# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:29:04 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 5-bromo-2-[(3R)-piperidin-3-ylamino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=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
 AJD  AJD  '5-bromo-2-[(3R)-piperidin-3-ylamino]benzoic acid'  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 PERFECT
;

data_comp_AJD
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
 AJD  OAA   O   OC    -1  -0.578   1.0372   3.5060   0.5255
 AJD  OAB   O   O      0  -0.600  -1.1184   3.0405   0.2816
 AJD  CAD   C   CR16   0  -0.229   1.2629  -1.4050  -0.2461
 AJD  CAE   C   CR16   0  -0.355  -0.0740  -1.0732  -0.3378
 AJD  CAF   C   CR16   0  -0.260   1.7875   0.8975   0.1751
 AJD  CAG   C   CH2    0  -0.436  -5.3388  -0.6517  -1.0010
 AJD  CAH   C   CH2    0  -0.290  -5.5719  -1.2436   0.3813
 AJD  CAI   C   CH2    0  -0.447  -4.1538   0.3094  -0.9900
 AJD  CAJ   C   CH2    0  -0.286  -3.2626  -0.9473   0.9733
 AJD  NAK   N   NH1    0  -0.598  -4.3579  -1.8888   0.8490
 AJD  CAM   C   C      0   0.449   0.0966   2.7223   0.3148
 AJD  CAN   C   CR6    0  -0.136   2.1978  -0.4121   0.0076
 AJD  CAO   C   CR6    0   0.362  -0.5229   0.2553  -0.1894
 AJD  CAP   C   CR6    0  -0.221   0.4471   1.2584   0.0881
 AJD  CAQ   C   CH1    0  -0.069  -2.9193  -0.3632  -0.3994
 AJD  HAD   H   HCR6   0   0.269   1.5605  -2.4381  -0.3728
 AJD  HAE   H   HCR6   0   0.265  -0.7802  -1.8691  -0.5306
 AJD  HAF   H   HCR6   0   0.260   2.5073   1.6780   0.3822
 AJD  HAH   H   HCH2   0   0.185  -5.9084  -0.4395   1.0576
 AJD  HAHA  H   HCH2   0   0.231  -6.3734  -1.9840   0.3435
 AJD  HAI   H   HCH2   0   0.240  -3.9371   0.6693  -1.9985
 AJD  HAIA  H   HCH2   0   0.215  -4.4066   1.1894  -0.3861
 AJD  HAJ   H   HCH2   0   0.184  -3.4907  -0.1070   1.6519
 AJD  HAJA  H   HCH2   0   0.234  -2.3939  -1.4639   1.3881
 AJD  HNAK  H   HNH1   0   0.352  -4.5271  -2.3313   1.7424
 AJD  HAQ   H   HCH1   0   0.224  -2.6459  -1.1921  -1.0615
 AJD  NAL   N   NH1    0  -0.711  -1.8324   0.5794  -0.3355
 AJD  HAG   H   HCH2   0   0.217  -5.1524  -1.4603  -1.7138
 AJD  HNAL  H   HNH1   0   0.388  -2.0230   1.5517  -0.0973
 AJD  BRAC  BR  BR     0  -0.091   4.0369  -0.8562   0.1352
 AJD  HAGA  H   HCH2   0   0.232  -6.2389  -0.1327  -1.3368

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
 AJD  OAA   CAM   deloc     1.242  0.020  1.242
 AJD  OAB   CAM   deloc     1.256  0.020  1.256
 AJD  BRAC  CAN   single    1.896  0.020  1.896
 AJD  CAD   CAE   aromatic  1.381  0.020  1.381
 AJD  CAD   CAN   aromatic  1.387  0.020  1.387
 AJD  CAD   HAD   single    0.930  0.020  1.080
 AJD  CAE   CAO   aromatic  1.410  0.020  1.410
 AJD  CAE   HAE   single    0.930  0.020  1.080
 AJD  CAF   CAN   aromatic  1.383  0.020  1.383
 AJD  CAF   CAP   aromatic  1.391  0.020  1.391
 AJD  CAF   HAF   single    0.930  0.020  1.080
 AJD  CAG   CAH   single    1.522  0.020  1.522
 AJD  CAG   CAI   single    1.526  0.020  1.526
 AJD  CAG   HAG   single    0.970  0.020  1.090
 AJD  CAG   HAGA  single    0.970  0.020  1.090
 AJD  CAH   NAK   single    1.452  0.020  1.452
 AJD  CAH   HAH   single    0.970  0.020  1.090
 AJD  CAH   HAHA  single    0.970  0.020  1.090
 AJD  CAI   CAQ   single    1.525  0.020  1.525
 AJD  CAI   HAI   single    0.970  0.020  1.090
 AJD  CAI   HAIA  single    0.970  0.020  1.090
 AJD  CAJ   NAK   single    1.450  0.020  1.450
 AJD  CAJ   CAQ   single    1.531  0.020  1.531
 AJD  CAJ   HAJ   single    0.970  0.020  1.090
 AJD  CAJ   HAJA  single    0.970  0.020  1.090
 AJD  NAK   HNAK  single    0.890  0.020  1.040
 AJD  NAL   CAO   single    1.357  0.020  1.357
 AJD  NAL   CAQ   single    1.440  0.020  1.440
 AJD  NAL   HNAL  single    0.890  0.020  1.040
 AJD  CAM   CAP   single    1.522  0.020  1.522
 AJD  CAO   CAP   aromatic  1.423  0.020  1.423
 AJD  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
 AJD  HAD   CAD  CAN   121.28  3.000
 AJD  HAD   CAD  CAE   119.20  3.000
 AJD  CAN   CAD  CAE   119.52  3.000
 AJD  HAE   CAE  CAO   120.29  3.000
 AJD  HAE   CAE  CAD   117.86  3.000
 AJD  CAO   CAE  CAD   121.85  3.000
 AJD  HAF   CAF  CAP   117.78  3.000
 AJD  HAF   CAF  CAN   120.60  3.000
 AJD  CAP   CAF  CAN   121.62  3.000
 AJD  HAGA  CAG  HAG   106.94  3.000
 AJD  HAGA  CAG  CAI   110.06  3.000
 AJD  HAG   CAG  CAI   109.75  3.000
 AJD  HAGA  CAG  CAH   109.75  3.000
 AJD  HAG   CAG  CAH   109.30  3.000
 AJD  CAI   CAG  CAH   110.94  3.000
 AJD  HAHA  CAH  HAH   106.95  3.000
 AJD  HAHA  CAH  NAK   108.88  3.000
 AJD  HAH   CAH  NAK   112.42  3.000
 AJD  HAHA  CAH  CAG   110.17  3.000
 AJD  HAH   CAH  CAG   108.67  3.000
 AJD  NAK   CAH  CAG   109.71  3.000
 AJD  HAIA  CAI  HAI   106.85  3.000
 AJD  HAIA  CAI  CAQ   109.10  3.000
 AJD  HAI   CAI  CAQ   110.02  3.000
 AJD  HAIA  CAI  CAG   109.29  3.000
 AJD  HAI   CAI  CAG   110.78  3.000
 AJD  CAQ   CAI  CAG   110.71  3.000
 AJD  HAJA  CAJ  HAJ   106.91  3.000
 AJD  HAJA  CAJ  CAQ   110.03  3.000
 AJD  HAJ   CAJ  CAQ   107.89  3.000
 AJD  HAJA  CAJ  NAK   109.04  3.000
 AJD  HAJ   CAJ  NAK   113.02  3.000
 AJD  CAQ   CAJ  NAK   109.90  3.000
 AJD  HNAK  NAK  CAJ   109.56  3.000
 AJD  HNAK  NAK  CAH   109.82  3.000
 AJD  CAJ   NAK  CAH   111.76  3.000
 AJD  CAP   CAM  OAB   117.54  3.000
 AJD  CAP   CAM  OAA   117.23  3.000
 AJD  OAB   CAM  OAA   125.23  3.000
 AJD  CAF   CAN  CAD   120.01  3.000
 AJD  CAF   CAN  BRAC  120.10  3.000
 AJD  CAD   CAN  BRAC  119.89  3.000
 AJD  CAP   CAO  NAL   120.70  3.000
 AJD  CAP   CAO  CAE   117.89  3.000
 AJD  NAL   CAO  CAE   121.39  3.000
 AJD  CAO   CAP  CAM   123.37  3.000
 AJD  CAO   CAP  CAF   119.09  3.000
 AJD  CAM   CAP  CAF   117.53  3.000
 AJD  HAQ   CAQ  NAL   109.50  3.000
 AJD  HAQ   CAQ  CAJ   108.01  3.000
 AJD  NAL   CAQ  CAJ   112.28  3.000
 AJD  HAQ   CAQ  CAI   107.56  3.000
 AJD  NAL   CAQ  CAI   109.85  3.000
 AJD  CAJ   CAQ  CAI   109.52  3.000
 AJD  HNAL  NAL  CAQ   119.59  3.000
 AJD  HNAL  NAL  CAO   112.53  3.000
 AJD  CAQ   NAL  CAO   125.23  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
 AJD  CONST_01  CAP   CAO  CAE  CAD     0.00   0.0  0
 AJD  CONST_02  CAP   CAF  CAN  CAD     0.00   0.0  0
 AJD  CONST_03  CAF   CAN  CAD  CAE     0.00   0.0  0
 AJD  CONST_04  CAF   CAP  CAO  CAE     0.00   0.0  0
 AJD  CONST_05  CAO   CAE  CAD  CAN     0.00   0.0  0
 AJD  CONST_06  CAO   CAP  CAF  CAN     0.00   0.0  0
 AJD  CONST_07  CAE   CAD  CAN  BRAC  180.00   0.0  0
 AJD  CONST_08  CAP   CAF  CAN  BRAC  180.00   0.0  0
 AJD  CONST_09  NAL   CAO  CAE  CAD   180.00   0.0  0
 AJD  CONST_10  CAM   CAP  CAO  CAE   180.00   0.0  0
 AJD  CONST_11  NAL   CAO  CAP  CAF   180.00   0.0  0
 AJD  CONST_12  CAN   CAF  CAP  CAM   180.00   0.0  0
 AJD  CONST_13  CAQ   NAL  CAO  CAE     0.00   0.0  0
 AJD  CONST_14  CAQ   NAL  CAO  CAP   180.00   0.0  0
 AJD  CONST_15  HAF   CAF  CAN  CAD   180.00   0.0  0
 AJD  CONST_16  HAD   CAD  CAN  CAF   180.00   0.0  0
 AJD  CONST_17  HAE   CAE  CAD  CAN   180.00   0.0  0
 AJD  CONST_18  HNAL  NAL  CAO  CAE   180.00   0.0  0
 AJD  Var_01    CAJ   NAK  CAH  CAG    61.63  30.0  1
 AJD  Var_02    CAQ   CAI  CAG  CAH    52.99  30.0  1
 AJD  Var_03    CAQ   CAJ  NAK  CAH   -62.96  30.0  1
 AJD  Var_04    NAK   CAH  CAG  CAI   -55.95  30.0  1
 AJD  Var_05    CAF   CAP  CAM  OAA     1.99  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
 AJD  chir_01  CAQ  CAI  CAJ  NAL  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
 AJD  plan-1  CAD   0.020
 AJD  plan-1  CAE   0.020
 AJD  plan-1  CAF   0.020
 AJD  plan-1  CAM   0.020
 AJD  plan-1  CAN   0.020
 AJD  plan-1  CAO   0.020
 AJD  plan-1  CAP   0.020
 AJD  plan-1  HAD   0.020
 AJD  plan-1  HAE   0.020
 AJD  plan-1  HAF   0.020
 AJD  plan-1  NAL   0.020
 AJD  plan-1  BRAC  0.020
 AJD  plan-2  CAO   0.020
 AJD  plan-2  CAQ   0.020
 AJD  plan-2  NAL   0.020
 AJD  plan-2  HNAL  0.020
 AJD  plan-3  OAA   0.020
 AJD  plan-3  OAB   0.020
 AJD  plan-3  CAM   0.020
 AJD  plan-3  CAP   0.020

