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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
PDA PDA '"2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOO' non-polymer 35 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDA
#
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
PDA OXT O OC -0.500 0.000 0.000 0.000
PDA C C C 0.000 -0.138 -1.210 -0.284
PDA O O OC -0.500 0.659 -2.056 0.180
PDA CA C CH1 0.000 -1.262 -1.649 -1.186
PDA HA H H 0.000 -1.909 -2.356 -0.647
PDA CB C CH3 0.000 -0.683 -2.333 -2.427
PDA HB3 H H 0.000 -0.114 -3.178 -2.133
PDA HB2 H H 0.000 -1.472 -2.643 -3.061
PDA HB1 H H 0.000 -0.059 -1.653 -2.947
PDA N N NH1 0.000 -2.050 -0.479 -1.594
PDA HN H H 0.000 -1.710 0.465 -1.709
PDA C4A C CH2 0.000 -3.425 -0.947 -1.804
PDA H4A1 H H 0.000 -3.811 -1.370 -0.874
PDA H4A2 H H 0.000 -3.434 -1.712 -2.583
PDA C4 C CR6 0.000 -4.290 0.212 -2.227
PDA C3 C CR6 0.000 -4.448 0.530 -3.572
PDA O3A O OH1 0.000 -3.820 -0.201 -4.531
PDA HOA H H 0.000 -4.392 -0.930 -4.806
PDA C2 C CR6 0.000 -5.252 1.603 -3.921
PDA C2A C CH3 0.000 -5.432 1.960 -5.374
PDA H2A3 H H 0.000 -5.598 3.002 -5.463
PDA H2A2 H H 0.000 -4.560 1.694 -5.913
PDA H2A1 H H 0.000 -6.264 1.435 -5.766
PDA C5 C CR6 0.000 -4.954 0.981 -1.287
PDA C6 C CR16 0.000 -5.736 2.039 -1.711
PDA H6 H H 0.000 -6.251 2.649 -0.980
PDA N1 N NRD6 0.000 -5.863 2.315 -2.995
PDA C5A C CH2 0.000 -4.816 0.677 0.183
PDA H5A1 H H 0.000 -3.765 0.748 0.471
PDA H5A2 H H 0.000 -5.179 -0.334 0.380
PDA OP4 O O2 0.000 -5.584 1.616 0.937
PDA P P P 0.000 -5.392 1.234 2.489
PDA OP1 O OP -0.666 -3.926 1.321 2.853
PDA OP2 O OP -0.666 -6.184 2.196 3.348
PDA OP3 O OP -0.666 -5.886 -0.176 2.725
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
PDA OXT n/a C START
PDA C OXT CA .
PDA O C . .
PDA CA C N .
PDA HA CA . .
PDA CB CA HB1 .
PDA HB3 CB . .
PDA HB2 CB . .
PDA HB1 CB . .
PDA N CA C4A .
PDA HN N . .
PDA C4A N C4 .
PDA H4A1 C4A . .
PDA H4A2 C4A . .
PDA C4 C4A C5 .
PDA C3 C4 C2 .
PDA O3A C3 HOA .
PDA HOA O3A . .
PDA C2 C3 C2A .
PDA C2A C2 H2A1 .
PDA H2A3 C2A . .
PDA H2A2 C2A . .
PDA H2A1 C2A . .
PDA C5 C4 C5A .
PDA C6 C5 N1 .
PDA H6 C6 . .
PDA N1 C6 . .
PDA C5A C5 OP4 .
PDA H5A1 C5A . .
PDA H5A2 C5A . .
PDA OP4 C5A P .
PDA P OP4 OP3 .
PDA OP1 P . .
PDA OP2 P . .
PDA OP3 P . END
PDA 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
PDA C4A N single 1.450 0.020
PDA N CA single 1.450 0.020
PDA HN N single 1.010 0.020
PDA N1 C2 double 1.350 0.020
PDA N1 C6 single 1.337 0.020
PDA C2A C2 single 1.506 0.020
PDA C2 C3 single 1.487 0.020
PDA H2A1 C2A single 1.059 0.020
PDA H2A2 C2A single 1.059 0.020
PDA H2A3 C2A single 1.059 0.020
PDA O3A C3 single 1.362 0.020
PDA C3 C4 double 1.487 0.020
PDA HOA O3A single 0.967 0.020
PDA C4 C4A single 1.511 0.020
PDA C5 C4 single 1.487 0.020
PDA H4A1 C4A single 1.092 0.020
PDA H4A2 C4A single 1.092 0.020
PDA C5A C5 single 1.511 0.020
PDA C6 C5 double 1.390 0.020
PDA OP4 C5A single 1.426 0.020
PDA H5A1 C5A single 1.092 0.020
PDA H5A2 C5A single 1.092 0.020
PDA P OP4 single 1.610 0.020
PDA OP1 P deloc 1.510 0.020
PDA OP2 P deloc 1.510 0.020
PDA OP3 P deloc 1.510 0.020
PDA H6 C6 single 1.083 0.020
PDA CB CA single 1.524 0.020
PDA CA C single 1.500 0.020
PDA HA CA single 1.099 0.020
PDA HB1 CB single 1.059 0.020
PDA HB2 CB single 1.059 0.020
PDA HB3 CB single 1.059 0.020
PDA O C deloc 1.250 0.020
PDA 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
PDA OXT C O 123.000 3.000
PDA OXT C CA 118.500 3.000
PDA O C CA 118.500 3.000
PDA C CA HA 108.810 3.000
PDA C CA CB 109.470 3.000
PDA C CA N 111.600 3.000
PDA HA CA CB 108.340 3.000
PDA HA CA N 108.550 3.000
PDA CB CA N 110.000 3.000
PDA CA CB HB3 109.470 3.000
PDA CA CB HB2 109.470 3.000
PDA CA CB HB1 109.470 3.000
PDA HB3 CB HB2 109.470 3.000
PDA HB3 CB HB1 109.470 3.000
PDA HB2 CB HB1 109.470 3.000
PDA CA N HN 118.500 3.000
PDA CA N C4A 120.000 3.000
PDA HN N C4A 118.500 3.000
PDA N C4A H4A1 109.470 3.000
PDA N C4A H4A2 109.470 3.000
PDA N C4A C4 109.500 3.000
PDA H4A1 C4A H4A2 107.900 3.000
PDA H4A1 C4A C4 109.470 3.000
PDA H4A2 C4A C4 109.470 3.000
PDA C4A C4 C3 120.000 3.000
PDA C4A C4 C5 120.000 3.000
PDA C3 C4 C5 120.000 3.000
PDA C4 C3 O3A 120.000 3.000
PDA C4 C3 C2 120.000 3.000
PDA O3A C3 C2 120.000 3.000
PDA C3 O3A HOA 109.470 3.000
PDA C3 C2 C2A 120.000 3.000
PDA C3 C2 N1 120.000 3.000
PDA C2A C2 N1 120.000 3.000
PDA C2 C2A H2A3 109.470 3.000
PDA C2 C2A H2A2 109.470 3.000
PDA C2 C2A H2A1 109.470 3.000
PDA H2A3 C2A H2A2 109.470 3.000
PDA H2A3 C2A H2A1 109.470 3.000
PDA H2A2 C2A H2A1 109.470 3.000
PDA C4 C5 C6 120.000 3.000
PDA C4 C5 C5A 120.000 3.000
PDA C6 C5 C5A 120.000 3.000
PDA C5 C6 H6 120.000 3.000
PDA C5 C6 N1 120.000 3.000
PDA H6 C6 N1 120.000 3.000
PDA C6 N1 C2 120.000 3.000
PDA C5 C5A H5A1 109.470 3.000
PDA C5 C5A H5A2 109.470 3.000
PDA C5 C5A OP4 109.470 3.000
PDA H5A1 C5A H5A2 107.900 3.000
PDA H5A1 C5A OP4 109.470 3.000
PDA H5A2 C5A OP4 109.470 3.000
PDA C5A OP4 P 120.500 3.000
PDA OP4 P OP1 108.200 3.000
PDA OP4 P OP2 108.200 3.000
PDA OP4 P OP3 108.200 3.000
PDA OP1 P OP2 119.900 3.000
PDA OP1 P OP3 119.900 3.000
PDA 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
PDA var_1 OXT C CA N -0.038 20.000 3
PDA var_2 C CA CB HB1 -60.071 20.000 3
PDA var_3 C CA N C4A -149.969 20.000 3
PDA var_4 CA N C4A C4 179.970 20.000 3
PDA var_5 N C4A C4 C5 -90.331 20.000 2
PDA CONST_1 C4A C4 C3 C2 180.000 0.000 0
PDA var_6 C4 C3 O3A HOA 90.081 20.000 1
PDA CONST_2 C4 C3 C2 C2A 180.000 0.000 0
PDA var_7 C3 C2 C2A H2A1 90.010 20.000 1
PDA CONST_3 C4A C4 C5 C5A 0.000 0.000 0
PDA CONST_4 C4 C5 C6 N1 0.000 0.000 0
PDA CONST_5 C5 C6 N1 C2 0.000 0.000 0
PDA CONST_6 C6 N1 C2 C3 0.000 0.000 0
PDA var_8 C4 C5 C5A OP4 179.447 20.000 2
PDA var_9 C5 C5A OP4 P -179.994 20.000 1
PDA var_10 C5A OP4 P OP3 -60.018 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
PDA chir_01 CA N CB C 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
PDA plan-1 N 0.020
PDA plan-1 C4A 0.020
PDA plan-1 CA 0.020
PDA plan-1 HN 0.020
PDA plan-2 N1 0.020
PDA plan-2 C2 0.020
PDA plan-2 C6 0.020
PDA plan-2 C3 0.020
PDA plan-2 C4 0.020
PDA plan-2 C5 0.020
PDA plan-2 C2A 0.020
PDA plan-2 O3A 0.020
PDA plan-2 C4A 0.020
PDA plan-2 C5A 0.020
PDA plan-2 H6 0.020
PDA plan-3 C 0.020
PDA plan-3 CA 0.020
PDA plan-3 O 0.020
PDA plan-3 OXT 0.020
# ------------------------------------------------------
|
