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#$Date: 2025-08-20 17:12:52 +0300 (Wed, 20 Aug 2025) $
#$Revision: 301832 $
#$URL: file:///home/coder/svn-repositories/cod/cif/4/10/48/4104873.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_4104873
loop_
_publ_author_name
'Panče Naumov'
'Yutaka Ozawa'
'Kei Ohkubo'
'Shunichi Fukuzumi'
_publ_section_title
;
 Structure and Spectroscopy of Oxyluciferin, the Light Emitter of the
 Firefly Bioluminescence
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              11590
_journal_page_last               11605
_journal_paper_doi               10.1021/ja904309q
_journal_volume                  131
_journal_year                    2009
_chemical_formula_sum            'C10 H6 N2 O2 S2'
_chemical_formula_weight         250.29
_chemical_name_common            'firefly oxylcuiferin'
_space_group_IT_number           14
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  '-P 2yn'
_symmetry_space_group_name_H-M   'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-97
_cell_angle_alpha                90.00
_cell_angle_beta                 99.260(5)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   4.8806(4)
_cell_length_b                   18.8242(14)
_cell_length_c                   11.1298(8)
_cell_measurement_temperature    293(2)
_cell_volume                     1009.21(13)
_computing_cell_refinement       'APEX2 software (Bruker, 2007)'
_computing_data_collection       'APEX2 software (Bruker, 2007)'
_computing_data_reduction        'SAINT (Bruker, 2007)'
_computing_molecular_graphics    'DIAMOND (Brandenburg, 2005)'
_computing_publication_material  'WinGX (Farrugia, 1999)'
_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 2008)'
_diffrn_ambient_temperature      293(2)
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.996
_diffrn_measurement_device_type  'Bruker SMART APEX2 diffractometer'
_diffrn_measurement_method       'ω scans'
_diffrn_radiation_monochromator  'multilayer confocal TXS mirror'
_diffrn_radiation_source         'rotating anode'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0554
_diffrn_reflns_av_sigmaI/netI    0.0439
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            14599
_diffrn_reflns_theta_full        26.39
_diffrn_reflns_theta_max         26.39
_diffrn_reflns_theta_min         2.15
_exptl_absorpt_coefficient_mu    0.510
_exptl_absorpt_correction_T_max  0.9676
_exptl_absorpt_correction_T_min  0.8579
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details   'SADABS (Sheldrick, 1996)'
_exptl_crystal_colour            red
_exptl_crystal_density_diffrn    1.647
_exptl_crystal_description       needle
_exptl_crystal_F_000             512
_exptl_crystal_size_max          0.310
_exptl_crystal_size_mid          0.100
_exptl_crystal_size_min          0.065
_refine_diff_density_max         0.327
_refine_diff_density_min         -0.252
_refine_diff_density_rms         0.064
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.037
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     157
_refine_ls_number_reflns         2056
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.037
_refine_ls_R_factor_all          0.0913
_refine_ls_R_factor_gt           0.0524
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[σ²(Fo²)+(0.0625P)²+0.8795P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1239
_refine_ls_wR_factor_ref         0.1412
_reflns_number_gt                1376
_reflns_number_total             2056
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja904309q_si_002.cif
_cod_data_source_block           oxyl5_0m
_cod_database_code               4104873
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x+1/2, y+1/2, -z+1/2'
'-x, -y, -z'
'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_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
S2 S 0.9528(2) 0.35354(5) 0.52678(7) 0.0495(3) Uani 1 1 d .
S1 S 1.2633(2) 0.47919(6) 0.84793(8) 0.0596(3) Uani 1 1 d .
O1 O 0.2981(7) 0.13395(15) 0.5014(3) 0.0650(9) Uani 1 1 d .
N2 N 0.8689(6) 0.35657(14) 0.7501(2) 0.0421(7) Uani 1 1 d .
O2 O 1.6876(6) 0.56015(15) 0.6241(3) 0.0688(8) Uani 1 1 d .
N1 N 1.3472(6) 0.47268(15) 0.6270(2) 0.0435(7) Uani 1 1 d .
C5 C 0.7093(7) 0.30001(18) 0.6931(3) 0.0426(8) Uani 1 1 d .
C4 C 1.0044(7) 0.38684(18) 0.6738(3) 0.0415(8) Uani 1 1 d .
C10 C 0.5419(7) 0.25345(18) 0.7514(3) 0.0470(9) Uani 1 1 d .
H10 H 0.5226 0.2596 0.8326 0.056 Uiso 1 1 calc R
C7 C 0.5956(7) 0.23506(19) 0.5049(3) 0.0472(9) Uani 1 1 d .
H7 H 0.6120 0.2290 0.4234 0.057 Uiso 1 1 calc R
C8 C 0.4364(7) 0.18956(19) 0.5607(3) 0.0471(8) Uani 1 1 d .
C6 C 0.7319(7) 0.29040(18) 0.5721(3) 0.0419(8) Uani 1 1 d .
C2 C 1.5003(9) 0.5339(2) 0.8022(4) 0.0572(11) Uani 1 1 d .
C1 C 1.1993(7) 0.44416(18) 0.7049(3) 0.0444(8) Uani 1 1 d .
C3 C 1.5170(7) 0.52382(19) 0.6844(3) 0.0472(8) Uani 1 1 d .
C9 C 0.4107(8) 0.1994(2) 0.6830(3) 0.0586(10) Uani 1 1 d .
H9 H 0.3006 0.1681 0.7189 0.070 Uiso 1 1 calc R
H2 H 1.593(8) 0.559(2) 0.845(3) 0.052(12) Uiso 1 1 d .
H1O H 0.328(9) 0.135(2) 0.436(4) 0.076(15) Uiso 1 1 d .
H2O H 1.668(11) 0.537(3) 0.533(5) 0.13(2) Uiso 1 1 d .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0033 0.0016 '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 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
S S 0.1246 0.1234 '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
C4 S2 C6 88.63(16)
C2 S1 C1 89.17(19)
C8 O1 H1O 107(3)
C4 N2 C5 110.0(3)
C3 O2 H2O 107(3)
C1 N1 C3 109.5(3)
C6 C5 N2 114.4(3)
C6 C5 C10 120.4(3)
N2 C5 C10 125.2(3)
N2 C4 C1 124.1(3)
N2 C4 S2 116.8(3)
C1 C4 S2 119.2(2)
C9 C10 C5 117.1(3)
C9 C10 H10 121.4
C5 C10 H10 121.4
C8 C7 C6 118.8(3)
C8 C7 H7 120.6
C6 C7 H7 120.6
O1 C8 C7 122.3(3)
O1 C8 C9 117.4(3)
C7 C8 C9 120.3(3)
C5 C6 C7 121.2(3)
C5 C6 S2 110.2(3)
C7 C6 S2 128.6(2)
C3 C2 S1 111.2(3)
C3 C2 H2 125(3)
S1 C2 H2 124(3)
N1 C1 C4 123.5(3)
N1 C1 S1 114.6(3)
C4 C1 S1 121.8(3)
O2 C3 C2 124.0(4)
O2 C3 N1 120.4(3)
C2 C3 N1 115.6(3)
C10 C9 C8 122.2(3)
C10 C9 H9 118.9
C8 C9 H9 118.9
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
S2 C4 1.732(3)
S2 C6 1.734(3)
S1 C2 1.688(5)
S1 C1 1.705(3)
O1 C8 1.358(4)
O1 H1O 0.77(4)
N2 C4 1.291(4)
N2 C5 1.408(4)
O2 C3 1.339(4)
O2 H2O 1.09(6)
N1 C1 1.328(4)
N1 C3 1.361(4)
C5 C6 1.381(4)
C5 C10 1.424(4)
C4 C1 1.443(5)
C10 C9 1.367(5)
C10 H10 0.9300
C7 C8 1.370(4)
C7 C6 1.388(5)
C7 H7 0.9300
C8 C9 1.398(4)
C2 C3 1.340(5)
C2 H2 0.76(4)
C9 H9 0.9300
loop_
_cod_related_entry_id
_cod_related_entry_database
_cod_related_entry_code
1 ChemSpider 16237274
2 PubChem 135967518
