# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:28:07 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1C(=O)N[C@H]2CCC(=O)NC2=O
#
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
 JNW  JNW  '2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid'  ligand  31  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JNW
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
 JNW  OAS  O  O      0  -0.569   0.7729  -0.3202   2.0504
 JNW  CAR  C  C      0   0.410   1.6328   0.5822   2.0323
 JNW  OAT  O  OC    -1  -0.582   2.1015   1.1932   3.0082
 JNW  CAQ  C  CR6    0  -0.113   2.1688   0.9575   0.6575
 JNW  CAP  C  CR16   0  -0.285   3.2449   1.8347   0.5438
 JNW  CAO  C  CR16   0  -0.248   3.7814   2.1614  -0.6918
 JNW  CAN  C  CR16   0  -0.253   3.2399   1.6111  -1.8459
 JNW  CAM  C  CR16   0  -0.273   2.1648   0.7406  -1.7508
 JNW  CAK  C  CR6    0  -0.059   1.6274   0.4135  -0.5082
 JNW  CAJ  C  C      0   0.515   0.4749  -0.5503  -0.5158
 JNW  OAL  O  O      0  -0.484   0.6289  -1.7411  -0.7239
 JNW  N    N  NH1    0  -0.618  -0.7397   0.0436  -0.4720
 JNW  CA   C  CH1    0  -0.236  -1.9595  -0.7325  -0.3889
 JNW  CB   C  CH2    0  -0.450  -2.2883  -1.2159   1.0171
 JNW  CG   C  CH2    0  -0.605  -2.6100  -0.0451   1.9269
 JNW  CD   C  C      0   0.552  -3.6690   0.8528   1.3584
 JNW  OE1  O  O      0  -0.432  -4.3773   1.5739   2.0234
 JNW  NE2  N  NH1    0  -0.676  -3.8098   0.8386  -0.0196
 JNW  C    C  C      0   0.548  -3.0806   0.1286  -0.9449
 JNW  O    O  O      0  -0.416  -3.3197   0.2200  -2.1261
 JNW  H2   H  HCR6   0   0.251   3.6678   2.2597   1.4442
 JNW  H3   H  HCR6   0   0.255   4.6213   2.8411  -0.7552
 JNW  H4   H  HCR6   0   0.258   3.6513   1.8562  -2.8164
 JNW  H5   H  HCR6   0   0.258   1.7387   0.3174  -2.6525
 JNW  H6   H  HNH1   0   0.402  -0.7627   1.0077  -0.1787
 JNW  H7   H  HCH1   0   0.307  -1.8631  -1.5848  -1.0616
 JNW  H8   H  HCH2   0   0.257  -3.1398  -1.8987   0.9623
 JNW  H9   H  HCH2   0   0.279  -1.4458  -1.7766   1.4155
 JNW  H10  H  HCH2   0   0.294  -2.9476  -0.3800   2.9075
 JNW  H11  H  HCH2   0   0.297  -1.7092   0.5513   2.1031
 JNW  H12  H  HNH1   0   0.416  -4.5386   1.4364  -0.3948

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
 JNW  OE1  CD   double    1.210  0.020  1.210
 JNW  NE2  CD   single    1.385  0.020  1.385
 JNW  NE2  C    single    1.376  0.020  1.376
 JNW  CD   CG   single    1.500  0.020  1.500
 JNW  O    C    double    1.209  0.020  1.209
 JNW  C    CA   single    1.519  0.020  1.519
 JNW  CG   CB   single    1.517  0.020  1.517
 JNW  CA   CB   single    1.523  0.020  1.523
 JNW  CA   N    single    1.448  0.020  1.448
 JNW  N    CAJ  single    1.353  0.020  1.353
 JNW  OAL  CAJ  double    1.219  0.020  1.219
 JNW  CAJ  CAK  single    1.502  0.020  1.502
 JNW  CAK  CAM  aromatic  1.393  0.020  1.393
 JNW  CAK  CAQ  aromatic  1.396  0.020  1.396
 JNW  CAM  CAN  aromatic  1.387  0.020  1.387
 JNW  OAS  CAR  deloc     1.247  0.020  1.247
 JNW  CAR  CAQ  single    1.523  0.020  1.523
 JNW  CAR  OAT  deloc     1.243  0.020  1.243
 JNW  CAQ  CAP  aromatic  1.393  0.020  1.393
 JNW  CAN  CAO  aromatic  1.388  0.020  1.388
 JNW  CAO  CAP  aromatic  1.386  0.020  1.386
 JNW  CAP  H2   single    0.930  0.020  1.080
 JNW  CAO  H3   single    0.930  0.020  1.080
 JNW  CAN  H4   single    0.930  0.020  1.080
 JNW  CAM  H5   single    0.930  0.020  1.080
 JNW  N    H6   single    0.890  0.020  1.040
 JNW  CA   H7   single    0.970  0.020  1.090
 JNW  CB   H8   single    0.970  0.020  1.090
 JNW  CB   H9   single    0.970  0.020  1.090
 JNW  CG   H10  single    0.970  0.020  1.090
 JNW  CG   H11  single    0.970  0.020  1.090
 JNW  NE2  H12  single    0.860  0.020  1.020

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
 JNW  CAQ  CAR  OAT  117.06  3.000
 JNW  OAT  CAR  OAS  127.19  3.000
 JNW  CAQ  CAR  OAS  115.75  3.000
 JNW  CAK  CAQ  CAP  118.49  3.000
 JNW  CAP  CAQ  CAR  120.06  3.000
 JNW  CAK  CAQ  CAR  121.44  3.000
 JNW  H2   CAP  CAO  119.87  3.000
 JNW  H2   CAP  CAQ  118.79  3.000
 JNW  CAO  CAP  CAQ  121.34  3.000
 JNW  H3   CAO  CAN  120.19  3.000
 JNW  H3   CAO  CAP  120.04  3.000
 JNW  CAN  CAO  CAP  119.78  3.000
 JNW  H4   CAN  CAM  119.90  3.000
 JNW  H4   CAN  CAO  120.49  3.000
 JNW  CAM  CAN  CAO  119.61  3.000
 JNW  H5   CAM  CAK  119.93  3.000
 JNW  H5   CAM  CAN  119.55  3.000
 JNW  CAK  CAM  CAN  120.52  3.000
 JNW  CAJ  CAK  CAM  116.25  3.000
 JNW  CAM  CAK  CAQ  120.26  3.000
 JNW  CAJ  CAK  CAQ  123.49  3.000
 JNW  N    CAJ  OAL  123.24  3.000
 JNW  OAL  CAJ  CAK  122.05  3.000
 JNW  N    CAJ  CAK  114.01  3.000
 JNW  H6   N    CA   118.47  3.000
 JNW  H6   N    CAJ  116.73  3.000
 JNW  CA   N    CAJ  121.52  3.000
 JNW  H7   CA   C    106.42  3.000
 JNW  H7   CA   CB   109.92  3.000
 JNW  C    CA   CB   111.01  3.000
 JNW  H7   CA   N    108.00  3.000
 JNW  CB   CA   N    113.89  3.000
 JNW  C    CA   N    107.27  3.000
 JNW  H9   CB   H8   107.45  3.000
 JNW  H9   CB   CG   110.02  3.000
 JNW  H8   CB   CG   110.31  3.000
 JNW  H9   CB   CA   109.55  3.000
 JNW  H8   CB   CA   108.69  3.000
 JNW  CG   CB   CA   110.76  3.000
 JNW  H11  CG   H10  106.11  3.000
 JNW  H11  CG   CD   108.41  3.000
 JNW  H10  CG   CD   107.83  3.000
 JNW  H11  CG   CB   110.03  3.000
 JNW  H10  CG   CB   111.60  3.000
 JNW  CD   CG   CB   112.60  3.000
 JNW  NE2  CD   OE1  119.56  3.000
 JNW  NE2  CD   CG   116.27  3.000
 JNW  OE1  CD   CG   124.17  3.000
 JNW  H12  NE2  C    115.86  3.000
 JNW  H12  NE2  CD   115.78  3.000
 JNW  C    NE2  CD   128.36  3.000
 JNW  O    C    NE2  120.90  3.000
 JNW  O    C    CA   123.14  3.000
 JNW  NE2  C    CA   115.95  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
 JNW  CONST_01  CAN  CAM  CAK  CAQ    0.00   0.0  0
 JNW  CONST_02  CAN  CAO  CAP  CAQ    0.00   0.0  0
 JNW  CONST_03  CAM  CAK  CAQ  CAP    0.00   0.0  0
 JNW  CONST_04  CAM  CAN  CAO  CAP    0.00   0.0  0
 JNW  CONST_05  CAK  CAM  CAN  CAO    0.00   0.0  0
 JNW  CONST_06  CAK  CAQ  CAP  CAO    0.00   0.0  0
 JNW  CONST_07  C    NE2  CD   CG     0.00   0.0  0
 JNW  CONST_08  CAM  CAK  CAQ  CAR  180.00   0.0  0
 JNW  CONST_09  CAO  CAP  CAQ  CAR  180.00   0.0  0
 JNW  CONST_10  CAJ  CAK  CAQ  CAP  180.00   0.0  0
 JNW  CONST_11  CAJ  CAK  CAM  CAN  180.00   0.0  0
 JNW  CONST_12  C    NE2  CD   OE1  180.00   0.0  0
 JNW  CONST_13  H5   CAM  CAK  CAQ  180.00   0.0  0
 JNW  CONST_14  H3   CAO  CAP  CAQ  180.00   0.0  0
 JNW  CONST_15  H4   CAN  CAO  CAP  180.00   0.0  0
 JNW  CONST_16  H2   CAP  CAO  CAN  180.00   0.0  0
 JNW  CONST_17  H12  NE2  CD   CG   180.00   0.0  0
 JNW  CONST_18  CA   N    CAJ  CAK  180.00   0.0  0
 JNW  CONST_19  CA   N    CAJ  OAL    0.00   0.0  0
 JNW  Var_01    CD   NE2  C    CA    -1.21  30.0  1
 JNW  Var_02    CD   CG   CB   CA    52.66  30.0  1
 JNW  Var_03    NE2  CD   CG   CB   -24.57  30.0  1
 JNW  Var_04    CAK  CAQ  CAR  OAS    6.14  30.0  2
 JNW  Var_05    N    CAJ  CAK  CAQ   84.39  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
 JNW  chir_01  CA  C  CB  N  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
 JNW  plan-1  CAR  0.020
 JNW  plan-1  CAQ  0.020
 JNW  plan-1  CAP  0.020
 JNW  plan-1  CAO  0.020
 JNW  plan-1  CAN  0.020
 JNW  plan-1  CAM  0.020
 JNW  plan-1  CAK  0.020
 JNW  plan-1  CAJ  0.020
 JNW  plan-1  H2   0.020
 JNW  plan-1  H3   0.020
 JNW  plan-1  H4   0.020
 JNW  plan-1  H5   0.020
 JNW  plan-2  CAK  0.020
 JNW  plan-2  CAJ  0.020
 JNW  plan-2  OAL  0.020
 JNW  plan-2  N    0.020
 JNW  plan-2  CA   0.020
 JNW  plan-2  H6   0.020
 JNW  plan-3  CA   0.020
 JNW  plan-3  NE2  0.020
 JNW  plan-3  C    0.020
 JNW  plan-3  O    0.020
 JNW  plan-4  CG   0.020
 JNW  plan-4  CD   0.020
 JNW  plan-4  OE1  0.020
 JNW  plan-4  NE2  0.020
 JNW  plan-4  C    0.020
 JNW  plan-4  H12  0.020
 JNW  plan-5  OAS  0.020
 JNW  plan-5  CAR  0.020
 JNW  plan-5  OAT  0.020
 JNW  plan-5  CAQ  0.020

