# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:05:46 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1OC(=C[C@H](O)[C@H]1O[S](O)(=O)=O)C(O)=O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 UAP  UAP  '4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid'  L-saccharide  22  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UAP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 UAP  S    S  S      0   1.562  -2.9675  -0.0779  -0.2893
 UAP  C1   C  CH1    0   0.265   0.4234   1.0371   0.6665
 UAP  O1   O  OH1    0  -0.641  -0.2432   2.2017   0.3889
 UAP  C2   C  CH1    0  -0.032  -0.3501  -0.1588   0.1169
 UAP  O2   O  OC2    0  -0.627  -1.6435  -0.1589   0.6894
 UAP  C3   C  CH1    0   0.040   0.3904  -1.4293   0.5078
 UAP  O3   O  OH1    0  -0.659  -0.0991  -2.4881  -0.2848
 UAP  C4   C  C1     0  -0.418   1.8672  -1.2287   0.3239
 UAP  C5   C  C      0   0.174   2.4264  -0.0414   0.0885
 UAP  O5   O  O2     0  -0.484   1.7021   1.1030   0.0518
 UAP  C6   C  C      0   0.375   3.9158   0.1589  -0.1715
 UAP  O1S  O  OS    -1  -0.734  -3.0589  -1.3842  -0.9405
 UAP  O2S  O  OS     0  -0.740  -4.0057   0.1786   0.7076
 UAP  O3S  O  OS     0  -0.735  -2.7248   1.0244  -1.2204
 UAP  O61  O  OC    -1  -0.595   4.2802   1.3269  -0.3818
 UAP  O62  O  O      0  -0.590   4.6171  -0.8685  -0.1502
 UAP  H1   H  HCH1   0   0.205   0.5778   0.8996   1.7497
 UAP  H2   H  HCH1   0   0.247  -0.3827  -0.0820  -0.9770
 UAP  H3   H  HCH1   0   0.218   0.1811  -1.6272   1.5702
 UAP  HO3  H  HOH1   0   0.451   0.2904  -3.3057   0.0407
 UAP  H4   H  H      0   0.253   2.5116  -2.0966   0.3747
 UAP  HO1  H  HOH1   0   0.465   0.0503   2.8877   0.9974

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
_chem_comp_bond.value_dist_neutron
 UAP  O2   S    single  1.648  0.020  1.648
 UAP  S    O2S  deloc   1.462  0.020  1.462
 UAP  S    O3S  deloc   1.463  0.020  1.463
 UAP  S    O1S  deloc   1.462  0.020  1.462
 UAP  O5   C1   single  1.420  0.020  1.420
 UAP  O1   C1   single  1.370  0.020  1.370
 UAP  C1   C2   single  1.527  0.020  1.527
 UAP  C1   H1   single  0.970  0.020  1.090
 UAP  O1   HO1  single  0.850  0.020  0.980
 UAP  C3   C2   single  1.522  0.020  1.522
 UAP  C2   O2   single  1.414  0.020  1.414
 UAP  C2   H2   single  0.970  0.020  1.090
 UAP  C4   C3   single  1.502  0.020  1.502
 UAP  O3   C3   single  1.410  0.020  1.410
 UAP  C3   H3   single  0.970  0.020  1.090
 UAP  O3   HO3  single  0.850  0.020  0.980
 UAP  C5   C4   double  1.333  0.020  1.333
 UAP  C4   H4   single  0.930  0.020  1.080
 UAP  C6   C5   single  1.525  0.020  1.525
 UAP  C5   O5   single  1.355  0.020  1.355
 UAP  O62  C6   deloc   1.244  0.020  1.244
 UAP  O61  C6   deloc   1.242  0.020  1.242

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
 UAP  O3S  S   O2S  114.80  3.000
 UAP  O3S  S   O1S  113.57  3.000
 UAP  O2S  S   O1S  114.59  3.000
 UAP  O1S  S   O2   105.71  3.000
 UAP  O3S  S   O2   106.35  3.000
 UAP  O2S  S   O2   100.03  3.000
 UAP  H1   C1  O5   107.75  3.000
 UAP  H1   C1  C2   109.08  3.000
 UAP  O5   C1  C2   109.67  3.000
 UAP  H1   C1  O1   111.91  3.000
 UAP  C2   C1  O1   110.27  3.000
 UAP  O5   C1  O1   108.11  3.000
 UAP  HO1  O1  C1   109.22  3.000
 UAP  H2   C2  C3   109.21  3.000
 UAP  H2   C2  O2   112.11  3.000
 UAP  C3   C2  O2   109.94  3.000
 UAP  H2   C2  C1   108.61  3.000
 UAP  O2   C2  C1   108.52  3.000
 UAP  C3   C2  C1   108.37  3.000
 UAP  C2   O2  S    119.62  3.000
 UAP  H3   C3  C4   109.22  3.000
 UAP  H3   C3  O3   109.96  3.000
 UAP  C4   C3  O3   111.89  3.000
 UAP  H3   C3  C2   107.79  3.000
 UAP  O3   C3  C2   108.28  3.000
 UAP  C4   C3  C2   109.61  3.000
 UAP  HO3  O3  C3   107.90  3.000
 UAP  H4   C4  C5   118.21  3.000
 UAP  H4   C4  C3   118.21  3.000
 UAP  C5   C4  C3   123.58  3.000
 UAP  C6   C5  O5   113.99  3.000
 UAP  O5   C5  C4   122.19  3.000
 UAP  C6   C5  C4   123.82  3.000
 UAP  C5   O5  C1   115.49  3.000
 UAP  O62  C6  O61  127.91  3.000
 UAP  O61  C6  C5   116.05  3.000
 UAP  O62  C6  C5   116.04  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
 UAP  Var_01  C4   C5  O5  C1    18.46  30.0  1
 UAP  Var_02  O5   C5  C4  C3     2.87  30.0  1
 UAP  Var_03  O62  C6  C5  C4    -0.24  30.0  2
 UAP  Var_04  O2S  S   O2  C2  -168.62  30.0  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
 UAP  chir_01  C1  O5  O1  C2  negativ
 UAP  chir_02  C2  O2  C1  C3  negativ
 UAP  chir_03  C3  O3  C2  C4  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
 UAP  plan-1  C5   0.020
 UAP  plan-1  C6   0.020
 UAP  plan-1  O61  0.020
 UAP  plan-1  O62  0.020

