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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
KDA KDA '(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID' non-polymer 36 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_KDA
#
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
KDA O1B O OC -0.500 0.000 0.000 0.000
KDA C1 C C 0.000 -0.742 0.854 -0.535
KDA O1A O OC -0.500 -0.255 1.711 -1.305
KDA C2 C CT 0.000 -2.221 0.851 -0.250
KDA O2 O O2 0.000 -2.593 2.095 0.343
KDA C9 C CH2 0.000 -1.840 2.218 1.551
KDA H91 H H 0.000 -0.773 2.202 1.318
KDA H92 H H 0.000 -2.079 1.384 2.215
KDA C10 C C1 0.000 -2.188 3.518 2.230
KDA H10 H H 0.000 -2.019 4.452 1.722
KDA C11 C C2 0.000 -2.696 3.512 3.437
KDA H112 H H 0.000 -2.865 2.577 3.940
KDA H111 H H 0.000 -2.943 4.441 3.917
KDA O6 O O2 0.000 -2.529 -0.213 0.649
KDA C6 C CH1 0.000 -3.895 -0.074 1.031
KDA H6 H H 0.000 -4.069 0.947 1.400
KDA C7 C CH1 0.000 -4.218 -1.076 2.141
KDA H7 H H 0.000 -4.046 -2.098 1.773
KDA C8 C CH2 0.000 -3.317 -0.810 3.347
KDA H81 H H 0.000 -3.488 0.205 3.711
KDA H82 H H 0.000 -2.271 -0.918 3.051
KDA O8 O OH1 0.000 -3.619 -1.746 4.384
KDA HO8 H H 0.000 -3.048 -1.577 5.146
KDA O7 O OH1 0.000 -5.586 -0.935 2.528
KDA HO7 H H 0.000 -5.737 -0.036 2.851
KDA C5 C CH1 0.000 -4.799 -0.340 -0.174
KDA H5 H H 0.000 -5.851 -0.251 0.130
KDA O5 O OH1 0.000 -4.557 -1.654 -0.678
KDA HO5 H H 0.000 -5.127 -1.815 -1.442
KDA C4 C CH1 0.000 -4.493 0.692 -1.265
KDA H4 H H 0.000 -4.780 1.694 -0.916
KDA O4 O OH1 0.000 -5.221 0.369 -2.452
KDA HO4 H H 0.000 -5.016 1.016 -3.141
KDA C3 C CH2 0.000 -2.990 0.660 -1.559
KDA H32 H H 0.000 -2.734 1.464 -2.253
KDA H31 H H 0.000 -2.722 -0.301 -2.003
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
KDA O1B n/a C1 START
KDA C1 O1B C2 .
KDA O1A C1 . .
KDA C2 C1 O6 .
KDA O2 C2 C9 .
KDA C9 O2 C10 .
KDA H91 C9 . .
KDA H92 C9 . .
KDA C10 C9 C11 .
KDA H10 C10 . .
KDA C11 C10 H111 .
KDA H112 C11 . .
KDA H111 C11 . .
KDA O6 C2 C6 .
KDA C6 O6 C5 .
KDA H6 C6 . .
KDA C7 C6 O7 .
KDA H7 C7 . .
KDA C8 C7 O8 .
KDA H81 C8 . .
KDA H82 C8 . .
KDA O8 C8 HO8 .
KDA HO8 O8 . .
KDA O7 C7 HO7 .
KDA HO7 O7 . .
KDA C5 C6 C4 .
KDA H5 C5 . .
KDA O5 C5 HO5 .
KDA HO5 O5 . .
KDA C4 C5 C3 .
KDA H4 C4 . .
KDA O4 C4 HO4 .
KDA HO4 O4 . .
KDA C3 C4 H31 .
KDA H32 C3 . .
KDA H31 C3 . END
KDA C2 C3 . 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
KDA O1A C1 deloc 1.250 0.020
KDA C1 O1B deloc 1.250 0.020
KDA C2 C1 single 1.507 0.020
KDA C2 C3 single 1.524 0.020
KDA O6 C2 single 1.426 0.020
KDA O2 C2 single 1.426 0.020
KDA C3 C4 single 1.524 0.020
KDA H31 C3 single 1.092 0.020
KDA H32 C3 single 1.092 0.020
KDA O4 C4 single 1.432 0.020
KDA C4 C5 single 1.524 0.020
KDA H4 C4 single 1.099 0.020
KDA HO4 O4 single 0.967 0.020
KDA O5 C5 single 1.432 0.020
KDA C5 C6 single 1.524 0.020
KDA H5 C5 single 1.099 0.020
KDA HO5 O5 single 0.967 0.020
KDA C6 O6 single 1.426 0.020
KDA C7 C6 single 1.524 0.020
KDA H6 C6 single 1.099 0.020
KDA O7 C7 single 1.432 0.020
KDA C8 C7 single 1.524 0.020
KDA H7 C7 single 1.099 0.020
KDA HO7 O7 single 0.967 0.020
KDA O8 C8 single 1.432 0.020
KDA H81 C8 single 1.092 0.020
KDA H82 C8 single 1.092 0.020
KDA HO8 O8 single 0.967 0.020
KDA C9 O2 single 1.426 0.020
KDA C10 C9 single 1.510 0.020
KDA H91 C9 single 1.092 0.020
KDA H92 C9 single 1.092 0.020
KDA C11 C10 double 1.320 0.020
KDA H10 C10 single 1.077 0.020
KDA H111 C11 single 1.077 0.020
KDA H112 C11 single 1.077 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
KDA O1B C1 O1A 123.000 3.000
KDA O1B C1 C2 118.500 3.000
KDA O1A C1 C2 118.500 3.000
KDA C1 C2 O2 109.470 3.000
KDA C1 C2 O6 109.470 3.000
KDA C1 C2 C3 109.470 3.000
KDA O2 C2 O6 109.500 3.000
KDA O2 C2 C3 109.470 3.000
KDA O6 C2 C3 109.470 3.000
KDA C2 O2 C9 111.800 3.000
KDA O2 C9 H91 109.470 3.000
KDA O2 C9 H92 109.470 3.000
KDA O2 C9 C10 109.500 3.000
KDA H91 C9 H92 107.900 3.000
KDA H91 C9 C10 109.470 3.000
KDA H92 C9 C10 109.470 3.000
KDA C9 C10 H10 120.000 3.000
KDA C9 C10 C11 120.000 3.000
KDA H10 C10 C11 120.000 3.000
KDA C10 C11 H112 120.000 3.000
KDA C10 C11 H111 120.000 3.000
KDA H112 C11 H111 120.000 3.000
KDA C2 O6 C6 111.800 3.000
KDA O6 C6 H6 109.470 3.000
KDA O6 C6 C7 109.470 3.000
KDA O6 C6 C5 109.470 3.000
KDA H6 C6 C7 108.340 3.000
KDA H6 C6 C5 108.340 3.000
KDA C7 C6 C5 111.000 3.000
KDA C6 C7 H7 108.340 3.000
KDA C6 C7 C8 111.000 3.000
KDA C6 C7 O7 109.470 3.000
KDA H7 C7 C8 108.340 3.000
KDA H7 C7 O7 109.470 3.000
KDA C8 C7 O7 109.470 3.000
KDA C7 C8 H81 109.470 3.000
KDA C7 C8 H82 109.470 3.000
KDA C7 C8 O8 109.470 3.000
KDA H81 C8 H82 107.900 3.000
KDA H81 C8 O8 109.470 3.000
KDA H82 C8 O8 109.470 3.000
KDA C8 O8 HO8 109.470 3.000
KDA C7 O7 HO7 109.470 3.000
KDA C6 C5 H5 108.340 3.000
KDA C6 C5 O5 109.470 3.000
KDA C6 C5 C4 111.000 3.000
KDA H5 C5 O5 109.470 3.000
KDA H5 C5 C4 108.340 3.000
KDA O5 C5 C4 109.470 3.000
KDA C5 O5 HO5 109.470 3.000
KDA C5 C4 H4 108.340 3.000
KDA C5 C4 O4 109.470 3.000
KDA C5 C4 C3 111.000 3.000
KDA H4 C4 O4 109.470 3.000
KDA H4 C4 C3 108.340 3.000
KDA O4 C4 C3 109.470 3.000
KDA C4 O4 HO4 109.470 3.000
KDA C4 C3 H32 109.470 3.000
KDA C4 C3 H31 109.470 3.000
KDA C4 C3 C2 111.000 3.000
KDA H32 C3 H31 107.900 3.000
KDA H32 C3 C2 109.470 3.000
KDA H31 C3 C2 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
KDA var_1 O1B C1 C2 O6 -0.082 20.000 1
KDA var_2 C1 C2 C3 C4 180.000 20.000 1
KDA var_3 C1 C2 O2 C9 -59.852 20.000 1
KDA var_4 C2 O2 C9 C10 -179.978 20.000 1
KDA var_5 O2 C9 C10 C11 119.968 20.000 1
KDA CONST_1 C9 C10 C11 H111 179.967 0.000 0
KDA var_6 C1 C2 O6 C6 180.000 20.000 1
KDA var_7 C2 O6 C6 C5 60.000 20.000 1
KDA var_8 O6 C6 C7 O7 179.791 20.000 3
KDA var_9 C6 C7 C8 O8 179.994 20.000 3
KDA var_10 C7 C8 O8 HO8 179.978 20.000 1
KDA var_11 C6 C7 O7 HO7 -59.976 20.000 1
KDA var_12 O6 C6 C5 C4 -60.000 20.000 3
KDA var_13 C6 C5 O5 HO5 -179.716 20.000 1
KDA var_14 C6 C5 C4 C3 60.000 20.000 3
KDA var_15 C5 C4 O4 HO4 -179.221 20.000 1
KDA var_16 C5 C4 C3 C2 -60.000 20.000 3
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
KDA chir_01 C2 C1 C3 O6 negativ
KDA chir_02 C4 C3 O4 C5 negativ
KDA chir_03 C5 C4 O5 C6 negativ
KDA chir_04 C6 C5 O6 C7 positiv
KDA chir_05 C7 C6 O7 C8 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
KDA plan-1 C1 0.020
KDA plan-1 O1A 0.020
KDA plan-1 O1B 0.020
KDA plan-1 C2 0.020
KDA plan-2 C10 0.020
KDA plan-2 C9 0.020
KDA plan-2 C11 0.020
KDA plan-2 H10 0.020
KDA plan-2 H111 0.020
KDA plan-2 H112 0.020
# ------------------------------------------------------
|
