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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
DG DG '2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE ' DNA 35 23 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DG
#
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
DG P P P 0.000 -0.056 -0.552 0.076
DG OP3 O OP -0.660 0.020 -2.009 0.478
DG OP1 O OP -0.660 -0.172 0.378 1.260
DG "O5'" O O2 0.000 -1.466 -0.414 -0.696
DG "C5'" C CH2 0.000 -1.980 0.791 -1.294
DG "H5'" H H 0.000 -1.199 1.313 -1.851
DG "H5''" H H 0.000 -2.392 1.458 -0.534
DG "C4'" C CH1 0.000 -3.092 0.360 -2.253
DG "H4'" H H 0.000 -2.689 -0.449 -2.879
DG "C3'" C CH1 0.000 -3.758 1.373 -3.192
DG "H3'" H H 0.000 -3.624 2.391 -2.801
DG "O3'" O OH1 0.000 -3.218 1.283 -4.520
DG "HO3'" H H 0.000 -3.707 1.875 -5.109
DG "C2'" C CH2 0.000 -5.268 0.993 -3.183
DG "H2' " H H 0.000 -5.554 0.561 -4.144
DG "H2''" H H 0.000 -5.879 1.877 -2.987
DG "C1'" C CH1 0.000 -5.488 -0.042 -2.067
DG "H1'" H H 0.000 -5.742 -0.995 -2.554
DG "O4'" O O2 0.000 -4.180 -0.201 -1.473
DG N9 N NR5 0.000 -6.561 0.242 -1.071
DG C4 C CR56 0.000 -7.783 -0.323 -0.980
DG C5 C CR56 0.000 -8.470 0.361 0.156
DG N7 N NRD5 0.000 -7.502 0.995 0.805
DG C8 C CR15 0.000 -6.341 0.713 0.168
DG H8 H H 0.000 -5.358 0.850 0.603
DG N3 N NRD6 0.000 -8.662 -0.949 -1.782
DG C2 C CR6 0.000 -9.985 -1.121 -1.470
DG N2 N NH2 0.000 -10.687 -1.850 -2.375
DG H22 H H 0.000 -10.227 -2.215 -3.197
DG H21 H H 0.000 -11.671 -2.027 -2.227
DG N1 N NR16 0.000 -10.616 -0.564 -0.437
DG H1 H H 0.000 -11.634 -0.721 -0.294
DG C6 C CR6 0.000 -9.926 0.195 0.408
DG O6 O O 0.000 -10.487 0.731 1.387
DG OP2 O OP -0.660 0.998 -0.164 -0.933
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
DG "O5'" n/a "C5'" START
DG P "O5'" OP2 .
DG OP3 P . .
DG OP1 P . .
DG "C5'" "O5'" "C4'" .
DG "H5'" "C5'" . .
DG "H5''" "C5'" . .
DG "C4'" "C5'" "C3'" .
DG "H4'" "C4'" . .
DG "C3'" "C4'" "C2'" .
DG "H3'" "C3'" . .
DG "O3'" "C3'" "HO3'" .
DG "HO3'" "O3'" . .
DG "C2'" "C3'" "C1'" .
DG "H2' " "C2'" . .
DG "H2''" "C2'" . .
DG "C1'" "C2'" N9 .
DG "H1'" "C1'" . .
DG "O4'" "C1'" . .
DG N9 "C1'" C4 .
DG C4 N9 N3 .
DG C5 C4 N7 .
DG N7 C5 C8 .
DG C8 N7 H8 .
DG H8 C8 . .
DG N3 C4 C2 .
DG C2 N3 N1 .
DG N2 C2 H21 .
DG H22 N2 . .
DG H21 N2 . .
DG N1 C2 C6 .
DG H1 N1 . .
DG C6 N1 O6 .
DG OP2 P . .
DG O6 C6 . END
DG "C4'" "O4'" . ADD
DG N9 C8 . ADD
DG C5 C6 . 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
DG OP3 P deloc 1.485 0.017
DG OP1 P deloc 1.485 0.017
DG OP2 P deloc 1.485 0.017
DG "O5'" P single 1.593 0.010
DG "C5'" "O5'" single 1.440 0.016
DG "C4'" "C5'" single 1.511 0.008
DG "C4'" "O4'" single 1.446 0.011
DG "C3'" "C4'" single 1.528 0.010
DG "O4'" "C1'" single 1.420 0.013
DG "O3'" "C3'" single 1.431 0.013
DG "C2'" "C3'" single 1.518 0.010
DG "C1'" "C2'" single 1.521 0.014
DG N9 "C1'" single 1.459 0.009
DG N9 C8 single 1.374 0.007
DG C4 N9 single 1.375 0.008
DG C8 N7 double 1.305 0.006
DG N7 C5 single 1.388 0.006
DG C5 C6 single 1.419 0.010
DG C5 C4 double 1.379 0.007
DG O6 C6 double 1.237 0.009
DG C6 N1 single 1.391 0.007
DG N1 C2 single 1.373 0.008
DG N2 C2 single 1.341 0.010
DG C2 N3 double 1.323 0.008
DG N3 C4 single 1.350 0.007
DG "H5'" "C5'" single 1.092 0.020
DG "H5''" "C5'" single 1.092 0.020
DG "H4'" "C4'" single 1.099 0.020
DG "H3'" "C3'" single 1.099 0.020
DG "HO3'" "O3'" single 0.967 0.020
DG "H2' " "C2'" single 1.092 0.020
DG "H2''" "C2'" single 1.092 0.020
DG "H1'" "C1'" single 1.099 0.020
DG H8 C8 single 1.083 0.020
DG H1 N1 single 1.040 0.020
DG H21 N2 single 1.010 0.020
DG H22 N2 single 1.010 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
DG OP3 P OP1 107.400 3.200
DG OP3 P "O5'" 104.000 1.900
DG OP1 P "O5'" 108.100 2.900
DG OP3 P OP2 108.300 3.200
DG OP1 P OP2 119.600 1.500
DG "O5'" P OP2 108.300 2.700
DG P "O5'" "C5'" 120.900 1.600
DG "O5'" "C5'" "H5'" 109.470 3.000
DG "O5'" "C5'" "H5''" 109.470 3.000
DG "O5'" "C5'" "C4'" 110.200 1.400
DG "H5'" "C5'" "H5''" 107.900 3.000
DG "H5'" "C5'" "C4'" 109.470 3.000
DG "H5''" "C5'" "C4'" 109.470 3.000
DG "C5'" "C4'" "H4'" 108.340 3.000
DG "C5'" "C4'" "C3'" 114.700 1.500
DG "C5'" "C4'" "O4'" 109.400 1.600
DG "H4'" "C4'" "C3'" 108.340 3.000
DG "H4'" "C4'" "O4'" 109.470 3.000
DG "C3'" "C4'" "O4'" 105.600 1.000
DG "C4'" "C3'" "H3'" 108.340 3.000
DG "C4'" "C3'" "O3'" 110.300 2.200
DG "C4'" "C3'" "C2'" 103.200 1.000
DG "H3'" "C3'" "O3'" 109.470 3.000
DG "H3'" "C3'" "C2'" 108.340 3.000
DG "O3'" "C3'" "C2'" 110.600 2.700
DG "C3'" "O3'" "HO3'" 109.470 3.000
DG "C3'" "C2'" "H2' " 109.470 3.000
DG "C3'" "C2'" "H2''" 109.470 3.000
DG "C3'" "C2'" "C1'" 102.700 1.400
DG "H2' " "C2'" "H2''" 107.900 3.000
DG "H2' " "C2'" "C1'" 109.470 3.000
DG "H2''" "C2'" "C1'" 109.470 3.000
DG "C2'" "C1'" "H1'" 108.340 3.000
DG "C2'" "C1'" "O4'" 106.100 1.100
DG "C2'" "C1'" N9 114.200 1.600
DG "H1'" "C1'" "O4'" 109.470 3.000
DG "H1'" "C1'" N9 109.470 3.000
DG "O4'" "C1'" N9 107.800 0.800
DG "C1'" "O4'" "C4'" 109.700 1.400
DG "C1'" N9 C4 126.500 1.300
DG "C1'" N9 C8 127.000 1.300
DG C4 N9 C8 106.400 0.400
DG N9 C4 C5 105.400 0.400
DG N9 C4 N3 126.000 0.600
DG C5 C4 N3 128.600 0.500
DG C4 C5 N7 110.800 0.400
DG C4 C5 C6 118.800 0.600
DG N7 C5 C6 130.400 0.600
DG C5 N7 C8 104.300 0.500
DG N7 C8 H8 126.000 3.000
DG N7 C8 N9 113.100 0.500
DG H8 C8 N9 126.000 3.000
DG C4 N3 C2 111.900 0.500
DG N3 C2 N2 119.900 0.700
DG N3 C2 N1 123.900 0.600
DG N2 C2 N1 116.200 0.900
DG C2 N2 H22 120.000 3.000
DG C2 N2 H21 120.000 3.000
DG H22 N2 H21 120.000 3.000
DG C2 N1 H1 120.000 3.000
DG C2 N1 C6 125.100 0.600
DG H1 N1 C6 120.000 3.000
DG N1 C6 O6 119.900 0.600
DG N1 C6 C5 111.500 0.500
DG O6 C6 C5 128.600 0.600
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
DG var_1 OP2 P "O5'" "C5'" -60.054 20.000 1
DG var_2 P "O5'" "C5'" "C4'" -179.992 20.000 1
DG var_3 "O5'" "C5'" "C4'" "C3'" 179.992 20.000 3
DG var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DG var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DG var_6 "C4'" "C3'" "O3'" "HO3'" 175.000 20.000 1
DG var_7 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DG var_8 "C3'" "C2'" "C1'" N9 120.000 20.000 3
DG var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DG var_10 "C2'" "C1'" N9 C4 90.187 20.000 1
DG CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
DG CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
DG CONST_3 N9 C4 C5 N7 0.000 0.000 0
DG CONST_4 C4 C5 C6 N1 0.000 0.000 0
DG CONST_5 C4 C5 N7 C8 0.000 0.000 0
DG CONST_6 C5 N7 C8 N9 0.000 0.000 0
DG CONST_7 N9 C4 N3 C2 180.000 0.000 0
DG CONST_8 C4 N3 C2 N1 0.000 0.000 0
DG CONST_9 N3 C2 N2 H21 180.000 0.000 0
DG CONST_10 N3 C2 N1 C6 0.000 0.000 0
DG CONST_11 C2 N1 C6 O6 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
DG chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DG chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DG 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
DG plan-1 N9 0.020
DG plan-1 "C1'" 0.020
DG plan-1 C8 0.020
DG plan-1 C4 0.020
DG plan-1 N7 0.020
DG plan-1 H8 0.020
DG plan-1 C5 0.020
DG plan-1 C6 0.020
DG plan-1 N1 0.020
DG plan-1 C2 0.020
DG plan-1 N3 0.020
DG plan-1 O6 0.020
DG plan-1 H1 0.020
DG plan-1 N2 0.020
DG plan-1 H22 0.020
DG plan-1 H21 0.020
DG plan-2 N2 0.020
DG plan-2 C2 0.020
DG plan-2 H21 0.020
DG plan-2 H22 0.020
# ------------------------------------------------------
# ------------------------------------------------------
# ------------------------------------------------------
|
