# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 01:56:00 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-D-galactopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@@H]([C@H](O[C@H]2OC(=C[C@H](O)[C@H]2O)C(O)=O)[C@H](O)[C@H]1O)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
 UNG  UNG  '4-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-D-galactopyranuronic acid'  ligand  40  24  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UNG
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
 UNG  C1    C  CH1   0   0.229   8.0993  12.6171  44.0110
 UNG  C2    C  CH1   0  -0.028   7.6806  11.9010  45.2873
 UNG  C3    C  CH1   0   0.009   8.5398  12.4030  46.4464
 UNG  C4    C  C1    0  -0.377   9.9735  12.4695  46.0149
 UNG  C5    C  C     0   0.273  10.3209  12.4307  44.7295
 UNG  C6    C  C     0   0.499  11.7209  12.4822  44.2340
 UNG  O1    O  O2    0  -0.483   7.9216  13.9724  44.2106
 UNG  O2    O  OH1   0  -0.658   6.3123  12.1207  45.4797
 UNG  O3    O  OH1   0  -0.659   8.3611  11.6247  47.6084
 UNG  O5    O  O2    0  -0.484   9.4452  12.3126  43.7063
 UNG  O6    O  O     0  -0.437  12.0080  12.3884  43.0677
 UNG  C1'   C  CH1   0   0.207   7.5984  17.4148  44.2652
 UNG  C2'   C  CH1   0   0.008   8.9654  16.7173  44.2797
 UNG  C3'   C  CH1   0   0.042   9.0846  15.7834  43.0845
 UNG  C4'   C  CH1   0  -0.051   7.8993  14.8111  43.0743
 UNG  C5'   C  CH1   0  -0.080   6.5976  15.6096  43.1171
 UNG  C6'   C  C     0   0.532   5.4188  14.6586  43.1643
 UNG  O2'   O  OH1   0  -0.664  10.0170  17.6425  44.2388
 UNG  O3'   O  OH1   0  -0.653  10.3214  15.1327  43.1604
 UNG  O5'   O  O2    0  -0.493   6.5615  16.4633  44.2310
 UNG  O6'   O  O     0  -0.449   5.2958  13.7609  42.3688
 UNG  OAC   O  OH1   0  -0.570   4.5498  14.9328  44.1145
 UNG  OAN   O  OH1   0  -0.589  12.6055  12.6260  45.2077
 UNG  H1    H  HCH1  0   0.257   7.5320  12.2513  43.1490
 UNG  H2    H  HCH1  0   0.234   7.8974  10.8315  45.1356
 UNG  H3    H  HCH1  0   0.264   8.2077  13.4102  46.7201
 UNG  HA    H  HOH1  0   0.455   6.0342  11.6189  46.2530
 UNG  H4C1  H  H     0   0.282  10.7305  12.5702  46.7802
 UNG  HB    H  HOH1  0   0.448   8.6914  10.7354  47.4369
 UNG  HAN   H  HOH1  0   0.491  13.5015  12.6390  44.8398
 UNG  H4'   H  HCH1  0   0.270   7.9236  14.2248  42.1474
 UNG  H1'   H  HCH1  0   0.242   7.4468  17.9470  45.2121
 UNG  H2'   H  HCH1  0   0.232   9.0053  16.1107  45.1949
 UNG  H3'   H  HCH1  0   0.224   9.0105  16.3759  42.1604
 UNG  HD    H  HOH1  0   0.454  10.0475  18.1076  45.0807
 UNG  HE    H  HOH1  0   0.450  10.4287  14.5799  42.3797
 UNG  H5'   H  HCH1  0   0.281   6.5057  16.1722  42.1765
 UNG  HAC   H  HOH1  0   0.486   3.8146  14.3017  44.0760
 UNG  O1'   O  OH1   0  -0.659   7.5537  18.2837  43.1848
 UNG  HC    H  HOH1  0   0.465   6.7980  18.8729  43.2839

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
 UNG  C1   C2    single  1.522  0.020  1.522
 UNG  C2   C3    single  1.528  0.020  1.528
 UNG  C3   C4    single  1.499  0.020  1.499
 UNG  C4   C5    double  1.332  0.020  1.332
 UNG  C5   C6    single  1.486  0.020  1.486
 UNG  C1   O1    single  1.381  0.020  1.381
 UNG  C2   O2    single  1.399  0.020  1.399
 UNG  C3   O3    single  1.410  0.020  1.410
 UNG  C1   O5    single  1.413  0.020  1.413
 UNG  C5   O5    single  1.352  0.020  1.352
 UNG  C6   O6    double  1.205  0.020  1.205
 UNG  C1'  C2'   single  1.535  0.020  1.535
 UNG  C2'  C3'   single  1.522  0.020  1.522
 UNG  O1   C4'   single  1.413  0.020  1.413
 UNG  C3'  C4'   single  1.533  0.020  1.533
 UNG  C4'  C5'   single  1.528  0.020  1.528
 UNG  C5'  C6'   single  1.515  0.020  1.515
 UNG  C1'  O1'   single  1.387  0.020  1.387
 UNG  C2'  O2'   single  1.401  0.020  1.401
 UNG  C3'  O3'   single  1.400  0.020  1.400
 UNG  C1'  O5'   single  1.408  0.020  1.408
 UNG  C5'  O5'   single  1.404  0.020  1.404
 UNG  C6'  O6'   double  1.206  0.020  1.206
 UNG  C6'  OAC   single  1.317  0.020  1.317
 UNG  C6   OAN   single  1.323  0.020  1.323
 UNG  C1   H1    single  0.970  0.020  1.090
 UNG  C2   H2    single  0.970  0.020  1.090
 UNG  C3   H3    single  0.970  0.020  1.090
 UNG  O2   HA    single  0.850  0.020  0.980
 UNG  C4   H4C1  single  0.930  0.020  1.080
 UNG  O3   HB    single  0.850  0.020  0.980
 UNG  OAN  HAN   single  0.850  0.020  0.980
 UNG  C4'  H4'   single  0.970  0.020  1.090
 UNG  C1'  H1'   single  0.970  0.020  1.090
 UNG  C2'  H2'   single  0.970  0.020  1.090
 UNG  O1'  HC    single  0.850  0.020  0.980
 UNG  C3'  H3'   single  0.970  0.020  1.090
 UNG  O2'  HD    single  0.850  0.020  0.980
 UNG  O3'  HE    single  0.850  0.020  0.980
 UNG  C5'  H5'   single  0.970  0.020  1.090
 UNG  OAC  HAC   single  0.850  0.020  0.980

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
 UNG  H1    C1   O5   104.58  3.000
 UNG  H1    C1   O1   112.02  3.000
 UNG  O5    C1   O1   111.41  3.000
 UNG  H1    C1   C2   111.13  3.000
 UNG  O5    C1   C2   109.96  3.000
 UNG  O1    C1   C2   107.76  3.000
 UNG  H2    C2   O2   111.33  3.000
 UNG  H2    C2   C3   108.22  3.000
 UNG  O2    C2   C3   113.21  3.000
 UNG  H2    C2   C1   106.68  3.000
 UNG  O2    C2   C1   108.09  3.000
 UNG  C3    C2   C1   109.08  3.000
 UNG  H3    C3   O3   105.26  3.000
 UNG  H3    C3   C4   108.73  3.000
 UNG  O3    C3   C4   112.52  3.000
 UNG  H3    C3   C2   108.73  3.000
 UNG  O3    C3   C2   111.88  3.000
 UNG  C4    C3   C2   109.52  3.000
 UNG  H4C1  C4   C5   120.21  3.000
 UNG  H4C1  C4   C3   118.04  3.000
 UNG  C5    C4   C3   121.74  3.000
 UNG  O5    C5   C6   111.16  3.000
 UNG  O5    C5   C4   124.33  3.000
 UNG  C6    C5   C4   124.50  3.000
 UNG  OAN   C6   O6   124.16  3.000
 UNG  OAN   C6   C5   112.84  3.000
 UNG  O6    C6   C5   122.99  3.000
 UNG  C4'   O1   C1   117.93  3.000
 UNG  HA    O2   C2   108.12  3.000
 UNG  HB    O3   C3   108.61  3.000
 UNG  C5    O5   C1   115.78  3.000
 UNG  H1'   C1'  O5'  104.31  3.000
 UNG  H1'   C1'  O1'  111.35  3.000
 UNG  O5'   C1'  O1'  112.38  3.000
 UNG  H1'   C1'  C2'  109.60  3.000
 UNG  O5'   C1'  C2'  110.43  3.000
 UNG  O1'   C1'  C2'  108.71  3.000
 UNG  H2'   C2'  O2'  111.20  3.000
 UNG  H2'   C2'  C3'  108.22  3.000
 UNG  O2'   C2'  C3'  108.87  3.000
 UNG  H2'   C2'  C1'  106.93  3.000
 UNG  O2'   C2'  C1'  111.60  3.000
 UNG  C3'   C2'  C1'  109.96  3.000
 UNG  H3'   C3'  O3'  110.82  3.000
 UNG  H3'   C3'  C4'  106.49  3.000
 UNG  O3'   C3'  C4'  112.88  3.000
 UNG  H3'   C3'  C2'  108.90  3.000
 UNG  O3'   C3'  C2'  108.18  3.000
 UNG  C4'   C3'  C2'  109.50  3.000
 UNG  H4'   C4'  C5'  108.78  3.000
 UNG  H4'   C4'  C3'  109.11  3.000
 UNG  C5'   C4'  C3'  109.10  3.000
 UNG  H4'   C4'  O1   111.22  3.000
 UNG  C5'   C4'  O1   107.54  3.000
 UNG  C3'   C4'  O1   111.04  3.000
 UNG  H5'   C5'  O5'  111.43  3.000
 UNG  H5'   C5'  C6'  106.42  3.000
 UNG  O5'   C5'  C6'  109.69  3.000
 UNG  H5'   C5'  C4'  108.33  3.000
 UNG  O5'   C5'  C4'  111.22  3.000
 UNG  C6'   C5'  C4'  109.61  3.000
 UNG  OAC   C6'  O6'  124.33  3.000
 UNG  OAC   C6'  C5'  113.91  3.000
 UNG  O6'   C6'  C5'  121.74  3.000
 UNG  HD    O2'  C2'  108.50  3.000
 UNG  HE    O3'  C3'  108.76  3.000
 UNG  C5'   O5'  C1'  114.29  3.000
 UNG  HAC   OAC  C6'  109.65  3.000
 UNG  HAN   OAN  C6   109.89  3.000
 UNG  HC    O1'  C1'  109.16  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
 UNG  CONST_01  HAN  OAN  C6   C5   180.00   0.0  0
 UNG  CONST_02  HAC  OAC  C6'  C5'  180.00   0.0  0
 UNG  Var_01    C4   C5   O5   C1    17.82  30.0  1
 UNG  Var_02    O5   C5   C4   C3    -0.90  30.0  1
 UNG  Var_03    O6   C6   C5   C4   176.76  30.0  2

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
 UNG  chir_01  C1   C2   O1   O5   negativ
 UNG  chir_02  C2   O2   C1   C3   negativ
 UNG  chir_03  C3   O3   C2   C4   positiv
 UNG  chir_04  C1'  C2'  O1'  O5'  negativ
 UNG  chir_05  C2'  O2'  C1'  C3'  negativ
 UNG  chir_06  C3'  O3'  C2'  C4'  positiv
 UNG  chir_07  C4'  O1   C5'  C3'  negativ
 UNG  chir_08  C5'  O5'  C4'  C6'  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
 UNG  plan-1  C5   0.020
 UNG  plan-1  C6   0.020
 UNG  plan-1  O6   0.020
 UNG  plan-1  OAN  0.020
 UNG  plan-1  HAN  0.020
 UNG  plan-2  C5'  0.020
 UNG  plan-2  C6'  0.020
 UNG  plan-2  O6'  0.020
 UNG  plan-2  OAC  0.020
 UNG  plan-2  HAC  0.020

