Hi,
Sorry. One correction in the restraint or dictionary file. There are
three rings in the molecules. Two rings (without B1 atom) are aromatic
and the ring with B1 is not. That might not affect the result of
refinement too much. Anyway, the new restraint file is attached again.
Best wishes,
Fei
On 2024-08-19 14:42, Hu, Wenhao wrote:
Dear Jon,
Thank you so much for all your effort! I really appreciate it. I’ve
just tried to load the files, but unfortunately, it still won’t open
and continues to show the error message I’ve attached here.
Thanks again for your help.
Best regards,
Martin
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon
Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
⚠ Caution: External sender
I made your cif into a pdb (attached) which looks OK. Maybe worth
trying with that.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent from Proton Mail Android
-------- Original Message --------
On 19/08/2024 12:42, Martin Hu <wenhao.hu...@ucl.ac.uk> 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623540130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=l0Po7pO%2B5QxANPgjMOPRsZzuCyiu1Jx0xQ%2BVH4J08qQ%3D&reserved=0
[1]
This message was issued to members of
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623550984%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=SmjT9S9fJbDmq64tKZuw8LlsPPiQ8rbnSD%2BBt4RF35Y%3D&reserved=0
[2], a mailing list hosted by
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623557690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ED9U15EbAizx%2FIHYsNo47dGsKlgUWbPQkfW4Dvl2P%2BA%3D&reserved=0
[3], terms & conditions are available at
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623565219%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=CNDtlF8SLHwoa8GmZ1ZjbeTyBljLAP4PXvK0ddmYY%2Bw%3D&reserved=0
[4]
#######################################################################
#
# 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
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccdc.cam.ac.uk%2Faccess%2FV1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623572595%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1UNcBtGEJl2mElc8AyyDvIzhkmQzINthVoWLdUFtKPk%3D&reserved=0
[5]
#
# 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623579764%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=qSQVtftKDaI3EdU4qaBw9xq%2B1%2FlGJjUkOJmmF7rAs4w%3D&reserved=0
[1]
This message was issued to members of
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623587236%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tv0hv3TqB9K5wnUBXLoSZoTwGUZabcYv6MF1ZR%2Bnl7s%3D&reserved=0
[2], a mailing list hosted by
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623594397%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=k%2FTrh9sIdYt6CK9mpJQQWx9RQBM%2F1yV4ZOuH0iO1qZs%3D&reserved=0
[3], terms & conditions are available at
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623601540%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=mtC89HrZkZFZL7ew%2FXxPQmwuaMPiEW3cBzKMXDT%2Fcss%3D&reserved=0
[4]
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623609403%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wThRROTTYEs2sTuXO0DltSD4trlT4HVPS%2B6CPUwoC%2F0%3D&reserved=0
[1]
This message was issued to members of
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623616705%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=qTSTVPdfiqJu5oQ2RVba7afb8RwqUpZo7qCje9RXJnU%3D&reserved=0
[2], a mailing list hosted by
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623624045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Jb9ow%2BXW4uQ%2FSqCO26Qw389kQD8sYtOQTYqxL%2FQQGLk%3D&reserved=0
[3], terms & conditions are available at
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623631243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=eFMOUTGwlhfqjyF9OHlUJuFplYhTzPGYnK1FfX5IOc4%3D&reserved=0
[4]
-------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
Links:
------
[1]
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
[2] http://www.jiscmail.ac.uk/CCP4BB
[3] http://www.jiscmail.ac.uk/
[4] https://www.jiscmail.ac.uk/policyandsecurity/
[5] http://www.ccdc.cam.ac.uk/access/V1
--
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk
Tel:+44 1223 4027844
########################################################################
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/
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
LIG LIG "Test_713483_mol_1" NON-POLYMER 21 14 .
#
data_comp_LIG
_chem_comp.pdbx_type HETAIN
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
LIG F1 F1 F F 0 0.069 1.353 1.618 0.069 1.353 1.618
LIG N2 N2 N NR5 1 0.958 3.487 2.281 0.958 3.487 2.281
LIG B1 B1 B B -1 -0.056 2.716 1.408 -0.056 2.716 1.408
LIG C5 C5 C CR16 0 2.111 4.516 0.440 2.111 4.516 0.440
LIG C6 C6 C CR56 0 1.959 4.320 1.806 1.959 4.320 1.806
LIG C7 C7 C CR15 0 2.666 4.832 2.904 2.666 4.832 2.904
LIG C8 C8 C CR15 0 2.089 4.304 4.039 2.089 4.304 4.039
LIG C9 C9 C CR15 0 1.046 3.485 3.624 1.046 3.485 3.624
LIG F2 F2 F F 0 -1.348 3.110 1.713 -1.348 3.110 1.713
LIG N1 N1 N NR5 0 0.268 3.057 -0.064 0.268 3.057 -0.064
LIG C1 C1 C CR15 0 -0.363 2.607 -1.164 -0.363 2.607 -1.164
LIG C2 C2 C CR15 0 0.222 3.141 -2.306 0.222 3.141 -2.306
LIG C3 C3 C CR15 0 1.256 3.953 -1.891 1.256 3.953 -1.891
LIG C4 C4 C CR56 0 1.283 3.899 -0.489 1.283 3.899 -0.489
LIG H5A H5A H H 0 2.790 5.081 0.136 2.790 5.081 0.136
LIG H7A H7A H H 0 3.399 5.425 2.870 3.399 5.425 2.870
LIG H8A H8A H H 0 2.351 4.468 4.929 2.351 4.468 4.929
LIG H9A H9A H H 0 0.480 2.998 4.199 0.480 2.998 4.199
LIG H1A H1A H H 0 -1.096 2.015 -1.159 -1.096 2.015 -1.159
LIG H2A H2A H H 0 -0.039 2.978 -3.197 -0.039 2.978 -3.197
LIG H3A H3A H H 0 1.836 4.450 -2.443 1.836 4.450 -2.443
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
LIG F1 F(B[6]N[5a,6]2F)
LIG N2 N[5a,6](C[5a,6]C[5a]C[6])(B[6]N[5a,6]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG B1 B[6](N[5a,6]C[5a,6]C[5a])2(F)2{2|H<1>,5|C<3>}
LIG C5 C[6](C[5a,6]N[5a,6]C[5a])2(H){1|B<4>,2|H<1>,4|C<3>}
LIG C6
C[5a,6](N[5a,6]C[5a]B[6])(C[6]C[5a,6]H)(C[5a]C[5a]H){1|C<3>,1|N<3>,2|F<1>,2|H<1>}
LIG C7 C[5a](C[5a,6]N[5a,6]C[6])(C[5a]C[5a]H)(H){1|B<4>,1|C<3>,2|H<1>}
LIG C8 C[5a](C[5a]C[5a,6]H)(C[5a]N[5a,6]H)(H){1|B<4>,1|C<3>}
LIG C9 C[5a](N[5a,6]C[5a,6]B[6])(C[5a]C[5a]H)(H){1|C<3>,1|H<1>,1|N<3>,2|F<1>}
LIG F2 F(B[6]N[5a,6]2F)
LIG N1 N[5a,6](C[5a,6]C[5a]C[6])(B[6]N[5a,6]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG C1 C[5a](N[5a,6]C[5a,6]B[6])(C[5a]C[5a]H)(H){1|C<3>,1|H<1>,1|N<3>,2|F<1>}
LIG C2 C[5a](C[5a]C[5a,6]H)(C[5a]N[5a,6]H)(H){1|B<4>,1|C<3>}
LIG C3 C[5a](C[5a,6]N[5a,6]C[6])(C[5a]C[5a]H)(H){1|B<4>,1|C<3>,2|H<1>}
LIG C4
C[5a,6](N[5a,6]C[5a]B[6])(C[6]C[5a,6]H)(C[5a]C[5a]H){1|C<3>,1|N<3>,2|F<1>,2|H<1>}
LIG H5A H(C[6]C[5a,6]2)
LIG H7A H(C[5a]C[5a,6]C[5a])
LIG H8A H(C[5a]C[5a]2)
LIG H9A H(C[5a]N[5a,6]C[5a])
LIG H1A H(C[5a]N[5a,6]C[5a])
LIG H2A H(C[5a]C[5a]2)
LIG H3A H(C[5a]C[5a,6]C[5a])
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
LIG F1 B1 SINGLE n 1.385 0.0107 1.385 0.0107
LIG N2 B1 SINGLE n 1.542 0.0100 1.542 0.0100
LIG N2 C9 DOUBLE y 1.346 0.0117 1.346 0.0117
LIG N2 C6 SINGLE y 1.385 0.0100 1.385 0.0100
LIG B1 F2 SINGLE n 1.385 0.0107 1.385 0.0107
LIG B1 N1 SINGLE n 1.542 0.0100 1.542 0.0100
LIG C5 C4 SINGLE n 1.388 0.0138 1.388 0.0138
LIG C5 C6 DOUBLE n 1.388 0.0138 1.388 0.0138
LIG C6 C7 SINGLE y 1.403 0.0116 1.403 0.0116
LIG C7 C8 DOUBLE y 1.378 0.0100 1.378 0.0100
LIG C8 C9 SINGLE y 1.389 0.0100 1.389 0.0100
LIG N1 C1 SINGLE y 1.346 0.0117 1.346 0.0117
LIG N1 C4 SINGLE y 1.385 0.0100 1.385 0.0100
LIG C1 C2 DOUBLE y 1.389 0.0100 1.389 0.0100
LIG C2 C3 SINGLE y 1.378 0.0100 1.378 0.0100
LIG C3 C4 DOUBLE y 1.403 0.0116 1.403 0.0116
LIG C5 H5A SINGLE n 1.085 0.0150 0.934 0.0100
LIG C7 H7A SINGLE n 1.085 0.0150 0.943 0.0123
LIG C8 H8A SINGLE n 1.085 0.0150 0.942 0.0100
LIG C9 H9A SINGLE n 1.085 0.0150 0.943 0.0100
LIG C1 H1A SINGLE n 1.085 0.0150 0.943 0.0100
LIG C2 H2A SINGLE n 1.085 0.0150 0.942 0.0100
LIG C3 H3A SINGLE n 1.085 0.0150 0.943 0.0123
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
LIG B1 N2 C9 127.009 1.50
LIG B1 N2 C6 125.646 1.50
LIG C9 N2 C6 107.346 1.50
LIG F1 B1 N2 110.377 1.50
LIG F1 B1 F2 109.494 1.50
LIG F1 B1 N1 110.377 1.50
LIG N2 B1 F2 110.377 1.50
LIG N2 B1 N1 106.070 1.50
LIG F2 B1 N1 110.377 1.50
LIG C4 C5 C6 122.931 1.50
LIG C4 C5 H5A 118.534 1.50
LIG C6 C5 H5A 118.534 1.50
LIG N2 C6 C5 120.882 1.50
LIG N2 C6 C7 108.218 1.50
LIG C5 C6 C7 130.900 1.50
LIG C6 C7 C8 107.117 1.50
LIG C6 C7 H7A 126.382 1.50
LIG C8 C7 H7A 126.501 1.50
LIG C7 C8 C9 107.016 1.50
LIG C7 C8 H8A 126.497 1.50
LIG C9 C8 H8A 126.487 1.50
LIG N2 C9 C8 110.304 1.50
LIG N2 C9 H9A 124.780 1.50
LIG C8 C9 H9A 124.916 1.50
LIG B1 N1 C1 127.009 1.50
LIG B1 N1 C4 125.646 1.50
LIG C1 N1 C4 107.346 1.50
LIG N1 C1 C2 110.304 1.50
LIG N1 C1 H1A 124.780 1.50
LIG C2 C1 H1A 124.916 1.50
LIG C1 C2 C3 107.016 1.50
LIG C1 C2 H2A 126.487 1.50
LIG C3 C2 H2A 126.497 1.50
LIG C2 C3 C4 107.117 1.50
LIG C2 C3 H3A 126.501 1.50
LIG C4 C3 H3A 126.382 1.50
LIG C5 C4 N1 120.882 1.50
LIG C5 C4 C3 130.900 1.50
LIG N1 C4 C3 108.218 1.50
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
LIG const_0 N1 C1 C2 C3 0.000 0.0 1
LIG const_1 H1A C1 C2 H2A 0.000 0.0 1
LIG const_2 C1 C2 C3 C4 0.000 0.0 1
LIG const_3 H2A C2 C3 H3A 0.000 0.0 1
LIG const_4 C2 C3 C4 N1 0.000 0.0 1
LIG const_5 H3A C3 C4 C5 0.000 0.0 1
LIG sp2_sp3_1 C9 N2 B1 F1 60.000 20.0 6
LIG const_6 C5 C6 N2 B1 0.000 0.0 1
LIG const_7 C7 C6 N2 C9 0.000 0.0 1
LIG const_8 C8 C9 N2 C6 0.000 0.0 1
LIG const_9 H9A C9 N2 B1 0.000 0.0 1
LIG sp2_sp3_2 C1 N1 B1 F1 -60.000 20.0 6
LIG sp2_sp2_1 N1 C4 C5 C6 0.000 5.0 1
LIG sp2_sp2_2 C3 C4 C5 H5A 0.000 5.0 1
LIG sp2_sp2_3 C4 C5 C6 N2 0.000 5.0 1
LIG sp2_sp2_4 H5A C5 C6 C7 0.000 5.0 1
LIG const_10 N2 C6 C7 C8 0.000 0.0 1
LIG const_11 C5 C6 C7 H7A 0.000 0.0 1
LIG const_12 C6 C7 C8 C9 0.000 0.0 1
LIG const_13 H7A C7 C8 H8A 0.000 0.0 1
LIG const_14 C7 C8 C9 N2 0.000 0.0 1
LIG const_15 H8A C8 C9 H9A 0.000 0.0 1
LIG const_16 C2 C1 N1 C4 0.000 0.0 1
LIG const_17 H1A C1 N1 B1 0.000 0.0 1
LIG const_18 C5 C4 N1 B1 0.000 0.0 1
LIG const_19 C3 C4 N1 C1 0.000 0.0 1
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
LIG chir_1 B1 F1 F2 N2 both
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
LIG plan-1 B1 0.020
LIG plan-1 C1 0.020
LIG plan-1 C2 0.020
LIG plan-1 C3 0.020
LIG plan-1 C4 0.020
LIG plan-1 C5 0.020
LIG plan-1 H1A 0.020
LIG plan-1 H2A 0.020
LIG plan-1 H3A 0.020
LIG plan-1 N1 0.020
LIG plan-2 B1 0.020
LIG plan-2 C5 0.020
LIG plan-2 C6 0.020
LIG plan-2 C7 0.020
LIG plan-2 C8 0.020
LIG plan-2 C9 0.020
LIG plan-2 H7A 0.020
LIG plan-2 H8A 0.020
LIG plan-2 H9A 0.020
LIG plan-2 N2 0.020
LIG plan-3 C4 0.020
LIG plan-3 C5 0.020
LIG plan-3 C6 0.020
LIG plan-3 H5A 0.020
loop_
_chem_comp_ring_atom.comp_id
_chem_comp_ring_atom.ring_serial_number
_chem_comp_ring_atom.atom_id
_chem_comp_ring_atom.is_aromatic_ring
LIG ring-1 N1 YES
LIG ring-1 C1 YES
LIG ring-1 C2 YES
LIG ring-1 C3 YES
LIG ring-1 C4 YES
LIG ring-2 N2 NO
LIG ring-2 B1 NO
LIG ring-2 C5 NO
LIG ring-2 C6 NO
LIG ring-2 N1 NO
LIG ring-2 C4 NO
LIG ring-3 N2 YES
LIG ring-3 C6 YES
LIG ring-3 C7 YES
LIG ring-3 C8 YES
LIG ring-3 C9 YES
loop_
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
LIG acedrg 295 "dictionary generator"
LIG acedrg_database 12 "data source"
LIG rdkit 2023.03.3 "Chemoinformatics tool"
LIG servalcat 0.4.74 'optimization tool'
########################################################################
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/
