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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
DBM DBM '9-(6-DEOXY-BETA-D-ALLOFURANOSYL)-6-M' non-polymer 36 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DBM
#
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
DBM "O3'" O OH1 0.000 0.000 0.000 0.000
DBM H4 H H 0.000 0.093 -0.611 0.743
DBM "C3'" C CH1 0.000 -0.844 -0.585 -0.993
DBM "H3'" H H 0.000 -0.403 -1.518 -1.371
DBM "C4'" C CH1 0.000 -1.091 0.401 -2.151
DBM "H4'" H H 0.000 -0.578 1.352 -1.948
DBM "C5'" C CH1 0.000 -0.579 -0.197 -3.462
DBM H1 H H 0.000 -1.105 -1.140 -3.664
DBM "C6'" C CH3 0.000 -0.835 0.786 -4.605
DBM "H6'3" H H 0.000 -1.875 0.973 -4.685
DBM "H6'2" H H 0.000 -0.328 1.696 -4.411
DBM "H6'1" H H 0.000 -0.481 0.373 -5.514
DBM "O5'" O OH1 0.000 0.825 -0.448 -3.355
DBM "H5'" H H 0.000 1.288 0.382 -3.177
DBM "C2'" C CH1 0.000 -2.259 -0.849 -0.416
DBM "H2'" H H 0.000 -2.682 -1.777 -0.825
DBM "O2'" O OH1 0.000 -2.228 -0.890 1.012
DBM H3 H H 0.000 -1.730 -1.667 1.301
DBM "C1'" C CH1 0.000 -3.050 0.385 -0.917
DBM "H1'" H H 0.000 -2.869 1.251 -0.265
DBM "O4'" O O2 0.000 -2.509 0.620 -2.234
DBM N9 N NR5 0.000 -4.482 0.088 -0.993
DBM C4 C CR56 0.000 -5.416 0.339 -0.020
DBM N3 N NRD6 0.000 -5.388 0.882 1.189
DBM C2 C CR16 0.000 -6.493 0.991 1.897
DBM H2 H H 0.000 -6.439 1.436 2.883
DBM N1 N NRD6 0.000 -7.664 0.577 1.449
DBM C6 C CR6 0.000 -7.788 0.028 0.254
DBM C7 C CH3 0.000 -9.131 -0.439 -0.244
DBM H73 H H 0.000 -9.893 0.162 0.181
DBM H72 H H 0.000 -9.164 -0.357 -1.299
DBM H71 H H 0.000 -9.280 -1.449 0.037
DBM C5 C CR56 0.000 -6.647 -0.110 -0.539
DBM N7 N NRD5 0.000 -6.399 -0.609 -1.774
DBM C8 C CR15 0.000 -5.130 -0.492 -2.042
DBM H8 H H 0.000 -4.659 -0.809 -2.964
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
DBM "O3'" n/a "C3'" START
DBM H4 "O3'" . .
DBM "C3'" "O3'" "C2'" .
DBM "H3'" "C3'" . .
DBM "C4'" "C3'" "C5'" .
DBM "H4'" "C4'" . .
DBM "C5'" "C4'" "O5'" .
DBM H1 "C5'" . .
DBM "C6'" "C5'" "H6'1" .
DBM "H6'3" "C6'" . .
DBM "H6'2" "C6'" . .
DBM "H6'1" "C6'" . .
DBM "O5'" "C5'" "H5'" .
DBM "H5'" "O5'" . .
DBM "C2'" "C3'" "C1'" .
DBM "H2'" "C2'" . .
DBM "O2'" "C2'" H3 .
DBM H3 "O2'" . .
DBM "C1'" "C2'" N9 .
DBM "H1'" "C1'" . .
DBM "O4'" "C1'" . .
DBM N9 "C1'" C4 .
DBM C4 N9 N3 .
DBM N3 C4 C2 .
DBM C2 N3 N1 .
DBM H2 C2 . .
DBM N1 C2 C6 .
DBM C6 N1 C5 .
DBM C7 C6 H71 .
DBM H73 C7 . .
DBM H72 C7 . .
DBM H71 C7 . .
DBM C5 C6 N7 .
DBM N7 C5 C8 .
DBM C8 N7 H8 .
DBM H8 C8 . END
DBM "C4'" "O4'" . ADD
DBM N9 C8 . ADD
DBM C5 C4 . 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
DBM "O5'" "C5'" single 1.432 0.020
DBM "H5'" "O5'" single 0.967 0.020
DBM "C6'" "C5'" single 1.524 0.020
DBM "C5'" "C4'" single 1.524 0.020
DBM H1 "C5'" single 1.099 0.020
DBM "H6'1" "C6'" single 1.059 0.020
DBM "H6'2" "C6'" single 1.059 0.020
DBM "H6'3" "C6'" single 1.059 0.020
DBM "C4'" "O4'" single 1.426 0.020
DBM "C4'" "C3'" single 1.524 0.020
DBM "H4'" "C4'" single 1.099 0.020
DBM "O4'" "C1'" single 1.426 0.020
DBM N9 "C1'" single 1.485 0.020
DBM "C1'" "C2'" single 1.524 0.020
DBM "H1'" "C1'" single 1.099 0.020
DBM N9 C8 single 1.337 0.020
DBM C4 N9 single 1.337 0.020
DBM C8 N7 double 1.350 0.020
DBM H8 C8 single 1.083 0.020
DBM N7 C5 single 1.350 0.020
DBM C5 C4 double 1.490 0.020
DBM C5 C6 single 1.490 0.020
DBM N3 C4 single 1.355 0.020
DBM C2 N3 double 1.337 0.020
DBM N1 C2 single 1.337 0.020
DBM H2 C2 single 1.083 0.020
DBM C6 N1 double 1.350 0.020
DBM C7 C6 single 1.506 0.020
DBM H71 C7 single 1.059 0.020
DBM H72 C7 single 1.059 0.020
DBM H73 C7 single 1.059 0.020
DBM "O2'" "C2'" single 1.432 0.020
DBM "C2'" "C3'" single 1.524 0.020
DBM "H2'" "C2'" single 1.099 0.020
DBM H3 "O2'" single 0.967 0.020
DBM "C3'" "O3'" single 1.432 0.020
DBM "H3'" "C3'" single 1.099 0.020
DBM H4 "O3'" single 0.967 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
DBM H4 "O3'" "C3'" 109.470 3.000
DBM "O3'" "C3'" "H3'" 109.470 3.000
DBM "O3'" "C3'" "C4'" 109.470 3.000
DBM "O3'" "C3'" "C2'" 109.470 3.000
DBM "H3'" "C3'" "C4'" 108.340 3.000
DBM "H3'" "C3'" "C2'" 108.340 3.000
DBM "C4'" "C3'" "C2'" 111.000 3.000
DBM "C3'" "C4'" "H4'" 108.340 3.000
DBM "C3'" "C4'" "C5'" 111.000 3.000
DBM "C3'" "C4'" "O4'" 109.470 3.000
DBM "H4'" "C4'" "C5'" 108.340 3.000
DBM "H4'" "C4'" "O4'" 109.470 3.000
DBM "C5'" "C4'" "O4'" 109.470 3.000
DBM "C4'" "C5'" H1 108.340 3.000
DBM "C4'" "C5'" "C6'" 111.000 3.000
DBM "C4'" "C5'" "O5'" 109.470 3.000
DBM H1 "C5'" "C6'" 108.340 3.000
DBM H1 "C5'" "O5'" 109.470 3.000
DBM "C6'" "C5'" "O5'" 109.470 3.000
DBM "C5'" "C6'" "H6'3" 109.470 3.000
DBM "C5'" "C6'" "H6'2" 109.470 3.000
DBM "C5'" "C6'" "H6'1" 109.470 3.000
DBM "H6'3" "C6'" "H6'2" 109.470 3.000
DBM "H6'3" "C6'" "H6'1" 109.470 3.000
DBM "H6'2" "C6'" "H6'1" 109.470 3.000
DBM "C5'" "O5'" "H5'" 109.470 3.000
DBM "C3'" "C2'" "H2'" 108.340 3.000
DBM "C3'" "C2'" "O2'" 109.470 3.000
DBM "C3'" "C2'" "C1'" 111.000 3.000
DBM "H2'" "C2'" "O2'" 109.470 3.000
DBM "H2'" "C2'" "C1'" 108.340 3.000
DBM "O2'" "C2'" "C1'" 109.470 3.000
DBM "C2'" "O2'" H3 109.470 3.000
DBM "C2'" "C1'" "H1'" 108.340 3.000
DBM "C2'" "C1'" "O4'" 109.470 3.000
DBM "C2'" "C1'" N9 109.470 3.000
DBM "H1'" "C1'" "O4'" 109.470 3.000
DBM "H1'" "C1'" N9 109.470 3.000
DBM "O4'" "C1'" N9 109.470 3.000
DBM "C1'" "O4'" "C4'" 111.800 3.000
DBM "C1'" N9 C4 126.000 3.000
DBM "C1'" N9 C8 126.000 3.000
DBM C4 N9 C8 108.000 3.000
DBM N9 C4 N3 132.000 3.000
DBM N9 C4 C5 108.000 3.000
DBM N3 C4 C5 120.000 3.000
DBM C4 N3 C2 120.000 3.000
DBM N3 C2 H2 120.000 3.000
DBM N3 C2 N1 120.000 3.000
DBM H2 C2 N1 120.000 3.000
DBM C2 N1 C6 120.000 3.000
DBM N1 C6 C7 120.000 3.000
DBM N1 C6 C5 120.000 3.000
DBM C7 C6 C5 120.000 3.000
DBM C6 C7 H73 109.470 3.000
DBM C6 C7 H72 109.470 3.000
DBM C6 C7 H71 109.470 3.000
DBM H73 C7 H72 109.470 3.000
DBM H73 C7 H71 109.470 3.000
DBM H72 C7 H71 109.470 3.000
DBM C6 C5 N7 132.000 3.000
DBM C6 C5 C4 120.000 3.000
DBM N7 C5 C4 108.000 3.000
DBM C5 N7 C8 108.000 3.000
DBM N7 C8 H8 126.000 3.000
DBM N7 C8 N9 108.000 3.000
DBM H8 C8 N9 126.000 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
DBM var_1 H4 "O3'" "C3'" "C2'" 61.471 20.000 1
DBM var_2 "O3'" "C3'" "C4'" "C5'" 120.000 20.000 3
DBM var_3 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
DBM var_4 "C3'" "C4'" "C5'" "O5'" -60.306 20.000 3
DBM var_5 "C4'" "C5'" "C6'" "H6'1" -179.991 20.000 3
DBM var_6 "C4'" "C5'" "O5'" "H5'" -60.016 20.000 1
DBM var_7 "O3'" "C3'" "C2'" "C1'" 90.000 20.000 3
DBM var_8 "C3'" "C2'" "O2'" H3 -67.258 20.000 1
DBM var_9 "C3'" "C2'" "C1'" N9 150.000 20.000 3
DBM var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DBM var_11 "C2'" "C1'" N9 C4 94.129 20.000 1
DBM CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
DBM CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
DBM CONST_3 N9 C4 N3 C2 180.000 0.000 0
DBM CONST_4 C4 N3 C2 N1 0.000 0.000 0
DBM CONST_5 N3 C2 N1 C6 0.000 0.000 0
DBM CONST_6 C2 N1 C6 C5 0.000 0.000 0
DBM var_12 N1 C6 C7 H71 -89.919 20.000 1
DBM CONST_7 N1 C6 C5 N7 180.000 0.000 0
DBM CONST_8 C6 C5 C4 N9 180.000 0.000 0
DBM CONST_9 C6 C5 N7 C8 180.000 0.000 0
DBM CONST_10 C5 N7 C8 N9 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
DBM chir_01 "C5'" "O5'" "C6'" "C4'" positiv
DBM chir_02 "C4'" "C5'" "O4'" "C3'" negativ
DBM chir_03 "C1'" "O4'" N9 "C2'" negativ
DBM chir_04 "C2'" "C1'" "O2'" "C3'" positiv
DBM chir_05 "C3'" "C4'" "C2'" "O3'" 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
DBM plan-1 N9 0.020
DBM plan-1 "C1'" 0.020
DBM plan-1 C8 0.020
DBM plan-1 C4 0.020
DBM plan-1 N7 0.020
DBM plan-1 H8 0.020
DBM plan-1 C5 0.020
DBM plan-1 C6 0.020
DBM plan-1 N3 0.020
DBM plan-1 C2 0.020
DBM plan-1 N1 0.020
DBM plan-1 H2 0.020
DBM plan-1 C7 0.020
# ------------------------------------------------------
|
