# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:51:21 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 3'-chloro-4'-(alpha-D-mannopyranosyloxy)biphenyl-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2Cl)c3ccc(cc3)C#N)[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
 CWK  CWK  3'-chloro-4'-(alpha-D-mannopyranosyloxy)biphenyl-4-carbonitrile  ligand  45  27  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CWK
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
 CWK  CL   CL  CL    0  -0.102   0.6234  -2.6156   1.0231
 CWK  C1   C   CH1   0   0.201   2.7063   0.1184  -1.4077
 CWK  O1   O   O2    0  -0.488   1.8285  -0.8332  -0.8363
 CWK  C2   C   CH1   0  -0.026   4.0853  -0.5481  -1.4306
 CWK  O2   O   OH1   0  -0.664   4.9840   0.2552  -2.1478
 CWK  C3   C   CH1   0   0.001   4.5924  -0.6927   0.0024
 CWK  O3   O   OH1   0  -0.671   5.9164  -1.1665   0.0560
 CWK  C4   C   CH1   0   0.031   4.5548   0.6521   0.7200
 CWK  O4   O   OH1   0  -0.675   4.8825   0.5076   2.0810
 CWK  C5   C   CH1   0  -0.016   3.1456   1.2426   0.6447
 CWK  O5   O   O2    0  -0.481   2.7050   1.3081  -0.7057
 CWK  C6   C   CH2   0  -0.159   3.0992   2.6506   1.1985
 CWK  O6   O   OH1   0  -0.666   1.7649   3.0973   1.2043
 CWK  CAA  C   CR6   0   0.469   0.5204  -0.5557  -0.7114
 CWK  CAB  C   CR16  0  -0.345  -0.1558   0.4611  -1.3774
 CWK  CAC  C   CR16  0  -0.291  -1.5188   0.6275  -1.1994
 CWK  CAD  C   CR6   0   0.060  -2.2495  -0.2017  -0.3513
 CWK  CAE  C   CR16  0  -0.259  -1.5689  -1.2133   0.3254
 CWK  CAF  C   CR6   0  -0.151  -0.2088  -1.3764   0.1517
 CWK  CAG  C   CR6   0   0.110  -3.6996  -0.0205  -0.1667
 CWK  CAH  C   CR16  0  -0.302  -4.5418  -1.1223   0.0024
 CWK  CAI  C   CR16  0  -0.222  -5.9024  -0.9578   0.1803
 CWK  CAJ  C   CR6   0  -0.011  -6.4472   0.3258   0.1885
 CWK  CAK  C   CR16  0  -0.222  -5.6215   1.4370   0.0187
 CWK  CAL  C   CR16  0  -0.301  -4.2627   1.2583  -0.1557
 CWK  CAN  C   CSP   0   0.055  -7.8505   0.5023   0.3703
 CWK  NAO  N   NS    0  -0.252  -8.9849   0.6446   0.5164
 CWK  H1   H   HCH1  0   0.267   2.3884   0.3640  -2.4276
 CWK  H5   H   HCH1  0   0.229   2.4690   0.6101   1.2375
 CWK  H2   H   HCH1  0   0.245   3.9840  -1.5427  -1.8855
 CWK  HO2  H   HOH1  0   0.459   4.7959   0.1665  -3.0871
 CWK  H3   H   HCH1  0   0.233   3.9155  -1.3771   0.5319
 CWK  HO3  H   HOH1  0   0.459   5.9083  -2.1245  -0.0314
 CWK  H4   H   HCH1  0   0.215   5.2526   1.3414   0.2211
 CWK  HO4  H   HOH1  0   0.453   5.7383   0.0685   2.1306
 CWK  H61  H   HCH2  0   0.214   3.5251   2.6322   2.2070
 CWK  H62  H   HCH2  0   0.196   3.7451   3.2957   0.5863
 CWK  HO6  H   HOH1  0   0.456   1.7402   3.9423   1.6622
 CWK  HAB  H   HCR6  0   0.291   0.3620   1.1276  -2.0525
 CWK  HAC  H   HCR6  0   0.269  -2.0158   1.4131  -1.7534
 CWK  HAE  H   HCR6  0   0.282  -2.0907  -1.8630   1.0161
 CWK  HAH  H   HCR6  0   0.272  -4.1373  -2.1257  -0.0249
 CWK  HAI  H   HCR6  0   0.284  -6.5417  -1.8211   0.3043
 CWK  HAK  H   HCR6  0   0.283  -6.0400   2.4342   0.0336
 CWK  HAL  H   HCR6  0   0.272  -3.6321   2.1308  -0.2624

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
 CWK  CL   CAF  single    1.728  0.020  1.728
 CWK  C1   O1   single    1.415  0.020  1.415
 CWK  C1   C2   single    1.532  0.020  1.532
 CWK  C1   O5   single    1.381  0.020  1.381
 CWK  C1   H1   single    0.970  0.020  1.090
 CWK  O1   CAA  single    1.343  0.020  1.343
 CWK  C2   O2   single    1.403  0.020  1.403
 CWK  C2   C3   single    1.527  0.020  1.527
 CWK  C2   H2   single    0.970  0.020  1.090
 CWK  O2   HO2  single    0.850  0.020  0.980
 CWK  C3   O3   single    1.407  0.020  1.407
 CWK  C3   C4   single    1.525  0.020  1.525
 CWK  C3   H3   single    0.970  0.020  1.090
 CWK  O3   HO3  single    0.850  0.020  0.980
 CWK  C4   O4   single    1.407  0.020  1.407
 CWK  C4   C5   single    1.530  0.020  1.530
 CWK  C4   H4   single    0.970  0.020  1.090
 CWK  O4   HO4  single    0.850  0.020  0.980
 CWK  C5   O5   single    1.422  0.020  1.422
 CWK  C5   C6   single    1.514  0.020  1.514
 CWK  C5   H5   single    0.970  0.020  1.090
 CWK  C6   O6   single    1.407  0.020  1.407
 CWK  C6   H61  single    0.970  0.020  1.090
 CWK  C6   H62  single    0.970  0.020  1.090
 CWK  O6   HO6  single    0.850  0.020  0.980
 CWK  CAA  CAB  aromatic  1.391  0.020  1.391
 CWK  CAA  CAF  aromatic  1.396  0.020  1.396
 CWK  CAB  CAC  aromatic  1.385  0.020  1.385
 CWK  CAB  HAB  single    0.930  0.020  1.080
 CWK  CAC  CAD  aromatic  1.393  0.020  1.393
 CWK  CAC  HAC  single    0.930  0.020  1.080
 CWK  CAD  CAE  aromatic  1.394  0.020  1.394
 CWK  CAD  CAG  single    1.473  0.020  1.473
 CWK  CAE  CAF  aromatic  1.381  0.020  1.381
 CWK  CAE  HAE  single    0.930  0.020  1.080
 CWK  CAG  CAH  aromatic  1.397  0.020  1.397
 CWK  CAG  CAL  aromatic  1.397  0.020  1.397
 CWK  CAH  CAI  aromatic  1.382  0.020  1.382
 CWK  CAH  HAH  single    0.930  0.020  1.080
 CWK  CAI  CAJ  aromatic  1.394  0.020  1.394
 CWK  CAI  HAI  single    0.930  0.020  1.080
 CWK  CAJ  CAK  aromatic  1.395  0.020  1.395
 CWK  CAJ  CAN  single    1.426  0.020  1.426
 CWK  CAK  CAL  aromatic  1.382  0.020  1.382
 CWK  CAK  HAK  single    0.930  0.020  1.080
 CWK  CAL  HAL  single    0.930  0.020  1.080
 CWK  CAN  NAO  triple    1.153  0.020  1.153

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
 CWK  H1   C1   O5   106.24  3.000
 CWK  H1   C1   C2   110.16  3.000
 CWK  O5   C1   C2   112.53  3.000
 CWK  H1   C1   O1   110.27  3.000
 CWK  O5   C1   O1   111.93  3.000
 CWK  C2   C1   O1   105.77  3.000
 CWK  CAA  O1   C1   120.19  3.000
 CWK  H2   C2   C3   109.49  3.000
 CWK  H2   C2   O2   111.46  3.000
 CWK  C3   C2   O2   108.74  3.000
 CWK  H2   C2   C1   108.50  3.000
 CWK  C3   C2   C1   109.03  3.000
 CWK  O2   C2   C1   109.59  3.000
 CWK  HO2  O2   C2   108.73  3.000
 CWK  H3   C3   C4   107.91  3.000
 CWK  H3   C3   O3   110.58  3.000
 CWK  C4   C3   O3   107.59  3.000
 CWK  H3   C3   C2   107.86  3.000
 CWK  C4   C3   C2   110.49  3.000
 CWK  O3   C3   C2   112.34  3.000
 CWK  HO3  O3   C3   108.90  3.000
 CWK  H4   C4   C5   108.66  3.000
 CWK  H4   C4   O4   110.80  3.000
 CWK  C5   C4   O4   107.56  3.000
 CWK  H4   C4   C3   108.87  3.000
 CWK  C5   C4   C3   109.87  3.000
 CWK  O4   C4   C3   111.03  3.000
 CWK  HO4  O4   C4   107.67  3.000
 CWK  H5   C5   C6   108.59  3.000
 CWK  H5   C5   O5   110.36  3.000
 CWK  C6   C5   O5   107.16  3.000
 CWK  H5   C5   C4   108.56  3.000
 CWK  C6   C5   C4   111.67  3.000
 CWK  O5   C5   C4   110.48  3.000
 CWK  C5   O5   C1   116.27  3.000
 CWK  H62  C6   H61  107.12  3.000
 CWK  H62  C6   O6   111.91  3.000
 CWK  H61  C6   O6   111.74  3.000
 CWK  H62  C6   C5   108.91  3.000
 CWK  H61  C6   C5   108.03  3.000
 CWK  O6   C6   C5   109.02  3.000
 CWK  HO6  O6   C6   107.78  3.000
 CWK  CAF  CAA  CAB  118.14  3.000
 CWK  CAF  CAA  O1   116.41  3.000
 CWK  CAB  CAA  O1   125.45  3.000
 CWK  HAB  CAB  CAC  118.54  3.000
 CWK  HAB  CAB  CAA  121.13  3.000
 CWK  CAC  CAB  CAA  120.33  3.000
 CWK  HAC  CAC  CAD  120.19  3.000
 CWK  HAC  CAC  CAB  118.26  3.000
 CWK  CAD  CAC  CAB  121.53  3.000
 CWK  CAG  CAD  CAE  120.59  3.000
 CWK  CAG  CAD  CAC  121.30  3.000
 CWK  CAE  CAD  CAC  118.12  3.000
 CWK  HAE  CAE  CAF  118.96  3.000
 CWK  HAE  CAE  CAD  120.65  3.000
 CWK  CAF  CAE  CAD  120.36  3.000
 CWK  CAE  CAF  CAA  121.51  3.000
 CWK  CAE  CAF  CL   119.70  3.000
 CWK  CAA  CAF  CL   118.79  3.000
 CWK  CAL  CAG  CAH  118.55  3.000
 CWK  CAL  CAG  CAD  120.68  3.000
 CWK  CAH  CAG  CAD  120.77  3.000
 CWK  HAH  CAH  CAI  118.79  3.000
 CWK  HAH  CAH  CAG  120.19  3.000
 CWK  CAI  CAH  CAG  121.01  3.000
 CWK  HAI  CAI  CAJ  120.21  3.000
 CWK  HAI  CAI  CAH  120.12  3.000
 CWK  CAJ  CAI  CAH  119.66  3.000
 CWK  CAN  CAJ  CAK  119.97  3.000
 CWK  CAN  CAJ  CAI  119.94  3.000
 CWK  CAK  CAJ  CAI  120.09  3.000
 CWK  HAK  CAK  CAL  120.10  3.000
 CWK  HAK  CAK  CAJ  120.25  3.000
 CWK  CAL  CAK  CAJ  119.64  3.000
 CWK  HAL  CAL  CAK  118.78  3.000
 CWK  HAL  CAL  CAG  120.16  3.000
 CWK  CAK  CAL  CAG  121.04  3.000
 CWK  NAO  CAN  CAJ  180.00  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
 CWK  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 CWK  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 CWK  CONST_03  CAE  CAF  CAA  CAB    0.00   0.0  0
 CWK  CONST_04  CAE  CAD  CAC  CAB    0.00   0.0  0
 CWK  CONST_05  CAG  CAD  CAC  CAB  180.00   0.0  0
 CWK  CONST_06  CAF  CAA  CAB  CAC    0.00   0.0  0
 CWK  CONST_07  CAF  CAE  CAD  CAC    0.00   0.0  0
 CWK  CONST_10  CAI  CAH  CAG  CAD  180.00   0.0  0
 CWK  CONST_11  CAK  CAL  CAG  CAD  180.00   0.0  0
 CWK  CONST_14  CAG  CAD  CAE  CAF  180.00   0.0  0
 CWK  CONST_15  CAJ  CAI  CAH  CAG    0.00   0.0  0
 CWK  CONST_16  CAJ  CAK  CAL  CAG    0.00   0.0  0
 CWK  CONST_17  CAK  CAL  CAG  CAH    0.00   0.0  0
 CWK  CONST_18  CAK  CAJ  CAI  CAH    0.00   0.0  0
 CWK  CONST_19  CAL  CAG  CAH  CAI    0.00   0.0  0
 CWK  CONST_20  CAL  CAK  CAJ  CAI    0.00   0.0  0
 CWK  CONST_21  CAB  CAA  CAF  CL   180.00   0.0  0
 CWK  CONST_22  CAD  CAE  CAF  CL   180.00   0.0  0
 CWK  CONST_23  CAC  CAB  CAA  O1   180.00   0.0  0
 CWK  CONST_24  CAE  CAF  CAA  O1   180.00   0.0  0
 CWK  CONST_25  CAN  CAJ  CAI  CAH  180.00   0.0  0
 CWK  CONST_26  CAN  CAJ  CAK  CAL  180.00   0.0  0
 CWK  CONST_27  HAC  CAC  CAB  CAA  180.00   0.0  0
 CWK  CONST_28  HAE  CAE  CAF  CAA  180.00   0.0  0
 CWK  CONST_29  HAB  CAB  CAC  CAD  180.00   0.0  0
 CWK  CONST_30  HAH  CAH  CAG  CAD    0.00   0.0  0
 CWK  CONST_31  HAL  CAL  CAG  CAD    0.00   0.0  0
 CWK  CONST_32  HAI  CAI  CAH  CAG  180.00   0.0  0
 CWK  CONST_33  HAK  CAK  CAL  CAG  180.00   0.0  0
 CWK  Var_01    CAB  CAA  O1   C1    16.56  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
 CWK  chir_01  C1  O1  C2  O5  positiv
 CWK  chir_02  C2  O2  C1  C3  positiv
 CWK  chir_03  C3  O3  C2  C4  positiv
 CWK  chir_04  C4  O4  C3  C5  negativ
 CWK  chir_05  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
 CWK  plan-1  CL   0.020
 CWK  plan-1  O1   0.020
 CWK  plan-1  CAA  0.020
 CWK  plan-1  CAB  0.020
 CWK  plan-1  CAC  0.020
 CWK  plan-1  CAD  0.020
 CWK  plan-1  CAE  0.020
 CWK  plan-1  CAF  0.020
 CWK  plan-1  CAG  0.020
 CWK  plan-1  HAB  0.020
 CWK  plan-1  HAC  0.020
 CWK  plan-1  HAE  0.020
 CWK  plan-2  CAD  0.020
 CWK  plan-2  CAG  0.020
 CWK  plan-2  CAH  0.020
 CWK  plan-2  CAI  0.020
 CWK  plan-2  CAJ  0.020
 CWK  plan-2  CAK  0.020
 CWK  plan-2  CAL  0.020
 CWK  plan-2  CAN  0.020
 CWK  plan-2  NAO  0.020
 CWK  plan-2  HAH  0.020
 CWK  plan-2  HAI  0.020
 CWK  plan-2  HAK  0.020
 CWK  plan-2  HAL  0.020

