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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
PYI PYI '1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)M' non-polymer 45 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PYI
#
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
PYI O3B O OP -0.666 0.000 0.000 0.000
PYI PB P P 0.000 0.000 0.000 0.000
PYI O1B O OP -0.666 0.000 0.000 0.000
PYI O2B O OP -0.666 0.000 0.000 0.000
PYI O3A O O2 0.000 0.000 0.000 0.000
PYI PA P P 0.000 0.000 0.000 0.000
PYI O1A O OP -0.500 0.000 0.000 0.000
PYI O2A O OP -0.500 0.000 0.000 0.000
PYI OM7 O O2 0.000 0.000 0.000 0.000
PYI CM7 C CH2 0.000 0.000 0.000 0.000
PYI HM71 H H 0.000 0.000 0.000 0.000
PYI HM72 H H 0.000 0.000 0.000 0.000
PYI CM6 C CH2 0.000 0.000 0.000 0.000
PYI HM61 H H 0.000 0.000 0.000 0.000
PYI HM62 H H 0.000 0.000 0.000 0.000
PYI C5 C CR6 0.000 0.000 0.000 0.000
PYI C6 C CR16 0.000 0.000 0.000 0.000
PYI H6 H H 0.000 0.000 0.000 0.000
PYI C1 C CR16 0.000 0.000 0.000 0.000
PYI H1 H H 0.000 0.000 0.000 0.000
PYI C2 C CR16 0.000 0.000 0.000 0.000
PYI H2 H H 0.000 0.000 0.000 0.000
PYI C4 C CR6 0.000 0.000 0.000 0.000
PYI CM4 C CH3 0.000 0.000 0.000 0.000
PYI HM43 H H 0.000 0.000 0.000 0.000
PYI HM42 H H 0.000 0.000 0.000 0.000
PYI HM41 H H 0.000 0.000 0.000 0.000
PYI N3 N NR6 1.000 0.000 0.000 0.000
PYI C7A C CH2 0.000 0.000 0.000 0.000
PYI H7A1 H H 0.000 0.000 0.000 0.000
PYI H7A2 H H 0.000 0.000 0.000 0.000
PYI C5A C CR6 0.000 0.000 0.000 0.000
PYI C6A C CR16 0.000 0.000 0.000 0.000
PYI H6A H H 0.000 0.000 0.000 0.000
PYI N1A N NRD6 0.000 0.000 0.000 0.000
PYI C4A C CR6 0.000 0.000 0.000 0.000
PYI N4A N NH2 0.000 0.000 0.000 0.000
PYI H4A2 H H 0.000 0.000 0.000 0.000
PYI H4A1 H H 0.000 0.000 0.000 0.000
PYI N3A N NRD6 0.000 0.000 0.000 0.000
PYI C2A C CR6 0.000 0.000 0.000 0.000
PYI CM2 C CH3 0.000 0.000 0.000 0.000
PYI HM23 H H 0.000 0.000 0.000 0.000
PYI HM22 H H 0.000 0.000 0.000 0.000
PYI HM21 H H 0.000 0.000 0.000 0.000
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
PYI O3B n/a PB START
PYI PB O3B O3A .
PYI O1B PB . .
PYI O2B PB . .
PYI O3A PB PA .
PYI PA O3A OM7 .
PYI O1A PA . .
PYI O2A PA . .
PYI OM7 PA CM7 .
PYI CM7 OM7 CM6 .
PYI HM71 CM7 . .
PYI HM72 CM7 . .
PYI CM6 CM7 C5 .
PYI HM61 CM6 . .
PYI HM62 CM6 . .
PYI C5 CM6 C4 .
PYI C6 C5 C1 .
PYI H6 C6 . .
PYI C1 C6 C2 .
PYI H1 C1 . .
PYI C2 C1 H2 .
PYI H2 C2 . .
PYI C4 C5 N3 .
PYI CM4 C4 HM41 .
PYI HM43 CM4 . .
PYI HM42 CM4 . .
PYI HM41 CM4 . .
PYI N3 C4 C7A .
PYI C7A N3 C5A .
PYI H7A1 C7A . .
PYI H7A2 C7A . .
PYI C5A C7A C4A .
PYI C6A C5A N1A .
PYI H6A C6A . .
PYI N1A C6A . .
PYI C4A C5A N3A .
PYI N4A C4A H4A1 .
PYI H4A2 N4A . .
PYI H4A1 N4A . .
PYI N3A C4A C2A .
PYI C2A N3A CM2 .
PYI CM2 C2A HM21 .
PYI HM23 CM2 . .
PYI HM22 CM2 . .
PYI HM21 CM2 . END
PYI C2A N1A . ADD
PYI N3 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
PYI CM2 C2A single 1.506 0.020
PYI HM21 CM2 single 1.059 0.020
PYI HM22 CM2 single 1.059 0.020
PYI HM23 CM2 single 1.059 0.020
PYI C2A N1A double 1.350 0.020
PYI C2A N3A single 1.350 0.020
PYI N1A C6A single 1.337 0.020
PYI C6A C5A double 1.390 0.020
PYI H6A C6A single 1.083 0.020
PYI C5A C7A single 1.511 0.020
PYI C4A C5A single 1.487 0.020
PYI C7A N3 single 1.465 0.020
PYI H7A1 C7A single 1.092 0.020
PYI H7A2 C7A single 1.092 0.020
PYI N3 C2 double 1.337 0.020
PYI N3 C4 single 1.410 0.020
PYI C2 C1 single 1.390 0.020
PYI H2 C2 single 1.083 0.020
PYI C1 C6 double 1.390 0.020
PYI H1 C1 single 1.083 0.020
PYI C6 C5 single 1.390 0.020
PYI H6 C6 single 1.083 0.020
PYI C5 CM6 single 1.511 0.020
PYI C4 C5 double 1.487 0.020
PYI CM6 CM7 single 1.524 0.020
PYI HM61 CM6 single 1.092 0.020
PYI HM62 CM6 single 1.092 0.020
PYI CM7 OM7 single 1.426 0.020
PYI HM71 CM7 single 1.092 0.020
PYI HM72 CM7 single 1.092 0.020
PYI OM7 PA single 1.610 0.020
PYI O1A PA deloc 1.510 0.020
PYI O2A PA deloc 1.510 0.020
PYI PA O3A single 1.610 0.020
PYI O3A PB single 1.610 0.020
PYI O1B PB deloc 1.510 0.020
PYI O2B PB deloc 1.510 0.020
PYI PB O3B deloc 1.510 0.020
PYI CM4 C4 single 1.506 0.020
PYI HM41 CM4 single 1.059 0.020
PYI HM42 CM4 single 1.059 0.020
PYI HM43 CM4 single 1.059 0.020
PYI N4A C4A single 1.355 0.020
PYI N3A C4A double 1.350 0.020
PYI H4A1 N4A single 1.010 0.020
PYI H4A2 N4A single 1.010 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
PYI O3B PB O1B 119.900 3.000
PYI O3B PB O2B 119.900 3.000
PYI O3B PB O3A 108.200 3.000
PYI O1B PB O2B 119.900 3.000
PYI O1B PB O3A 108.200 3.000
PYI O2B PB O3A 108.200 3.000
PYI PB O3A PA 120.500 3.000
PYI O3A PA O1A 108.200 3.000
PYI O3A PA O2A 108.200 3.000
PYI O3A PA OM7 102.600 3.000
PYI O1A PA O2A 119.900 3.000
PYI O1A PA OM7 108.200 3.000
PYI O2A PA OM7 108.200 3.000
PYI PA OM7 CM7 120.500 3.000
PYI OM7 CM7 HM71 109.470 3.000
PYI OM7 CM7 HM72 109.470 3.000
PYI OM7 CM7 CM6 109.470 3.000
PYI HM71 CM7 HM72 107.900 3.000
PYI HM71 CM7 CM6 109.470 3.000
PYI HM72 CM7 CM6 109.470 3.000
PYI CM7 CM6 HM61 109.470 3.000
PYI CM7 CM6 HM62 109.470 3.000
PYI CM7 CM6 C5 109.470 3.000
PYI HM61 CM6 HM62 107.900 3.000
PYI HM61 CM6 C5 109.470 3.000
PYI HM62 CM6 C5 109.470 3.000
PYI CM6 C5 C6 120.000 3.000
PYI CM6 C5 C4 120.000 3.000
PYI C6 C5 C4 120.000 3.000
PYI C5 C6 H6 120.000 3.000
PYI C5 C6 C1 120.000 3.000
PYI H6 C6 C1 120.000 3.000
PYI C6 C1 H1 120.000 3.000
PYI C6 C1 C2 120.000 3.000
PYI H1 C1 C2 120.000 3.000
PYI C1 C2 H2 120.000 3.000
PYI C1 C2 N3 120.000 3.000
PYI H2 C2 N3 120.000 3.000
PYI C5 C4 CM4 120.000 3.000
PYI C5 C4 N3 120.000 3.000
PYI CM4 C4 N3 120.000 3.000
PYI C4 CM4 HM43 109.470 3.000
PYI C4 CM4 HM42 109.470 3.000
PYI C4 CM4 HM41 109.470 3.000
PYI HM43 CM4 HM42 109.470 3.000
PYI HM43 CM4 HM41 109.470 3.000
PYI HM42 CM4 HM41 109.470 3.000
PYI C4 N3 C7A 120.000 3.000
PYI C4 N3 C2 120.000 3.000
PYI C7A N3 C2 120.000 3.000
PYI N3 C7A H7A1 109.470 3.000
PYI N3 C7A H7A2 109.470 3.000
PYI N3 C7A C5A 109.500 3.000
PYI H7A1 C7A H7A2 107.900 3.000
PYI H7A1 C7A C5A 109.470 3.000
PYI H7A2 C7A C5A 109.470 3.000
PYI C7A C5A C6A 120.000 3.000
PYI C7A C5A C4A 120.000 3.000
PYI C6A C5A C4A 120.000 3.000
PYI C5A C6A H6A 120.000 3.000
PYI C5A C6A N1A 120.000 3.000
PYI H6A C6A N1A 120.000 3.000
PYI C6A N1A C2A 120.000 3.000
PYI C5A C4A N4A 120.000 3.000
PYI C5A C4A N3A 120.000 3.000
PYI N4A C4A N3A 120.000 3.000
PYI C4A N4A H4A2 120.000 3.000
PYI C4A N4A H4A1 120.000 3.000
PYI H4A2 N4A H4A1 120.000 3.000
PYI C4A N3A C2A 120.000 3.000
PYI N3A C2A CM2 120.000 3.000
PYI N3A C2A N1A 120.000 3.000
PYI CM2 C2A N1A 120.000 3.000
PYI C2A CM2 HM23 109.470 3.000
PYI C2A CM2 HM22 109.470 3.000
PYI C2A CM2 HM21 109.470 3.000
PYI HM23 CM2 HM22 109.470 3.000
PYI HM23 CM2 HM21 109.470 3.000
PYI HM22 CM2 HM21 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
PYI var_1 O3B PB O3A PA 0.000 20.000 1
PYI var_2 PB O3A PA OM7 0.000 20.000 1
PYI var_3 O3A PA OM7 CM7 0.000 20.000 1
PYI var_4 PA OM7 CM7 CM6 0.000 20.000 1
PYI var_5 OM7 CM7 CM6 C5 0.000 20.000 3
PYI var_6 CM7 CM6 C5 C4 0.000 20.000 2
PYI CONST_1 CM6 C5 C6 C1 0.000 0.000 0
PYI CONST_2 C5 C6 C1 C2 0.000 0.000 0
PYI CONST_3 C6 C1 C2 N3 0.000 0.000 0
PYI CONST_4 CM6 C5 C4 N3 0.000 0.000 0
PYI var_7 C5 C4 CM4 HM41 0.000 20.000 1
PYI CONST_5 C5 C4 N3 C7A 0.000 0.000 0
PYI CONST_6 C4 N3 C2 C1 0.000 0.000 0
PYI var_8 C4 N3 C7A C5A 0.000 20.000 1
PYI var_9 N3 C7A C5A C4A 0.000 20.000 2
PYI CONST_7 C7A C5A C6A N1A 0.000 0.000 0
PYI CONST_8 C5A C6A N1A C2A 0.000 0.000 0
PYI CONST_9 C7A C5A C4A N3A 0.000 0.000 0
PYI CONST_10 C5A C4A N4A H4A1 0.000 0.000 0
PYI CONST_11 C5A C4A N3A C2A 0.000 0.000 0
PYI CONST_12 C4A N3A C2A CM2 0.000 0.000 0
PYI CONST_13 N3A C2A N1A C6A 0.000 0.000 0
PYI var_10 N3A C2A CM2 HM21 0.000 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
PYI plan-1 C2A 0.020
PYI plan-1 CM2 0.020
PYI plan-1 N1A 0.020
PYI plan-1 N3A 0.020
PYI plan-1 C6A 0.020
PYI plan-1 C5A 0.020
PYI plan-1 C4A 0.020
PYI plan-1 H6A 0.020
PYI plan-1 C7A 0.020
PYI plan-1 N4A 0.020
PYI plan-1 H4A2 0.020
PYI plan-1 H4A1 0.020
PYI plan-2 N3 0.020
PYI plan-2 C7A 0.020
PYI plan-2 C2 0.020
PYI plan-2 C4 0.020
PYI plan-2 C1 0.020
PYI plan-2 C6 0.020
PYI plan-2 C5 0.020
PYI plan-2 H2 0.020
PYI plan-2 H1 0.020
PYI plan-2 H6 0.020
PYI plan-2 CM6 0.020
PYI plan-2 CM4 0.020
PYI plan-3 N4A 0.020
PYI plan-3 C4A 0.020
PYI plan-3 H4A1 0.020
PYI plan-3 H4A2 0.020
# ------------------------------------------------------
|
