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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
DGI DGI '2'-DEOXYGUANOSINE-5'-DIPHOSPHATE ' non-polymer 39 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DGI
#
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
DGI O6 O O 0.000 0.000 0.000 0.000
DGI C6 C CR6 0.000 -0.886 0.661 0.515
DGI C5 C CR56 0.000 -2.243 0.438 0.186
DGI N7 N NRD5 0.000 -2.883 -0.416 -0.649
DGI C8 C CR15 0.000 -4.165 -0.206 -0.580
DGI H8 H H 0.000 -4.916 -0.747 -1.142
DGI N1 N NR16 0.000 -0.593 1.629 1.413
DGI HN1 H H 0.000 0.398 1.817 1.666
DGI C2 C CR6 0.000 -1.591 2.359 1.986
DGI N2 N NH2 0.000 -1.265 3.331 2.898
DGI HN22 H H 0.000 -0.296 3.499 3.143
DGI HN21 H H 0.000 -1.991 3.888 3.334
DGI N3 N NRD6 0.000 -2.855 2.162 1.689
DGI C4 C CR56 0.000 -3.221 1.225 0.805
DGI N9 N NR5 0.000 -4.422 0.800 0.306
DGI "C1'" C CH1 0.000 -5.742 1.327 0.659
DGI "H1'" H H 0.000 -5.761 1.602 1.723
DGI "O4'" O O2 0.000 -6.751 0.339 0.392
DGI "C2'" C CH2 0.000 -6.063 2.561 -0.206
DGI "H2'" H H 0.000 -5.278 2.762 -0.939
DGI "H2''" H H 0.000 -6.230 3.454 0.399
DGI "C3'" C CH1 0.000 -7.371 2.179 -0.940
DGI "H3'" H H 0.000 -7.159 1.802 -1.950
DGI "O3'" O OH1 0.000 -8.270 3.289 -0.989
DGI "HO3'" H H 0.000 -7.860 4.013 -1.481
DGI "C4'" C CH1 0.000 -7.933 1.052 -0.036
DGI "H4'" H H 0.000 -8.462 1.477 0.829
DGI "C5'" C CH2 0.000 -8.861 0.134 -0.834
DGI "H5'" H H 0.000 -8.285 -0.385 -1.604
DGI "H5''" H H 0.000 -9.644 0.731 -1.308
DGI "O5'" O O2 0.000 -9.456 -0.824 0.045
DGI PA P P 0.000 -10.414 -1.751 -0.857
DGI O1A O OP -0.500 -9.631 -2.331 -1.976
DGI O2A O OP -0.500 -11.524 -0.932 -1.402
DGI O3A O O2 0.000 -11.017 -2.938 0.048
DGI PB P P 0.000 -11.502 -4.094 -0.964
DGI O1B O OP -0.666 -12.156 -3.463 -2.174
DGI O2B O OP -0.666 -10.308 -4.912 -1.405
DGI O3B O OP -0.666 -12.498 -4.991 -0.263
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
DGI O6 n/a C6 START
DGI C6 O6 N1 .
DGI C5 C6 N7 .
DGI N7 C5 C8 .
DGI C8 N7 H8 .
DGI H8 C8 . .
DGI N1 C6 C2 .
DGI HN1 N1 . .
DGI C2 N1 N3 .
DGI N2 C2 HN21 .
DGI HN22 N2 . .
DGI HN21 N2 . .
DGI N3 C2 C4 .
DGI C4 N3 N9 .
DGI N9 C4 "C1'" .
DGI "C1'" N9 "C2'" .
DGI "H1'" "C1'" . .
DGI "O4'" "C1'" . .
DGI "C2'" "C1'" "C3'" .
DGI "H2'" "C2'" . .
DGI "H2''" "C2'" . .
DGI "C3'" "C2'" "C4'" .
DGI "H3'" "C3'" . .
DGI "O3'" "C3'" "HO3'" .
DGI "HO3'" "O3'" . .
DGI "C4'" "C3'" "C5'" .
DGI "H4'" "C4'" . .
DGI "C5'" "C4'" "O5'" .
DGI "H5'" "C5'" . .
DGI "H5''" "C5'" . .
DGI "O5'" "C5'" PA .
DGI PA "O5'" O3A .
DGI O1A PA . .
DGI O2A PA . .
DGI O3A PA PB .
DGI PB O3A O3B .
DGI O1B PB . .
DGI O2B PB . .
DGI O3B PB . END
DGI "C4'" "O4'" . ADD
DGI N9 C8 . ADD
DGI C5 C4 . 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
DGI O1B PB deloc 1.510 0.020
DGI O2B PB deloc 1.510 0.020
DGI O3B PB deloc 1.510 0.020
DGI PB O3A single 1.610 0.020
DGI O3A PA single 1.610 0.020
DGI O1A PA deloc 1.510 0.020
DGI O2A PA deloc 1.510 0.020
DGI PA "O5'" single 1.610 0.020
DGI "O5'" "C5'" single 1.426 0.020
DGI "C5'" "C4'" single 1.524 0.020
DGI "H5'" "C5'" single 1.092 0.020
DGI "H5''" "C5'" single 1.092 0.020
DGI "C4'" "O4'" single 1.426 0.020
DGI "C4'" "C3'" single 1.524 0.020
DGI "H4'" "C4'" single 1.099 0.020
DGI "O4'" "C1'" single 1.426 0.020
DGI "O3'" "C3'" single 1.432 0.020
DGI "C3'" "C2'" single 1.524 0.020
DGI "H3'" "C3'" single 1.099 0.020
DGI "HO3'" "O3'" single 0.967 0.020
DGI "C2'" "C1'" single 1.524 0.020
DGI "H2'" "C2'" single 1.092 0.020
DGI "H2''" "C2'" single 1.092 0.020
DGI "C1'" N9 single 1.485 0.020
DGI "H1'" "C1'" single 1.099 0.020
DGI N9 C8 single 1.337 0.020
DGI N9 C4 single 1.337 0.020
DGI C8 N7 double 1.350 0.020
DGI H8 C8 single 1.083 0.020
DGI N7 C5 single 1.350 0.020
DGI C5 C4 double 1.490 0.020
DGI C5 C6 single 1.490 0.020
DGI C4 N3 single 1.355 0.020
DGI N3 C2 double 1.350 0.020
DGI N2 C2 single 1.355 0.020
DGI C2 N1 single 1.337 0.020
DGI HN21 N2 single 1.010 0.020
DGI HN22 N2 single 1.010 0.020
DGI N1 C6 single 1.337 0.020
DGI HN1 N1 single 1.040 0.020
DGI C6 O6 double 1.250 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
DGI O6 C6 C5 120.000 3.000
DGI O6 C6 N1 120.000 3.000
DGI C5 C6 N1 120.000 3.000
DGI C6 C5 N7 132.000 3.000
DGI C6 C5 C4 120.000 3.000
DGI N7 C5 C4 108.000 3.000
DGI C5 N7 C8 108.000 3.000
DGI N7 C8 H8 126.000 3.000
DGI N7 C8 N9 108.000 3.000
DGI H8 C8 N9 126.000 3.000
DGI C6 N1 HN1 120.000 3.000
DGI C6 N1 C2 120.000 3.000
DGI HN1 N1 C2 120.000 3.000
DGI N1 C2 N2 120.000 3.000
DGI N1 C2 N3 120.000 3.000
DGI N2 C2 N3 120.000 3.000
DGI C2 N2 HN22 120.000 3.000
DGI C2 N2 HN21 120.000 3.000
DGI HN22 N2 HN21 120.000 3.000
DGI C2 N3 C4 120.000 3.000
DGI N3 C4 N9 132.000 3.000
DGI N3 C4 C5 120.000 3.000
DGI N9 C4 C5 108.000 3.000
DGI C4 N9 "C1'" 126.000 3.000
DGI C4 N9 C8 108.000 3.000
DGI "C1'" N9 C8 126.000 3.000
DGI N9 "C1'" "H1'" 109.470 3.000
DGI N9 "C1'" "O4'" 109.470 3.000
DGI N9 "C1'" "C2'" 109.470 3.000
DGI "H1'" "C1'" "O4'" 109.470 3.000
DGI "H1'" "C1'" "C2'" 108.340 3.000
DGI "O4'" "C1'" "C2'" 109.470 3.000
DGI "C1'" "O4'" "C4'" 111.800 3.000
DGI "C1'" "C2'" "H2'" 109.470 3.000
DGI "C1'" "C2'" "H2''" 109.470 3.000
DGI "C1'" "C2'" "C3'" 111.000 3.000
DGI "H2'" "C2'" "H2''" 107.900 3.000
DGI "H2'" "C2'" "C3'" 109.470 3.000
DGI "H2''" "C2'" "C3'" 109.470 3.000
DGI "C2'" "C3'" "H3'" 108.340 3.000
DGI "C2'" "C3'" "O3'" 109.470 3.000
DGI "C2'" "C3'" "C4'" 111.000 3.000
DGI "H3'" "C3'" "O3'" 109.470 3.000
DGI "H3'" "C3'" "C4'" 108.340 3.000
DGI "O3'" "C3'" "C4'" 109.470 3.000
DGI "C3'" "O3'" "HO3'" 109.470 3.000
DGI "C3'" "C4'" "H4'" 108.340 3.000
DGI "C3'" "C4'" "C5'" 111.000 3.000
DGI "C3'" "C4'" "O4'" 109.470 3.000
DGI "H4'" "C4'" "C5'" 108.340 3.000
DGI "H4'" "C4'" "O4'" 109.470 3.000
DGI "C5'" "C4'" "O4'" 109.470 3.000
DGI "C4'" "C5'" "H5'" 109.470 3.000
DGI "C4'" "C5'" "H5''" 109.470 3.000
DGI "C4'" "C5'" "O5'" 109.470 3.000
DGI "H5'" "C5'" "H5''" 107.900 3.000
DGI "H5'" "C5'" "O5'" 109.470 3.000
DGI "H5''" "C5'" "O5'" 109.470 3.000
DGI "C5'" "O5'" PA 120.500 3.000
DGI "O5'" PA O1A 108.200 3.000
DGI "O5'" PA O2A 108.200 3.000
DGI "O5'" PA O3A 102.600 3.000
DGI O1A PA O2A 119.900 3.000
DGI O1A PA O3A 108.200 3.000
DGI O2A PA O3A 108.200 3.000
DGI PA O3A PB 120.500 3.000
DGI O3A PB O1B 108.200 3.000
DGI O3A PB O2B 108.200 3.000
DGI O3A PB O3B 108.200 3.000
DGI O1B PB O2B 119.900 3.000
DGI O1B PB O3B 119.900 3.000
DGI 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
DGI CONST_1 O6 C6 C5 N7 0.000 0.000 0
DGI CONST_2 C6 C5 C4 N3 0.000 0.000 0
DGI CONST_3 C6 C5 N7 C8 180.000 0.000 0
DGI CONST_4 C5 N7 C8 N9 0.000 0.000 0
DGI CONST_5 O6 C6 N1 C2 180.000 0.000 0
DGI CONST_6 C6 N1 C2 N3 0.000 0.000 0
DGI CONST_7 N1 C2 N2 HN21 179.744 0.000 0
DGI CONST_8 N1 C2 N3 C4 0.000 0.000 0
DGI CONST_9 C2 N3 C4 N9 180.000 0.000 0
DGI CONST_10 N3 C4 N9 "C1'" 0.000 0.000 0
DGI CONST_11 C4 N9 C8 N7 0.000 0.000 0
DGI var_1 C4 N9 "C1'" "C2'" 85.264 20.000 1
DGI var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
DGI var_3 N9 "C1'" "C2'" "C3'" 120.000 20.000 3
DGI var_4 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
DGI var_5 "C2'" "C3'" "O3'" "HO3'" 61.464 20.000 1
DGI var_6 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
DGI var_7 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
DGI var_8 "C3'" "C4'" "C5'" "O5'" -174.972 20.000 3
DGI var_9 "C4'" "C5'" "O5'" PA -179.988 20.000 1
DGI var_10 "C5'" "O5'" PA O3A 174.985 20.000 1
DGI var_11 "O5'" PA O3A PB -160.007 20.000 1
DGI var_12 PA O3A PB O3B -159.996 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
DGI chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DGI chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DGI chir_03 "C1'" "O4'" "C2'" N9 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
DGI plan-1 N9 0.020
DGI plan-1 "C1'" 0.020
DGI plan-1 C8 0.020
DGI plan-1 C4 0.020
DGI plan-1 N7 0.020
DGI plan-1 H8 0.020
DGI plan-1 C5 0.020
DGI plan-1 C6 0.020
DGI plan-1 N3 0.020
DGI plan-1 C2 0.020
DGI plan-1 N1 0.020
DGI plan-1 N2 0.020
DGI plan-1 HN1 0.020
DGI plan-1 O6 0.020
DGI plan-1 HN22 0.020
DGI plan-1 HN21 0.020
DGI plan-2 N2 0.020
DGI plan-2 C2 0.020
DGI plan-2 HN21 0.020
DGI plan-2 HN22 0.020
# ------------------------------------------------------
|
