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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
ATD ATD 'THYMIDINE-3'-PHOSPHATE ' non-polymer 34 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ATD
#
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
ATD O4 O O 0.000 0.000 0.000 0.000
ATD C4 C CR6 0.000 -1.200 -0.187 -0.076
ATD N3 N NR16 0.000 -2.035 0.841 -0.335
ATD H3 H H 0.000 -1.651 1.798 -0.473
ATD C2 C CR6 0.000 -3.362 0.633 -0.418
ATD O2 O O 0.000 -4.102 1.569 -0.648
ATD C5 C CR6 0.000 -1.734 -1.485 0.100
ATD C5M C CH3 0.000 -0.824 -2.652 0.387
ATD H73 H H 0.000 -1.082 -3.081 1.320
ATD H72 H H 0.000 -0.931 -3.379 -0.376
ATD H71 H H 0.000 0.181 -2.318 0.417
ATD C6 C CR16 0.000 -3.069 -1.666 0.012
ATD H6 H H 0.000 -3.495 -2.653 0.146
ATD N1 N NR6 0.000 -3.881 -0.596 -0.249
ATD "C1'" C CH1 0.000 -5.330 -0.791 -0.345
ATD "H1'" H H 0.000 -5.584 -1.845 -0.170
ATD "O4'" O O2 0.000 -6.010 0.049 0.601
ATD "C2'" C CH2 0.000 -5.843 -0.338 -1.734
ATD "H2'" H H 0.000 -5.799 -1.123 -2.492
ATD "H2''" H H 0.000 -5.346 0.558 -2.111
ATD "C3'" C CH1 0.000 -7.325 -0.011 -1.409
ATD "H3'" H H 0.000 -7.941 -0.921 -1.443
ATD "O3'" O O2 0.000 -7.836 0.980 -2.301
ATD P P P 0.000 -9.104 0.328 -3.047
ATD OP2 O OP -0.666 -9.693 1.333 -4.012
ATD OP1 O OP -0.666 -10.148 -0.061 -2.024
ATD OP3 O OP -0.666 -8.662 -0.902 -3.809
ATD "C4'" C CH1 0.000 -7.232 0.533 0.032
ATD "H4'" H H 0.000 -7.226 1.632 0.015
ATD "C5'" C CH2 0.000 -8.421 0.033 0.855
ATD "H5'" H H 0.000 -8.412 -1.059 0.880
ATD "H5''" H H 0.000 -9.350 0.378 0.397
ATD "O5'" O OH1 0.000 -8.327 0.542 2.187
ATD "HO'5" H H 0.000 -9.079 0.226 2.706
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
ATD O4 n/a C4 START
ATD C4 O4 C5 .
ATD N3 C4 C2 .
ATD H3 N3 . .
ATD C2 N3 O2 .
ATD O2 C2 . .
ATD C5 C4 C6 .
ATD C5M C5 H71 .
ATD H73 C5M . .
ATD H72 C5M . .
ATD H71 C5M . .
ATD C6 C5 N1 .
ATD H6 C6 . .
ATD N1 C6 "C1'" .
ATD "C1'" N1 "C2'" .
ATD "H1'" "C1'" . .
ATD "O4'" "C1'" . .
ATD "C2'" "C1'" "C3'" .
ATD "H2'" "C2'" . .
ATD "H2''" "C2'" . .
ATD "C3'" "C2'" "C4'" .
ATD "H3'" "C3'" . .
ATD "O3'" "C3'" P .
ATD P "O3'" OP3 .
ATD OP2 P . .
ATD OP1 P . .
ATD OP3 P . .
ATD "C4'" "C3'" "C5'" .
ATD "H4'" "C4'" . .
ATD "C5'" "C4'" "O5'" .
ATD "H5'" "C5'" . .
ATD "H5''" "C5'" . .
ATD "O5'" "C5'" "HO'5" .
ATD "HO'5" "O5'" . END
ATD "C4'" "O4'" . ADD
ATD N1 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
ATD OP1 P deloc 1.510 0.020
ATD OP2 P deloc 1.510 0.020
ATD OP3 P deloc 1.510 0.020
ATD P "O3'" single 1.610 0.020
ATD "O5'" "C5'" single 1.432 0.020
ATD "HO'5" "O5'" single 0.967 0.020
ATD "C5'" "C4'" single 1.524 0.020
ATD "H5'" "C5'" single 1.092 0.020
ATD "H5''" "C5'" single 1.092 0.020
ATD "C4'" "O4'" single 1.426 0.020
ATD "C4'" "C3'" single 1.524 0.020
ATD "H4'" "C4'" single 1.099 0.020
ATD "O4'" "C1'" single 1.426 0.020
ATD "O3'" "C3'" single 1.426 0.020
ATD "C3'" "C2'" single 1.524 0.020
ATD "H3'" "C3'" single 1.099 0.020
ATD "C2'" "C1'" single 1.524 0.020
ATD "H2'" "C2'" single 1.092 0.020
ATD "H2''" "C2'" single 1.092 0.020
ATD "C1'" N1 single 1.465 0.020
ATD "H1'" "C1'" single 1.099 0.020
ATD N1 C2 single 1.410 0.020
ATD N1 C6 single 1.337 0.020
ATD O2 C2 double 1.250 0.020
ATD C2 N3 single 1.337 0.020
ATD N3 C4 single 1.337 0.020
ATD H3 N3 single 1.040 0.020
ATD C4 O4 double 1.250 0.020
ATD C5 C4 single 1.487 0.020
ATD C5M C5 single 1.506 0.020
ATD C6 C5 double 1.390 0.020
ATD H71 C5M single 1.059 0.020
ATD H72 C5M single 1.059 0.020
ATD H73 C5M single 1.059 0.020
ATD H6 C6 single 1.083 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
ATD O4 C4 N3 120.000 3.000
ATD O4 C4 C5 120.000 3.000
ATD N3 C4 C5 120.000 3.000
ATD C4 N3 H3 120.000 3.000
ATD C4 N3 C2 120.000 3.000
ATD H3 N3 C2 120.000 3.000
ATD N3 C2 O2 120.000 3.000
ATD N3 C2 N1 120.000 3.000
ATD O2 C2 N1 120.000 3.000
ATD C4 C5 C5M 120.000 3.000
ATD C4 C5 C6 120.000 3.000
ATD C5M C5 C6 120.000 3.000
ATD C5 C5M H73 109.470 3.000
ATD C5 C5M H72 109.470 3.000
ATD C5 C5M H71 109.470 3.000
ATD H73 C5M H72 109.470 3.000
ATD H73 C5M H71 109.470 3.000
ATD H72 C5M H71 109.470 3.000
ATD C5 C6 H6 120.000 3.000
ATD C5 C6 N1 120.000 3.000
ATD H6 C6 N1 120.000 3.000
ATD C6 N1 "C1'" 120.000 3.000
ATD C6 N1 C2 120.000 3.000
ATD "C1'" N1 C2 120.000 3.000
ATD N1 "C1'" "H1'" 109.470 3.000
ATD N1 "C1'" "O4'" 109.470 3.000
ATD N1 "C1'" "C2'" 109.470 3.000
ATD "H1'" "C1'" "O4'" 109.470 3.000
ATD "H1'" "C1'" "C2'" 108.340 3.000
ATD "O4'" "C1'" "C2'" 109.470 3.000
ATD "C1'" "O4'" "C4'" 111.800 3.000
ATD "C1'" "C2'" "H2'" 109.470 3.000
ATD "C1'" "C2'" "H2''" 109.470 3.000
ATD "C1'" "C2'" "C3'" 111.000 3.000
ATD "H2'" "C2'" "H2''" 107.900 3.000
ATD "H2'" "C2'" "C3'" 109.470 3.000
ATD "H2''" "C2'" "C3'" 109.470 3.000
ATD "C2'" "C3'" "H3'" 108.340 3.000
ATD "C2'" "C3'" "O3'" 109.470 3.000
ATD "C2'" "C3'" "C4'" 111.000 3.000
ATD "H3'" "C3'" "O3'" 109.470 3.000
ATD "H3'" "C3'" "C4'" 108.340 3.000
ATD "O3'" "C3'" "C4'" 109.470 3.000
ATD "C3'" "O3'" P 120.500 3.000
ATD "O3'" P OP2 108.200 3.000
ATD "O3'" P OP1 108.200 3.000
ATD "O3'" P OP3 108.200 3.000
ATD OP2 P OP1 119.900 3.000
ATD OP2 P OP3 119.900 3.000
ATD OP1 P OP3 119.900 3.000
ATD "C3'" "C4'" "H4'" 108.340 3.000
ATD "C3'" "C4'" "C5'" 111.000 3.000
ATD "C3'" "C4'" "O4'" 109.470 3.000
ATD "H4'" "C4'" "C5'" 108.340 3.000
ATD "H4'" "C4'" "O4'" 109.470 3.000
ATD "C5'" "C4'" "O4'" 109.470 3.000
ATD "C4'" "C5'" "H5'" 109.470 3.000
ATD "C4'" "C5'" "H5''" 109.470 3.000
ATD "C4'" "C5'" "O5'" 109.470 3.000
ATD "H5'" "C5'" "H5''" 107.900 3.000
ATD "H5'" "C5'" "O5'" 109.470 3.000
ATD "H5''" "C5'" "O5'" 109.470 3.000
ATD "C5'" "O5'" "HO'5" 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
ATD CONST_1 O4 C4 N3 C2 180.000 0.000 0
ATD CONST_2 C4 N3 C2 O2 180.000 0.000 0
ATD CONST_3 O4 C4 C5 C6 180.000 0.000 0
ATD var_1 C4 C5 C5M H71 -0.218 20.000 1
ATD CONST_4 C4 C5 C6 N1 0.000 0.000 0
ATD CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
ATD CONST_6 C6 N1 C2 N3 0.000 0.000 0
ATD var_2 C6 N1 "C1'" "C2'" -121.392 20.000 1
ATD var_3 N1 "C1'" "O4'" "C4'" 150.000 20.000 1
ATD var_4 N1 "C1'" "C2'" "C3'" -150.000 20.000 3
ATD var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
ATD var_6 "C2'" "C3'" "O3'" P 121.458 20.000 1
ATD var_7 "C3'" "O3'" P OP3 -60.016 20.000 1
ATD var_8 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
ATD var_9 "C3'" "C4'" "O4'" "C1'" 0.000 20.000 1
ATD var_10 "C3'" "C4'" "C5'" "O5'" -179.969 20.000 3
ATD var_11 "C4'" "C5'" "O5'" "HO'5" 179.995 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
ATD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
ATD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
ATD chir_03 "C1'" "O4'" "C2'" N1 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
ATD plan-1 N1 0.020
ATD plan-1 "C1'" 0.020
ATD plan-1 C2 0.020
ATD plan-1 C6 0.020
ATD plan-1 N3 0.020
ATD plan-1 C4 0.020
ATD plan-1 C5 0.020
ATD plan-1 O2 0.020
ATD plan-1 H3 0.020
ATD plan-1 O4 0.020
ATD plan-1 C5M 0.020
ATD plan-1 H6 0.020
# ------------------------------------------------------
|
