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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
P P '. ' DNA 42 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_P
#
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
P OP3 O OP -0.666 0.000 0.000 0.000
P P P P 0.000 -0.739 0.559 1.196
P OP1 O OP -0.666 -0.874 -0.516 2.252
P OP2 O OP -0.666 0.033 1.730 1.765
P "O5'" O O2 0.000 -2.203 1.050 0.741
P "C5'" C CH2 0.000 -3.183 1.533 1.662
P "H5'" H H 0.000 -2.792 2.409 2.183
P "H5''" H H 0.000 -3.414 0.751 2.389
P "C4'" C CH1 0.000 -4.454 1.914 0.901
P "H4'" H H 0.000 -4.230 2.656 0.122
P "C3'" C CH1 0.000 -5.532 2.453 1.875
P "H3'" H H 0.000 -5.514 1.900 2.825
P "C2'" C CH2 0.000 -6.841 2.172 1.098
P "H2'" H H 0.000 -7.195 3.053 0.559
P "H2''" H H 0.000 -7.635 1.803 1.751
P "C1'" C CH1 0.000 -6.453 1.073 0.089
P "H1'" H H 0.000 -6.578 1.445 -0.937
P "O4'" O O2 0.000 -5.073 0.744 0.326
P N9 N NR5 0.000 -7.290 -0.112 0.296
P C4 C CR56 0.000 -8.531 -0.330 -0.238
P C5 C CR56 0.000 -8.944 -1.580 0.236
P N7 N NRD5 0.000 -7.952 -2.059 1.025
P C8 C CR15 0.000 -6.977 -1.197 1.063
P H8 H H 0.000 -6.057 -1.323 1.619
P N3 N NRD6 0.000 -9.324 0.354 -1.068
P C2 C CR6 0.000 -10.506 -0.106 -1.432
P N2 N NH1 0.000 -11.228 0.637 -2.340
P H2 H H 0.000 -10.775 1.351 -2.892
P C6A C CH2 0.000 -12.666 0.378 -2.496
P H6A1 H H 0.000 -13.036 0.825 -3.421
P H6A2 H H 0.000 -13.221 0.784 -1.649
P C7A C CH2 0.000 -12.854 -1.146 -2.551
P H7A1 H H 0.000 -12.280 -1.565 -3.381
P H7A2 H H 0.000 -13.910 -1.389 -2.682
P C8A C CH2 0.000 -12.353 -1.737 -1.233
P H8A1 H H 0.000 -12.368 -2.827 -1.306
P H8A2 H H 0.000 -13.017 -1.418 -0.427
P N1 N NR6 0.000 -10.989 -1.285 -0.951
P C6 C CR6 0.000 -10.212 -2.062 -0.157
P O6 O O 0.000 -10.602 -3.157 0.212
P "O3'" O OH1 0.000 -5.364 3.854 2.098
P "HO3'" H H 0.000 -6.016 4.239 2.701
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
P OP3 n/a P START
P P OP3 "O5'" .
P OP1 P . .
P OP2 P . .
P "O5'" P "C5'" .
P "C5'" "O5'" "C4'" .
P "H5'" "C5'" . .
P "H5''" "C5'" . .
P "C4'" "C5'" "C3'" .
P "H4'" "C4'" . .
P "C3'" "C4'" "O3'" .
P "H3'" "C3'" . .
P "C2'" "C3'" "C1'" .
P "H2'" "C2'" . .
P "H2''" "C2'" . .
P "C1'" "C2'" N9 .
P "H1'" "C1'" . .
P "O4'" "C1'" . .
P N9 "C1'" C4 .
P C4 N9 N3 .
P C5 C4 N7 .
P N7 C5 C8 .
P C8 N7 H8 .
P H8 C8 . .
P N3 C4 C2 .
P C2 N3 N2 .
P N2 C2 C6A .
P H2 N2 . .
P C6A N2 C7A .
P H6A1 C6A . .
P H6A2 C6A . .
P C7A C6A C8A .
P H7A1 C7A . .
P H7A2 C7A . .
P C8A C7A N1 .
P H8A1 C8A . .
P H8A2 C8A . .
P N1 C8A C6 .
P C6 N1 O6 .
P O6 C6 . .
P "O3'" "C3'" . END
P "HO3'" "O3'" . .
P "C4'" "O4'" . ADD
P N9 C8 . ADD
P C5 C6 . ADD
P 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
P OP1 P deloc 1.510 0.020
P OP2 P deloc 1.510 0.020
P P OP3 deloc 1.510 0.020
P "O5'" P single 1.610 0.020
P "C5'" "O5'" single 1.426 0.020
P "C4'" "C5'" single 1.524 0.020
P "H5'" "C5'" single 1.092 0.020
P "H5''" "C5'" single 1.092 0.020
P "C4'" "O4'" single 1.426 0.020
P "C3'" "C4'" single 1.524 0.020
P "H4'" "C4'" single 1.099 0.020
P "O4'" "C1'" single 1.426 0.020
P "O3'" "C3'" single 1.432 0.020
P "C2'" "C3'" single 1.524 0.020
P "H3'" "C3'" single 1.099 0.020
P "HO3'" "O3'" single 0.967 0.020
P "C1'" "C2'" single 1.524 0.020
P "H2'" "C2'" single 1.092 0.020
P "H2''" "C2'" single 1.092 0.020
P N9 "C1'" single 1.485 0.020
P "H1'" "C1'" single 1.099 0.020
P N9 C8 single 1.337 0.020
P C4 N9 single 1.337 0.020
P C8 N7 double 1.350 0.020
P H8 C8 single 1.083 0.020
P N7 C5 single 1.350 0.020
P C5 C6 single 1.490 0.020
P C5 C4 double 1.490 0.020
P O6 C6 double 1.250 0.020
P C6 N1 single 1.410 0.020
P N1 C2 single 1.410 0.020
P N1 C8A single 1.465 0.020
P N2 C2 single 1.350 0.020
P C2 N3 double 1.350 0.020
P C6A N2 single 1.450 0.020
P H2 N2 single 1.010 0.020
P N3 C4 single 1.355 0.020
P C7A C6A single 1.524 0.020
P H6A1 C6A single 1.092 0.020
P H6A2 C6A single 1.092 0.020
P C8A C7A single 1.524 0.020
P H7A1 C7A single 1.092 0.020
P H7A2 C7A single 1.092 0.020
P H8A1 C8A single 1.092 0.020
P H8A2 C8A single 1.092 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
P OP3 P OP1 119.900 3.000
P OP3 P OP2 119.900 3.000
P OP3 P "O5'" 108.200 3.000
P OP1 P OP2 119.900 3.000
P OP1 P "O5'" 108.200 3.000
P OP2 P "O5'" 108.200 3.000
P P "O5'" "C5'" 120.500 3.000
P "O5'" "C5'" "H5'" 109.470 3.000
P "O5'" "C5'" "H5''" 109.470 3.000
P "O5'" "C5'" "C4'" 109.470 3.000
P "H5'" "C5'" "H5''" 107.900 3.000
P "H5'" "C5'" "C4'" 109.470 3.000
P "H5''" "C5'" "C4'" 109.470 3.000
P "C5'" "C4'" "H4'" 108.340 3.000
P "C5'" "C4'" "C3'" 111.000 3.000
P "C5'" "C4'" "O4'" 109.470 3.000
P "H4'" "C4'" "C3'" 108.340 3.000
P "H4'" "C4'" "O4'" 109.470 3.000
P "C3'" "C4'" "O4'" 109.470 3.000
P "C4'" "C3'" "H3'" 108.340 3.000
P "C4'" "C3'" "C2'" 111.000 3.000
P "C4'" "C3'" "O3'" 109.470 3.000
P "H3'" "C3'" "C2'" 108.340 3.000
P "H3'" "C3'" "O3'" 109.470 3.000
P "C2'" "C3'" "O3'" 109.470 3.000
P "C3'" "C2'" "H2'" 109.470 3.000
P "C3'" "C2'" "H2''" 109.470 3.000
P "C3'" "C2'" "C1'" 111.000 3.000
P "H2'" "C2'" "H2''" 107.900 3.000
P "H2'" "C2'" "C1'" 109.470 3.000
P "H2''" "C2'" "C1'" 109.470 3.000
P "C2'" "C1'" "H1'" 108.340 3.000
P "C2'" "C1'" "O4'" 109.470 3.000
P "C2'" "C1'" N9 109.470 3.000
P "H1'" "C1'" "O4'" 109.470 3.000
P "H1'" "C1'" N9 109.470 3.000
P "O4'" "C1'" N9 109.470 3.000
P "C1'" "O4'" "C4'" 111.800 3.000
P "C1'" N9 C4 126.000 3.000
P "C1'" N9 C8 126.000 3.000
P C4 N9 C8 108.000 3.000
P N9 C4 C5 108.000 3.000
P N9 C4 N3 132.000 3.000
P C5 C4 N3 120.000 3.000
P C4 C5 N7 108.000 3.000
P C4 C5 C6 120.000 3.000
P N7 C5 C6 132.000 3.000
P C5 N7 C8 108.000 3.000
P N7 C8 H8 126.000 3.000
P N7 C8 N9 108.000 3.000
P H8 C8 N9 126.000 3.000
P C4 N3 C2 120.000 3.000
P N3 C2 N2 120.000 3.000
P N3 C2 N1 120.000 3.000
P N2 C2 N1 120.000 3.000
P C2 N2 H2 120.000 3.000
P C2 N2 C6A 120.000 3.000
P H2 N2 C6A 118.500 3.000
P N2 C6A H6A1 109.470 3.000
P N2 C6A H6A2 109.470 3.000
P N2 C6A C7A 112.000 3.000
P H6A1 C6A H6A2 107.900 3.000
P H6A1 C6A C7A 109.470 3.000
P H6A2 C6A C7A 109.470 3.000
P C6A C7A H7A1 109.470 3.000
P C6A C7A H7A2 109.470 3.000
P C6A C7A C8A 111.000 3.000
P H7A1 C7A H7A2 107.900 3.000
P H7A1 C7A C8A 109.470 3.000
P H7A2 C7A C8A 109.470 3.000
P C7A C8A H8A1 109.470 3.000
P C7A C8A H8A2 109.470 3.000
P C7A C8A N1 109.470 3.000
P H8A1 C8A H8A2 107.900 3.000
P H8A1 C8A N1 109.470 3.000
P H8A2 C8A N1 109.470 3.000
P C8A N1 C6 120.000 3.000
P C8A N1 C2 120.000 3.000
P C6 N1 C2 120.000 3.000
P N1 C6 O6 120.000 3.000
P N1 C6 C5 120.000 3.000
P O6 C6 C5 120.000 3.000
P "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
P var_1 OP3 P "O5'" "C5'" 175.019 20.000 1
P var_2 P "O5'" "C5'" "C4'" 179.958 20.000 1
P var_3 "O5'" "C5'" "C4'" "C3'" -179.516 20.000 3
P var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
P var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
P var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
P var_7 "C3'" "C2'" "C1'" N9 120.000 20.000 3
P var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
P var_9 "C2'" "C1'" N9 C4 85.401 20.000 1
P CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
P CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
P CONST_3 N9 C4 C5 N7 0.000 0.000 0
P CONST_4 C4 C5 C6 N1 0.000 0.000 0
P CONST_5 C4 C5 N7 C8 0.000 0.000 0
P CONST_6 C5 N7 C8 N9 0.000 0.000 0
P CONST_7 N9 C4 N3 C2 180.000 0.000 0
P CONST_8 C4 N3 C2 N2 180.000 0.000 0
P var_10 N3 C2 N2 C6A -150.000 20.000 1
P var_11 C2 N2 C6A C7A -30.000 20.000 3
P var_12 N2 C6A C7A C8A 60.000 20.000 3
P var_13 C6A C7A C8A N1 -60.000 20.000 3
P var_14 C7A C8A N1 C6 -150.000 20.000 1
P CONST_9 C8A N1 C2 N3 180.000 0.000 0
P CONST_10 C8A N1 C6 O6 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
P chir_01 "C4'" "C5'" "O4'" "C3'" negativ
P chir_02 "C3'" "C4'" "O3'" "C2'" negativ
P chir_03 "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
P plan-1 N9 0.020
P plan-1 "C1'" 0.020
P plan-1 C8 0.020
P plan-1 C4 0.020
P plan-1 N7 0.020
P plan-1 H8 0.020
P plan-1 C5 0.020
P plan-1 C6 0.020
P plan-1 N1 0.020
P plan-1 C2 0.020
P plan-1 N3 0.020
P plan-1 O6 0.020
P plan-1 C8A 0.020
P plan-1 N2 0.020
P plan-1 H2 0.020
P plan-2 N2 0.020
P plan-2 C2 0.020
P plan-2 C6A 0.020
P plan-2 H2 0.020
# ------------------------------------------------------
|
