# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:19:05 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-]C(=O)c1cc(Br)ccc1N[C@H]2CCCNC2
#
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
 AKD  AKD  5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate  ligand  31  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AKD
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
 AKD  OAA   O   OC    -1  -0.578   1.0638   3.5977  -0.2035
 AKD  OAB   O   O      0  -0.601  -1.0939   3.0935  -0.1011
 AKD  CAD   C   CR16   0  -0.228   1.3136  -1.3558   0.2234
 AKD  CAE   C   CR16   0  -0.358  -0.0289  -1.0415   0.2867
 AKD  CAF   C   CR16   0  -0.260   1.8295   0.9734  -0.0267
 AKD  CAG   C   C      0  -0.446  -5.2906  -0.6976   0.9617
 AKD  CAH   C   C      0  -0.314  -5.5281  -1.2565  -0.4391
 AKD  CAI   C   C      0  -0.448  -4.1247   0.2862   0.9624
 AKD  CAJ   C   C      0  -0.312  -3.2235  -0.9052  -1.0426
 AKD  NAK   N   NR16   0  -0.577  -4.3407  -1.8327  -1.0518
 AKD  CAM   C   C      0   0.449   0.1256   2.7901  -0.0993
 AKD  CAN   C   CR6    0  -0.138   2.2473  -0.3414   0.0691
 AKD  CAO   C   CR6    0   0.366  -0.4867   0.2905   0.2072
 AKD  CAP   C   CR6    0  -0.221   0.4835   1.3176   0.0342
 AKD  CAQ   C   CR16   0  -0.077  -2.8834  -0.3559   0.3517
 AKD  HAD   H   HCR6   0   0.268   1.6164  -2.3929   0.2924
 AKD  HAE   H   HCR6   0   0.263  -0.7322  -1.8550   0.3988
 AKD  HAF   H   HCR6   0   0.260   2.5488   1.7713  -0.1528
 AKD  HAGA  H   H      0   0.217  -5.0790  -1.5208   1.6524
 AKD  HAH   H   H      0   0.235  -6.3134  -2.0146  -0.4195
 AKD  HAHA  H   H      0   0.214  -5.8863  -0.4506  -1.0891
 AKD  HAI   H   H      0   0.218  -4.3959   1.1734   0.3772
 AKD  HAIA  H   H      0   0.240  -3.9068   0.6309   1.9761
 AKD  HAJ   H   H      0   0.237  -2.3499  -1.3952  -1.4791
 AKD  HAJA  H   H      0   0.214  -3.4691  -0.0586  -1.6944
 AKD  HNAK  H   HNR6   0   0.340  -4.0794  -2.6718  -0.5463
 AKD  HAQ   H   HCR6   0   0.221  -2.6014  -1.2005   0.9933
 AKD  BRAC  BR  BR     0  -0.092   4.0944  -0.7613  -0.0169
 AKD  NAL   N   NH1    0  -0.712  -1.8025   0.5948   0.3197
 AKD  HAG   H   H      0   0.230  -6.1973  -0.2090   1.3272
 AKD  HNAL  H   HNH1   0   0.389  -1.9945   1.5812   0.1498

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
 AKD  OAA   CAM   deloc     1.242  0.020  1.242
 AKD  OAB   CAM   deloc     1.257  0.020  1.257
 AKD  BRAC  CAN   single    1.896  0.020  1.896
 AKD  CAD   CAE   aromatic  1.380  0.020  1.380
 AKD  CAD   CAN   aromatic  1.387  0.020  1.387
 AKD  CAE   CAO   aromatic  1.411  0.020  1.411
 AKD  CAF   CAN   aromatic  1.383  0.020  1.383
 AKD  CAF   CAP   aromatic  1.391  0.020  1.391
 AKD  CAG   CAH   single    1.527  0.020  1.527
 AKD  CAG   CAI   single    1.526  0.020  1.526
 AKD  CAH   NAK   single    1.455  0.020  1.455
 AKD  CAI   CAQ   single    1.525  0.020  1.525
 AKD  CAJ   NAK   single    1.452  0.020  1.452
 AKD  CAJ   CAQ   single    1.537  0.020  1.537
 AKD  NAL   CAO   single    1.355  0.020  1.355
 AKD  NAL   CAQ   single    1.440  0.020  1.440
 AKD  CAM   CAP   single    1.521  0.020  1.521
 AKD  CAO   CAP   aromatic  1.423  0.020  1.423
 AKD  CAD   HAD   single    0.930  0.020  1.080
 AKD  CAE   HAE   single    0.930  0.020  1.080
 AKD  CAF   HAF   single    0.930  0.020  1.080
 AKD  CAG   HAG   single    0.970  0.020  1.090
 AKD  CAG   HAGA  single    0.970  0.020  1.090
 AKD  CAH   HAH   single    0.970  0.020  1.090
 AKD  CAH   HAHA  single    0.970  0.020  1.090
 AKD  CAI   HAI   single    0.970  0.020  1.090
 AKD  CAI   HAIA  single    0.970  0.020  1.090
 AKD  CAJ   HAJ   single    0.970  0.020  1.090
 AKD  CAJ   HAJA  single    0.970  0.020  1.090
 AKD  NAK   HNAK  single    0.890  0.020  1.040
 AKD  NAL   HNAL  single    0.860  0.020  1.020
 AKD  CAQ   HAQ   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
 AKD  HAD   CAD  CAN   121.29  3.000
 AKD  HAD   CAD  CAE   119.16  3.000
 AKD  CAN   CAD  CAE   119.55  3.000
 AKD  HAE   CAE  CAO   120.35  3.000
 AKD  HAE   CAE  CAD   117.78  3.000
 AKD  CAO   CAE  CAD   121.87  3.000
 AKD  HAF   CAF  CAP   117.79  3.000
 AKD  HAF   CAF  CAN   120.57  3.000
 AKD  CAP   CAF  CAN   121.65  3.000
 AKD  HAGA  CAG  HAG   106.58  3.000
 AKD  HAGA  CAG  CAI   109.68  3.000
 AKD  HAG   CAG  CAI   110.21  3.000
 AKD  HAGA  CAG  CAH   109.49  3.000
 AKD  HAG   CAG  CAH   109.97  3.000
 AKD  CAI   CAG  CAH   110.82  3.000
 AKD  HAHA  CAH  HAH   106.63  3.000
 AKD  HAHA  CAH  NAK   107.96  3.000
 AKD  HAH   CAH  NAK   108.64  3.000
 AKD  HAHA  CAH  CAG   109.02  3.000
 AKD  HAH   CAH  CAG   110.46  3.000
 AKD  NAK   CAH  CAG   113.85  3.000
 AKD  HAIA  CAI  HAI   106.81  3.000
 AKD  HAIA  CAI  CAQ   110.00  3.000
 AKD  HAI   CAI  CAQ   109.16  3.000
 AKD  HAIA  CAI  CAG   110.87  3.000
 AKD  HAI   CAI  CAG   109.42  3.000
 AKD  CAQ   CAI  CAG   110.50  3.000
 AKD  HAJA  CAJ  HAJ   106.73  3.000
 AKD  HAJA  CAJ  CAQ   108.24  3.000
 AKD  HAJ   CAJ  CAQ   110.23  3.000
 AKD  HAJA  CAJ  NAK   108.49  3.000
 AKD  HAJ   CAJ  NAK   109.03  3.000
 AKD  CAQ   CAJ  NAK   113.85  3.000
 AKD  HNAK  NAK  CAJ   109.10  3.000
 AKD  HNAK  NAK  CAH   109.16  3.000
 AKD  CAJ   NAK  CAH   111.85  3.000
 AKD  CAP   CAM  OAB   117.53  3.000
 AKD  CAP   CAM  OAA   117.32  3.000
 AKD  OAB   CAM  OAA   125.15  3.000
 AKD  CAF   CAN  CAD   119.98  3.000
 AKD  CAF   CAN  BRAC  120.11  3.000
 AKD  CAD   CAN  BRAC  119.91  3.000
 AKD  CAP   CAO  NAL   120.66  3.000
 AKD  CAP   CAO  CAE   117.84  3.000
 AKD  NAL   CAO  CAE   121.49  3.000
 AKD  CAO   CAP  CAM   123.28  3.000
 AKD  CAO   CAP  CAF   119.11  3.000
 AKD  CAM   CAP  CAF   117.61  3.000
 AKD  HAQ   CAQ  NAL   109.15  3.000
 AKD  HAQ   CAQ  CAJ   108.19  3.000
 AKD  NAL   CAQ  CAJ   112.46  3.000
 AKD  HAQ   CAQ  CAI   107.40  3.000
 AKD  NAL   CAQ  CAI   109.99  3.000
 AKD  CAJ   CAQ  CAI   109.49  3.000
 AKD  HNAL  NAL  CAQ   120.08  3.000
 AKD  HNAL  NAL  CAO   112.73  3.000
 AKD  CAQ   NAL  CAO   125.63  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
 AKD  CONST_01  CAP   CAO  CAE  CAD     0.00   0.0  0
 AKD  CONST_02  CAP   CAF  CAN  CAD     0.00   0.0  0
 AKD  CONST_03  CAF   CAN  CAD  CAE     0.00   0.0  0
 AKD  CONST_04  CAF   CAP  CAO  CAE     0.00   0.0  0
 AKD  CONST_05  CAO   CAE  CAD  CAN     0.00   0.0  0
 AKD  CONST_06  CAO   CAP  CAF  CAN     0.00   0.0  0
 AKD  CONST_07  CAE   CAD  CAN  BRAC  180.00   0.0  0
 AKD  CONST_08  CAP   CAF  CAN  BRAC  180.00   0.0  0
 AKD  CONST_09  NAL   CAO  CAE  CAD   180.00   0.0  0
 AKD  CONST_10  CAM   CAP  CAO  CAE   180.00   0.0  0
 AKD  CONST_11  NAL   CAO  CAP  CAF   180.00   0.0  0
 AKD  CONST_12  CAN   CAF  CAP  CAM   180.00   0.0  0
 AKD  CONST_13  CAQ   NAL  CAO  CAE     0.00   0.0  0
 AKD  CONST_14  CAQ   NAL  CAO  CAP   180.00   0.0  0
 AKD  CONST_15  HAF   CAF  CAN  CAD   180.00   0.0  0
 AKD  CONST_16  HAD   CAD  CAN  CAF   180.00   0.0  0
 AKD  CONST_17  HAE   CAE  CAD  CAN   180.00   0.0  0
 AKD  CONST_18  HNAL  NAL  CAO  CAE   180.00   0.0  0
 AKD  Var_01    CAJ   NAK  CAH  CAG   -53.09  30.0  1
 AKD  Var_02    CAQ   CAI  CAG  CAH   -53.61  30.0  1
 AKD  Var_03    CAQ   CAJ  NAK  CAH    54.46  30.0  1
 AKD  Var_04    NAK   CAH  CAG  CAI    53.23  30.0  1
 AKD  Var_05    CAF   CAP  CAM  OAA    -2.66  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
 AKD  chir_01  CAQ  CAI  CAJ  NAL  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
 AKD  plan-1  CAD   0.020
 AKD  plan-1  CAE   0.020
 AKD  plan-1  CAF   0.020
 AKD  plan-1  CAM   0.020
 AKD  plan-1  CAN   0.020
 AKD  plan-1  CAO   0.020
 AKD  plan-1  CAP   0.020
 AKD  plan-1  HAD   0.020
 AKD  plan-1  HAE   0.020
 AKD  plan-1  HAF   0.020
 AKD  plan-1  BRAC  0.020
 AKD  plan-1  NAL   0.020
 AKD  plan-2  CAO   0.020
 AKD  plan-2  CAQ   0.020
 AKD  plan-2  NAL   0.020
 AKD  plan-2  HNAL  0.020
 AKD  plan-3  OAA   0.020
 AKD  plan-3  OAB   0.020
 AKD  plan-3  CAM   0.020
 AKD  plan-3  CAP   0.020

