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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
PYP PYP '2'-DEOXYRIBOFURANOSYLPYRENE-5'-MONOP' non-polymer 45 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PYP
#
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
PYP O3P O OP -0.666 0.000 0.000 0.000
PYP P P P 0.000 -0.938 -0.359 -1.131
PYP O1P O OP -0.666 -0.310 -1.438 -1.986
PYP O2P O OP -0.666 -1.200 0.866 -1.979
PYP "O5'" O O2 0.000 -2.329 -0.898 -0.524
PYP "C5'" C CH2 0.000 -3.385 -1.416 -1.336
PYP "H5'1" H H 0.000 -3.022 -2.281 -1.896
PYP "H5'2" H H 0.000 -3.717 -0.645 -2.035
PYP "C4'" C CH1 0.000 -4.554 -1.836 -0.445
PYP "H4'" H H 0.000 -4.205 -2.541 0.323
PYP "C3'" C CH1 0.000 -5.654 -2.495 -1.301
PYP "H3'" H H 0.000 -5.380 -2.473 -2.365
PYP "O3'" O OH1 0.000 -5.886 -3.838 -0.871
PYP H3T H H 0.000 -6.578 -4.236 -1.416
PYP "C2'" C CH2 0.000 -6.907 -1.621 -1.046
PYP "H2'2" H H 0.000 -7.819 -2.208 -0.922
PYP "H2'1" H H 0.000 -7.064 -0.865 -1.818
PYP "C1'" C CH1 0.000 -6.552 -0.927 0.294
PYP "H1'" H H 0.000 -6.761 -1.594 1.142
PYP "O4'" O O2 0.000 -5.134 -0.679 0.180
PYP C10 C CR6 0.000 -7.308 0.368 0.438
PYP C1 C CR16 0.000 -6.718 1.626 -0.056
PYP H1 H H 0.000 -5.740 1.614 -0.521
PYP C11 C CR66 0.000 -8.495 0.380 1.004
PYP C9 C CR16 0.000 -9.115 -0.856 1.507
PYP H9 H H 0.000 -8.576 -1.790 1.409
PYP C15 C CR66 0.000 -9.218 1.656 1.134
PYP C12 C CR66 0.000 -8.700 2.780 0.697
PYP C3 C CR16 0.000 -9.455 4.035 0.845
PYP H3 H H 0.000 -9.033 4.966 0.486
PYP C2 C CR16 0.000 -7.370 2.764 0.064
PYP H2 H H 0.000 -6.931 3.684 -0.302
PYP C16 C CR66 0.000 -10.547 1.649 1.770
PYP C13 C CR66 0.000 -11.223 2.766 1.904
PYP C5 C CR16 0.000 -12.549 2.735 2.544
PYP H5 H H 0.000 -13.117 3.649 2.662
PYP C4 C CR16 0.000 -10.644 4.029 1.415
PYP H4 H H 0.000 -11.196 4.954 1.524
PYP C14 C CR66 0.000 -11.091 0.365 2.246
PYP C8 C CR16 0.000 -10.298 -0.863 2.072
PYP H8 H H 0.000 -10.705 -1.803 2.423
PYP C7 C CR16 0.000 -12.275 0.340 2.815
PYP H7 H H 0.000 -12.688 -0.597 3.169
PYP C6 C CR16 0.000 -13.041 1.590 2.971
PYP H6 H H 0.000 -14.017 1.567 3.440
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
PYP O3P n/a P START
PYP P O3P "O5'" .
PYP O1P P . .
PYP O2P P . .
PYP "O5'" P "C5'" .
PYP "C5'" "O5'" "C4'" .
PYP "H5'1" "C5'" . .
PYP "H5'2" "C5'" . .
PYP "C4'" "C5'" "C3'" .
PYP "H4'" "C4'" . .
PYP "C3'" "C4'" "C2'" .
PYP "H3'" "C3'" . .
PYP "O3'" "C3'" H3T .
PYP H3T "O3'" . .
PYP "C2'" "C3'" "C1'" .
PYP "H2'2" "C2'" . .
PYP "H2'1" "C2'" . .
PYP "C1'" "C2'" C10 .
PYP "H1'" "C1'" . .
PYP "O4'" "C1'" . .
PYP C10 "C1'" C11 .
PYP C1 C10 H1 .
PYP H1 C1 . .
PYP C11 C10 C15 .
PYP C9 C11 H9 .
PYP H9 C9 . .
PYP C15 C11 C16 .
PYP C12 C15 C2 .
PYP C3 C12 H3 .
PYP H3 C3 . .
PYP C2 C12 H2 .
PYP H2 C2 . .
PYP C16 C15 C14 .
PYP C13 C16 C4 .
PYP C5 C13 H5 .
PYP H5 C5 . .
PYP C4 C13 H4 .
PYP H4 C4 . .
PYP C14 C16 C7 .
PYP C8 C14 H8 .
PYP H8 C8 . .
PYP C7 C14 C6 .
PYP H7 C7 . .
PYP C6 C7 H6 .
PYP H6 C6 . END
PYP "C4'" "O4'" . ADD
PYP C1 C2 . ADD
PYP C3 C4 . ADD
PYP C5 C6 . ADD
PYP C8 C9 . 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
PYP O1P P deloc 1.510 0.020
PYP O2P P deloc 1.510 0.020
PYP "O5'" P single 1.610 0.020
PYP P O3P deloc 1.510 0.020
PYP "C5'" "O5'" single 1.426 0.020
PYP "C4'" "C5'" single 1.524 0.020
PYP "H5'1" "C5'" single 1.092 0.020
PYP "H5'2" "C5'" single 1.092 0.020
PYP "C4'" "O4'" single 1.426 0.020
PYP "C3'" "C4'" single 1.524 0.020
PYP "H4'" "C4'" single 1.099 0.020
PYP "O4'" "C1'" single 1.426 0.020
PYP C10 "C1'" single 1.480 0.020
PYP "C1'" "C2'" single 1.524 0.020
PYP "H1'" "C1'" single 1.099 0.020
PYP C1 C2 double 1.390 0.020
PYP C1 C10 single 1.390 0.020
PYP H1 C1 single 1.083 0.020
PYP C2 C12 single 1.390 0.020
PYP H2 C2 single 1.083 0.020
PYP C3 C4 double 1.390 0.020
PYP C3 C12 single 1.390 0.020
PYP H3 C3 single 1.083 0.020
PYP C4 C13 single 1.390 0.020
PYP H4 C4 single 1.083 0.020
PYP C5 C6 double 1.390 0.020
PYP C5 C13 single 1.390 0.020
PYP H5 C5 single 1.083 0.020
PYP C6 C7 single 1.390 0.020
PYP H6 C6 single 1.083 0.020
PYP C7 C14 double 1.390 0.020
PYP H7 C7 single 1.083 0.020
PYP C8 C9 double 1.390 0.020
PYP C8 C14 single 1.390 0.020
PYP H8 C8 single 1.083 0.020
PYP C9 C11 single 1.390 0.020
PYP H9 C9 single 1.083 0.020
PYP C11 C10 double 1.490 0.020
PYP C15 C11 single 1.490 0.020
PYP C12 C15 double 1.490 0.020
PYP C13 C16 double 1.490 0.020
PYP C14 C16 single 1.490 0.020
PYP C16 C15 single 1.490 0.020
PYP "C2'" "C3'" single 1.524 0.020
PYP "H2'2" "C2'" single 1.092 0.020
PYP "H2'1" "C2'" single 1.092 0.020
PYP "O3'" "C3'" single 1.432 0.020
PYP "H3'" "C3'" single 1.099 0.020
PYP 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
PYP O3P P O1P 119.900 3.000
PYP O3P P O2P 119.900 3.000
PYP O3P P "O5'" 108.200 3.000
PYP O1P P O2P 119.900 3.000
PYP O1P P "O5'" 108.200 3.000
PYP O2P P "O5'" 108.200 3.000
PYP P "O5'" "C5'" 120.500 3.000
PYP "O5'" "C5'" "H5'1" 109.470 3.000
PYP "O5'" "C5'" "H5'2" 109.470 3.000
PYP "O5'" "C5'" "C4'" 109.470 3.000
PYP "H5'1" "C5'" "H5'2" 107.900 3.000
PYP "H5'1" "C5'" "C4'" 109.470 3.000
PYP "H5'2" "C5'" "C4'" 109.470 3.000
PYP "C5'" "C4'" "H4'" 108.340 3.000
PYP "C5'" "C4'" "C3'" 111.000 3.000
PYP "C5'" "C4'" "O4'" 109.470 3.000
PYP "H4'" "C4'" "C3'" 108.340 3.000
PYP "H4'" "C4'" "O4'" 109.470 3.000
PYP "C3'" "C4'" "O4'" 109.470 3.000
PYP "C4'" "C3'" "H3'" 108.340 3.000
PYP "C4'" "C3'" "O3'" 109.470 3.000
PYP "C4'" "C3'" "C2'" 111.000 3.000
PYP "H3'" "C3'" "O3'" 109.470 3.000
PYP "H3'" "C3'" "C2'" 108.340 3.000
PYP "O3'" "C3'" "C2'" 109.470 3.000
PYP "C3'" "O3'" H3T 109.470 3.000
PYP "C3'" "C2'" "H2'2" 109.470 3.000
PYP "C3'" "C2'" "H2'1" 109.470 3.000
PYP "C3'" "C2'" "C1'" 111.000 3.000
PYP "H2'2" "C2'" "H2'1" 107.900 3.000
PYP "H2'2" "C2'" "C1'" 109.470 3.000
PYP "H2'1" "C2'" "C1'" 109.470 3.000
PYP "C2'" "C1'" "H1'" 108.340 3.000
PYP "C2'" "C1'" "O4'" 109.470 3.000
PYP "C2'" "C1'" C10 109.470 3.000
PYP "H1'" "C1'" "O4'" 109.470 3.000
PYP "H1'" "C1'" C10 109.470 3.000
PYP "O4'" "C1'" C10 109.470 3.000
PYP "C1'" "O4'" "C4'" 111.800 3.000
PYP "C1'" C10 C1 120.000 3.000
PYP "C1'" C10 C11 120.000 3.000
PYP C1 C10 C11 120.000 3.000
PYP C10 C1 H1 120.000 3.000
PYP C10 C1 C2 120.000 3.000
PYP H1 C1 C2 120.000 3.000
PYP C10 C11 C9 120.000 3.000
PYP C10 C11 C15 120.000 3.000
PYP C9 C11 C15 120.000 3.000
PYP C11 C9 H9 120.000 3.000
PYP C11 C9 C8 120.000 3.000
PYP H9 C9 C8 120.000 3.000
PYP C11 C15 C12 120.000 3.000
PYP C11 C15 C16 120.000 3.000
PYP C12 C15 C16 120.000 3.000
PYP C15 C12 C3 120.000 3.000
PYP C15 C12 C2 120.000 3.000
PYP C3 C12 C2 120.000 3.000
PYP C12 C3 H3 120.000 3.000
PYP C12 C3 C4 120.000 3.000
PYP H3 C3 C4 120.000 3.000
PYP C12 C2 H2 120.000 3.000
PYP C12 C2 C1 120.000 3.000
PYP H2 C2 C1 120.000 3.000
PYP C15 C16 C13 120.000 3.000
PYP C15 C16 C14 120.000 3.000
PYP C13 C16 C14 120.000 3.000
PYP C16 C13 C5 120.000 3.000
PYP C16 C13 C4 120.000 3.000
PYP C5 C13 C4 120.000 3.000
PYP C13 C5 H5 120.000 3.000
PYP C13 C5 C6 120.000 3.000
PYP H5 C5 C6 120.000 3.000
PYP C13 C4 H4 120.000 3.000
PYP C13 C4 C3 120.000 3.000
PYP H4 C4 C3 120.000 3.000
PYP C16 C14 C8 120.000 3.000
PYP C16 C14 C7 120.000 3.000
PYP C8 C14 C7 120.000 3.000
PYP C14 C8 H8 120.000 3.000
PYP C14 C8 C9 120.000 3.000
PYP H8 C8 C9 120.000 3.000
PYP C14 C7 H7 120.000 3.000
PYP C14 C7 C6 120.000 3.000
PYP H7 C7 C6 120.000 3.000
PYP C7 C6 H6 120.000 3.000
PYP C7 C6 C5 120.000 3.000
PYP H6 C6 C5 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
PYP var_1 O3P P "O5'" "C5'" -174.991 20.000 1
PYP var_2 P "O5'" "C5'" "C4'" 179.994 20.000 1
PYP var_3 "O5'" "C5'" "C4'" "C3'" -175.703 20.000 3
PYP var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
PYP var_5 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
PYP var_6 "C4'" "C3'" "O3'" H3T 179.975 20.000 1
PYP var_7 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
PYP var_8 "C3'" "C2'" "C1'" C10 150.000 20.000 3
PYP var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
PYP var_10 "C2'" "C1'" C10 C11 89.455 20.000 1
PYP CONST_1 "C1'" C10 C1 C2 180.000 0.000 0
PYP CONST_2 C10 C1 C2 C12 0.000 0.000 0
PYP CONST_3 "C1'" C10 C11 C15 180.000 0.000 0
PYP CONST_4 C10 C11 C9 C8 180.000 0.000 0
PYP CONST_5 C10 C11 C15 C16 180.000 0.000 0
PYP CONST_6 C11 C15 C12 C2 0.000 0.000 0
PYP CONST_7 C15 C12 C3 C4 0.000 0.000 0
PYP CONST_8 C12 C3 C4 C13 0.000 0.000 0
PYP CONST_9 C15 C12 C2 C1 0.000 0.000 0
PYP CONST_10 C11 C15 C16 C14 0.000 0.000 0
PYP CONST_11 C15 C16 C13 C4 0.000 0.000 0
PYP CONST_12 C16 C13 C5 C6 0.000 0.000 0
PYP CONST_13 C13 C5 C6 C7 0.000 0.000 0
PYP CONST_14 C16 C13 C4 C3 0.000 0.000 0
PYP CONST_15 C15 C16 C14 C7 180.000 0.000 0
PYP CONST_16 C16 C14 C8 C9 0.000 0.000 0
PYP CONST_17 C14 C8 C9 C11 0.000 0.000 0
PYP CONST_18 C16 C14 C7 C6 0.000 0.000 0
PYP CONST_19 C14 C7 C6 C5 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
PYP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
PYP chir_02 "C1'" "O4'" C10 "C2'" negativ
PYP chir_03 "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
PYP plan-1 C1 0.020
PYP plan-1 C2 0.020
PYP plan-1 C10 0.020
PYP plan-1 H1 0.020
PYP plan-1 C12 0.020
PYP plan-1 H2 0.020
PYP plan-1 "C1'" 0.020
PYP plan-1 C11 0.020
PYP plan-1 C9 0.020
PYP plan-1 C15 0.020
PYP plan-1 C3 0.020
PYP plan-1 C16 0.020
PYP plan-1 C13 0.020
PYP plan-1 C14 0.020
PYP plan-1 C4 0.020
PYP plan-1 C5 0.020
PYP plan-1 C6 0.020
PYP plan-1 C7 0.020
PYP plan-1 C8 0.020
PYP plan-1 H3 0.020
PYP plan-1 H4 0.020
PYP plan-1 H5 0.020
PYP plan-1 H6 0.020
PYP plan-1 H7 0.020
PYP plan-1 H8 0.020
PYP plan-1 H9 0.020
# ------------------------------------------------------
|
