# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:26:58 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1N2CCN(CC2)C(=O)c3cn(Cc4ccccc4)cn3
#
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
 2WL  2WL  (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone  ligand  48  27  .  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_2WL
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
 2WL  CL1  CL  CL    0  -0.114   5.6323  -1.5337  -1.0945
 2WL  C2   C   CR6   0  -0.103   5.6421   0.0330  -0.3501
 2WL  C3   C   CR16  0  -0.217   6.8507   0.6990  -0.2341
 2WL  C4   C   CR16  0  -0.278   6.9039   1.9220   0.4193
 2WL  C5   C   CR16  0  -0.243   5.7433   2.4635   0.9499
 2WL  C6   C   CR16  0  -0.327   4.5341   1.7986   0.8086
 2WL  C1   C   CR6   0   0.390   4.4492   0.5681   0.1540
 2WL  N1   N   NT    0  -0.505   3.2471  -0.1355   0.0119
 2WL  C10  C   CH2   0  -0.303   2.6677  -0.1267  -1.3268
 2WL  C9   C   CH2   0  -0.325   1.6020  -1.2032  -1.4257
 2WL  C7   C   CH2   0  -0.301   2.2345   0.0781   1.0281
 2WL  C8   C   CH2   0  -0.333   1.1682  -1.0033   0.9315
 2WL  N4   N   NT    0  -0.463   0.5880  -1.0174  -0.4016
 2WL  C21  C   C     0   0.503  -0.6202  -0.5116  -0.7432
 2WL  O1   O   O     0  -0.498  -0.8927  -0.1937  -1.8977
 2WL  C11  C   CR5   0  -0.027  -1.6751  -0.3668   0.2833
 2WL  C20  C   CR15  0  -0.034  -2.7573   0.4617   0.1273
 2WL  N2   N   N     0  -0.456  -1.7861  -1.0559   1.4603
 2WL  C12  C   CR15  0   0.099  -2.9003  -0.6461   2.0003
 2WL  N3   N   NR5   0  -0.401  -3.5208   0.2814   1.2337
 2WL  C13  C   CH2   0  -0.407  -4.7871   0.9352   1.5168
 2WL  C14  C   CR6   0   0.122  -5.8510   0.5443   0.5262
 2WL  C15  C   CR16  0  -0.302  -6.3452   1.4743  -0.3802
 2WL  C19  C   CR16  0  -0.283  -6.3423  -0.7590   0.4987
 2WL  C18  C   CR16  0  -0.241  -7.3122  -1.1244  -0.4219
 2WL  C17  C   CR16  0  -0.262  -7.8034  -0.1886  -1.3259
 2WL  C16  C   CR16  0  -0.241  -7.3193   1.1110  -1.3030
 2WL  H1   H   HCR6  0   0.276   7.7513   0.2534  -0.6350
 2WL  H2   H   HCR6  0   0.264   7.8501   2.4360   0.5207
 2WL  H3   H   HCR6  0   0.262   5.7725   3.4135   1.4673
 2WL  H4   H   HCR6  0   0.271   3.6368   2.2480   1.2138
 2WL  H5   H   HCH2  0   0.226   2.2272   0.8550  -1.5581
 2WL  H6   H   HCH2  0   0.255   3.4373  -0.3197  -2.0726
 2WL  H7   H   HCH2  0   0.267   1.1455  -1.1950  -2.4113
 2WL  H8   H   HCH2  0   0.250   2.0657  -2.1820  -1.2733
 2WL  H9   H   HCH2  0   0.260   2.6970   0.0278   2.0153
 2WL  H10  H   HCH2  0   0.216   1.7456   1.0610   0.9403
 2WL  H11  H   HCH2  0   0.244   1.6180  -1.9806   1.1266
 2WL  H12  H   HCH2  0   0.287   0.4067  -0.8383   1.6847
 2WL  H13  H   HCR5  0   0.304  -3.0279   1.1480  -0.6577
 2WL  H14  H   HCR5  0   0.292  -3.3110  -0.9801   2.9413
 2WL  H15  H   HCH2  0   0.293  -5.0751   0.6565   2.5307
 2WL  H16  H   HCH2  0   0.292  -4.6336   2.0144   1.5102
 2WL  H17  H   HCR6  0   0.258  -5.9688   2.4903  -0.3676
 2WL  H18  H   HCR6  0   0.254  -5.9667  -1.4946   1.2010
 2WL  H19  H   HCR6  0   0.260  -7.6885  -2.1391  -0.4329
 2WL  H20  H   HCR6  0   0.260  -8.5615  -0.4735  -2.0440
 2WL  H21  H   HCR6  0   0.259  -7.6971   1.8441  -2.0037

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
 2WL  CL1  C2   single    1.735  0.020  1.735
 2WL  C9   C10  single    1.518  0.020  1.518
 2WL  C9   N4   single    1.453  0.020  1.453
 2WL  C2   C3   aromatic  1.385  0.020  1.385
 2WL  C2   C1   aromatic  1.401  0.020  1.401
 2WL  C10  N1   single    1.459  0.020  1.459
 2WL  C3   C4   aromatic  1.388  0.020  1.388
 2WL  O1   C21  double    1.228  0.020  1.228
 2WL  N1   C1   single    1.400  0.020  1.400
 2WL  N1   C7   single    1.450  0.020  1.450
 2WL  N4   C21  single    1.354  0.020  1.354
 2WL  N4   C8   single    1.454  0.020  1.454
 2WL  C1   C6   aromatic  1.396  0.020  1.396
 2WL  C21  C11  single    1.479  0.020  1.479
 2WL  C4   C5   aromatic  1.386  0.020  1.386
 2WL  C8   C7   single    1.522  0.020  1.522
 2WL  C6   C5   aromatic  1.387  0.020  1.387
 2WL  C11  N2   aromatic  1.368  0.020  1.368
 2WL  C11  C20  aromatic  1.372  0.020  1.372
 2WL  N2   C12  aromatic  1.304  0.020  1.304
 2WL  C20  N3   aromatic  1.356  0.020  1.356
 2WL  C12  N3   aromatic  1.354  0.020  1.354
 2WL  N3   C13  single    1.453  0.020  1.453
 2WL  C13  C14  single    1.505  0.020  1.505
 2WL  C14  C19  aromatic  1.393  0.020  1.393
 2WL  C14  C15  aromatic  1.390  0.020  1.390
 2WL  C19  C18  aromatic  1.386  0.020  1.386
 2WL  C15  C16  aromatic  1.390  0.020  1.390
 2WL  C18  C17  aromatic  1.391  0.020  1.391
 2WL  C16  C17  aromatic  1.387  0.020  1.387
 2WL  C3   H1   single    0.930  0.020  1.080
 2WL  C4   H2   single    0.930  0.020  1.080
 2WL  C5   H3   single    0.930  0.020  1.080
 2WL  C6   H4   single    0.930  0.020  1.080
 2WL  C10  H5   single    0.970  0.020  1.090
 2WL  C10  H6   single    0.970  0.020  1.090
 2WL  C9   H7   single    0.970  0.020  1.090
 2WL  C9   H8   single    0.970  0.020  1.090
 2WL  C7   H9   single    0.970  0.020  1.090
 2WL  C7   H10  single    0.970  0.020  1.090
 2WL  C8   H11  single    0.970  0.020  1.090
 2WL  C8   H12  single    0.970  0.020  1.090
 2WL  C20  H13  single    0.930  0.020  1.080
 2WL  C12  H14  single    0.930  0.020  1.080
 2WL  C13  H15  single    0.970  0.020  1.090
 2WL  C13  H16  single    0.970  0.020  1.090
 2WL  C15  H17  single    0.930  0.020  1.080
 2WL  C19  H18  single    0.930  0.020  1.080
 2WL  C18  H19  single    0.930  0.020  1.080
 2WL  C17  H20  single    0.930  0.020  1.080
 2WL  C16  H21  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
 2WL  C1   C2   C3   121.95  3.000
 2WL  C1   C2   CL1  119.64  3.000
 2WL  C3   C2   CL1  118.37  3.000
 2WL  H1   C3   C4   120.37  3.000
 2WL  H1   C3   C2   119.83  3.000
 2WL  C4   C3   C2   119.78  3.000
 2WL  H2   C4   C5   120.72  3.000
 2WL  H2   C4   C3   119.77  3.000
 2WL  C5   C4   C3   119.50  3.000
 2WL  H3   C5   C6   119.54  3.000
 2WL  H3   C5   C4   120.22  3.000
 2WL  C6   C5   C4   120.23  3.000
 2WL  H4   C6   C1   119.41  3.000
 2WL  H4   C6   C5   119.05  3.000
 2WL  C1   C6   C5   121.54  3.000
 2WL  N1   C1   C6   122.86  3.000
 2WL  C6   C1   C2   116.97  3.000
 2WL  N1   C1   C2   120.17  3.000
 2WL  C7   N1   C10  111.39  3.000
 2WL  C7   N1   C1   117.02  3.000
 2WL  C10  N1   C1   115.54  3.000
 2WL  H6   C10  H5   107.28  3.000
 2WL  H6   C10  C9   109.02  3.000
 2WL  H5   C10  C9   109.75  3.000
 2WL  H6   C10  N1   110.29  3.000
 2WL  H5   C10  N1   110.93  3.000
 2WL  C9   C10  N1   109.53  3.000
 2WL  H8   C9   H7   108.14  3.000
 2WL  H8   C9   N4   108.18  3.000
 2WL  H7   C9   N4   110.20  3.000
 2WL  H8   C9   C10  109.14  3.000
 2WL  H7   C9   C10  110.41  3.000
 2WL  N4   C9   C10  110.69  3.000
 2WL  H10  C7   H9   107.54  3.000
 2WL  H10  C7   C8   108.55  3.000
 2WL  H9   C7   C8   108.76  3.000
 2WL  H10  C7   N1   112.68  3.000
 2WL  H9   C7   N1   109.34  3.000
 2WL  C8   C7   N1   109.88  3.000
 2WL  H12  C8   H11  107.52  3.000
 2WL  H12  C8   N4   110.99  3.000
 2WL  H11  C8   N4   108.61  3.000
 2WL  H12  C8   C7   109.88  3.000
 2WL  H11  C8   C7   109.61  3.000
 2WL  N4   C8   C7   110.16  3.000
 2WL  C21  N4   C8   125.73  3.000
 2WL  C8   N4   C9   111.65  3.000
 2WL  C21  N4   C9   119.52  3.000
 2WL  C11  C21  O1   117.96  3.000
 2WL  C11  C21  N4   119.87  3.000
 2WL  O1   C21  N4   122.15  3.000
 2WL  N2   C11  C20  109.75  3.000
 2WL  C20  C11  C21  122.88  3.000
 2WL  N2   C11  C21  127.27  3.000
 2WL  H13  C20  N3   122.53  3.000
 2WL  H13  C20  C11  131.74  3.000
 2WL  N3   C20  C11  105.73  3.000
 2WL  C12  N2   C11  105.50  3.000
 2WL  H14  C12  N3   122.08  3.000
 2WL  H14  C12  N2   126.06  3.000
 2WL  N3   C12  N2   111.86  3.000
 2WL  C13  N3   C12  126.68  3.000
 2WL  C13  N3   C20  126.14  3.000
 2WL  C12  N3   C20  107.15  3.000
 2WL  H16  C13  H15  107.21  3.000
 2WL  H16  C13  C14  110.65  3.000
 2WL  H15  C13  C14  111.04  3.000
 2WL  H16  C13  N3   108.76  3.000
 2WL  H15  C13  N3   107.24  3.000
 2WL  C14  C13  N3   111.77  3.000
 2WL  C19  C14  C15  119.20  3.000
 2WL  C15  C14  C13  120.45  3.000
 2WL  C19  C14  C13  120.34  3.000
 2WL  H17  C15  C16  119.75  3.000
 2WL  H17  C15  C14  119.76  3.000
 2WL  C16  C15  C14  120.49  3.000
 2WL  H18  C19  C18  119.59  3.000
 2WL  H18  C19  C14  119.99  3.000
 2WL  C18  C19  C14  120.43  3.000
 2WL  H19  C18  C17  120.10  3.000
 2WL  H19  C18  C19  119.81  3.000
 2WL  C17  C18  C19  120.09  3.000
 2WL  H20  C17  C16  120.13  3.000
 2WL  H20  C17  C18  120.10  3.000
 2WL  C16  C17  C18  119.77  3.000
 2WL  H21  C16  C17  120.14  3.000
 2WL  H21  C16  C15  119.83  3.000
 2WL  C17  C16  C15  120.03  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
 2WL  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 2WL  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 2WL  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 2WL  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 2WL  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 2WL  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 2WL  CONST_07  N3   C12  N2   C11     0.00   0.0  0
 2WL  CONST_08  C12  N3   C20  C11     0.00   0.0  0
 2WL  CONST_09  C12  N2   C11  C20     0.00   0.0  0
 2WL  CONST_10  N2   C12  N3   C20     0.00   0.0  0
 2WL  CONST_11  N3   C20  C11  N2      0.00   0.0  0
 2WL  CONST_12  C17  C18  C19  C14     0.00   0.0  0
 2WL  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 2WL  CONST_14  C18  C19  C14  C15     0.00   0.0  0
 2WL  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 2WL  CONST_16  C16  C15  C14  C19     0.00   0.0  0
 2WL  CONST_17  C16  C17  C18  C19     0.00   0.0  0
 2WL  CONST_18  N1   C1   C2   C3    180.00   0.0  0
 2WL  CONST_19  N1   C1   C6   C5    180.00   0.0  0
 2WL  CONST_20  C4   C3   C2   CL1   180.00   0.0  0
 2WL  CONST_21  N1   C1   C2   CL1     0.00   0.0  0
 2WL  CONST_22  C6   C1   C2   CL1   180.00   0.0  0
 2WL  CONST_23  C12  N2   C11  C21   180.00   0.0  0
 2WL  CONST_24  N3   C20  C11  C21   180.00   0.0  0
 2WL  CONST_25  C13  N3   C20  C11   180.00   0.0  0
 2WL  CONST_26  C13  N3   C12  N2    180.00   0.0  0
 2WL  CONST_27  C18  C19  C14  C13   180.00   0.0  0
 2WL  CONST_28  C16  C15  C14  C13   180.00   0.0  0
 2WL  CONST_29  C11  C21  N4   C9    180.00   0.0  0
 2WL  CONST_31  H2   C4   C3   C2    180.00   0.0  0
 2WL  CONST_32  H4   C6   C1   C2    180.00   0.0  0
 2WL  CONST_33  H3   C5   C4   C3    180.00   0.0  0
 2WL  CONST_34  H1   C3   C4   C5    180.00   0.0  0
 2WL  CONST_35  H14  C12  N2   C11   180.00   0.0  0
 2WL  CONST_36  H13  C20  C11  N2    180.00   0.0  0
 2WL  CONST_37  H19  C18  C19  C14   180.00   0.0  0
 2WL  CONST_38  H21  C16  C15  C14   180.00   0.0  0
 2WL  CONST_39  H18  C19  C14  C15   180.00   0.0  0
 2WL  CONST_40  H20  C17  C16  C15   180.00   0.0  0
 2WL  CONST_41  H17  C15  C14  C19   180.00   0.0  0
 2WL  CONST_42  O1   C21  N4   C9      0.00   0.0  0
 2WL  Var_01    C10  N1   C1   C2    -74.66  30.0  3
 2WL  Var_02    C9   C10  N1   C1    165.05  30.0  1
 2WL  Var_03    C8   C7   N1   C1   -165.39  30.0  1
 2WL  Var_04    N4   C9   C10  N1     56.47  30.0  1
 2WL  Var_05    N4   C8   C7   N1    -56.87  30.0  1
 2WL  Var_06    C8   N4   C9   C10   -56.72  30.0  1
 2WL  Var_07    C7   C8   N4   C9     56.58  30.0  1
 2WL  Var_08    N2   C11  C21  N4    -23.17  30.0  2
 2WL  Var_09    C14  C13  N3   C20    64.47  30.0  2
 2WL  Var_10    C19  C14  C13  N3     67.64  30.0  2

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
 2WL  plan-1  C21  0.020
 2WL  plan-1  C11  0.020
 2WL  plan-1  C20  0.020
 2WL  plan-1  N2   0.020
 2WL  plan-1  C12  0.020
 2WL  plan-1  N3   0.020
 2WL  plan-1  C13  0.020
 2WL  plan-1  H13  0.020
 2WL  plan-1  H14  0.020
 2WL  plan-2  CL1  0.020
 2WL  plan-2  C2   0.020
 2WL  plan-2  C3   0.020
 2WL  plan-2  C4   0.020
 2WL  plan-2  C5   0.020
 2WL  plan-2  C6   0.020
 2WL  plan-2  C1   0.020
 2WL  plan-2  N1   0.020
 2WL  plan-2  H1   0.020
 2WL  plan-2  H2   0.020
 2WL  plan-2  H3   0.020
 2WL  plan-2  H4   0.020
 2WL  plan-3  C13  0.020
 2WL  plan-3  C14  0.020
 2WL  plan-3  C15  0.020
 2WL  plan-3  C19  0.020
 2WL  plan-3  C18  0.020
 2WL  plan-3  C17  0.020
 2WL  plan-3  C16  0.020
 2WL  plan-3  H17  0.020
 2WL  plan-3  H18  0.020
 2WL  plan-3  H19  0.020
 2WL  plan-3  H20  0.020
 2WL  plan-3  H21  0.020
 2WL  plan-4  C9   0.020
 2WL  plan-4  C8   0.020
 2WL  plan-4  N4   0.020
 2WL  plan-4  C21  0.020
 2WL  plan-4  O1   0.020
 2WL  plan-4  C11  0.020

