#------------------------------------------------------------------------------ #$Date: 2025-08-19 11:43:10 +0100 (Tue, 19 Aug 2025) $ #$Revision: 301803 $ #$URL: svn://www.crystallography.net/cod/cif/2/20/24/2202488.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_2202488 loop_ _publ_author_name 'A. Sivalakshmidevi' 'K. Vyas' 'S. D. V. N. Sivaram' 'P. Veerabhadra Swamy' 'Ramachandra Puranik' 'P. Sairam' ' G. Om Reddy ' _publ_section_title ; 2'-Deoxy-2',2'-difluorocytidine monohydrochloride (Gemcitabine hydrochloride) ; _journal_issue 10 _journal_name_full 'Acta Crystallographica Section E' _journal_page_first o1435 _journal_page_last o1437 _journal_paper_doi 10.1107/S1600536803018816 _journal_volume 59 _journal_year 2003 _chemical_formula_iupac 'C9 H12 F2 N3 O4 1+, Cl 1-' _chemical_formula_moiety 'C9 H12 F2 N3 O4 1+, Cl 1-' _chemical_formula_sum 'C9 H12 Cl F2 N3 O4' _chemical_formula_weight 299.66 _chemical_name_common 'Gemcitabine Hydrochloride' _chemical_name_systematic ; 2'-deoxy-2',2'-difluorocytidine monohydrochloride ; _space_group_IT_number 19 _symmetry_cell_setting orthorhombic _symmetry_space_group_name_Hall 'P 2ac 2ab' _symmetry_space_group_name_H-M 'P 21 21 21' _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 11.4680(7) _cell_length_b 15.5987(9) _cell_length_c 6.706(2) _cell_measurement_reflns_used 25 _cell_measurement_temperature 298.2 _cell_measurement_theta_max 24.8 _cell_measurement_theta_min 22.6 _cell_volume 1199.6(4) _computing_cell_refinement 'MSC/AFC Diffractometer Control Software' _computing_data_collection ; MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1994) ; _computing_data_reduction 'TEXSAN (Molecular Structure Corporation, 1995)' _computing_molecular_graphics 'CrystalStructure (Rigaku/MSC, 2003)' _computing_publication_material CrystalStructure _computing_structure_refinement 'CRYSTALS (Watkin et al., 1996)' _computing_structure_solution 'SIR92 (Altomare et al., 1993)' _diffrn_ambient_temperature 298.2 _diffrn_measured_fraction_theta_full 0.9631 _diffrn_measured_fraction_theta_max 0.9631 _diffrn_measurement_device_type 'Rigaku AFC-7S' _diffrn_measurement_method \w-2\q _diffrn_radiation_monochromator graphite _diffrn_radiation_source 'X-ray tube' _diffrn_radiation_type 'Cu K\a' _diffrn_radiation_wavelength 1.5418 _diffrn_reflns_av_R_equivalents 0.028 _diffrn_reflns_av_sigmaI/netI 0.030 _diffrn_reflns_limit_h_max 13 _diffrn_reflns_limit_h_min -13 _diffrn_reflns_limit_k_max 18 _diffrn_reflns_limit_k_min -18 _diffrn_reflns_limit_l_max 7 _diffrn_reflns_limit_l_min -7 _diffrn_reflns_number 2540 _diffrn_reflns_reduction_process 'Lp corrections applied' _diffrn_reflns_theta_full 67.86 _diffrn_reflns_theta_max 67.86 _diffrn_reflns_theta_min 2.84 _diffrn_standards_decay_% 1.26 _diffrn_standards_interval_count 150 _diffrn_standards_number 3 _exptl_absorpt_coefficient_mu 3.266 _exptl_absorpt_correction_T_max 0.271 _exptl_absorpt_correction_T_min 0.175 _exptl_absorpt_correction_type '\y scan' _exptl_absorpt_process_details '(North et al., 1968)' _exptl_crystal_colour Colourless _exptl_crystal_density_diffrn 1.659 _exptl_crystal_density_method 'not measured' _exptl_crystal_description block _exptl_crystal_F_000 616.00 _exptl_crystal_size_max 0.50 _exptl_crystal_size_mid 0.50 _exptl_crystal_size_min 0.40 _refine_diff_density_max 0.77 _refine_diff_density_min -0.57 _refine_ls_abs_structure_details 'Flack (1983), 828 Friedel pairs' _refine_ls_abs_structure_Flack 0.00(3) _refine_ls_extinction_coef 110(9) _refine_ls_extinction_method 'Larson (1970), eq. 22' _refine_ls_goodness_of_fit_ref 1.134 _refine_ls_hydrogen_treatment mixed _refine_ls_number_parameters 191 _refine_ls_number_reflns 2082 _refine_ls_R_factor_gt 0.0600 _refine_ls_shift/su_max 0.0410 _refine_ls_structure_factor_coef F _refine_ls_weighting_details ; Chebychev polynomial with 3 parameters (Carruthers & Watkin, 1979): 2.0710, 1.3167 and 0.0135 ; _refine_ls_weighting_scheme calc _refine_ls_wR_factor_ref 0.0600 _reflns_number_gt 2032 _reflns_number_total 2083 _reflns_threshold_expression F^2^>2\s(F^2^) _cod_data_source_file ci6255.cif _cod_data_source_block I _cod_database_code 2202488 loop_ _symmetry_equiv_pos_as_xyz ' +x, +y, +z' '1/2-x, -y,1/2+z' '1/2+x,1/2-y, -z' ' -x,1/2+y,1/2-z' 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 Cl1 0.0417(5) 0.0547(6) 0.0594(7) 0.0008(4) -0.0157(5) 0.0127(5) F1 0.0353(12) 0.0560(10) 0.096(2) -0.0140(10) -0.0137(13) 0.0210(10) F2 0.096(2) 0.0560(10) 0.0406(13) -0.0140(10) -0.0130(10) 0.0013(12) O2 0.0243(11) 0.0478(13) 0.052(2) 0.0051(10) -0.0004(10) 0.0037(12) O1' 0.0440(10) 0.0345(12) 0.043(2) 0.0044(10) -0.0051(12) 0.0029(10) O3' 0.0438(13) 0.0309(11) 0.060(2) -0.0003(10) 0.0000(10) -0.0007(13) O5' 0.0330(13) 0.058(2) 0.085(3) -0.0011(12) 0.0030(10) -0.015(2) N1 0.0266(13) 0.0324(13) 0.048(2) 0.0028(11) 0.0010(13) 0.0075(13) N3 0.0292(13) 0.0312(13) 0.048(2) 0.0024(11) -0.0036(13) 0.0063(12) N4 0.037(2) 0.048(2) 0.057(2) 0.0000(10) 0.005(2) 0.014(2) C2 0.0290(10) 0.0260(10) 0.040(2) 0.0015(11) -0.0010(10) 0.001(2) C4 0.029(2) 0.0290(10) 0.049(2) -0.0026(13) 0.002(2) 0.0020(10) C5 0.026(2) 0.037(2) 0.050(2) 0.0023(13) 0.000(2) 0.000(2) C6 0.0230(10) 0.034(2) 0.051(2) 0.0041(13) -0.001(2) 0.007(2) C1' 0.030(2) 0.041(2) 0.040(2) 0.0020(10) 0.002(2) 0.008(2) C2' 0.037(2) 0.047(2) 0.037(2) -0.010(2) 0.000(2) 0.004(2) C3' 0.030(2) 0.036(2) 0.043(2) -0.0002(13) 0.005(2) 0.001(2) C4' 0.033(2) 0.034(2) 0.038(2) 0.0018(13) 0.004(2) 0.006(2) C5' 0.048(2) 0.045(2) 0.052(3) 0.006(2) -0.010(2) 0.000(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_thermal_displace_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_type_symbol Cl1 0.28824(8) 0.32194(6) -0.4814(2) 0.0519(3) Uani . . 1.000 Cl F1 0.2745(2) -0.0581(2) 0.2133(5) 0.0624(8) Uani . . 1.000 F F2 0.3973(3) -0.0299(2) -0.0220(4) 0.0642(9) Uani . . 1.000 F O2 0.2558(2) 0.1739(2) 0.0510(4) 0.0414(9) Uani . . 1.000 O O1' 0.4719(2) 0.0592(2) 0.4248(4) 0.0405(8) Uani . . 1.000 O O3' 0.4475(2) -0.1666(2) 0.3127(5) 0.0449(9) Uani . . 1.000 O O5' 0.6978(2) -0.0162(2) 0.4448(6) 0.0587(13) Uani . . 1.000 O N1 0.4392(2) 0.1239(2) 0.1166(5) 0.0357(9) Uani . . 1.000 N N3 0.4038(2) 0.2137(2) -0.1546(5) 0.0361(9) Uani . . 1.000 N N4 0.5456(3) 0.2519(2) -0.3770(6) 0.0473(12) Uani . . 1.000 N C2 0.3600(3) 0.1713(2) 0.0061(6) 0.0317(8) Uani . . 1.000 C C4 0.5166(3) 0.2106(2) -0.2169(6) 0.0357(10) Uani . . 1.000 C C5 0.5958(3) 0.1621(2) -0.0999(6) 0.0377(12) Uani . . 1.000 C C6 0.5561(3) 0.1200(2) 0.0610(6) 0.0360(10) Uani . . 1.000 C C1' 0.3942(3) 0.0638(2) 0.2623(6) 0.0370(12) Uani . . 1.000 C C2' 0.3848(3) -0.0274(2) 0.1796(6) 0.0403(12) Uani . . 1.000 C C3' 0.4747(3) -0.0792(2) 0.2913(6) 0.0363(12) Uani . . 1.000 C C4' 0.4883(3) -0.0290(2) 0.4822(6) 0.0350(12) Uani . . 1.000 C C5' 0.6065(4) -0.0360(3) 0.5778(7) 0.0483(14) Uani . . 1.000 C H1 0.35140 0.24810 -0.22950 0.0434 Uiso calc . 1.000 H H2 0.67610 0.15960 -0.13460 0.0450 Uiso calc . 1.000 H H3 0.60870 0.08660 0.13820 0.0440 Uiso calc . 1.000 H H4 0.62410 0.25070 -0.42250 0.0570 Uiso calc . 1.000 H H5 0.48850 0.28320 -0.44910 0.0570 Uiso calc . 1.000 H H6 0.31990 0.08240 0.30750 0.0450 Uiso calc . 1.000 H H9 0.54610 -0.07540 0.21990 0.0430 Uiso calc . 1.000 H H10 0.42970 -0.04540 0.57460 0.0422 Uiso calc . 1.000 H H11 0.61680 -0.09300 0.62460 0.0580 Uiso calc . 1.000 H H12 0.60990 0.00260 0.68720 0.0580 Uiso calc . 1.000 H H13 0.384(6) -0.169(4) 0.400(3) 0.10(2) Uiso . . 1.000 H H14 0.709(5) 0.0425(13) 0.460(10) 0.10(2) Uiso . . 1.000 H loop_ _atom_type_symbol _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C 0.017 0.009 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.1) ; H 0.000 0.000 ;International Tables for Crystallography (1992, Vol. C, Table 6.1.1.2) ; Cl 0.348 0.702 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.1) ; F 0.069 0.053 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.1) ; N 0.029 0.018 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.1) ; O 0.047 0.032 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.1) ; loop_ _diffrn_standard_refln_index_h _diffrn_standard_refln_index_k _diffrn_standard_refln_index_l -1 -4 1 -1 -2 1 1 -4 1 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 C1' O1' C4' 109.7(3) yes C3' O3' H13 106(4) no C5' O5' H14 104(4) no C2 N1 C1' 118.2(3) yes C6 N1 C1' 119.7(3) yes C2 N1 C6 120.7(3) yes C2 N3 C4 125.2(3) yes C2 N3 H1 117.40 no C4 N3 H1 117.36 no H4 N4 H5 119.99 no C4 N4 H5 120.06 no C4 N4 H4 119.95 no O2 C2 N3 122.4(3) yes O2 C2 N1 121.5(3) yes N1 C2 N3 116.2(3) yes N3 C4 N4 118.8(3) yes N3 C4 C5 117.3(3) yes N4 C4 C5 124.0(3) yes C4 C5 C6 119.2(3) no N1 C6 C5 121.3(3) yes O1' C1' N1 109.2(3) yes O1' C1' C2' 106.1(3) yes N1 C1' C2' 112.5(3) yes C1' C2' C3' 105.6(3) no F1 C2' F2 104.5(3) yes F1 C2' C1' 109.3(3) yes F1 C2' C3' 111.2(3) yes F2 C2' C1' 112.3(3) yes F2 C2' C3' 114.0(3) yes O3' C3' C2' 114.7(3) yes O3' C3' C4' 116.1(3) yes C2' C3' C4' 102.4(3) no O1' C4' C3' 104.8(3) yes O1' C4' C5' 107.5(3) yes C3' C4' C5' 114.7(3) no O5' C5' C4' 112.6(4) yes C4 C5 H2 120.44 no C6 C5 H2 120.34 no N1 C6 H3 119.28 no C5 C6 H3 119.38 no O1' C1' H6 109.63 no N1 C1' H6 109.70 no C2' C1' H6 109.65 no O3' C3' H9 107.64 no C2' C3' H9 107.77 no C4' C3' H9 107.82 no O1' C4' H10 109.83 no C3' C4' H10 109.93 no C5' C4' H10 109.90 no O5' C5' H11 108.76 no O5' C5' H12 108.62 no C4' C5' H11 108.71 no C4' C5' H12 108.68 no H11 C5' H12 109.45 no loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag F1 C2' . . 1.371(4) yes F2 C2' . . 1.360(5) yes O2 C2 . . 1.233(4) yes O1' C1' . . 1.409(5) yes O1' C4' . . 1.441(4) yes O3' C3' . . 1.406(4) yes O5' C5' . . 1.410(6) yes O3' H13 . . 0.94(5) no O5' H14 . . 0.93(2) no N1 C6 . . 1.393(4) yes N1 C2 . . 1.386(5) yes N1 C1' . . 1.449(5) yes N3 C4 . . 1.360(4) yes N3 C2 . . 1.361(5) yes N4 C4 . . 1.295(5) yes N3 H1 . . 0.95 no N4 H4 . . 0.95 no N4 H5 . . 0.95 no C4 C5 . . 1.419(5) no C5 C6 . . 1.343(5) no C1' C2' . . 1.531(5) no C2' C3' . . 1.509(5) no C3' C4' . . 1.509(5) no C4' C5' . . 1.503(6) no C5 H2 . . 0.95 no C6 H3 . . 0.95 no C1' H6 . . 0.95 no C3' H9 . . 0.95 no C4' H10 . . 0.95 no C5' H11 . . 0.95 no C5' H12 . . 0.95 no loop_ _geom_contact_atom_site_label_1 _geom_contact_atom_site_label_2 _geom_contact_distance _geom_contact_site_symmetry_2 _geom_contact_publ_flag Cl1 N3 3.068(3) . no Cl1 N4 3.224(4) . no Cl1 C4 3.608(4) . no Cl1 N4 3.158(4) 3_454 no Cl1 C5 3.580(4) 3_454 no Cl1 O5' 3.212(3) 3_455 no Cl1 H1 2.1691 . no Cl1 H5 2.3846 . no Cl1 H2 2.8927 3_454 no Cl1 H4 2.2896 3_454 no Cl1 H14 2.31(3) 3_455 no Cl1 H9 2.9549 4_654 no Cl1 H11 2.9447 4_655 no F1 O3' 2.692(4) . no F1 C2 3.058(5) 2_555 no F1 F2 2.986(4) 2_555 no F1 O2 2.918(4) 2_555 no F2 C6 3.016(5) . no F2 O3' 3.149(4) . no F2 N1 2.617(4) . no F2 C2 3.173(5) . no F2 F1 2.986(4) 2_554 no F1 H13 2.48(6) . no F2 H10 2.7413 1_554 no F2 H6 2.8605 2_554 no O2 F1 2.918(4) 2_554 no O2 O3' 2.829(4) 2_554 no O2 C5 3.165(4) 3_455 no O1' C4 3.408(5) 1_556 no O1' O5' 2.848(4) . no O3' O2 2.829(4) 2_555 no O3' F1 2.692(4) . no O3' C5 3.331(5) 4_645 no O3' F2 3.149(4) . no O3' N4 3.187(5) 4_644 no O3' C4 3.345(5) 4_645 no O5' C5 3.297(4) 2_655 no O5' Cl1 3.212(3) 3_555 no O5' O1' 2.848(4) . no O5' C6 3.346(4) 2_655 no O2 H6 2.3529 . no O2 H13 1.90(6) 2_554 no O2 H2 2.8098 3_455 no O1' H14 2.74(6) . no O1' H3 2.5175 . no O3' H5 2.6641 4_644 no O5' H9 2.4807 . no O5' H2 2.7163 2_655 no O5' H3 2.7950 2_655 no O5' H12 2.8094 2_654 no O5' H3 2.8005 . no N1 F2 2.617(4) . no N3 Cl1 3.068(3) . no N4 Cl1 3.224(4) . no N4 Cl1 3.158(4) 3_554 no N4 O3' 3.187(5) 4_654 no C2 F2 3.173(5) . no C2 F1 3.058(5) 2_554 no C4 O3' 3.345(5) 4_655 no C4 Cl1 3.608(4) . no C4 O1' 3.408(5) 1_554 no C5 Cl1 3.580(4) 3_554 no C5 O2 3.165(4) 3_555 no C5 O5' 3.297(4) 2_654 no C5 O3' 3.331(5) 4_655 no C6 F2 3.016(5) . no C6 O5' 3.346(4) 2_654 no C6 C3' 3.593(5) . no C3' C6 3.593(5) . no C2 H13 2.89(7) 2_554 no C4 H13 3.06(5) 4_655 no C5 H12 2.8731 1_554 no C5 H13 2.97(6) 4_655 no H1 Cl1 2.1691 . no H1 H5 2.2227 . no H2 H4 2.4703 . no H2 O5' 2.7163 2_654 no H2 Cl1 2.8927 3_554 no H2 O2 2.8098 3_555 no H3 O1' 2.5175 . no H3 O5' 2.8005 . no H3 H14 2.5403 . no H3 O5' 2.7950 2_654 no H4 H2 2.4703 . no H4 Cl1 2.2896 3_554 no H5 Cl1 2.3846 . no H5 H1 2.2227 . no H5 O3' 2.6641 4_654 no H6 O2 2.3529 . no H6 F2 2.8605 2_555 no H9 O5' 2.4807 . no H9 Cl1 2.9549 4_644 no H10 F2 2.7413 1_556 no H10 H13 2.3158 . no H11 Cl1 2.9447 4_645 no H12 C5 2.8731 1_556 no H12 O5' 2.8094 2_655 no H13 F1 2.48(6) . no H13 H10 2.3158 . no H13 O2 1.90(6) 2_555 no H13 C2 2.89(7) 2_555 no H13 C4 3.06(5) 4_645 no H13 C5 2.97(6) 4_645 no H14 O1' 2.74(6) . no H14 H3 2.5403 . no H14 Cl1 2.31(3) 3_555 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 N3 H1 Cl1 . 0.95 2.17 3.068(3) 157 yes N4 H4 Cl1 3_554 0.95 2.29 3.158(4) 151 yes N4 H5 Cl1 . 0.95 2.38 3.224(4) 147 yes O3' H13 O2 2_555 0.94(5) 1.90(6) 2.829(4) 173(5) yes O5' H14 Cl1 3_555 0.93(2) 2.31(3) 3.212(3) 165(5) yes C1' H6 O2 . 0.95 2.35 2.734(5) 103 yes C3' H9 O5' . 0.95 2.48 2.928(4) 109 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_publ_flag C4' O1' C1' N1 -136.1(3) no C4' O1' C1' C2' -14.6(4) no C1' O1' C4' C3' 30.9(3) no C1' O1' C4' C5' 153.3(3) no C6 N1 C2 O2 178.4(3) no C1' N1 C2 O2 12.1(5) no C1' N1 C2 N3 -167.3(3) no C6 N1 C2 N3 -0.9(5) no C2 N1 C1' O1' -147.2(3) no C2 N1 C6 C5 0.3(5) no C1' N1 C6 C5 166.5(3) no C6 N1 C1' C2' -71.2(4) no C2 N1 C1' C2' 95.3(4) no C6 N1 C1' O1' 46.3(4) no C2 N3 C4 N4 177.6(3) no C4 N3 C2 O2 -177.1(3) no C2 N3 C4 C5 -2.8(5) no C4 N3 C2 N1 2.3(5) no N3 C4 C5 C6 1.9(5) no N4 C4 C5 C6 -178.4(4) no C4 C5 C6 N1 -0.8(5) no O1' C1' C2' F1 112.5(3) no O1' C1' C2' F2 -132.0(3) no N1 C1' C2' C3' 112.1(3) no O1' C1' C2' C3' -7.2(4) no N1 C1' C2' F1 -128.2(3) no N1 C1' C2' F2 -12.7(4) no F2 C2' C3' O3' -85.0(4) no F2 C2' C3' C4' 148.4(3) no C1' C2' C3' O3' 151.3(3) no F1 C2' C3' C4' -93.7(3) no F1 C2' C3' O3' 32.9(5) no C1' C2' C3' C4' 24.7(4) no O3' C3' C4' O1' -159.2(3) no O3' C3' C4' C5' 83.1(4) no C2' C3' C4' C5' -151.1(3) no C2' C3' C4' O1' -33.5(3) no C3' C4' C5' O5' 52.9(5) no O1' C4' C5' O5' -63.2(4) no loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 ChemSpider 54752 2 PubChem 135501939