# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 12:39:56 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-({4-[(4-methoxypyridin-2-yl)amino]piperidin-1-yl}carbonyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccnc(NC2CCN(CC2)C(=O)c3ccc(cc3)C#N)c1
#
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
 328  328  4-({4-[(4-methoxypyridin-2-yl)amino]piperidin-1-yl}carbonyl)benzonitrile  ligand  45  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_328
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
 328  C1    C  CR16  0  -0.245  -4.1892   0.5576   0.9956
 328  C2    C  CR16  0  -0.227  -5.4326  -0.0354   1.1228
 328  C3    C  CR6   0   0.004  -6.0485  -0.5830  -0.0016
 328  C7    C  CSP   0   0.060  -7.3282  -1.2031   0.1243
 328  C9    C  CH3   0  -0.438   7.5651   1.0448   1.2556
 328  C10   C  CH2   0  -0.329   0.0016   1.8004   0.2711
 328  C12   C  CH2   0  -0.330  -1.0751  -0.2421   1.0214
 328  C13   C  CH2   0  -0.431  -0.0229  -1.0900   0.3140
 328  C14   C  CH1   0  -0.083   1.3000  -0.3410   0.1895
 328  C15   C  CH2   0  -0.438   1.0698   1.0164  -0.4786
 328  C19   C  CR6   0   0.478   5.6129   0.0385   0.3629
 328  C20   C  CR16  0  -0.476   6.3402  -0.7050  -0.5705
 328  C21   C  CR16  0  -0.065   5.6139  -1.5260  -1.4156
 328  C24   C  CR16  0  -0.507   4.2291  -0.0817   0.3972
 328  N25   N  NS    0  -0.247  -8.3618  -1.7021   0.2232
 328  C6    C  CR6   0  -0.065  -3.5634   0.6181  -0.2466
 328  C5    C  CR16  0  -0.259  -4.1946   0.0874  -1.3678
 328  C4    C  CR16  0  -0.230  -5.4278  -0.5270  -1.2489
 328  N17   N  NH1   0  -0.667   2.2602  -1.1647  -0.5050
 328  N11   N  NT    0  -0.442  -1.2370   1.0411   0.3535
 328  O8    O  O     0  -0.479  -2.2540   2.2802  -1.2499
 328  O18   O  O2    0  -0.463   6.1575   0.8822   1.2460
 328  C23   C  CR6   0   0.500   3.6055  -0.9528  -0.5023
 328  N22   N  N     0  -0.478   4.2980  -1.6628  -1.4040
 328  H1    H  HCR6  0   0.286  -3.7126   0.9817   1.8699
 328  H2    H  HCR6  0   0.287  -5.9218  -0.0745   2.0862
 328  H9    H  HCH3  0   0.262   7.7842   1.7722   2.0331
 328  H9A   H  HCH3  0   0.233   8.0802   0.1113   1.4910
 328  H9B   H  HCH3  0   0.233   7.9366   1.4260   0.3023
 328  H10   H  HCH2  0   0.253   0.3367   1.9997   1.2935
 328  H10A  H  HCH2  0   0.271  -0.1878   2.7602  -0.2007
 328  H12   H  HCH2  0   0.280  -2.0177  -0.7820   1.0534
 328  H12A  H  HCH2  0   0.254  -0.7747  -0.0587   2.0568
 328  H13   H  HCH2  0   0.259   0.1212  -2.0170   0.8725
 328  H13A  H  HCH2  0   0.236  -0.3905  -1.3610  -0.6813
 328  H14   H  HCH1  0   0.240   1.6750  -0.1700   1.2054
 328  H15   H  HCH2  0   0.235   0.7576   0.8639  -1.5163
 328  H15A  H  HCH2  0   0.252   1.9942   1.5975  -0.5009
 328  H20   H  HCR6  0   0.278   7.4154  -0.6577  -0.6593
 328  H21   H  HCR6  0   0.258   6.1447  -2.1140  -2.1574
 328  H24   H  HCR6  0   0.270   3.6659   0.4984   1.1157
 328  H5    H  HCR6  0   0.279  -3.7210   0.1457  -2.3387
 328  H4    H  HCR6  0   0.287  -5.9112  -0.9521  -2.1176
 328  HN17  H  HNH1  0   0.374   1.9235  -1.6682  -1.3122
 328  C16   C  C     0   0.528  -2.2801   1.3715  -0.4311

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
 328  C1   C2    aromatic  1.383  0.020  1.383
 328  C1   C6    aromatic  1.392  0.020  1.392
 328  C2   C3    aromatic  1.394  0.020  1.394
 328  C3   C7    single    1.428  0.020  1.428
 328  C3   C4    aromatic  1.394  0.020  1.394
 328  C7   N25   triple    1.152  0.020  1.152
 328  C9   O18   single    1.417  0.020  1.417
 328  C10  C15   single    1.522  0.020  1.522
 328  C10  N11   single    1.455  0.020  1.455
 328  C12  C13   single    1.525  0.020  1.525
 328  C12  N11   single    1.456  0.020  1.456
 328  C13  C14   single    1.525  0.020  1.525
 328  C14  C15   single    1.530  0.020  1.530
 328  C14  N17   single    1.443  0.020  1.443
 328  C16  C6    single    1.500  0.020  1.500
 328  C16  N11   single    1.346  0.020  1.346
 328  C16  O8    double    1.223  0.020  1.223
 328  C19  C20   aromatic  1.397  0.020  1.397
 328  C19  C24   aromatic  1.390  0.020  1.390
 328  C19  O18   single    1.337  0.020  1.337
 328  C20  C21   aromatic  1.384  0.020  1.384
 328  C21  N22   aromatic  1.323  0.020  1.323
 328  C24  C23   aromatic  1.399  0.020  1.399
 328  C6   C5    aromatic  1.392  0.020  1.392
 328  C5   C4    aromatic  1.383  0.020  1.383
 328  N17  C23   single    1.362  0.020  1.362
 328  C23  N22   aromatic  1.340  0.020  1.340
 328  C1   H1    single    0.930  0.020  1.080
 328  C2   H2    single    0.930  0.020  1.080
 328  C9   H9    single    0.970  0.020  1.090
 328  C9   H9A   single    0.970  0.020  1.090
 328  C9   H9B   single    0.970  0.020  1.090
 328  C10  H10   single    0.970  0.020  1.090
 328  C10  H10A  single    0.970  0.020  1.090
 328  C12  H12   single    0.970  0.020  1.090
 328  C12  H12A  single    0.970  0.020  1.090
 328  C13  H13   single    0.970  0.020  1.090
 328  C13  H13A  single    0.970  0.020  1.090
 328  C14  H14   single    0.970  0.020  1.090
 328  C15  H15   single    0.970  0.020  1.090
 328  C15  H15A  single    0.970  0.020  1.090
 328  C20  H20   single    0.930  0.020  1.080
 328  C21  H21   single    0.930  0.020  1.080
 328  C24  H24   single    0.930  0.020  1.080
 328  C5   H5    single    0.930  0.020  1.080
 328  C4   H4    single    0.930  0.020  1.080
 328  N17  HN17  single    0.890  0.020  1.040

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
 328  H1    C1   C6   120.39  3.000
 328  H1    C1   C2   119.31  3.000
 328  C6    C1   C2   120.30  3.000
 328  H2    C2   C3   120.30  3.000
 328  H2    C2   C1   120.27  3.000
 328  C3    C2   C1   119.43  3.000
 328  C4    C3   C7   119.69  3.000
 328  C4    C3   C2   120.60  3.000
 328  C7    C3   C2   119.71  3.000
 328  N25   C7   C3   180.00  3.000
 328  H9B   C9   H9A  109.04  3.000
 328  H9B   C9   H9   108.80  3.000
 328  H9A   C9   H9   108.84  3.000
 328  H9B   C9   O18  111.85  3.000
 328  H9A   C9   O18  111.83  3.000
 328  H9    C9   O18  106.37  3.000
 328  H10A  C10  H10  107.36  3.000
 328  H10A  C10  N11  109.71  3.000
 328  H10   C10  N11  107.63  3.000
 328  H10A  C10  C15  111.32  3.000
 328  H10   C10  C15  109.82  3.000
 328  N11   C10  C15  110.88  3.000
 328  H12A  C12  H12  107.07  3.000
 328  H12A  C12  N11  108.49  3.000
 328  H12   C12  N11  110.80  3.000
 328  H12A  C12  C13  110.05  3.000
 328  H12   C12  C13  109.62  3.000
 328  N11   C12  C13  110.73  3.000
 328  H13A  C13  H13  107.40  3.000
 328  H13A  C13  C14  109.78  3.000
 328  H13   C13  C14  110.14  3.000
 328  H13A  C13  C12  109.12  3.000
 328  H13   C13  C12  109.01  3.000
 328  C14   C13  C12  111.30  3.000
 328  H14   C14  N17  107.90  3.000
 328  H14   C14  C15  108.52  3.000
 328  N17   C14  C15  113.34  3.000
 328  H14   C14  C13  107.31  3.000
 328  N17   C14  C13  109.64  3.000
 328  C15   C14  C13  109.92  3.000
 328  H15A  C15  H15  107.24  3.000
 328  H15A  C15  C14  110.71  3.000
 328  H15   C15  C14  109.47  3.000
 328  H15A  C15  C10  109.26  3.000
 328  H15   C15  C10  109.78  3.000
 328  C14   C15  C10  110.32  3.000
 328  O18   C19  C24  116.35  3.000
 328  O18   C19  C20  124.39  3.000
 328  C24   C19  C20  119.26  3.000
 328  H20   C20  C21  119.88  3.000
 328  H20   C20  C19  123.35  3.000
 328  C21   C20  C19  116.77  3.000
 328  H21   C21  N22  115.88  3.000
 328  H21   C21  C20  118.82  3.000
 328  N22   C21  C20  125.30  3.000
 328  H24   C24  C23  121.94  3.000
 328  H24   C24  C19  119.24  3.000
 328  C23   C24  C19  118.82  3.000
 328  C5    C6   C16  118.72  3.000
 328  C5    C6   C1   119.89  3.000
 328  C16   C6   C1   121.08  3.000
 328  H5    C5   C4   119.44  3.000
 328  H5    C5   C6   120.26  3.000
 328  C4    C5   C6   120.30  3.000
 328  H4    C4   C5   120.28  3.000
 328  H4    C4   C3   120.26  3.000
 328  C5    C4   C3   119.45  3.000
 328  HN17  N17  C23  114.13  3.000
 328  HN17  N17  C14  116.59  3.000
 328  C23   N17  C14  124.57  3.000
 328  C16   N11  C12  124.74  3.000
 328  C16   N11  C10  119.90  3.000
 328  C12   N11  C10  113.03  3.000
 328  C19   O18  C9   118.78  3.000
 328  N22   C23  N17  115.25  3.000
 328  N22   C23  C24  122.14  3.000
 328  N17   C23  C24  122.58  3.000
 328  C23   N22  C21  117.71  3.000
 328  O8    C16  N11  123.76  3.000
 328  O8    C16  C6   118.28  3.000
 328  N11   C16  C6   117.91  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
 328  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 328  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 328  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 328  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 328  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 328  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 328  CONST_07  N22   C21  C20  C19    0.00   0.0  0
 328  CONST_08  N22   C23  C24  C19    0.00   0.0  0
 328  CONST_09  C23   C24  C19  C20    0.00   0.0  0
 328  CONST_10  C23   N22  C21  C20    0.00   0.0  0
 328  CONST_11  C24   C19  C20  C21    0.00   0.0  0
 328  CONST_12  C24   C23  N22  C21    0.00   0.0  0
 328  CONST_13  C7    C3   C2   C1   180.00   0.0  0
 328  CONST_14  C16   C6   C1   C2   180.00   0.0  0
 328  CONST_15  C5    C4   C3   C7   180.00   0.0  0
 328  CONST_16  C4    C5   C6   C16  180.00   0.0  0
 328  CONST_17  N17   C23  C24  C19  180.00   0.0  0
 328  CONST_18  O18   C19  C20  C21  180.00   0.0  0
 328  CONST_19  N17   C23  N22  C21  180.00   0.0  0
 328  CONST_20  C23   C24  C19  O18  180.00   0.0  0
 328  CONST_21  C6    C16  N11  C10  180.00   0.0  0
 328  CONST_23  C24   C23  N17  C14    0.00   0.0  0
 328  CONST_24  N22   C23  N17  C14  180.00   0.0  0
 328  CONST_25  H5    C5   C6   C1   180.00   0.0  0
 328  CONST_26  H4    C4   C3   C2   180.00   0.0  0
 328  CONST_27  H1    C1   C2   C3   180.00   0.0  0
 328  CONST_28  H21   C21  C20  C19  180.00   0.0  0
 328  CONST_29  H24   C24  C19  C20  180.00   0.0  0
 328  CONST_30  H20   C20  C19  C24  180.00   0.0  0
 328  CONST_31  H2    C2   C1   C6   180.00   0.0  0
 328  CONST_32  O8    C16  N11  C10    0.00   0.0  0
 328  CONST_34  HN17  N17  C23  C24  180.00   0.0  0
 328  Var_01    C13   C12  N11  C10  -57.55  30.0  1
 328  Var_02    C15   C10  N11  C12   58.80  30.0  1
 328  Var_03    N11   C12  C13  C14   54.79  30.0  1
 328  Var_04    N11   C10  C15  C14  -56.52  30.0  1
 328  Var_05    N11   C16  C6   C1    55.93  30.0  2
 328  Var_06    C20   C19  O18  C9    -0.20  30.0  1
 328  Var_07    H9    C9   O18  C19  179.46  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
 328  chir_01  C14  C13  C15  N17  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
 328  plan-1  C1    0.020
 328  plan-1  C2    0.020
 328  plan-1  C3    0.020
 328  plan-1  C7    0.020
 328  plan-1  N25   0.020
 328  plan-1  C6    0.020
 328  plan-1  C5    0.020
 328  plan-1  C4    0.020
 328  plan-1  H1    0.020
 328  plan-1  H2    0.020
 328  plan-1  H5    0.020
 328  plan-1  H4    0.020
 328  plan-1  C16   0.020
 328  plan-2  C19   0.020
 328  plan-2  C20   0.020
 328  plan-2  C21   0.020
 328  plan-2  C24   0.020
 328  plan-2  N17   0.020
 328  plan-2  O18   0.020
 328  plan-2  C23   0.020
 328  plan-2  N22   0.020
 328  plan-2  H20   0.020
 328  plan-2  H21   0.020
 328  plan-2  H24   0.020
 328  plan-3  C14   0.020
 328  plan-3  N17   0.020
 328  plan-3  C23   0.020
 328  plan-3  HN17  0.020
 328  plan-4  C10   0.020
 328  plan-4  C12   0.020
 328  plan-4  C6    0.020
 328  plan-4  N11   0.020
 328  plan-4  O8    0.020
 328  plan-4  C16   0.020

