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#$Date: 2025-08-19 21:17:10 +0300 (Tue, 19 Aug 2025) $
#$Revision: 301807 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/24/35/2243556.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_2243556
loop_
_publ_author_name
'Katsuumi, Natsuki'
'Onami, Yuika'
'Pradhan, Sayantan'
'Haraguchi, Tomoyuki'
'Akitsu, Takashiro'
_publ_section_title
;
 Crystal structure and Hirshfeld surface analysis of
 (aqua-κO)(methanol-κO)[N-(2-oxidobenzylidene)threoninato-κ³O,N,O']copper(II)
;
_journal_issue                   9
_journal_name_full               'Acta Crystallographica Section E'
_journal_page_first              1539
_journal_page_last               1542
_journal_paper_doi               10.1107/S2056989020011706
_journal_volume                  76
_journal_year                    2020
_chemical_absolute_configuration syn
_chemical_formula_iupac          '[Cu (C11 H11 N O4) (C H4 O) (H2 O)]'
_chemical_formula_moiety         'C12 H17 Cu N O6'
_chemical_formula_sum            'C12 H17 Cu N O6'
_chemical_formula_weight         334.80
_chemical_name_systematic
(Aqua-κO)(methanol-κO)[N-(2-oxidobenzylidene)threoninato-κ³O,N,O']copper(II)
_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
_audit_creation_method           SHELXL-2016/6
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.0614(4)
_cell_length_b                   11.0738(6)
_cell_length_c                   17.6541(10)
_cell_measurement_reflns_used    3748
_cell_measurement_temperature    173
_cell_measurement_theta_max      27.1527
_cell_measurement_theta_min      3.4748
_cell_volume                     1380.49(13)
_computing_cell_refinement
;
APEX3 (Bruker, 2017)
;
_computing_data_collection
;
APEX3 (Bruker, 2017)
;
_computing_data_reduction
;
SAINT (Bruker, 2017)
;
_computing_molecular_graphics
;
Mercury (Macrae et al.,  2020)
;
_computing_publication_material
;
SHELXTL (Sheldrick, 2008)
;
_computing_structure_refinement
;
SHELXL2016/6 (Sheldrick, 2015b)
;
_computing_structure_solution
;
SHELXT2014/5 (Sheldrick, 2015a)
;
_diffrn_ambient_temperature      173
_diffrn_detector_area_resol_mean 7.3910
_diffrn_measured_fraction_theta_full 0.984
_diffrn_measured_fraction_theta_max 0.887
_diffrn_measurement_device_type  'Bruker APEXIII CCD'
_diffrn_measurement_method       'φ and ω scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0783
_diffrn_reflns_av_unetI/netI     0.0630
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            21250
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         31.151
_diffrn_reflns_theta_min         2.307
_diffrn_source                   'fine-focus sealed tube'
_exptl_absorpt_coefficient_mu    1.606
_exptl_absorpt_correction_T_max  0.70
_exptl_absorpt_correction_T_min  0.65
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(SADABS; Bruker, 2017)
;
_exptl_crystal_colour            green
_exptl_crystal_density_diffrn    1.611
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             692
_exptl_crystal_size_max          0.577
_exptl_crystal_size_mid          0.247
_exptl_crystal_size_min          0.105
_refine_diff_density_max         1.40
_refine_diff_density_min         -2.47
_refine_ls_abs_structure_details
;
Flack x determined using 1080 quotients
[(I⁺)-(I⁻)]/[(I⁺)+(I⁻)]
(Parsons et al.,  2013)
;
_refine_ls_abs_structure_Flack   0.013(6)
_refine_ls_extinction_coef       0.0061(19)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4^
_refine_ls_extinction_method
;
SHELXL-2016/6 (Sheldrick, 2015b)
;
_refine_ls_goodness_of_fit_ref   1.325
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     195
_refine_ls_number_reflns         3706
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.325
_refine_ls_R_factor_all          0.0843
_refine_ls_R_factor_gt           0.0281
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.0366P)²+0.3357P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0643
_refine_ls_wR_factor_ref         0.0965
_reflns_number_gt                2981
_reflns_number_total             3706
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            is5551sup1.cif
_cod_data_source_block           I
_cod_database_code               2243556
_cod_database_fobs_code          2243556
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
loop_
_space_group_symop_operation_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_type_symbol
_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_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
Cu Cu1 0.61538(6) 0.62966(4) 0.57142(2) 0.01921(15) Uani d 1 . .
N N1 0.5954(4) 0.5019(3) 0.64462(16) 0.0182(6) Uani d 1 . .
O O1 0.1357(4) 0.6119(3) 0.68853(17) 0.0321(7) Uani d 1 . .
C C1 0.2945(5) 0.6045(4) 0.6605(2) 0.0213(8) Uani d 1 . .
O O2 0.3562(4) 0.6679(3) 0.60469(15) 0.0236(6) Uani d 1 . .
C C2 0.9302(5) 0.4684(4) 0.5454(2) 0.0226(8) Uani d 1 . .
O O3 0.5999(5) 0.7596(3) 0.49822(19) 0.0312(7) Uani d 1 . .
H H3 0.681(8) 0.770(5) 0.467(3) 0.030(14) Uiso d 1 . .
H H2 0.510(9) 0.813(6) 0.497(4) 0.043(16) Uiso d 1 . .
C C3 1.1020(7) 0.4402(4) 0.5083(2) 0.0305(9) Uani d 1 . .
H H3A 1.143887 0.489273 0.468909 0.037 Uiso calc 1 . .
O O4 0.8381(4) 0.5673(3) 0.52418(16) 0.0238(6) Uani d 1 . .
C C4 1.2084(6) 0.3414(5) 0.5293(3) 0.0357(11) Uani d 1 . .
H H4A 1.321203 0.325388 0.504001 0.043 Uiso calc 1 . .
C C5 1.1509(7) 0.2654(4) 0.5873(3) 0.0359(11) Uani d 1 . .
H H5A 1.225553 0.200181 0.601761 0.043 Uiso calc 1 . .
O O5 0.5433(4) 0.6871(3) 0.76923(17) 0.0270(7) Uani d 1 . .
H H5 0.630851 0.694020 0.739006 0.040 Uiso calc 1 . .
C C6 0.9816(7) 0.2880(4) 0.6233(3) 0.0295(10) Uani d 1 . .
H H6A 0.940205 0.235879 0.661122 0.035 Uiso calc 1 . .
O O6 0.8220(4) 0.7368(3) 0.66221(19) 0.0277(7) Uani d 1 . .
H H4 0.914663 0.694152 0.670341 0.043(16) Uiso calc 1 . .
C C7 0.8696(6) 0.3893(3) 0.6037(2) 0.0225(8) Uani d 1 . .
C C8 0.7002(5) 0.4070(3) 0.6473(2) 0.0203(8) Uani d 1 . .
H H7A 0.663550 0.345351 0.679967 0.024 Uiso calc 1 . .
C C9 0.4331(5) 0.5140(4) 0.6951(2) 0.0205(8) Uani d 1 . .
H H8A 0.370634 0.435523 0.700865 0.025 Uiso calc 1 . .
C C10 0.4885(6) 0.5637(4) 0.7740(2) 0.0224(8) Uani d 1 . .
H H10A 0.373683 0.561185 0.805101 0.027 Uiso calc 1 . .
C C11 0.6344(7) 0.4869(4) 0.8141(2) 0.0310(9) Uani d 1 . .
H H11A 0.597899 0.403518 0.811274 0.046 Uiso calc 1 . .
H H11B 0.642361 0.510986 0.866273 0.046 Uiso calc 1 . .
H H11C 0.755515 0.497466 0.790346 0.046 Uiso calc 1 . .
C C12 0.8794(7) 0.8592(4) 0.6574(3) 0.0387(10) Uani d 1 . .
H H12A 0.990908 0.865077 0.626517 0.058 Uiso calc 1 . .
H H12B 0.906569 0.889230 0.707250 0.058 Uiso calc 1 . .
H H12C 0.779612 0.906256 0.635190 0.058 Uiso calc 1 . .
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'
Cu Cu 0.3201 1.2651 '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'
O O 0.0106 0.0060 '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_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
O4 Cu1 N1 . . 95.03(13) n
O4 Cu1 O3 . . 91.37(14) n
N1 Cu1 O3 . . 172.54(15) n
O4 Cu1 O2 . . 166.91(13) n
N1 Cu1 O2 . . 83.64(13) n
O3 Cu1 O2 . . 89.26(13) n
C8 N1 C9 . . 120.3(3) ?
C8 N1 Cu1 . . 125.8(3) ?
C9 N1 Cu1 . . 113.6(2) ?
O1 C1 O2 . . 125.6(4) ?
O1 C1 C9 . . 117.9(4) ?
O2 C1 C9 . . 116.6(3) ?
C1 O2 Cu1 . . 115.3(2) ?
O4 C2 C3 . . 118.1(4) ?
O4 C2 C7 . . 124.5(4) ?
C3 C2 C7 . . 117.4(4) ?
Cu1 O3 H3 . . 122(4) ?
Cu1 O3 H2 . . 124(4) ?
H3 O3 H2 . . 114(5) ?
C4 C3 C2 . . 121.2(4) ?
C4 C3 H3A . . 119.4 ?
C2 C3 H3A . . 119.4 ?
C2 O4 Cu1 . . 125.3(3) ?
C3 C4 C5 . . 121.4(4) ?
C3 C4 H4A . . 119.3 ?
C5 C4 H4A . . 119.3 ?
C6 C5 C4 . . 119.0(4) ?
C6 C5 H5A . . 120.5 ?
C4 C5 H5A . . 120.5 ?
C10 O5 H5 . . 109.5 ?
C5 C6 C7 . . 121.1(4) ?
C5 C6 H6A . . 119.4 ?
C7 C6 H6A . . 119.4 ?
C12 O6 H4 . . 109.5 ?
C6 C7 C2 . . 119.9(4) ?
C6 C7 C8 . . 116.3(4) ?
C2 C7 C8 . . 123.8(4) ?
N1 C8 C7 . . 124.8(4) ?
N1 C8 H7A . . 117.6 ?
C7 C8 H7A . . 117.6 ?
N1 C9 C1 . . 108.7(3) ?
N1 C9 C10 . . 112.6(3) ?
C1 C9 C10 . . 106.8(3) ?
N1 C9 H8A . . 109.6 ?
C1 C9 H8A . . 109.6 ?
C10 C9 H8A . . 109.6 ?
O5 C10 C11 . . 112.5(3) ?
O5 C10 C9 . . 110.9(3) ?
C11 C10 C9 . . 113.2(3) ?
O5 C10 H10A . . 106.6 ?
C11 C10 H10A . . 106.6 ?
C9 C10 H10A . . 106.6 ?
C10 C11 H11A . . 109.5 ?
C10 C11 H11B . . 109.5 ?
H11A C11 H11B . . 109.5 ?
C10 C11 H11C . . 109.5 ?
H11A C11 H11C . . 109.5 ?
H11B C11 H11C . . 109.5 ?
O6 C12 H12A . . 109.5 ?
O6 C12 H12B . . 109.5 ?
H12A C12 H12B . . 109.5 ?
O6 C12 H12C . . 109.5 ?
H12A C12 H12C . . 109.5 ?
H12B C12 H12C . . 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
Cu1 O6 . 2.471(3) n
Cu1 O4 . 1.910(3) n
Cu1 N1 . 1.922(3) n
Cu1 O3 . 1.937(3) n
Cu1 O2 . 1.968(3) n
N1 C8 . 1.286(5) n
N1 C9 . 1.458(5) ?
O1 C1 . 1.228(5) ?
C1 O2 . 1.286(5) ?
C1 C9 . 1.528(5) ?
C2 O4 . 1.327(5) ?
C2 C3 . 1.414(6) ?
C2 C7 . 1.418(6) ?
O3 H3 . 0.81(6) ?
O3 H2 . 0.87(7) ?
C3 C4 . 1.378(7) ?
C3 H3A . 0.9300 ?
C4 C5 . 1.387(7) ?
C4 H4A . 0.9300 ?
C5 C6 . 1.376(7) ?
C5 H5A . 0.9300 ?
O5 C10 . 1.423(5) ?
O5 H5 . 0.8200 ?
C6 C7 . 1.415(6) ?
C6 H6A . 0.9300 ?
O6 C12 . 1.417(5) ?
O6 H4 . 0.8200 ?
C7 C8 . 1.436(6) ?
C8 H7A . 0.9300 ?
C9 C10 . 1.548(6) ?
C9 H8A . 0.9800 ?
C10 C11 . 1.512(6) ?
C10 H10A . 0.9800 ?
C11 H11A . 0.9600 ?
C11 H11B . 0.9600 ?
C11 H11C . 0.9600 ?
C12 H12A . 0.9600 ?
C12 H12B . 0.9600 ?
C12 H12C . 0.9600 ?
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
O3 H2 O4 4_466 0.87(7) 1.84(7) 2.692(4) 169(6)
O3 H3 O2 4_566 0.81(6) 1.89(6) 2.687(4) 167(6)
O5 H5 O6 . 0.82 1.97 2.783(4) 171
O6 H4 O1 1_655 0.82 1.84 2.653(4) 175
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 PubChem 168326807
