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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
PED PED 'PENTANE-3,4-DIOL-5-PHOSPHATE ' non-polymer 23 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PED
#
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
PED O3P O OP -0.666 0.000 0.000 0.000
PED P P P 0.000 -1.126 0.228 0.984
PED O1P O OP -0.666 -1.443 1.706 1.055
PED O2P O OP -0.666 -0.707 -0.265 2.352
PED "O5'" O O2 0.000 -2.433 -0.579 0.501
PED "C5'" C CH2 0.000 -2.847 0.008 -0.735
PED "H5'1" H H 0.000 -2.042 -0.082 -1.468
PED "H5'2" H H 0.000 -3.077 1.064 -0.577
PED "C4'" C CH1 0.000 -4.092 -0.716 -1.251
PED "H4'1" H H 0.000 -4.871 -0.703 -0.476
PED "O4'" O OH1 0.000 -3.759 -2.069 -1.569
PED "HO'4" H H 0.000 -3.073 -2.080 -2.250
PED "C3'" C CH1 0.000 -4.608 -0.011 -2.506
PED "H3'" H H 0.000 -3.829 -0.025 -3.281
PED "O3'" O OH1 0.000 -4.942 1.342 -2.190
PED H3T H H 0.000 -5.627 1.353 -1.508
PED "C2'" C CH2 0.000 -5.853 -0.735 -3.023
PED "H2'1" H H 0.000 -6.656 -0.646 -2.288
PED "H2'2" H H 0.000 -5.620 -1.790 -3.180
PED "C1'" C CH3 0.000 -6.297 -0.106 -4.345
PED "H1'3" H H 0.000 -5.518 -0.192 -5.060
PED "H1'2" H H 0.000 -7.160 -0.605 -4.706
PED "H1'1" H H 0.000 -6.522 0.919 -4.195
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
PED O3P n/a P START
PED P O3P "O5'" .
PED O1P P . .
PED O2P P . .
PED "O5'" P "C5'" .
PED "C5'" "O5'" "C4'" .
PED "H5'1" "C5'" . .
PED "H5'2" "C5'" . .
PED "C4'" "C5'" "C3'" .
PED "H4'1" "C4'" . .
PED "O4'" "C4'" "HO'4" .
PED "HO'4" "O4'" . .
PED "C3'" "C4'" "C2'" .
PED "H3'" "C3'" . .
PED "O3'" "C3'" H3T .
PED H3T "O3'" . .
PED "C2'" "C3'" "C1'" .
PED "H2'1" "C2'" . .
PED "H2'2" "C2'" . .
PED "C1'" "C2'" "H1'1" .
PED "H1'3" "C1'" . .
PED "H1'2" "C1'" . .
PED "H1'1" "C1'" . END
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
PED O1P P deloc 1.510 0.020
PED O2P P deloc 1.510 0.020
PED P O3P deloc 1.510 0.020
PED "O5'" P single 1.610 0.020
PED "C5'" "O5'" single 1.426 0.020
PED "C2'" "C3'" single 1.524 0.020
PED "C1'" "C2'" single 1.513 0.020
PED "H2'1" "C2'" single 1.092 0.020
PED "H2'2" "C2'" single 1.092 0.020
PED "C4'" "C5'" single 1.524 0.020
PED "H5'1" "C5'" single 1.092 0.020
PED "H5'2" "C5'" single 1.092 0.020
PED "O4'" "C4'" single 1.432 0.020
PED "C3'" "C4'" single 1.524 0.020
PED "H4'1" "C4'" single 1.099 0.020
PED "HO'4" "O4'" single 0.967 0.020
PED "O3'" "C3'" single 1.432 0.020
PED "H3'" "C3'" single 1.099 0.020
PED "H1'1" "C1'" single 1.059 0.020
PED "H1'2" "C1'" single 1.059 0.020
PED "H1'3" "C1'" single 1.059 0.020
PED H3T "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
PED O3P P O1P 119.900 3.000
PED O3P P O2P 119.900 3.000
PED O3P P "O5'" 108.200 3.000
PED O1P P O2P 119.900 3.000
PED O1P P "O5'" 108.200 3.000
PED O2P P "O5'" 108.200 3.000
PED P "O5'" "C5'" 120.500 3.000
PED "O5'" "C5'" "H5'1" 109.470 3.000
PED "O5'" "C5'" "H5'2" 109.470 3.000
PED "O5'" "C5'" "C4'" 109.470 3.000
PED "H5'1" "C5'" "H5'2" 107.900 3.000
PED "H5'1" "C5'" "C4'" 109.470 3.000
PED "H5'2" "C5'" "C4'" 109.470 3.000
PED "C5'" "C4'" "H4'1" 108.340 3.000
PED "C5'" "C4'" "O4'" 109.470 3.000
PED "C5'" "C4'" "C3'" 111.000 3.000
PED "H4'1" "C4'" "O4'" 109.470 3.000
PED "H4'1" "C4'" "C3'" 108.340 3.000
PED "O4'" "C4'" "C3'" 109.470 3.000
PED "C4'" "O4'" "HO'4" 109.470 3.000
PED "C4'" "C3'" "H3'" 108.340 3.000
PED "C4'" "C3'" "O3'" 109.470 3.000
PED "C4'" "C3'" "C2'" 111.000 3.000
PED "H3'" "C3'" "O3'" 109.470 3.000
PED "H3'" "C3'" "C2'" 108.340 3.000
PED "O3'" "C3'" "C2'" 109.470 3.000
PED "C3'" "O3'" H3T 109.470 3.000
PED "C3'" "C2'" "H2'1" 109.470 3.000
PED "C3'" "C2'" "H2'2" 109.470 3.000
PED "C3'" "C2'" "C1'" 111.000 3.000
PED "H2'1" "C2'" "H2'2" 107.900 3.000
PED "H2'1" "C2'" "C1'" 109.470 3.000
PED "H2'2" "C2'" "C1'" 109.470 3.000
PED "C2'" "C1'" "H1'3" 109.470 3.000
PED "C2'" "C1'" "H1'2" 109.470 3.000
PED "C2'" "C1'" "H1'1" 109.470 3.000
PED "H1'3" "C1'" "H1'2" 109.470 3.000
PED "H1'3" "C1'" "H1'1" 109.470 3.000
PED "H1'2" "C1'" "H1'1" 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
PED var_1 O3P P "O5'" "C5'" -64.977 20.000 1
PED var_2 P "O5'" "C5'" "C4'" -179.966 20.000 1
PED var_3 "O5'" "C5'" "C4'" "C3'" 174.989 20.000 3
PED var_4 "C5'" "C4'" "O4'" "HO'4" -59.944 20.000 1
PED var_5 "C5'" "C4'" "C3'" "C2'" 179.969 20.000 3
PED var_6 "C4'" "C3'" "O3'" H3T -59.950 20.000 1
PED var_7 "C4'" "C3'" "C2'" "C1'" -175.046 20.000 3
PED var_8 "C3'" "C2'" "C1'" "H1'1" -59.960 20.000 3
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
PED chir_01 "C4'" "C5'" "O4'" "C3'" positiv
PED chir_02 "C3'" "C2'" "C4'" "O3'" positiv
# ------------------------------------------------------
|
