# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:58:22 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-[(4-chlorophenyl)methyl]-4-(3-imidazol-1-ylpropyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CN2CCN(CCCn3ccnc3)CC2=O)cc1
#
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
 9KE  9KE  1-[(4-chlorophenyl)methyl]-4-(3-imidazol-1-ylpropyl)piperazin-2-one  ligand  44  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9KE
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
 9KE  C10  C   CR15  0  -0.219   7.9841  -0.0021  -0.6573
 9KE  C13  C   CH2   0  -0.318   0.2259   1.0174   1.2238
 9KE  C17  C   CR6   0   0.135  -3.5163   0.7741  -0.9139
 9KE  C20  C   CR6   0  -0.053  -5.8004  -0.1854   0.3432
 9KE  C22  C   CR16  0  -0.196  -4.8763  -1.0832  -0.1736
 9KE  C02  C   C     0   0.542  -0.2558  -0.0453  -1.3085
 9KE  C03  C   CH2   0  -0.388   1.0211  -0.3209  -0.5406
 9KE  N04  N   NT    0  -0.429   1.3840   0.6936   0.4207
 9KE  C05  C   CH2   0  -0.263   2.5248   0.3098   1.2304
 9KE  C06  C   CH2   0  -0.465   3.8013   0.1365   0.4188
 9KE  C07  C   CH2   0  -0.295   5.0029  -0.0192   1.3405
 9KE  N08  N   NR5   0  -0.398   6.2321  -0.2476   0.6093
 9KE  C09  C   CR15  0  -0.108   6.9500   0.6839  -0.0864
 9KE  N11  N   N     0  -0.458   7.9096  -1.3263  -0.3308
 9KE  C12  C   CR15  0   0.093   6.8464  -1.4347   0.4250
 9KE  C14  C   CH2   0  -0.265  -0.8041   1.6919   0.3503
 9KE  N15  N   NT    0  -0.452  -1.0654   0.9272  -0.8566
 9KE  C16  C   CH2   0  -0.405  -2.2688   1.2902  -1.5834
 9KE  C18  C   CR16  0  -0.314  -4.4580   1.6498  -0.3876
 9KE  C19  C   CR16  0  -0.198  -5.6045   1.1808   0.2415
 9KE  CL1  CL  CL    0  -0.131  -7.2246  -0.7896   1.1269
 9KE  C23  C   CR16  0  -0.297  -3.7404  -0.5966  -0.7990
 9KE  H1   H   HCR5  0   0.249   8.7750   0.3906  -1.2780
 9KE  H2   H   HCH2  0   0.214  -0.2081   0.1258   1.7075
 9KE  H3   H   HCH2  0   0.260   0.5098   1.7074   2.0195
 9KE  H4   H   HCR6  0   0.279  -5.0420  -2.1488  -0.0924
 9KE  H5   H   HCH2  0   0.236   0.8927  -1.3131  -0.0711
 9KE  H6   H   HCH2  0   0.277   1.8044  -0.4335  -1.2920
 9KE  H8   H   HCH2  0   0.241   2.6787   1.1026   1.9681
 9KE  H9   H   HCH2  0   0.202   2.3283  -0.6142   1.8015
 9KE  H10  H   HCH2  0   0.246   3.7419  -0.7435  -0.2263
 9KE  H11  H   HCH2  0   0.242   3.9387   1.0060  -0.2293
 9KE  H12  H   HCH2  0   0.265   5.1285   0.8685   1.9621
 9KE  H13  H   HCH2  0   0.265   4.8598  -0.8635   2.0160
 9KE  H14  H   HCR5  0   0.287   6.6734   1.7250  -0.1077
 9KE  H15  H   HCR5  0   0.278   6.4749  -2.3453   0.8720
 9KE  H16  H   HCH2  0   0.250  -1.7394   1.7944   0.9052
 9KE  H17  H   HCH2  0   0.246  -0.4703   2.6981   0.0802
 9KE  H18  H   HCH2  0   0.282  -2.1947   0.9088  -2.6001
 9KE  H19  H   HCH2  0   0.272  -2.3091   2.3799  -1.6521
 9KE  H20  H   HCR6  0   0.267  -4.3021   2.7192  -0.4656
 9KE  H21  H   HCR6  0   0.280  -6.3288   1.8746   0.6464
 9KE  H22  H   HCR6  0   0.263  -3.0244  -1.2981  -1.2089
 9KE  O01  O   O     0  -0.519  -0.5107  -0.7250  -2.2964

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
 9KE  C16  N15  single    1.452  0.020  1.452
 9KE  C16  C17  single    1.507  0.020  1.507
 9KE  O01  C02  double    1.226  0.020  1.226
 9KE  N15  C02  single    1.344  0.020  1.344
 9KE  N15  C14  single    1.452  0.020  1.452
 9KE  C02  C03  single    1.515  0.020  1.515
 9KE  C23  C17  aromatic  1.394  0.020  1.394
 9KE  C23  C22  aromatic  1.385  0.020  1.385
 9KE  C17  C18  aromatic  1.389  0.020  1.389
 9KE  C14  C13  single    1.510  0.020  1.510
 9KE  C03  N04  single    1.444  0.020  1.444
 9KE  C22  C20  aromatic  1.388  0.020  1.388
 9KE  C18  C19  aromatic  1.389  0.020  1.389
 9KE  C13  N04  single    1.446  0.020  1.446
 9KE  C20  C19  aromatic  1.384  0.020  1.384
 9KE  C20  CL1  single    1.734  0.020  1.734
 9KE  N04  C05  single    1.451  0.020  1.451
 9KE  C05  C06  single    1.523  0.020  1.523
 9KE  C06  C07  single    1.522  0.020  1.522
 9KE  C07  N08  single    1.448  0.020  1.448
 9KE  N08  C09  aromatic  1.366  0.020  1.366
 9KE  N08  C12  aromatic  1.349  0.020  1.349
 9KE  C09  C10  aromatic  1.366  0.020  1.366
 9KE  C12  N11  aromatic  1.309  0.020  1.309
 9KE  C10  N11  aromatic  1.366  0.020  1.366
 9KE  C10  H1   single    0.930  0.020  1.080
 9KE  C13  H2   single    0.970  0.020  1.090
 9KE  C13  H3   single    0.970  0.020  1.090
 9KE  C22  H4   single    0.930  0.020  1.080
 9KE  C03  H5   single    0.970  0.020  1.090
 9KE  C03  H6   single    0.970  0.020  1.090
 9KE  C05  H8   single    0.970  0.020  1.090
 9KE  C05  H9   single    0.970  0.020  1.090
 9KE  C06  H10  single    0.970  0.020  1.090
 9KE  C06  H11  single    0.970  0.020  1.090
 9KE  C07  H12  single    0.970  0.020  1.090
 9KE  C07  H13  single    0.970  0.020  1.090
 9KE  C09  H14  single    0.930  0.020  1.080
 9KE  C12  H15  single    0.930  0.020  1.080
 9KE  C14  H16  single    0.970  0.020  1.090
 9KE  C14  H17  single    0.970  0.020  1.090
 9KE  C16  H18  single    0.970  0.020  1.090
 9KE  C16  H19  single    0.970  0.020  1.090
 9KE  C18  H20  single    0.930  0.020  1.080
 9KE  C19  H21  single    0.930  0.020  1.080
 9KE  C23  H22  single    0.930  0.020  1.080

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
 9KE  H1   C10  N11  122.02  3.000
 9KE  H1   C10  C09  127.77  3.000
 9KE  N11  C10  C09  110.22  3.000
 9KE  H3   C13  H2   107.08  3.000
 9KE  H3   C13  C14  108.49  3.000
 9KE  H2   C13  C14  110.27  3.000
 9KE  H3   C13  N04  109.77  3.000
 9KE  H2   C13  N04  112.18  3.000
 9KE  C14  C13  N04  108.98  3.000
 9KE  C23  C17  C18  118.66  3.000
 9KE  C18  C17  C16  120.90  3.000
 9KE  C23  C17  C16  120.43  3.000
 9KE  CL1  C20  C19  119.56  3.000
 9KE  CL1  C20  C22  119.31  3.000
 9KE  C19  C20  C22  121.12  3.000
 9KE  H4   C22  C23  120.38  3.000
 9KE  H4   C22  C20  120.48  3.000
 9KE  C23  C22  C20  119.14  3.000
 9KE  N15  C02  C03  117.97  3.000
 9KE  C03  C02  O01  118.86  3.000
 9KE  N15  C02  O01  123.16  3.000
 9KE  H6   C03  H5   106.45  3.000
 9KE  H6   C03  N04  110.52  3.000
 9KE  H5   C03  N04  112.16  3.000
 9KE  H6   C03  C02  105.95  3.000
 9KE  H5   C03  C02  106.30  3.000
 9KE  N04  C03  C02  114.92  3.000
 9KE  C05  N04  C03  112.54  3.000
 9KE  C05  N04  C13  112.28  3.000
 9KE  C03  N04  C13  109.01  3.000
 9KE  H9   C05  H8   106.43  3.000
 9KE  H9   C05  C06  109.25  3.000
 9KE  H8   C05  C06  108.91  3.000
 9KE  H9   C05  N04  111.73  3.000
 9KE  H8   C05  N04  107.17  3.000
 9KE  C06  C05  N04  113.07  3.000
 9KE  H11  C06  H10  107.30  3.000
 9KE  H11  C06  C07  109.94  3.000
 9KE  H10  C06  C07  108.54  3.000
 9KE  H11  C06  C05  109.32  3.000
 9KE  H10  C06  C05  111.15  3.000
 9KE  C07  C06  C05  110.53  3.000
 9KE  H13  C07  H12  106.98  3.000
 9KE  H13  C07  N08  107.57  3.000
 9KE  H12  C07  N08  108.55  3.000
 9KE  H13  C07  C06  110.53  3.000
 9KE  H12  C07  C06  110.65  3.000
 9KE  N08  C07  C06  112.35  3.000
 9KE  C12  N08  C09  106.92  3.000
 9KE  C12  N08  C07  126.45  3.000
 9KE  C09  N08  C07  126.54  3.000
 9KE  H14  C09  N08  122.28  3.000
 9KE  H14  C09  C10  132.17  3.000
 9KE  N08  C09  C10  105.56  3.000
 9KE  C12  N11  C10  105.23  3.000
 9KE  H15  C12  N11  126.02  3.000
 9KE  H15  C12  N08  121.90  3.000
 9KE  N11  C12  N08  112.08  3.000
 9KE  H17  C14  H16  107.48  3.000
 9KE  H17  C14  N15  109.51  3.000
 9KE  H16  C14  N15  108.50  3.000
 9KE  H17  C14  C13  110.23  3.000
 9KE  H16  C14  C13  109.41  3.000
 9KE  N15  C14  C13  111.61  3.000
 9KE  C16  N15  C14  115.69  3.000
 9KE  C14  N15  C02  123.51  3.000
 9KE  C16  N15  C02  120.79  3.000
 9KE  H19  C16  H18  107.05  3.000
 9KE  H19  C16  N15  108.14  3.000
 9KE  H18  C16  N15  108.88  3.000
 9KE  H19  C16  C17  109.81  3.000
 9KE  H18  C16  C17  110.57  3.000
 9KE  N15  C16  C17  112.22  3.000
 9KE  H20  C18  C19  118.98  3.000
 9KE  H20  C18  C17  119.82  3.000
 9KE  C19  C18  C17  121.20  3.000
 9KE  H21  C19  C18  120.37  3.000
 9KE  H21  C19  C20  120.72  3.000
 9KE  C18  C19  C20  118.90  3.000
 9KE  H22  C23  C22  119.05  3.000
 9KE  H22  C23  C17  119.97  3.000
 9KE  C22  C23  C17  120.97  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
 9KE  CONST_01  C12  N08  C09  C10     0.00   0.0  0
 9KE  CONST_02  N08  C12  N11  C10     0.00   0.0  0
 9KE  CONST_03  C20  C22  C23  C17     0.00   0.0  0
 9KE  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 9KE  CONST_05  C18  C17  C23  C22     0.00   0.0  0
 9KE  CONST_06  C18  C19  C20  C22     0.00   0.0  0
 9KE  CONST_07  N11  C10  C09  N08     0.00   0.0  0
 9KE  CONST_08  N11  C12  N08  C09     0.00   0.0  0
 9KE  CONST_09  C12  N11  C10  C09     0.00   0.0  0
 9KE  CONST_10  C23  C17  C18  C19     0.00   0.0  0
 9KE  CONST_11  C23  C22  C20  C19     0.00   0.0  0
 9KE  CONST_12  C14  N15  C02  C03     0.00   0.0  0
 9KE  CONST_13  C07  N08  C09  C10   180.00   0.0  0
 9KE  CONST_14  C16  C17  C23  C22   180.00   0.0  0
 9KE  CONST_15  N11  C12  N08  C07   180.00   0.0  0
 9KE  CONST_16  C19  C18  C17  C16   180.00   0.0  0
 9KE  CONST_17  CL1  C20  C19  C18   180.00   0.0  0
 9KE  CONST_18  C23  C22  C20  CL1   180.00   0.0  0
 9KE  CONST_19  C14  N15  C02  O01   180.00   0.0  0
 9KE  CONST_20  C16  N15  C02  C03   180.00   0.0  0
 9KE  CONST_21  H15  C12  N11  C10   180.00   0.0  0
 9KE  CONST_22  H4   C22  C23  C17   180.00   0.0  0
 9KE  CONST_23  H21  C19  C18  C17   180.00   0.0  0
 9KE  CONST_24  H22  C23  C22  C20   180.00   0.0  0
 9KE  CONST_25  H20  C18  C19  C20   180.00   0.0  0
 9KE  CONST_26  H1   C10  C09  N08   180.00   0.0  0
 9KE  CONST_27  H14  C09  C10  N11   180.00   0.0  0
 9KE  CONST_28  C16  N15  C02  O01     0.00   0.0  0
 9KE  Var_01    C02  N15  C14  C13   -16.50  30.0  1
 9KE  Var_02    C02  C03  N04  C13    48.20  30.0  1
 9KE  Var_03    C14  C13  N04  C03   -67.05  30.0  1
 9KE  Var_04    N15  C02  C03  N04   -13.58  30.0  1
 9KE  Var_05    N15  C14  C13  N04    50.86  30.0  1
 9KE  Var_06    C23  C17  C16  N15   -64.36  30.0  2
 9KE  Var_07    C06  C05  N04  C13  -172.69  30.0  3
 9KE  Var_08    C09  N08  C07  C06    75.20  30.0  2
 9KE  Var_09    C07  C06  C05  N04   169.92  30.0  3
 9KE  Var_10    N08  C07  C06  C05   177.38  30.0  3

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
 9KE  plan-1  C10  0.020
 9KE  plan-1  C07  0.020
 9KE  plan-1  N08  0.020
 9KE  plan-1  C09  0.020
 9KE  plan-1  N11  0.020
 9KE  plan-1  C12  0.020
 9KE  plan-1  H1   0.020
 9KE  plan-1  H14  0.020
 9KE  plan-1  H15  0.020
 9KE  plan-2  C17  0.020
 9KE  plan-2  C20  0.020
 9KE  plan-2  C22  0.020
 9KE  plan-2  C16  0.020
 9KE  plan-2  C18  0.020
 9KE  plan-2  C19  0.020
 9KE  plan-2  CL1  0.020
 9KE  plan-2  C23  0.020
 9KE  plan-2  H4   0.020
 9KE  plan-2  H20  0.020
 9KE  plan-2  H21  0.020
 9KE  plan-2  H22  0.020
 9KE  plan-3  C02  0.020
 9KE  plan-3  C03  0.020
 9KE  plan-3  C14  0.020
 9KE  plan-3  N15  0.020
 9KE  plan-3  C16  0.020
 9KE  plan-3  O01  0.020

