# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:50:46 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3S)-N~1~-(2-aminoethyl)-N~3~-(4-chloro-3-fluorophenyl)piperidine-1,3-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC(=O)N1CCC[C@@H](C1)C(=O)Nc2ccc(Cl)c(F)c2
#
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
 O51  O51  (3S)-N~1~-(2-aminoethyl)-N~3~-(4-chloro-3-fluorophenyl)piperidine-1,3-dicarboxamide  ligand  43  23  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O51
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
 O51  C02  C   CH2   0  -0.312   7.4841   0.7897   0.4581
 O51  C03  C   CH2   0  -0.249   6.1416   1.2689  -0.0725
 O51  C05  C   C     0   0.729   4.1013   0.2851  -0.9780
 O51  C07  C   CH2   0  -0.285   1.9246  -0.6547  -1.5188
 O51  C08  C   CH1   0  -0.425   0.9918  -0.6706  -0.3056
 O51  C09  C   C     0   0.583  -0.4584  -0.5423  -0.7172
 O51  O10  O   O     0  -0.460  -0.8851  -0.9794  -1.7703
 O51  C12  C   CR6   0   0.408  -2.6095   0.2862   0.2248
 O51  C13  C   CR16  0  -0.495  -3.4662  -0.1107  -0.8018
 O51  C14  C   CR6   0   0.654  -4.8161   0.1495  -0.6787
 O51  C16  C   CR6   0  -0.260  -5.3531   0.7910   0.4219
 O51  C18  C   CR16  0  -0.197  -4.4975   1.1866   1.4385
 O51  C19  C   CR16  0  -0.367  -3.1425   0.9377   1.3414
 O51  C20  C   CH2   0  -0.427   1.1854  -1.9656   0.5013
 O51  C21  C   CH2   0  -0.434   2.6545  -2.1805   0.8505
 O51  C22  C   CH2   0  -0.351   3.5194  -2.0791  -0.3987
 O51  F15  F   F     0  -0.297  -5.6325  -0.2348  -1.6622
 O51  N01  N   NH2   0  -0.801   8.3753   1.9250   0.6269
 O51  N04  N   NH1   0  -0.691   5.2456   0.1469  -0.2535
 O51  N06  N   NT    0  -0.489   3.2964  -0.8180  -1.0824
 O51  N11  N   NH1   0  -0.749  -1.2344   0.0725   0.2171
 O51  O23  O   O     0  -0.548   3.8344   1.3356  -1.5550
 O51  CL1  CL  CL    0  -0.096  -7.0490   1.0810   0.5087
 O51  H1   H   HCH2  0   0.224   7.3410   0.3213   1.4360
 O51  H2   H   HCH2  0   0.203   7.8717   0.0088  -0.2105
 O51  H3   H   HCH2  0   0.220   5.7274   2.0171   0.6123
 O51  H4   H   HCH2  0   0.233   6.2882   1.7614  -1.0349
 O51  H5   H   HCH2  0   0.244   1.6774  -1.4767  -2.1955
 O51  H6   H   HCH2  0   0.273   1.8258   0.2705  -2.0802
 O51  H7   H   HCH1  0   0.273   1.2563   0.1770   0.3373
 O51  H8   H   HCR6  0   0.310  -3.1078  -0.6114  -1.6867
 O51  H9   H   HCR6  0   0.293  -4.8911   1.6905   2.3103
 O51  H10  H   HCR6  0   0.286  -2.4916   1.2525   2.1472
 O51  H11  H   HCH2  0   0.254   0.5821  -1.9367   1.4110
 O51  H12  H   HCH2  0   0.237   0.8228  -2.8130  -0.0893
 O51  H13  H   HCH2  0   0.232   2.9795  -1.4357   1.5832
 O51  H14  H   HCH2  0   0.247   2.7870  -3.1615   1.3106
 O51  H15  H   HCH2  0   0.260   4.5743  -2.2233  -0.1732
 O51  H16  H   HCH2  0   0.254   3.2560  -2.8821  -1.0946
 O51  H17  H   HNH2  0   0.352   9.2241   1.6231   1.0864
 O51  H18  H   HNH2  0   0.342   8.6624   2.2668  -0.2818
 O51  H20  H   HNH1  0   0.397   5.2889  -0.5594   0.4619
 O51  H21  H   HNH1  0   0.423  -0.7519   0.4109   1.0363

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
 O51  N01  C02  single    1.453  0.020  1.453
 O51  C02  C03  single    1.521  0.020  1.521
 O51  C03  N04  single    1.447  0.020  1.447
 O51  O23  C05  double    1.228  0.020  1.228
 O51  N04  C05  single    1.361  0.020  1.361
 O51  C05  N06  single    1.369  0.020  1.369
 O51  N06  C22  single    1.452  0.020  1.452
 O51  N06  C07  single    1.449  0.020  1.449
 O51  C22  C21  single    1.523  0.020  1.523
 O51  C07  C08  single    1.530  0.020  1.530
 O51  C21  C20  single    1.525  0.020  1.525
 O51  C20  C08  single    1.538  0.020  1.538
 O51  C08  C09  single    1.513  0.020  1.513
 O51  O10  C09  double    1.217  0.020  1.217
 O51  C09  N11  single    1.361  0.020  1.361
 O51  N11  C12  single    1.392  0.020  1.392
 O51  C12  C13  aromatic  1.395  0.020  1.395
 O51  C12  C19  aromatic  1.398  0.020  1.398
 O51  C13  C14  aromatic  1.380  0.020  1.380
 O51  C19  C18  aromatic  1.381  0.020  1.381
 O51  C14  F15  single    1.335  0.020  1.335
 O51  C14  C16  aromatic  1.382  0.020  1.382
 O51  C18  C16  aromatic  1.386  0.020  1.386
 O51  C16  CL1  single    1.723  0.020  1.723
 O51  C02  H1   single    0.970  0.020  1.090
 O51  C02  H2   single    0.970  0.020  1.090
 O51  C03  H3   single    0.970  0.020  1.090
 O51  C03  H4   single    0.970  0.020  1.090
 O51  C07  H5   single    0.970  0.020  1.090
 O51  C07  H6   single    0.970  0.020  1.090
 O51  C08  H7   single    0.970  0.020  1.090
 O51  C13  H8   single    0.930  0.020  1.080
 O51  C18  H9   single    0.930  0.020  1.080
 O51  C19  H10  single    0.930  0.020  1.080
 O51  C20  H11  single    0.970  0.020  1.090
 O51  C20  H12  single    0.970  0.020  1.090
 O51  C21  H13  single    0.970  0.020  1.090
 O51  C21  H14  single    0.970  0.020  1.090
 O51  C22  H15  single    0.970  0.020  1.090
 O51  C22  H16  single    0.970  0.020  1.090
 O51  N01  H17  single    0.890  0.020  1.040
 O51  N01  H18  single    0.890  0.020  1.040
 O51  N04  H20  single    0.890  0.020  1.040
 O51  N11  H21  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
 O51  H2   C02  H1   106.61  3.000
 O51  H2   C02  N01  114.18  3.000
 O51  H1   C02  N01  108.12  3.000
 O51  H2   C02  C03  108.85  3.000
 O51  H1   C02  C03  109.35  3.000
 O51  N01  C02  C03  109.62  3.000
 O51  H4   C03  H3   107.09  3.000
 O51  H4   C03  N04  108.83  3.000
 O51  H3   C03  N04  111.94  3.000
 O51  H4   C03  C02  109.35  3.000
 O51  H3   C03  C02  109.32  3.000
 O51  N04  C03  C02  110.23  3.000
 O51  O23  C05  N06  121.70  3.000
 O51  N06  C05  N04  116.93  3.000
 O51  O23  C05  N04  121.30  3.000
 O51  H6   C07  H5   107.45  3.000
 O51  H6   C07  N06  109.73  3.000
 O51  H5   C07  N06  108.41  3.000
 O51  H6   C07  C08  111.28  3.000
 O51  H5   C07  C08  110.19  3.000
 O51  N06  C07  C08  109.70  3.000
 O51  H7   C08  C20  108.24  3.000
 O51  H7   C08  C09  108.98  3.000
 O51  C20  C08  C09  109.56  3.000
 O51  H7   C08  C07  108.05  3.000
 O51  C09  C08  C07  111.57  3.000
 O51  C20  C08  C07  110.36  3.000
 O51  N11  C09  O10  123.78  3.000
 O51  N11  C09  C08  113.45  3.000
 O51  O10  C09  C08  122.75  3.000
 O51  N11  C12  C19  116.91  3.000
 O51  C19  C12  C13  119.09  3.000
 O51  N11  C12  C13  124.00  3.000
 O51  H8   C13  C14  119.07  3.000
 O51  H8   C13  C12  122.15  3.000
 O51  C14  C13  C12  118.78  3.000
 O51  F15  C14  C16  118.86  3.000
 O51  C16  C14  C13  122.57  3.000
 O51  F15  C14  C13  118.57  3.000
 O51  CL1  C16  C18  121.50  3.000
 O51  CL1  C16  C14  120.04  3.000
 O51  C18  C16  C14  118.46  3.000
 O51  H9   C18  C19  119.86  3.000
 O51  H9   C18  C16  119.98  3.000
 O51  C19  C18  C16  120.17  3.000
 O51  H10  C19  C18  119.02  3.000
 O51  H10  C19  C12  120.04  3.000
 O51  C18  C19  C12  120.94  3.000
 O51  H12  C20  H11  106.68  3.000
 O51  H12  C20  C21  109.48  3.000
 O51  H11  C20  C21  110.19  3.000
 O51  H12  C20  C08  109.09  3.000
 O51  H11  C20  C08  110.19  3.000
 O51  C21  C20  C08  111.10  3.000
 O51  H14  C21  H13  107.06  3.000
 O51  H14  C21  C22  109.68  3.000
 O51  H13  C21  C22  109.59  3.000
 O51  H14  C21  C20  109.88  3.000
 O51  H13  C21  C20  110.09  3.000
 O51  C22  C21  C20  110.48  3.000
 O51  H16  C22  H15  105.52  3.000
 O51  H16  C22  N06  107.51  3.000
 O51  H15  C22  N06  111.20  3.000
 O51  H16  C22  C21  109.63  3.000
 O51  H15  C22  C21  111.82  3.000
 O51  N06  C22  C21  110.92  3.000
 O51  H18  N01  H17  105.70  3.000
 O51  H18  N01  C02  109.48  3.000
 O51  H17  N01  C02  109.53  3.000
 O51  H20  N04  C05  119.06  3.000
 O51  H20  N04  C03  115.38  3.000
 O51  C05  N04  C03  120.55  3.000
 O51  C22  N06  C07  112.66  3.000
 O51  C07  N06  C05  119.26  3.000
 O51  C22  N06  C05  124.99  3.000
 O51  H21  N11  C12  114.61  3.000
 O51  H21  N11  C09  115.85  3.000
 O51  C12  N11  C09  129.53  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
 O51  CONST_01  C16  C14  C13  C12     0.00   0.0  0
 O51  CONST_02  C16  C18  C19  C12     0.00   0.0  0
 O51  CONST_03  C18  C19  C12  C13     0.00   0.0  0
 O51  CONST_04  C18  C16  C14  C13     0.00   0.0  0
 O51  CONST_05  C19  C12  C13  C14     0.00   0.0  0
 O51  CONST_06  C19  C18  C16  C14     0.00   0.0  0
 O51  CONST_07  F15  C14  C13  C12   180.00   0.0  0
 O51  CONST_08  CL1  C16  C14  C13   180.00   0.0  0
 O51  CONST_09  N11  C12  C13  C14   180.00   0.0  0
 O51  CONST_10  N11  C12  C19  C18   180.00   0.0  0
 O51  CONST_11  F15  C14  C16  C18   180.00   0.0  0
 O51  CONST_12  CL1  C16  C18  C19   180.00   0.0  0
 O51  CONST_13  H9   C18  C19  C12   180.00   0.0  0
 O51  CONST_14  H10  C19  C12  C13   180.00   0.0  0
 O51  CONST_15  H8   C13  C14  C16   180.00   0.0  0
 O51  CONST_17  C12  N11  C09  C08   180.00   0.0  0
 O51  CONST_18  O23  C05  N06  C22   180.00   0.0  0
 O51  CONST_19  C13  C12  N11  C09     0.00   0.0  0
 O51  CONST_20  C19  C12  N11  C09   180.00   0.0  0
 O51  CONST_22  N04  C05  N06  C22     0.00   0.0  0
 O51  CONST_23  H21  N11  C12  C13   180.00   0.0  0
 O51  CONST_24  C12  N11  C09  O10     0.00   0.0  0
 O51  CONST_25  N06  C05  N04  C03   180.00   0.0  0
 O51  CONST_27  O23  C05  N04  C03     0.00   0.0  0
 O51  Var_01    C21  C22  N06  C07   -60.79  30.0  1
 O51  Var_02    C22  N06  C07  C08    61.20  30.0  1
 O51  Var_03    C22  C21  C20  C08   -51.76  30.0  1
 O51  Var_04    N06  C22  C21  C20    54.90  30.0  1
 O51  Var_05    C05  N04  C03  C02  -165.90  30.0  3
 O51  Var_06    N04  C03  C02  N01   179.65  30.0  3
 O51  Var_07    H17  N01  C02  C03   172.99  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
 O51  chir_01  C08  C07  C20  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
 O51  plan-1  C12  0.020
 O51  plan-1  C13  0.020
 O51  plan-1  C14  0.020
 O51  plan-1  C16  0.020
 O51  plan-1  C18  0.020
 O51  plan-1  C19  0.020
 O51  plan-1  F15  0.020
 O51  plan-1  N11  0.020
 O51  plan-1  CL1  0.020
 O51  plan-1  H8   0.020
 O51  plan-1  H9   0.020
 O51  plan-1  H10  0.020
 O51  plan-2  C03  0.020
 O51  plan-2  C05  0.020
 O51  plan-2  C07  0.020
 O51  plan-2  C22  0.020
 O51  plan-2  N04  0.020
 O51  plan-2  N06  0.020
 O51  plan-2  O23  0.020
 O51  plan-2  H20  0.020
 O51  plan-3  C08  0.020
 O51  plan-3  C09  0.020
 O51  plan-3  O10  0.020
 O51  plan-3  C12  0.020
 O51  plan-3  N11  0.020
 O51  plan-3  H21  0.020

