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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
UPF UPF 'URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLU' non-polymer 57 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_UPF
#
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
UPF "F2'" F F 0.000 0.000 0.000 0.000
UPF "C2'" C CH1 0.000 -0.187 0.663 1.218
UPF "H2'" H H 0.000 0.549 1.473 1.313
UPF "C3'" C CH1 0.000 -0.012 -0.327 2.373
UPF "H3'" H H 0.000 -0.675 -1.190 2.224
UPF "O3'" O OH1 0.000 1.347 -0.768 2.425
UPF HO3A H H 0.000 1.575 -1.203 1.592
UPF "C4'" C CH1 0.000 -0.376 0.381 3.684
UPF "H4'" H H 0.000 -0.365 -0.345 4.509
UPF "O4'" O OH1 0.000 0.572 1.416 3.946
UPF "HO4'" H H 0.000 1.456 1.031 4.024
UPF "C5'" C CH1 0.000 -1.777 0.984 3.551
UPF "H5'" H H 0.000 -2.498 0.186 3.325
UPF "C6'" C CH2 0.000 -2.164 1.663 4.865
UPF "H6'1" H H 0.000 -1.446 2.455 5.090
UPF "H6'2" H H 0.000 -2.156 0.926 5.671
UPF "O6'" O OH1 0.000 -3.472 2.225 4.744
UPF "HO6'" H H 0.000 -3.717 2.654 5.575
UPF "O5'" O O2 0.000 -1.788 1.946 2.498
UPF "C1'" C CH1 0.000 -1.600 1.246 1.270
UPF "H1'" H H 0.000 -1.742 1.939 0.429
UPF O3B O O2 0.000 -2.555 0.187 1.179
UPF PB P P 0.000 -3.857 0.794 0.453
UPF O1B O OP -0.500 -3.486 1.287 -0.896
UPF O2B O OP -0.500 -4.394 1.916 1.259
UPF O3A O O2 0.000 -4.980 -0.352 0.315
UPF PA P P 0.000 -6.246 0.321 -0.414
UPF O1A O OP -0.500 -5.839 0.822 -1.749
UPF O2A O OP -0.500 -6.745 1.451 0.407
UPF O5D O O2 0.000 -7.412 -0.774 -0.585
UPF C5D C CH2 0.000 -8.503 -0.120 -1.235
UPF "H5'1" H H 0.000 -8.175 0.254 -2.207
UPF "H5'2" H H 0.000 -8.842 0.717 -0.621
UPF C4D C CH1 0.000 -9.651 -1.111 -1.429
UPF H4D H H 0.000 -9.312 -1.961 -2.036
UPF C3D C CH1 0.000 -10.836 -0.412 -2.123
UPF H3D H H 0.000 -10.616 0.654 -2.278
UPF O3D O OH1 0.000 -11.142 -1.046 -3.367
UPF "HO3'" H H 0.000 -11.923 -0.631 -3.756
UPF C2D C CH1 0.000 -12.011 -0.583 -1.124
UPF H2D H H 0.000 -12.130 0.316 -0.503
UPF "O2'" O OH1 0.000 -13.225 -0.890 -1.813
UPF "HO2'" H H 0.000 -13.499 -0.126 -2.338
UPF O4D O O2 0.000 -10.116 -1.577 -0.151
UPF C1D C CH1 0.000 -11.539 -1.786 -0.270
UPF H1D H H 0.000 -11.749 -2.732 -0.787
UPF N1 N NR6 0.000 -12.175 -1.767 1.049
UPF C6 C CR16 0.000 -12.882 -2.859 1.475
UPF H6 H H 0.000 -12.970 -3.732 0.840
UPF C5 C CR16 0.000 -13.468 -2.843 2.691
UPF H5 H H 0.000 -14.030 -3.699 3.041
UPF C4 C CR6 0.000 -13.338 -1.689 3.503
UPF O4 O O 0.000 -13.856 -1.651 4.604
UPF N3 N NR16 0.000 -12.633 -0.635 3.046
UPF HN3 H H 0.000 -12.535 0.217 3.634
UPF C2 C CR6 0.000 -12.054 -0.681 1.831
UPF O2 O O 0.000 -11.422 0.278 1.432
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
UPF "F2'" n/a "C2'" START
UPF "C2'" "F2'" "C3'" .
UPF "H2'" "C2'" . .
UPF "C3'" "C2'" "C4'" .
UPF "H3'" "C3'" . .
UPF "O3'" "C3'" HO3A .
UPF HO3A "O3'" . .
UPF "C4'" "C3'" "C5'" .
UPF "H4'" "C4'" . .
UPF "O4'" "C4'" "HO4'" .
UPF "HO4'" "O4'" . .
UPF "C5'" "C4'" "O5'" .
UPF "H5'" "C5'" . .
UPF "C6'" "C5'" "O6'" .
UPF "H6'1" "C6'" . .
UPF "H6'2" "C6'" . .
UPF "O6'" "C6'" "HO6'" .
UPF "HO6'" "O6'" . .
UPF "O5'" "C5'" "C1'" .
UPF "C1'" "O5'" O3B .
UPF "H1'" "C1'" . .
UPF O3B "C1'" PB .
UPF PB O3B O3A .
UPF O1B PB . .
UPF O2B PB . .
UPF O3A PB PA .
UPF PA O3A O5D .
UPF O1A PA . .
UPF O2A PA . .
UPF O5D PA C5D .
UPF C5D O5D C4D .
UPF "H5'1" C5D . .
UPF "H5'2" C5D . .
UPF C4D C5D O4D .
UPF H4D C4D . .
UPF C3D C4D C2D .
UPF H3D C3D . .
UPF O3D C3D "HO3'" .
UPF "HO3'" O3D . .
UPF C2D C3D "O2'" .
UPF H2D C2D . .
UPF "O2'" C2D "HO2'" .
UPF "HO2'" "O2'" . .
UPF O4D C4D C1D .
UPF C1D O4D N1 .
UPF H1D C1D . .
UPF N1 C1D C6 .
UPF C6 N1 C5 .
UPF H6 C6 . .
UPF C5 C6 C4 .
UPF H5 C5 . .
UPF C4 C5 N3 .
UPF O4 C4 . .
UPF N3 C4 C2 .
UPF HN3 N3 . .
UPF C2 N3 O2 .
UPF O2 C2 . END
UPF N1 C2 . ADD
UPF C1D C2D . ADD
UPF "C1'" "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
UPF N1 C2 single 1.410 0.020
UPF C6 N1 single 1.337 0.020
UPF N1 C1D single 1.465 0.020
UPF C2 N3 single 1.337 0.020
UPF O2 C2 double 1.250 0.020
UPF N3 C4 single 1.337 0.020
UPF HN3 N3 single 1.040 0.020
UPF C4 C5 single 1.390 0.020
UPF O4 C4 double 1.250 0.020
UPF C5 C6 double 1.390 0.020
UPF H5 C5 single 1.083 0.020
UPF H6 C6 single 1.083 0.020
UPF C1D C2D single 1.524 0.020
UPF C1D O4D single 1.426 0.020
UPF H1D C1D single 1.099 0.020
UPF "O2'" C2D single 1.432 0.020
UPF C2D C3D single 1.524 0.020
UPF H2D C2D single 1.099 0.020
UPF "HO2'" "O2'" single 0.967 0.020
UPF C3D C4D single 1.524 0.020
UPF O3D C3D single 1.432 0.020
UPF H3D C3D single 1.099 0.020
UPF O4D C4D single 1.426 0.020
UPF C4D C5D single 1.524 0.020
UPF H4D C4D single 1.099 0.020
UPF "HO3'" O3D single 0.967 0.020
UPF C5D O5D single 1.426 0.020
UPF "H5'1" C5D single 1.092 0.020
UPF "H5'2" C5D single 1.092 0.020
UPF O5D PA single 1.610 0.020
UPF O1A PA deloc 1.510 0.020
UPF O2A PA deloc 1.510 0.020
UPF PA O3A single 1.610 0.020
UPF O3A PB single 1.610 0.020
UPF O1B PB deloc 1.510 0.020
UPF O2B PB deloc 1.510 0.020
UPF PB O3B single 1.610 0.020
UPF O3B "C1'" single 1.426 0.020
UPF "C1'" "C2'" single 1.524 0.020
UPF "C1'" "O5'" single 1.426 0.020
UPF "H1'" "C1'" single 1.099 0.020
UPF "C3'" "C2'" single 1.524 0.020
UPF "C2'" "F2'" single 1.370 0.020
UPF "H2'" "C2'" single 1.099 0.020
UPF "C4'" "C3'" single 1.524 0.020
UPF "O3'" "C3'" single 1.432 0.020
UPF "H3'" "C3'" single 1.099 0.020
UPF "C5'" "C4'" single 1.524 0.020
UPF "O4'" "C4'" single 1.432 0.020
UPF "H4'" "C4'" single 1.099 0.020
UPF "C6'" "C5'" single 1.524 0.020
UPF "O5'" "C5'" single 1.426 0.020
UPF "H5'" "C5'" single 1.099 0.020
UPF "O6'" "C6'" single 1.432 0.020
UPF "H6'1" "C6'" single 1.092 0.020
UPF "H6'2" "C6'" single 1.092 0.020
UPF HO3A "O3'" single 0.967 0.020
UPF "HO4'" "O4'" single 0.967 0.020
UPF "HO6'" "O6'" 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
UPF "F2'" "C2'" "H2'" 109.500 3.000
UPF "F2'" "C2'" "C3'" 109.500 3.000
UPF "F2'" "C2'" "C1'" 109.500 3.000
UPF "H2'" "C2'" "C3'" 108.340 3.000
UPF "H2'" "C2'" "C1'" 108.340 3.000
UPF "C3'" "C2'" "C1'" 111.000 3.000
UPF "C2'" "C3'" "H3'" 108.340 3.000
UPF "C2'" "C3'" "O3'" 109.470 3.000
UPF "C2'" "C3'" "C4'" 111.000 3.000
UPF "H3'" "C3'" "O3'" 109.470 3.000
UPF "H3'" "C3'" "C4'" 108.340 3.000
UPF "O3'" "C3'" "C4'" 109.470 3.000
UPF "C3'" "O3'" HO3A 109.470 3.000
UPF "C3'" "C4'" "H4'" 108.340 3.000
UPF "C3'" "C4'" "O4'" 109.470 3.000
UPF "C3'" "C4'" "C5'" 111.000 3.000
UPF "H4'" "C4'" "O4'" 109.470 3.000
UPF "H4'" "C4'" "C5'" 108.340 3.000
UPF "O4'" "C4'" "C5'" 109.470 3.000
UPF "C4'" "O4'" "HO4'" 109.470 3.000
UPF "C4'" "C5'" "H5'" 108.340 3.000
UPF "C4'" "C5'" "C6'" 111.000 3.000
UPF "C4'" "C5'" "O5'" 109.470 3.000
UPF "H5'" "C5'" "C6'" 108.340 3.000
UPF "H5'" "C5'" "O5'" 109.470 3.000
UPF "C6'" "C5'" "O5'" 109.470 3.000
UPF "C5'" "C6'" "H6'1" 109.470 3.000
UPF "C5'" "C6'" "H6'2" 109.470 3.000
UPF "C5'" "C6'" "O6'" 109.470 3.000
UPF "H6'1" "C6'" "H6'2" 107.900 3.000
UPF "H6'1" "C6'" "O6'" 109.470 3.000
UPF "H6'2" "C6'" "O6'" 109.470 3.000
UPF "C6'" "O6'" "HO6'" 109.470 3.000
UPF "C5'" "O5'" "C1'" 111.800 3.000
UPF "O5'" "C1'" "H1'" 109.470 3.000
UPF "O5'" "C1'" O3B 109.470 3.000
UPF "O5'" "C1'" "C2'" 109.470 3.000
UPF "H1'" "C1'" O3B 109.470 3.000
UPF "H1'" "C1'" "C2'" 108.340 3.000
UPF O3B "C1'" "C2'" 109.470 3.000
UPF "C1'" O3B PB 120.500 3.000
UPF O3B PB O1B 108.200 3.000
UPF O3B PB O2B 108.200 3.000
UPF O3B PB O3A 102.600 3.000
UPF O1B PB O2B 119.900 3.000
UPF O1B PB O3A 108.200 3.000
UPF O2B PB O3A 108.200 3.000
UPF PB O3A PA 120.500 3.000
UPF O3A PA O1A 108.200 3.000
UPF O3A PA O2A 108.200 3.000
UPF O3A PA O5D 102.600 3.000
UPF O1A PA O2A 119.900 3.000
UPF O1A PA O5D 108.200 3.000
UPF O2A PA O5D 108.200 3.000
UPF PA O5D C5D 120.500 3.000
UPF O5D C5D "H5'1" 109.470 3.000
UPF O5D C5D "H5'2" 109.470 3.000
UPF O5D C5D C4D 109.470 3.000
UPF "H5'1" C5D "H5'2" 107.900 3.000
UPF "H5'1" C5D C4D 109.470 3.000
UPF "H5'2" C5D C4D 109.470 3.000
UPF C5D C4D H4D 108.340 3.000
UPF C5D C4D C3D 111.000 3.000
UPF C5D C4D O4D 109.470 3.000
UPF H4D C4D C3D 108.340 3.000
UPF H4D C4D O4D 109.470 3.000
UPF C3D C4D O4D 109.470 3.000
UPF C4D C3D H3D 108.340 3.000
UPF C4D C3D O3D 109.470 3.000
UPF C4D C3D C2D 111.000 3.000
UPF H3D C3D O3D 109.470 3.000
UPF H3D C3D C2D 108.340 3.000
UPF O3D C3D C2D 109.470 3.000
UPF C3D O3D "HO3'" 109.470 3.000
UPF C3D C2D H2D 108.340 3.000
UPF C3D C2D "O2'" 109.470 3.000
UPF C3D C2D C1D 111.000 3.000
UPF H2D C2D "O2'" 109.470 3.000
UPF H2D C2D C1D 108.340 3.000
UPF "O2'" C2D C1D 109.470 3.000
UPF C2D "O2'" "HO2'" 109.470 3.000
UPF C4D O4D C1D 111.800 3.000
UPF O4D C1D H1D 109.470 3.000
UPF O4D C1D N1 109.470 3.000
UPF O4D C1D C2D 109.470 3.000
UPF H1D C1D N1 109.470 3.000
UPF H1D C1D C2D 108.340 3.000
UPF N1 C1D C2D 109.470 3.000
UPF C1D N1 C6 120.000 3.000
UPF C1D N1 C2 120.000 3.000
UPF C6 N1 C2 120.000 3.000
UPF N1 C6 H6 120.000 3.000
UPF N1 C6 C5 120.000 3.000
UPF H6 C6 C5 120.000 3.000
UPF C6 C5 H5 120.000 3.000
UPF C6 C5 C4 120.000 3.000
UPF H5 C5 C4 120.000 3.000
UPF C5 C4 O4 120.000 3.000
UPF C5 C4 N3 120.000 3.000
UPF O4 C4 N3 120.000 3.000
UPF C4 N3 HN3 120.000 3.000
UPF C4 N3 C2 120.000 3.000
UPF HN3 N3 C2 120.000 3.000
UPF N3 C2 O2 120.000 3.000
UPF N3 C2 N1 120.000 3.000
UPF O2 C2 N1 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
UPF var_1 "F2'" "C2'" "C3'" "C4'" 180.000 20.000 3
UPF var_2 "C2'" "C3'" "O3'" HO3A -60.039 20.000 1
UPF var_3 "C2'" "C3'" "C4'" "C5'" 60.000 20.000 3
UPF var_4 "C3'" "C4'" "O4'" "HO4'" -60.045 20.000 1
UPF var_5 "C3'" "C4'" "C5'" "O5'" -60.000 20.000 3
UPF var_6 "C4'" "C5'" "C6'" "O6'" -179.926 20.000 3
UPF var_7 "C5'" "C6'" "O6'" "HO6'" 179.949 20.000 1
UPF var_8 "C4'" "C5'" "O5'" "C1'" 60.000 20.000 1
UPF var_9 "C5'" "O5'" "C1'" O3B 60.000 20.000 1
UPF var_10 "O5'" "C1'" "C2'" "F2'" 180.000 20.000 3
UPF var_11 "O5'" "C1'" O3B PB 90.065 20.000 1
UPF var_12 "C1'" O3B PB O3A 179.966 20.000 1
UPF var_13 O3B PB O3A PA 179.932 20.000 1
UPF var_14 PB O3A PA O5D 179.969 20.000 1
UPF var_15 O3A PA O5D C5D -179.981 20.000 1
UPF var_16 PA O5D C5D C4D -179.976 20.000 1
UPF var_17 O5D C5D C4D O4D 61.714 20.000 3
UPF var_18 C5D C4D C3D C2D -120.000 20.000 3
UPF var_19 C4D C3D O3D "HO3'" 176.206 20.000 1
UPF var_20 C4D C3D C2D "O2'" -150.000 20.000 3
UPF var_21 C3D C2D "O2'" "HO2'" -67.287 20.000 1
UPF var_22 C5D C4D O4D C1D 150.000 20.000 1
UPF var_23 C4D O4D C1D N1 -150.000 20.000 1
UPF var_24 O4D C1D C2D C3D 30.000 20.000 3
UPF var_25 O4D C1D N1 C6 -121.448 20.000 1
UPF CONST_1 C1D N1 C2 N3 180.000 0.000 0
UPF CONST_2 C1D N1 C6 C5 180.000 0.000 0
UPF CONST_3 N1 C6 C5 C4 0.000 0.000 0
UPF CONST_4 C6 C5 C4 N3 0.000 0.000 0
UPF CONST_5 C5 C4 N3 C2 0.000 0.000 0
UPF CONST_6 C4 N3 C2 O2 180.000 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
UPF chir_01 C1D N1 C2D O4D negativ
UPF chir_02 C2D C1D "O2'" C3D positiv
UPF chir_03 C3D C2D C4D O3D negativ
UPF chir_04 C4D C3D O4D C5D positiv
UPF chir_05 "C1'" O3B "C2'" "O5'" positiv
UPF chir_06 "C2'" "C1'" "C3'" "F2'" negativ
UPF chir_07 "C3'" "C2'" "C4'" "O3'" positiv
UPF chir_08 "C4'" "C3'" "C5'" "O4'" positiv
UPF chir_09 "C5'" "C4'" "C6'" "O5'" 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
UPF plan-1 N1 0.020
UPF plan-1 C2 0.020
UPF plan-1 C6 0.020
UPF plan-1 C1D 0.020
UPF plan-1 N3 0.020
UPF plan-1 C4 0.020
UPF plan-1 C5 0.020
UPF plan-1 O2 0.020
UPF plan-1 HN3 0.020
UPF plan-1 O4 0.020
UPF plan-1 H5 0.020
UPF plan-1 H6 0.020
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