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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
S2M S2M '2'-O-[2-(METHOXY)ETHYL]-2-THIOTHYMID' DNA 45 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_S2M
#
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
S2M OP3 O OP -0.666 0.000 0.000 0.000
S2M P P P 0.000 -0.530 1.416 0.049
S2M OP2 O OP -0.666 -1.420 1.497 -1.172
S2M OP1 O OP -0.666 0.531 2.491 0.149
S2M "O5'" O O2 0.000 -1.575 1.370 1.285
S2M "C5'" C CH2 0.000 -2.598 0.391 1.268
S2M "H5'" H H 0.000 -2.156 -0.607 1.248
S2M "H5''" H H 0.000 -3.226 0.527 0.385
S2M "C4'" C CH1 0.000 -3.444 0.549 2.524
S2M "H4'" H H 0.000 -2.807 0.459 3.415
S2M "C3'" C CH1 0.000 -4.591 -0.451 2.607
S2M "H3'" H H 0.000 -4.330 -1.416 2.151
S2M "C2'" C CH1 0.000 -5.687 0.260 1.843
S2M "H2'" H H 0.000 -5.523 0.146 0.762
S2M "O2'" O O2 0.000 -6.974 -0.213 2.186
S2M "CA'" C CH2 0.000 -7.118 -1.603 1.913
S2M "HA'1" H H 0.000 -6.372 -2.167 2.477
S2M "HA'2" H H 0.000 -6.979 -1.785 0.845
S2M "CB'" C CH2 0.000 -8.507 -2.047 2.326
S2M "HB'1" H H 0.000 -8.633 -3.110 2.109
S2M "HB'2" H H 0.000 -9.255 -1.473 1.775
S2M "OC'" O O2 0.000 -8.670 -1.825 3.721
S2M "CD'" C CH3 0.000 -9.968 -2.204 4.161
S2M "HD'3" H H 0.000 -10.337 -2.977 3.540
S2M "HD'2" H H 0.000 -9.914 -2.548 5.161
S2M "HD'1" H H 0.000 -10.615 -1.368 4.108
S2M "C1'" C CH1 0.000 -5.468 1.707 2.248
S2M "H1'" H H 0.000 -6.026 1.920 3.171
S2M "O4'" O O2 0.000 -4.059 1.855 2.492
S2M N1 N NR6 0.000 -5.864 2.630 1.223
S2M C6 C CR16 0.000 -4.934 2.942 0.225
S2M H6 H H 0.000 -3.965 2.462 0.280
S2M C5 C CR6 0.000 -5.146 3.788 -0.791
S2M C5M C CH3 0.000 -4.124 4.092 -1.840
S2M H73 H H 0.000 -4.526 4.786 -2.530
S2M H72 H H 0.000 -3.264 4.506 -1.381
S2M H71 H H 0.000 -3.862 3.200 -2.344
S2M C2 C CR6 0.000 -7.130 3.273 1.192
S2M S2 S S1 0.000 -8.356 3.071 2.327
S2M N3 N NR16 0.000 -7.352 4.148 0.130
S2M H3 H H 0.000 -8.282 4.614 0.098
S2M C4 C CR6 0.000 -6.466 4.463 -0.887
S2M O4 O O 0.000 -6.727 5.240 -1.801
S2M "O3'" O OH1 0.000 -4.954 -0.589 3.981
S2M "HO3'" H H 0.000 -4.548 0.157 4.448
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
S2M OP3 n/a P START
S2M P OP3 "O5'" .
S2M OP2 P . .
S2M OP1 P . .
S2M "O5'" P "C5'" .
S2M "C5'" "O5'" "C4'" .
S2M "H5'" "C5'" . .
S2M "H5''" "C5'" . .
S2M "C4'" "C5'" "C3'" .
S2M "H4'" "C4'" . .
S2M "C3'" "C4'" "O3'" .
S2M "H3'" "C3'" . .
S2M "C2'" "C3'" "C1'" .
S2M "H2'" "C2'" . .
S2M "O2'" "C2'" "CA'" .
S2M "CA'" "O2'" "CB'" .
S2M "HA'1" "CA'" . .
S2M "HA'2" "CA'" . .
S2M "CB'" "CA'" "OC'" .
S2M "HB'1" "CB'" . .
S2M "HB'2" "CB'" . .
S2M "OC'" "CB'" "CD'" .
S2M "CD'" "OC'" "HD'1" .
S2M "HD'3" "CD'" . .
S2M "HD'2" "CD'" . .
S2M "HD'1" "CD'" . .
S2M "C1'" "C2'" N1 .
S2M "H1'" "C1'" . .
S2M "O4'" "C1'" . .
S2M N1 "C1'" C2 .
S2M C6 N1 C5 .
S2M H6 C6 . .
S2M C5 C6 C5M .
S2M C5M C5 H71 .
S2M H73 C5M . .
S2M H72 C5M . .
S2M H71 C5M . .
S2M C2 N1 N3 .
S2M S2 C2 . .
S2M N3 C2 C4 .
S2M H3 N3 . .
S2M C4 N3 O4 .
S2M O4 C4 . .
S2M "O3'" "C3'" . END
S2M "HO3'" "O3'" . .
S2M C4 C5 . ADD
S2M "C4'" "O4'" . 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
S2M O4 C4 double 1.250 0.020
S2M C4 C5 single 1.487 0.020
S2M C4 N3 single 1.337 0.020
S2M C5 C6 double 1.390 0.020
S2M C5M C5 single 1.506 0.020
S2M C6 N1 single 1.337 0.020
S2M H6 C6 single 1.083 0.020
S2M H71 C5M single 1.059 0.020
S2M H72 C5M single 1.059 0.020
S2M H73 C5M single 1.059 0.020
S2M N3 C2 single 1.337 0.020
S2M H3 N3 single 1.040 0.020
S2M S2 C2 double 1.595 0.020
S2M C2 N1 single 1.410 0.020
S2M "C5'" "O5'" single 1.426 0.020
S2M "C4'" "C5'" single 1.524 0.020
S2M "H5'" "C5'" single 1.092 0.020
S2M "H5''" "C5'" single 1.092 0.020
S2M "O5'" P single 1.610 0.020
S2M OP2 P deloc 1.510 0.020
S2M OP1 P deloc 1.510 0.020
S2M P OP3 deloc 1.510 0.020
S2M "C4'" "O4'" single 1.426 0.020
S2M "C3'" "C4'" single 1.524 0.020
S2M "H4'" "C4'" single 1.099 0.020
S2M "O4'" "C1'" single 1.426 0.020
S2M N1 "C1'" single 1.465 0.020
S2M "C1'" "C2'" single 1.524 0.020
S2M "H1'" "C1'" single 1.099 0.020
S2M "C2'" "C3'" single 1.524 0.020
S2M "O2'" "C2'" single 1.426 0.020
S2M "H2'" "C2'" single 1.099 0.020
S2M "O3'" "C3'" single 1.432 0.020
S2M "H3'" "C3'" single 1.099 0.020
S2M "HO3'" "O3'" single 0.967 0.020
S2M "CA'" "O2'" single 1.426 0.020
S2M "CB'" "CA'" single 1.524 0.020
S2M "HA'1" "CA'" single 1.092 0.020
S2M "HA'2" "CA'" single 1.092 0.020
S2M "OC'" "CB'" single 1.426 0.020
S2M "HB'1" "CB'" single 1.092 0.020
S2M "HB'2" "CB'" single 1.092 0.020
S2M "CD'" "OC'" single 1.426 0.020
S2M "HD'1" "CD'" single 1.059 0.020
S2M "HD'2" "CD'" single 1.059 0.020
S2M "HD'3" "CD'" single 1.059 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
S2M OP3 P OP2 119.900 3.000
S2M OP3 P OP1 119.900 3.000
S2M OP3 P "O5'" 108.200 3.000
S2M OP2 P OP1 119.900 3.000
S2M OP2 P "O5'" 108.200 3.000
S2M OP1 P "O5'" 108.200 3.000
S2M P "O5'" "C5'" 120.500 3.000
S2M "O5'" "C5'" "H5'" 109.470 3.000
S2M "O5'" "C5'" "H5''" 109.470 3.000
S2M "O5'" "C5'" "C4'" 109.470 3.000
S2M "H5'" "C5'" "H5''" 107.900 3.000
S2M "H5'" "C5'" "C4'" 109.470 3.000
S2M "H5''" "C5'" "C4'" 109.470 3.000
S2M "C5'" "C4'" "H4'" 108.340 3.000
S2M "C5'" "C4'" "C3'" 111.000 3.000
S2M "C5'" "C4'" "O4'" 109.470 3.000
S2M "H4'" "C4'" "C3'" 108.340 3.000
S2M "H4'" "C4'" "O4'" 109.470 3.000
S2M "C3'" "C4'" "O4'" 109.470 3.000
S2M "C4'" "C3'" "H3'" 108.340 3.000
S2M "C4'" "C3'" "C2'" 111.000 3.000
S2M "C4'" "C3'" "O3'" 109.470 3.000
S2M "H3'" "C3'" "C2'" 108.340 3.000
S2M "H3'" "C3'" "O3'" 109.470 3.000
S2M "C2'" "C3'" "O3'" 109.470 3.000
S2M "C3'" "C2'" "H2'" 108.340 3.000
S2M "C3'" "C2'" "O2'" 109.470 3.000
S2M "C3'" "C2'" "C1'" 111.000 3.000
S2M "H2'" "C2'" "O2'" 109.470 3.000
S2M "H2'" "C2'" "C1'" 108.340 3.000
S2M "O2'" "C2'" "C1'" 109.470 3.000
S2M "C2'" "O2'" "CA'" 111.800 3.000
S2M "O2'" "CA'" "HA'1" 109.470 3.000
S2M "O2'" "CA'" "HA'2" 109.470 3.000
S2M "O2'" "CA'" "CB'" 109.470 3.000
S2M "HA'1" "CA'" "HA'2" 107.900 3.000
S2M "HA'1" "CA'" "CB'" 109.470 3.000
S2M "HA'2" "CA'" "CB'" 109.470 3.000
S2M "CA'" "CB'" "HB'1" 109.470 3.000
S2M "CA'" "CB'" "HB'2" 109.470 3.000
S2M "CA'" "CB'" "OC'" 109.470 3.000
S2M "HB'1" "CB'" "HB'2" 107.900 3.000
S2M "HB'1" "CB'" "OC'" 109.470 3.000
S2M "HB'2" "CB'" "OC'" 109.470 3.000
S2M "CB'" "OC'" "CD'" 111.800 3.000
S2M "OC'" "CD'" "HD'3" 109.470 3.000
S2M "OC'" "CD'" "HD'2" 109.470 3.000
S2M "OC'" "CD'" "HD'1" 109.470 3.000
S2M "HD'3" "CD'" "HD'2" 109.470 3.000
S2M "HD'3" "CD'" "HD'1" 109.470 3.000
S2M "HD'2" "CD'" "HD'1" 109.470 3.000
S2M "C2'" "C1'" "H1'" 108.340 3.000
S2M "C2'" "C1'" "O4'" 109.470 3.000
S2M "C2'" "C1'" N1 109.470 3.000
S2M "H1'" "C1'" "O4'" 109.470 3.000
S2M "H1'" "C1'" N1 109.470 3.000
S2M "O4'" "C1'" N1 109.470 3.000
S2M "C1'" "O4'" "C4'" 111.800 3.000
S2M "C1'" N1 C6 120.000 3.000
S2M "C1'" N1 C2 120.000 3.000
S2M C6 N1 C2 120.000 3.000
S2M N1 C6 H6 120.000 3.000
S2M N1 C6 C5 120.000 3.000
S2M H6 C6 C5 120.000 3.000
S2M C6 C5 C5M 120.000 3.000
S2M C6 C5 C4 120.000 3.000
S2M C5M C5 C4 120.000 3.000
S2M C5 C5M H73 109.470 3.000
S2M C5 C5M H72 109.470 3.000
S2M C5 C5M H71 109.470 3.000
S2M H73 C5M H72 109.470 3.000
S2M H73 C5M H71 109.470 3.000
S2M H72 C5M H71 109.470 3.000
S2M N1 C2 S2 120.000 3.000
S2M N1 C2 N3 120.000 3.000
S2M S2 C2 N3 120.000 3.000
S2M C2 N3 H3 120.000 3.000
S2M C2 N3 C4 120.000 3.000
S2M H3 N3 C4 120.000 3.000
S2M N3 C4 O4 120.000 3.000
S2M N3 C4 C5 120.000 3.000
S2M O4 C4 C5 120.000 3.000
S2M "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
S2M var_1 OP3 P "O5'" "C5'" -54.172 20.000 1
S2M var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
S2M var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
S2M var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
S2M var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
S2M var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
S2M var_7 "C3'" "C2'" "O2'" "CA'" -59.966 20.000 1
S2M var_8 "C2'" "O2'" "CA'" "CB'" 179.001 20.000 1
S2M var_9 "O2'" "CA'" "CB'" "OC'" -60.850 20.000 3
S2M var_10 "CA'" "CB'" "OC'" "CD'" 179.032 20.000 1
S2M var_11 "CB'" "OC'" "CD'" "HD'1" -91.506 20.000 1
S2M var_12 "C3'" "C2'" "C1'" N1 150.000 20.000 3
S2M var_13 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
S2M var_14 "C2'" "C1'" N1 C2 96.408 20.000 1
S2M CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
S2M CONST_2 N1 C6 C5 C5M 180.000 0.000 0
S2M var_15 C6 C5 C5M H71 60.054 20.000 1
S2M CONST_3 "C1'" N1 C2 N3 180.000 0.000 0
S2M CONST_4 N1 C2 N3 C4 0.000 0.000 0
S2M CONST_5 C2 N3 C4 O4 180.000 0.000 0
S2M CONST_6 N3 C4 C5 C6 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
S2M chir_01 "C4'" "C5'" "O4'" "C3'" negativ
S2M chir_02 "C1'" "O4'" N1 "C2'" negativ
S2M chir_03 "C2'" "C1'" "C3'" "O2'" negativ
S2M chir_04 "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
S2M plan-1 C4 0.020
S2M plan-1 C5 0.020
S2M plan-1 N3 0.020
S2M plan-1 O4 0.020
S2M plan-1 C6 0.020
S2M plan-1 C2 0.020
S2M plan-1 N1 0.020
S2M plan-1 C5M 0.020
S2M plan-1 H6 0.020
S2M plan-1 H3 0.020
S2M plan-1 S2 0.020
S2M plan-1 "C1'" 0.020
# ------------------------------------------------------
|
