# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 05:21:44 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-O-alpha-D-galactopyranuronosyl-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]2O[C@@H]([C@H](O)[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
 AD0  AD0  '4-O-alpha-D-galactopyranuronosyl-alpha-D-galactopyranuronic acid'  ligand  43  25  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AD0
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
 AD0  C1   C  CH1   0   0.232  -4.6866  13.9649   98.4370
 AD0  C2   C  CH1   0  -0.011  -3.8370  15.1314   97.9221
 AD0  C3   C  CH1   0   0.006  -2.5041  14.6134   97.3991
 AD0  C4   C  CH1   0  -0.001  -1.8050  13.7790   98.4719
 AD0  C5   C  CH1   0  -0.085  -2.7716  12.7091   98.9723
 AD0  C6   C  C     0   0.510  -2.1820  11.9513  100.1422
 AD0  O1   O  O2    0  -0.502  -5.0364  13.1691   97.3520
 AD0  O2   O  OH1   0  -0.664  -4.4689  15.8376   96.8847
 AD0  O3   O  OH1   0  -0.675  -1.6307  15.6598   97.0499
 AD0  O4   O  OH1   0  -0.669  -1.4162  14.5519   99.5789
 AD0  O5   O  O2    0  -0.488  -3.9813  13.2617   99.4187
 AD0  O6   O  OH1   0  -0.595  -1.0876  11.2989   99.7750
 AD0  C1'  C  CH1   0   0.222  -6.2173  10.9633   94.9317
 AD0  O60  O  O     0  -0.424  -2.6419  11.9270  101.2515
 AD0  C2'  C  CH1   0  -0.024  -5.3116  10.5247   96.0865
 AD0  C3'  C  CH1   0   0.044  -5.9349  10.9124   97.4226
 AD0  C4'  C  CH1   0  -0.016  -6.2217  12.4099   97.4427
 AD0  C5'  C  CH1   0  -0.083  -7.0835  12.7497   96.2257
 AD0  C6'  C  C     0   0.531  -7.3371  14.2435   96.1849
 AD0  O2'  O  OH1   0  -0.670  -5.1004   9.1351   96.0955
 AD0  O3'  O  OH1   0  -0.659  -5.1070  10.5821   98.5035
 AD0  O5'  O  O2    0  -0.496  -6.4729  12.3460   95.0269
 AD0  O6'  O  OH1   0  -0.571  -7.1283  14.7876   95.0039
 AD0  OAP  O  O     0  -0.450  -7.7343  14.8488   97.1494
 AD0  H1   H  HCH1  0   0.246  -5.5795  14.3460   98.9468
 AD0  H2   H  HCH1  0   0.233  -3.6431  15.7868   98.7807
 AD0  H3   H  HCH1  0   0.223  -2.6912  13.9583   96.5362
 AD0  HA   H  HOH1  0   0.458  -5.1321  16.4207   97.2659
 AD0  H4   H  HCH1  0   0.247  -0.9431  13.2783   98.0101
 AD0  HB   H  HOH1  0   0.456  -2.1090  16.2835   96.4930
 AD0  H5   H  HCH1  0   0.282  -2.9364  11.9875   98.1631
 AD0  HC   H  HOH1  0   0.455  -0.9036  15.3018   99.2574
 AD0  H6   H  HOH1  0   0.487  -0.7100  10.8266  100.5320
 AD0  H4'  H  HCH1  0   0.265  -6.7818  12.6569   98.3519
 AD0  H1'  H  HCH1  0   0.241  -5.6889  10.8511   93.9780
 AD0  H2'  H  HCH1  0   0.240  -4.3628  11.0654   95.9758
 AD0  H3'  H  HCH1  0   0.223  -6.9084  10.4072   97.5170
 AD0  HE   H  HOH1  0   0.461  -4.3906   8.9245   95.4818
 AD0  HF   H  HOH1  0   0.450  -4.8312   9.6658   98.3913
 AD0  H5'  H  HCH1  0   0.280  -8.0677  12.2757   96.3552
 AD0  H6'  H  HOH1  0   0.485  -7.3306  15.7350   95.0419
 AD0  O1'  O  OH1   0  -0.660  -7.3784  10.2058   94.9601
 AD0  HD   H  HOH1  0   0.465  -7.8386  10.2997   94.1193

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
 AD0  C1   C2   single  1.532  0.020  1.532
 AD0  C2   C3   single  1.523  0.020  1.523
 AD0  C3   C4   single  1.528  0.020  1.528
 AD0  C4   C5   single  1.526  0.020  1.526
 AD0  C5   C6   single  1.513  0.020  1.513
 AD0  C1   O1   single  1.390  0.020  1.390
 AD0  C2   O2   single  1.405  0.020  1.405
 AD0  C3   O3   single  1.407  0.020  1.407
 AD0  C4   O4   single  1.405  0.020  1.405
 AD0  C5   O5   single  1.403  0.020  1.403
 AD0  C1   O5   single  1.398  0.020  1.398
 AD0  C6   O6   single  1.326  0.020  1.326
 AD0  C6   O60  double  1.201  0.020  1.201
 AD0  C1'  C2'  single  1.532  0.020  1.532
 AD0  C2'  C3'  single  1.524  0.020  1.524
 AD0  O1   C4'  single  1.411  0.020  1.411
 AD0  C3'  C4'  single  1.525  0.020  1.525
 AD0  C4'  C5'  single  1.529  0.020  1.529
 AD0  C5'  C6'  single  1.516  0.020  1.516
 AD0  C1'  O1'  single  1.387  0.020  1.387
 AD0  C2'  O2'  single  1.406  0.020  1.406
 AD0  C3'  O3'  single  1.401  0.020  1.401
 AD0  C1'  O5'  single  1.409  0.020  1.409
 AD0  C5'  O5'  single  1.405  0.020  1.405
 AD0  C6'  O6'  single  1.317  0.020  1.317
 AD0  C6'  OAP  double  1.206  0.020  1.206
 AD0  C1   H1   single  0.970  0.020  1.090
 AD0  C2   H2   single  0.970  0.020  1.090
 AD0  C3   H3   single  0.970  0.020  1.090
 AD0  O2   HA   single  0.850  0.020  0.980
 AD0  C4   H4   single  0.970  0.020  1.090
 AD0  O3   HB   single  0.850  0.020  0.980
 AD0  C5   H5   single  0.970  0.020  1.090
 AD0  O4   HC   single  0.850  0.020  0.980
 AD0  O6   H6   single  0.850  0.020  0.980
 AD0  C4'  H4'  single  0.970  0.020  1.090
 AD0  C1'  H1'  single  0.970  0.020  1.090
 AD0  C2'  H2'  single  0.970  0.020  1.090
 AD0  O1'  HD   single  0.850  0.020  0.980
 AD0  C3'  H3'  single  0.970  0.020  1.090
 AD0  O2'  HE   single  0.850  0.020  0.980
 AD0  O3'  HF   single  0.850  0.020  0.980
 AD0  C5'  H5'  single  0.970  0.020  1.090
 AD0  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
 AD0  H1   C1   O5   105.01  3.000
 AD0  H1   C1   O1   110.91  3.000
 AD0  O5   C1   O1   112.76  3.000
 AD0  H1   C1   C2   110.07  3.000
 AD0  O5   C1   C2   109.82  3.000
 AD0  O1   C1   C2   108.24  3.000
 AD0  H2   C2   O2   110.91  3.000
 AD0  H2   C2   C3   108.49  3.000
 AD0  O2   C2   C3   108.13  3.000
 AD0  H2   C2   C1   106.84  3.000
 AD0  O2   C2   C1   112.42  3.000
 AD0  C3   C2   C1   109.99  3.000
 AD0  H3   C3   O3   110.72  3.000
 AD0  H3   C3   C4   107.67  3.000
 AD0  O3   C3   C4   107.24  3.000
 AD0  H3   C3   C2   108.86  3.000
 AD0  O3   C3   C2   112.06  3.000
 AD0  C4   C3   C2   110.19  3.000
 AD0  H4   C4   O4   111.40  3.000
 AD0  H4   C4   C5   108.37  3.000
 AD0  O4   C4   C5   107.61  3.000
 AD0  H4   C4   C3   108.22  3.000
 AD0  O4   C4   C3   112.29  3.000
 AD0  C5   C4   C3   108.85  3.000
 AD0  H5   C5   O5   111.37  3.000
 AD0  H5   C5   C6   107.43  3.000
 AD0  O5   C5   C6   106.69  3.000
 AD0  H5   C5   C4   108.33  3.000
 AD0  O5   C5   C4   111.98  3.000
 AD0  C6   C5   C4   110.96  3.000
 AD0  O60  C6   O6   124.18  3.000
 AD0  O60  C6   C5   125.10  3.000
 AD0  O6   C6   C5   110.72  3.000
 AD0  C4'  O1   C1   117.99  3.000
 AD0  HA   O2   C2   108.79  3.000
 AD0  HB   O3   C3   108.47  3.000
 AD0  HC   O4   C4   108.20  3.000
 AD0  C5   O5   C1   114.18  3.000
 AD0  H6   O6   C6   110.19  3.000
 AD0  H1'  C1'  O5'  104.28  3.000
 AD0  H1'  C1'  O1'  111.44  3.000
 AD0  O5'  C1'  O1'  112.50  3.000
 AD0  H1'  C1'  C2'  109.98  3.000
 AD0  O5'  C1'  C2'  109.71  3.000
 AD0  O1'  C1'  C2'  108.86  3.000
 AD0  H2'  C2'  O2'  110.96  3.000
 AD0  H2'  C2'  C3'  108.45  3.000
 AD0  O2'  C2'  C3'  107.89  3.000
 AD0  H2'  C2'  C1'  107.10  3.000
 AD0  O2'  C2'  C1'  112.13  3.000
 AD0  C3'  C2'  C1'  110.26  3.000
 AD0  H3'  C3'  O3'  110.38  3.000
 AD0  H3'  C3'  C4'  106.45  3.000
 AD0  O3'  C3'  C4'  109.42  3.000
 AD0  H3'  C3'  C2'  108.67  3.000
 AD0  O3'  C3'  C2'  112.01  3.000
 AD0  C4'  C3'  C2'  109.77  3.000
 AD0  H4'  C4'  C5'  108.78  3.000
 AD0  H4'  C4'  C3'  109.17  3.000
 AD0  C5'  C4'  C3'  108.28  3.000
 AD0  H4'  C4'  O1   111.19  3.000
 AD0  C5'  C4'  O1   107.62  3.000
 AD0  C3'  C4'  O1   111.70  3.000
 AD0  H5'  C5'  O5'  111.44  3.000
 AD0  H5'  C5'  C6'  106.15  3.000
 AD0  O5'  C5'  C6'  109.45  3.000
 AD0  H5'  C5'  C4'  108.34  3.000
 AD0  O5'  C5'  C4'  111.73  3.000
 AD0  C6'  C5'  C4'  109.55  3.000
 AD0  OAP  C6'  O6'  124.19  3.000
 AD0  OAP  C6'  C5'  121.89  3.000
 AD0  O6'  C6'  C5'  113.88  3.000
 AD0  HE   O2'  C2'  108.87  3.000
 AD0  HF   O3'  C3'  107.67  3.000
 AD0  C5'  O5'  C1'  114.74  3.000
 AD0  H6'  O6'  C6'  109.60  3.000
 AD0  HD   O1'  C1'  109.21  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
 AD0  CONST_01  H6   O6   C6   C5   180.00  0.0  0
 AD0  CONST_02  H6'  O6'  C6'  C5'  180.00  0.0  0

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
 AD0  chir_01  C1   C2   O1   O5   negativ
 AD0  chir_02  C2   O2   C1   C3   negativ
 AD0  chir_03  C3   O3   C2   C4   positiv
 AD0  chir_04  C4   O4   C3   C5   positiv
 AD0  chir_05  C5   O5   C4   C6   negativ
 AD0  chir_06  C1'  C2'  O1'  O5'  negativ
 AD0  chir_07  C2'  O2'  C1'  C3'  negativ
 AD0  chir_08  C3'  O3'  C2'  C4'  positiv
 AD0  chir_09  C4'  O1   C5'  C3'  negativ
 AD0  chir_10  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
 AD0  plan-1  C5   0.020
 AD0  plan-1  C6   0.020
 AD0  plan-1  O6   0.020
 AD0  plan-1  O60  0.020
 AD0  plan-1  H6   0.020
 AD0  plan-2  C5'  0.020
 AD0  plan-2  C6'  0.020
 AD0  plan-2  O6'  0.020
 AD0  plan-2  OAP  0.020
 AD0  plan-2  H6'  0.020

