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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
IU IU '5-IODOURIDINE-5'-MONOPHOSPHATE ' RNA 32 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_IU
#
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
IU OP3 O OP -0.666 0.000 0.000 0.000
IU P P P 0.000 -0.530 1.416 0.049
IU OP1 O OP -0.666 0.531 2.491 0.149
IU OP2 O OP -0.666 -1.420 1.497 -1.172
IU "O5'" O O2 0.000 -1.575 1.370 1.285
IU "C5'" C CH2 0.000 -2.598 0.391 1.268
IU "H5'" H H 0.000 -2.156 -0.607 1.248
IU "H5''" H H 0.000 -3.226 0.527 0.385
IU "C4'" C CH1 0.000 -3.444 0.549 2.524
IU "H4'" H H 0.000 -2.807 0.459 3.415
IU "C3'" C CH1 0.000 -4.591 -0.451 2.607
IU "H3'" H H 0.000 -4.330 -1.416 2.151
IU "C2'" C CH1 0.000 -5.687 0.260 1.843
IU "H2'" H H 0.000 -5.523 0.146 0.762
IU "O2'" O OH1 0.000 -6.974 -0.213 2.186
IU "HO2'" H H 0.000 -7.640 0.379 1.813
IU "C1'" C CH1 0.000 -5.468 1.707 2.248
IU "H1'" H H 0.000 -6.026 1.920 3.171
IU "O4'" O O2 0.000 -4.059 1.855 2.492
IU N1 N NR6 0.000 -5.864 2.630 1.223
IU C6 C CR16 0.000 -4.948 2.949 0.226
IU H6 H H 0.000 -3.971 2.483 0.269
IU C5 C CR6 0.000 -5.193 3.793 -0.785
IU C4 C CR6 0.000 -6.528 4.445 -0.861
IU O4 O O 0.000 -6.830 5.230 -1.756
IU N3 N NR16 0.000 -7.401 4.091 0.159
IU H3 H H 0.000 -8.343 4.529 0.134
IU C2 C CR6 0.000 -7.152 3.209 1.216
IU O2 O O 0.000 -8.013 2.973 2.065
IU I5 I I 0.000 -3.789 4.209 -2.216
IU "O3'" O OH1 0.000 -4.954 -0.589 3.981
IU "HO3'" H H 0.000 -4.548 0.157 4.448
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
IU OP3 n/a P START
IU P OP3 "O5'" .
IU OP1 P . .
IU OP2 P . .
IU "O5'" P "C5'" .
IU "C5'" "O5'" "C4'" .
IU "H5'" "C5'" . .
IU "H5''" "C5'" . .
IU "C4'" "C5'" "C3'" .
IU "H4'" "C4'" . .
IU "C3'" "C4'" "O3'" .
IU "H3'" "C3'" . .
IU "C2'" "C3'" "C1'" .
IU "H2'" "C2'" . .
IU "O2'" "C2'" "HO2'" .
IU "HO2'" "O2'" . .
IU "C1'" "C2'" N1 .
IU "H1'" "C1'" . .
IU "O4'" "C1'" . .
IU N1 "C1'" C6 .
IU C6 N1 C5 .
IU H6 C6 . .
IU C5 C6 I5 .
IU C4 C5 N3 .
IU O4 C4 . .
IU N3 C4 C2 .
IU H3 N3 . .
IU C2 N3 O2 .
IU O2 C2 . .
IU I5 C5 . .
IU "O3'" "C3'" . END
IU "HO3'" "O3'" . .
IU "C4'" "O4'" . ADD
IU 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
IU OP1 P deloc 1.510 0.020
IU OP2 P deloc 1.510 0.020
IU P OP3 deloc 1.510 0.020
IU "O5'" P single 1.610 0.020
IU "C5'" "O5'" single 1.426 0.020
IU "C4'" "C5'" single 1.524 0.020
IU "H5'" "C5'" single 1.092 0.020
IU "H5''" "C5'" single 1.092 0.020
IU "C4'" "O4'" single 1.426 0.020
IU "C3'" "C4'" single 1.524 0.020
IU "H4'" "C4'" single 1.099 0.020
IU "O4'" "C1'" single 1.426 0.020
IU "O3'" "C3'" single 1.432 0.020
IU "C2'" "C3'" single 1.524 0.020
IU "H3'" "C3'" single 1.099 0.020
IU "HO3'" "O3'" single 0.967 0.020
IU "O2'" "C2'" single 1.432 0.020
IU "C1'" "C2'" single 1.524 0.020
IU "H2'" "C2'" single 1.099 0.020
IU "HO2'" "O2'" single 0.967 0.020
IU N1 "C1'" single 1.465 0.020
IU "H1'" "C1'" single 1.099 0.020
IU N1 C2 single 1.410 0.020
IU C6 N1 single 1.337 0.020
IU O2 C2 double 1.250 0.020
IU C2 N3 single 1.337 0.020
IU N3 C4 single 1.337 0.020
IU H3 N3 single 1.040 0.020
IU O4 C4 double 1.250 0.020
IU C4 C5 single 1.487 0.020
IU C5 C6 double 1.390 0.020
IU I5 C5 single 2.090 0.020
IU 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
IU OP3 P OP1 119.900 3.000
IU OP3 P OP2 119.900 3.000
IU OP3 P "O5'" 108.200 3.000
IU OP1 P OP2 119.900 3.000
IU OP1 P "O5'" 108.200 3.000
IU OP2 P "O5'" 108.200 3.000
IU P "O5'" "C5'" 120.500 3.000
IU "O5'" "C5'" "H5'" 109.470 3.000
IU "O5'" "C5'" "H5''" 109.470 3.000
IU "O5'" "C5'" "C4'" 109.470 3.000
IU "H5'" "C5'" "H5''" 107.900 3.000
IU "H5'" "C5'" "C4'" 109.470 3.000
IU "H5''" "C5'" "C4'" 109.470 3.000
IU "C5'" "C4'" "H4'" 108.340 3.000
IU "C5'" "C4'" "C3'" 111.000 3.000
IU "C5'" "C4'" "O4'" 109.470 3.000
IU "H4'" "C4'" "C3'" 108.340 3.000
IU "H4'" "C4'" "O4'" 109.470 3.000
IU "C3'" "C4'" "O4'" 109.470 3.000
IU "C4'" "C3'" "H3'" 108.340 3.000
IU "C4'" "C3'" "C2'" 111.000 3.000
IU "C4'" "C3'" "O3'" 109.470 3.000
IU "H3'" "C3'" "C2'" 108.340 3.000
IU "H3'" "C3'" "O3'" 109.470 3.000
IU "C2'" "C3'" "O3'" 109.470 3.000
IU "C3'" "C2'" "H2'" 108.340 3.000
IU "C3'" "C2'" "O2'" 109.470 3.000
IU "C3'" "C2'" "C1'" 111.000 3.000
IU "H2'" "C2'" "O2'" 109.470 3.000
IU "H2'" "C2'" "C1'" 108.340 3.000
IU "O2'" "C2'" "C1'" 109.470 3.000
IU "C2'" "O2'" "HO2'" 109.470 3.000
IU "C2'" "C1'" "H1'" 108.340 3.000
IU "C2'" "C1'" "O4'" 109.470 3.000
IU "C2'" "C1'" N1 109.470 3.000
IU "H1'" "C1'" "O4'" 109.470 3.000
IU "H1'" "C1'" N1 109.470 3.000
IU "O4'" "C1'" N1 109.470 3.000
IU "C1'" "O4'" "C4'" 111.800 3.000
IU "C1'" N1 C6 120.000 3.000
IU "C1'" N1 C2 120.000 3.000
IU C6 N1 C2 120.000 3.000
IU N1 C6 H6 120.000 3.000
IU N1 C6 C5 120.000 3.000
IU H6 C6 C5 120.000 3.000
IU C6 C5 C4 120.000 3.000
IU C6 C5 I5 120.000 3.000
IU C4 C5 I5 120.000 3.000
IU C5 C4 O4 120.000 3.000
IU C5 C4 N3 120.000 3.000
IU O4 C4 N3 120.000 3.000
IU C4 N3 H3 120.000 3.000
IU C4 N3 C2 120.000 3.000
IU H3 N3 C2 120.000 3.000
IU N3 C2 O2 120.000 3.000
IU N3 C2 N1 120.000 3.000
IU O2 C2 N1 120.000 3.000
IU "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
IU var_1 OP3 P "O5'" "C5'" -54.172 20.000 1
IU var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
IU var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
IU var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
IU var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
IU var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
IU var_7 "C3'" "C2'" "O2'" "HO2'" 168.831 20.000 1
IU var_8 "C3'" "C2'" "C1'" N1 150.000 20.000 3
IU var_9 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
IU var_10 "C2'" "C1'" N1 C6 -85.657 20.000 1
IU CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
IU CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
IU CONST_3 N1 C6 C5 I5 180.000 0.000 0
IU CONST_4 C6 C5 C4 N3 0.000 0.000 0
IU CONST_5 C5 C4 N3 C2 0.000 0.000 0
IU 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
IU chir_01 "C4'" "C5'" "O4'" "C3'" negativ
IU chir_02 "C3'" "C4'" "O3'" "C2'" negativ
IU chir_03 "C2'" "C3'" "O2'" "C1'" negativ
IU chir_04 "C1'" "O4'" "C2'" N1 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
IU plan-1 N1 0.020
IU plan-1 "C1'" 0.020
IU plan-1 C2 0.020
IU plan-1 C6 0.020
IU plan-1 N3 0.020
IU plan-1 C4 0.020
IU plan-1 C5 0.020
IU plan-1 O2 0.020
IU plan-1 H3 0.020
IU plan-1 O4 0.020
IU plan-1 I5 0.020
IU plan-1 H6 0.020
# ------------------------------------------------------
|
