#------------------------------------------------------------------------------
#$Date: 2025-08-22 00:24:23 +0200 (Fri, 22 Aug 2025) $
#$Revision: 301857 $
#$URL: svn://saulius.grazulis.lt/cod-secondary/cif/7/11/27/7112731.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_7112731
loop_
_publ_author_name
'Lou, Chenguang'
'Xiao, Qiang'
'Tailor, Radha R.'
'Ben Gaied, Nouha'
'Gale, Nittaya'
'Light, Mark E.'
'Fox, Keith R.'
'Brown, Tom'
_publ_section_title
;
 2′-Substituted 2-amino-3-methylpyridine ribonucleosides in
 triplex-forming oligonucleotides: triplex stability is determined by
 chemical environment
;
_journal_issue                   6
_journal_name_full               MedChemComm
_journal_page_first              550
_journal_paper_doi               10.1039/c1md00068c
_journal_volume                  2
_journal_year                    2011
_chemical_absolute_configuration syn
_chemical_formula_sum            'C12 H18 N2 O4'
_chemical_formula_weight         254.28
_space_group_IT_number           146
_symmetry_cell_setting           hexagonal
_symmetry_space_group_name_Hall  'R 3'
_symmetry_space_group_name_H-M   'R 3 :H'
_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                 90.00
_cell_angle_gamma                120.00
_cell_formula_units_Z            9
_cell_length_a                   25.4843(4)
_cell_length_b                   25.4843(4)
_cell_length_c                   4.97850(10)
_cell_measurement_reflns_used    19504
_cell_measurement_temperature    120(2)
_cell_measurement_theta_max      27.48
_cell_measurement_theta_min      2.91
_cell_volume                     2800.11(8)
_computing_cell_refinement
'DENZO (Otwinowski & Minor, 1997) & COLLECT (Hooft, R.W.W., 1998)'
_computing_data_collection       'COLLECT (Hooft, R.W.W., 1998)'
_computing_data_reduction
'DENZO (Otwinowski & Minor, 1997) & COLLECT (Hooft, R.W.W., 1998)'
_computing_molecular_graphics    'CAMERON (Watkin, et al., 1993)'
_computing_publication_material  'WINGX (Farrugia, 1998)'
_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1997)'
_diffrn_ambient_temperature      120(2)
_diffrn_detector_area_resol_mean 9.091
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type  'Bruker-Nonius CCD camera on κ-goniostat'
_diffrn_measurement_method       'φ & ω scans to fill the asymmetric unit'
_diffrn_radiation_monochromator  '10cm confocal mirrors'
_diffrn_radiation_source         'Bruker Nonius FR591 Rotating Anode'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0461
_diffrn_reflns_av_sigmaI/netI    0.0266
_diffrn_reflns_limit_h_max       33
_diffrn_reflns_limit_h_min       -32
_diffrn_reflns_limit_k_max       33
_diffrn_reflns_limit_k_min       -32
_diffrn_reflns_limit_l_max       6
_diffrn_reflns_limit_l_min       -6
_diffrn_reflns_number            12291
_diffrn_reflns_theta_full        27.44
_diffrn_reflns_theta_max         27.44
_diffrn_reflns_theta_min         3.20
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.102
_exptl_absorpt_correction_T_max  0.9959
_exptl_absorpt_correction_T_min  0.9599
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS V2.10 (Sheldrick, G.M., 2003)
;
_exptl_crystal_colour            Colourless
_exptl_crystal_density_diffrn    1.357
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       Rod
_exptl_crystal_F_000             1224
_exptl_crystal_size_max          0.3
_exptl_crystal_size_mid          0.07
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.189
_refine_diff_density_min         -0.166
_refine_diff_density_rms         0.040
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.014
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     167
_refine_ls_number_reflns         1428
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.013
_refine_ls_R_factor_all          0.0383
_refine_ls_R_factor_gt           0.0342
_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)+(0.0254P)²+3.9360P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0720
_refine_ls_wR_factor_ref         0.0747
_reflns_number_gt                1333
_reflns_number_total             1428
_reflns_threshold_expression     >2σ(I)
_cod_data_source_file            c1md00068c.txt
_cod_data_source_block           2009sot0799
_cod_depositor_comments
;
The following automatic conversions were performed:

'_symmetry_cell_setting' value 'Hexagonal' changed to 'hexagonal'
according to
/usr/data/users/saulius/automatic-downloads/retrospective/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 
;
_cod_original_sg_symbol_H-M      R3
_cod_database_code               7112731
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-y, x-y, z'
'-x+y, -x, z'
'x+2/3, y+1/3, z+1/3'
'-y+2/3, x-y+1/3, z+1/3'
'-x+y+2/3, -x+1/3, z+1/3'
'x+1/3, y+2/3, z+2/3'
'-y+1/3, x-y+2/3, z+2/3'
'-x+y+1/3, -x+2/3, z+2/3'
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
C1 C 0.63588(12) 0.40237(11) 0.5455(5) 0.0259(5) Uani 1 1 d .
H1A H 0.6611 0.4089 0.6994 0.039 Uiso 1 1 calc R
H1B H 0.6134 0.3599 0.5050 0.039 Uiso 1 1 calc R
H1C H 0.6083 0.4167 0.5832 0.039 Uiso 1 1 calc R
C2 C 0.70636(10) 0.49776(10) 0.3638(5) 0.0163(4) Uani 1 1 d .
H2 H 0.7222 0.5061 0.5477 0.020 Uiso 1 1 calc R
C3 C 0.67268(10) 0.53247(10) 0.3060(4) 0.0177(5) Uani 1 1 d .
H3 H 0.6463 0.5296 0.4551 0.021 Uiso 1 1 calc R
C4 C 0.72556(10) 0.59667(10) 0.2694(4) 0.0169(4) Uani 1 1 d .
H4 H 0.7152 0.6180 0.1345 0.020 Uiso 1 1 calc R
C5 C 0.74659(11) 0.63393(11) 0.5259(5) 0.0220(5) Uani 1 1 d .
H5A H 0.7532 0.6109 0.6638 0.026 Uiso 1 1 calc R
H5B H 0.7848 0.6706 0.4929 0.026 Uiso 1 1 calc R
C6 C 0.75857(10) 0.52704(10) 0.1646(4) 0.0163(4) Uani 1 1 d .
H6 H 0.7432 0.5113 -0.0155 0.020 Uiso 1 1 calc R
C7 C 0.81206(10) 0.51943(10) 0.2211(4) 0.0173(4) Uani 1 1 d .
C8 C 0.85520(11) 0.55274(10) 0.4179(5) 0.0200(5) Uani 1 1 d .
H8 H 0.8510 0.5810 0.5201 0.024 Uiso 1 1 calc R
C9 C 0.90402(11) 0.54435(11) 0.4628(5) 0.0211(5) Uani 1 1 d .
C10 C 0.90758(11) 0.50007(11) 0.3046(5) 0.0220(5) Uani 1 1 d .
C11 C 0.81966(11) 0.47668(11) 0.0817(5) 0.0200(5) Uani 1 1 d .
H11 H 0.7910 0.4538 -0.0480 0.024 Uiso 1 1 calc R
C12 C 0.95202(12) 0.58042(12) 0.6679(5) 0.0287(6) Uani 1 1 d .
H12A H 0.9895 0.6068 0.5783 0.043 Uiso 1 1 calc R
H12B H 0.9573 0.5533 0.7840 0.043 Uiso 1 1 calc R
H12C H 0.9399 0.6042 0.7723 0.043 Uiso 1 1 calc R
N1 N 0.86564(9) 0.46621(9) 0.1216(4) 0.0230(4) Uani 1 1 d .
N2 N 0.95437(10) 0.48878(12) 0.3348(5) 0.0337(5) Uani 1 1 d .
H91 H 0.9556 0.4613 0.2392 0.040 Uiso 1 1 calc R
H92 H 0.9826 0.5092 0.4495 0.040 Uiso 1 1 calc R
O1 O 0.67295(8) 0.43460(7) 0.3201(3) 0.0209(3) Uani 1 1 d .
O2 O 0.64084(8) 0.51396(7) 0.0577(3) 0.0221(4) Uani 1 1 d .
H2A H 0.6138 0.4785 0.0686 0.033 Uiso 1 1 calc R
O3 O 0.70357(9) 0.64946(8) 0.6184(4) 0.0277(4) Uani 1 1 d .
H3A H 0.7041 0.6756 0.5204 0.042 Uiso 1 1 calc R
O4 O 0.77620(7) 0.59010(7) 0.1733(3) 0.0191(3) Uani 1 1 d .
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 0.0000 '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 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0106 0.0000 '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
O1 C2 C6 109.86(18)
O1 C2 C3 115.81(19)
C6 C2 C3 101.47(17)
O2 C3 C4 107.67(18)
O2 C3 C2 111.20(18)
C4 C3 C2 101.06(18)
O4 C4 C5 106.91(18)
O4 C4 C3 105.87(17)
C5 C4 C3 114.62(19)
O3 C5 C4 111.6(2)
O4 C6 C7 110.10(18)
O4 C6 C2 103.67(17)
C7 C6 C2 116.32(18)
C11 C7 C8 116.9(2)
C11 C7 C6 120.2(2)
C8 C7 C6 122.9(2)
C9 C8 C7 121.0(2)
C8 C9 C10 117.1(2)
C8 C9 C12 122.4(2)
C10 C9 C12 120.6(2)
N1 C10 N2 116.0(2)
N1 C10 C9 122.9(2)
N2 C10 C9 121.1(2)
N1 C11 C7 124.2(2)
C10 N1 C11 117.9(2)
C2 O1 C1 112.48(17)
C6 O4 C4 109.74(16)
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
C1 O1 1.432(3)
C2 O1 1.412(3)
C2 C6 1.522(3)
C2 C3 1.537(3)
C3 O2 1.424(3)
C3 C4 1.524(3)
C4 O4 1.462(3)
C4 C5 1.520(3)
C5 O3 1.416(3)
C6 O4 1.437(3)
C6 C7 1.496(3)
C7 C11 1.385(3)
C7 C8 1.399(3)
C8 C9 1.382(3)
C9 C10 1.416(3)
C9 C12 1.503(3)
C10 N1 1.340(3)
C10 N2 1.367(3)
C11 N1 1.340(3)
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
N2 H91 O2 0.86 2.56 3.203(3) 132.8 3_665
N2 H92 O4 0.86 2.29 2.934(3) 131.4 5_655
O2 H2A N1 0.82 2.04 2.846(3) 165.7 2_655
O3 H3A O3 0.82 1.89 2.687(2) 165.2 8_654
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 PubChem 139184597
