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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
XAE XAE '"3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERY' DNA 40 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XAE
#
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
XAE OP3 O OP -0.666 0.000 0.000 0.000
XAE P P P 0.000 -0.474 1.289 0.635
XAE OP1 O OP -0.666 -0.856 2.143 -0.554
XAE OP2 O OP -0.666 0.503 1.924 1.600
XAE "O5'" O O2 0.000 -1.900 0.871 1.281
XAE "C5'" C CH2 0.000 -2.871 0.271 0.444
XAE "H5'1" H H 0.000 -2.478 -0.659 0.028
XAE "H5'2" H H 0.000 -3.130 0.952 -0.370
XAE "C4'" C CH1 0.000 -4.108 -0.026 1.270
XAE "H4'" H H 0.000 -3.836 -0.684 2.108
XAE "C3'" C CH1 0.000 -5.233 -0.666 0.475
XAE "H3'" H H 0.000 -5.310 -0.203 -0.519
XAE "C2'" C CH2 0.000 -6.443 -0.316 1.313
XAE "H2'1" H H 0.000 -6.609 -1.028 2.124
XAE "H2'2" H H 0.000 -7.353 -0.226 0.717
XAE "C1'" C CH1 0.000 -6.079 1.044 1.896
XAE "H1'" H H 0.000 -6.351 1.054 2.961
XAE "O4'" O O2 0.000 -4.653 1.199 1.786
XAE N9 N NR5 0.000 -6.743 2.168 1.234
XAE C10 C CR56 0.000 -7.931 2.747 1.600
XAE C11 C CR56 0.000 -8.126 3.756 0.667
XAE CP C CR16 0.000 -9.276 4.553 0.763
XAE HP H H 0.000 -9.460 5.349 0.053
XAE C5 C CR66 0.000 -10.189 4.293 1.807
XAE N7 N NRD5 0.000 -7.092 3.795 -0.239
XAE C8 C CR15 0.000 -6.281 2.829 0.130
XAE H8 H H 0.000 -5.357 2.585 -0.380
XAE CD C CR16 0.000 -8.828 2.481 2.637
XAE HD H H 0.000 -8.636 1.682 3.343
XAE C4 C CR66 0.000 -9.975 3.265 2.745
XAE N3 N NRD6 0.000 -10.852 3.029 3.734
XAE C2 C CR16 0.000 -11.943 3.821 3.786
XAE H2 H H 0.000 -12.645 3.624 4.586
XAE N1 N NRD6 0.000 -12.252 4.826 2.953
XAE C6 C CR6 0.000 -11.353 5.037 1.972
XAE N6 N NH2 0.000 -11.641 6.090 1.068
XAE HN62 H H 0.000 -12.599 6.284 0.771
XAE HN61 H H 0.000 -10.897 6.680 0.690
XAE "O3'" O OH1 0.000 -5.079 -2.065 0.354
XAE "HO3'" H H 0.000 -5.316 -2.443 1.215
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
XAE OP3 n/a P START
XAE P OP3 "O5'" .
XAE OP1 P . .
XAE OP2 P . .
XAE "O5'" P "C5'" .
XAE "C5'" "O5'" "C4'" .
XAE "H5'1" "C5'" . .
XAE "H5'2" "C5'" . .
XAE "C4'" "C5'" "C3'" .
XAE "H4'" "C4'" . .
XAE "C3'" "C4'" "O3'" .
XAE "H3'" "C3'" . .
XAE "C2'" "C3'" "C1'" .
XAE "H2'1" "C2'" . .
XAE "H2'2" "C2'" . .
XAE "C1'" "C2'" N9 .
XAE "H1'" "C1'" . .
XAE "O4'" "C1'" . .
XAE N9 "C1'" C10 .
XAE C10 N9 CD .
XAE C11 C10 N7 .
XAE CP C11 C5 .
XAE HP CP . .
XAE C5 CP . .
XAE N7 C11 C8 .
XAE C8 N7 H8 .
XAE H8 C8 . .
XAE CD C10 C4 .
XAE HD CD . .
XAE C4 CD N3 .
XAE N3 C4 C2 .
XAE C2 N3 N1 .
XAE H2 C2 . .
XAE N1 C2 C6 .
XAE C6 N1 N6 .
XAE N6 C6 HN61 .
XAE HN62 N6 . .
XAE HN61 N6 . .
XAE "O3'" "C3'" . END
XAE "HO3'" "O3'" . .
XAE "C4'" "O4'" . ADD
XAE N9 C8 . ADD
XAE C5 C4 . ADD
XAE 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
XAE P OP3 deloc 1.510 0.020
XAE "O5'" P single 1.610 0.020
XAE OP1 P deloc 1.510 0.020
XAE OP2 P deloc 1.510 0.020
XAE "C4'" "C5'" single 1.524 0.020
XAE "C5'" "O5'" single 1.426 0.020
XAE "H5'1" "C5'" single 1.092 0.020
XAE "H5'2" "C5'" single 1.092 0.020
XAE "C4'" "O4'" single 1.426 0.020
XAE "C3'" "C4'" single 1.524 0.020
XAE "H4'" "C4'" single 1.099 0.020
XAE "O4'" "C1'" single 1.426 0.020
XAE "O3'" "C3'" single 1.432 0.020
XAE "C2'" "C3'" single 1.524 0.020
XAE "H3'" "C3'" single 1.099 0.020
XAE "C1'" "C2'" single 1.524 0.020
XAE "H2'1" "C2'" single 1.092 0.020
XAE "H2'2" "C2'" single 1.092 0.020
XAE N9 "C1'" single 1.485 0.020
XAE "H1'" "C1'" single 1.099 0.020
XAE C10 N9 single 1.337 0.020
XAE N9 C8 single 1.337 0.020
XAE C8 N7 double 1.350 0.020
XAE H8 C8 single 1.083 0.020
XAE N7 C11 single 1.350 0.020
XAE C5 C4 single 1.490 0.020
XAE C5 C6 single 1.490 0.020
XAE C5 CP double 1.390 0.020
XAE N3 C4 single 1.350 0.020
XAE C4 CD double 1.390 0.020
XAE C6 N1 double 1.350 0.020
XAE N6 C6 single 1.355 0.020
XAE HN61 N6 single 1.010 0.020
XAE HN62 N6 single 1.010 0.020
XAE N1 C2 single 1.337 0.020
XAE C2 N3 double 1.337 0.020
XAE H2 C2 single 1.083 0.020
XAE CD C10 single 1.390 0.020
XAE C11 C10 double 1.490 0.020
XAE CP C11 single 1.390 0.020
XAE HP CP single 1.083 0.020
XAE HD CD single 1.083 0.020
XAE "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
XAE OP3 P OP1 119.900 3.000
XAE OP3 P OP2 119.900 3.000
XAE OP3 P "O5'" 108.200 3.000
XAE OP1 P OP2 119.900 3.000
XAE OP1 P "O5'" 108.200 3.000
XAE OP2 P "O5'" 108.200 3.000
XAE P "O5'" "C5'" 120.500 3.000
XAE "O5'" "C5'" "H5'1" 109.470 3.000
XAE "O5'" "C5'" "H5'2" 109.470 3.000
XAE "O5'" "C5'" "C4'" 109.470 3.000
XAE "H5'1" "C5'" "H5'2" 107.900 3.000
XAE "H5'1" "C5'" "C4'" 109.470 3.000
XAE "H5'2" "C5'" "C4'" 109.470 3.000
XAE "C5'" "C4'" "H4'" 108.340 3.000
XAE "C5'" "C4'" "C3'" 111.000 3.000
XAE "C5'" "C4'" "O4'" 109.470 3.000
XAE "H4'" "C4'" "C3'" 108.340 3.000
XAE "H4'" "C4'" "O4'" 109.470 3.000
XAE "C3'" "C4'" "O4'" 109.470 3.000
XAE "C4'" "C3'" "H3'" 108.340 3.000
XAE "C4'" "C3'" "C2'" 111.000 3.000
XAE "C4'" "C3'" "O3'" 109.470 3.000
XAE "H3'" "C3'" "C2'" 108.340 3.000
XAE "H3'" "C3'" "O3'" 109.470 3.000
XAE "C2'" "C3'" "O3'" 109.470 3.000
XAE "C3'" "C2'" "H2'1" 109.470 3.000
XAE "C3'" "C2'" "H2'2" 109.470 3.000
XAE "C3'" "C2'" "C1'" 111.000 3.000
XAE "H2'1" "C2'" "H2'2" 107.900 3.000
XAE "H2'1" "C2'" "C1'" 109.470 3.000
XAE "H2'2" "C2'" "C1'" 109.470 3.000
XAE "C2'" "C1'" "H1'" 108.340 3.000
XAE "C2'" "C1'" "O4'" 109.470 3.000
XAE "C2'" "C1'" N9 109.470 3.000
XAE "H1'" "C1'" "O4'" 109.470 3.000
XAE "H1'" "C1'" N9 109.470 3.000
XAE "O4'" "C1'" N9 109.470 3.000
XAE "C1'" "O4'" "C4'" 111.800 3.000
XAE "C1'" N9 C10 126.000 3.000
XAE "C1'" N9 C8 126.000 3.000
XAE C10 N9 C8 108.000 3.000
XAE N9 C10 C11 108.000 3.000
XAE N9 C10 CD 132.000 3.000
XAE C11 C10 CD 120.000 3.000
XAE C10 C11 CP 120.000 3.000
XAE C10 C11 N7 108.000 3.000
XAE CP C11 N7 132.000 3.000
XAE C11 CP HP 120.000 3.000
XAE C11 CP C5 120.000 3.000
XAE HP CP C5 120.000 3.000
XAE CP C5 C4 120.000 3.000
XAE CP C5 C6 120.000 3.000
XAE C4 C5 C6 120.000 3.000
XAE C11 N7 C8 108.000 3.000
XAE N7 C8 H8 126.000 3.000
XAE N7 C8 N9 108.000 3.000
XAE H8 C8 N9 126.000 3.000
XAE C10 CD HD 120.000 3.000
XAE C10 CD C4 120.000 3.000
XAE HD CD C4 120.000 3.000
XAE CD C4 N3 120.000 3.000
XAE CD C4 C5 120.000 3.000
XAE N3 C4 C5 120.000 3.000
XAE C4 N3 C2 120.000 3.000
XAE N3 C2 H2 120.000 3.000
XAE N3 C2 N1 120.000 3.000
XAE H2 C2 N1 120.000 3.000
XAE C2 N1 C6 120.000 3.000
XAE N1 C6 N6 120.000 3.000
XAE N1 C6 C5 120.000 3.000
XAE N6 C6 C5 120.000 3.000
XAE C6 N6 HN62 120.000 3.000
XAE C6 N6 HN61 120.000 3.000
XAE HN62 N6 HN61 120.000 3.000
XAE "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
XAE var_1 OP3 P "O5'" "C5'" -54.207 20.000 1
XAE var_2 P "O5'" "C5'" "C4'" 179.969 20.000 1
XAE var_3 "O5'" "C5'" "C4'" "C3'" 179.534 20.000 3
XAE var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
XAE var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
XAE var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
XAE var_7 "C3'" "C2'" "C1'" N9 90.000 20.000 3
XAE var_8 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
XAE var_9 "C2'" "C1'" N9 C10 92.438 20.000 1
XAE CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
XAE CONST_2 "C1'" N9 C10 CD 0.000 0.000 0
XAE CONST_3 N9 C10 C11 N7 0.000 0.000 0
XAE CONST_4 C10 C11 CP C5 0.000 0.000 0
XAE CONST_5 C11 CP C5 C4 0.000 0.000 0
XAE CONST_6 CP C5 C4 CD 0.000 0.000 0
XAE CONST_7 CP C5 C6 N1 180.000 0.000 0
XAE CONST_8 C10 C11 N7 C8 0.000 0.000 0
XAE CONST_9 C11 N7 C8 N9 0.000 0.000 0
XAE CONST_10 N9 C10 CD C4 180.000 0.000 0
XAE CONST_11 C10 CD C4 N3 180.000 0.000 0
XAE CONST_12 CD C4 N3 C2 180.000 0.000 0
XAE CONST_13 C4 N3 C2 N1 0.000 0.000 0
XAE CONST_14 N3 C2 N1 C6 0.000 0.000 0
XAE CONST_15 C2 N1 C6 N6 180.000 0.000 0
XAE CONST_16 N1 C6 N6 HN61 143.391 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
XAE chir_01 "C4'" "C5'" "O4'" "C3'" negativ
XAE chir_02 "C3'" "C4'" "C2'" "O3'" positiv
XAE 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
XAE plan-1 N9 0.020
XAE plan-1 "C1'" 0.020
XAE plan-1 C8 0.020
XAE plan-1 C10 0.020
XAE plan-1 N7 0.020
XAE plan-1 H8 0.020
XAE plan-1 C11 0.020
XAE plan-1 C5 0.020
XAE plan-1 C4 0.020
XAE plan-1 C6 0.020
XAE plan-1 CP 0.020
XAE plan-1 CD 0.020
XAE plan-1 N3 0.020
XAE plan-1 N6 0.020
XAE plan-1 N1 0.020
XAE plan-1 C2 0.020
XAE plan-1 H2 0.020
XAE plan-1 HP 0.020
XAE plan-1 HD 0.020
XAE plan-1 HN62 0.020
XAE plan-1 HN61 0.020
XAE plan-2 N6 0.020
XAE plan-2 C6 0.020
XAE plan-2 HN61 0.020
XAE plan-2 HN62 0.020
# ------------------------------------------------------
|
