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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
SOS SOS '"[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(F' DNA 53 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SOS
#
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
SOS OP3 O OP -0.666 0.000 0.000 0.000
SOS P P P 0.000 -1.142 0.165 -0.978
SOS OP2 O OP -0.666 -1.889 -1.146 -0.865
SOS OP1 O OP -0.666 -0.732 0.557 -2.381
SOS "O5'" O O2 0.000 -2.110 1.224 -0.228
SOS "C5'" C CH2 0.000 -2.541 0.931 1.090
SOS "H5'" H H 0.000 -1.676 0.838 1.750
SOS "H5''" H H 0.000 -3.104 -0.005 1.096
SOS "C4'" C CH1 0.000 -3.432 2.065 1.576
SOS "H4'" H H 0.000 -2.846 2.994 1.589
SOS "C6'" C CH2 0.000 -4.673 2.277 0.698
SOS "H6'2" H H 0.000 -4.957 1.353 0.189
SOS "H6'1" H H 0.000 -4.502 3.061 -0.043
SOS "C3'" C CH1 0.000 -4.000 1.823 2.972
SOS "H3'" H H 0.000 -4.371 0.793 3.064
SOS "C2'" C CH2 0.000 -5.155 2.814 3.032
SOS "H2'" H H 0.000 -4.813 3.837 3.197
SOS "H2''" H H 0.000 -5.887 2.549 3.798
SOS "C1'" C CH1 0.000 -5.800 2.706 1.650
SOS "H1'" H H 0.000 -6.186 3.689 1.346
SOS N9 N NH1 0.000 -6.873 1.741 1.647
SOS HN9 H H 0.000 -6.911 1.056 2.388
SOS C4 C CR6 0.000 -7.811 1.719 0.709
SOS N3 N NRD6 0.000 -7.754 2.662 -0.308
SOS C2 C CR6 0.000 -8.662 2.662 -1.240
SOS N2 N NH2 0.000 -8.659 3.568 -2.269
SOS HN22 H H 0.000 -9.513 3.770 -2.774
SOS HN21 H H 0.000 -7.802 4.040 -2.531
SOS N1 N NR16 0.000 -9.694 1.743 -1.254
SOS HN1 H H 0.000 -10.389 1.791 -2.027
SOS C6 C CR6 0.000 -9.847 0.766 -0.297
SOS O6 O O 0.000 -10.757 -0.057 -0.294
SOS C5 C CR6 0.000 -8.796 0.790 0.755
SOS N7 N N 0.000 -8.902 -0.163 1.731
SOS C8 C C1 0.000 -9.045 0.222 3.060
SOS H8 H H 0.000 -9.065 1.282 3.249
SOS O8 O O 0.000 -9.152 -0.505 4.043
SOS C9 C CH2 0.000 -8.865 -1.576 1.372
SOS H91 H H 0.000 -9.292 -1.686 0.373
SOS H92 H H 0.000 -9.477 -2.126 2.091
SOS C10 C CR6 0.000 -7.466 -2.122 1.383
SOS C15 C CR16 0.000 -6.700 -2.073 0.225
SOS H15 H H 0.000 -7.109 -1.643 -0.681
SOS C11 C CR16 0.000 -6.952 -2.670 2.552
SOS H11 H H 0.000 -7.556 -2.703 3.450
SOS C12 C CR16 0.000 -5.652 -3.177 2.563
SOS H12 H H 0.000 -5.246 -3.606 3.470
SOS C13 C CR16 0.000 -4.876 -3.132 1.404
SOS H13 H H 0.000 -3.867 -3.525 1.412
SOS C14 C CR16 0.000 -5.401 -2.580 0.236
SOS H14 H H 0.000 -4.799 -2.545 -0.664
SOS "O3'" O OH1 0.000 -3.034 2.093 3.970
SOS "HO3'" H H 0.000 -3.496 2.526 4.707
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
SOS OP3 n/a P START
SOS P OP3 "O5'" .
SOS OP2 P . .
SOS OP1 P . .
SOS "O5'" P "C5'" .
SOS "C5'" "O5'" "C4'" .
SOS "H5'" "C5'" . .
SOS "H5''" "C5'" . .
SOS "C4'" "C5'" "C3'" .
SOS "H4'" "C4'" . .
SOS "C6'" "C4'" "H6'1" .
SOS "H6'2" "C6'" . .
SOS "H6'1" "C6'" . .
SOS "C3'" "C4'" "O3'" .
SOS "H3'" "C3'" . .
SOS "C2'" "C3'" "C1'" .
SOS "H2'" "C2'" . .
SOS "H2''" "C2'" . .
SOS "C1'" "C2'" N9 .
SOS "H1'" "C1'" . .
SOS N9 "C1'" C4 .
SOS HN9 N9 . .
SOS C4 N9 C5 .
SOS N3 C4 C2 .
SOS C2 N3 N1 .
SOS N2 C2 HN21 .
SOS HN22 N2 . .
SOS HN21 N2 . .
SOS N1 C2 C6 .
SOS HN1 N1 . .
SOS C6 N1 O6 .
SOS O6 C6 . .
SOS C5 C4 N7 .
SOS N7 C5 C9 .
SOS C8 N7 O8 .
SOS H8 C8 . .
SOS O8 C8 . .
SOS C9 N7 C10 .
SOS H91 C9 . .
SOS H92 C9 . .
SOS C10 C9 C11 .
SOS C15 C10 H15 .
SOS H15 C15 . .
SOS C11 C10 C12 .
SOS H11 C11 . .
SOS C12 C11 C13 .
SOS H12 C12 . .
SOS C13 C12 C14 .
SOS H13 C13 . .
SOS C14 C13 H14 .
SOS H14 C14 . .
SOS "O3'" "C3'" . END
SOS "HO3'" "O3'" . .
SOS C15 C14 . ADD
SOS C5 C6 . ADD
SOS "C1'" "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
SOS P OP3 deloc 1.510 0.020
SOS C15 C10 single 1.390 0.020
SOS C15 C14 double 1.390 0.020
SOS H15 C15 single 1.083 0.020
SOS C14 C13 single 1.390 0.020
SOS H14 C14 single 1.083 0.020
SOS C13 C12 double 1.390 0.020
SOS H13 C13 single 1.083 0.020
SOS C12 C11 single 1.390 0.020
SOS H12 C12 single 1.083 0.020
SOS C11 C10 double 1.390 0.020
SOS H11 C11 single 1.083 0.020
SOS C10 C9 single 1.511 0.020
SOS C9 N7 single 1.455 0.020
SOS H91 C9 single 1.092 0.020
SOS H92 C9 single 1.092 0.020
SOS C8 N7 single 1.260 0.020
SOS N7 C5 single 1.400 0.020
SOS O8 C8 double 1.220 0.020
SOS H8 C8 single 1.077 0.020
SOS C5 C6 single 1.487 0.020
SOS C5 C4 double 1.487 0.020
SOS O6 C6 double 1.250 0.020
SOS C6 N1 single 1.337 0.020
SOS N1 C2 single 1.337 0.020
SOS HN1 N1 single 1.040 0.020
SOS C2 N3 double 1.350 0.020
SOS N2 C2 single 1.355 0.020
SOS HN21 N2 single 1.010 0.020
SOS HN22 N2 single 1.010 0.020
SOS N3 C4 single 1.350 0.020
SOS C4 N9 single 1.350 0.020
SOS N9 "C1'" single 1.450 0.020
SOS HN9 N9 single 1.010 0.020
SOS "C1'" "C2'" single 1.524 0.020
SOS "C1'" "C6'" single 1.524 0.020
SOS "H1'" "C1'" single 1.099 0.020
SOS "C6'" "C4'" single 1.524 0.020
SOS "H6'1" "C6'" single 1.092 0.020
SOS "H6'2" "C6'" single 1.092 0.020
SOS "C2'" "C3'" single 1.524 0.020
SOS "H2'" "C2'" single 1.092 0.020
SOS "H2''" "C2'" single 1.092 0.020
SOS "C3'" "C4'" single 1.524 0.020
SOS "O3'" "C3'" single 1.432 0.020
SOS "H3'" "C3'" single 1.099 0.020
SOS "HO3'" "O3'" single 0.967 0.020
SOS "C4'" "C5'" single 1.524 0.020
SOS "H4'" "C4'" single 1.099 0.020
SOS "C5'" "O5'" single 1.426 0.020
SOS "H5'" "C5'" single 1.092 0.020
SOS "H5''" "C5'" single 1.092 0.020
SOS "O5'" P single 1.610 0.020
SOS OP1 P deloc 1.510 0.020
SOS OP2 P deloc 1.510 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
SOS OP3 P OP2 119.900 3.000
SOS OP3 P OP1 119.900 3.000
SOS OP3 P "O5'" 108.200 3.000
SOS OP2 P OP1 119.900 3.000
SOS OP2 P "O5'" 108.200 3.000
SOS OP1 P "O5'" 108.200 3.000
SOS P "O5'" "C5'" 120.500 3.000
SOS "O5'" "C5'" "H5'" 109.470 3.000
SOS "O5'" "C5'" "H5''" 109.470 3.000
SOS "O5'" "C5'" "C4'" 109.470 3.000
SOS "H5'" "C5'" "H5''" 107.900 3.000
SOS "H5'" "C5'" "C4'" 109.470 3.000
SOS "H5''" "C5'" "C4'" 109.470 3.000
SOS "C5'" "C4'" "H4'" 108.340 3.000
SOS "C5'" "C4'" "C6'" 109.470 3.000
SOS "C5'" "C4'" "C3'" 111.000 3.000
SOS "H4'" "C4'" "C6'" 108.340 3.000
SOS "H4'" "C4'" "C3'" 108.340 3.000
SOS "C6'" "C4'" "C3'" 111.000 3.000
SOS "C4'" "C6'" "H6'2" 109.470 3.000
SOS "C4'" "C6'" "H6'1" 109.470 3.000
SOS "C4'" "C6'" "C1'" 111.000 3.000
SOS "H6'2" "C6'" "H6'1" 107.900 3.000
SOS "H6'2" "C6'" "C1'" 109.470 3.000
SOS "H6'1" "C6'" "C1'" 109.470 3.000
SOS "C4'" "C3'" "H3'" 108.340 3.000
SOS "C4'" "C3'" "C2'" 111.000 3.000
SOS "C4'" "C3'" "O3'" 109.470 3.000
SOS "H3'" "C3'" "C2'" 108.340 3.000
SOS "H3'" "C3'" "O3'" 109.470 3.000
SOS "C2'" "C3'" "O3'" 109.470 3.000
SOS "C3'" "C2'" "H2'" 109.470 3.000
SOS "C3'" "C2'" "H2''" 109.470 3.000
SOS "C3'" "C2'" "C1'" 111.000 3.000
SOS "H2'" "C2'" "H2''" 107.900 3.000
SOS "H2'" "C2'" "C1'" 109.470 3.000
SOS "H2''" "C2'" "C1'" 109.470 3.000
SOS "C2'" "C1'" "H1'" 108.340 3.000
SOS "C2'" "C1'" N9 110.000 3.000
SOS "C2'" "C1'" "C6'" 109.470 3.000
SOS "H1'" "C1'" N9 108.550 3.000
SOS "H1'" "C1'" "C6'" 108.340 3.000
SOS N9 "C1'" "C6'" 110.000 3.000
SOS "C1'" N9 HN9 118.500 3.000
SOS "C1'" N9 C4 120.000 3.000
SOS HN9 N9 C4 120.000 3.000
SOS N9 C4 N3 120.000 3.000
SOS N9 C4 C5 120.000 3.000
SOS N3 C4 C5 120.000 3.000
SOS C4 N3 C2 120.000 3.000
SOS N3 C2 N2 120.000 3.000
SOS N3 C2 N1 120.000 3.000
SOS N2 C2 N1 120.000 3.000
SOS C2 N2 HN22 120.000 3.000
SOS C2 N2 HN21 120.000 3.000
SOS HN22 N2 HN21 120.000 3.000
SOS C2 N1 HN1 120.000 3.000
SOS C2 N1 C6 120.000 3.000
SOS HN1 N1 C6 120.000 3.000
SOS N1 C6 O6 120.000 3.000
SOS N1 C6 C5 120.000 3.000
SOS O6 C6 C5 120.000 3.000
SOS C4 C5 N7 120.000 3.000
SOS C4 C5 C6 120.000 3.000
SOS N7 C5 C6 120.000 3.000
SOS C5 N7 C8 120.000 3.000
SOS C5 N7 C9 120.000 3.000
SOS C8 N7 C9 120.000 3.000
SOS N7 C8 H8 120.000 3.000
SOS N7 C8 O8 120.000 3.000
SOS H8 C8 O8 123.000 3.000
SOS N7 C9 H91 109.470 3.000
SOS N7 C9 H92 109.470 3.000
SOS N7 C9 C10 109.470 3.000
SOS H91 C9 H92 107.900 3.000
SOS H91 C9 C10 109.470 3.000
SOS H92 C9 C10 109.470 3.000
SOS C9 C10 C15 120.000 3.000
SOS C9 C10 C11 120.000 3.000
SOS C15 C10 C11 120.000 3.000
SOS C10 C15 H15 120.000 3.000
SOS C10 C15 C14 120.000 3.000
SOS H15 C15 C14 120.000 3.000
SOS C10 C11 H11 120.000 3.000
SOS C10 C11 C12 120.000 3.000
SOS H11 C11 C12 120.000 3.000
SOS C11 C12 H12 120.000 3.000
SOS C11 C12 C13 120.000 3.000
SOS H12 C12 C13 120.000 3.000
SOS C12 C13 H13 120.000 3.000
SOS C12 C13 C14 120.000 3.000
SOS H13 C13 C14 120.000 3.000
SOS C13 C14 H14 120.000 3.000
SOS C13 C14 C15 120.000 3.000
SOS H14 C14 C15 120.000 3.000
SOS "C3'" "O3'" "HO3'" 109.470 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
SOS var_1 OP3 P "O5'" "C5'" -54.216 20.000 1
SOS var_2 P "O5'" "C5'" "C4'" -179.995 20.000 1
SOS var_3 "O5'" "C5'" "C4'" "C3'" 177.670 20.000 3
SOS var_4 "C5'" "C4'" "C6'" "C1'" 150.000 20.000 3
SOS var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
SOS var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
SOS var_7 "C3'" "C2'" "C1'" N9 90.000 20.000 3
SOS var_8 "C2'" "C1'" "C6'" "C4'" 0.000 20.000 3
SOS var_9 "C2'" "C1'" N9 C4 161.161 20.000 3
SOS var_10 "C1'" N9 C4 C5 179.974 20.000 1
SOS CONST_1 N9 C4 N3 C2 180.000 0.000 0
SOS CONST_2 C4 N3 C2 N1 0.000 0.000 0
SOS CONST_3 N3 C2 N2 HN21 22.124 0.000 0
SOS CONST_4 N3 C2 N1 C6 0.000 0.000 0
SOS CONST_5 C2 N1 C6 O6 180.000 0.000 0
SOS CONST_6 N9 C4 C5 N7 0.000 0.000 0
SOS CONST_7 C4 C5 C6 N1 0.000 0.000 0
SOS var_11 C4 C5 N7 C9 -120.032 20.000 1
SOS var_12 C5 N7 C8 O8 179.983 20.000 1
SOS var_13 C5 N7 C9 C10 90.002 20.000 1
SOS var_14 N7 C9 C10 C11 90.009 20.000 2
SOS CONST_8 C9 C10 C15 C14 180.000 0.000 0
SOS CONST_9 C10 C15 C14 C13 0.000 0.000 0
SOS CONST_10 C9 C10 C11 C12 180.000 0.000 0
SOS CONST_11 C10 C11 C12 C13 0.000 0.000 0
SOS CONST_12 C11 C12 C13 C14 0.000 0.000 0
SOS CONST_13 C12 C13 C14 C15 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
SOS chir_01 "C1'" N9 "C6'" "C2'" positiv
SOS chir_02 "C3'" "C2'" "O3'" "C4'" positiv
SOS chir_03 "C4'" "C6'" "C3'" "C5'" 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
SOS plan-1 C15 0.020
SOS plan-1 C14 0.020
SOS plan-1 C10 0.020
SOS plan-1 H15 0.020
SOS plan-1 C13 0.020
SOS plan-1 C12 0.020
SOS plan-1 C11 0.020
SOS plan-1 H14 0.020
SOS plan-1 H13 0.020
SOS plan-1 H12 0.020
SOS plan-1 H11 0.020
SOS plan-1 C9 0.020
SOS plan-2 N7 0.020
SOS plan-2 C9 0.020
SOS plan-2 C8 0.020
SOS plan-2 C5 0.020
SOS plan-2 H8 0.020
SOS plan-3 C8 0.020
SOS plan-3 N7 0.020
SOS plan-3 O8 0.020
SOS plan-3 H8 0.020
SOS plan-4 C5 0.020
SOS plan-4 N7 0.020
SOS plan-4 C6 0.020
SOS plan-4 C4 0.020
SOS plan-4 N1 0.020
SOS plan-4 C2 0.020
SOS plan-4 N3 0.020
SOS plan-4 O6 0.020
SOS plan-4 HN1 0.020
SOS plan-4 N2 0.020
SOS plan-4 N9 0.020
SOS plan-4 HN22 0.020
SOS plan-4 HN21 0.020
SOS plan-4 HN9 0.020
SOS plan-5 N2 0.020
SOS plan-5 C2 0.020
SOS plan-5 HN21 0.020
SOS plan-5 HN22 0.020
SOS plan-6 N9 0.020
SOS plan-6 C4 0.020
SOS plan-6 "C1'" 0.020
SOS plan-6 HN9 0.020
# ------------------------------------------------------
|
