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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
2DA 2DA '2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPH' non-polymer 33 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2DA
#
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
2DA OP2 O OP -0.666 0.000 0.000 0.000
2DA P P P 0.000 -1.129 0.954 -0.326
2DA OP3 O OP -0.666 -0.807 1.697 -1.604
2DA OP1 O OP -0.666 -1.295 1.943 0.807
2DA "O5'" O O2 0.000 -2.494 0.124 -0.516
2DA "C5'" C CH2 0.000 -3.516 1.073 -0.820
2DA "H5'" H H 0.000 -3.254 1.607 -1.736
2DA "H5''" H H 0.000 -3.606 1.786 0.002
2DA "C4'" C CH1 0.000 -4.849 0.345 -1.015
2DA "H4'" H H 0.000 -4.762 -0.412 -1.806
2DA "C3'" C CH2 0.000 -5.978 1.353 -1.347
2DA "H3'1" H H 0.000 -6.054 1.572 -2.414
2DA "H3'2" H H 0.000 -5.892 2.288 -0.790
2DA "C2'" C CH2 0.000 -7.241 0.588 -0.884
2DA "H2'" H H 0.000 -7.741 0.083 -1.714
2DA "H2''" H H 0.000 -7.952 1.242 -0.376
2DA "C1'" C CH1 0.000 -6.705 -0.461 0.108
2DA "H1'" H H 0.000 -6.910 -1.472 -0.270
2DA "O4'" O O2 0.000 -5.287 -0.260 0.223
2DA N9 N NR5 0.000 -7.339 -0.280 1.416
2DA C4 C CR56 0.000 -8.498 -0.877 1.847
2DA C5 C CR56 0.000 -8.717 -0.402 3.149
2DA N7 N NRD5 0.000 -7.696 0.437 3.445
2DA C8 C CR15 0.000 -6.889 0.513 2.428
2DA H8 H H 0.000 -5.991 1.118 2.391
2DA N3 N NRD6 0.000 -9.366 -1.731 1.315
2DA C2 C CR16 0.000 -10.416 -2.133 2.000
2DA H2 H H 0.000 -11.104 -2.829 1.538
2DA N1 N NRD6 0.000 -10.662 -1.719 3.229
2DA C6 C CR6 0.000 -9.849 -0.865 3.843
2DA N6 N NH2 0.000 -10.113 -0.437 5.131
2DA HN62 H H 0.000 -9.490 0.216 5.596
2DA HN61 H H 0.000 -10.934 -0.770 5.627
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
2DA OP2 n/a P START
2DA P OP2 "O5'" .
2DA OP3 P . .
2DA OP1 P . .
2DA "O5'" P "C5'" .
2DA "C5'" "O5'" "C4'" .
2DA "H5'" "C5'" . .
2DA "H5''" "C5'" . .
2DA "C4'" "C5'" "C3'" .
2DA "H4'" "C4'" . .
2DA "C3'" "C4'" "C2'" .
2DA "H3'1" "C3'" . .
2DA "H3'2" "C3'" . .
2DA "C2'" "C3'" "C1'" .
2DA "H2'" "C2'" . .
2DA "H2''" "C2'" . .
2DA "C1'" "C2'" N9 .
2DA "H1'" "C1'" . .
2DA "O4'" "C1'" . .
2DA N9 "C1'" C4 .
2DA C4 N9 N3 .
2DA C5 C4 N7 .
2DA N7 C5 C8 .
2DA C8 N7 H8 .
2DA H8 C8 . .
2DA N3 C4 C2 .
2DA C2 N3 N1 .
2DA H2 C2 . .
2DA N1 C2 C6 .
2DA C6 N1 N6 .
2DA N6 C6 HN61 .
2DA HN62 N6 . .
2DA HN61 N6 . END
2DA "C4'" "O4'" . ADD
2DA N9 C8 . ADD
2DA 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
2DA OP1 P deloc 1.510 0.020
2DA P OP2 deloc 1.510 0.020
2DA OP3 P deloc 1.510 0.020
2DA "O5'" P single 1.610 0.020
2DA "C5'" "O5'" single 1.426 0.020
2DA "C4'" "C5'" single 1.524 0.020
2DA "H5'" "C5'" single 1.092 0.020
2DA "H5''" "C5'" single 1.092 0.020
2DA "C4'" "O4'" single 1.426 0.020
2DA "C3'" "C4'" single 1.524 0.020
2DA "H4'" "C4'" single 1.099 0.020
2DA "O4'" "C1'" single 1.426 0.020
2DA "C2'" "C3'" single 1.524 0.020
2DA "H3'1" "C3'" single 1.092 0.020
2DA "H3'2" "C3'" single 1.092 0.020
2DA "C1'" "C2'" single 1.524 0.020
2DA "H2'" "C2'" single 1.092 0.020
2DA "H2''" "C2'" single 1.092 0.020
2DA N9 "C1'" single 1.485 0.020
2DA "H1'" "C1'" single 1.099 0.020
2DA N9 C8 single 1.337 0.020
2DA C4 N9 single 1.337 0.020
2DA C8 N7 double 1.350 0.020
2DA H8 C8 single 1.083 0.020
2DA N7 C5 single 1.350 0.020
2DA C5 C6 single 1.490 0.020
2DA C5 C4 double 1.490 0.020
2DA N6 C6 single 1.355 0.020
2DA C6 N1 double 1.350 0.020
2DA HN61 N6 single 1.010 0.020
2DA HN62 N6 single 1.010 0.020
2DA N1 C2 single 1.337 0.020
2DA C2 N3 double 1.337 0.020
2DA H2 C2 single 1.083 0.020
2DA 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
2DA OP2 P OP3 119.900 3.000
2DA OP2 P OP1 119.900 3.000
2DA OP2 P "O5'" 108.200 3.000
2DA OP3 P OP1 119.900 3.000
2DA OP3 P "O5'" 108.200 3.000
2DA OP1 P "O5'" 108.200 3.000
2DA P "O5'" "C5'" 120.500 3.000
2DA "O5'" "C5'" "H5'" 109.470 3.000
2DA "O5'" "C5'" "H5''" 109.470 3.000
2DA "O5'" "C5'" "C4'" 109.470 3.000
2DA "H5'" "C5'" "H5''" 107.900 3.000
2DA "H5'" "C5'" "C4'" 109.470 3.000
2DA "H5''" "C5'" "C4'" 109.470 3.000
2DA "C5'" "C4'" "H4'" 108.340 3.000
2DA "C5'" "C4'" "C3'" 109.470 3.000
2DA "C5'" "C4'" "O4'" 109.470 3.000
2DA "H4'" "C4'" "C3'" 108.340 3.000
2DA "H4'" "C4'" "O4'" 109.470 3.000
2DA "C3'" "C4'" "O4'" 109.470 3.000
2DA "C4'" "C3'" "H3'1" 109.470 3.000
2DA "C4'" "C3'" "H3'2" 109.470 3.000
2DA "C4'" "C3'" "C2'" 111.000 3.000
2DA "H3'1" "C3'" "H3'2" 107.900 3.000
2DA "H3'1" "C3'" "C2'" 109.470 3.000
2DA "H3'2" "C3'" "C2'" 109.470 3.000
2DA "C3'" "C2'" "H2'" 109.470 3.000
2DA "C3'" "C2'" "H2''" 109.470 3.000
2DA "C3'" "C2'" "C1'" 111.000 3.000
2DA "H2'" "C2'" "H2''" 107.900 3.000
2DA "H2'" "C2'" "C1'" 109.470 3.000
2DA "H2''" "C2'" "C1'" 109.470 3.000
2DA "C2'" "C1'" "H1'" 108.340 3.000
2DA "C2'" "C1'" "O4'" 109.470 3.000
2DA "C2'" "C1'" N9 109.470 3.000
2DA "H1'" "C1'" "O4'" 109.470 3.000
2DA "H1'" "C1'" N9 109.470 3.000
2DA "O4'" "C1'" N9 109.470 3.000
2DA "C1'" "O4'" "C4'" 111.800 3.000
2DA "C1'" N9 C4 126.000 3.000
2DA "C1'" N9 C8 126.000 3.000
2DA C4 N9 C8 108.000 3.000
2DA N9 C4 C5 108.000 3.000
2DA N9 C4 N3 132.000 3.000
2DA C5 C4 N3 120.000 3.000
2DA C4 C5 N7 108.000 3.000
2DA C4 C5 C6 120.000 3.000
2DA N7 C5 C6 132.000 3.000
2DA C5 N7 C8 108.000 3.000
2DA N7 C8 H8 126.000 3.000
2DA N7 C8 N9 108.000 3.000
2DA H8 C8 N9 126.000 3.000
2DA C4 N3 C2 120.000 3.000
2DA N3 C2 H2 120.000 3.000
2DA N3 C2 N1 120.000 3.000
2DA H2 C2 N1 120.000 3.000
2DA C2 N1 C6 120.000 3.000
2DA N1 C6 N6 120.000 3.000
2DA N1 C6 C5 120.000 3.000
2DA N6 C6 C5 120.000 3.000
2DA C6 N6 HN62 120.000 3.000
2DA C6 N6 HN61 120.000 3.000
2DA 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
2DA var_1 OP2 P "O5'" "C5'" -179.979 20.000 1
2DA var_2 P "O5'" "C5'" "C4'" 179.991 20.000 1
2DA var_3 "O5'" "C5'" "C4'" "C3'" -179.996 20.000 3
2DA var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
2DA var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
2DA var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
2DA var_7 "C3'" "C2'" "C1'" N9 120.000 20.000 3
2DA var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
2DA var_9 "C2'" "C1'" N9 C4 90.217 20.000 1
2DA CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
2DA CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
2DA CONST_3 N9 C4 C5 N7 0.000 0.000 0
2DA CONST_4 C4 C5 C6 N1 0.000 0.000 0
2DA CONST_5 C4 C5 N7 C8 0.000 0.000 0
2DA CONST_6 C5 N7 C8 N9 0.000 0.000 0
2DA CONST_7 N9 C4 N3 C2 180.000 0.000 0
2DA CONST_8 C4 N3 C2 N1 0.000 0.000 0
2DA CONST_9 N3 C2 N1 C6 0.000 0.000 0
2DA CONST_10 C2 N1 C6 N6 180.000 0.000 0
2DA CONST_11 N1 C6 N6 HN61 0.003 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
2DA chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2DA chir_02 "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
2DA plan-1 N9 0.020
2DA plan-1 "C1'" 0.020
2DA plan-1 C8 0.020
2DA plan-1 C4 0.020
2DA plan-1 N7 0.020
2DA plan-1 H8 0.020
2DA plan-1 C5 0.020
2DA plan-1 C6 0.020
2DA plan-1 N1 0.020
2DA plan-1 C2 0.020
2DA plan-1 N3 0.020
2DA plan-1 N6 0.020
2DA plan-1 H2 0.020
2DA plan-1 HN62 0.020
2DA plan-1 HN61 0.020
2DA plan-2 N6 0.020
2DA plan-2 C6 0.020
2DA plan-2 HN61 0.020
2DA plan-2 HN62 0.020
# ------------------------------------------------------
|
