# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 13:31:25 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: hexyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O
#
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
 4YA  4YA  'hexyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside'  ligand  62  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4YA
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
 4YA  C1   C  CH1   0   0.237  -2.0229  -1.3138   0.6416
 4YA  C2   C  CH1   0  -0.036  -2.6138  -2.4625  -0.1804
 4YA  O2   O  OH1   0  -0.670  -3.6218  -2.0189  -1.0566
 4YA  C3   C  CH1   0   0.019  -1.5015  -3.2057  -0.9205
 4YA  O3   O  OH1   0  -0.673  -1.9978  -4.3158  -1.6254
 4YA  C4   C  CH1   0  -0.002  -0.4407  -3.6655   0.0683
 4YA  O4   O  OH1   0  -0.674  -1.0104  -4.6402   0.9097
 4YA  C5   C  CH1   0   0.011   0.0698  -2.4427   0.8336
 4YA  O5   O  O2    0  -0.494  -1.0018  -1.7589   1.4758
 4YA  C6   C  CH3   0  -0.714   1.0840  -2.7887   1.9037
 4YA  O6   O  OH1   0  -0.668   0.3736   5.5727  -0.8064
 4YA  C6B  C  CH3   0  -0.662   7.8758  -1.5958  -0.0696
 4YA  C5B  C  CH2   0  -0.420   6.9207  -0.4434  -0.3473
 4YA  C4B  C  CH2   0  -0.405   5.4901  -0.7425   0.0830
 4YA  C3B  C  CH2   0  -0.420   4.5244   0.3973  -0.2155
 4YA  C2B  C  CH2   0  -0.461   3.0984   0.0983   0.2300
 4YA  C1B  C  CH2   0  -0.136   2.1484   1.2199  -0.1363
 4YA  C1A  C  CH1   0   0.310  -0.1748   1.5848  -0.2534
 4YA  O5A  O  O2    0  -0.496  -0.1168   2.9416   0.1028
 4YA  C5A  C  CH1   0  -0.008  -1.1046   3.7324  -0.5233
 4YA  C6A  C  CH2   0  -0.165  -0.8331   5.1839  -0.1957
 4YA  C4A  C  CH1   0  -0.025  -2.4954   3.2826  -0.0748
 4YA  O4A  O  OH1   0  -0.672  -2.6886   3.4572   1.3083
 4YA  C3A  C  CH1   0   0.020  -2.6485   1.7985  -0.4098
 4YA  O3A  O  OH1   0  -0.661  -3.8599   1.2594   0.0446
 4YA  C2A  C  CH1   0  -0.001  -1.5078   0.9834   0.1945
 4YA  O2A  O  O2    0  -0.523  -1.5865  -0.3454  -0.2719
 4YA  H1   H  HCH1  0   0.242  -2.7859  -0.8949   1.3055
 4YA  H2   H  HCH1  0   0.246  -3.0963  -3.1542   0.5157
 4YA  H3   H  HOH1  0   0.442  -3.3209  -1.2007  -1.4687
 4YA  H4   H  HCH1  0   0.213  -1.0070  -2.5033  -1.6088
 4YA  H5   H  HOH1  0   0.447  -2.6582  -3.9904  -2.2458
 4YA  H6   H  HCH1  0   0.229   0.4091  -4.0783  -0.4953
 4YA  H7   H  HOH1  0   0.455  -0.3090  -5.0539   1.4207
 4YA  H8   H  HCH1  0   0.230   0.5517  -1.7794   0.1070
 4YA  H9   H  HCH3  0   0.228   0.6498  -3.3902   2.7039
 4YA  H10  H  HCH3  0   0.235   1.9160  -3.3452   1.4704
 4YA  H11  H  HCH3  0   0.249   1.4936  -1.8831   2.3500
 4YA  H12  H  HOH1  0   0.456   0.5466   6.4874  -0.5669
 4YA  H13  H  HCH3  0   0.216   7.9160  -1.8274   0.9963
 4YA  H14  H  HCH3  0   0.216   7.5604  -2.5024  -0.5900
 4YA  H15  H  HCH3  0   0.226   8.8902  -1.3637  -0.3959
 4YA  H16  H  HCH2  0   0.211   7.2721   0.4567   0.1667
 4YA  H17  H  HCH2  0   0.211   6.9346  -0.2066  -1.4158
 4YA  H18  H  HCH2  0   0.208   5.1424  -1.6520  -0.4193
 4YA  H19  H  HCH2  0   0.209   5.4714  -0.9641   1.1557
 4YA  H20  H  HCH2  0   0.214   4.8772   1.3108   0.2752
 4YA  H21  H  HCH2  0   0.213   4.5374   0.6066  -1.2908
 4YA  H22  H  HCH2  0   0.222   2.7555  -0.8334  -0.2308
 4YA  H23  H  HCH2  0   0.223   3.0768  -0.0605   1.3125
 4YA  H24  H  HCH2  0   0.201   2.1106   1.3342  -1.2279
 4YA  H25  H  HCH2  0   0.208   2.5126   2.1688   0.2731
 4YA  H26  H  HCH1  0   0.180  -0.0881   1.4923  -1.3548
 4YA  H27  H  HCH1  0   0.219  -1.0528   3.6112  -1.6184
 4YA  H28  H  HCH2  0   0.202  -0.7936   5.3123   0.8930
 4YA  H29  H  HCH2  0   0.204  -1.6830   5.7762  -0.5613
 4YA  H30  H  HCH1  0   0.240  -3.2411   3.8437  -0.6542
 4YA  H31  H  HOH1  0   0.458  -3.0452   4.3353   1.4653
 4YA  H32  H  HCH1  0   0.222  -2.5683   1.7122  -1.5042
 4YA  H33  H  HOH1  0   0.455  -4.5614   1.5260  -0.5571
 4YA  H34  H  HCH1  0   0.242  -1.5558   1.0220   1.2904
 4YA  O1   O  O2    0  -0.487   0.8552   0.9246   0.3695

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
 4YA  C6   C5   single  1.514  0.020  1.514
 4YA  O4   C4   single  1.408  0.020  1.408
 4YA  C5   O5   single  1.424  0.020  1.424
 4YA  C5   C4   single  1.530  0.020  1.530
 4YA  O5   C1   single  1.392  0.020  1.392
 4YA  C4   C3   single  1.521  0.020  1.521
 4YA  O4A  C4A  single  1.407  0.020  1.407
 4YA  O1   C1B  single  1.420  0.020  1.420
 4YA  O1   C1A  single  1.373  0.020  1.373
 4YA  C1   C2   single  1.531  0.020  1.531
 4YA  C1   O2A  single  1.401  0.020  1.401
 4YA  O5A  C1A  single  1.404  0.020  1.404
 4YA  O5A  C5A  single  1.412  0.020  1.412
 4YA  C2A  C1A  single  1.529  0.020  1.529
 4YA  C2A  O2A  single  1.411  0.020  1.411
 4YA  C2A  C3A  single  1.527  0.020  1.527
 4YA  C1B  C2B  single  1.515  0.020  1.515
 4YA  O3A  C3A  single  1.402  0.020  1.402
 4YA  C6A  C5A  single  1.513  0.020  1.513
 4YA  C6A  O6   single  1.407  0.020  1.407
 4YA  C4A  C3A  single  1.529  0.020  1.529
 4YA  C4A  C5A  single  1.529  0.020  1.529
 4YA  C3   C2   single  1.529  0.020  1.529
 4YA  C3   O3   single  1.406  0.020  1.406
 4YA  C2   O2   single  1.407  0.020  1.407
 4YA  C2B  C3B  single  1.524  0.020  1.524
 4YA  C3B  C4B  single  1.523  0.020  1.523
 4YA  C4B  C5B  single  1.524  0.020  1.524
 4YA  C5B  C6B  single  1.522  0.020  1.522
 4YA  C1   H1   single  0.970  0.020  1.090
 4YA  C2   H2   single  0.970  0.020  1.090
 4YA  O2   H3   single  0.850  0.020  0.980
 4YA  C3   H4   single  0.970  0.020  1.090
 4YA  O3   H5   single  0.850  0.020  0.980
 4YA  C4   H6   single  0.970  0.020  1.090
 4YA  O4   H7   single  0.850  0.020  0.980
 4YA  C5   H8   single  0.970  0.020  1.090
 4YA  C6   H9   single  0.970  0.020  1.090
 4YA  C6   H10  single  0.970  0.020  1.090
 4YA  C6   H11  single  0.970  0.020  1.090
 4YA  O6   H12  single  0.850  0.020  0.980
 4YA  C6B  H13  single  0.970  0.020  1.090
 4YA  C6B  H14  single  0.970  0.020  1.090
 4YA  C6B  H15  single  0.970  0.020  1.090
 4YA  C5B  H16  single  0.970  0.020  1.090
 4YA  C5B  H17  single  0.970  0.020  1.090
 4YA  C4B  H18  single  0.970  0.020  1.090
 4YA  C4B  H19  single  0.970  0.020  1.090
 4YA  C3B  H20  single  0.970  0.020  1.090
 4YA  C3B  H21  single  0.970  0.020  1.090
 4YA  C2B  H22  single  0.970  0.020  1.090
 4YA  C2B  H23  single  0.970  0.020  1.090
 4YA  C1B  H24  single  0.970  0.020  1.090
 4YA  C1B  H25  single  0.970  0.020  1.090
 4YA  C1A  H26  single  0.970  0.020  1.090
 4YA  C5A  H27  single  0.970  0.020  1.090
 4YA  C6A  H28  single  0.970  0.020  1.090
 4YA  C6A  H29  single  0.970  0.020  1.090
 4YA  C4A  H30  single  0.970  0.020  1.090
 4YA  O4A  H31  single  0.850  0.020  0.980
 4YA  C3A  H32  single  0.970  0.020  1.090
 4YA  O3A  H33  single  0.850  0.020  0.980
 4YA  C2A  H34  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
 4YA  H1   C1   O2A  110.37  3.000
 4YA  H1   C1   O5   105.68  3.000
 4YA  O2A  C1   O5   112.54  3.000
 4YA  H1   C1   C2   110.10  3.000
 4YA  O2A  C1   C2   106.79  3.000
 4YA  O5   C1   C2   111.41  3.000
 4YA  H2   C2   C3   108.77  3.000
 4YA  H2   C2   O2   106.24  3.000
 4YA  C3   C2   O2   111.90  3.000
 4YA  H2   C2   C1   107.64  3.000
 4YA  O2   C2   C1   111.97  3.000
 4YA  C3   C2   C1   110.10  3.000
 4YA  H3   O2   C2   108.06  3.000
 4YA  H4   C3   C4   106.62  3.000
 4YA  H4   C3   O3   110.43  3.000
 4YA  C4   C3   O3   109.48  3.000
 4YA  H4   C3   C2   108.63  3.000
 4YA  O3   C3   C2   111.70  3.000
 4YA  C4   C3   C2   109.85  3.000
 4YA  H5   O3   C3   107.36  3.000
 4YA  H6   C4   C5   107.36  3.000
 4YA  H6   C4   O4   111.04  3.000
 4YA  C5   C4   O4   112.91  3.000
 4YA  H6   C4   C3   108.61  3.000
 4YA  C5   C4   C3   108.43  3.000
 4YA  O4   C4   C3   108.39  3.000
 4YA  H7   O4   C4   108.68  3.000
 4YA  H8   C5   C6   108.20  3.000
 4YA  H8   C5   O5   109.84  3.000
 4YA  C6   C5   O5   107.15  3.000
 4YA  H8   C5   C4   107.39  3.000
 4YA  O5   C5   C4   110.99  3.000
 4YA  C6   C5   C4   113.22  3.000
 4YA  C5   O5   C1   115.80  3.000
 4YA  H11  C6   H10  107.46  3.000
 4YA  H11  C6   H9   107.90  3.000
 4YA  H10  C6   H9   108.27  3.000
 4YA  H11  C6   C5   110.57  3.000
 4YA  H10  C6   C5   110.29  3.000
 4YA  H9   C6   C5   112.19  3.000
 4YA  H12  O6   C6A  108.00  3.000
 4YA  H15  C6B  H14  107.63  3.000
 4YA  H15  C6B  H13  107.64  3.000
 4YA  H14  C6B  H13  107.46  3.000
 4YA  H15  C6B  C5B  111.59  3.000
 4YA  H14  C6B  C5B  111.12  3.000
 4YA  H13  C6B  C5B  111.21  3.000
 4YA  H17  C5B  H16  106.05  3.000
 4YA  H17  C5B  C4B  109.28  3.000
 4YA  H16  C5B  C4B  109.29  3.000
 4YA  H17  C5B  C6B  109.50  3.000
 4YA  H16  C5B  C6B  109.60  3.000
 4YA  C4B  C5B  C6B  112.89  3.000
 4YA  H19  C4B  H18  106.00  3.000
 4YA  H19  C4B  C3B  109.42  3.000
 4YA  H18  C4B  C3B  109.27  3.000
 4YA  H19  C4B  C5B  109.41  3.000
 4YA  H18  C4B  C5B  109.36  3.000
 4YA  C3B  C4B  C5B  113.14  3.000
 4YA  H21  C3B  H20  106.06  3.000
 4YA  H21  C3B  C2B  109.61  3.000
 4YA  H20  C3B  C2B  109.52  3.000
 4YA  H21  C3B  C4B  109.13  3.000
 4YA  H20  C3B  C4B  109.39  3.000
 4YA  C2B  C3B  C4B  112.90  3.000
 4YA  H23  C2B  H22  106.66  3.000
 4YA  H23  C2B  C1B  109.53  3.000
 4YA  H22  C2B  C1B  109.39  3.000
 4YA  H23  C2B  C3B  109.65  3.000
 4YA  H22  C2B  C3B  109.71  3.000
 4YA  C1B  C2B  C3B  111.77  3.000
 4YA  H25  C1B  H24  107.02  3.000
 4YA  H25  C1B  C2B  110.02  3.000
 4YA  H24  C1B  C2B  109.82  3.000
 4YA  H25  C1B  O1   110.47  3.000
 4YA  H24  C1B  O1   110.14  3.000
 4YA  C2B  C1B  O1   109.34  3.000
 4YA  H26  C1A  C2A  109.05  3.000
 4YA  H26  C1A  O5A  109.23  3.000
 4YA  C2A  C1A  O5A  109.98  3.000
 4YA  H26  C1A  O1   110.61  3.000
 4YA  C2A  C1A  O1   109.39  3.000
 4YA  O5A  C1A  O1   108.58  3.000
 4YA  C5A  O5A  C1A  113.57  3.000
 4YA  H27  C5A  C4A  107.55  3.000
 4YA  H27  C5A  C6A  108.18  3.000
 4YA  C4A  C5A  C6A  112.46  3.000
 4YA  H27  C5A  O5A  110.24  3.000
 4YA  C4A  C5A  O5A  109.97  3.000
 4YA  C6A  C5A  O5A  108.42  3.000
 4YA  H29  C6A  H28  107.17  3.000
 4YA  H29  C6A  C5A  107.85  3.000
 4YA  H28  C6A  C5A  109.49  3.000
 4YA  H29  C6A  O6   111.71  3.000
 4YA  H28  C6A  O6   111.56  3.000
 4YA  C5A  C6A  O6   108.97  3.000
 4YA  H30  C4A  C3A  108.19  3.000
 4YA  H30  C4A  O4A  111.22  3.000
 4YA  C3A  C4A  O4A  108.79  3.000
 4YA  H30  C4A  C5A  108.21  3.000
 4YA  C3A  C4A  C5A  108.20  3.000
 4YA  O4A  C4A  C5A  112.12  3.000
 4YA  H31  O4A  C4A  108.97  3.000
 4YA  H32  C3A  C2A  107.29  3.000
 4YA  H32  C3A  O3A  110.80  3.000
 4YA  C2A  C3A  O3A  108.18  3.000
 4YA  H32  C3A  C4A  106.66  3.000
 4YA  O3A  C3A  C4A  112.88  3.000
 4YA  C2A  C3A  C4A  110.90  3.000
 4YA  H33  O3A  C3A  108.72  3.000
 4YA  H34  C2A  O2A  111.15  3.000
 4YA  H34  C2A  C3A  110.11  3.000
 4YA  O2A  C2A  C3A  109.30  3.000
 4YA  H34  C2A  C1A  108.46  3.000
 4YA  C3A  C2A  C1A  108.99  3.000
 4YA  O2A  C2A  C1A  108.79  3.000
 4YA  C2A  O2A  C1   116.94  3.000
 4YA  C1A  O1   C1B  114.95  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
 4YA  Var_01  H24  C1B  O1   C1A   -37.85  30.0  3
 4YA  Var_02  C3B  C2B  C1B  O1   -176.63  30.0  3
 4YA  Var_03  C3B  C4B  C5B  C6B  -178.95  30.0  1
 4YA  Var_04  C2B  C3B  C4B  C5B  -179.41  30.0  2
 4YA  Var_05  C1B  C2B  C3B  C4B  -177.35  30.0  1
 4YA  Var_06  H13  C6B  C5B  C4B   -60.45  30.0  3

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
 4YA  chir_01  C1   O5   C2   O2A  positiv
 4YA  chir_02  C2   O2   C1   C3   positiv
 4YA  chir_03  C3   O3   C2   C4   negativ
 4YA  chir_04  C4   O4   C3   C5   negativ
 4YA  chir_05  C5   O5   C4   C6   positiv
 4YA  chir_06  C1A  O5A  O1   C2A  negativ
 4YA  chir_07  C5A  O5A  C6A  C4A  positiv
 4YA  chir_08  C4A  O4A  C5A  C3A  negativ
 4YA  chir_09  C3A  O3A  C2A  C4A  positiv
 4YA  chir_10  C2A  O2A  C3A  C1A  positiv

