# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:23:26 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 6-chloro-1-[(3-chloro-4-fluorophenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Cn2c3cc(Cl)ccc3nc2N4CCNCC4)cc1Cl
#
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
 FW7  FW7  6-chloro-1-[(3-chloro-4-fluorophenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole  ligand  42  25  .  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_FW7
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
 FW7  C4    C   CR16  0  -0.269  -0.2829  -2.0918   0.2552
 FW7  C5    C   CR6   0   0.124   0.3112  -1.3153  -0.7366
 FW7  C6    C   CH2   0  -0.451  -0.5183  -0.3326  -1.5228
 FW7  C8    C   CR5   0   0.692  -2.0364   0.9165   0.0709
 FW7  C10   C   CR56  0   0.167  -0.7067   2.4151   0.7900
 FW7  C13   C   CR6   0  -0.064   1.8345   3.1559   0.0358
 FW7  C15   C   CR16  0  -0.268   1.2422   2.1158  -0.6630
 FW7  C21   C   CH2   0  -0.303  -4.8445  -1.2990   0.8914
 FW7  C22   C   CH2   0  -0.296  -3.9839  -0.0610   1.0620
 FW7  C24   C   CR6   0  -0.216   2.4312  -2.3339  -0.2305
 FW7  C11   C   CR16  0  -0.345  -0.0843   3.4575   1.4663
 FW7  C12   C   CR16  0  -0.233   1.1956   3.8244   1.0816
 FW7  C16   C   CR56  0   0.350  -0.0368   1.7667  -0.2592
 FW7  C18   C   CH2   0  -0.328  -3.8338   0.1205  -1.3462
 FW7  C19   C   CH2   0  -0.297  -4.6907  -1.1216  -1.4857
 FW7  C2    C   CR6   0   0.606   1.8239  -3.0904   0.7560
 FW7  C23   C   CR16  0  -0.262   1.6721  -1.4444  -0.9769
 FW7  C3    C   CR16  0  -0.402   0.4698  -2.9793   1.0052
 FW7  F1    F   F     0  -0.293   2.5625  -3.9384   1.4732
 FW7  N17   N   NT    0  -0.539  -3.0910   0.0550  -0.0840
 FW7  N20   N   NH1   0  -0.600  -5.5879  -1.2112  -0.3508
 FW7  N7    N   NR5   0  -0.554  -0.9096   0.8047  -0.7106
 FW7  N9    N   N     0  -0.494  -1.9540   1.8666   0.9612
 FW7  CL25  CL  CL    0  -0.089   4.1212  -2.5064  -0.5138
 FW7  H1    H   HCR6  0   0.274  -1.3467  -2.0091   0.4414
 FW7  H2    H   HCH2  0   0.299   0.0266   0.0295  -2.3950
 FW7  H3    H   HCH2  0   0.303  -1.4128  -0.8216  -1.8995
 FW7  H4    H   HCR6  0   0.283   1.7594   1.6194  -1.4728
 FW7  H5    H   HCH2  0   0.200  -4.1938  -2.1869   0.9377
 FW7  H6    H   HCH2  0   0.242  -5.5431  -1.3610   1.7276
 FW7  H7    H   HCH2  0   0.223  -4.6224   0.8263   1.1598
 FW7  H8    H   HCH2  0   0.253  -3.3897  -0.1475   1.9707
 FW7  H9    H   HCR6  0   0.263  -0.5836   3.9732   2.2760
 FW7  H10   H   HCR6  0   0.274   1.7046   4.6299   1.5931
 FW7  H11   H   HCH2  0   0.260  -3.1499   0.1971  -2.1903
 FW7  H12   H   HCH2  0   0.240  -4.4710   1.0148  -1.3619
 FW7  H13   H   HCH2  0   0.243  -5.2732  -1.0506  -2.4057
 FW7  H14   H   HCH2  0   0.201  -4.0270  -1.9960  -1.5795
 FW7  H15   H   HCR6  0   0.290   2.1524  -0.8578  -1.7498
 FW7  H16   H   HCR6  0   0.293   0.0134  -3.5855   1.7767
 FW7  H17   H   HNH1  0   0.359  -6.1897  -2.0177  -0.4492
 FW7  CL14  CL  CL    0  -0.136   3.4402   3.6484  -0.4099

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
 FW7  F1   C2    single    1.334  0.020  1.334
 FW7  C3   C2    aromatic  1.381  0.020  1.381
 FW7  C3   C4    aromatic  1.384  0.020  1.384
 FW7  N20  C21   single    1.450  0.020  1.450
 FW7  N20  C19   single    1.450  0.020  1.450
 FW7  C21  C22   single    1.517  0.020  1.517
 FW7  C2   C24   aromatic  1.383  0.020  1.383
 FW7  C19  C18   single    1.515  0.020  1.515
 FW7  C4   C5    aromatic  1.393  0.020  1.393
 FW7  C24  CL25  single    1.722  0.020  1.722
 FW7  C24  C23   aromatic  1.387  0.020  1.387
 FW7  C22  N17   single    1.457  0.020  1.457
 FW7  N17  C18   single    1.466  0.020  1.466
 FW7  N17  C8    single    1.371  0.020  1.371
 FW7  C5   C23   aromatic  1.388  0.020  1.388
 FW7  C5   C6    single    1.507  0.020  1.507
 FW7  C6   N7    single    1.451  0.020  1.451
 FW7  C8   N7    aromatic  1.376  0.020  1.376
 FW7  C8   N9    aromatic  1.305  0.020  1.305
 FW7  N7   C16   aromatic  1.375  0.020  1.375
 FW7  N9   C10   aromatic  1.373  0.020  1.373
 FW7  C16  C10   aromatic  1.404  0.020  1.404
 FW7  C16  C15   aromatic  1.386  0.020  1.386
 FW7  C10  C11   aromatic  1.390  0.020  1.390
 FW7  C15  C13   aromatic  1.386  0.020  1.386
 FW7  C11  C12   aromatic  1.386  0.020  1.386
 FW7  C13  C12   aromatic  1.396  0.020  1.396
 FW7  C13  CL14  single    1.738  0.020  1.738
 FW7  C4   H1    single    0.930  0.020  1.080
 FW7  C6   H2    single    0.970  0.020  1.090
 FW7  C6   H3    single    0.970  0.020  1.090
 FW7  C15  H4    single    0.930  0.020  1.080
 FW7  C21  H5    single    0.970  0.020  1.090
 FW7  C21  H6    single    0.970  0.020  1.090
 FW7  C22  H7    single    0.970  0.020  1.090
 FW7  C22  H8    single    0.970  0.020  1.090
 FW7  C11  H9    single    0.930  0.020  1.080
 FW7  C12  H10   single    0.930  0.020  1.080
 FW7  C18  H11   single    0.970  0.020  1.090
 FW7  C18  H12   single    0.970  0.020  1.090
 FW7  C19  H13   single    0.970  0.020  1.090
 FW7  C19  H14   single    0.970  0.020  1.090
 FW7  C23  H15   single    0.930  0.020  1.080
 FW7  C3   H16   single    0.930  0.020  1.080
 FW7  N20  H17   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
 FW7  H1    C4   C3   119.32  3.000
 FW7  H1    C4   C5   119.92  3.000
 FW7  C3    C4   C5   120.75  3.000
 FW7  C23   C5   C6   120.66  3.000
 FW7  C6    C5   C4   120.01  3.000
 FW7  C23   C5   C4   119.32  3.000
 FW7  H3    C6   H2   106.47  3.000
 FW7  H3    C6   N7   108.95  3.000
 FW7  H2    C6   N7   108.80  3.000
 FW7  H3    C6   C5   109.90  3.000
 FW7  H2    C6   C5   111.02  3.000
 FW7  N7    C6   C5   111.55  3.000
 FW7  N9    C8   N7   113.27  3.000
 FW7  N9    C8   N17  125.70  3.000
 FW7  N7    C8   N17  120.99  3.000
 FW7  N9    C10  C16  110.01  3.000
 FW7  C16   C10  C11  119.77  3.000
 FW7  N9    C10  C11  130.21  3.000
 FW7  CL14  C13  C12  118.64  3.000
 FW7  CL14  C13  C15  118.57  3.000
 FW7  C12   C13  C15  122.79  3.000
 FW7  H4    C15  C16  122.94  3.000
 FW7  H4    C15  C13  121.17  3.000
 FW7  C16   C15  C13  115.88  3.000
 FW7  H6    C21  H5   107.46  3.000
 FW7  H6    C21  N20  109.36  3.000
 FW7  H5    C21  N20  112.80  3.000
 FW7  H6    C21  C22  108.86  3.000
 FW7  H5    C21  C22  108.53  3.000
 FW7  N20   C21  C22  109.73  3.000
 FW7  H8    C22  H7   107.90  3.000
 FW7  H8    C22  N17  109.16  3.000
 FW7  H7    C22  N17  111.23  3.000
 FW7  H8    C22  C21  109.78  3.000
 FW7  H7    C22  C21  109.86  3.000
 FW7  N17   C22  C21  108.90  3.000
 FW7  CL25  C24  C23  120.84  3.000
 FW7  C23   C24  C2   119.61  3.000
 FW7  CL25  C24  C2   119.55  3.000
 FW7  H9    C11  C12  120.51  3.000
 FW7  H9    C11  C10  121.00  3.000
 FW7  C12   C11  C10  118.50  3.000
 FW7  H10   C12  C11  120.04  3.000
 FW7  H10   C12  C13  119.71  3.000
 FW7  C11   C12  C13  120.25  3.000
 FW7  N7    C16  C15  131.79  3.000
 FW7  C15   C16  C10  122.81  3.000
 FW7  N7    C16  C10  105.40  3.000
 FW7  H12   C18  H11  107.22  3.000
 FW7  H12   C18  N17  110.04  3.000
 FW7  H11   C18  N17  110.63  3.000
 FW7  H12   C18  C19  109.76  3.000
 FW7  H11   C18  C19  109.96  3.000
 FW7  N17   C18  C19  109.22  3.000
 FW7  H14   C19  H13  107.55  3.000
 FW7  H14   C19  N20  112.98  3.000
 FW7  H13   C19  N20  109.50  3.000
 FW7  H14   C19  C18  108.52  3.000
 FW7  H13   C19  C18  109.04  3.000
 FW7  N20   C19  C18  109.18  3.000
 FW7  F1    C2   C3   119.79  3.000
 FW7  C3    C2   C24  121.00  3.000
 FW7  F1    C2   C24  119.21  3.000
 FW7  H15   C23  C24  119.26  3.000
 FW7  H15   C23  C5   120.54  3.000
 FW7  C24   C23  C5   120.20  3.000
 FW7  H16   C3   C2   119.80  3.000
 FW7  H16   C3   C4   121.07  3.000
 FW7  C2    C3   C4   119.12  3.000
 FW7  C18   N17  C22  111.73  3.000
 FW7  C18   N17  C8   117.33  3.000
 FW7  C22   N17  C8   115.63  3.000
 FW7  H17   N20  C19  109.97  3.000
 FW7  H17   N20  C21  109.89  3.000
 FW7  C19   N20  C21  110.92  3.000
 FW7  C16   N7   C8   106.05  3.000
 FW7  C16   N7   C6   124.11  3.000
 FW7  C8    N7   C6   127.04  3.000
 FW7  C10   N9   C8   105.26  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
 FW7  CONST_01  C24   C2   C3   C4      0.00   0.0  0
 FW7  CONST_02  C24   C23  C5   C4      0.00   0.0  0
 FW7  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 FW7  CONST_04  C2    C24  C23  C5      0.00   0.0  0
 FW7  CONST_05  C10   C16  N7   C8      0.00   0.0  0
 FW7  CONST_06  C15   C16  N7   C8    180.00   0.0  0
 FW7  CONST_07  C16   C10  N9   C8      0.00   0.0  0
 FW7  CONST_08  C11   C10  N9   C8    180.00   0.0  0
 FW7  CONST_09  N7    C8   N9   C10     0.00   0.0  0
 FW7  CONST_10  C13   C15  C16  C10     0.00   0.0  0
 FW7  CONST_11  C13   C12  C11  C10     0.00   0.0  0
 FW7  CONST_12  N7    C16  C15  C13   180.00   0.0  0
 FW7  CONST_13  N9    C10  C16  C15   180.00   0.0  0
 FW7  CONST_14  C11   C10  C16  C15     0.00   0.0  0
 FW7  CONST_15  C11   C12  C13  C15     0.00   0.0  0
 FW7  CONST_16  N7    C16  C10  C11   180.00   0.0  0
 FW7  CONST_17  N9    C10  C11  C12   180.00   0.0  0
 FW7  CONST_18  C16   C10  C11  C12     0.00   0.0  0
 FW7  CONST_19  C16   C15  C13  C12     0.00   0.0  0
 FW7  CONST_20  N9    C8   N7   C16     0.00   0.0  0
 FW7  CONST_21  C3    C2   C24  C23     0.00   0.0  0
 FW7  CONST_22  C3    C4   C5   C23     0.00   0.0  0
 FW7  CONST_23  N9    C10  C16  N7      0.00   0.0  0
 FW7  CONST_24  N17   C8   N9   C10   180.00   0.0  0
 FW7  CONST_25  N17   C8   N7   C16   180.00   0.0  0
 FW7  CONST_26  F1    C2   C3   C4    180.00   0.0  0
 FW7  CONST_27  CL25  C24  C23  C5    180.00   0.0  0
 FW7  CONST_28  C3    C4   C5   C6    180.00   0.0  0
 FW7  CONST_29  C24   C23  C5   C6    180.00   0.0  0
 FW7  CONST_34  CL14  C13  C12  C11   180.00   0.0  0
 FW7  CONST_35  CL14  C13  C15  C16   180.00   0.0  0
 FW7  CONST_36  F1    C2   C24  C23   180.00   0.0  0
 FW7  CONST_37  CL25  C24  C2   C3    180.00   0.0  0
 FW7  CONST_38  H15   C23  C5   C4    180.00   0.0  0
 FW7  CONST_39  H16   C3   C4   C5    180.00   0.0  0
 FW7  CONST_40  H4    C15  C16  C10   180.00   0.0  0
 FW7  CONST_41  H10   C12  C11  C10   180.00   0.0  0
 FW7  CONST_42  H9    C11  C12  C13   180.00   0.0  0
 FW7  CONST_43  H1    C4   C3   C2    180.00   0.0  0
 FW7  Var_01    C21   C22  N17  C8   -164.47  30.0  1
 FW7  Var_02    C19   C18  N17  C8    164.82  30.0  1
 FW7  Var_03    C18   C19  N20  C21   -60.35  30.0  1
 FW7  Var_04    C19   N20  C21  C22    60.42  30.0  1
 FW7  Var_05    N7    C8   N17  C22   158.52  30.0  2
 FW7  Var_06    N20   C21  C22  N17   -57.87  30.0  1
 FW7  Var_07    N20   C19  C18  N17    58.09  30.0  1
 FW7  Var_08    N7    C6   C5   C4     71.14  30.0  2
 FW7  Var_09    C8    N7   C6   C5    -88.93  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
 FW7  plan-1  C4    0.020
 FW7  plan-1  C5    0.020
 FW7  plan-1  C6    0.020
 FW7  plan-1  C24   0.020
 FW7  plan-1  C2    0.020
 FW7  plan-1  C23   0.020
 FW7  plan-1  C3    0.020
 FW7  plan-1  F1    0.020
 FW7  plan-1  CL25  0.020
 FW7  plan-1  H1    0.020
 FW7  plan-1  H15   0.020
 FW7  plan-1  H16   0.020
 FW7  plan-2  C6    0.020
 FW7  plan-2  C8    0.020
 FW7  plan-2  C10   0.020
 FW7  plan-2  C13   0.020
 FW7  plan-2  C15   0.020
 FW7  plan-2  C11   0.020
 FW7  plan-2  C12   0.020
 FW7  plan-2  C16   0.020
 FW7  plan-2  N17   0.020
 FW7  plan-2  N7    0.020
 FW7  plan-2  N9    0.020
 FW7  plan-2  H4    0.020
 FW7  plan-2  H9    0.020
 FW7  plan-2  H10   0.020
 FW7  plan-2  CL14  0.020

