#------------------------------------------------------------------------------ #$Date: 2020-05-08 08:29:32 +0100 (Fri, 08 May 2020) $ #$Revision: 251898 $ #$URL: svn://www.crystallography.net/cod/cif/3/50/01/3500100.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_3500100 loop_ _publ_author_name 'Thierry Maris' _publ_section_references ; Dolomanov, O.V., Bourhis, L.J., Gildea, R.J, Howard, J.A.K. & Puschmann, H. (2009), J. Appl. Cryst. 42, 339-341. Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122. ; _journal_name_full 'Personal communication to COD' _journal_year 2020 _chemical_absolute_configuration ad _chemical_formula_moiety 'C8 H12 N4 O4' _chemical_formula_sum 'C8 H12 N4 O4' _chemical_formula_weight 228.22 _chemical_name_systematic 4-amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-1,3,5-triazin-2(1H)-one _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' _atom_sites_solution_hydrogens mixed _atom_sites_solution_primary dual _audit_creation_date 2020-05-05 _audit_creation_method ; Olex2 1.3 (compiled 2020.02.04 svn.rd84adfe8 for OlexSys, GUI svn.r6032) ; _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 5.6352(2) _cell_length_b 7.1096(3) _cell_length_c 24.7718(9) _cell_measurement_reflns_used 9856 _cell_measurement_temperature 150 _cell_measurement_theta_max 60.667 _cell_measurement_theta_min 3.105 _cell_volume 992.46(7) _computing_cell_refinement ; SAINT (2013) V8.37A; Integration Software for Single Crystal Data. Bruker AXS Inc., Madison, WI 53719-1173. ; _computing_data_collection ; APEX 2 (2013) Bruker AXS Inc., Madison, WI 53719-1173. ; _computing_data_reduction ; SAINT (2013) V8.37A; Integration Software for Single Crystal Data. Bruker AXS Inc., Madison, WI 53719-1173. ; _computing_molecular_graphics 'Olex2 1.3 (Dolomanov et al., 2009)' _computing_publication_material 'Olex2 1.3 (Dolomanov et al., 2009)' _computing_structure_refinement 'XL (Sheldrick, 2008)' _computing_structure_solution 'XT (Sheldrick, 2015)' _diffrn_ambient_temperature 150 _diffrn_detector 'CMOS Area detector' _diffrn_detector_area_resol_mean 10.24 _diffrn_detector_type 'Bruker Photon 100 CMOS Detector' _diffrn_measured_fraction_theta_full 1.000 _diffrn_measured_fraction_theta_max 0.999 _diffrn_measurement_device 'k-geometry diffractometer' _diffrn_measurement_device_type 'Bruker Venture Metaljet' _diffrn_measurement_method '\w and \f scans' _diffrn_radiation_collimation 'Focusing mirrors' _diffrn_radiation_monochromator 'Helios MX Mirror Optics' _diffrn_radiation_probe x-ray _diffrn_radiation_type GaK\a _diffrn_radiation_wavelength 1.34139 _diffrn_reflns_av_R_equivalents 0.0301 _diffrn_reflns_av_unetI/netI 0.0156 _diffrn_reflns_Laue_measured_fraction_full 1.000 _diffrn_reflns_Laue_measured_fraction_max 0.999 _diffrn_reflns_limit_h_max 7 _diffrn_reflns_limit_h_min -6 _diffrn_reflns_limit_k_max 9 _diffrn_reflns_limit_k_min -9 _diffrn_reflns_limit_l_max 32 _diffrn_reflns_limit_l_min -32 _diffrn_reflns_number 19796 _diffrn_reflns_point_group_measured_fraction_full 1.000 _diffrn_reflns_point_group_measured_fraction_max 1.000 _diffrn_reflns_theta_full 53.594 _diffrn_reflns_theta_max 60.636 _diffrn_reflns_theta_min 3.104 _diffrn_source 'Metal Jet' _diffrn_source_target Ga _diffrn_source_type 'Gallium Liquid Metal Jet Source' _exptl_absorpt_coefficient_mu 0.680 _exptl_absorpt_correction_T_max 0.7519 _exptl_absorpt_correction_T_min 0.6651 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details ; SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.1207 before and 0.0537 after correction. The Ratio of minimum to maximum transmission is 0.8846. The \l/2 correction factor is Not present. ; _exptl_crystal_colour 'clear light colourless' _exptl_crystal_colour_lustre clear _exptl_crystal_colour_modifier light _exptl_crystal_colour_primary colourless _exptl_crystal_density_diffrn 1.527 _exptl_crystal_description Block _exptl_crystal_F_000 480 _exptl_crystal_recrystallization_method 'The material was used as supplied' _exptl_crystal_size_max 0.234 _exptl_crystal_size_mid 0.088 _exptl_crystal_size_min 0.07 _exptl_special_details ; X-ray crystallographic data for I were collected from a single crystal sample, which was mounted on a loop fiber. Data were collected using a Bruker Venture diffractometer equipped with a Photon 100 CMOS Detector, a Helios MX optics and a Kappa goniometer. The crystal-to-detector distance was 4.0 cm, and the data collection was carried out in 1024 x 1024 pixel mode. ; _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; _refine_diff_density_max 0.187 _refine_diff_density_min -0.204 _refine_diff_density_rms 0.045 _refine_ls_abs_structure_details ; Flack x determined using 861 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259). ; _refine_ls_abs_structure_Flack -0.08(7) _refine_ls_extinction_coef 0.0249(18) _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ _refine_ls_extinction_method 'SHELXL-2018/3 (Sheldrick 2018)' _refine_ls_goodness_of_fit_ref 1.099 _refine_ls_hydrogen_treatment mixed _refine_ls_matrix_type full _refine_ls_number_parameters 162 _refine_ls_number_reflns 2290 _refine_ls_number_restraints 1 _refine_ls_restrained_S_all 1.098 _refine_ls_R_factor_all 0.0312 _refine_ls_R_factor_gt 0.0296 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'w=1/[\s^2^(Fo^2^)+(0.0361P)^2^+0.2430P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0734 _refine_ls_wR_factor_ref 0.0751 _refine_special_details ; _shelx_SHELXL_version_number 2018/3 1. Fixed Uiso At 1.2 times of: All C(H) groups, All C(H,H) groups 2. Restrained distances H3-H6 2.2 with sigma of 0.002 3.a Ternary CH refined with riding coordinates: C4(H4C), C6(H6), C7(H7) 3.b Secondary CH2 refined with riding coordinates: C5(H5A,H5B), C8(H8A,H8B) 3.c Aromatic/amide H refined with riding coordinates: C3(H3A) ; _reflns_Friedel_coverage 0.672 _reflns_Friedel_fraction_full 1.000 _reflns_Friedel_fraction_max 1.000 _reflns_number_gt 2193 _reflns_number_total 2290 _reflns_special_details ; Reflections were merged by SHELXL according to the crystal class for the calculation of statistics and refinement. _reflns_Friedel_fraction is defined as the number of unique Friedel pairs measured divided by the number that would be possible theoretically, ignoring centric projections and systematic absences. ; _reflns_threshold_expression 'I > 2\s(I)' _cod_data_source_file deci.cif _cod_data_source_block deci2 _cod_database_code 3500100 loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 'x, y, z' 2 '-x+1/2, -y, z+1/2' 3 '-x, y+1/2, -z+1/2' 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 O1 O 0.4990(3) 0.79117(18) 0.35110(5) 0.0335(3) Uani 1 1 d . . . . . O2 O 0.9036(2) 0.3190(2) 0.36026(5) 0.0276(3) Uani 1 1 d . . . . . O3 O 1.1117(3) 0.5027(2) 0.46475(6) 0.0357(3) Uani 1 1 d . . . . . H3 H 1.133(5) 0.534(3) 0.5010(16) 0.087(12) Uiso 1 1 d D . . . . O4 O 0.6785(3) 0.0230(2) 0.42587(6) 0.0402(4) Uani 1 1 d . . . . . H4 H 0.611(6) -0.056(5) 0.4042(13) 0.069(10) Uiso 1 1 d . . . . . N1 N 0.5574(2) 0.4775(2) 0.33621(6) 0.0226(3) Uani 1 1 d . . . . . N2 N 0.2405(3) 0.6401(2) 0.29573(6) 0.0242(3) Uani 1 1 d . . . . . N3 N 0.3041(3) 0.3104(2) 0.27873(6) 0.0231(3) Uani 1 1 d . . . . . N4 N 0.0008(3) 0.4756(2) 0.23839(6) 0.0257(3) Uani 1 1 d . . . . . H4A H -0.088(5) 0.577(4) 0.2342(10) 0.036(6) Uiso 1 1 d . . . . . H4B H -0.050(5) 0.375(4) 0.2261(10) 0.039(7) Uiso 1 1 d . . . . . C1 C 0.4314(3) 0.6470(2) 0.32842(7) 0.0243(4) Uani 1 1 d . . . . . C2 C 0.1842(3) 0.4780(2) 0.27169(7) 0.0215(3) Uani 1 1 d . . . . . C3 C 0.4851(3) 0.3192(2) 0.31119(7) 0.0237(3) Uani 1 1 d . . . . . H3A H 0.571956 0.206942 0.317684 0.028 Uiso 1 1 calc R U . . . C4 C 0.7681(3) 0.4808(3) 0.37208(7) 0.0241(4) Uani 1 1 d . . . . . H4C H 0.864200 0.596338 0.364845 0.029 Uiso 1 1 calc R U . . . C5 C 0.7073(3) 0.4695(3) 0.43207(7) 0.0267(4) Uani 1 1 d . . . . . H5A H 0.686411 0.596190 0.447929 0.032 Uiso 1 1 calc R U . . . H5B H 0.561798 0.394504 0.438252 0.032 Uiso 1 1 calc R U . . . C6 C 0.9261(3) 0.3712(3) 0.45503(7) 0.0261(4) Uani 1 1 d . . . . . H6 H 0.886341 0.298788 0.488437 0.031 Uiso 1 1 calc DR U . . . C7 C 1.0019(3) 0.2395(3) 0.40902(7) 0.0256(4) Uani 1 1 d . . . . . H7 H 1.178827 0.243275 0.406179 0.031 Uiso 1 1 calc R U . . . C8 C 0.9264(4) 0.0364(3) 0.41436(8) 0.0330(4) Uani 1 1 d . . . . . H8A H 0.961533 -0.031276 0.380354 0.040 Uiso 1 1 calc R U . . . H8B H 1.017790 -0.024202 0.443729 0.040 Uiso 1 1 calc R U . . . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 O1 0.0349(7) 0.0271(6) 0.0385(7) -0.0059(5) -0.0114(6) -0.0018(6) O2 0.0235(6) 0.0390(7) 0.0202(5) 0.0021(5) -0.0004(5) 0.0077(6) O3 0.0306(7) 0.0445(8) 0.0320(7) -0.0025(6) -0.0085(6) -0.0111(7) O4 0.0443(9) 0.0447(8) 0.0317(7) -0.0133(6) 0.0097(6) -0.0177(7) N1 0.0201(7) 0.0272(7) 0.0205(6) 0.0012(6) -0.0031(5) -0.0008(6) N2 0.0246(7) 0.0213(6) 0.0266(7) 0.0016(6) -0.0036(6) -0.0011(6) N3 0.0227(7) 0.0218(7) 0.0248(7) -0.0008(5) -0.0017(6) 0.0014(6) N4 0.0272(7) 0.0199(7) 0.0299(7) 0.0004(6) -0.0086(7) 0.0002(6) C1 0.0242(8) 0.0239(8) 0.0249(8) 0.0013(6) -0.0015(6) -0.0017(7) C2 0.0218(7) 0.0229(8) 0.0198(7) 0.0024(6) 0.0014(6) -0.0011(7) C3 0.0225(7) 0.0264(8) 0.0221(7) 0.0003(6) 0.0013(6) 0.0021(7) C4 0.0185(7) 0.0292(8) 0.0246(8) 0.0002(7) -0.0022(6) -0.0010(7) C5 0.0226(8) 0.0344(9) 0.0230(8) -0.0031(7) -0.0018(7) 0.0000(7) C6 0.0230(8) 0.0324(9) 0.0227(7) 0.0005(7) -0.0035(6) -0.0041(7) C7 0.0191(7) 0.0363(9) 0.0213(7) 0.0029(6) -0.0024(6) -0.0007(7) C8 0.0388(10) 0.0329(10) 0.0274(8) -0.0011(7) 0.0021(8) 0.0000(8) loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0140 0.0070 '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 0.0250 0.0140 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0390 0.0250 '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_site_symmetry_1 _geom_angle_site_symmetry_3 C4 O2 C7 110.68(13) . . C6 O3 H3 114.6(11) . . C8 O4 H4 111(2) . . C1 N1 C4 118.10(14) . . C3 N1 C1 119.87(14) . . C3 N1 C4 122.03(14) . . C2 N2 C1 119.32(15) . . C3 N3 C2 114.84(14) . . H4A N4 H4B 118(2) . . C2 N4 H4A 120.3(16) . . C2 N4 H4B 120.7(18) . . O1 C1 N1 119.56(15) . . O1 C1 N2 123.56(16) . . N2 C1 N1 116.89(15) . . N2 C2 N3 124.90(15) . . N4 C2 N2 118.38(16) . . N4 C2 N3 116.72(15) . . N1 C3 H3A 117.9 . . N3 C3 N1 124.16(16) . . N3 C3 H3A 117.9 . . O2 C4 N1 107.22(13) . . O2 C4 H4C 109.8 . . O2 C4 C5 106.25(14) . . N1 C4 H4C 109.8 . . N1 C4 C5 113.74(14) . . C5 C4 H4C 109.8 . . C4 C5 H5A 111.4 . . C4 C5 H5B 111.4 . . H5A C5 H5B 109.3 . . C6 C5 C4 101.87(14) . . C6 C5 H5A 111.4 . . C6 C5 H5B 111.4 . . O3 C6 C5 110.82(16) . . O3 C6 H6 111.3 . . O3 C6 C7 108.78(15) . . C5 C6 H6 111.3 . . C5 C6 C7 103.13(14) . . C7 C6 H6 111.3 . . O2 C7 C6 105.99(14) . . O2 C7 H7 108.2 . . O2 C7 C8 109.83(15) . . C6 C7 H7 108.2 . . C8 C7 C6 116.07(15) . . C8 C7 H7 108.2 . . O4 C8 C7 110.87(16) . . O4 C8 H8A 109.5 . . O4 C8 H8B 109.5 . . C7 C8 H8A 109.5 . . C7 C8 H8B 109.5 . . H8A C8 H8B 108.1 . . loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 O1 C1 1.229(2) . O2 C4 1.412(2) . O2 C7 1.444(2) . O3 H3 0.93(4) . O3 C6 1.423(2) . O4 H4 0.87(4) . O4 C8 1.429(3) . N1 C1 1.412(2) . N1 C3 1.348(2) . N1 C4 1.483(2) . N2 C1 1.347(2) . N2 C2 1.335(2) . N3 C2 1.381(2) . N3 C3 1.301(2) . N4 H4A 0.88(3) . N4 H4B 0.83(3) . N4 C2 1.322(2) . C3 H3A 0.9500 . C4 H4C 1.0000 . C4 C5 1.527(2) . C5 H5A 0.9900 . C5 H5B 0.9900 . C5 C6 1.527(2) . C6 H6 1.0000 . C6 C7 1.535(3) . C7 H7 1.0000 . C7 C8 1.511(3) . C8 H8A 0.9900 . C8 H8B 0.9900 . loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A _geom_hbond_publ_flag O3 H3 O4 0.93(4) 1.87(4) 2.742(2) 154(2) 4_556 yes O4 H4 O1 0.87(4) 1.82(4) 2.678(2) 171(3) 1_545 yes N4 H4A N3 0.88(3) 2.08(3) 2.966(2) 177(2) 3 yes N4 H4B N2 0.83(3) 2.05(3) 2.873(2) 168(3) 3_545 yes 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 O2 C4 C5 C6 32.76(17) . . . . O2 C7 C8 O4 -69.84(19) . . . . O3 C6 C7 O2 -94.88(16) . . . . O3 C6 C7 C8 142.91(16) . . . . N1 C4 C5 C6 150.47(15) . . . . C1 N1 C3 N3 1.0(2) . . . . C1 N1 C4 O2 -161.69(14) . . . . C1 N1 C4 C5 81.16(19) . . . . C1 N2 C2 N3 2.0(3) . . . . C1 N2 C2 N4 -177.85(15) . . . . C2 N2 C1 O1 178.22(17) . . . . C2 N2 C1 N1 -1.7(2) . . . . C2 N3 C3 N1 -0.8(2) . . . . C3 N1 C1 O1 -179.59(16) . . . . C3 N1 C1 N2 0.3(2) . . . . C3 N1 C4 O2 18.1(2) . . . . C3 N1 C4 C5 -99.05(19) . . . . C3 N3 C2 N2 -0.7(2) . . . . C3 N3 C2 N4 179.13(15) . . . . C4 O2 C7 C6 -2.38(18) . . . . C4 O2 C7 C8 123.73(16) . . . . C4 N1 C1 O1 0.2(2) . . . . C4 N1 C1 N2 -179.89(15) . . . . C4 N1 C3 N3 -178.80(16) . . . . C4 C5 C6 O3 83.23(17) . . . . C4 C5 C6 C7 -33.03(18) . . . . C5 C6 C7 O2 22.82(18) . . . . C5 C6 C7 C8 -99.39(18) . . . . C6 C7 C8 O4 50.3(2) . . . . C7 O2 C4 N1 -141.30(14) . . . . C7 O2 C4 C5 -19.34(18) . . . . _cod_database_fobs_code 3500100