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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
PD7 PD7 '(2R)-3-(phosphonooxy)propane-1,2-diy' non-polymer 57 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PD7
#
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
PD7 "O'" O O -0.500 0.000 0.000 0.000
PD7 "C'" C C 0.000 -0.906 -0.650 -0.568
PD7 "C1'" C CH2 0.000 -0.579 -1.526 -1.749
PD7 "H1'" H H 0.000 -1.142 -1.187 -2.621
PD7 "H1'A" H H 0.000 -0.850 -2.559 -1.522
PD7 "C2'" C CH2 0.000 0.920 -1.444 -2.045
PD7 "H2'" H H 0.000 1.482 -1.782 -1.173
PD7 "H2'A" H H 0.000 1.190 -0.410 -2.272
PD7 "C3'" C CH2 0.000 1.252 -2.334 -3.245
PD7 "H3'" H H 0.000 0.688 -1.995 -4.117
PD7 "H3'A" H H 0.000 0.981 -3.367 -3.017
PD7 "C4'" C CH2 0.000 2.751 -2.251 -3.541
PD7 "H4'" H H 0.000 3.313 -2.589 -2.668
PD7 "H4'A" H H 0.000 3.020 -1.217 -3.768
PD7 "C5'" C CH2 0.000 3.084 -3.142 -4.740
PD7 "H5'" H H 0.000 2.519 -2.803 -5.612
PD7 "H5'A" H H 0.000 2.813 -4.175 -4.512
PD7 "C6'" C CH3 0.000 4.582 -3.059 -5.037
PD7 "H6'B" H H 0.000 5.132 -3.388 -4.193
PD7 "H6'A" H H 0.000 4.816 -3.674 -5.869
PD7 "H6'" H H 0.000 4.847 -2.056 -5.259
PD7 O2 O O2 -0.500 -2.084 -0.570 -0.155
PD7 C2 C CH1 0.000 -2.413 0.300 1.017
PD7 H2 H H 0.000 -1.533 0.349 1.673
PD7 C1 C CH2 0.000 -2.735 1.713 0.528
PD7 H1 H H 0.000 -1.930 2.065 -0.120
PD7 H1A H H 0.000 -2.828 2.381 1.386
PD7 O3P O O2 0.000 -3.963 1.696 -0.201
PD7 P P P 0.000 -4.609 3.015 -0.862
PD7 O2P O OP -0.666 -5.836 2.630 -1.659
PD7 O1P O OP -0.666 -3.597 3.667 -1.778
PD7 O4P O OP -0.666 -5.001 3.986 0.229
PD7 C3 C CH2 0.000 -3.594 -0.243 1.825
PD7 H3 H H 0.000 -3.685 0.360 2.731
PD7 H3A H H 0.000 -3.366 -1.275 2.098
PD7 O3 O O2 -0.500 -4.879 -0.199 1.063
PD7 "C''" C C 0.000 -5.937 -0.608 1.591
PD7 "O''" O O -0.500 -5.919 -1.056 2.759
PD7 "C1''" C CH2 0.000 -7.233 -0.556 0.824
PD7 "H1''" H H 0.000 -7.142 -1.160 -0.082
PD7 H1AA H H 0.000 -7.452 0.478 0.550
PD7 "C2''" C CH2 0.000 -8.364 -1.106 1.694
PD7 "H2''" H H 0.000 -8.452 -0.502 2.599
PD7 H2AA H H 0.000 -8.142 -2.139 1.968
PD7 "C3''" C CH2 0.000 -9.679 -1.054 0.915
PD7 "H3''" H H 0.000 -9.589 -1.658 0.009
PD7 H3AA H H 0.000 -9.898 -0.020 0.641
PD7 "C4''" C CH2 0.000 -10.810 -1.604 1.785
PD7 "H4''" H H 0.000 -10.898 -0.999 2.690
PD7 H4AA H H 0.000 -10.589 -2.637 2.059
PD7 "C5''" C CH2 0.000 -12.126 -1.552 1.006
PD7 "H5''" H H 0.000 -12.035 -2.155 0.100
PD7 H5AA H H 0.000 -12.345 -0.518 0.732
PD7 "C6''" C CH3 0.000 -13.257 -2.102 1.876
PD7 H6AB H H 0.000 -13.347 -1.518 2.756
PD7 H6AA H H 0.000 -14.170 -2.067 1.339
PD7 "H6''" H H 0.000 -13.046 -3.107 2.143
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
PD7 "O'" n/a "C'" START
PD7 "C'" "O'" O2 .
PD7 "C1'" "C'" "C2'" .
PD7 "H1'" "C1'" . .
PD7 "H1'A" "C1'" . .
PD7 "C2'" "C1'" "C3'" .
PD7 "H2'" "C2'" . .
PD7 "H2'A" "C2'" . .
PD7 "C3'" "C2'" "C4'" .
PD7 "H3'" "C3'" . .
PD7 "H3'A" "C3'" . .
PD7 "C4'" "C3'" "C5'" .
PD7 "H4'" "C4'" . .
PD7 "H4'A" "C4'" . .
PD7 "C5'" "C4'" "C6'" .
PD7 "H5'" "C5'" . .
PD7 "H5'A" "C5'" . .
PD7 "C6'" "C5'" "H6'" .
PD7 "H6'B" "C6'" . .
PD7 "H6'A" "C6'" . .
PD7 "H6'" "C6'" . .
PD7 O2 "C'" C2 .
PD7 C2 O2 C3 .
PD7 H2 C2 . .
PD7 C1 C2 O3P .
PD7 H1 C1 . .
PD7 H1A C1 . .
PD7 O3P C1 P .
PD7 P O3P O4P .
PD7 O2P P . .
PD7 O1P P . .
PD7 O4P P . .
PD7 C3 C2 O3 .
PD7 H3 C3 . .
PD7 H3A C3 . .
PD7 O3 C3 "C''" .
PD7 "C''" O3 "C1''" .
PD7 "O''" "C''" . .
PD7 "C1''" "C''" "C2''" .
PD7 "H1''" "C1''" . .
PD7 H1AA "C1''" . .
PD7 "C2''" "C1''" "C3''" .
PD7 "H2''" "C2''" . .
PD7 H2AA "C2''" . .
PD7 "C3''" "C2''" "C4''" .
PD7 "H3''" "C3''" . .
PD7 H3AA "C3''" . .
PD7 "C4''" "C3''" "C5''" .
PD7 "H4''" "C4''" . .
PD7 H4AA "C4''" . .
PD7 "C5''" "C4''" "C6''" .
PD7 "H5''" "C5''" . .
PD7 H5AA "C5''" . .
PD7 "C6''" "C5''" "H6''" .
PD7 H6AB "C6''" . .
PD7 H6AA "C6''" . .
PD7 "H6''" "C6''" . 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
PD7 "O''" "C''" deloc 1.220 0.020
PD7 "C1''" "C''" single 1.510 0.020
PD7 "C''" O3 deloc 1.454 0.020
PD7 "C2''" "C1''" single 1.524 0.020
PD7 "H1''" "C1''" single 1.092 0.020
PD7 H1AA "C1''" single 1.092 0.020
PD7 "C3''" "C2''" single 1.524 0.020
PD7 "H2''" "C2''" single 1.092 0.020
PD7 H2AA "C2''" single 1.092 0.020
PD7 "C4''" "C3''" single 1.524 0.020
PD7 "H3''" "C3''" single 1.092 0.020
PD7 H3AA "C3''" single 1.092 0.020
PD7 "C5''" "C4''" single 1.524 0.020
PD7 "H4''" "C4''" single 1.092 0.020
PD7 H4AA "C4''" single 1.092 0.020
PD7 "C6''" "C5''" single 1.513 0.020
PD7 "H5''" "C5''" single 1.092 0.020
PD7 H5AA "C5''" single 1.092 0.020
PD7 "H6''" "C6''" single 1.059 0.020
PD7 H6AA "C6''" single 1.059 0.020
PD7 H6AB "C6''" single 1.059 0.020
PD7 O3 C3 single 1.426 0.020
PD7 C3 C2 single 1.524 0.020
PD7 H3 C3 single 1.092 0.020
PD7 H3A C3 single 1.092 0.020
PD7 C2 O2 single 1.426 0.020
PD7 C1 C2 single 1.524 0.020
PD7 H2 C2 single 1.099 0.020
PD7 O3P C1 single 1.426 0.020
PD7 H1 C1 single 1.092 0.020
PD7 H1A C1 single 1.092 0.020
PD7 P O3P single 1.610 0.020
PD7 O1P P deloc 1.510 0.020
PD7 O2P P deloc 1.510 0.020
PD7 O4P P deloc 1.510 0.020
PD7 O2 "C'" deloc 1.454 0.020
PD7 "C1'" "C'" single 1.510 0.020
PD7 "C'" "O'" deloc 1.220 0.020
PD7 "C2'" "C1'" single 1.524 0.020
PD7 "H1'" "C1'" single 1.092 0.020
PD7 "H1'A" "C1'" single 1.092 0.020
PD7 "C3'" "C2'" single 1.524 0.020
PD7 "H2'" "C2'" single 1.092 0.020
PD7 "H2'A" "C2'" single 1.092 0.020
PD7 "C4'" "C3'" single 1.524 0.020
PD7 "H3'" "C3'" single 1.092 0.020
PD7 "H3'A" "C3'" single 1.092 0.020
PD7 "C5'" "C4'" single 1.524 0.020
PD7 "H4'" "C4'" single 1.092 0.020
PD7 "H4'A" "C4'" single 1.092 0.020
PD7 "C6'" "C5'" single 1.513 0.020
PD7 "H5'" "C5'" single 1.092 0.020
PD7 "H5'A" "C5'" single 1.092 0.020
PD7 "H6'" "C6'" single 1.059 0.020
PD7 "H6'A" "C6'" single 1.059 0.020
PD7 "H6'B" "C6'" single 1.059 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
PD7 "O'" "C'" "C1'" 120.500 3.000
PD7 "O'" "C'" O2 119.000 3.000
PD7 "C1'" "C'" O2 120.000 3.000
PD7 "C'" "C1'" "H1'" 109.470 3.000
PD7 "C'" "C1'" "H1'A" 109.470 3.000
PD7 "C'" "C1'" "C2'" 109.470 3.000
PD7 "H1'" "C1'" "H1'A" 107.900 3.000
PD7 "H1'" "C1'" "C2'" 109.470 3.000
PD7 "H1'A" "C1'" "C2'" 109.470 3.000
PD7 "C1'" "C2'" "H2'" 109.470 3.000
PD7 "C1'" "C2'" "H2'A" 109.470 3.000
PD7 "C1'" "C2'" "C3'" 111.000 3.000
PD7 "H2'" "C2'" "H2'A" 107.900 3.000
PD7 "H2'" "C2'" "C3'" 109.470 3.000
PD7 "H2'A" "C2'" "C3'" 109.470 3.000
PD7 "C2'" "C3'" "H3'" 109.470 3.000
PD7 "C2'" "C3'" "H3'A" 109.470 3.000
PD7 "C2'" "C3'" "C4'" 111.000 3.000
PD7 "H3'" "C3'" "H3'A" 107.900 3.000
PD7 "H3'" "C3'" "C4'" 109.470 3.000
PD7 "H3'A" "C3'" "C4'" 109.470 3.000
PD7 "C3'" "C4'" "H4'" 109.470 3.000
PD7 "C3'" "C4'" "H4'A" 109.470 3.000
PD7 "C3'" "C4'" "C5'" 111.000 3.000
PD7 "H4'" "C4'" "H4'A" 107.900 3.000
PD7 "H4'" "C4'" "C5'" 109.470 3.000
PD7 "H4'A" "C4'" "C5'" 109.470 3.000
PD7 "C4'" "C5'" "H5'" 109.470 3.000
PD7 "C4'" "C5'" "H5'A" 109.470 3.000
PD7 "C4'" "C5'" "C6'" 111.000 3.000
PD7 "H5'" "C5'" "H5'A" 107.900 3.000
PD7 "H5'" "C5'" "C6'" 109.470 3.000
PD7 "H5'A" "C5'" "C6'" 109.470 3.000
PD7 "C5'" "C6'" "H6'B" 109.470 3.000
PD7 "C5'" "C6'" "H6'A" 109.470 3.000
PD7 "C5'" "C6'" "H6'" 109.470 3.000
PD7 "H6'B" "C6'" "H6'A" 109.470 3.000
PD7 "H6'B" "C6'" "H6'" 109.470 3.000
PD7 "H6'A" "C6'" "H6'" 109.470 3.000
PD7 "C'" O2 C2 111.800 3.000
PD7 O2 C2 H2 109.470 3.000
PD7 O2 C2 C1 109.470 3.000
PD7 O2 C2 C3 109.470 3.000
PD7 H2 C2 C1 108.340 3.000
PD7 H2 C2 C3 108.340 3.000
PD7 C1 C2 C3 109.470 3.000
PD7 C2 C1 H1 109.470 3.000
PD7 C2 C1 H1A 109.470 3.000
PD7 C2 C1 O3P 109.470 3.000
PD7 H1 C1 H1A 107.900 3.000
PD7 H1 C1 O3P 109.470 3.000
PD7 H1A C1 O3P 109.470 3.000
PD7 C1 O3P P 120.500 3.000
PD7 O3P P O2P 108.200 3.000
PD7 O3P P O1P 108.200 3.000
PD7 O3P P O4P 108.200 3.000
PD7 O2P P O1P 119.900 3.000
PD7 O2P P O4P 119.900 3.000
PD7 O1P P O4P 119.900 3.000
PD7 C2 C3 H3 109.470 3.000
PD7 C2 C3 H3A 109.470 3.000
PD7 C2 C3 O3 109.470 3.000
PD7 H3 C3 H3A 107.900 3.000
PD7 H3 C3 O3 109.470 3.000
PD7 H3A C3 O3 109.470 3.000
PD7 C3 O3 "C''" 120.000 3.000
PD7 O3 "C''" "O''" 119.000 3.000
PD7 O3 "C''" "C1''" 120.000 3.000
PD7 "O''" "C''" "C1''" 120.500 3.000
PD7 "C''" "C1''" "H1''" 109.470 3.000
PD7 "C''" "C1''" H1AA 109.470 3.000
PD7 "C''" "C1''" "C2''" 109.470 3.000
PD7 "H1''" "C1''" H1AA 107.900 3.000
PD7 "H1''" "C1''" "C2''" 109.470 3.000
PD7 H1AA "C1''" "C2''" 109.470 3.000
PD7 "C1''" "C2''" "H2''" 109.470 3.000
PD7 "C1''" "C2''" H2AA 109.470 3.000
PD7 "C1''" "C2''" "C3''" 111.000 3.000
PD7 "H2''" "C2''" H2AA 107.900 3.000
PD7 "H2''" "C2''" "C3''" 109.470 3.000
PD7 H2AA "C2''" "C3''" 109.470 3.000
PD7 "C2''" "C3''" "H3''" 109.470 3.000
PD7 "C2''" "C3''" H3AA 109.470 3.000
PD7 "C2''" "C3''" "C4''" 111.000 3.000
PD7 "H3''" "C3''" H3AA 107.900 3.000
PD7 "H3''" "C3''" "C4''" 109.470 3.000
PD7 H3AA "C3''" "C4''" 109.470 3.000
PD7 "C3''" "C4''" "H4''" 109.470 3.000
PD7 "C3''" "C4''" H4AA 109.470 3.000
PD7 "C3''" "C4''" "C5''" 111.000 3.000
PD7 "H4''" "C4''" H4AA 107.900 3.000
PD7 "H4''" "C4''" "C5''" 109.470 3.000
PD7 H4AA "C4''" "C5''" 109.470 3.000
PD7 "C4''" "C5''" "H5''" 109.470 3.000
PD7 "C4''" "C5''" H5AA 109.470 3.000
PD7 "C4''" "C5''" "C6''" 111.000 3.000
PD7 "H5''" "C5''" H5AA 107.900 3.000
PD7 "H5''" "C5''" "C6''" 109.470 3.000
PD7 H5AA "C5''" "C6''" 109.470 3.000
PD7 "C5''" "C6''" H6AB 109.470 3.000
PD7 "C5''" "C6''" H6AA 109.470 3.000
PD7 "C5''" "C6''" "H6''" 109.470 3.000
PD7 H6AB "C6''" H6AA 109.470 3.000
PD7 H6AB "C6''" "H6''" 109.470 3.000
PD7 H6AA "C6''" "H6''" 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
PD7 var_1 "O'" "C'" "C1'" "C2'" 0.049 20.000 3
PD7 var_2 "C'" "C1'" "C2'" "C3'" -179.996 20.000 3
PD7 var_3 "C1'" "C2'" "C3'" "C4'" 180.000 20.000 3
PD7 var_4 "C2'" "C3'" "C4'" "C5'" 179.973 20.000 3
PD7 var_5 "C3'" "C4'" "C5'" "C6'" 179.974 20.000 3
PD7 var_6 "C4'" "C5'" "C6'" "H6'" -59.959 20.000 3
PD7 var_7 "O'" "C'" O2 C2 0.001 20.000 1
PD7 var_8 "C'" O2 C2 C3 -149.393 20.000 1
PD7 var_9 O2 C2 C1 O3P 68.292 20.000 3
PD7 var_10 C2 C1 O3P P 179.991 20.000 1
PD7 var_11 C1 O3P P O4P -64.981 20.000 1
PD7 var_12 O2 C2 C3 O3 -66.726 20.000 3
PD7 var_13 C2 C3 O3 "C''" -179.974 20.000 1
PD7 var_14 C3 O3 "C''" "C1''" 179.704 20.000 1
PD7 var_15 O3 "C''" "C1''" "C2''" -179.699 20.000 3
PD7 var_16 "C''" "C1''" "C2''" "C3''" -179.965 20.000 3
PD7 var_17 "C1''" "C2''" "C3''" "C4''" 180.000 20.000 3
PD7 var_18 "C2''" "C3''" "C4''" "C5''" 180.000 20.000 3
PD7 var_19 "C3''" "C4''" "C5''" "C6''" 179.964 20.000 3
PD7 var_20 "C4''" "C5''" "C6''" "H6''" -60.018 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
PD7 chir_01 C2 C3 C1 O2 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
PD7 plan-1 "C''" 0.020
PD7 plan-1 "O''" 0.020
PD7 plan-1 "C1''" 0.020
PD7 plan-1 O3 0.020
PD7 plan-2 "C'" 0.020
PD7 plan-2 O2 0.020
PD7 plan-2 "O'" 0.020
PD7 plan-2 "C1'" 0.020
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