# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 04:44:00 2020
#   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  38  24  .  2021-08-24  2021-08-24  
;
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   0.312   2.4432  -3.0203  -0.8410
 UNG  C2    C  CH1    0  -0.047   3.6456  -3.0140   0.0851
 UNG  C3    C  CH1    0  -0.018   3.6756  -4.3552   0.8367
 UNG  C4    C  C1     0  -0.395   3.3858  -5.4830  -0.1017
 UNG  C5    C  C      0   0.200   2.8834  -5.2852  -1.3238
 UNG  C6    C  C      0   0.379   2.5672  -6.3948  -2.3207
 UNG  O1    O  O2     0  -0.499   2.3376  -1.8419  -1.5266
 UNG  O2    O  OH1    0  -0.667   4.7908  -2.8399  -0.7061
 UNG  O3    O  OH1    0  -0.666   2.8004  -4.3474   1.9522
 UNG  O5    O  O2     0  -0.497   2.5832  -4.0574  -1.7960
 UNG  O6    O  O      0  -0.581   2.9376  -7.5384  -2.0084
 UNG  C1'   C  CH1    0   0.220   1.6070  -0.0939  -4.3883
 UNG  C2'   C  CH1    0  -0.008   1.4476  -1.6228  -4.3374
 UNG  C3'   C  CH1    0   0.012   0.5106  -2.0025  -3.1952
 UNG  C4'   C  CH1    0  -0.028   1.0391  -1.3901  -1.8914
 UNG  C5'   C  CH1    0  -0.131   1.1596   0.1168  -2.0649
 UNG  C6'   C  C      0   0.400   1.6814   0.7945  -0.7791
 UNG  O2'   O  OH1    0  -0.667   0.9352  -2.1373  -5.5384
 UNG  O3'   O  OH1    0  -0.696   0.2225  -3.3725  -3.1362
 UNG  O5'   O  O2     0  -0.494   2.0154   0.4161  -3.1525
 UNG  O6'   O  O      0  -0.593   2.6493   1.5632  -0.8768
 UNG  OAC   O  OC    -1  -0.616   1.0305   0.5160   0.2466
 UNG  OAN   O  OC    -1  -0.584   1.9557  -6.0411  -3.3448
 UNG  H1    H  HCH1   0   0.199   1.5404  -3.2187  -0.2380
 UNG  H2    H  HCH1   0   0.237   3.5155  -2.2022   0.8133
 UNG  H3    H  HCH1   0   0.246   4.6796  -4.4777   1.2596
 UNG  HA    H  HOH1   0   0.456   5.5560  -2.7948  -0.1248
 UNG  H4C1  H  H      0   0.253   3.5891  -6.4959   0.2167
 UNG  HB    H  HOH1   0   0.443   1.9188  -4.5875   1.6498
 UNG  H4'   H  HCH1   0   0.244   0.3277  -1.5977  -1.0833
 UNG  H2'   H  HCH1   0   0.217   2.4436  -2.0392  -4.1286
 UNG  H3'   H  HCH1   0   0.227  -0.4580  -1.5193  -3.3704
 UNG  HD    H  HOH1   0   0.450   1.5896  -2.0024  -6.2308
 UNG  HE    H  HOH1   0   0.454   1.0350  -3.8973  -3.0694
 UNG  H5'   H  HCH1   0   0.227   0.1500   0.5105  -2.2513
 UNG  O1'   O  OH1    0  -0.667   0.4033   0.4553  -4.8274
 UNG  HC    H  HOH1   0   0.458   0.5459   1.3861  -5.0294
 UNG  H1'   H  HCH1   0   0.221   2.4232   0.1620  -5.0776

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  1.518  0.020  1.518
 UNG  C2   C3    single  1.538  0.020  1.538
 UNG  C3   C4    single  1.495  0.020  1.495
 UNG  C4   C5    double  1.336  0.020  1.336
 UNG  C5   C6    single  1.525  0.020  1.525
 UNG  C1   O1    single  1.367  0.020  1.367
 UNG  C2   O2    single  1.403  0.020  1.403
 UNG  C3   O3    single  1.418  0.020  1.418
 UNG  C1   O5    single  1.417  0.020  1.417
 UNG  C5   O5    single  1.349  0.020  1.349
 UNG  C6   O6    deloc   1.242  0.020  1.242
 UNG  C1'  C2'   single  1.538  0.020  1.538
 UNG  C2'  C3'   single  1.525  0.020  1.525
 UNG  O1   C4'   single  1.422  0.020  1.422
 UNG  C3'  C4'   single  1.534  0.020  1.534
 UNG  C4'  C5'   single  1.522  0.020  1.522
 UNG  C5'  C6'   single  1.544  0.020  1.544
 UNG  C1'  O1'   single  1.394  0.020  1.394
 UNG  C2'  O2'   single  1.403  0.020  1.403
 UNG  C3'  O3'   single  1.401  0.020  1.401
 UNG  C1'  O5'   single  1.398  0.020  1.398
 UNG  C5'  O5'   single  1.416  0.020  1.416
 UNG  C6'  O6'   deloc   1.240  0.020  1.240
 UNG  C6'  OAC   deloc   1.246  0.020  1.246
 UNG  C6   OAN   deloc   1.244  0.020  1.244
 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  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

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   108.52  3.000
 UNG  H1    C1   O1   111.45  3.000
 UNG  O5    C1   O1   107.49  3.000
 UNG  H1    C1   C2   108.39  3.000
 UNG  O5    C1   C2   109.64  3.000
 UNG  O1    C1   C2   111.31  3.000
 UNG  H2    C2   O2   112.27  3.000
 UNG  H2    C2   C3   108.84  3.000
 UNG  O2    C2   C3   111.59  3.000
 UNG  H2    C2   C1   108.29  3.000
 UNG  O2    C2   C1   107.65  3.000
 UNG  C3    C2   C1   108.06  3.000
 UNG  H3    C3   O3   105.21  3.000
 UNG  H3    C3   C4   109.59  3.000
 UNG  O3    C3   C4   112.22  3.000
 UNG  H3    C3   C2   107.69  3.000
 UNG  O3    C3   C2   111.57  3.000
 UNG  C4    C3   C2   110.32  3.000
 UNG  H4C1  C4   C5   118.61  3.000
 UNG  H4C1  C4   C3   119.04  3.000
 UNG  C5    C4   C3   122.36  3.000
 UNG  O5    C5   C6   112.78  3.000
 UNG  O5    C5   C4   122.58  3.000
 UNG  C6    C5   C4   124.63  3.000
 UNG  OAN   C6   O6   127.98  3.000
 UNG  OAN   C6   C5   115.67  3.000
 UNG  O6    C6   C5   116.35  3.000
 UNG  C4'   O1   C1   118.22  3.000
 UNG  HA    O2   C2   108.32  3.000
 UNG  HB    O3   C3   108.47  3.000
 UNG  C5    O5   C1   116.88  3.000
 UNG  H1'   C1'  O5'  104.64  3.000
 UNG  H1'   C1'  O1'  110.62  3.000
 UNG  O5'   C1'  O1'  112.77  3.000
 UNG  H1'   C1'  C2'  109.23  3.000
 UNG  O5'   C1'  C2'  111.33  3.000
 UNG  O1'   C1'  C2'  108.21  3.000
 UNG  H2'   C2'  O2'  110.76  3.000
 UNG  H2'   C2'  C3'  108.66  3.000
 UNG  O2'   C2'  C3'  108.99  3.000
 UNG  H2'   C2'  C1'  106.79  3.000
 UNG  O2'   C2'  C1'  111.96  3.000
 UNG  C3'   C2'  C1'  109.63  3.000
 UNG  H3'   C3'  O3'  104.83  3.000
 UNG  H3'   C3'  C4'  105.32  3.000
 UNG  O3'   C3'  C4'  115.17  3.000
 UNG  H3'   C3'  C2'  108.25  3.000
 UNG  O3'   C3'  C2'  113.65  3.000
 UNG  C4'   C3'  C2'  108.99  3.000
 UNG  H4'   C4'  C5'  108.84  3.000
 UNG  H4'   C4'  C3'  109.10  3.000
 UNG  C5'   C4'  C3'  109.01  3.000
 UNG  H4'   C4'  O1   110.07  3.000
 UNG  C5'   C4'  O1   105.75  3.000
 UNG  C3'   C4'  O1   113.93  3.000
 UNG  H5'   C5'  O5'  110.43  3.000
 UNG  H5'   C5'  C6'  107.11  3.000
 UNG  O5'   C5'  C6'  110.03  3.000
 UNG  H5'   C5'  C4'  107.53  3.000
 UNG  O5'   C5'  C4'  110.17  3.000
 UNG  C6'   C5'  C4'  111.49  3.000
 UNG  OAC   C6'  O6'  127.67  3.000
 UNG  OAC   C6'  C5'  114.25  3.000
 UNG  O6'   C6'  C5'  118.05  3.000
 UNG  HD    O2'  C2'  108.43  3.000
 UNG  HE    O3'  C3'  111.09  3.000
 UNG  C5'   O5'  C1'  115.18  3.000
 UNG  HC    O1'  C1'  108.61  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  Var_01  C4  C5  O5  C1  -18.06  30.0  1
 UNG  Var_02  O5  C5  C4  C3   -0.92  30.0  1
 UNG  Var_03  O6  C6  C5  C4   -7.73  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-2  C5'  0.020
 UNG  plan-2  C6'  0.020
 UNG  plan-2  O6'  0.020
 UNG  plan-2  OAC  0.020

