# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:15:47 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  32  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  -0.430   1.6580  -1.4380   1.4597
 JNW  CAR  C  C     0   0.520   2.6393  -0.7773   1.2190
 JNW  OAT  O  OH1   0  -0.589   3.8009  -0.9474   1.8300
 JNW  CAQ  C  CR6   0  -0.086   2.6626   0.3167   0.2155
 JNW  CAP  C  CR16  0  -0.257   3.7276   1.2130   0.1479
 JNW  CAO  C  CR16  0  -0.242   3.7075   2.2627  -0.7568
 JNW  CAN  C  CR16  0  -0.232   2.6205   2.4268  -1.6016
 JNW  CAM  C  CR16  0  -0.253   1.5572   1.5365  -1.5442
 JNW  CAK  C  CR6   0  -0.043   1.5713   0.4808  -0.6430
 JNW  CAJ  C  C     0   0.503   0.4260  -0.4911  -0.7085
 JNW  OAL  O  O     0  -0.460   0.5062  -1.5228  -1.3482
 JNW  N    N  NH1   0  -0.610  -0.6860  -0.0594  -0.0861
 JNW  CA   C  CH1   0  -0.246  -1.8957  -0.8454   0.0156
 JNW  CB   C  CH2   0  -0.462  -2.4520  -0.8547   1.4289
 JNW  CG   C  CH2   0  -0.605  -3.0296   0.4980   1.8110
 JNW  CD   C  C     0   0.557  -4.0203   1.0078   0.8040
 JNW  OE1  O  O     0  -0.429  -4.9073   1.7866   1.0672
 JNW  NE2  N  NH1   0  -0.683  -3.8613   0.5547  -0.4921
 JNW  C    C  C     0   0.581  -2.9037  -0.3002  -0.9861
 JNW  O    O  O     0  -0.420  -2.8629  -0.5698  -2.1634
 JNW  H1   H  HOH1  0   0.491   3.7291  -1.6565   2.4865
 JNW  H2   H  HCR6  0   0.276   4.5762   1.1041   0.8085
 JNW  H3   H  HCR6  0   0.273   4.5393   2.9526  -0.7971
 JNW  H4   H  HCR6  0   0.275   2.5969   3.2467  -2.3067
 JNW  H5   H  HCR6  0   0.273   0.7140   1.6653  -2.2111
 JNW  H6   H  HNH1  0   0.417  -0.6241   0.7926   0.4501
 JNW  H7   H  HCH1  0   0.314  -1.6616  -1.8631  -0.2965
 JNW  H8   H  HCH2  0   0.274  -3.2321  -1.6161   1.4895
 JNW  H9   H  HCH2  0   0.281  -1.6659  -1.1456   2.1252
 JNW  H10  H  HCH2  0   0.304  -3.5250   0.4544   2.7803
 JNW  H11  H  HCH2  0   0.290  -2.2469   1.2578   1.9127
 JNW  H12  H  HNH1  0   0.418  -4.5181   0.9225  -1.1722

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    1.209  0.020  1.209
 JNW  NE2  CD   single    1.382  0.020  1.382
 JNW  NE2  C    single    1.375  0.020  1.375
 JNW  CD   CG   single    1.502  0.020  1.502
 JNW  O    C    double    1.208  0.020  1.208
 JNW  C    CA   single    1.522  0.020  1.522
 JNW  CG   CB   single    1.520  0.020  1.520
 JNW  CA   CB   single    1.519  0.020  1.519
 JNW  CA   N    single    1.446  0.020  1.446
 JNW  N    CAJ  single    1.345  0.020  1.345
 JNW  OAL  CAJ  double    1.217  0.020  1.217
 JNW  CAJ  CAK  single    1.504  0.020  1.504
 JNW  CAK  CAM  aromatic  1.388  0.020  1.388
 JNW  CAK  CAQ  aromatic  1.398  0.020  1.398
 JNW  CAM  CAN  aromatic  1.388  0.020  1.388
 JNW  OAS  CAR  double    1.207  0.020  1.207
 JNW  CAR  CAQ  single    1.485  0.020  1.485
 JNW  CAR  OAT  single    1.324  0.020  1.324
 JNW  CAQ  CAP  aromatic  1.394  0.020  1.394
 JNW  CAN  CAO  aromatic  1.386  0.020  1.386
 JNW  CAO  CAP  aromatic  1.386  0.020  1.386
 JNW  OAT  H1   single    0.850  0.020  0.980
 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    0.860  0.020  1.020
 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  113.14  3.000
 JNW  OAT  CAR  OAS  123.44  3.000
 JNW  CAQ  CAR  OAS  123.42  3.000
 JNW  H1   OAT  CAR  109.99  3.000
 JNW  CAK  CAQ  CAP  119.42  3.000
 JNW  CAP  CAQ  CAR  121.25  3.000
 JNW  CAK  CAQ  CAR  119.29  3.000
 JNW  H2   CAP  CAO  119.12  3.000
 JNW  H2   CAP  CAQ  120.37  3.000
 JNW  CAO  CAP  CAQ  120.51  3.000
 JNW  H3   CAO  CAN  120.33  3.000
 JNW  H3   CAO  CAP  119.76  3.000
 JNW  CAN  CAO  CAP  119.92  3.000
 JNW  H4   CAN  CAM  119.76  3.000
 JNW  H4   CAN  CAO  120.27  3.000
 JNW  CAM  CAN  CAO  119.97  3.000
 JNW  H5   CAM  CAK  119.88  3.000
 JNW  H5   CAM  CAN  119.66  3.000
 JNW  CAK  CAM  CAN  120.45  3.000
 JNW  CAJ  CAK  CAM  117.10  3.000
 JNW  CAM  CAK  CAQ  119.73  3.000
 JNW  CAJ  CAK  CAQ  123.05  3.000
 JNW  N    CAJ  OAL  124.74  3.000
 JNW  OAL  CAJ  CAK  121.39  3.000
 JNW  N    CAJ  CAK  113.70  3.000
 JNW  H6   N    CA   118.23  3.000
 JNW  H6   N    CAJ  117.79  3.000
 JNW  CA   N    CAJ  123.33  3.000
 JNW  H7   CA   C    106.76  3.000
 JNW  H7   CA   CB   109.84  3.000
 JNW  C    CA   CB   111.84  3.000
 JNW  H7   CA   N    107.92  3.000
 JNW  CB   CA   N    112.03  3.000
 JNW  C    CA   N    108.24  3.000
 JNW  H9   CB   H8   107.09  3.000
 JNW  H9   CB   CG   110.56  3.000
 JNW  H8   CB   CG   109.59  3.000
 JNW  H9   CB   CA   109.39  3.000
 JNW  H8   CB   CA   108.52  3.000
 JNW  CG   CB   CA   111.57  3.000
 JNW  H11  CG   H10  105.66  3.000
 JNW  H11  CG   CD   107.34  3.000
 JNW  H10  CG   CD   108.07  3.000
 JNW  H11  CG   CB   111.66  3.000
 JNW  H10  CG   CB   111.16  3.000
 JNW  CD   CG   CB   112.60  3.000
 JNW  NE2  CD   OE1  119.96  3.000
 JNW  NE2  CD   CG   116.21  3.000
 JNW  OE1  CD   CG   123.82  3.000
 JNW  H12  NE2  C    115.80  3.000
 JNW  H12  NE2  CD   115.81  3.000
 JNW  C    NE2  CD   128.36  3.000
 JNW  O    C    NE2  120.80  3.000
 JNW  O    C    CA   122.61  3.000
 JNW  NE2  C    CA   116.57  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  CONST_20  H6   N    CAJ  CAK    0.00   0.0  0
 JNW  CONST_21  H1   OAT  CAR  CAQ  180.00   0.0  0
 JNW  Var_01    CD   NE2  C    CA     1.15  30.0  1
 JNW  Var_02    CD   CG   CB   CA    52.24  30.0  1
 JNW  Var_03    NE2  CD   CG   CB   -26.55  30.0  1
 JNW  Var_04    CAK  CAQ  CAR  OAS   -9.84  30.0  2
 JNW  Var_05    N    CAJ  CAK  CAQ  103.52  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
 JNW  plan-5  H1   0.020

