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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
XCL XCL '"[(1S,4R,6R)-6-HYDROXY-4-(CYTOSIN-9-' DNA 35 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XCL
#
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
XCL OP3 O OP -0.666 0.000 0.000 0.000
XCL P P P 0.000 -0.021 -1.465 0.379
XCL OP1 O OP -0.666 0.118 -1.601 1.879
XCL OP2 O OP -0.666 1.126 -2.179 -0.302
XCL "O5'" O O2 0.000 -1.415 -2.120 -0.093
XCL "C5'" C CH2 0.000 -2.446 -1.487 0.668
XCL "H5'" H H 0.000 -2.435 -0.413 0.472
XCL "H5''" H H 0.000 -2.274 -1.663 1.732
XCL "C4'" C CH1 0.000 -3.805 -2.067 0.266
XCL "H4'" H H 0.000 -3.784 -3.159 0.385
XCL "C3'" C CH1 0.000 -4.893 -1.479 1.167
XCL "H3'" H H 0.000 -4.796 -0.385 1.197
XCL "C2'" C CH2 0.000 -6.261 -1.861 0.588
XCL "H2'" H H 0.000 -7.053 -1.564 1.278
XCL "H2''" H H 0.000 -6.308 -2.940 0.424
XCL "C1'" C CH1 0.000 -6.443 -1.132 -0.746
XCL "H1'" H H 0.000 -7.325 -1.534 -1.263
XCL "C7'" C C1 0.000 -5.229 -1.325 -1.607
XCL "H7'" H H 0.000 -5.320 -1.114 -2.659
XCL "C6'" C C1 0.000 -4.083 -1.727 -1.169
XCL "H6'" H H 0.000 -3.277 -1.825 -1.876
XCL N1 N NR6 0.000 -6.637 0.298 -0.493
XCL C6 C CR16 0.000 -5.595 1.055 -0.050
XCL H6 H H 0.000 -4.625 0.605 0.122
XCL C2 C CR6 0.000 -7.843 0.856 -0.701
XCL N3 N NRD6 0.000 -8.047 2.154 -0.481
XCL C4 C CR6 0.000 -7.063 2.931 -0.048
XCL N4 N NH2 0.000 -7.285 4.270 0.176
XCL HN42 H H 0.000 -6.534 4.865 0.506
XCL HN41 H H 0.000 -8.202 4.671 0.013
XCL C5 C CR16 0.000 -5.786 2.378 0.173
XCL H5 H H 0.000 -4.969 3.001 0.517
XCL O2 O O 0.000 -8.765 0.163 -1.099
XCL "O3'" O OH1 0.000 -4.766 -2.009 2.488
XCL "HO3'" H H 0.000 -5.480 -1.623 3.014
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
XCL OP3 n/a P START
XCL P OP3 "O5'" .
XCL OP1 P . .
XCL OP2 P . .
XCL "O5'" P "C5'" .
XCL "C5'" "O5'" "C4'" .
XCL "H5'" "C5'" . .
XCL "H5''" "C5'" . .
XCL "C4'" "C5'" "C3'" .
XCL "H4'" "C4'" . .
XCL "C3'" "C4'" "O3'" .
XCL "H3'" "C3'" . .
XCL "C2'" "C3'" "C1'" .
XCL "H2'" "C2'" . .
XCL "H2''" "C2'" . .
XCL "C1'" "C2'" N1 .
XCL "H1'" "C1'" . .
XCL "C7'" "C1'" "C6'" .
XCL "H7'" "C7'" . .
XCL "C6'" "C7'" "H6'" .
XCL "H6'" "C6'" . .
XCL N1 "C1'" C2 .
XCL C6 N1 H6 .
XCL H6 C6 . .
XCL C2 N1 O2 .
XCL N3 C2 C4 .
XCL C4 N3 C5 .
XCL N4 C4 HN41 .
XCL HN42 N4 . .
XCL HN41 N4 . .
XCL C5 C4 H5 .
XCL H5 C5 . .
XCL O2 C2 . .
XCL "O3'" "C3'" . END
XCL "HO3'" "O3'" . .
XCL "C4'" "C6'" . ADD
XCL C6 C5 . 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
XCL OP1 P deloc 1.510 0.020
XCL OP2 P deloc 1.510 0.020
XCL "O5'" P single 1.610 0.020
XCL P OP3 deloc 1.510 0.020
XCL "C5'" "O5'" single 1.426 0.020
XCL "C4'" "C5'" single 1.524 0.020
XCL "H5'" "C5'" single 1.092 0.020
XCL "H5''" "C5'" single 1.092 0.020
XCL "C4'" "C6'" single 1.510 0.020
XCL "C3'" "C4'" single 1.524 0.020
XCL "H4'" "C4'" single 1.099 0.020
XCL "C6'" "C7'" double 1.330 0.020
XCL "H6'" "C6'" single 1.077 0.020
XCL "C7'" "C1'" single 1.510 0.020
XCL "H7'" "C7'" single 1.077 0.020
XCL "O3'" "C3'" single 1.432 0.020
XCL "C2'" "C3'" single 1.524 0.020
XCL "H3'" "C3'" single 1.099 0.020
XCL "HO3'" "O3'" single 0.967 0.020
XCL "C1'" "C2'" single 1.524 0.020
XCL "H2'" "C2'" single 1.092 0.020
XCL "H2''" "C2'" single 1.092 0.020
XCL N1 "C1'" single 1.465 0.020
XCL "H1'" "C1'" single 1.099 0.020
XCL C6 C5 double 1.390 0.020
XCL C6 N1 single 1.337 0.020
XCL H6 C6 single 1.083 0.020
XCL C5 C4 single 1.390 0.020
XCL H5 C5 single 1.083 0.020
XCL N4 C4 single 1.355 0.020
XCL C4 N3 double 1.350 0.020
XCL HN41 N4 single 1.010 0.020
XCL HN42 N4 single 1.010 0.020
XCL N3 C2 single 1.350 0.020
XCL O2 C2 double 1.250 0.020
XCL C2 N1 single 1.410 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
XCL OP3 P OP1 119.900 3.000
XCL OP3 P OP2 119.900 3.000
XCL OP3 P "O5'" 108.200 3.000
XCL OP1 P OP2 119.900 3.000
XCL OP1 P "O5'" 108.200 3.000
XCL OP2 P "O5'" 108.200 3.000
XCL P "O5'" "C5'" 120.500 3.000
XCL "O5'" "C5'" "H5'" 109.470 3.000
XCL "O5'" "C5'" "H5''" 109.470 3.000
XCL "O5'" "C5'" "C4'" 109.470 3.000
XCL "H5'" "C5'" "H5''" 107.900 3.000
XCL "H5'" "C5'" "C4'" 109.470 3.000
XCL "H5''" "C5'" "C4'" 109.470 3.000
XCL "C5'" "C4'" "H4'" 108.340 3.000
XCL "C5'" "C4'" "C3'" 111.000 3.000
XCL "C5'" "C4'" "C6'" 109.470 3.000
XCL "H4'" "C4'" "C3'" 108.340 3.000
XCL "H4'" "C4'" "C6'" 108.810 3.000
XCL "C3'" "C4'" "C6'" 109.470 3.000
XCL "C4'" "C3'" "H3'" 108.340 3.000
XCL "C4'" "C3'" "C2'" 111.000 3.000
XCL "C4'" "C3'" "O3'" 109.470 3.000
XCL "H3'" "C3'" "C2'" 108.340 3.000
XCL "H3'" "C3'" "O3'" 109.470 3.000
XCL "C2'" "C3'" "O3'" 109.470 3.000
XCL "C3'" "C2'" "H2'" 109.470 3.000
XCL "C3'" "C2'" "H2''" 109.470 3.000
XCL "C3'" "C2'" "C1'" 111.000 3.000
XCL "H2'" "C2'" "H2''" 107.900 3.000
XCL "H2'" "C2'" "C1'" 109.470 3.000
XCL "H2''" "C2'" "C1'" 109.470 3.000
XCL "C2'" "C1'" "H1'" 108.340 3.000
XCL "C2'" "C1'" "C7'" 109.470 3.000
XCL "C2'" "C1'" N1 109.470 3.000
XCL "H1'" "C1'" "C7'" 108.810 3.000
XCL "H1'" "C1'" N1 109.470 3.000
XCL "C7'" "C1'" N1 109.500 3.000
XCL "C1'" "C7'" "H7'" 120.000 3.000
XCL "C1'" "C7'" "C6'" 120.000 3.000
XCL "H7'" "C7'" "C6'" 120.000 3.000
XCL "C7'" "C6'" "H6'" 120.000 3.000
XCL "C7'" "C6'" "C4'" 120.000 3.000
XCL "H6'" "C6'" "C4'" 120.000 3.000
XCL "C1'" N1 C6 120.000 3.000
XCL "C1'" N1 C2 120.000 3.000
XCL C6 N1 C2 120.000 3.000
XCL N1 C6 H6 120.000 3.000
XCL N1 C6 C5 120.000 3.000
XCL H6 C6 C5 120.000 3.000
XCL N1 C2 N3 120.000 3.000
XCL N1 C2 O2 120.000 3.000
XCL N3 C2 O2 120.000 3.000
XCL C2 N3 C4 120.000 3.000
XCL N3 C4 N4 120.000 3.000
XCL N3 C4 C5 120.000 3.000
XCL N4 C4 C5 120.000 3.000
XCL C4 N4 HN42 120.000 3.000
XCL C4 N4 HN41 120.000 3.000
XCL HN42 N4 HN41 120.000 3.000
XCL C4 C5 H5 120.000 3.000
XCL C4 C5 C6 120.000 3.000
XCL H5 C5 C6 120.000 3.000
XCL "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
XCL var_1 OP3 P "O5'" "C5'" -65.004 20.000 1
XCL var_2 P "O5'" "C5'" "C4'" 179.984 20.000 1
XCL var_3 "O5'" "C5'" "C4'" "C3'" 174.990 20.000 3
XCL var_4 "C5'" "C4'" "C6'" "C7'" -150.000 20.000 1
XCL var_5 "C5'" "C4'" "C3'" "O3'" -60.000 20.000 3
XCL var_6 "C4'" "C3'" "C2'" "C1'" -60.000 20.000 3
XCL var_7 "C3'" "C2'" "C1'" N1 -60.000 20.000 3
XCL var_8 "C2'" "C1'" "C7'" "C6'" -30.000 20.000 1
XCL var_9 "C1'" "C7'" "C6'" "C4'" 0.000 20.000 1
XCL var_10 "C2'" "C1'" N1 C2 -109.569 20.000 1
XCL CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
XCL CONST_2 N1 C6 C5 C4 0.000 0.000 0
XCL CONST_3 "C1'" N1 C2 O2 0.000 0.000 0
XCL CONST_4 N1 C2 N3 C4 0.000 0.000 0
XCL CONST_5 C2 N3 C4 C5 0.000 0.000 0
XCL CONST_6 N3 C4 N4 HN41 0.046 0.000 0
XCL CONST_7 N3 C4 C5 C6 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
XCL chir_01 "C4'" "C5'" "C6'" "C3'" positiv
XCL chir_02 "C3'" "C4'" "O3'" "C2'" positiv
XCL chir_03 "C1'" "C7'" "C2'" N1 negativ
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
XCL plan-1 "C6'" 0.020
XCL plan-1 "C4'" 0.020
XCL plan-1 "C7'" 0.020
XCL plan-1 "H6'" 0.020
XCL plan-1 "H7'" 0.020
XCL plan-2 "C7'" 0.020
XCL plan-2 "C6'" 0.020
XCL plan-2 "C1'" 0.020
XCL plan-2 "H7'" 0.020
XCL plan-2 "H6'" 0.020
XCL plan-3 C6 0.020
XCL plan-3 C5 0.020
XCL plan-3 N1 0.020
XCL plan-3 H6 0.020
XCL plan-3 C4 0.020
XCL plan-3 N3 0.020
XCL plan-3 C2 0.020
XCL plan-3 H5 0.020
XCL plan-3 N4 0.020
XCL plan-3 O2 0.020
XCL plan-3 "C1'" 0.020
XCL plan-3 HN42 0.020
XCL plan-3 HN41 0.020
XCL plan-4 N4 0.020
XCL plan-4 C4 0.020
XCL plan-4 HN41 0.020
XCL plan-4 HN42 0.020
# ------------------------------------------------------
|
