#------------------------------------------------------------------------------ #$Date: 2017-10-13 02:48:21 +0200 (Fri, 13 Oct 2017) $ #$Revision: 201957 $ #$URL: svn://www.crystallography.net/cod/cif/2/01/26/2012676.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided by IUCr Journals, http://journals.iucr.org/. # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_2012676 loop_ _publ_author_name 'Pop, Mihaela' 'Borodi, Gheorghe' 'Goubitz, Kees' 'Peschar, Ren\'e' 'Fraanje, Jan' 'Fenesan, Ioan' 'Schenk, Henk' _publ_section_title 5,5-Dimethyl-2-[6-methyl-2-(methylsulfanyl)pyrimidin-4-yloxy]-1,3,2-dioxaphosphorinane-2-thione _journal_issue 5 _journal_name_full 'Acta Crystallographica Section C' _journal_page_first o280 _journal_page_last o281 _journal_paper_doi 10.1107/S0108270102005218 _journal_volume 58 _journal_year 2002 _chemical_formula_moiety 'C11 H17 N2 O3 P S2' _chemical_formula_sum 'C11 H17 N2 O3 P S2' _chemical_formula_weight 320.36 _chemical_name_systematic ; 5,5-Dimethyl-2-[6-methyl-2-(methylsulfanyl)pyrimidin-4-yloxy]- 1,3,2-dioxaphosphorinane-2-thione ; _space_group_IT_number 14 _symmetry_cell_setting monoclinic _symmetry_space_group_name_Hall '-P 2ybc' _symmetry_space_group_name_H-M 'P 1 21/c 1' _atom_sites_solution_hydrogens geom _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _audit_creation_method SHELXL97 _cell_angle_alpha 90 _cell_angle_beta 90.23(2) _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 9.900(2) _cell_length_b 9.330(2) _cell_length_c 17.010(3) _cell_measurement_reflns_used 23 _cell_measurement_temperature 293(2) _cell_measurement_theta_max 43.50 _cell_measurement_theta_min 40.01 _cell_volume 1571.2(5) _computing_cell_refinement 'local program' _computing_data_collection 'CAD-4-PC Software (Enraf-Nonius, 1992)' _computing_data_reduction 'Please provide missing details' _computing_molecular_graphics 'Please provide missing details' _computing_structure_refinement 'SHELXL97 (Sheldrick, 1997)' _computing_structure_solution 'SIR97 (Altomare et al., 1997)' _diffrn_ambient_temperature 293 _diffrn_measured_fraction_theta_full 0.889 _diffrn_measured_fraction_theta_max 0.889 _diffrn_measurement_device_type 'Enraf-Nonius CAD-4' _diffrn_measurement_method \w/2\q _diffrn_radiation_monochromator graphite _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.5418 _diffrn_reflns_av_R_equivalents 0.089 _diffrn_reflns_av_sigmaI/netI 0.055 _diffrn_reflns_limit_h_max 11 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_k_max 12 _diffrn_reflns_limit_k_min -3 _diffrn_reflns_limit_l_max 10 _diffrn_reflns_limit_l_min -21 _diffrn_reflns_number 3703 _diffrn_reflns_theta_full 87.88 _diffrn_reflns_theta_max 74.04 _diffrn_reflns_theta_min 4.47 _diffrn_standards_decay_% 6 _diffrn_standards_interval_time 60 _diffrn_standards_number 2 _exptl_absorpt_coefficient_mu 4.093 _exptl_absorpt_correction_type none _exptl_crystal_colour colourless _exptl_crystal_density_diffrn 1.354 _exptl_crystal_density_meas ? _exptl_crystal_density_method 'not measured' _exptl_crystal_description prism _exptl_crystal_F_000 672 _exptl_crystal_size_max 0.30 _exptl_crystal_size_mid 0.30 _exptl_crystal_size_min 0.25 _refine_diff_density_max 0.97 _refine_diff_density_min -0.48 _refine_ls_extinction_coef 0.0099(9) _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ _refine_ls_extinction_method 'SHELXL97 (Sheldrick, 1997)' _refine_ls_goodness_of_fit_ref 1.067 _refine_ls_hydrogen_treatment constr _refine_ls_matrix_type full _refine_ls_number_parameters 177 _refine_ls_number_reflns 3185 _refine_ls_number_restraints 0 _refine_ls_restrained_S_all 1.067 _refine_ls_R_factor_all 0.069 _refine_ls_R_factor_gt 0.059 _refine_ls_shift/su_max 0.005 _refine_ls_shift/su_mean 0.000 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'calc w = 1/[\s^2^(Fo^2^)+(0.0947P)^2^+0.4685P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.145 _refine_ls_wR_factor_ref 0.154 _reflns_number_gt 2626 _reflns_number_total 3185 _reflns_threshold_expression I>2\s(I) _cod_data_source_file av1105.cif _cod_data_source_block I _cod_depositor_comments ; The following automatic conversions were performed: '_exptl_crystal_density_meas' value 'not measured' was changed to '?' - the value is perceived as not measured. Automatic conversion script Id: cif_fix_values 3008 2015-01-20 13:52:24Z robertas ; _cod_original_sg_symbol_Hall -P_2ybc _cod_original_sg_symbol_H-M 'P 21/c' _cod_database_code 2012676 _cod_database_fobs_code 2012676 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y+1/2, -z+1/2' '-x, -y, -z' 'x, -y-1/2, z-1/2' loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_type_symbol S1 0.50695(10) 0.27240(12) 0.02876(5) 0.0789(3) Uani d . 1 . . S S2 1.15227(8) 0.29194(7) -0.12452(5) 0.0601(3) Uani d . 1 . . S P1 0.63259(6) 0.20343(6) 0.10651(3) 0.0426(2) Uani d . 1 . . P O1 0.59314(19) 0.05838(18) 0.13681(10) 0.0499(5) Uani d . 1 . . O O2 0.6484(2) 0.29258(17) 0.18254(10) 0.0525(5) Uani d . 1 . . O O3 0.79901(19) 0.1961(2) 0.08193(10) 0.0506(5) Uani d . 1 . . O N1 0.9551(2) 0.2350(2) -0.01586(11) 0.0413(4) Uani d . 1 . . N N2 0.9768(2) 0.0878(2) -0.12732(11) 0.0443(5) Uani d . 1 . . N C1 0.6699(3) 0.0057(3) 0.20605(15) 0.0514(6) Uani d . 1 . . C H11 0.6356 -0.0879 0.2206 0.062 Uiso calc R 1 . . H H12 0.7639 -0.0057 0.1915 0.062 Uiso calc R 1 . . H C2 0.6620(3) 0.1019(3) 0.27525(13) 0.0439(5) Uani d . 1 . . C C3 0.7234(3) 0.2374(3) 0.25065(15) 0.0519(6) Uani d . 1 . . C H31 0.8172 0.2221 0.2368 0.062 Uiso calc R 1 . . H H32 0.7201 0.3062 0.2934 0.062 Uiso calc R 1 . . H C4 0.8506(2) 0.1555(3) 0.00940(13) 0.0405(5) Uani d . 1 . . C C5 0.8019(3) 0.0422(3) -0.02909(15) 0.0467(6) Uani d . 1 . . C H5 0.7287 -0.0111 -0.0112 0.056 Uiso calc R 1 . . H C6 0.8707(2) 0.0101(3) -0.09910(14) 0.0446(5) Uani d . 1 . . C C7 1.0128(2) 0.1962(2) -0.08401(13) 0.0411(5) Uani d . 1 . . C C8 0.5069(3) 0.1200(3) 0.30306(17) 0.0566(7) Uani d . 1 . . C H81 0.5027 0.1871 0.3458 0.085 Uiso calc R 1 . . H H82 0.4724 0.0290 0.3200 0.085 Uiso calc R 1 . . H H83 0.4534 0.1549 0.2599 0.085 Uiso calc R 1 . . H C9 0.7536(4) 0.0437(4) 0.3418(2) 0.0765(10) Uani d . 1 . . C H91 0.8444 0.0344 0.3229 0.115 Uiso calc R 1 . . H H92 0.7210 -0.0483 0.3585 0.115 Uiso calc R 1 . . H H93 0.7522 0.1090 0.3854 0.115 Uiso calc R 1 . . H C10 0.8316(3) -0.1128(4) -0.1458(2) 0.0676(8) Uani d . 1 . . C H101 0.8286 -0.0862 -0.2004 0.101 Uiso calc R 1 . . H H102 0.7439 -0.1452 -0.1297 0.101 Uiso calc R 1 . . H H103 0.8962 -0.1883 -0.1385 0.101 Uiso calc R 1 . . H C11 1.1717(4) 0.4290(3) -0.0566(2) 0.0749(10) Uani d . 1 . . C H111 1.0992 0.4966 -0.0626 0.112 Uiso calc R 1 . . H H112 1.2563 0.4766 -0.0653 0.112 Uiso calc R 1 . . H H113 1.1703 0.3899 -0.0044 0.112 Uiso calc R 1 . . H loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 S1 0.0765(6) 0.1059(7) 0.0545(4) 0.0255(5) 0.0013(4) 0.0224(4) S2 0.0704(5) 0.0480(4) 0.0623(4) -0.0066(3) 0.0303(4) -0.0028(3) P1 0.0525(4) 0.0401(3) 0.0352(3) -0.0003(2) 0.0082(2) 0.0018(2) O1 0.0707(12) 0.0371(8) 0.0420(9) -0.0136(8) 0.0056(8) -0.0069(7) O2 0.0845(13) 0.0286(8) 0.0445(9) -0.0027(8) 0.0128(9) -0.0006(6) O3 0.0556(10) 0.0607(11) 0.0356(8) -0.0061(8) 0.0103(7) -0.0027(7) N1 0.0487(11) 0.0373(9) 0.0380(10) 0.0036(8) 0.0064(8) 0.0028(7) N2 0.0496(11) 0.0435(10) 0.0399(10) 0.0053(8) 0.0018(8) 0.0001(8) C1 0.0703(17) 0.0319(11) 0.0519(14) 0.0010(11) 0.0079(12) 0.0001(10) C2 0.0549(14) 0.0396(11) 0.0371(11) -0.0041(10) 0.0012(10) 0.0025(9) C3 0.0669(16) 0.0429(13) 0.0459(13) -0.0167(12) 0.0012(12) -0.0056(10) C4 0.0442(12) 0.0432(11) 0.0340(10) 0.0054(9) 0.0017(9) 0.0048(9) C5 0.0492(13) 0.0478(13) 0.0432(12) -0.0039(10) 0.0034(10) 0.0045(10) C6 0.0478(13) 0.0449(12) 0.0410(11) 0.0027(10) -0.0049(10) -0.0004(10) C7 0.0480(12) 0.0363(11) 0.0391(11) 0.0070(9) 0.0034(9) 0.0051(9) C8 0.0670(17) 0.0551(15) 0.0479(14) -0.0059(13) 0.0168(12) 0.0008(11) C9 0.094(2) 0.077(2) 0.0583(17) 0.0038(19) -0.0166(17) 0.0156(16) C10 0.0710(19) 0.0692(19) 0.0625(17) -0.0128(15) -0.0033(15) -0.0192(15) C11 0.083(2) 0.0472(15) 0.095(2) -0.0125(15) 0.0310(19) -0.0128(16) 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' P P 0.2955 0.4335 '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 C11 S2 C7 101.30(13) O1 P1 O2 102.92(9) O1 P1 O3 107.56(11) O2 P1 O3 97.58(11) O1 P1 S1 111.69(9) O2 P1 S1 117.31(9) O3 P1 S1 117.93(7) C1 O1 P1 116.01(15) C3 O2 P1 121.45(16) C4 O3 P1 126.04(16) C7 N1 C4 117.2(2) C7 N2 C6 115.0(2) C2 C1 O1 113.7(2) C2 C1 H11 108.8 O1 C1 H11 108.8 C2 C1 H12 108.8 O1 C1 H12 108.8 H11 C1 H12 107.7 C3 C2 C1 105.8(2) C3 C2 C9 105.6(2) C1 C2 C9 109.7(2) C3 C2 C8 112.9(2) C1 C2 C8 110.4(2) C9 C2 C8 112.2(2) C2 C3 O2 108.6(2) C2 C3 H31 110.0 O2 C3 H31 110.0 C2 C3 H32 110.0 O2 C3 H32 110.0 H31 C3 H32 108.3 C5 C4 N1 123.9(2) C5 C4 O3 121.2(2) N1 C4 O3 114.8(2) C4 C5 C6 114.1(2) C4 C5 H5 122.9 C6 C5 H5 122.9 N2 C6 C5 124.1(2) N2 C6 C10 115.6(2) C5 C6 C10 120.2(2) N2 C7 N1 125.6(2) N2 C7 S2 112.39(17) N1 C7 S2 122.02(18) C2 C8 H81 109.5 C2 C8 H82 109.5 H81 C8 H82 109.5 C2 C8 H83 109.5 H81 C8 H83 109.5 H82 C8 H83 109.5 C2 C9 H91 109.5 C2 C9 H92 109.5 H91 C9 H92 109.5 C2 C9 H93 109.5 H91 C9 H93 109.5 H92 C9 H93 109.5 C6 C10 H101 109.5 C6 C10 H102 109.5 H101 C10 H102 109.5 C6 C10 H103 109.5 H101 C10 H103 109.5 H102 C10 H103 109.5 S2 C11 H111 109.5 S2 C11 H112 109.5 H111 C11 H112 109.5 S2 C11 H113 109.5 H111 C11 H113 109.5 H112 C11 H113 109.5 loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag S1 P1 . 1.9227(10) ? S2 C11 . 1.734(3) ? S2 C7 . 1.785(3) ? P1 O1 . 1.5004(18) ? P1 O2 . 1.5452(18) ? P1 O3 . 1.7028(19) ? O1 C1 . 1.483(3) ? O2 C3 . 1.467(3) ? O3 C4 . 1.390(3) ? N1 C7 . 1.344(3) ? N1 C4 . 1.344(3) ? N2 C7 . 1.300(3) ? N2 C6 . 1.365(3) ? C1 C2 . 1.482(3) ? C1 H11 . 0.9700 ? C1 H12 . 0.9700 ? C2 C3 . 1.465(3) ? C2 C9 . 1.546(4) ? C2 C8 . 1.617(4) ? C3 H31 . 0.9700 ? C3 H32 . 0.9700 ? C4 C5 . 1.333(4) ? C5 C6 . 1.407(3) ? C5 H5 . 0.9300 ? C6 C10 . 1.447(4) ? C8 H81 . 0.9600 ? C8 H82 . 0.9600 ? C8 H83 . 0.9600 ? C9 H91 . 0.9600 ? C9 H92 . 0.9600 ? C9 H93 . 0.9600 ? C10 H101 . 0.9600 ? C10 H102 . 0.9600 ? C10 H103 . 0.9600 ? C11 H111 . 0.9600 ? C11 H112 . 0.9600 ? C11 H113 . 0.9600 ? 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_publ_flag P1 O1 C1 C2 58.1(3) yes O1 C1 C2 C3 -62.2(3) yes C1 C2 C3 O2 58.7(3) yes C2 C3 O2 P1 -57.6(3) yes C3 O2 P1 O1 46.5(2) yes O2 P1 O1 C1 -43.60(19) yes loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 ChemSpider 4402205