# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:36:28 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-[(4-fluorophenyl)methyl]-4-(3-imidazol-1-ylpropyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(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
 9KB  9KB  1-[(4-fluorophenyl)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_9KB
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
 9KB  C10  C  CR15  0  -0.219   7.6110  -0.2796  -0.7288
 9KB  C13  C  CH2   0  -0.318  -0.1258   1.4906   0.7045
 9KB  C17  C  CR6   0   0.125  -3.9504   0.1688  -0.8745
 9KB  C20  C  CR6   0   0.516  -6.1190  -0.2697   0.7868
 9KB  C22  C  CR16  0  -0.397  -5.2453  -1.3125   0.5358
 9KB  C02  C  C     0   0.543  -0.6818  -0.6193  -1.0340
 9KB  C03  C  CH2   0  -0.391   0.6386  -0.4951  -0.3018
 9KB  N04  N  NT    0  -0.428   1.0081   0.8507   0.0741
 9KB  C05  C  CH2   0  -0.264   2.1803   0.8732   0.9299
 9KB  C06  C  CH2   0  -0.463   3.4329   0.3445   0.2461
 9KB  C07  C  CH2   0  -0.295   4.6563   0.5627   1.1256
 9KB  N08  N  NR5   0  -0.398   5.8648   0.0279   0.5324
 9KB  C09  C  CR15  0  -0.108   6.6217   0.6171  -0.4408
 9KB  N11  N  N     0  -0.457   7.4701  -1.4003   0.0390
 9KB  C12  C  CR15  0   0.094   6.4117  -1.1811   0.7774
 9KB  C14  C  CH2   0  -0.268  -1.2242   1.6716  -0.3145
 9KB  N15  N  NT    0  -0.449  -1.5102   0.4376  -1.0240
 9KB  C16  C  CH2   0  -0.413  -2.7594   0.4085  -1.7657
 9KB  C18  C  CR16  0  -0.292  -4.8500   1.1911  -0.5963
 9KB  C19  C  CR16  0  -0.400  -5.9433   0.9827   0.2361
 9KB  F21  F  F     0  -0.316  -7.1740  -0.4864   1.5897
 9KB  C23  C  CR16  0  -0.277  -4.1623  -1.0834  -0.2982
 9KB  H1   H  HCR5  0   0.249   8.4145  -0.1707  -1.4409
 9KB  H2   H  HCH2  0   0.214  -0.4962   0.9147   1.5693
 9KB  H3   H  HCH2  0   0.260   0.1668   2.4741   1.0749
 9KB  H4   H  HCR6  0   0.279  -5.4103  -2.2858   0.9795
 9KB  H5   H  HCH2  0   0.236   0.5725  -1.1663   0.5742
 9KB  H6   H  HCH2  0   0.278   1.3911  -0.9267  -0.9639
 9KB  H8   H  HCH2  0   0.242   2.3490   1.9124   1.2253
 9KB  H9   H  HCH2  0   0.201   2.0059   0.3057   1.8608
 9KB  H10  H  HCH2  0   0.246   3.3399  -0.7234   0.0351
 9KB  H11  H  HCH2  0   0.242   3.5689   0.8542  -0.7114
 9KB  H12  H  HCH2  0   0.265   4.8101   1.6260   1.3132
 9KB  H13  H  HCH2  0   0.265   4.5207   0.0834   2.0960
 9KB  H14  H  HCR5  0   0.287   6.4010   1.5992  -0.8254
 9KB  H15  H  HCR5  0   0.278   5.9985  -1.8570   1.5120
 9KB  H16  H  HCH2  0   0.250  -2.1337   2.0026   0.1922
 9KB  H17  H  HCH2  0   0.245  -0.9518   2.4501  -1.0335
 9KB  H18  H  HCH2  0   0.280  -2.6947  -0.3609  -2.5329
 9KB  H19  H  HCH2  0   0.271  -2.8675   1.3668  -2.2802
 9KB  H20  H  HCR6  0   0.266  -4.7043   2.1711  -1.0348
 9KB  H21  H  HCR6  0   0.280  -6.6409   1.7818   0.4497
 9KB  H22  H  HCR6  0   0.264  -3.4759  -1.8946  -0.5073
 9KB  O01  O  O     0  -0.519  -0.9511  -1.6774  -1.5917

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
 9KB  O01  C02  double    1.226  0.020  1.226
 9KB  C16  N15  single    1.453  0.020  1.453
 9KB  C16  C17  single    1.507  0.020  1.507
 9KB  C02  N15  single    1.343  0.020  1.343
 9KB  C02  C03  single    1.515  0.020  1.515
 9KB  N15  C14  single    1.452  0.020  1.452
 9KB  C17  C18  aromatic  1.390  0.020  1.390
 9KB  C17  C23  aromatic  1.395  0.020  1.395
 9KB  C18  C19  aromatic  1.390  0.020  1.390
 9KB  C03  N04  single    1.445  0.020  1.445
 9KB  C14  C13  single    1.509  0.020  1.509
 9KB  C13  N04  single    1.447  0.020  1.447
 9KB  C23  C22  aromatic  1.386  0.020  1.386
 9KB  C19  C20  aromatic  1.379  0.020  1.379
 9KB  N04  C05  single    1.452  0.020  1.452
 9KB  C05  C06  single    1.522  0.020  1.522
 9KB  C22  C20  aromatic  1.383  0.020  1.383
 9KB  C20  F21  single    1.343  0.020  1.343
 9KB  C06  C07  single    1.522  0.020  1.522
 9KB  C07  N08  single    1.449  0.020  1.449
 9KB  N08  C09  aromatic  1.366  0.020  1.366
 9KB  N08  C12  aromatic  1.349  0.020  1.349
 9KB  C09  C10  aromatic  1.366  0.020  1.366
 9KB  C12  N11  aromatic  1.309  0.020  1.309
 9KB  C10  N11  aromatic  1.366  0.020  1.366
 9KB  C10  H1   single    0.930  0.020  1.080
 9KB  C13  H2   single    0.970  0.020  1.090
 9KB  C13  H3   single    0.970  0.020  1.090
 9KB  C22  H4   single    0.930  0.020  1.080
 9KB  C03  H5   single    0.970  0.020  1.090
 9KB  C03  H6   single    0.970  0.020  1.090
 9KB  C05  H8   single    0.970  0.020  1.090
 9KB  C05  H9   single    0.970  0.020  1.090
 9KB  C06  H10  single    0.970  0.020  1.090
 9KB  C06  H11  single    0.970  0.020  1.090
 9KB  C07  H12  single    0.970  0.020  1.090
 9KB  C07  H13  single    0.970  0.020  1.090
 9KB  C09  H14  single    0.930  0.020  1.080
 9KB  C12  H15  single    0.930  0.020  1.080
 9KB  C14  H16  single    0.970  0.020  1.090
 9KB  C14  H17  single    0.970  0.020  1.090
 9KB  C16  H18  single    0.970  0.020  1.090
 9KB  C16  H19  single    0.970  0.020  1.090
 9KB  C18  H20  single    0.930  0.020  1.080
 9KB  C19  H21  single    0.930  0.020  1.080
 9KB  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
 9KB  H1   C10  N11  122.04  3.000
 9KB  H1   C10  C09  127.75  3.000
 9KB  N11  C10  C09  110.21  3.000
 9KB  H3   C13  H2   107.13  3.000
 9KB  H3   C13  C14  108.45  3.000
 9KB  H2   C13  C14  110.34  3.000
 9KB  H3   C13  N04  109.66  3.000
 9KB  H2   C13  N04  111.96  3.000
 9KB  C14  C13  N04  109.22  3.000
 9KB  C23  C17  C18  118.65  3.000
 9KB  C23  C17  C16  120.49  3.000
 9KB  C18  C17  C16  120.86  3.000
 9KB  F21  C20  C19  119.02  3.000
 9KB  F21  C20  C22  118.88  3.000
 9KB  C19  C20  C22  122.11  3.000
 9KB  H4   C22  C23  120.96  3.000
 9KB  H4   C22  C20  120.47  3.000
 9KB  C23  C22  C20  118.56  3.000
 9KB  N15  C02  C03  118.00  3.000
 9KB  C03  C02  O01  118.82  3.000
 9KB  N15  C02  O01  123.17  3.000
 9KB  H6   C03  H5   106.37  3.000
 9KB  H6   C03  N04  110.47  3.000
 9KB  H5   C03  N04  112.00  3.000
 9KB  H6   C03  C02  105.98  3.000
 9KB  H5   C03  C02  106.32  3.000
 9KB  N04  C03  C02  115.14  3.000
 9KB  C05  N04  C03  111.97  3.000
 9KB  C05  N04  C13  111.67  3.000
 9KB  C03  N04  C13  108.96  3.000
 9KB  H9   C05  H8   106.56  3.000
 9KB  H9   C05  C06  109.29  3.000
 9KB  H8   C05  C06  108.93  3.000
 9KB  H9   C05  N04  111.20  3.000
 9KB  H8   C05  N04  107.37  3.000
 9KB  C06  C05  N04  113.23  3.000
 9KB  H11  C06  H10  107.29  3.000
 9KB  H11  C06  C07  109.83  3.000
 9KB  H10  C06  C07  108.67  3.000
 9KB  H11  C06  C05  109.51  3.000
 9KB  H10  C06  C05  110.87  3.000
 9KB  C07  C06  C05  110.61  3.000
 9KB  H13  C07  H12  107.03  3.000
 9KB  H13  C07  N08  107.81  3.000
 9KB  H12  C07  N08  108.22  3.000
 9KB  H13  C07  C06  110.55  3.000
 9KB  H12  C07  C06  110.64  3.000
 9KB  N08  C07  C06  112.39  3.000
 9KB  C12  N08  C09  106.93  3.000
 9KB  C12  N08  C07  126.48  3.000
 9KB  C09  N08  C07  126.48  3.000
 9KB  H14  C09  N08  122.26  3.000
 9KB  H14  C09  C10  132.18  3.000
 9KB  N08  C09  C10  105.56  3.000
 9KB  C12  N11  C10  105.25  3.000
 9KB  H15  C12  N11  126.01  3.000
 9KB  H15  C12  N08  121.94  3.000
 9KB  N11  C12  N08  112.05  3.000
 9KB  H17  C14  H16  107.25  3.000
 9KB  H17  C14  N15  109.43  3.000
 9KB  H16  C14  N15  108.68  3.000
 9KB  H17  C14  C13  110.35  3.000
 9KB  H16  C14  C13  109.21  3.000
 9KB  N15  C14  C13  111.80  3.000
 9KB  C16  N15  C14  115.83  3.000
 9KB  C14  N15  C02  123.44  3.000
 9KB  C16  N15  C02  120.72  3.000
 9KB  H19  C16  H18  107.09  3.000
 9KB  H19  C16  N15  107.92  3.000
 9KB  H18  C16  N15  108.83  3.000
 9KB  H19  C16  C17  109.86  3.000
 9KB  H18  C16  C17  110.57  3.000
 9KB  N15  C16  C17  112.38  3.000
 9KB  H20  C18  C19  118.94  3.000
 9KB  H20  C18  C17  119.82  3.000
 9KB  C19  C18  C17  121.24  3.000
 9KB  H21  C19  C18  120.97  3.000
 9KB  H21  C19  C20  120.64  3.000
 9KB  C18  C19  C20  118.39  3.000
 9KB  H22  C23  C22  119.19  3.000
 9KB  H22  C23  C17  119.77  3.000
 9KB  C22  C23  C17  121.05  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
 9KB  CONST_01  C12  N08  C09  C10     0.00   0.0  0
 9KB  CONST_02  N08  C12  N11  C10     0.00   0.0  0
 9KB  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 9KB  CONST_04  C20  C22  C23  C17     0.00   0.0  0
 9KB  CONST_05  C18  C17  C23  C22     0.00   0.0  0
 9KB  CONST_06  C18  C19  C20  C22     0.00   0.0  0
 9KB  CONST_07  N11  C10  C09  N08     0.00   0.0  0
 9KB  CONST_08  N11  C12  N08  C09     0.00   0.0  0
 9KB  CONST_09  C12  N11  C10  C09     0.00   0.0  0
 9KB  CONST_10  C23  C17  C18  C19     0.00   0.0  0
 9KB  CONST_11  C23  C22  C20  C19     0.00   0.0  0
 9KB  CONST_12  C14  N15  C02  C03     0.00   0.0  0
 9KB  CONST_13  C07  N08  C09  C10   180.00   0.0  0
 9KB  CONST_14  C16  C17  C23  C22   180.00   0.0  0
 9KB  CONST_15  N11  C12  N08  C07   180.00   0.0  0
 9KB  CONST_16  C19  C18  C17  C16   180.00   0.0  0
 9KB  CONST_17  F21  C20  C19  C18   180.00   0.0  0
 9KB  CONST_18  C23  C22  C20  F21   180.00   0.0  0
 9KB  CONST_19  C14  N15  C02  O01   180.00   0.0  0
 9KB  CONST_20  C16  N15  C02  C03   180.00   0.0  0
 9KB  CONST_21  H15  C12  N11  C10   180.00   0.0  0
 9KB  CONST_22  H21  C19  C18  C17   180.00   0.0  0
 9KB  CONST_23  H4   C22  C23  C17   180.00   0.0  0
 9KB  CONST_24  H20  C18  C19  C20   180.00   0.0  0
 9KB  CONST_25  H22  C23  C22  C20   180.00   0.0  0
 9KB  CONST_26  H1   C10  C09  N08   180.00   0.0  0
 9KB  CONST_27  H14  C09  C10  N11   180.00   0.0  0
 9KB  CONST_28  C16  N15  C02  O01     0.00   0.0  0
 9KB  Var_01    C02  N15  C14  C13   -16.47  30.0  1
 9KB  Var_02    C02  C03  N04  C13    47.87  30.0  1
 9KB  Var_03    C14  C13  N04  C03   -66.44  30.0  1
 9KB  Var_04    N15  C02  C03  N04   -13.69  30.0  1
 9KB  Var_05    N15  C14  C13  N04    50.57  30.0  1
 9KB  Var_06    C18  C17  C16  N15   107.92  30.0  2
 9KB  Var_07    C06  C05  N04  C13  -173.80  30.0  3
 9KB  Var_08    C09  N08  C07  C06    79.85  30.0  2
 9KB  Var_09    C07  C06  C05  N04   172.58  30.0  3
 9KB  Var_10    N08  C07  C06  C05   177.85  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
 9KB  plan-1  C10  0.020
 9KB  plan-1  C07  0.020
 9KB  plan-1  N08  0.020
 9KB  plan-1  C09  0.020
 9KB  plan-1  N11  0.020
 9KB  plan-1  C12  0.020
 9KB  plan-1  H1   0.020
 9KB  plan-1  H14  0.020
 9KB  plan-1  H15  0.020
 9KB  plan-2  C17  0.020
 9KB  plan-2  C20  0.020
 9KB  plan-2  C22  0.020
 9KB  plan-2  C16  0.020
 9KB  plan-2  C18  0.020
 9KB  plan-2  C19  0.020
 9KB  plan-2  F21  0.020
 9KB  plan-2  C23  0.020
 9KB  plan-2  H4   0.020
 9KB  plan-2  H20  0.020
 9KB  plan-2  H21  0.020
 9KB  plan-2  H22  0.020
 9KB  plan-3  C02  0.020
 9KB  plan-3  C03  0.020
 9KB  plan-3  C14  0.020
 9KB  plan-3  N15  0.020
 9KB  plan-3  C16  0.020
 9KB  plan-3  O01  0.020

