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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
XCS XCS '"(1R)-1-(4-AMINO-6-METHYL-2-OXO-1,2-' DNA 41 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XCS
#
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
XCS OP3 O OP -0.666 0.000 0.000 0.000
XCS P P P 0.000 0.413 -1.371 0.488
XCS OP2 O OP -0.666 1.757 -1.433 1.180
XCS OP1 O OP -0.666 0.292 -2.233 -0.749
XCS "O5'" O O2 0.000 -0.842 -1.852 1.390
XCS "C5'" C CH2 0.000 -2.137 -1.825 0.816
XCS "H5'1" H H 0.000 -2.167 -2.474 -0.062
XCS "H5'2" H H 0.000 -2.389 -0.804 0.520
XCS "C4'" C CH1 0.000 -3.141 -2.319 1.849
XCS "H4'" H H 0.000 -2.867 -3.330 2.181
XCS "C3'" C CH1 0.000 -4.571 -2.316 1.330
XCS "H3'" H H 0.000 -4.598 -2.448 0.239
XCS "C2'" C CH2 0.000 -5.080 -0.949 1.727
XCS "H2'1" H H 0.000 -6.159 -0.930 1.892
XCS "H2'2" H H 0.000 -4.808 -0.171 1.011
XCS "C1'" C CH1 0.000 -4.358 -0.702 3.048
XCS "H1'" H H 0.000 -4.955 -1.145 3.857
XCS "O4'" O O2 0.000 -3.107 -1.411 2.969
XCS C8 C CR6 0.000 -4.164 0.763 3.348
XCS C6 C CR66 0.000 -5.087 1.495 4.097
XCS ND N NR16 0.000 -6.233 0.870 4.593
XCS HND H H 0.000 -6.382 -0.140 4.394
XCS C2 C CR6 0.000 -7.179 1.554 5.341
XCS O2 O O 0.000 -8.176 0.962 5.759
XCS CD C CR16 0.000 -3.024 1.396 2.858
XCS HD H H 0.000 -2.302 0.837 2.276
XCS C7 C CR6 0.000 -2.811 2.750 3.117
XCS C7A C CH3 0.000 -1.588 3.424 2.591
XCS H7A3 H H 0.000 -0.842 2.698 2.401
XCS H7A2 H H 0.000 -1.826 3.932 1.694
XCS H7A1 H H 0.000 -1.234 4.117 3.308
XCS CP C CR16 0.000 -3.739 3.480 3.867
XCS HP H H 0.000 -3.570 4.531 4.066
XCS C5 C CR66 0.000 -4.883 2.847 4.359
XCS C4 C CR6 0.000 -5.925 3.539 5.167
XCS N3 N NRD6 0.000 -6.976 2.895 5.602
XCS N4 N NH2 0.000 -5.779 4.873 5.459
XCS HN42 H H 0.000 -5.830 5.196 6.419
XCS HN41 H H 0.000 -5.620 5.546 4.718
XCS "O3'" O OH1 0.000 -5.333 -3.324 1.990
XCS "HO3'" H H 0.000 -5.031 -3.340 2.910
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
XCS OP3 n/a P START
XCS P OP3 "O5'" .
XCS OP2 P . .
XCS OP1 P . .
XCS "O5'" P "C5'" .
XCS "C5'" "O5'" "C4'" .
XCS "H5'1" "C5'" . .
XCS "H5'2" "C5'" . .
XCS "C4'" "C5'" "C3'" .
XCS "H4'" "C4'" . .
XCS "C3'" "C4'" "O3'" .
XCS "H3'" "C3'" . .
XCS "C2'" "C3'" "C1'" .
XCS "H2'1" "C2'" . .
XCS "H2'2" "C2'" . .
XCS "C1'" "C2'" C8 .
XCS "H1'" "C1'" . .
XCS "O4'" "C1'" . .
XCS C8 "C1'" CD .
XCS C6 C8 ND .
XCS ND C6 C2 .
XCS HND ND . .
XCS C2 ND O2 .
XCS O2 C2 . .
XCS CD C8 C7 .
XCS HD CD . .
XCS C7 CD CP .
XCS C7A C7 H7A1 .
XCS H7A3 C7A . .
XCS H7A2 C7A . .
XCS H7A1 C7A . .
XCS CP C7 C5 .
XCS HP CP . .
XCS C5 CP C4 .
XCS C4 C5 N4 .
XCS N3 C4 . .
XCS N4 C4 HN41 .
XCS HN42 N4 . .
XCS HN41 N4 . .
XCS "O3'" "C3'" . END
XCS "HO3'" "O3'" . .
XCS C6 C5 . ADD
XCS C2 N3 . ADD
XCS "C4'" "O4'" . 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
XCS P OP3 deloc 1.510 0.020
XCS "O5'" P single 1.610 0.020
XCS OP1 P deloc 1.510 0.020
XCS OP2 P deloc 1.510 0.020
XCS ND C6 single 1.337 0.020
XCS C6 C5 double 1.490 0.020
XCS C6 C8 single 1.490 0.020
XCS O2 C2 double 1.250 0.020
XCS C2 N3 single 1.350 0.020
XCS C2 ND single 1.337 0.020
XCS N3 C4 double 1.350 0.020
XCS N4 C4 single 1.355 0.020
XCS C4 C5 single 1.490 0.020
XCS HN41 N4 single 1.010 0.020
XCS HN42 N4 single 1.010 0.020
XCS C5 CP single 1.390 0.020
XCS "C5'" "O5'" single 1.426 0.020
XCS "C4'" "C5'" single 1.524 0.020
XCS "H5'1" "C5'" single 1.092 0.020
XCS "H5'2" "C5'" single 1.092 0.020
XCS "C4'" "O4'" single 1.426 0.020
XCS "C3'" "C4'" single 1.524 0.020
XCS "H4'" "C4'" single 1.099 0.020
XCS "O4'" "C1'" single 1.426 0.020
XCS C8 "C1'" single 1.480 0.020
XCS "C1'" "C2'" single 1.524 0.020
XCS "H1'" "C1'" single 1.099 0.020
XCS HND ND single 1.040 0.020
XCS CP C7 double 1.390 0.020
XCS HP CP single 1.083 0.020
XCS CD C8 double 1.390 0.020
XCS C7 CD single 1.390 0.020
XCS HD CD single 1.083 0.020
XCS C7A C7 single 1.506 0.020
XCS H7A1 C7A single 1.059 0.020
XCS H7A2 C7A single 1.059 0.020
XCS H7A3 C7A single 1.059 0.020
XCS "C2'" "C3'" single 1.524 0.020
XCS "H2'1" "C2'" single 1.092 0.020
XCS "H2'2" "C2'" single 1.092 0.020
XCS "O3'" "C3'" single 1.432 0.020
XCS "H3'" "C3'" single 1.099 0.020
XCS "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
XCS OP3 P OP2 119.900 3.000
XCS OP3 P OP1 119.900 3.000
XCS OP3 P "O5'" 108.200 3.000
XCS OP2 P OP1 119.900 3.000
XCS OP2 P "O5'" 108.200 3.000
XCS OP1 P "O5'" 108.200 3.000
XCS P "O5'" "C5'" 120.500 3.000
XCS "O5'" "C5'" "H5'1" 109.470 3.000
XCS "O5'" "C5'" "H5'2" 109.470 3.000
XCS "O5'" "C5'" "C4'" 109.470 3.000
XCS "H5'1" "C5'" "H5'2" 107.900 3.000
XCS "H5'1" "C5'" "C4'" 109.470 3.000
XCS "H5'2" "C5'" "C4'" 109.470 3.000
XCS "C5'" "C4'" "H4'" 108.340 3.000
XCS "C5'" "C4'" "C3'" 111.000 3.000
XCS "C5'" "C4'" "O4'" 109.470 3.000
XCS "H4'" "C4'" "C3'" 108.340 3.000
XCS "H4'" "C4'" "O4'" 109.470 3.000
XCS "C3'" "C4'" "O4'" 109.470 3.000
XCS "C4'" "C3'" "H3'" 108.340 3.000
XCS "C4'" "C3'" "C2'" 111.000 3.000
XCS "C4'" "C3'" "O3'" 109.470 3.000
XCS "H3'" "C3'" "C2'" 108.340 3.000
XCS "H3'" "C3'" "O3'" 109.470 3.000
XCS "C2'" "C3'" "O3'" 109.470 3.000
XCS "C3'" "C2'" "H2'1" 109.470 3.000
XCS "C3'" "C2'" "H2'2" 109.470 3.000
XCS "C3'" "C2'" "C1'" 111.000 3.000
XCS "H2'1" "C2'" "H2'2" 107.900 3.000
XCS "H2'1" "C2'" "C1'" 109.470 3.000
XCS "H2'2" "C2'" "C1'" 109.470 3.000
XCS "C2'" "C1'" "H1'" 108.340 3.000
XCS "C2'" "C1'" "O4'" 109.470 3.000
XCS "C2'" "C1'" C8 109.470 3.000
XCS "H1'" "C1'" "O4'" 109.470 3.000
XCS "H1'" "C1'" C8 109.470 3.000
XCS "O4'" "C1'" C8 109.470 3.000
XCS "C1'" "O4'" "C4'" 111.800 3.000
XCS "C1'" C8 C6 120.000 3.000
XCS "C1'" C8 CD 120.000 3.000
XCS C6 C8 CD 120.000 3.000
XCS C8 C6 ND 120.000 3.000
XCS C8 C6 C5 120.000 3.000
XCS ND C6 C5 120.000 3.000
XCS C6 ND HND 120.000 3.000
XCS C6 ND C2 120.000 3.000
XCS HND ND C2 120.000 3.000
XCS ND C2 O2 120.000 3.000
XCS ND C2 N3 120.000 3.000
XCS O2 C2 N3 120.000 3.000
XCS C8 CD HD 120.000 3.000
XCS C8 CD C7 120.000 3.000
XCS HD CD C7 120.000 3.000
XCS CD C7 C7A 120.000 3.000
XCS CD C7 CP 120.000 3.000
XCS C7A C7 CP 120.000 3.000
XCS C7 C7A H7A3 109.470 3.000
XCS C7 C7A H7A2 109.470 3.000
XCS C7 C7A H7A1 109.470 3.000
XCS H7A3 C7A H7A2 109.470 3.000
XCS H7A3 C7A H7A1 109.470 3.000
XCS H7A2 C7A H7A1 109.470 3.000
XCS C7 CP HP 120.000 3.000
XCS C7 CP C5 120.000 3.000
XCS HP CP C5 120.000 3.000
XCS CP C5 C4 120.000 3.000
XCS CP C5 C6 120.000 3.000
XCS C4 C5 C6 120.000 3.000
XCS C5 C4 N3 120.000 3.000
XCS C5 C4 N4 120.000 3.000
XCS N3 C4 N4 120.000 3.000
XCS C4 N3 C2 120.000 3.000
XCS C4 N4 HN42 120.000 3.000
XCS C4 N4 HN41 120.000 3.000
XCS HN42 N4 HN41 120.000 3.000
XCS "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
XCS var_1 OP3 P "O5'" "C5'" 53.189 20.000 1
XCS var_2 P "O5'" "C5'" "C4'" -179.998 20.000 1
XCS var_3 "O5'" "C5'" "C4'" "C3'" 179.539 20.000 3
XCS var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
XCS var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
XCS var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
XCS var_7 "C3'" "C2'" "C1'" C8 150.000 20.000 3
XCS var_8 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
XCS var_9 "C2'" "C1'" C8 CD -87.897 20.000 1
XCS CONST_1 "C1'" C8 C6 ND 0.000 0.000 0
XCS CONST_2 C8 C6 C5 CP 0.000 0.000 0
XCS CONST_3 C8 C6 ND C2 180.000 0.000 0
XCS CONST_4 C6 ND C2 O2 180.000 0.000 0
XCS CONST_5 ND C2 N3 C4 0.000 0.000 0
XCS CONST_6 "C1'" C8 CD C7 180.000 0.000 0
XCS CONST_7 C8 CD C7 CP 0.000 0.000 0
XCS var_10 CD C7 C7A H7A1 -142.307 20.000 1
XCS CONST_8 CD C7 CP C5 0.000 0.000 0
XCS CONST_9 C7 CP C5 C4 180.000 0.000 0
XCS CONST_10 CP C5 C4 N4 0.000 0.000 0
XCS CONST_11 C5 C4 N3 C2 0.000 0.000 0
XCS CONST_12 C5 C4 N4 HN41 53.430 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
XCS chir_01 "C4'" "C5'" "O4'" "C3'" negativ
XCS chir_02 "C1'" "O4'" C8 "C2'" negativ
XCS chir_03 "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
XCS plan-1 C6 0.020
XCS plan-1 C5 0.020
XCS plan-1 ND 0.020
XCS plan-1 C8 0.020
XCS plan-1 CP 0.020
XCS plan-1 CD 0.020
XCS plan-1 C7 0.020
XCS plan-1 C4 0.020
XCS plan-1 C2 0.020
XCS plan-1 HND 0.020
XCS plan-1 HP 0.020
XCS plan-1 HD 0.020
XCS plan-1 "C1'" 0.020
XCS plan-1 C7A 0.020
XCS plan-1 N3 0.020
XCS plan-1 O2 0.020
XCS plan-1 N4 0.020
XCS plan-1 HN42 0.020
XCS plan-1 HN41 0.020
XCS plan-2 N4 0.020
XCS plan-2 C4 0.020
XCS plan-2 HN41 0.020
XCS plan-2 HN42 0.020
# ------------------------------------------------------
|
