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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
PDX PDX '2,3-DI-O-SULFO-ALPHA-D-GLUCOPYRANOSE' non-polymer 32 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDX
#
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
PDX O2X O OS 0.000 0.000 0.000 0.000
PDX "S'" S ST 0.000 -1.195 -0.617 0.455
PDX O1X O OS 0.000 -1.343 -1.319 1.682
PDX O3X O OH1 0.000 -1.592 -1.603 -0.634
PDX "HO'" H H 0.000 -1.034 -2.359 -0.782
PDX O3 O O2 0.000 -2.247 0.482 0.480
PDX C3 C CH1 0.000 -3.447 -0.105 0.985
PDX H3 H H 0.000 -3.284 -1.176 1.173
PDX C2 C CH1 0.000 -4.577 0.072 -0.034
PDX H2 H H 0.000 -4.669 1.134 -0.300
PDX O2 O O2 0.000 -4.288 -0.690 -1.207
PDX S S ST 0.000 -4.684 0.168 -2.400
PDX O2S O OS 0.000 -5.910 0.790 -2.037
PDX O3S O OH1 0.000 -3.666 1.295 -2.508
PDX H3S H H 0.000 -3.769 1.929 -3.208
PDX O1S O OS 0.000 -4.483 -0.645 -3.547
PDX C4 C CH1 0.000 -3.852 0.590 2.290
PDX H4 H H 0.000 -3.913 1.674 2.125
PDX O4 O OH1 0.000 -2.882 0.313 3.301
PDX HB H H 0.000 -3.140 0.752 4.122
PDX C5 C CH1 0.000 -5.217 0.061 2.733
PDX H5 H H 0.000 -5.159 -1.027 2.873
PDX C6 C CH2 0.000 -5.616 0.722 4.054
PDX H6C1 H H 0.000 -5.671 1.804 3.916
PDX H6C2 H H 0.000 -4.867 0.491 4.815
PDX O6 O OH1 0.000 -6.889 0.228 4.471
PDX H6 H H 0.000 -7.139 0.646 5.305
PDX O5 O O2 0.000 -6.196 0.359 1.739
PDX C1 C CH1 0.000 -5.888 -0.416 0.584
PDX H1 H H 0.000 -6.698 -0.314 -0.151
PDX O1 O OH1 0.000 -5.754 -1.790 0.955
PDX HA H H 0.000 -6.583 -2.101 1.342
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
PDX O2X n/a "S'" START
PDX "S'" O2X O3 .
PDX O1X "S'" . .
PDX O3X "S'" "HO'" .
PDX "HO'" O3X . .
PDX O3 "S'" C3 .
PDX C3 O3 C4 .
PDX H3 C3 . .
PDX C2 C3 O2 .
PDX H2 C2 . .
PDX O2 C2 S .
PDX S O2 O1S .
PDX O2S S . .
PDX O3S S H3S .
PDX H3S O3S . .
PDX O1S S . .
PDX C4 C3 C5 .
PDX H4 C4 . .
PDX O4 C4 HB .
PDX HB O4 . .
PDX C5 C4 O5 .
PDX H5 C5 . .
PDX C6 C5 O6 .
PDX H6C1 C6 . .
PDX H6C2 C6 . .
PDX O6 C6 H6 .
PDX H6 O6 . .
PDX O5 C5 C1 .
PDX C1 O5 O1 .
PDX H1 C1 . .
PDX O1 C1 HA .
PDX HA O1 . END
PDX C1 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
PDX C1 C2 single 1.524 0.020
PDX O1 C1 single 1.432 0.020
PDX C1 O5 single 1.426 0.020
PDX H1 C1 single 1.099 0.020
PDX C2 C3 single 1.524 0.020
PDX O2 C2 single 1.426 0.020
PDX H2 C2 single 1.099 0.020
PDX C4 C3 single 1.524 0.020
PDX C3 O3 single 1.426 0.020
PDX H3 C3 single 1.099 0.020
PDX C5 C4 single 1.524 0.020
PDX O4 C4 single 1.432 0.020
PDX H4 C4 single 1.099 0.020
PDX C6 C5 single 1.524 0.020
PDX O5 C5 single 1.426 0.020
PDX H5 C5 single 1.099 0.020
PDX O6 C6 single 1.432 0.020
PDX H6C1 C6 single 1.092 0.020
PDX H6C2 C6 single 1.092 0.020
PDX HA O1 single 0.967 0.020
PDX S O2 single 1.535 0.020
PDX O3 "S'" single 1.535 0.020
PDX HB O4 single 0.967 0.020
PDX H6 O6 single 0.967 0.020
PDX O1S S double 1.436 0.020
PDX O2S S double 1.436 0.020
PDX O3S S single 1.635 0.020
PDX H3S O3S single 0.967 0.020
PDX O1X "S'" double 1.436 0.020
PDX "S'" O2X double 1.436 0.020
PDX O3X "S'" single 1.635 0.020
PDX "HO'" O3X 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
PDX O2X "S'" O1X 109.500 3.000
PDX O2X "S'" O3X 109.500 3.000
PDX O2X "S'" O3 109.500 3.000
PDX O1X "S'" O3X 109.500 3.000
PDX O1X "S'" O3 109.500 3.000
PDX O3X "S'" O3 109.500 3.000
PDX "S'" O3X "HO'" 120.000 3.000
PDX "S'" O3 C3 120.000 3.000
PDX O3 C3 H3 109.470 3.000
PDX O3 C3 C2 109.470 3.000
PDX O3 C3 C4 109.470 3.000
PDX H3 C3 C2 108.340 3.000
PDX H3 C3 C4 108.340 3.000
PDX C2 C3 C4 111.000 3.000
PDX C3 C2 H2 108.340 3.000
PDX C3 C2 O2 109.470 3.000
PDX C3 C2 C1 111.000 3.000
PDX H2 C2 O2 109.470 3.000
PDX H2 C2 C1 108.340 3.000
PDX O2 C2 C1 109.470 3.000
PDX C2 O2 S 120.000 3.000
PDX O2 S O3S 109.500 3.000
PDX O2 S O2S 109.500 3.000
PDX O2 S O1S 109.500 3.000
PDX O3S S O2S 109.500 3.000
PDX O3S S O1S 109.500 3.000
PDX O2S S O1S 109.500 3.000
PDX S O3S H3S 120.000 3.000
PDX C3 C4 H4 108.340 3.000
PDX C3 C4 O4 109.470 3.000
PDX C3 C4 C5 111.000 3.000
PDX H4 C4 O4 109.470 3.000
PDX H4 C4 C5 108.340 3.000
PDX O4 C4 C5 109.470 3.000
PDX C4 O4 HB 109.470 3.000
PDX C4 C5 H5 108.340 3.000
PDX C4 C5 C6 111.000 3.000
PDX C4 C5 O5 109.470 3.000
PDX H5 C5 C6 108.340 3.000
PDX H5 C5 O5 109.470 3.000
PDX C6 C5 O5 109.470 3.000
PDX C5 C6 H6C1 109.470 3.000
PDX C5 C6 H6C2 109.470 3.000
PDX C5 C6 O6 109.470 3.000
PDX H6C1 C6 H6C2 107.900 3.000
PDX H6C1 C6 O6 109.470 3.000
PDX H6C2 C6 O6 109.470 3.000
PDX C6 O6 H6 109.470 3.000
PDX C5 O5 C1 111.800 3.000
PDX O5 C1 H1 109.470 3.000
PDX O5 C1 O1 109.470 3.000
PDX O5 C1 C2 109.470 3.000
PDX H1 C1 O1 109.470 3.000
PDX H1 C1 C2 108.340 3.000
PDX O1 C1 C2 109.470 3.000
PDX C1 O1 HA 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
PDX var_1 O2X "S'" O3X "HO'" 67.350 20.000 1
PDX var_2 O2X "S'" O3 C3 -177.783 20.000 1
PDX var_3 "S'" O3 C3 C4 118.254 20.000 1
PDX var_4 O3 C3 C2 O2 60.000 20.000 3
PDX var_5 C3 C2 O2 S -139.104 20.000 1
PDX var_6 C2 O2 S O1S -175.745 20.000 1
PDX var_7 O2 S O3S H3S -179.938 20.000 1
PDX var_8 O3 C3 C4 C5 180.000 20.000 3
PDX var_9 C3 C4 O4 HB -179.982 20.000 1
PDX var_10 C3 C4 C5 O5 -60.000 20.000 3
PDX var_11 C4 C5 C6 O6 -179.900 20.000 3
PDX var_12 C5 C6 O6 H6 179.988 20.000 1
PDX var_13 C4 C5 O5 C1 60.000 20.000 1
PDX var_14 C5 O5 C1 O1 60.000 20.000 1
PDX var_15 O5 C1 C2 C3 60.000 20.000 3
PDX var_16 O5 C1 O1 HA 59.949 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
PDX chir_01 C1 C2 O1 O5 negativ
PDX chir_02 C2 C1 C3 O2 negativ
PDX chir_03 C3 C2 C4 O3 positiv
PDX chir_04 C4 C3 C5 O4 negativ
PDX chir_05 C5 C4 C6 O5 negativ
PDX chir_06 S O2 O1S O2S negativ
PDX chir_07 "S'" O3 O1X O2X positiv
# ------------------------------------------------------
|
