# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:55:01 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-2-(piperazin-1-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2nc(N3CCNCC3)n(Cc4ccc(F)c(Cl)c4)c2cc1C
#
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
 FW4  FW4  1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-2-(piperazin-1-yl)-1H-benzimidazole  ligand  48  26  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FW4
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
 FW4  C10  C   CH3   0  -0.737   5.0727   2.3975   0.8566
 FW4  C13  C   CR16  0  -0.396   3.7655  -0.3760  -1.3921
 FW4  C21  C   CH2   0  -0.306  -2.3254  -3.3611  -1.0003
 FW4  C22  C   CH2   0  -0.291  -0.9052  -2.8729  -1.2186
 FW4  C24  C   CR16  0  -0.404  -1.2392   3.1942   0.2753
 FW4  C02  C   CR6   0  -0.221  -2.7974   1.4122  -0.1494
 FW4  C03  C   CR16  0  -0.236  -1.9816   0.5285   0.5353
 FW4  C04  C   CR6   0   0.126  -0.7844   0.9655   1.0925
 FW4  N06  N   NR5   0  -0.549   1.0596  -0.6250   0.8583
 FW4  C07  C   CR56  0   0.352   2.2429  -0.0487   0.4473
 FW4  C08  C   CR16  0  -0.369   3.0304   0.9613   0.9799
 FW4  C09  C   CR6   0   0.051   4.1982   1.3059   0.3098
 FW4  C11  C   CR6   0   0.057   4.5680   0.6340  -0.8788
 FW4  C12  C   CH3   0  -0.737   5.8329   1.0171  -1.5935
 FW4  C14  C   CR56  0   0.158   2.5929  -0.7205  -0.7276
 FW4  N15  N   N     0  -0.493   1.6528  -1.6830  -1.0215
 FW4  C16  C   CR5   0   0.670   0.7630  -1.5890  -0.0737
 FW4  N17  N   NT    0  -0.540  -0.3934  -2.3279   0.0317
 FW4  C18  C   CH2   0  -0.317  -0.4360  -3.3093   1.1178
 FW4  C19  C   CH2   0  -0.303  -1.8598  -3.7954   1.3025
 FW4  N20  N   NH1   0  -0.599  -2.3423  -4.3542   0.0555
 FW4  C23  C   CR16  0  -0.273  -0.4258   2.3028   0.9596
 FW4  C25  C   CR6   0   0.606  -2.4184   2.7385  -0.2767
 FW4  F26  F   F     0  -0.293  -3.2113   3.5805  -0.9418
 FW4  H1   H   HCH3  0   0.241   6.0829   2.0383   1.0640
 FW4  H2   H   HCH3  0   0.240   5.1731   3.2267   0.1527
 FW4  H3   H   HCH3  0   0.249   4.6701   2.8000   1.7852
 FW4  H4   H   HCR6  0   0.242   4.0501  -0.8908  -2.3023
 FW4  H5   H   HCH2  0   0.193  -2.9694  -2.4933  -0.7833
 FW4  H6   H   HCH2  0   0.244  -2.6911  -3.8096  -1.9255
 FW4  H7   H   HCH2  0   0.218  -0.2838  -3.7006  -1.5839
 FW4  H8   H   HCH2  0   0.250  -0.8978  -2.0893  -1.9755
 FW4  H9   H   HCR6  0   0.293  -0.9630   4.2353   0.1720
 FW4  H10  H   HCR6  0   0.280  -2.2784  -0.5078   0.6261
 FW4  H11  H   HCH2  0   0.296   0.7039   0.4784   2.5668
 FW4  H12  H   HCH2  0   0.293  -0.4558  -0.7899   2.2840
 FW4  H13  H   HCR6  0   0.256   2.7606   1.4732   1.8966
 FW4  H14  H   HCH3  0   0.240   5.8012   2.0507  -1.9460
 FW4  H15  H   HCH3  0   0.239   6.7090   0.9356  -0.9462
 FW4  H16  H   HCH3  0   0.249   6.0039   0.3801  -2.4604
 FW4  H17  H   HCH2  0   0.233   0.2206  -4.1604   0.8912
 FW4  H18  H   HCH2  0   0.254  -0.0776  -2.8619   2.0444
 FW4  H19  H   HCH2  0   0.245  -1.8752  -4.5649   2.0758
 FW4  H20  H   HCH2  0   0.200  -2.4744  -2.9548   1.6634
 FW4  H21  H   HNH1  0   0.359  -3.2795  -4.7136   0.1777
 FW4  H23  H   HCR6  0   0.269   0.4958   2.6647   1.3957
 FW4  C05  C   CH2   0  -0.449   0.1250  -0.0160   1.7872
 FW4  CL1  CL  CL    0  -0.091  -4.2796   0.8783  -0.8472

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
 FW4  C21  N20  single    1.450  0.020  1.450
 FW4  C21  C22  single    1.518  0.020  1.518
 FW4  N20  C19  single    1.449  0.020  1.449
 FW4  F26  C25  single    1.334  0.020  1.334
 FW4  C24  C25  aromatic  1.379  0.020  1.379
 FW4  C24  C23  aromatic  1.387  0.020  1.387
 FW4  C19  C18  single    1.516  0.020  1.516
 FW4  C25  C02  aromatic  1.385  0.020  1.385
 FW4  C23  C04  aromatic  1.391  0.020  1.391
 FW4  C22  N17  single    1.457  0.020  1.457
 FW4  C18  N17  single    1.464  0.020  1.464
 FW4  C02  CL1  single    1.723  0.020  1.723
 FW4  C02  C03  aromatic  1.384  0.020  1.384
 FW4  N17  C16  single    1.376  0.020  1.376
 FW4  C04  C03  aromatic  1.391  0.020  1.391
 FW4  C04  C05  single    1.508  0.020  1.508
 FW4  C05  N06  single    1.452  0.020  1.452
 FW4  C16  N06  aromatic  1.373  0.020  1.373
 FW4  C16  N15  aromatic  1.303  0.020  1.303
 FW4  N06  C07  aromatic  1.379  0.020  1.379
 FW4  N15  C14  aromatic  1.377  0.020  1.377
 FW4  C07  C14  aromatic  1.398  0.020  1.398
 FW4  C07  C08  aromatic  1.387  0.020  1.387
 FW4  C14  C13  aromatic  1.391  0.020  1.391
 FW4  C08  C09  aromatic  1.390  0.020  1.390
 FW4  C13  C11  aromatic  1.388  0.020  1.388
 FW4  C09  C11  aromatic  1.415  0.020  1.415
 FW4  C09  C10  single    1.502  0.020  1.502
 FW4  C11  C12  single    1.503  0.020  1.503
 FW4  C10  H1   single    0.970  0.020  1.090
 FW4  C10  H2   single    0.970  0.020  1.090
 FW4  C10  H3   single    0.970  0.020  1.090
 FW4  C13  H4   single    0.930  0.020  1.080
 FW4  C21  H5   single    0.970  0.020  1.090
 FW4  C21  H6   single    0.970  0.020  1.090
 FW4  C22  H7   single    0.970  0.020  1.090
 FW4  C22  H8   single    0.970  0.020  1.090
 FW4  C24  H9   single    0.930  0.020  1.080
 FW4  C03  H10  single    0.930  0.020  1.080
 FW4  C05  H11  single    0.970  0.020  1.090
 FW4  C05  H12  single    0.970  0.020  1.090
 FW4  C08  H13  single    0.930  0.020  1.080
 FW4  C12  H14  single    0.970  0.020  1.090
 FW4  C12  H15  single    0.970  0.020  1.090
 FW4  C12  H16  single    0.970  0.020  1.090
 FW4  C18  H17  single    0.970  0.020  1.090
 FW4  C18  H18  single    0.970  0.020  1.090
 FW4  C19  H19  single    0.970  0.020  1.090
 FW4  C19  H20  single    0.970  0.020  1.090
 FW4  N20  H21  single    0.890  0.020  1.040
 FW4  C23  H23  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
 FW4  H3   C10  H2   107.63  3.000
 FW4  H3   C10  H1   107.55  3.000
 FW4  H2   C10  H1   106.68  3.000
 FW4  H3   C10  C09  111.34  3.000
 FW4  H2   C10  C09  111.76  3.000
 FW4  H1   C10  C09  111.64  3.000
 FW4  H4   C13  C14  120.32  3.000
 FW4  H4   C13  C11  120.28  3.000
 FW4  C14  C13  C11  119.40  3.000
 FW4  H6   C21  H5   107.14  3.000
 FW4  H6   C21  N20  109.39  3.000
 FW4  H5   C21  N20  112.91  3.000
 FW4  H6   C21  C22  108.89  3.000
 FW4  H5   C21  C22  108.77  3.000
 FW4  N20  C21  C22  109.64  3.000
 FW4  H8   C22  H7   107.90  3.000
 FW4  H8   C22  N17  108.95  3.000
 FW4  H7   C22  N17  111.65  3.000
 FW4  H8   C22  C21  109.73  3.000
 FW4  H7   C22  C21  109.58  3.000
 FW4  N17  C22  C21  109.01  3.000
 FW4  H9   C24  C25  119.86  3.000
 FW4  H9   C24  C23  121.04  3.000
 FW4  C25  C24  C23  119.10  3.000
 FW4  C25  C02  C03  119.71  3.000
 FW4  C03  C02  CL1  120.64  3.000
 FW4  C25  C02  CL1  119.66  3.000
 FW4  H10  C03  C04  120.23  3.000
 FW4  H10  C03  C02  119.44  3.000
 FW4  C04  C03  C02  120.33  3.000
 FW4  C23  C04  C05  120.96  3.000
 FW4  C05  C04  C03  119.95  3.000
 FW4  C23  C04  C03  119.06  3.000
 FW4  C16  N06  C07  106.05  3.000
 FW4  C07  N06  C05  124.60  3.000
 FW4  C16  N06  C05  126.14  3.000
 FW4  C14  C07  C08  122.04  3.000
 FW4  C08  C07  N06  132.62  3.000
 FW4  C14  C07  N06  105.33  3.000
 FW4  H13  C08  C09  119.99  3.000
 FW4  H13  C08  C07  121.82  3.000
 FW4  C09  C08  C07  118.20  3.000
 FW4  C11  C09  C08  120.47  3.000
 FW4  C11  C09  C10  119.93  3.000
 FW4  C08  C09  C10  119.60  3.000
 FW4  C12  C11  C09  119.91  3.000
 FW4  C12  C11  C13  119.75  3.000
 FW4  C09  C11  C13  120.34  3.000
 FW4  H16  C12  H15  107.58  3.000
 FW4  H16  C12  H14  107.52  3.000
 FW4  H15  C12  H14  106.57  3.000
 FW4  H16  C12  C11  111.20  3.000
 FW4  H15  C12  C11  111.98  3.000
 FW4  H14  C12  C11  111.73  3.000
 FW4  N15  C14  C07  110.14  3.000
 FW4  C07  C14  C13  119.56  3.000
 FW4  N15  C14  C13  130.29  3.000
 FW4  C16  N15  C14  105.10  3.000
 FW4  N17  C16  N15  126.20  3.000
 FW4  N15  C16  N06  113.37  3.000
 FW4  N17  C16  N06  120.42  3.000
 FW4  C18  N17  C16  116.17  3.000
 FW4  C16  N17  C22  115.49  3.000
 FW4  C18  N17  C22  112.05  3.000
 FW4  H18  C18  H17  107.27  3.000
 FW4  H18  C18  C19  109.70  3.000
 FW4  H17  C18  C19  109.76  3.000
 FW4  H18  C18  N17  110.24  3.000
 FW4  H17  C18  N17  110.41  3.000
 FW4  C19  C18  N17  109.43  3.000
 FW4  H20  C19  H19  107.34  3.000
 FW4  H20  C19  N20  112.97  3.000
 FW4  H19  C19  N20  109.47  3.000
 FW4  H20  C19  C18  108.61  3.000
 FW4  H19  C19  C18  109.01  3.000
 FW4  N20  C19  C18  109.36  3.000
 FW4  H21  N20  C19  109.97  3.000
 FW4  H21  N20  C21  110.02  3.000
 FW4  C19  N20  C21  111.02  3.000
 FW4  H23  C23  C04  120.18  3.000
 FW4  H23  C23  C24  118.90  3.000
 FW4  C04  C23  C24  120.91  3.000
 FW4  F26  C25  C02  119.17  3.000
 FW4  C02  C25  C24  120.89  3.000
 FW4  F26  C25  C24  119.94  3.000
 FW4  H12  C05  H11  106.24  3.000
 FW4  H12  C05  N06  109.73  3.000
 FW4  H11  C05  N06  107.82  3.000
 FW4  H12  C05  C04  110.59  3.000
 FW4  H11  C05  C04  110.78  3.000
 FW4  N06  C05  C04  111.51  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
 FW4  CONST_01  C16  N15  C14  C13  180.00   0.0  0
 FW4  CONST_02  N06  C07  C14  C13  180.00   0.0  0
 FW4  CONST_03  C08  C07  C14  C13    0.00   0.0  0
 FW4  CONST_04  C08  C09  C11  C13    0.00   0.0  0
 FW4  CONST_05  C03  C02  C25  C24    0.00   0.0  0
 FW4  CONST_06  C03  C04  C23  C24    0.00   0.0  0
 FW4  CONST_07  C23  C24  C25  C02    0.00   0.0  0
 FW4  CONST_08  C23  C04  C03  C02    0.00   0.0  0
 FW4  CONST_09  C25  C24  C23  C04    0.00   0.0  0
 FW4  CONST_10  C25  C02  C03  C04    0.00   0.0  0
 FW4  CONST_11  C14  N15  C16  N06    0.00   0.0  0
 FW4  CONST_12  N15  C14  C07  N06    0.00   0.0  0
 FW4  CONST_13  C09  C08  C07  N06  180.00   0.0  0
 FW4  CONST_14  N15  C16  N06  C07    0.00   0.0  0
 FW4  CONST_15  C16  N15  C14  C07    0.00   0.0  0
 FW4  CONST_16  C11  C13  C14  C07    0.00   0.0  0
 FW4  CONST_17  C11  C09  C08  C07    0.00   0.0  0
 FW4  CONST_18  C16  N06  C07  C08  180.00   0.0  0
 FW4  CONST_19  N15  C14  C07  C08  180.00   0.0  0
 FW4  CONST_20  C14  C07  C08  C09    0.00   0.0  0
 FW4  CONST_21  C14  C13  C11  C09    0.00   0.0  0
 FW4  CONST_22  N15  C14  C13  C11  180.00   0.0  0
 FW4  CONST_23  C16  N06  C07  C14    0.00   0.0  0
 FW4  CONST_24  N17  C16  N06  C07  180.00   0.0  0
 FW4  CONST_25  N17  C16  N15  C14  180.00   0.0  0
 FW4  CONST_26  C07  C08  C09  C10  180.00   0.0  0
 FW4  CONST_27  C13  C11  C09  C10  180.00   0.0  0
 FW4  CONST_28  CL1  C02  C25  C24  180.00   0.0  0
 FW4  CONST_29  C05  C04  C23  C24  180.00   0.0  0
 FW4  CONST_30  C04  C03  C02  CL1  180.00   0.0  0
 FW4  CONST_31  C05  C04  C03  C02  180.00   0.0  0
 FW4  CONST_32  F26  C25  C02  C03  180.00   0.0  0
 FW4  CONST_37  C12  C11  C09  C08  180.00   0.0  0
 FW4  CONST_38  C14  C13  C11  C12  180.00   0.0  0
 FW4  CONST_39  F26  C25  C24  C23  180.00   0.0  0
 FW4  CONST_40  H9   C24  C25  C02  180.00   0.0  0
 FW4  CONST_41  H23  C23  C04  C03  180.00   0.0  0
 FW4  CONST_42  H13  C08  C07  N06    0.00   0.0  0
 FW4  CONST_43  H4   C13  C14  C07  180.00   0.0  0
 FW4  CONST_44  H10  C03  C04  C23  180.00   0.0  0
 FW4  Var_01    C18  C19  N20  C21  -60.16  30.0  1
 FW4  Var_02    C18  N17  C22  C21   57.42  30.0  1
 FW4  Var_03    C19  N20  C21  C22   60.54  30.0  1
 FW4  Var_04    C19  C18  N17  C22  -57.45  30.0  1
 FW4  Var_05    N06  C16  N17  C22  154.59  30.0  2
 FW4  Var_06    N20  C21  C22  N17  -57.83  30.0  1
 FW4  Var_07    N20  C19  C18  N17   57.33  30.0  1
 FW4  Var_08    N06  C05  C04  C03   88.79  30.0  2
 FW4  Var_09    C16  N06  C05  C04  -74.39  30.0  2
 FW4  Var_10    H14  C12  C11  C13  117.18  30.0  2
 FW4  Var_11    H1   C10  C09  C08  121.48  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
 FW4  plan-1  C24  0.020
 FW4  plan-1  C02  0.020
 FW4  plan-1  C03  0.020
 FW4  plan-1  C04  0.020
 FW4  plan-1  C23  0.020
 FW4  plan-1  C25  0.020
 FW4  plan-1  F26  0.020
 FW4  plan-1  H9   0.020
 FW4  plan-1  H10  0.020
 FW4  plan-1  H23  0.020
 FW4  plan-1  C05  0.020
 FW4  plan-1  CL1  0.020
 FW4  plan-2  C10  0.020
 FW4  plan-2  C13  0.020
 FW4  plan-2  N06  0.020
 FW4  plan-2  C07  0.020
 FW4  plan-2  C08  0.020
 FW4  plan-2  C09  0.020
 FW4  plan-2  C11  0.020
 FW4  plan-2  C12  0.020
 FW4  plan-2  C14  0.020
 FW4  plan-2  N15  0.020
 FW4  plan-2  C16  0.020
 FW4  plan-2  N17  0.020
 FW4  plan-2  H4   0.020
 FW4  plan-2  H13  0.020
 FW4  plan-2  C05  0.020

