# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:03:12 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-[(4-cyanophenyl)methyl]morpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccc(cc1)C#N)N2CCOCC2
#
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
 JGG  JGG  N-[(4-cyanophenyl)methyl]morpholine-4-carboxamide  ligand  33  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JGG
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
 JGG  C13   C  CH2   0  -0.191  -4.1332   0.4288  -1.7017
 JGG  C15   C  CH2   0  -0.181  -3.9916   1.9253   0.0562
 JGG  C01   C  CR16  0  -0.296   2.7165  -1.5052   0.7191
 JGG  C02   C  CR16  0  -0.226   3.7784  -1.3105  -0.1456
 JGG  C03   C  CR6   0  -0.013   3.8467  -0.1358  -0.8939
 JGG  C04   C  CR16  0  -0.227   2.8521   0.8345  -0.7677
 JGG  C05   C  CR16  0  -0.278   1.7990   0.6246   0.1038
 JGG  C06   C  CR6   0   0.123   1.7176  -0.5450   0.8552
 JGG  C07   C  CH2   0  -0.336   0.5987  -0.7669   1.8436
 JGG  N08   N  NH1   0  -0.693  -0.6551  -0.1706   1.4707
 JGG  C09   C  C     0   0.761  -1.3439  -0.6484   0.4013
 JGG  O10   O  O     0  -0.537  -0.9277  -1.6197  -0.2212
 JGG  N11   N  NT    0  -0.515  -2.4918   0.0070   0.0444
 JGG  C12   C  CH2   0  -0.308  -3.3600  -0.6260  -0.9362
 JGG  O14   O  O2    0  -0.481  -4.8609   1.2713  -0.8360
 JGG  C16   C  CH2   0  -0.332  -3.1928   0.9472   0.9023
 JGG  N18   N  NS    0  -0.256   5.8079   0.2455  -2.5245
 JGG  H132  H  HCH2  0   0.207  -3.4378   1.0177  -2.3160
 JGG  H131  H  HCH2  0   0.244  -4.8479  -0.0540  -2.3698
 JGG  H151  H  HCH2  0   0.209  -3.2942   2.5747  -0.4912
 JGG  H152  H  HCH2  0   0.247  -4.5969   2.5550   0.7089
 JGG  H011  H  HCR6  0   0.265   2.6640  -2.4228   1.2922
 JGG  H021  H  HCR6  0   0.280   4.5457  -2.0659  -0.2476
 JGG  H041  H  HCR6  0   0.279   2.9048   1.7455  -1.3487
 JGG  H051  H  HCR6  0   0.261   1.0295   1.3803   0.1934
 JGG  H071  H  HCH2  0   0.259   0.4790  -1.8377   2.0193
 JGG  H072  H  HCH2  0   0.281   0.8867  -0.3293   2.8010
 JGG  H081  H  HNH1  0   0.406  -0.9411   0.6537   1.9661
 JGG  H121  H  HCH2  0   0.231  -4.0583  -1.3132  -0.4411
 JGG  H122  H  HCH2  0   0.265  -2.7655  -1.2073  -1.6362
 JGG  H162  H  HCH2  0   0.255  -2.5023   1.5454   1.4947
 JGG  H161  H  HCH2  0   0.243  -3.8544   0.4172   1.5984
 JGG  C17   C  CSP   0   0.053   4.9324   0.0733  -1.7947

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
 JGG  O14  C13   single    1.410  0.020  1.410
 JGG  O14  C15   single    1.407  0.020  1.407
 JGG  C13  C12   single    1.515  0.020  1.515
 JGG  C15  C16   single    1.520  0.020  1.520
 JGG  N18  C17   triple    1.153  0.020  1.153
 JGG  C17  C03   single    1.426  0.020  1.426
 JGG  C02  C03   aromatic  1.395  0.020  1.395
 JGG  C02  C01   aromatic  1.383  0.020  1.383
 JGG  C16  N11   single    1.453  0.020  1.453
 JGG  C12  N11   single    1.455  0.020  1.455
 JGG  C03  C04   aromatic  1.395  0.020  1.395
 JGG  C01  C06   aromatic  1.392  0.020  1.392
 JGG  N11  C09   single    1.369  0.020  1.369
 JGG  C09  O10   double    1.226  0.020  1.226
 JGG  C09  N08   single    1.359  0.020  1.359
 JGG  C04  C05   aromatic  1.383  0.020  1.383
 JGG  C06  C05   aromatic  1.393  0.020  1.393
 JGG  C06  C07   single    1.509  0.020  1.509
 JGG  N08  C07   single    1.438  0.020  1.438
 JGG  C13  H132  single    0.970  0.020  1.090
 JGG  C13  H131  single    0.970  0.020  1.090
 JGG  C15  H151  single    0.970  0.020  1.090
 JGG  C15  H152  single    0.970  0.020  1.090
 JGG  C01  H011  single    0.930  0.020  1.080
 JGG  C02  H021  single    0.930  0.020  1.080
 JGG  C04  H041  single    0.930  0.020  1.080
 JGG  C05  H051  single    0.930  0.020  1.080
 JGG  C07  H071  single    0.970  0.020  1.090
 JGG  C07  H072  single    0.970  0.020  1.090
 JGG  N08  H081  single    0.860  0.020  1.020
 JGG  C12  H121  single    0.970  0.020  1.090
 JGG  C12  H122  single    0.970  0.020  1.090
 JGG  C16  H162  single    0.970  0.020  1.090
 JGG  C16  H161  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
 JGG  H131  C13  H132  108.02  3.000
 JGG  H131  C13  O14   107.59  3.000
 JGG  H132  C13  O14   110.46  3.000
 JGG  H131  C13  C12   109.61  3.000
 JGG  H132  C13  C12   109.42  3.000
 JGG  O14   C13  C12   111.66  3.000
 JGG  H152  C15  H151  108.01  3.000
 JGG  H152  C15  C16   109.28  3.000
 JGG  H151  C15  C16   108.91  3.000
 JGG  H152  C15  O14   107.76  3.000
 JGG  H151  C15  O14   110.54  3.000
 JGG  C16   C15  O14   112.25  3.000
 JGG  H011  C01  C06   119.85  3.000
 JGG  H011  C01  C02   119.15  3.000
 JGG  C06   C01  C02   120.99  3.000
 JGG  H021  C02  C03   120.20  3.000
 JGG  H021  C02  C01   120.35  3.000
 JGG  C03   C02  C01   119.45  3.000
 JGG  C04   C03  C02   120.16  3.000
 JGG  C04   C03  C17   119.86  3.000
 JGG  C02   C03  C17   119.98  3.000
 JGG  H041  C04  C05   120.22  3.000
 JGG  H041  C04  C03   120.15  3.000
 JGG  C05   C04  C03   119.62  3.000
 JGG  H051  C05  C06   120.02  3.000
 JGG  H051  C05  C04   119.18  3.000
 JGG  C06   C05  C04   120.80  3.000
 JGG  C07   C06  C05   121.34  3.000
 JGG  C07   C06  C01   119.64  3.000
 JGG  C05   C06  C01   118.98  3.000
 JGG  H072  C07  H071  106.32  3.000
 JGG  H072  C07  N08   106.94  3.000
 JGG  H071  C07  N08   110.67  3.000
 JGG  H072  C07  C06   108.66  3.000
 JGG  H071  C07  C06   109.32  3.000
 JGG  N08   C07  C06   114.56  3.000
 JGG  H081  N08  C09   122.21  3.000
 JGG  H081  N08  C07   117.47  3.000
 JGG  C09   N08  C07   120.03  3.000
 JGG  N11   C09  O10   122.09  3.000
 JGG  O10   C09  N08   120.39  3.000
 JGG  N11   C09  N08   117.51  3.000
 JGG  C16   N11  C12   113.05  3.000
 JGG  C12   N11  C09   117.89  3.000
 JGG  C16   N11  C09   124.08  3.000
 JGG  H122  C12  H121  107.67  3.000
 JGG  H122  C12  N11   109.91  3.000
 JGG  H121  C12  N11   110.37  3.000
 JGG  H122  C12  C13   109.02  3.000
 JGG  H121  C12  C13   109.81  3.000
 JGG  N11   C12  C13   110.01  3.000
 JGG  C15   O14  C13   110.37  3.000
 JGG  H161  C16  H162  107.62  3.000
 JGG  H161  C16  N11   110.67  3.000
 JGG  H162  C16  N11   111.76  3.000
 JGG  H161  C16  C15   110.32  3.000
 JGG  H162  C16  C15   106.41  3.000
 JGG  N11   C16  C15   109.95  3.000
 JGG  N18   C17  C03   180.00  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
 JGG  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 JGG  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 JGG  CONST_03  C05   C04  C03  C02     0.00   0.0  0
 JGG  CONST_04  C05   C06  C01  C02     0.00   0.0  0
 JGG  CONST_05  C06   C01  C02  C03     0.00   0.0  0
 JGG  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 JGG  CONST_07  C01   C02  C03  C17   180.00   0.0  0
 JGG  CONST_08  C05   C04  C03  C17   180.00   0.0  0
 JGG  CONST_09  C07   C06  C01  C02   180.00   0.0  0
 JGG  CONST_10  C07   C06  C05  C04   180.00   0.0  0
 JGG  CONST_11  H051  C05  C06  C01   180.00   0.0  0
 JGG  CONST_12  H041  C04  C03  C02   180.00   0.0  0
 JGG  CONST_13  H011  C01  C02  C03   180.00   0.0  0
 JGG  CONST_14  H021  C02  C03  C04   180.00   0.0  0
 JGG  CONST_15  C16   N11  C09  O10   180.00   0.0  0
 JGG  CONST_16  C12   N11  C09  O10     0.00   0.0  0
 JGG  CONST_18  C12   N11  C09  N08   180.00   0.0  0
 JGG  CONST_19  N11   C09  N08  C07   180.00   0.0  0
 JGG  CONST_20  H081  N08  C09  N11     0.00   0.0  0
 JGG  CONST_21  O10   C09  N08  C07     0.00   0.0  0
 JGG  Var_01    C16   C15  O14  C13   -59.09  30.0  1
 JGG  Var_02    C16   N11  C12  C13    52.00  30.0  1
 JGG  Var_03    C12   C13  O14  C15    59.63  30.0  1
 JGG  Var_04    C12   N11  C16  C15   -51.15  30.0  1
 JGG  Var_05    O14   C15  C16  N11    54.42  30.0  1
 JGG  Var_06    O14   C13  C12  N11   -55.71  30.0  1
 JGG  Var_07    N08   C07  C06  C01  -149.47  30.0  2
 JGG  Var_08    C09   N08  C07  C06    67.92  30.0  1

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
 JGG  plan-1  C01   0.020
 JGG  plan-1  C02   0.020
 JGG  plan-1  C03   0.020
 JGG  plan-1  C04   0.020
 JGG  plan-1  C05   0.020
 JGG  plan-1  C06   0.020
 JGG  plan-1  C07   0.020
 JGG  plan-1  N18   0.020
 JGG  plan-1  H011  0.020
 JGG  plan-1  H021  0.020
 JGG  plan-1  H041  0.020
 JGG  plan-1  H051  0.020
 JGG  plan-1  C17   0.020
 JGG  plan-2  C07   0.020
 JGG  plan-2  N08   0.020
 JGG  plan-2  C09   0.020
 JGG  plan-2  O10   0.020
 JGG  plan-2  N11   0.020
 JGG  plan-2  C12   0.020
 JGG  plan-2  C16   0.020
 JGG  plan-2  H081  0.020

