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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
CKB CKB '1-beta-D-glucopyranosyl-5-methylpyri' non-polymer 36 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CKB
#
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
CKB O4 O O 0.000 0.000 0.000 0.000
CKB C4 C CR6 0.000 -1.207 0.041 0.159
CKB N3 N NR16 0.000 -2.036 -0.078 -0.896
CKB HN3 H H 0.000 -1.644 -0.205 -1.851
CKB C2 C CR6 0.000 -3.370 -0.033 -0.719
CKB O2 O O 0.000 -4.106 -0.148 -1.680
CKB C5 C CR6 0.000 -1.751 0.212 1.455
CKB C7 C CH3 0.000 -0.846 0.347 2.653
CKB H7B H H 0.000 -1.018 1.280 3.123
CKB H7A H H 0.000 -1.047 -0.436 3.337
CKB H7 H H 0.000 0.164 0.291 2.340
CKB C6 C CR16 0.000 -3.092 0.255 1.604
CKB H6 H H 0.000 -3.526 0.387 2.588
CKB N1 N NR6 0.000 -3.900 0.130 0.506
CKB "C1'" C CH1 0.000 -5.355 0.175 0.668
CKB "H1'" H H 0.000 -5.604 0.222 1.738
CKB "O5'" O O2 0.000 -5.935 -0.999 0.095
CKB "C5'" C CH1 0.000 -7.357 -1.070 0.221
CKB "H5'" H H 0.000 -7.632 -1.039 1.284
CKB "C6'" C CH2 0.000 -7.860 -2.374 -0.399
CKB "H6'" H H 0.000 -7.512 -2.444 -1.431
CKB "H6'A" H H 0.000 -8.952 -2.386 -0.383
CKB "O6'" O OH1 0.000 -7.360 -3.483 0.351
CKB "HO6'" H H 0.000 -7.679 -4.307 -0.041
CKB "C4'" C CH1 0.000 -7.991 0.119 -0.505
CKB "H4'" H H 0.000 -7.750 0.067 -1.576
CKB "O4'" O OH1 0.000 -9.409 0.083 -0.332
CKB "HO4'" H H 0.000 -9.808 0.837 -0.787
CKB "C3'" C CH1 0.000 -7.436 1.421 0.081
CKB "H3'" H H 0.000 -7.720 1.499 1.140
CKB "O3'" O OH1 0.000 -7.967 2.534 -0.640
CKB "HO3'" H H 0.000 -8.931 2.537 -0.562
CKB "C2'" C CH1 0.000 -5.910 1.414 -0.041
CKB "H2'" H H 0.000 -5.626 1.388 -1.102
CKB "O2'" O OH1 0.000 -5.376 2.591 0.569
CKB "HO2'" H H 0.000 -5.726 3.372 0.121
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
CKB O4 n/a C4 START
CKB C4 O4 C5 .
CKB N3 C4 C2 .
CKB HN3 N3 . .
CKB C2 N3 O2 .
CKB O2 C2 . .
CKB C5 C4 C6 .
CKB C7 C5 H7 .
CKB H7B C7 . .
CKB H7A C7 . .
CKB H7 C7 . .
CKB C6 C5 N1 .
CKB H6 C6 . .
CKB N1 C6 "C1'" .
CKB "C1'" N1 "O5'" .
CKB "H1'" "C1'" . .
CKB "O5'" "C1'" "C5'" .
CKB "C5'" "O5'" "C4'" .
CKB "H5'" "C5'" . .
CKB "C6'" "C5'" "O6'" .
CKB "H6'" "C6'" . .
CKB "H6'A" "C6'" . .
CKB "O6'" "C6'" "HO6'" .
CKB "HO6'" "O6'" . .
CKB "C4'" "C5'" "C3'" .
CKB "H4'" "C4'" . .
CKB "O4'" "C4'" "HO4'" .
CKB "HO4'" "O4'" . .
CKB "C3'" "C4'" "C2'" .
CKB "H3'" "C3'" . .
CKB "O3'" "C3'" "HO3'" .
CKB "HO3'" "O3'" . .
CKB "C2'" "C3'" "O2'" .
CKB "H2'" "C2'" . .
CKB "O2'" "C2'" "HO2'" .
CKB "HO2'" "O2'" . END
CKB C2 N1 . ADD
CKB "C1'" "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
CKB C2 N1 single 1.410 0.020
CKB C2 N3 single 1.337 0.020
CKB O2 C2 double 1.250 0.020
CKB C5 C4 single 1.487 0.020
CKB N3 C4 single 1.337 0.020
CKB C4 O4 double 1.250 0.020
CKB C6 C5 double 1.390 0.020
CKB C7 C5 single 1.506 0.020
CKB N1 C6 single 1.337 0.020
CKB "C1'" N1 single 1.465 0.020
CKB "C1'" "C2'" single 1.524 0.020
CKB "O5'" "C1'" single 1.426 0.020
CKB "C2'" "C3'" single 1.524 0.020
CKB "O2'" "C2'" single 1.432 0.020
CKB "C3'" "C4'" single 1.524 0.020
CKB "O3'" "C3'" single 1.432 0.020
CKB "C4'" "C5'" single 1.524 0.020
CKB "O4'" "C4'" single 1.432 0.020
CKB "C6'" "C5'" single 1.524 0.020
CKB "C5'" "O5'" single 1.426 0.020
CKB "O6'" "C6'" single 1.432 0.020
CKB H6 C6 single 1.083 0.020
CKB H7 C7 single 1.059 0.020
CKB H7A C7 single 1.059 0.020
CKB H7B C7 single 1.059 0.020
CKB HN3 N3 single 1.040 0.020
CKB "H1'" "C1'" single 1.099 0.020
CKB "H2'" "C2'" single 1.099 0.020
CKB "H3'" "C3'" single 1.099 0.020
CKB "H4'" "C4'" single 1.099 0.020
CKB "H5'" "C5'" single 1.099 0.020
CKB "H6'" "C6'" single 1.092 0.020
CKB "H6'A" "C6'" single 1.092 0.020
CKB "HO6'" "O6'" single 0.967 0.020
CKB "HO2'" "O2'" single 0.967 0.020
CKB "HO3'" "O3'" single 0.967 0.020
CKB "HO4'" "O4'" 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
CKB O4 C4 N3 120.000 3.000
CKB O4 C4 C5 120.000 3.000
CKB N3 C4 C5 120.000 3.000
CKB C4 N3 HN3 120.000 3.000
CKB C4 N3 C2 120.000 3.000
CKB HN3 N3 C2 120.000 3.000
CKB N3 C2 O2 120.000 3.000
CKB N3 C2 N1 120.000 3.000
CKB O2 C2 N1 120.000 3.000
CKB C4 C5 C7 120.000 3.000
CKB C4 C5 C6 120.000 3.000
CKB C7 C5 C6 120.000 3.000
CKB C5 C7 H7B 109.470 3.000
CKB C5 C7 H7A 109.470 3.000
CKB C5 C7 H7 109.470 3.000
CKB H7B C7 H7A 109.470 3.000
CKB H7B C7 H7 109.470 3.000
CKB H7A C7 H7 109.470 3.000
CKB C5 C6 H6 120.000 3.000
CKB C5 C6 N1 120.000 3.000
CKB H6 C6 N1 120.000 3.000
CKB C6 N1 "C1'" 120.000 3.000
CKB C6 N1 C2 120.000 3.000
CKB "C1'" N1 C2 120.000 3.000
CKB N1 "C1'" "H1'" 109.470 3.000
CKB N1 "C1'" "O5'" 109.470 3.000
CKB N1 "C1'" "C2'" 109.470 3.000
CKB "H1'" "C1'" "O5'" 109.470 3.000
CKB "H1'" "C1'" "C2'" 108.340 3.000
CKB "O5'" "C1'" "C2'" 109.470 3.000
CKB "C1'" "O5'" "C5'" 111.800 3.000
CKB "O5'" "C5'" "H5'" 109.470 3.000
CKB "O5'" "C5'" "C6'" 109.470 3.000
CKB "O5'" "C5'" "C4'" 109.470 3.000
CKB "H5'" "C5'" "C6'" 108.340 3.000
CKB "H5'" "C5'" "C4'" 108.340 3.000
CKB "C6'" "C5'" "C4'" 111.000 3.000
CKB "C5'" "C6'" "H6'" 109.470 3.000
CKB "C5'" "C6'" "H6'A" 109.470 3.000
CKB "C5'" "C6'" "O6'" 109.470 3.000
CKB "H6'" "C6'" "H6'A" 107.900 3.000
CKB "H6'" "C6'" "O6'" 109.470 3.000
CKB "H6'A" "C6'" "O6'" 109.470 3.000
CKB "C6'" "O6'" "HO6'" 109.470 3.000
CKB "C5'" "C4'" "H4'" 108.340 3.000
CKB "C5'" "C4'" "O4'" 109.470 3.000
CKB "C5'" "C4'" "C3'" 111.000 3.000
CKB "H4'" "C4'" "O4'" 109.470 3.000
CKB "H4'" "C4'" "C3'" 108.340 3.000
CKB "O4'" "C4'" "C3'" 109.470 3.000
CKB "C4'" "O4'" "HO4'" 109.470 3.000
CKB "C4'" "C3'" "H3'" 108.340 3.000
CKB "C4'" "C3'" "O3'" 109.470 3.000
CKB "C4'" "C3'" "C2'" 111.000 3.000
CKB "H3'" "C3'" "O3'" 109.470 3.000
CKB "H3'" "C3'" "C2'" 108.340 3.000
CKB "O3'" "C3'" "C2'" 109.470 3.000
CKB "C3'" "O3'" "HO3'" 109.470 3.000
CKB "C3'" "C2'" "H2'" 108.340 3.000
CKB "C3'" "C2'" "O2'" 109.470 3.000
CKB "C3'" "C2'" "C1'" 111.000 3.000
CKB "H2'" "C2'" "O2'" 109.470 3.000
CKB "H2'" "C2'" "C1'" 108.340 3.000
CKB "O2'" "C2'" "C1'" 109.470 3.000
CKB "C2'" "O2'" "HO2'" 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
CKB CONST_1 O4 C4 N3 C2 180.000 0.000 0
CKB CONST_2 C4 N3 C2 O2 180.000 0.000 0
CKB CONST_3 N3 C2 N1 C6 0.000 0.000 0
CKB CONST_4 O4 C4 C5 C6 180.000 0.000 0
CKB var_1 C4 C5 C7 H7 0.028 20.000 1
CKB CONST_5 C4 C5 C6 N1 0.000 0.000 0
CKB CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
CKB var_2 C6 N1 "C1'" "O5'" -125.085 20.000 1
CKB var_3 N1 "C1'" "C2'" "C3'" 180.000 20.000 3
CKB var_4 N1 "C1'" "O5'" "C5'" 180.000 20.000 1
CKB var_5 "C1'" "O5'" "C5'" "C4'" 60.000 20.000 1
CKB var_6 "O5'" "C5'" "C6'" "O6'" 65.000 20.000 3
CKB var_7 "C5'" "C6'" "O6'" "HO6'" 179.957 20.000 1
CKB var_8 "O5'" "C5'" "C4'" "C3'" -60.000 20.000 3
CKB var_9 "C5'" "C4'" "O4'" "HO4'" 179.698 20.000 1
CKB var_10 "C5'" "C4'" "C3'" "C2'" 60.000 20.000 3
CKB var_11 "C4'" "C3'" "O3'" "HO3'" 60.397 20.000 1
CKB var_12 "C4'" "C3'" "C2'" "O2'" 180.000 20.000 3
CKB var_13 "C3'" "C2'" "O2'" "HO2'" -60.355 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
CKB chir_01 "C1'" N1 "C2'" "O5'" negativ
CKB chir_02 "C2'" "C1'" "C3'" "O2'" negativ
CKB chir_03 "C3'" "C2'" "C4'" "O3'" positiv
CKB chir_04 "C4'" "C3'" "C5'" "O4'" negativ
CKB chir_05 "C5'" "C4'" "C6'" "O5'" negativ
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
CKB plan-1 C2 0.020
CKB plan-1 N1 0.020
CKB plan-1 N3 0.020
CKB plan-1 O2 0.020
CKB plan-1 C4 0.020
CKB plan-1 C5 0.020
CKB plan-1 C6 0.020
CKB plan-1 O4 0.020
CKB plan-1 C7 0.020
CKB plan-1 H6 0.020
CKB plan-1 "C1'" 0.020
CKB plan-1 HN3 0.020
# ------------------------------------------------------
|
