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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
P2T P2T '. ' DNA 44 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_P2T
#
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
P2T OP3 O OP -0.666 0.000 0.000 0.000
P2T P P P 0.000 -0.530 1.416 0.049
P2T OP1 O OP -0.666 0.531 2.491 0.149
P2T OP2 O OP -0.666 -1.420 1.497 -1.172
P2T "O5'" O O2 0.000 -1.575 1.370 1.285
P2T "C5'" C CH2 0.000 -2.598 0.391 1.268
P2T "H5'" H H 0.000 -2.156 -0.607 1.248
P2T "H5''" H H 0.000 -3.226 0.527 0.385
P2T "C4'" C CH1 0.000 -3.444 0.549 2.524
P2T "H4'" H H 0.000 -2.807 0.459 3.415
P2T "C3'" C CH1 0.000 -4.591 -0.451 2.607
P2T "H3'" H H 0.000 -4.330 -1.416 2.151
P2T "C2'" C CH1 0.000 -5.687 0.260 1.843
P2T "H2'" H H 0.000 -5.523 0.146 0.762
P2T "O2'" O O2 0.000 -6.974 -0.213 2.186
P2T "CB'" C CH2 0.000 -7.118 -1.603 1.913
P2T "HB'1" H H 0.000 -6.394 -2.172 2.501
P2T "HB'2" H H 0.000 -6.948 -1.791 0.851
P2T "CC'" C CH2 0.000 -8.527 -2.033 2.287
P2T "HC'1" H H 0.000 -9.233 -1.451 1.690
P2T "HC'2" H H 0.000 -8.682 -1.815 3.346
P2T "CD'" C CH3 0.000 -8.751 -3.514 2.036
P2T "HD'3" H H 0.000 -9.742 -3.774 2.304
P2T "HD'2" H H 0.000 -8.597 -3.727 1.009
P2T "HD'1" H H 0.000 -8.069 -4.079 2.618
P2T "C1'" C CH1 0.000 -5.468 1.707 2.248
P2T "H1'" H H 0.000 -6.026 1.920 3.171
P2T "O4'" O O2 0.000 -4.059 1.855 2.492
P2T N1 N NR6 0.000 -5.864 2.630 1.223
P2T C2 C CR6 0.000 -7.152 3.209 1.216
P2T O2 O O 0.000 -8.013 2.975 2.065
P2T N3 N NR16 0.000 -7.401 4.090 0.157
P2T HN3 H H 0.000 -8.344 4.528 0.129
P2T C4 C CR6 0.000 -6.526 4.441 -0.860
P2T C5 C CR6 0.000 -5.190 3.791 -0.785
P2T C5M C CH3 0.000 -4.190 4.118 -1.847
P2T H73 H H 0.000 -4.589 4.859 -2.488
P2T H72 H H 0.000 -3.304 4.480 -1.394
P2T H71 H H 0.000 -3.972 3.246 -2.404
P2T C6 C CR16 0.000 -4.948 2.948 0.226
P2T H6 H H 0.000 -3.972 2.481 0.271
P2T O4 O O 0.000 -6.811 5.225 -1.761
P2T "O3'" O OH1 0.000 -4.954 -0.589 3.981
P2T "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
P2T OP3 n/a P START
P2T P OP3 "O5'" .
P2T OP1 P . .
P2T OP2 P . .
P2T "O5'" P "C5'" .
P2T "C5'" "O5'" "C4'" .
P2T "H5'" "C5'" . .
P2T "H5''" "C5'" . .
P2T "C4'" "C5'" "C3'" .
P2T "H4'" "C4'" . .
P2T "C3'" "C4'" "O3'" .
P2T "H3'" "C3'" . .
P2T "C2'" "C3'" "C1'" .
P2T "H2'" "C2'" . .
P2T "O2'" "C2'" "CB'" .
P2T "CB'" "O2'" "CC'" .
P2T "HB'1" "CB'" . .
P2T "HB'2" "CB'" . .
P2T "CC'" "CB'" "CD'" .
P2T "HC'1" "CC'" . .
P2T "HC'2" "CC'" . .
P2T "CD'" "CC'" "HD'1" .
P2T "HD'3" "CD'" . .
P2T "HD'2" "CD'" . .
P2T "HD'1" "CD'" . .
P2T "C1'" "C2'" N1 .
P2T "H1'" "C1'" . .
P2T "O4'" "C1'" . .
P2T N1 "C1'" C2 .
P2T C2 N1 N3 .
P2T O2 C2 . .
P2T N3 C2 C4 .
P2T HN3 N3 . .
P2T C4 N3 O4 .
P2T C5 C4 C6 .
P2T C5M C5 H71 .
P2T H73 C5M . .
P2T H72 C5M . .
P2T H71 C5M . .
P2T C6 C5 H6 .
P2T H6 C6 . .
P2T O4 C4 . .
P2T "O3'" "C3'" . END
P2T "HO3'" "O3'" . .
P2T "C4'" "O4'" . ADD
P2T N1 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
P2T OP1 P deloc 1.510 0.020
P2T OP2 P deloc 1.510 0.020
P2T "O5'" P single 1.610 0.020
P2T P OP3 deloc 1.510 0.020
P2T "C5'" "O5'" single 1.426 0.020
P2T "C4'" "C5'" single 1.524 0.020
P2T "H5'" "C5'" single 1.092 0.020
P2T "H5''" "C5'" single 1.092 0.020
P2T "C4'" "O4'" single 1.426 0.020
P2T "C3'" "C4'" single 1.524 0.020
P2T "H4'" "C4'" single 1.099 0.020
P2T "O4'" "C1'" single 1.426 0.020
P2T N1 "C1'" single 1.465 0.020
P2T "C1'" "C2'" single 1.524 0.020
P2T "H1'" "C1'" single 1.099 0.020
P2T N1 C6 single 1.337 0.020
P2T C2 N1 single 1.410 0.020
P2T C6 C5 double 1.390 0.020
P2T H6 C6 single 1.083 0.020
P2T O2 C2 double 1.250 0.020
P2T N3 C2 single 1.337 0.020
P2T C4 N3 single 1.337 0.020
P2T HN3 N3 single 1.040 0.020
P2T O4 C4 double 1.250 0.020
P2T C5 C4 single 1.487 0.020
P2T C5M C5 single 1.506 0.020
P2T H71 C5M single 1.059 0.020
P2T H72 C5M single 1.059 0.020
P2T H73 C5M single 1.059 0.020
P2T "O2'" "C2'" single 1.426 0.020
P2T "C2'" "C3'" single 1.524 0.020
P2T "H2'" "C2'" single 1.099 0.020
P2T "CB'" "O2'" single 1.426 0.020
P2T "CC'" "CB'" single 1.524 0.020
P2T "HB'1" "CB'" single 1.092 0.020
P2T "HB'2" "CB'" single 1.092 0.020
P2T "CD'" "CC'" single 1.513 0.020
P2T "HC'1" "CC'" single 1.092 0.020
P2T "HC'2" "CC'" single 1.092 0.020
P2T "HD'1" "CD'" single 1.059 0.020
P2T "HD'2" "CD'" single 1.059 0.020
P2T "HD'3" "CD'" single 1.059 0.020
P2T "O3'" "C3'" single 1.432 0.020
P2T "H3'" "C3'" single 1.099 0.020
P2T "HO3'" "O3'" single 0.967 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
P2T OP3 P OP1 119.900 3.000
P2T OP3 P OP2 119.900 3.000
P2T OP3 P "O5'" 108.200 3.000
P2T OP1 P OP2 119.900 3.000
P2T OP1 P "O5'" 108.200 3.000
P2T OP2 P "O5'" 108.200 3.000
P2T P "O5'" "C5'" 120.500 3.000
P2T "O5'" "C5'" "H5'" 109.470 3.000
P2T "O5'" "C5'" "H5''" 109.470 3.000
P2T "O5'" "C5'" "C4'" 109.470 3.000
P2T "H5'" "C5'" "H5''" 107.900 3.000
P2T "H5'" "C5'" "C4'" 109.470 3.000
P2T "H5''" "C5'" "C4'" 109.470 3.000
P2T "C5'" "C4'" "H4'" 108.340 3.000
P2T "C5'" "C4'" "C3'" 111.000 3.000
P2T "C5'" "C4'" "O4'" 109.470 3.000
P2T "H4'" "C4'" "C3'" 108.340 3.000
P2T "H4'" "C4'" "O4'" 109.470 3.000
P2T "C3'" "C4'" "O4'" 109.470 3.000
P2T "C4'" "C3'" "H3'" 108.340 3.000
P2T "C4'" "C3'" "C2'" 111.000 3.000
P2T "C4'" "C3'" "O3'" 109.470 3.000
P2T "H3'" "C3'" "C2'" 108.340 3.000
P2T "H3'" "C3'" "O3'" 109.470 3.000
P2T "C2'" "C3'" "O3'" 109.470 3.000
P2T "C3'" "C2'" "H2'" 108.340 3.000
P2T "C3'" "C2'" "O2'" 109.470 3.000
P2T "C3'" "C2'" "C1'" 111.000 3.000
P2T "H2'" "C2'" "O2'" 109.470 3.000
P2T "H2'" "C2'" "C1'" 108.340 3.000
P2T "O2'" "C2'" "C1'" 109.470 3.000
P2T "C2'" "O2'" "CB'" 111.800 3.000
P2T "O2'" "CB'" "HB'1" 109.470 3.000
P2T "O2'" "CB'" "HB'2" 109.470 3.000
P2T "O2'" "CB'" "CC'" 109.470 3.000
P2T "HB'1" "CB'" "HB'2" 107.900 3.000
P2T "HB'1" "CB'" "CC'" 109.470 3.000
P2T "HB'2" "CB'" "CC'" 109.470 3.000
P2T "CB'" "CC'" "HC'1" 109.470 3.000
P2T "CB'" "CC'" "HC'2" 109.470 3.000
P2T "CB'" "CC'" "CD'" 111.000 3.000
P2T "HC'1" "CC'" "HC'2" 107.900 3.000
P2T "HC'1" "CC'" "CD'" 109.470 3.000
P2T "HC'2" "CC'" "CD'" 109.470 3.000
P2T "CC'" "CD'" "HD'3" 109.470 3.000
P2T "CC'" "CD'" "HD'2" 109.470 3.000
P2T "CC'" "CD'" "HD'1" 109.470 3.000
P2T "HD'3" "CD'" "HD'2" 109.470 3.000
P2T "HD'3" "CD'" "HD'1" 109.470 3.000
P2T "HD'2" "CD'" "HD'1" 109.470 3.000
P2T "C2'" "C1'" "H1'" 108.340 3.000
P2T "C2'" "C1'" "O4'" 109.470 3.000
P2T "C2'" "C1'" N1 109.470 3.000
P2T "H1'" "C1'" "O4'" 109.470 3.000
P2T "H1'" "C1'" N1 109.470 3.000
P2T "O4'" "C1'" N1 109.470 3.000
P2T "C1'" "O4'" "C4'" 111.800 3.000
P2T "C1'" N1 C2 120.000 3.000
P2T "C1'" N1 C6 120.000 3.000
P2T C2 N1 C6 120.000 3.000
P2T N1 C2 O2 120.000 3.000
P2T N1 C2 N3 120.000 3.000
P2T O2 C2 N3 120.000 3.000
P2T C2 N3 HN3 120.000 3.000
P2T C2 N3 C4 120.000 3.000
P2T HN3 N3 C4 120.000 3.000
P2T N3 C4 C5 120.000 3.000
P2T N3 C4 O4 120.000 3.000
P2T C5 C4 O4 120.000 3.000
P2T C4 C5 C5M 120.000 3.000
P2T C4 C5 C6 120.000 3.000
P2T C5M C5 C6 120.000 3.000
P2T C5 C5M H73 109.470 3.000
P2T C5 C5M H72 109.470 3.000
P2T C5 C5M H71 109.470 3.000
P2T H73 C5M H72 109.470 3.000
P2T H73 C5M H71 109.470 3.000
P2T H72 C5M H71 109.470 3.000
P2T C5 C6 H6 120.000 3.000
P2T C5 C6 N1 120.000 3.000
P2T H6 C6 N1 120.000 3.000
P2T "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
P2T var_1 OP3 P "O5'" "C5'" -54.172 20.000 1
P2T var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
P2T var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
P2T var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
P2T var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
P2T var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
P2T var_7 "C3'" "C2'" "O2'" "CB'" -59.966 20.000 1
P2T var_8 "C2'" "O2'" "CB'" "CC'" -179.187 20.000 1
P2T var_9 "O2'" "CB'" "CC'" "CD'" -179.417 20.000 3
P2T var_10 "CB'" "CC'" "CD'" "HD'1" 60.234 20.000 3
P2T var_11 "C3'" "C2'" "C1'" N1 150.000 20.000 3
P2T var_12 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
P2T var_13 "C2'" "C1'" N1 C2 94.305 20.000 1
P2T CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
P2T CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
P2T CONST_3 N1 C2 N3 C4 0.000 0.000 0
P2T CONST_4 C2 N3 C4 O4 180.000 0.000 0
P2T CONST_5 N3 C4 C5 C6 0.000 0.000 0
P2T var_14 C4 C5 C5M H71 -115.793 20.000 1
P2T CONST_6 C4 C5 C6 N1 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
P2T chir_01 "C4'" "C5'" "O4'" "C3'" negativ
P2T chir_02 "C1'" "O4'" N1 "C2'" negativ
P2T chir_03 "C2'" "C1'" "O2'" "C3'" positiv
P2T chir_04 "C3'" "C4'" "C2'" "O3'" 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
P2T plan-1 N1 0.020
P2T plan-1 "C1'" 0.020
P2T plan-1 C6 0.020
P2T plan-1 C2 0.020
P2T plan-1 N3 0.020
P2T plan-1 C4 0.020
P2T plan-1 C5 0.020
P2T plan-1 H6 0.020
P2T plan-1 O2 0.020
P2T plan-1 HN3 0.020
P2T plan-1 O4 0.020
P2T plan-1 C5M 0.020
# ------------------------------------------------------
|
