#------------------------------------------------------------------------------
#$Date: 2024-03-23 05:14:53 +0200 (Sat, 23 Mar 2024) $
#$Revision: 290612 $
#$URL: file:///home/coder/svn-repositories/cod/cif/1/57/12/1571263.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_1571263
loop_
_publ_author_name
'Olech, Barbara'
'Brázda, Petr'
'Palatinus, Lukas'
'Dominiak, Paulina Maria'
_publ_section_title
;
 Dynamical refinement with multipolar electron scattering factors.
;
_journal_coeditor_code           OF5004
_journal_issue                   3
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524001763
_journal_volume                  11
_journal_year                    2024
_chemical_formula_sum            'C5 H6 N2 O2'
_chemical_formula_weight         126.1
_chemical_name_common            1-methyluracil
_space_group_IT_number           72
_space_group_name_Hall           '-I 2 2c'
_space_group_name_H-M_alt        'I b a m'
_symmetry_cell_setting           orthorhombic
_symmetry_Int_Tables_number      72
_symmetry_space_group_name_Hall  '-I 2 2c'
_symmetry_space_group_name_H-M   'I b a m'
_audit_creation_method           'Jana2020 1.3.51'
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   13.1931
_cell_length_b                   13.214
_cell_length_c                   6.213
_cell_measurement_reflns_used    2334
_cell_measurement_temperature    100
_cell_measurement_theta_max      0.90
_cell_measurement_theta_min      0.05
_cell_volume                     1083.135
_computing_cell_refinement
;
PETS2 (Palatinus, L., et al. Acta Crystallogr. B 2019)
Optical distortions in PETS2 (Brazda, P., et al IUCrJ 2022) 
;
_computing_data_reduction
;
PETS2 (Palatinus, L., et al. Acta Crystallogr. B 2019).
;
_computing_structure_refinement
;
Jana2006 (Petricek et al., 2014). Dynamical refinement (Palatinus, L. et al.
 2015).
;
_computing_structure_solution
;
Superflip (Palatinus et al., 2007).
;
_diffrn_ambient_temperature      100
_diffrn_detector
;
SIS Veleta CCD 14 bit camera
;
_diffrn_detector_area_resol_mean 2048.2048
_diffrn_measured_fraction_theta_full 0.7
_diffrn_measured_fraction_theta_max 0.69
_diffrn_measurement_device       TEM
_diffrn_measurement_device_type  'Tecnai G2 20'
_diffrn_measurement_method
;
precession assisted 3D ED
;
_diffrn_measurement_specimen_support
;
Cu grid with carbon foil
;
_diffrn_radiation_probe          electron
_diffrn_radiation_source         LaB6
_diffrn_radiation_type           electron
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_unetI/netI     0.0426
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            21381
_diffrn_reflns_reduction_process 'data integration with PETS2'
_diffrn_reflns_theta_full        0.64
_diffrn_reflns_theta_max         1.29
_diffrn_reflns_theta_min         0.08
_diffrn_source                   'electron microscope'
_diffrn_source_voltage           200
_exptl_absorpt_correction_type   none
_exptl_crystal_density_diffrn    1.5468
_exptl_crystal_description
;
platelet
;
_exptl_crystal_F_000             192.856
_exptl_crystal_size_max          0.005
_exptl_crystal_size_mid          0.003
_exptl_crystal_size_min          0.0002
_refine_diff_density_max         0.07
_refine_diff_density_min         -0.09
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_gt    0.0000
_refine_ls_goodness_of_fit_ref   2.7600
_refine_ls_hydrogen_treatment    refall
_refine_ls_number_constraints    0
_refine_ls_number_parameters     166
_refine_ls_number_reflns         11582
_refine_ls_number_restraints     0
_refine_ls_R_factor_all          0.1273
_refine_ls_R_factor_gt           0.0892
_refine_ls_shift/su_max          0.0432
_refine_ls_shift/su_mean         0.0021
_refine_ls_structure_factor_coef F
_refine_ls_weighting_details
'calc w=1/[σ²(Fo)+(0.01P)²+0.0000P] where P=Fo'
_refine_ls_weighting_scheme      sigma
_refine_ls_wR_factor_gt          0.0959
_refine_ls_wR_factor_ref         0.0988
_reflns_number_gt                5409
_reflns_number_total             11582
_reflns_threshold_expression     I>3σ(I)
_cod_data_source_file            of5004.cif
_cod_data_source_block           TAAM
_cod_original_sg_symbol_Hall     '-I -2xab;-2yab;-2z'
_cod_database_code               1571263
_jana_m50_file
;
Version Jana2020
title
cell 13.1931 13.214 6.213 90 90 90
esdcell 0 0 0 0 0 0
spgroup Ibam 72 3
lattice I
symmetry x y z
symmetry -x -y z
symmetry -x y -z+1/2
symmetry x -y -z+1/2
symmetry -x -y -z
symmetry x y -z
symmetry x -y z+1/2
symmetry -x y z+1/2
unitsnumb 8
atlist C5 H6 N2 O2
formtab 40
atom C atradius 0.77 color 128073041
wffile Default
FFCore 2
FFVal 0 2 2
nslater 2 2 2 3 4 5 6 7
ZSlater 3.13 3.13 3.13 3.13 3.13 3.13 3.13 3.13
atom H atradius 0.46 color 255204204
wffile Default
FFCore 0
FFVal 1
nslater 1 1 2 3 4 5 6 7
ZSlater 1.915 1.915 1.915 1.915 1.915 1.915 1.915 1.915
atom N atradius 0.74 color 176185230
wffile Default
FFCore 2
FFVal 0 2 3
nslater 2 2 2 3 4 5 6 7
ZSlater 3.811 3.811 3.811 3.811 3.811 3.811 3.811 3.811
atom O atradius 0.74 color 254003000
wffile Default
FFCore 2
FFVal 0 2 4
nslater 2 2 2 3 4 5 6 7
ZSlater 4.497 4.497 4.497 4.497 4.497 4.497 4.497 4.497
densities
wavefile wavefj.dat
usemottform
roundmethod 1
end
*******************************************************************************
contour
end contour
dist
  angles 1 dhmax 1.6 expdmax 20
  selfirst O(4) O(2) N(3) H(3) N(1) C(2) C(6) H(6) C(4) C(5) H(5) C(7) H(7a)
  selfirst H(7b)
  selsecnd O(4) O(2) N(3) H(3) N(1) C(2) C(6) H(6) C(4) C(5) H(5) C(7) H(7a)
  selsecnd H(7b)
end dist
fourier
  addbord 0 maptype 6
end fourier
refine
  cycles 7 fsquare 0 autkeys 0 autspec 0 callfour 1 wilsonmod 0 uisolim 0
end refine
;
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 -x,-y,z
3 -x,y,-z+1/2
4 x,-y,-z+1/2
5 -x,-y,-z
6 x,y,-z
7 x,-y,z+1/2
8 -x,y,z+1/2
9 x+1/2,y+1/2,z+1/2
10 -x+1/2,-y+1/2,z+1/2
11 -x+1/2,y+1/2,-z
12 x+1/2,-y+1/2,-z
13 -x+1/2,-y+1/2,-z+1/2
14 x+1/2,y+1/2,-z+1/2
15 x+1/2,-y+1/2,z
16 -x+1/2,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_adp_type
_atom_site_U_iso_or_equiv
_atom_site_site_symmetry_multiplicity
_atom_site_occupancy
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
O(4) O 0.13550(8) 1.01867(7) 0 Uani 0.0156(8) 8 1 d . . .
O(2) O -0.04562(7) 0.72573(8) 0 Uani 0.0183(8) 8 1 d . . .
N(3) N 0.04746(8) 0.87090(8) 0 Uani 0.0144(9) 8 1 d . . .
H(3) H -0.0242(5) 0.9095(4) 0 Uiso 0.0237(17) 8 1 d . . .
N(1) N 0.12678(7) 0.71385(8) 0 Uani 0.0132(9) 8 1 d . . .
C(2) C 0.03763(8) 0.76699(9) 0 Uani 0.0144(10) 8 1 d . . .
C(6) C 0.21882(9) 0.76141(9) 0 Uani 0.0132(10) 8 1 d . . .
H(6) H 0.2830(5) 0.7139(5) 0 Uiso 0.0261(18) 8 1 d . . .
C(4) C 0.13727(9) 0.92548(8) 0 Uani 0.0137(9) 8 1 d . . .
C(5) C 0.22774(8) 0.86473(9) 0 Uani 0.0184(10) 8 1 d . . .
H(5) H 0.3000(5) 0.8986(5) 0 Uiso 0.0289(19) 8 1 d . . .
C(7) C 0.12037(10) 0.60355(10) 0 Uani 0.0298(12) 8 1 d . . .
H(7a) H 0.1980(6) 0.5782(5) 0 Uiso 0.029(2) 8 1 d . . .
H(7b) H 0.0776(5) 0.5793(4) -0.141(2) Uiso 0.0410(19) 16 1 d . . .
loop_
_atom_type_symbol
_atom_type_scat_source
C International_Tables_Vol_C
H International_Tables_Vol_C
N International_Tables_Vol_C
O International_Tables_Vol_C
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_2
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
H(3) N(3) C(2) . . . 113.0(3) ?
H(3) N(3) C(4) . . . 120.3(3) ?
C(2) N(3) C(4) . . . 126.72(10) ?
C(2) N(1) C(6) . . . 121.80(10) ?
C(2) N(1) C(7) . . . 117.52(10) ?
C(6) N(1) C(7) . . . 120.68(10) ?
O(2) C(2) N(3) . . . 121.79(11) ?
O(2) C(2) N(1) . . . 122.76(11) ?
N(3) C(2) N(1) . . . 115.45(10) ?
N(1) C(6) H(6) . . . 116.1(4) ?
N(1) C(6) C(5) . . . 122.28(11) ?
H(6) C(6) C(5) . . . 121.7(4) ?
O(4) C(4) N(3) . . . 120.24(11) ?
O(4) C(4) C(5) . . . 125.01(11) ?
N(3) C(4) C(5) . . . 114.75(9) ?
C(6) C(5) C(4) . . . 119.00(10) ?
C(6) C(5) H(5) . . . 120.1(4) ?
C(4) C(5) H(5) . . . 120.9(4) ?
N(1) C(7) H(7a) . . . 104.8(4) ?
N(1) C(7) H(7b) . . . 108.9(3) ?
N(1) C(7) H(7b) . . 6_555 108.9(3) ?
H(7a) C(7) H(7b) . . . 113.6(4) ?
H(7a) C(7) H(7b) . . 6_555 113.6(4) ?
H(7b) C(7) H(7b) . . 6_555 107.0(7) ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
O(4) C(4) . . 1.2316(14) ?
O(2) C(2) . . 1.2263(14) ?
N(3) H(3) . . 1.074(7) ?
N(3) C(2) . . 1.3792(16) ?
N(3) C(4) . . 1.3872(15) ?
N(1) C(2) . . 1.3698(15) ?
N(1) C(6) . . 1.3673(15) ?
N(1) C(7) . . 1.4600(16) ?
C(6) H(6) . . 1.054(7) ?
C(6) C(5) . . 1.3703(17) ?
C(4) C(5) . . 1.4384(16) ?
C(5) H(5) . . 1.053(7) ?
C(7) H(7a) . . 1.078(8) ?
C(7) H(7b) . . 1.091(11) ?
C(7) H(7b) . 6_555 1.091(11) ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_site_symmetry_D
_geom_hbond_site_symmetry_H
_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
N(3) H(3) O(4) . . 2_575 1.074(7) 1.749(7) 2.8205(14) 175.5(5) ?
C(6) H(6) O(2) . . 12_565 1.054(7) 2.398(7) 3.1123(15) 124.0(5) ?
C(7) H(7a) O(4) . . 11_545 1.078(8) 2.333(8) 3.4105(17) 178.4(5) ?
loop_
_reflns_scale_group_code
_reflns_scale_meas_intensity
1%1 1204.886
2%1 1266.473
3%1 1319.221
4%1 1341.887
5%1 1363.165
6%1 1354.089
7%1 1337.564
8%1 1328.390
9%1 1308.158
10%1 1278.552
11%1 1192.958
12%1 1181.725
13%1 1233.701
14%1 1286.617
15%1 1210.885
16%1 1176.374
17%1 1111.546
18%1 1112.868
19%1 1103.479
20%1 1116.650
21%1 1112.653
22%1 1104.982
23%1 1158.712
24%1 1106.476
25%1 1110.357
26%1 1075.415
27%1 1584.405
28%1 1541.458
29%1 1617.380
30%1 1567.996
31%1 1511.449
32%1 1499.315
33%1 1474.633
34%1 1451.162
35%1 1371.661
36%1 1367.323
37%1 1353.074
38%1 1328.690
39%1 1353.764
40%1 1345.171
2%2 1387.351
3%2 1338.913
4%2 1293.850
5%2 1311.917
6%2 1275.365
7%2 1318.825
8%2 1277.573
9%2 1532.263
10%2 1498.298
11%2 1497.080
12%2 1419.630
13%2 1451.346
14%2 1479.979
15%2 1535.932
16%2 1492.804
17%2 1577.183
18%2 1503.872
19%2 1699.306
20%2 1614.497
21%2 1655.131
22%2 1648.665
23%2 1686.154
24%2 1647.435
25%2 2135.043
26%2 2165.585
27%2 2125.474
28%2 2150.950
29%2 2159.871
30%2 2147.713
32%2 2125.671
33%2 2219.182
34%2 2232.665
35%2 2133.076
36%2 2126.563
37%2 2015.305
38%2 1966.516
39%2 1828.950
40%2 1774.801
46%2 1551.062
50%2 2143.452
52%2 2134.831
53%2 2106.941
54%2 2063.853
55%2 1758.571
58%2 1654.628
59%2 1668.908
60%2 1609.816
61%2 1588.561
62%2 1538.959
63%2 1529.674
64%2 1510.230
65%2 1485.249
66%2 1425.162
67%2 1382.324
