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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
CH CH 'N3-PROTONATED CYTIDINE-5'-MONOPHOSPH' RNA 34 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CH
#
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
CH OP3 O OP -0.666 0.000 0.000 0.000
CH P P P 0.000 0.000 0.000 0.000
CH OP1 O OP -0.666 0.000 0.000 0.000
CH OP2 O OP -0.666 0.000 0.000 0.000
CH "O5'" O O2 0.000 0.000 0.000 0.000
CH "C5'" C CH2 0.000 0.000 0.000 0.000
CH "H5'" H H 0.000 0.000 0.000 0.000
CH "H5''" H H 0.000 0.000 0.000 0.000
CH "C4'" C CH1 0.000 0.000 0.000 0.000
CH "H4'" H H 0.000 0.000 0.000 0.000
CH "C3'" C CH1 0.000 0.000 0.000 0.000
CH "H3'" H H 0.000 0.000 0.000 0.000
CH "C2'" C CH1 0.000 0.000 0.000 0.000
CH "H2'" H H 0.000 0.000 0.000 0.000
CH "O2'" O OH1 0.000 0.000 0.000 0.000
CH "HO2'" H H 0.000 0.000 0.000 0.000
CH "C1'" C CH1 0.000 0.000 0.000 0.000
CH "H1'" H H 0.000 0.000 0.000 0.000
CH "O4'" O O2 0.000 0.000 0.000 0.000
CH N1 N NR6 1.000 0.000 0.000 0.000
CH C6 C CR16 0.000 0.000 0.000 0.000
CH H6 H H 0.000 0.000 0.000 0.000
CH C5 C CR16 0.000 0.000 0.000 0.000
CH H5 H H 0.000 0.000 0.000 0.000
CH C4 C CR6 0.000 0.000 0.000 0.000
CH N4 N NH2 0.000 0.000 0.000 0.000
CH H42 H H 0.000 0.000 0.000 0.000
CH H41 H H 0.000 0.000 0.000 0.000
CH N3 N NR16 0.000 0.000 0.000 0.000
CH HN3 H H 0.000 0.000 0.000 0.000
CH C2 C CR6 0.000 0.000 0.000 0.000
CH O2 O O 0.000 0.000 0.000 0.000
CH "O3'" O OH1 0.000 0.000 0.000 0.000
CH "HO3'" H H 0.000 0.000 0.000 0.000
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
CH OP3 n/a P START
CH P OP3 "O5'" .
CH OP1 P . .
CH OP2 P . .
CH "O5'" P "C5'" .
CH "C5'" "O5'" "C4'" .
CH "H5'" "C5'" . .
CH "H5''" "C5'" . .
CH "C4'" "C5'" "C3'" .
CH "H4'" "C4'" . .
CH "C3'" "C4'" "O3'" .
CH "H3'" "C3'" . .
CH "C2'" "C3'" "C1'" .
CH "H2'" "C2'" . .
CH "O2'" "C2'" "HO2'" .
CH "HO2'" "O2'" . .
CH "C1'" "C2'" N1 .
CH "H1'" "C1'" . .
CH "O4'" "C1'" . .
CH N1 "C1'" C6 .
CH C6 N1 C5 .
CH H6 C6 . .
CH C5 C6 C4 .
CH H5 C5 . .
CH C4 C5 N3 .
CH N4 C4 H41 .
CH H42 N4 . .
CH H41 N4 . .
CH N3 C4 C2 .
CH HN3 N3 . .
CH C2 N3 O2 .
CH O2 C2 . .
CH "O3'" "C3'" . END
CH "HO3'" "O3'" . .
CH "C4'" "O4'" . ADD
CH 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
CH P OP3 deloc 1.510 0.020
CH OP1 P deloc 1.510 0.020
CH OP2 P deloc 1.510 0.020
CH "O5'" P single 1.610 0.020
CH "C5'" "O5'" single 1.426 0.020
CH "C4'" "C5'" single 1.524 0.020
CH "H5'" "C5'" single 1.092 0.020
CH "H5''" "C5'" single 1.092 0.020
CH "C4'" "O4'" single 1.426 0.020
CH "C3'" "C4'" single 1.524 0.020
CH "H4'" "C4'" single 1.099 0.020
CH "O4'" "C1'" single 1.426 0.020
CH "O3'" "C3'" single 1.432 0.020
CH "C2'" "C3'" single 1.524 0.020
CH "H3'" "C3'" single 1.099 0.020
CH "HO3'" "O3'" single 0.967 0.020
CH "O2'" "C2'" single 1.432 0.020
CH "C1'" "C2'" single 1.524 0.020
CH "H2'" "C2'" single 1.099 0.020
CH "HO2'" "O2'" single 0.967 0.020
CH N1 "C1'" single 1.465 0.020
CH "H1'" "C1'" single 1.099 0.020
CH N1 C2 single 1.410 0.020
CH C6 N1 double 1.337 0.020
CH O2 C2 double 1.250 0.020
CH C2 N3 single 1.337 0.020
CH N3 C4 single 1.337 0.020
CH HN3 N3 single 1.040 0.020
CH N4 C4 single 1.355 0.020
CH C4 C5 double 1.390 0.020
CH H41 N4 single 1.010 0.020
CH H42 N4 single 1.010 0.020
CH C5 C6 single 1.390 0.020
CH H5 C5 single 1.083 0.020
CH 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
CH OP3 P OP1 119.900 3.000
CH OP3 P OP2 119.900 3.000
CH OP3 P "O5'" 108.200 3.000
CH OP1 P OP2 119.900 3.000
CH OP1 P "O5'" 108.200 3.000
CH OP2 P "O5'" 108.200 3.000
CH P "O5'" "C5'" 120.500 3.000
CH "O5'" "C5'" "H5'" 109.470 3.000
CH "O5'" "C5'" "H5''" 109.470 3.000
CH "O5'" "C5'" "C4'" 109.470 3.000
CH "H5'" "C5'" "H5''" 107.900 3.000
CH "H5'" "C5'" "C4'" 109.470 3.000
CH "H5''" "C5'" "C4'" 109.470 3.000
CH "C5'" "C4'" "H4'" 108.340 3.000
CH "C5'" "C4'" "C3'" 111.000 3.000
CH "C5'" "C4'" "O4'" 109.470 3.000
CH "H4'" "C4'" "C3'" 108.340 3.000
CH "H4'" "C4'" "O4'" 109.470 3.000
CH "C3'" "C4'" "O4'" 109.470 3.000
CH "C4'" "C3'" "H3'" 108.340 3.000
CH "C4'" "C3'" "C2'" 111.000 3.000
CH "C4'" "C3'" "O3'" 109.470 3.000
CH "H3'" "C3'" "C2'" 108.340 3.000
CH "H3'" "C3'" "O3'" 109.470 3.000
CH "C2'" "C3'" "O3'" 109.470 3.000
CH "C3'" "C2'" "H2'" 108.340 3.000
CH "C3'" "C2'" "O2'" 109.470 3.000
CH "C3'" "C2'" "C1'" 111.000 3.000
CH "H2'" "C2'" "O2'" 109.470 3.000
CH "H2'" "C2'" "C1'" 108.340 3.000
CH "O2'" "C2'" "C1'" 109.470 3.000
CH "C2'" "O2'" "HO2'" 109.470 3.000
CH "C2'" "C1'" "H1'" 108.340 3.000
CH "C2'" "C1'" "O4'" 109.470 3.000
CH "C2'" "C1'" N1 109.470 3.000
CH "H1'" "C1'" "O4'" 109.470 3.000
CH "H1'" "C1'" N1 109.470 3.000
CH "O4'" "C1'" N1 109.470 3.000
CH "C1'" "O4'" "C4'" 111.800 3.000
CH "C1'" N1 C6 120.000 3.000
CH "C1'" N1 C2 120.000 3.000
CH C6 N1 C2 120.000 3.000
CH N1 C6 H6 120.000 3.000
CH N1 C6 C5 120.000 3.000
CH H6 C6 C5 120.000 3.000
CH C6 C5 H5 120.000 3.000
CH C6 C5 C4 120.000 3.000
CH H5 C5 C4 120.000 3.000
CH C5 C4 N4 120.000 3.000
CH C5 C4 N3 120.000 3.000
CH N4 C4 N3 120.000 3.000
CH C4 N4 H42 120.000 3.000
CH C4 N4 H41 120.000 3.000
CH H42 N4 H41 120.000 3.000
CH C4 N3 HN3 120.000 3.000
CH C4 N3 C2 120.000 3.000
CH HN3 N3 C2 120.000 3.000
CH N3 C2 O2 120.000 3.000
CH N3 C2 N1 120.000 3.000
CH O2 C2 N1 120.000 3.000
CH "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
CH var_1 OP3 P "O5'" "C5'" 0.000 20.000 1
CH var_2 P "O5'" "C5'" "C4'" 0.000 20.000 1
CH var_3 "O5'" "C5'" "C4'" "C3'" 0.000 20.000 3
CH var_4 "C5'" "C4'" "O4'" "C1'" 0.000 20.000 1
CH var_5 "C5'" "C4'" "C3'" "O3'" 0.000 20.000 3
CH var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
CH var_7 "C3'" "C2'" "O2'" "HO2'" 0.000 20.000 1
CH var_8 "C3'" "C2'" "C1'" N1 0.000 20.000 3
CH var_9 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
CH var_10 "C2'" "C1'" N1 C6 0.000 20.000 1
CH CONST_1 "C1'" N1 C2 N3 0.000 0.000 0
CH CONST_2 "C1'" N1 C6 C5 0.000 0.000 0
CH CONST_3 N1 C6 C5 C4 0.000 0.000 0
CH CONST_4 C6 C5 C4 N3 0.000 0.000 0
CH CONST_5 C5 C4 N4 H41 0.000 0.000 0
CH CONST_6 C5 C4 N3 C2 0.000 0.000 0
CH CONST_7 C4 N3 C2 O2 0.000 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
CH chir_01 "C4'" "C5'" "O4'" "C3'" positiv
CH chir_02 "C3'" "C4'" "O3'" "C2'" positiv
CH chir_03 "C2'" "C3'" "O2'" "C1'" positiv
CH 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
CH plan-1 N1 0.020
CH plan-1 "C1'" 0.020
CH plan-1 C2 0.020
CH plan-1 C6 0.020
CH plan-1 N3 0.020
CH plan-1 C4 0.020
CH plan-1 C5 0.020
CH plan-1 O2 0.020
CH plan-1 HN3 0.020
CH plan-1 N4 0.020
CH plan-1 H5 0.020
CH plan-1 H6 0.020
CH plan-1 H42 0.020
CH plan-1 H41 0.020
CH plan-2 N4 0.020
CH plan-2 C4 0.020
CH plan-2 H41 0.020
CH plan-2 H42 0.020
# ------------------------------------------------------
|
