# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:22:45 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: N~1~-phenylpiperidine-1,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C1CCN(CC1)C(=O)Nc2ccccc2
#
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
 T0J  T0J  N~1~-phenylpiperidine-1,4-dicarboxamide  ligand  35  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T0J
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
 T0J  C10   C  C     0   0.717   0.6034  -0.5475   0.8083
 T0J  N12   N  NH1   0  -0.784   1.5191   0.4481   0.5551
 T0J  C13   C  CR6   0   0.371   2.7825   0.2567  -0.0115
 T0J  C15   C  CR16  0  -0.252   4.3035  -0.7699  -1.5721
 T0J  C17   C  CR16  0  -0.247   5.0835   0.9866  -0.1486
 T0J  C02   C  C     0   0.536  -4.0710   0.1805  -1.0855
 T0J  C04   C  CH1   0  -0.389  -3.1905   0.1781   0.1509
 T0J  C05   C  CH2   0  -0.415  -2.0899   1.2353  -0.0059
 T0J  C06   C  CH2   0  -0.343  -1.1350   1.2006   1.1817
 T0J  C08   C  CH2   0  -0.324  -1.6116  -1.1269   1.5913
 T0J  C09   C  CH2   0  -0.421  -2.5811  -1.1956   0.4183
 T0J  C14   C  CR16  0  -0.298   3.0328  -0.6719  -1.0237
 T0J  C16   C  CR16  0  -0.276   5.3373   0.0516  -1.1426
 T0J  C18   C  CR16  0  -0.344   3.8214   1.0853   0.4160
 T0J  N01   N  NH2   0  -0.802  -5.1674   0.9476  -0.9978
 T0J  N07   N  NT    0  -0.484  -0.5753  -0.1317   1.3584
 T0J  O03   O  O     0  -0.492  -3.7789  -0.4466  -2.0948
 T0J  O11   O  O     0  -0.515   0.8486  -1.7236   0.5841
 T0J  H121  H  HNH1  0   0.409   1.4161   1.3164   1.0553
 T0J  H151  H  HCR6  0   0.256   4.4789  -1.4960  -2.3557
 T0J  H171  H  HCR6  0   0.257   5.8714   1.6427   0.1983
 T0J  H041  H  HCH1  0   0.254  -3.7982   0.4577   1.0193
 T0J  H052  H  HCH2  0   0.239  -1.5249   1.0567  -0.9254
 T0J  H051  H  HCH2  0   0.253  -2.5278   2.2331  -0.0831
 T0J  H062  H  HCH2  0   0.263  -0.3646   1.9565   1.0546
 T0J  H061  H  HCH2  0   0.253  -1.6671   1.4669   2.0988
 T0J  H081  H  HCH2  0   0.244  -2.1445  -0.8414   2.5029
 T0J  H082  H  HCH2  0   0.266  -1.1581  -2.0964   1.7776
 T0J  H092  H  HCH2  0   0.247  -3.3672  -1.9211   0.6407
 T0J  H091  H  HCH2  0   0.235  -2.0521  -1.5541  -0.4670
 T0J  H141  H  HCR6  0   0.264   2.2460  -1.3101  -1.3955
 T0J  H161  H  HCR6  0   0.253   6.3231  -0.0317  -1.5801
 T0J  H181  H  HCR6  0   0.265   3.6393   1.8135   1.1980
 T0J  H012  H  HNH2  0   0.406  -5.3856   1.4657  -0.1647
 T0J  H011  H  HNH2  0   0.399  -5.7705   1.0745  -1.7945

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
 T0J  C02  N01   single    1.341  0.020  1.341
 T0J  O03  C02   double    1.224  0.020  1.224
 T0J  C04  C02   single    1.518  0.020  1.518
 T0J  C05  C04   single    1.534  0.020  1.534
 T0J  C06  C05   single    1.524  0.020  1.524
 T0J  N07  C06   single    1.456  0.020  1.456
 T0J  C09  C08   single    1.523  0.020  1.523
 T0J  C08  N07   single    1.456  0.020  1.456
 T0J  C10  N07   single    1.366  0.020  1.366
 T0J  O11  C10   double    1.222  0.020  1.222
 T0J  N12  C10   single    1.376  0.020  1.376
 T0J  C13  N12   single    1.398  0.020  1.398
 T0J  C14  C13   aromatic  1.396  0.020  1.396
 T0J  C15  C14   aromatic  1.387  0.020  1.387
 T0J  C16  C15   aromatic  1.389  0.020  1.389
 T0J  C17  C16   aromatic  1.388  0.020  1.388
 T0J  C18  C17   aromatic  1.386  0.020  1.386
 T0J  C04  C09   single    1.526  0.020  1.526
 T0J  C13  C18   aromatic  1.396  0.020  1.396
 T0J  N12  H121  single    0.890  0.020  1.040
 T0J  C15  H151  single    0.930  0.020  1.080
 T0J  C17  H171  single    0.930  0.020  1.080
 T0J  C04  H041  single    0.970  0.020  1.090
 T0J  C05  H052  single    0.970  0.020  1.090
 T0J  C05  H051  single    0.970  0.020  1.090
 T0J  C06  H062  single    0.970  0.020  1.090
 T0J  C06  H061  single    0.970  0.020  1.090
 T0J  C08  H081  single    0.970  0.020  1.090
 T0J  C08  H082  single    0.970  0.020  1.090
 T0J  C09  H092  single    0.970  0.020  1.090
 T0J  C09  H091  single    0.970  0.020  1.090
 T0J  C14  H141  single    0.930  0.020  1.080
 T0J  C16  H161  single    0.930  0.020  1.080
 T0J  C18  H181  single    0.930  0.020  1.080
 T0J  N01  H012  single    0.860  0.020  1.020
 T0J  N01  H011  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
 T0J  O11   C10  N07   122.69  3.000
 T0J  O11   C10  N12   121.93  3.000
 T0J  N07   C10  N12   115.35  3.000
 T0J  H121  N12  C13   114.31  3.000
 T0J  H121  N12  C10   117.65  3.000
 T0J  C13   N12  C10   125.24  3.000
 T0J  C18   C13  C14   118.91  3.000
 T0J  C18   C13  N12   117.86  3.000
 T0J  C14   C13  N12   123.15  3.000
 T0J  H151  C15  C16   120.01  3.000
 T0J  H151  C15  C14   118.81  3.000
 T0J  C16   C15  C14   121.18  3.000
 T0J  H171  C17  C18   119.28  3.000
 T0J  H171  C17  C16   120.31  3.000
 T0J  C18   C17  C16   120.40  3.000
 T0J  O03   C02  N01   122.84  3.000
 T0J  O03   C02  C04   122.18  3.000
 T0J  N01   C02  C04   114.95  3.000
 T0J  H041  C04  C09   108.18  3.000
 T0J  H041  C04  C05   107.63  3.000
 T0J  C09   C04  C05   110.59  3.000
 T0J  H041  C04  C02   108.87  3.000
 T0J  C09   C04  C02   112.07  3.000
 T0J  C05   C04  C02   109.38  3.000
 T0J  H051  C05  H052  107.27  3.000
 T0J  H051  C05  C06   109.08  3.000
 T0J  H052  C05  C06   109.13  3.000
 T0J  H051  C05  C04   110.43  3.000
 T0J  H052  C05  C04   110.11  3.000
 T0J  C06   C05  C04   110.74  3.000
 T0J  H061  C06  H062  105.89  3.000
 T0J  H061  C06  N07   107.96  3.000
 T0J  H062  C06  N07   112.22  3.000
 T0J  H061  C06  C05   110.07  3.000
 T0J  H062  C06  C05   109.70  3.000
 T0J  N07   C06  C05   110.87  3.000
 T0J  H082  C08  H081  107.06  3.000
 T0J  H082  C08  N07   109.90  3.000
 T0J  H081  C08  N07   107.56  3.000
 T0J  H082  C08  C09   110.95  3.000
 T0J  H081  C08  C09   110.08  3.000
 T0J  N07   C08  C09   111.14  3.000
 T0J  H091  C09  H092  107.19  3.000
 T0J  H091  C09  C08   109.31  3.000
 T0J  H092  C09  C08   109.34  3.000
 T0J  H091  C09  C04   110.30  3.000
 T0J  H092  C09  C04   110.24  3.000
 T0J  C08   C09  C04   110.39  3.000
 T0J  H141  C14  C15   119.32  3.000
 T0J  H141  C14  C13   120.82  3.000
 T0J  C15   C14  C13   119.85  3.000
 T0J  H161  C16  C17   120.54  3.000
 T0J  H161  C16  C15   120.52  3.000
 T0J  C17   C16  C15   118.94  3.000
 T0J  H181  C18  C17   119.64  3.000
 T0J  H181  C18  C13   119.65  3.000
 T0J  C17   C18  C13   120.71  3.000
 T0J  H011  N01  H012  117.44  3.000
 T0J  H011  N01  C02   120.65  3.000
 T0J  H012  N01  C02   121.78  3.000
 T0J  C08   N07  C06   111.80  3.000
 T0J  C08   N07  C10   118.08  3.000
 T0J  C06   N07  C10   124.17  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
 T0J  CONST_01  C16   C15  C14  C13    0.00   0.0  0
 T0J  CONST_02  C16   C17  C18  C13    0.00   0.0  0
 T0J  CONST_03  C18   C13  C14  C15    0.00   0.0  0
 T0J  CONST_04  C18   C17  C16  C15    0.00   0.0  0
 T0J  CONST_05  C14   C15  C16  C17    0.00   0.0  0
 T0J  CONST_06  C14   C13  C18  C17    0.00   0.0  0
 T0J  CONST_07  C15   C14  C13  N12  180.00   0.0  0
 T0J  CONST_08  C17   C18  C13  N12  180.00   0.0  0
 T0J  CONST_09  H151  C15  C14  C13  180.00   0.0  0
 T0J  CONST_10  H171  C17  C18  C13  180.00   0.0  0
 T0J  CONST_11  H181  C18  C13  C14  180.00   0.0  0
 T0J  CONST_12  H161  C16  C15  C14  180.00   0.0  0
 T0J  CONST_13  H141  C14  C15  C16  180.00   0.0  0
 T0J  CONST_15  O11   C10  N07  C08    0.00   0.0  0
 T0J  CONST_18  N07   C10  N12  C13  180.00   0.0  0
 T0J  CONST_20  C08   N07  C10  N12  180.00   0.0  0
 T0J  CONST_22  O11   C10  N12  C13    0.00   0.0  0
 T0J  CONST_23  H012  N01  C02  C04    0.00   0.0  0
 T0J  CONST_24  H011  N01  C02  C04  180.00   0.0  0
 T0J  Var_01    N07   C06  C05  C04   55.63  30.0  1
 T0J  Var_02    N07   C08  C09  C04  -56.31  30.0  1
 T0J  Var_03    C08   N07  C06  C05  -59.67  30.0  1
 T0J  Var_04    C09   C08  N07  C06   60.16  30.0  1

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
 T0J  chir_01  C04  C02  C05  C09  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
 T0J  plan-1  N12   0.020
 T0J  plan-1  C13   0.020
 T0J  plan-1  C15   0.020
 T0J  plan-1  C17   0.020
 T0J  plan-1  C14   0.020
 T0J  plan-1  C16   0.020
 T0J  plan-1  C18   0.020
 T0J  plan-1  H151  0.020
 T0J  plan-1  H171  0.020
 T0J  plan-1  H141  0.020
 T0J  plan-1  H161  0.020
 T0J  plan-1  H181  0.020
 T0J  plan-2  C10   0.020
 T0J  plan-2  N12   0.020
 T0J  plan-2  C13   0.020
 T0J  plan-2  C06   0.020
 T0J  plan-2  C08   0.020
 T0J  plan-2  N07   0.020
 T0J  plan-2  O11   0.020
 T0J  plan-2  H121  0.020
 T0J  plan-3  C02   0.020
 T0J  plan-3  C04   0.020
 T0J  plan-3  N01   0.020
 T0J  plan-3  O03   0.020
 T0J  plan-3  H012  0.020
 T0J  plan-3  H011  0.020

