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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
DPB DPB '"(S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHON' non-polymer 47 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DPB
#
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
DPB OP1 O O 0.000 0.000 0.000 0.000
DPB P P P 0.000 -0.911 0.251 1.140
DPB OP3 O OH1 0.000 -0.868 -1.004 2.147
DPB HOP3 H H 0.000 -0.035 -1.259 2.565
DPB OP2 O OH1 0.000 -0.443 1.581 1.917
DPB HOP2 H H 0.000 -0.935 1.887 2.692
DPB "C6'" C CT 0.000 -2.626 0.478 0.515
DPB "O5'" O O2 0.000 -3.451 0.764 1.635
DPB "C5'" C CH2 0.000 -4.784 1.013 1.230
DPB "H5'" H H 0.000 -5.403 1.179 2.114
DPB "H5''" H H 0.000 -5.161 0.147 0.682
DPB "C4'" C CH1 0.000 -4.834 2.249 0.330
DPB "H4'" H H 0.000 -4.681 3.166 0.917
DPB "O4'" O O2 0.000 -6.115 2.271 -0.327
DPB C7 C CR6 0.000 -3.043 -0.828 -0.111
DPB C8 C CR16 0.000 -2.411 -1.278 -1.256
DPB H8 H H 0.000 -1.617 -0.692 -1.702
DPB C9 C CR16 0.000 -2.792 -2.476 -1.830
DPB H9 H H 0.000 -2.297 -2.828 -2.727
DPB C10 C CR16 0.000 -3.805 -3.224 -1.261
DPB H10 H H 0.000 -4.105 -4.162 -1.712
DPB C11 C CR16 0.000 -4.436 -2.775 -0.116
DPB H11 H H 0.000 -5.232 -3.360 0.329
DPB C12 C CR16 0.000 -4.052 -1.579 0.461
DPB H12 H H 0.000 -4.542 -1.230 1.362
DPB "O3'" O O2 0.000 -2.602 1.503 -0.445
DPB "C3'" C CH1 0.000 -3.790 2.137 -0.787
DPB "H3'" H H 0.000 -3.535 3.160 -1.098
DPB "C2'" C CH2 0.000 -4.535 1.479 -1.959
DPB "H2'" H H 0.000 -4.271 0.425 -2.067
DPB "H2''" H H 0.000 -4.350 1.998 -2.901
DPB "C1'" C CH1 0.000 -6.025 1.601 -1.587
DPB "H1'" H H 0.000 -6.544 2.194 -2.353
DPB N1 N NR6 0.000 -6.634 0.270 -1.507
DPB C6 C CR16 0.000 -7.206 -0.144 -0.335
DPB H6 H H 0.000 -7.208 0.509 0.530
DPB C5 C CR6 0.000 -7.767 -1.370 -0.261
DPB C5M C CH3 0.000 -8.402 -1.843 1.021
DPB H73 H H 0.000 -8.316 -2.896 1.090
DPB H72 H H 0.000 -7.910 -1.395 1.846
DPB H71 H H 0.000 -9.425 -1.571 1.030
DPB C4 C CR6 0.000 -7.747 -2.206 -1.402
DPB O4 O O 0.000 -8.247 -3.316 -1.359
DPB N3 N NR16 0.000 -7.177 -1.760 -2.540
DPB H3 H H 0.000 -7.164 -2.366 -3.385
DPB C2 C CR6 0.000 -6.626 -0.534 -2.586
DPB O2 O O 0.000 -6.111 -0.146 -3.617
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
DPB OP1 n/a P START
DPB P OP1 "C6'" .
DPB OP3 P HOP3 .
DPB HOP3 OP3 . .
DPB OP2 P HOP2 .
DPB HOP2 OP2 . .
DPB "C6'" P "O3'" .
DPB "O5'" "C6'" "C5'" .
DPB "C5'" "O5'" "C4'" .
DPB "H5'" "C5'" . .
DPB "H5''" "C5'" . .
DPB "C4'" "C5'" "O4'" .
DPB "H4'" "C4'" . .
DPB "O4'" "C4'" . .
DPB C7 "C6'" C8 .
DPB C8 C7 C9 .
DPB H8 C8 . .
DPB C9 C8 C10 .
DPB H9 C9 . .
DPB C10 C9 C11 .
DPB H10 C10 . .
DPB C11 C10 C12 .
DPB H11 C11 . .
DPB C12 C11 H12 .
DPB H12 C12 . .
DPB "O3'" "C6'" "C3'" .
DPB "C3'" "O3'" "C2'" .
DPB "H3'" "C3'" . .
DPB "C2'" "C3'" "C1'" .
DPB "H2'" "C2'" . .
DPB "H2''" "C2'" . .
DPB "C1'" "C2'" N1 .
DPB "H1'" "C1'" . .
DPB N1 "C1'" C6 .
DPB C6 N1 C5 .
DPB H6 C6 . .
DPB C5 C6 C4 .
DPB C5M C5 H71 .
DPB H73 C5M . .
DPB H72 C5M . .
DPB H71 C5M . .
DPB C4 C5 N3 .
DPB O4 C4 . .
DPB N3 C4 C2 .
DPB H3 N3 . .
DPB C2 N3 O2 .
DPB O2 C2 . END
DPB C12 C7 . ADD
DPB C2 N1 . ADD
DPB "C1'" "O4'" . ADD
DPB "C4'" "C3'" . 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
DPB C12 C11 double 1.390 0.020
DPB C11 C10 single 1.390 0.020
DPB H11 C11 single 1.083 0.020
DPB C12 C7 single 1.390 0.020
DPB H12 C12 single 1.083 0.020
DPB C8 C7 double 1.390 0.020
DPB C7 "C6'" single 1.500 0.020
DPB C9 C8 single 1.390 0.020
DPB H8 C8 single 1.083 0.020
DPB C10 C9 double 1.390 0.020
DPB H9 C9 single 1.083 0.020
DPB H10 C10 single 1.083 0.020
DPB C2 N1 single 1.410 0.020
DPB C2 N3 single 1.337 0.020
DPB O2 C2 double 1.250 0.020
DPB C6 N1 single 1.337 0.020
DPB N1 "C1'" single 1.465 0.020
DPB C5 C6 double 1.390 0.020
DPB H6 C6 single 1.083 0.020
DPB C4 C5 single 1.487 0.020
DPB C5M C5 single 1.506 0.020
DPB N3 C4 single 1.337 0.020
DPB O4 C4 double 1.250 0.020
DPB H3 N3 single 1.040 0.020
DPB H71 C5M single 1.059 0.020
DPB H72 C5M single 1.059 0.020
DPB H73 C5M single 1.059 0.020
DPB "C1'" "O4'" single 1.426 0.020
DPB "C1'" "C2'" single 1.524 0.020
DPB "H1'" "C1'" single 1.099 0.020
DPB "O4'" "C4'" single 1.426 0.020
DPB "C4'" "C3'" single 1.524 0.020
DPB "C4'" "C5'" single 1.524 0.020
DPB "H4'" "C4'" single 1.099 0.020
DPB "C2'" "C3'" single 1.524 0.020
DPB "C3'" "O3'" single 1.426 0.020
DPB "H3'" "C3'" single 1.099 0.020
DPB "H2'" "C2'" single 1.092 0.020
DPB "H2''" "C2'" single 1.092 0.020
DPB "C5'" "O5'" single 1.426 0.020
DPB "H5'" "C5'" single 1.092 0.020
DPB "H5''" "C5'" single 1.092 0.020
DPB "O5'" "C6'" single 1.426 0.020
DPB "O3'" "C6'" single 1.426 0.020
DPB "C6'" P single 1.812 0.020
DPB OP2 P single 1.610 0.020
DPB P OP1 double 1.480 0.020
DPB OP3 P single 1.610 0.020
DPB HOP2 OP2 single 0.967 0.020
DPB HOP3 OP3 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
DPB OP1 P OP3 109.500 3.000
DPB OP1 P OP2 109.500 3.000
DPB OP1 P "C6'" 109.500 3.000
DPB OP3 P OP2 109.500 3.000
DPB OP3 P "C6'" 109.500 3.000
DPB OP2 P "C6'" 109.500 3.000
DPB P OP3 HOP3 120.000 3.000
DPB P OP2 HOP2 120.000 3.000
DPB P "C6'" "O5'" 109.500 3.000
DPB P "C6'" C7 109.500 3.000
DPB P "C6'" "O3'" 109.500 3.000
DPB "O5'" "C6'" C7 109.500 3.000
DPB "O5'" "C6'" "O3'" 109.500 3.000
DPB C7 "C6'" "O3'" 109.500 3.000
DPB "C6'" "O5'" "C5'" 111.800 3.000
DPB "O5'" "C5'" "H5'" 109.470 3.000
DPB "O5'" "C5'" "H5''" 109.470 3.000
DPB "O5'" "C5'" "C4'" 109.470 3.000
DPB "H5'" "C5'" "H5''" 107.900 3.000
DPB "H5'" "C5'" "C4'" 109.470 3.000
DPB "H5''" "C5'" "C4'" 109.470 3.000
DPB "C5'" "C4'" "H4'" 108.340 3.000
DPB "C5'" "C4'" "O4'" 109.470 3.000
DPB "C5'" "C4'" "C3'" 111.000 3.000
DPB "H4'" "C4'" "O4'" 109.470 3.000
DPB "H4'" "C4'" "C3'" 108.340 3.000
DPB "O4'" "C4'" "C3'" 109.470 3.000
DPB "C4'" "O4'" "C1'" 111.800 3.000
DPB "C6'" C7 C8 120.000 3.000
DPB "C6'" C7 C12 120.000 3.000
DPB C8 C7 C12 120.000 3.000
DPB C7 C8 H8 120.000 3.000
DPB C7 C8 C9 120.000 3.000
DPB H8 C8 C9 120.000 3.000
DPB C8 C9 H9 120.000 3.000
DPB C8 C9 C10 120.000 3.000
DPB H9 C9 C10 120.000 3.000
DPB C9 C10 H10 120.000 3.000
DPB C9 C10 C11 120.000 3.000
DPB H10 C10 C11 120.000 3.000
DPB C10 C11 H11 120.000 3.000
DPB C10 C11 C12 120.000 3.000
DPB H11 C11 C12 120.000 3.000
DPB C11 C12 H12 120.000 3.000
DPB C11 C12 C7 120.000 3.000
DPB H12 C12 C7 120.000 3.000
DPB "C6'" "O3'" "C3'" 111.800 3.000
DPB "O3'" "C3'" "H3'" 109.470 3.000
DPB "O3'" "C3'" "C2'" 109.470 3.000
DPB "O3'" "C3'" "C4'" 109.470 3.000
DPB "H3'" "C3'" "C2'" 108.340 3.000
DPB "H3'" "C3'" "C4'" 108.340 3.000
DPB "C2'" "C3'" "C4'" 111.000 3.000
DPB "C3'" "C2'" "H2'" 109.470 3.000
DPB "C3'" "C2'" "H2''" 109.470 3.000
DPB "C3'" "C2'" "C1'" 111.000 3.000
DPB "H2'" "C2'" "H2''" 107.900 3.000
DPB "H2'" "C2'" "C1'" 109.470 3.000
DPB "H2''" "C2'" "C1'" 109.470 3.000
DPB "C2'" "C1'" "H1'" 108.340 3.000
DPB "C2'" "C1'" N1 109.470 3.000
DPB "C2'" "C1'" "O4'" 109.470 3.000
DPB "H1'" "C1'" N1 109.470 3.000
DPB "H1'" "C1'" "O4'" 109.470 3.000
DPB N1 "C1'" "O4'" 109.470 3.000
DPB "C1'" N1 C6 120.000 3.000
DPB "C1'" N1 C2 120.000 3.000
DPB C6 N1 C2 120.000 3.000
DPB N1 C6 H6 120.000 3.000
DPB N1 C6 C5 120.000 3.000
DPB H6 C6 C5 120.000 3.000
DPB C6 C5 C5M 120.000 3.000
DPB C6 C5 C4 120.000 3.000
DPB C5M C5 C4 120.000 3.000
DPB C5 C5M H73 109.470 3.000
DPB C5 C5M H72 109.470 3.000
DPB C5 C5M H71 109.470 3.000
DPB H73 C5M H72 109.470 3.000
DPB H73 C5M H71 109.470 3.000
DPB H72 C5M H71 109.470 3.000
DPB C5 C4 O4 120.000 3.000
DPB C5 C4 N3 120.000 3.000
DPB O4 C4 N3 120.000 3.000
DPB C4 N3 H3 120.000 3.000
DPB C4 N3 C2 120.000 3.000
DPB H3 N3 C2 120.000 3.000
DPB N3 C2 O2 120.000 3.000
DPB N3 C2 N1 120.000 3.000
DPB 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
DPB var_1 OP1 P OP3 HOP3 60.005 20.000 1
DPB var_2 OP1 P OP2 HOP2 -179.970 20.000 1
DPB var_3 OP1 P "C6'" "O3'" -54.979 20.000 1
DPB var_4 P "C6'" "O5'" "C5'" 180.000 20.000 1
DPB var_5 "C6'" "O5'" "C5'" "C4'" -60.000 20.000 1
DPB var_6 "O5'" "C5'" "C4'" "O4'" 180.000 20.000 3
DPB var_7 "C5'" "C4'" "C3'" "O3'" -30.000 20.000 3
DPB var_8 "C5'" "C4'" "O4'" "C1'" -90.000 20.000 1
DPB var_9 P "C6'" C7 C8 -66.470 20.000 1
DPB CONST_1 "C6'" C7 C8 C9 180.000 0.000 0
DPB CONST_2 C7 C8 C9 C10 0.000 0.000 0
DPB CONST_3 C8 C9 C10 C11 0.000 0.000 0
DPB CONST_4 C9 C10 C11 C12 0.000 0.000 0
DPB CONST_5 C10 C11 C12 C7 0.000 0.000 0
DPB CONST_6 C11 C12 C7 "C6'" 180.000 0.000 0
DPB var_10 P "C6'" "O3'" "C3'" -150.000 20.000 1
DPB var_11 "C6'" "O3'" "C3'" "C2'" -90.000 20.000 1
DPB var_12 "O3'" "C3'" "C2'" "C1'" 150.000 20.000 3
DPB var_13 "C3'" "C2'" "C1'" N1 -120.000 20.000 3
DPB var_14 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DPB var_15 "C2'" "C1'" N1 C6 120.715 20.000 1
DPB CONST_7 "C1'" N1 C6 C5 180.000 0.000 0
DPB CONST_8 N1 C6 C5 C4 0.000 0.000 0
DPB var_16 C6 C5 C5M H71 89.993 20.000 1
DPB CONST_9 C6 C5 C4 N3 0.000 0.000 0
DPB CONST_10 C5 C4 N3 C2 0.000 0.000 0
DPB CONST_11 C4 N3 C2 O2 180.000 0.000 0
DPB CONST_12 N3 C2 N1 "C1'" 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
DPB chir_01 "C1'" N1 "O4'" "C2'" negativ
DPB chir_02 "C4'" "O4'" "C3'" "C5'" positiv
DPB chir_03 "C3'" "C4'" "C2'" "O3'" positiv
DPB chir_04 "C6'" C7 "O5'" "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
DPB plan-1 C12 0.020
DPB plan-1 C7 0.020
DPB plan-1 C11 0.020
DPB plan-1 H12 0.020
DPB plan-1 C8 0.020
DPB plan-1 C9 0.020
DPB plan-1 C10 0.020
DPB plan-1 "C6'" 0.020
DPB plan-1 H8 0.020
DPB plan-1 H9 0.020
DPB plan-1 H10 0.020
DPB plan-1 H11 0.020
DPB plan-2 C2 0.020
DPB plan-2 N1 0.020
DPB plan-2 N3 0.020
DPB plan-2 O2 0.020
DPB plan-2 C6 0.020
DPB plan-2 C5 0.020
DPB plan-2 C4 0.020
DPB plan-2 "C1'" 0.020
DPB plan-2 H6 0.020
DPB plan-2 C5M 0.020
DPB plan-2 O4 0.020
DPB plan-2 H3 0.020
# ------------------------------------------------------
|
