116(4) 0.7266(4) 0.28227(14) 0.0706(12) Uani 1 1 d . .
H10A H -0.007470 0.741216 0.322990 0.106 Uiso 1 1 calc R U
H10B H -0.015163 0.640427 0.273259 0.106 Uiso 1 1 calc R U
H10C H -0.064496 0.780921 0.260041 0.106 Uiso 1 1 calc R U
C11 C 0.2897(6) 0.9223(3) 0.28306(15) 0.0669(10) Uani 1 1 d . .
H11A H 0.214591 0.977153 0.260776 0.100 Uiso 1 1 calc R U
H11B H 0.411960 0.940373 0.274481 0.100 Uiso 1 1 calc R U
H11C H 0.268178 0.935355 0.323759 0.100 Uiso 1 1 calc R U
C12 C 0.2948(4) 0.7241(3) 0.18779(10) 0.0400(7) Uani 1 1 d . .
C13 C 0.1913(5) 0.8125(3) 0.14915(13) 0.0626(10) Uani 1 1 d . .
H13A H 0.211500 0.790936 0.109160 0.094 Uiso 1 1 calc R U
H13B H 0.229597 0.897424 0.155983 0.094 Uiso 1 1 calc R U
H13C H 0.066809 0.805405 0.157750 0.094 Uiso 1 1 calc R U
C14 C 0.4913(5) 0.7421(4) 0.17831(14) 0.0642(9) Uani 1 1 d . .
H14A H 0.518619 0.730372 0.137898 0.096 Uiso 1 1 calc R U
H14B H 0.555988 0.681874 0.201110 0.096 Uiso 1 1 calc R U
H14C H 0.524549 0.825724 0.189892 0.096 Uiso 1 1 calc R U
C15 C 0.2466(5) 0.5909(3) 0.17362(12) 0.0524(8) Uani 1 1 d . .
H15A H 0.279167 0.572846 0.134137 0.079 Uiso 1 1 calc R U
H15B H 0.120829 0.579590 0.178332 0.079 Uiso 1 1 calc R U
H15C H 0.308783 0.534960 0.199306 0.079 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 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Si Si 0.2541 0.3302 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
S S 0.3331 0.5567 'International Tables 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
C2 S1 S2 98.58(7)
C4 S2 S1 97.26(7)
O3 Si1 C10 110.79(16)
O3 Si1 C11 108.97(15)
C10 Si1 C11 108.6(2)
O3 Si1 C12 103.64(11)
C10 Si1 C12 112.76(14)
C11 Si1 C12 111.95(15)
C6 O3 Si1 125.52(16)
C1 N1 C4 119.37(19)
C1 N1 C7 126.3(2)
C4 N1 C7 113.54(19)
C3 N2 C2 118.02(18)
C3 N2 C9 119.7(2)
C2 N2 C9 121.10(18)
O1 C1 N1 124.6(2)
O1 C1 C2 123.8(2)
N1 C1 C2 111.6(2)
N2 C2 C8 113.65(19)
N2 C2 C1 110.99(18)
C8 C2 C1 111.0(2)
N2 C2 S1 111.56(16)
C8 C2 S1 106.22(16)
C1 C2 S1 102.82(15)
O2 C3 N2 125.1(2)
O2 C3 C4 122.9(2)
N2 C3 C4 112.01(19)
N1 C4 C5 104.28(18)
N1 C4 C3 111.60(18)
C5 C4 C3 116.22(19)
N1 C4 S2 111.67(15)
C5 C4 S2 109.33(16)
C3 C4 S2 103.92(15)
C4 C5 C6 103.55(19)
C4 C5 H5A 111.1
C6 C5 H5A 111.1
C4 C5 H5B 111.1
C6 C5 H5B 111.1
H5A C5 H5B 109.0
O3 C6 C7 110.8(2)
O3 C6 C5 110.4(2)
C7 C6 C5 105.1(2)
O3 C6 H6 110.1
C7 C6 H6 110.1
C5 C6 H6 110.1
N1 C7 C6 103.2(2)
N1 C7 H7A 111.1
C6 C7 H7A 111.1
N1 C7 H7B 111.1
C6 C7 H7B 111.1
H7A C7 H7B 109.1
C2 C8 H8A 109.5
C2 C8 H8B 109.5
H8A C8 H8B 109.5
C2 C8 H8C 109.5
H8A C8 H8C 109.5
H8B C8 H8C 109.5
N2 C9 H9A 109.5
N2 C9 H9B 109.5
H9A C9 H9B 109.5
N2 C9 H9C 109.5
H9A C9 H9C 109.5
H9B C9 H9C 109.5
Si1 C10 H10A 109.5
Si1 C10 H10B 109.5
H10A C10 H10B 109.5
Si1 C10 H10C 109.5
H10A C10 H10C 109.5
H10B C10 H10C 109.5
Si1 C11 H11A 109.5
Si1 C11 H11B 109.5
H11A C11 H11B 109.5
Si1 C11 H11C 109.5
H11A C11 H11C 109.5
H11B C11 H11C 109.5
C15 C12 C14 109.1(3)
C15 C12 C13 109.6(2)
C14 C12 C13 110.0(3)
C15 C12 Si1 110.25(19)
C14 C12 Si1 109.1(2)
C13 C12 Si1 108.9(2)
C12 C13 H13A 109.5
C12 C13 H13B 109.5
H13A C13 H13B 109.5
C12 C13 H13C 109.5
H13A C13 H13C 109.5
H13B C13 H13C 109.5
C12 C14 H14A 109.5
C12 C14 H14B 109.5
H14A C14 H14B 109.5
C12 C14 H14C 109.5
H14A C14 H14C 109.5
H14B C14 H14C 109.5
C12 C15 H15A 109.5
C12 C15 H15B 109.5
H15A C15 H15B 109.5
C12 C15 H15C 109.5
H15A C15 H15C 109.5
H15B C15 H15C 109.5
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
S1 C2 1.890(2)
S1 S2 2.0762(8)
S2 C4 1.873(2)
Si1 O3 1.6448(19)
Si1 C10 1.848(3)
Si1 C11 1.860(3)
Si1 C12 1.883(3)
O1 C1 1.221(3)
O2 C3 1.217(3)
O3 C6 1.422(3)
N1 C1 1.344(3)
N1 C4 1.440(3)
N1 C7 1.465(3)
N2 C3 1.366(3)
N2 C2 1.450(3)
N2 C9 1.466(3)
C1 C2 1.534(3)
C2 C8 1.515(3)
C3 C4 1.518(3)
C4 C5 1.517(3)
C5 C6 1.537(4)
C5 H5A 0.9900
C5 H5B 0.9900
C6 C7 1.529(4)
C6 H6 1.0000
C7 H7A 0.9900
C7 H7B 0.9900
C8 H8A 0.9800
C8 H8B 0.9800
C8 H8C 0.9800
C9 H9A 0.9800
C9 H9B 0.9800
C9 H9C 0.9800
C10 H10A 0.9800
C10 H10B 0.9800
C10 H10C 0.9800
C11 H11A 0.9800
C11 H11B 0.9800
C11 H11C 0.9800
C12 C15 1.527(4)
C12 C14 1.538(4)
C12 C13 1.541(4)
C13 H13A 0.9800
C13 H13B 0.9800
C13 H13C 0.9800
C14 H14A 0.9800
C14 H14B 0.9800
C14 H14C 0.9800
C15 H15A 0.9800
C15 H15B 0.9800
C15 H15C 0.9800
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
C10 Si1 O3 C6 -68.7(3)
C11 Si1 O3 C6 50.7(3)
C12 Si1 O3 C6 170.1(2)
C4 N1 C1 O1 177.1(2)
C7 N1 C1 O1 7.7(4)
C4 N1 C1 C2 -1.0(3)
C7 N1 C1 C2 -170.5(2)
C3 N2 C2 C8 173.9(2)
C9 N2 C2 C8 -18.6(3)
C3 N2 C2 C1 48.0(3)
C9 N2 C2 C1 -144.5(2)
C3 N2 C2 S1 -66.1(2)
C9 N2 C2 S1 101.5(2)
O1 C1 C2 N2 135.8(2)
N1 C1 C2 N2 -46.1(3)
O1 C1 C2 C8 8.4(3)
N1 C1 C2 C8 -173.4(2)
O1 C1 C2 S1 -104.8(2)
N1 C1 C2 S1 73.3(2)
S2 S1 C2 N2 49.85(16)
S2 S1 C2 C8 174.19(15)
S2 S1 C2 C1 -69.15(14)
C2 N2 C3 O2 176.1(2)
C9 N2 C3 O2 8.4(3)
C2 N2 C3 C4 -2.4(3)
C9 N2 C3 C4 -170.1(2)
C1 N1 C4 C5 173.2(2)
C7 N1 C4 C5 -16.0(2)
C1 N1 C4 C3 47.0(3)
C7 N1 C4 C3 -142.3(2)
C1 N1 C4 S2 -68.9(2)
C7 N1 C4 S2 101.90(19)
O2 C3 C4 N1 136.8(2)
N2 C3 C4 N1 -44.7(2)
O2 C3 C4 C5 17.4(3)
N2 C3 C4 C5 -164.1(2)
O2 C3 C4 S2 -102.7(2)
N2 C3 C4 S2 75.8(2)
S1 S2 C4 N1 50.39(16)
S1 S2 C4 C5 165.27(15)
S1 S2 C4 C3 -70.04(14)
N1 C4 C5 C6 29.0(2)
C3 C4 C5 C6 152.2(2)
S2 C4 C5 C6 -90.6(2)
Si1 O3 C6 C7 118.5(2)
Si1 O3 C6 C5 -125.5(2)
C4 C5 C6 O3 -151.4(2)
C4 C5 C6 C7 -31.9(2)
C1 N1 C7 C6 166.0(2)
C4 N1 C7 C6 -4.0(2)
O3 C6 C7 N1 141.4(2)
C5 C6 C7 N1 22.2(2)
O3 Si1 C12 C15 64.9(2)
C10 Si1 C12 C15 -54.9(3)
C11 Si1 C12 C15 -177.8(2)
O3 Si1 C12 C14 -54.8(3)
C10 Si1 C12 C14 -174.7(3)
C11 Si1 C12 C14 62.4(3)
O3 Si1 C12 C13 -174.9(2)
C10 Si1 C12 C13 65.3(3)
C11 Si1 C12 C13 -57.6(3)
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 PubChem 139188957
