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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
DDN DDN '3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOP' DNA 33 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DDN
#
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
DDN OP3 O OP -0.666 0.000 0.000 0.000
DDN P P P 0.000 -0.497 0.394 -1.374
DDN OP1 O OP -0.666 0.105 -0.527 -2.412
DDN OP2 O OP -0.666 -0.087 1.821 -1.667
DDN "O5'" O O2 0.000 -2.102 0.278 -1.418
DDN "C5'" C CH2 0.000 -2.604 1.075 -0.344
DDN "H5'" H H 0.000 -2.286 2.111 -0.481
DDN "H5''" H H 0.000 -2.212 0.697 0.602
DDN "C4'" C CH1 0.000 -4.132 1.007 -0.329
DDN "H4'" H H 0.000 -4.537 1.313 -1.304
DDN "C3'" C CH1 0.000 -4.708 1.898 0.793
DDN "H3'" H H 0.000 -3.963 2.045 1.587
DDN "C2'" C CH2 0.000 -5.918 1.100 1.329
DDN "H2'" H H 0.000 -6.857 1.641 1.198
DDN "H2''" H H 0.000 -5.798 0.830 2.380
DDN "C1'" C CH1 0.000 -5.934 -0.181 0.465
DDN "H1'" H H 0.000 -6.617 -0.059 -0.387
DDN "O4'" O O2 0.000 -4.574 -0.330 0.001
DDN N1 N NR6 0.000 -6.328 -1.336 1.274
DDN C6 C CR16 0.000 -7.520 -1.976 0.969
DDN H6 H H 0.000 -8.124 -1.609 0.148
DDN C5 C CR16 0.000 -7.933 -3.023 1.660
DDN H5 H H 0.000 -8.866 -3.517 1.419
DDN C4 C CH1 0.000 -7.064 -3.511 2.801
DDN H4 H H 0.000 -7.666 -3.482 3.719
DDN O4 O OH1 0.000 -6.726 -4.875 2.543
DDN HO4 H H 0.000 -6.170 -5.210 3.259
DDN N3 N NR16 0.000 -5.815 -2.776 3.057
DDN HN3 H H 0.000 -5.178 -3.060 3.829
DDN C2 C CR6 0.000 -5.516 -1.725 2.266
DDN O2 O O 0.000 -4.488 -1.108 2.465
DDN "O3'" O OH1 0.000 -5.132 3.157 0.266
DDN H1 H H 0.000 -5.508 3.657 1.004
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
DDN OP3 n/a P START
DDN P OP3 "O5'" .
DDN OP1 P . .
DDN OP2 P . .
DDN "O5'" P "C5'" .
DDN "C5'" "O5'" "C4'" .
DDN "H5'" "C5'" . .
DDN "H5''" "C5'" . .
DDN "C4'" "C5'" "C3'" .
DDN "H4'" "C4'" . .
DDN "C3'" "C4'" "O3'" .
DDN "H3'" "C3'" . .
DDN "C2'" "C3'" "C1'" .
DDN "H2'" "C2'" . .
DDN "H2''" "C2'" . .
DDN "C1'" "C2'" N1 .
DDN "H1'" "C1'" . .
DDN "O4'" "C1'" . .
DDN N1 "C1'" C6 .
DDN C6 N1 C5 .
DDN H6 C6 . .
DDN C5 C6 C4 .
DDN H5 C5 . .
DDN C4 C5 N3 .
DDN H4 C4 . .
DDN O4 C4 HO4 .
DDN HO4 O4 . .
DDN N3 C4 C2 .
DDN HN3 N3 . .
DDN C2 N3 O2 .
DDN O2 C2 . .
DDN "O3'" "C3'" . END
DDN H1 "O3'" . .
DDN "C4'" "O4'" . ADD
DDN N1 C2 . 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
DDN P OP3 deloc 1.510 0.020
DDN OP1 P deloc 1.510 0.020
DDN OP2 P deloc 1.510 0.020
DDN "O5'" P single 1.610 0.020
DDN "C5'" "O5'" single 1.426 0.020
DDN "C4'" "C5'" single 1.524 0.020
DDN "H5'" "C5'" single 1.092 0.020
DDN "H5''" "C5'" single 1.092 0.020
DDN "C4'" "O4'" single 1.426 0.020
DDN "C3'" "C4'" single 1.524 0.020
DDN "H4'" "C4'" single 1.099 0.020
DDN "O4'" "C1'" single 1.426 0.020
DDN "O3'" "C3'" single 1.432 0.020
DDN "C2'" "C3'" single 1.524 0.020
DDN "H3'" "C3'" single 1.099 0.020
DDN H1 "O3'" single 0.967 0.020
DDN "C1'" "C2'" single 1.524 0.020
DDN "H2'" "C2'" single 1.092 0.020
DDN "H2''" "C2'" single 1.092 0.020
DDN N1 "C1'" single 1.465 0.020
DDN "H1'" "C1'" single 1.099 0.020
DDN N1 C2 single 1.410 0.020
DDN C6 N1 single 1.337 0.020
DDN O2 C2 double 1.250 0.020
DDN C2 N3 single 1.337 0.020
DDN N3 C4 single 1.465 0.020
DDN HN3 N3 single 1.040 0.020
DDN O4 C4 single 1.432 0.020
DDN C4 C5 single 1.460 0.020
DDN H4 C4 single 1.099 0.020
DDN HO4 O4 single 0.967 0.020
DDN C5 C6 double 1.390 0.020
DDN H5 C5 single 1.083 0.020
DDN H6 C6 single 1.083 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
DDN OP3 P OP1 119.900 3.000
DDN OP3 P OP2 119.900 3.000
DDN OP3 P "O5'" 108.200 3.000
DDN OP1 P OP2 119.900 3.000
DDN OP1 P "O5'" 108.200 3.000
DDN OP2 P "O5'" 108.200 3.000
DDN P "O5'" "C5'" 120.500 3.000
DDN "O5'" "C5'" "H5'" 109.470 3.000
DDN "O5'" "C5'" "H5''" 109.470 3.000
DDN "O5'" "C5'" "C4'" 109.470 3.000
DDN "H5'" "C5'" "H5''" 107.900 3.000
DDN "H5'" "C5'" "C4'" 109.470 3.000
DDN "H5''" "C5'" "C4'" 109.470 3.000
DDN "C5'" "C4'" "H4'" 108.340 3.000
DDN "C5'" "C4'" "C3'" 111.000 3.000
DDN "C5'" "C4'" "O4'" 109.470 3.000
DDN "H4'" "C4'" "C3'" 108.340 3.000
DDN "H4'" "C4'" "O4'" 109.470 3.000
DDN "C3'" "C4'" "O4'" 109.470 3.000
DDN "C4'" "C3'" "H3'" 108.340 3.000
DDN "C4'" "C3'" "C2'" 111.000 3.000
DDN "C4'" "C3'" "O3'" 109.470 3.000
DDN "H3'" "C3'" "C2'" 108.340 3.000
DDN "H3'" "C3'" "O3'" 109.470 3.000
DDN "C2'" "C3'" "O3'" 109.470 3.000
DDN "C3'" "C2'" "H2'" 109.470 3.000
DDN "C3'" "C2'" "H2''" 109.470 3.000
DDN "C3'" "C2'" "C1'" 111.000 3.000
DDN "H2'" "C2'" "H2''" 107.900 3.000
DDN "H2'" "C2'" "C1'" 109.470 3.000
DDN "H2''" "C2'" "C1'" 109.470 3.000
DDN "C2'" "C1'" "H1'" 108.340 3.000
DDN "C2'" "C1'" "O4'" 109.470 3.000
DDN "C2'" "C1'" N1 109.470 3.000
DDN "H1'" "C1'" "O4'" 109.470 3.000
DDN "H1'" "C1'" N1 109.470 3.000
DDN "O4'" "C1'" N1 109.470 3.000
DDN "C1'" "O4'" "C4'" 111.800 3.000
DDN "C1'" N1 C6 120.000 3.000
DDN "C1'" N1 C2 120.000 3.000
DDN C6 N1 C2 120.000 3.000
DDN N1 C6 H6 120.000 3.000
DDN N1 C6 C5 120.000 3.000
DDN H6 C6 C5 120.000 3.000
DDN C6 C5 H5 120.000 3.000
DDN C6 C5 C4 120.000 3.000
DDN H5 C5 C4 120.000 3.000
DDN C5 C4 H4 109.500 3.000
DDN C5 C4 O4 109.500 3.000
DDN C5 C4 N3 109.500 3.000
DDN H4 C4 O4 109.470 3.000
DDN H4 C4 N3 109.500 3.000
DDN O4 C4 N3 109.500 3.000
DDN C4 O4 HO4 109.470 3.000
DDN C4 N3 HN3 120.000 3.000
DDN C4 N3 C2 120.000 3.000
DDN HN3 N3 C2 120.000 3.000
DDN N3 C2 O2 120.000 3.000
DDN N3 C2 N1 120.000 3.000
DDN O2 C2 N1 120.000 3.000
DDN "C3'" "O3'" H1 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
DDN var_1 OP3 P "O5'" "C5'" 54.962 20.000 1
DDN var_2 P "O5'" "C5'" "C4'" -179.965 20.000 1
DDN var_3 "O5'" "C5'" "C4'" "C3'" -178.119 20.000 3
DDN var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DDN var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
DDN var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
DDN var_7 "C3'" "C2'" "C1'" N1 150.000 20.000 3
DDN var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DDN var_9 "C2'" "C1'" N1 C6 115.035 20.000 1
DDN CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DDN CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DDN CONST_3 N1 C6 C5 C4 0.000 0.000 0
DDN CONST_4 C6 C5 C4 N3 0.000 0.000 0
DDN var_10 C5 C4 O4 HO4 179.995 20.000 1
DDN CONST_5 C5 C4 N3 C2 0.000 0.000 0
DDN CONST_6 C4 N3 C2 O2 180.000 0.000 0
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
DDN chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DDN chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DDN chir_03 "C1'" "O4'" "C2'" N1 positiv
DDN chir_04 C4 N3 O4 C5 positiv
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
DDN plan-1 N1 0.020
DDN plan-1 "C1'" 0.020
DDN plan-1 C2 0.020
DDN plan-1 C6 0.020
DDN plan-1 N3 0.020
DDN plan-1 C4 0.020
DDN plan-1 C5 0.020
DDN plan-1 O2 0.020
DDN plan-1 HN3 0.020
DDN plan-1 H5 0.020
DDN plan-1 H6 0.020
# ------------------------------------------------------
|
