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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
TBD TBD '2*-DEOXY-THYMIDINE-5*-ALPHA BORANO D' non-polymer 42 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TBD
#
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
TBD O4 O O 0.000 0.000 0.000 0.000
TBD C4 C CR6 0.000 0.000 0.000 0.000
TBD C5 C CR6 0.000 0.000 0.000 0.000
TBD C5A C CH3 0.000 0.000 0.000 0.000
TBD HCA3 H H 0.000 0.000 0.000 0.000
TBD HCA2 H H 0.000 0.000 0.000 0.000
TBD HCA1 H H 0.000 0.000 0.000 0.000
TBD C6 C CR16 0.000 0.000 0.000 0.000
TBD HC6 H H 0.000 0.000 0.000 0.000
TBD N3 N NR16 0.000 0.000 0.000 0.000
TBD HN3 H H 0.000 0.000 0.000 0.000
TBD C2 C CR6 0.000 0.000 0.000 0.000
TBD O2 O O 0.000 0.000 0.000 0.000
TBD N1 N NR6 0.000 0.000 0.000 0.000
TBD "C1'" C CH1 0.000 0.000 0.000 0.000
TBD "H1'C" H H 0.000 0.000 0.000 0.000
TBD "O4'" O O2 0.000 0.000 0.000 0.000
TBD "C2'" C CH2 0.000 0.000 0.000 0.000
TBD "H2'1" H H 0.000 0.000 0.000 0.000
TBD "H2'2" H H 0.000 0.000 0.000 0.000
TBD "C3'" C CH1 0.000 0.000 0.000 0.000
TBD "H3'C" H H 0.000 0.000 0.000 0.000
TBD "O3'" O OH1 0.000 0.000 0.000 0.000
TBD "H3'O" H H 0.000 0.000 0.000 0.000
TBD "C4'" C CH1 0.000 0.000 0.000 0.000
TBD "H4'C" H H 0.000 0.000 0.000 0.000
TBD "C5'" C CH2 0.000 0.000 0.000 0.000
TBD "H5'1" H H 0.000 0.000 0.000 0.000
TBD "H5'2" H H 0.000 0.000 0.000 0.000
TBD "O5'" O O2 0.000 0.000 0.000 0.000
TBD PA P P 1.000 0.000 0.000 0.000
TBD O2A O OH1 0.000 0.000 0.000 0.000
TBD H2AO H H 0.000 0.000 0.000 0.000
TBD B1A B B -1.000 0.000 0.000 0.000
TBD H3B H H 0.000 0.000 0.000 0.000
TBD H2B H H 0.000 0.000 0.000 0.000
TBD H1B H H 0.000 0.000 0.000 0.000
TBD O3A O O2 0.000 0.000 0.000 0.000
TBD PB P P 0.000 0.000 0.000 0.000
TBD O1B O OP -0.666 0.000 0.000 0.000
TBD O2B O OP -0.666 0.000 0.000 0.000
TBD O3B O OP -0.666 0.000 0.000 0.000
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
TBD O4 n/a C4 START
TBD C4 O4 N3 .
TBD C5 C4 C6 .
TBD C5A C5 HCA1 .
TBD HCA3 C5A . .
TBD HCA2 C5A . .
TBD HCA1 C5A . .
TBD C6 C5 HC6 .
TBD HC6 C6 . .
TBD N3 C4 C2 .
TBD HN3 N3 . .
TBD C2 N3 N1 .
TBD O2 C2 . .
TBD N1 C2 "C1'" .
TBD "C1'" N1 "C2'" .
TBD "H1'C" "C1'" . .
TBD "O4'" "C1'" . .
TBD "C2'" "C1'" "C3'" .
TBD "H2'1" "C2'" . .
TBD "H2'2" "C2'" . .
TBD "C3'" "C2'" "C4'" .
TBD "H3'C" "C3'" . .
TBD "O3'" "C3'" "H3'O" .
TBD "H3'O" "O3'" . .
TBD "C4'" "C3'" "C5'" .
TBD "H4'C" "C4'" . .
TBD "C5'" "C4'" "O5'" .
TBD "H5'1" "C5'" . .
TBD "H5'2" "C5'" . .
TBD "O5'" "C5'" PA .
TBD PA "O5'" O3A .
TBD O2A PA H2AO .
TBD H2AO O2A . .
TBD B1A PA H1B .
TBD H3B B1A . .
TBD H2B B1A . .
TBD H1B B1A . .
TBD O3A PA PB .
TBD PB O3A O3B .
TBD O1B PB . .
TBD O2B PB . .
TBD O3B PB . END
TBD "C4'" "O4'" . ADD
TBD N1 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
TBD O1B PB deloc 1.510 0.020
TBD O2B PB deloc 1.510 0.020
TBD O3B PB deloc 1.510 0.020
TBD PB O3A single 1.610 0.020
TBD O3A PA single 1.610 0.020
TBD B1A PA single 1.850 0.020
TBD O2A PA single 1.610 0.020
TBD PA "O5'" single 1.610 0.020
TBD H1B B1A single 1.133 0.020
TBD H2B B1A single 1.133 0.020
TBD H3B B1A single 1.133 0.020
TBD H2AO O2A single 0.967 0.020
TBD "O5'" "C5'" single 1.426 0.020
TBD "C5'" "C4'" single 1.524 0.020
TBD "H5'1" "C5'" single 1.092 0.020
TBD "H5'2" "C5'" single 1.092 0.020
TBD "C4'" "O4'" single 1.426 0.020
TBD "C4'" "C3'" single 1.524 0.020
TBD "H4'C" "C4'" single 1.099 0.020
TBD "O4'" "C1'" single 1.426 0.020
TBD "C1'" N1 single 1.465 0.020
TBD "C2'" "C1'" single 1.524 0.020
TBD "H1'C" "C1'" single 1.099 0.020
TBD N1 C6 single 1.337 0.020
TBD N1 C2 single 1.410 0.020
TBD C6 C5 double 1.390 0.020
TBD HC6 C6 single 1.083 0.020
TBD O2 C2 double 1.250 0.020
TBD C2 N3 single 1.337 0.020
TBD N3 C4 single 1.337 0.020
TBD HN3 N3 single 1.040 0.020
TBD C4 O4 double 1.250 0.020
TBD C5 C4 single 1.487 0.020
TBD C5A C5 single 1.506 0.020
TBD HCA1 C5A single 1.059 0.020
TBD HCA2 C5A single 1.059 0.020
TBD HCA3 C5A single 1.059 0.020
TBD "C3'" "C2'" single 1.524 0.020
TBD "H2'1" "C2'" single 1.092 0.020
TBD "H2'2" "C2'" single 1.092 0.020
TBD "O3'" "C3'" single 1.432 0.020
TBD "H3'C" "C3'" single 1.099 0.020
TBD "H3'O" "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
TBD O4 C4 C5 120.000 3.000
TBD O4 C4 N3 120.000 3.000
TBD C5 C4 N3 120.000 3.000
TBD C4 C5 C5A 120.000 3.000
TBD C4 C5 C6 120.000 3.000
TBD C5A C5 C6 120.000 3.000
TBD C5 C5A HCA3 109.470 3.000
TBD C5 C5A HCA2 109.470 3.000
TBD C5 C5A HCA1 109.470 3.000
TBD HCA3 C5A HCA2 109.470 3.000
TBD HCA3 C5A HCA1 109.470 3.000
TBD HCA2 C5A HCA1 109.470 3.000
TBD C5 C6 HC6 120.000 3.000
TBD C5 C6 N1 120.000 3.000
TBD HC6 C6 N1 120.000 3.000
TBD C4 N3 HN3 120.000 3.000
TBD C4 N3 C2 120.000 3.000
TBD HN3 N3 C2 120.000 3.000
TBD N3 C2 O2 120.000 3.000
TBD N3 C2 N1 120.000 3.000
TBD O2 C2 N1 120.000 3.000
TBD C2 N1 "C1'" 120.000 3.000
TBD C2 N1 C6 120.000 3.000
TBD "C1'" N1 C6 120.000 3.000
TBD N1 "C1'" "H1'C" 109.470 3.000
TBD N1 "C1'" "O4'" 109.470 3.000
TBD N1 "C1'" "C2'" 109.470 3.000
TBD "H1'C" "C1'" "O4'" 109.470 3.000
TBD "H1'C" "C1'" "C2'" 108.340 3.000
TBD "O4'" "C1'" "C2'" 109.470 3.000
TBD "C1'" "O4'" "C4'" 111.800 3.000
TBD "C1'" "C2'" "H2'1" 109.470 3.000
TBD "C1'" "C2'" "H2'2" 109.470 3.000
TBD "C1'" "C2'" "C3'" 111.000 3.000
TBD "H2'1" "C2'" "H2'2" 107.900 3.000
TBD "H2'1" "C2'" "C3'" 109.470 3.000
TBD "H2'2" "C2'" "C3'" 109.470 3.000
TBD "C2'" "C3'" "H3'C" 108.340 3.000
TBD "C2'" "C3'" "O3'" 109.470 3.000
TBD "C2'" "C3'" "C4'" 111.000 3.000
TBD "H3'C" "C3'" "O3'" 109.470 3.000
TBD "H3'C" "C3'" "C4'" 108.340 3.000
TBD "O3'" "C3'" "C4'" 109.470 3.000
TBD "C3'" "O3'" "H3'O" 109.470 3.000
TBD "C3'" "C4'" "H4'C" 108.340 3.000
TBD "C3'" "C4'" "C5'" 111.000 3.000
TBD "C3'" "C4'" "O4'" 109.470 3.000
TBD "H4'C" "C4'" "C5'" 108.340 3.000
TBD "H4'C" "C4'" "O4'" 109.470 3.000
TBD "C5'" "C4'" "O4'" 109.470 3.000
TBD "C4'" "C5'" "H5'1" 109.470 3.000
TBD "C4'" "C5'" "H5'2" 109.470 3.000
TBD "C4'" "C5'" "O5'" 109.470 3.000
TBD "H5'1" "C5'" "H5'2" 107.900 3.000
TBD "H5'1" "C5'" "O5'" 109.470 3.000
TBD "H5'2" "C5'" "O5'" 109.470 3.000
TBD "C5'" "O5'" PA 120.500 3.000
TBD "O5'" PA O2A 109.500 3.000
TBD "O5'" PA B1A 109.500 3.000
TBD "O5'" PA O3A 102.600 3.000
TBD O2A PA B1A 109.500 3.000
TBD O2A PA O3A 109.500 3.000
TBD B1A PA O3A 109.500 3.000
TBD PA O2A H2AO 120.000 3.000
TBD PA B1A H3B 120.000 3.000
TBD PA B1A H2B 120.000 3.000
TBD PA B1A H1B 120.000 3.000
TBD H3B B1A H2B 120.000 3.000
TBD H3B B1A H1B 120.000 3.000
TBD H2B B1A H1B 120.000 3.000
TBD PA O3A PB 120.500 3.000
TBD O3A PB O1B 108.200 3.000
TBD O3A PB O2B 108.200 3.000
TBD O3A PB O3B 108.200 3.000
TBD O1B PB O2B 119.900 3.000
TBD O1B PB O3B 119.900 3.000
TBD O2B PB O3B 119.900 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
TBD CONST_1 O4 C4 C5 C6 0.000 0.000 0
TBD var_1 C4 C5 C5A HCA1 0.000 20.000 1
TBD CONST_2 C4 C5 C6 N1 0.000 0.000 0
TBD CONST_3 O4 C4 N3 C2 0.000 0.000 0
TBD CONST_4 C4 N3 C2 N1 0.000 0.000 0
TBD CONST_5 N3 C2 N1 "C1'" 0.000 0.000 0
TBD CONST_6 C2 N1 C6 C5 0.000 0.000 0
TBD var_2 C2 N1 "C1'" "C2'" 0.000 20.000 1
TBD var_3 N1 "C1'" "O4'" "C4'" 0.000 20.000 1
TBD var_4 N1 "C1'" "C2'" "C3'" 0.000 20.000 3
TBD var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
TBD var_6 "C2'" "C3'" "O3'" "H3'O" 0.000 20.000 1
TBD var_7 "C2'" "C3'" "C4'" "C5'" 0.000 20.000 3
TBD var_8 "C3'" "C4'" "O4'" "C1'" 0.000 20.000 1
TBD var_9 "C3'" "C4'" "C5'" "O5'" 0.000 20.000 3
TBD var_10 "C4'" "C5'" "O5'" PA 0.000 20.000 1
TBD var_11 "C5'" "O5'" PA O3A 0.000 20.000 1
TBD var_12 "O5'" PA O2A H2AO 0.000 20.000 1
TBD var_13 "O5'" PA B1A H1B 0.000 20.000 1
TBD var_14 "O5'" PA O3A PB 0.000 20.000 1
TBD var_15 PA O3A PB O3B 0.000 20.000 1
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
TBD chir_01 "C4'" "C5'" "O4'" "C3'" positiv
TBD chir_02 "C1'" "O4'" N1 "C2'" positiv
TBD 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
TBD plan-1 N1 0.020
TBD plan-1 "C1'" 0.020
TBD plan-1 C6 0.020
TBD plan-1 C2 0.020
TBD plan-1 N3 0.020
TBD plan-1 C4 0.020
TBD plan-1 C5 0.020
TBD plan-1 HC6 0.020
TBD plan-1 O2 0.020
TBD plan-1 HN3 0.020
TBD plan-1 O4 0.020
TBD plan-1 C5A 0.020
# ------------------------------------------------------
|
