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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
AD2 AD2 '2'-DEOXY-ADENOSINE-3'-5'-DIPHOSPHATE' non-polymer 37 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AD2
#
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
AD2 O6P O OP -0.666 0.000 0.000 0.000
AD2 P2 P P 0.000 -0.377 -0.632 1.322
AD2 O5P O OP -0.666 0.949 -1.117 1.867
AD2 O4P O OP -0.666 -1.464 -1.680 1.243
AD2 "O3'" O O2 0.000 -0.725 0.650 2.240
AD2 "C3'" C CH1 0.000 -1.846 1.436 1.891
AD2 "H3'" H H 0.000 -1.701 1.891 0.902
AD2 "C2'" C CH2 0.000 -3.119 0.620 1.914
AD2 "H2'2" H H 0.000 -3.116 -0.138 2.700
AD2 "H2'1" H H 0.000 -3.327 0.144 0.953
AD2 "C4'" C CH1 0.000 -2.146 2.507 2.927
AD2 "H4'" H H 0.000 -1.978 2.097 3.933
AD2 "C5'" C CH2 0.000 -1.320 3.768 2.755
AD2 "H5'1" H H 0.000 -1.509 4.204 1.772
AD2 "H5'2" H H 0.000 -0.258 3.531 2.849
AD2 "O5'" O O2 0.000 -1.689 4.693 3.761
AD2 P1 P P 0.000 -0.947 6.132 3.799
AD2 OP2 O OP -0.666 -1.128 6.665 2.394
AD2 OP1 O OP -0.666 -1.404 7.058 4.905
AD2 OP3 O OP -0.666 0.518 5.756 3.843
AD2 "O4'" O O2 0.000 -3.540 2.815 2.766
AD2 "C1'" C CH1 0.000 -4.193 1.659 2.212
AD2 "H1'" H H 0.000 -4.879 1.248 2.966
AD2 N9 N NR5 0.000 -4.973 2.057 1.038
AD2 C8 C CR15 0.000 -4.654 3.055 0.154
AD2 H8 H H 0.000 -3.766 3.670 0.234
AD2 N7 N NRD5 0.000 -5.549 3.181 -0.802
AD2 C5 C CR56 0.000 -6.492 2.222 -0.529
AD2 C4 C CR56 0.000 -6.153 1.512 0.611
AD2 C6 C CR6 0.000 -7.673 1.857 -1.169
AD2 N6 N NH2 0.000 -8.093 2.524 -2.332
AD2 H62 H H 0.000 -8.748 3.304 -2.281
AD2 H61 H H 0.000 -7.752 2.242 -3.250
AD2 N1 N NRD6 0.000 -8.415 0.848 -0.656
AD2 C2 C CR16 0.000 -7.959 0.243 0.467
AD2 H2 H H 0.000 -8.577 -0.560 0.850
AD2 N3 N NRD6 0.000 -6.837 0.504 1.174
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
AD2 O6P n/a P2 START
AD2 P2 O6P "O3'" .
AD2 O5P P2 . .
AD2 O4P P2 . .
AD2 "O3'" P2 "C3'" .
AD2 "C3'" "O3'" "C4'" .
AD2 "H3'" "C3'" . .
AD2 "C2'" "C3'" "H2'1" .
AD2 "H2'2" "C2'" . .
AD2 "H2'1" "C2'" . .
AD2 "C4'" "C3'" "O4'" .
AD2 "H4'" "C4'" . .
AD2 "C5'" "C4'" "O5'" .
AD2 "H5'1" "C5'" . .
AD2 "H5'2" "C5'" . .
AD2 "O5'" "C5'" P1 .
AD2 P1 "O5'" OP3 .
AD2 OP2 P1 . .
AD2 OP1 P1 . .
AD2 OP3 P1 . .
AD2 "O4'" "C4'" "C1'" .
AD2 "C1'" "O4'" N9 .
AD2 "H1'" "C1'" . .
AD2 N9 "C1'" C8 .
AD2 C8 N9 N7 .
AD2 H8 C8 . .
AD2 N7 C8 C5 .
AD2 C5 N7 C6 .
AD2 C4 C5 . .
AD2 C6 C5 N1 .
AD2 N6 C6 H61 .
AD2 H62 N6 . .
AD2 H61 N6 . .
AD2 N1 C6 C2 .
AD2 C2 N1 N3 .
AD2 H2 C2 . .
AD2 N3 C2 . END
AD2 N9 C4 . ADD
AD2 C4 N3 . ADD
AD2 "C2'" "C1'" . 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
AD2 OP1 P1 deloc 1.510 0.020
AD2 OP2 P1 deloc 1.510 0.020
AD2 P1 "O5'" single 1.610 0.020
AD2 OP3 P1 deloc 1.510 0.020
AD2 "O5'" "C5'" single 1.426 0.020
AD2 O5P P2 deloc 1.510 0.020
AD2 O4P P2 deloc 1.510 0.020
AD2 P2 O6P deloc 1.510 0.020
AD2 "O3'" P2 single 1.610 0.020
AD2 N9 C4 single 1.337 0.020
AD2 C8 N9 single 1.337 0.020
AD2 N9 "C1'" single 1.485 0.020
AD2 C4 N3 double 1.355 0.020
AD2 C4 C5 single 1.490 0.020
AD2 N3 C2 single 1.337 0.020
AD2 C2 N1 double 1.337 0.020
AD2 H2 C2 single 1.083 0.020
AD2 N1 C6 single 1.350 0.020
AD2 N6 C6 single 1.355 0.020
AD2 C6 C5 double 1.490 0.020
AD2 H61 N6 single 1.010 0.020
AD2 H62 N6 single 1.010 0.020
AD2 C5 N7 single 1.350 0.020
AD2 N7 C8 double 1.350 0.020
AD2 H8 C8 single 1.083 0.020
AD2 "C2'" "C1'" single 1.524 0.020
AD2 "C2'" "C3'" single 1.524 0.020
AD2 "H2'1" "C2'" single 1.092 0.020
AD2 "H2'2" "C2'" single 1.092 0.020
AD2 "C5'" "C4'" single 1.524 0.020
AD2 "H5'1" "C5'" single 1.092 0.020
AD2 "H5'2" "C5'" single 1.092 0.020
AD2 "O4'" "C4'" single 1.426 0.020
AD2 "C4'" "C3'" single 1.524 0.020
AD2 "H4'" "C4'" single 1.099 0.020
AD2 "C1'" "O4'" single 1.426 0.020
AD2 "H1'" "C1'" single 1.099 0.020
AD2 "C3'" "O3'" single 1.426 0.020
AD2 "H3'" "C3'" single 1.099 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
AD2 O6P P2 O5P 119.900 3.000
AD2 O6P P2 O4P 119.900 3.000
AD2 O6P P2 "O3'" 108.200 3.000
AD2 O5P P2 O4P 119.900 3.000
AD2 O5P P2 "O3'" 108.200 3.000
AD2 O4P P2 "O3'" 108.200 3.000
AD2 P2 "O3'" "C3'" 120.500 3.000
AD2 "O3'" "C3'" "H3'" 109.470 3.000
AD2 "O3'" "C3'" "C2'" 109.470 3.000
AD2 "O3'" "C3'" "C4'" 109.470 3.000
AD2 "H3'" "C3'" "C2'" 108.340 3.000
AD2 "H3'" "C3'" "C4'" 108.340 3.000
AD2 "C2'" "C3'" "C4'" 111.000 3.000
AD2 "C3'" "C2'" "H2'2" 109.470 3.000
AD2 "C3'" "C2'" "H2'1" 109.470 3.000
AD2 "C3'" "C2'" "C1'" 111.000 3.000
AD2 "H2'2" "C2'" "H2'1" 107.900 3.000
AD2 "H2'2" "C2'" "C1'" 109.470 3.000
AD2 "H2'1" "C2'" "C1'" 109.470 3.000
AD2 "C3'" "C4'" "H4'" 108.340 3.000
AD2 "C3'" "C4'" "C5'" 111.000 3.000
AD2 "C3'" "C4'" "O4'" 109.470 3.000
AD2 "H4'" "C4'" "C5'" 108.340 3.000
AD2 "H4'" "C4'" "O4'" 109.470 3.000
AD2 "C5'" "C4'" "O4'" 109.470 3.000
AD2 "C4'" "C5'" "H5'1" 109.470 3.000
AD2 "C4'" "C5'" "H5'2" 109.470 3.000
AD2 "C4'" "C5'" "O5'" 109.470 3.000
AD2 "H5'1" "C5'" "H5'2" 107.900 3.000
AD2 "H5'1" "C5'" "O5'" 109.470 3.000
AD2 "H5'2" "C5'" "O5'" 109.470 3.000
AD2 "C5'" "O5'" P1 120.500 3.000
AD2 "O5'" P1 OP2 108.200 3.000
AD2 "O5'" P1 OP1 108.200 3.000
AD2 "O5'" P1 OP3 108.200 3.000
AD2 OP2 P1 OP1 119.900 3.000
AD2 OP2 P1 OP3 119.900 3.000
AD2 OP1 P1 OP3 119.900 3.000
AD2 "C4'" "O4'" "C1'" 111.800 3.000
AD2 "O4'" "C1'" "H1'" 109.470 3.000
AD2 "O4'" "C1'" N9 109.470 3.000
AD2 "O4'" "C1'" "C2'" 109.470 3.000
AD2 "H1'" "C1'" N9 109.470 3.000
AD2 "H1'" "C1'" "C2'" 108.340 3.000
AD2 N9 "C1'" "C2'" 109.470 3.000
AD2 "C1'" N9 C8 126.000 3.000
AD2 "C1'" N9 C4 126.000 3.000
AD2 C8 N9 C4 108.000 3.000
AD2 N9 C8 H8 126.000 3.000
AD2 N9 C8 N7 108.000 3.000
AD2 H8 C8 N7 126.000 3.000
AD2 C8 N7 C5 108.000 3.000
AD2 N7 C5 C4 108.000 3.000
AD2 N7 C5 C6 132.000 3.000
AD2 C4 C5 C6 120.000 3.000
AD2 C5 C4 N9 108.000 3.000
AD2 C5 C4 N3 120.000 3.000
AD2 N9 C4 N3 132.000 3.000
AD2 C5 C6 N6 120.000 3.000
AD2 C5 C6 N1 120.000 3.000
AD2 N6 C6 N1 120.000 3.000
AD2 C6 N6 H62 120.000 3.000
AD2 C6 N6 H61 120.000 3.000
AD2 H62 N6 H61 120.000 3.000
AD2 C6 N1 C2 120.000 3.000
AD2 N1 C2 H2 120.000 3.000
AD2 N1 C2 N3 120.000 3.000
AD2 H2 C2 N3 120.000 3.000
AD2 C2 N3 C4 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
AD2 var_1 O6P P2 "O3'" "C3'" 65.687 20.000 1
AD2 var_2 P2 "O3'" "C3'" "C4'" 173.426 20.000 1
AD2 var_3 "O3'" "C3'" "C2'" "C1'" 150.000 20.000 3
AD2 var_4 "C3'" "C2'" "C1'" "O4'" -30.000 20.000 3
AD2 var_5 "O3'" "C3'" "C4'" "O4'" -150.000 20.000 3
AD2 var_6 "C3'" "C4'" "C5'" "O5'" 179.534 20.000 3
AD2 var_7 "C4'" "C5'" "O5'" P1 179.969 20.000 1
AD2 var_8 "C5'" "O5'" P1 OP3 -54.207 20.000 1
AD2 var_9 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
AD2 var_10 "C4'" "O4'" "C1'" N9 -120.000 20.000 1
AD2 var_11 "O4'" "C1'" N9 C8 32.955 20.000 1
AD2 CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
AD2 CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
AD2 CONST_3 N9 C8 N7 C5 0.000 0.000 0
AD2 CONST_4 C8 N7 C5 C6 180.000 0.000 0
AD2 CONST_5 N7 C5 C4 N9 0.000 0.000 0
AD2 CONST_6 C5 C4 N3 C2 0.000 0.000 0
AD2 CONST_7 N7 C5 C6 N1 180.000 0.000 0
AD2 CONST_8 C5 C6 N6 H61 85.363 0.000 0
AD2 CONST_9 C5 C6 N1 C2 0.000 0.000 0
AD2 CONST_10 C6 N1 C2 N3 0.000 0.000 0
AD2 CONST_11 N1 C2 N3 C4 0.000 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
AD2 chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AD2 chir_02 "C1'" N9 "C2'" "O4'" negativ
AD2 chir_03 "C3'" "C2'" "C4'" "O3'" negativ
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
AD2 plan-1 N9 0.020
AD2 plan-1 C4 0.020
AD2 plan-1 C8 0.020
AD2 plan-1 "C1'" 0.020
AD2 plan-1 N7 0.020
AD2 plan-1 N3 0.020
AD2 plan-1 C5 0.020
AD2 plan-1 C2 0.020
AD2 plan-1 N1 0.020
AD2 plan-1 C6 0.020
AD2 plan-1 H2 0.020
AD2 plan-1 N6 0.020
AD2 plan-1 H8 0.020
AD2 plan-1 H62 0.020
AD2 plan-1 H61 0.020
AD2 plan-2 N6 0.020
AD2 plan-2 C6 0.020
AD2 plan-2 H61 0.020
AD2 plan-2 H62 0.020
# ------------------------------------------------------
|
