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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
PDP PDP 'PYRIDOXAL-5'-DIPHOSPHATE ' non-polymer 28 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDP
#
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
PDP O3B O OP -0.666 0.000 0.000 0.000
PDP PB P P 0.000 -0.341 1.168 0.899
PDP O1B O OP -0.666 -0.641 2.386 0.053
PDP O2B O OP -0.666 0.832 1.463 1.808
PDP O3A O O2 0.000 -1.631 0.802 1.790
PDP PA P P 0.000 -2.835 0.502 0.764
PDP O1A O OP -0.500 -3.090 1.706 -0.064
PDP O2A O OP -0.500 -2.463 -0.632 -0.116
PDP O5A O O2 0.000 -4.164 0.127 1.590
PDP C5A C CH2 0.000 -5.190 -0.127 0.630
PDP H5A1 H H 0.000 -4.886 -0.954 -0.016
PDP H5A2 H H 0.000 -5.349 0.767 0.023
PDP C5 C CR6 0.000 -6.467 -0.486 1.342
PDP C6 C CR16 0.000 -6.512 -0.528 2.720
PDP H6 H H 0.000 -5.619 -0.301 3.289
PDP N1 N NRD6 0.000 -7.625 -0.840 3.356
PDP C4 C CR6 0.000 -7.629 -0.783 0.615
PDP C4A C C1 0.000 -7.630 -0.750 -0.857
PDP H4A H H 0.000 -6.730 -0.495 -1.391
PDP O4A O O 0.000 -8.644 -1.009 -1.468
PDP C3 C CR6 0.000 -8.791 -1.116 1.333
PDP O3 O OH1 0.000 -9.944 -1.412 0.682
PDP HO3 H H 0.000 -9.977 -2.362 0.505
PDP C2 C CR6 0.000 -8.740 -1.127 2.720
PDP C2A C CH3 0.000 -9.977 -1.476 3.507
PDP H2A3 H H 0.000 -10.578 -2.142 2.944
PDP H2A2 H H 0.000 -9.697 -1.938 4.418
PDP H2A1 H H 0.000 -10.526 -0.594 3.713
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
PDP O3B n/a PB START
PDP PB O3B O3A .
PDP O1B PB . .
PDP O2B PB . .
PDP O3A PB PA .
PDP PA O3A O5A .
PDP O1A PA . .
PDP O2A PA . .
PDP O5A PA C5A .
PDP C5A O5A C5 .
PDP H5A1 C5A . .
PDP H5A2 C5A . .
PDP C5 C5A C4 .
PDP C6 C5 N1 .
PDP H6 C6 . .
PDP N1 C6 . .
PDP C4 C5 C3 .
PDP C4A C4 O4A .
PDP H4A C4A . .
PDP O4A C4A . .
PDP C3 C4 C2 .
PDP O3 C3 HO3 .
PDP HO3 O3 . .
PDP C2 C3 C2A .
PDP C2A C2 H2A1 .
PDP H2A3 C2A . .
PDP H2A2 C2A . .
PDP H2A1 C2A . END
PDP N1 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
PDP N1 C2 double 1.350 0.020
PDP N1 C6 single 1.337 0.020
PDP C2A C2 single 1.506 0.020
PDP C2 C3 single 1.487 0.020
PDP H2A1 C2A single 1.059 0.020
PDP H2A2 C2A single 1.059 0.020
PDP H2A3 C2A single 1.059 0.020
PDP O3 C3 single 1.362 0.020
PDP C3 C4 double 1.487 0.020
PDP HO3 O3 single 0.967 0.020
PDP C4A C4 single 1.480 0.020
PDP C4 C5 single 1.487 0.020
PDP O4A C4A double 1.220 0.020
PDP H4A C4A single 1.077 0.020
PDP C6 C5 double 1.390 0.020
PDP C5 C5A single 1.511 0.020
PDP H6 C6 single 1.083 0.020
PDP C5A O5A single 1.426 0.020
PDP H5A1 C5A single 1.092 0.020
PDP H5A2 C5A single 1.092 0.020
PDP O5A PA single 1.610 0.020
PDP O1A PA deloc 1.510 0.020
PDP PA O3A single 1.610 0.020
PDP O2A PA deloc 1.510 0.020
PDP O3A PB single 1.610 0.020
PDP O1B PB deloc 1.510 0.020
PDP O2B PB deloc 1.510 0.020
PDP PB O3B deloc 1.510 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
PDP O3B PB O1B 119.900 3.000
PDP O3B PB O2B 119.900 3.000
PDP O3B PB O3A 108.200 3.000
PDP O1B PB O2B 119.900 3.000
PDP O1B PB O3A 108.200 3.000
PDP O2B PB O3A 108.200 3.000
PDP PB O3A PA 120.500 3.000
PDP O3A PA O1A 108.200 3.000
PDP O3A PA O2A 108.200 3.000
PDP O3A PA O5A 102.600 3.000
PDP O1A PA O2A 119.900 3.000
PDP O1A PA O5A 108.200 3.000
PDP O2A PA O5A 108.200 3.000
PDP PA O5A C5A 120.500 3.000
PDP O5A C5A H5A1 109.470 3.000
PDP O5A C5A H5A2 109.470 3.000
PDP O5A C5A C5 109.470 3.000
PDP H5A1 C5A H5A2 107.900 3.000
PDP H5A1 C5A C5 109.470 3.000
PDP H5A2 C5A C5 109.470 3.000
PDP C5A C5 C6 120.000 3.000
PDP C5A C5 C4 120.000 3.000
PDP C6 C5 C4 120.000 3.000
PDP C5 C6 H6 120.000 3.000
PDP C5 C6 N1 120.000 3.000
PDP H6 C6 N1 120.000 3.000
PDP C6 N1 C2 120.000 3.000
PDP C5 C4 C4A 120.000 3.000
PDP C5 C4 C3 120.000 3.000
PDP C4A C4 C3 120.000 3.000
PDP C4 C4A H4A 120.000 3.000
PDP C4 C4A O4A 120.000 3.000
PDP H4A C4A O4A 123.000 3.000
PDP C4 C3 O3 120.000 3.000
PDP C4 C3 C2 120.000 3.000
PDP O3 C3 C2 120.000 3.000
PDP C3 O3 HO3 109.470 3.000
PDP C3 C2 C2A 120.000 3.000
PDP C3 C2 N1 120.000 3.000
PDP C2A C2 N1 120.000 3.000
PDP C2 C2A H2A3 109.470 3.000
PDP C2 C2A H2A2 109.470 3.000
PDP C2 C2A H2A1 109.470 3.000
PDP H2A3 C2A H2A2 109.470 3.000
PDP H2A3 C2A H2A1 109.470 3.000
PDP H2A2 C2A H2A1 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
PDP var_1 O3B PB O3A PA -60.026 20.000 1
PDP var_2 PB O3A PA O5A 179.989 20.000 1
PDP var_3 O3A PA O5A C5A -179.998 20.000 1
PDP var_4 PA O5A C5A C5 179.977 20.000 1
PDP var_5 O5A C5A C5 C4 -179.974 20.000 2
PDP CONST_1 C5A C5 C6 N1 180.000 0.000 0
PDP CONST_2 C5 C6 N1 C2 0.000 0.000 0
PDP CONST_3 C6 N1 C2 C3 0.000 0.000 0
PDP CONST_4 C5A C5 C4 C3 180.000 0.000 0
PDP var_6 C5 C4 C4A O4A -179.998 20.000 1
PDP CONST_5 C5 C4 C3 C2 0.000 0.000 0
PDP var_7 C4 C3 O3 HO3 89.936 20.000 1
PDP CONST_6 C4 C3 C2 C2A 180.000 0.000 0
PDP var_8 C3 C2 C2A H2A1 -90.313 20.000 1
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
PDP plan-1 N1 0.020
PDP plan-1 C2 0.020
PDP plan-1 C6 0.020
PDP plan-1 C3 0.020
PDP plan-1 C4 0.020
PDP plan-1 C5 0.020
PDP plan-1 C2A 0.020
PDP plan-1 O3 0.020
PDP plan-1 C4A 0.020
PDP plan-1 C5A 0.020
PDP plan-1 H6 0.020
PDP plan-1 H4A 0.020
PDP plan-2 C4A 0.020
PDP plan-2 C4 0.020
PDP plan-2 O4A 0.020
PDP plan-2 H4A 0.020
# ------------------------------------------------------
|
