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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
D3 D3 '1-(2-DEOXY-BETA-D-RIBOFURANOSYL)-4-(' DNA 52 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_D3
#
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
D3 OP3 O OP -0.666 0.000 0.000 0.000
D3 P P P 0.000 -1.259 0.556 -0.628
D3 OP1 O OP -0.666 -1.992 -0.550 -1.355
D3 OP2 O OP -0.666 -0.894 1.648 -1.609
D3 "O5'" O O2 0.000 -2.209 1.163 0.522
D3 "C5'" C CH2 0.000 -2.518 0.089 1.411
D3 "H5'" H H 0.000 -1.594 -0.306 1.838
D3 "H5''" H H 0.000 -3.031 -0.702 0.861
D3 "C4'" C CH1 0.000 -3.423 0.601 2.534
D3 "H4'" H H 0.000 -2.914 1.390 3.104
D3 "C3'" C CH1 0.000 -3.838 -0.555 3.470
D3 "H3'" H H 0.000 -3.779 -1.517 2.942
D3 "C2'" C CH2 0.000 -5.302 -0.232 3.845
D3 "H2'" H H 0.000 -5.426 -0.074 4.919
D3 "H2''" H H 0.000 -5.993 -1.008 3.511
D3 "C1'" C CH1 0.000 -5.600 1.084 3.092
D3 "H1'" H H 0.000 -5.427 1.948 3.750
D3 "O4'" O O2 0.000 -4.667 1.098 1.990
D3 N1A N NR5 0.000 -6.979 1.087 2.598
D3 C5A C CR15 0.000 -7.402 0.631 1.381
D3 H5A H H 0.000 -6.786 0.202 0.601
D3 C4A C CR5 0.000 -8.747 0.821 1.340
D3 N3A N NRD5 0.000 -9.116 1.387 2.507
D3 C2A C CR15 0.000 -8.064 1.546 3.259
D3 H2A H H 0.000 -8.060 1.976 4.253
D3 C1B C CR6 0.000 -9.646 0.474 0.213
D3 C6B C CR16 0.000 -9.232 0.687 -1.102
D3 H6B H H 0.000 -8.253 1.106 -1.300
D3 C5B C CR16 0.000 -10.069 0.363 -2.150
D3 H5B H H 0.000 -9.746 0.529 -3.170
D3 C4B C CR16 0.000 -11.319 -0.172 -1.901
D3 H4B H H 0.000 -11.972 -0.424 -2.727
D3 C3B C CR6 0.000 -11.739 -0.389 -0.595
D3 C2B C CR16 0.000 -10.902 -0.071 0.464
D3 H2B H H 0.000 -11.225 -0.246 1.483
D3 N N NH1 0.000 -13.005 -0.930 -0.348
D3 HN H H 0.000 -13.401 -1.600 -0.992
D3 C C C 0.000 -13.695 -0.559 0.747
D3 C1C C CR6 0.000 -14.976 -1.218 1.074
D3 C6C C CR16 0.000 -15.477 -2.225 0.246
D3 H6C H H 0.000 -14.930 -2.520 -0.641
D3 C5C C CR16 0.000 -16.670 -2.842 0.561
D3 H5C H H 0.000 -17.054 -3.631 -0.075
D3 C4C C CR16 0.000 -17.377 -2.457 1.684
D3 H4C H H 0.000 -18.316 -2.941 1.923
D3 C3C C CR16 0.000 -16.890 -1.456 2.506
D3 H3C H H 0.000 -17.448 -1.159 3.385
D3 C2C C CR16 0.000 -15.694 -0.835 2.208
D3 H2C H H 0.000 -15.313 -0.052 2.852
D3 O O O 0.000 -13.264 0.322 1.467
D3 "O3'" O OH1 0.000 -3.015 -0.574 4.637
D3 "HO3'" H H 0.000 -3.338 -1.294 5.196
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
D3 OP3 n/a P START
D3 P OP3 "O5'" .
D3 OP1 P . .
D3 OP2 P . .
D3 "O5'" P "C5'" .
D3 "C5'" "O5'" "C4'" .
D3 "H5'" "C5'" . .
D3 "H5''" "C5'" . .
D3 "C4'" "C5'" "C3'" .
D3 "H4'" "C4'" . .
D3 "C3'" "C4'" "O3'" .
D3 "H3'" "C3'" . .
D3 "C2'" "C3'" "C1'" .
D3 "H2'" "C2'" . .
D3 "H2''" "C2'" . .
D3 "C1'" "C2'" N1A .
D3 "H1'" "C1'" . .
D3 "O4'" "C1'" . .
D3 N1A "C1'" C5A .
D3 C5A N1A C4A .
D3 H5A C5A . .
D3 C4A C5A C1B .
D3 N3A C4A C2A .
D3 C2A N3A H2A .
D3 H2A C2A . .
D3 C1B C4A C6B .
D3 C6B C1B C5B .
D3 H6B C6B . .
D3 C5B C6B C4B .
D3 H5B C5B . .
D3 C4B C5B C3B .
D3 H4B C4B . .
D3 C3B C4B N .
D3 C2B C3B H2B .
D3 H2B C2B . .
D3 N C3B C .
D3 HN N . .
D3 C N O .
D3 C1C C C6C .
D3 C6C C1C C5C .
D3 H6C C6C . .
D3 C5C C6C C4C .
D3 H5C C5C . .
D3 C4C C5C C3C .
D3 H4C C4C . .
D3 C3C C4C C2C .
D3 H3C C3C . .
D3 C2C C3C H2C .
D3 H2C C2C . .
D3 O C . .
D3 "O3'" "C3'" . END
D3 "HO3'" "O3'" . .
D3 "C4'" "O4'" . ADD
D3 N1A C2A . ADD
D3 C1B C2B . ADD
D3 C1C C2C . 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
D3 OP1 P deloc 1.510 0.020
D3 OP2 P deloc 1.510 0.020
D3 P OP3 deloc 1.510 0.020
D3 "O5'" P single 1.610 0.020
D3 "C5'" "O5'" single 1.426 0.020
D3 "C4'" "C5'" single 1.524 0.020
D3 "H5'" "C5'" single 1.092 0.020
D3 "H5''" "C5'" single 1.092 0.020
D3 "C4'" "O4'" single 1.426 0.020
D3 "C3'" "C4'" single 1.524 0.020
D3 "H4'" "C4'" single 1.099 0.020
D3 "O4'" "C1'" single 1.426 0.020
D3 "O3'" "C3'" single 1.432 0.020
D3 "C2'" "C3'" single 1.524 0.020
D3 "H3'" "C3'" single 1.099 0.020
D3 "HO3'" "O3'" single 0.967 0.020
D3 "C1'" "C2'" single 1.524 0.020
D3 "H2'" "C2'" single 1.092 0.020
D3 "H2''" "C2'" single 1.092 0.020
D3 N1A "C1'" single 1.485 0.020
D3 "H1'" "C1'" single 1.099 0.020
D3 N1A C2A single 1.337 0.020
D3 C5A N1A single 1.337 0.020
D3 C2A N3A double 1.350 0.020
D3 H2A C2A single 1.083 0.020
D3 N3A C4A single 1.350 0.020
D3 C4A C5A double 1.387 0.020
D3 C1B C4A single 1.490 0.020
D3 H5A C5A single 1.083 0.020
D3 C1B C2B double 1.390 0.020
D3 C6B C1B single 1.390 0.020
D3 C2B C3B single 1.390 0.020
D3 H2B C2B single 1.083 0.020
D3 C3B C4B double 1.390 0.020
D3 N C3B single 1.350 0.020
D3 C4B C5B single 1.390 0.020
D3 H4B C4B single 1.083 0.020
D3 C5B C6B double 1.390 0.020
D3 H5B C5B single 1.083 0.020
D3 H6B C6B single 1.083 0.020
D3 C N single 1.330 0.020
D3 HN N single 1.010 0.020
D3 O C double 1.220 0.020
D3 C1C C single 1.500 0.020
D3 C1C C2C double 1.390 0.020
D3 C6C C1C single 1.390 0.020
D3 C2C C3C single 1.390 0.020
D3 H2C C2C single 1.083 0.020
D3 C3C C4C double 1.390 0.020
D3 H3C C3C single 1.083 0.020
D3 C4C C5C single 1.390 0.020
D3 H4C C4C single 1.083 0.020
D3 C5C C6C double 1.390 0.020
D3 H5C C5C single 1.083 0.020
D3 H6C C6C 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
D3 OP3 P OP1 119.900 3.000
D3 OP3 P OP2 119.900 3.000
D3 OP3 P "O5'" 108.200 3.000
D3 OP1 P OP2 119.900 3.000
D3 OP1 P "O5'" 108.200 3.000
D3 OP2 P "O5'" 108.200 3.000
D3 P "O5'" "C5'" 120.500 3.000
D3 "O5'" "C5'" "H5'" 109.470 3.000
D3 "O5'" "C5'" "H5''" 109.470 3.000
D3 "O5'" "C5'" "C4'" 109.470 3.000
D3 "H5'" "C5'" "H5''" 107.900 3.000
D3 "H5'" "C5'" "C4'" 109.470 3.000
D3 "H5''" "C5'" "C4'" 109.470 3.000
D3 "C5'" "C4'" "H4'" 108.340 3.000
D3 "C5'" "C4'" "C3'" 111.000 3.000
D3 "C5'" "C4'" "O4'" 109.470 3.000
D3 "H4'" "C4'" "C3'" 108.340 3.000
D3 "H4'" "C4'" "O4'" 109.470 3.000
D3 "C3'" "C4'" "O4'" 109.470 3.000
D3 "C4'" "C3'" "H3'" 108.340 3.000
D3 "C4'" "C3'" "C2'" 111.000 3.000
D3 "C4'" "C3'" "O3'" 109.470 3.000
D3 "H3'" "C3'" "C2'" 108.340 3.000
D3 "H3'" "C3'" "O3'" 109.470 3.000
D3 "C2'" "C3'" "O3'" 109.470 3.000
D3 "C3'" "C2'" "H2'" 109.470 3.000
D3 "C3'" "C2'" "H2''" 109.470 3.000
D3 "C3'" "C2'" "C1'" 111.000 3.000
D3 "H2'" "C2'" "H2''" 107.900 3.000
D3 "H2'" "C2'" "C1'" 109.470 3.000
D3 "H2''" "C2'" "C1'" 109.470 3.000
D3 "C2'" "C1'" "H1'" 108.340 3.000
D3 "C2'" "C1'" "O4'" 109.470 3.000
D3 "C2'" "C1'" N1A 109.470 3.000
D3 "H1'" "C1'" "O4'" 109.470 3.000
D3 "H1'" "C1'" N1A 109.470 3.000
D3 "O4'" "C1'" N1A 109.470 3.000
D3 "C1'" "O4'" "C4'" 111.800 3.000
D3 "C1'" N1A C5A 126.000 3.000
D3 "C1'" N1A C2A 126.000 3.000
D3 C5A N1A C2A 108.000 3.000
D3 N1A C5A H5A 126.000 3.000
D3 N1A C5A C4A 108.000 3.000
D3 H5A C5A C4A 126.000 3.000
D3 C5A C4A N3A 108.000 3.000
D3 C5A C4A C1B 126.000 3.000
D3 N3A C4A C1B 126.000 3.000
D3 C4A N3A C2A 108.000 3.000
D3 N3A C2A H2A 126.000 3.000
D3 N3A C2A N1A 108.000 3.000
D3 H2A C2A N1A 126.000 3.000
D3 C4A C1B C6B 120.000 3.000
D3 C4A C1B C2B 120.000 3.000
D3 C6B C1B C2B 120.000 3.000
D3 C1B C6B H6B 120.000 3.000
D3 C1B C6B C5B 120.000 3.000
D3 H6B C6B C5B 120.000 3.000
D3 C6B C5B H5B 120.000 3.000
D3 C6B C5B C4B 120.000 3.000
D3 H5B C5B C4B 120.000 3.000
D3 C5B C4B H4B 120.000 3.000
D3 C5B C4B C3B 120.000 3.000
D3 H4B C4B C3B 120.000 3.000
D3 C4B C3B C2B 120.000 3.000
D3 C4B C3B N 120.000 3.000
D3 C2B C3B N 120.000 3.000
D3 C3B C2B H2B 120.000 3.000
D3 C3B C2B C1B 120.000 3.000
D3 H2B C2B C1B 120.000 3.000
D3 C3B N HN 120.000 3.000
D3 C3B N C 120.000 3.000
D3 HN N C 120.000 3.000
D3 N C C1C 120.000 3.000
D3 N C O 123.000 3.000
D3 C1C C O 120.500 3.000
D3 C C1C C6C 120.000 3.000
D3 C C1C C2C 120.000 3.000
D3 C6C C1C C2C 120.000 3.000
D3 C1C C6C H6C 120.000 3.000
D3 C1C C6C C5C 120.000 3.000
D3 H6C C6C C5C 120.000 3.000
D3 C6C C5C H5C 120.000 3.000
D3 C6C C5C C4C 120.000 3.000
D3 H5C C5C C4C 120.000 3.000
D3 C5C C4C H4C 120.000 3.000
D3 C5C C4C C3C 120.000 3.000
D3 H4C C4C C3C 120.000 3.000
D3 C4C C3C H3C 120.000 3.000
D3 C4C C3C C2C 120.000 3.000
D3 H3C C3C C2C 120.000 3.000
D3 C3C C2C H2C 120.000 3.000
D3 C3C C2C C1C 120.000 3.000
D3 H2C C2C C1C 120.000 3.000
D3 "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
D3 var_1 OP3 P "O5'" "C5'" -60.018 20.000 1
D3 var_2 P "O5'" "C5'" "C4'" -179.991 20.000 1
D3 var_3 "O5'" "C5'" "C4'" "C3'" 176.914 20.000 3
D3 var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
D3 var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
D3 var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
D3 var_7 "C3'" "C2'" "C1'" N1A 150.000 20.000 3
D3 var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
D3 var_9 "C2'" "C1'" N1A C5A -90.290 20.000 1
D3 CONST_1 "C1'" N1A C2A N3A 180.000 0.000 0
D3 CONST_2 "C1'" N1A C5A C4A 180.000 0.000 0
D3 CONST_3 N1A C5A C4A C1B 180.000 0.000 0
D3 CONST_4 C5A C4A N3A C2A 0.000 0.000 0
D3 CONST_5 C4A N3A C2A N1A 0.000 0.000 0
D3 var_10 C5A C4A C1B C6B -39.425 20.000 1
D3 CONST_6 C4A C1B C2B C3B 180.000 0.000 0
D3 CONST_7 C4A C1B C6B C5B 180.000 0.000 0
D3 CONST_8 C1B C6B C5B C4B 0.000 0.000 0
D3 CONST_9 C6B C5B C4B C3B 0.000 0.000 0
D3 CONST_10 C5B C4B C3B N 180.000 0.000 0
D3 CONST_11 C4B C3B C2B C1B 0.000 0.000 0
D3 var_11 C4B C3B N C -146.691 20.000 1
D3 CONST_12 C3B N C O 0.000 0.000 0
D3 var_12 N C C1C C6C -0.166 20.000 1
D3 CONST_13 C C1C C2C C3C 180.000 0.000 0
D3 CONST_14 C C1C C6C C5C 180.000 0.000 0
D3 CONST_15 C1C C6C C5C C4C 0.000 0.000 0
D3 CONST_16 C6C C5C C4C C3C 0.000 0.000 0
D3 CONST_17 C5C C4C C3C C2C 0.000 0.000 0
D3 CONST_18 C4C C3C C2C C1C 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
D3 chir_01 "C4'" "C5'" "O4'" "C3'" negativ
D3 chir_02 "C3'" "C4'" "O3'" "C2'" negativ
D3 chir_03 "C1'" "O4'" "C2'" N1A 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
D3 plan-1 N1A 0.020
D3 plan-1 "C1'" 0.020
D3 plan-1 C2A 0.020
D3 plan-1 C5A 0.020
D3 plan-1 N3A 0.020
D3 plan-1 C4A 0.020
D3 plan-1 H2A 0.020
D3 plan-1 C1B 0.020
D3 plan-1 H5A 0.020
D3 plan-2 C1B 0.020
D3 plan-2 C4A 0.020
D3 plan-2 C2B 0.020
D3 plan-2 C6B 0.020
D3 plan-2 C3B 0.020
D3 plan-2 C4B 0.020
D3 plan-2 C5B 0.020
D3 plan-2 H2B 0.020
D3 plan-2 N 0.020
D3 plan-2 H4B 0.020
D3 plan-2 H5B 0.020
D3 plan-2 H6B 0.020
D3 plan-2 HN 0.020
D3 plan-3 N 0.020
D3 plan-3 C3B 0.020
D3 plan-3 C 0.020
D3 plan-3 HN 0.020
D3 plan-4 C 0.020
D3 plan-4 N 0.020
D3 plan-4 O 0.020
D3 plan-4 C1C 0.020
D3 plan-4 HN 0.020
D3 plan-5 C1C 0.020
D3 plan-5 C 0.020
D3 plan-5 C2C 0.020
D3 plan-5 C6C 0.020
D3 plan-5 C3C 0.020
D3 plan-5 C4C 0.020
D3 plan-5 C5C 0.020
D3 plan-5 H2C 0.020
D3 plan-5 H3C 0.020
D3 plan-5 H4C 0.020
D3 plan-5 H5C 0.020
D3 plan-5 H6C 0.020
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