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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
2GT 2GT '. ' DNA 40 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2GT
#
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
2GT OP3 O OP -0.666 0.000 0.000 0.000
2GT P P P 0.000 -0.530 1.416 0.049
2GT OP1 O OP -0.666 0.531 2.491 0.149
2GT OP2 O OP -0.666 -1.420 1.497 -1.172
2GT "O5'" O O2 0.000 -1.575 1.370 1.285
2GT "C5'" C CH2 0.000 -2.598 0.391 1.268
2GT "H5'" H H 0.000 -2.156 -0.607 1.248
2GT "H5''" H H 0.000 -3.226 0.527 0.385
2GT "C4'" C CH1 0.000 -3.444 0.549 2.524
2GT "H4'" H H 0.000 -2.807 0.459 3.415
2GT "C3'" C CH1 0.000 -4.591 -0.451 2.607
2GT "H3'" H H 0.000 -4.330 -1.416 2.151
2GT "C2'" C CH1 0.000 -5.687 0.260 1.843
2GT "H2'" H H 0.000 -5.523 0.146 0.762
2GT "O2'" O O2 0.000 -6.974 -0.213 2.186
2GT "CB'" C CH2 0.000 -7.118 -1.603 1.913
2GT "HB'1" H H 0.000 -6.373 -2.156 2.490
2GT "HB'2" H H 0.000 -6.951 -1.774 0.848
2GT "CC'" C CSP 0.000 -8.458 -2.061 2.278
2GT "CD'" C CSP1 0.000 -9.558 -2.439 2.578
2GT "HD'" H H 0.000 -10.437 -2.740 2.818
2GT "C1'" C CH1 0.000 -5.468 1.707 2.248
2GT "H1'" H H 0.000 -6.026 1.920 3.171
2GT "O4'" O O2 0.000 -4.059 1.855 2.492
2GT N1 N NR6 0.000 -5.864 2.630 1.223
2GT C2 C CR6 0.000 -7.152 3.209 1.216
2GT O2 O O 0.000 -8.013 2.975 2.065
2GT N3 N NR16 0.000 -7.401 4.090 0.157
2GT HN3 H H 0.000 -8.344 4.528 0.129
2GT C4 C CR6 0.000 -6.526 4.441 -0.860
2GT C5 C CR6 0.000 -5.190 3.791 -0.785
2GT C5M C CH3 0.000 -4.190 4.118 -1.847
2GT H73 H H 0.000 -4.589 4.859 -2.488
2GT H72 H H 0.000 -3.304 4.480 -1.394
2GT H71 H H 0.000 -3.972 3.246 -2.404
2GT C6 C CR16 0.000 -4.948 2.948 0.226
2GT H6 H H 0.000 -3.972 2.481 0.271
2GT O4 O O 0.000 -6.811 5.225 -1.761
2GT "O3'" O OH1 0.000 -4.954 -0.589 3.981
2GT "HO3'" H H 0.000 -4.548 0.157 4.448
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
2GT OP3 n/a P START
2GT P OP3 "O5'" .
2GT OP1 P . .
2GT OP2 P . .
2GT "O5'" P "C5'" .
2GT "C5'" "O5'" "C4'" .
2GT "H5'" "C5'" . .
2GT "H5''" "C5'" . .
2GT "C4'" "C5'" "C3'" .
2GT "H4'" "C4'" . .
2GT "C3'" "C4'" "O3'" .
2GT "H3'" "C3'" . .
2GT "C2'" "C3'" "C1'" .
2GT "H2'" "C2'" . .
2GT "O2'" "C2'" "CB'" .
2GT "CB'" "O2'" "CC'" .
2GT "HB'1" "CB'" . .
2GT "HB'2" "CB'" . .
2GT "CC'" "CB'" "CD'" .
2GT "CD'" "CC'" "HD'" .
2GT "HD'" "CD'" . .
2GT "C1'" "C2'" N1 .
2GT "H1'" "C1'" . .
2GT "O4'" "C1'" . .
2GT N1 "C1'" C2 .
2GT C2 N1 N3 .
2GT O2 C2 . .
2GT N3 C2 C4 .
2GT HN3 N3 . .
2GT C4 N3 O4 .
2GT C5 C4 C6 .
2GT C5M C5 H71 .
2GT H73 C5M . .
2GT H72 C5M . .
2GT H71 C5M . .
2GT C6 C5 H6 .
2GT H6 C6 . .
2GT O4 C4 . .
2GT "O3'" "C3'" . END
2GT "HO3'" "O3'" . .
2GT "C4'" "O4'" . ADD
2GT N1 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
2GT OP1 P deloc 1.510 0.020
2GT OP2 P deloc 1.510 0.020
2GT "O5'" P single 1.610 0.020
2GT P OP3 deloc 1.510 0.020
2GT "C5'" "O5'" single 1.426 0.020
2GT "C4'" "C5'" single 1.524 0.020
2GT "H5'" "C5'" single 1.092 0.020
2GT "H5''" "C5'" single 1.092 0.020
2GT "C4'" "O4'" single 1.426 0.020
2GT "C3'" "C4'" single 1.524 0.020
2GT "H4'" "C4'" single 1.099 0.020
2GT "O4'" "C1'" single 1.426 0.020
2GT N1 "C1'" single 1.465 0.020
2GT "C1'" "C2'" single 1.524 0.020
2GT "H1'" "C1'" single 1.099 0.020
2GT N1 C6 single 1.337 0.020
2GT C2 N1 single 1.410 0.020
2GT C6 C5 double 1.390 0.020
2GT H6 C6 single 1.083 0.020
2GT O2 C2 double 1.250 0.020
2GT N3 C2 single 1.337 0.020
2GT C4 N3 single 1.337 0.020
2GT HN3 N3 single 1.040 0.020
2GT O4 C4 double 1.250 0.020
2GT C5 C4 single 1.487 0.020
2GT C5M C5 single 1.506 0.020
2GT H71 C5M single 1.059 0.020
2GT H72 C5M single 1.059 0.020
2GT H73 C5M single 1.059 0.020
2GT "O2'" "C2'" single 1.426 0.020
2GT "C2'" "C3'" single 1.524 0.020
2GT "H2'" "C2'" single 1.099 0.020
2GT "CB'" "O2'" single 1.426 0.020
2GT "CC'" "CB'" single 1.470 0.020
2GT "HB'1" "CB'" single 1.092 0.020
2GT "HB'2" "CB'" single 1.092 0.020
2GT "CD'" "CC'" triple 1.278 0.020
2GT "HD'" "CD'" single 1.022 0.020
2GT "O3'" "C3'" single 1.432 0.020
2GT "H3'" "C3'" single 1.099 0.020
2GT "HO3'" "O3'" 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
2GT OP3 P OP1 119.900 3.000
2GT OP3 P OP2 119.900 3.000
2GT OP3 P "O5'" 108.200 3.000
2GT OP1 P OP2 119.900 3.000
2GT OP1 P "O5'" 108.200 3.000
2GT OP2 P "O5'" 108.200 3.000
2GT P "O5'" "C5'" 120.500 3.000
2GT "O5'" "C5'" "H5'" 109.470 3.000
2GT "O5'" "C5'" "H5''" 109.470 3.000
2GT "O5'" "C5'" "C4'" 109.470 3.000
2GT "H5'" "C5'" "H5''" 107.900 3.000
2GT "H5'" "C5'" "C4'" 109.470 3.000
2GT "H5''" "C5'" "C4'" 109.470 3.000
2GT "C5'" "C4'" "H4'" 108.340 3.000
2GT "C5'" "C4'" "C3'" 111.000 3.000
2GT "C5'" "C4'" "O4'" 109.470 3.000
2GT "H4'" "C4'" "C3'" 108.340 3.000
2GT "H4'" "C4'" "O4'" 109.470 3.000
2GT "C3'" "C4'" "O4'" 109.470 3.000
2GT "C4'" "C3'" "H3'" 108.340 3.000
2GT "C4'" "C3'" "C2'" 111.000 3.000
2GT "C4'" "C3'" "O3'" 109.470 3.000
2GT "H3'" "C3'" "C2'" 108.340 3.000
2GT "H3'" "C3'" "O3'" 109.470 3.000
2GT "C2'" "C3'" "O3'" 109.470 3.000
2GT "C3'" "C2'" "H2'" 108.340 3.000
2GT "C3'" "C2'" "O2'" 109.470 3.000
2GT "C3'" "C2'" "C1'" 111.000 3.000
2GT "H2'" "C2'" "O2'" 109.470 3.000
2GT "H2'" "C2'" "C1'" 108.340 3.000
2GT "O2'" "C2'" "C1'" 109.470 3.000
2GT "C2'" "O2'" "CB'" 111.800 3.000
2GT "O2'" "CB'" "HB'1" 109.470 3.000
2GT "O2'" "CB'" "HB'2" 109.470 3.000
2GT "O2'" "CB'" "CC'" 109.500 3.000
2GT "HB'1" "CB'" "HB'2" 107.900 3.000
2GT "HB'1" "CB'" "CC'" 109.500 3.000
2GT "HB'2" "CB'" "CC'" 109.500 3.000
2GT "CB'" "CC'" "CD'" 180.000 3.000
2GT "CC'" "CD'" "HD'" 179.966 3.000
2GT "C2'" "C1'" "H1'" 108.340 3.000
2GT "C2'" "C1'" "O4'" 109.470 3.000
2GT "C2'" "C1'" N1 109.470 3.000
2GT "H1'" "C1'" "O4'" 109.470 3.000
2GT "H1'" "C1'" N1 109.470 3.000
2GT "O4'" "C1'" N1 109.470 3.000
2GT "C1'" "O4'" "C4'" 111.800 3.000
2GT "C1'" N1 C2 120.000 3.000
2GT "C1'" N1 C6 120.000 3.000
2GT C2 N1 C6 120.000 3.000
2GT N1 C2 O2 120.000 3.000
2GT N1 C2 N3 120.000 3.000
2GT O2 C2 N3 120.000 3.000
2GT C2 N3 HN3 120.000 3.000
2GT C2 N3 C4 120.000 3.000
2GT HN3 N3 C4 120.000 3.000
2GT N3 C4 C5 120.000 3.000
2GT N3 C4 O4 120.000 3.000
2GT C5 C4 O4 120.000 3.000
2GT C4 C5 C5M 120.000 3.000
2GT C4 C5 C6 120.000 3.000
2GT C5M C5 C6 120.000 3.000
2GT C5 C5M H73 109.470 3.000
2GT C5 C5M H72 109.470 3.000
2GT C5 C5M H71 109.470 3.000
2GT H73 C5M H72 109.470 3.000
2GT H73 C5M H71 109.470 3.000
2GT H72 C5M H71 109.470 3.000
2GT C5 C6 H6 120.000 3.000
2GT C5 C6 N1 120.000 3.000
2GT H6 C6 N1 120.000 3.000
2GT "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
2GT var_1 OP3 P "O5'" "C5'" -54.172 20.000 1
2GT var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
2GT var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
2GT var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
2GT var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
2GT var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
2GT var_7 "C3'" "C2'" "O2'" "CB'" -59.966 20.000 1
2GT var_8 "C2'" "O2'" "CB'" "CC'" -179.993 20.000 1
2GT var_9 "O2'" "CB'" "CC'" "CD'" -166.004 20.000 1
2GT var_10 "CB'" "CC'" "CD'" "HD'" 179.937 20.000 1
2GT var_11 "C3'" "C2'" "C1'" N1 150.000 20.000 3
2GT var_12 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
2GT var_13 "C2'" "C1'" N1 C2 94.305 20.000 1
2GT CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
2GT CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
2GT CONST_3 N1 C2 N3 C4 0.000 0.000 0
2GT CONST_4 C2 N3 C4 O4 180.000 0.000 0
2GT CONST_5 N3 C4 C5 C6 0.000 0.000 0
2GT var_14 C4 C5 C5M H71 -115.793 20.000 1
2GT CONST_6 C4 C5 C6 N1 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
2GT chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2GT chir_02 "C1'" "O4'" N1 "C2'" negativ
2GT chir_03 "C2'" "C1'" "O2'" "C3'" positiv
2GT chir_04 "C3'" "C4'" "C2'" "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
2GT plan-1 N1 0.020
2GT plan-1 "C1'" 0.020
2GT plan-1 C6 0.020
2GT plan-1 C2 0.020
2GT plan-1 N3 0.020
2GT plan-1 C4 0.020
2GT plan-1 C5 0.020
2GT plan-1 H6 0.020
2GT plan-1 O2 0.020
2GT plan-1 HN3 0.020
2GT plan-1 O4 0.020
2GT plan-1 C5M 0.020
# ------------------------------------------------------
|
