# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 11:08:59 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(Nc1ccccc1)=C/2C(=O)N[C@@H](Cc3ccccc3)C/2=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
 N16  N16  (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione  ligand  41  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N16
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
 N16  CD1   C  CR16  0  -0.300  -5.1838   0.7849  -0.3072
 N16  CE1   C  CR16  0  -0.239  -6.3402   0.1135  -0.6768
 N16  CZ    C  CR16  0  -0.270  -6.5389  -1.2037  -0.2808
 N16  CE2   C  CR16  0  -0.240  -5.5752  -1.8396   0.4895
 N16  CD2   C  CR16  0  -0.317  -4.4184  -1.1635   0.8576
 N16  CG    C  CR6   0   0.120  -4.2076   0.1556   0.4645
 N16  CB    C  CH2   0  -0.513  -2.9338   0.8722   0.8141
 N16  CA    C  CH1   0  -0.137  -1.9287   0.8308  -0.3412
 N16  C     C  C     0   0.320  -0.6103   1.5108   0.0350
 N16  O     O  O     0  -0.445  -0.5607   2.6699   0.4145
 N16  N     N  NH1   0  -0.662  -1.5150  -0.5042  -0.6879
 N16  CAR   C  C     0   0.571  -0.1870  -0.7118  -0.5846
 N16  OAB   O  O     0  -0.520   0.3860  -1.7726  -0.8466
 N16  CAT   C  C     0  -0.374   0.4259   0.5322  -0.1249
 N16  CAQ   C  C     0   0.427   1.7931   0.6867   0.0953
 N16  CAA   C  CH3   0  -0.754   2.3650   1.9997   0.5126
 N16  NAO   N  NH1   0  -0.728   2.5932  -0.3572  -0.0984
 N16  CAV   C  CR6   0   0.304   3.9829  -0.4500   0.1145
 N16  CAL   C  CR16  0  -0.273   4.5717  -0.0329   1.3042
 N16  CAH   C  CR16  0  -0.252   5.9418  -0.1675   1.4774
 N16  CAE   C  CR16  0  -0.256   6.7248  -0.7388   0.4836
 N16  CAI   C  CR16  0  -0.249   6.1291  -1.1786  -0.6916
 N16  CAM   C  CR16  0  -0.302   4.7634  -1.0331  -0.8798
 N16  HD1   H  HCR6  0   0.250  -5.0384   1.8128  -0.6201
 N16  HE1   H  HCR6  0   0.255  -7.0885   0.6195  -1.2733
 N16  HZ    H  HCR6  0   0.255  -7.4407  -1.7284  -0.5687
 N16  HE2   H  HCR6  0   0.255  -5.7238  -2.8636   0.8074
 N16  HD2   H  HCR6  0   0.251  -3.6747  -1.6666   1.4644
 N16  HB    H  HCH2  0   0.263  -3.1376   1.9191   1.0463
 N16  HBA   H  HCH2  0   0.259  -2.4767   0.4249   1.7002
 N16  HA    H  HCH1  0   0.289  -2.3544   1.3451  -1.2107
 N16  HN    H  HNH1  0   0.399  -2.1447  -1.2025  -1.0503
 N16  HAA   H  HCH3  0   0.281   2.2526   2.1371   1.5891
 N16  HAAA  H  HCH3  0   0.272   3.4217   2.0790   0.2708
 N16  HAAB  H  HCH3  0   0.286   1.8303   2.8124   0.0314
 N16  HNAO  H  HNH1  0   0.430   2.1231  -1.1884  -0.4633
 N16  HAL   H  HCR6  0   0.277   3.9680   0.3802   2.1015
 N16  HAH   H  HCR6  0   0.266   6.3936   0.1655   2.4023
 N16  HAE   H  HCR6  0   0.262   7.7916  -0.8477   0.6271
 N16  HAI   H  HCR6  0   0.265   6.7286  -1.6308  -1.4706
 N16  HAM   H  HCR6  0   0.274   4.3005  -1.3668  -1.8001

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
 N16  CAI  CAM   aromatic  1.386  0.020  1.386
 N16  CAI  CAE   aromatic  1.389  0.020  1.389
 N16  CAM  CAV   aromatic  1.392  0.020  1.392
 N16  CAE  CAH   aromatic  1.388  0.020  1.388
 N16  CAV  NAO   single    1.409  0.020  1.409
 N16  CAV  CAL   aromatic  1.391  0.020  1.391
 N16  NAO  CAQ   single    1.329  0.020  1.329
 N16  OAB  CAR   double    1.234  0.020  1.234
 N16  CAH  CAL   aromatic  1.388  0.020  1.388
 N16  CAQ  CAA   single    1.492  0.020  1.492
 N16  CAQ  CAT   double    1.393  0.020  1.393
 N16  CAR  CAT   single    1.461  0.020  1.461
 N16  CAR  N     single    1.348  0.020  1.348
 N16  CAT  C     single    1.434  0.020  1.434
 N16  N    CA    single    1.440  0.020  1.440
 N16  C    CA    single    1.530  0.020  1.530
 N16  C    O     double    1.221  0.020  1.221
 N16  CA   CB    single    1.532  0.020  1.532
 N16  CB   CG    single    1.503  0.020  1.503
 N16  CD2  CG    aromatic  1.393  0.020  1.393
 N16  CD2  CE2   aromatic  1.390  0.020  1.390
 N16  CG   CD1   aromatic  1.394  0.020  1.394
 N16  CD1  CE1   aromatic  1.387  0.020  1.387
 N16  CE2  CZ    aromatic  1.388  0.020  1.388
 N16  CZ   CE1   aromatic  1.390  0.020  1.390
 N16  CD1  HD1   single    0.930  0.020  1.080
 N16  CE1  HE1   single    0.930  0.020  1.080
 N16  CZ   HZ    single    0.930  0.020  1.080
 N16  CE2  HE2   single    0.930  0.020  1.080
 N16  CD2  HD2   single    0.930  0.020  1.080
 N16  CB   HB    single    0.970  0.020  1.090
 N16  CB   HBA   single    0.970  0.020  1.090
 N16  CA   HA    single    0.970  0.020  1.090
 N16  N    HN    single    0.860  0.020  1.020
 N16  CAA  HAA   single    0.970  0.020  1.090
 N16  CAA  HAAA  single    0.970  0.020  1.090
 N16  CAA  HAAB  single    0.970  0.020  1.090
 N16  NAO  HNAO  single    0.860  0.020  1.020
 N16  CAL  HAL   single    0.930  0.020  1.080
 N16  CAH  HAH   single    0.930  0.020  1.080
 N16  CAE  HAE   single    0.930  0.020  1.080
 N16  CAI  HAI   single    0.930  0.020  1.080
 N16  CAM  HAM   single    0.930  0.020  1.080

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
 N16  HD1   CD1  CG    119.59  3.000
 N16  HD1   CD1  CE1   119.58  3.000
 N16  CG    CD1  CE1   120.84  3.000
 N16  HE1   CE1  CZ    120.08  3.000
 N16  HE1   CE1  CD1   119.79  3.000
 N16  CZ    CE1  CD1   120.13  3.000
 N16  HZ    CZ   CE2   120.27  3.000
 N16  HZ    CZ   CE1   120.18  3.000
 N16  CE2   CZ   CE1   119.55  3.000
 N16  HE2   CE2  CD2   119.78  3.000
 N16  HE2   CE2  CZ    120.07  3.000
 N16  CD2   CE2  CZ    120.15  3.000
 N16  HD2   CD2  CG    119.60  3.000
 N16  HD2   CD2  CE2   119.59  3.000
 N16  CG    CD2  CE2   120.80  3.000
 N16  CB    CG   CD2   120.95  3.000
 N16  CD2   CG   CD1   118.54  3.000
 N16  CB    CG   CD1   120.46  3.000
 N16  HBA   CB   HB    107.34  3.000
 N16  HBA   CB   CA    109.03  3.000
 N16  HB    CB   CA    107.99  3.000
 N16  HBA   CB   CG    110.37  3.000
 N16  HB    CB   CG    110.39  3.000
 N16  CA    CB   CG    111.58  3.000
 N16  HA    CA   N     110.83  3.000
 N16  HA    CA   C     108.72  3.000
 N16  N     CA   C     102.92  3.000
 N16  HA    CA   CB    109.31  3.000
 N16  C     CA   CB    111.58  3.000
 N16  N     CA   CB    113.28  3.000
 N16  CAT   C    O     130.79  3.000
 N16  O     C    CA    122.23  3.000
 N16  CAT   C    CA    106.96  3.000
 N16  HN    N    CAR   122.44  3.000
 N16  HN    N    CA    123.33  3.000
 N16  CAR   N    CA    114.04  3.000
 N16  CAT   CAR  OAB   127.16  3.000
 N16  CAT   CAR  N     107.83  3.000
 N16  OAB   CAR  N     125.00  3.000
 N16  CAQ   CAT  CAR   123.77  3.000
 N16  CAR   CAT  C     108.24  3.000
 N16  CAQ   CAT  C     127.99  3.000
 N16  NAO   CAQ  CAA   120.08  3.000
 N16  CAA   CAQ  CAT   121.20  3.000
 N16  NAO   CAQ  CAT   118.71  3.000
 N16  HAAB  CAA  HAAA  109.00  3.000
 N16  HAAB  CAA  HAA   107.00  3.000
 N16  HAAA  CAA  HAA   108.09  3.000
 N16  HAAB  CAA  CAQ   110.26  3.000
 N16  HAAA  CAA  CAQ   112.01  3.000
 N16  HAA   CAA  CAQ   110.33  3.000
 N16  HNAO  NAO  CAV   116.99  3.000
 N16  HNAO  NAO  CAQ   114.44  3.000
 N16  CAV   NAO  CAQ   128.56  3.000
 N16  CAM   CAV  CAL   119.94  3.000
 N16  CAL   CAV  NAO   121.78  3.000
 N16  CAM   CAV  NAO   118.21  3.000
 N16  HAL   CAL  CAH   119.74  3.000
 N16  HAL   CAL  CAV   120.56  3.000
 N16  CAH   CAL  CAV   119.70  3.000
 N16  HAH   CAH  CAE   120.21  3.000
 N16  HAH   CAH  CAL   119.29  3.000
 N16  CAE   CAH  CAL   120.50  3.000
 N16  HAE   CAE  CAI   120.21  3.000
 N16  HAE   CAE  CAH   120.18  3.000
 N16  CAI   CAE  CAH   119.61  3.000
 N16  HAI   CAI  CAM   119.47  3.000
 N16  HAI   CAI  CAE   120.26  3.000
 N16  CAM   CAI  CAE   120.27  3.000
 N16  HAM   CAM  CAI   120.28  3.000
 N16  HAM   CAM  CAV   119.77  3.000
 N16  CAI   CAM  CAV   119.96  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
 N16  CONST_01  CE2  CD2  CG   CD1    0.00   0.0  0
 N16  CONST_02  CE2  CZ   CE1  CD1    0.00   0.0  0
 N16  CONST_03  CD2  CG   CD1  CE1    0.00   0.0  0
 N16  CONST_04  CD2  CE2  CZ   CE1    0.00   0.0  0
 N16  CONST_05  CG   CD2  CE2  CZ     0.00   0.0  0
 N16  CONST_06  CG   CD1  CE1  CZ     0.00   0.0  0
 N16  CONST_07  CAE  CAI  CAM  CAV    0.00   0.0  0
 N16  CONST_08  CAE  CAH  CAL  CAV    0.00   0.0  0
 N16  CONST_09  CAI  CAM  CAV  CAL    0.00   0.0  0
 N16  CONST_10  CAI  CAE  CAH  CAL    0.00   0.0  0
 N16  CONST_11  CAM  CAI  CAE  CAH    0.00   0.0  0
 N16  CONST_12  CAM  CAV  CAL  CAH    0.00   0.0  0
 N16  CONST_13  CAT  CAR  N    CA     0.00   0.0  0
 N16  CONST_14  CB   CG   CD1  CE1  180.00   0.0  0
 N16  CONST_15  CB   CG   CD2  CE2  180.00   0.0  0
 N16  CONST_16  CAI  CAM  CAV  NAO  180.00   0.0  0
 N16  CONST_17  CAH  CAL  CAV  NAO  180.00   0.0  0
 N16  CONST_18  OAB  CAR  N    CA   180.00   0.0  0
 N16  CONST_19  HD2  CD2  CG   CD1  180.00   0.0  0
 N16  CONST_20  HZ   CZ   CE1  CD1  180.00   0.0  0
 N16  CONST_21  HE2  CE2  CZ   CE1  180.00   0.0  0
 N16  CONST_22  HD1  CD1  CE1  CZ   180.00   0.0  0
 N16  CONST_23  HE1  CE1  CZ   CE2  180.00   0.0  0
 N16  CONST_24  HAI  CAI  CAM  CAV  180.00   0.0  0
 N16  CONST_25  HAH  CAH  CAL  CAV  180.00   0.0  0
 N16  CONST_26  HAM  CAM  CAV  CAL  180.00   0.0  0
 N16  CONST_27  HAE  CAE  CAH  CAL  180.00   0.0  0
 N16  CONST_28  HAL  CAL  CAH  CAE  180.00   0.0  0
 N16  CONST_29  HN   N    CAR  CAT  180.00   0.0  0
 N16  CONST_30  CAV  NAO  CAQ  CAT  180.00   0.0  0
 N16  CONST_34  CAV  NAO  CAQ  CAA    0.00   0.0  0
 N16  Var_01    CAR  CAT  C    CA     0.21  30.0  1
 N16  Var_02    N    CAR  CAT  C     -0.42  30.0  1
 N16  Var_03    CA   CB   CG   CD1  -80.50  30.0  2
 N16  Var_04    NAO  CAQ  CAT  C    179.26  30.0  2
 N16  Var_05    HAA  CAA  CAQ  CAT   82.04  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
 N16  chir_01  CA  N  C  CB  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
 N16  plan-1  CD1   0.020
 N16  plan-1  CE1   0.020
 N16  plan-1  CZ    0.020
 N16  plan-1  CE2   0.020
 N16  plan-1  CD2   0.020
 N16  plan-1  CG    0.020
 N16  plan-1  CB    0.020
 N16  plan-1  HD1   0.020
 N16  plan-1  HE1   0.020
 N16  plan-1  HZ    0.020
 N16  plan-1  HE2   0.020
 N16  plan-1  HD2   0.020
 N16  plan-2  NAO   0.020
 N16  plan-2  CAV   0.020
 N16  plan-2  CAL   0.020
 N16  plan-2  CAH   0.020
 N16  plan-2  CAE   0.020
 N16  plan-2  CAI   0.020
 N16  plan-2  CAM   0.020
 N16  plan-2  HAL   0.020
 N16  plan-2  HAH   0.020
 N16  plan-2  HAE   0.020
 N16  plan-2  HAI   0.020
 N16  plan-2  HAM   0.020
 N16  plan-3  CAQ   0.020
 N16  plan-3  NAO   0.020
 N16  plan-3  CAV   0.020
 N16  plan-3  HNAO  0.020
 N16  plan-4  CA    0.020
 N16  plan-4  C     0.020
 N16  plan-4  O     0.020
 N16  plan-4  CAT   0.020
 N16  plan-5  CA    0.020
 N16  plan-5  N     0.020
 N16  plan-5  CAR   0.020
 N16  plan-5  OAB   0.020
 N16  plan-5  CAT   0.020
 N16  plan-5  HN    0.020

