# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 20:55:21 2021
#   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  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_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   0.204  -2.9543   2.6870  54.2842
 UNF  C2    C  CH1   0  -0.031  -1.6428   3.4114  53.9849
 UNF  C3    C  CH1   0   0.024  -1.6466   3.8456  52.5271
 UNF  C4    C  C1    0  -0.346  -2.1636   2.7202  51.6781
 UNF  C5    C  C     0   0.277  -2.8036   1.6747  52.1945
 UNF  C6    C  C     0   0.499  -3.2939   0.5672  51.3368
 UNF  O1    O  O2    0  -0.481  -3.9865   3.5667  53.9947
 UNF  O2    O  OH1   0  -0.646  -1.4805   4.5253  54.8185
 UNF  O3    O  OH1   0  -0.649  -0.3336   4.2104  52.1654
 UNF  O5    O  O2    0  -0.479  -3.0522   1.5103  53.5132
 UNF  O6    O  O     0  -0.432  -3.2663   0.5919  50.1311
 UNF  C1'   C  CH1   0   0.283  -6.8942   5.4050  53.3987
 UNF  C2'   C  CH1   0  -0.050  -6.3912   4.3280  52.4422
 UNF  C3'   C  CH1   0   0.060  -6.2154   3.0254  53.2219
 UNF  C4'   C  CH1   0   0.001  -5.2856   3.2270  54.4154
 UNF  C5'   C  CH1   0  -0.072  -5.8306   4.3992  55.2394
 UNF  C6'   C  C     0   0.536  -4.9029   4.7603  56.3832
 UNF  O2'   O  OH1   0  -0.636  -7.2350   4.1321  51.3330
 UNF  O3'   O  OH1   0  -0.640  -5.7416   1.9917  52.4126
 UNF  O5'   O  O2    0  -0.476  -5.9774   5.5480  54.4602
 UNF  O6'   O  OH1   0  -0.581  -4.6453   3.6946  57.1309
 UNF  OAC   O  O     0  -0.407  -4.4835   5.8595  56.6062
 UNF  OAN   O  OH1   0  -0.568  -3.7366  -0.4607  52.0408
 UNF  H1    H  HCH1  0   0.261  -2.9878   2.3428  55.3233
 UNF  H2    H  HCH1  0   0.258  -0.8363   2.6810  54.1269
 UNF  H3    H  HCH1  0   0.242  -2.3254   4.7028  52.4197
 UNF  HA    H  HOH1  0   0.439  -0.9424   4.2670  55.5692
 UNF  H41C  H  H     0   0.263  -2.0301   2.7757  50.6062
 UNF  HB    H  HOH1  0   0.434  -0.3847   4.8258  51.4313
 UNF  HAN   H  HOH1  0   0.457  -4.0279  -1.1535  51.4350
 UNF  H4'   H  HCH1  0   0.261  -5.2949   2.3172  55.0261
 UNF  H1'   H  HCH1  0   0.152  -7.8730   5.0931  53.8185
 UNF  H2'   H  HCH1  0   0.264  -5.4256   4.6409  52.0342
 UNF  H3'   H  HCH1  0   0.177  -7.1999   2.7560  53.6498
 UNF  HD    H  HOH1  0   0.423  -8.1367   3.9770  51.6311
 UNF  HE    H  HOH1  0   0.435  -6.2403   2.0192  51.5893
 UNF  H5'   H  HCH1  0   0.251  -6.7915   4.0910  55.6877
 UNF  H6'   H  HOH1  0   0.463  -4.0912   3.9426  57.8827
 UNF  O1'   O  OH1   0  -0.616  -6.9924   6.6018  52.7402
 UNF  HC    H  HOH1  0   0.442  -7.5234   7.2049  53.2685

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  1.528  0.020  1.528
 UNF  C1   O1    single  1.387  0.020  1.387
 UNF  C1   O5    single  1.410  0.020  1.410
 UNF  C2   C3    single  1.521  0.020  1.521
 UNF  C2   O2    single  1.401  0.020  1.401
 UNF  C3   C4    single  1.502  0.020  1.502
 UNF  C3   O3    single  1.410  0.020  1.410
 UNF  C4   C5    double  1.330  0.020  1.330
 UNF  C5   C6    single  1.484  0.020  1.484
 UNF  C5   O5    single  1.352  0.020  1.352
 UNF  C6   O6    double  1.206  0.020  1.206
 UNF  C6   OAN   single  1.322  0.020  1.322
 UNF  O1   C4'   single  1.407  0.020  1.407
 UNF  C1'  C2'   single  1.526  0.020  1.526
 UNF  C1'  O1'   single  1.370  0.020  1.370
 UNF  C1'  O5'   single  1.410  0.020  1.410
 UNF  C2'  C3'   single  1.528  0.020  1.528
 UNF  C2'  O2'   single  1.407  0.020  1.407
 UNF  C3'  C4'   single  1.526  0.020  1.526
 UNF  C3'  O3'   single  1.396  0.020  1.396
 UNF  C4'  C5'   single  1.533  0.020  1.533
 UNF  C5'  C6'   single  1.516  0.020  1.516
 UNF  C5'  O5'   single  1.396  0.020  1.396
 UNF  C6'  O6'   single  1.327  0.020  1.327
 UNF  C6'  OAC   double  1.197  0.020  1.197
 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  OAN  HAN   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
 UNF  O6'  H6'   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
 UNF  H1    C1   O5   104.74  3.000
 UNF  H1    C1   O1   112.00  3.000
 UNF  O5    C1   O1   111.31  3.000
 UNF  H1    C1   C2   111.17  3.000
 UNF  O5    C1   C2   110.37  3.000
 UNF  O1    C1   C2   107.29  3.000
 UNF  H2    C2   O2   111.54  3.000
 UNF  H2    C2   C3   108.41  3.000
 UNF  O2    C2   C3   110.10  3.000
 UNF  H2    C2   C1   106.85  3.000
 UNF  O2    C2   C1   111.10  3.000
 UNF  C3    C2   C1   108.72  3.000
 UNF  H3    C3   O3   110.39  3.000
 UNF  H3    C3   C4   108.47  3.000
 UNF  O3    C3   C4   111.68  3.000
 UNF  H3    C3   C2   108.54  3.000
 UNF  O3    C3   C2   108.50  3.000
 UNF  C4    C3   C2   109.20  3.000
 UNF  H41C  C4   C5   118.98  3.000
 UNF  H41C  C4   C3   118.65  3.000
 UNF  C5    C4   C3   122.36  3.000
 UNF  O5    C5   C6   114.34  3.000
 UNF  O5    C5   C4   124.24  3.000
 UNF  C6    C5   C4   121.41  3.000
 UNF  OAN   C6   O6   123.76  3.000
 UNF  OAN   C6   C5   112.52  3.000
 UNF  O6    C6   C5   123.70  3.000
 UNF  C4'   O1   C1   118.14  3.000
 UNF  HA    O2   C2   108.47  3.000
 UNF  HB    O3   C3   108.22  3.000
 UNF  C5    O5   C1   114.78  3.000
 UNF  H1'   C1'  O5'  108.50  3.000
 UNF  H1'   C1'  O1'  111.36  3.000
 UNF  O5'   C1'  O1'  108.67  3.000
 UNF  H1'   C1'  C2'  109.24  3.000
 UNF  O5'   C1'  C2'  109.22  3.000
 UNF  O1'   C1'  C2'  109.82  3.000
 UNF  H2'   C2'  O2'  105.96  3.000
 UNF  H2'   C2'  C3'  109.43  3.000
 UNF  O2'   C2'  C3'  110.64  3.000
 UNF  H2'   C2'  C1'  108.84  3.000
 UNF  O2'   C2'  C1'  113.25  3.000
 UNF  C3'   C2'  C1'  108.65  3.000
 UNF  H3'   C3'  O3'  110.23  3.000
 UNF  H3'   C3'  C4'  105.77  3.000
 UNF  O3'   C3'  C4'  110.15  3.000
 UNF  H3'   C3'  C2'  107.60  3.000
 UNF  O3'   C3'  C2'  111.99  3.000
 UNF  C4'   C3'  C2'  110.88  3.000
 UNF  H4'   C4'  C5'  109.41  3.000
 UNF  H4'   C4'  C3'  108.72  3.000
 UNF  C5'   C4'  C3'  107.74  3.000
 UNF  H4'   C4'  O1   112.02  3.000
 UNF  C5'   C4'  O1   107.72  3.000
 UNF  C3'   C4'  O1   111.13  3.000
 UNF  H5'   C5'  O5'  111.39  3.000
 UNF  H5'   C5'  C6'  107.02  3.000
 UNF  O5'   C5'  C6'  106.82  3.000
 UNF  H5'   C5'  C4'  108.31  3.000
 UNF  O5'   C5'  C4'  111.51  3.000
 UNF  C6'   C5'  C4'  111.72  3.000
 UNF  OAC   C6'  O6'  124.35  3.000
 UNF  OAC   C6'  C5'  124.99  3.000
 UNF  O6'   C6'  C5'  110.64  3.000
 UNF  HD    O2'  C2'  109.89  3.000
 UNF  HE    O3'  C3'  107.38  3.000
 UNF  C5'   O5'  C1'  113.91  3.000
 UNF  H6'   O6'  C6'  110.10  3.000
 UNF  HAN   OAN  C6   108.95  3.000
 UNF  HC    O1'  C1'  108.87  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  CONST_01  HAN  OAN  C6   C5   180.00   0.0  0
 UNF  CONST_02  H6'  O6'  C6'  C5'  180.00   0.0  0
 UNF  Var_01    C4   C5   O5   C1    18.26  30.0  1
 UNF  Var_02    O5   C5   C4   C3    -0.17  30.0  1
 UNF  Var_03    O6   C6   C5   C4    -7.35  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-1  HAN  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
 UNF  plan-2  H6'  0.020

