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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
DT DT 'THYMIDINE-5'-MONOPHOSPHATE ' DNA 34 21 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DT
#
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
DT P P P 0.000 0.013 0.030 -0.075
DT OP3 O OP -0.660 -0.589 -1.011 0.843
DT OP1 O OP -0.660 1.224 -0.476 -0.823
DT "O5'" O O2 0.000 -1.088 0.308 -1.228
DT "C5'" C CH2 0.000 -2.338 0.881 -0.836
DT "H5'" H H 0.000 -2.128 1.849 -0.377
DT "H5''" H H 0.000 -2.786 0.217 -0.093
DT "C4'" C CH1 0.000 -3.297 1.066 -1.994
DT "H4'" H H 0.000 -2.865 1.792 -2.697
DT "C3'" C CH1 0.000 -4.742 1.504 -1.654
DT "H3'" H H 0.000 -4.810 2.046 -0.700
DT "O3'" O OH1 0.000 -5.174 2.295 -2.776
DT "HO3'" H H 0.000 -6.104 2.537 -2.662
DT "C2'" C CH2 0.000 -5.532 0.173 -1.644
DT "H2' " H H 0.000 -6.535 0.301 -2.056
DT "H2''" H H 0.000 -5.604 -0.240 -0.636
DT "C1'" C CH1 0.000 -4.722 -0.794 -2.543
DT "H1'" H H 0.000 -5.182 -0.794 -3.542
DT "O4'" O O2 0.000 -3.408 -0.212 -2.658
DT N1 N NR6 0.000 -4.674 -2.184 -2.064
DT C6 C CR16 0.000 -3.621 -2.648 -1.371
DT H6 H H 0.000 -2.786 -1.975 -1.217
DT C5 C CR6 0.000 -3.521 -3.938 -0.831
DT C7 C CH3 0.000 -2.368 -4.279 0.074
DT H73 H H 0.000 -1.463 -4.228 -0.473
DT H72 H H 0.000 -2.334 -3.589 0.877
DT H71 H H 0.000 -2.496 -5.258 0.455
DT C4 C CR6 0.000 -4.533 -4.912 -1.261
DT N3 N NR16 0.000 -5.439 -4.431 -2.127
DT H3 H H 0.000 -6.159 -5.099 -2.467
DT C2 C CR6 0.000 -5.511 -3.170 -2.601
DT O2 O O 0.000 -6.474 -2.893 -3.352
DT O4 O O 0.000 -4.557 -6.109 -0.904
DT OP2 O OP -0.660 0.258 1.360 0.609
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
DT "O5'" n/a "C5'" START
DT P "O5'" OP2 .
DT OP3 P . .
DT OP1 P . .
DT "C5'" "O5'" "C4'" .
DT "H5'" "C5'" . .
DT "H5''" "C5'" . .
DT "C4'" "C5'" "C3'" .
DT "H4'" "C4'" . .
DT "C3'" "C4'" "C2'" .
DT "H3'" "C3'" . .
DT "O3'" "C3'" "HO3'" .
DT "HO3'" "O3'" . .
DT "C2'" "C3'" "C1'" .
DT "H2' " "C2'" . .
DT "H2''" "C2'" . .
DT "C1'" "C2'" N1 .
DT "H1'" "C1'" . .
DT "O4'" "C1'" . .
DT N1 "C1'" C6 .
DT C6 N1 C5 .
DT H6 C6 . .
DT C5 C6 C4 .
DT C7 C5 H71 .
DT H73 C7 . .
DT H72 C7 . .
DT H71 C7 . .
DT C4 C5 O4 .
DT N3 C4 C2 .
DT H3 N3 . .
DT C2 N3 O2 .
DT O2 C2 . .
DT OP2 P . .
DT O4 C4 . END
DT "C4'" "O4'" . ADD
DT N1 C2 . 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
DT OP3 P deloc 1.485 0.017
DT OP1 P deloc 1.485 0.017
DT OP2 P deloc 1.485 0.017
DT "O5'" P single 1.593 0.010
DT "C5'" "O5'" single 1.440 0.016
DT "C4'" "C5'" single 1.511 0.008
DT "C4'" "O4'" single 1.446 0.011
DT "C3'" "C4'" single 1.528 0.010
DT "O4'" "C1'" single 1.420 0.013
DT "O3'" "C3'" single 1.431 0.013
DT "C2'" "C3'" single 1.518 0.010
DT "C1'" "C2'" single 1.521 0.014
DT N1 "C1'" single 1.473 0.014
DT N1 C2 single 1.376 0.008
DT C6 N1 single 1.378 0.007
DT O2 C2 double 1.220 0.008
DT C2 N3 single 1.373 0.008
DT N3 C4 single 1.382 0.008
DT O4 C4 double 1.228 0.009
DT C4 C5 single 1.445 0.009
DT C7 C5 single 1.496 0.006
DT C5 C6 double 1.339 0.007
DT "H5'" "C5'" single 1.092 0.020
DT "H5''" "C5'" single 1.092 0.020
DT "H4'" "C4'" single 1.099 0.020
DT "H3'" "C3'" single 1.099 0.020
DT "HO3'" "O3'" single 0.967 0.020
DT "H2' " "C2'" single 1.092 0.020
DT "H2''" "C2'" single 1.092 0.020
DT "H1'" "C1'" single 1.099 0.020
DT H3 N3 single 1.040 0.020
DT H71 C7 single 1.059 0.020
DT H72 C7 single 1.059 0.020
DT H73 C7 single 1.059 0.020
DT H6 C6 single 1.083 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
DT OP3 P OP1 107.400 3.200
DT OP3 P "O5'" 104.000 1.900
DT OP1 P "O5'" 108.100 2.900
DT OP3 P OP2 108.300 3.200
DT OP1 P OP2 119.600 1.500
DT "O5'" P OP2 108.300 2.700
DT P "O5'" "C5'" 120.900 1.600
DT "O5'" "C5'" "H5'" 109.470 3.000
DT "O5'" "C5'" "H5''" 109.470 3.000
DT "O5'" "C5'" "C4'" 110.200 1.400
DT "H5'" "C5'" "H5''" 107.900 3.000
DT "H5'" "C5'" "C4'" 109.470 3.000
DT "H5''" "C5'" "C4'" 109.470 3.000
DT "C5'" "C4'" "H4'" 108.340 3.000
DT "C5'" "C4'" "C3'" 114.700 1.500
DT "C5'" "C4'" "O4'" 109.400 1.600
DT "H4'" "C4'" "C3'" 108.340 3.000
DT "H4'" "C4'" "O4'" 109.470 3.000
DT "C3'" "C4'" "O4'" 105.600 1.000
DT "C4'" "C3'" "H3'" 108.340 3.000
DT "C4'" "C3'" "O3'" 110.300 2.200
DT "C4'" "C3'" "C2'" 103.200 1.000
DT "H3'" "C3'" "O3'" 109.470 3.000
DT "H3'" "C3'" "C2'" 108.340 3.000
DT "O3'" "C3'" "C2'" 110.600 2.700
DT "C3'" "O3'" "HO3'" 109.470 3.000
DT "C3'" "C2'" "H2' " 109.470 3.000
DT "C3'" "C2'" "H2''" 109.470 3.000
DT "C3'" "C2'" "C1'" 102.700 1.400
DT "H2' " "C2'" "H2''" 107.900 3.000
DT "H2' " "C2'" "C1'" 109.470 3.000
DT "H2''" "C2'" "C1'" 109.470 3.000
DT "C2'" "C1'" "H1'" 108.340 3.000
DT "C2'" "C1'" "O4'" 106.100 1.100
DT "C2'" "C1'" N1 114.200 1.600
DT "H1'" "C1'" "O4'" 109.470 3.000
DT "H1'" "C1'" N1 109.470 3.000
DT "O4'" "C1'" N1 107.800 0.800
DT "C1'" "O4'" "C4'" 109.700 1.400
DT "C1'" N1 C6 120.400 1.500
DT "C1'" N1 C2 118.200 1.600
DT C6 N1 C2 121.300 0.500
DT N1 C6 H6 120.000 3.000
DT N1 C6 C5 123.700 0.600
DT H6 C6 C5 120.000 3.000
DT C6 C5 C7 122.900 0.600
DT C6 C5 C4 118.000 0.600
DT C7 C5 C4 119.000 0.600
DT C5 C7 H73 109.470 3.000
DT C5 C7 H72 109.470 3.000
DT C5 C7 H71 109.470 3.000
DT H73 C7 H72 109.470 3.000
DT H73 C7 H71 109.470 3.000
DT H72 C7 H71 109.470 3.000
DT C5 C4 N3 115.200 0.600
DT C5 C4 O4 124.900 0.700
DT N3 C4 O4 119.900 0.600
DT C4 N3 H3 120.000 3.000
DT C4 N3 C2 127.200 0.600
DT H3 N3 C2 120.000 3.000
DT N3 C2 O2 122.300 0.600
DT N3 C2 N1 114.600 0.600
DT O2 C2 N1 123.100 0.800
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
DT var_1 OP2 P "O5'" "C5'" -54.229 20.000 1
DT var_2 P "O5'" "C5'" "C4'" 179.971 20.000 1
DT var_3 "O5'" "C5'" "C4'" "C3'" 179.531 20.000 3
DT var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
DT var_5 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
DT var_6 "C4'" "C3'" "O3'" "HO3'" 175.000 20.000 1
DT var_7 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
DT var_8 "C3'" "C2'" "C1'" N1 150.000 20.000 3
DT var_9 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
DT var_10 "C2'" "C1'" N1 C6 -86.506 20.000 1
DT CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DT CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DT CONST_3 N1 C6 C5 C4 0.000 0.000 0
DT var_11 C6 C5 C7 H71 175.000 20.000 1
DT CONST_4 C6 C5 C4 O4 180.000 0.000 0
DT CONST_5 C5 C4 N3 C2 0.000 0.000 0
DT CONST_6 C4 N3 C2 O2 180.000 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
DT chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DT chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DT chir_03 "C1'" "O4'" "C2'" N1 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
DT plan-1 N1 0.020
DT plan-1 "C1'" 0.020
DT plan-1 C2 0.020
DT plan-1 C6 0.020
DT plan-1 N3 0.020
DT plan-1 C4 0.020
DT plan-1 C5 0.020
DT plan-1 O2 0.020
DT plan-1 H3 0.020
DT plan-1 O4 0.020
DT plan-1 C7 0.020
DT plan-1 H6 0.020
# ------------------------------------------------------
# ------------------------------------------------------
# ------------------------------------------------------
|
