#------------------------------------------------------------------------------
#$Date: 2016-03-26 22:20:56 +0200 (Sat, 26 Mar 2016) $
#$Revision: 180501 $
#$URL: svn://www.crystallography.net/cod/cif/7/21/70/7217012.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_7217012
loop_
_publ_author_name
'Yu, Hongchuan'
'Schlegel, Mark K.'
'McLaughlin, Larry W.'
_publ_section_title
;
 The synthesis and structural characterization of both diastereomers of
 5’-(hydroxymethyl)-6,5’-cyclo-2’,5’-dideoxyuridine
 cyclonucleosides
;
_journal_name_full               'RSC Advances'
_journal_paper_doi               10.1039/c4ra04784b
_journal_year                    2014
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C10 H12 N2 O5'
_chemical_formula_sum            'C10 H12 N2 O5'
_chemical_formula_weight         240.22
_chemical_name_systematic
; 
 ? 
;
_space_group_IT_number           4
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-97
_cell_angle_alpha                90.00
_cell_angle_beta                 102.701(5)
_cell_angle_gamma                90.00
_cell_formula_units_Z            2
_cell_length_a                   7.8546(6)
_cell_length_b                   5.0786(4)
_cell_length_c                   12.4411(9)
_cell_measurement_reflns_used    3587
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      66.17
_cell_measurement_theta_min      3.64
_cell_volume                     484.14(6)
_computing_cell_refinement       'SAINT (Bruker, 2010)'
_computing_data_collection       'APEX2 (Bruker, 2010)'
_computing_data_reduction        'SAINT (Bruker, 2010)'
_computing_molecular_graphics    'Bruker SHELXTL'
_computing_publication_material  'Bruker SHELXTL'
_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 2008)'
_diffrn_ambient_temperature      100(2)
_diffrn_measured_fraction_theta_full 0.978
_diffrn_measured_fraction_theta_max 0.978
_diffrn_measurement_device_type  'Bruker Kappa DUO CCD diffractometer'
_diffrn_measurement_method       'φ and ω scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0311
_diffrn_reflns_av_sigmaI/netI    0.0324
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       5
_diffrn_reflns_limit_k_min       -5
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            4042
_diffrn_reflns_theta_full        66.17
_diffrn_reflns_theta_max         66.17
_diffrn_reflns_theta_min         3.64
_diffrn_source                   'microfocus sealed tube'
_diffrn_source_type              'Incoatec I\uS'
_exptl_absorpt_coefficient_mu    1.145
_exptl_absorpt_correction_T_max  0.9344
_exptl_absorpt_correction_T_min  0.8469
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
Sheldrick, G.M. (2008). SADABS v2008/1. Bruker AXS Inc. Madison, WI USA.
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.648
_exptl_crystal_density_meas      ?
_exptl_crystal_density_method    none
_exptl_crystal_description       block
_exptl_crystal_F_000             252
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.152
_refine_diff_density_min         -0.218
_refine_diff_density_rms         0.044
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0.1(2)
_refine_ls_extinction_coef       na
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.063
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     175
_refine_ls_number_reflns         1588
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.063
_refine_ls_R_factor_all          0.0297
_refine_ls_R_factor_gt           0.0288
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[σ²(Fo²)+(0.0515P)²+0.0553P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0755
_refine_ls_wR_factor_ref         0.0763
_reflns_number_gt                1544
_reflns_number_total             1588
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            c4ra04784b2.cif
_cod_data_source_block           C10H12N2O5
_cod_depositor_comments
;
The following automatic conversions were performed:

'_symmetry_cell_setting' value 'Monoclinic' changed to 'monoclinic'
according to
/usr/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 from 2011-04-26.

Automatic conversion script
Id: cif_fix_values 2281 2013-09-26 08:29:07Z andrius 

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_H-M      P2(1)
_cod_database_code               7217012
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, 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_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
O1 O 0.38147(16) 0.6865(3) 0.48718(10) 0.0219(3) Uani 1 1 d .
O2 O -0.01175(16) 0.0238(3) 0.39123(10) 0.0216(3) Uani 1 1 d .
O3 O 0.45671(15) 0.7287(3) 0.18133(10) 0.0159(3) Uani 1 1 d .
O4 O 0.18897(15) 0.4317(3) -0.05922(9) 0.0186(3) Uani 1 1 d .
H4O H 0.194(3) 0.289(6) -0.087(2) 0.028 Uiso 1 1 d .
O5 O 0.80225(15) 0.4305(3) 0.15229(10) 0.0185(3) Uani 1 1 d .
H5O H 0.824(3) 0.302(6) 0.1238(19) 0.028 Uiso 1 1 d .
N1 N 0.18010(18) 0.3628(3) 0.43539(12) 0.0172(4) Uani 1 1 d .
H1N H 0.137(3) 0.392(6) 0.4885(18) 0.021 Uiso 1 1 d .
N2 N 0.36052(18) 0.4927(3) 0.31921(11) 0.0152(3) Uani 1 1 d .
C1 C 0.3130(2) 0.5245(4) 0.41933(14) 0.0164(4) Uani 1 1 d .
C2 C 0.1047(2) 0.1591(4) 0.36795(14) 0.0163(4) Uani 1 1 d .
C3 C 0.1691(2) 0.1313(4) 0.26875(15) 0.0167(4) Uani 1 1 d .
H3 H 0.1276 -0.0088 0.2193 0.020 Uiso 1 1 calc R
C4 C 0.2869(2) 0.3009(4) 0.24505(14) 0.0147(4) Uani 1 1 d .
C5 C 0.3295(2) 0.3073(4) 0.13188(14) 0.0148(4) Uani 1 1 d .
H5 H 0.348(3) 0.129(5) 0.1118(17) 0.018 Uiso 1 1 d .
C6 C 0.4863(2) 0.4818(4) 0.13048(14) 0.0155(4) Uani 1 1 d .
H6 H 0.495(3) 0.519(5) 0.0566(17) 0.019 Uiso 1 1 d .
C7 C 0.6578(2) 0.3734(4) 0.20169(15) 0.0158(4) Uani 1 1 d .
H7 H 0.647(3) 0.186(6) 0.2132(17) 0.019 Uiso 1 1 d .
C8 C 0.6753(2) 0.5270(4) 0.30996(14) 0.0174(4) Uani 1 1 d .
H8A H 0.6951 0.4064 0.3741 0.021 Uiso 1 1 calc R
H8B H 0.7724 0.6552 0.3198 0.021 Uiso 1 1 calc R
C9 C 0.5002(2) 0.6664(4) 0.29548(14) 0.0163(4) Uani 1 1 d .
H9 H 0.498(3) 0.827(5) 0.3360(17) 0.020 Uiso 1 1 d .
C10 C 0.1663(2) 0.4120(4) 0.05043(14) 0.0171(4) Uani 1 1 d .
H10A H 0.0669 0.2931 0.0517 0.020 Uiso 1 1 calc R
H10B H 0.1367 0.5879 0.0753 0.020 Uiso 1 1 calc R
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'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
C9 O3 C6 102.56(14)
C10 O4 H4O 112.5(18)
C7 O5 H5O 107.3(19)
C1 N1 C2 126.60(15)
C1 N1 H1N 118.0(18)
C2 N1 H1N 115.3(18)
C4 N2 C1 121.81(15)
C4 N2 C9 120.38(14)
C1 N2 C9 117.76(14)
O1 C1 N1 122.46(16)
O1 C1 N2 122.46(16)
N1 C1 N2 115.07(16)
O2 C2 N1 121.19(16)
O2 C2 C3 124.56(17)
N1 C2 C3 114.19(16)
C4 C3 C2 120.93(17)
C4 C3 H3 119.5
C2 C3 H3 119.5
C3 C4 N2 120.94(16)
C3 C4 C5 121.38(16)
N2 C4 C5 117.38(15)
C4 C5 C6 111.58(14)
C4 C5 C10 107.19(13)
C6 C5 C10 110.48(15)
C4 C5 H5 107.3(13)
C6 C5 H5 112.3(12)
C10 C5 H5 107.8(12)
O3 C6 C5 106.98(13)
O3 C6 C7 105.20(14)
C5 C6 C7 113.14(16)
O3 C6 H6 107.5(15)
C5 C6 H6 110.7(13)
C7 C6 H6 112.8(12)
O5 C7 C8 110.27(14)
O5 C7 C6 110.81(14)
C8 C7 C6 102.78(14)
O5 C7 H7 111.4(13)
C8 C7 H7 111.3(13)
C6 C7 H7 110.0(12)
C9 C8 C7 103.18(13)
C9 C8 H8A 111.1
C7 C8 H8A 111.1
C9 C8 H8B 111.1
C7 C8 H8B 111.1
H8A C8 H8B 109.1
O3 C9 N2 107.76(13)
O3 C9 C8 103.53(13)
N2 C9 C8 112.80(16)
O3 C9 H9 107.8(13)
N2 C9 H9 107.6(13)
C8 C9 H9 116.8(12)
O4 C10 C5 113.23(13)
O4 C10 H10A 108.9
C5 C10 H10A 108.9
O4 C10 H10B 108.9
C5 C10 H10B 108.9
H10A C10 H10B 107.7
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
O1 C1 1.217(2)
O2 C2 1.229(2)
O3 C9 1.421(2)
O3 C6 1.446(2)
O4 C10 1.4175(19)
O4 H4O 0.81(3)
O5 C7 1.434(2)
O5 H5O 0.78(3)
N1 C1 1.376(2)
N1 C2 1.381(2)
N1 H1N 0.82(2)
N2 C4 1.379(2)
N2 C1 1.386(2)
N2 C9 1.487(2)
C2 C3 1.440(2)
C3 C4 1.343(3)
C3 H3 0.9500
C4 C5 1.518(2)
C5 C6 1.520(3)
C5 C10 1.543(2)
C5 H5 0.96(3)
C6 C7 1.542(2)
C6 H6 0.95(2)
C7 C8 1.536(2)
C7 H7 0.97(3)
C8 C9 1.522(2)
C8 H8A 0.9900
C8 H8B 0.9900
C9 H9 0.96(3)
C10 H10A 0.9900
C10 H10B 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
O4 H4O O5 0.81(3) 1.99(3) 2.803(2) 177(3) 2_645
O5 H5O O4 0.78(3) 2.04(3) 2.793(2) 163(3) 2_645
N1 H1N O2 0.82(2) 2.07(3) 2.885(2) 170(3) 2_556
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
C2 N1 C1 O1 -174.10(17)
C2 N1 C1 N2 7.2(2)
C4 N2 C1 O1 177.25(16)
C9 N2 C1 O1 -0.3(2)
C4 N2 C1 N1 -4.0(2)
C9 N2 C1 N1 178.43(15)
C1 N1 C2 O2 178.76(16)
C1 N1 C2 C3 -3.9(2)
O2 C2 C3 C4 174.53(17)
N1 C2 C3 C4 -2.7(2)
C2 C3 C4 N2 5.5(3)
C2 C3 C4 C5 -168.00(16)
C1 N2 C4 C3 -2.0(3)
C9 N2 C4 C3 175.50(16)
C1 N2 C4 C5 171.76(14)
C9 N2 C4 C5 -10.8(2)
C3 C4 C5 C6 -170.66(17)
N2 C4 C5 C6 15.6(2)
C3 C4 C5 C10 68.3(2)
N2 C4 C5 C10 -105.45(17)
C9 O3 C6 C5 78.40(15)
C9 O3 C6 C7 -42.17(16)
C4 C5 C6 O3 -48.95(17)
C10 C5 C6 O3 70.19(18)
C4 C5 C6 C7 66.42(19)
C10 C5 C6 C7 -174.44(14)
O3 C6 C7 O5 -98.75(17)
C5 C6 C7 O5 144.81(15)
O3 C6 C7 C8 19.03(18)
C5 C6 C7 C8 -97.40(17)
O5 C7 C8 C9 127.49(16)
C6 C7 C8 C9 9.33(18)
C6 O3 C9 N2 -71.34(16)
C6 O3 C9 C8 48.37(17)
C4 N2 C9 O3 39.0(2)
C1 N2 C9 O3 -143.44(15)
C4 N2 C9 C8 -74.68(19)
C1 N2 C9 C8 102.91(17)
C7 C8 C9 O3 -35.37(18)
C7 C8 C9 N2 80.83(17)
C4 C5 C10 O4 179.19(15)
C6 C5 C10 O4 57.4(2)
