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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
PB5 PB5 'N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDI' non-polymer 42 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PB5
#
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
PB5 O42 O O 0.000 0.000 0.000 0.000
PB5 C9 C C 0.000 -0.698 0.994 0.004
PB5 N10 N NH1 0.000 -0.130 2.217 0.003
PB5 H10 H H 0.000 -0.711 3.043 0.007
PB5 C11 C CH2 0.000 1.329 2.346 -0.003
PB5 H111 H H 0.000 1.733 1.866 -0.897
PB5 H112 H H 0.000 1.741 1.864 0.886
PB5 C12 C CR6 0.000 1.704 3.806 -0.003
PB5 C34 C CR16 0.000 1.878 4.484 -1.194
PB5 H34 H H 0.000 1.747 3.959 -2.133
PB5 N33 N NRD6 0.000 2.201 5.762 -1.202
PB5 C32 C CR16 0.000 2.379 6.440 -0.085
PB5 H32 H H 0.000 2.648 7.488 -0.132
PB5 C31 C CR16 0.000 2.228 5.826 1.145
PB5 H31 H H 0.000 2.376 6.387 2.060
PB5 C30 C CR16 0.000 1.884 4.484 1.193
PB5 H30 H H 0.000 1.758 3.977 2.142
PB5 C3 C CR6 0.000 -2.177 0.863 0.003
PB5 C2 C CR16 0.000 -2.777 -0.398 -0.002
PB5 H2 H H 0.000 -2.177 -1.300 -0.006
PB5 N4 N NRD6 0.000 -2.951 1.943 0.014
PB5 C5 C CR16 0.000 -4.263 1.837 0.008
PB5 H5 H H 0.000 -4.863 2.739 0.008
PB5 N6 N NRD6 0.000 -4.869 0.668 0.004
PB5 C1 C CR6 0.000 -4.172 -0.464 0.000
PB5 C15 C C 0.000 -4.865 -1.777 -0.006
PB5 O41 O O 0.000 -4.219 -2.805 -0.011
PB5 N16 N NH1 0.000 -6.212 -1.827 -0.005
PB5 H16 H H 0.000 -6.750 -0.972 -0.001
PB5 C17 C CH2 0.000 -6.897 -3.123 -0.011
PB5 H171 H H 0.000 -6.610 -3.689 0.877
PB5 H172 H H 0.000 -6.611 -3.681 -0.905
PB5 C18 C CR6 0.000 -8.387 -2.903 -0.009
PB5 C25 C CR16 0.000 -9.083 -2.795 -1.204
PB5 H25 H H 0.000 -8.567 -2.866 -2.153
PB5 C24 C CR16 0.000 -10.453 -2.594 -1.154
PB5 H24 H H 0.000 -11.028 -2.506 -2.068
PB5 C23 C CR16 0.000 -11.077 -2.508 0.076
PB5 H23 H H 0.000 -12.147 -2.351 0.124
PB5 N22 N NRD6 0.000 -10.384 -2.616 1.193
PB5 C21 C CR16 0.000 -9.080 -2.812 1.183
PB5 H21 H H 0.000 -8.545 -2.904 2.121
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
PB5 O42 n/a C9 START
PB5 C9 O42 C3 .
PB5 N10 C9 C11 .
PB5 H10 N10 . .
PB5 C11 N10 C12 .
PB5 H111 C11 . .
PB5 H112 C11 . .
PB5 C12 C11 C34 .
PB5 C34 C12 N33 .
PB5 H34 C34 . .
PB5 N33 C34 C32 .
PB5 C32 N33 C31 .
PB5 H32 C32 . .
PB5 C31 C32 C30 .
PB5 H31 C31 . .
PB5 C30 C31 H30 .
PB5 H30 C30 . .
PB5 C3 C9 N4 .
PB5 C2 C3 H2 .
PB5 H2 C2 . .
PB5 N4 C3 C5 .
PB5 C5 N4 N6 .
PB5 H5 C5 . .
PB5 N6 C5 C1 .
PB5 C1 N6 C15 .
PB5 C15 C1 N16 .
PB5 O41 C15 . .
PB5 N16 C15 C17 .
PB5 H16 N16 . .
PB5 C17 N16 C18 .
PB5 H171 C17 . .
PB5 H172 C17 . .
PB5 C18 C17 C25 .
PB5 C25 C18 C24 .
PB5 H25 C25 . .
PB5 C24 C25 C23 .
PB5 H24 C24 . .
PB5 C23 C24 N22 .
PB5 H23 C23 . .
PB5 N22 C23 C21 .
PB5 C21 N22 H21 .
PB5 H21 C21 . END
PB5 C1 C2 . ADD
PB5 C12 C30 . ADD
PB5 C21 C18 . 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
PB5 C1 C2 double 1.390 0.020
PB5 C1 N6 single 1.350 0.020
PB5 C15 C1 single 1.500 0.020
PB5 C2 C3 single 1.390 0.020
PB5 H2 C2 single 1.083 0.020
PB5 C3 C9 single 1.500 0.020
PB5 N4 C3 double 1.350 0.020
PB5 N6 C5 double 1.337 0.020
PB5 N10 C9 single 1.330 0.020
PB5 C9 O42 double 1.220 0.020
PB5 C12 C11 single 1.511 0.020
PB5 C11 N10 single 1.450 0.020
PB5 H111 C11 single 1.092 0.020
PB5 H112 C11 single 1.092 0.020
PB5 C12 C30 single 1.390 0.020
PB5 C34 C12 double 1.390 0.020
PB5 N16 C15 single 1.330 0.020
PB5 O41 C15 double 1.220 0.020
PB5 C21 C18 single 1.390 0.020
PB5 C21 N22 double 1.337 0.020
PB5 H21 C21 single 1.083 0.020
PB5 C23 C24 double 1.390 0.020
PB5 C24 C25 single 1.390 0.020
PB5 H24 C24 single 1.083 0.020
PB5 C30 C31 double 1.390 0.020
PB5 H30 C30 single 1.083 0.020
PB5 C31 C32 single 1.390 0.020
PB5 H31 C31 single 1.083 0.020
PB5 C32 N33 double 1.337 0.020
PB5 H32 C32 single 1.083 0.020
PB5 N33 C34 single 1.337 0.020
PB5 H34 C34 single 1.083 0.020
PB5 C5 N4 single 1.337 0.020
PB5 H5 C5 single 1.083 0.020
PB5 H10 N10 single 1.010 0.020
PB5 C17 N16 single 1.450 0.020
PB5 H16 N16 single 1.010 0.020
PB5 C18 C17 single 1.511 0.020
PB5 H171 C17 single 1.092 0.020
PB5 H172 C17 single 1.092 0.020
PB5 C25 C18 double 1.390 0.020
PB5 N22 C23 single 1.337 0.020
PB5 H23 C23 single 1.083 0.020
PB5 H25 C25 single 1.083 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
PB5 O42 C9 N10 123.000 3.000
PB5 O42 C9 C3 120.500 3.000
PB5 N10 C9 C3 120.000 3.000
PB5 C9 N10 H10 120.000 3.000
PB5 C9 N10 C11 121.500 3.000
PB5 H10 N10 C11 118.500 3.000
PB5 N10 C11 H111 109.470 3.000
PB5 N10 C11 H112 109.470 3.000
PB5 N10 C11 C12 109.500 3.000
PB5 H111 C11 H112 107.900 3.000
PB5 H111 C11 C12 109.470 3.000
PB5 H112 C11 C12 109.470 3.000
PB5 C11 C12 C34 120.000 3.000
PB5 C11 C12 C30 120.000 3.000
PB5 C34 C12 C30 120.000 3.000
PB5 C12 C34 H34 120.000 3.000
PB5 C12 C34 N33 120.000 3.000
PB5 H34 C34 N33 120.000 3.000
PB5 C34 N33 C32 120.000 3.000
PB5 N33 C32 H32 120.000 3.000
PB5 N33 C32 C31 120.000 3.000
PB5 H32 C32 C31 120.000 3.000
PB5 C32 C31 H31 120.000 3.000
PB5 C32 C31 C30 120.000 3.000
PB5 H31 C31 C30 120.000 3.000
PB5 C31 C30 H30 120.000 3.000
PB5 C31 C30 C12 120.000 3.000
PB5 H30 C30 C12 120.000 3.000
PB5 C9 C3 C2 120.000 3.000
PB5 C9 C3 N4 120.000 3.000
PB5 C2 C3 N4 120.000 3.000
PB5 C3 C2 H2 120.000 3.000
PB5 C3 C2 C1 120.000 3.000
PB5 H2 C2 C1 120.000 3.000
PB5 C3 N4 C5 120.000 3.000
PB5 N4 C5 H5 120.000 3.000
PB5 N4 C5 N6 120.000 3.000
PB5 H5 C5 N6 120.000 3.000
PB5 C5 N6 C1 120.000 3.000
PB5 N6 C1 C15 120.000 3.000
PB5 N6 C1 C2 120.000 3.000
PB5 C15 C1 C2 120.000 3.000
PB5 C1 C15 O41 120.500 3.000
PB5 C1 C15 N16 120.000 3.000
PB5 O41 C15 N16 123.000 3.000
PB5 C15 N16 H16 120.000 3.000
PB5 C15 N16 C17 121.500 3.000
PB5 H16 N16 C17 118.500 3.000
PB5 N16 C17 H171 109.470 3.000
PB5 N16 C17 H172 109.470 3.000
PB5 N16 C17 C18 109.500 3.000
PB5 H171 C17 H172 107.900 3.000
PB5 H171 C17 C18 109.470 3.000
PB5 H172 C17 C18 109.470 3.000
PB5 C17 C18 C25 120.000 3.000
PB5 C17 C18 C21 120.000 3.000
PB5 C25 C18 C21 120.000 3.000
PB5 C18 C25 H25 120.000 3.000
PB5 C18 C25 C24 120.000 3.000
PB5 H25 C25 C24 120.000 3.000
PB5 C25 C24 H24 120.000 3.000
PB5 C25 C24 C23 120.000 3.000
PB5 H24 C24 C23 120.000 3.000
PB5 C24 C23 H23 120.000 3.000
PB5 C24 C23 N22 120.000 3.000
PB5 H23 C23 N22 120.000 3.000
PB5 C23 N22 C21 120.000 3.000
PB5 N22 C21 H21 120.000 3.000
PB5 N22 C21 C18 120.000 3.000
PB5 H21 C21 C18 120.000 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
PB5 CONST_1 O42 C9 N10 C11 0.000 0.000 0
PB5 var_1 C9 N10 C11 C12 179.997 20.000 3
PB5 var_2 N10 C11 C12 C34 -90.261 20.000 2
PB5 CONST_2 C11 C12 C30 C31 180.000 0.000 0
PB5 CONST_3 C11 C12 C34 N33 180.000 0.000 0
PB5 CONST_4 C12 C34 N33 C32 0.000 0.000 0
PB5 CONST_5 C34 N33 C32 C31 0.000 0.000 0
PB5 CONST_6 N33 C32 C31 C30 0.000 0.000 0
PB5 CONST_7 C32 C31 C30 C12 0.000 0.000 0
PB5 var_3 O42 C9 C3 N4 179.715 20.000 1
PB5 CONST_8 C9 C3 C2 C1 180.000 0.000 0
PB5 CONST_9 C9 C3 N4 C5 180.000 0.000 0
PB5 CONST_10 C3 N4 C5 N6 0.000 0.000 0
PB5 CONST_11 N4 C5 N6 C1 0.000 0.000 0
PB5 CONST_12 C5 N6 C1 C15 180.000 0.000 0
PB5 CONST_13 N6 C1 C2 C3 0.000 0.000 0
PB5 var_4 N6 C1 C15 N16 -0.057 20.000 1
PB5 CONST_14 C1 C15 N16 C17 180.000 0.000 0
PB5 var_5 C15 N16 C17 C18 -179.979 20.000 3
PB5 var_6 N16 C17 C18 C25 89.982 20.000 2
PB5 CONST_15 C17 C18 C25 C24 180.000 0.000 0
PB5 CONST_16 C18 C25 C24 C23 0.000 0.000 0
PB5 CONST_17 C25 C24 C23 N22 0.000 0.000 0
PB5 CONST_18 C24 C23 N22 C21 0.000 0.000 0
PB5 CONST_19 C23 N22 C21 C18 0.000 0.000 0
PB5 CONST_20 N22 C21 C18 C17 180.000 0.000 0
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
PB5 plan-1 C1 0.020
PB5 plan-1 C2 0.020
PB5 plan-1 N6 0.020
PB5 plan-1 C15 0.020
PB5 plan-1 C3 0.020
PB5 plan-1 N4 0.020
PB5 plan-1 C5 0.020
PB5 plan-1 H2 0.020
PB5 plan-1 C9 0.020
PB5 plan-1 H5 0.020
PB5 plan-2 C9 0.020
PB5 plan-2 C3 0.020
PB5 plan-2 N10 0.020
PB5 plan-2 O42 0.020
PB5 plan-2 H10 0.020
PB5 plan-3 C12 0.020
PB5 plan-3 C11 0.020
PB5 plan-3 C30 0.020
PB5 plan-3 C34 0.020
PB5 plan-3 C31 0.020
PB5 plan-3 C32 0.020
PB5 plan-3 N33 0.020
PB5 plan-3 H30 0.020
PB5 plan-3 H31 0.020
PB5 plan-3 H32 0.020
PB5 plan-3 H34 0.020
PB5 plan-4 C15 0.020
PB5 plan-4 C1 0.020
PB5 plan-4 N16 0.020
PB5 plan-4 O41 0.020
PB5 plan-4 H16 0.020
PB5 plan-5 C21 0.020
PB5 plan-5 C18 0.020
PB5 plan-5 N22 0.020
PB5 plan-5 H21 0.020
PB5 plan-5 C24 0.020
PB5 plan-5 C23 0.020
PB5 plan-5 C25 0.020
PB5 plan-5 H24 0.020
PB5 plan-5 C17 0.020
PB5 plan-5 H23 0.020
PB5 plan-5 H25 0.020
PB5 plan-6 N10 0.020
PB5 plan-6 C9 0.020
PB5 plan-6 C11 0.020
PB5 plan-6 H10 0.020
PB5 plan-7 N16 0.020
PB5 plan-7 C15 0.020
PB5 plan-7 C17 0.020
PB5 plan-7 H16 0.020
# ------------------------------------------------------
|
