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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
THD THD '"2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDIN' non-polymer 49 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_THD
#
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
THD O3B O OP -0.666 0.000 0.000 0.000
THD PB P P 0.000 -0.199 1.333 -0.687
THD O1B O OP -0.666 -0.544 1.103 -2.143
THD O2B O OP -0.666 1.076 2.143 -0.592
THD O3A O O2 0.000 -1.399 2.131 0.029
THD PA P P 0.000 -2.715 1.215 -0.109
THD O1A O OP -0.500 -3.014 0.992 -1.545
THD O2A O OP -0.500 -2.482 -0.089 0.556
THD O7 O O2 0.000 -3.961 1.958 0.589
THD C7 C CH2 0.000 -5.093 1.100 0.434
THD H7C1 H H 0.000 -4.891 0.141 0.917
THD H7C2 H H 0.000 -5.283 0.937 -0.629
THD C6 C CH2 0.000 -6.318 1.750 1.080
THD H6C1 H H 0.000 -6.518 2.709 0.597
THD H6C2 H H 0.000 -6.126 1.913 2.143
THD C5 C CR5 0.000 -7.512 0.845 0.917
THD S1 S S2 0.000 -8.701 0.796 -0.412
THD C2 C CR5 0.000 -9.714 -0.538 0.208
THD C8 C C 0.000 -10.808 -1.089 -0.325
THD C9 C CH2 0.000 -11.270 -0.672 -1.696
THD H9C1 H H 0.000 -10.592 0.086 -2.093
THD H9C2 H H 0.000 -12.278 -0.257 -1.629
THD O10 O OH1 0.000 -11.277 -1.807 -2.563
THD H10 H H 0.000 -11.575 -1.538 -3.442
THD O9 O OH1 0.000 -11.505 -2.032 0.374
THD H9 H H 0.000 -12.390 -1.698 0.587
THD C4 C CR5 0.000 -7.942 -0.118 1.726
THD CM4 C CH3 0.000 -7.197 -0.411 3.003
THD HM43 H H 0.000 -7.843 -0.267 3.830
THD HM42 H H 0.000 -6.858 -1.414 2.991
THD HM41 H H 0.000 -6.367 0.242 3.085
THD N3 N NR5 0.000 -9.059 -0.842 1.409
THD "C7'" C CH2 0.000 -9.547 -1.907 2.288
THD "H7'1" H H 0.000 -8.718 -2.295 2.884
THD "H7'2" H H 0.000 -9.967 -2.713 1.684
THD "C5'" C CR6 0.000 -10.610 -1.355 3.202
THD "C6'" C CR16 0.000 -10.987 -0.029 3.130
THD "H6'" H H 0.000 -10.520 0.635 2.412
THD "N1'" N NRD6 0.000 -11.925 0.423 3.949
THD "C4'" C CR6 0.000 -11.240 -2.172 4.142
THD "N4'" N NH2 0.000 -10.898 -3.509 4.255
THD "H4'2" H H 0.000 -10.184 -3.912 3.654
THD "H4'1" H H 0.000 -11.356 -4.103 4.939
THD "N3'" N NRD6 0.000 -12.169 -1.644 4.934
THD "C2'" C CR6 0.000 -12.501 -0.373 4.827
THD CM2 C CH3 0.000 -13.562 0.186 5.738
THD HM23 H H 0.000 -13.554 -0.342 6.656
THD HM22 H H 0.000 -13.368 1.211 5.918
THD HM21 H H 0.000 -14.511 0.082 5.280
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
THD O3B n/a PB START
THD PB O3B O3A .
THD O1B PB . .
THD O2B PB . .
THD O3A PB PA .
THD PA O3A O7 .
THD O1A PA . .
THD O2A PA . .
THD O7 PA C7 .
THD C7 O7 C6 .
THD H7C1 C7 . .
THD H7C2 C7 . .
THD C6 C7 C5 .
THD H6C1 C6 . .
THD H6C2 C6 . .
THD C5 C6 C4 .
THD S1 C5 C2 .
THD C2 S1 C8 .
THD C8 C2 O9 .
THD C9 C8 O10 .
THD H9C1 C9 . .
THD H9C2 C9 . .
THD O10 C9 H10 .
THD H10 O10 . .
THD O9 C8 H9 .
THD H9 O9 . .
THD C4 C5 N3 .
THD CM4 C4 HM41 .
THD HM43 CM4 . .
THD HM42 CM4 . .
THD HM41 CM4 . .
THD N3 C4 "C7'" .
THD "C7'" N3 "C5'" .
THD "H7'1" "C7'" . .
THD "H7'2" "C7'" . .
THD "C5'" "C7'" "C4'" .
THD "C6'" "C5'" "N1'" .
THD "H6'" "C6'" . .
THD "N1'" "C6'" . .
THD "C4'" "C5'" "N3'" .
THD "N4'" "C4'" "H4'1" .
THD "H4'2" "N4'" . .
THD "H4'1" "N4'" . .
THD "N3'" "C4'" "C2'" .
THD "C2'" "N3'" CM2 .
THD CM2 "C2'" HM21 .
THD HM23 CM2 . .
THD HM22 CM2 . .
THD HM21 CM2 . END
THD "N1'" "C2'" . ADD
THD N3 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
THD "N1'" "C2'" double 1.350 0.020
THD "N1'" "C6'" single 1.337 0.020
THD CM2 "C2'" single 1.506 0.020
THD "C2'" "N3'" single 1.350 0.020
THD HM21 CM2 single 1.059 0.020
THD HM22 CM2 single 1.059 0.020
THD HM23 CM2 single 1.059 0.020
THD "N3'" "C4'" double 1.350 0.020
THD "N4'" "C4'" single 1.355 0.020
THD "C4'" "C5'" single 1.487 0.020
THD "H4'1" "N4'" single 1.010 0.020
THD "H4'2" "N4'" single 1.010 0.020
THD "C6'" "C5'" double 1.390 0.020
THD "C5'" "C7'" single 1.511 0.020
THD "H6'" "C6'" single 1.083 0.020
THD "C7'" N3 single 1.462 0.020
THD "H7'1" "C7'" single 1.092 0.020
THD "H7'2" "C7'" single 1.092 0.020
THD N3 C2 single 1.337 0.020
THD N3 C4 single 1.337 0.020
THD C2 S1 single 1.745 0.020
THD C8 C2 double 1.490 0.020
THD S1 C5 single 1.745 0.020
THD C4 C5 double 1.490 0.020
THD C5 C6 single 1.510 0.020
THD CM4 C4 single 1.506 0.020
THD HM41 CM4 single 1.059 0.020
THD HM42 CM4 single 1.059 0.020
THD HM43 CM4 single 1.059 0.020
THD C6 C7 single 1.524 0.020
THD H6C1 C6 single 1.092 0.020
THD H6C2 C6 single 1.092 0.020
THD C7 O7 single 1.426 0.020
THD H7C1 C7 single 1.092 0.020
THD H7C2 C7 single 1.092 0.020
THD O7 PA single 1.610 0.020
THD O1A PA deloc 1.510 0.020
THD O2A PA deloc 1.510 0.020
THD PA O3A single 1.610 0.020
THD O3A PB single 1.610 0.020
THD O1B PB deloc 1.510 0.020
THD O2B PB deloc 1.510 0.020
THD PB O3B deloc 1.510 0.020
THD O9 C8 single 1.330 0.020
THD C9 C8 single 1.510 0.020
THD H9 O9 single 0.967 0.020
THD O10 C9 single 1.432 0.020
THD H9C1 C9 single 1.092 0.020
THD H9C2 C9 single 1.092 0.020
THD H10 O10 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
THD O3B PB O1B 119.900 3.000
THD O3B PB O2B 119.900 3.000
THD O3B PB O3A 108.200 3.000
THD O1B PB O2B 119.900 3.000
THD O1B PB O3A 108.200 3.000
THD O2B PB O3A 108.200 3.000
THD PB O3A PA 120.500 3.000
THD O3A PA O1A 108.200 3.000
THD O3A PA O2A 108.200 3.000
THD O3A PA O7 102.600 3.000
THD O1A PA O2A 119.900 3.000
THD O1A PA O7 108.200 3.000
THD O2A PA O7 108.200 3.000
THD PA O7 C7 120.500 3.000
THD O7 C7 H7C1 109.470 3.000
THD O7 C7 H7C2 109.470 3.000
THD O7 C7 C6 109.470 3.000
THD H7C1 C7 H7C2 107.900 3.000
THD H7C1 C7 C6 109.470 3.000
THD H7C2 C7 C6 109.470 3.000
THD C7 C6 H6C1 109.470 3.000
THD C7 C6 H6C2 109.470 3.000
THD C7 C6 C5 109.470 3.000
THD H6C1 C6 H6C2 107.900 3.000
THD H6C1 C6 C5 109.470 3.000
THD H6C2 C6 C5 109.470 3.000
THD C6 C5 S1 108.000 3.000
THD C6 C5 C4 126.000 3.000
THD S1 C5 C4 108.000 3.000
THD C5 S1 C2 97.993 3.000
THD S1 C2 C8 108.000 3.000
THD S1 C2 N3 108.000 3.000
THD C8 C2 N3 126.000 3.000
THD C2 C8 C9 116.500 3.000
THD C2 C8 O9 120.000 3.000
THD C9 C8 O9 120.500 3.000
THD C8 C9 H9C1 109.470 3.000
THD C8 C9 H9C2 109.470 3.000
THD C8 C9 O10 109.500 3.000
THD H9C1 C9 H9C2 107.900 3.000
THD H9C1 C9 O10 109.470 3.000
THD H9C2 C9 O10 109.470 3.000
THD C9 O10 H10 109.470 3.000
THD C8 O9 H9 109.470 3.000
THD C5 C4 CM4 126.000 3.000
THD C5 C4 N3 108.000 3.000
THD CM4 C4 N3 126.000 3.000
THD C4 CM4 HM43 109.470 3.000
THD C4 CM4 HM42 109.470 3.000
THD C4 CM4 HM41 109.470 3.000
THD HM43 CM4 HM42 109.470 3.000
THD HM43 CM4 HM41 109.470 3.000
THD HM42 CM4 HM41 109.470 3.000
THD C4 N3 "C7'" 126.000 3.000
THD C4 N3 C2 108.000 3.000
THD "C7'" N3 C2 126.000 3.000
THD N3 "C7'" "H7'1" 109.500 3.000
THD N3 "C7'" "H7'2" 109.500 3.000
THD N3 "C7'" "C5'" 109.500 3.000
THD "H7'1" "C7'" "H7'2" 107.900 3.000
THD "H7'1" "C7'" "C5'" 109.470 3.000
THD "H7'2" "C7'" "C5'" 109.470 3.000
THD "C7'" "C5'" "C6'" 120.000 3.000
THD "C7'" "C5'" "C4'" 120.000 3.000
THD "C6'" "C5'" "C4'" 120.000 3.000
THD "C5'" "C6'" "H6'" 120.000 3.000
THD "C5'" "C6'" "N1'" 120.000 3.000
THD "H6'" "C6'" "N1'" 120.000 3.000
THD "C6'" "N1'" "C2'" 120.000 3.000
THD "C5'" "C4'" "N4'" 120.000 3.000
THD "C5'" "C4'" "N3'" 120.000 3.000
THD "N4'" "C4'" "N3'" 120.000 3.000
THD "C4'" "N4'" "H4'2" 120.000 3.000
THD "C4'" "N4'" "H4'1" 120.000 3.000
THD "H4'2" "N4'" "H4'1" 120.000 3.000
THD "C4'" "N3'" "C2'" 120.000 3.000
THD "N3'" "C2'" CM2 120.000 3.000
THD "N3'" "C2'" "N1'" 120.000 3.000
THD CM2 "C2'" "N1'" 120.000 3.000
THD "C2'" CM2 HM23 109.470 3.000
THD "C2'" CM2 HM22 109.470 3.000
THD "C2'" CM2 HM21 109.470 3.000
THD HM23 CM2 HM22 109.470 3.000
THD HM23 CM2 HM21 109.470 3.000
THD HM22 CM2 HM21 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
THD var_1 O3B PB O3A PA -60.016 20.000 1
THD var_2 PB O3A PA O7 -179.967 20.000 1
THD var_3 O3A PA O7 C7 -179.973 20.000 1
THD var_4 PA O7 C7 C6 179.992 20.000 1
THD var_5 O7 C7 C6 C5 -179.985 20.000 3
THD var_6 C7 C6 C5 C4 90.029 20.000 2
THD CONST_1 C6 C5 S1 C2 180.000 0.000 0
THD CONST_2 C5 S1 C2 C8 180.000 0.000 0
THD CONST_3 S1 C2 C8 O9 -174.360 0.000 0
THD var_7 C2 C8 C9 O10 119.957 20.000 3
THD var_8 C8 C9 O10 H10 179.965 20.000 1
THD var_9 C2 C8 O9 H9 115.206 20.000 1
THD CONST_4 C6 C5 C4 N3 180.000 0.000 0
THD var_10 C5 C4 CM4 HM41 -0.023 20.000 1
THD CONST_5 C5 C4 N3 "C7'" 180.000 0.000 0
THD CONST_6 C4 N3 C2 S1 0.000 0.000 0
THD var_11 C4 N3 "C7'" "C5'" 94.860 20.000 1
THD var_12 N3 "C7'" "C5'" "C4'" -179.992 20.000 2
THD CONST_7 "C7'" "C5'" "C6'" "N1'" 180.000 0.000 0
THD CONST_8 "C5'" "C6'" "N1'" "C2'" 0.000 0.000 0
THD CONST_9 "C6'" "N1'" "C2'" "N3'" 0.000 0.000 0
THD CONST_10 "C7'" "C5'" "C4'" "N3'" 180.000 0.000 0
THD CONST_11 "C5'" "C4'" "N4'" "H4'1" -179.999 0.000 0
THD CONST_12 "C5'" "C4'" "N3'" "C2'" 0.000 0.000 0
THD CONST_13 "C4'" "N3'" "C2'" CM2 180.000 0.000 0
THD var_13 "N3'" "C2'" CM2 HM21 -90.239 20.000 1
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
THD plan-1 "N1'" 0.020
THD plan-1 "C2'" 0.020
THD plan-1 "C6'" 0.020
THD plan-1 "N3'" 0.020
THD plan-1 "C4'" 0.020
THD plan-1 "C5'" 0.020
THD plan-1 CM2 0.020
THD plan-1 "N4'" 0.020
THD plan-1 "C7'" 0.020
THD plan-1 "H6'" 0.020
THD plan-1 "H4'2" 0.020
THD plan-1 "H4'1" 0.020
THD plan-2 "N4'" 0.020
THD plan-2 "C4'" 0.020
THD plan-2 "H4'1" 0.020
THD plan-2 "H4'2" 0.020
THD plan-3 N3 0.020
THD plan-3 "C7'" 0.020
THD plan-3 C2 0.020
THD plan-3 C4 0.020
THD plan-3 S1 0.020
THD plan-3 C5 0.020
THD plan-3 C8 0.020
THD plan-3 C6 0.020
THD plan-3 CM4 0.020
THD plan-3 O9 0.020
THD plan-3 C9 0.020
# ------------------------------------------------------
|
