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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
UPS UPS '2'-deoxy-5'-O-thiophosphonouridine ' non-polymer 33 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_UPS
#
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
UPS O4 O O 0.000 0.000 0.000 0.000
UPS C4 C CR6 0.000 -1.168 0.282 0.191
UPS N3 N NR16 0.000 -2.087 0.066 -0.771
UPS HN3 H H 0.000 -1.797 -0.345 -1.682
UPS C2 C CR6 0.000 -3.379 0.379 -0.558
UPS O2 O O 0.000 -4.197 0.178 -1.436
UPS C5 C CR16 0.000 -1.575 0.841 1.427
UPS H5 H H 0.000 -0.853 1.018 2.214
UPS C6 C CR16 0.000 -2.877 1.151 1.611
UPS H6 H H 0.000 -3.205 1.587 2.546
UPS N1 N NR6 0.000 -3.779 0.911 0.610
UPS "C1'" C CH1 0.000 -5.191 1.242 0.812
UPS "H1'" H H 0.000 -5.357 1.601 1.838
UPS "O4'" O O2 0.000 -6.021 0.092 0.540
UPS "C2'" C CH2 0.000 -5.645 2.307 -0.211
UPS "H2'" H H 0.000 -5.029 2.300 -1.113
UPS "H2'A" H H 0.000 -5.649 3.312 0.217
UPS "C3'" C CH1 0.000 -7.090 1.892 -0.568
UPS "H3'" H H 0.000 -7.171 1.660 -1.639
UPS "O3'" O OH1 0.000 -8.011 2.925 -0.209
UPS "HO3'" H H 0.000 -7.842 3.709 -0.748
UPS "C4'" C CH1 0.000 -7.338 0.626 0.280
UPS "H4'" H H 0.000 -7.838 0.889 1.223
UPS "C5'" C CH2 0.000 -8.177 -0.385 -0.503
UPS "H5'" H H 0.000 -7.612 -0.732 -1.371
UPS "H5'A" H H 0.000 -9.100 0.092 -0.840
UPS "O5'" O O2 0.000 -8.493 -1.496 0.337
UPS P P P 0.000 -9.367 -2.754 -0.162
UPS S1P S S1 0.000 -10.852 -2.142 -1.106
UPS OP2 O OH1 0.000 -9.856 -3.607 1.113
UPS HOP2 H H 0.000 -10.395 -4.400 0.985
UPS OP3 O OH1 0.000 -8.468 -3.685 -1.120
UPS HOP3 H H 0.000 -7.655 -4.085 -0.781
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
UPS O4 n/a C4 START
UPS C4 O4 C5 .
UPS N3 C4 C2 .
UPS HN3 N3 . .
UPS C2 N3 O2 .
UPS O2 C2 . .
UPS C5 C4 C6 .
UPS H5 C5 . .
UPS C6 C5 N1 .
UPS H6 C6 . .
UPS N1 C6 "C1'" .
UPS "C1'" N1 "C2'" .
UPS "H1'" "C1'" . .
UPS "O4'" "C1'" . .
UPS "C2'" "C1'" "C3'" .
UPS "H2'" "C2'" . .
UPS "H2'A" "C2'" . .
UPS "C3'" "C2'" "C4'" .
UPS "H3'" "C3'" . .
UPS "O3'" "C3'" "HO3'" .
UPS "HO3'" "O3'" . .
UPS "C4'" "C3'" "C5'" .
UPS "H4'" "C4'" . .
UPS "C5'" "C4'" "O5'" .
UPS "H5'" "C5'" . .
UPS "H5'A" "C5'" . .
UPS "O5'" "C5'" P .
UPS P "O5'" OP3 .
UPS S1P P . .
UPS OP2 P HOP2 .
UPS HOP2 OP2 . .
UPS OP3 P HOP3 .
UPS HOP3 OP3 . END
UPS "C4'" "O4'" . ADD
UPS 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
UPS OP3 P single 1.610 0.020
UPS S1P P double 1.950 0.020
UPS OP2 P single 1.610 0.020
UPS P "O5'" single 1.610 0.020
UPS HOP3 OP3 single 0.967 0.020
UPS HOP2 OP2 single 0.967 0.020
UPS "O5'" "C5'" single 1.426 0.020
UPS "C5'" "C4'" single 1.524 0.020
UPS "H5'" "C5'" single 1.092 0.020
UPS "H5'A" "C5'" single 1.092 0.020
UPS "C4'" "C3'" single 1.524 0.020
UPS "C4'" "O4'" single 1.426 0.020
UPS "H4'" "C4'" single 1.099 0.020
UPS "O4'" "C1'" single 1.426 0.020
UPS "C2'" "C1'" single 1.524 0.020
UPS "C1'" N1 single 1.465 0.020
UPS "H1'" "C1'" single 1.099 0.020
UPS N1 C6 single 1.337 0.020
UPS N1 C2 single 1.410 0.020
UPS O2 C2 double 1.250 0.020
UPS C2 N3 single 1.337 0.020
UPS N3 C4 single 1.337 0.020
UPS C5 C4 single 1.390 0.020
UPS C4 O4 double 1.250 0.020
UPS C6 C5 double 1.390 0.020
UPS H5 C5 single 1.083 0.020
UPS H6 C6 single 1.083 0.020
UPS "C3'" "C2'" single 1.524 0.020
UPS "H2'" "C2'" single 1.092 0.020
UPS "H2'A" "C2'" single 1.092 0.020
UPS "O3'" "C3'" single 1.432 0.020
UPS "H3'" "C3'" single 1.099 0.020
UPS "HO3'" "O3'" single 0.967 0.020
UPS HN3 N3 single 1.040 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
UPS O4 C4 N3 120.000 3.000
UPS O4 C4 C5 120.000 3.000
UPS N3 C4 C5 120.000 3.000
UPS C4 N3 HN3 120.000 3.000
UPS C4 N3 C2 120.000 3.000
UPS HN3 N3 C2 120.000 3.000
UPS N3 C2 O2 120.000 3.000
UPS N3 C2 N1 120.000 3.000
UPS O2 C2 N1 120.000 3.000
UPS C4 C5 H5 120.000 3.000
UPS C4 C5 C6 120.000 3.000
UPS H5 C5 C6 120.000 3.000
UPS C5 C6 H6 120.000 3.000
UPS C5 C6 N1 120.000 3.000
UPS H6 C6 N1 120.000 3.000
UPS C6 N1 "C1'" 120.000 3.000
UPS C6 N1 C2 120.000 3.000
UPS "C1'" N1 C2 120.000 3.000
UPS N1 "C1'" "H1'" 109.470 3.000
UPS N1 "C1'" "O4'" 109.470 3.000
UPS N1 "C1'" "C2'" 109.470 3.000
UPS "H1'" "C1'" "O4'" 109.470 3.000
UPS "H1'" "C1'" "C2'" 108.340 3.000
UPS "O4'" "C1'" "C2'" 109.470 3.000
UPS "C1'" "O4'" "C4'" 111.800 3.000
UPS "C1'" "C2'" "H2'" 109.470 3.000
UPS "C1'" "C2'" "H2'A" 109.470 3.000
UPS "C1'" "C2'" "C3'" 111.000 3.000
UPS "H2'" "C2'" "H2'A" 107.900 3.000
UPS "H2'" "C2'" "C3'" 109.470 3.000
UPS "H2'A" "C2'" "C3'" 109.470 3.000
UPS "C2'" "C3'" "H3'" 108.340 3.000
UPS "C2'" "C3'" "O3'" 109.470 3.000
UPS "C2'" "C3'" "C4'" 111.000 3.000
UPS "H3'" "C3'" "O3'" 109.470 3.000
UPS "H3'" "C3'" "C4'" 108.340 3.000
UPS "O3'" "C3'" "C4'" 109.470 3.000
UPS "C3'" "O3'" "HO3'" 109.470 3.000
UPS "C3'" "C4'" "H4'" 108.340 3.000
UPS "C3'" "C4'" "C5'" 111.000 3.000
UPS "C3'" "C4'" "O4'" 109.470 3.000
UPS "H4'" "C4'" "C5'" 108.340 3.000
UPS "H4'" "C4'" "O4'" 109.470 3.000
UPS "C5'" "C4'" "O4'" 109.470 3.000
UPS "C4'" "C5'" "H5'" 109.470 3.000
UPS "C4'" "C5'" "H5'A" 109.470 3.000
UPS "C4'" "C5'" "O5'" 109.470 3.000
UPS "H5'" "C5'" "H5'A" 107.900 3.000
UPS "H5'" "C5'" "O5'" 109.470 3.000
UPS "H5'A" "C5'" "O5'" 109.470 3.000
UPS "C5'" "O5'" P 120.500 3.000
UPS "O5'" P S1P 109.500 3.000
UPS "O5'" P OP2 109.500 3.000
UPS "O5'" P OP3 109.500 3.000
UPS S1P P OP2 109.500 3.000
UPS S1P P OP3 109.500 3.000
UPS OP2 P OP3 109.500 3.000
UPS P OP2 HOP2 120.000 3.000
UPS P OP3 HOP3 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
UPS CONST_1 O4 C4 N3 C2 180.000 0.000 0
UPS CONST_2 C4 N3 C2 O2 180.000 0.000 0
UPS CONST_3 O4 C4 C5 C6 180.000 0.000 0
UPS CONST_4 C4 C5 C6 N1 0.000 0.000 0
UPS CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
UPS CONST_6 C6 N1 C2 N3 0.000 0.000 0
UPS var_1 C6 N1 "C1'" "C2'" 118.182 20.000 1
UPS var_2 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
UPS var_3 N1 "C1'" "C2'" "C3'" 150.000 20.000 3
UPS var_4 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
UPS var_5 "C2'" "C3'" "O3'" "HO3'" 65.316 20.000 1
UPS var_6 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
UPS var_7 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
UPS var_8 "C3'" "C4'" "C5'" "O5'" -175.012 20.000 3
UPS var_9 "C4'" "C5'" "O5'" P -179.980 20.000 1
UPS var_10 "C5'" "O5'" P OP3 74.983 20.000 1
UPS var_11 "O5'" P OP2 HOP2 -179.988 20.000 1
UPS var_12 "O5'" P OP3 HOP3 60.048 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
UPS chir_01 "C4'" "C5'" "O4'" "C3'" negativ
UPS chir_02 "C1'" "O4'" N1 "C2'" negativ
UPS chir_03 "C3'" "C4'" "C2'" "O3'" 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
UPS plan-1 N1 0.020
UPS plan-1 "C1'" 0.020
UPS plan-1 C2 0.020
UPS plan-1 C6 0.020
UPS plan-1 N3 0.020
UPS plan-1 C4 0.020
UPS plan-1 C5 0.020
UPS plan-1 O2 0.020
UPS plan-1 HN3 0.020
UPS plan-1 O4 0.020
UPS plan-1 H5 0.020
UPS plan-1 H6 0.020
# ------------------------------------------------------
|
