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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
TDX TDX 'THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE' non-polymer 56 34 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TDX
#
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
TDX O2B O OP -0.500 0.000 0.000 0.000
TDX PB P P 0.000 -0.767 0.066 -1.268
TDX O1B O OP -0.500 -1.011 -1.307 -1.770
TDX "O1'" O O2 0.000 0.074 0.896 -2.360
TDX "C1'" C CH1 0.000 1.306 0.199 -2.550
TDX "H1'" H H 0.000 1.582 -0.316 -1.619
TDX "C2'" C CH1 0.000 2.404 1.197 -2.924
TDX "H2'" H H 0.000 3.348 0.660 -3.093
TDX "O2'" O OH1 0.000 2.574 2.140 -1.862
TDX "HO2'" H H 0.000 2.831 1.673 -1.056
TDX "C3'" C CH1 0.000 1.997 1.934 -4.202
TDX "H3'" H H 0.000 1.112 2.555 -4.004
TDX "O3'" O OH1 0.000 3.074 2.761 -4.646
TDX HO3A H H 0.000 2.817 3.214 -5.461
TDX "C4'" C CH1 0.000 1.667 0.896 -5.280
TDX "H4'" H H 0.000 2.579 0.345 -5.552
TDX "O4'" O OH1 0.000 1.144 1.553 -6.436
TDX "HO4'" H H 0.000 0.931 0.894 -7.111
TDX "C5'" C CH2 0.000 0.625 -0.080 -4.730
TDX H5D H H 0.000 0.367 -0.806 -5.504
TDX H5B H H 0.000 -0.270 0.474 -4.441
TDX "O5'" O O2 0.000 1.153 -0.760 -3.593
TDX O3A O O2 0.000 -2.177 0.799 -1.004
TDX PA P P 0.000 -2.961 -0.079 0.093
TDX O1A O OP -0.500 -3.171 -1.450 -0.431
TDX O2A O OP -0.500 -2.160 -0.144 1.340
TDX O5B O O2 0.000 -4.385 0.599 0.405
TDX C5B C CH2 0.000 -5.029 -0.223 1.380
TDX "H5'1" H H 0.000 -4.414 -0.268 2.281
TDX "H5'2" H H 0.000 -5.158 -1.230 0.979
TDX C4B C CH1 0.000 -6.398 0.370 1.724
TDX H4B H H 0.000 -6.292 1.403 2.084
TDX C3B C CH1 0.000 -7.122 -0.503 2.781
TDX H3B H H 0.000 -6.931 -1.570 2.604
TDX O3B O OH1 0.000 -6.732 -0.128 4.104
TDX "HO3'" H H 0.000 -7.262 -0.619 4.747
TDX C2B C CH2 0.000 -8.608 -0.158 2.523
TDX "H2'2" H H 0.000 -8.977 0.604 3.213
TDX "H2'1" H H 0.000 -9.249 -1.041 2.581
TDX O4B O O2 0.000 -7.280 0.319 0.580
TDX C1B C CH1 0.000 -8.623 0.397 1.086
TDX H1B H H 0.000 -8.960 1.443 1.093
TDX N1 N NR6 0.000 -9.518 -0.408 0.251
TDX C2 C CR6 0.000 -9.279 -1.722 0.093
TDX O2 O O 0.000 -8.321 -2.227 0.646
TDX N3 N NR16 0.000 -10.085 -2.486 -0.668
TDX H3 H H 0.000 -9.882 -3.499 -0.781
TDX C6 C CR16 0.000 -10.590 0.184 -0.360
TDX H6 H H 0.000 -10.775 1.242 -0.228
TDX C5 C CR6 0.000 -11.414 -0.559 -1.130
TDX C5M C CH3 0.000 -12.599 0.075 -1.811
TDX H5M3 H H 0.000 -13.244 0.492 -1.081
TDX H5M2 H H 0.000 -12.264 0.838 -2.464
TDX H5M1 H H 0.000 -13.122 -0.660 -2.365
TDX C4 C CR6 0.000 -11.153 -1.941 -1.284
TDX O4 O O 0.000 -11.883 -2.631 -1.973
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
TDX O2B n/a PB START
TDX PB O2B O3A .
TDX O1B PB . .
TDX "O1'" PB "C1'" .
TDX "C1'" "O1'" "C2'" .
TDX "H1'" "C1'" . .
TDX "C2'" "C1'" "C3'" .
TDX "H2'" "C2'" . .
TDX "O2'" "C2'" "HO2'" .
TDX "HO2'" "O2'" . .
TDX "C3'" "C2'" "C4'" .
TDX "H3'" "C3'" . .
TDX "O3'" "C3'" HO3A .
TDX HO3A "O3'" . .
TDX "C4'" "C3'" "C5'" .
TDX "H4'" "C4'" . .
TDX "O4'" "C4'" "HO4'" .
TDX "HO4'" "O4'" . .
TDX "C5'" "C4'" "O5'" .
TDX H5D "C5'" . .
TDX H5B "C5'" . .
TDX "O5'" "C5'" . .
TDX O3A PB PA .
TDX PA O3A O5B .
TDX O1A PA . .
TDX O2A PA . .
TDX O5B PA C5B .
TDX C5B O5B C4B .
TDX "H5'1" C5B . .
TDX "H5'2" C5B . .
TDX C4B C5B O4B .
TDX H4B C4B . .
TDX C3B C4B C2B .
TDX H3B C3B . .
TDX O3B C3B "HO3'" .
TDX "HO3'" O3B . .
TDX C2B C3B "H2'1" .
TDX "H2'2" C2B . .
TDX "H2'1" C2B . .
TDX O4B C4B C1B .
TDX C1B O4B N1 .
TDX H1B C1B . .
TDX N1 C1B C6 .
TDX C2 N1 N3 .
TDX O2 C2 . .
TDX N3 C2 H3 .
TDX H3 N3 . .
TDX C6 N1 C5 .
TDX H6 C6 . .
TDX C5 C6 C4 .
TDX C5M C5 H5M1 .
TDX H5M3 C5M . .
TDX H5M2 C5M . .
TDX H5M1 C5M . .
TDX C4 C5 O4 .
TDX O4 C4 . END
TDX C4 N3 . ADD
TDX C1B C2B . ADD
TDX "C1'" "O5'" . 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
TDX O4 C4 double 1.250 0.020
TDX C4 N3 single 1.337 0.020
TDX C4 C5 single 1.487 0.020
TDX N3 C2 single 1.337 0.020
TDX H3 N3 single 1.040 0.020
TDX O2 C2 double 1.250 0.020
TDX C2 N1 single 1.410 0.020
TDX C5M C5 single 1.506 0.020
TDX C5 C6 double 1.390 0.020
TDX H5M1 C5M single 1.059 0.020
TDX H5M2 C5M single 1.059 0.020
TDX H5M3 C5M single 1.059 0.020
TDX C6 N1 single 1.337 0.020
TDX H6 C6 single 1.083 0.020
TDX N1 C1B single 1.465 0.020
TDX C1B C2B single 1.524 0.020
TDX C1B O4B single 1.426 0.020
TDX H1B C1B single 1.099 0.020
TDX C2B C3B single 1.524 0.020
TDX "H2'1" C2B single 1.092 0.020
TDX "H2'2" C2B single 1.092 0.020
TDX O3B C3B single 1.432 0.020
TDX C3B C4B single 1.524 0.020
TDX H3B C3B single 1.099 0.020
TDX "HO3'" O3B single 0.967 0.020
TDX O4B C4B single 1.426 0.020
TDX C4B C5B single 1.524 0.020
TDX H4B C4B single 1.099 0.020
TDX C5B O5B single 1.426 0.020
TDX "H5'1" C5B single 1.092 0.020
TDX "H5'2" C5B single 1.092 0.020
TDX O5B PA single 1.610 0.020
TDX O1A PA deloc 1.510 0.020
TDX O2A PA deloc 1.510 0.020
TDX PA O3A single 1.610 0.020
TDX O3A PB single 1.610 0.020
TDX O1B PB deloc 1.510 0.020
TDX PB O2B deloc 1.510 0.020
TDX "O1'" PB single 1.610 0.020
TDX "C1'" "O1'" single 1.426 0.020
TDX "C1'" "O5'" single 1.426 0.020
TDX "C2'" "C1'" single 1.524 0.020
TDX "H1'" "C1'" single 1.099 0.020
TDX "O5'" "C5'" single 1.426 0.020
TDX "C5'" "C4'" single 1.524 0.020
TDX H5B "C5'" single 1.092 0.020
TDX H5D "C5'" single 1.092 0.020
TDX "O2'" "C2'" single 1.432 0.020
TDX "C3'" "C2'" single 1.524 0.020
TDX "H2'" "C2'" single 1.099 0.020
TDX "HO2'" "O2'" single 0.967 0.020
TDX "O3'" "C3'" single 1.432 0.020
TDX "C4'" "C3'" single 1.524 0.020
TDX "H3'" "C3'" single 1.099 0.020
TDX HO3A "O3'" single 0.967 0.020
TDX "O4'" "C4'" single 1.432 0.020
TDX "H4'" "C4'" single 1.099 0.020
TDX "HO4'" "O4'" 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
TDX O2B PB O1B 119.900 3.000
TDX O2B PB "O1'" 108.200 3.000
TDX O2B PB O3A 108.200 3.000
TDX O1B PB "O1'" 108.200 3.000
TDX O1B PB O3A 108.200 3.000
TDX "O1'" PB O3A 102.600 3.000
TDX PB "O1'" "C1'" 120.500 3.000
TDX "O1'" "C1'" "H1'" 109.470 3.000
TDX "O1'" "C1'" "C2'" 109.470 3.000
TDX "O1'" "C1'" "O5'" 109.470 3.000
TDX "H1'" "C1'" "C2'" 108.340 3.000
TDX "H1'" "C1'" "O5'" 109.470 3.000
TDX "C2'" "C1'" "O5'" 109.470 3.000
TDX "C1'" "C2'" "H2'" 108.340 3.000
TDX "C1'" "C2'" "O2'" 109.470 3.000
TDX "C1'" "C2'" "C3'" 111.000 3.000
TDX "H2'" "C2'" "O2'" 109.470 3.000
TDX "H2'" "C2'" "C3'" 108.340 3.000
TDX "O2'" "C2'" "C3'" 109.470 3.000
TDX "C2'" "O2'" "HO2'" 109.470 3.000
TDX "C2'" "C3'" "H3'" 108.340 3.000
TDX "C2'" "C3'" "O3'" 109.470 3.000
TDX "C2'" "C3'" "C4'" 111.000 3.000
TDX "H3'" "C3'" "O3'" 109.470 3.000
TDX "H3'" "C3'" "C4'" 108.340 3.000
TDX "O3'" "C3'" "C4'" 109.470 3.000
TDX "C3'" "O3'" HO3A 109.470 3.000
TDX "C3'" "C4'" "H4'" 108.340 3.000
TDX "C3'" "C4'" "O4'" 109.470 3.000
TDX "C3'" "C4'" "C5'" 111.000 3.000
TDX "H4'" "C4'" "O4'" 109.470 3.000
TDX "H4'" "C4'" "C5'" 108.340 3.000
TDX "O4'" "C4'" "C5'" 109.470 3.000
TDX "C4'" "O4'" "HO4'" 109.470 3.000
TDX "C4'" "C5'" H5D 109.470 3.000
TDX "C4'" "C5'" H5B 109.470 3.000
TDX "C4'" "C5'" "O5'" 109.470 3.000
TDX H5D "C5'" H5B 107.900 3.000
TDX H5D "C5'" "O5'" 109.470 3.000
TDX H5B "C5'" "O5'" 109.470 3.000
TDX "C5'" "O5'" "C1'" 111.800 3.000
TDX PB O3A PA 120.500 3.000
TDX O3A PA O1A 108.200 3.000
TDX O3A PA O2A 108.200 3.000
TDX O3A PA O5B 102.600 3.000
TDX O1A PA O2A 119.900 3.000
TDX O1A PA O5B 108.200 3.000
TDX O2A PA O5B 108.200 3.000
TDX PA O5B C5B 120.500 3.000
TDX O5B C5B "H5'1" 109.470 3.000
TDX O5B C5B "H5'2" 109.470 3.000
TDX O5B C5B C4B 109.470 3.000
TDX "H5'1" C5B "H5'2" 107.900 3.000
TDX "H5'1" C5B C4B 109.470 3.000
TDX "H5'2" C5B C4B 109.470 3.000
TDX C5B C4B H4B 108.340 3.000
TDX C5B C4B C3B 111.000 3.000
TDX C5B C4B O4B 109.470 3.000
TDX H4B C4B C3B 108.340 3.000
TDX H4B C4B O4B 109.470 3.000
TDX C3B C4B O4B 109.470 3.000
TDX C4B C3B H3B 108.340 3.000
TDX C4B C3B O3B 109.470 3.000
TDX C4B C3B C2B 111.000 3.000
TDX H3B C3B O3B 109.470 3.000
TDX H3B C3B C2B 108.340 3.000
TDX O3B C3B C2B 109.470 3.000
TDX C3B O3B "HO3'" 109.470 3.000
TDX C3B C2B "H2'2" 109.470 3.000
TDX C3B C2B "H2'1" 109.470 3.000
TDX C3B C2B C1B 111.000 3.000
TDX "H2'2" C2B "H2'1" 107.900 3.000
TDX "H2'2" C2B C1B 109.470 3.000
TDX "H2'1" C2B C1B 109.470 3.000
TDX C4B O4B C1B 111.800 3.000
TDX O4B C1B H1B 109.470 3.000
TDX O4B C1B N1 109.470 3.000
TDX O4B C1B C2B 109.470 3.000
TDX H1B C1B N1 109.470 3.000
TDX H1B C1B C2B 108.340 3.000
TDX N1 C1B C2B 109.470 3.000
TDX C1B N1 C2 120.000 3.000
TDX C1B N1 C6 120.000 3.000
TDX C2 N1 C6 120.000 3.000
TDX N1 C2 O2 120.000 3.000
TDX N1 C2 N3 120.000 3.000
TDX O2 C2 N3 120.000 3.000
TDX C2 N3 H3 120.000 3.000
TDX C2 N3 C4 120.000 3.000
TDX H3 N3 C4 120.000 3.000
TDX N1 C6 H6 120.000 3.000
TDX N1 C6 C5 120.000 3.000
TDX H6 C6 C5 120.000 3.000
TDX C6 C5 C5M 120.000 3.000
TDX C6 C5 C4 120.000 3.000
TDX C5M C5 C4 120.000 3.000
TDX C5 C5M H5M3 109.470 3.000
TDX C5 C5M H5M2 109.470 3.000
TDX C5 C5M H5M1 109.470 3.000
TDX H5M3 C5M H5M2 109.470 3.000
TDX H5M3 C5M H5M1 109.470 3.000
TDX H5M2 C5M H5M1 109.470 3.000
TDX C5 C4 O4 120.000 3.000
TDX C5 C4 N3 120.000 3.000
TDX O4 C4 N3 120.000 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
TDX var_1 O2B PB "O1'" "C1'" 60.026 20.000 1
TDX var_2 PB "O1'" "C1'" "C2'" -149.877 20.000 1
TDX var_3 "O1'" "C1'" "O5'" "C5'" 60.000 20.000 1
TDX var_4 "O1'" "C1'" "C2'" "C3'" -60.000 20.000 3
TDX var_5 "C1'" "C2'" "O2'" "HO2'" 60.426 20.000 1
TDX var_6 "C1'" "C2'" "C3'" "C4'" -60.000 20.000 3
TDX var_7 "C2'" "C3'" "O3'" HO3A 179.122 20.000 1
TDX var_8 "C2'" "C3'" "C4'" "C5'" 60.000 20.000 3
TDX var_9 "C3'" "C4'" "O4'" "HO4'" -179.563 20.000 1
TDX var_10 "C3'" "C4'" "C5'" "O5'" -60.000 20.000 3
TDX var_11 "C4'" "C5'" "O5'" "C1'" 60.000 20.000 1
TDX var_12 O2B PB O3A PA -59.941 20.000 1
TDX var_13 PB O3A PA O5B -179.986 20.000 1
TDX var_14 O3A PA O5B C5B 179.973 20.000 1
TDX var_15 PA O5B C5B C4B 179.959 20.000 1
TDX var_16 O5B C5B C4B O4B 65.689 20.000 3
TDX var_17 C5B C4B C3B C2B -150.000 20.000 3
TDX var_18 C4B C3B O3B "HO3'" 174.119 20.000 1
TDX var_19 C4B C3B C2B C1B 30.000 20.000 3
TDX var_20 C5B C4B O4B C1B 150.000 20.000 1
TDX var_21 C4B O4B C1B N1 -150.000 20.000 1
TDX var_22 O4B C1B C2B C3B 0.000 20.000 3
TDX var_23 O4B C1B N1 C6 -121.661 20.000 1
TDX CONST_1 C1B N1 C2 N3 180.000 0.000 0
TDX CONST_2 N1 C2 N3 C4 0.000 0.000 0
TDX CONST_3 C1B N1 C6 C5 180.000 0.000 0
TDX CONST_4 N1 C6 C5 C4 0.000 0.000 0
TDX var_24 C6 C5 C5M H5M1 179.976 20.000 1
TDX CONST_5 C6 C5 C4 O4 180.000 0.000 0
TDX CONST_6 C5 C4 N3 C2 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
TDX chir_01 C1B N1 C2B O4B negativ
TDX chir_02 C3B C2B O3B C4B positiv
TDX chir_03 C4B C3B O4B C5B positiv
TDX chir_04 "C1'" "O1'" "O5'" "C2'" negativ
TDX chir_05 "C2'" "C1'" "O2'" "C3'" positiv
TDX chir_06 "C3'" "C2'" "O3'" "C4'" negativ
TDX chir_07 "C4'" "C5'" "C3'" "O4'" 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
TDX plan-1 C4 0.020
TDX plan-1 O4 0.020
TDX plan-1 N3 0.020
TDX plan-1 C5 0.020
TDX plan-1 C2 0.020
TDX plan-1 C6 0.020
TDX plan-1 N1 0.020
TDX plan-1 H3 0.020
TDX plan-1 O2 0.020
TDX plan-1 C5M 0.020
TDX plan-1 H6 0.020
TDX plan-1 C1B 0.020
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