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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
PSU PSU 'PSEUDOURIDINE-5'-MONOPHOSPHATE ' RNA 32 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PSU
#
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
PSU OP3 O OP -0.666 0.000 0.000 0.000
PSU P P P 0.000 -1.224 0.219 -0.862
PSU OP1 O OP -0.666 -1.686 -1.105 -1.430
PSU OP2 O OP -0.666 -0.881 1.162 -1.994
PSU "O5'" O O2 0.000 -2.402 0.859 0.032
PSU "C5'" C CH2 0.000 -2.679 -0.072 1.078
PSU "H5'" H H 0.000 -1.778 -0.227 1.675
PSU "H5''" H H 0.000 -2.993 -1.024 0.643
PSU "C4'" C CH1 0.000 -3.795 0.477 1.968
PSU "H4'" H H 0.000 -3.486 1.429 2.422
PSU "O4'" O O2 0.000 -5.008 0.657 1.201
PSU "C1'" C CH1 0.000 -6.074 0.689 2.174
PSU "H1'" H H 0.000 -6.118 1.673 2.661
PSU C5 C CR6 0.000 -7.393 0.368 1.520
PSU C4 C CR6 0.000 -7.556 -0.829 0.785
PSU O4 O O 0.000 -6.631 -1.615 0.676
PSU N3 N NR16 0.000 -8.748 -1.098 0.212
PSU HN3 H H 0.000 -8.879 -1.979 -0.324
PSU C6 C CR16 0.000 -8.434 1.221 1.626
PSU H6 H H 0.000 -8.327 2.143 2.183
PSU N1 N NR16 0.000 -9.625 0.914 1.026
PSU HN1 H H 0.000 -10.426 1.572 1.107
PSU C2 C CR6 0.000 -9.768 -0.229 0.333
PSU O2 O O 0.000 -10.835 -0.482 -0.192
PSU "C3'" C CH1 0.000 -4.171 -0.543 3.064
PSU "H3'" H H 0.000 -3.905 -1.562 2.749
PSU "C2'" C CH1 0.000 -5.703 -0.402 3.202
PSU "H2'" H H 0.000 -6.201 -1.350 2.953
PSU "O2'" O OH1 0.000 -6.051 0.011 4.524
PSU "HO2'" H H 0.000 -5.757 -0.657 5.158
PSU "O3'" O OH1 0.000 -3.525 -0.216 4.295
PSU "HO3'" H H 0.000 -3.821 -0.867 4.947
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
PSU OP3 n/a P START
PSU P OP3 "O5'" .
PSU OP1 P . .
PSU OP2 P . .
PSU "O5'" P "C5'" .
PSU "C5'" "O5'" "C4'" .
PSU "H5'" "C5'" . .
PSU "H5''" "C5'" . .
PSU "C4'" "C5'" "C3'" .
PSU "H4'" "C4'" . .
PSU "O4'" "C4'" "C1'" .
PSU "C1'" "O4'" C5 .
PSU "H1'" "C1'" . .
PSU C5 "C1'" C6 .
PSU C4 C5 N3 .
PSU O4 C4 . .
PSU N3 C4 HN3 .
PSU HN3 N3 . .
PSU C6 C5 N1 .
PSU H6 C6 . .
PSU N1 C6 C2 .
PSU HN1 N1 . .
PSU C2 N1 O2 .
PSU O2 C2 . .
PSU "C3'" "C4'" "O3'" .
PSU "H3'" "C3'" . .
PSU "C2'" "C3'" "O2'" .
PSU "H2'" "C2'" . .
PSU "O2'" "C2'" "HO2'" .
PSU "HO2'" "O2'" . .
PSU "O3'" "C3'" . END
PSU "HO3'" "O3'" . .
PSU C2 N3 . ADD
PSU "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
PSU C2 N1 single 1.337 0.020
PSU N1 C6 single 1.337 0.020
PSU HN1 N1 single 1.040 0.020
PSU C2 N3 single 1.337 0.020
PSU O2 C2 double 1.250 0.020
PSU N3 C4 single 1.337 0.020
PSU HN3 N3 single 1.040 0.020
PSU C4 C5 single 1.487 0.020
PSU O4 C4 double 1.250 0.020
PSU C6 C5 double 1.390 0.020
PSU C5 "C1'" single 1.480 0.020
PSU H6 C6 single 1.083 0.020
PSU "C1'" "C2'" single 1.524 0.020
PSU "C1'" "O4'" single 1.426 0.020
PSU "H1'" "C1'" single 1.099 0.020
PSU "O2'" "C2'" single 1.432 0.020
PSU "C2'" "C3'" single 1.524 0.020
PSU "H2'" "C2'" single 1.099 0.020
PSU "HO2'" "O2'" single 0.967 0.020
PSU "C3'" "C4'" single 1.524 0.020
PSU "O3'" "C3'" single 1.432 0.020
PSU "H3'" "C3'" single 1.099 0.020
PSU "O4'" "C4'" single 1.426 0.020
PSU "C4'" "C5'" single 1.524 0.020
PSU "H4'" "C4'" single 1.099 0.020
PSU "HO3'" "O3'" single 0.967 0.020
PSU "C5'" "O5'" single 1.426 0.020
PSU "H5'" "C5'" single 1.092 0.020
PSU "H5''" "C5'" single 1.092 0.020
PSU "O5'" P single 1.610 0.020
PSU OP1 P deloc 1.510 0.020
PSU OP2 P deloc 1.510 0.020
PSU P OP3 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
PSU OP3 P OP1 119.900 3.000
PSU OP3 P OP2 119.900 3.000
PSU OP3 P "O5'" 108.200 3.000
PSU OP1 P OP2 119.900 3.000
PSU OP1 P "O5'" 108.200 3.000
PSU OP2 P "O5'" 108.200 3.000
PSU P "O5'" "C5'" 120.500 3.000
PSU "O5'" "C5'" "H5'" 109.470 3.000
PSU "O5'" "C5'" "H5''" 109.470 3.000
PSU "O5'" "C5'" "C4'" 109.470 3.000
PSU "H5'" "C5'" "H5''" 107.900 3.000
PSU "H5'" "C5'" "C4'" 109.470 3.000
PSU "H5''" "C5'" "C4'" 109.470 3.000
PSU "C5'" "C4'" "H4'" 108.340 3.000
PSU "C5'" "C4'" "O4'" 109.470 3.000
PSU "C5'" "C4'" "C3'" 111.000 3.000
PSU "H4'" "C4'" "O4'" 109.470 3.000
PSU "H4'" "C4'" "C3'" 108.340 3.000
PSU "O4'" "C4'" "C3'" 109.470 3.000
PSU "C4'" "O4'" "C1'" 111.800 3.000
PSU "O4'" "C1'" "H1'" 109.470 3.000
PSU "O4'" "C1'" C5 109.470 3.000
PSU "O4'" "C1'" "C2'" 109.470 3.000
PSU "H1'" "C1'" C5 109.470 3.000
PSU "H1'" "C1'" "C2'" 108.340 3.000
PSU C5 "C1'" "C2'" 109.470 3.000
PSU "C1'" C5 C4 120.000 3.000
PSU "C1'" C5 C6 120.000 3.000
PSU C4 C5 C6 120.000 3.000
PSU C5 C4 O4 120.000 3.000
PSU C5 C4 N3 120.000 3.000
PSU O4 C4 N3 120.000 3.000
PSU C4 N3 HN3 120.000 3.000
PSU C4 N3 C2 120.000 3.000
PSU HN3 N3 C2 120.000 3.000
PSU C5 C6 H6 120.000 3.000
PSU C5 C6 N1 120.000 3.000
PSU H6 C6 N1 120.000 3.000
PSU C6 N1 HN1 120.000 3.000
PSU C6 N1 C2 120.000 3.000
PSU HN1 N1 C2 120.000 3.000
PSU N1 C2 O2 120.000 3.000
PSU N1 C2 N3 120.000 3.000
PSU O2 C2 N3 120.000 3.000
PSU "C4'" "C3'" "H3'" 108.340 3.000
PSU "C4'" "C3'" "C2'" 111.000 3.000
PSU "C4'" "C3'" "O3'" 109.470 3.000
PSU "H3'" "C3'" "C2'" 108.340 3.000
PSU "H3'" "C3'" "O3'" 109.470 3.000
PSU "C2'" "C3'" "O3'" 109.470 3.000
PSU "C3'" "C2'" "H2'" 108.340 3.000
PSU "C3'" "C2'" "O2'" 109.470 3.000
PSU "C3'" "C2'" "C1'" 111.000 3.000
PSU "H2'" "C2'" "O2'" 109.470 3.000
PSU "H2'" "C2'" "C1'" 108.340 3.000
PSU "O2'" "C2'" "C1'" 109.470 3.000
PSU "C2'" "O2'" "HO2'" 109.470 3.000
PSU "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
PSU var_1 OP3 P "O5'" "C5'" -60.027 20.000 1
PSU var_2 P "O5'" "C5'" "C4'" -179.975 20.000 1
PSU var_3 "O5'" "C5'" "C4'" "C3'" 176.904 20.000 3
PSU var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
PSU var_5 "C4'" "O4'" "C1'" C5 -150.000 20.000 1
PSU var_6 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
PSU var_7 "O4'" "C1'" C5 C6 -124.656 20.000 1
PSU CONST_1 "C1'" C5 C4 N3 180.000 0.000 0
PSU CONST_2 C5 C4 N3 C2 0.000 0.000 0
PSU CONST_3 "C1'" C5 C6 N1 180.000 0.000 0
PSU CONST_4 C5 C6 N1 C2 0.000 0.000 0
PSU CONST_5 C6 N1 C2 O2 180.000 0.000 0
PSU CONST_6 N1 C2 N3 C4 0.000 0.000 0
PSU var_8 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
PSU var_9 "C4'" "C3'" "C2'" "O2'" -120.000 20.000 3
PSU var_10 "C3'" "C2'" "O2'" "HO2'" -61.439 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
PSU chir_01 "C1'" C5 "C2'" "O4'" negativ
PSU chir_02 "C2'" "C1'" "O2'" "C3'" positiv
PSU chir_03 "C3'" "C2'" "C4'" "O3'" negativ
PSU chir_04 "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
PSU plan-1 C2 0.020
PSU plan-1 N3 0.020
PSU plan-1 O2 0.020
PSU plan-1 N1 0.020
PSU plan-1 C4 0.020
PSU plan-1 C5 0.020
PSU plan-1 C6 0.020
PSU plan-1 HN3 0.020
PSU plan-1 O4 0.020
PSU plan-1 "C1'" 0.020
PSU plan-1 H6 0.020
PSU plan-1 HN1 0.020
# ------------------------------------------------------
|
