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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
XUG XUG '. ' DNA 39 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XUG
#
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
XUG OP3 O OP -0.666 0.000 0.000 0.000
XUG P P P 0.000 -0.477 0.068 -1.434
XUG OP1 O OP -0.666 -0.245 1.513 -1.818
XUG OP2 O OP -0.666 -1.885 -0.473 -1.321
XUG "O5'" O O2 0.000 0.314 -0.817 -2.494
XUG "C5'" C CH2 0.000 -0.419 -1.347 -3.575
XUG "H5'" H H 0.000 -0.260 -0.753 -4.478
XUG "H5''" H H 0.000 -1.486 -1.374 -3.342
XUG "C4'" C CH1 0.000 0.084 -2.752 -3.800
XUG "H4'" H H 0.000 1.150 -2.740 -4.064
XUG "O4'" O O2 0.000 -0.138 -3.581 -2.659
XUG "C3'" C CH1 0.000 -0.727 -3.359 -4.912
XUG "H3'" H H 0.000 -1.747 -2.953 -4.876
XUG "C2'" C CH1 0.000 -0.769 -4.827 -4.574
XUG "H2'" H H 0.000 -1.690 -5.300 -4.942
XUG "SE2'" SE SE 0.000 0.833 -5.708 -5.291
XUG "CA'" C CH3 0.000 0.234 -7.581 -5.138
XUG "HA'3" H H 0.000 -0.748 -7.607 -4.741
XUG "HA'2" H H 0.000 0.239 -8.033 -6.095
XUG "HA'1" H H 0.000 0.888 -8.110 -4.494
XUG "C1'" C CH1 0.000 -0.704 -4.832 -3.060
XUG "H1'" H H 0.000 -0.079 -5.665 -2.708
XUG N9 N NR5 0.000 -2.083 -4.961 -2.528
XUG C8 C CR15 0.000 -2.770 -4.034 -1.847
XUG H8 H H 0.000 -2.406 -3.048 -1.587
XUG N7 N NRD5 0.000 -3.991 -4.527 -1.538
XUG C4 C CR56 0.000 -2.854 -6.040 -2.657
XUG C5 C CR56 0.000 -4.063 -5.778 -2.035
XUG N3 N NRD6 0.000 -2.648 -7.237 -3.249
XUG C2 C CR6 0.000 -3.612 -8.181 -3.240
XUG N2 N NH2 0.000 -3.368 -9.365 -3.843
XUG HN22 H H 0.000 -2.477 -9.528 -4.290
XUG HN21 H H 0.000 -4.075 -10.085 -3.846
XUG N1 N NR16 0.000 -4.802 -7.950 -2.637
XUG HN1 H H 0.000 -5.533 -8.689 -2.639
XUG C6 C CR6 0.000 -5.047 -6.765 -2.031
XUG O6 O O 0.000 -6.150 -6.563 -1.481
XUG "O3'" O OH1 0.000 -0.146 -3.052 -6.175
XUG "HO3'" H H 0.000 -0.373 -2.163 -6.420
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
XUG OP3 n/a P START
XUG P OP3 "O5'" .
XUG OP1 P . .
XUG OP2 P . .
XUG "O5'" P "C5'" .
XUG "C5'" "O5'" "C4'" .
XUG "H5'" "C5'" . .
XUG "H5''" "C5'" . .
XUG "C4'" "C5'" "C3'" .
XUG "H4'" "C4'" . .
XUG "O4'" "C4'" . .
XUG "C3'" "C4'" "O3'" .
XUG "H3'" "C3'" . .
XUG "C2'" "C3'" "C1'" .
XUG "H2'" "C2'" . .
XUG "SE2'" "C2'" "CA'" .
XUG "CA'" "SE2'" "HA'1" .
XUG "HA'3" "CA'" . .
XUG "HA'2" "CA'" . .
XUG "HA'1" "CA'" . .
XUG "C1'" "C2'" N9 .
XUG "H1'" "C1'" . .
XUG N9 "C1'" C4 .
XUG C8 N9 N7 .
XUG H8 C8 . .
XUG N7 C8 . .
XUG C4 N9 N3 .
XUG C5 C4 . .
XUG N3 C4 C2 .
XUG C2 N3 N1 .
XUG N2 C2 HN21 .
XUG HN22 N2 . .
XUG HN21 N2 . .
XUG N1 C2 C6 .
XUG HN1 N1 . .
XUG C6 N1 O6 .
XUG O6 C6 . .
XUG "O3'" "C3'" . END
XUG "HO3'" "O3'" . .
XUG C6 C5 . ADD
XUG C5 N7 . ADD
XUG "C1'" "O4'" . 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
XUG O6 C6 double 1.250 0.020
XUG C6 C5 single 1.490 0.020
XUG C6 N1 single 1.337 0.020
XUG C5 N7 single 1.350 0.020
XUG C5 C4 double 1.490 0.020
XUG N7 C8 double 1.350 0.020
XUG C8 N9 single 1.337 0.020
XUG H8 C8 single 1.083 0.020
XUG N1 C2 single 1.337 0.020
XUG HN1 N1 single 1.040 0.020
XUG N2 C2 single 1.355 0.020
XUG C2 N3 double 1.350 0.020
XUG HN21 N2 single 1.010 0.020
XUG HN22 N2 single 1.010 0.020
XUG N3 C4 single 1.355 0.020
XUG C4 N9 single 1.337 0.020
XUG N9 "C1'" single 1.485 0.020
XUG "C1'" "O4'" single 1.426 0.020
XUG "C1'" "C2'" single 1.524 0.020
XUG "H1'" "C1'" single 1.099 0.020
XUG "O4'" "C4'" single 1.426 0.020
XUG "SE2'" "C2'" single 1.970 0.020
XUG "C2'" "C3'" single 1.524 0.020
XUG "H2'" "C2'" single 1.099 0.020
XUG "CA'" "SE2'" single 1.970 0.020
XUG "HA'1" "CA'" single 1.059 0.020
XUG "HA'2" "CA'" single 1.059 0.020
XUG "HA'3" "CA'" single 1.059 0.020
XUG "O3'" "C3'" single 1.432 0.020
XUG "C3'" "C4'" single 1.524 0.020
XUG "H3'" "C3'" single 1.099 0.020
XUG "HO3'" "O3'" single 0.967 0.020
XUG "C4'" "C5'" single 1.524 0.020
XUG "H4'" "C4'" single 1.099 0.020
XUG "C5'" "O5'" single 1.426 0.020
XUG "H5'" "C5'" single 1.092 0.020
XUG "H5''" "C5'" single 1.092 0.020
XUG "O5'" P single 1.610 0.020
XUG OP1 P deloc 1.510 0.020
XUG OP2 P deloc 1.510 0.020
XUG 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
XUG OP3 P OP1 119.900 3.000
XUG OP3 P OP2 119.900 3.000
XUG OP3 P "O5'" 108.200 3.000
XUG OP1 P OP2 119.900 3.000
XUG OP1 P "O5'" 108.200 3.000
XUG OP2 P "O5'" 108.200 3.000
XUG P "O5'" "C5'" 120.500 3.000
XUG "O5'" "C5'" "H5'" 109.470 3.000
XUG "O5'" "C5'" "H5''" 109.470 3.000
XUG "O5'" "C5'" "C4'" 109.470 3.000
XUG "H5'" "C5'" "H5''" 107.900 3.000
XUG "H5'" "C5'" "C4'" 109.470 3.000
XUG "H5''" "C5'" "C4'" 109.470 3.000
XUG "C5'" "C4'" "H4'" 108.340 3.000
XUG "C5'" "C4'" "O4'" 109.470 3.000
XUG "C5'" "C4'" "C3'" 111.000 3.000
XUG "H4'" "C4'" "O4'" 109.470 3.000
XUG "H4'" "C4'" "C3'" 108.340 3.000
XUG "O4'" "C4'" "C3'" 109.470 3.000
XUG "C4'" "O4'" "C1'" 111.800 3.000
XUG "C4'" "C3'" "H3'" 108.340 3.000
XUG "C4'" "C3'" "C2'" 111.000 3.000
XUG "C4'" "C3'" "O3'" 109.470 3.000
XUG "H3'" "C3'" "C2'" 108.340 3.000
XUG "H3'" "C3'" "O3'" 109.470 3.000
XUG "C2'" "C3'" "O3'" 109.470 3.000
XUG "C3'" "C2'" "H2'" 108.340 3.000
XUG "C3'" "C2'" "SE2'" 109.500 3.000
XUG "C3'" "C2'" "C1'" 111.000 3.000
XUG "H2'" "C2'" "SE2'" 109.500 3.000
XUG "H2'" "C2'" "C1'" 108.340 3.000
XUG "SE2'" "C2'" "C1'" 109.500 3.000
XUG "C2'" "SE2'" "CA'" 98.000 3.000
XUG "SE2'" "CA'" "HA'3" 109.500 3.000
XUG "SE2'" "CA'" "HA'2" 109.500 3.000
XUG "SE2'" "CA'" "HA'1" 109.500 3.000
XUG "HA'3" "CA'" "HA'2" 109.470 3.000
XUG "HA'3" "CA'" "HA'1" 109.470 3.000
XUG "HA'2" "CA'" "HA'1" 109.470 3.000
XUG "C2'" "C1'" "H1'" 108.340 3.000
XUG "C2'" "C1'" N9 109.470 3.000
XUG "C2'" "C1'" "O4'" 109.470 3.000
XUG "H1'" "C1'" N9 109.470 3.000
XUG "H1'" "C1'" "O4'" 109.470 3.000
XUG N9 "C1'" "O4'" 109.470 3.000
XUG "C1'" N9 C8 126.000 3.000
XUG "C1'" N9 C4 126.000 3.000
XUG C8 N9 C4 108.000 3.000
XUG N9 C8 H8 126.000 3.000
XUG N9 C8 N7 108.000 3.000
XUG H8 C8 N7 126.000 3.000
XUG C8 N7 C5 108.000 3.000
XUG N9 C4 C5 108.000 3.000
XUG N9 C4 N3 132.000 3.000
XUG C5 C4 N3 120.000 3.000
XUG C4 C5 C6 120.000 3.000
XUG C4 C5 N7 108.000 3.000
XUG C6 C5 N7 132.000 3.000
XUG C4 N3 C2 120.000 3.000
XUG N3 C2 N2 120.000 3.000
XUG N3 C2 N1 120.000 3.000
XUG N2 C2 N1 120.000 3.000
XUG C2 N2 HN22 120.000 3.000
XUG C2 N2 HN21 120.000 3.000
XUG HN22 N2 HN21 120.000 3.000
XUG C2 N1 HN1 120.000 3.000
XUG C2 N1 C6 120.000 3.000
XUG HN1 N1 C6 120.000 3.000
XUG N1 C6 O6 120.000 3.000
XUG N1 C6 C5 120.000 3.000
XUG O6 C6 C5 120.000 3.000
XUG "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
XUG var_1 OP3 P "O5'" "C5'" 147.267 20.000 1
XUG var_2 P "O5'" "C5'" "C4'" -139.843 20.000 1
XUG var_3 "O5'" "C5'" "C4'" "C3'" 177.595 20.000 3
XUG var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
XUG var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
XUG var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
XUG var_7 "C3'" "C2'" "SE2'" "CA'" -165.114 20.000 1
XUG var_8 "C2'" "SE2'" "CA'" "HA'1" -119.336 20.000 1
XUG var_9 "C3'" "C2'" "C1'" N9 90.000 20.000 3
XUG var_10 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
XUG var_11 "C2'" "C1'" N9 C4 67.090 20.000 1
XUG CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
XUG CONST_2 N9 C8 N7 C5 0.000 0.000 0
XUG CONST_3 "C1'" N9 C4 N3 0.000 0.000 0
XUG CONST_4 N9 C4 C5 C6 180.000 0.000 0
XUG CONST_5 C4 C5 N7 C8 0.000 0.000 0
XUG CONST_6 N9 C4 N3 C2 180.000 0.000 0
XUG CONST_7 C4 N3 C2 N1 0.000 0.000 0
XUG CONST_8 N3 C2 N2 HN21 179.901 0.000 0
XUG CONST_9 N3 C2 N1 C6 0.000 0.000 0
XUG CONST_10 C2 N1 C6 O6 180.000 0.000 0
XUG CONST_11 N1 C6 C5 C4 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
XUG chir_01 "C1'" N9 "O4'" "C2'" positiv
XUG chir_02 "C2'" "C1'" "SE2'" "C3'" positiv
XUG chir_03 "C3'" "C2'" "O3'" "C4'" positiv
XUG chir_04 "C4'" "O4'" "C3'" "C5'" 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
XUG plan-1 C6 0.020
XUG plan-1 C5 0.020
XUG plan-1 N1 0.020
XUG plan-1 O6 0.020
XUG plan-1 C2 0.020
XUG plan-1 N3 0.020
XUG plan-1 N7 0.020
XUG plan-1 C4 0.020
XUG plan-1 C8 0.020
XUG plan-1 N9 0.020
XUG plan-1 H8 0.020
XUG plan-1 HN1 0.020
XUG plan-1 N2 0.020
XUG plan-1 "C1'" 0.020
XUG plan-1 HN22 0.020
XUG plan-1 HN21 0.020
XUG plan-2 N2 0.020
XUG plan-2 C2 0.020
XUG plan-2 HN21 0.020
XUG plan-2 HN22 0.020
# ------------------------------------------------------
|
