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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
D4D D4D '. ' non-polymer 35 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_D4D
#
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
D4D O4 O O 0.000 0.000 0.000 0.000
D4D C4 C CR6 0.000 -1.018 0.630 0.224
D4D N3 N NR16 0.000 -2.106 0.465 -0.555
D4D HN3 H H 0.000 -2.076 -0.204 -1.351
D4D C2 C CR6 0.000 -3.230 1.163 -0.308
D4D O2 O O 0.000 -4.201 1.006 -1.022
D4D C5 C CR6 0.000 -1.072 1.536 1.311
D4D C5M C CH3 0.000 0.127 1.736 2.200
D4D H5M3 H H 0.000 1.012 1.571 1.641
D4D H5M2 H H 0.000 0.127 2.726 2.576
D4D H5M1 H H 0.000 0.086 1.051 3.007
D4D C6 C CR16 0.000 -2.213 2.223 1.536
D4D H66 H H 0.000 -2.273 2.923 2.360
D4D N1 N NR6 0.000 -3.294 2.030 0.719
D4D "C1'" C CH1 0.000 -4.531 2.775 0.963
D4D "H1'C" H H 0.000 -4.446 3.357 1.891
D4D "O4'" O O2 0.000 -5.648 1.870 1.045
D4D "C2'" C C1 0.000 -4.828 3.691 -0.202
D4D "H2'C" H H 0.000 -4.113 4.312 -0.714
D4D "C3'" C C1 0.000 -6.108 3.601 -0.481
D4D "H3'C" H H 0.000 -6.621 4.134 -1.264
D4D "C4'" C CH1 0.000 -6.739 2.623 0.482
D4D "H4'C" H H 0.000 -7.276 3.163 1.274
D4D "C5'" C CH2 0.000 -7.698 1.690 -0.262
D4D "H5'1" H H 0.000 -7.138 1.100 -0.991
D4D "H5'2" H H 0.000 -8.454 2.283 -0.780
D4D "O5'" O O2 0.000 -8.333 0.816 0.673
D4D PA P P 0.000 -9.321 -0.132 -0.174
D4D O1A O OP -0.500 -8.554 -0.814 -1.244
D4D O2A O OP -0.500 -10.395 0.690 -0.781
D4D O3A O O2 0.000 -9.974 -1.234 0.802
D4D PB P P 0.000 -10.497 -2.434 -0.135
D4D O1B O OP -0.666 -9.333 -3.325 -0.510
D4D O2B O OP -0.666 -11.118 -1.861 -1.389
D4D O3B O OP -0.666 -11.532 -3.245 0.614
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
D4D O4 n/a C4 START
D4D C4 O4 C5 .
D4D N3 C4 C2 .
D4D HN3 N3 . .
D4D C2 N3 O2 .
D4D O2 C2 . .
D4D C5 C4 C6 .
D4D C5M C5 H5M1 .
D4D H5M3 C5M . .
D4D H5M2 C5M . .
D4D H5M1 C5M . .
D4D C6 C5 N1 .
D4D H66 C6 . .
D4D N1 C6 "C1'" .
D4D "C1'" N1 "C2'" .
D4D "H1'C" "C1'" . .
D4D "O4'" "C1'" . .
D4D "C2'" "C1'" "C3'" .
D4D "H2'C" "C2'" . .
D4D "C3'" "C2'" "C4'" .
D4D "H3'C" "C3'" . .
D4D "C4'" "C3'" "C5'" .
D4D "H4'C" "C4'" . .
D4D "C5'" "C4'" "O5'" .
D4D "H5'1" "C5'" . .
D4D "H5'2" "C5'" . .
D4D "O5'" "C5'" PA .
D4D PA "O5'" O3A .
D4D O1A PA . .
D4D O2A PA . .
D4D O3A PA PB .
D4D PB O3A O3B .
D4D O1B PB . .
D4D O2B PB . .
D4D O3B PB . END
D4D "C4'" "O4'" . ADD
D4D 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
D4D O1A PA deloc 1.510 0.020
D4D O2A PA deloc 1.510 0.020
D4D O3A PA single 1.610 0.020
D4D PA "O5'" single 1.610 0.020
D4D PB O3A single 1.610 0.020
D4D O1B PB deloc 1.510 0.020
D4D O2B PB deloc 1.510 0.020
D4D O3B PB deloc 1.510 0.020
D4D "O5'" "C5'" single 1.426 0.020
D4D "C5'" "C4'" single 1.524 0.020
D4D "H5'1" "C5'" single 1.092 0.020
D4D "H5'2" "C5'" single 1.092 0.020
D4D "C4'" "O4'" single 1.426 0.020
D4D "C4'" "C3'" single 1.510 0.020
D4D "H4'C" "C4'" single 1.099 0.020
D4D "O4'" "C1'" single 1.426 0.020
D4D "C3'" "C2'" double 1.330 0.020
D4D "H3'C" "C3'" single 1.077 0.020
D4D "C2'" "C1'" single 1.510 0.020
D4D "H2'C" "C2'" single 1.077 0.020
D4D "C1'" N1 single 1.465 0.020
D4D "H1'C" "C1'" single 1.099 0.020
D4D N1 C2 single 1.410 0.020
D4D N1 C6 single 1.337 0.020
D4D O2 C2 double 1.250 0.020
D4D C2 N3 single 1.337 0.020
D4D N3 C4 single 1.337 0.020
D4D HN3 N3 single 1.040 0.020
D4D C4 O4 double 1.250 0.020
D4D C5 C4 single 1.487 0.020
D4D C5M C5 single 1.506 0.020
D4D C6 C5 double 1.390 0.020
D4D H5M1 C5M single 1.059 0.020
D4D H5M2 C5M single 1.059 0.020
D4D H5M3 C5M single 1.059 0.020
D4D H66 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
D4D O4 C4 N3 120.000 3.000
D4D O4 C4 C5 120.000 3.000
D4D N3 C4 C5 120.000 3.000
D4D C4 N3 HN3 120.000 3.000
D4D C4 N3 C2 120.000 3.000
D4D HN3 N3 C2 120.000 3.000
D4D N3 C2 O2 120.000 3.000
D4D N3 C2 N1 120.000 3.000
D4D O2 C2 N1 120.000 3.000
D4D C4 C5 C5M 120.000 3.000
D4D C4 C5 C6 120.000 3.000
D4D C5M C5 C6 120.000 3.000
D4D C5 C5M H5M3 109.470 3.000
D4D C5 C5M H5M2 109.470 3.000
D4D C5 C5M H5M1 109.470 3.000
D4D H5M3 C5M H5M2 109.470 3.000
D4D H5M3 C5M H5M1 109.470 3.000
D4D H5M2 C5M H5M1 109.470 3.000
D4D C5 C6 H66 120.000 3.000
D4D C5 C6 N1 120.000 3.000
D4D H66 C6 N1 120.000 3.000
D4D C6 N1 "C1'" 120.000 3.000
D4D C6 N1 C2 120.000 3.000
D4D "C1'" N1 C2 120.000 3.000
D4D N1 "C1'" "H1'C" 109.470 3.000
D4D N1 "C1'" "O4'" 109.470 3.000
D4D N1 "C1'" "C2'" 109.500 3.000
D4D "H1'C" "C1'" "O4'" 109.470 3.000
D4D "H1'C" "C1'" "C2'" 108.810 3.000
D4D "O4'" "C1'" "C2'" 109.500 3.000
D4D "C1'" "O4'" "C4'" 111.800 3.000
D4D "C1'" "C2'" "H2'C" 120.000 3.000
D4D "C1'" "C2'" "C3'" 120.000 3.000
D4D "H2'C" "C2'" "C3'" 120.000 3.000
D4D "C2'" "C3'" "H3'C" 120.000 3.000
D4D "C2'" "C3'" "C4'" 120.000 3.000
D4D "H3'C" "C3'" "C4'" 120.000 3.000
D4D "C3'" "C4'" "H4'C" 108.810 3.000
D4D "C3'" "C4'" "C5'" 109.470 3.000
D4D "C3'" "C4'" "O4'" 109.500 3.000
D4D "H4'C" "C4'" "C5'" 108.340 3.000
D4D "H4'C" "C4'" "O4'" 109.470 3.000
D4D "C5'" "C4'" "O4'" 109.470 3.000
D4D "C4'" "C5'" "H5'1" 109.470 3.000
D4D "C4'" "C5'" "H5'2" 109.470 3.000
D4D "C4'" "C5'" "O5'" 109.470 3.000
D4D "H5'1" "C5'" "H5'2" 107.900 3.000
D4D "H5'1" "C5'" "O5'" 109.470 3.000
D4D "H5'2" "C5'" "O5'" 109.470 3.000
D4D "C5'" "O5'" PA 120.500 3.000
D4D "O5'" PA O1A 108.200 3.000
D4D "O5'" PA O2A 108.200 3.000
D4D "O5'" PA O3A 102.600 3.000
D4D O1A PA O2A 119.900 3.000
D4D O1A PA O3A 108.200 3.000
D4D O2A PA O3A 108.200 3.000
D4D PA O3A PB 120.500 3.000
D4D O3A PB O1B 108.200 3.000
D4D O3A PB O2B 108.200 3.000
D4D O3A PB O3B 108.200 3.000
D4D O1B PB O2B 119.900 3.000
D4D O1B PB O3B 119.900 3.000
D4D 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
D4D CONST_1 O4 C4 N3 C2 180.000 0.000 0
D4D CONST_2 C4 N3 C2 O2 180.000 0.000 0
D4D CONST_3 O4 C4 C5 C6 180.000 0.000 0
D4D var_1 C4 C5 C5M H5M1 -90.280 20.000 1
D4D CONST_4 C4 C5 C6 N1 0.000 0.000 0
D4D CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
D4D CONST_6 C6 N1 C2 N3 0.000 0.000 0
D4D var_2 C6 N1 "C1'" "C2'" 116.077 20.000 1
D4D var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
D4D var_4 N1 "C1'" "C2'" "C3'" 150.000 20.000 1
D4D var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 1
D4D var_6 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 1
D4D var_7 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
D4D var_8 "C3'" "C4'" "C5'" "O5'" -177.208 20.000 3
D4D var_9 "C4'" "C5'" "O5'" PA -179.971 20.000 1
D4D var_10 "C5'" "O5'" PA O3A 174.969 20.000 1
D4D var_11 "O5'" PA O3A PB -160.004 20.000 1
D4D var_12 PA O3A PB O3B -159.960 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
D4D chir_01 "C4'" "C5'" "O4'" "C3'" negativ
D4D chir_02 "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
D4D plan-1 "C3'" 0.020
D4D plan-1 "C4'" 0.020
D4D plan-1 "C2'" 0.020
D4D plan-1 "H3'C" 0.020
D4D plan-1 "H2'C" 0.020
D4D plan-2 "C2'" 0.020
D4D plan-2 "C3'" 0.020
D4D plan-2 "C1'" 0.020
D4D plan-2 "H2'C" 0.020
D4D plan-2 "H3'C" 0.020
D4D plan-3 N1 0.020
D4D plan-3 "C1'" 0.020
D4D plan-3 C2 0.020
D4D plan-3 C6 0.020
D4D plan-3 N3 0.020
D4D plan-3 C4 0.020
D4D plan-3 C5 0.020
D4D plan-3 O2 0.020
D4D plan-3 HN3 0.020
D4D plan-3 O4 0.020
D4D plan-3 C5M 0.020
D4D plan-3 H66 0.020
# ------------------------------------------------------
|
