Dear all,
The attached is a restraint file generated by aceDRG, using your
713483.txt as the input file. The latest version of aceDRG, currently
not released yet and under the final testing, can generate restraint or
dictionary files of ligands using input files in form of small molecule
cif files from CSD or COD. The things under testing are deciding
bond-orders and charges, the rest of the chemistry are already within
the released version of aceDRG. We will try to release that version,
which will deal with the molecules with metal as well, as soon as
possible. Meanwhile, please try that file and tell us (me, Garib, or
Paul) if you see any problem.
Best wishes,
Fei
On 2024-08-19 15:02, Paul Emsley wrote:
On 19/08/2024 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.
Martin,
These are not restraints. They are not in mmCIF format (as Philip
Jeffrey says) - which is the format Coot expects for restraints. Coot
- an indeed any other program - will continue to give you error
messages if you read in a small molecule cif files as if they were
restraints.
We, in the CCP4 world, typically use Acedrg to generate restraints.
You will need to generate a suitable input for Acedrg given your cif
file. The author of Acedrg would be in a good place to help you with
that. Have you ever played Street Fighter?
Paul.
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--
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
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#
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 0.057 1.314 1.644 0.057 1.314 1.644
LIG N2 N2 N NR5 1 0.974 3.504 2.269 0.974 3.504 2.269
LIG B1 B1 B B -1 -0.090 2.690 1.420 -0.090 2.690 1.420
LIG C5 C5 C CR16 0 2.169 4.568 0.423 2.169 4.568 0.423
LIG C6 C6 C CR56 0 1.978 4.340 1.782 1.978 4.340 1.782
LIG C7 C7 C CR15 0 2.676 4.844 2.916 2.676 4.844 2.916
LIG C8 C8 C CR15 0 2.072 4.295 4.049 2.072 4.295 4.049
LIG C9 C9 C CR15 0 1.027 3.474 3.626 1.027 3.474 3.626
LIG F2 F2 F F 0 -1.390 3.106 1.740 -1.390 3.106 1.740
LIG N1 N1 N NR5 0 0.294 3.080 -0.067 0.294 3.080 -0.067
LIG C1 C1 C CR15 0 -0.365 2.606 -1.156 -0.365 2.606 -1.156
LIG C2 C2 C CR15 0 0.224 3.143 -2.301 0.224 3.143 -2.301
LIG C3 C3 C CR15 0 1.275 3.971 -1.899 1.275 3.971 -1.899
LIG C4 C4 C CR56 0 1.320 3.930 -0.477 1.320 3.930 -0.477
LIG H5A H5A H H 0 2.855 5.138 0.120 2.855 5.138 0.120
LIG H7A H7A H H 0 3.408 5.435 2.903 3.408 5.435 2.903
LIG H8A H8A H H 0 2.324 4.451 4.939 2.324 4.451 4.939
LIG H9A H9A H H 0 0.446 2.974 4.188 0.446 2.974 4.188
LIG H1A H1A H H 0 -1.103 2.009 -1.135 -1.103 2.009 -1.135
LIG H2A H2A H H 0 -0.040 2.978 -3.187 -0.040 2.978 -3.187
LIG H3A H3A H H 0 1.847 4.463 -2.462 1.847 4.463 -2.462
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
LIG F1 F(B[6a]N[5a,6a]2F)
LIG N2
N[5a,6a](C[5a,6a]C[5a]C[6a])(B[6a]N[5a,6a]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG B1 B[6a](N[5a,6a]C[5a,6a]C[5a])2(F)2{2|H<1>,5|C<3>}
LIG C5 C[6a](C[5a,6a]N[5a,6a]C[5a])2(H){1|B<4>,2|H<1>,4|C<3>}
LIG C6
C[5a,6a](N[5a,6a]B[6a]C[5a])(C[6a]C[5a,6a]H)(C[5a]C[5a]H){1|C<3>,1|N<3>,2|F<1>,2|H<1>}
LIG C7 C[5a](C[5a,6a]N[5a,6a]C[6a])(C[5a]C[5a]H)(H){1|B<4>,1|C<3>,2|H<1>}
LIG C8 C[5a](C[5a]C[5a,6a]H)(C[5a]N[5a,6a]H)(H){1|B<4>,1|C<3>}
LIG C9
C[5a](N[5a,6a]C[5a,6a]B[6a])(C[5a]C[5a]H)(H){1|C<3>,1|H<1>,1|N<3>,2|F<1>}
LIG F2 F(B[6a]N[5a,6a]2F)
LIG N1
N[5a,6a](C[5a,6a]C[5a]C[6a])(B[6a]N[5a,6a]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG C1
C[5a](N[5a,6a]C[5a,6a]B[6a])(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,6a]H)(C[5a]N[5a,6a]H)(H){1|B<4>,1|C<3>}
LIG C3 C[5a](C[5a,6a]N[5a,6a]C[6a])(C[5a]C[5a]H)(H){1|B<4>,1|C<3>,2|H<1>}
LIG C4
C[5a,6a](N[5a,6a]B[6a]C[5a])(C[6a]C[5a,6a]H)(C[5a]C[5a]H){1|C<3>,1|N<3>,2|F<1>,2|H<1>}
LIG H5A H(C[6a]C[5a,6a]2)
LIG H7A H(C[5a]C[5a,6a]C[5a])
LIG H8A H(C[5a]C[5a]2)
LIG H9A H(C[5a]N[5a,6a]C[5a])
LIG H1A H(C[5a]N[5a,6a]C[5a])
LIG H2A H(C[5a]C[5a]2)
LIG H3A H(C[5a]C[5a,6a]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 1.401 0.0100 1.401 0.0100
LIG N2 B1 SINGLE y 1.587 0.0143 1.587 0.0143
LIG N2 C9 DOUBLE y 1.351 0.0177 1.351 0.0177
LIG N2 C6 SINGLE y 1.390 0.0166 1.390 0.0166
LIG B1 F2 SINGLE n 1.401 0.0100 1.401 0.0100
LIG B1 N1 SINGLE y 1.587 0.0143 1.587 0.0143
LIG C5 C4 SINGLE y 1.390 0.0109 1.390 0.0109
LIG C5 C6 DOUBLE y 1.390 0.0109 1.390 0.0109
LIG C6 C7 SINGLE y 1.429 0.0200 1.429 0.0200
LIG C7 C8 DOUBLE y 1.399 0.0100 1.399 0.0100
LIG C8 C9 SINGLE y 1.395 0.0200 1.395 0.0200
LIG N1 C1 SINGLE y 1.351 0.0177 1.351 0.0177
LIG N1 C4 SINGLE y 1.390 0.0166 1.390 0.0166
LIG C1 C2 DOUBLE y 1.395 0.0200 1.395 0.0200
LIG C2 C3 SINGLE y 1.399 0.0100 1.399 0.0100
LIG C3 C4 DOUBLE y 1.429 0.0200 1.429 0.0200
LIG C5 H5A SINGLE n 1.085 0.0150 0.942 0.0161
LIG C7 H7A SINGLE n 1.085 0.0150 0.941 0.0107
LIG C8 H8A SINGLE n 1.085 0.0150 0.939 0.0109
LIG C9 H9A SINGLE n 1.085 0.0150 0.950 0.0100
LIG C1 H1A SINGLE n 1.085 0.0150 0.950 0.0100
LIG C2 H2A SINGLE n 1.085 0.0150 0.939 0.0109
LIG C3 H3A SINGLE n 1.085 0.0150 0.941 0.0107
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 124.124 1.74
LIG B1 N2 C6 127.841 1.50
LIG C9 N2 C6 108.035 2.64
LIG F1 B1 N2 109.471 3.00
LIG F1 B1 F2 109.471 3.00
LIG F1 B1 N1 109.471 3.00
LIG N2 B1 F2 109.471 3.00
LIG N2 B1 N1 103.607 3.00
LIG F2 B1 N1 109.471 3.00
LIG C4 C5 C6 116.550 2.75
LIG C4 C5 H5A 121.725 1.50
LIG C6 C5 H5A 121.725 1.50
LIG N2 C6 C5 120.340 3.00
LIG N2 C6 C7 107.813 3.00
LIG C5 C6 C7 131.847 3.00
LIG C6 C7 C8 107.878 1.50
LIG C6 C7 H7A 125.977 1.50
LIG C8 C7 H7A 126.146 1.50
LIG C7 C8 C9 108.555 1.50
LIG C7 C8 H8A 125.722 1.50
LIG C9 C8 H8A 125.719 1.50
LIG N2 C9 C8 107.724 2.45
LIG N2 C9 H9A 125.957 2.22
LIG C8 C9 H9A 126.319 1.50
LIG B1 N1 C1 124.124 1.74
LIG B1 N1 C4 127.841 1.50
LIG C1 N1 C4 108.035 2.64
LIG N1 C1 C2 107.724 2.45
LIG N1 C1 H1A 125.957 2.22
LIG C2 C1 H1A 126.319 1.50
LIG C1 C2 C3 108.555 1.50
LIG C1 C2 H2A 125.719 1.50
LIG C3 C2 H2A 125.722 1.50
LIG C2 C3 C4 107.878 1.50
LIG C2 C3 H3A 126.146 1.50
LIG C4 C3 H3A 125.977 1.50
LIG C5 C4 N1 120.340 3.00
LIG C5 C4 C3 131.847 3.00
LIG N1 C4 C3 107.813 3.00
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 const_10 N1 C4 C5 C6 0.000 0.0 1
LIG const_11 C3 C4 C5 H5A 0.000 0.0 1
LIG const_12 C4 C5 C6 N2 0.000 0.0 1
LIG const_13 H5A C5 C6 C7 0.000 0.0 1
LIG const_14 N2 C6 C7 C8 0.000 0.0 1
LIG const_15 C5 C6 C7 H7A 0.000 0.0 1
LIG const_16 C6 C7 C8 C9 0.000 0.0 1
LIG const_17 H7A C7 C8 H8A 0.000 0.0 1
LIG const_18 C7 C8 C9 N2 0.000 0.0 1
LIG const_19 H8A C8 C9 H9A 0.000 0.0 1
LIG const_20 C2 C1 N1 C4 0.000 0.0 1
LIG const_21 H1A C1 N1 B1 0.000 0.0 1
LIG const_22 C5 C4 N1 B1 0.000 0.0 1
LIG const_23 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 C1 0.020
LIG plan-2 C3 0.020
LIG plan-2 C4 0.020
LIG plan-2 C5 0.020
LIG plan-2 C6 0.020
LIG plan-2 C7 0.020
LIG plan-2 C9 0.020
LIG plan-2 H5A 0.020
LIG plan-2 N1 0.020
LIG plan-2 N2 0.020
LIG plan-3 B1 0.020
LIG plan-3 C5 0.020
LIG plan-3 C6 0.020
LIG plan-3 C7 0.020
LIG plan-3 C8 0.020
LIG plan-3 C9 0.020
LIG plan-3 H7A 0.020
LIG plan-3 H8A 0.020
LIG plan-3 H9A 0.020
LIG plan-3 N2 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 YES
LIG ring-2 B1 YES
LIG ring-2 C5 YES
LIG ring-2 C6 YES
LIG ring-2 N1 YES
LIG ring-2 C4 YES
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'
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