#------------------------------------------------------------------------------
#$Date: 2025-10-16 02:16:41 +0300 (Thu, 16 Oct 2025) $
#$Revision: 302878 $
#$URL: file:///home/coder/svn-repositories/cod/cif/7/25/09/7250995.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_7250995
loop_
_publ_author_name
'Marasinghe, Aloka A.'
'Averkiev, Boris B.'
'Aakeröy, Christer B.'
_publ_section_title
;
 Examining intermolecular interactions in crystal structures of
 amide-substituted 2-aminopyrimidine derivatives
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/D5CE00839E
_journal_year                    2025
_chemical_formula_moiety         'C6 H6 Cl N3 O'
_chemical_formula_sum            'C6 H6 Cl N3 O'
_chemical_formula_weight         171.59
_chemical_melting_point          480.0(10)
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)acetamide
_space_group_crystal_system      orthorhombic
_space_group_IT_number           66
_space_group_name_Hall           '-C 2 2c'
_space_group_name_H-M_alt        'C c c m'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-09-18
_audit_creation_method
;
Olex2 1.5-ac5-024
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2025-08-25 deposited with the CCDC.	2025-10-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   11.52290(10)
_cell_length_b                   18.7942(3)
_cell_length_c                   6.59400(10)
_cell_measurement_reflns_used    2685
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.6120
_cell_measurement_theta_min      4.4910
_cell_volume                     1428.02(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      210.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  tₑₓₚ   ω     θ     κ     φ   Frames
#--------------------------------------------------------------------------
  1  ω     70.00 106.00   0.50    0.40    --  113.25-100.00   6.00   72
  2  ω     44.00  94.00   0.50    0.40    --  113.25 -94.00  60.00  100
  3  ω     43.00  76.00   0.50    0.40    --  113.25-140.00 -59.00   66
  4  ω     44.00 103.00   0.50    0.40    --  113.25 -94.00 -60.00  118
  5  ω     69.00 102.00   0.50    0.40    --  113.25 -77.00   0.00   66
  6  ω     45.00  70.00   0.50    0.40    --  113.25 -77.00  60.00   50
  7  ω     42.00  67.00   0.50    0.40    --  113.25 -61.00 150.00   50
  8  ω     44.00  69.00   0.50    0.40    --  113.25 -61.00   0.00   50
  9  ω     52.00  92.00   0.50    0.40    --  113.25 -77.00-150.00   80
 10  ω     46.00  71.00   0.50    0.40    --  113.25 -61.00-180.00   50
 11  ω    106.00 158.00   0.50    0.40    --  113.25  15.00 -60.00  104
 12  ω    109.00 170.00   0.50    0.40    --  113.25 100.00 111.00  122
 13  ω    111.00 161.00   0.50    0.40    --  113.25 125.00 120.00  100
 14  ω    -30.00  11.00   0.50    0.10    --  -48.07  24.00 -31.00   82
 15  ω    -77.00 -52.00   0.50    0.40    --  -91.75 140.00  -0.00   50
 16  ω    -25.00  15.00   0.50    0.10    --  -48.07  19.00  30.00   80
 17  ω   -118.00 -69.00   0.50    0.10    --  -48.07-140.00 -59.00   98
 18  ω   -110.00 -71.00   0.50    0.10    --  -48.07-130.00 113.00   78
 19  ω   -146.00-121.00   0.50    0.40    --  -91.75 -24.00 164.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       'ω scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0165669000
_diffrn_orient_matrix_UB_12      0.0399850000
_diffrn_orient_matrix_UB_13      0.2019257000
_diffrn_orient_matrix_UB_21      -0.0377563000
_diffrn_orient_matrix_UB_22      0.0669995000
_diffrn_orient_matrix_UB_23      -0.1172848000
_diffrn_orient_matrix_UB_31      -0.1271654000
_diffrn_orient_matrix_UB_32      -0.0251050000
_diffrn_orient_matrix_UB_33      0.0085577000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0210
_diffrn_reflns_av_unetI/netI     0.0181
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            3405
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.885
_diffrn_reflns_theta_min         4.501
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.261
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.85607
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.133a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.596
_exptl_crystal_description       irregular
_exptl_crystal_F_000             704
_exptl_crystal_recrystallization_method
'crystallized from acetonitrile, methanol, ethylacetate'
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.308
_refine_diff_density_min         -0.381
_refine_diff_density_rms         0.127
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.147
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     71
_refine_ls_number_reflns         854
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.147
_refine_ls_R_factor_all          0.0397
_refine_ls_R_factor_gt           0.0385
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.0703P)²+0.2779P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1004
_refine_ls_wR_factor_ref         0.1020
_reflns_Friedel_coverage         0.000
_reflns_number_gt                808
_reflns_number_total             854
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_932_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '479-481' was changed to
'480.0(10)' -- the average value was taken and precision was
estimated.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 
;
_cod_database_code               7250995
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C6H6Cl1N3O
_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.
;
_shelx_estimated_absorpt_t_max   0.727
_shelx_estimated_absorpt_t_min   0.549
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Others
 Fixed Sof: H10A(0.5) H10B(0.5) H10C(0.5)
3.a Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
3.b Idealised Me refined as rotating group:
 C10(H10A,H10B,H10C)
;
_shelx_res_file
;
TITL exp_932_auto_a.res in Cccm
    exp_932_auto.res
    created by SHELXL-2018/3 at 16:39:38 on 18-Sep-2024
REM Old TITL exp_932_auto in Cccm
REM SHELXT solution in Cccm: R1 0.157, Rweak 0.006, Alpha 0.026
REM <I/s> 0.508 for 61 systematic absences, Orientation as input
REM Formula found by SHELXT: C10 N7 O Cl
CELL 1.54184 11.5229 18.7942 6.594 90 90 90
ZERR 8 0.0001 0.0003 0.0001 0 0 0
LATT 7
SYMM -X,-Y,+Z
SYMM -X,+Y,0.5-Z
SYMM +X,-Y,0.5-Z
SFAC C H Cl N O
UNIT 48 48 8 24 8
EQIV $1 1-X,1-Y,1-Z

L.S. 6
PLAN  5
SIZE 0.08 0.14 0.16
TEMP -63
HTAB N7 N2_$1
BOND
fmap 2
acta
REM <olex2.extras>
REM <HklSrc "%.\\exp_932_auto.hkl">
REM </olex2.extras>

WGHT    0.070300    0.277900
FVAR       2.62379
CL1   3    0.404151    0.201716    0.500000    10.50000    0.02748    0.02455 =
         0.06639    0.00000    0.00000   -0.00583
C1    1    0.605509    0.399565    0.500000    10.50000    0.02256    0.02226 =
         0.03033    0.00000    0.00000   -0.00035
N2    4    0.489035    0.405709    0.500000    10.50000    0.02262    0.02269 =
         0.03622    0.00000    0.00000    0.00263
C3    1    0.428086    0.345753    0.500000    10.50000    0.02232    0.02583 =
         0.03582    0.00000    0.00000   -0.00099
AFIX  43
H3    2    0.346593    0.348022    0.500000    10.50000   -1.20000
AFIX   0
C4    1    0.482332    0.279719    0.500000    10.50000    0.02459    0.02169 =
         0.03820    0.00000    0.00000   -0.00214
C5    1    0.602498    0.278904    0.500000    10.50000    0.02479    0.02192 =
         0.04349    0.00000    0.00000    0.00074
AFIX  43
H5    2    0.641110    0.234846    0.500000    10.50000   -1.20000
AFIX   0
N6    4    0.665391    0.338588    0.500000    10.50000    0.02168    0.02238 =
         0.04196    0.00000    0.00000    0.00007
N7    4    0.661915    0.464354    0.500000    10.50000    0.02276    0.01953 =
         0.04743    0.00000    0.00000    0.00164
H7    2    0.620338    0.501223    0.500000    10.50000    0.04046
C8    1    0.778586    0.482801    0.500000    10.50000    0.02561    0.02449 =
         0.04471    0.00000    0.00000   -0.00329
O9    5    0.801405    0.546401    0.500000    10.50000    0.03103    0.02337 =
         0.07207    0.00000    0.00000   -0.00398
C10   1    0.870129    0.426665    0.500000    10.50000    0.02278    0.02982 =
         0.07073    0.00000    0.00000   -0.00071
PART -1
AFIX 137
H10A  2    0.856315    0.393869    0.610990    10.50000   -1.50000
H10B  2    0.945694    0.448659    0.516527    10.50000   -1.50000
H10C  2    0.867899    0.400970    0.372483    10.50000   -1.50000
AFIX   0
HKLF 4




REM  exp_932_auto_a.res in Cccm
REM wR2 = 0.1020, GooF = S = 1.147, Restrained GooF = 1.147 for all data
REM R1 = 0.0385 for 808 Fo > 4sig(Fo) and 0.0397 for all 854 data
REM 71 parameters refined using 0 restraints

END

WGHT      0.0703      0.2779

REM Highest difference peak  0.308,  deepest hole -0.381,  1-sigma level  0.127
Q1    1   0.7289  0.2252  0.7642  11.00000  0.05    0.31
Q2    1   1.0000  0.4726  0.7500  10.50000  0.05    0.28
Q3    1   0.2571  0.3110  0.2773  11.00000  0.05    0.28
Q4    1   0.5000  0.5000  0.2500  10.25000  0.05    0.28
Q5    1   1.0000  0.4055  0.2500  10.50000  0.05    0.27
;
_shelx_res_checksum              84297
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.301
_oxdiff_exptl_absorpt_empirical_full_min 0.846
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, -y, z'
'-x, y, -z+1/2'
'x, -y, -z+1/2'
'x+1/2, y+1/2, z'
'-x+1/2, -y+1/2, z'
'-x+1/2, y+1/2, -z+1/2'
'x+1/2, -y+1/2, -z+1/2'
'-x, -y, -z'
'x, y, -z'
'x, -y, z-1/2'
'-x, y, z-1/2'
'-x+1/2, -y+1/2, -z'
'x+1/2, y+1/2, -z'
'x+1/2, -y+1/2, z-1/2'
'-x+1/2, y+1/2, z-1/2'
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_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
Cl1 Cl 0.40415(4) 0.20172(2) 0.500000 0.0395(2) Uani 1 2 d S T P . .
C1 C 0.60551(15) 0.39956(10) 0.500000 0.0250(4) Uani 1 2 d S T P . .
N2 N 0.48904(13) 0.40571(8) 0.500000 0.0272(3) Uani 1 2 d S T P . .
C3 C 0.42809(16) 0.34575(10) 0.500000 0.0280(4) Uani 1 2 d S T P . .
H3 H 0.346593 0.348022 0.500000 0.034 Uiso 1 2 calc R U P . .
C4 C 0.48233(15) 0.27972(9) 0.500000 0.0282(4) Uani 1 2 d S T P . .
C5 C 0.60250(15) 0.27890(11) 0.500000 0.0301(4) Uani 1 2 d S T P . .
H5 H 0.641110 0.234846 0.500000 0.036 Uiso 1 2 calc R U P . .
N6 N 0.66539(13) 0.33859(8) 0.500000 0.0287(4) Uani 1 2 d S T P . .
N7 N 0.66192(13) 0.46435(8) 0.500000 0.0299(4) Uani 1 2 d S T P . .
H7 H 0.620(2) 0.5012(19) 0.500000 0.040(6) Uiso 1 2 d S . P . .
C8 C 0.77859(15) 0.48280(10) 0.500000 0.0316(4) Uani 1 2 d S T P . .
O9 O 0.80140(13) 0.54640(8) 0.500000 0.0422(4) Uani 1 2 d S T P . .
C10 C 0.87013(18) 0.42667(11) 0.500000 0.0411(5) Uani 1 2 d S T P . .
H10A H 0.856315 0.393869 0.610990 0.062 Uiso 0.5 1 calc R U P A -1
H10B H 0.945694 0.448659 0.516527 0.062 Uiso 0.5 1 calc R U P A -1
H10C H 0.867899 0.400970 0.372483 0.062 Uiso 0.5 1 calc R U P A -1
loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_23
_atom_site_aniso_U_13
_atom_site_aniso_U_12
Cl1 0.0275(3) 0.0245(3) 0.0664(4) 0.000 0.000 -0.00583(14)
C1 0.0226(8) 0.0223(9) 0.0303(8) 0.000 0.000 -0.0003(6)
N2 0.0226(7) 0.0227(7) 0.0362(7) 0.000 0.000 0.0026(5)
C3 0.0223(7) 0.0258(9) 0.0358(8) 0.000 0.000 -0.0010(7)
C4 0.0246(8) 0.0217(8) 0.0382(8) 0.000 0.000 -0.0021(7)
C5 0.0248(8) 0.0219(9) 0.0435(9) 0.000 0.000 0.0007(6)
N6 0.0217(7) 0.0224(7) 0.0420(8) 0.000 0.000 0.0001(5)
N7 0.0228(7) 0.0195(7) 0.0474(8) 0.000 0.000 0.0016(6)
C8 0.0256(8) 0.0245(10) 0.0447(9) 0.000 0.000 -0.0033(6)
O9 0.0310(7) 0.0234(7) 0.0721(10) 0.000 0.000 -0.0040(5)
C10 0.0228(9) 0.0298(10) 0.0707(14) 0.000 0.000 -0.0007(8)
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0181 0.0091 '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'
Cl Cl 0.3639 0.7018 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0492 0.0322 '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_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
N2 C1 N7 113.17(16) . . ?
N6 C1 N2 125.97(17) . . ?
N6 C1 N7 120.86(16) . . ?
C3 N2 C1 117.02(15) . . ?
N2 C3 C4 121.33(17) . . ?
C3 C4 Cl1 121.70(14) . . ?
C5 C4 Cl1 120.94(15) . . ?
C5 C4 C3 117.37(17) . . ?
N6 C5 C4 122.23(18) . . ?
C5 N6 C1 116.08(16) . . ?
C1 N7 C8 132.55(16) . . ?
N7 C8 C10 120.53(16) . . ?
O9 C8 N7 116.87(17) . . ?
O9 C8 C10 122.60(17) . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Cl1 C4 1.7207(18) . ?
C1 N2 1.347(2) . ?
C1 N6 1.338(2) . ?
C1 N7 1.380(2) . ?
N2 C3 1.328(2) . ?
C3 C4 1.390(2) . ?
C4 C5 1.385(3) . ?
C5 N6 1.335(3) . ?
N7 C8 1.388(2) . ?
C8 O9 1.224(2) . ?
C8 C10 1.492(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
_geom_hbond_publ_flag
N7 H7 N2 0.84(3) 2.16(3) 2.998(2) 179(3) 9_666 yes
