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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
DUD DUD 'DEOXYURIDINE-5'-DIPHOSPHATE ' non-polymer 35 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DUD
#
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
DUD O3B O OP -0.666 0.000 0.000 0.000
DUD PB P P 0.000 -0.999 0.233 -1.113
DUD O1B O OP -0.666 -1.416 -1.097 -1.703
DUD O2B O OP -0.666 -0.364 1.085 -2.190
DUD O3A O O2 0.000 -2.293 0.988 -0.523
DUD PA P P 0.000 -2.915 0.030 0.611
DUD O1A O OP -0.500 -3.295 -1.270 0.006
DUD O2A O OP -0.500 -1.907 -0.195 1.675
DUD "O5'" O O2 0.000 -4.219 0.727 1.245
DUD "C5'" C CH2 0.000 -4.724 -0.166 2.240
DUD "H5'1" H H 0.000 -3.959 -0.329 3.003
DUD "H5'2" H H 0.000 -4.980 -1.120 1.774
DUD "C4'" C CH1 0.000 -5.970 0.439 2.886
DUD "H4'" H H 0.000 -5.723 1.394 3.370
DUD "C3'" C CH1 0.000 -6.582 -0.540 3.912
DUD "H3'" H H 0.000 -6.295 -1.574 3.677
DUD "O3'" O OH1 0.000 -6.173 -0.197 5.238
DUD "HO3'" H H 0.000 -6.590 -0.800 5.869
DUD "C2'" C CH2 0.000 -8.107 -0.352 3.750
DUD "H2'2" H H 0.000 -8.576 0.009 4.667
DUD "H2'1" H H 0.000 -8.601 -1.271 3.427
DUD "O4'" O O2 0.000 -7.006 0.630 1.897
DUD "C1'" C CH1 0.000 -8.238 0.719 2.646
DUD "H1'" H H 0.000 -8.342 1.717 3.094
DUD N1 N NR6 0.000 -9.385 0.425 1.784
DUD C6 C CR16 0.000 -10.403 1.333 1.677
DUD H6 H H 0.000 -10.361 2.264 2.229
DUD C5 C CR16 0.000 -11.460 1.062 0.881
DUD H5 H H 0.000 -12.273 1.772 0.787
DUD C4 C CR6 0.000 -11.491 -0.162 0.171
DUD O4 O O 0.000 -12.434 -0.428 -0.553
DUD N3 N NR16 0.000 -10.468 -1.030 0.304
DUD HN3 H H 0.000 -10.486 -1.934 -0.211
DUD C2 C CR6 0.000 -9.424 -0.732 1.100
DUD O2 O O 0.000 -8.509 -1.525 1.209
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
DUD O3B n/a PB START
DUD PB O3B O3A .
DUD O1B PB . .
DUD O2B PB . .
DUD O3A PB PA .
DUD PA O3A "O5'" .
DUD O1A PA . .
DUD O2A PA . .
DUD "O5'" PA "C5'" .
DUD "C5'" "O5'" "C4'" .
DUD "H5'1" "C5'" . .
DUD "H5'2" "C5'" . .
DUD "C4'" "C5'" "O4'" .
DUD "H4'" "C4'" . .
DUD "C3'" "C4'" "C2'" .
DUD "H3'" "C3'" . .
DUD "O3'" "C3'" "HO3'" .
DUD "HO3'" "O3'" . .
DUD "C2'" "C3'" "H2'1" .
DUD "H2'2" "C2'" . .
DUD "H2'1" "C2'" . .
DUD "O4'" "C4'" "C1'" .
DUD "C1'" "O4'" N1 .
DUD "H1'" "C1'" . .
DUD N1 "C1'" C6 .
DUD C6 N1 C5 .
DUD H6 C6 . .
DUD C5 C6 C4 .
DUD H5 C5 . .
DUD C4 C5 N3 .
DUD O4 C4 . .
DUD N3 C4 C2 .
DUD HN3 N3 . .
DUD C2 N3 O2 .
DUD O2 C2 . END
DUD N1 C2 . ADD
DUD "C1'" "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
DUD N1 C2 single 1.410 0.020
DUD C6 N1 single 1.337 0.020
DUD N1 "C1'" single 1.465 0.020
DUD C2 N3 single 1.337 0.020
DUD O2 C2 double 1.250 0.020
DUD N3 C4 single 1.337 0.020
DUD HN3 N3 single 1.040 0.020
DUD C4 C5 single 1.390 0.020
DUD O4 C4 double 1.250 0.020
DUD C5 C6 double 1.390 0.020
DUD H5 C5 single 1.083 0.020
DUD H6 C6 single 1.083 0.020
DUD "C1'" "C2'" single 1.524 0.020
DUD "C1'" "O4'" single 1.426 0.020
DUD "H1'" "C1'" single 1.099 0.020
DUD "C2'" "C3'" single 1.524 0.020
DUD "H2'1" "C2'" single 1.092 0.020
DUD "H2'2" "C2'" single 1.092 0.020
DUD "C3'" "C4'" single 1.524 0.020
DUD "O3'" "C3'" single 1.432 0.020
DUD "H3'" "C3'" single 1.099 0.020
DUD "O4'" "C4'" single 1.426 0.020
DUD "C4'" "C5'" single 1.524 0.020
DUD "H4'" "C4'" single 1.099 0.020
DUD "HO3'" "O3'" single 0.967 0.020
DUD "C5'" "O5'" single 1.426 0.020
DUD "H5'1" "C5'" single 1.092 0.020
DUD "H5'2" "C5'" single 1.092 0.020
DUD "O5'" PA single 1.610 0.020
DUD O1A PA deloc 1.510 0.020
DUD O2A PA deloc 1.510 0.020
DUD PA O3A single 1.610 0.020
DUD O3A PB single 1.610 0.020
DUD O1B PB deloc 1.510 0.020
DUD O2B PB deloc 1.510 0.020
DUD PB O3B deloc 1.510 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
DUD O3B PB O1B 119.900 3.000
DUD O3B PB O2B 119.900 3.000
DUD O3B PB O3A 108.200 3.000
DUD O1B PB O2B 119.900 3.000
DUD O1B PB O3A 108.200 3.000
DUD O2B PB O3A 108.200 3.000
DUD PB O3A PA 120.500 3.000
DUD O3A PA O1A 108.200 3.000
DUD O3A PA O2A 108.200 3.000
DUD O3A PA "O5'" 102.600 3.000
DUD O1A PA O2A 119.900 3.000
DUD O1A PA "O5'" 108.200 3.000
DUD O2A PA "O5'" 108.200 3.000
DUD PA "O5'" "C5'" 120.500 3.000
DUD "O5'" "C5'" "H5'1" 109.470 3.000
DUD "O5'" "C5'" "H5'2" 109.470 3.000
DUD "O5'" "C5'" "C4'" 109.470 3.000
DUD "H5'1" "C5'" "H5'2" 107.900 3.000
DUD "H5'1" "C5'" "C4'" 109.470 3.000
DUD "H5'2" "C5'" "C4'" 109.470 3.000
DUD "C5'" "C4'" "H4'" 108.340 3.000
DUD "C5'" "C4'" "C3'" 111.000 3.000
DUD "C5'" "C4'" "O4'" 109.470 3.000
DUD "H4'" "C4'" "C3'" 108.340 3.000
DUD "H4'" "C4'" "O4'" 109.470 3.000
DUD "C3'" "C4'" "O4'" 109.470 3.000
DUD "C4'" "C3'" "H3'" 108.340 3.000
DUD "C4'" "C3'" "O3'" 109.470 3.000
DUD "C4'" "C3'" "C2'" 111.000 3.000
DUD "H3'" "C3'" "O3'" 109.470 3.000
DUD "H3'" "C3'" "C2'" 108.340 3.000
DUD "O3'" "C3'" "C2'" 109.470 3.000
DUD "C3'" "O3'" "HO3'" 109.470 3.000
DUD "C3'" "C2'" "H2'2" 109.470 3.000
DUD "C3'" "C2'" "H2'1" 109.470 3.000
DUD "C3'" "C2'" "C1'" 111.000 3.000
DUD "H2'2" "C2'" "H2'1" 107.900 3.000
DUD "H2'2" "C2'" "C1'" 109.470 3.000
DUD "H2'1" "C2'" "C1'" 109.470 3.000
DUD "C4'" "O4'" "C1'" 111.800 3.000
DUD "O4'" "C1'" "H1'" 109.470 3.000
DUD "O4'" "C1'" N1 109.470 3.000
DUD "O4'" "C1'" "C2'" 109.470 3.000
DUD "H1'" "C1'" N1 109.470 3.000
DUD "H1'" "C1'" "C2'" 108.340 3.000
DUD N1 "C1'" "C2'" 109.470 3.000
DUD "C1'" N1 C6 120.000 3.000
DUD "C1'" N1 C2 120.000 3.000
DUD C6 N1 C2 120.000 3.000
DUD N1 C6 H6 120.000 3.000
DUD N1 C6 C5 120.000 3.000
DUD H6 C6 C5 120.000 3.000
DUD C6 C5 H5 120.000 3.000
DUD C6 C5 C4 120.000 3.000
DUD H5 C5 C4 120.000 3.000
DUD C5 C4 O4 120.000 3.000
DUD C5 C4 N3 120.000 3.000
DUD O4 C4 N3 120.000 3.000
DUD C4 N3 HN3 120.000 3.000
DUD C4 N3 C2 120.000 3.000
DUD HN3 N3 C2 120.000 3.000
DUD N3 C2 O2 120.000 3.000
DUD N3 C2 N1 120.000 3.000
DUD O2 C2 N1 120.000 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
DUD var_1 O3B PB O3A PA -60.022 20.000 1
DUD var_2 PB O3A PA "O5'" -179.978 20.000 1
DUD var_3 O3A PA "O5'" "C5'" -179.990 20.000 1
DUD var_4 PA "O5'" "C5'" "C4'" 179.984 20.000 1
DUD var_5 "O5'" "C5'" "C4'" "O4'" 61.426 20.000 3
DUD var_6 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DUD var_7 "C4'" "C3'" "O3'" "HO3'" 178.043 20.000 1
DUD var_8 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
DUD var_9 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DUD var_10 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
DUD var_11 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
DUD var_12 "O4'" "C1'" N1 C6 -124.514 20.000 1
DUD CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DUD CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DUD CONST_3 N1 C6 C5 C4 0.000 0.000 0
DUD CONST_4 C6 C5 C4 N3 0.000 0.000 0
DUD CONST_5 C5 C4 N3 C2 0.000 0.000 0
DUD 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
DUD chir_01 "C1'" N1 "C2'" "O4'" negativ
DUD chir_02 "C3'" "C2'" "C4'" "O3'" negativ
DUD chir_03 "C4'" "C3'" "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
DUD plan-1 N1 0.020
DUD plan-1 C2 0.020
DUD plan-1 C6 0.020
DUD plan-1 "C1'" 0.020
DUD plan-1 N3 0.020
DUD plan-1 C4 0.020
DUD plan-1 C5 0.020
DUD plan-1 O2 0.020
DUD plan-1 HN3 0.020
DUD plan-1 O4 0.020
DUD plan-1 H5 0.020
DUD plan-1 H6 0.020
# ------------------------------------------------------
|
