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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
ADY ADY '3'-OXO-ADENOSINE ' non-polymer 30 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ADY
#
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
ADY "O3'" O O 0.000 0.000 0.000 0.000
ADY "C3'" C C 0.000 -1.186 0.174 0.152
ADY "C4'" C CH1 0.000 -1.863 1.216 1.021
ADY "H4'" H H 0.000 -1.594 1.055 2.074
ADY "C5'" C CH2 0.000 -1.431 2.618 0.585
ADY "H5'1" H H 0.000 -1.787 2.808 -0.430
ADY "H5'2" H H 0.000 -0.342 2.686 0.606
ADY "O5'" O OH1 0.000 -1.988 3.587 1.475
ADY "HO5'" H H 0.000 -1.715 4.473 1.198
ADY "C2'" C CH1 0.000 -2.329 -0.608 -0.485
ADY "H2'" H H 0.000 -2.542 -0.233 -1.496
ADY "O2'" O OH1 0.000 -2.033 -2.007 -0.517
ADY "HO2'" H H 0.000 -1.242 -2.156 -1.052
ADY "C1'" C CH1 0.000 -3.509 -0.307 0.472
ADY "H1'" H H 0.000 -3.472 -0.964 1.353
ADY "O4'" O O2 0.000 -3.283 1.069 0.853
ADY N9 N NR5 0.000 -4.790 -0.447 -0.224
ADY C4 C CR56 0.000 -5.516 -1.603 -0.364
ADY C5 C CR56 0.000 -6.658 -1.255 -1.104
ADY N7 N NRD5 0.000 -6.578 0.072 -1.363
ADY C8 C CR15 0.000 -5.481 0.548 -0.851
ADY H8 H H 0.000 -5.164 1.582 -0.913
ADY N3 N NRD6 0.000 -5.356 -2.863 0.024
ADY C2 C CR16 0.000 -6.257 -3.776 -0.274
ADY H2 H H 0.000 -6.095 -4.794 0.056
ADY N1 N NRD6 0.000 -7.349 -3.497 -0.961
ADY C6 C CR6 0.000 -7.595 -2.264 -1.391
ADY N6 N NH2 0.000 -8.743 -1.980 -2.111
ADY HN62 H H 0.000 -8.927 -1.037 -2.438
ADY HN61 H H 0.000 -9.414 -2.713 -2.320
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
ADY "O3'" n/a "C3'" START
ADY "C3'" "O3'" "C2'" .
ADY "C4'" "C3'" "C5'" .
ADY "H4'" "C4'" . .
ADY "C5'" "C4'" "O5'" .
ADY "H5'1" "C5'" . .
ADY "H5'2" "C5'" . .
ADY "O5'" "C5'" "HO5'" .
ADY "HO5'" "O5'" . .
ADY "C2'" "C3'" "C1'" .
ADY "H2'" "C2'" . .
ADY "O2'" "C2'" "HO2'" .
ADY "HO2'" "O2'" . .
ADY "C1'" "C2'" N9 .
ADY "H1'" "C1'" . .
ADY "O4'" "C1'" . .
ADY N9 "C1'" C4 .
ADY C4 N9 N3 .
ADY C5 C4 N7 .
ADY N7 C5 C8 .
ADY C8 N7 H8 .
ADY H8 C8 . .
ADY N3 C4 C2 .
ADY C2 N3 N1 .
ADY H2 C2 . .
ADY N1 C2 C6 .
ADY C6 N1 N6 .
ADY N6 C6 HN61 .
ADY HN62 N6 . .
ADY HN61 N6 . END
ADY "C4'" "O4'" . ADD
ADY N9 C8 . ADD
ADY C5 C6 . 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
ADY "O5'" "C5'" single 1.432 0.020
ADY "HO5'" "O5'" single 0.967 0.020
ADY "C5'" "C4'" single 1.524 0.020
ADY "H5'1" "C5'" single 1.092 0.020
ADY "H5'2" "C5'" single 1.092 0.020
ADY "C4'" "O4'" single 1.426 0.020
ADY "C4'" "C3'" single 1.500 0.020
ADY "H4'" "C4'" single 1.099 0.020
ADY "O4'" "C1'" single 1.426 0.020
ADY "C3'" "O3'" double 1.220 0.020
ADY "C2'" "C3'" single 1.500 0.020
ADY "O2'" "C2'" single 1.432 0.020
ADY "C1'" "C2'" single 1.524 0.020
ADY "H2'" "C2'" single 1.099 0.020
ADY "HO2'" "O2'" single 0.967 0.020
ADY N9 "C1'" single 1.485 0.020
ADY "H1'" "C1'" single 1.099 0.020
ADY N9 C8 single 1.337 0.020
ADY C4 N9 single 1.337 0.020
ADY C8 N7 double 1.350 0.020
ADY H8 C8 single 1.083 0.020
ADY N7 C5 single 1.350 0.020
ADY C5 C6 single 1.490 0.020
ADY C5 C4 double 1.490 0.020
ADY N6 C6 single 1.355 0.020
ADY C6 N1 double 1.350 0.020
ADY HN61 N6 single 1.010 0.020
ADY HN62 N6 single 1.010 0.020
ADY N1 C2 single 1.337 0.020
ADY C2 N3 double 1.337 0.020
ADY H2 C2 single 1.083 0.020
ADY N3 C4 single 1.355 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
ADY "O3'" "C3'" "C4'" 120.500 3.000
ADY "O3'" "C3'" "C2'" 120.500 3.000
ADY "C4'" "C3'" "C2'" 120.000 3.000
ADY "C3'" "C4'" "H4'" 108.810 3.000
ADY "C3'" "C4'" "C5'" 109.470 3.000
ADY "C3'" "C4'" "O4'" 109.470 3.000
ADY "H4'" "C4'" "C5'" 108.340 3.000
ADY "H4'" "C4'" "O4'" 109.470 3.000
ADY "C5'" "C4'" "O4'" 109.470 3.000
ADY "C4'" "C5'" "H5'1" 109.470 3.000
ADY "C4'" "C5'" "H5'2" 109.470 3.000
ADY "C4'" "C5'" "O5'" 109.470 3.000
ADY "H5'1" "C5'" "H5'2" 107.900 3.000
ADY "H5'1" "C5'" "O5'" 109.470 3.000
ADY "H5'2" "C5'" "O5'" 109.470 3.000
ADY "C5'" "O5'" "HO5'" 109.470 3.000
ADY "C3'" "C2'" "H2'" 108.810 3.000
ADY "C3'" "C2'" "O2'" 109.470 3.000
ADY "C3'" "C2'" "C1'" 109.470 3.000
ADY "H2'" "C2'" "O2'" 109.470 3.000
ADY "H2'" "C2'" "C1'" 108.340 3.000
ADY "O2'" "C2'" "C1'" 109.470 3.000
ADY "C2'" "O2'" "HO2'" 109.470 3.000
ADY "C2'" "C1'" "H1'" 108.340 3.000
ADY "C2'" "C1'" "O4'" 109.470 3.000
ADY "C2'" "C1'" N9 109.470 3.000
ADY "H1'" "C1'" "O4'" 109.470 3.000
ADY "H1'" "C1'" N9 109.470 3.000
ADY "O4'" "C1'" N9 109.470 3.000
ADY "C1'" "O4'" "C4'" 111.800 3.000
ADY "C1'" N9 C4 126.000 3.000
ADY "C1'" N9 C8 126.000 3.000
ADY C4 N9 C8 108.000 3.000
ADY N9 C4 C5 108.000 3.000
ADY N9 C4 N3 132.000 3.000
ADY C5 C4 N3 120.000 3.000
ADY C4 C5 N7 108.000 3.000
ADY C4 C5 C6 120.000 3.000
ADY N7 C5 C6 132.000 3.000
ADY C5 N7 C8 108.000 3.000
ADY N7 C8 H8 126.000 3.000
ADY N7 C8 N9 108.000 3.000
ADY H8 C8 N9 126.000 3.000
ADY C4 N3 C2 120.000 3.000
ADY N3 C2 H2 120.000 3.000
ADY N3 C2 N1 120.000 3.000
ADY H2 C2 N1 120.000 3.000
ADY C2 N1 C6 120.000 3.000
ADY N1 C6 N6 120.000 3.000
ADY N1 C6 C5 120.000 3.000
ADY N6 C6 C5 120.000 3.000
ADY C6 N6 HN62 120.000 3.000
ADY C6 N6 HN61 120.000 3.000
ADY HN62 N6 HN61 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
ADY var_1 "O3'" "C3'" "C4'" "C5'" 60.000 20.000 3
ADY var_2 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
ADY var_3 "C3'" "C4'" "C5'" "O5'" -175.335 20.000 3
ADY var_4 "C4'" "C5'" "O5'" "HO5'" -179.979 20.000 1
ADY var_5 "O3'" "C3'" "C2'" "C1'" 150.000 20.000 3
ADY var_6 "C3'" "C2'" "O2'" "HO2'" -61.460 20.000 1
ADY var_7 "C3'" "C2'" "C1'" N9 150.000 20.000 3
ADY var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
ADY var_9 "C2'" "C1'" N9 C4 87.428 20.000 1
ADY CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
ADY CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
ADY CONST_3 N9 C4 C5 N7 0.000 0.000 0
ADY CONST_4 C4 C5 C6 N1 0.000 0.000 0
ADY CONST_5 C4 C5 N7 C8 0.000 0.000 0
ADY CONST_6 C5 N7 C8 N9 0.000 0.000 0
ADY CONST_7 N9 C4 N3 C2 180.000 0.000 0
ADY CONST_8 C4 N3 C2 N1 0.000 0.000 0
ADY CONST_9 N3 C2 N1 C6 0.000 0.000 0
ADY CONST_10 C2 N1 C6 N6 180.000 0.000 0
ADY CONST_11 N1 C6 N6 HN61 -0.017 0.000 0
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
ADY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
ADY chir_02 "C2'" "C3'" "O2'" "C1'" negativ
ADY chir_03 "C1'" "O4'" "C2'" N9 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
ADY plan-1 "C3'" 0.020
ADY plan-1 "C4'" 0.020
ADY plan-1 "O3'" 0.020
ADY plan-1 "C2'" 0.020
ADY plan-2 N9 0.020
ADY plan-2 "C1'" 0.020
ADY plan-2 C8 0.020
ADY plan-2 C4 0.020
ADY plan-2 N7 0.020
ADY plan-2 H8 0.020
ADY plan-2 C5 0.020
ADY plan-2 C6 0.020
ADY plan-2 N1 0.020
ADY plan-2 C2 0.020
ADY plan-2 N3 0.020
ADY plan-2 N6 0.020
ADY plan-2 H2 0.020
ADY plan-2 HN62 0.020
ADY plan-2 HN61 0.020
ADY plan-3 N6 0.020
ADY plan-3 C6 0.020
ADY plan-3 HN61 0.020
ADY plan-3 HN62 0.020
# ------------------------------------------------------
|
