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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
OMG OMG 'O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE' RNA 39 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_OMG
#
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
OMG OP3 O OP -0.666 0.000 0.000 0.000
OMG P P P 0.000 -1.168 -0.115 0.955
OMG OP1 O OP -0.666 -1.575 1.265 1.424
OMG OP2 O OP -0.666 -0.761 -0.953 2.148
OMG "O5'" O O2 0.000 -2.408 -0.816 0.205
OMG "C5'" C CH2 0.000 -2.743 0.018 -0.905
OMG "H5'" H H 0.000 -1.882 0.099 -1.571
OMG "H5''" H H 0.000 -3.017 1.011 -0.543
OMG "C4'" C CH1 0.000 -3.923 -0.594 -1.664
OMG "H4'" H H 0.000 -3.659 -1.601 -2.015
OMG "C3'" C CH1 0.000 -4.293 0.298 -2.865
OMG "H3'" H H 0.000 -3.666 1.200 -2.880
OMG "C2'" C CH1 0.000 -5.773 0.673 -2.617
OMG "H2'" H H 0.000 -5.852 1.661 -2.143
OMG "O2'" O O2 0.000 -6.520 0.630 -3.835
OMG CM2 C CH3 0.000 -6.527 1.958 -4.362
OMG HM23 H H 0.000 -6.981 2.613 -3.665
OMG HM22 H H 0.000 -5.531 2.271 -4.543
OMG HM21 H H 0.000 -7.073 1.975 -5.270
OMG "C1'" C CH1 0.000 -6.233 -0.443 -1.646
OMG "H1'" H H 0.000 -6.485 -1.358 -2.201
OMG "O4'" O O2 0.000 -5.077 -0.660 -0.810
OMG N9 N NR5 0.000 -7.374 0.004 -0.843
OMG C4 C CR56 0.000 -8.696 -0.203 -1.131
OMG C5 C CR56 0.000 -9.416 0.393 -0.089
OMG N7 N NRD5 0.000 -8.515 0.934 0.766
OMG C8 C CR15 0.000 -7.312 0.705 0.326
OMG H8 H H 0.000 -6.399 1.023 0.814
OMG N3 N NRD6 0.000 -9.351 -0.821 -2.118
OMG C2 C CR6 0.000 -10.664 -0.872 -2.137
OMG N2 N NH2 0.000 -11.291 -1.514 -3.175
OMG HN22 H H 0.000 -12.303 -1.565 -3.209
OMG HN21 H H 0.000 -10.747 -1.942 -3.916
OMG N1 N NR16 0.000 -11.421 -0.306 -1.156
OMG HN1 H H 0.000 -12.458 -0.364 -1.203
OMG C6 C CR6 0.000 -10.829 0.332 -0.122
OMG O6 O O 0.000 -11.498 0.842 0.762
OMG "O3'" O OH1 0.000 -4.158 -0.425 -4.089
OMG "HO3'" H H 0.000 -3.218 -0.631 -4.190
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
OMG OP3 n/a P START
OMG P OP3 "O5'" .
OMG OP1 P . .
OMG OP2 P . .
OMG "O5'" P "C5'" .
OMG "C5'" "O5'" "C4'" .
OMG "H5'" "C5'" . .
OMG "H5''" "C5'" . .
OMG "C4'" "C5'" "C3'" .
OMG "H4'" "C4'" . .
OMG "C3'" "C4'" "O3'" .
OMG "H3'" "C3'" . .
OMG "C2'" "C3'" "C1'" .
OMG "H2'" "C2'" . .
OMG "O2'" "C2'" CM2 .
OMG CM2 "O2'" HM21 .
OMG HM23 CM2 . .
OMG HM22 CM2 . .
OMG HM21 CM2 . .
OMG "C1'" "C2'" N9 .
OMG "H1'" "C1'" . .
OMG "O4'" "C1'" . .
OMG N9 "C1'" C4 .
OMG C4 N9 N3 .
OMG C5 C4 N7 .
OMG N7 C5 C8 .
OMG C8 N7 H8 .
OMG H8 C8 . .
OMG N3 C4 C2 .
OMG C2 N3 N1 .
OMG N2 C2 HN21 .
OMG HN22 N2 . .
OMG HN21 N2 . .
OMG N1 C2 C6 .
OMG HN1 N1 . .
OMG C6 N1 O6 .
OMG O6 C6 . .
OMG "O3'" "C3'" . END
OMG "HO3'" "O3'" . .
OMG "C4'" "O4'" . ADD
OMG N9 C8 . ADD
OMG C5 C6 . 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
OMG OP1 P deloc 1.510 0.020
OMG OP2 P deloc 1.510 0.020
OMG P OP3 deloc 1.510 0.020
OMG "O5'" P single 1.610 0.020
OMG "C5'" "O5'" single 1.426 0.020
OMG "C4'" "C5'" single 1.524 0.020
OMG "H5'" "C5'" single 1.092 0.020
OMG "H5''" "C5'" single 1.092 0.020
OMG "C4'" "O4'" single 1.426 0.020
OMG "C3'" "C4'" single 1.524 0.020
OMG "H4'" "C4'" single 1.099 0.020
OMG "O4'" "C1'" single 1.426 0.020
OMG "O3'" "C3'" single 1.432 0.020
OMG "C2'" "C3'" single 1.524 0.020
OMG "H3'" "C3'" single 1.099 0.020
OMG "HO3'" "O3'" single 0.967 0.020
OMG "O2'" "C2'" single 1.426 0.020
OMG "C1'" "C2'" single 1.524 0.020
OMG "H2'" "C2'" single 1.099 0.020
OMG CM2 "O2'" single 1.426 0.020
OMG HM21 CM2 single 1.059 0.020
OMG HM22 CM2 single 1.059 0.020
OMG HM23 CM2 single 1.059 0.020
OMG N9 "C1'" single 1.485 0.020
OMG "H1'" "C1'" single 1.099 0.020
OMG N9 C8 single 1.337 0.020
OMG C4 N9 single 1.337 0.020
OMG C8 N7 double 1.350 0.020
OMG H8 C8 single 1.083 0.020
OMG N7 C5 single 1.350 0.020
OMG C5 C6 single 1.490 0.020
OMG C5 C4 double 1.490 0.020
OMG O6 C6 double 1.250 0.020
OMG C6 N1 single 1.337 0.020
OMG N1 C2 single 1.337 0.020
OMG HN1 N1 single 1.040 0.020
OMG N2 C2 single 1.355 0.020
OMG C2 N3 double 1.350 0.020
OMG HN21 N2 single 1.010 0.020
OMG HN22 N2 single 1.010 0.020
OMG N3 C4 single 1.355 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
OMG OP3 P OP1 119.900 3.000
OMG OP3 P OP2 119.900 3.000
OMG OP3 P "O5'" 108.200 3.000
OMG OP1 P OP2 119.900 3.000
OMG OP1 P "O5'" 108.200 3.000
OMG OP2 P "O5'" 108.200 3.000
OMG P "O5'" "C5'" 120.500 3.000
OMG "O5'" "C5'" "H5'" 109.470 3.000
OMG "O5'" "C5'" "H5''" 109.470 3.000
OMG "O5'" "C5'" "C4'" 109.470 3.000
OMG "H5'" "C5'" "H5''" 107.900 3.000
OMG "H5'" "C5'" "C4'" 109.470 3.000
OMG "H5''" "C5'" "C4'" 109.470 3.000
OMG "C5'" "C4'" "H4'" 108.340 3.000
OMG "C5'" "C4'" "C3'" 111.000 3.000
OMG "C5'" "C4'" "O4'" 109.470 3.000
OMG "H4'" "C4'" "C3'" 108.340 3.000
OMG "H4'" "C4'" "O4'" 109.470 3.000
OMG "C3'" "C4'" "O4'" 109.470 3.000
OMG "C4'" "C3'" "H3'" 108.340 3.000
OMG "C4'" "C3'" "C2'" 111.000 3.000
OMG "C4'" "C3'" "O3'" 109.470 3.000
OMG "H3'" "C3'" "C2'" 108.340 3.000
OMG "H3'" "C3'" "O3'" 109.470 3.000
OMG "C2'" "C3'" "O3'" 109.470 3.000
OMG "C3'" "C2'" "H2'" 108.340 3.000
OMG "C3'" "C2'" "O2'" 109.470 3.000
OMG "C3'" "C2'" "C1'" 111.000 3.000
OMG "H2'" "C2'" "O2'" 109.470 3.000
OMG "H2'" "C2'" "C1'" 108.340 3.000
OMG "O2'" "C2'" "C1'" 109.470 3.000
OMG "C2'" "O2'" CM2 111.800 3.000
OMG "O2'" CM2 HM23 109.470 3.000
OMG "O2'" CM2 HM22 109.470 3.000
OMG "O2'" CM2 HM21 109.470 3.000
OMG HM23 CM2 HM22 109.470 3.000
OMG HM23 CM2 HM21 109.470 3.000
OMG HM22 CM2 HM21 109.470 3.000
OMG "C2'" "C1'" "H1'" 108.340 3.000
OMG "C2'" "C1'" "O4'" 109.470 3.000
OMG "C2'" "C1'" N9 109.470 3.000
OMG "H1'" "C1'" "O4'" 109.470 3.000
OMG "H1'" "C1'" N9 109.470 3.000
OMG "O4'" "C1'" N9 109.470 3.000
OMG "C1'" "O4'" "C4'" 111.800 3.000
OMG "C1'" N9 C4 126.000 3.000
OMG "C1'" N9 C8 126.000 3.000
OMG C4 N9 C8 108.000 3.000
OMG N9 C4 C5 108.000 3.000
OMG N9 C4 N3 132.000 3.000
OMG C5 C4 N3 120.000 3.000
OMG C4 C5 N7 108.000 3.000
OMG C4 C5 C6 120.000 3.000
OMG N7 C5 C6 132.000 3.000
OMG C5 N7 C8 108.000 3.000
OMG N7 C8 H8 126.000 3.000
OMG N7 C8 N9 108.000 3.000
OMG H8 C8 N9 126.000 3.000
OMG C4 N3 C2 120.000 3.000
OMG N3 C2 N2 120.000 3.000
OMG N3 C2 N1 120.000 3.000
OMG N2 C2 N1 120.000 3.000
OMG C2 N2 HN22 120.000 3.000
OMG C2 N2 HN21 120.000 3.000
OMG HN22 N2 HN21 120.000 3.000
OMG C2 N1 HN1 120.000 3.000
OMG C2 N1 C6 120.000 3.000
OMG HN1 N1 C6 120.000 3.000
OMG N1 C6 O6 120.000 3.000
OMG N1 C6 C5 120.000 3.000
OMG O6 C6 C5 120.000 3.000
OMG "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
OMG var_1 OP3 P "O5'" "C5'" -60.077 20.000 1
OMG var_2 P "O5'" "C5'" "C4'" -179.943 20.000 1
OMG var_3 "O5'" "C5'" "C4'" "C3'" -179.989 20.000 3
OMG var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
OMG var_5 "C5'" "C4'" "C3'" "O3'" 120.000 20.000 3
OMG var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
OMG var_7 "C3'" "C2'" "O2'" CM2 -94.325 20.000 1
OMG var_8 "C2'" "O2'" CM2 HM21 -179.988 20.000 1
OMG var_9 "C3'" "C2'" "C1'" N9 150.000 20.000 3
OMG var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
OMG var_11 "C2'" "C1'" N9 C4 94.137 20.000 1
OMG CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
OMG CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
OMG CONST_3 N9 C4 C5 N7 0.000 0.000 0
OMG CONST_4 C4 C5 C6 N1 0.000 0.000 0
OMG CONST_5 C4 C5 N7 C8 0.000 0.000 0
OMG CONST_6 C5 N7 C8 N9 0.000 0.000 0
OMG CONST_7 N9 C4 N3 C2 180.000 0.000 0
OMG CONST_8 C4 N3 C2 N1 0.000 0.000 0
OMG CONST_9 N3 C2 N2 HN21 -0.007 0.000 0
OMG CONST_10 N3 C2 N1 C6 0.000 0.000 0
OMG CONST_11 C2 N1 C6 O6 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
OMG chir_01 "C4'" "C5'" "O4'" "C3'" negativ
OMG chir_02 "C3'" "C4'" "O3'" "C2'" negativ
OMG chir_03 "C2'" "C3'" "O2'" "C1'" negativ
OMG chir_04 "C1'" "O4'" "C2'" N9 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
OMG plan-1 N9 0.020
OMG plan-1 "C1'" 0.020
OMG plan-1 C8 0.020
OMG plan-1 C4 0.020
OMG plan-1 N7 0.020
OMG plan-1 H8 0.020
OMG plan-1 C5 0.020
OMG plan-1 C6 0.020
OMG plan-1 N1 0.020
OMG plan-1 C2 0.020
OMG plan-1 N3 0.020
OMG plan-1 O6 0.020
OMG plan-1 HN1 0.020
OMG plan-1 N2 0.020
OMG plan-1 HN22 0.020
OMG plan-1 HN21 0.020
OMG plan-2 N2 0.020
OMG plan-2 C2 0.020
OMG plan-2 HN21 0.020
OMG plan-2 HN22 0.020
# ------------------------------------------------------
|
