#------------------------------------------------------------------------------ #$Date: 2025-08-19 20:21:09 +0100 (Tue, 19 Aug 2025) $ #$Revision: 301810 $ #$URL: svn://www.crystallography.net/cod/cif/3/50/01/3500112.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_3500112 loop_ _publ_author_name 'Thierry Maris' _publ_section_references ; Dolomanov, O.V., Bourhis, L.J., Gildea, R.J, Howard, J.A.K. & Puschmann, H. (2009), J. Appl. Cryst. 42, 339-341. Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122. ; _publ_section_title ; Indole in Pnma at 100 K ; _journal_name_full 'Personal communication to COD' _journal_year 2020 _chemical_formula_moiety 'C8 H7 N' _chemical_formula_sum 'C8 H7 N' _chemical_formula_weight 117.15 _chemical_name_common indole _chemical_name_systematic ; 1H-Indole ; _space_group_crystal_system orthorhombic _space_group_IT_number 62 _space_group_name_Hall '-P 2ac 2n' _space_group_name_H-M_alt 'P n m a' _atom_sites_solution_hydrogens geom _atom_sites_solution_primary dual _audit_creation_date 2014-04-04 _audit_creation_method ; Olex2 1.2 (compiled 2014.03.20 svn.r2914 for OlexSys, GUI svn.r4816) ; _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 7.6434(2) _cell_length_b 14.6714(5) _cell_length_c 5.5496(2) _cell_measurement_reflns_used 8039 _cell_measurement_temperature 150 _cell_measurement_theta_max 68.33 _cell_measurement_theta_min 3.01 _cell_volume 622.33(3) _computing_cell_refinement 'SAINT v8.34A (Bruker, 2013)' _computing_data_collection 'APEX2 (Bruker, 2013)' _computing_data_reduction 'SAINT v8.34A (Bruker, 2013)' _computing_molecular_graphics 'Olex2 (Dolomanov et al., 2009)' _computing_publication_material 'Olex2 (Dolomanov et al., 2009)' _computing_structure_refinement 'XL (Sheldrick, 2008)' _computing_structure_solution 'XM (Sheldrick, 2008)' _diffrn_ambient_temperature 150 _diffrn_measured_fraction_theta_full 0.969 _diffrn_measured_fraction_theta_max 0.970 _diffrn_measurement_device_type 'Bruker APEX-II CCD' _diffrn_measurement_method '\f and \w scans' _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.54178 _diffrn_reflns_av_R_equivalents 0.0525 _diffrn_reflns_av_unetI/netI 0.0220 _diffrn_reflns_Laue_measured_fraction_full 0.969 _diffrn_reflns_Laue_measured_fraction_max 0.970 _diffrn_reflns_limit_h_max 9 _diffrn_reflns_limit_h_min -8 _diffrn_reflns_limit_k_max 17 _diffrn_reflns_limit_k_min -17 _diffrn_reflns_limit_l_max 6 _diffrn_reflns_limit_l_min -6 _diffrn_reflns_number 9008 _diffrn_reflns_point_group_measured_fraction_full 0.969 _diffrn_reflns_point_group_measured_fraction_max 0.970 _diffrn_reflns_theta_full 67.679 _diffrn_reflns_theta_max 68.316 _diffrn_reflns_theta_min 8.541 _diffrn_source 'Incoatec Mircosource' _diffrn_standards_number 0 _exptl_absorpt_coefficient_mu 0.576 _exptl_absorpt_correction_T_max 0.7531 _exptl_absorpt_correction_T_min 0.6154 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details ; SADABS-2012/1 (Bruker,2012) was used for absorption correction. wR2(int) was 0.1059 before and 0.0656 after correction. The Ratio of minimum to maximum transmission is 0.8172. The \l/2 correction factor is 0.0015. ; _exptl_crystal_colour colourless _exptl_crystal_colour_primary colourless _exptl_crystal_density_diffrn 1.250 _exptl_crystal_description Block _exptl_crystal_F_000 248 _exptl_crystal_size_max 0.364 _exptl_crystal_size_mid 0.18 _exptl_crystal_size_min 0.15 _exptl_special_details ; ? ; _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; _refine_diff_density_max 0.104 _refine_diff_density_min -0.090 _refine_diff_density_rms 0.020 _refine_ls_extinction_coef . _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.129 _refine_ls_hydrogen_treatment constr _refine_ls_matrix_type full _refine_ls_number_parameters 82 _refine_ls_number_reflns 579 _refine_ls_number_restraints 28 _refine_ls_restrained_S_all 1.154 _refine_ls_R_factor_all 0.0317 _refine_ls_R_factor_gt 0.0315 _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/[\s^2^(Fo^2^)+(0.0535P)^2^+0.0306P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0862 _refine_ls_wR_factor_ref 0.0863 _refine_special_details ; 1. Fixed Uiso At 1.2 times of: All C(H) groups, All N(H) groups 2. Restrained distances N1-C2 = N1-C9 1.38 with sigma of 0.02 C3-C4 1.47 with sigma of 0.02 C4-C9 1.43 with sigma of 0.02 C4-C5 \\sim C6-C7 \\sim C8-C9 with sigma of 0.02 C4-C6 \\sim C5-C7 \\sim C6-C8 \\sim C7-C9 \\sim C8-C4 \\sim C9-C5 with sigma of 0.02 3. Restrained planarity N1, C2, C3, C4, C5, C6, C7, C8, C9 with sigma of 0.1 4. Others Fixed Sof: N1(0.5) H1(0.5) C2(0.5) H2(0.5) C3(0.5) H3(0.5) C4(0.5) C5(0.5) H5(0.5) C6(0.5) H6(0.5) C7(0.5) H7(0.5) C8(0.5) H8(0.5) C9(0.5) 5.a Aromatic/amide H refined with riding coordinates: N1(H1), C2(H2), C3(H3), C5(H5), C6(H6), C7(H7), C8(H8) ; _reflns_Friedel_coverage 0.000 _reflns_Friedel_fraction_full . _reflns_Friedel_fraction_max . _reflns_number_gt 573 _reflns_number_total 579 _reflns_special_details ; Reflections were merged by SHELXL according to the crystal class for the calculation of statistics and refinement. _reflns_Friedel_fraction is defined as the number of unique Friedel pairs measured divided by the number that would be possible theoretically, ignoring centric projections and systematic absences. ; _reflns_threshold_expression 'I > 2\s(I)' _cod_data_source_file indole.cif _cod_data_source_block indole _cod_database_code 3500112 _cod_database_fobs_code 3500112 _vrf_plat088_indole ; PROBLEM: Poor Data / Parameter Ratio .................... 5.68 RESPONSE: The structure is disordered with the molecule lying over a mirror plane. The refinement involve the complete molecules and this situation generates a large number of parameters. However, this is counterbalanced by the use of numerous restraints applied on distances and atomic displacement parameters that links many of these parameters. ; _shelxl_version_number 2014-3 loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 'x, y, z' 2 '-x+1/2, -y, z+1/2' 3 'x+1/2, -y+1/2, -z+1/2' 4 '-x, y+1/2, -z' 5 '-x, -y, -z' 6 'x-1/2, y, -z-1/2' 7 '-x-1/2, y-1/2, z-1/2' 8 'x, -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_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 N1 N 0.2507(12) 0.1676(6) 1.2379(14) 0.0478(14) Uani 0.5 1 d D . P A -1 H1 H 0.3094 0.1620 1.3735 0.057 Uiso 0.5 1 calc R . P A -1 C2 C 0.1931(12) 0.0999(8) 1.0989(17) 0.058(2) Uani 0.5 1 d D . P A -1 H2 H 0.2090 0.0372 1.1351 0.070 Uiso 0.5 1 calc R . P A -1 C3 C 0.1092(6) 0.1309(3) 0.9000(9) 0.0524(9) Uani 0.5 1 d D . P A -1 H3 H 0.0586 0.0952 0.7754 0.063 Uiso 0.5 1 calc R . P A -1 C4 C 0.11227(15) 0.22716(8) 0.9152(2) 0.0371(5) Uani 0.5 1 d D . P A -1 C5 C 0.05234(17) 0.29838(11) 0.7706(2) 0.0418(4) Uani 0.5 1 d . . P A -1 H5 H -0.0086 0.2863 0.6249 0.050 Uiso 0.5 1 calc R . P A -1 C6 C 0.0834(6) 0.3866(3) 0.8436(8) 0.0440(7) Uani 0.5 1 d . . P A -1 H6 H 0.0421 0.4351 0.7453 0.053 Uiso 0.5 1 calc R . P A -1 C7 C 0.1718(12) 0.4078(8) 1.0529(17) 0.0466(12) Uani 0.5 1 d . . P A -1 H7 H 0.1921 0.4696 1.0957 0.056 Uiso 0.5 1 calc R . P A -1 C8 C 0.2306(15) 0.3378(8) 1.2002(18) 0.0464(13) Uani 0.5 1 d . . P A -1 H8 H 0.2899 0.3513 1.3464 0.056 Uiso 0.5 1 calc R . P A -1 C9 C 0.20202(14) 0.2466(8) 1.13170(19) 0.0371(6) Uani 0.5 1 d D . 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 N1 0.034(2) 0.069(2) 0.040(3) 0.0164(17) -0.0027(14) 0.0088(14) C2 0.046(2) 0.058(4) 0.071(4) 0.009(3) 0.006(2) 0.009(2) C3 0.0420(16) 0.054(2) 0.061(3) -0.0172(15) 0.0094(15) -0.0065(12) C4 0.0228(6) 0.0570(15) 0.0314(6) -0.0026(5) 0.0040(4) -0.0019(5) C5 0.0257(7) 0.0687(9) 0.0309(7) 0.0055(6) -0.0021(5) -0.0029(6) C6 0.0324(13) 0.0507(18) 0.0489(17) 0.0141(11) 0.0040(11) 0.0004(10) C7 0.041(2) 0.0451(16) 0.053(2) -0.0011(18) 0.0067(18) -0.0030(15) C8 0.033(2) 0.073(3) 0.033(2) -0.0073(17) -0.0055(15) -0.0064(15) C9 0.0236(5) 0.0577(16) 0.0299(6) -0.012(3) 0.0019(4) -0.003(2) 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' 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 C2 N1 H1 126.4 . . C2 N1 C9 107.2(6) . . C9 N1 H1 126.4 . . N1 C2 H2 123.9 . . N1 C2 C3 112.2(8) . . C3 C2 H2 123.9 . . C2 C3 H3 126.9 . . C2 C3 C4 106.1(5) . . C4 C3 H3 126.9 . . C5 C4 C3 135.1(2) . . C5 C4 C9 119.9(5) . . C9 C4 C3 105.1(5) . . C4 C5 H5 120.7 . . C6 C5 C4 118.57(18) . . C6 C5 H5 120.7 . . C5 C6 H6 118.5 . . C5 C6 C7 123.0(5) . . C7 C6 H6 118.5 . . C6 C7 H7 120.4 . . C6 C7 C8 119.2(8) . . C8 C7 H7 120.4 . . C7 C8 H8 120.2 . . C7 C8 C9 119.6(7) . . C9 C8 H8 120.2 . . N1 C9 C4 109.4(7) . . N1 C9 C8 130.8(2) . . C8 C9 C4 119.8(6) . . loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 N1 H1 0.8800 . N1 C2 1.332(11) . N1 C9 1.352(10) . C2 H2 0.9500 . C2 C3 1.355(11) . C3 H3 0.9500 . C3 C4 1.415(5) . C4 C5 1.3950(18) . C4 C9 1.412(3) . C5 H5 0.9500 . C5 C6 1.377(6) . C6 H6 0.9500 . C6 C7 1.380(10) . C7 H7 0.9500 . C7 C8 1.388(12) . C8 H8 0.9500 . C8 C9 1.409(12) . loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 N1 C2 C3 C4 -0.6(5) . . . . C2 N1 C9 C4 -0.8(6) . . . . C2 N1 C9 C8 -179.2(7) . . . . C2 C3 C4 C5 179.0(4) . . . . C2 C3 C4 C9 0.1(5) . . . . C3 C4 C5 C6 -178.49(14) . . . . C3 C4 C9 N1 0.5(5) . . . . C3 C4 C9 C8 179.0(6) . . . . C4 C5 C6 C7 0.3(6) . . . . C5 C4 C9 N1 -178.6(5) . . . . C5 C4 C9 C8 0.0(6) . . . . C5 C6 C7 C8 -1.0(7) . . . . C6 C7 C8 C9 1.1(9) . . . . C7 C8 C9 N1 177.6(8) . . . . C7 C8 C9 C4 -0.6(10) . . . . C9 N1 C2 C3 0.9(6) . . . . C9 C4 C5 C6 0.2(3) . . . . loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 PubChem 798