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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
3AD 3AD '3'-DEOXYADENOSINE ' non-polymer 31 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_3AD
#
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
3AD "O2'" O OH1 0.000 0.000 0.000 0.000
3AD "HO2'" H H 0.000 0.831 0.493 -0.033
3AD "C2'" C CH1 0.000 -0.799 0.486 1.080
3AD "H2'" H H 0.000 -1.038 1.549 0.932
3AD "C3'" C CH2 0.000 -0.072 0.277 2.430
3AD "H3'1" H H 0.000 0.057 1.214 2.975
3AD "H3'2" H H 0.000 0.899 -0.205 2.302
3AD "C4'" C CH1 0.000 -1.012 -0.656 3.222
3AD "H4'" H H 0.000 -0.706 -1.704 3.096
3AD "C5'" C CH2 0.000 -1.016 -0.279 4.705
3AD "H5'1" H H 0.000 -1.306 0.768 4.812
3AD "H5'2" H H 0.000 -0.015 -0.422 5.118
3AD "O5'" O OH1 0.000 -1.945 -1.107 5.404
3AD "HO5'" H H 0.000 -1.948 -0.867 6.341
3AD "C1'" C CH1 0.000 -2.093 -0.343 1.221
3AD "H1'" H H 0.000 -1.955 -1.343 0.786
3AD "O4'" O O2 0.000 -2.317 -0.443 2.644
3AD N9 N NR5 0.000 -3.213 0.343 0.575
3AD C4 C CR56 0.000 -3.623 0.183 -0.724
3AD C5 C CR56 0.000 -4.720 1.043 -0.895
3AD N7 N NRD5 0.000 -4.925 1.666 0.291
3AD C8 C CR15 0.000 -4.040 1.259 1.154
3AD H8 H H 0.000 -3.970 1.598 2.180
3AD N3 N NRD6 0.000 -3.217 -0.556 -1.752
3AD C2 C CR16 0.000 -3.835 -0.488 -2.912
3AD H2 H H 0.000 -3.478 -1.103 -3.729
3AD N1 N NRD6 0.000 -4.873 0.301 -3.117
3AD C6 C CR6 0.000 -5.350 1.075 -2.149
3AD N6 N NH2 0.000 -6.439 1.899 -2.374
3AD HN62 H H 0.000 -6.801 2.489 -1.632
3AD HN61 H H 0.000 -6.888 1.923 -3.284
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
3AD "O2'" n/a "C2'" START
3AD "HO2'" "O2'" . .
3AD "C2'" "O2'" "C1'" .
3AD "H2'" "C2'" . .
3AD "C3'" "C2'" "C4'" .
3AD "H3'1" "C3'" . .
3AD "H3'2" "C3'" . .
3AD "C4'" "C3'" "C5'" .
3AD "H4'" "C4'" . .
3AD "C5'" "C4'" "O5'" .
3AD "H5'1" "C5'" . .
3AD "H5'2" "C5'" . .
3AD "O5'" "C5'" "HO5'" .
3AD "HO5'" "O5'" . .
3AD "C1'" "C2'" N9 .
3AD "H1'" "C1'" . .
3AD "O4'" "C1'" . .
3AD N9 "C1'" C4 .
3AD C4 N9 N3 .
3AD C5 C4 N7 .
3AD N7 C5 C8 .
3AD C8 N7 H8 .
3AD H8 C8 . .
3AD N3 C4 C2 .
3AD C2 N3 N1 .
3AD H2 C2 . .
3AD N1 C2 C6 .
3AD C6 N1 N6 .
3AD N6 C6 HN61 .
3AD HN62 N6 . .
3AD HN61 N6 . END
3AD "C4'" "O4'" . ADD
3AD N9 C8 . ADD
3AD 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
3AD "O5'" "C5'" single 1.432 0.020
3AD "HO5'" "O5'" single 0.967 0.020
3AD "C5'" "C4'" single 1.524 0.020
3AD "H5'1" "C5'" single 1.092 0.020
3AD "H5'2" "C5'" single 1.092 0.020
3AD "C4'" "O4'" single 1.426 0.020
3AD "C4'" "C3'" single 1.524 0.020
3AD "H4'" "C4'" single 1.099 0.020
3AD "O4'" "C1'" single 1.426 0.020
3AD "C3'" "C2'" single 1.524 0.020
3AD "H3'1" "C3'" single 1.092 0.020
3AD "H3'2" "C3'" single 1.092 0.020
3AD "C2'" "O2'" single 1.432 0.020
3AD "C1'" "C2'" single 1.524 0.020
3AD "H2'" "C2'" single 1.099 0.020
3AD "HO2'" "O2'" single 0.967 0.020
3AD N9 "C1'" single 1.485 0.020
3AD "H1'" "C1'" single 1.099 0.020
3AD N9 C8 single 1.337 0.020
3AD C4 N9 single 1.337 0.020
3AD C8 N7 double 1.350 0.020
3AD H8 C8 single 1.083 0.020
3AD N7 C5 single 1.350 0.020
3AD C5 C6 single 1.490 0.020
3AD C5 C4 double 1.490 0.020
3AD N6 C6 single 1.355 0.020
3AD C6 N1 double 1.350 0.020
3AD HN61 N6 single 1.010 0.020
3AD HN62 N6 single 1.010 0.020
3AD N1 C2 single 1.337 0.020
3AD C2 N3 double 1.337 0.020
3AD H2 C2 single 1.083 0.020
3AD 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
3AD "HO2'" "O2'" "C2'" 109.470 3.000
3AD "O2'" "C2'" "H2'" 109.470 3.000
3AD "O2'" "C2'" "C3'" 109.470 3.000
3AD "O2'" "C2'" "C1'" 109.470 3.000
3AD "H2'" "C2'" "C3'" 108.340 3.000
3AD "H2'" "C2'" "C1'" 108.340 3.000
3AD "C3'" "C2'" "C1'" 111.000 3.000
3AD "C2'" "C3'" "H3'1" 109.470 3.000
3AD "C2'" "C3'" "H3'2" 109.470 3.000
3AD "C2'" "C3'" "C4'" 111.000 3.000
3AD "H3'1" "C3'" "H3'2" 107.900 3.000
3AD "H3'1" "C3'" "C4'" 109.470 3.000
3AD "H3'2" "C3'" "C4'" 109.470 3.000
3AD "C3'" "C4'" "H4'" 108.340 3.000
3AD "C3'" "C4'" "C5'" 109.470 3.000
3AD "C3'" "C4'" "O4'" 109.470 3.000
3AD "H4'" "C4'" "C5'" 108.340 3.000
3AD "H4'" "C4'" "O4'" 109.470 3.000
3AD "C5'" "C4'" "O4'" 109.470 3.000
3AD "C4'" "C5'" "H5'1" 109.470 3.000
3AD "C4'" "C5'" "H5'2" 109.470 3.000
3AD "C4'" "C5'" "O5'" 109.470 3.000
3AD "H5'1" "C5'" "H5'2" 107.900 3.000
3AD "H5'1" "C5'" "O5'" 109.470 3.000
3AD "H5'2" "C5'" "O5'" 109.470 3.000
3AD "C5'" "O5'" "HO5'" 109.470 3.000
3AD "C2'" "C1'" "H1'" 108.340 3.000
3AD "C2'" "C1'" "O4'" 109.470 3.000
3AD "C2'" "C1'" N9 109.470 3.000
3AD "H1'" "C1'" "O4'" 109.470 3.000
3AD "H1'" "C1'" N9 109.470 3.000
3AD "O4'" "C1'" N9 109.470 3.000
3AD "C1'" "O4'" "C4'" 111.800 3.000
3AD "C1'" N9 C4 126.000 3.000
3AD "C1'" N9 C8 126.000 3.000
3AD C4 N9 C8 108.000 3.000
3AD N9 C4 C5 108.000 3.000
3AD N9 C4 N3 132.000 3.000
3AD C5 C4 N3 120.000 3.000
3AD C4 C5 N7 108.000 3.000
3AD C4 C5 C6 120.000 3.000
3AD N7 C5 C6 132.000 3.000
3AD C5 N7 C8 108.000 3.000
3AD N7 C8 H8 126.000 3.000
3AD N7 C8 N9 108.000 3.000
3AD H8 C8 N9 126.000 3.000
3AD C4 N3 C2 120.000 3.000
3AD N3 C2 H2 120.000 3.000
3AD N3 C2 N1 120.000 3.000
3AD H2 C2 N1 120.000 3.000
3AD C2 N1 C6 120.000 3.000
3AD N1 C6 N6 120.000 3.000
3AD N1 C6 C5 120.000 3.000
3AD N6 C6 C5 120.000 3.000
3AD C6 N6 HN62 120.000 3.000
3AD C6 N6 HN61 120.000 3.000
3AD 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
3AD var_1 "HO2'" "O2'" "C2'" "C1'" -176.155 20.000 1
3AD var_2 "O2'" "C2'" "C3'" "C4'" -120.000 20.000 3
3AD var_3 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
3AD var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
3AD var_5 "C3'" "C4'" "C5'" "O5'" 176.884 20.000 3
3AD var_6 "C4'" "C5'" "O5'" "HO5'" -179.885 20.000 1
3AD var_7 "O2'" "C2'" "C1'" N9 -90.000 20.000 3
3AD var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
3AD var_9 "C2'" "C1'" N9 C4 91.458 20.000 1
3AD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
3AD CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
3AD CONST_3 N9 C4 C5 N7 0.000 0.000 0
3AD CONST_4 C4 C5 C6 N1 0.000 0.000 0
3AD CONST_5 C4 C5 N7 C8 0.000 0.000 0
3AD CONST_6 C5 N7 C8 N9 0.000 0.000 0
3AD CONST_7 N9 C4 N3 C2 180.000 0.000 0
3AD CONST_8 C4 N3 C2 N1 0.000 0.000 0
3AD CONST_9 N3 C2 N1 C6 0.000 0.000 0
3AD CONST_10 C2 N1 C6 N6 180.000 0.000 0
3AD CONST_11 N1 C6 N6 HN61 0.001 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
3AD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
3AD chir_02 "C2'" "C3'" "O2'" "C1'" negativ
3AD 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
3AD plan-1 N9 0.020
3AD plan-1 "C1'" 0.020
3AD plan-1 C8 0.020
3AD plan-1 C4 0.020
3AD plan-1 N7 0.020
3AD plan-1 H8 0.020
3AD plan-1 C5 0.020
3AD plan-1 C6 0.020
3AD plan-1 N1 0.020
3AD plan-1 C2 0.020
3AD plan-1 N3 0.020
3AD plan-1 N6 0.020
3AD plan-1 H2 0.020
3AD plan-1 HN62 0.020
3AD plan-1 HN61 0.020
3AD plan-2 N6 0.020
3AD plan-2 C6 0.020
3AD plan-2 HN61 0.020
3AD plan-2 HN62 0.020
# ------------------------------------------------------
|
