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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
3DT 3DT '3-methylthymidine ' non-polymer 34 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_3DT
#
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
3DT O4 O O 0.000 0.000 0.000 0.000
3DT C4 C CR6 0.000 -1.216 -0.060 0.004
3DT N3 N NR6 0.000 -1.841 -1.221 -0.282
3DT CN C CH3 0.000 -1.052 -2.415 -0.597
3DT HNB H H 0.000 -0.126 -2.371 -0.085
3DT HNA H H 0.000 -1.583 -3.279 -0.292
3DT HN H H 0.000 -0.877 -2.457 -1.640
3DT C2 C CR6 0.000 -3.185 -1.286 -0.278
3DT O2 O O 0.000 -3.735 -2.339 -0.538
3DT C5 C CR6 0.000 -1.987 1.088 0.307
3DT C7 C CH3 0.000 -1.314 2.396 0.630
3DT H7B H H 0.000 -1.615 3.131 -0.072
3DT H7A H H 0.000 -1.590 2.705 1.604
3DT H7 H H 0.000 -0.263 2.274 0.583
3DT C6 C CR16 0.000 -3.334 0.994 0.304
3DT H6 H H 0.000 -3.941 1.861 0.534
3DT N1 N NR6 0.000 -3.929 -0.202 0.009
3DT "C1'" C CH1 0.000 -5.391 -0.304 -0.001
3DT "H1'" H H 0.000 -5.695 -1.295 -0.365
3DT "O4'" O O2 0.000 -5.946 0.720 -0.843
3DT "C4'" C CH1 0.000 -7.199 1.121 -0.249
3DT "H4'" H H 0.000 -7.987 0.390 -0.476
3DT "C5'" C CH2 0.000 -7.603 2.516 -0.733
3DT "H5'" H H 0.000 -6.756 3.197 -0.626
3DT "H5'A" H H 0.000 -8.439 2.880 -0.133
3DT "O5'" O OH1 0.000 -7.992 2.450 -2.106
3DT "HO5'" H H 0.000 -8.246 3.331 -2.411
3DT "C3'" C CH1 0.000 -6.891 1.139 1.269
3DT "H3'" H H 0.000 -6.385 2.071 1.555
3DT "O3'" O OH1 0.000 -8.084 0.950 2.034
3DT "HO3'" H H 0.000 -7.856 0.872 2.970
3DT "C2'" C CH2 0.000 -5.941 -0.074 1.421
3DT "H2'A" H H 0.000 -6.470 -0.968 1.757
3DT "H2'" H H 0.000 -5.115 0.136 2.103
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
3DT O4 n/a C4 START
3DT C4 O4 C5 .
3DT N3 C4 C2 .
3DT CN N3 HN .
3DT HNB CN . .
3DT HNA CN . .
3DT HN CN . .
3DT C2 N3 O2 .
3DT O2 C2 . .
3DT C5 C4 C6 .
3DT C7 C5 H7 .
3DT H7B C7 . .
3DT H7A C7 . .
3DT H7 C7 . .
3DT C6 C5 N1 .
3DT H6 C6 . .
3DT N1 C6 "C1'" .
3DT "C1'" N1 "O4'" .
3DT "H1'" "C1'" . .
3DT "O4'" "C1'" "C4'" .
3DT "C4'" "O4'" "C3'" .
3DT "H4'" "C4'" . .
3DT "C5'" "C4'" "O5'" .
3DT "H5'" "C5'" . .
3DT "H5'A" "C5'" . .
3DT "O5'" "C5'" "HO5'" .
3DT "HO5'" "O5'" . .
3DT "C3'" "C4'" "C2'" .
3DT "H3'" "C3'" . .
3DT "O3'" "C3'" "HO3'" .
3DT "HO3'" "O3'" . .
3DT "C2'" "C3'" "H2'" .
3DT "H2'A" "C2'" . .
3DT "H2'" "C2'" . END
3DT N1 C2 . ADD
3DT "C1'" "C2'" . 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
3DT N1 C2 single 1.410 0.020
3DT N1 C6 single 1.337 0.020
3DT "C1'" N1 single 1.465 0.020
3DT O2 C2 double 1.250 0.020
3DT C2 N3 single 1.410 0.020
3DT N3 C4 single 1.410 0.020
3DT CN N3 single 1.465 0.020
3DT C4 O4 double 1.250 0.020
3DT C5 C4 single 1.487 0.020
3DT C6 C5 double 1.390 0.020
3DT C7 C5 single 1.506 0.020
3DT "C1'" "C2'" single 1.524 0.020
3DT "O4'" "C1'" single 1.426 0.020
3DT "C2'" "C3'" single 1.524 0.020
3DT "O3'" "C3'" single 1.432 0.020
3DT "C3'" "C4'" single 1.524 0.020
3DT "C4'" "O4'" single 1.426 0.020
3DT "C5'" "C4'" single 1.524 0.020
3DT "O5'" "C5'" single 1.432 0.020
3DT H6 C6 single 1.083 0.020
3DT H7 C7 single 1.059 0.020
3DT H7A C7 single 1.059 0.020
3DT H7B C7 single 1.059 0.020
3DT HN CN single 1.059 0.020
3DT HNA CN single 1.059 0.020
3DT HNB CN single 1.059 0.020
3DT "H1'" "C1'" single 1.099 0.020
3DT "H2'" "C2'" single 1.092 0.020
3DT "H2'A" "C2'" single 1.092 0.020
3DT "H3'" "C3'" single 1.099 0.020
3DT "HO3'" "O3'" single 0.967 0.020
3DT "H4'" "C4'" single 1.099 0.020
3DT "H5'" "C5'" single 1.092 0.020
3DT "H5'A" "C5'" single 1.092 0.020
3DT "HO5'" "O5'" 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
3DT O4 C4 N3 120.000 3.000
3DT O4 C4 C5 120.000 3.000
3DT N3 C4 C5 120.000 3.000
3DT C4 N3 CN 120.000 3.000
3DT C4 N3 C2 120.000 3.000
3DT CN N3 C2 120.000 3.000
3DT N3 CN HNB 109.470 3.000
3DT N3 CN HNA 109.470 3.000
3DT N3 CN HN 109.470 3.000
3DT HNB CN HNA 109.470 3.000
3DT HNB CN HN 109.470 3.000
3DT HNA CN HN 109.470 3.000
3DT N3 C2 O2 120.000 3.000
3DT N3 C2 N1 120.000 3.000
3DT O2 C2 N1 120.000 3.000
3DT C4 C5 C7 120.000 3.000
3DT C4 C5 C6 120.000 3.000
3DT C7 C5 C6 120.000 3.000
3DT C5 C7 H7B 109.470 3.000
3DT C5 C7 H7A 109.470 3.000
3DT C5 C7 H7 109.470 3.000
3DT H7B C7 H7A 109.470 3.000
3DT H7B C7 H7 109.470 3.000
3DT H7A C7 H7 109.470 3.000
3DT C5 C6 H6 120.000 3.000
3DT C5 C6 N1 120.000 3.000
3DT H6 C6 N1 120.000 3.000
3DT C6 N1 "C1'" 120.000 3.000
3DT C6 N1 C2 120.000 3.000
3DT "C1'" N1 C2 120.000 3.000
3DT N1 "C1'" "H1'" 109.470 3.000
3DT N1 "C1'" "O4'" 109.470 3.000
3DT N1 "C1'" "C2'" 109.470 3.000
3DT "H1'" "C1'" "O4'" 109.470 3.000
3DT "H1'" "C1'" "C2'" 108.340 3.000
3DT "O4'" "C1'" "C2'" 109.470 3.000
3DT "C1'" "O4'" "C4'" 111.800 3.000
3DT "O4'" "C4'" "H4'" 109.470 3.000
3DT "O4'" "C4'" "C5'" 109.470 3.000
3DT "O4'" "C4'" "C3'" 109.470 3.000
3DT "H4'" "C4'" "C5'" 108.340 3.000
3DT "H4'" "C4'" "C3'" 108.340 3.000
3DT "C5'" "C4'" "C3'" 111.000 3.000
3DT "C4'" "C5'" "H5'" 109.470 3.000
3DT "C4'" "C5'" "H5'A" 109.470 3.000
3DT "C4'" "C5'" "O5'" 109.470 3.000
3DT "H5'" "C5'" "H5'A" 107.900 3.000
3DT "H5'" "C5'" "O5'" 109.470 3.000
3DT "H5'A" "C5'" "O5'" 109.470 3.000
3DT "C5'" "O5'" "HO5'" 109.470 3.000
3DT "C4'" "C3'" "H3'" 108.340 3.000
3DT "C4'" "C3'" "O3'" 109.470 3.000
3DT "C4'" "C3'" "C2'" 111.000 3.000
3DT "H3'" "C3'" "O3'" 109.470 3.000
3DT "H3'" "C3'" "C2'" 108.340 3.000
3DT "O3'" "C3'" "C2'" 109.470 3.000
3DT "C3'" "O3'" "HO3'" 109.470 3.000
3DT "C3'" "C2'" "H2'A" 109.470 3.000
3DT "C3'" "C2'" "H2'" 109.470 3.000
3DT "C3'" "C2'" "C1'" 111.000 3.000
3DT "H2'A" "C2'" "H2'" 107.900 3.000
3DT "H2'A" "C2'" "C1'" 109.470 3.000
3DT "H2'" "C2'" "C1'" 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
3DT CONST_1 O4 C4 N3 C2 180.000 0.000 0
3DT var_1 C4 N3 CN HN -90.069 20.000 1
3DT CONST_2 C4 N3 C2 O2 180.000 0.000 0
3DT CONST_3 O4 C4 C5 C6 180.000 0.000 0
3DT var_2 C4 C5 C7 H7 -0.023 20.000 1
3DT CONST_4 C4 C5 C6 N1 0.000 0.000 0
3DT CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
3DT CONST_6 C6 N1 C2 N3 0.000 0.000 0
3DT var_3 C6 N1 "C1'" "O4'" 52.531 20.000 1
3DT var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
3DT var_5 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
3DT var_6 "C1'" "O4'" "C4'" "C3'" 30.000 20.000 1
3DT var_7 "O4'" "C4'" "C5'" "O5'" 70.875 20.000 3
3DT var_8 "C4'" "C5'" "O5'" "HO5'" -179.966 20.000 1
3DT var_9 "O4'" "C4'" "C3'" "C2'" -30.000 20.000 3
3DT var_10 "C4'" "C3'" "O3'" "HO3'" 174.113 20.000 1
3DT var_11 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
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
3DT chir_01 "C1'" N1 "C2'" "O4'" negativ
3DT chir_02 "C3'" "C2'" "O3'" "C4'" positiv
3DT chir_03 "C4'" "C3'" "O4'" "C5'" 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
3DT plan-1 N1 0.020
3DT plan-1 C2 0.020
3DT plan-1 C6 0.020
3DT plan-1 "C1'" 0.020
3DT plan-1 N3 0.020
3DT plan-1 C4 0.020
3DT plan-1 C5 0.020
3DT plan-1 O2 0.020
3DT plan-1 CN 0.020
3DT plan-1 O4 0.020
3DT plan-1 C7 0.020
3DT plan-1 H6 0.020
# ------------------------------------------------------
|
