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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
PDU PDU '5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONO' DNA 40 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDU
#
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
PDU OP3 O OP -0.666 0.000 0.000 0.000
PDU P P P 0.000 -1.186 0.517 -0.784
PDU OP1 O OP -0.666 -1.512 1.925 -0.335
PDU OP2 O OP -0.666 -0.852 0.522 -2.259
PDU "O5'" O O2 0.000 -2.458 -0.435 -0.525
PDU "C5'" C CH2 0.000 -3.540 0.103 -1.287
PDU "H5'" H H 0.000 -3.270 0.111 -2.345
PDU "H5''" H H 0.000 -3.744 1.123 -0.956
PDU "C4'" C CH1 0.000 -4.786 -0.761 -1.083
PDU "H4'" H H 0.000 -4.583 -1.804 -1.364
PDU "C3'" C CH1 0.000 -5.978 -0.200 -1.902
PDU "H3'" H H 0.000 -5.973 0.899 -1.898
PDU "C2'" C CH2 0.000 -7.194 -0.749 -1.118
PDU "H2''" H H 0.000 -7.592 -1.661 -1.568
PDU "H2'" H H 0.000 -7.992 -0.009 -1.031
PDU "C1'" C CH1 0.000 -6.631 -1.068 0.280
PDU "H1'" H H 0.000 -6.721 -2.144 0.483
PDU "O4'" O O2 0.000 -5.246 -0.684 0.284
PDU N1 N NR6 0.000 -7.361 -0.307 1.297
PDU C6 C CR16 0.000 -8.029 -0.970 2.291
PDU H6 H H 0.000 -8.017 -2.052 2.326
PDU C5 C CR6 0.000 -8.703 -0.270 3.226
PDU C5A C CH2 0.000 -9.444 -0.982 4.328
PDU H5A1 H H 0.000 -9.789 -1.952 3.965
PDU H5A2 H H 0.000 -10.303 -0.382 4.634
PDU C5B C CH2 0.000 -8.510 -1.185 5.523
PDU H5B1 H H 0.000 -8.166 -0.214 5.885
PDU H5B2 H H 0.000 -7.651 -1.784 5.215
PDU C5M C CH3 0.000 -9.264 -1.909 6.641
PDU H73 H H 0.000 -10.099 -1.330 6.942
PDU H72 H H 0.000 -9.599 -2.853 6.292
PDU H71 H H 0.000 -8.620 -2.052 7.471
PDU C4 C CR6 0.000 -8.707 1.144 3.158
PDU N3 N NR16 0.000 -8.033 1.760 2.166
PDU H3 H H 0.000 -8.026 2.799 2.112
PDU C2 C CR6 0.000 -7.369 1.037 1.245
PDU O2 O O 0.000 -6.770 1.605 0.354
PDU O4 O O 0.000 -9.308 1.798 3.991
PDU "O3'" O OH1 0.000 -5.962 -0.704 -3.239
PDU "HO3'" H H 0.000 -6.774 -0.395 -3.663
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
PDU OP3 n/a P START
PDU P OP3 "O5'" .
PDU OP1 P . .
PDU OP2 P . .
PDU "O5'" P "C5'" .
PDU "C5'" "O5'" "C4'" .
PDU "H5'" "C5'" . .
PDU "H5''" "C5'" . .
PDU "C4'" "C5'" "C3'" .
PDU "H4'" "C4'" . .
PDU "C3'" "C4'" "O3'" .
PDU "H3'" "C3'" . .
PDU "C2'" "C3'" "C1'" .
PDU "H2''" "C2'" . .
PDU "H2'" "C2'" . .
PDU "C1'" "C2'" N1 .
PDU "H1'" "C1'" . .
PDU "O4'" "C1'" . .
PDU N1 "C1'" C6 .
PDU C6 N1 C5 .
PDU H6 C6 . .
PDU C5 C6 C4 .
PDU C5A C5 C5B .
PDU H5A1 C5A . .
PDU H5A2 C5A . .
PDU C5B C5A C5M .
PDU H5B1 C5B . .
PDU H5B2 C5B . .
PDU C5M C5B H71 .
PDU H73 C5M . .
PDU H72 C5M . .
PDU H71 C5M . .
PDU C4 C5 O4 .
PDU N3 C4 C2 .
PDU H3 N3 . .
PDU C2 N3 O2 .
PDU O2 C2 . .
PDU O4 C4 . .
PDU "O3'" "C3'" . END
PDU "HO3'" "O3'" . .
PDU "C4'" "O4'" . ADD
PDU 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
PDU P OP3 deloc 1.510 0.020
PDU OP1 P deloc 1.510 0.020
PDU OP2 P deloc 1.510 0.020
PDU "O5'" P single 1.610 0.020
PDU "C5'" "O5'" single 1.426 0.020
PDU "C4'" "C5'" single 1.524 0.020
PDU "H5'" "C5'" single 1.092 0.020
PDU "H5''" "C5'" single 1.092 0.020
PDU "C4'" "O4'" single 1.426 0.020
PDU "C3'" "C4'" single 1.524 0.020
PDU "H4'" "C4'" single 1.099 0.020
PDU "O4'" "C1'" single 1.426 0.020
PDU "O3'" "C3'" single 1.432 0.020
PDU "C2'" "C3'" single 1.524 0.020
PDU "H3'" "C3'" single 1.099 0.020
PDU "HO3'" "O3'" single 0.967 0.020
PDU "C1'" "C2'" single 1.524 0.020
PDU "H2''" "C2'" single 1.092 0.020
PDU "H2'" "C2'" single 1.092 0.020
PDU N1 "C1'" single 1.465 0.020
PDU "H1'" "C1'" single 1.099 0.020
PDU N1 C2 single 1.410 0.020
PDU C6 N1 single 1.337 0.020
PDU O2 C2 double 1.250 0.020
PDU C2 N3 single 1.337 0.020
PDU N3 C4 single 1.337 0.020
PDU H3 N3 single 1.040 0.020
PDU O4 C4 double 1.250 0.020
PDU C4 C5 single 1.487 0.020
PDU C5A C5 single 1.511 0.020
PDU C5 C6 double 1.390 0.020
PDU C5B C5A single 1.524 0.020
PDU H5A1 C5A single 1.092 0.020
PDU H5A2 C5A single 1.092 0.020
PDU C5M C5B single 1.513 0.020
PDU H5B1 C5B single 1.092 0.020
PDU H5B2 C5B single 1.092 0.020
PDU H71 C5M single 1.059 0.020
PDU H72 C5M single 1.059 0.020
PDU H73 C5M single 1.059 0.020
PDU H6 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
PDU OP3 P OP1 119.900 3.000
PDU OP3 P OP2 119.900 3.000
PDU OP3 P "O5'" 108.200 3.000
PDU OP1 P OP2 119.900 3.000
PDU OP1 P "O5'" 108.200 3.000
PDU OP2 P "O5'" 108.200 3.000
PDU P "O5'" "C5'" 120.500 3.000
PDU "O5'" "C5'" "H5'" 109.470 3.000
PDU "O5'" "C5'" "H5''" 109.470 3.000
PDU "O5'" "C5'" "C4'" 109.470 3.000
PDU "H5'" "C5'" "H5''" 107.900 3.000
PDU "H5'" "C5'" "C4'" 109.470 3.000
PDU "H5''" "C5'" "C4'" 109.470 3.000
PDU "C5'" "C4'" "H4'" 108.340 3.000
PDU "C5'" "C4'" "C3'" 111.000 3.000
PDU "C5'" "C4'" "O4'" 109.470 3.000
PDU "H4'" "C4'" "C3'" 108.340 3.000
PDU "H4'" "C4'" "O4'" 109.470 3.000
PDU "C3'" "C4'" "O4'" 109.470 3.000
PDU "C4'" "C3'" "H3'" 108.340 3.000
PDU "C4'" "C3'" "C2'" 111.000 3.000
PDU "C4'" "C3'" "O3'" 109.470 3.000
PDU "H3'" "C3'" "C2'" 108.340 3.000
PDU "H3'" "C3'" "O3'" 109.470 3.000
PDU "C2'" "C3'" "O3'" 109.470 3.000
PDU "C3'" "C2'" "H2''" 109.470 3.000
PDU "C3'" "C2'" "H2'" 109.470 3.000
PDU "C3'" "C2'" "C1'" 111.000 3.000
PDU "H2''" "C2'" "H2'" 107.900 3.000
PDU "H2''" "C2'" "C1'" 109.470 3.000
PDU "H2'" "C2'" "C1'" 109.470 3.000
PDU "C2'" "C1'" "H1'" 108.340 3.000
PDU "C2'" "C1'" "O4'" 109.470 3.000
PDU "C2'" "C1'" N1 109.470 3.000
PDU "H1'" "C1'" "O4'" 109.470 3.000
PDU "H1'" "C1'" N1 109.470 3.000
PDU "O4'" "C1'" N1 109.470 3.000
PDU "C1'" "O4'" "C4'" 111.800 3.000
PDU "C1'" N1 C6 120.000 3.000
PDU "C1'" N1 C2 120.000 3.000
PDU C6 N1 C2 120.000 3.000
PDU N1 C6 H6 120.000 3.000
PDU N1 C6 C5 120.000 3.000
PDU H6 C6 C5 120.000 3.000
PDU C6 C5 C5A 120.000 3.000
PDU C6 C5 C4 120.000 3.000
PDU C5A C5 C4 120.000 3.000
PDU C5 C5A H5A1 109.470 3.000
PDU C5 C5A H5A2 109.470 3.000
PDU C5 C5A C5B 109.470 3.000
PDU H5A1 C5A H5A2 107.900 3.000
PDU H5A1 C5A C5B 109.470 3.000
PDU H5A2 C5A C5B 109.470 3.000
PDU C5A C5B H5B1 109.470 3.000
PDU C5A C5B H5B2 109.470 3.000
PDU C5A C5B C5M 111.000 3.000
PDU H5B1 C5B H5B2 107.900 3.000
PDU H5B1 C5B C5M 109.470 3.000
PDU H5B2 C5B C5M 109.470 3.000
PDU C5B C5M H73 109.470 3.000
PDU C5B C5M H72 109.470 3.000
PDU C5B C5M H71 109.470 3.000
PDU H73 C5M H72 109.470 3.000
PDU H73 C5M H71 109.470 3.000
PDU H72 C5M H71 109.470 3.000
PDU C5 C4 N3 120.000 3.000
PDU C5 C4 O4 120.000 3.000
PDU N3 C4 O4 120.000 3.000
PDU C4 N3 H3 120.000 3.000
PDU C4 N3 C2 120.000 3.000
PDU H3 N3 C2 120.000 3.000
PDU N3 C2 O2 120.000 3.000
PDU N3 C2 N1 120.000 3.000
PDU O2 C2 N1 120.000 3.000
PDU "C3'" "O3'" "HO3'" 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
PDU var_1 OP3 P "O5'" "C5'" 179.958 20.000 1
PDU var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
PDU var_3 "O5'" "C5'" "C4'" "C3'" -179.930 20.000 3
PDU var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
PDU var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
PDU var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
PDU var_7 "C3'" "C2'" "C1'" N1 120.000 20.000 3
PDU var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
PDU var_9 "C2'" "C1'" N1 C6 120.332 20.000 1
PDU CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
PDU CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
PDU CONST_3 N1 C6 C5 C4 0.000 0.000 0
PDU var_10 C6 C5 C5A C5B 89.901 20.000 2
PDU var_11 C5 C5A C5B C5M -179.958 20.000 3
PDU var_12 C5A C5B C5M H71 -179.990 20.000 3
PDU CONST_4 C6 C5 C4 O4 180.000 0.000 0
PDU CONST_5 C5 C4 N3 C2 0.000 0.000 0
PDU 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
PDU chir_01 "C4'" "C5'" "O4'" "C3'" negativ
PDU chir_02 "C3'" "C4'" "O3'" "C2'" negativ
PDU chir_03 "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
PDU plan-1 N1 0.020
PDU plan-1 "C1'" 0.020
PDU plan-1 C2 0.020
PDU plan-1 C6 0.020
PDU plan-1 N3 0.020
PDU plan-1 C4 0.020
PDU plan-1 C5 0.020
PDU plan-1 O2 0.020
PDU plan-1 H3 0.020
PDU plan-1 O4 0.020
PDU plan-1 C5A 0.020
PDU plan-1 H6 0.020
# ------------------------------------------------------
|
