REFMAC (CCP4: Supported Program)

User's manual for the program refmac version 5.0.*

DICTIONARY

Example of minimum description

# ---   My monomer for LAP
#
data_comp_list
#
#  List of ligand in this dictionary file. In this case only one. Last item "M" 
# shows that program should expect minimum description. 
#  File is cif style so format is not important. There should be space between 
#  items.
#
loop_
_chem_comp.id
_chem_comp.name
_chem_comp.desc_level
LAP       '.                                   '  M
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_LAP
#
# List of elements present in the ligand
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol

LAP C1  C
LAP C2  C
LAP C3  C
LAP C4  C
LAP C5  C
LAP C6  C
LAP O1  O
LAP O2  O
LAP O3  O
LAP O4  O
LAP O5  O
LAP O6  O
LAP P1  P
LAP O11 O
LAP O12 O
LAP O13 O
LAP P4  P
LAP O41 O
LAP O42 O
LAP O43 O
LAP P5  P
LAP O51 O
LAP O52 O
LAP O53 O
#
#   List of connectivity. I.e. what is bound to what with what bond order (only
#   single and double should be given. Program will work out atomic types 
#   according to number of bonds.) Hydrogens will be added.
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type

LAP C1 C2  single
LAP C1 O1  single
LAP C1 C6  single
LAP C2 O2  single
LAP C2 C3  single
LAP C3 O3  single
LAP C3 C4  single
LAP C4 O4  single
LAP C4 C5  single
LAP C5 O5  single
LAP C5 O5  single
LAP C5 C6  single
LAP O1 P1  single
LAP P1 O11 single
LAP P1 O12 double
LAP P1 O13 single
LAP O4 P4  single
LAP P4 O41 single
LAP P4 O42 double
LAP P4 O43 single
LAP O5 P5  single
LAP P5 O51 single
LAP P5 O52 double
LAP P5 O53 single
#
#  chiral volume signs should be added here
#----------------------------------------------