#------------------------------------------------------------------------------
#$Date: 2017-10-13 03:08:28 +0300 (Fri, 13 Oct 2017) $
#$Revision: 201955 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/00/82/2008239.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_2008239
loop_
_publ_author_name
'Audette, Gerald F.'
'Zoghaib, Wajdi M.'
'Gupta, Sagar V.'
'Quail, J. Wilson'
'Delbaere, Louis T. J.'
_publ_section_title
;
 N,N-Dimethyl-5-methoxymethyl-2'-deoxycytidine
;
_journal_issue                   3
_journal_name_full               'Acta Crystallographica Section C'
_journal_page_first              427
_journal_page_last               430
_journal_paper_doi               10.1107/S0108270198013249
_journal_volume                  55
_journal_year                    1999
_chemical_formula_sum            'C13 H21 N3 O5'
_chemical_formula_weight         299.33
_chemical_name_systematic
;
1-(4-hydroxy-5-hydroxymethyltetrahydrofuran-2-yl)-5-methoxymethyl-
4-dimethylamino-(1H)-pyrimidin-2-one
;
_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                90.00
_cell_angle_beta                 90.00
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   4.906(3)
_cell_length_b                   14.838(5)
_cell_length_c                   19.488(3)
_cell_measurement_reflns_used    25
_cell_measurement_temperature    123(2)
_cell_measurement_theta_max      26.26
_cell_measurement_theta_min      8.30
_cell_volume                     1418.6(10)
_computing_cell_refinement       'SET4 in CAD-4 EXPRESS'
_computing_data_collection       'CAD-4 EXPRESS (Enraf-Nonius, 1992)'
_computing_data_reduction        'Xtal 3.4 (Hall et al., 1995)'
_computing_molecular_graphics    'ORTEPII (Johnson, 1976)'
_computing_structure_refinement  'SHELXL97 (Sheldrick, 1997)'
_computing_structure_solution    'Xtal 3.4'
_diffrn_ambient_temperature      123(2)
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device_type  'Nonius CAD-4'
_diffrn_measurement_method       'ω scan b/P/b'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_source         'fine-focus sealed tube'
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.70930
_diffrn_reflns_av_R_equivalents  0.000
_diffrn_reflns_av_sigmaI/netI    0.035
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -1
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -2
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            1702
_diffrn_reflns_theta_full        26.26
_diffrn_reflns_theta_max         26.26
_diffrn_reflns_theta_min         2.50
_diffrn_standards_decay_%        none
_diffrn_standards_interval_time  '240 min'
_diffrn_standards_number         3
_exptl_absorpt_coefficient_mu    0.108
_exptl_absorpt_correction_T_max  0.984
_exptl_absorpt_correction_T_min  0.878
_exptl_absorpt_correction_type   \y-scan
_exptl_absorpt_process_details   '(North et al., 1968)'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.401
_exptl_crystal_density_meas      ?
_exptl_crystal_description       rod-like
_exptl_crystal_F_000             640
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.20
_exptl_crystal_size_min          0.15
_refine_diff_density_max         0.188
_refine_diff_density_min         -0.189
_refine_ls_abs_structure_details 'Flack (1983)'
_refine_ls_abs_structure_Flack   -1.1(17)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.065
_refine_ls_hydrogen_treatment    'H atoms: see below'
_refine_ls_matrix_type           full
_refine_ls_number_parameters     195
_refine_ls_number_reflns         1702
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.065
_refine_ls_R_factor_all          0.046
_refine_ls_R_factor_gt           0.037
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w = 1/[σ²(Fo²)+(0.0498P)²+0.1106P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_ref         0.090
_reflns_number_gt                1447
_reflns_number_total             1702
_reflns_threshold_expression     I>2σ(I)
_cod_data_source_file            da1046.cif
_cod_data_source_block           nndm
_cod_depositor_comments
;
The following automatic conversions were performed:
'_symmetry_cell_setting' value 'Orthorhombic' changed to 'orthorhombic'
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_enum 1527 2010-12-29 10:47:43Z saulius 

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_database_code               2008239
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x+1/2, -y, z+1/2'
'-x, y+1/2, -z+1/2'
'x+1/2, -y+1/2, -z'
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 0.6289(4) 0.47274(13) 0.79232(9) 0.0133(5) Uani d . 1 . . N
C2 0.4454(5) 0.40153(15) 0.78546(11) 0.0132(5) Uani d . 1 . . C
O2 0.4453(4) 0.35869(10) 0.73069(8) 0.0164(4) Uani d . 1 . . O
N3 0.2817(5) 0.38125(13) 0.83915(10) 0.0152(5) Uani d . 1 . . N
C4 0.2759(6) 0.43372(16) 0.89572(12) 0.0156(5) Uani d . 1 . . C
N4 0.1113(5) 0.40614(14) 0.94646(10) 0.0201(5) Uani d . 1 . . N
C41 0.1385(7) 0.43465(19) 1.01777(12) 0.0277(7) Uani d . 1 . . C
H41A 0.0050 0.4801 1.0277 0.042 Uiso calc R 1 . . H
H41B 0.3178 0.4588 1.0251 0.042 Uiso calc R 1 . . H
H41C 0.1107 0.3838 1.0475 0.042 Uiso calc R 1 . . H
C42 -0.0888(6) 0.33463(17) 0.93607(13) 0.0229(6) Uani d . 1 . . C
H42A -0.0091 0.2776 0.9479 0.034 Uiso calc R 1 . . H
H42B -0.1440 0.3337 0.8888 0.034 Uiso calc R 1 . . H
H42C -0.2448 0.3455 0.9646 0.034 Uiso calc R 1 . . H
C5 0.4352(6) 0.51518(15) 0.89906(12) 0.0166(6) Uani d . 1 . . C
C51 0.4032(7) 0.59130(16) 0.95016(12) 0.0209(6) Uani d . 1 . . C
H51A 0.4363 0.6484 0.9273 0.025 Uiso calc R 1 . . H
H51B 0.2179 0.5918 0.9675 0.025 Uiso calc R 1 . . H
O52 0.5884(5) 0.58149(11) 1.00594(8) 0.0257(5) Uani d . 1 . . O
C53 0.5433(9) 0.65000(18) 1.05599(14) 0.0377(9) Uani d . 1 . . C
H53A 0.5478 0.7080 1.0342 0.057 Uiso calc R 1 . . H
H53B 0.6832 0.6470 1.0904 0.057 Uiso calc R 1 . . H
H53C 0.3685 0.6411 1.0771 0.057 Uiso calc R 1 . . H
C6 0.6101(6) 0.52928(15) 0.84664(11) 0.0149(5) Uani d . 1 . . C
H6 0.7220 0.5798 0.8479 0.018 Uiso calc R 1 . . H
C1' 0.8207(5) 0.48986(16) 0.73401(11) 0.0135(5) Uani d . 1 . . C
H1' 0.9021 0.4330 0.7187 0.016 Uiso calc R 1 . . H
C2' 0.6805(6) 0.53625(15) 0.67419(11) 0.0144(5) Uani d . 1 . . C
H2'1 0.4891 0.5202 0.6718 0.017 Uiso calc R 1 . . H
H2'2 0.7677 0.5215 0.6310 0.017 Uiso calc R 1 . . H
C3' 0.7180(6) 0.63544(15) 0.69218(11) 0.0132(5) Uani d . 1 . . C
H3' 0.5862 0.6528 0.7276 0.016 Uiso calc R 1 . . H
O3' 0.6857(4) 0.69126(11) 0.63390(8) 0.0199(4) Uani d . 1 . . O
H3'1 0.6982 0.7443 0.6454 0.030 Uiso calc R 1 . . H
C4' 1.0037(5) 0.63561(15) 0.72227(12) 0.0131(5) Uani d . 1 . . C
H4' 1.1356 0.6372 0.6845 0.016 Uiso calc R 1 . . H
O4' 1.0270(4) 0.54919(10) 0.75711(8) 0.0137(4) Uani d . 1 . . O
C5' 1.0693(6) 0.71161(15) 0.77180(12) 0.0166(5) Uani d . 1 . . C
H5'1 1.2412 0.6987 0.7943 0.020 Uiso calc R 1 . . H
H5'2 1.0913 0.7671 0.7460 0.020 Uiso calc R 1 . . H
O5' 0.8647(4) 0.72446(10) 0.82263(8) 0.0177(4) Uani d . 1 . . O
H5' 0.7554 0.7624 0.8093 0.026 Uiso calc R 1 . . H
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'
O O 0.0106 0.0060 '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'
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
C6 N1 C2 120.0(2) ?
C6 N1 C1' 122.1(2) ?
C2 N1 C1' 117.49(19) ?
O2 C2 N3 123.4(2) yes
O2 C2 N1 118.1(2) ?
N3 C2 N1 118.5(2) ?
C4 N3 C2 121.0(2) ?
N4 C4 N3 116.0(2) ?
N4 C4 C5 123.3(2) ?
N3 C4 C5 120.6(2) ?
C4 N4 C41 124.0(2) yes
C4 N4 C42 121.6(2) yes
C41 N4 C42 113.9(2) yes
N4 C41 H41A 109.5 ?
N4 C41 H41B 109.5 ?
H41A C41 H41B 109.5 ?
N4 C41 H41C 109.5 ?
H41A C41 H41C 109.5 ?
H41B C41 H41C 109.5 ?
N4 C42 H42A 109.5 ?
N4 C42 H42B 109.5 ?
H42A C42 H42B 109.5 ?
N4 C42 H42C 109.5 ?
H42A C42 H42C 109.5 ?
H42B C42 H42C 109.5 ?
C6 C5 C4 116.1(2) ?
C6 C5 C51 116.6(2) ?
C4 C5 C51 126.8(2) yes
O52 C51 C5 111.1(2) yes
O52 C51 H51A 109.4 ?
C5 C51 H51A 109.4 ?
O52 C51 H51B 109.4 ?
C5 C51 H51B 109.4 ?
H51A C51 H51B 108.0 ?
C51 O52 C53 110.5(2) yes
O52 C53 H53A 109.5 ?
O52 C53 H53B 109.5 ?
H53A C53 H53B 109.5 ?
O52 C53 H53C 109.5 ?
H53A C53 H53C 109.5 ?
H53B C53 H53C 109.5 ?
C5 C6 N1 122.6(2) ?
C5 C6 H6 118.7 ?
N1 C6 H6 118.7 ?
O4' C1' N1 108.29(17) ?
O4' C1' C2' 106.62(19) ?
N1 C1' C2' 112.02(19) ?
O4' C1' H1' 109.9 ?
N1 C1' H1' 109.9 ?
C2' C1' H1' 109.9 ?
C1' C2' C3' 101.92(18) ?
C1' C2' H2'1 111.4 ?
C3' C2' H2'1 111.4 ?
C1' C2' H2'2 111.4 ?
C3' C2' H2'2 111.4 ?
H2'1 C2' H2'2 109.3 ?
O3' C3' C4' 114.4(2) ?
O3' C3' C2' 111.55(17) ?
C4' C3' C2' 101.6(2) ?
O3' C3' H3' 109.7 ?
C4' C3' H3' 109.7 ?
C2' C3' H3' 109.7 ?
C3' O3' H3'1 109.5 ?
O4' C4' C5' 109.94(17) ?
O4' C4' C3' 104.54(19) ?
C5' C4' C3' 116.2(2) ?
O4' C4' H4' 108.6 ?
C5' C4' H4' 108.6 ?
C3' C4' H4' 108.6 ?
C1' O4' C4' 110.10(17) ?
O5' C5' C4' 113.1(2) ?
O5' C5' H5'1 109.0 ?
C4' C5' H5'1 109.0 ?
O5' C5' H5'2 109.0 ?
C4' C5' H5'2 109.0 ?
H5'1 C5' H5'2 107.8 ?
C5' O5' H5' 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
N1 C6 . 1.354(3) ?
N1 C2 . 1.394(3) ?
N1 C1' . 1.497(3) ?
C2 O2 . 1.242(3) yes
C2 N3 . 1.353(3) ?
N3 C4 . 1.350(3) ?
C4 N4 . 1.341(3) yes
C4 C5 . 1.441(4) ?
N4 C41 . 1.459(3) yes
N4 C42 . 1.460(4) yes
C41 H41A . 0.9600 ?
C41 H41B . 0.9600 ?
C41 H41C . 0.9600 ?
C42 H42A . 0.9600 ?
C42 H42B . 0.9600 ?
C42 H42C . 0.9600 ?
C5 C6 . 1.350(3) ?
C5 C51 . 1.514(3) yes
C51 O52 . 1.424(3) yes
C51 H51A . 0.9700 ?
C51 H51B . 0.9700 ?
O52 C53 . 1.426(3) yes
C53 H53A . 0.9600 ?
C53 H53B . 0.9600 ?
C53 H53C . 0.9600 ?
C6 H6 . 0.9300 ?
C1' O4' . 1.415(3) ?
C1' C2' . 1.519(3) ?
C1' H1' . 0.9800 ?
C2' C3' . 1.524(3) ?
C2' H2'1 . 0.9700 ?
C2' H2'2 . 0.9700 ?
C3' O3' . 1.415(3) ?
C3' C4' . 1.519(4) ?
C3' H3' . 0.9800 ?
O3' H3'1 . 0.8200 ?
C4' O4' . 1.455(3) ?
C4' C5' . 1.519(3) ?
C4' H4' . 0.9800 ?
C5' O5' . 1.423(3) ?
C5' H5'1 . 0.9700 ?
C5' H5'2 . 0.9700 ?
O5' H5' . 0.8200 ?
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
O3' H3'1 N3 3_656 0.82 2.06 2.872(3) 172.3 yes
O5' H5' O2 3_656 0.82 1.90 2.713(2) 169.8 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
C6 N1 C2 O2 170.5(2) ?
C1' N1 C2 O2 -2.5(3) ?
C6 N1 C2 N3 -11.1(3) ?
C1' N1 C2 N3 176.0(2) ?
O2 C2 N3 C4 -175.3(2) ?
N1 C2 N3 C4 6.3(3) ?
C2 N3 C4 N4 -178.4(2) ?
C2 N3 C4 C5 2.9(4) ?
N3 C4 N4 C41 159.5(2) yes
C5 C4 N4 C41 -21.8(4) ?
N3 C4 N4 C42 -11.8(4) yes
C5 C4 N4 C42 166.8(2) ?
N4 C4 C5 C6 174.0(2) ?
N3 C4 C5 C6 -7.4(4) ?
N4 C4 C5 C51 -13.9(4) ?
N3 C4 C5 C51 164.7(2) ?
C6 C5 C51 O52 -91.9(3) yes
C4 C5 C51 O52 96.1(3) ?
C5 C51 O52 C53 -176.0(2) ?
C4 C5 C6 N1 2.7(4) ?
C51 C5 C6 N1 -170.3(2) ?
C2 N1 C6 C5 6.5(4) ?
C1' N1 C6 C5 179.1(2) ?
C6 N1 C1' O4' 20.8(3) ?
C2 N1 C1' O4' -166.46(19) yes
C6 N1 C1' C2' -96.5(3) ?
C2 N1 C1' C2' 76.2(3) ?
O4' C1' C2' C3' -29.1(2) yes
N1 C1' C2' C3' 89.2(2) ?
C1' C2' C3' O3' 160.3(2) ?
C1' C2' C3' C4' 38.0(2) yes
O3' C3' C4' O4' -154.46(18) ?
C2' C3' C4' O4' -34.1(2) yes
O3' C3' C4' C5' 84.2(2) ?
C2' C3' C4' C5' -155.5(2) ?
N1 C1' O4' C4' -112.9(2) ?
C2' C1' O4' C4' 7.9(2) yes
C5' C4' O4' C1' 142.3(2) ?
C3' C4' O4' C1' 16.9(2) yes
O4' C4' C5' O5' -70.7(3) ?
C3' C4' C5' O5' 47.7(3) yes
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 ChemSpider 21105674
