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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
XTY XTY '"(1R)-1,4-ANHYDRO-2-DEOXY-1-(6-METHY' DNA 40 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XTY
#
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
XTY OP3 O OP -0.666 0.000 0.000 0.000
XTY P P P 0.000 -0.392 0.982 1.082
XTY OP1 O OP -0.666 -1.243 1.992 0.345
XTY OP2 O OP -0.666 0.764 1.561 1.869
XTY "O5'" O O2 0.000 -1.464 0.144 1.960
XTY "C5'" C CH2 0.000 -2.577 -0.431 1.299
XTY "H5'1" H H 0.000 -2.232 -1.139 0.542
XTY "H5'2" H H 0.000 -3.169 0.352 0.821
XTY "C4'" C CH1 0.000 -3.432 -1.161 2.327
XTY "H4'" H H 0.000 -2.829 -1.922 2.841
XTY "C3'" C CH1 0.000 -4.666 -1.807 1.714
XTY "H3'" H H 0.000 -4.494 -2.072 0.661
XTY "C2'" C CH2 0.000 -5.719 -0.730 1.842
XTY "H2'1" H H 0.000 -6.730 -1.134 1.924
XTY "H2'2" H H 0.000 -5.683 -0.004 1.028
XTY "C1'" C CH1 0.000 -5.334 -0.049 3.151
XTY "H1'" H H 0.000 -5.810 -0.594 3.978
XTY "O4'" O O2 0.000 -3.906 -0.188 3.279
XTY C8 C CR6 0.000 -5.774 1.393 3.216
XTY C6 C CR66 0.000 -7.001 1.768 3.766
XTY N N NR16 0.000 -7.861 0.784 4.277
XTY HN H H 0.000 -7.559 -0.210 4.231
XTY C2 C CR6 0.000 -9.092 1.073 4.838
XTY O2 O O 0.000 -9.839 0.198 5.281
XTY CD C CR16 0.000 -4.916 2.369 2.707
XTY HD H H 0.000 -3.963 2.081 2.280
XTY C7 C CR6 0.000 -5.282 3.714 2.748
XTY C7A C CH3 0.000 -4.360 4.753 2.202
XTY H7A3 H H 0.000 -3.511 4.281 1.783
XTY H7A2 H H 0.000 -4.863 5.309 1.456
XTY H7A1 H H 0.000 -4.059 5.398 2.984
XTY CP C CR16 0.000 -6.508 4.092 3.298
XTY HP H H 0.000 -6.792 5.137 3.329
XTY C5 C CR66 0.000 -7.368 3.115 3.806
XTY C4 C CR6 0.000 -8.669 3.489 4.393
XTY N3 N NR16 0.000 -9.433 2.426 4.864
XTY HN3 H H 0.000 -10.355 2.665 5.280
XTY O4 O O 0.000 -9.029 4.660 4.446
XTY "O3'" O OH1 0.000 -5.049 -2.949 2.477
XTY "HO3'" H H 0.000 -4.926 -3.720 1.901
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
XTY OP3 n/a P START
XTY P OP3 "O5'" .
XTY OP1 P . .
XTY OP2 P . .
XTY "O5'" P "C5'" .
XTY "C5'" "O5'" "C4'" .
XTY "H5'1" "C5'" . .
XTY "H5'2" "C5'" . .
XTY "C4'" "C5'" "C3'" .
XTY "H4'" "C4'" . .
XTY "C3'" "C4'" "O3'" .
XTY "H3'" "C3'" . .
XTY "C2'" "C3'" "C1'" .
XTY "H2'1" "C2'" . .
XTY "H2'2" "C2'" . .
XTY "C1'" "C2'" C8 .
XTY "H1'" "C1'" . .
XTY "O4'" "C1'" . .
XTY C8 "C1'" CD .
XTY C6 C8 N .
XTY N C6 C2 .
XTY HN N . .
XTY C2 N O2 .
XTY O2 C2 . .
XTY CD C8 C7 .
XTY HD CD . .
XTY C7 CD CP .
XTY C7A C7 H7A1 .
XTY H7A3 C7A . .
XTY H7A2 C7A . .
XTY H7A1 C7A . .
XTY CP C7 C5 .
XTY HP CP . .
XTY C5 CP C4 .
XTY C4 C5 O4 .
XTY N3 C4 HN3 .
XTY HN3 N3 . .
XTY O4 C4 . .
XTY "O3'" "C3'" . END
XTY "HO3'" "O3'" . .
XTY "C4'" "O4'" . ADD
XTY C2 N3 . ADD
XTY 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
XTY P OP3 deloc 1.510 0.020
XTY OP2 P deloc 1.510 0.020
XTY "O5'" P single 1.610 0.020
XTY OP1 P deloc 1.510 0.020
XTY "C4'" "C5'" single 1.524 0.020
XTY "C5'" "O5'" single 1.426 0.020
XTY "H5'1" "C5'" single 1.092 0.020
XTY "H5'2" "C5'" single 1.092 0.020
XTY "C4'" "O4'" single 1.426 0.020
XTY "C3'" "C4'" single 1.524 0.020
XTY "H4'" "C4'" single 1.099 0.020
XTY "O4'" "C1'" single 1.426 0.020
XTY "C2'" "C3'" single 1.524 0.020
XTY "O3'" "C3'" single 1.432 0.020
XTY "H3'" "C3'" single 1.099 0.020
XTY "C1'" "C2'" single 1.524 0.020
XTY "H2'1" "C2'" single 1.092 0.020
XTY "H2'2" "C2'" single 1.092 0.020
XTY C8 "C1'" single 1.480 0.020
XTY "H1'" "C1'" single 1.099 0.020
XTY C2 N3 single 1.337 0.020
XTY O2 C2 double 1.250 0.020
XTY C2 N single 1.337 0.020
XTY N3 C4 single 1.337 0.020
XTY HN3 N3 single 1.040 0.020
XTY O4 C4 double 1.250 0.020
XTY C4 C5 single 1.490 0.020
XTY C5 CP double 1.390 0.020
XTY C5 C6 single 1.490 0.020
XTY N C6 single 1.337 0.020
XTY C6 C8 double 1.490 0.020
XTY HN N single 1.040 0.020
XTY CP C7 single 1.390 0.020
XTY HP CP single 1.083 0.020
XTY C7 CD double 1.390 0.020
XTY CD C8 single 1.390 0.020
XTY HD CD single 1.083 0.020
XTY C7A C7 single 1.506 0.020
XTY H7A1 C7A single 1.059 0.020
XTY H7A2 C7A single 1.059 0.020
XTY H7A3 C7A single 1.059 0.020
XTY "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
XTY OP3 P OP1 119.900 3.000
XTY OP3 P OP2 119.900 3.000
XTY OP3 P "O5'" 108.200 3.000
XTY OP1 P OP2 119.900 3.000
XTY OP1 P "O5'" 108.200 3.000
XTY OP2 P "O5'" 108.200 3.000
XTY P "O5'" "C5'" 120.500 3.000
XTY "O5'" "C5'" "H5'1" 109.470 3.000
XTY "O5'" "C5'" "H5'2" 109.470 3.000
XTY "O5'" "C5'" "C4'" 109.470 3.000
XTY "H5'1" "C5'" "H5'2" 107.900 3.000
XTY "H5'1" "C5'" "C4'" 109.470 3.000
XTY "H5'2" "C5'" "C4'" 109.470 3.000
XTY "C5'" "C4'" "H4'" 108.340 3.000
XTY "C5'" "C4'" "C3'" 111.000 3.000
XTY "C5'" "C4'" "O4'" 109.470 3.000
XTY "H4'" "C4'" "C3'" 108.340 3.000
XTY "H4'" "C4'" "O4'" 109.470 3.000
XTY "C3'" "C4'" "O4'" 109.470 3.000
XTY "C4'" "C3'" "H3'" 108.340 3.000
XTY "C4'" "C3'" "C2'" 111.000 3.000
XTY "C4'" "C3'" "O3'" 109.470 3.000
XTY "H3'" "C3'" "C2'" 108.340 3.000
XTY "H3'" "C3'" "O3'" 109.470 3.000
XTY "C2'" "C3'" "O3'" 109.470 3.000
XTY "C3'" "C2'" "H2'1" 109.470 3.000
XTY "C3'" "C2'" "H2'2" 109.470 3.000
XTY "C3'" "C2'" "C1'" 111.000 3.000
XTY "H2'1" "C2'" "H2'2" 107.900 3.000
XTY "H2'1" "C2'" "C1'" 109.470 3.000
XTY "H2'2" "C2'" "C1'" 109.470 3.000
XTY "C2'" "C1'" "H1'" 108.340 3.000
XTY "C2'" "C1'" "O4'" 109.470 3.000
XTY "C2'" "C1'" C8 109.470 3.000
XTY "H1'" "C1'" "O4'" 109.470 3.000
XTY "H1'" "C1'" C8 109.470 3.000
XTY "O4'" "C1'" C8 109.470 3.000
XTY "C1'" "O4'" "C4'" 111.800 3.000
XTY "C1'" C8 C6 120.000 3.000
XTY "C1'" C8 CD 120.000 3.000
XTY C6 C8 CD 120.000 3.000
XTY C8 C6 N 120.000 3.000
XTY C8 C6 C5 120.000 3.000
XTY N C6 C5 120.000 3.000
XTY C6 N HN 120.000 3.000
XTY C6 N C2 120.000 3.000
XTY HN N C2 120.000 3.000
XTY N C2 O2 120.000 3.000
XTY N C2 N3 120.000 3.000
XTY O2 C2 N3 120.000 3.000
XTY C8 CD HD 120.000 3.000
XTY C8 CD C7 120.000 3.000
XTY HD CD C7 120.000 3.000
XTY CD C7 C7A 120.000 3.000
XTY CD C7 CP 120.000 3.000
XTY C7A C7 CP 120.000 3.000
XTY C7 C7A H7A3 109.470 3.000
XTY C7 C7A H7A2 109.470 3.000
XTY C7 C7A H7A1 109.470 3.000
XTY H7A3 C7A H7A2 109.470 3.000
XTY H7A3 C7A H7A1 109.470 3.000
XTY H7A2 C7A H7A1 109.470 3.000
XTY C7 CP HP 120.000 3.000
XTY C7 CP C5 120.000 3.000
XTY HP CP C5 120.000 3.000
XTY CP C5 C4 120.000 3.000
XTY CP C5 C6 120.000 3.000
XTY C4 C5 C6 120.000 3.000
XTY C5 C4 N3 120.000 3.000
XTY C5 C4 O4 120.000 3.000
XTY N3 C4 O4 120.000 3.000
XTY C4 N3 HN3 120.000 3.000
XTY C4 N3 C2 120.000 3.000
XTY HN3 N3 C2 120.000 3.000
XTY "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
XTY var_1 OP3 P "O5'" "C5'" -54.222 20.000 1
XTY var_2 P "O5'" "C5'" "C4'" -179.998 20.000 1
XTY var_3 "O5'" "C5'" "C4'" "C3'" 179.539 20.000 3
XTY var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
XTY var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
XTY var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
XTY var_7 "C3'" "C2'" "C1'" C8 150.000 20.000 3
XTY var_8 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
XTY var_9 "C2'" "C1'" C8 CD -87.894 20.000 1
XTY CONST_1 "C1'" C8 C6 N 0.000 0.000 0
XTY CONST_2 C8 C6 N C2 180.000 0.000 0
XTY CONST_3 C6 N C2 O2 180.000 0.000 0
XTY CONST_4 N C2 N3 C4 0.000 0.000 0
XTY CONST_5 "C1'" C8 CD C7 180.000 0.000 0
XTY CONST_6 C8 CD C7 CP 0.000 0.000 0
XTY var_10 CD C7 C7A H7A1 -116.954 20.000 1
XTY CONST_7 CD C7 CP C5 0.000 0.000 0
XTY CONST_8 C7 CP C5 C4 180.000 0.000 0
XTY CONST_9 CP C5 C6 C8 0.000 0.000 0
XTY CONST_10 CP C5 C4 O4 0.000 0.000 0
XTY CONST_11 C5 C4 N3 C2 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
XTY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
XTY chir_02 "C3'" "C4'" "C2'" "O3'" positiv
XTY chir_03 "C1'" "O4'" "C2'" C8 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
XTY plan-1 C2 0.020
XTY plan-1 O2 0.020
XTY plan-1 N3 0.020
XTY plan-1 N 0.020
XTY plan-1 C4 0.020
XTY plan-1 HN3 0.020
XTY plan-1 O4 0.020
XTY plan-1 C5 0.020
XTY plan-1 C6 0.020
XTY plan-1 CP 0.020
XTY plan-1 CD 0.020
XTY plan-1 C8 0.020
XTY plan-1 C7 0.020
XTY plan-1 HN 0.020
XTY plan-1 HP 0.020
XTY plan-1 HD 0.020
XTY plan-1 "C1'" 0.020
XTY plan-1 C7A 0.020
# ------------------------------------------------------
|
