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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
AD3 AD3 '3-DEAZA-ADENOSINE ' non-polymer 33 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AD3
#
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
AD3 "O2'" O OH1 0.000 0.000 0.000 0.000
AD3 "HO2'" H H 0.000 0.824 0.505 -0.025
AD3 "C2'" C CH1 0.000 -0.833 0.502 1.047
AD3 "H2'" H H 0.000 -1.083 1.557 0.867
AD3 "C3'" C CH1 0.000 -0.136 0.338 2.419
AD3 "H3'" H H 0.000 -0.040 1.311 2.920
AD3 "O3'" O OH1 0.000 1.147 -0.272 2.260
AD3 "HO3'" H H 0.000 1.541 -0.423 3.130
AD3 "C4'" C CH1 0.000 -1.081 -0.588 3.213
AD3 "H4'" H H 0.000 -0.757 -1.634 3.121
AD3 "C5'" C CH2 0.000 -1.127 -0.173 4.683
AD3 "H5'1" H H 0.000 -1.435 0.872 4.756
AD3 "H5'2" H H 0.000 -0.135 -0.291 5.125
AD3 "O5'" O OH1 0.000 -2.063 -0.997 5.383
AD3 "HO5'" H H 0.000 -2.091 -0.733 6.312
AD3 "C1'" C CH1 0.000 -2.118 -0.343 1.179
AD3 "H1'" H H 0.000 -1.956 -1.351 0.773
AD3 "O4'" O O2 0.000 -2.376 -0.408 2.598
AD3 N9 N NR5 0.000 -3.231 0.312 0.488
AD3 C4 C CR56 0.000 -3.608 0.113 -0.818
AD3 C5 C CR56 0.000 -4.713 0.952 -1.038
AD3 N7 N NRD5 0.000 -4.955 1.600 0.127
AD3 C8 C CR15 0.000 -4.085 1.229 1.021
AD3 H8 H H 0.000 -4.046 1.596 2.039
AD3 C3 C CR16 0.000 -3.151 -0.679 -1.869
AD3 H3 H H 0.000 -2.298 -1.333 -1.734
AD3 C2 C CR16 0.000 -3.794 -0.618 -3.074
AD3 H2 H H 0.000 -3.441 -1.232 -3.894
AD3 N1 N NRD6 0.000 -4.837 0.174 -3.263
AD3 C6 C CR6 0.000 -5.316 0.948 -2.305
AD3 N6 N NH2 0.000 -6.415 1.761 -2.555
AD3 HN62 H H 0.000 -6.792 2.360 -1.825
AD3 HN61 H H 0.000 -6.856 1.768 -3.470
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
AD3 "O2'" n/a "C2'" START
AD3 "HO2'" "O2'" . .
AD3 "C2'" "O2'" "C1'" .
AD3 "H2'" "C2'" . .
AD3 "C3'" "C2'" "C4'" .
AD3 "H3'" "C3'" . .
AD3 "O3'" "C3'" "HO3'" .
AD3 "HO3'" "O3'" . .
AD3 "C4'" "C3'" "C5'" .
AD3 "H4'" "C4'" . .
AD3 "C5'" "C4'" "O5'" .
AD3 "H5'1" "C5'" . .
AD3 "H5'2" "C5'" . .
AD3 "O5'" "C5'" "HO5'" .
AD3 "HO5'" "O5'" . .
AD3 "C1'" "C2'" N9 .
AD3 "H1'" "C1'" . .
AD3 "O4'" "C1'" . .
AD3 N9 "C1'" C4 .
AD3 C4 N9 C3 .
AD3 C5 C4 N7 .
AD3 N7 C5 C8 .
AD3 C8 N7 H8 .
AD3 H8 C8 . .
AD3 C3 C4 C2 .
AD3 H3 C3 . .
AD3 C2 C3 N1 .
AD3 H2 C2 . .
AD3 N1 C2 C6 .
AD3 C6 N1 N6 .
AD3 N6 C6 HN61 .
AD3 HN62 N6 . .
AD3 HN61 N6 . END
AD3 "C4'" "O4'" . ADD
AD3 N9 C8 . ADD
AD3 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
AD3 "O5'" "C5'" single 1.432 0.020
AD3 "HO5'" "O5'" single 0.967 0.020
AD3 "C5'" "C4'" single 1.524 0.020
AD3 "H5'1" "C5'" single 1.092 0.020
AD3 "H5'2" "C5'" single 1.092 0.020
AD3 "C4'" "O4'" single 1.426 0.020
AD3 "C4'" "C3'" single 1.524 0.020
AD3 "H4'" "C4'" single 1.099 0.020
AD3 "O4'" "C1'" single 1.426 0.020
AD3 "O3'" "C3'" single 1.432 0.020
AD3 "C3'" "C2'" single 1.524 0.020
AD3 "H3'" "C3'" single 1.099 0.020
AD3 "HO3'" "O3'" single 0.967 0.020
AD3 "C2'" "O2'" single 1.432 0.020
AD3 "C1'" "C2'" single 1.524 0.020
AD3 "H2'" "C2'" single 1.099 0.020
AD3 "HO2'" "O2'" single 0.967 0.020
AD3 N9 "C1'" single 1.485 0.020
AD3 "H1'" "C1'" single 1.099 0.020
AD3 N9 C8 single 1.337 0.020
AD3 C4 N9 single 1.337 0.020
AD3 C8 N7 double 1.350 0.020
AD3 H8 C8 single 1.083 0.020
AD3 N7 C5 single 1.350 0.020
AD3 C5 C6 single 1.490 0.020
AD3 C5 C4 double 1.490 0.020
AD3 N6 C6 single 1.355 0.020
AD3 C6 N1 double 1.350 0.020
AD3 HN61 N6 single 1.010 0.020
AD3 HN62 N6 single 1.010 0.020
AD3 N1 C2 single 1.337 0.020
AD3 C2 C3 double 1.390 0.020
AD3 H2 C2 single 1.083 0.020
AD3 C3 C4 single 1.390 0.020
AD3 H3 C3 single 1.083 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
AD3 "HO2'" "O2'" "C2'" 109.470 3.000
AD3 "O2'" "C2'" "H2'" 109.470 3.000
AD3 "O2'" "C2'" "C3'" 109.470 3.000
AD3 "O2'" "C2'" "C1'" 109.470 3.000
AD3 "H2'" "C2'" "C3'" 108.340 3.000
AD3 "H2'" "C2'" "C1'" 108.340 3.000
AD3 "C3'" "C2'" "C1'" 111.000 3.000
AD3 "C2'" "C3'" "H3'" 108.340 3.000
AD3 "C2'" "C3'" "O3'" 109.470 3.000
AD3 "C2'" "C3'" "C4'" 111.000 3.000
AD3 "H3'" "C3'" "O3'" 109.470 3.000
AD3 "H3'" "C3'" "C4'" 108.340 3.000
AD3 "O3'" "C3'" "C4'" 109.470 3.000
AD3 "C3'" "O3'" "HO3'" 109.470 3.000
AD3 "C3'" "C4'" "H4'" 108.340 3.000
AD3 "C3'" "C4'" "C5'" 111.000 3.000
AD3 "C3'" "C4'" "O4'" 109.470 3.000
AD3 "H4'" "C4'" "C5'" 108.340 3.000
AD3 "H4'" "C4'" "O4'" 109.470 3.000
AD3 "C5'" "C4'" "O4'" 109.470 3.000
AD3 "C4'" "C5'" "H5'1" 109.470 3.000
AD3 "C4'" "C5'" "H5'2" 109.470 3.000
AD3 "C4'" "C5'" "O5'" 109.470 3.000
AD3 "H5'1" "C5'" "H5'2" 107.900 3.000
AD3 "H5'1" "C5'" "O5'" 109.470 3.000
AD3 "H5'2" "C5'" "O5'" 109.470 3.000
AD3 "C5'" "O5'" "HO5'" 109.470 3.000
AD3 "C2'" "C1'" "H1'" 108.340 3.000
AD3 "C2'" "C1'" "O4'" 109.470 3.000
AD3 "C2'" "C1'" N9 109.470 3.000
AD3 "H1'" "C1'" "O4'" 109.470 3.000
AD3 "H1'" "C1'" N9 109.470 3.000
AD3 "O4'" "C1'" N9 109.470 3.000
AD3 "C1'" "O4'" "C4'" 111.800 3.000
AD3 "C1'" N9 C4 126.000 3.000
AD3 "C1'" N9 C8 126.000 3.000
AD3 C4 N9 C8 108.000 3.000
AD3 N9 C4 C5 108.000 3.000
AD3 N9 C4 C3 132.000 3.000
AD3 C5 C4 C3 120.000 3.000
AD3 C4 C5 N7 108.000 3.000
AD3 C4 C5 C6 120.000 3.000
AD3 N7 C5 C6 132.000 3.000
AD3 C5 N7 C8 108.000 3.000
AD3 N7 C8 H8 126.000 3.000
AD3 N7 C8 N9 108.000 3.000
AD3 H8 C8 N9 126.000 3.000
AD3 C4 C3 H3 120.000 3.000
AD3 C4 C3 C2 120.000 3.000
AD3 H3 C3 C2 120.000 3.000
AD3 C3 C2 H2 120.000 3.000
AD3 C3 C2 N1 120.000 3.000
AD3 H2 C2 N1 120.000 3.000
AD3 C2 N1 C6 120.000 3.000
AD3 N1 C6 N6 120.000 3.000
AD3 N1 C6 C5 120.000 3.000
AD3 N6 C6 C5 120.000 3.000
AD3 C6 N6 HN62 120.000 3.000
AD3 C6 N6 HN61 120.000 3.000
AD3 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
AD3 var_1 "HO2'" "O2'" "C2'" "C1'" -176.176 20.000 1
AD3 var_2 "O2'" "C2'" "C3'" "C4'" -120.000 20.000 3
AD3 var_3 "C2'" "C3'" "O3'" "HO3'" -176.135 20.000 1
AD3 var_4 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
AD3 var_5 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
AD3 var_6 "C3'" "C4'" "C5'" "O5'" 176.852 20.000 3
AD3 var_7 "C4'" "C5'" "O5'" "HO5'" 179.990 20.000 1
AD3 var_8 "O2'" "C2'" "C1'" N9 -90.000 20.000 3
AD3 var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AD3 var_10 "C2'" "C1'" N9 C4 91.554 20.000 1
AD3 CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AD3 CONST_2 "C1'" N9 C4 C3 0.000 0.000 0
AD3 CONST_3 N9 C4 C5 N7 0.000 0.000 0
AD3 CONST_4 C4 C5 C6 N1 0.000 0.000 0
AD3 CONST_5 C4 C5 N7 C8 0.000 0.000 0
AD3 CONST_6 C5 N7 C8 N9 0.000 0.000 0
AD3 CONST_7 N9 C4 C3 C2 180.000 0.000 0
AD3 CONST_8 C4 C3 C2 N1 0.000 0.000 0
AD3 CONST_9 C3 C2 N1 C6 0.000 0.000 0
AD3 CONST_10 C2 N1 C6 N6 180.000 0.000 0
AD3 CONST_11 N1 C6 N6 HN61 -0.015 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
AD3 chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AD3 chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AD3 chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AD3 chir_04 "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
AD3 plan-1 N9 0.020
AD3 plan-1 "C1'" 0.020
AD3 plan-1 C8 0.020
AD3 plan-1 C4 0.020
AD3 plan-1 N7 0.020
AD3 plan-1 H8 0.020
AD3 plan-1 C5 0.020
AD3 plan-1 C6 0.020
AD3 plan-1 N1 0.020
AD3 plan-1 C2 0.020
AD3 plan-1 C3 0.020
AD3 plan-1 N6 0.020
AD3 plan-1 H2 0.020
AD3 plan-1 H3 0.020
AD3 plan-1 HN62 0.020
AD3 plan-1 HN61 0.020
AD3 plan-2 N6 0.020
AD3 plan-2 C6 0.020
AD3 plan-2 HN61 0.020
AD3 plan-2 HN62 0.020
# ------------------------------------------------------
|
