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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
PDG PDG '"N-({3-HYDROXY-2-METHYL-5-[(PHOSPHON' non-polymer 40 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDG
#
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
PDG OXT O OC -0.500 0.000 0.000 0.000
PDG CA C C 0.000 -1.224 -0.190 0.176
PDG OA O OC -0.500 -1.611 -1.019 1.030
PDG CAA C CH1 0.000 -2.232 0.576 -0.641
PDG HAA H H 0.000 -2.103 1.653 -0.464
PDG CBA C CH2 0.000 -2.021 0.275 -2.126
PDG HBA1 H H 0.000 -2.235 -0.779 -2.316
PDG HBA2 H H 0.000 -0.985 0.489 -2.396
PDG CGA C CH2 0.000 -2.959 1.147 -2.962
PDG HGA1 H H 0.000 -2.744 2.200 -2.770
PDG HGA2 H H 0.000 -3.994 0.932 -2.689
PDG CDA C C 0.000 -2.751 0.848 -4.425
PDG OE2 O OC -0.500 -1.906 -0.006 -4.775
PDG OE1 O OC -0.500 -3.422 1.456 -5.288
PDG NA N NH1 0.000 -3.589 0.175 -0.247
PDG HNA H H 0.000 -4.163 -0.527 -0.692
PDG C4A C CH2 0.000 -3.949 0.992 0.918
PDG H4A1 H H 0.000 -3.920 2.049 0.644
PDG H4A2 H H 0.000 -3.238 0.807 1.726
PDG C4 C CR6 0.000 -5.338 0.629 1.376
PDG C3 C CR6 0.000 -6.452 1.287 0.863
PDG O3 O OH1 0.000 -6.306 2.274 -0.058
PDG HO3 H H 0.000 -6.328 1.892 -0.946
PDG C2 C CR6 0.000 -7.714 0.926 1.314
PDG C2A C CH3 0.000 -8.929 1.633 0.773
PDG H2A3 H H 0.000 -8.738 1.955 -0.218
PDG H2A2 H H 0.000 -9.755 0.970 0.776
PDG H2A1 H H 0.000 -9.149 2.473 1.380
PDG C5 C CR6 0.000 -5.538 -0.372 2.313
PDG C6 C CR16 0.000 -6.826 -0.679 2.710
PDG H6 H H 0.000 -6.989 -1.460 3.442
PDG N1 N NRD6 0.000 -7.861 -0.031 2.209
PDG C5A C CH2 0.000 -4.364 -1.117 2.894
PDG H5A1 H H 0.000 -3.702 -0.413 3.402
PDG H5A2 H H 0.000 -3.817 -1.616 2.092
PDG OP4 O O2 0.000 -4.833 -2.091 3.829
PDG P P P 0.000 -3.534 -2.845 4.407
PDG OP1 O OP -0.666 -2.570 -1.827 4.976
PDG OP2 O OP -0.666 -3.953 -3.807 5.497
PDG OP3 O OP -0.666 -2.858 -3.611 3.291
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
PDG OXT n/a CA START
PDG CA OXT CAA .
PDG OA CA . .
PDG CAA CA NA .
PDG HAA CAA . .
PDG CBA CAA CGA .
PDG HBA1 CBA . .
PDG HBA2 CBA . .
PDG CGA CBA CDA .
PDG HGA1 CGA . .
PDG HGA2 CGA . .
PDG CDA CGA OE1 .
PDG OE2 CDA . .
PDG OE1 CDA . .
PDG NA CAA C4A .
PDG HNA NA . .
PDG C4A NA C4 .
PDG H4A1 C4A . .
PDG H4A2 C4A . .
PDG C4 C4A C5 .
PDG C3 C4 C2 .
PDG O3 C3 HO3 .
PDG HO3 O3 . .
PDG C2 C3 C2A .
PDG C2A C2 H2A1 .
PDG H2A3 C2A . .
PDG H2A2 C2A . .
PDG H2A1 C2A . .
PDG C5 C4 C5A .
PDG C6 C5 N1 .
PDG H6 C6 . .
PDG N1 C6 . .
PDG C5A C5 OP4 .
PDG H5A1 C5A . .
PDG H5A2 C5A . .
PDG OP4 C5A P .
PDG P OP4 OP3 .
PDG OP1 P . .
PDG OP2 P . .
PDG OP3 P . END
PDG 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
PDG N1 C2 double 1.350 0.020
PDG N1 C6 single 1.337 0.020
PDG C2A C2 single 1.506 0.020
PDG C2 C3 single 1.487 0.020
PDG H2A1 C2A single 1.059 0.020
PDG H2A2 C2A single 1.059 0.020
PDG H2A3 C2A single 1.059 0.020
PDG O3 C3 single 1.362 0.020
PDG C3 C4 double 1.487 0.020
PDG HO3 O3 single 0.967 0.020
PDG C4 C4A single 1.511 0.020
PDG C5 C4 single 1.487 0.020
PDG C4A NA single 1.450 0.020
PDG H4A1 C4A single 1.092 0.020
PDG H4A2 C4A single 1.092 0.020
PDG C6 C5 double 1.390 0.020
PDG C5A C5 single 1.511 0.020
PDG H6 C6 single 1.083 0.020
PDG OP4 C5A single 1.426 0.020
PDG H5A1 C5A single 1.092 0.020
PDG H5A2 C5A single 1.092 0.020
PDG P OP4 single 1.610 0.020
PDG OP1 P deloc 1.510 0.020
PDG OP2 P deloc 1.510 0.020
PDG OP3 P deloc 1.510 0.020
PDG NA CAA single 1.450 0.020
PDG HNA NA single 1.010 0.020
PDG CBA CAA single 1.524 0.020
PDG CAA CA single 1.500 0.020
PDG HAA CAA single 1.099 0.020
PDG CGA CBA single 1.524 0.020
PDG HBA1 CBA single 1.092 0.020
PDG HBA2 CBA single 1.092 0.020
PDG CDA CGA single 1.510 0.020
PDG HGA1 CGA single 1.092 0.020
PDG HGA2 CGA single 1.092 0.020
PDG OE1 CDA deloc 1.250 0.020
PDG OE2 CDA deloc 1.250 0.020
PDG OA CA deloc 1.250 0.020
PDG CA 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
PDG OXT CA OA 123.000 3.000
PDG OXT CA CAA 118.500 3.000
PDG OA CA CAA 118.500 3.000
PDG CA CAA HAA 108.810 3.000
PDG CA CAA CBA 109.470 3.000
PDG CA CAA NA 111.600 3.000
PDG HAA CAA CBA 108.340 3.000
PDG HAA CAA NA 108.550 3.000
PDG CBA CAA NA 110.000 3.000
PDG CAA CBA HBA1 109.470 3.000
PDG CAA CBA HBA2 109.470 3.000
PDG CAA CBA CGA 111.000 3.000
PDG HBA1 CBA HBA2 107.900 3.000
PDG HBA1 CBA CGA 109.470 3.000
PDG HBA2 CBA CGA 109.470 3.000
PDG CBA CGA HGA1 109.470 3.000
PDG CBA CGA HGA2 109.470 3.000
PDG CBA CGA CDA 109.470 3.000
PDG HGA1 CGA HGA2 107.900 3.000
PDG HGA1 CGA CDA 109.470 3.000
PDG HGA2 CGA CDA 109.470 3.000
PDG CGA CDA OE2 118.500 3.000
PDG CGA CDA OE1 118.500 3.000
PDG OE2 CDA OE1 123.000 3.000
PDG CAA NA HNA 118.500 3.000
PDG CAA NA C4A 120.000 3.000
PDG HNA NA C4A 118.500 3.000
PDG NA C4A H4A1 109.470 3.000
PDG NA C4A H4A2 109.470 3.000
PDG NA C4A C4 109.500 3.000
PDG H4A1 C4A H4A2 107.900 3.000
PDG H4A1 C4A C4 109.470 3.000
PDG H4A2 C4A C4 109.470 3.000
PDG C4A C4 C3 120.000 3.000
PDG C4A C4 C5 120.000 3.000
PDG C3 C4 C5 120.000 3.000
PDG C4 C3 O3 120.000 3.000
PDG C4 C3 C2 120.000 3.000
PDG O3 C3 C2 120.000 3.000
PDG C3 O3 HO3 109.470 3.000
PDG C3 C2 C2A 120.000 3.000
PDG C3 C2 N1 120.000 3.000
PDG C2A C2 N1 120.000 3.000
PDG C2 C2A H2A3 109.470 3.000
PDG C2 C2A H2A2 109.470 3.000
PDG C2 C2A H2A1 109.470 3.000
PDG H2A3 C2A H2A2 109.470 3.000
PDG H2A3 C2A H2A1 109.470 3.000
PDG H2A2 C2A H2A1 109.470 3.000
PDG C4 C5 C6 120.000 3.000
PDG C4 C5 C5A 120.000 3.000
PDG C6 C5 C5A 120.000 3.000
PDG C5 C6 H6 120.000 3.000
PDG C5 C6 N1 120.000 3.000
PDG H6 C6 N1 120.000 3.000
PDG C6 N1 C2 120.000 3.000
PDG C5 C5A H5A1 109.470 3.000
PDG C5 C5A H5A2 109.470 3.000
PDG C5 C5A OP4 109.470 3.000
PDG H5A1 C5A H5A2 107.900 3.000
PDG H5A1 C5A OP4 109.470 3.000
PDG H5A2 C5A OP4 109.470 3.000
PDG C5A OP4 P 120.500 3.000
PDG OP4 P OP1 108.200 3.000
PDG OP4 P OP2 108.200 3.000
PDG OP4 P OP3 108.200 3.000
PDG OP1 P OP2 119.900 3.000
PDG OP1 P OP3 119.900 3.000
PDG 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
PDG var_1 OXT CA CAA NA 179.992 20.000 3
PDG var_2 CA CAA CBA CGA -174.955 20.000 3
PDG var_3 CAA CBA CGA CDA -179.966 20.000 3
PDG var_4 CBA CGA CDA OE1 -179.978 20.000 3
PDG var_5 CA CAA NA C4A 84.984 20.000 3
PDG var_6 CAA NA C4A C4 -179.957 20.000 3
PDG var_7 NA C4A C4 C5 89.916 20.000 2
PDG CONST_1 C4A C4 C3 C2 180.000 0.000 0
PDG var_8 C4 C3 O3 HO3 90.044 20.000 1
PDG CONST_2 C4 C3 C2 C2A 180.000 0.000 0
PDG var_9 C3 C2 C2A H2A1 -90.278 20.000 1
PDG CONST_3 C4A C4 C5 C5A 0.000 0.000 0
PDG CONST_4 C4 C5 C6 N1 0.000 0.000 0
PDG CONST_5 C5 C6 N1 C2 0.000 0.000 0
PDG CONST_6 C6 N1 C2 C3 0.000 0.000 0
PDG var_10 C4 C5 C5A OP4 -179.990 20.000 2
PDG var_11 C5 C5A OP4 P 179.962 20.000 1
PDG var_12 C5A OP4 P OP3 -65.055 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
PDG chir_01 CAA NA CBA CA 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
PDG plan-1 N1 0.020
PDG plan-1 C2 0.020
PDG plan-1 C6 0.020
PDG plan-1 C3 0.020
PDG plan-1 C4 0.020
PDG plan-1 C5 0.020
PDG plan-1 C2A 0.020
PDG plan-1 O3 0.020
PDG plan-1 C4A 0.020
PDG plan-1 C5A 0.020
PDG plan-1 H6 0.020
PDG plan-2 NA 0.020
PDG plan-2 C4A 0.020
PDG plan-2 CAA 0.020
PDG plan-2 HNA 0.020
PDG plan-3 CDA 0.020
PDG plan-3 CGA 0.020
PDG plan-3 OE1 0.020
PDG plan-3 OE2 0.020
PDG plan-4 CA 0.020
PDG plan-4 CAA 0.020
PDG plan-4 OA 0.020
PDG plan-4 OXT 0.020
# ------------------------------------------------------
|
