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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
PDE PDE 'PARA-NITROPHENYL PHOSPHONOBUTANOYL D' non-polymer 40 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDE
#
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
PDE O5 O O -1.000 0.000 0.000 0.000
PDE N1 N N 1.000 -0.722 0.375 -0.907
PDE O4 O O 0.000 -0.315 1.194 -1.710
PDE C4 C CR6 0.000 -2.094 -0.166 -1.031
PDE C3 C CR16 0.000 -2.554 -1.097 -0.118
PDE HC3 H H 0.000 -1.910 -1.430 0.686
PDE C2 C CR16 0.000 -3.835 -1.603 -0.231
PDE HC2 H H 0.000 -4.195 -2.331 0.484
PDE C5 C CR16 0.000 -2.913 0.259 -2.061
PDE HC5 H H 0.000 -2.551 0.990 -2.773
PDE C6 C CR16 0.000 -4.193 -0.247 -2.181
PDE HC6 H H 0.000 -4.831 0.081 -2.992
PDE C1 C CR6 0.000 -4.659 -1.177 -1.263
PDE O1 O O2 0.000 -5.918 -1.673 -1.377
PDE P1 P P 0.000 -6.880 -0.704 -0.523
PDE O3 O O 0.000 -6.715 0.691 -0.990
PDE O2 O OH1 0.000 -6.489 -0.799 1.036
PDE HO2 H H 0.000 -6.543 -1.647 1.497
PDE C8 C CH2 0.000 -8.615 -1.218 -0.747
PDE HC81 H H 0.000 -8.756 -2.214 -0.324
PDE HC82 H H 0.000 -8.852 -1.239 -1.813
PDE C9 C CH2 0.000 -9.537 -0.224 -0.038
PDE HC91 H H 0.000 -9.393 0.772 -0.462
PDE HC92 H H 0.000 -9.297 -0.203 1.028
PDE C10 C CH2 0.000 -10.993 -0.655 -0.225
PDE H101 H H 0.000 -11.135 -1.652 0.199
PDE H102 H H 0.000 -11.231 -0.678 -1.291
PDE C11 C C 0.000 -11.900 0.324 0.474
PDE O6 O O 0.000 -11.430 1.273 1.064
PDE N2 N NH1 0.000 -13.236 0.145 0.443
PDE HN2 H H 0.000 -13.629 -0.646 -0.048
PDE C12 C CH1 0.000 -14.118 1.097 1.122
PDE H12 H H 0.000 -13.631 1.458 2.039
PDE C1D C CH3 0.000 -14.403 2.279 0.195
PDE H1D3 H H 0.000 -14.873 1.931 -0.689
PDE H1D2 H H 0.000 -15.041 2.968 0.685
PDE H1D1 H H 0.000 -13.493 2.759 -0.056
PDE C13 C C 0.000 -15.414 0.413 1.478
PDE O7 O OC -0.500 -15.589 -0.790 1.183
PDE O8 O OC -0.500 -16.315 1.051 2.068
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
PDE O5 n/a N1 START
PDE N1 O5 C4 .
PDE O4 N1 . .
PDE C4 N1 C5 .
PDE C3 C4 C2 .
PDE HC3 C3 . .
PDE C2 C3 HC2 .
PDE HC2 C2 . .
PDE C5 C4 C6 .
PDE HC5 C5 . .
PDE C6 C5 C1 .
PDE HC6 C6 . .
PDE C1 C6 O1 .
PDE O1 C1 P1 .
PDE P1 O1 C8 .
PDE O3 P1 . .
PDE O2 P1 HO2 .
PDE HO2 O2 . .
PDE C8 P1 C9 .
PDE HC81 C8 . .
PDE HC82 C8 . .
PDE C9 C8 C10 .
PDE HC91 C9 . .
PDE HC92 C9 . .
PDE C10 C9 C11 .
PDE H101 C10 . .
PDE H102 C10 . .
PDE C11 C10 N2 .
PDE O6 C11 . .
PDE N2 C11 C12 .
PDE HN2 N2 . .
PDE C12 N2 C13 .
PDE H12 C12 . .
PDE C1D C12 H1D1 .
PDE H1D3 C1D . .
PDE H1D2 C1D . .
PDE H1D1 C1D . .
PDE C13 C12 O8 .
PDE O7 C13 . .
PDE O8 C13 . END
PDE 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
PDE P1 O1 single 1.610 0.020
PDE O2 P1 single 1.610 0.020
PDE O3 P1 double 1.480 0.020
PDE C8 P1 single 1.812 0.020
PDE O1 C1 single 1.370 0.020
PDE HO2 O2 single 0.967 0.020
PDE C9 C8 single 1.524 0.020
PDE HC81 C8 single 1.092 0.020
PDE HC82 C8 single 1.092 0.020
PDE C10 C9 single 1.524 0.020
PDE HC91 C9 single 1.092 0.020
PDE HC92 C9 single 1.092 0.020
PDE C11 C10 single 1.510 0.020
PDE H101 C10 single 1.092 0.020
PDE H102 C10 single 1.092 0.020
PDE N2 C11 single 1.330 0.020
PDE O6 C11 double 1.220 0.020
PDE C12 N2 single 1.450 0.020
PDE HN2 N2 single 1.010 0.020
PDE C1D C12 single 1.524 0.020
PDE C13 C12 single 1.500 0.020
PDE H12 C12 single 1.099 0.020
PDE H1D1 C1D single 1.059 0.020
PDE H1D2 C1D single 1.059 0.020
PDE H1D3 C1D single 1.059 0.020
PDE O7 C13 deloc 1.250 0.020
PDE O8 C13 deloc 1.250 0.020
PDE C1 C2 double 1.390 0.020
PDE C1 C6 single 1.390 0.020
PDE C2 C3 single 1.390 0.020
PDE HC2 C2 single 1.083 0.020
PDE C6 C5 double 1.390 0.020
PDE HC6 C6 single 1.083 0.020
PDE C5 C4 single 1.390 0.020
PDE C3 C4 double 1.390 0.020
PDE C4 N1 single 1.400 0.020
PDE HC5 C5 single 1.083 0.020
PDE HC3 C3 single 1.083 0.020
PDE O4 N1 double 1.220 0.020
PDE N1 O5 single 1.400 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
PDE O5 N1 O4 120.000 3.000
PDE O5 N1 C4 120.000 3.000
PDE O4 N1 C4 120.000 3.000
PDE N1 C4 C3 120.000 3.000
PDE N1 C4 C5 120.000 3.000
PDE C3 C4 C5 120.000 3.000
PDE C4 C3 HC3 120.000 3.000
PDE C4 C3 C2 120.000 3.000
PDE HC3 C3 C2 120.000 3.000
PDE C3 C2 HC2 120.000 3.000
PDE C3 C2 C1 120.000 3.000
PDE HC2 C2 C1 120.000 3.000
PDE C4 C5 HC5 120.000 3.000
PDE C4 C5 C6 120.000 3.000
PDE HC5 C5 C6 120.000 3.000
PDE C5 C6 HC6 120.000 3.000
PDE C5 C6 C1 120.000 3.000
PDE HC6 C6 C1 120.000 3.000
PDE C6 C1 O1 120.000 3.000
PDE C6 C1 C2 120.000 3.000
PDE O1 C1 C2 120.000 3.000
PDE C1 O1 P1 120.000 3.000
PDE O1 P1 O3 109.500 3.000
PDE O1 P1 O2 109.500 3.000
PDE O1 P1 C8 109.500 3.000
PDE O3 P1 O2 109.500 3.000
PDE O3 P1 C8 109.500 3.000
PDE O2 P1 C8 109.500 3.000
PDE P1 O2 HO2 120.000 3.000
PDE P1 C8 HC81 109.500 3.000
PDE P1 C8 HC82 109.500 3.000
PDE P1 C8 C9 109.500 3.000
PDE HC81 C8 HC82 107.900 3.000
PDE HC81 C8 C9 109.470 3.000
PDE HC82 C8 C9 109.470 3.000
PDE C8 C9 HC91 109.470 3.000
PDE C8 C9 HC92 109.470 3.000
PDE C8 C9 C10 111.000 3.000
PDE HC91 C9 HC92 107.900 3.000
PDE HC91 C9 C10 109.470 3.000
PDE HC92 C9 C10 109.470 3.000
PDE C9 C10 H101 109.470 3.000
PDE C9 C10 H102 109.470 3.000
PDE C9 C10 C11 109.470 3.000
PDE H101 C10 H102 107.900 3.000
PDE H101 C10 C11 109.470 3.000
PDE H102 C10 C11 109.470 3.000
PDE C10 C11 O6 120.500 3.000
PDE C10 C11 N2 116.500 3.000
PDE O6 C11 N2 123.000 3.000
PDE C11 N2 HN2 120.000 3.000
PDE C11 N2 C12 121.500 3.000
PDE HN2 N2 C12 118.500 3.000
PDE N2 C12 H12 108.550 3.000
PDE N2 C12 C1D 110.000 3.000
PDE N2 C12 C13 111.600 3.000
PDE H12 C12 C1D 108.340 3.000
PDE H12 C12 C13 108.810 3.000
PDE C1D C12 C13 109.470 3.000
PDE C12 C1D H1D3 109.470 3.000
PDE C12 C1D H1D2 109.470 3.000
PDE C12 C1D H1D1 109.470 3.000
PDE H1D3 C1D H1D2 109.470 3.000
PDE H1D3 C1D H1D1 109.470 3.000
PDE H1D2 C1D H1D1 109.470 3.000
PDE C12 C13 O7 118.500 3.000
PDE C12 C13 O8 118.500 3.000
PDE O7 C13 O8 123.000 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
PDE var_1 O5 N1 C4 C5 179.998 20.000 1
PDE CONST_1 N1 C4 C3 C2 180.000 0.000 0
PDE CONST_2 C4 C3 C2 C1 0.000 0.000 0
PDE CONST_3 N1 C4 C5 C6 180.000 0.000 0
PDE CONST_4 C4 C5 C6 C1 0.000 0.000 0
PDE CONST_5 C5 C6 C1 O1 180.000 0.000 0
PDE CONST_6 C6 C1 C2 C3 0.000 0.000 0
PDE var_2 C6 C1 O1 P1 -90.294 20.000 1
PDE var_3 C1 O1 P1 C8 175.012 20.000 1
PDE var_4 O1 P1 O2 HO2 -60.043 20.000 1
PDE var_5 O1 P1 C8 C9 -175.024 20.000 1
PDE var_6 P1 C8 C9 C10 -179.998 20.000 3
PDE var_7 C8 C9 C10 C11 -179.980 20.000 3
PDE var_8 C9 C10 C11 N2 -179.991 20.000 3
PDE CONST_7 C10 C11 N2 C12 180.000 0.000 0
PDE var_9 C11 N2 C12 C13 -155.021 20.000 3
PDE var_10 N2 C12 C1D H1D1 -60.030 20.000 3
PDE var_11 N2 C12 C13 O8 -179.964 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
PDE chir_01 C12 N2 C1D C13 negativ
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
PDE plan-1 C11 0.020
PDE plan-1 C10 0.020
PDE plan-1 N2 0.020
PDE plan-1 O6 0.020
PDE plan-1 HN2 0.020
PDE plan-2 N2 0.020
PDE plan-2 C11 0.020
PDE plan-2 C12 0.020
PDE plan-2 HN2 0.020
PDE plan-3 C13 0.020
PDE plan-3 C12 0.020
PDE plan-3 O7 0.020
PDE plan-3 O8 0.020
PDE plan-4 C1 0.020
PDE plan-4 O1 0.020
PDE plan-4 C2 0.020
PDE plan-4 C6 0.020
PDE plan-4 C4 0.020
PDE plan-4 C5 0.020
PDE plan-4 C3 0.020
PDE plan-4 HC2 0.020
PDE plan-4 HC6 0.020
PDE plan-4 N1 0.020
PDE plan-4 HC5 0.020
PDE plan-4 HC3 0.020
PDE plan-5 N1 0.020
PDE plan-5 C4 0.020
PDE plan-5 O4 0.020
PDE plan-5 O5 0.020
# ------------------------------------------------------
|
