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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
DFT DFT '1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUOR' DNA 34 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DFT
#
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
DFT OP3 O OP -0.666 0.000 0.000 0.000
DFT P P P 0.000 -0.900 0.397 -1.149
DFT OP1 O OP -0.666 -1.150 -0.804 -2.035
DFT OP2 O OP -0.666 -0.234 1.489 -1.957
DFT "O5'" O O2 0.000 -2.302 0.937 -0.570
DFT "C5'" C CH2 0.000 -2.880 -0.133 0.178
DFT "H5'" H H 0.000 -2.207 -0.413 0.990
DFT "H5''" H H 0.000 -3.035 -0.992 -0.478
DFT "C4'" C CH1 0.000 -4.222 0.316 0.758
DFT "H4'" H H 0.000 -4.074 1.192 1.405
DFT "C3'" C CH1 0.000 -4.854 -0.831 1.568
DFT "H3'" H H 0.000 -4.229 -1.734 1.508
DFT "C2'" C CH2 0.000 -6.220 -1.072 0.883
DFT "H2'" H H 0.000 -7.030 -1.244 1.595
DFT "H2''" H H 0.000 -6.195 -1.889 0.158
DFT "C1'" C CH1 0.000 -6.454 0.269 0.144
DFT "H1'" H H 0.000 -6.857 1.025 0.833
DFT "O4'" O O2 0.000 -5.135 0.645 -0.305
DFT C1 C CR6 0.000 -7.379 0.075 -1.029
DFT C6 C CR16 0.000 -6.865 -0.281 -2.261
DFT H6 H H 0.000 -5.798 -0.420 -2.383
DFT C5 C CR6 0.000 -7.712 -0.460 -3.338
DFT C5M C CH3 0.000 -7.150 -0.850 -4.681
DFT H73 H H 0.000 -7.767 -0.460 -5.449
DFT H72 H H 0.000 -6.171 -0.459 -4.782
DFT H71 H H 0.000 -7.118 -1.906 -4.757
DFT C4 C CR6 0.000 -9.075 -0.276 -3.185
DFT C3 C CR16 0.000 -9.592 0.076 -1.951
DFT H3 H H 0.000 -10.659 0.211 -1.828
DFT F4 F F 0.000 -9.904 -0.451 -4.239
DFT C2 C CR6 0.000 -8.743 0.255 -0.873
DFT F2 F F 0.000 -9.245 0.605 0.332
DFT "O3'" O OH1 0.000 -5.039 -0.443 2.931
DFT "HO3'" H H 0.000 -5.489 -1.176 3.372
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
DFT OP3 n/a P START
DFT P OP3 "O5'" .
DFT OP1 P . .
DFT OP2 P . .
DFT "O5'" P "C5'" .
DFT "C5'" "O5'" "C4'" .
DFT "H5'" "C5'" . .
DFT "H5''" "C5'" . .
DFT "C4'" "C5'" "C3'" .
DFT "H4'" "C4'" . .
DFT "C3'" "C4'" "O3'" .
DFT "H3'" "C3'" . .
DFT "C2'" "C3'" "C1'" .
DFT "H2'" "C2'" . .
DFT "H2''" "C2'" . .
DFT "C1'" "C2'" C1 .
DFT "H1'" "C1'" . .
DFT "O4'" "C1'" . .
DFT C1 "C1'" C2 .
DFT C6 C1 C5 .
DFT H6 C6 . .
DFT C5 C6 C4 .
DFT C5M C5 H71 .
DFT H73 C5M . .
DFT H72 C5M . .
DFT H71 C5M . .
DFT C4 C5 F4 .
DFT C3 C4 H3 .
DFT H3 C3 . .
DFT F4 C4 . .
DFT C2 C1 F2 .
DFT F2 C2 . .
DFT "O3'" "C3'" . END
DFT "HO3'" "O3'" . .
DFT "C4'" "O4'" . ADD
DFT C2 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
DFT OP1 P deloc 1.510 0.020
DFT OP2 P deloc 1.510 0.020
DFT P OP3 deloc 1.510 0.020
DFT "O5'" P single 1.610 0.020
DFT "C5'" "O5'" single 1.426 0.020
DFT "C4'" "C5'" single 1.524 0.020
DFT "H5'" "C5'" single 1.092 0.020
DFT "H5''" "C5'" single 1.092 0.020
DFT "C4'" "O4'" single 1.426 0.020
DFT "C3'" "C4'" single 1.524 0.020
DFT "H4'" "C4'" single 1.099 0.020
DFT "O4'" "C1'" single 1.426 0.020
DFT "O3'" "C3'" single 1.432 0.020
DFT "C2'" "C3'" single 1.524 0.020
DFT "H3'" "C3'" single 1.099 0.020
DFT "HO3'" "O3'" single 0.967 0.020
DFT "C1'" "C2'" single 1.524 0.020
DFT "H2'" "C2'" single 1.092 0.020
DFT "H2''" "C2'" single 1.092 0.020
DFT C1 "C1'" single 1.480 0.020
DFT "H1'" "C1'" single 1.099 0.020
DFT C2 C3 double 1.390 0.020
DFT F2 C2 single 1.345 0.020
DFT C2 C1 single 1.487 0.020
DFT C4 C5 double 1.487 0.020
DFT F4 C4 single 1.345 0.020
DFT C3 C4 single 1.390 0.020
DFT C5M C5 single 1.506 0.020
DFT C5 C6 single 1.390 0.020
DFT H71 C5M single 1.059 0.020
DFT H72 C5M single 1.059 0.020
DFT H73 C5M single 1.059 0.020
DFT C6 C1 double 1.390 0.020
DFT H6 C6 single 1.083 0.020
DFT H3 C3 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
DFT OP3 P OP1 119.900 3.000
DFT OP3 P OP2 119.900 3.000
DFT OP3 P "O5'" 108.200 3.000
DFT OP1 P OP2 119.900 3.000
DFT OP1 P "O5'" 108.200 3.000
DFT OP2 P "O5'" 108.200 3.000
DFT P "O5'" "C5'" 120.500 3.000
DFT "O5'" "C5'" "H5'" 109.470 3.000
DFT "O5'" "C5'" "H5''" 109.470 3.000
DFT "O5'" "C5'" "C4'" 109.470 3.000
DFT "H5'" "C5'" "H5''" 107.900 3.000
DFT "H5'" "C5'" "C4'" 109.470 3.000
DFT "H5''" "C5'" "C4'" 109.470 3.000
DFT "C5'" "C4'" "H4'" 108.340 3.000
DFT "C5'" "C4'" "C3'" 111.000 3.000
DFT "C5'" "C4'" "O4'" 109.470 3.000
DFT "H4'" "C4'" "C3'" 108.340 3.000
DFT "H4'" "C4'" "O4'" 109.470 3.000
DFT "C3'" "C4'" "O4'" 109.470 3.000
DFT "C4'" "C3'" "H3'" 108.340 3.000
DFT "C4'" "C3'" "C2'" 111.000 3.000
DFT "C4'" "C3'" "O3'" 109.470 3.000
DFT "H3'" "C3'" "C2'" 108.340 3.000
DFT "H3'" "C3'" "O3'" 109.470 3.000
DFT "C2'" "C3'" "O3'" 109.470 3.000
DFT "C3'" "C2'" "H2'" 109.470 3.000
DFT "C3'" "C2'" "H2''" 109.470 3.000
DFT "C3'" "C2'" "C1'" 111.000 3.000
DFT "H2'" "C2'" "H2''" 107.900 3.000
DFT "H2'" "C2'" "C1'" 109.470 3.000
DFT "H2''" "C2'" "C1'" 109.470 3.000
DFT "C2'" "C1'" "H1'" 108.340 3.000
DFT "C2'" "C1'" "O4'" 109.470 3.000
DFT "C2'" "C1'" C1 109.470 3.000
DFT "H1'" "C1'" "O4'" 109.470 3.000
DFT "H1'" "C1'" C1 109.470 3.000
DFT "O4'" "C1'" C1 109.470 3.000
DFT "C1'" "O4'" "C4'" 111.800 3.000
DFT "C1'" C1 C6 120.000 3.000
DFT "C1'" C1 C2 120.000 3.000
DFT C6 C1 C2 120.000 3.000
DFT C1 C6 H6 120.000 3.000
DFT C1 C6 C5 120.000 3.000
DFT H6 C6 C5 120.000 3.000
DFT C6 C5 C5M 120.000 3.000
DFT C6 C5 C4 120.000 3.000
DFT C5M C5 C4 120.000 3.000
DFT C5 C5M H73 109.470 3.000
DFT C5 C5M H72 109.470 3.000
DFT C5 C5M H71 109.470 3.000
DFT H73 C5M H72 109.470 3.000
DFT H73 C5M H71 109.470 3.000
DFT H72 C5M H71 109.470 3.000
DFT C5 C4 C3 120.000 3.000
DFT C5 C4 F4 120.000 3.000
DFT C3 C4 F4 120.000 3.000
DFT C4 C3 H3 120.000 3.000
DFT C4 C3 C2 120.000 3.000
DFT H3 C3 C2 120.000 3.000
DFT C1 C2 F2 120.000 3.000
DFT C1 C2 C3 120.000 3.000
DFT F2 C2 C3 120.000 3.000
DFT "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
DFT var_1 OP3 P "O5'" "C5'" -60.096 20.000 1
DFT var_2 P "O5'" "C5'" "C4'" -179.961 20.000 1
DFT var_3 "O5'" "C5'" "C4'" "C3'" -179.937 20.000 3
DFT var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DFT var_5 "C5'" "C4'" "C3'" "O3'" 120.000 20.000 3
DFT var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
DFT var_7 "C3'" "C2'" "C1'" C1 150.000 20.000 3
DFT var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DFT var_9 "C2'" "C1'" C1 C2 92.205 20.000 1
DFT CONST_1 "C1'" C1 C6 C5 180.000 0.000 0
DFT CONST_2 C1 C6 C5 C4 0.000 0.000 0
DFT var_10 C6 C5 C5M H71 89.993 20.000 1
DFT CONST_3 C6 C5 C4 F4 180.000 0.000 0
DFT CONST_4 C5 C4 C3 C2 0.000 0.000 0
DFT CONST_5 "C1'" C1 C2 F2 0.000 0.000 0
DFT CONST_6 C1 C2 C3 C4 0.000 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
DFT chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DFT chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DFT chir_03 "C1'" "O4'" "C2'" C1 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
DFT plan-1 C2 0.020
DFT plan-1 C3 0.020
DFT plan-1 F2 0.020
DFT plan-1 C1 0.020
DFT plan-1 C4 0.020
DFT plan-1 C5 0.020
DFT plan-1 C6 0.020
DFT plan-1 F4 0.020
DFT plan-1 C5M 0.020
DFT plan-1 H6 0.020
DFT plan-1 H3 0.020
DFT plan-1 "C1'" 0.020
# ------------------------------------------------------
|
