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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
TYD TYD 'THYMIDINE-5'-DIPHOSPHATE ' non-polymer 38 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TYD
#
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
TYD O4 O O 0.000 0.000 0.000 0.000
TYD C4 C CR6 0.000 -1.135 -0.295 0.328
TYD N3 N NR16 0.000 -2.116 0.630 0.295
TYD HN3 H H 0.000 -1.902 1.600 -0.012
TYD C2 C CR6 0.000 -3.370 0.301 0.657
TYD O2 O O 0.000 -4.243 1.148 0.625
TYD C5 C CR6 0.000 -1.440 -1.615 0.738
TYD C5M C CH3 0.000 -0.363 -2.669 0.780
TYD H53 H H 0.000 -0.265 -3.034 1.769
TYD H52 H H 0.000 -0.624 -3.466 0.133
TYD H51 H H 0.000 0.556 -2.247 0.466
TYD C6 C CR16 0.000 -2.706 -1.916 1.096
TYD H6 H H 0.000 -2.957 -2.920 1.417
TYD N1 N NR6 0.000 -3.670 -0.947 1.052
TYD "C1'" C CH1 0.000 -5.045 -1.274 1.441
TYD "H1'" H H 0.000 -5.112 -2.334 1.723
TYD "O4'" O O2 0.000 -5.940 -1.000 0.350
TYD "C2'" C CH2 0.000 -5.478 -0.389 2.626
TYD "H2'1" H H 0.000 -4.708 0.334 2.900
TYD "H2'2" H H 0.000 -5.748 -0.982 3.502
TYD "C3'" C CH1 0.000 -6.728 0.359 2.102
TYD "H3'" H H 0.000 -6.460 1.362 1.740
TYD "O3'" O OH1 0.000 -7.737 0.435 3.111
TYD "HO3'" H H 0.000 -7.397 0.929 3.870
TYD "C4'" C CH1 0.000 -7.184 -0.546 0.931
TYD "H4'" H H 0.000 -7.768 -1.398 1.306
TYD "C5'" C CH2 0.000 -7.996 0.255 -0.087
TYD "H5'1" H H 0.000 -7.382 1.067 -0.483
TYD "H5'2" H H 0.000 -8.879 0.674 0.402
TYD "O5'" O O2 0.000 -8.402 -0.602 -1.155
TYD PA P P 0.000 -9.248 0.304 -2.183
TYD O1A O OP -0.500 -8.394 1.406 -2.688
TYD O2A O OP -0.500 -10.427 0.872 -1.486
TYD O3A O O2 0.000 -9.741 -0.604 -3.417
TYD PB P P 0.000 -10.575 0.360 -4.399
TYD O1B O OP -0.666 -9.684 1.483 -4.881
TYD O2B O OP -0.666 -11.070 -0.436 -5.587
TYD O3B O OP -0.666 -11.758 0.939 -3.654
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
TYD O4 n/a C4 START
TYD C4 O4 C5 .
TYD N3 C4 C2 .
TYD HN3 N3 . .
TYD C2 N3 O2 .
TYD O2 C2 . .
TYD C5 C4 C6 .
TYD C5M C5 H51 .
TYD H53 C5M . .
TYD H52 C5M . .
TYD H51 C5M . .
TYD C6 C5 N1 .
TYD H6 C6 . .
TYD N1 C6 "C1'" .
TYD "C1'" N1 "C2'" .
TYD "H1'" "C1'" . .
TYD "O4'" "C1'" . .
TYD "C2'" "C1'" "C3'" .
TYD "H2'1" "C2'" . .
TYD "H2'2" "C2'" . .
TYD "C3'" "C2'" "C4'" .
TYD "H3'" "C3'" . .
TYD "O3'" "C3'" "HO3'" .
TYD "HO3'" "O3'" . .
TYD "C4'" "C3'" "C5'" .
TYD "H4'" "C4'" . .
TYD "C5'" "C4'" "O5'" .
TYD "H5'1" "C5'" . .
TYD "H5'2" "C5'" . .
TYD "O5'" "C5'" PA .
TYD PA "O5'" O3A .
TYD O1A PA . .
TYD O2A PA . .
TYD O3A PA PB .
TYD PB O3A O3B .
TYD O1B PB . .
TYD O2B PB . .
TYD O3B PB . END
TYD "C4'" "O4'" . ADD
TYD 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
TYD O1A PA deloc 1.510 0.020
TYD O2A PA deloc 1.510 0.020
TYD O3A PA single 1.610 0.020
TYD PA "O5'" single 1.610 0.020
TYD PB O3A single 1.610 0.020
TYD O1B PB deloc 1.510 0.020
TYD O2B PB deloc 1.510 0.020
TYD O3B PB deloc 1.510 0.020
TYD "O5'" "C5'" single 1.426 0.020
TYD "C5'" "C4'" single 1.524 0.020
TYD "H5'1" "C5'" single 1.092 0.020
TYD "H5'2" "C5'" single 1.092 0.020
TYD "C4'" "O4'" single 1.426 0.020
TYD "C4'" "C3'" single 1.524 0.020
TYD "H4'" "C4'" single 1.099 0.020
TYD "O4'" "C1'" single 1.426 0.020
TYD "O3'" "C3'" single 1.432 0.020
TYD "C3'" "C2'" single 1.524 0.020
TYD "H3'" "C3'" single 1.099 0.020
TYD "HO3'" "O3'" single 0.967 0.020
TYD "C2'" "C1'" single 1.524 0.020
TYD "H2'1" "C2'" single 1.092 0.020
TYD "H2'2" "C2'" single 1.092 0.020
TYD "C1'" N1 single 1.465 0.020
TYD "H1'" "C1'" single 1.099 0.020
TYD N1 C2 single 1.410 0.020
TYD N1 C6 single 1.337 0.020
TYD O2 C2 double 1.250 0.020
TYD C2 N3 single 1.337 0.020
TYD N3 C4 single 1.337 0.020
TYD HN3 N3 single 1.040 0.020
TYD C4 O4 double 1.250 0.020
TYD C5 C4 single 1.487 0.020
TYD C5M C5 single 1.506 0.020
TYD C6 C5 double 1.390 0.020
TYD H51 C5M single 1.059 0.020
TYD H52 C5M single 1.059 0.020
TYD H53 C5M single 1.059 0.020
TYD 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
TYD O4 C4 N3 120.000 3.000
TYD O4 C4 C5 120.000 3.000
TYD N3 C4 C5 120.000 3.000
TYD C4 N3 HN3 120.000 3.000
TYD C4 N3 C2 120.000 3.000
TYD HN3 N3 C2 120.000 3.000
TYD N3 C2 O2 120.000 3.000
TYD N3 C2 N1 120.000 3.000
TYD O2 C2 N1 120.000 3.000
TYD C4 C5 C5M 120.000 3.000
TYD C4 C5 C6 120.000 3.000
TYD C5M C5 C6 120.000 3.000
TYD C5 C5M H53 109.470 3.000
TYD C5 C5M H52 109.470 3.000
TYD C5 C5M H51 109.470 3.000
TYD H53 C5M H52 109.470 3.000
TYD H53 C5M H51 109.470 3.000
TYD H52 C5M H51 109.470 3.000
TYD C5 C6 H6 120.000 3.000
TYD C5 C6 N1 120.000 3.000
TYD H6 C6 N1 120.000 3.000
TYD C6 N1 "C1'" 120.000 3.000
TYD C6 N1 C2 120.000 3.000
TYD "C1'" N1 C2 120.000 3.000
TYD N1 "C1'" "H1'" 109.470 3.000
TYD N1 "C1'" "O4'" 109.470 3.000
TYD N1 "C1'" "C2'" 109.470 3.000
TYD "H1'" "C1'" "O4'" 109.470 3.000
TYD "H1'" "C1'" "C2'" 108.340 3.000
TYD "O4'" "C1'" "C2'" 109.470 3.000
TYD "C1'" "O4'" "C4'" 111.800 3.000
TYD "C1'" "C2'" "H2'1" 109.470 3.000
TYD "C1'" "C2'" "H2'2" 109.470 3.000
TYD "C1'" "C2'" "C3'" 111.000 3.000
TYD "H2'1" "C2'" "H2'2" 107.900 3.000
TYD "H2'1" "C2'" "C3'" 109.470 3.000
TYD "H2'2" "C2'" "C3'" 109.470 3.000
TYD "C2'" "C3'" "H3'" 108.340 3.000
TYD "C2'" "C3'" "O3'" 109.470 3.000
TYD "C2'" "C3'" "C4'" 111.000 3.000
TYD "H3'" "C3'" "O3'" 109.470 3.000
TYD "H3'" "C3'" "C4'" 108.340 3.000
TYD "O3'" "C3'" "C4'" 109.470 3.000
TYD "C3'" "O3'" "HO3'" 109.470 3.000
TYD "C3'" "C4'" "H4'" 108.340 3.000
TYD "C3'" "C4'" "C5'" 111.000 3.000
TYD "C3'" "C4'" "O4'" 109.470 3.000
TYD "H4'" "C4'" "C5'" 108.340 3.000
TYD "H4'" "C4'" "O4'" 109.470 3.000
TYD "C5'" "C4'" "O4'" 109.470 3.000
TYD "C4'" "C5'" "H5'1" 109.470 3.000
TYD "C4'" "C5'" "H5'2" 109.470 3.000
TYD "C4'" "C5'" "O5'" 109.470 3.000
TYD "H5'1" "C5'" "H5'2" 107.900 3.000
TYD "H5'1" "C5'" "O5'" 109.470 3.000
TYD "H5'2" "C5'" "O5'" 109.470 3.000
TYD "C5'" "O5'" PA 120.500 3.000
TYD "O5'" PA O1A 108.200 3.000
TYD "O5'" PA O2A 108.200 3.000
TYD "O5'" PA O3A 102.600 3.000
TYD O1A PA O2A 119.900 3.000
TYD O1A PA O3A 108.200 3.000
TYD O2A PA O3A 108.200 3.000
TYD PA O3A PB 120.500 3.000
TYD O3A PB O1B 108.200 3.000
TYD O3A PB O2B 108.200 3.000
TYD O3A PB O3B 108.200 3.000
TYD O1B PB O2B 119.900 3.000
TYD O1B PB O3B 119.900 3.000
TYD O2B PB O3B 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
TYD CONST_1 O4 C4 N3 C2 180.000 0.000 0
TYD CONST_2 C4 N3 C2 O2 180.000 0.000 0
TYD CONST_3 O4 C4 C5 C6 180.000 0.000 0
TYD var_1 C4 C5 C5M H51 -0.288 20.000 1
TYD CONST_4 C4 C5 C6 N1 0.000 0.000 0
TYD CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
TYD CONST_6 C6 N1 C2 N3 0.000 0.000 0
TYD var_2 C6 N1 "C1'" "C2'" 120.291 20.000 1
TYD var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
TYD var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
TYD var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
TYD var_6 "C2'" "C3'" "O3'" "HO3'" 61.430 20.000 1
TYD var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
TYD var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
TYD var_9 "C3'" "C4'" "C5'" "O5'" 179.960 20.000 3
TYD var_10 "C4'" "C5'" "O5'" PA 180.000 20.000 1
TYD var_11 "C5'" "O5'" PA O3A -179.919 20.000 1
TYD var_12 "O5'" PA O3A PB -179.996 20.000 1
TYD var_13 PA O3A PB O3B -60.083 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
TYD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
TYD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
TYD chir_03 "C1'" "O4'" "C2'" N1 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
TYD plan-1 N1 0.020
TYD plan-1 "C1'" 0.020
TYD plan-1 C2 0.020
TYD plan-1 C6 0.020
TYD plan-1 N3 0.020
TYD plan-1 C4 0.020
TYD plan-1 C5 0.020
TYD plan-1 O2 0.020
TYD plan-1 HN3 0.020
TYD plan-1 O4 0.020
TYD plan-1 C5M 0.020
TYD plan-1 H6 0.020
# ------------------------------------------------------
|
