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#$Date: 2025-03-27 01:37:20 +0200 (Thu, 27 Mar 2025) $
#$Revision: 298608 $
#$URL: file:///home/coder/svn-repositories/cod/cif/7/25/01/7250184.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_7250184
loop_
_publ_author_name
'Zhang, Qi'
'Zhu, Yitong'
'Xu, Yisheng'
'Yang, Huaiyu'
'Li, Wei'
'Zhang, Xiangyang'
_publ_section_title
;
 Different Thermal and Solubility Properties with Identical Crystal
 Structure - Case of Lenalidomide Hydrate
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/D4CE00798K
_journal_year                    2025
_chemical_formula_moiety         'C13 H13 N3 O3, 2(H2 O)'
_chemical_formula_sum            'C13 H17 N3 O5'
_chemical_formula_weight         295.29
_chemical_name_common            'Lenalidomide Dihydrate'
_chemical_name_systematic
3-(4-Amino-1-oxoisoindolin-2-yl)piperidine-2,6-dione
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2dhzc8
_audit_creation_date             2017-06-28
_audit_creation_method
;
Olex2 1.2
(compiled 2017.03.28 svn.r3405 for OlexSys, GUI svn.r5337)
;
_audit_update_record
;
2022-11-15 deposited with the CCDC.	2025-03-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 99.231(6)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.4300(14)
_cell_length_b                   8.8535(10)
_cell_length_c                   11.7594(12)
_cell_measurement_reflns_used    2137
_cell_measurement_temperature    281(2)
_cell_measurement_theta_max      70.01
_cell_measurement_theta_min      3.33
_cell_volume                     1380.1(3)
_computing_cell_refinement       'SAINT v8.37A (Bruker, 2015)'
_computing_data_reduction        'SAINT v8.37A (Bruker, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      281.59
_diffrn_measured_fraction_theta_full 0.988
_diffrn_measured_fraction_theta_max 0.986
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       'φ and ω scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0808
_diffrn_reflns_av_unetI/netI     0.0615
_diffrn_reflns_Laue_measured_fraction_full 0.988
_diffrn_reflns_Laue_measured_fraction_max 0.986
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            13400
_diffrn_reflns_point_group_measured_fraction_full 0.988
_diffrn_reflns_point_group_measured_fraction_max 0.986
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         70.195
_diffrn_reflns_theta_min         3.334
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.933
_exptl_absorpt_correction_T_max  0.7533
_exptl_absorpt_correction_T_min  0.5737
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.1301 before and 0.0878 after correction. The Ratio of minimum to maximum transmission is 0.7616. The λ/2 correction factor is Not present.'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.421
_exptl_crystal_description       block
_exptl_crystal_F_000             624
_exptl_crystal_recrystallization_method 'Re-crystallisation from solvent'
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.15
_refine_diff_density_max         0.245
_refine_diff_density_min         -0.216
_refine_diff_density_rms         0.061
_refine_ls_extinction_coef       0.026(4)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2014/8 (Sheldrick 2014'
_refine_ls_goodness_of_fit_ref   1.063
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     210
_refine_ls_number_reflns         2590
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.063
_refine_ls_R_factor_all          0.1059
_refine_ls_R_factor_gt           0.0806
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.1511P)²+0.4709P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2268
_refine_ls_wR_factor_ref         0.2677
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1784
_reflns_number_total             2590
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            d4ce00798k2.cif
_cod_data_source_block           d8v17156
_cod_database_code               7250184
_shelx_shelxl_version_number     2014/8
_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   0.873
_shelx_estimated_absorpt_t_min   0.821
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All O(H,H) groups
2.a Free rotating group:
 O5(H5A,H5B)
2.b Ternary CH refined with riding coordinates:
 C9(H9)
2.c Secondary CH2 refined with riding coordinates:
 C1(H1C,H1D), C11(H11A,H11B), C12(H12A,H12B)
2.d Aromatic/amide H refined with riding coordinates:
 N3(H3), C4(H4), C5(H5), C6(H6)
;
_olex2_submission_special_instructions 'No special instructions were received'
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -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
O1 O 0.6853(2) 0.4405(3) 0.9440(2) 0.0769(8) Uani 1 1 d . . . . .
O2 O 0.7995(3) 0.4745(4) 0.6636(3) 0.1051(12) Uani 1 1 d . . . . .
O3 O 0.5302(2) 0.6393(3) 0.4216(2) 0.0803(8) Uani 1 1 d . . . . .
N1 N 1.0480(3) 0.8359(4) 1.0137(4) 0.0813(10) Uani 1 1 d . . . . .
H1A H 1.111(3) 0.845(4) 1.053(4) 0.073(11) Uiso 1 1 d . . . . .
H1B H 1.031(4) 0.865(5) 0.941(5) 0.104(18) Uiso 1 1 d . . . . .
N2 N 0.7564(2) 0.6336(3) 0.8529(3) 0.0685(8) Uani 1 1 d . . . . .
N3 N 0.6656(2) 0.5632(4) 0.5439(3) 0.0688(8) Uani 1 1 d . . . . .
H3 H 0.6840 0.5117 0.4888 0.083 Uiso 1 1 calc R . . . .
C1 C 0.8460(3) 0.7306(4) 0.8719(3) 0.0665(9) Uani 1 1 d . . . . .
H1C H 0.8276 0.8364 0.8735 0.080 Uiso 1 1 calc R . . . .
H1D H 0.8879 0.7150 0.8131 0.080 Uiso 1 1 calc R . . . .
C2 C 0.8979(3) 0.6785(4) 0.9873(3) 0.0623(9) Uani 1 1 d . . . . .
C3 C 0.9895(3) 0.7222(4) 1.0505(3) 0.0644(9) Uani 1 1 d . . . . .
C4 C 1.0217(3) 0.6455(4) 1.1539(3) 0.0685(9) Uani 1 1 d . . . . .
H4 H 1.0830 0.6722 1.1981 0.082 Uiso 1 1 calc R . . . .
C5 C 0.9654(3) 0.5311(4) 1.1927(3) 0.0705(10) Uani 1 1 d . . . . .
H5 H 0.9895 0.4831 1.2619 0.085 Uiso 1 1 calc R . . . .
C6 C 0.8743(3) 0.4873(4) 1.1305(3) 0.0676(9) Uani 1 1 d . . . . .
H6 H 0.8360 0.4107 1.1561 0.081 Uiso 1 1 calc R . . . .
C7 C 0.8425(3) 0.5630(4) 1.0276(3) 0.0608(8) Uani 1 1 d . . . . .
C8 C 0.7528(3) 0.5357(4) 0.9411(3) 0.0648(9) Uani 1 1 d . . . . .
C9 C 0.6830(3) 0.6307(4) 0.7482(3) 0.0689(10) Uani 1 1 d . . . . .
H9 H 0.6251 0.5724 0.7652 0.083 Uiso 1 1 calc R . . . .
C10 C 0.7238(3) 0.5481(4) 0.6513(3) 0.0726(10) Uani 1 1 d . . . . .
C11 C 0.6433(3) 0.7836(4) 0.7056(3) 0.0712(10) Uani 1 1 d . . . . .
H11A H 0.6965 0.8418 0.6794 0.085 Uiso 1 1 calc R . . . .
H11B H 0.6198 0.8388 0.7675 0.085 Uiso 1 1 calc R . . . .
C12 C 0.5564(3) 0.7595(5) 0.6065(3) 0.0763(11) Uani 1 1 d . . . . .
H12A H 0.4986 0.7209 0.6374 0.092 Uiso 1 1 calc R . . . .
H12B H 0.5375 0.8562 0.5707 0.092 Uiso 1 1 calc R . . . .
C13 C 0.5811(3) 0.6522(4) 0.5161(3) 0.0661(9) Uani 1 1 d . . . . .
O4 O 0.3779(3) 0.8487(5) 0.3470(3) 0.1062(13) Uani 1 1 d . . . . .
H4A H 0.357(3) 0.880(5) 0.407(4) 0.079(13) Uiso 1 1 d . . . . .
H4B H 0.428(5) 0.762(7) 0.369(5) 0.13(2) Uiso 1 1 d . . . . .
O5 O 0.2776(2) 0.8598(3) 0.1256(3) 0.0802(8) Uani 1 1 d . . . . .
H5A H 0.2868 0.7733 0.0977 0.120 Uiso 1 1 d G . . . .
H5B H 0.3092 0.8651 0.1941 0.120 Uiso 1 1 d G . . . .
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'
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
H1A N1 H1B 123(4) . . ?
C3 N1 H1A 116(3) . . ?
C3 N1 H1B 116(3) . . ?
C8 N2 C1 112.7(3) . . ?
C8 N2 C9 122.3(3) . . ?
C9 N2 C1 124.8(3) . . ?
C10 N3 H3 116.7 . . ?
C13 N3 H3 116.7 . . ?
C13 N3 C10 126.6(3) . . ?
N2 C1 H1C 111.3 . . ?
N2 C1 H1D 111.3 . . ?
N2 C1 C2 102.1(3) . . ?
H1C C1 H1D 109.2 . . ?
C2 C1 H1C 111.3 . . ?
C2 C1 H1D 111.3 . . ?
C3 C2 C1 130.2(3) . . ?
C3 C2 C7 119.9(3) . . ?
C7 C2 C1 109.8(3) . . ?
N1 C3 C4 120.7(3) . . ?
C2 C3 N1 122.2(4) . . ?
C2 C3 C4 117.1(3) . . ?
C3 C4 H4 119.0 . . ?
C5 C4 C3 122.1(3) . . ?
C5 C4 H4 119.0 . . ?
C4 C5 H5 119.4 . . ?
C6 C5 C4 121.2(3) . . ?
C6 C5 H5 119.4 . . ?
C5 C6 H6 121.6 . . ?
C5 C6 C7 116.7(4) . . ?
C7 C6 H6 121.6 . . ?
C2 C7 C8 108.0(3) . . ?
C6 C7 C2 123.0(3) . . ?
C6 C7 C8 128.9(3) . . ?
O1 C8 N2 124.7(3) . . ?
O1 C8 C7 127.9(3) . . ?
N2 C8 C7 107.4(3) . . ?
N2 C9 H9 106.9 . . ?
N2 C9 C10 111.4(3) . . ?
N2 C9 C11 114.9(3) . . ?
C10 C9 H9 106.9 . . ?
C11 C9 H9 106.9 . . ?
C11 C9 C10 109.4(3) . . ?
O2 C10 N3 120.5(4) . . ?
O2 C10 C9 124.8(3) . . ?
N3 C10 C9 114.7(3) . . ?
C9 C11 H11A 110.0 . . ?
C9 C11 H11B 110.0 . . ?
C9 C11 C12 108.3(3) . . ?
H11A C11 H11B 108.4 . . ?
C12 C11 H11A 110.0 . . ?
C12 C11 H11B 110.0 . . ?
C11 C12 H12A 108.8 . . ?
C11 C12 H12B 108.8 . . ?
H12A C12 H12B 107.7 . . ?
C13 C12 C11 113.6(3) . . ?
C13 C12 H12A 108.8 . . ?
C13 C12 H12B 108.8 . . ?
O3 C13 N3 119.1(3) . . ?
O3 C13 C12 123.5(3) . . ?
N3 C13 C12 117.4(3) . . ?
H4A O4 H4B 109(5) . . ?
H5A O5 H5B 109.5 . . ?
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
O1 C8 1.243(4) . ?
O2 C10 1.197(5) . ?
O3 C13 1.213(4) . ?
N1 H1A 0.90(4) . ?
N1 H1B 0.89(5) . ?
N1 C3 1.389(5) . ?
N2 C1 1.465(4) . ?
N2 C8 1.358(5) . ?
N2 C9 1.449(5) . ?
N3 H3 0.8600 . ?
N3 C10 1.381(4) . ?
N3 C13 1.377(4) . ?
C1 H1C 0.9700 . ?
C1 H1D 0.9700 . ?
C1 C2 1.496(5) . ?
C2 C3 1.386(5) . ?
C2 C7 1.392(5) . ?
C3 C4 1.399(5) . ?
C4 H4 0.9300 . ?
C4 C5 1.384(6) . ?
C5 H5 0.9300 . ?
C5 C6 1.376(5) . ?
C6 H6 0.9300 . ?
C6 C7 1.389(5) . ?
C7 C8 1.467(5) . ?
C9 H9 0.9800 . ?
C9 C10 1.527(6) . ?
C9 C11 1.511(5) . ?
C11 H11A 0.9700 . ?
C11 H11B 0.9700 . ?
C11 C12 1.527(5) . ?
C12 H12A 0.9700 . ?
C12 H12B 0.9700 . ?
C12 C13 1.502(5) . ?
O4 H4A 0.85(5) . ?
O4 H4B 1.02(7) . ?
O5 H5A 0.8502 . ?
O5 H5B 0.8500 . ?
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
N3 H3 O5 0.86 2.03 2.878(4) 170.4 2_645
O4 H4A O1 0.85(5) 2.00(5) 2.844(5) 175(4) 2_656
O4 H4B O3 1.02(7) 1.79(7) 2.795(4) 168(5) .
O5 H5A O1 0.85 2.01 2.849(4) 171.6 3_666
O5 H5B O4 0.85 1.89 2.735(4) 172.4 .
