#------------------------------------------------------------------------------ #$Date: 2016-02-20 00:18:51 +0200 (Sat, 20 Feb 2016) $ #$Revision: 176760 $ #$URL: file:///home/coder/svn-repositories/cod/cif/2/01/38/2013873.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_2013873 loop_ _publ_author_name 'Low, John N.' 'Cobo, Justo' 'Cruz, Silvia' 'Quiroga, Jairo' 'Glidewell, Christopher' _publ_section_title ;4-Amino-5-(2-hydroxy-4,4-dimethyl-6-oxocyclohexenylmethyl)-1-methyl-2-(methylsulfanyl)pyrimidin-6(1H)-one: hydrogen-bonded chains are \p-stacked in pairs ; _journal_issue 3 _journal_name_full 'Acta Crystallographica Section C' _journal_page_first o191 _journal_page_last o193 _journal_paper_doi 10.1107/S0108270104001118 _journal_volume 60 _journal_year 2004 _chemical_formula_iupac 'C15 H21 N3 O3 S' _chemical_formula_moiety 'C15 H21 N3 O3 S' _chemical_formula_sum 'C15 H21 N3 O3 S' _chemical_formula_weight 323.41 _chemical_name_systematic ; 4-Amino-1-methyl-5-(2-hydroxy-4,4-dimethyl-2-oxocyclohexenylmethyl)- 2-(methylsulfanyl)pyrimidin-6(1H)-one ; _space_group_IT_number 14 _symmetry_cell_setting monoclinic _symmetry_space_group_name_Hall '-P 2yn' _symmetry_space_group_name_H-M 'P 1 21/n 1' _atom_sites_solution_hydrogens geom _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _cell_angle_alpha 90.00 _cell_angle_beta 93.128(2) _cell_angle_gamma 90.00 _cell_formula_units_Z 4 _cell_length_a 7.5524(2) _cell_length_b 7.1370(3) _cell_length_c 28.6208(11) _cell_measurement_reflns_used 3586 _cell_measurement_temperature 120(2) _cell_measurement_theta_max 28.18 _cell_measurement_theta_min 3.35 _cell_volume 1540.41(10) _computing_cell_refinement 'DENZO--SMN (Otwinowski & Minor, 1997)' _computing_data_collection 'KappaCCD Server Software (Nonius, 1997)' _computing_data_reduction DENZO--SMN _computing_molecular_graphics ' PLATON (Spek, 2003)' _computing_publication_material 'SHELXL97 and PRPKAPPA (Ferguson, 1999)' _computing_structure_refinement 'SHELXL97 (Sheldrick, 1997)' _computing_structure_solution 'OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997)' _diffrn_ambient_temperature 120(2) _diffrn_measured_fraction_theta_full 0.996 _diffrn_measured_fraction_theta_max 0.949 _diffrn_measurement_device_type 'Nonius KappaCCD' _diffrn_measurement_method '\f scans, and \w scans with \k offsets' _diffrn_radiation_monochromator graphite _diffrn_radiation_source 'rotating anode' _diffrn_radiation_type 'Mo K\a' _diffrn_radiation_wavelength 0.71073 _diffrn_reflns_av_R_equivalents 0.0708 _diffrn_reflns_av_sigmaI/netI 0.0538 _diffrn_reflns_limit_h_max 9 _diffrn_reflns_limit_h_min -9 _diffrn_reflns_limit_k_max 9 _diffrn_reflns_limit_k_min -8 _diffrn_reflns_limit_l_max 37 _diffrn_reflns_limit_l_min -37 _diffrn_reflns_number 18675 _diffrn_reflns_theta_full 26.50 _diffrn_reflns_theta_max 28.18 _diffrn_reflns_theta_min 3.35 _diffrn_standards_decay_% negligible _exptl_absorpt_coefficient_mu 0.226 _exptl_absorpt_correction_T_max 0.956 _exptl_absorpt_correction_T_min 0.868 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details '(SORTAV; Blessing 1995, 1997)' _exptl_crystal_colour colourless _exptl_crystal_density_diffrn 1.394 _exptl_crystal_density_method 'not measured' _exptl_crystal_description block _exptl_crystal_F_000 664 _exptl_crystal_size_max 0.50 _exptl_crystal_size_mid 0.30 _exptl_crystal_size_min 0.20 _refine_diff_density_max 0.278 _refine_diff_density_min -0.293 _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.011 _refine_ls_hydrogen_treatment constr _refine_ls_matrix_type full _refine_ls_number_parameters 204 _refine_ls_number_reflns 3586 _refine_ls_number_restraints 0 _refine_ls_restrained_S_all 1.011 _refine_ls_R_factor_all 0.0702 _refine_ls_R_factor_gt 0.0422 _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/[\s^2^(Fo^2^)+(0.0505P)^2^+0.5167P] where P = (Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0988 _refine_ls_wR_factor_ref 0.1091 _reflns_number_gt 2600 _reflns_number_total 3586 _reflns_threshold_expression I>2\s(I) _cod_data_source_file sk1697.cif _cod_data_source_block I _cod_depositor_comments ; The following automatic conversions were performed: '_exptl_absorpt_correction_type' value 'Multi-scan' changed to 'multi-scan' according to /home/saulius/struct/CIF-dictionaries/cif_core.dic dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29. Automatic conversion script Id: cif_fix_values 1715 2011-07-08 13:25:40Z adriana ; _cod_original_cell_volume 1540.40(10) _cod_original_sg_symbol_H-M 'P 21/n' _cod_database_code 2013873 _cod_database_fobs_code 2013873 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x+1/2, -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 N1 0.7539(2) 0.3798(2) 0.49141(5) 0.0198(3) Uani d . 1 . . N C2 0.7498(2) 0.5505(3) 0.51029(6) 0.0194(4) Uani d . 1 . . C N3 0.6955(2) 0.6963(2) 0.48764(5) 0.0213(3) Uani d . 1 . . N C4 0.6362(2) 0.6744(2) 0.44168(6) 0.0200(4) Uani d . 1 . . C N4 0.5820(2) 0.8288(2) 0.41993(5) 0.0255(4) Uani d . 1 . . N C5 0.6339(2) 0.5062(2) 0.41944(6) 0.0194(4) Uani d . 1 . . C C6 0.7005(2) 0.3536(3) 0.44411(6) 0.0208(4) Uani d . 1 . . C O6 0.71906(19) 0.19762(17) 0.42643(4) 0.0262(3) Uani d . 1 . . O C11 0.8209(3) 0.2222(3) 0.51881(7) 0.0260(4) Uani d . 1 . . C S2 0.82976(6) 0.56773(7) 0.568820(15) 0.02358(14) Uani d . 1 . . S C21 0.7849(3) 0.8037(3) 0.57990(7) 0.0307(5) Uani d . 1 . . C C57 0.5750(2) 0.4850(3) 0.36838(6) 0.0206(4) Uani d . 1 . . C C51 0.7154(2) 0.5431(3) 0.33565(6) 0.0191(4) Uani d . 1 . . C C52 0.8609(2) 0.4398(2) 0.32941(6) 0.0198(4) Uani d . 1 . . C O52 0.88973(18) 0.27490(17) 0.34900(4) 0.0238(3) Uani d . 1 . . O C53 1.0093(2) 0.4934(3) 0.29979(6) 0.0217(4) Uani d . 1 . . C C54 1.0156(2) 0.6982(3) 0.28889(6) 0.0226(4) Uani d . 1 . . C C55 0.8268(2) 0.7601(3) 0.27475(6) 0.0229(4) Uani d . 1 . . C C56 0.6944(2) 0.7138(3) 0.31032(6) 0.0211(4) Uani d . 1 . . C O56 0.5690(2) 0.8186(2) 0.31668(6) 0.0277(4) Uani d . 1 . . O C541 1.0852(3) 0.8074(3) 0.33172(7) 0.0297(4) Uani d . 1 . . C C542 1.1342(3) 0.7320(3) 0.24834(8) 0.0325(5) Uani d . 1 . . C H11A 0.7994 0.1061 0.5011 0.039 Uiso calc R 1 . . H H11B 0.7602 0.2160 0.5482 0.039 Uiso calc R 1 . . H H11C 0.9486 0.2376 0.5257 0.039 Uiso calc R 1 . . H H21A 0.8014 0.8281 0.6136 0.046 Uiso calc R 1 . . H H21B 0.6623 0.8323 0.5693 0.046 Uiso calc R 1 . . H H21C 0.8660 0.8829 0.5630 0.046 Uiso calc R 1 . . H H4A 0.5433 0.8241 0.3904 0.031 Uiso calc R 1 . . H H4B 0.5845 0.9364 0.4350 0.031 Uiso calc R 1 . . H H57A 0.5428 0.3525 0.3622 0.025 Uiso calc R 1 . . H H57B 0.4675 0.5620 0.3617 0.025 Uiso calc R 1 . . H H52 0.8159 0.2569 0.3695 0.036 Uiso calc R 1 . . H H53A 0.9975 0.4225 0.2701 0.026 Uiso calc R 1 . . H H53B 1.1229 0.4564 0.3161 0.026 Uiso calc R 1 . . H H54A 1.0781 0.9420 0.3251 0.044 Uiso calc R 1 . . H H54B 1.2089 0.7725 0.3394 0.044 Uiso calc R 1 . . H H54C 1.0134 0.7780 0.3583 0.044 Uiso calc R 1 . . H H54G 1.1285 0.8644 0.2393 0.049 Uiso calc R 1 . . H H54H 1.0936 0.6543 0.2216 0.049 Uiso calc R 1 . . H H54I 1.2568 0.6989 0.2580 0.049 Uiso calc R 1 . . H H55A 0.8263 0.8972 0.2695 0.027 Uiso calc R 1 . . H H55B 0.7894 0.6992 0.2447 0.027 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 N1 0.0252(8) 0.0148(7) 0.0195(7) 0.0005(6) 0.0023(6) 0.0021(6) C2 0.0188(9) 0.0199(9) 0.0198(8) -0.0010(7) 0.0037(7) 0.0001(7) N3 0.0263(8) 0.0177(8) 0.0197(7) 0.0002(6) 0.0005(6) 0.0009(6) C4 0.0209(9) 0.0184(9) 0.0207(9) 0.0000(7) 0.0026(7) 0.0020(7) N4 0.0377(10) 0.0171(8) 0.0211(8) 0.0043(7) -0.0038(7) -0.0001(6) C5 0.0222(9) 0.0174(9) 0.0188(8) -0.0026(7) 0.0025(7) 0.0003(7) C6 0.0243(10) 0.0185(10) 0.0200(9) -0.0034(7) 0.0057(7) 0.0010(7) O6 0.0401(8) 0.0141(7) 0.0243(7) -0.0012(6) 0.0027(6) 0.0004(5) C11 0.0349(11) 0.0189(10) 0.0241(9) 0.0032(8) 0.0019(8) 0.0045(7) S2 0.0294(3) 0.0223(3) 0.0187(2) 0.0011(2) -0.00129(17) 0.00093(18) C21 0.0402(12) 0.0274(11) 0.0236(10) 0.0053(9) -0.0058(8) -0.0036(8) C57 0.0234(9) 0.0186(9) 0.0198(9) -0.0014(7) 0.0009(7) 0.0002(7) C51 0.0209(9) 0.0201(9) 0.0160(8) -0.0010(7) -0.0015(7) -0.0001(7) C52 0.0276(10) 0.0156(9) 0.0157(8) -0.0016(7) -0.0023(7) -0.0016(7) O52 0.0325(8) 0.0161(7) 0.0231(7) 0.0029(6) 0.0045(5) 0.0023(5) C53 0.0254(10) 0.0204(9) 0.0194(9) 0.0014(8) 0.0014(7) -0.0003(7) C54 0.0236(10) 0.0205(10) 0.0238(9) -0.0012(8) 0.0014(7) 0.0011(7) C55 0.0272(10) 0.0198(9) 0.0215(9) -0.0010(8) 0.0000(7) 0.0036(7) C56 0.0233(10) 0.0218(10) 0.0178(8) 0.0002(8) -0.0032(7) -0.0007(7) O56 0.0291(7) 0.0261(7) 0.0273(7) 0.0080(6) 0.0029(6) 0.0057(6) C541 0.0291(11) 0.0234(10) 0.0359(11) -0.0024(8) -0.0041(8) -0.0036(9) C542 0.0311(11) 0.0297(11) 0.0376(11) -0.0017(9) 0.0095(9) 0.0061(9) 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 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 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' S S 0.1246 0.1234 '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 _geom_angle_publ_flag C2 N1 C6 120.05(15) no C2 N1 C11 120.37(15) no C6 N1 C11 119.52(15) no N1 C11 H11A 109.5 no N1 C11 H11B 109.5 no H11A C11 H11B 109.5 no N1 C11 H11C 109.5 no H11A C11 H11C 109.5 no H11B C11 H11C 109.5 no N3 C2 N1 123.40(16) no N3 C2 S2 120.69(14) no N1 C2 S2 115.90(13) no C21 S2 C2 100.40(9) no S2 C21 H21A 109.5 no S2 C21 H21B 109.5 no H21A C21 H21B 109.5 no S2 C21 H21C 109.5 no H21A C21 H21C 109.5 no H21B C21 H21C 109.5 no C2 N3 C4 118.04(15) no N4 C4 C5 121.40(16) no N4 C4 N3 115.66(16) no C5 C4 N3 122.95(16) no C4 N4 H4A 120.0 no C4 N4 H4B 120.0 no H4A N4 H4B 120.0 no C4 C5 C6 117.60(16) no C4 C5 C57 122.47(16) no C6 C5 C57 119.76(16) no C51 C57 C5 113.09(15) no C51 C57 H57A 109.0 no C5 C57 H57A 109.0 no C51 C57 H57B 109.0 no C5 C57 H57B 109.0 no H57A C57 H57B 107.8 no C52 C51 C56 118.16(16) no C52 C51 C57 122.62(16) no C56 C51 C57 119.21(16) no O52 C52 C51 123.45(16) no O52 C52 C53 111.08(15) no C51 C52 C53 125.47(16) no C52 O52 H52 109.5 no C52 C53 C54 113.76(15) no C52 C53 H53A 108.8 no C54 C53 H53A 108.8 no C52 C53 H53B 108.8 no C54 C53 H53B 108.8 no H53A C53 H53B 107.7 no C53 C54 C541 110.23(15) no C53 C54 C542 109.89(16) no C541 C54 C542 109.97(16) no C53 C54 C55 107.32(15) no C541 C54 C55 110.01(16) no C542 C54 C55 109.37(15) no C54 C541 H54A 109.5 no C54 C541 H54B 109.5 no H54A C541 H54B 109.5 no C54 C541 H54C 109.5 no H54A C541 H54C 109.5 no H54B C541 H54C 109.5 no C54 C542 H54G 109.5 no C54 C542 H54H 109.5 no H54G C542 H54H 109.5 no C54 C542 H54I 109.5 no H54G C542 H54I 109.5 no H54H C542 H54I 109.5 no C56 C55 C54 113.82(15) no C56 C55 H55A 108.8 no C54 C55 H55A 108.8 no C56 C55 H55B 108.8 no C54 C55 H55B 108.8 no H55A C55 H55B 107.7 no O56 C56 C51 120.84(17) no O56 C56 C55 120.90(16) no C51 C56 C55 118.24(16) no O6 C6 C5 123.32(17) no O6 C6 N1 118.86(16) no C5 C6 N1 117.80(16) no 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 N1 C2 . 1.334(2) y C2 N3 . 1.282(2) y N3 C4 . 1.375(2) y C4 C5 . 1.359(3) y C5 C6 . 1.378(3) y C6 N1 . 1.404(2) y C2 S2 . 1.7536(18) y S2 C21 . 1.750(2) y N1 C11 . 1.447(2) y C4 N4 . 1.319(2) y C6 O6 . 1.234(2) y C51 C52 . 1.343(3) y C52 O52 . 1.317(2) y C51 C56 . 1.423(3) y C56 O56 . 1.227(2) y C11 H11A . 0.98 no C11 H11B . 0.98 no C11 H11C . 0.98 no C21 H21A . 0.98 no C21 H21B . 0.98 no C21 H21C . 0.98 no N4 H4A . 0.88 no N4 H4B . 0.88 no C5 C57 . 1.512(2) no C57 C51 . 1.511(2) no C57 H57A . 0.99 no C57 H57B . 0.99 no C52 C53 . 1.491(3) no O52 H52 . 0.84 no C53 C54 . 1.496(3) no C53 H53A . 0.99 no C53 H53B . 0.99 no C54 C541 . 1.522(3) no C54 C542 . 1.523(3) no C54 C55 . 1.526(3) no C541 H54A . 0.98 no C541 H54B . 0.98 no C541 H54C . 0.98 no C542 H54G . 0.98 no C542 H54H . 0.98 no C542 H54I . 0.98 no C55 C56 . 1.503(3) no C55 H55A . 0.99 no C55 H55B . 0.99 no loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_site_symmetry_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_publ_flag O52 H52 O6 . 0.84 1.87 2.681(2) 161 y N4 H4A O56 . 0.88 2.13 2.952(2) 155 y N4 H4B O6 1_565 0.88 2.14 2.831(3) 134 y 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 C6 N1 C2 N3 1.5(3) no C11 N1 C2 N3 178.55(17) no C6 N1 C2 S2 -176.98(13) no C11 N1 C2 S2 0.1(2) no N3 C2 S2 C21 5.73(17) no N1 C2 S2 C21 -175.76(15) no N1 C2 N3 C4 0.9(3) no S2 C2 N3 C4 179.25(13) no C2 N3 C4 N4 -179.89(16) no C2 N3 C4 C5 -0.4(3) no N4 C4 C5 C6 177.06(17) no N3 C4 C5 C6 -2.4(3) no N4 C4 C5 C57 1.8(3) no N3 C4 C5 C57 -177.65(16) no C4 C5 C57 C51 78.6(2) y C6 C5 C57 C51 -96.5(2) no C5 C57 C51 C56 -106.97(18) no C56 C51 C52 O52 -176.21(15) no C57 C51 C52 O52 3.9(3) no C56 C51 C52 C53 3.4(3) y C57 C51 C52 C53 -176.43(16) no O52 C52 C53 C54 -161.73(15) no C51 C52 C53 C54 18.6(3) y C52 C53 C54 C55 -45.3(2) y C52 C53 C54 C541 74.5(2) y C52 C53 C54 C542 -164.09(15) y C5 C57 C51 C52 72.9(2) y C52 C51 C56 O56 -175.95(17) no C57 C51 C56 O56 3.9(3) no C52 C51 C56 C55 5.7(2) y C57 C51 C56 C55 -174.49(15) no C54 C55 C56 O56 145.49(17) no C54 C55 C56 C51 -36.1(2) y C53 C54 C55 C56 54.6(2) y C56 C55 C54 C541 -65.4(2) y C56 C56 C54 C542 173.75(16) y C4 C5 C6 O6 -173.71(18) no C57 C5 C6 O6 1.6(3) no C4 C5 C6 N1 4.6(3) no C57 C5 C6 N1 179.92(15) no C2 N1 C6 O6 174.12(17) no C11 N1 C6 O6 -3.0(3) no C2 N1 C6 C5 -4.2(2) no C11 N1 C6 C5 178.66(16) no