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global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
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
DXD DXD '(1S,3S,4R)-4-(PHOSPHOOXYMETHYL)-CYCL' DNA 24 13 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DXD
#
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
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
DXD OP3 O OP -0.666 0.000 0.000 0.000
DXD P P P 0.000 -1.007 0.559 0.981
DXD OP1 O OP -0.666 -0.446 0.919 2.338
DXD OP2 O OP -0.666 -1.637 1.703 0.217
DXD "O5'" O O2 0.000 -2.163 -0.574 0.997
DXD "C5'" C CH2 0.000 -2.742 -0.968 -0.236
DXD "H5'1" H H 0.000 -1.971 -1.375 -0.894
DXD "H5'2" H H 0.000 -3.212 -0.107 -0.716
DXD "C4'" C CH1 0.000 -3.792 -2.034 0.037
DXD "H4'" H H 0.000 -3.308 -2.915 0.480
DXD "C3'" C CH1 0.000 -4.559 -2.455 -1.217
DXD "H3'" H H 0.000 -4.766 -1.574 -1.840
DXD "C2'" C CH2 0.000 -5.875 -3.049 -0.702
DXD "H2'1" H H 0.000 -5.861 -4.140 -0.751
DXD "H2'2" H H 0.000 -6.727 -2.671 -1.271
DXD "C1'" C CH1 0.000 -5.996 -2.603 0.759
DXD "H1'" H H 0.000 -6.990 -2.180 0.958
DXD "O6'" O OH1 0.000 -5.745 -3.726 1.599
DXD "H7'" H H 0.000 -6.199 -4.501 1.243
DXD "C6'" C CH2 0.000 -4.908 -1.554 0.961
DXD "H6'2" H H 0.000 -4.542 -1.522 1.990
DXD "H6'1" H H 0.000 -5.228 -0.554 0.659
DXD "O3'" O OH1 0.000 -3.817 -3.405 -1.961
DXD "HO3'" H H 0.000 -4.019 -4.280 -1.586
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
DXD OP3 n/a P START
DXD P OP3 "O5'" .
DXD OP1 P . .
DXD OP2 P . .
DXD "O5'" P "C5'" .
DXD "C5'" "O5'" "C4'" .
DXD "H5'1" "C5'" . .
DXD "H5'2" "C5'" . .
DXD "C4'" "C5'" "C3'" .
DXD "H4'" "C4'" . .
DXD "C3'" "C4'" "O3'" .
DXD "H3'" "C3'" . .
DXD "C2'" "C3'" "C1'" .
DXD "H2'1" "C2'" . .
DXD "H2'2" "C2'" . .
DXD "C1'" "C2'" "C6'" .
DXD "H1'" "C1'" . .
DXD "O6'" "C1'" "H7'" .
DXD "H7'" "O6'" . .
DXD "C6'" "C1'" "H6'1" .
DXD "H6'2" "C6'" . .
DXD "H6'1" "C6'" . .
DXD "O3'" "C3'" . END
DXD "HO3'" "O3'" . .
DXD "C4'" "C6'" . ADD
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
DXD OP1 P deloc 1.510 0.020
DXD OP2 P deloc 1.510 0.020
DXD "O5'" P single 1.610 0.020
DXD P OP3 deloc 1.510 0.020
DXD "C5'" "O5'" single 1.426 0.020
DXD "C4'" "C5'" single 1.524 0.020
DXD "H5'1" "C5'" single 1.092 0.020
DXD "H5'2" "C5'" single 1.092 0.020
DXD "C4'" "C6'" single 1.524 0.020
DXD "C3'" "C4'" single 1.524 0.020
DXD "H4'" "C4'" single 1.099 0.020
DXD "C6'" "C1'" single 1.524 0.020
DXD "O6'" "C1'" single 1.432 0.020
DXD "C1'" "C2'" single 1.524 0.020
DXD "H1'" "C1'" single 1.099 0.020
DXD "H6'1" "C6'" single 1.092 0.020
DXD "H6'2" "C6'" single 1.092 0.020
DXD "H7'" "O6'" single 0.967 0.020
DXD "C2'" "C3'" single 1.524 0.020
DXD "H2'1" "C2'" single 1.092 0.020
DXD "H2'2" "C2'" single 1.092 0.020
DXD "O3'" "C3'" single 1.432 0.020
DXD "H3'" "C3'" single 1.099 0.020
DXD "HO3'" "O3'" single 0.967 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
DXD OP3 P OP1 119.900 3.000
DXD OP3 P OP2 119.900 3.000
DXD OP3 P "O5'" 108.200 3.000
DXD OP1 P OP2 119.900 3.000
DXD OP1 P "O5'" 108.200 3.000
DXD OP2 P "O5'" 108.200 3.000
DXD P "O5'" "C5'" 120.500 3.000
DXD "O5'" "C5'" "H5'1" 109.470 3.000
DXD "O5'" "C5'" "H5'2" 109.470 3.000
DXD "O5'" "C5'" "C4'" 109.470 3.000
DXD "H5'1" "C5'" "H5'2" 107.900 3.000
DXD "H5'1" "C5'" "C4'" 109.470 3.000
DXD "H5'2" "C5'" "C4'" 109.470 3.000
DXD "C5'" "C4'" "H4'" 108.340 3.000
DXD "C5'" "C4'" "C3'" 111.000 3.000
DXD "C5'" "C4'" "C6'" 109.470 3.000
DXD "H4'" "C4'" "C3'" 108.340 3.000
DXD "H4'" "C4'" "C6'" 108.340 3.000
DXD "C3'" "C4'" "C6'" 111.000 3.000
DXD "C4'" "C3'" "H3'" 108.340 3.000
DXD "C4'" "C3'" "C2'" 111.000 3.000
DXD "C4'" "C3'" "O3'" 109.470 3.000
DXD "H3'" "C3'" "C2'" 108.340 3.000
DXD "H3'" "C3'" "O3'" 109.470 3.000
DXD "C2'" "C3'" "O3'" 109.470 3.000
DXD "C3'" "C2'" "H2'1" 109.470 3.000
DXD "C3'" "C2'" "H2'2" 109.470 3.000
DXD "C3'" "C2'" "C1'" 111.000 3.000
DXD "H2'1" "C2'" "H2'2" 107.900 3.000
DXD "H2'1" "C2'" "C1'" 109.470 3.000
DXD "H2'2" "C2'" "C1'" 109.470 3.000
DXD "C2'" "C1'" "H1'" 108.340 3.000
DXD "C2'" "C1'" "O6'" 109.470 3.000
DXD "C2'" "C1'" "C6'" 109.470 3.000
DXD "H1'" "C1'" "O6'" 109.470 3.000
DXD "H1'" "C1'" "C6'" 108.340 3.000
DXD "O6'" "C1'" "C6'" 109.470 3.000
DXD "C1'" "O6'" "H7'" 109.470 3.000
DXD "C1'" "C6'" "H6'2" 109.470 3.000
DXD "C1'" "C6'" "H6'1" 109.470 3.000
DXD "C1'" "C6'" "C4'" 111.000 3.000
DXD "H6'2" "C6'" "H6'1" 107.900 3.000
DXD "H6'2" "C6'" "C4'" 109.470 3.000
DXD "H6'1" "C6'" "C4'" 109.470 3.000
DXD "C3'" "O3'" "HO3'" 109.470 3.000
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
DXD var_1 OP3 P "O5'" "C5'" -54.236 20.000 1
DXD var_2 P "O5'" "C5'" "C4'" -179.991 20.000 1
DXD var_3 "O5'" "C5'" "C4'" "C3'" 175.541 20.000 3
DXD var_4 "C5'" "C4'" "C6'" "C1'" 150.000 20.000 3
DXD var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
DXD var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DXD var_7 "C3'" "C2'" "C1'" "C6'" 0.000 20.000 3
DXD var_8 "C2'" "C1'" "O6'" "H7'" -42.988 20.000 1
DXD var_9 "C2'" "C1'" "C6'" "C4'" -30.000 20.000 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
DXD chir_01 "C4'" "C5'" "C6'" "C3'" negativ
DXD chir_02 "C1'" "C6'" "O6'" "C2'" positiv
DXD chir_03 "C3'" "C4'" "C2'" "O3'" positiv
# ------------------------------------------------------
|
