# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:51:32 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2R)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@]1(CCCCC1=O)c2ccccc2Cl
#
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
 RKE  RKE  (2R)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone  ligand  32  16  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RKE
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
 RKE  CAA   C   CR16  0  -0.222  -3.2728   1.0772   0.0993
 RKE  CAB   C   CR16  0  -0.282  -3.7214  -0.2265  -0.0310
 RKE  CAC   C   CR16  0  -0.364  -1.9110   1.3405   0.1454
 RKE  CAD   C   CR16  0  -0.195  -2.7998  -1.2594  -0.1055
 RKE  CAE   C   CR6   0   0.304  -0.9567   0.3308   0.0536
 RKE  CAF   C   CR6   0  -0.118  -1.4442  -0.9728  -0.0610
 RKE  CAG   C   C     0   0.425   1.2299  -0.1185   1.2110
 RKE  CAH   C   CH2   0  -0.548   2.7075  -0.3829   1.0807
 RKE  CAI   C   CH2   0  -0.443   3.1600  -0.7190  -0.3360
 RKE  CAJ   C   CH2   0  -0.439   2.6626   0.3244  -1.3235
 RKE  CAK   C   CH2   0  -0.461   1.1409   0.3672  -1.3167
 RKE  CAL   C   CT    0  -0.080   0.5359   0.6549   0.0699
 RKE  NAN   N   NH1   0  -0.610   0.8615   2.0156   0.4762
 RKE  OAO   O   O     0  -0.399   0.6231  -0.3656   2.2279
 RKE  CLAP  CL  CL    0  -0.129  -0.3577  -2.3349  -0.1232
 RKE  HAA   H   HCR6  0   0.263  -3.9787   1.8938   0.1695
 RKE  HAB   H   HCR6  0   0.267  -4.7798  -0.4470  -0.0672
 RKE  HAC   H   HCR6  0   0.261  -1.5904   2.3662   0.2621
 RKE  HAD   H   HCR6  0   0.279  -3.1326  -2.2851  -0.1917
 RKE  HAH   H   HCH2  0   0.268   3.2133   0.5313   1.4092
 RKE  HAHA  H   HCH2  0   0.263   2.9837  -1.1643   1.7905
 RKE  HAI   H   HCH2  0   0.245   4.2489  -0.7883  -0.3586
 RKE  HAIA  H   HCH2  0   0.224   2.7787  -1.7034  -0.6228
 RKE  HAJ   H   HCH2  0   0.226   3.0874   1.3012  -1.0753
 RKE  HAJA  H   HCH2  0   0.242   3.0033   0.0825  -2.3322
 RKE  HAK   H   HCH2  0   0.259   0.7647   1.1085  -2.0240
 RKE  HAKA  H   HCH2  0   0.249   0.7735  -0.5915  -1.6819
 RKE  HAM   H   HCH3  0   0.251   0.9178   4.0338   0.0543
 RKE  HAMA  H   HCH3  0   0.237   1.6713   3.0397  -1.1764
 RKE  HAMB  H   HCH3  0   0.209  -0.0875   3.1548  -1.0949
 RKE  HNAN  H   HNH1  0   0.362   0.3620   2.2665   1.3182
 RKE  CAM   C   CH3   0  -0.542   0.8254   3.0962  -0.4918

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
 RKE  CAA  CAB   aromatic  1.385  0.020  1.385
 RKE  CAA  CAC   aromatic  1.388  0.020  1.388
 RKE  CAB  CAD   aromatic  1.386  0.020  1.386
 RKE  CAC  CAE   aromatic  1.392  0.020  1.392
 RKE  CAD  CAF   aromatic  1.386  0.020  1.386
 RKE  CAE  CAF   aromatic  1.396  0.020  1.396
 RKE  CAE  CAL   single    1.528  0.020  1.528
 RKE  CAF  CLAP  single    1.743  0.020  1.743
 RKE  CAG  CAH   single    1.507  0.020  1.507
 RKE  CAG  CAL   single    1.543  0.020  1.543
 RKE  CAG  OAO   double    1.210  0.020  1.210
 RKE  CAH  CAI   single    1.525  0.020  1.525
 RKE  CAI  CAJ   single    1.520  0.020  1.520
 RKE  CAJ  CAK   single    1.522  0.020  1.522
 RKE  CAK  CAL   single    1.540  0.020  1.540
 RKE  CAL  NAN   single    1.457  0.020  1.457
 RKE  CAM  NAN   single    1.451  0.020  1.451
 RKE  CAA  HAA   single    0.930  0.020  1.080
 RKE  CAB  HAB   single    0.930  0.020  1.080
 RKE  CAC  HAC   single    0.930  0.020  1.080
 RKE  CAD  HAD   single    0.930  0.020  1.080
 RKE  CAH  HAH   single    0.970  0.020  1.090
 RKE  CAH  HAHA  single    0.970  0.020  1.090
 RKE  CAI  HAI   single    0.970  0.020  1.090
 RKE  CAI  HAIA  single    0.970  0.020  1.090
 RKE  CAJ  HAJ   single    0.970  0.020  1.090
 RKE  CAJ  HAJA  single    0.970  0.020  1.090
 RKE  CAK  HAK   single    0.970  0.020  1.090
 RKE  CAK  HAKA  single    0.970  0.020  1.090
 RKE  CAM  HAM   single    0.970  0.020  1.090
 RKE  CAM  HAMA  single    0.970  0.020  1.090
 RKE  CAM  HAMB  single    0.970  0.020  1.090
 RKE  NAN  HNAN  single    0.890  0.020  1.040

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
 RKE  HAA   CAA  CAC   119.67  3.000
 RKE  HAA   CAA  CAB   120.36  3.000
 RKE  CAC   CAA  CAB   119.97  3.000
 RKE  HAB   CAB  CAD   119.79  3.000
 RKE  HAB   CAB  CAA   120.79  3.000
 RKE  CAD   CAB  CAA   119.41  3.000
 RKE  HAC   CAC  CAE   119.47  3.000
 RKE  HAC   CAC  CAA   118.34  3.000
 RKE  CAE   CAC  CAA   122.19  3.000
 RKE  HAD   CAD  CAF   119.96  3.000
 RKE  HAD   CAD  CAB   120.41  3.000
 RKE  CAF   CAD  CAB   119.63  3.000
 RKE  CAL   CAE  CAF   122.69  3.000
 RKE  CAL   CAE  CAC   121.01  3.000
 RKE  CAF   CAE  CAC   116.31  3.000
 RKE  CLAP  CAF  CAE   120.98  3.000
 RKE  CLAP  CAF  CAD   116.54  3.000
 RKE  CAE   CAF  CAD   122.48  3.000
 RKE  OAO   CAG  CAL   119.89  3.000
 RKE  OAO   CAG  CAH   121.92  3.000
 RKE  CAL   CAG  CAH   117.71  3.000
 RKE  HAHA  CAH  HAH   106.60  3.000
 RKE  HAHA  CAH  CAI   111.80  3.000
 RKE  HAH   CAH  CAI   109.00  3.000
 RKE  HAHA  CAH  CAG   108.52  3.000
 RKE  HAH   CAH  CAG   106.29  3.000
 RKE  CAI   CAH  CAG   114.21  3.000
 RKE  HAIA  CAI  HAI   106.58  3.000
 RKE  HAIA  CAI  CAJ   109.47  3.000
 RKE  HAI   CAI  CAJ   110.89  3.000
 RKE  HAIA  CAI  CAH   109.79  3.000
 RKE  HAI   CAI  CAH   109.23  3.000
 RKE  CAJ   CAI  CAH   110.80  3.000
 RKE  HAJA  CAJ  HAJ   106.64  3.000
 RKE  HAJA  CAJ  CAK   108.80  3.000
 RKE  HAJ   CAJ  CAK   111.22  3.000
 RKE  HAJA  CAJ  CAI   110.24  3.000
 RKE  HAJ   CAJ  CAI   109.79  3.000
 RKE  CAK   CAJ  CAI   110.09  3.000
 RKE  HAKA  CAK  HAK   105.31  3.000
 RKE  HAKA  CAK  CAL   109.49  3.000
 RKE  HAK   CAK  CAL   108.74  3.000
 RKE  HAKA  CAK  CAJ   108.10  3.000
 RKE  HAK   CAK  CAJ   111.15  3.000
 RKE  CAL   CAK  CAJ   113.70  3.000
 RKE  NAN   CAL  CAK   109.74  3.000
 RKE  NAN   CAL  CAG    99.29  3.000
 RKE  CAK   CAL  CAG   113.30  3.000
 RKE  NAN   CAL  CAE   114.81  3.000
 RKE  CAK   CAL  CAE   109.55  3.000
 RKE  CAG   CAL  CAE   109.94  3.000
 RKE  HNAN  NAN  CAM   111.01  3.000
 RKE  HNAN  NAN  CAL   110.71  3.000
 RKE  CAM   NAN  CAL   120.26  3.000
 RKE  HAMB  CAM  HAMA  107.68  3.000
 RKE  HAMB  CAM  HAM   107.50  3.000
 RKE  HAMA  CAM  HAM   107.09  3.000
 RKE  HAMB  CAM  NAN   115.32  3.000
 RKE  HAMA  CAM  NAN   111.17  3.000
 RKE  HAM   CAM  NAN   107.73  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
 RKE  CONST_01  CAF   CAD  CAB  CAA    0.00   0.0  0
 RKE  CONST_02  CAF   CAE  CAC  CAA    0.00   0.0  0
 RKE  CONST_03  CAE   CAC  CAA  CAB    0.00   0.0  0
 RKE  CONST_04  CAE   CAF  CAD  CAB    0.00   0.0  0
 RKE  CONST_05  CAD   CAB  CAA  CAC    0.00   0.0  0
 RKE  CONST_06  CAD   CAF  CAE  CAC    0.00   0.0  0
 RKE  CONST_07  CAL   CAE  CAC  CAA  180.00   0.0  0
 RKE  CONST_08  CAL   CAE  CAF  CAD  180.00   0.0  0
 RKE  CONST_09  CLAP  CAF  CAD  CAB  180.00   0.0  0
 RKE  CONST_10  CLAP  CAF  CAE  CAC  180.00   0.0  0
 RKE  CONST_11  CLAP  CAF  CAE  CAL    0.00   0.0  0
 RKE  CONST_12  HAD   CAD  CAB  CAA  180.00   0.0  0
 RKE  CONST_13  HAC   CAC  CAA  CAB  180.00   0.0  0
 RKE  CONST_14  HAB   CAB  CAA  CAC  180.00   0.0  0
 RKE  CONST_15  HAA   CAA  CAB  CAD  180.00   0.0  0
 RKE  Var_01    CAJ   CAI  CAH  CAG   51.50  30.0  1
 RKE  Var_02    CAK   CAJ  CAI  CAH  -60.75  30.0  1
 RKE  Var_03    CAL   CAG  CAH  CAI  -38.29  30.0  1
 RKE  Var_04    CAL   CAK  CAJ  CAI   57.17  30.0  1
 RKE  Var_05    HAM   CAM  NAN  CAL  169.71  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
 RKE  chir_01  CAL  CAG  CAK  CAE  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
 RKE  plan-1  CAA   0.020
 RKE  plan-1  CAB   0.020
 RKE  plan-1  CAC   0.020
 RKE  plan-1  CAD   0.020
 RKE  plan-1  CAE   0.020
 RKE  plan-1  CAF   0.020
 RKE  plan-1  CAL   0.020
 RKE  plan-1  CLAP  0.020
 RKE  plan-1  HAA   0.020
 RKE  plan-1  HAB   0.020
 RKE  plan-1  HAC   0.020
 RKE  plan-1  HAD   0.020
 RKE  plan-2  CAG   0.020
 RKE  plan-2  CAH   0.020
 RKE  plan-2  CAL   0.020
 RKE  plan-2  OAO   0.020

