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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
D33 D33 '1-(2-deoxy-5-O-phosphono-beta-D-eryt' DNA 28 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_D33
#
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
D33 OP3 O OP -0.666 0.000 0.000 0.000
D33 P P P 0.000 -1.040 -0.475 -0.991
D33 OP1 O OP -0.666 -0.573 -1.763 -1.634
D33 OP2 O OP -0.666 -1.240 0.579 -2.057
D33 "O5'" O O2 0.000 -2.433 -0.733 -0.224
D33 "C5'" C CH2 0.000 -3.583 -1.287 -0.865
D33 "H15'" H H 0.000 -3.340 -2.279 -1.252
D33 "H25'" H H 0.000 -3.886 -0.639 -1.691
D33 "C4'" C CH1 0.000 -4.727 -1.397 0.145
D33 "H4'" H H 0.000 -4.419 -1.995 1.015
D33 "C3'" C CH1 0.000 -5.986 -2.008 -0.521
D33 "H3'" H H 0.000 -6.095 -1.650 -1.554
D33 "C2'" C CH2 0.000 -7.124 -1.463 0.376
D33 "H22'" H H 0.000 -7.434 -2.189 1.130
D33 "H12'" H H 0.000 -7.993 -1.154 -0.209
D33 "C1'" C CH1 0.000 -6.504 -0.234 1.068
D33 "H1'" H H 0.000 -6.475 -0.391 2.155
D33 "O4'" O O2 0.000 -5.168 -0.086 0.559
D33 N1 N NR5 0.000 -7.291 0.962 0.757
D33 C2 C CR15 0.000 -7.237 1.681 -0.384
D33 H22 H H 0.000 -6.597 1.473 -1.232
D33 N3 N NRD5 0.000 -8.085 2.670 -0.296
D33 C4 C CR15 0.000 -8.696 2.623 0.898
D33 H44 H H 0.000 -9.444 3.318 1.257
D33 C5 C CR15 0.000 -8.216 1.560 1.570
D33 H55 H H 0.000 -8.505 1.240 2.563
D33 "O3'" O OH1 0.000 -5.944 -3.436 -0.479
D33 "HO3'" H H 0.000 -6.710 -3.865 -0.883
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
D33 OP3 n/a P START
D33 P OP3 "O5'" .
D33 OP1 P . .
D33 OP2 P . .
D33 "O5'" P "C5'" .
D33 "C5'" "O5'" "C4'" .
D33 "H15'" "C5'" . .
D33 "H25'" "C5'" . .
D33 "C4'" "C5'" "C3'" .
D33 "H4'" "C4'" . .
D33 "C3'" "C4'" "O3'" .
D33 "H3'" "C3'" . .
D33 "C2'" "C3'" "C1'" .
D33 "H22'" "C2'" . .
D33 "H12'" "C2'" . .
D33 "C1'" "C2'" N1 .
D33 "H1'" "C1'" . .
D33 "O4'" "C1'" . .
D33 N1 "C1'" C2 .
D33 C2 N1 N3 .
D33 H22 C2 . .
D33 N3 C2 C4 .
D33 C4 N3 C5 .
D33 H44 C4 . .
D33 C5 C4 H55 .
D33 H55 C5 . .
D33 "O3'" "C3'" . END
D33 "HO3'" "O3'" . .
D33 C5 N1 . ADD
D33 "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
D33 H44 C4 single 1.083 0.020
D33 C5 C4 double 1.380 0.020
D33 N3 C2 double 1.350 0.020
D33 C5 N1 single 1.337 0.020
D33 C2 N1 single 1.337 0.020
D33 "O5'" P single 1.610 0.020
D33 OP2 P deloc 1.510 0.020
D33 OP1 P deloc 1.510 0.020
D33 "C5'" "O5'" single 1.426 0.020
D33 "C4'" "C5'" single 1.524 0.020
D33 "H25'" "C5'" single 1.092 0.020
D33 "C4'" "O4'" single 1.426 0.020
D33 "C3'" "C4'" single 1.524 0.020
D33 "O4'" "C1'" single 1.426 0.020
D33 N1 "C1'" single 1.485 0.020
D33 "C1'" "C2'" single 1.524 0.020
D33 C4 N3 single 1.350 0.020
D33 "H22'" "C2'" single 1.092 0.020
D33 "H12'" "C2'" single 1.092 0.020
D33 "C2'" "C3'" single 1.524 0.020
D33 "H3'" "C3'" single 1.099 0.020
D33 "O3'" "C3'" single 1.432 0.020
D33 "HO3'" "O3'" single 0.967 0.020
D33 "H15'" "C5'" single 1.092 0.020
D33 "H4'" "C4'" single 1.099 0.020
D33 "H1'" "C1'" single 1.099 0.020
D33 H55 C5 single 1.083 0.020
D33 H22 C2 single 1.083 0.020
D33 P OP3 deloc 1.510 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
D33 OP3 P OP1 119.900 3.000
D33 OP3 P OP2 119.900 3.000
D33 OP3 P "O5'" 108.200 3.000
D33 OP1 P OP2 119.900 3.000
D33 OP1 P "O5'" 108.200 3.000
D33 OP2 P "O5'" 108.200 3.000
D33 P "O5'" "C5'" 120.500 3.000
D33 "O5'" "C5'" "H15'" 109.470 3.000
D33 "O5'" "C5'" "H25'" 109.470 3.000
D33 "O5'" "C5'" "C4'" 109.470 3.000
D33 "H15'" "C5'" "H25'" 107.900 3.000
D33 "H15'" "C5'" "C4'" 109.470 3.000
D33 "H25'" "C5'" "C4'" 109.470 3.000
D33 "C5'" "C4'" "H4'" 108.340 3.000
D33 "C5'" "C4'" "C3'" 111.000 3.000
D33 "C5'" "C4'" "O4'" 109.470 3.000
D33 "H4'" "C4'" "C3'" 108.340 3.000
D33 "H4'" "C4'" "O4'" 109.470 3.000
D33 "C3'" "C4'" "O4'" 109.470 3.000
D33 "C4'" "C3'" "H3'" 108.340 3.000
D33 "C4'" "C3'" "C2'" 111.000 3.000
D33 "C4'" "C3'" "O3'" 109.470 3.000
D33 "H3'" "C3'" "C2'" 108.340 3.000
D33 "H3'" "C3'" "O3'" 109.470 3.000
D33 "C2'" "C3'" "O3'" 109.470 3.000
D33 "C3'" "C2'" "H22'" 109.470 3.000
D33 "C3'" "C2'" "H12'" 109.470 3.000
D33 "C3'" "C2'" "C1'" 111.000 3.000
D33 "H22'" "C2'" "H12'" 107.900 3.000
D33 "H22'" "C2'" "C1'" 109.470 3.000
D33 "H12'" "C2'" "C1'" 109.470 3.000
D33 "C2'" "C1'" "H1'" 108.340 3.000
D33 "C2'" "C1'" "O4'" 109.470 3.000
D33 "C2'" "C1'" N1 109.470 3.000
D33 "H1'" "C1'" "O4'" 109.470 3.000
D33 "H1'" "C1'" N1 109.470 3.000
D33 "O4'" "C1'" N1 109.470 3.000
D33 "C1'" "O4'" "C4'" 111.800 3.000
D33 "C1'" N1 C2 126.000 3.000
D33 "C1'" N1 C5 126.000 3.000
D33 C2 N1 C5 108.000 3.000
D33 N1 C2 H22 126.000 3.000
D33 N1 C2 N3 108.000 3.000
D33 H22 C2 N3 126.000 3.000
D33 C2 N3 C4 108.000 3.000
D33 N3 C4 H44 126.000 3.000
D33 N3 C4 C5 108.000 3.000
D33 H44 C4 C5 126.000 3.000
D33 C4 C5 H55 126.000 3.000
D33 C4 C5 N1 108.000 3.000
D33 H55 C5 N1 126.000 3.000
D33 "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
D33 var_1 OP3 P "O5'" "C5'" -174.972 20.000 1
D33 var_2 P "O5'" "C5'" "C4'" 179.979 20.000 1
D33 var_3 "O5'" "C5'" "C4'" "C3'" -179.486 20.000 3
D33 var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
D33 var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
D33 var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
D33 var_7 "C3'" "C2'" "C1'" N1 120.000 20.000 3
D33 var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
D33 var_9 "C2'" "C1'" N1 C2 -79.346 20.000 1
D33 CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
D33 CONST_2 N1 C2 N3 C4 0.000 0.000 0
D33 CONST_3 C2 N3 C4 C5 0.000 0.000 0
D33 CONST_4 N3 C4 C5 N1 0.000 0.000 0
D33 CONST_5 C4 C5 N1 "C1'" 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
D33 chir_01 "C4'" "C5'" "O4'" "C3'" negativ
D33 chir_02 "C1'" N1 "O4'" "C2'" positiv
D33 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
D33 plan-1 C5 0.020
D33 plan-1 N1 0.020
D33 plan-1 C4 0.020
D33 plan-1 H55 0.020
D33 plan-1 C2 0.020
D33 plan-1 N3 0.020
D33 plan-1 H22 0.020
D33 plan-1 "C1'" 0.020
D33 plan-1 H44 0.020
# ------------------------------------------------------
|
