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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
PST PST 'THYMIDINE-5'-THIOPHOSPHATE ' non-polymer 36 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PST
#
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
PST O4 O O 0.000 0.000 0.000 0.000
PST C4 C CR6 0.000 -1.179 -0.223 0.209
PST N3 N NR16 0.000 -2.112 0.694 -0.117
PST HN3 H H 0.000 -1.824 1.596 -0.549
PST C2 C CR6 0.000 -3.415 0.447 0.115
PST O2 O O 0.000 -4.246 1.286 -0.179
PST C5 C CR6 0.000 -1.582 -1.449 0.789
PST C5M C CH3 0.000 -0.559 -2.492 1.159
PST H73 H H 0.000 -0.610 -2.683 2.199
PST H72 H H 0.000 -0.758 -3.385 0.626
PST H71 H H 0.000 0.408 -2.140 0.911
PST C6 C CR16 0.000 -2.896 -1.669 1.011
PST H6 H H 0.000 -3.224 -2.600 1.458
PST N1 N NR6 0.000 -3.811 -0.711 0.669
PST "C1'" C CH1 0.000 -5.236 -0.951 0.910
PST "H1'" H H 0.000 -5.378 -1.947 1.353
PST "O4'" O O2 0.000 -5.963 -0.859 -0.326
PST "C2'" C CH2 0.000 -5.796 0.128 1.857
PST "H2'" H H 0.000 -5.045 0.878 2.112
PST "H2''" H H 0.000 -6.204 -0.303 2.773
PST "C3'" C CH1 0.000 -6.934 0.791 1.044
PST "H3'" H H 0.000 -6.584 1.713 0.560
PST "O3'" O OH1 0.000 -8.069 1.051 1.873
PST HO3 H H 0.000 -7.818 1.663 2.579
PST "C4'" C CH1 0.000 -7.257 -0.298 -0.010
PST "H4'" H H 0.000 -7.917 -1.066 0.418
PST "C5'" C CH2 0.000 -7.895 0.327 -1.252
PST "H5'" H H 0.000 -7.204 1.051 -1.690
PST "H5''" H H 0.000 -8.820 0.833 -0.970
PST "O5'" O O2 0.000 -8.182 -0.696 -2.207
PST P P P 0.000 -8.847 0.029 -3.481
PST SP S S1 0.000 -7.649 1.270 -4.184
PST OP2 O OH1 0.000 -10.195 0.780 -3.027
PST HOP2 H H 0.000 -10.922 0.275 -2.640
PST OP1 O OH1 0.000 -9.198 -1.072 -4.602
PST HOP1 H H 0.000 -9.605 -0.800 -5.436
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
PST O4 n/a C4 START
PST C4 O4 C5 .
PST N3 C4 C2 .
PST HN3 N3 . .
PST C2 N3 O2 .
PST O2 C2 . .
PST C5 C4 C6 .
PST C5M C5 H71 .
PST H73 C5M . .
PST H72 C5M . .
PST H71 C5M . .
PST C6 C5 N1 .
PST H6 C6 . .
PST N1 C6 "C1'" .
PST "C1'" N1 "C2'" .
PST "H1'" "C1'" . .
PST "O4'" "C1'" . .
PST "C2'" "C1'" "C3'" .
PST "H2'" "C2'" . .
PST "H2''" "C2'" . .
PST "C3'" "C2'" "C4'" .
PST "H3'" "C3'" . .
PST "O3'" "C3'" HO3 .
PST HO3 "O3'" . .
PST "C4'" "C3'" "C5'" .
PST "H4'" "C4'" . .
PST "C5'" "C4'" "O5'" .
PST "H5'" "C5'" . .
PST "H5''" "C5'" . .
PST "O5'" "C5'" P .
PST P "O5'" OP1 .
PST SP P . .
PST OP2 P HOP2 .
PST HOP2 OP2 . .
PST OP1 P HOP1 .
PST HOP1 OP1 . END
PST "C4'" "O4'" . ADD
PST 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
PST OP1 P single 1.610 0.020
PST OP2 P single 1.610 0.020
PST SP P double 1.950 0.020
PST P "O5'" single 1.610 0.020
PST HOP1 OP1 single 0.967 0.020
PST HOP2 OP2 single 0.967 0.020
PST "O5'" "C5'" single 1.426 0.020
PST "C5'" "C4'" single 1.524 0.020
PST "H5'" "C5'" single 1.092 0.020
PST "H5''" "C5'" single 1.092 0.020
PST "C4'" "O4'" single 1.426 0.020
PST "C4'" "C3'" single 1.524 0.020
PST "H4'" "C4'" single 1.099 0.020
PST "O4'" "C1'" single 1.426 0.020
PST "O3'" "C3'" single 1.432 0.020
PST "C3'" "C2'" single 1.524 0.020
PST "H3'" "C3'" single 1.099 0.020
PST HO3 "O3'" single 0.967 0.020
PST "C2'" "C1'" single 1.524 0.020
PST "H2'" "C2'" single 1.092 0.020
PST "H2''" "C2'" single 1.092 0.020
PST "C1'" N1 single 1.465 0.020
PST "H1'" "C1'" single 1.099 0.020
PST N1 C2 single 1.410 0.020
PST N1 C6 single 1.337 0.020
PST O2 C2 double 1.250 0.020
PST C2 N3 single 1.337 0.020
PST N3 C4 single 1.337 0.020
PST HN3 N3 single 1.040 0.020
PST C4 O4 double 1.250 0.020
PST C5 C4 single 1.487 0.020
PST C5M C5 single 1.506 0.020
PST C6 C5 double 1.390 0.020
PST H71 C5M single 1.059 0.020
PST H72 C5M single 1.059 0.020
PST H73 C5M single 1.059 0.020
PST H6 C6 single 1.083 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
PST O4 C4 N3 120.000 3.000
PST O4 C4 C5 120.000 3.000
PST N3 C4 C5 120.000 3.000
PST C4 N3 HN3 120.000 3.000
PST C4 N3 C2 120.000 3.000
PST HN3 N3 C2 120.000 3.000
PST N3 C2 O2 120.000 3.000
PST N3 C2 N1 120.000 3.000
PST O2 C2 N1 120.000 3.000
PST C4 C5 C5M 120.000 3.000
PST C4 C5 C6 120.000 3.000
PST C5M C5 C6 120.000 3.000
PST C5 C5M H73 109.470 3.000
PST C5 C5M H72 109.470 3.000
PST C5 C5M H71 109.470 3.000
PST H73 C5M H72 109.470 3.000
PST H73 C5M H71 109.470 3.000
PST H72 C5M H71 109.470 3.000
PST C5 C6 H6 120.000 3.000
PST C5 C6 N1 120.000 3.000
PST H6 C6 N1 120.000 3.000
PST C6 N1 "C1'" 120.000 3.000
PST C6 N1 C2 120.000 3.000
PST "C1'" N1 C2 120.000 3.000
PST N1 "C1'" "H1'" 109.470 3.000
PST N1 "C1'" "O4'" 109.470 3.000
PST N1 "C1'" "C2'" 109.470 3.000
PST "H1'" "C1'" "O4'" 109.470 3.000
PST "H1'" "C1'" "C2'" 108.340 3.000
PST "O4'" "C1'" "C2'" 109.470 3.000
PST "C1'" "O4'" "C4'" 111.800 3.000
PST "C1'" "C2'" "H2'" 109.470 3.000
PST "C1'" "C2'" "H2''" 109.470 3.000
PST "C1'" "C2'" "C3'" 111.000 3.000
PST "H2'" "C2'" "H2''" 107.900 3.000
PST "H2'" "C2'" "C3'" 109.470 3.000
PST "H2''" "C2'" "C3'" 109.470 3.000
PST "C2'" "C3'" "H3'" 108.340 3.000
PST "C2'" "C3'" "O3'" 109.470 3.000
PST "C2'" "C3'" "C4'" 111.000 3.000
PST "H3'" "C3'" "O3'" 109.470 3.000
PST "H3'" "C3'" "C4'" 108.340 3.000
PST "O3'" "C3'" "C4'" 109.470 3.000
PST "C3'" "O3'" HO3 109.470 3.000
PST "C3'" "C4'" "H4'" 108.340 3.000
PST "C3'" "C4'" "C5'" 111.000 3.000
PST "C3'" "C4'" "O4'" 109.470 3.000
PST "H4'" "C4'" "C5'" 108.340 3.000
PST "H4'" "C4'" "O4'" 109.470 3.000
PST "C5'" "C4'" "O4'" 109.470 3.000
PST "C4'" "C5'" "H5'" 109.470 3.000
PST "C4'" "C5'" "H5''" 109.470 3.000
PST "C4'" "C5'" "O5'" 109.470 3.000
PST "H5'" "C5'" "H5''" 107.900 3.000
PST "H5'" "C5'" "O5'" 109.470 3.000
PST "H5''" "C5'" "O5'" 109.470 3.000
PST "C5'" "O5'" P 120.500 3.000
PST "O5'" P SP 109.500 3.000
PST "O5'" P OP2 109.500 3.000
PST "O5'" P OP1 109.500 3.000
PST SP P OP2 109.500 3.000
PST SP P OP1 109.500 3.000
PST OP2 P OP1 109.500 3.000
PST P OP2 HOP2 120.000 3.000
PST P OP1 HOP1 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
PST CONST_1 O4 C4 N3 C2 180.000 0.000 0
PST CONST_2 C4 N3 C2 O2 180.000 0.000 0
PST CONST_3 O4 C4 C5 C6 180.000 0.000 0
PST var_1 C4 C5 C5M H71 -0.252 20.000 1
PST CONST_4 C4 C5 C6 N1 0.000 0.000 0
PST CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
PST CONST_6 C6 N1 C2 N3 0.000 0.000 0
PST var_2 C6 N1 "C1'" "C2'" 120.241 20.000 1
PST var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
PST var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
PST var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
PST var_6 "C2'" "C3'" "O3'" HO3 61.429 20.000 1
PST var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
PST var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
PST var_9 "C3'" "C4'" "C5'" "O5'" -179.981 20.000 3
PST var_10 "C4'" "C5'" "O5'" P -179.981 20.000 1
PST var_11 "C5'" "O5'" P OP1 179.991 20.000 1
PST var_12 "O5'" P OP2 HOP2 -59.958 20.000 1
PST var_13 "O5'" P OP1 HOP1 179.984 20.000 1
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
PST chir_01 "C4'" "C5'" "O4'" "C3'" negativ
PST chir_02 "C3'" "C4'" "O3'" "C2'" negativ
PST chir_03 "C1'" "O4'" "C2'" N1 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
PST plan-1 N1 0.020
PST plan-1 "C1'" 0.020
PST plan-1 C2 0.020
PST plan-1 C6 0.020
PST plan-1 N3 0.020
PST plan-1 C4 0.020
PST plan-1 C5 0.020
PST plan-1 O2 0.020
PST plan-1 HN3 0.020
PST plan-1 O4 0.020
PST plan-1 C5M 0.020
PST plan-1 H6 0.020
# ------------------------------------------------------
|
