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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
2DT 2DT '3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE ' non-polymer 33 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2DT
#
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
2DT O4 O O 0.000 0.000 0.000 0.000
2DT C4 C CR6 0.000 -1.186 -0.183 0.204
2DT C5 C CR6 0.000 -1.630 -1.386 0.802
2DT C5M C CH3 0.000 -0.642 -2.453 1.196
2DT H73 H H 0.000 -0.705 -2.625 2.239
2DT H72 H H 0.000 -0.863 -3.349 0.677
2DT H71 H H 0.000 0.338 -2.135 0.950
2DT C6 C CR16 0.000 -2.951 -1.564 1.016
2DT H6 H H 0.000 -3.309 -2.477 1.476
2DT N3 N NR16 0.000 -2.090 0.755 -0.145
2DT HN3 H H 0.000 -1.773 1.639 -0.591
2DT C2 C CR6 0.000 -3.401 0.552 0.081
2DT O2 O O 0.000 -4.203 1.408 -0.234
2DT N1 N NR6 0.000 -3.836 -0.586 0.651
2DT "C1'" C CH1 0.000 -5.269 -0.779 0.886
2DT "H1'" H H 0.000 -5.444 -1.762 1.345
2DT "O4'" O O2 0.000 -5.983 -0.687 -0.357
2DT "C4'" C CH1 0.000 -7.262 -0.082 -0.061
2DT "H4'" H H 0.000 -7.947 -0.822 0.374
2DT "C3'" C CH2 0.000 -6.915 1.014 0.977
2DT "H3'1" H H 0.000 -7.755 1.266 1.627
2DT "H3'2" H H 0.000 -6.523 1.925 0.520
2DT "C2'" C CH2 0.000 -5.803 0.332 1.809
2DT "H2''" H H 0.000 -6.193 -0.113 2.727
2DT "H2'" H H 0.000 -4.994 1.022 2.055
2DT "C5'" C CH2 0.000 -7.872 0.539 -1.320
2DT "H5''" H H 0.000 -7.157 1.235 -1.764
2DT "H5'" H H 0.000 -8.784 1.077 -1.053
2DT "O5'" O O2 0.000 -8.182 -0.490 -2.259
2DT P P P 0.000 -8.816 0.232 -3.550
2DT OP3 O OP -0.666 -10.066 0.983 -3.145
2DT OP1 O OP -0.666 -7.810 1.201 -4.130
2DT OP2 O OP -0.666 -9.169 -0.811 -4.588
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
2DT O4 n/a C4 START
2DT C4 O4 N3 .
2DT C5 C4 C6 .
2DT C5M C5 H71 .
2DT H73 C5M . .
2DT H72 C5M . .
2DT H71 C5M . .
2DT C6 C5 H6 .
2DT H6 C6 . .
2DT N3 C4 C2 .
2DT HN3 N3 . .
2DT C2 N3 N1 .
2DT O2 C2 . .
2DT N1 C2 "C1'" .
2DT "C1'" N1 "O4'" .
2DT "H1'" "C1'" . .
2DT "O4'" "C1'" "C4'" .
2DT "C4'" "O4'" "C5'" .
2DT "H4'" "C4'" . .
2DT "C3'" "C4'" "C2'" .
2DT "H3'1" "C3'" . .
2DT "H3'2" "C3'" . .
2DT "C2'" "C3'" "H2'" .
2DT "H2''" "C2'" . .
2DT "H2'" "C2'" . .
2DT "C5'" "C4'" "O5'" .
2DT "H5''" "C5'" . .
2DT "H5'" "C5'" . .
2DT "O5'" "C5'" P .
2DT P "O5'" OP2 .
2DT OP3 P . .
2DT OP1 P . .
2DT OP2 P . END
2DT N1 C6 . ADD
2DT "C2'" "C1'" . 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
2DT OP1 P deloc 1.510 0.020
2DT OP2 P deloc 1.510 0.020
2DT OP3 P deloc 1.510 0.020
2DT P "O5'" single 1.610 0.020
2DT "O5'" "C5'" single 1.426 0.020
2DT N1 C6 single 1.337 0.020
2DT N1 C2 single 1.410 0.020
2DT "C1'" N1 single 1.465 0.020
2DT C6 C5 double 1.390 0.020
2DT H6 C6 single 1.083 0.020
2DT O2 C2 double 1.250 0.020
2DT C2 N3 single 1.337 0.020
2DT N3 C4 single 1.337 0.020
2DT HN3 N3 single 1.040 0.020
2DT C4 O4 double 1.250 0.020
2DT C5 C4 single 1.487 0.020
2DT C5M C5 single 1.506 0.020
2DT H71 C5M single 1.059 0.020
2DT H72 C5M single 1.059 0.020
2DT H73 C5M single 1.059 0.020
2DT "C2'" "C1'" single 1.524 0.020
2DT "C2'" "C3'" single 1.524 0.020
2DT "H2'" "C2'" single 1.092 0.020
2DT "H2''" "C2'" single 1.092 0.020
2DT "C5'" "C4'" single 1.524 0.020
2DT "H5'" "C5'" single 1.092 0.020
2DT "H5''" "C5'" single 1.092 0.020
2DT "C4'" "O4'" single 1.426 0.020
2DT "C3'" "C4'" single 1.524 0.020
2DT "H4'" "C4'" single 1.099 0.020
2DT "O4'" "C1'" single 1.426 0.020
2DT "H1'" "C1'" single 1.099 0.020
2DT "H3'1" "C3'" single 1.092 0.020
2DT "H3'2" "C3'" single 1.092 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
2DT O4 C4 C5 120.000 3.000
2DT O4 C4 N3 120.000 3.000
2DT C5 C4 N3 120.000 3.000
2DT C4 C5 C5M 120.000 3.000
2DT C4 C5 C6 120.000 3.000
2DT C5M C5 C6 120.000 3.000
2DT C5 C5M H73 109.470 3.000
2DT C5 C5M H72 109.470 3.000
2DT C5 C5M H71 109.470 3.000
2DT H73 C5M H72 109.470 3.000
2DT H73 C5M H71 109.470 3.000
2DT H72 C5M H71 109.470 3.000
2DT C5 C6 H6 120.000 3.000
2DT C5 C6 N1 120.000 3.000
2DT H6 C6 N1 120.000 3.000
2DT C4 N3 HN3 120.000 3.000
2DT C4 N3 C2 120.000 3.000
2DT HN3 N3 C2 120.000 3.000
2DT N3 C2 O2 120.000 3.000
2DT N3 C2 N1 120.000 3.000
2DT O2 C2 N1 120.000 3.000
2DT C2 N1 "C1'" 120.000 3.000
2DT C2 N1 C6 120.000 3.000
2DT "C1'" N1 C6 120.000 3.000
2DT N1 "C1'" "H1'" 109.470 3.000
2DT N1 "C1'" "O4'" 109.470 3.000
2DT N1 "C1'" "C2'" 109.470 3.000
2DT "H1'" "C1'" "O4'" 109.470 3.000
2DT "H1'" "C1'" "C2'" 108.340 3.000
2DT "O4'" "C1'" "C2'" 109.470 3.000
2DT "C1'" "O4'" "C4'" 111.800 3.000
2DT "O4'" "C4'" "H4'" 109.470 3.000
2DT "O4'" "C4'" "C3'" 109.470 3.000
2DT "O4'" "C4'" "C5'" 109.470 3.000
2DT "H4'" "C4'" "C3'" 108.340 3.000
2DT "H4'" "C4'" "C5'" 108.340 3.000
2DT "C3'" "C4'" "C5'" 109.470 3.000
2DT "C4'" "C3'" "H3'1" 109.470 3.000
2DT "C4'" "C3'" "H3'2" 109.470 3.000
2DT "C4'" "C3'" "C2'" 111.000 3.000
2DT "H3'1" "C3'" "H3'2" 107.900 3.000
2DT "H3'1" "C3'" "C2'" 109.470 3.000
2DT "H3'2" "C3'" "C2'" 109.470 3.000
2DT "C3'" "C2'" "H2''" 109.470 3.000
2DT "C3'" "C2'" "H2'" 109.470 3.000
2DT "C3'" "C2'" "C1'" 111.000 3.000
2DT "H2''" "C2'" "H2'" 107.900 3.000
2DT "H2''" "C2'" "C1'" 109.470 3.000
2DT "H2'" "C2'" "C1'" 109.470 3.000
2DT "C4'" "C5'" "H5''" 109.470 3.000
2DT "C4'" "C5'" "H5'" 109.470 3.000
2DT "C4'" "C5'" "O5'" 109.470 3.000
2DT "H5''" "C5'" "H5'" 107.900 3.000
2DT "H5''" "C5'" "O5'" 109.470 3.000
2DT "H5'" "C5'" "O5'" 109.470 3.000
2DT "C5'" "O5'" P 120.500 3.000
2DT "O5'" P OP3 108.200 3.000
2DT "O5'" P OP1 108.200 3.000
2DT "O5'" P OP2 108.200 3.000
2DT OP3 P OP1 119.900 3.000
2DT OP3 P OP2 119.900 3.000
2DT OP1 P OP2 119.900 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
2DT CONST_1 O4 C4 C5 C6 180.000 0.000 0
2DT var_1 C4 C5 C5M H71 -0.197 20.000 1
2DT CONST_2 C4 C5 C6 N1 0.000 0.000 0
2DT CONST_3 O4 C4 N3 C2 180.000 0.000 0
2DT CONST_4 C4 N3 C2 N1 0.000 0.000 0
2DT CONST_5 N3 C2 N1 "C1'" 180.000 0.000 0
2DT CONST_6 C2 N1 C6 C5 0.000 0.000 0
2DT var_2 C2 N1 "C1'" "O4'" 58.405 20.000 1
2DT var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
2DT var_4 "C1'" "O4'" "C4'" "C5'" 150.000 20.000 1
2DT var_5 "O4'" "C4'" "C3'" "C2'" -30.000 20.000 3
2DT var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
2DT var_7 "C3'" "C2'" "C1'" N1 120.000 20.000 3
2DT var_8 "O4'" "C4'" "C5'" "O5'" 65.687 20.000 3
2DT var_9 "C4'" "C5'" "O5'" P 179.996 20.000 1
2DT var_10 "C5'" "O5'" P OP2 -179.985 20.000 1
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
2DT chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2DT chir_02 "C1'" N1 "C2'" "O4'" 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
2DT plan-1 N1 0.020
2DT plan-1 C6 0.020
2DT plan-1 C2 0.020
2DT plan-1 "C1'" 0.020
2DT plan-1 N3 0.020
2DT plan-1 C4 0.020
2DT plan-1 C5 0.020
2DT plan-1 H6 0.020
2DT plan-1 O2 0.020
2DT plan-1 HN3 0.020
2DT plan-1 O4 0.020
2DT plan-1 C5M 0.020
# ------------------------------------------------------
|
