# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:00:25 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: biphenyl-4-yl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2)c3ccccc3)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 3X8  3X8  'biphenyl-4-yl alpha-D-mannopyranoside'  ligand  44  24  .  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_3X8
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
 3X8  C4   C  CH1   0   0.029   4.2427   0.6547   0.3319
 3X8  C5   C  CH1   0  -0.014   2.9138   1.3436   0.0121
 3X8  C6   C  CH2   0  -0.160   3.1206   2.7576  -0.4873
 3X8  C3   C  CH1   0   0.002   3.9909  -0.8123   0.6644
 3X8  CAH  C  CR16  0  -0.315  -5.3311  -1.2540   0.5071
 3X8  CAI  C  CR16  0  -0.239  -6.7112  -1.1231   0.4579
 3X8  CAJ  C  CR16  0  -0.269  -7.2866   0.0483  -0.0169
 3X8  CAK  C  CR16  0  -0.240  -6.4674   1.0863  -0.4416
 3X8  CAL  C  CR16  0  -0.315  -5.0873   0.9557  -0.3890
 3X8  CAG  C  CR6   0   0.094  -4.4957  -0.2167   0.0862
 3X8  CAD  C  CR6   0   0.071  -3.0276  -0.3596   0.1417
 3X8  CAC  C  CR16  0  -0.297  -2.4085  -1.0573   1.1819
 3X8  CAB  C  CR16  0  -0.335  -1.0354  -1.2082   1.2282
 3X8  CAE  C  CR16  0  -0.301  -2.2077   0.1931  -0.8396
 3X8  CAF  C  CR16  0  -0.343  -0.8264   0.0604  -0.8034
 3X8  CAA  C  CR6   0   0.373  -0.2337  -0.6587   0.2301
 3X8  O1   O  O2    0  -0.504   1.0983  -0.8756   0.3531
 3X8  C1   C  CH1   0   0.201   1.9464  -0.6960  -0.7565
 3X8  O5   O  O2    0  -0.489   2.2204   0.6396  -1.0080
 3X8  O6   O  OH1   0  -0.667   1.8646   3.3687  -0.6598
 3X8  O4   O  OH1   0  -0.675   4.8172   1.3304   1.4246
 3X8  O3   O  OH1   0  -0.672   5.2384  -1.4173   0.9055
 3X8  C2   C  CH1   0  -0.021   3.2220  -1.4937  -0.4645
 3X8  O2   O  OH1   0  -0.665   4.0376  -1.5226  -1.6063
 3X8  H41  H  HCH1  0   0.216   4.8931   0.7158  -0.5530
 3X8  H5   H  HCH1  0   0.231   2.3113   1.3763   0.9308
 3X8  H62  H  HCH2  0   0.212   3.7349   3.2940   0.2435
 3X8  H61  H  HCH2  0   0.197   3.6918   2.7235  -1.4260
 3X8  H31  H  HCH1  0   0.231   3.3641  -0.8462   1.5660
 3X8  HAI  H  HCR6  0   0.257  -7.3376  -1.9435   0.7840
 3X8  HAJ  H  HCR6  0   0.256  -8.3632   0.1508  -0.0569
 3X8  HAK  H  HCR6  0   0.257  -6.9032   2.0060  -0.8096
 3X8  HAL  H  HCR6  0   0.252  -4.4660   1.7849  -0.7043
 3X8  HAC  H  HCR6  0   0.256  -3.0031  -1.4847   1.9796
 3X8  HAB  H  HCR6  0   0.265  -0.5752  -1.7537   2.0424
 3X8  HAE  H  HCR6  0   0.257  -2.6485   0.7333  -1.6683
 3X8  HAF  H  HCR6  0   0.283  -0.2381   0.5273  -1.5802
 3X8  H1   H  HCH1  0   0.264   1.4608  -1.0781  -1.6631
 3X8  H63  H  HOH1  0   0.456   2.0142   4.2742  -0.9457
 3X8  H42  H  HOH1  0   0.453   5.6330   0.8753   1.6585
 3X8  H32  H  HOH1  0   0.458   5.1010  -2.2062   1.4383
 3X8  H21  H  HCH1  0   0.241   2.9339  -2.5068  -0.1529
 3X8  H22  H  HOH1  0   0.458   3.6369  -2.1085  -2.2559
 3X8  HAH  H  HCR6  0   0.253  -4.9012  -2.1829   0.8600

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
 3X8  CAJ  CAK  aromatic  1.389  0.020  1.389
 3X8  CAJ  CAI  aromatic  1.389  0.020  1.389
 3X8  CAK  CAL  aromatic  1.387  0.020  1.387
 3X8  CAI  CAH  aromatic  1.387  0.020  1.387
 3X8  CAL  CAG  aromatic  1.396  0.020  1.396
 3X8  CAH  CAG  aromatic  1.397  0.020  1.397
 3X8  CAG  CAD  single    1.476  0.020  1.476
 3X8  CAD  CAE  aromatic  1.393  0.020  1.393
 3X8  CAD  CAC  aromatic  1.397  0.020  1.397
 3X8  CAE  CAF  aromatic  1.388  0.020  1.388
 3X8  CAC  CAB  aromatic  1.382  0.020  1.382
 3X8  CAF  CAA  aromatic  1.392  0.020  1.392
 3X8  CAB  CAA  aromatic  1.393  0.020  1.393
 3X8  CAA  O1   single    1.355  0.020  1.355
 3X8  O1   C1   single    1.408  0.020  1.408
 3X8  C1   O5   single    1.386  0.020  1.386
 3X8  C1   C2   single    1.533  0.020  1.533
 3X8  O5   C5   single    1.420  0.020  1.420
 3X8  C5   C6   single    1.514  0.020  1.514
 3X8  C5   C4   single    1.531  0.020  1.531
 3X8  C2   C3   single    1.526  0.020  1.526
 3X8  C2   O2   single    1.403  0.020  1.403
 3X8  C6   O6   single    1.407  0.020  1.407
 3X8  C3   C4   single    1.525  0.020  1.525
 3X8  C3   O3   single    1.407  0.020  1.407
 3X8  C4   O4   single    1.407  0.020  1.407
 3X8  C4   H41  single    0.970  0.020  1.090
 3X8  C5   H5   single    0.970  0.020  1.090
 3X8  C6   H62  single    0.970  0.020  1.090
 3X8  C6   H61  single    0.970  0.020  1.090
 3X8  C3   H31  single    0.970  0.020  1.090
 3X8  CAH  HAH  single    0.930  0.020  1.080
 3X8  CAI  HAI  single    0.930  0.020  1.080
 3X8  CAJ  HAJ  single    0.930  0.020  1.080
 3X8  CAK  HAK  single    0.930  0.020  1.080
 3X8  CAL  HAL  single    0.930  0.020  1.080
 3X8  CAC  HAC  single    0.930  0.020  1.080
 3X8  CAB  HAB  single    0.930  0.020  1.080
 3X8  CAE  HAE  single    0.930  0.020  1.080
 3X8  CAF  HAF  single    0.930  0.020  1.080
 3X8  C1   H1   single    0.970  0.020  1.090
 3X8  O6   H63  single    0.850  0.020  0.980
 3X8  O4   H42  single    0.850  0.020  0.980
 3X8  O3   H32  single    0.850  0.020  0.980
 3X8  C2   H21  single    0.970  0.020  1.090
 3X8  O2   H22  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
 3X8  H41  C4   O4   110.89  3.000
 3X8  H41  C4   C3   109.05  3.000
 3X8  O4   C4   C3   111.10  3.000
 3X8  H41  C4   C5   108.68  3.000
 3X8  O4   C4   C5   107.49  3.000
 3X8  C3   C4   C5   109.58  3.000
 3X8  H5   C5   O5   110.34  3.000
 3X8  H5   C5   C6   108.83  3.000
 3X8  O5   C5   C6   107.02  3.000
 3X8  H5   C5   C4   108.34  3.000
 3X8  C6   C5   C4   111.76  3.000
 3X8  O5   C5   C4   110.54  3.000
 3X8  H61  C6   H62  107.08  3.000
 3X8  H61  C6   O6   111.87  3.000
 3X8  H62  C6   O6   111.70  3.000
 3X8  H61  C6   C5   108.88  3.000
 3X8  H62  C6   C5   108.30  3.000
 3X8  O6   C6   C5   108.91  3.000
 3X8  H31  C3   C2   107.80  3.000
 3X8  H31  C3   O3   110.60  3.000
 3X8  C2   C3   O3   112.42  3.000
 3X8  H31  C3   C4   107.63  3.000
 3X8  O3   C3   C4   107.73  3.000
 3X8  C2   C3   C4   110.57  3.000
 3X8  HAH  CAH  CAG  119.86  3.000
 3X8  HAH  CAH  CAI  119.18  3.000
 3X8  CAG  CAH  CAI  120.95  3.000
 3X8  HAI  CAI  CAJ  120.17  3.000
 3X8  HAI  CAI  CAH  119.57  3.000
 3X8  CAJ  CAI  CAH  120.26  3.000
 3X8  HAJ  CAJ  CAK  120.31  3.000
 3X8  HAJ  CAJ  CAI  120.31  3.000
 3X8  CAK  CAJ  CAI  119.38  3.000
 3X8  HAK  CAK  CAL  119.57  3.000
 3X8  HAK  CAK  CAJ  120.11  3.000
 3X8  CAL  CAK  CAJ  120.32  3.000
 3X8  HAL  CAL  CAG  119.92  3.000
 3X8  HAL  CAL  CAK  119.18  3.000
 3X8  CAG  CAL  CAK  120.89  3.000
 3X8  CAD  CAG  CAL  121.03  3.000
 3X8  CAD  CAG  CAH  120.77  3.000
 3X8  CAL  CAG  CAH  118.20  3.000
 3X8  CAE  CAD  CAC  117.50  3.000
 3X8  CAC  CAD  CAG  121.14  3.000
 3X8  CAE  CAD  CAG  121.36  3.000
 3X8  HAC  CAC  CAB  118.53  3.000
 3X8  HAC  CAC  CAD  120.15  3.000
 3X8  CAB  CAC  CAD  121.31  3.000
 3X8  HAB  CAB  CAA  119.53  3.000
 3X8  HAB  CAB  CAC  120.17  3.000
 3X8  CAA  CAB  CAC  120.31  3.000
 3X8  HAE  CAE  CAF  118.21  3.000
 3X8  HAE  CAE  CAD  119.83  3.000
 3X8  CAF  CAE  CAD  121.96  3.000
 3X8  HAF  CAF  CAA  121.69  3.000
 3X8  HAF  CAF  CAE  118.80  3.000
 3X8  CAA  CAF  CAE  119.51  3.000
 3X8  O1   CAA  CAF  124.66  3.000
 3X8  O1   CAA  CAB  115.94  3.000
 3X8  CAF  CAA  CAB  119.39  3.000
 3X8  C1   O1   CAA  120.01  3.000
 3X8  H1   C1   C2   110.15  3.000
 3X8  H1   C1   O5   105.85  3.000
 3X8  C2   C1   O5   111.81  3.000
 3X8  H1   C1   O1   109.88  3.000
 3X8  C2   C1   O1   106.55  3.000
 3X8  O5   C1   O1   112.64  3.000
 3X8  C1   O5   C5   116.34  3.000
 3X8  H63  O6   C6   107.85  3.000
 3X8  H42  O4   C4   107.91  3.000
 3X8  H32  O3   C3   108.72  3.000
 3X8  H21  C2   O2   111.36  3.000
 3X8  H21  C2   C1   108.42  3.000
 3X8  O2   C2   C1   109.84  3.000
 3X8  H21  C2   C3   109.52  3.000
 3X8  O2   C2   C3   108.55  3.000
 3X8  C1   C2   C3   109.13  3.000
 3X8  H22  O2   C2   108.65  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
 3X8  CONST_01  CAK  CAJ  CAI  CAH    0.00  0.0  0
 3X8  CONST_02  CAK  CAL  CAG  CAH    0.00  0.0  0
 3X8  CONST_05  CAL  CAK  CAJ  CAI    0.00  0.0  0
 3X8  CONST_06  CAL  CAG  CAH  CAI    0.00  0.0  0
 3X8  CONST_07  CAD  CAG  CAH  CAI  180.00  0.0  0
 3X8  CONST_08  CAG  CAL  CAK  CAJ    0.00  0.0  0
 3X8  CONST_09  CAG  CAH  CAI  CAJ    0.00  0.0  0
 3X8  CONST_10  CAD  CAG  CAL  CAK  180.00  0.0  0
 3X8  CONST_13  CAF  CAE  CAD  CAG  180.00  0.0  0
 3X8  CONST_14  CAB  CAC  CAD  CAG  180.00  0.0  0
 3X8  CONST_15  CAA  CAF  CAE  CAD    0.00  0.0  0
 3X8  CONST_16  CAA  CAB  CAC  CAD    0.00  0.0  0
 3X8  CONST_17  CAF  CAE  CAD  CAC    0.00  0.0  0
 3X8  CONST_18  CAF  CAA  CAB  CAC    0.00  0.0  0
 3X8  CONST_19  CAE  CAD  CAC  CAB    0.00  0.0  0
 3X8  CONST_20  CAE  CAF  CAA  CAB    0.00  0.0  0
 3X8  CONST_21  O1   CAA  CAB  CAC  180.00  0.0  0
 3X8  CONST_22  O1   CAA  CAF  CAE  180.00  0.0  0
 3X8  CONST_23  HAJ  CAJ  CAI  CAH  180.00  0.0  0
 3X8  CONST_24  HAL  CAL  CAG  CAH  180.00  0.0  0
 3X8  CONST_25  HAK  CAK  CAJ  CAI  180.00  0.0  0
 3X8  CONST_26  HAH  CAH  CAI  CAJ  180.00  0.0  0
 3X8  CONST_27  HAI  CAI  CAJ  CAK  180.00  0.0  0
 3X8  CONST_28  HAE  CAE  CAD  CAG    0.00  0.0  0
 3X8  CONST_29  HAC  CAC  CAD  CAG    0.00  0.0  0
 3X8  CONST_30  HAF  CAF  CAE  CAD  180.00  0.0  0
 3X8  CONST_31  HAB  CAB  CAC  CAD  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
 3X8  chir_01  C4  C5  C3  O4  positiv
 3X8  chir_02  C5  O5  C4  C6  negativ
 3X8  chir_03  C3  O3  C4  C2  negativ
 3X8  chir_04  C1  O5  O1  C2  positiv
 3X8  chir_05  C2  O2  C1  C3  positiv

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
 3X8  plan-1  CAH  0.020
 3X8  plan-1  CAI  0.020
 3X8  plan-1  CAJ  0.020
 3X8  plan-1  CAK  0.020
 3X8  plan-1  CAL  0.020
 3X8  plan-1  CAG  0.020
 3X8  plan-1  CAD  0.020
 3X8  plan-1  HAI  0.020
 3X8  plan-1  HAJ  0.020
 3X8  plan-1  HAK  0.020
 3X8  plan-1  HAL  0.020
 3X8  plan-1  HAH  0.020
 3X8  plan-2  CAG  0.020
 3X8  plan-2  CAD  0.020
 3X8  plan-2  CAC  0.020
 3X8  plan-2  CAB  0.020
 3X8  plan-2  CAE  0.020
 3X8  plan-2  CAF  0.020
 3X8  plan-2  CAA  0.020
 3X8  plan-2  O1   0.020
 3X8  plan-2  HAC  0.020
 3X8  plan-2  HAB  0.020
 3X8  plan-2  HAE  0.020
 3X8  plan-2  HAF  0.020

