#------------------------------------------------------------------------------
#$Date: 2024-08-07 00:33:12 +0300 (Wed, 07 Aug 2024) $
#$Revision: 293973 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/31/25/2312562.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_2312562
loop_
_publ_author_name
'Kumar, Anil'
'Jha, Kunal Kumar'
'Olech, Barbara'
'Goral, Tomasz'
'Malinska, Maura'
'Woźniak, Krzysztof'
'Dominiak, Paulina Maria'
_publ_section_title
;
TAAM refinement on high-resolution experimental and simulated 3D
ED/MicroED data for organic molecules.
;
_journal_coeditor_code EQ3017
_journal_issue 'Pt 7'
_journal_name_full
'Acta crystallographica. Section C, Structural chemistry'
_journal_page_first 264
_journal_page_last 277
_journal_paper_doi 10.1107/S2053229624005357
_journal_volume 80
_journal_year 2024
_chemical_absolute_configuration unk
_chemical_formula_iupac 'C H4 N2 O'
_chemical_formula_moiety 'C H4 N2 O'
_chemical_formula_sum 'C H4 N2 O'
_chemical_formula_weight 60.056
_chemical_name_systematic
;
Urea
;
_space_group_crystal_system tetragonal
_space_group_IT_number 113
_space_group_name_Hall 'P -4 2ab'
_space_group_name_H-M_alt 'P -4 21 m'
_atom_sites_solution_primary dual
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2022.06.10 svn.r3fa896fb for OlexSys, GUI svn.r6535)
;
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 2
_cell_length_a 5.596(3)
_cell_length_b 5.596(3)
_cell_length_c 4.7164(17)
_cell_measurement_reflns_used 950
_cell_measurement_temperature 81.00
_cell_measurement_theta_max 1.2820
_cell_measurement_theta_min 0.1280
_cell_volume 147.70(12)
_computing_cell_refinement
;
CrysAlis PRO (Rigaku OD, 2024)
;
_computing_data_collection
;
CrysAlis PRO (Rigaku OD, 2024)
;
_computing_data_reduction
;
CrysAlis PRO (Rigaku OD, 2024)
;
_computing_molecular_graphics
;
OLEX2 (Dolomanov et al., 2009)
;
_computing_publication_material
;
OLEX2 (Dolomanov et al., 2009)
;
_computing_structure_refinement
;
olex2.refine (Bourhis et al., 2015)
;
_computing_structure_solution
;
SHELXT (Sheldrick, 2015)
;
_diffrn_ambient_temperature 81.00
_diffrn_detector 'CCD plate'
_diffrn_measured_fraction_theta_full 0.9118
_diffrn_measured_fraction_theta_max 0.9322
_diffrn_measurement_device
'ThermoFisher 200kV Glacios TEM with CetaD CMOS'
_diffrn_measurement_method 'continuous rotation electron diffraction'
_diffrn_radiation_monochromator none
_diffrn_radiation_probe electron
_diffrn_radiation_type electron
_diffrn_radiation_wavelength 0.02510
_diffrn_reflns_av_R_equivalents 0.1297
_diffrn_reflns_av_unetI/netI 0.0941
_diffrn_reflns_limit_h_max 9
_diffrn_reflns_limit_h_min -9
_diffrn_reflns_limit_k_max 8
_diffrn_reflns_limit_k_min -8
_diffrn_reflns_limit_l_max 8
_diffrn_reflns_limit_l_min -8
_diffrn_reflns_number 1772
_diffrn_reflns_theta_full 0.8629
_diffrn_reflns_theta_max 1.28
_diffrn_reflns_theta_min 0.15
_diffrn_source 'electron diffractometer'
_exptl_absorpt_coefficient_mu 0.000
_exptl_absorpt_correction_T_max 1.00000
_exptl_absorpt_correction_T_min 0.54585
_exptl_absorpt_correction_type multi-scan
_exptl_absorpt_process_details
;
(CrysAlis PRO; Rigaku OD, 2024)
;
_exptl_crystal_density_diffrn 1.350
_exptl_crystal_description Plate
_exptl_crystal_F_000 21.314
_refine_diff_density_max 0.2350
_refine_diff_density_min -0.2457
_refine_ls_abs_structure_details
;
Hooft, R.W.W., Straver, L.H. & Spek, A.L. (2010). J. Appl. Cryst. 43,
665-668.
;
_refine_ls_abs_structure_Flack 0E1(2)
_refine_ls_goodness_of_fit_ref 1.3349
_refine_ls_hydrogen_treatment refall
_refine_ls_matrix_type full
_refine_ls_number_constraints 0
_refine_ls_number_parameters 21
_refine_ls_number_reflns 457
_refine_ls_number_restraints 0
_refine_ls_restrained_S_all 1.3349
_refine_ls_R_factor_all 0.1801
_refine_ls_R_factor_gt 0.1628
_refine_ls_shift/su_max -0.0005
_refine_ls_shift/su_mean 0.0002
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme calc
_refine_ls_wR_factor_gt 0.3709
_refine_ls_wR_factor_ref 0.3866
_reflns_number_gt 344
_reflns_number_total 457
_reflns_threshold_expression I>=2u(I)
_iucr_refine_instructions_details
;
TITL urea_657_gain_2 in P-42(1)m
REM P-42(1)m (#113 in standard setting)
REM SFAC C H N O
CELL 0.0251 5.596142 5.596142 4.716384 90 90 90
ZERR 2 0.002664 0.002664 0.001729 0 0 0
LATT -1
SYMM -X,-Y,+Z
SYMM +Y,-X,-Z
SYMM -Y,+X,-Z
SYMM 0.5-X,0.5+Y,-Z
SYMM 0.5+X,0.5-Y,-Z
SYMM 0.5-Y,0.5-X,+Z
SYMM 0.5+Y,0.5+X,+Z
SFAC C 0.731 36.995 1.195 11.297 0.456 2.814 0.125 0.346 0 0 0 0 0.77 12.011
SFAC H 0.375 15.495 0.141 4.126 0.022 0.025 -0.101 46.884 0 0 0 0 0.32 1.008
SFAC N 0.572 28.846 1.042 9.054 0.465 2.421 0.131 0.317 0 0 0 0 0.75 14.007
SFAC O 0.455 23.78 0.917 7.622 0.472 2.144 0.138 0.296 0 0 0 0 0.73 15.999
UNIT 2 8 4 2
L.S. 4
PLAN 20
TEMP -192.15
CONF
list 3
fmap 2
MORE -1
BOND $H
ACTA
SHEL 100 0.56
WGHT 0.2
FVAR 155.258985
REM
REM
REM
O1 4 0.50000 1.00000 0.40428 10.25000 0.02231 0.02231 0.00504 =
0.00000 -0.00000 0.00287
C1 1 0.50000 1.00000 0.67006 10.25000 0.02055 0.02055 0.00603 =
0.00000 -0.00000 0.00206
N1 3 0.64453 0.85547 0.82208 10.50000 0.02887 0.02887 0.00880 =
0.00089 -0.00089 0.01396
H1 2 0.76210 0.73790 0.72616 10.50000 0.02243
H2 2 0.61416 0.88584 1.06417 10.50000 0.07855
HKLF 4
END
Q1 1 0.5 1 1.066667 11 0.05 0.23
Q2 1 0.7 0.8 1.266667 11 0.05 0.23
Q3 1 0.35 0.85 0.733333 11 0.05 0.16
Q4 1 0.85 0.65 0.533333 11 0.05 0.15
Q5 1 0.95 0.85 0.466667 11 0.05 0.14
REM The information below was added by Olex2.
REM
REM R1 = 0.1628 for 344 Fo > 4sig(Fo) and 0.1801 for all 457 data
REM 21 parameters refined using 0 restraints
REM Highest difference peak 0.2350, deepest hole -0.2457
REM Mean Shift 0.0002, Max Shift -0.0005.
REM +++ Tabular Listing of Refinement Information +++
REM R1_all = 0.1801
REM R1_gt = 0.1628
REM wR_ref = 0.3866
REM GOOF = 1.3349
REM Shift_max = -0.0005
REM Shift_mean = 0.0002
REM Reflections_all = 457
REM Reflections_gt = 344
REM Parameters = 21
REM Hole = -0.315
REM Peak = 0.239
REM Flack = 1(23)
;
_cod_data_source_file eq3017.cif
_cod_data_source_block UreaTAAM
_cod_original_cell_volume 147.70(11)
_cod_original_sg_symbol_Hall ' P -4 2ab'
_cod_database_code 2312562
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 y,-x,-z
3 -y,x,-z
4 x+1/2,-y+1/2,-z
5 -x+1/2,y+1/2,-z
6 -x,-y,z
7 -y+1/2,-x+1/2,z
8 y+1/2,x+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_occupancy
O O1 0.5 1.0 0.4043(8) 0.0166(9) Uani 1.000000
C C1 0.5 1.0 0.6701(12) 0.0157(10) Uani 1.000000
N N1 0.6445(6) 0.8555(6) 0.8221(8) 0.0222(10) Uani 1.000000
H H1 0.762(3) 0.738(3) 0.726(5) 0.022(5) Uiso 1.000000
H H2 0.614(11) 0.886(11) 1.064(9) 0.079(16) Uiso 1.000000
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
O1 0.0223(14) 0.0223(14) 0.0050(12) 0.003(2) -0.000000 0.000000
C1 0.0205(16) 0.0205(16) 0.0060(15) 0.002(3) -0.000000 0.000000
N1 0.0289(14) 0.0289(14) 0.0088(10) 0.014(2) -0.0009(8) 0.0009(8)
loop_
_atom_type_symbol
_atom_type_scat_dispersion_source
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C custom 0.00000 0.00000 'NoSpherA2: Chem.Sci. 2021, DOI:10.1039/D0SC05526C'
H custom 0.00000 0.00000 'NoSpherA2: Chem.Sci. 2021, DOI:10.1039/D0SC05526C'
N custom 0.00000 0.00000 'NoSpherA2: Chem.Sci. 2021, DOI:10.1039/D0SC05526C'
O custom 0.00000 0.00000 'NoSpherA2: Chem.Sci. 2021, DOI:10.1039/D0SC05526C'
loop_
_diffrn_refln_index_h
_diffrn_refln_index_k
_diffrn_refln_index_l
0 0 -1
0 0 1
0 0 2
0 0 -2
0 0 3
0 0 -3
0 0 -4
0 0 4
0 0 -5
0 0 5
0 0 6
0 0 -6
0 0 -7
0 0 7
0 0 -8
0 0 8
1 0 -1
0 1 2
0 -1 -2
-1 0 -2
0 -1 2
0 1 -2
0 -1 3
0 1 -3
-1 0 -3
0 -1 -3
1 0 -3
0 1 3
0 1 -4
0 -1 4
0 -1 -4
0 1 4
0 -1 -5
0 1 -5
0 -1 5
0 1 5
1 0 5
-1 0 5
-1 0 -5
1 0 -5
0 1 6
0 -1 6
1 0 -6
0 1 -6
-1 0 -6
0 -1 -6
1 0 7
-1 0 -7
0 1 7
-1 0 7
1 0 -7
0 1 -7
0 -1 -7
0 -1 7
-1 0 8
0 1 8
0 -1 8
-1 0 -8
1 0 8
0 1 -8
0 -1 -8
1 0 -8
1 -1 8
1 1 -8
-1 -1 -8
-1 1 8
-1 -1 -7
1 -1 7
1 1 -7
-1 1 7
-1 -1 -6
1 1 -6
-1 1 6
1 -1 6
-1 -1 -5
1 1 -5
1 -1 5
-1 1 5
1 -1 4
-1 -1 -4
1 1 -4
-1 1 4
1 -1 3
-1 -1 -3
-1 1 3
1 1 -3
1 1 -2
-1 1 2
1 -1 2
-1 -1 -2
-1 1 1
1 -1 1
-1 -1 1
1 -1 -1
-1 -1 2
-1 1 -2
1 1 2
1 -1 -2
1 -1 -3
-1 1 -3
-1 -1 3
1 1 3
1 -1 -4
-1 -1 4
1 1 4
-1 1 -4
1 -1 -5
-1 -1 5
1 1 5
-1 1 -5
1 1 6
-1 1 -6
-1 -1 6
1 -1 -6
1 1 7
-1 -1 7
-1 1 -7
1 -1 -7
1 1 8
-1 1 -8
-1 -1 8
1 -1 -8
-2 0 1
2 0 -1
2 0 -2
0 -2 2
2 0 2
0 2 -2
-2 0 -2
-2 0 2
2 0 -3
-2 0 3
-2 0 -3
0 2 -3
0 -2 -3
0 -2 3
0 2 3
2 0 3
2 0 4
0 -2 4
0 2 4
0 -2 -4
-2 0 4
2 0 -4
0 2 -5
-2 0 -5
0 -2 -5
0 2 5
0 -2 5
0 2 -6
-2 0 -6
0 2 6
0 -2 6
0 -2 -6
0 -2 7
0 -2 -7
-2 0 -7
0 2 7
-2 0 7
2 0 -7
2 0 7
0 2 -7
0 2 -8
0 -2 -8
-2 0 8
-2 0 -8
0 -2 8
0 2 8
2 0 8
-1 2 8
2 1 -8
2 -1 8
-2 -1 -8
-1 -2 -8
1 -2 8
-2 1 8
1 2 -8
1 2 -7
-1 2 7
2 -1 7
-1 -2 -7
-2 1 7
1 -2 7
2 1 -7
-2 -1 -7
-1 -2 -6
2 -1 6
-2 1 6
1 -2 6
2 1 -6
-1 2 6
1 2 -6
-2 -1 -6
1 -2 5
-1 -2 -5
1 2 -5
-1 2 5
-2 -1 -5
2 1 -5
-2 1 5
2 -1 5
-1 -2 -4
2 1 -4
-1 2 4
1 2 -4
-2 1 4
-2 -1 -4
2 -1 4
1 -2 4
-2 1 3
-1 2 3
1 -2 3
-1 -2 -3
-2 -1 -3
1 2 -3
2 1 -3
2 -1 3
-1 2 2
1 2 -2
1 -2 2
2 1 -2
-2 1 2
1 2 -1
2 1 -1
-2 1 1
-2 -1 0
-2 -1 1
2 -1 -1
-1 -2 1
2 -1 -2
-1 -2 2
2 1 2
-2 1 -2
-2 -1 2
1 -2 -2
-2 -1 3
2 -1 -3
-1 2 -3
1 2 3
1 -2 -3
2 1 3
-1 -2 3
-2 1 -3
2 1 4
-2 -1 4
2 -1 -4
-1 -2 4
-2 1 -4
1 2 4
-1 2 -4
1 -2 -4
2 1 5
2 -1 -5
-2 -1 5
-1 2 -5
-1 -2 5
1 -2 -5
1 2 5
-2 1 -5
-1 2 -6
-2 -1 6
1 2 6
2 -1 -6
2 1 6
1 -2 -6
-1 -2 6
-2 1 -6
2 1 7
-2 1 -7
1 2 7
1 -2 -7
-2 -1 7
-1 2 -7
-1 -2 7
2 -1 -7
-1 2 -8
-2 1 -8
1 -2 -8
1 2 8
2 -1 -8
-1 -2 8
-2 -1 8
2 1 8
2 -2 8
-2 -2 -8
2 2 -7
2 -2 7
-2 -2 -7
-2 2 7
2 2 -6
-2 -2 -6
-2 2 6
2 -2 6
2 -2 5
-2 2 5
2 2 -5
-2 -2 -5
-2 2 4
2 2 -4
2 -2 4
-2 -2 -4
2 -2 3
-2 -2 -3
2 2 -3
-2 2 3
-2 2 2
2 2 -2
2 -2 2
2 2 -1
-2 -2 1
-2 2 -2
2 -2 -2
-2 -2 2
-2 -2 3
-2 2 -3
2 -2 -3
2 2 3
2 -2 -4
-2 -2 4
2 2 4
-2 2 -4
2 -2 -5
-2 2 -5
-2 -2 5
2 2 5
-2 -2 6
2 2 6
-2 2 -6
2 -2 -6
-2 -2 7
2 2 7
2 -2 -7
-2 2 -7
-2 2 -8
2 2 8
3 0 0
-3 0 0
3 0 -1
-3 0 1
-3 0 -1
0 -3 2
-3 0 2
3 0 2
3 0 -2
-3 0 -2
0 3 -2
-3 0 3
3 0 3
0 -3 3
0 3 -3
-3 0 -3
3 0 -3
0 3 4
-3 0 -4
3 0 -4
0 -3 4
3 0 4
-3 0 4
0 3 -4
0 -3 -4
0 3 5
0 -3 -5
-3 0 -5
0 3 -5
3 0 5
3 0 -5
-3 0 5
0 -3 5
0 -3 -6
0 3 6
0 3 -6
3 0 6
0 -3 6
-3 0 6
-3 0 -6
3 0 -6
0 3 7
0 -3 -7
3 0 7
0 -3 7
-3 0 7
3 0 -7
0 3 -7
-3 0 -7
0 3 8
0 -3 -8
0 -3 8
0 3 -8
3 1 -7
-1 3 7
-3 1 7
1 -3 7
-3 -1 -7
3 -1 7
-1 -3 -7
1 3 -7
-1 -3 -6
1 -3 6
-3 1 6
3 -1 6
-1 3 6
1 3 -6
3 1 -6
-3 -1 -6
1 3 -5
1 -3 5
-1 3 5
3 -1 5
3 1 -5
-1 -3 -5
-3 -1 -5
-3 1 5
-1 -3 -4
-3 -1 -4
-3 1 4
1 3 -4
3 1 -4
3 -1 4
-1 3 4
1 -3 4
3 1 -3
3 -1 3
1 3 -3
-3 -1 -3
-3 1 3
1 -3 3
-3 1 2
1 -3 2
-3 -1 -2
3 1 -2
3 -1 2
1 3 -2
-3 1 1
3 1 -1
-3 -1 0
3 1 0
-3 -1 1
3 -1 -1
3 -1 -2
-1 -3 2
-3 -1 2
3 1 2
-3 1 -2
3 1 3
-1 3 -3
3 -1 -3
1 -3 -3
-3 1 -3
-3 -1 3
-1 -3 3
1 3 4
-1 -3 4
3 1 4
-3 1 -4
3 -1 -4
-1 3 -4
1 -3 -4
-3 -1 4
-3 1 -5
-3 -1 5
3 -1 -5
3 1 5
1 3 5
-1 3 -5
-1 -3 5
1 3 6
-3 1 -6
-1 -3 6
3 -1 -6
1 -3 -6
3 1 6
-1 3 -6
-3 -1 6
-3 1 -7
1 -3 -7
1 3 7
-1 -3 7
-1 3 -7
3 1 7
3 -1 -7
-3 -1 7
-3 -2 -7
-2 3 7
3 -2 7
-3 2 7
3 2 -7
2 3 -7
2 -3 7
-2 -3 -7
-2 -3 -6
-2 3 6
2 3 -6
3 -2 6
-3 2 6
-3 -2 -6
2 -3 6
3 2 -6
-3 2 5
-2 3 5
-3 -2 -5
2 -3 5
3 2 -5
-2 -3 -5
3 -2 5
2 3 -5
-3 -2 -4
-2 3 4
2 -3 4
-3 2 4
-2 -3 -4
3 2 -4
3 -2 4
2 3 -4
-3 -2 -3
-3 2 3
-2 3 3
2 3 -3
3 -2 3
2 -3 3
-3 2 2
3 2 -2
2 3 -2
3 2 -1
-3 -2 1
3 -2 -2
-3 -2 2
-2 -3 2
-3 2 -3
-2 3 -3
-2 -3 3
-3 -2 3
3 -2 -3
3 2 3
2 -3 -3
-3 2 -4
-3 -2 4
3 2 4
2 -3 -4
3 -2 -4
-2 -3 4
-2 3 -4
3 -2 -5
3 2 5
-3 -2 5
-2 3 -5
2 3 5
-2 -3 5
2 -3 -5
-3 2 -5
3 2 6
-3 -2 6
2 3 6
-2 -3 6
-3 2 -6
-2 3 -6
2 -3 -6
3 -2 -6
3 2 7
2 -3 -7
2 3 7
3 -2 -7
-3 2 -7
-3 -2 7
-2 3 -7
-2 -3 7
-3 -3 -7
3 3 -7
-3 3 7
3 -3 7
-3 -3 -6
-3 3 6
3 3 -6
3 -3 6
3 -3 5
-3 -3 -5
-3 3 5
3 3 -5
-3 -3 -4
-3 3 4
3 3 -4
-3 3 3
3 -3 3
3 3 -2
3 3 -1
-3 -3 1
-3 -3 2
3 -3 -3
-3 -3 3
-3 -3 4
3 -3 -4
-3 -3 5
-3 3 -5
3 3 5
3 -3 -5
-3 -3 6
3 -3 -6
3 3 6
-3 3 -6
3 3 7
-3 -3 7
-3 3 -7
3 -3 -7
-4 0 0
4 0 0
4 0 -1
-4 0 1
-4 0 -1
4 0 2
-4 0 2
-4 0 -3
-4 0 3
4 0 3
4 0 -3
0 -4 3
0 4 -3
0 -4 -4
-4 0 4
4 0 4
4 0 -4
-4 0 -4
0 -4 4
0 4 -4
0 -4 5
0 -4 -5
-4 0 -5
-4 0 5
0 4 5
0 4 -5
0 -4 6
0 -4 -6
-4 0 -6
4 0 -6
0 4 6
0 4 -6
-4 0 6
4 0 6
0 -4 -7
4 0 7
0 4 7
4 0 -7
-4 0 -7
-4 0 7
0 -4 7
0 4 -7
4 1 -7
4 -1 7
-4 1 7
-1 4 7
-1 -4 -7
1 -4 7
-4 -1 -7
1 4 -7
4 -1 6
-1 -4 -6
-4 -1 -6
-4 1 6
4 1 -6
1 4 -6
1 -4 6
-1 4 6
4 1 -5
-1 -4 -5
4 -1 5
1 -4 5
-4 1 5
1 4 -5
-4 -1 -5
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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
N1 C1 O1 6_675 . 122.1(3) ?
N1 C1 O1 . . 122.1(3) ?
N1 C1 N1 . 6_675 115.8(5) ?
H1 N1 C1 . 6_675 122.0(13) ?
H2 N1 C1 . 6_675 110(4) ?
H2 N1 H1 . . 128(4) ?
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
O1 C1 . 1.254(7) ?
C1 N1 6_675 1.350(5) ?
C1 N1 . 1.350(5) ?
N1 H1 . 1.03(3) ?
N1 H2 . 1.17(4) ?