Dear Martin, My approach to your problem is to download an MOL2 of the small-molecule compound from WebCSD rather than the small-molecule CIF file. MOL2 files have the advantage that both the coordinates and the CCDC-curated bond orders are included in the file. MOL2 files can be read by AceDRG, Grade2, and eLBOW.
I have recorded a YouTube video showing how to download a MOL2 file for your ligand from WebCSD, use it in the Grade Web Server to produce restraints and use them in COOT. Please see https://youtu.be/Sx6haYQ3tSY for the YouTube video. I will send you the Grade Web Server tarball off the bulletin board. I hope this is useful! Best regards, Oliver > On 19 Aug 2024, at 12:42, Martin Hu <[email protected]> wrote: > > Dear All, > > Thank you all for your help. I’ve tried several approaches to input this > file, including changing the format to mmCIF, importing it as coordinates, > and checking the restraints in the file. However, I am still unable to > install the experimental ligand structure into the protein. It seems that > COOT or JLigand cannot read the restraints from the CIF file. > > I’m wondering if anyone has faced a similar problem before, and if there is a > way to input the experimental structure and save its restraints so that it > can be refined with the overall protein structure in Refmac? > > I’ve attached the original CIF file here for your reference (in .txt format). > > Sincerely, > Martin > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ####################################################################### > # > # This file contains crystal structure data downloaded from the > # Cambridge Structural Database (CSD) hosted by the Cambridge > # Crystallographic Data Centre (CCDC). > # > # Full information about CCDC data access policies and citation > # guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 > # > # Audit and citation data items may have been added by the CCDC. > # Please retain this information to preserve the provenance of > # this file and to allow appropriate attribution of the data. > # > ####################################################################### > > data_twin5 > _audit_block_doi 10.5517/ccryflp > _database_code_depnum_ccdc_archive 'CCDC 713483' > loop_ > _citation_id > _citation_doi > _citation_year > 1 10.1016/j.dyepig.2009.03.001 2009 > _audit_update_record > ; > 2008-12-13 deposited with the CCDC. 2024-08-19 downloaded from the CCDC. > ; > > > > _audit_creation_method SHELXL-97 > > _chemical_name_systematic > ; > > ? > > ; > > _chemical_name_common ? > > _chemical_melting_point ? > > _chemical_formula_moiety 'C9 H7 B F2 N2' > > _chemical_formula_sum 'C9 H7 B F2 N2' > > _chemical_formula_weight 191.98 > > > > 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' > B B 0.0013 0.0007 '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' > F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' > > > > _symmetry_cell_setting Monoclinic > > _symmetry_space_group_name_H-M C2/c > _symmetry_space_group_name_Hall '-C 2yc' > > > > loop_ > > _symmetry_equiv_pos_as_xyz > > > > > > > > > 'x, y, z' > '-x, y, -z+1/2' > 'x+1/2, y+1/2, z' > '-x+1/2, y+1/2, -z+1/2' > '-x, -y, -z' > 'x, -y, z-1/2' > '-x+1/2, -y+1/2, -z' > 'x+1/2, -y+1/2, z-1/2' > > > > _cell_length_a 10.126(4) > > _cell_length_b 10.196(4) > > _cell_length_c 17.143(6) > > _cell_angle_alpha 90.00 > > _cell_angle_beta 102.285(6) > > _cell_angle_gamma 90.00 > > _cell_volume 1729.5(11) > > _cell_formula_units_Z 8 > > _cell_measurement_temperature 296(2) > > _cell_measurement_reflns_used 32 > > _cell_measurement_theta_min 2.45 > > _cell_measurement_theta_max 12.33 > > > > _exptl_crystal_description plate > > _exptl_crystal_colour orange > > _exptl_crystal_size_max 0.20 > > _exptl_crystal_size_mid 0.20 > > _exptl_crystal_size_min 0.04 > > _exptl_crystal_density_meas 'not measured' > > _exptl_crystal_density_diffrn 1.475 > > _exptl_crystal_density_method 'not measured' > > _exptl_crystal_F_000 784 > > _exptl_absorpt_coefficient_mu 0.119 > > _exptl_absorpt_correction_type multi-scan > > _exptl_absorpt_correction_T_min 0.9766 > > _exptl_absorpt_correction_T_max 0.9953 > > _exptl_absorpt_process_details twinabs > > > > _exptl_special_details > ; > > ? > > ; > > > > _diffrn_ambient_temperature 296(2) > > _diffrn_radiation_wavelength 0.71073 > > _diffrn_radiation_type MoK\a > > _diffrn_radiation_source 'fine-focus sealed tube' > > _diffrn_radiation_monochromator graphite > > _diffrn_measurement_device_type 'CCD area detector' > > _diffrn_measurement_method 'phi and omega scans' > > _diffrn_detector_area_resol_mean ? > > _diffrn_standards_number ? > > _diffrn_standards_interval_count ? > > _diffrn_standards_interval_time ? > > _diffrn_standards_decay_% ? > > _diffrn_reflns_number 3845 > > _diffrn_reflns_av_R_equivalents 0.0000 > > _diffrn_reflns_av_sigmaI/netI 0.2541 > > _diffrn_reflns_limit_h_min -11 > > _diffrn_reflns_limit_h_max 11 > > _diffrn_reflns_limit_k_min -11 > > _diffrn_reflns_limit_k_max 11 > > _diffrn_reflns_limit_l_min -19 > > _diffrn_reflns_limit_l_max 20 > > _diffrn_reflns_theta_min 2.43 > > _diffrn_reflns_theta_max 24.77 > > _reflns_number_total 3845 > > _reflns_number_gt 1360 > > _reflns_threshold_expression >2sigma(I) > > > > _computing_data_collection 'Bruker APEX II' > > _computing_cell_refinement 'Bruker APEX II' > > _computing_data_reduction 'Bruker APEX II' > > _computing_structure_solution 'SHELXS-97 (Sheldrick, 1990)' > > _computing_structure_refinement 'SHELXL-97 (Sheldrick, 1997)' > > _computing_molecular_graphics 'Bruker SHELXTL' > > _computing_publication_material 'Bruker SHELXTL' > > > > _refine_special_details > ; > > Refinement of F^2^ against ALL reflections. The weighted R-factor wR and > > goodness of fit S are based on F^2^, conventional R-factors R are based > > on F, with F set to zero for negative F^2^. The threshold expression of > > F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is > > not relevant to the choice of reflections for refinement. R-factors based > > on F^2^ are statistically about twice as large as those based on F, and R- > > factors based on ALL data will be even larger. > > ; > > > > _refine_ls_structure_factor_coef Fsqd > > _refine_ls_matrix_type full > > _refine_ls_weighting_scheme calc > > _refine_ls_weighting_details > 'calc w=1/[\s^2^(Fo^2^)+(0.1025P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' > > _atom_sites_solution_primary direct > > _atom_sites_solution_secondary difmap > > _atom_sites_solution_hydrogens geom > > _refine_ls_hydrogen_treatment refall > > _refine_ls_extinction_method SHELXL > > _refine_ls_extinction_coef 0.0053(16) > > _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ > > _refine_ls_number_reflns 3845 > > _refine_ls_number_parameters 129 > > _refine_ls_number_restraints 0 > > _refine_ls_R_factor_all 0.2818 > > _refine_ls_R_factor_gt 0.1029 > > _refine_ls_wR_factor_ref 0.2803 > > _refine_ls_wR_factor_gt 0.1990 > > _refine_ls_goodness_of_fit_ref 1.004 > > _refine_ls_restrained_S_all 1.004 > > _refine_ls_shift/su_max 0.000 > > _refine_ls_shift/su_mean 0.000 > > > > 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 > > _atom_site_disorder_assembly > > _atom_site_disorder_group > > > > > > > > > > > > > > > > > > > > > > F1 F 0.0587(3) 0.1257(4) 0.09256(19) 0.0773(12) Uani 1 1 d . . . > F2 F -0.0926(3) 0.2839(3) 0.10355(19) 0.0796(13) Uani 1 1 d . . . > N1 N 0.0270(6) 0.3022(5) -0.0036(3) 0.0592(14) Uani 1 1 d . . . > N2 N 0.1431(5) 0.3421(4) 0.1373(3) 0.0582(15) Uani 1 1 d . . . > B1 B 0.0302(8) 0.2605(8) 0.0838(5) 0.062(2) Uani 1 1 d . . . > C1 C -0.0617(7) 0.2670(7) -0.0700(5) 0.076(2) Uani 1 1 d . . . > H1A H -0.1374 0.2152 -0.0703 0.092 Uiso 1 1 calc R . . > C2 C -0.0270(8) 0.3169(7) -0.1378(4) 0.076(2) Uani 1 1 d . . . > H2A H -0.0726 0.3045 -0.1904 0.092 Uiso 1 1 calc R . . > C3 C 0.0882(8) 0.3883(6) -0.1116(4) 0.0696(19) Uani 1 1 d . . . > H3A H 0.1350 0.4356 -0.1434 0.084 Uiso 1 1 calc R . . > C4 C 0.1228(7) 0.3776(6) -0.0288(4) 0.0583(17) Uani 1 1 d . . . > C5 C 0.2233(6) 0.4346(6) 0.0274(4) 0.0634(18) Uani 1 1 d . . . > H5A H 0.2867 0.4867 0.0099 0.076 Uiso 1 1 calc R . . > C6 C 0.2352(6) 0.4185(6) 0.1085(4) 0.0562(17) Uani 1 1 d . . . > C7 C 0.3230(7) 0.4738(6) 0.1728(5) 0.068(2) Uani 1 1 d . . . > H7A H 0.3941 0.5301 0.1700 0.082 Uiso 1 1 calc R . . > C8 C 0.2876(7) 0.4315(7) 0.2418(4) 0.075(2) Uani 1 1 d . . . > H8A H 0.3286 0.4536 0.2939 0.090 Uiso 1 1 calc R . . > C9 C 0.1766(7) 0.3482(6) 0.2168(4) 0.071(2) Uani 1 1 d . . . > H9A H 0.1324 0.3033 0.2510 0.085 Uiso 1 1 calc R . . > > > > 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 > > > > > > > > > > > > > > > F1 0.086(3) 0.061(3) 0.086(3) 0.008(2) 0.023(2) -0.007(2) > F2 0.055(2) 0.103(3) 0.089(3) -0.004(2) 0.0317(19) -0.010(2) > N1 0.057(4) 0.057(4) 0.065(4) 0.006(3) 0.017(3) 0.000(3) > N2 0.053(4) 0.058(4) 0.067(4) 0.008(3) 0.024(3) -0.007(3) > B1 0.053(6) 0.058(6) 0.080(6) 0.011(5) 0.026(5) 0.002(5) > C1 0.064(5) 0.088(6) 0.077(5) -0.003(4) 0.015(4) -0.014(4) > C2 0.083(6) 0.090(6) 0.059(5) 0.000(4) 0.023(4) 0.003(5) > C3 0.077(6) 0.066(5) 0.070(5) 0.012(4) 0.026(4) -0.002(4) > C4 0.049(5) 0.059(5) 0.068(5) 0.008(4) 0.015(4) 0.002(4) > C5 0.053(5) 0.062(5) 0.079(5) 0.018(4) 0.023(4) -0.003(4) > C6 0.059(5) 0.052(4) 0.058(5) 0.002(4) 0.013(4) -0.006(4) > C7 0.063(5) 0.066(5) 0.082(5) -0.004(4) 0.031(4) -0.007(4) > C8 0.055(5) 0.088(6) 0.076(5) -0.016(4) 0.000(4) 0.004(4) > C9 0.069(5) 0.100(6) 0.047(5) 0.019(4) 0.018(4) 0.003(4) > > > > _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. > > ; > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > F1 B1 1.405(8) . ? > F2 B1 1.378(7) . ? > N1 C1 1.340(7) . ? > N1 C4 1.377(7) . ? > N1 B1 1.551(8) . ? > N2 C9 1.335(6) . ? > N2 C6 1.384(6) . ? > N2 B1 1.547(8) . ? > C1 C2 1.382(7) . ? > C1 H1A 0.9300 . ? > C2 C3 1.367(7) . ? > C2 H2A 0.9300 . ? > C3 C4 1.393(7) . ? > C3 H3A 0.9300 . ? > C4 C5 1.373(7) . ? > C5 C6 1.380(7) . ? > C5 H5A 0.9300 . ? > C6 C7 1.381(7) . ? > C7 C8 1.375(7) . ? > C7 H7A 0.9300 . ? > C8 C9 1.401(7) . ? > C8 H8A 0.9300 . ? > C9 H9A 0.9300 . ? > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > C1 N1 C4 105.8(5) . . ? > C1 N1 B1 128.2(6) . . ? > C4 N1 B1 125.8(6) . . ? > C9 N2 C6 107.1(5) . . ? > C9 N2 B1 128.7(6) . . ? > C6 N2 B1 124.1(5) . . ? > F2 B1 F1 108.6(6) . . ? > F2 B1 N2 110.7(6) . . ? > F1 B1 N2 110.7(6) . . ? > F2 B1 N1 110.8(6) . . ? > F1 B1 N1 109.5(6) . . ? > N2 B1 N1 106.6(6) . . ? > N1 C1 C2 111.8(6) . . ? > N1 C1 H1A 124.1 . . ? > C2 C1 H1A 124.1 . . ? > C3 C2 C1 105.7(6) . . ? > C3 C2 H2A 127.1 . . ? > C1 C2 H2A 127.1 . . ? > C2 C3 C4 107.8(6) . . ? > C2 C3 H3A 126.1 . . ? > C4 C3 H3A 126.1 . . ? > C5 C4 N1 118.9(6) . . ? > C5 C4 C3 132.1(7) . . ? > N1 C4 C3 108.8(6) . . ? > C4 C5 C6 123.3(6) . . ? > C4 C5 H5A 118.3 . . ? > C6 C5 H5A 118.3 . . ? > C5 C6 N2 120.3(6) . . ? > C5 C6 C7 131.3(7) . . ? > N2 C6 C7 108.3(6) . . ? > C8 C7 C6 108.5(6) . . ? > C8 C7 H7A 125.8 . . ? > C6 C7 H7A 125.8 . . ? > C7 C8 C9 105.5(6) . . ? > C7 C8 H8A 127.3 . . ? > C9 C8 H8A 127.3 . . ? > N2 C9 C8 110.7(6) . . ? > N2 C9 H9A 124.7 . . ? > C8 C9 H9A 124.7 . . ? > > > > 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 > > _geom_torsion_publ_flag > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > C9 N2 B1 F2 53.6(9) . . . . ? > C6 N2 B1 F2 -130.6(6) . . . . ? > C9 N2 B1 F1 -66.9(8) . . . . ? > C6 N2 B1 F1 108.9(6) . . . . ? > C9 N2 B1 N1 174.2(5) . . . . ? > C6 N2 B1 N1 -10.0(8) . . . . ? > C1 N1 B1 F2 -53.0(9) . . . . ? > C4 N1 B1 F2 131.8(6) . . . . ? > C1 N1 B1 F1 66.8(8) . . . . ? > C4 N1 B1 F1 -108.4(6) . . . . ? > C1 N1 B1 N2 -173.5(6) . . . . ? > C4 N1 B1 N2 11.3(8) . . . . ? > C4 N1 C1 C2 0.0(7) . . . . ? > B1 N1 C1 C2 -175.9(6) . . . . ? > N1 C1 C2 C3 -0.9(8) . . . . ? > C1 C2 C3 C4 1.4(7) . . . . ? > C1 N1 C4 C5 176.1(5) . . . . ? > B1 N1 C4 C5 -7.8(9) . . . . ? > C1 N1 C4 C3 0.9(7) . . . . ? > B1 N1 C4 C3 177.0(5) . . . . ? > C2 C3 C4 C5 -175.9(7) . . . . ? > C2 C3 C4 N1 -1.5(7) . . . . ? > N1 C4 C5 C6 1.1(9) . . . . ? > C3 C4 C5 C6 175.1(6) . . . . ? > C4 C5 C6 N2 -0.1(9) . . . . ? > C4 C5 C6 C7 -175.4(6) . . . . ? > C9 N2 C6 C5 -177.9(5) . . . . ? > B1 N2 C6 C5 5.6(9) . . . . ? > C9 N2 C6 C7 -1.6(6) . . . . ? > B1 N2 C6 C7 -178.2(6) . . . . ? > C5 C6 C7 C8 176.3(6) . . . . ? > N2 C6 C7 C8 0.6(7) . . . . ? > C6 C7 C8 C9 0.6(7) . . . . ? > C6 N2 C9 C8 2.0(7) . . . . ? > B1 N2 C9 C8 178.4(6) . . . . ? > C7 C8 C9 N2 -1.6(7) . . . . ? > > > > _diffrn_measured_fraction_theta_max 0.987 > > _diffrn_reflns_theta_full 24.77 > > _diffrn_measured_fraction_theta_full 0.987 > > _refine_diff_density_max 0.181 > > _refine_diff_density_min -0.178 > > _refine_diff_density_rms 0.049 > > > > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
