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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
PPS PPS '. ' non-polymer 43 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PPS
#
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
PPS O3P O OP -0.666 0.000 0.000 0.000
PPS P1 P P 0.000 0.608 0.315 -1.349
PPS O1P O OP -0.666 2.065 0.721 -1.324
PPS O2P O OP -0.666 0.581 -0.825 -2.344
PPS "O3'" O O2 0.000 -0.110 1.509 -2.164
PPS "C3'" C CH1 0.000 -1.474 1.361 -2.498
PPS "H3'" H H 0.000 -1.597 0.500 -3.170
PPS "C4'" C CH1 0.000 -2.041 2.606 -3.158
PPS "H4'" H H 0.000 -1.663 3.498 -2.639
PPS "C5'" C CH2 0.000 -1.715 2.709 -4.636
PPS "H5'1" H H 0.000 -2.121 1.844 -5.166
PPS "H5'2" H H 0.000 -0.633 2.744 -4.776
PPS "O5'" O O2 0.000 -2.298 3.895 -5.149
PPS P2 P P 0.000 -2.097 4.241 -6.716
PPS O4P O OP -0.500 -0.699 4.407 -7.182
PPS O5P O OP -0.500 -2.843 3.165 -7.413
PPS O6P O O2 0.000 -3.067 5.525 -6.897
PPS S2 S ST 0.000 -2.575 6.867 -6.105
PPS OS2 O OS 0.000 -1.265 7.248 -6.596
PPS OS3 O OS 0.000 -2.804 6.671 -4.686
PPS OS1 O OH1 0.000 -3.637 7.992 -6.620
PPS HO1 H H 0.000 -4.583 7.793 -6.632
PPS "C2'" C CH1 0.000 -2.378 1.197 -1.291
PPS "H2'" H H 0.000 -2.454 0.141 -0.995
PPS "O2'" O OH1 0.000 -1.937 2.005 -0.201
PPS "HO2'" H H 0.000 -1.720 1.438 0.551
PPS "C1'" C CH1 0.000 -3.721 1.723 -1.798
PPS "H1'" H H 0.000 -4.158 2.372 -1.026
PPS "O4'" O O2 0.000 -3.463 2.515 -2.977
PPS N9 N NR5 0.000 -4.683 0.667 -2.121
PPS C8 C CR15 0.000 -4.786 0.007 -3.318
PPS H8 H H 0.000 -4.151 0.204 -4.173
PPS N7 N NRD5 0.000 -5.747 -0.892 -3.310
PPS C5 C CR56 0.000 -6.290 -0.813 -2.052
PPS C4 C CR56 0.000 -5.643 0.150 -1.297
PPS C6 C CR6 0.000 -7.330 -1.502 -1.435
PPS N6 N NH2 0.000 -8.043 -2.497 -2.127
PPS HN62 H H 0.000 -8.784 -3.025 -1.668
PPS HN61 H H 0.000 -7.833 -2.710 -3.101
PPS N1 N NRD6 0.000 -7.650 -1.202 -0.153
PPS C2 C CR16 0.000 -6.928 -0.234 0.461
PPS H2 H H 0.000 -7.209 -0.019 1.484
PPS N3 N NRD6 0.000 -5.905 0.499 -0.028
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
PPS O3P n/a P1 START
PPS P1 O3P "O3'" .
PPS O1P P1 . .
PPS O2P P1 . .
PPS "O3'" P1 "C3'" .
PPS "C3'" "O3'" "C2'" .
PPS "H3'" "C3'" . .
PPS "C4'" "C3'" "C5'" .
PPS "H4'" "C4'" . .
PPS "C5'" "C4'" "O5'" .
PPS "H5'1" "C5'" . .
PPS "H5'2" "C5'" . .
PPS "O5'" "C5'" P2 .
PPS P2 "O5'" O6P .
PPS O4P P2 . .
PPS O5P P2 . .
PPS O6P P2 S2 .
PPS S2 O6P OS1 .
PPS OS2 S2 . .
PPS OS3 S2 . .
PPS OS1 S2 HO1 .
PPS HO1 OS1 . .
PPS "C2'" "C3'" "C1'" .
PPS "H2'" "C2'" . .
PPS "O2'" "C2'" "HO2'" .
PPS "HO2'" "O2'" . .
PPS "C1'" "C2'" N9 .
PPS "H1'" "C1'" . .
PPS "O4'" "C1'" . .
PPS N9 "C1'" C8 .
PPS C8 N9 N7 .
PPS H8 C8 . .
PPS N7 C8 C5 .
PPS C5 N7 C6 .
PPS C4 C5 . .
PPS C6 C5 N1 .
PPS N6 C6 HN61 .
PPS HN62 N6 . .
PPS HN61 N6 . .
PPS N1 C6 C2 .
PPS C2 N1 N3 .
PPS H2 C2 . .
PPS N3 C2 . END
PPS "C4'" "O4'" . ADD
PPS N9 C4 . ADD
PPS C4 N3 . 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
PPS OS1 S2 single 1.635 0.020
PPS OS2 S2 double 1.436 0.020
PPS OS3 S2 double 1.436 0.020
PPS S2 O6P single 1.535 0.020
PPS HO1 OS1 single 0.967 0.020
PPS O6P P2 single 1.610 0.020
PPS O4P P2 deloc 1.510 0.020
PPS O5P P2 deloc 1.510 0.020
PPS P2 "O5'" single 1.610 0.020
PPS "O5'" "C5'" single 1.426 0.020
PPS "C5'" "C4'" single 1.524 0.020
PPS "H5'1" "C5'" single 1.092 0.020
PPS "H5'2" "C5'" single 1.092 0.020
PPS "C4'" "O4'" single 1.426 0.020
PPS "C4'" "C3'" single 1.524 0.020
PPS "H4'" "C4'" single 1.099 0.020
PPS "O4'" "C1'" single 1.426 0.020
PPS N9 "C1'" single 1.485 0.020
PPS "C1'" "C2'" single 1.524 0.020
PPS "H1'" "C1'" single 1.099 0.020
PPS N9 C4 single 1.337 0.020
PPS C8 N9 single 1.337 0.020
PPS C4 N3 single 1.355 0.020
PPS C4 C5 double 1.490 0.020
PPS N3 C2 double 1.337 0.020
PPS C2 N1 single 1.337 0.020
PPS H2 C2 single 1.083 0.020
PPS N1 C6 double 1.350 0.020
PPS N6 C6 single 1.355 0.020
PPS C6 C5 single 1.490 0.020
PPS HN61 N6 single 1.010 0.020
PPS HN62 N6 single 1.010 0.020
PPS C5 N7 single 1.350 0.020
PPS N7 C8 double 1.350 0.020
PPS H8 C8 single 1.083 0.020
PPS "O2'" "C2'" single 1.432 0.020
PPS "C2'" "C3'" single 1.524 0.020
PPS "H2'" "C2'" single 1.099 0.020
PPS "HO2'" "O2'" single 0.967 0.020
PPS "C3'" "O3'" single 1.426 0.020
PPS "H3'" "C3'" single 1.099 0.020
PPS "O3'" P1 single 1.610 0.020
PPS O1P P1 deloc 1.510 0.020
PPS O2P P1 deloc 1.510 0.020
PPS P1 O3P 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
PPS O3P P1 O1P 119.900 3.000
PPS O3P P1 O2P 119.900 3.000
PPS O3P P1 "O3'" 108.200 3.000
PPS O1P P1 O2P 119.900 3.000
PPS O1P P1 "O3'" 108.200 3.000
PPS O2P P1 "O3'" 108.200 3.000
PPS P1 "O3'" "C3'" 120.500 3.000
PPS "O3'" "C3'" "H3'" 109.470 3.000
PPS "O3'" "C3'" "C4'" 109.470 3.000
PPS "O3'" "C3'" "C2'" 109.470 3.000
PPS "H3'" "C3'" "C4'" 108.340 3.000
PPS "H3'" "C3'" "C2'" 108.340 3.000
PPS "C4'" "C3'" "C2'" 111.000 3.000
PPS "C3'" "C4'" "H4'" 108.340 3.000
PPS "C3'" "C4'" "C5'" 111.000 3.000
PPS "C3'" "C4'" "O4'" 109.470 3.000
PPS "H4'" "C4'" "C5'" 108.340 3.000
PPS "H4'" "C4'" "O4'" 109.470 3.000
PPS "C5'" "C4'" "O4'" 109.470 3.000
PPS "C4'" "C5'" "H5'1" 109.470 3.000
PPS "C4'" "C5'" "H5'2" 109.470 3.000
PPS "C4'" "C5'" "O5'" 109.470 3.000
PPS "H5'1" "C5'" "H5'2" 107.900 3.000
PPS "H5'1" "C5'" "O5'" 109.470 3.000
PPS "H5'2" "C5'" "O5'" 109.470 3.000
PPS "C5'" "O5'" P2 120.500 3.000
PPS "O5'" P2 O4P 108.200 3.000
PPS "O5'" P2 O5P 108.200 3.000
PPS "O5'" P2 O6P 102.600 3.000
PPS O4P P2 O5P 119.900 3.000
PPS O4P P2 O6P 108.200 3.000
PPS O5P P2 O6P 108.200 3.000
PPS P2 O6P S2 120.000 3.000
PPS O6P S2 OS2 109.500 3.000
PPS O6P S2 OS3 109.500 3.000
PPS O6P S2 OS1 109.500 3.000
PPS OS2 S2 OS3 109.500 3.000
PPS OS2 S2 OS1 109.500 3.000
PPS OS3 S2 OS1 109.500 3.000
PPS S2 OS1 HO1 120.000 3.000
PPS "C3'" "C2'" "H2'" 108.340 3.000
PPS "C3'" "C2'" "O2'" 109.470 3.000
PPS "C3'" "C2'" "C1'" 111.000 3.000
PPS "H2'" "C2'" "O2'" 109.470 3.000
PPS "H2'" "C2'" "C1'" 108.340 3.000
PPS "O2'" "C2'" "C1'" 109.470 3.000
PPS "C2'" "O2'" "HO2'" 109.470 3.000
PPS "C2'" "C1'" "H1'" 108.340 3.000
PPS "C2'" "C1'" "O4'" 109.470 3.000
PPS "C2'" "C1'" N9 109.470 3.000
PPS "H1'" "C1'" "O4'" 109.470 3.000
PPS "H1'" "C1'" N9 109.470 3.000
PPS "O4'" "C1'" N9 109.470 3.000
PPS "C1'" "O4'" "C4'" 111.800 3.000
PPS "C1'" N9 C8 126.000 3.000
PPS "C1'" N9 C4 126.000 3.000
PPS C8 N9 C4 108.000 3.000
PPS N9 C8 H8 126.000 3.000
PPS N9 C8 N7 108.000 3.000
PPS H8 C8 N7 126.000 3.000
PPS C8 N7 C5 108.000 3.000
PPS N7 C5 C4 108.000 3.000
PPS N7 C5 C6 132.000 3.000
PPS C4 C5 C6 120.000 3.000
PPS C5 C4 N9 108.000 3.000
PPS C5 C4 N3 120.000 3.000
PPS N9 C4 N3 132.000 3.000
PPS C5 C6 N6 120.000 3.000
PPS C5 C6 N1 120.000 3.000
PPS N6 C6 N1 120.000 3.000
PPS C6 N6 HN62 120.000 3.000
PPS C6 N6 HN61 120.000 3.000
PPS HN62 N6 HN61 120.000 3.000
PPS C6 N1 C2 120.000 3.000
PPS N1 C2 H2 120.000 3.000
PPS N1 C2 N3 120.000 3.000
PPS H2 C2 N3 120.000 3.000
PPS C2 N3 C4 120.000 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
PPS var_1 O3P P1 "O3'" "C3'" -59.982 20.000 1
PPS var_2 P1 "O3'" "C3'" "C2'" 59.996 20.000 1
PPS var_3 "O3'" "C3'" "C4'" "C5'" 90.000 20.000 3
PPS var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
PPS var_5 "C3'" "C4'" "C5'" "O5'" 179.549 20.000 3
PPS var_6 "C4'" "C5'" "O5'" P2 -179.976 20.000 1
PPS var_7 "C5'" "O5'" P2 O6P 172.701 20.000 1
PPS var_8 "O5'" P2 O6P S2 67.449 20.000 1
PPS var_9 P2 O6P S2 OS1 173.653 20.000 1
PPS var_10 O6P S2 OS1 HO1 46.855 20.000 1
PPS var_11 "O3'" "C3'" "C2'" "C1'" 150.000 20.000 3
PPS var_12 "C3'" "C2'" "O2'" "HO2'" -119.150 20.000 1
PPS var_13 "C3'" "C2'" "C1'" N9 90.000 20.000 3
PPS var_14 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
PPS var_15 "C2'" "C1'" N9 C8 -86.378 20.000 1
PPS CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
PPS CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
PPS CONST_3 N9 C8 N7 C5 0.000 0.000 0
PPS CONST_4 C8 N7 C5 C6 180.000 0.000 0
PPS CONST_5 N7 C5 C4 N9 0.000 0.000 0
PPS CONST_6 C5 C4 N3 C2 0.000 0.000 0
PPS CONST_7 N7 C5 C6 N1 180.000 0.000 0
PPS CONST_8 C5 C6 N6 HN61 -2.052 0.000 0
PPS CONST_9 C5 C6 N1 C2 0.000 0.000 0
PPS CONST_10 C6 N1 C2 N3 0.000 0.000 0
PPS CONST_11 N1 C2 N3 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
PPS chir_01 S2 OS1 OS2 OS3 negativ
PPS chir_02 "C4'" "C5'" "O4'" "C3'" negativ
PPS chir_03 "C1'" "O4'" N9 "C2'" negativ
PPS chir_04 "C2'" "C1'" "O2'" "C3'" positiv
PPS chir_05 "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
PPS plan-1 N9 0.020
PPS plan-1 "C1'" 0.020
PPS plan-1 C4 0.020
PPS plan-1 C8 0.020
PPS plan-1 N7 0.020
PPS plan-1 N3 0.020
PPS plan-1 C5 0.020
PPS plan-1 C2 0.020
PPS plan-1 N1 0.020
PPS plan-1 C6 0.020
PPS plan-1 H2 0.020
PPS plan-1 N6 0.020
PPS plan-1 H8 0.020
PPS plan-1 HN62 0.020
PPS plan-1 HN61 0.020
PPS plan-2 N6 0.020
PPS plan-2 C6 0.020
PPS plan-2 HN61 0.020
PPS plan-2 HN62 0.020
# ------------------------------------------------------
|
