# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 10:58:06 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-[cis-4-(aminomethyl)-4-(3-chlorophenyl)cyclohexyl]piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@]1(CC[C@@H](CC1)N2CCCCC2=O)c3cccc(Cl)c3
#
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
 2KV  2KV  1-[cis-4-(aminomethyl)-4-(3-chlorophenyl)cyclohexyl]piperidin-2-one  ligand  47  22  .  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_2KV
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
 2KV  C2   C   C     0   0.546   4.1447   0.3875   0.5715
 2KV  C3   C   CR6   0  -0.162  -0.8242   0.6164   0.1182
 2KV  C11  C   C     0  -0.440   1.2642  -0.6980   0.8807
 2KV  C12  C   CR6   0  -0.024  -4.4599  -0.5448   0.1969
 2KV  C13  C   CH2   0  -0.279   4.0317  -1.4734  -1.0729
 2KV  C16  C   CH2   0  -0.274  -0.7104   1.6996   1.2132
 2KV  C17  C   CH2   0  -0.551   5.6440   0.1879   0.6749
 2KV  C18  C   CR16  0  -0.300  -2.9180   1.2434  -1.2031
 2KV  C19  C   CR16  0  -0.250  -4.2722   1.1234  -1.4784
 2KV  C20  C   CR16  0  -0.245  -5.0654   0.2252  -0.7797
 2KV  C21  C   CH2   0  -0.469   5.5403  -1.4154  -1.1846
 2KV  C22  C   CH2   0  -0.450   6.1522  -1.1519   0.1765
 2KV  N1   N   NT    0  -0.484   3.4517  -0.3811  -0.2925
 2KV  C4   C   CR6   0   0.205  -2.3033   0.4607  -0.2243
 2KV  C5   C   CR16  0  -0.044   1.9923  -0.2813  -0.3923
 2KV  O6   O   O     0  -0.523   3.6121   1.2612   1.2507
 2KV  C7   C   CR16  0  -0.276  -3.1069  -0.4385   0.4775
 2KV  C8   C   C     0  -0.458  -0.0182   0.9994  -1.1375
 2KV  C9   C   C     0  -0.442  -0.2486  -0.7059   0.6668
 2KV  C10  C   C     0  -0.436   1.4872   1.0642  -0.8991
 2KV  N15  N   NH2   0  -0.792  -1.1476   3.0084   0.7610
 2KV  H1   H   H     0   0.237   1.5794  -1.7043   1.1699
 2KV  H2   H   H     0   0.238   1.5317  -0.0367   1.7041
 2KV  H3   H   HCH2  0   0.251   3.5913  -1.4406  -2.0714
 2KV  H4   H   HCH2  0   0.234   3.7296  -2.4275  -0.6263
 2KV  H5   H   HCH2  0   0.230  -1.3466   1.3935   2.0483
 2KV  H6   H   HCH2  0   0.216   0.3145   1.7089   1.6043
 2KV  H7   H   HCH2  0   0.262   6.1077   0.9948   0.0974
 2KV  H8   H   HCH2  0   0.264   5.9191   0.3637   1.7160
 2KV  H9   H   HCR6  0   0.247  -2.3427   1.9604  -1.7687
 2KV  H10  H   HCR6  0   0.261  -4.7208   1.7403  -2.2464
 2KV  H11  H   HCR6  0   0.275  -6.1211   0.1291  -0.9931
 2KV  H12  H   HCH2  0   0.250   5.8885  -2.3578  -1.6102
 2KV  H13  H   HCH2  0   0.232   5.8331  -0.6222  -1.8785
 2KV  H14  H   HCH2  0   0.246   7.2419  -1.1435   0.1251
 2KV  H15  H   HCH2  0   0.228   5.8760  -1.9485   0.8735
 2KV  H16  H   HCR6  0   0.236   1.7220  -1.0153  -1.1595
 2KV  H17  H   HCR6  0   0.264  -2.6897  -1.0649   1.2531
 2KV  H18  H   H     0   0.234  -0.2251   0.2586  -1.9180
 2KV  H19  H   H     0   0.243  -0.3474   1.9591  -1.5409
 2KV  H20  H   H     0   0.237  -0.7209  -0.9610   1.6188
 2KV  H21  H   H     0   0.234  -0.5026  -1.5106  -0.0318
 2KV  H22  H   H     0   0.240   1.7276   1.8540  -0.1879
 2KV  H23  H   H     0   0.235   1.9882   1.3152  -1.8377
 2KV  H24  H   HNH2  0   0.351  -1.2500   3.6161   1.5633
 2KV  H25  H   HNH2  0   0.342  -0.4246   3.4334   0.1944
 2KV  CL1  CL  CL    0  -0.140  -5.4185  -1.6801   1.0998

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
 2KV  C22  C17  single    1.517  0.020  1.517
 2KV  C22  C21  single    1.515  0.020  1.515
 2KV  C17  C2   single    1.516  0.020  1.516
 2KV  C10  C8   single    1.526  0.020  1.526
 2KV  C10  C5   single    1.524  0.020  1.524
 2KV  O6   C2   double    1.228  0.020  1.228
 2KV  C2   N1   single    1.348  0.020  1.348
 2KV  C21  C13  single    1.514  0.020  1.514
 2KV  C8   C3   single    1.540  0.020  1.540
 2KV  CL1  C12  single    1.739  0.020  1.739
 2KV  N1   C13  single    1.462  0.020  1.462
 2KV  N1   C5   single    1.466  0.020  1.466
 2KV  C5   C11  single    1.525  0.020  1.525
 2KV  C7   C12  aromatic  1.386  0.020  1.386
 2KV  C7   C4   aromatic  1.395  0.020  1.395
 2KV  C12  C20  aromatic  1.383  0.020  1.383
 2KV  C16  C3   single    1.544  0.020  1.544
 2KV  C16  N15  single    1.452  0.020  1.452
 2KV  C3   C4   single    1.526  0.020  1.526
 2KV  C3   C9   single    1.543  0.020  1.543
 2KV  C4   C18  aromatic  1.396  0.020  1.396
 2KV  C11  C9   single    1.528  0.020  1.528
 2KV  C20  C19  aromatic  1.387  0.020  1.387
 2KV  C18  C19  aromatic  1.387  0.020  1.387
 2KV  C11  H1   single    0.970  0.020  1.090
 2KV  C11  H2   single    0.970  0.020  1.090
 2KV  C13  H3   single    0.970  0.020  1.090
 2KV  C13  H4   single    0.970  0.020  1.090
 2KV  C16  H5   single    0.970  0.020  1.090
 2KV  C16  H6   single    0.970  0.020  1.090
 2KV  C17  H7   single    0.970  0.020  1.090
 2KV  C17  H8   single    0.970  0.020  1.090
 2KV  C18  H9   single    0.930  0.020  1.080
 2KV  C19  H10  single    0.930  0.020  1.080
 2KV  C20  H11  single    0.930  0.020  1.080
 2KV  C21  H12  single    0.970  0.020  1.090
 2KV  C21  H13  single    0.970  0.020  1.090
 2KV  C22  H14  single    0.970  0.020  1.090
 2KV  C22  H15  single    0.970  0.020  1.090
 2KV  C5   H16  single    0.970  0.020  1.090
 2KV  C7   H17  single    0.930  0.020  1.080
 2KV  C8   H18  single    0.970  0.020  1.090
 2KV  C8   H19  single    0.970  0.020  1.090
 2KV  C9   H20  single    0.970  0.020  1.090
 2KV  C9   H21  single    0.970  0.020  1.090
 2KV  C10  H22  single    0.970  0.020  1.090
 2KV  C10  H23  single    0.970  0.020  1.090
 2KV  N15  H24  single    0.890  0.020  1.040
 2KV  N15  H25  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
 2KV  O6   C2   N1   122.49  3.000
 2KV  N1   C2   C17  118.49  3.000
 2KV  O6   C2   C17  119.00  3.000
 2KV  C9   C3   C8   107.93  3.000
 2KV  C9   C3   C4   110.72  3.000
 2KV  C8   C3   C4   110.45  3.000
 2KV  C9   C3   C16  108.75  3.000
 2KV  C4   C3   C16  107.58  3.000
 2KV  C8   C3   C16  111.40  3.000
 2KV  H2   C11  H1   106.74  3.000
 2KV  H2   C11  C9   110.61  3.000
 2KV  H1   C11  C9   108.52  3.000
 2KV  H2   C11  C5   110.36  3.000
 2KV  H1   C11  C5   109.56  3.000
 2KV  C9   C11  C5   110.94  3.000
 2KV  CL1  C12  C7   118.89  3.000
 2KV  C7   C12  C20  121.85  3.000
 2KV  CL1  C12  C20  119.26  3.000
 2KV  H4   C13  H3   106.72  3.000
 2KV  H4   C13  N1   108.88  3.000
 2KV  H3   C13  N1   107.80  3.000
 2KV  H4   C13  C21  109.76  3.000
 2KV  H3   C13  C21  109.47  3.000
 2KV  N1   C13  C21  113.95  3.000
 2KV  H6   C16  H5   105.88  3.000
 2KV  H6   C16  N15  112.63  3.000
 2KV  H5   C16  N15  108.36  3.000
 2KV  H6   C16  C3   109.12  3.000
 2KV  H5   C16  C3   107.59  3.000
 2KV  N15  C16  C3   112.91  3.000
 2KV  H8   C17  H7   106.12  3.000
 2KV  H8   C17  C22  111.80  3.000
 2KV  H7   C17  C22  109.61  3.000
 2KV  H8   C17  C2   107.05  3.000
 2KV  H7   C17  C2   106.60  3.000
 2KV  C22  C17  C2   115.16  3.000
 2KV  H9   C18  C4   120.34  3.000
 2KV  H9   C18  C19  118.28  3.000
 2KV  C4   C18  C19  121.37  3.000
 2KV  H10  C19  C20  119.30  3.000
 2KV  H10  C19  C18  119.74  3.000
 2KV  C20  C19  C18  120.95  3.000
 2KV  H11  C20  C19  121.10  3.000
 2KV  H11  C20  C12  121.15  3.000
 2KV  C19  C20  C12  117.76  3.000
 2KV  H13  C21  H12  107.07  3.000
 2KV  H13  C21  C22  109.61  3.000
 2KV  H12  C21  C22  111.82  3.000
 2KV  H13  C21  C13  109.95  3.000
 2KV  H12  C21  C13  108.28  3.000
 2KV  C22  C21  C13  110.05  3.000
 2KV  H15  C22  H14  106.73  3.000
 2KV  H15  C22  C21  110.10  3.000
 2KV  H14  C22  C21  111.24  3.000
 2KV  H15  C22  C17  110.44  3.000
 2KV  H14  C22  C17  110.08  3.000
 2KV  C21  C22  C17  108.26  3.000
 2KV  C5   N1   C13  114.16  3.000
 2KV  C5   N1   C2   121.10  3.000
 2KV  C13  N1   C2   124.34  3.000
 2KV  C7   C4   C18  117.41  3.000
 2KV  C18  C4   C3   121.80  3.000
 2KV  C7   C4   C3   120.73  3.000
 2KV  H16  C5   C10  106.08  3.000
 2KV  H16  C5   N1   104.34  3.000
 2KV  C10  C5   N1   114.37  3.000
 2KV  H16  C5   C11  106.49  3.000
 2KV  N1   C5   C11  113.57  3.000
 2KV  C10  C5   C11  111.15  3.000
 2KV  H17  C7   C4   120.81  3.000
 2KV  H17  C7   C12  118.54  3.000
 2KV  C4   C7   C12  120.65  3.000
 2KV  H19  C8   H18  105.91  3.000
 2KV  H19  C8   C10  108.54  3.000
 2KV  H18  C8   C10  109.04  3.000
 2KV  H19  C8   C3   111.22  3.000
 2KV  H18  C8   C3   108.28  3.000
 2KV  C10  C8   C3   113.54  3.000
 2KV  H21  C9   H20  106.49  3.000
 2KV  H21  C9   C11  108.83  3.000
 2KV  H20  C9   C11  107.89  3.000
 2KV  H21  C9   C3   108.44  3.000
 2KV  H20  C9   C3   110.40  3.000
 2KV  C11  C9   C3   114.50  3.000
 2KV  H23  C10  H22  107.03  3.000
 2KV  H23  C10  C8   109.14  3.000
 2KV  H22  C10  C8   110.51  3.000
 2KV  H23  C10  C5   109.66  3.000
 2KV  H22  C10  C5   110.47  3.000
 2KV  C8   C10  C5   109.97  3.000
 2KV  H25  N15  H24  105.31  3.000
 2KV  H25  N15  C16  109.73  3.000
 2KV  H24  N15  C16  108.96  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
 2KV  CONST_01  C18  C4   C7   C12    0.00   0.0  0
 2KV  CONST_02  C18  C19  C20  C12    0.00   0.0  0
 2KV  CONST_03  C7   C12  C20  C19    0.00   0.0  0
 2KV  CONST_04  C7   C4   C18  C19    0.00   0.0  0
 2KV  CONST_05  C4   C7   C12  C20    0.00   0.0  0
 2KV  CONST_06  C4   C18  C19  C20    0.00   0.0  0
 2KV  CONST_07  C12  C7   C4   C3   180.00   0.0  0
 2KV  CONST_08  C19  C18  C4   C3   180.00   0.0  0
 2KV  CONST_09  C17  C2   N1   C13    0.00   0.0  0
 2KV  CONST_10  C5   N1   C2   C17  180.00   0.0  0
 2KV  CONST_11  CL1  C12  C20  C19  180.00   0.0  0
 2KV  CONST_12  CL1  C12  C7   C4   180.00   0.0  0
 2KV  CONST_13  O6   C2   N1   C13  180.00   0.0  0
 2KV  CONST_14  O6   C2   N1   C5     0.00   0.0  0
 2KV  CONST_15  H17  C7   C4   C3     0.00   0.0  0
 2KV  CONST_16  H9   C18  C4   C3     0.00   0.0  0
 2KV  CONST_17  H10  C19  C20  C12  180.00   0.0  0
 2KV  CONST_18  H11  C20  C19  C18  180.00   0.0  0
 2KV  Var_01    C21  C22  C17  C2    48.38  30.0  1
 2KV  Var_02    C21  C13  N1   C2   -18.47  30.0  1
 2KV  Var_03    C5   C10  C8   C3    58.23  30.0  1
 2KV  Var_04    C5   C11  C9   C3   -53.87  30.0  1
 2KV  Var_05    C17  C22  C21  C13  -61.06  30.0  1
 2KV  Var_06    N1   C2   C17  C22  -20.60  30.0  1
 2KV  Var_07    N1   C13  C21  C22   46.75  30.0  1
 2KV  Var_08    H24  N15  C16  C3   167.24  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
 2KV  chir_01  C3  C8  C4   C9   negativ
 2KV  chir_02  C5  N1  C11  C10  negativ

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
 2KV  plan-1  C3   0.020
 2KV  plan-1  C12  0.020
 2KV  plan-1  C18  0.020
 2KV  plan-1  C19  0.020
 2KV  plan-1  C20  0.020
 2KV  plan-1  C4   0.020
 2KV  plan-1  C7   0.020
 2KV  plan-1  H9   0.020
 2KV  plan-1  H10  0.020
 2KV  plan-1  H11  0.020
 2KV  plan-1  H17  0.020
 2KV  plan-1  CL1  0.020
 2KV  plan-2  C2   0.020
 2KV  plan-2  C13  0.020
 2KV  plan-2  C17  0.020
 2KV  plan-2  N1   0.020
 2KV  plan-2  C5   0.020
 2KV  plan-2  O6   0.020

