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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
YRR YRR '3-HYDROXY-PYRROLIDIN-2-YLMETHYL-MONO' DNA 22 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_YRR
#
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
YRR OP3 O OP -0.666 0.000 0.000 0.000
YRR P P P 0.000 -0.869 1.235 -0.083
YRR OP1 O OP -0.666 -0.482 2.228 -1.158
YRR OP2 O OP -0.666 -0.840 1.777 1.329
YRR "O5'" O O2 0.000 -2.370 0.640 -0.211
YRR "C5'" C CH2 0.000 -2.811 -0.296 0.755
YRR HC51 H H 0.000 -2.781 0.156 1.749
YRR HC52 H H 0.000 -2.167 -1.177 0.738
YRR "C4'" C CH1 0.000 -4.239 -0.702 0.424
YRR HC4 H H 0.000 -4.265 -1.191 -0.560
YRR "C3'" C CH1 0.000 -5.213 0.479 0.439
YRR HC3 H H 0.000 -4.785 1.326 0.993
YRR "C2'" C CH2 0.000 -6.466 -0.042 1.137
YRR HC21 H H 0.000 -7.362 0.116 0.534
YRR HC22 H H 0.000 -6.603 0.416 2.119
YRR "C1'" C CH2 0.000 -6.220 -1.533 1.302
YRR HC11 H H 0.000 -6.537 -2.108 0.429
YRR HC12 H H 0.000 -6.696 -1.940 2.196
YRR "N4'" N NH1 0.000 -4.769 -1.615 1.441
YRR HN4 H H 0.000 -4.245 -2.178 2.095
YRR "O3'" O OH1 0.000 -5.513 0.856 -0.898
YRR "HO3'" H H 0.000 -4.666 0.927 -1.367
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
YRR OP3 n/a P START
YRR P OP3 "O5'" .
YRR OP1 P . .
YRR OP2 P . .
YRR "O5'" P "C5'" .
YRR "C5'" "O5'" "C4'" .
YRR HC51 "C5'" . .
YRR HC52 "C5'" . .
YRR "C4'" "C5'" "C3'" .
YRR HC4 "C4'" . .
YRR "C3'" "C4'" "O3'" .
YRR HC3 "C3'" . .
YRR "C2'" "C3'" "C1'" .
YRR HC21 "C2'" . .
YRR HC22 "C2'" . .
YRR "C1'" "C2'" "N4'" .
YRR HC11 "C1'" . .
YRR HC12 "C1'" . .
YRR "N4'" "C1'" HN4 .
YRR HN4 "N4'" . .
YRR "O3'" "C3'" . END
YRR "HO3'" "O3'" . .
YRR "C4'" "N4'" . 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
YRR P OP3 deloc 1.510 0.020
YRR OP1 P deloc 1.510 0.020
YRR OP2 P deloc 1.510 0.020
YRR "O5'" P single 1.610 0.020
YRR "C5'" "O5'" single 1.426 0.020
YRR "C4'" "C5'" single 1.524 0.020
YRR HC51 "C5'" single 1.092 0.020
YRR HC52 "C5'" single 1.092 0.020
YRR "C4'" "N4'" single 1.450 0.020
YRR "C3'" "C4'" single 1.524 0.020
YRR HC4 "C4'" single 1.099 0.020
YRR "N4'" "C1'" single 1.450 0.020
YRR HN4 "N4'" single 1.010 0.020
YRR "O3'" "C3'" single 1.432 0.020
YRR "C2'" "C3'" single 1.524 0.020
YRR HC3 "C3'" single 1.099 0.020
YRR "HO3'" "O3'" single 0.967 0.020
YRR "C1'" "C2'" single 1.524 0.020
YRR HC21 "C2'" single 1.092 0.020
YRR HC22 "C2'" single 1.092 0.020
YRR HC11 "C1'" single 1.092 0.020
YRR HC12 "C1'" single 1.092 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
YRR OP3 P OP1 119.900 3.000
YRR OP3 P OP2 119.900 3.000
YRR OP3 P "O5'" 108.200 3.000
YRR OP1 P OP2 119.900 3.000
YRR OP1 P "O5'" 108.200 3.000
YRR OP2 P "O5'" 108.200 3.000
YRR P "O5'" "C5'" 120.500 3.000
YRR "O5'" "C5'" HC51 109.470 3.000
YRR "O5'" "C5'" HC52 109.470 3.000
YRR "O5'" "C5'" "C4'" 109.470 3.000
YRR HC51 "C5'" HC52 107.900 3.000
YRR HC51 "C5'" "C4'" 109.470 3.000
YRR HC52 "C5'" "C4'" 109.470 3.000
YRR "C5'" "C4'" HC4 108.340 3.000
YRR "C5'" "C4'" "C3'" 111.000 3.000
YRR "C5'" "C4'" "N4'" 110.000 3.000
YRR HC4 "C4'" "C3'" 108.340 3.000
YRR HC4 "C4'" "N4'" 108.550 3.000
YRR "C3'" "C4'" "N4'" 110.000 3.000
YRR "C4'" "C3'" HC3 108.340 3.000
YRR "C4'" "C3'" "C2'" 111.000 3.000
YRR "C4'" "C3'" "O3'" 109.470 3.000
YRR HC3 "C3'" "C2'" 108.340 3.000
YRR HC3 "C3'" "O3'" 109.470 3.000
YRR "C2'" "C3'" "O3'" 109.470 3.000
YRR "C3'" "C2'" HC21 109.470 3.000
YRR "C3'" "C2'" HC22 109.470 3.000
YRR "C3'" "C2'" "C1'" 111.000 3.000
YRR HC21 "C2'" HC22 107.900 3.000
YRR HC21 "C2'" "C1'" 109.470 3.000
YRR HC22 "C2'" "C1'" 109.470 3.000
YRR "C2'" "C1'" HC11 109.470 3.000
YRR "C2'" "C1'" HC12 109.470 3.000
YRR "C2'" "C1'" "N4'" 112.000 3.000
YRR HC11 "C1'" HC12 107.900 3.000
YRR HC11 "C1'" "N4'" 109.470 3.000
YRR HC12 "C1'" "N4'" 109.470 3.000
YRR "C1'" "N4'" HN4 118.500 3.000
YRR "C1'" "N4'" "C4'" 120.000 3.000
YRR HN4 "N4'" "C4'" 118.500 3.000
YRR "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
YRR var_1 OP3 P "O5'" "C5'" 53.189 20.000 1
YRR var_2 P "O5'" "C5'" "C4'" 179.974 20.000 1
YRR var_3 "O5'" "C5'" "C4'" "C3'" -60.488 20.000 3
YRR var_4 "C5'" "C4'" "N4'" "C1'" 150.000 20.000 3
YRR var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
YRR var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
YRR var_7 "C3'" "C2'" "C1'" "N4'" 30.000 20.000 3
YRR var_8 "C2'" "C1'" "N4'" "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
YRR chir_01 "C4'" "C5'" "N4'" "C3'" negativ
YRR chir_02 "C3'" "C4'" "O3'" "C2'" 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
YRR plan-1 "N4'" 0.020
YRR plan-1 "C4'" 0.000
YRR plan-1 "C1'" 0.000
YRR plan-1 HN4 0.000
# ------------------------------------------------------
|
