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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
DPY DPY '. ' non-polymer 34 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DPY
#
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
DPY O3P O OP -0.666 0.000 0.000 0.000
DPY P P P 0.000 -0.554 -1.213 0.715
DPY O1P O OP -0.666 0.096 -2.527 0.341
DPY O2P O OP -0.666 -0.453 -0.832 2.175
DPY "O5'" O O2 0.000 -2.140 -1.122 0.403
DPY "C5'" C CH2 0.000 -2.825 0.076 0.723
DPY "H5'1" H H 0.000 -2.391 0.910 0.168
DPY "H5'2" H H 0.000 -2.747 0.272 1.794
DPY "C4'" C CH1 0.000 -4.286 -0.083 0.341
DPY "H4'" H H 0.000 -4.358 -0.313 -0.731
DPY "C3'" C CH1 0.000 -5.131 1.141 0.649
DPY "H3'" H H 0.000 -4.842 1.574 1.617
DPY "O3'" O OH1 0.000 -5.058 2.116 -0.370
DPY H3T H H 0.000 -4.134 2.244 -0.621
DPY "C2'" C CH2 0.000 -6.514 0.535 0.733
DPY "H2'2" H H 0.000 -6.975 0.406 -0.249
DPY "H2'1" H H 0.000 -7.185 1.109 1.376
DPY "O4'" O O2 0.000 -4.871 -1.155 1.097
DPY "C1'" C CH1 0.000 -6.253 -0.833 1.358
DPY "H1'" H H 0.000 -6.887 -1.575 0.853
DPY C1 C CR6 0.000 -6.550 -0.872 2.840
DPY C6 C CR16 0.000 -5.564 -0.525 3.758
DPY H6 H H 0.000 -4.582 -0.226 3.412
DPY C5 C CR16 0.000 -5.841 -0.563 5.120
DPY H5 H H 0.000 -5.087 -0.298 5.851
DPY C4 C CR6 0.000 -7.112 -0.950 5.513
DPY C8 C C 0.000 -7.457 -1.008 6.922
DPY O82 O OC -0.500 -8.638 -1.373 7.113
DPY O81 O OC -0.500 -6.689 -0.729 7.869
DPY N3 N NRD6 0.000 -8.097 -1.294 4.654
DPY C2 C CR6 0.000 -7.790 -1.247 3.337
DPY C7 C C 0.000 -8.876 -1.623 2.444
DPY O71 O OC -0.500 -9.046 -1.183 1.285
DPY O72 O OC -0.500 -9.651 -2.458 2.961
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
DPY O3P n/a P START
DPY P O3P "O5'" .
DPY O1P P . .
DPY O2P P . .
DPY "O5'" P "C5'" .
DPY "C5'" "O5'" "C4'" .
DPY "H5'1" "C5'" . .
DPY "H5'2" "C5'" . .
DPY "C4'" "C5'" "O4'" .
DPY "H4'" "C4'" . .
DPY "C3'" "C4'" "C2'" .
DPY "H3'" "C3'" . .
DPY "O3'" "C3'" H3T .
DPY H3T "O3'" . .
DPY "C2'" "C3'" "H2'1" .
DPY "H2'2" "C2'" . .
DPY "H2'1" "C2'" . .
DPY "O4'" "C4'" "C1'" .
DPY "C1'" "O4'" C1 .
DPY "H1'" "C1'" . .
DPY C1 "C1'" C6 .
DPY C6 C1 C5 .
DPY H6 C6 . .
DPY C5 C6 C4 .
DPY H5 C5 . .
DPY C4 C5 N3 .
DPY C8 C4 O81 .
DPY O82 C8 . .
DPY O81 C8 . .
DPY N3 C4 C2 .
DPY C2 N3 C7 .
DPY C7 C2 O72 .
DPY O71 C7 . .
DPY O72 C7 . END
DPY C1 C2 . ADD
DPY "C2'" "C1'" . 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
DPY O1P P deloc 1.510 0.020
DPY O2P P deloc 1.510 0.020
DPY "O5'" P single 1.610 0.020
DPY P O3P deloc 1.510 0.020
DPY "C5'" "O5'" single 1.426 0.020
DPY C1 C2 double 1.487 0.020
DPY C6 C1 single 1.390 0.020
DPY C1 "C1'" single 1.480 0.020
DPY C7 C2 single 1.500 0.020
DPY C2 N3 single 1.350 0.020
DPY O71 C7 deloc 1.250 0.020
DPY O72 C7 deloc 1.250 0.020
DPY N3 C4 double 1.350 0.020
DPY C8 C4 single 1.500 0.020
DPY C4 C5 single 1.390 0.020
DPY O81 C8 deloc 1.250 0.020
DPY O82 C8 deloc 1.250 0.020
DPY C5 C6 double 1.390 0.020
DPY H5 C5 single 1.083 0.020
DPY H6 C6 single 1.083 0.020
DPY "C2'" "C1'" single 1.524 0.020
DPY "C2'" "C3'" single 1.524 0.020
DPY "H2'1" "C2'" single 1.092 0.020
DPY "H2'2" "C2'" single 1.092 0.020
DPY "C4'" "C5'" single 1.524 0.020
DPY "H5'1" "C5'" single 1.092 0.020
DPY "H5'2" "C5'" single 1.092 0.020
DPY "O4'" "C4'" single 1.426 0.020
DPY "C3'" "C4'" single 1.524 0.020
DPY "H4'" "C4'" single 1.099 0.020
DPY "C1'" "O4'" single 1.426 0.020
DPY "H1'" "C1'" single 1.099 0.020
DPY "O3'" "C3'" single 1.432 0.020
DPY "H3'" "C3'" single 1.099 0.020
DPY H3T "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
DPY O3P P O1P 119.900 3.000
DPY O3P P O2P 119.900 3.000
DPY O3P P "O5'" 108.200 3.000
DPY O1P P O2P 119.900 3.000
DPY O1P P "O5'" 108.200 3.000
DPY O2P P "O5'" 108.200 3.000
DPY P "O5'" "C5'" 120.500 3.000
DPY "O5'" "C5'" "H5'1" 109.470 3.000
DPY "O5'" "C5'" "H5'2" 109.470 3.000
DPY "O5'" "C5'" "C4'" 109.470 3.000
DPY "H5'1" "C5'" "H5'2" 107.900 3.000
DPY "H5'1" "C5'" "C4'" 109.470 3.000
DPY "H5'2" "C5'" "C4'" 109.470 3.000
DPY "C5'" "C4'" "H4'" 108.340 3.000
DPY "C5'" "C4'" "C3'" 111.000 3.000
DPY "C5'" "C4'" "O4'" 109.470 3.000
DPY "H4'" "C4'" "C3'" 108.340 3.000
DPY "H4'" "C4'" "O4'" 109.470 3.000
DPY "C3'" "C4'" "O4'" 109.470 3.000
DPY "C4'" "C3'" "H3'" 108.340 3.000
DPY "C4'" "C3'" "O3'" 109.470 3.000
DPY "C4'" "C3'" "C2'" 111.000 3.000
DPY "H3'" "C3'" "O3'" 109.470 3.000
DPY "H3'" "C3'" "C2'" 108.340 3.000
DPY "O3'" "C3'" "C2'" 109.470 3.000
DPY "C3'" "O3'" H3T 109.470 3.000
DPY "C3'" "C2'" "H2'2" 109.470 3.000
DPY "C3'" "C2'" "H2'1" 109.470 3.000
DPY "C3'" "C2'" "C1'" 111.000 3.000
DPY "H2'2" "C2'" "H2'1" 107.900 3.000
DPY "H2'2" "C2'" "C1'" 109.470 3.000
DPY "H2'1" "C2'" "C1'" 109.470 3.000
DPY "C4'" "O4'" "C1'" 111.800 3.000
DPY "O4'" "C1'" "H1'" 109.470 3.000
DPY "O4'" "C1'" C1 109.470 3.000
DPY "O4'" "C1'" "C2'" 109.470 3.000
DPY "H1'" "C1'" C1 109.470 3.000
DPY "H1'" "C1'" "C2'" 108.340 3.000
DPY C1 "C1'" "C2'" 109.470 3.000
DPY "C1'" C1 C6 120.000 3.000
DPY "C1'" C1 C2 120.000 3.000
DPY C6 C1 C2 120.000 3.000
DPY C1 C6 H6 120.000 3.000
DPY C1 C6 C5 120.000 3.000
DPY H6 C6 C5 120.000 3.000
DPY C6 C5 H5 120.000 3.000
DPY C6 C5 C4 120.000 3.000
DPY H5 C5 C4 120.000 3.000
DPY C5 C4 C8 120.000 3.000
DPY C5 C4 N3 120.000 3.000
DPY C8 C4 N3 120.000 3.000
DPY C4 C8 O82 120.000 3.000
DPY C4 C8 O81 120.000 3.000
DPY O82 C8 O81 123.000 3.000
DPY C4 N3 C2 120.000 3.000
DPY N3 C2 C7 120.000 3.000
DPY N3 C2 C1 120.000 3.000
DPY C7 C2 C1 120.000 3.000
DPY C2 C7 O71 120.000 3.000
DPY C2 C7 O72 120.000 3.000
DPY O71 C7 O72 123.000 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
DPY var_1 O3P P "O5'" "C5'" -54.236 20.000 1
DPY var_2 P "O5'" "C5'" "C4'" -179.963 20.000 1
DPY var_3 "O5'" "C5'" "C4'" "O4'" 61.661 20.000 3
DPY var_4 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DPY var_5 "C4'" "C3'" "O3'" H3T -46.204 20.000 1
DPY var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DPY var_7 "C3'" "C2'" "C1'" "O4'" -30.000 20.000 3
DPY var_8 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DPY var_9 "C4'" "O4'" "C1'" C1 -120.000 20.000 1
DPY var_10 "O4'" "C1'" C1 C6 32.099 20.000 1
DPY CONST_1 "C1'" C1 C2 N3 180.000 0.000 0
DPY CONST_2 "C1'" C1 C6 C5 180.000 0.000 0
DPY CONST_3 C1 C6 C5 C4 0.000 0.000 0
DPY CONST_4 C6 C5 C4 N3 0.000 0.000 0
DPY var_11 C5 C4 C8 O81 0.147 20.000 1
DPY CONST_5 C5 C4 N3 C2 0.000 0.000 0
DPY CONST_6 C4 N3 C2 C7 180.000 0.000 0
DPY var_12 N3 C2 C7 O72 -30.132 20.000 1
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
DPY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DPY chir_02 "C1'" C1 "C2'" "O4'" negativ
DPY chir_03 "C3'" "C2'" "C4'" "O3'" negativ
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
DPY plan-1 C1 0.020
DPY plan-1 C2 0.020
DPY plan-1 C6 0.020
DPY plan-1 "C1'" 0.020
DPY plan-1 N3 0.020
DPY plan-1 C4 0.020
DPY plan-1 C5 0.020
DPY plan-1 C7 0.020
DPY plan-1 C8 0.020
DPY plan-1 H5 0.020
DPY plan-1 H6 0.020
DPY plan-2 C7 0.020
DPY plan-2 C2 0.020
DPY plan-2 O71 0.020
DPY plan-2 O72 0.020
DPY plan-3 C8 0.020
DPY plan-3 C4 0.020
DPY plan-3 O81 0.020
DPY plan-3 O82 0.020
# ------------------------------------------------------
|
