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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
2BD 2BD '. ' DNA 44 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2BD
#
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
2BD OP3 O OP -0.666 0.000 0.000 0.000
2BD P P P 0.000 -1.225 0.721 0.519
2BD OP1 O OP -0.666 -1.389 0.702 2.023
2BD OP2 O OP -0.666 -1.108 2.096 -0.101
2BD "O5'" O O2 0.000 -2.431 0.028 -0.310
2BD "C5'" C CH2 0.000 -2.353 0.005 -1.725
2BD "H5'" H H 0.000 -1.459 -0.539 -2.038
2BD "H5''" H H 0.000 -2.310 1.026 -2.110
2BD "C4'" C CH1 0.000 -3.591 -0.693 -2.269
2BD "H4'" H H 0.000 -3.659 -1.708 -1.853
2BD "C3'" C CH1 0.000 -3.607 -0.758 -3.793
2BD "H3'" H H 0.000 -2.591 -0.759 -4.211
2BD "C2'" C CH2 0.000 -4.374 0.484 -4.184
2BD "H2'" H H 0.000 -4.897 0.385 -5.137
2BD "H2''" H H 0.000 -3.755 1.384 -4.201
2BD "C1'" C CH1 0.000 -5.389 0.585 -3.054
2BD "H1'" H H 0.000 -6.246 -0.060 -3.294
2BD "O4'" O O2 0.000 -4.748 0.075 -1.873
2BD N9 N NR5 0.000 -5.881 1.937 -2.809
2BD C8 C CR15 0.000 -5.291 2.875 -1.998
2BD H8 H H 0.000 -4.377 2.702 -1.442
2BD N7 N NRD5 0.000 -5.963 4.009 -1.971
2BD C4 C CR56 0.000 -7.000 2.515 -3.331
2BD C5 C CR56 0.000 -7.024 3.782 -2.800
2BD N3 N NRD6 0.000 -7.875 1.936 -4.180
2BD C2 C CR16 0.000 -8.843 2.748 -4.498
2BD H2 H H 0.000 -9.596 2.369 -5.177
2BD N1 N NR6 0.000 -9.003 4.074 -4.044
2BD CAN C CH1 0.000 -10.143 4.842 -4.515
2BD HAN H H 0.000 -10.098 5.850 -4.079
2BD CAO C CH2 0.000 -11.457 4.181 -4.101
2BD HAO1 H H 0.000 -11.511 3.177 -4.528
2BD HAO2 H H 0.000 -12.296 4.776 -4.467
2BD OAP O OH1 0.000 -11.514 4.099 -2.681
2BD HAP H H 0.000 -10.658 3.804 -2.343
2BD CAL C C1 0.000 -10.035 4.952 -6.008
2BD HAL2 H H 0.000 -10.103 4.048 -6.590
2BD CAM C C2 0.000 -9.860 6.108 -6.659
2BD HAM2 H H 0.000 -9.788 7.037 -6.112
2BD HAM1 H H 0.000 -9.789 6.123 -7.737
2BD C6 C CR6 0.000 -8.095 4.682 -3.146
2BD O6 O O 0.000 -8.173 5.821 -2.700
2BD "O3'" O OH1 0.000 -4.353 -1.899 -4.213
2BD "HO3'" H H 0.000 -4.610 -2.373 -3.408
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
2BD OP3 n/a P START
2BD P OP3 "O5'" .
2BD OP1 P . .
2BD OP2 P . .
2BD "O5'" P "C5'" .
2BD "C5'" "O5'" "C4'" .
2BD "H5'" "C5'" . .
2BD "H5''" "C5'" . .
2BD "C4'" "C5'" "C3'" .
2BD "H4'" "C4'" . .
2BD "C3'" "C4'" "O3'" .
2BD "H3'" "C3'" . .
2BD "C2'" "C3'" "C1'" .
2BD "H2'" "C2'" . .
2BD "H2''" "C2'" . .
2BD "C1'" "C2'" N9 .
2BD "H1'" "C1'" . .
2BD "O4'" "C1'" . .
2BD N9 "C1'" C4 .
2BD C8 N9 N7 .
2BD H8 C8 . .
2BD N7 C8 . .
2BD C4 N9 N3 .
2BD C5 C4 . .
2BD N3 C4 C2 .
2BD C2 N3 N1 .
2BD H2 C2 . .
2BD N1 C2 C6 .
2BD CAN N1 CAL .
2BD HAN CAN . .
2BD CAO CAN OAP .
2BD HAO1 CAO . .
2BD HAO2 CAO . .
2BD OAP CAO HAP .
2BD HAP OAP . .
2BD CAL CAN CAM .
2BD HAL2 CAL . .
2BD CAM CAL HAM1 .
2BD HAM2 CAM . .
2BD HAM1 CAM . .
2BD C6 N1 O6 .
2BD O6 C6 . .
2BD "O3'" "C3'" . END
2BD "HO3'" "O3'" . .
2BD "C4'" "O4'" . ADD
2BD C6 C5 . ADD
2BD C5 N7 . 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
2BD OP1 P deloc 1.510 0.020
2BD OP2 P deloc 1.510 0.020
2BD P OP3 deloc 1.510 0.020
2BD "O5'" P single 1.610 0.020
2BD "C5'" "O5'" single 1.426 0.020
2BD "C4'" "C5'" single 1.524 0.020
2BD "H5'" "C5'" single 1.092 0.020
2BD "H5''" "C5'" single 1.092 0.020
2BD "C4'" "O4'" single 1.426 0.020
2BD "C3'" "C4'" single 1.524 0.020
2BD "H4'" "C4'" single 1.099 0.020
2BD "O4'" "C1'" single 1.426 0.020
2BD N9 "C1'" single 1.485 0.020
2BD "C1'" "C2'" single 1.524 0.020
2BD "H1'" "C1'" single 1.099 0.020
2BD O6 C6 double 1.250 0.020
2BD C6 C5 single 1.490 0.020
2BD C6 N1 single 1.410 0.020
2BD C5 N7 single 1.350 0.020
2BD C5 C4 double 1.490 0.020
2BD N7 C8 double 1.350 0.020
2BD C8 N9 single 1.337 0.020
2BD H8 C8 single 1.083 0.020
2BD C4 N9 single 1.337 0.020
2BD N3 C4 single 1.355 0.020
2BD C2 N3 double 1.337 0.020
2BD N1 C2 single 1.337 0.020
2BD H2 C2 single 1.083 0.020
2BD CAN N1 single 1.465 0.020
2BD CAL CAN single 1.510 0.020
2BD CAO CAN single 1.524 0.020
2BD HAN CAN single 1.099 0.020
2BD CAM CAL double 1.320 0.020
2BD HAL2 CAL single 1.077 0.020
2BD HAM1 CAM single 1.077 0.020
2BD HAM2 CAM single 1.077 0.020
2BD OAP CAO single 1.432 0.020
2BD HAO1 CAO single 1.092 0.020
2BD HAO2 CAO single 1.092 0.020
2BD HAP OAP single 0.967 0.020
2BD "C2'" "C3'" single 1.524 0.020
2BD "H2'" "C2'" single 1.092 0.020
2BD "H2''" "C2'" single 1.092 0.020
2BD "O3'" "C3'" single 1.432 0.020
2BD "H3'" "C3'" single 1.099 0.020
2BD "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
2BD OP3 P OP1 119.900 3.000
2BD OP3 P OP2 119.900 3.000
2BD OP3 P "O5'" 108.200 3.000
2BD OP1 P OP2 119.900 3.000
2BD OP1 P "O5'" 108.200 3.000
2BD OP2 P "O5'" 108.200 3.000
2BD P "O5'" "C5'" 120.500 3.000
2BD "O5'" "C5'" "H5'" 109.470 3.000
2BD "O5'" "C5'" "H5''" 109.470 3.000
2BD "O5'" "C5'" "C4'" 109.470 3.000
2BD "H5'" "C5'" "H5''" 107.900 3.000
2BD "H5'" "C5'" "C4'" 109.470 3.000
2BD "H5''" "C5'" "C4'" 109.470 3.000
2BD "C5'" "C4'" "H4'" 108.340 3.000
2BD "C5'" "C4'" "C3'" 111.000 3.000
2BD "C5'" "C4'" "O4'" 109.470 3.000
2BD "H4'" "C4'" "C3'" 108.340 3.000
2BD "H4'" "C4'" "O4'" 109.470 3.000
2BD "C3'" "C4'" "O4'" 109.470 3.000
2BD "C4'" "C3'" "H3'" 108.340 3.000
2BD "C4'" "C3'" "C2'" 111.000 3.000
2BD "C4'" "C3'" "O3'" 109.470 3.000
2BD "H3'" "C3'" "C2'" 108.340 3.000
2BD "H3'" "C3'" "O3'" 109.470 3.000
2BD "C2'" "C3'" "O3'" 109.470 3.000
2BD "C3'" "C2'" "H2'" 109.470 3.000
2BD "C3'" "C2'" "H2''" 109.470 3.000
2BD "C3'" "C2'" "C1'" 111.000 3.000
2BD "H2'" "C2'" "H2''" 107.900 3.000
2BD "H2'" "C2'" "C1'" 109.470 3.000
2BD "H2''" "C2'" "C1'" 109.470 3.000
2BD "C2'" "C1'" "H1'" 108.340 3.000
2BD "C2'" "C1'" "O4'" 109.470 3.000
2BD "C2'" "C1'" N9 109.470 3.000
2BD "H1'" "C1'" "O4'" 109.470 3.000
2BD "H1'" "C1'" N9 109.470 3.000
2BD "O4'" "C1'" N9 109.470 3.000
2BD "C1'" "O4'" "C4'" 111.800 3.000
2BD "C1'" N9 C8 126.000 3.000
2BD "C1'" N9 C4 126.000 3.000
2BD C8 N9 C4 108.000 3.000
2BD N9 C8 H8 126.000 3.000
2BD N9 C8 N7 108.000 3.000
2BD H8 C8 N7 126.000 3.000
2BD C8 N7 C5 108.000 3.000
2BD N9 C4 C5 108.000 3.000
2BD N9 C4 N3 132.000 3.000
2BD C5 C4 N3 120.000 3.000
2BD C4 C5 C6 120.000 3.000
2BD C4 C5 N7 108.000 3.000
2BD C6 C5 N7 132.000 3.000
2BD C4 N3 C2 120.000 3.000
2BD N3 C2 H2 120.000 3.000
2BD N3 C2 N1 120.000 3.000
2BD H2 C2 N1 120.000 3.000
2BD C2 N1 CAN 120.000 3.000
2BD C2 N1 C6 120.000 3.000
2BD CAN N1 C6 120.000 3.000
2BD N1 CAN HAN 109.470 3.000
2BD N1 CAN CAO 109.470 3.000
2BD N1 CAN CAL 109.500 3.000
2BD HAN CAN CAO 108.340 3.000
2BD HAN CAN CAL 108.810 3.000
2BD CAO CAN CAL 109.470 3.000
2BD CAN CAO HAO1 109.470 3.000
2BD CAN CAO HAO2 109.470 3.000
2BD CAN CAO OAP 109.470 3.000
2BD HAO1 CAO HAO2 107.900 3.000
2BD HAO1 CAO OAP 109.470 3.000
2BD HAO2 CAO OAP 109.470 3.000
2BD CAO OAP HAP 109.470 3.000
2BD CAN CAL HAL2 120.000 3.000
2BD CAN CAL CAM 120.000 3.000
2BD HAL2 CAL CAM 120.000 3.000
2BD CAL CAM HAM2 120.000 3.000
2BD CAL CAM HAM1 120.000 3.000
2BD HAM2 CAM HAM1 120.000 3.000
2BD N1 C6 O6 120.000 3.000
2BD N1 C6 C5 120.000 3.000
2BD O6 C6 C5 120.000 3.000
2BD "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
2BD var_1 OP3 P "O5'" "C5'" -54.182 20.000 1
2BD var_2 P "O5'" "C5'" "C4'" 179.971 20.000 1
2BD var_3 "O5'" "C5'" "C4'" "C3'" 179.520 20.000 3
2BD var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
2BD var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
2BD var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
2BD var_7 "C3'" "C2'" "C1'" N9 150.000 20.000 3
2BD var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
2BD var_9 "C2'" "C1'" N9 C4 93.453 20.000 1
2BD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
2BD CONST_2 N9 C8 N7 C5 0.000 0.000 0
2BD CONST_3 "C1'" N9 C4 N3 0.000 0.000 0
2BD CONST_4 N9 C4 C5 C6 180.000 0.000 0
2BD CONST_5 C4 C5 N7 C8 0.000 0.000 0
2BD CONST_6 N9 C4 N3 C2 180.000 0.000 0
2BD CONST_7 C4 N3 C2 N1 0.000 0.000 0
2BD CONST_8 N3 C2 N1 C6 0.000 0.000 0
2BD var_10 C2 N1 CAN CAL -60.854 20.000 1
2BD var_11 N1 CAN CAO OAP 60.016 20.000 3
2BD var_12 CAN CAO OAP HAP -43.683 20.000 1
2BD var_13 N1 CAN CAL CAM -115.592 20.000 1
2BD CONST_9 CAN CAL CAM HAM1 179.941 0.000 0
2BD CONST_10 C2 N1 C6 O6 180.000 0.000 0
2BD CONST_11 N1 C6 C5 C4 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
2BD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2BD chir_02 "C1'" "O4'" N9 "C2'" negativ
2BD chir_03 CAN N1 CAL CAO negativ
2BD chir_04 "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
2BD plan-1 C6 0.020
2BD plan-1 O6 0.020
2BD plan-1 C5 0.020
2BD plan-1 N1 0.020
2BD plan-1 N3 0.020
2BD plan-1 C2 0.020
2BD plan-1 N7 0.020
2BD plan-1 C4 0.020
2BD plan-1 C8 0.020
2BD plan-1 N9 0.020
2BD plan-1 H8 0.020
2BD plan-1 "C1'" 0.020
2BD plan-1 H2 0.020
2BD plan-1 CAN 0.020
2BD plan-2 CAL 0.020
2BD plan-2 CAN 0.020
2BD plan-2 CAM 0.020
2BD plan-2 HAL2 0.020
2BD plan-2 HAM1 0.020
2BD plan-2 HAM2 0.020
# ------------------------------------------------------
|
