Your file has stray carriage returns and some "!"'s too. I have
removed them. Try this version.
Dale Tronrud
Mareike Kurz wrote:
> Dear Cooters,
> I modeled a small molecule using PRODRG2, but can't read the .cif file into
> coot. The errors message says, that the cif dictionary contains no
> restraints. I had this problem before and we found out that there were empty
> geometry loops at the end of the file. I had a look for this, but this time
> the file looks fine, but I still can't use.
> I have attached the file. If anyone would be so kind and have a look and it
> and maybe could fix, that would be great.
> Kind regards, Mareike
#
#
# WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to
# establish equivalence between model and topology. If
# you use O or other programmes that produce defective
# PDB files you must restore these columns, otherwise
# REFMAC5 will not recognise this topology.
#
#
# This file was generated by PRODRG version 071121.0636
# PRODRG written/copyrighted by Daan van Aalten
# and Alexander Schuettelkopf
#
# Questions/comments to [log in to unmask]
#
# When using this software in a publication, cite:
# A. W. Schuettelkopf and D. M. F. van Aalten (2004).
# PRODRG - a tool for high-throughput crystallography
# of protein-ligand complexes.
# Acta Crystallogr. D60, 1355--1363.
#
#
global_
_lib_name prodrg_lib
_lib_version 71121
_lib_update ?
#
# ---------------
#
data_comp_list
#
loop_
_chem_comp.id
_chem_comp.th!
ree_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
DRG DRG 'DRG ' non-polymer 14 6 .
#
# ---------------
#
data_comp_DRG
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
DRG OAA O OH1 -0.102
DRG HAA H HOH1 0.040
DRG CAD C CH2 0.049
DRG 1HAD H HCH2 0.000
DRG 2HAD H HCH2 0.000
DRG CAF C CH1 0.087
DRG 1HAF H HCH1 0.000
DRG OAC O OH1 -0.102
DRG HAC H HOH1 0.040
DRG CAE C CH2 0.050
DRG 1HAE H HCH2 0.000
DRG 2HAE H HCH2 0.000
DRG OAB O OH1 -0.102
DRG HAB H HOH1 0.040
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
DRG OAA n/a CAD START
DRG HAA OAA . .
DRG CAD OAA CAF .
DRG 1HAD CAD . .
DRG 2HAD CAD . .
DRG CAF CAD CAE .
DRG 1HAF CAF . .
DRG OAC CAF HAC .
DRG HAC OAC . .
DRG CAE CAF OAB .
DRG 1HAE CAE . .
DRG 2HAE CAE . .
DRG OAB CAE HAB .
DRG HAB OAB . END
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
DRG OAA HAA single 1.000 0.027
DRG OAA CAD single 1.430 0.025
DRG CAD CAF single 1.530 0.025
DRG CAF OAC single 1.430 0.025
DRG CAF CAE single 1.530 0.025
DRG OAC HAC single 1.000 0.027
DRG CAE OAB single 1.430 0.025
DRG OAB HAB single 1.000 0.027
DRG CAD 1HAD single 1.000 0.020
DRG CAD 2HAD single 1.000 0.020
DRG CAF 1HAF single 1.000 0.020
DRG CAE 1HAE single 1.000 0.020
DRG CAE 2HAE single 1.000 0.020
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
DRG HAA OAA CAD 109.500 3.158
DRG OAA CAD CAF 109.500 2.727
DRG CAD CAF OAC 109.500 2.727
DRG CAD CAF CAE 109.500 2.727
DRG OAC CAF CAE 109.500 2.727
DRG CAF OAC HAC 109.500 3.158
DRG CAF CAE OAB 109.500 2.727
DRG CAE OAB HAB 109.500 3.158
DRG OAA CAD 1HAD 109.500 3.300
DRG OAA CAD 2HAD 109.500 3.300
DRG CAD CAF 1HAF 109.500 3.300
DRG CAF CAE 1HAE 109.500 3.300
DRG CAF CAE 2HAE 109.500 3.300
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
DRG var_001 CAF CAD OAA HAA 60.000 13.333 3
DRG var_002 OAA CAD CAF CAE 60.000 2.857 3
DRG var_003 CAD CAF OAC HAC 60.000 13.333 3
DRG var_004 OAB CAE CAF CAD 60.000 2.857 3
DRG var_005 CAF CAE OAB HAB 60.000 13.333 3
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
DRG chir_001 CAF CAD CAE OAC positiv
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