# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 01:40:15 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-beta-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
 UNF  UNF  '4-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-beta-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 PERFECT
;

data_comp_UNF
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
 UNF  C1    C  CH1    0   0.291  -0.9033   0.2548   0.3112
 UNF  C2    C  CH1    0  -0.052  -1.3239   1.1343   1.4738
 UNF  C3    C  CH1    0  -0.016  -2.7876   1.5384   1.2489
 UNF  C4    C  C1     0  -0.397  -3.5693   0.3605   0.7649
 UNF  C5    C  C      0   0.176  -2.9949  -0.7800   0.3641
 UNF  C6    C  C      0   0.369  -3.7910  -2.0218  -0.0349
 UNF  O1    O  O2     0  -0.502   0.4242  -0.0822   0.4133
 UNF  O2    O  OH1    0  -0.668  -1.1617   0.3955   2.6569
 UNF  O3    O  OH1    0  -0.665  -2.9009   2.6643   0.3944
 UNF  O5    O  O2     0  -0.466  -1.6575  -0.9430   0.2878
 UNF  O6    O  O      0  -0.591  -5.0293  -1.8964  -0.0456
 UNF  C1'   C  CH1    0   0.261   3.8660   0.0383   0.0613
 UNF  C2'   C  CH1    0  -0.031   3.1191  -1.2647   0.3377
 UNF  C3'   C  CH1    0   0.032   2.0320  -1.4550  -0.7137
 UNF  C4'   C  CH1    0  -0.027   1.1486  -0.2196  -0.7978
 UNF  C5'   C  CH1    0  -0.094   2.0267   1.0135  -1.0088
 UNF  C6'   C  C      0   0.401   1.1863   2.3060  -1.1112
 UNF  O2'   O  OH1    0  -0.674   3.9804  -2.3770   0.2575
 UNF  O3'   O  OH1    0  -0.660   1.2368  -2.5821  -0.4636
 UNF  O5'   O  O2     0  -0.490   2.9716   1.1185   0.0321
 UNF  O6'   O  OC    -1  -0.612   0.3354   2.2901  -2.0239
 UNF  OAC   O  O      0  -0.582   1.4302   3.2232  -0.3161
 UNF  OAN   O  OC    -1  -0.590  -3.1255  -3.0341  -0.3031
 UNF  H1    H  HCH1   0   0.203  -1.1048   0.8046  -0.6212
 UNF  H2    H  HCH1   0   0.233  -0.6969   2.0362   1.4580
 UNF  H3    H  HCH1   0   0.242  -3.1949   1.8748   2.2093
 UNF  HA    H  HOH1   0   0.454  -1.3807   0.9678   3.3987
 UNF  H41C  H  H      0   0.245  -4.6491   0.4127   0.7723
 UNF  HB    H  HOH1   0   0.438  -2.7642   2.3745  -0.5135
 UNF  H4'   H  HCH1   0   0.249   0.4715  -0.3255  -1.6523
 UNF  H2'   H  HCH1   0   0.221   2.6515  -1.1956   1.3307
 UNF  H3'   H  HCH1   0   0.208   2.5327  -1.5372  -1.6932
 UNF  HD    H  HOH1   0   0.455   4.5565  -2.3737   1.0281
 UNF  HE    H  HOH1   0   0.447   1.8149  -3.3517  -0.4431
 UNF  H5'   H  HCH1   0   0.214   2.5452   0.8877  -1.9753
 UNF  O1'   O  OH1    0  -0.665   4.7747   0.2443   1.0835
 UNF  HC    H  HOH1   0   0.464   5.4729   0.8328   0.7788
 UNF  H1'   H  HCH1   0   0.178   4.3759  -0.0449  -0.9165

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
 UNF  C1   C2    single  1.517  0.020  1.517
 UNF  C1   O1    single  1.373  0.020  1.373
 UNF  C1   O5    single  1.416  0.020  1.416
 UNF  C2   C3    single  1.535  0.020  1.535
 UNF  C2   O2    single  1.404  0.020  1.404
 UNF  C3   C4    single  1.494  0.020  1.494
 UNF  C3   O3    single  1.418  0.020  1.418
 UNF  C4   C5    double  1.338  0.020  1.338
 UNF  C5   C6    single  1.528  0.020  1.528
 UNF  C5   O5    single  1.349  0.020  1.349
 UNF  C6   O6    deloc   1.245  0.020  1.245
 UNF  C6   OAN   deloc   1.241  0.020  1.241
 UNF  O1   C4'   single  1.418  0.020  1.418
 UNF  C1'  C2'   single  1.527  0.020  1.527
 UNF  C1'  O1'   single  1.383  0.020  1.383
 UNF  C1'  O5'   single  1.403  0.020  1.403
 UNF  C2'  C3'   single  1.524  0.020  1.524
 UNF  C2'  O2'   single  1.409  0.020  1.409
 UNF  C3'  C4'   single  1.521  0.020  1.521
 UNF  C3'  O3'   single  1.402  0.020  1.402
 UNF  C4'  C5'   single  1.528  0.020  1.528
 UNF  C5'  C6'   single  1.545  0.020  1.545
 UNF  C5'  O5'   single  1.410  0.020  1.410
 UNF  C6'  O6'   deloc   1.248  0.020  1.248
 UNF  C6'  OAC   deloc   1.238  0.020  1.238
 UNF  C1   H1    single  0.970  0.020  1.090
 UNF  C2   H2    single  0.970  0.020  1.090
 UNF  C3   H3    single  0.970  0.020  1.090
 UNF  O2   HA    single  0.850  0.020  0.980
 UNF  C4   H41C  single  0.930  0.020  1.080
 UNF  O3   HB    single  0.850  0.020  0.980
 UNF  C4'  H4'   single  0.970  0.020  1.090
 UNF  C1'  H1'   single  0.970  0.020  1.090
 UNF  C2'  H2'   single  0.970  0.020  1.090
 UNF  O1'  HC    single  0.850  0.020  0.980
 UNF  C3'  H3'   single  0.970  0.020  1.090
 UNF  O2'  HD    single  0.850  0.020  0.980
 UNF  O3'  HE    single  0.850  0.020  0.980
 UNF  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
 UNF  H1    C1   O5   108.12  3.000
 UNF  H1    C1   O1   111.25  3.000
 UNF  O5    C1   O1   107.97  3.000
 UNF  H1    C1   C2   107.98  3.000
 UNF  O5    C1   C2   110.82  3.000
 UNF  O1    C1   C2   110.68  3.000
 UNF  H2    C2   O2   112.22  3.000
 UNF  H2    C2   C3   109.03  3.000
 UNF  O2    C2   C3   111.84  3.000
 UNF  H2    C2   C1   107.86  3.000
 UNF  O2    C2   C1   107.97  3.000
 UNF  C3    C2   C1   107.74  3.000
 UNF  H3    C3   O3   104.75  3.000
 UNF  H3    C3   C4   109.35  3.000
 UNF  O3    C3   C4   112.88  3.000
 UNF  H3    C3   C2   107.87  3.000
 UNF  O3    C3   C2   111.93  3.000
 UNF  C4    C3   C2   109.81  3.000
 UNF  H41C  C4   C5   118.16  3.000
 UNF  H41C  C4   C3   118.83  3.000
 UNF  C5    C4   C3   122.97  3.000
 UNF  O5    C5   C6   113.79  3.000
 UNF  O5    C5   C4   123.04  3.000
 UNF  C6    C5   C4   123.16  3.000
 UNF  OAN   C6   O6   127.87  3.000
 UNF  OAN   C6   C5   116.11  3.000
 UNF  O6    C6   C5   116.02  3.000
 UNF  C4'   O1   C1   117.00  3.000
 UNF  HA    O2   C2   108.08  3.000
 UNF  HB    O3   C3   108.54  3.000
 UNF  C5    O5   C1   115.15  3.000
 UNF  H1'   C1'  O5'  109.49  3.000
 UNF  H1'   C1'  O1'  111.20  3.000
 UNF  O5'   C1'  O1'  108.64  3.000
 UNF  H1'   C1'  C2'  108.74  3.000
 UNF  O5'   C1'  C2'  110.43  3.000
 UNF  O1'   C1'  C2'  108.33  3.000
 UNF  H2'   C2'  O2'  111.16  3.000
 UNF  H2'   C2'  C3'  109.11  3.000
 UNF  O2'   C2'  C3'  107.35  3.000
 UNF  H2'   C2'  C1'  108.52  3.000
 UNF  O2'   C2'  C1'  111.37  3.000
 UNF  C3'   C2'  C1'  109.29  3.000
 UNF  H3'   C3'  O3'  110.85  3.000
 UNF  H3'   C3'  C4'  105.97  3.000
 UNF  O3'   C3'  C4'  109.48  3.000
 UNF  H3'   C3'  C2'  107.34  3.000
 UNF  O3'   C3'  C2'  112.45  3.000
 UNF  C4'   C3'  C2'  110.55  3.000
 UNF  H4'   C4'  C5'  109.00  3.000
 UNF  H4'   C4'  C3'  108.88  3.000
 UNF  C5'   C4'  C3'  109.22  3.000
 UNF  H4'   C4'  O1   111.09  3.000
 UNF  C5'   C4'  O1   109.47  3.000
 UNF  C3'   C4'  O1   109.16  3.000
 UNF  H5'   C5'  O5'  109.88  3.000
 UNF  H5'   C5'  C6'  107.02  3.000
 UNF  O5'   C5'  C6'  110.56  3.000
 UNF  H5'   C5'  C4'  107.38  3.000
 UNF  O5'   C5'  C4'  110.08  3.000
 UNF  C6'   C5'  C4'  111.81  3.000
 UNF  OAC   C6'  O6'  127.84  3.000
 UNF  OAC   C6'  C5'  118.04  3.000
 UNF  O6'   C6'  C5'  114.12  3.000
 UNF  HD    O2'  C2'  108.53  3.000
 UNF  HE    O3'  C3'  107.82  3.000
 UNF  C5'   O5'  C1'  112.67  3.000
 UNF  HC    O1'  C1'  109.49  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
 UNF  Var_01  C4  C5  O5  C1  -16.14  30.0  1
 UNF  Var_02  O5  C5  C4  C3   -3.94  30.0  1
 UNF  Var_03  O6  C6  C5  C4    4.16  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
 UNF  chir_01  C1   C2   O1   O5   negativ
 UNF  chir_02  C2   O2   C1   C3   negativ
 UNF  chir_03  C3   O3   C2   C4   positiv
 UNF  chir_04  C1'  C2'  O1'  O5'  positiv
 UNF  chir_05  C2'  O2'  C1'  C3'  negativ
 UNF  chir_06  C3'  O3'  C2'  C4'  positiv
 UNF  chir_07  C4'  O1   C5'  C3'  negativ
 UNF  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
 UNF  plan-1  C5   0.020
 UNF  plan-1  C6   0.020
 UNF  plan-1  O6   0.020
 UNF  plan-1  OAN  0.020
 UNF  plan-2  C5'  0.020
 UNF  plan-2  C6'  0.020
 UNF  plan-2  O6'  0.020
 UNF  plan-2  OAC  0.020

