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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
AYD AYD '. ' non-polymer 41 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AYD
#
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
AYD O3B O OP -0.666 0.000 0.000 0.000
AYD PB P P 0.000 -0.025 0.633 1.374
AYD O1B O OP -0.666 0.326 2.101 1.259
AYD O2B O OP -0.666 0.984 -0.057 2.265
AYD O3A O O2 0.000 -1.497 0.481 2.008
AYD PA P P 0.000 -2.440 1.547 1.257
AYD O1A O OP -0.500 -2.185 1.490 -0.203
AYD O2A O OP -0.500 -2.142 2.911 1.758
AYD O7 O O2 0.000 -3.984 1.195 1.545
AYD C7 C CH2 0.000 -4.767 2.096 0.761
AYD H71 H H 0.000 -4.528 1.961 -0.296
AYD H72 H H 0.000 -4.542 3.124 1.056
AYD C6 C CH2 0.000 -6.253 1.813 0.991
AYD H61 H H 0.000 -6.490 1.948 2.048
AYD H62 H H 0.000 -6.477 0.786 0.697
AYD C5 C C1 0.000 -7.080 2.765 0.164
AYD H5 H H 0.000 -6.922 3.828 0.247
AYD C4 C C 0.000 -7.996 2.297 -0.663
AYD CM4 C CH3 0.000 -8.727 3.236 -1.587
AYD HM43 H H 0.000 -8.553 2.952 -2.592
AYD HM42 H H 0.000 -9.766 3.195 -1.384
AYD HM41 H H 0.000 -8.378 4.225 -1.435
AYD N3 N NH1 0.000 -8.286 0.938 -0.680
AYD HN3 H H 0.000 -7.746 0.299 -0.114
AYD "C7'" C CH2 0.000 -9.375 0.433 -1.520
AYD "H7'1" H H 0.000 -9.170 0.674 -2.565
AYD "H7'2" H H 0.000 -10.314 0.901 -1.217
AYD "C5'" C CR6 0.000 -9.481 -1.061 -1.358
AYD "C6'" C CR16 0.000 -8.938 -1.915 -2.299
AYD "H6'" H H 0.000 -8.427 -1.520 -3.167
AYD "N1'" N NRD6 0.000 -9.051 -3.224 -2.125
AYD "C4'" C CR6 0.000 -10.125 -1.618 -0.252
AYD "N4'" N NH2 0.000 -10.686 -0.804 0.720
AYD "H4'2" H H 0.000 -10.627 0.207 0.643
AYD "H4'1" H H 0.000 -11.162 -1.208 1.521
AYD "N3'" N NRD6 0.000 -10.202 -2.942 -0.150
AYD "C2'" C CR6 0.000 -9.670 -3.719 -1.072
AYD CM2 C CH3 0.000 -9.773 -5.214 -0.917
AYD HM23 H H 0.000 -10.660 -5.455 -0.392
AYD HM22 H H 0.000 -9.795 -5.668 -1.874
AYD HM21 H H 0.000 -8.935 -5.571 -0.376
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
AYD O3B n/a PB START
AYD PB O3B O3A .
AYD O1B PB . .
AYD O2B PB . .
AYD O3A PB PA .
AYD PA O3A O7 .
AYD O1A PA . .
AYD O2A PA . .
AYD O7 PA C7 .
AYD C7 O7 C6 .
AYD H71 C7 . .
AYD H72 C7 . .
AYD C6 C7 C5 .
AYD H61 C6 . .
AYD H62 C6 . .
AYD C5 C6 C4 .
AYD H5 C5 . .
AYD C4 C5 N3 .
AYD CM4 C4 HM41 .
AYD HM43 CM4 . .
AYD HM42 CM4 . .
AYD HM41 CM4 . .
AYD N3 C4 "C7'" .
AYD HN3 N3 . .
AYD "C7'" N3 "C5'" .
AYD "H7'1" "C7'" . .
AYD "H7'2" "C7'" . .
AYD "C5'" "C7'" "C4'" .
AYD "C6'" "C5'" "N1'" .
AYD "H6'" "C6'" . .
AYD "N1'" "C6'" . .
AYD "C4'" "C5'" "N3'" .
AYD "N4'" "C4'" "H4'1" .
AYD "H4'2" "N4'" . .
AYD "H4'1" "N4'" . .
AYD "N3'" "C4'" "C2'" .
AYD "C2'" "N3'" CM2 .
AYD CM2 "C2'" HM21 .
AYD HM23 CM2 . .
AYD HM22 CM2 . .
AYD HM21 CM2 . END
AYD "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
AYD "N1'" "C2'" double 1.350 0.020
AYD "N1'" "C6'" single 1.337 0.020
AYD CM2 "C2'" single 1.506 0.020
AYD "C2'" "N3'" single 1.350 0.020
AYD HM21 CM2 single 1.059 0.020
AYD HM22 CM2 single 1.059 0.020
AYD HM23 CM2 single 1.059 0.020
AYD "N3'" "C4'" double 1.350 0.020
AYD "N4'" "C4'" single 1.355 0.020
AYD "C4'" "C5'" single 1.487 0.020
AYD "H4'1" "N4'" single 1.010 0.020
AYD "H4'2" "N4'" single 1.010 0.020
AYD "C6'" "C5'" double 1.390 0.020
AYD "C5'" "C7'" single 1.511 0.020
AYD "H6'" "C6'" single 1.083 0.020
AYD "C7'" N3 single 1.450 0.020
AYD "H7'1" "C7'" single 1.092 0.020
AYD "H7'2" "C7'" single 1.092 0.020
AYD N3 C4 single 1.330 0.020
AYD HN3 N3 single 1.010 0.020
AYD C4 C5 double 1.340 0.020
AYD C5 C6 single 1.510 0.020
AYD H5 C5 single 1.077 0.020
AYD CM4 C4 single 1.500 0.020
AYD HM41 CM4 single 1.059 0.020
AYD HM42 CM4 single 1.059 0.020
AYD HM43 CM4 single 1.059 0.020
AYD C6 C7 single 1.524 0.020
AYD H61 C6 single 1.092 0.020
AYD H62 C6 single 1.092 0.020
AYD C7 O7 single 1.426 0.020
AYD H71 C7 single 1.092 0.020
AYD H72 C7 single 1.092 0.020
AYD O7 PA single 1.610 0.020
AYD O1A PA deloc 1.510 0.020
AYD O2A PA deloc 1.510 0.020
AYD PA O3A single 1.610 0.020
AYD O3A PB single 1.610 0.020
AYD O1B PB deloc 1.510 0.020
AYD O2B PB deloc 1.510 0.020
AYD PB O3B deloc 1.510 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
AYD O3B PB O1B 119.900 3.000
AYD O3B PB O2B 119.900 3.000
AYD O3B PB O3A 108.200 3.000
AYD O1B PB O2B 119.900 3.000
AYD O1B PB O3A 108.200 3.000
AYD O2B PB O3A 108.200 3.000
AYD PB O3A PA 120.500 3.000
AYD O3A PA O1A 108.200 3.000
AYD O3A PA O2A 108.200 3.000
AYD O3A PA O7 102.600 3.000
AYD O1A PA O2A 119.900 3.000
AYD O1A PA O7 108.200 3.000
AYD O2A PA O7 108.200 3.000
AYD PA O7 C7 120.500 3.000
AYD O7 C7 H71 109.470 3.000
AYD O7 C7 H72 109.470 3.000
AYD O7 C7 C6 109.470 3.000
AYD H71 C7 H72 107.900 3.000
AYD H71 C7 C6 109.470 3.000
AYD H72 C7 C6 109.470 3.000
AYD C7 C6 H61 109.470 3.000
AYD C7 C6 H62 109.470 3.000
AYD C7 C6 C5 109.470 3.000
AYD H61 C6 H62 107.900 3.000
AYD H61 C6 C5 109.470 3.000
AYD H62 C6 C5 109.470 3.000
AYD C6 C5 H5 120.000 3.000
AYD C6 C5 C4 120.500 3.000
AYD H5 C5 C4 120.000 3.000
AYD C5 C4 CM4 120.000 3.000
AYD C5 C4 N3 120.000 3.000
AYD CM4 C4 N3 116.500 3.000
AYD C4 CM4 HM43 109.470 3.000
AYD C4 CM4 HM42 109.470 3.000
AYD C4 CM4 HM41 109.470 3.000
AYD HM43 CM4 HM42 109.470 3.000
AYD HM43 CM4 HM41 109.470 3.000
AYD HM42 CM4 HM41 109.470 3.000
AYD C4 N3 HN3 120.000 3.000
AYD C4 N3 "C7'" 121.500 3.000
AYD HN3 N3 "C7'" 118.500 3.000
AYD N3 "C7'" "H7'1" 109.470 3.000
AYD N3 "C7'" "H7'2" 109.470 3.000
AYD N3 "C7'" "C5'" 109.500 3.000
AYD "H7'1" "C7'" "H7'2" 107.900 3.000
AYD "H7'1" "C7'" "C5'" 109.470 3.000
AYD "H7'2" "C7'" "C5'" 109.470 3.000
AYD "C7'" "C5'" "C6'" 120.000 3.000
AYD "C7'" "C5'" "C4'" 120.000 3.000
AYD "C6'" "C5'" "C4'" 120.000 3.000
AYD "C5'" "C6'" "H6'" 120.000 3.000
AYD "C5'" "C6'" "N1'" 120.000 3.000
AYD "H6'" "C6'" "N1'" 120.000 3.000
AYD "C6'" "N1'" "C2'" 120.000 3.000
AYD "C5'" "C4'" "N4'" 120.000 3.000
AYD "C5'" "C4'" "N3'" 120.000 3.000
AYD "N4'" "C4'" "N3'" 120.000 3.000
AYD "C4'" "N4'" "H4'2" 120.000 3.000
AYD "C4'" "N4'" "H4'1" 120.000 3.000
AYD "H4'2" "N4'" "H4'1" 120.000 3.000
AYD "C4'" "N3'" "C2'" 120.000 3.000
AYD "N3'" "C2'" CM2 120.000 3.000
AYD "N3'" "C2'" "N1'" 120.000 3.000
AYD CM2 "C2'" "N1'" 120.000 3.000
AYD "C2'" CM2 HM23 109.470 3.000
AYD "C2'" CM2 HM22 109.470 3.000
AYD "C2'" CM2 HM21 109.470 3.000
AYD HM23 CM2 HM22 109.470 3.000
AYD HM23 CM2 HM21 109.470 3.000
AYD 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
AYD var_1 O3B PB O3A PA -75.013 20.000 1
AYD var_2 PB O3A PA O7 164.984 20.000 1
AYD var_3 O3A PA O7 C7 -174.985 20.000 1
AYD var_4 PA O7 C7 C6 -179.989 20.000 1
AYD var_5 O7 C7 C6 C5 179.988 20.000 3
AYD var_6 C7 C6 C5 C4 125.955 20.000 1
AYD CONST_1 C6 C5 C4 N3 6.024 0.000 0
AYD var_7 C5 C4 CM4 HM41 0.022 20.000 1
AYD CONST_2 C5 C4 N3 "C7'" 180.000 0.000 0
AYD var_8 C4 N3 "C7'" "C5'" 179.983 20.000 3
AYD var_9 N3 "C7'" "C5'" "C4'" 79.703 20.000 2
AYD CONST_3 "C7'" "C5'" "C6'" "N1'" 180.000 0.000 0
AYD CONST_4 "C5'" "C6'" "N1'" "C2'" 0.000 0.000 0
AYD CONST_5 "C6'" "N1'" "C2'" "N3'" 0.000 0.000 0
AYD CONST_6 "C7'" "C5'" "C4'" "N3'" 180.000 0.000 0
AYD CONST_7 "C5'" "C4'" "N4'" "H4'1" 179.440 0.000 0
AYD CONST_8 "C5'" "C4'" "N3'" "C2'" 0.000 0.000 0
AYD CONST_9 "C4'" "N3'" "C2'" CM2 180.000 0.000 0
AYD var_10 "N3'" "C2'" CM2 HM21 -89.944 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
AYD plan-1 "N1'" 0.020
AYD plan-1 "C2'" 0.020
AYD plan-1 "C6'" 0.020
AYD plan-1 "N3'" 0.020
AYD plan-1 "C4'" 0.020
AYD plan-1 "C5'" 0.020
AYD plan-1 CM2 0.020
AYD plan-1 "N4'" 0.020
AYD plan-1 "C7'" 0.020
AYD plan-1 "H6'" 0.020
AYD plan-1 "H4'2" 0.020
AYD plan-1 "H4'1" 0.020
AYD plan-2 "N4'" 0.020
AYD plan-2 "C4'" 0.020
AYD plan-2 "H4'1" 0.020
AYD plan-2 "H4'2" 0.020
AYD plan-3 N3 0.020
AYD plan-3 "C7'" 0.020
AYD plan-3 C4 0.020
AYD plan-3 HN3 0.020
AYD plan-4 C5 0.020
AYD plan-4 C4 0.020
AYD plan-4 C6 0.020
AYD plan-4 H5 0.020
AYD plan-4 N3 0.020
AYD plan-4 CM4 0.020
AYD plan-4 HN3 0.020
# ------------------------------------------------------
|
