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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
PDD PDD 'N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE ' non-polymer 35 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDD
#
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
PDD OXT O OC -0.500 0.000 0.000 0.000
PDD C C C 0.000 -1.180 -0.334 0.245
PDD O O OC -0.500 -1.413 -1.362 0.919
PDD CA C CH1 0.000 -2.324 0.500 -0.272
PDD HA H H 0.000 -2.247 1.518 0.134
PDD CB C CH3 0.000 -2.263 0.555 -1.801
PDD HB3 H H 0.000 -3.066 1.143 -2.166
PDD HB2 H H 0.000 -1.345 0.987 -2.104
PDD HB1 H H 0.000 -2.338 -0.426 -2.195
PDD N N NH1 0.000 -3.597 -0.099 0.146
PDD H H H 0.000 -3.779 -1.079 0.305
PDD C4A C CH2 0.000 -4.556 1.004 0.289
PDD H4A1 H H 0.000 -4.664 1.518 -0.668
PDD H4A2 H H 0.000 -4.191 1.708 1.040
PDD C4 C CR6 0.000 -5.892 0.456 0.720
PDD C3 C CR6 0.000 -6.206 0.323 2.068
PDD O3A O OH1 0.000 -5.311 0.687 3.024
PDD HO3 H H 0.000 -5.445 1.617 3.253
PDD C2 C CR6 0.000 -7.447 -0.185 2.423
PDD C2A C CH3 0.000 -7.802 -0.335 3.880
PDD H2A3 H H 0.000 -8.470 -1.149 3.999
PDD H2A2 H H 0.000 -6.923 -0.516 4.442
PDD H2A1 H H 0.000 -8.264 0.553 4.225
PDD C5 C CR6 0.000 -6.837 0.076 -0.218
PDD C6 C CR16 0.000 -8.050 -0.426 0.214
PDD H6 H H 0.000 -8.791 -0.732 -0.515
PDD N1 N NRD6 0.000 -8.318 -0.539 1.500
PDD C5A C CH2 0.000 -6.545 0.201 -1.691
PDD H5A1 H H 0.000 -5.667 -0.399 -1.939
PDD H5A2 H H 0.000 -6.349 1.247 -1.935
PDD OP4 O O2 0.000 -7.669 -0.263 -2.441
PDD P P P 0.000 -7.288 -0.102 -3.996
PDD OP1 O OP -0.666 -6.059 -0.929 -4.303
PDD OP2 O OP -0.666 -8.442 -0.579 -4.850
PDD OP3 O OP -0.666 -7.005 1.354 -4.299
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
PDD OXT n/a C START
PDD C OXT CA .
PDD O C . .
PDD CA C N .
PDD HA CA . .
PDD CB CA HB1 .
PDD HB3 CB . .
PDD HB2 CB . .
PDD HB1 CB . .
PDD N CA C4A .
PDD H N . .
PDD C4A N C4 .
PDD H4A1 C4A . .
PDD H4A2 C4A . .
PDD C4 C4A C5 .
PDD C3 C4 C2 .
PDD O3A C3 HO3 .
PDD HO3 O3A . .
PDD C2 C3 C2A .
PDD C2A C2 H2A1 .
PDD H2A3 C2A . .
PDD H2A2 C2A . .
PDD H2A1 C2A . .
PDD C5 C4 C5A .
PDD C6 C5 N1 .
PDD H6 C6 . .
PDD N1 C6 . .
PDD C5A C5 OP4 .
PDD H5A1 C5A . .
PDD H5A2 C5A . .
PDD OP4 C5A P .
PDD P OP4 OP3 .
PDD OP1 P . .
PDD OP2 P . .
PDD OP3 P . END
PDD 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
PDD C4A N single 1.450 0.020
PDD N CA single 1.450 0.020
PDD H N single 1.010 0.020
PDD N1 C2 double 1.350 0.020
PDD N1 C6 single 1.337 0.020
PDD C2A C2 single 1.506 0.020
PDD C2 C3 single 1.487 0.020
PDD H2A1 C2A single 1.059 0.020
PDD H2A2 C2A single 1.059 0.020
PDD H2A3 C2A single 1.059 0.020
PDD O3A C3 single 1.362 0.020
PDD C3 C4 double 1.487 0.020
PDD HO3 O3A single 0.967 0.020
PDD C4 C4A single 1.511 0.020
PDD C5 C4 single 1.487 0.020
PDD H4A1 C4A single 1.092 0.020
PDD H4A2 C4A single 1.092 0.020
PDD C5A C5 single 1.511 0.020
PDD C6 C5 double 1.390 0.020
PDD OP4 C5A single 1.426 0.020
PDD H5A1 C5A single 1.092 0.020
PDD H5A2 C5A single 1.092 0.020
PDD P OP4 single 1.610 0.020
PDD OP1 P deloc 1.510 0.020
PDD OP2 P deloc 1.510 0.020
PDD OP3 P deloc 1.510 0.020
PDD H6 C6 single 1.083 0.020
PDD CB CA single 1.524 0.020
PDD CA C single 1.500 0.020
PDD HA CA single 1.099 0.020
PDD HB1 CB single 1.059 0.020
PDD HB2 CB single 1.059 0.020
PDD HB3 CB single 1.059 0.020
PDD O C deloc 1.250 0.020
PDD C OXT deloc 1.250 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
PDD OXT C O 123.000 3.000
PDD OXT C CA 118.500 3.000
PDD O C CA 118.500 3.000
PDD C CA HA 108.810 3.000
PDD C CA CB 109.470 3.000
PDD C CA N 111.600 3.000
PDD HA CA CB 108.340 3.000
PDD HA CA N 108.550 3.000
PDD CB CA N 110.000 3.000
PDD CA CB HB3 109.470 3.000
PDD CA CB HB2 109.470 3.000
PDD CA CB HB1 109.470 3.000
PDD HB3 CB HB2 109.470 3.000
PDD HB3 CB HB1 109.470 3.000
PDD HB2 CB HB1 109.470 3.000
PDD CA N H 118.500 3.000
PDD CA N C4A 120.000 3.000
PDD H N C4A 118.500 3.000
PDD N C4A H4A1 109.470 3.000
PDD N C4A H4A2 109.470 3.000
PDD N C4A C4 109.500 3.000
PDD H4A1 C4A H4A2 107.900 3.000
PDD H4A1 C4A C4 109.470 3.000
PDD H4A2 C4A C4 109.470 3.000
PDD C4A C4 C3 120.000 3.000
PDD C4A C4 C5 120.000 3.000
PDD C3 C4 C5 120.000 3.000
PDD C4 C3 O3A 120.000 3.000
PDD C4 C3 C2 120.000 3.000
PDD O3A C3 C2 120.000 3.000
PDD C3 O3A HO3 109.470 3.000
PDD C3 C2 C2A 120.000 3.000
PDD C3 C2 N1 120.000 3.000
PDD C2A C2 N1 120.000 3.000
PDD C2 C2A H2A3 109.470 3.000
PDD C2 C2A H2A2 109.470 3.000
PDD C2 C2A H2A1 109.470 3.000
PDD H2A3 C2A H2A2 109.470 3.000
PDD H2A3 C2A H2A1 109.470 3.000
PDD H2A2 C2A H2A1 109.470 3.000
PDD C4 C5 C6 120.000 3.000
PDD C4 C5 C5A 120.000 3.000
PDD C6 C5 C5A 120.000 3.000
PDD C5 C6 H6 120.000 3.000
PDD C5 C6 N1 120.000 3.000
PDD H6 C6 N1 120.000 3.000
PDD C6 N1 C2 120.000 3.000
PDD C5 C5A H5A1 109.470 3.000
PDD C5 C5A H5A2 109.470 3.000
PDD C5 C5A OP4 109.470 3.000
PDD H5A1 C5A H5A2 107.900 3.000
PDD H5A1 C5A OP4 109.470 3.000
PDD H5A2 C5A OP4 109.470 3.000
PDD C5A OP4 P 120.500 3.000
PDD OP4 P OP1 108.200 3.000
PDD OP4 P OP2 108.200 3.000
PDD OP4 P OP3 108.200 3.000
PDD OP1 P OP2 119.900 3.000
PDD OP1 P OP3 119.900 3.000
PDD OP2 P OP3 119.900 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
PDD var_1 OXT C CA N 179.962 20.000 3
PDD var_2 C CA CB HB1 60.095 20.000 3
PDD var_3 C CA N C4A 149.969 20.000 3
PDD var_4 CA N C4A C4 -179.964 20.000 3
PDD var_5 N C4A C4 C5 -90.248 20.000 2
PDD CONST_1 C4A C4 C3 C2 180.000 0.000 0
PDD var_6 C4 C3 O3A HO3 89.991 20.000 1
PDD CONST_2 C4 C3 C2 C2A 180.000 0.000 0
PDD var_7 C3 C2 C2A H2A1 90.072 20.000 1
PDD CONST_3 C4A C4 C5 C5A 0.000 0.000 0
PDD CONST_4 C4 C5 C6 N1 0.000 0.000 0
PDD CONST_5 C5 C6 N1 C2 0.000 0.000 0
PDD CONST_6 C6 N1 C2 C3 0.000 0.000 0
PDD var_8 C4 C5 C5A OP4 179.543 20.000 2
PDD var_9 C5 C5A OP4 P 179.998 20.000 1
PDD var_10 C5A OP4 P OP3 -60.026 20.000 1
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
PDD chir_01 CA N CB C 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
PDD plan-1 N 0.020
PDD plan-1 C4A 0.020
PDD plan-1 CA 0.020
PDD plan-1 H 0.020
PDD plan-2 N1 0.020
PDD plan-2 C2 0.020
PDD plan-2 C6 0.020
PDD plan-2 C3 0.020
PDD plan-2 C4 0.020
PDD plan-2 C5 0.020
PDD plan-2 C2A 0.020
PDD plan-2 O3A 0.020
PDD plan-2 C4A 0.020
PDD plan-2 C5A 0.020
PDD plan-2 H6 0.020
PDD plan-3 C 0.020
PDD plan-3 CA 0.020
PDD plan-3 O 0.020
PDD plan-3 OXT 0.020
# ------------------------------------------------------
|
