# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:16:44 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cn2c3cc(Cl)ccc3nc2N4CCNCC4)cc(C)c1F
#
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
 FV4  FV4  6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-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_FV4
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
 FV4  N1   N   N     0  -0.496  -0.1901   2.5092  -1.0346
 FV4  N3   N   NH1   0  -0.601   4.4245   3.1358   0.6829
 FV4  C4   C   CH2   0  -0.451   0.3003   0.0392   1.5681
 FV4  C5   C   CR5   0   0.691   0.5002   1.9647  -0.0695
 FV4  C6   C   CR56  0   0.164  -1.4303   1.9240  -0.9655
 FV4  C7   C   CR16  0  -0.346  -2.5621   2.1211  -1.7480
 FV4  C8   C   CR16  0  -0.234  -3.7050   1.3941  -1.4539
 FV4  C10  C   CR16  0  -0.270  -2.5992   0.2668   0.4091
 FV4  C13  C   CH2   0  -0.299   4.0864   2.5156  -0.5836
 FV4  C15  C   CH2   0  -0.328   2.1639   2.8170   1.4826
 FV4  C17  C   CR6   0  -0.066   1.8630  -2.5371  -0.7455
 FV4  N    N   NR5   0  -0.553  -0.2188   1.0496   0.6626
 FV4  C1   C   CR6   0  -0.071   0.0277  -3.6007   0.4806
 FV4  C11  C   CR56  0   0.353  -1.4703   1.0080   0.0976
 FV4  C12  C   CH2   0  -0.298   2.6178   2.7459  -0.8905
 FV4  C14  C   CH2   0  -0.294   3.6343   2.5828   1.7661
 FV4  C16  C   CR16  0  -0.343   1.5954  -1.3537  -0.0694
 FV4  C18  C   CH3   0  -0.716   2.9683  -2.6426  -1.7528
 FV4  C19  C   CR6   0   0.498   1.0590  -3.6269  -0.4425
 FV4  C2   C   CR16  0  -0.367  -0.2024  -2.3896   1.1297
 FV4  C3   C   CR6   0   0.159   0.5675  -1.2663   0.8644
 FV4  C9   C   CR6   0  -0.063  -3.7071   0.4855  -0.3939
 FV4  N2   N   NT    0  -0.541   1.8220   2.1999   0.2003
 FV4  CL   CL  CL    0  -0.138  -5.1590  -0.4132  -0.0691
 FV4  H1   H   HNH1  0   0.359   5.4088   3.0088   0.8761
 FV4  H3   H   HCH2  0   0.298   1.2143   0.4116   2.0242
 FV4  H4   H   HCH2  0   0.292  -0.4168  -0.0961   2.3783
 FV4  H5   H   HCR6  0   0.263  -2.5557   2.8238  -2.5708
 FV4  H6   H   HCR6  0   0.273  -4.5985   1.5272  -2.0484
 FV4  H7   H   HCR6  0   0.282  -2.6264  -0.4453   1.2224
 FV4  H8   H   HCH2  0   0.242   4.6883   2.9622  -1.3768
 FV4  H9   H   HCH2  0   0.197   4.2805   1.4308  -0.5948
 FV4  H10  H   HCH2  0   0.260   1.5581   2.3989   2.2853
 FV4  H11  H   HCH2  0   0.241   1.9575   3.8950   1.4482
 FV4  H12  H   HCH3  0   0.251  -1.2514  -5.2222  -0.1416
 FV4  H13  H   HCH3  0   0.252  -0.1903  -5.6193   1.2007
 FV4  H14  H   HCH3  0   0.250  -1.5924  -4.5913   1.4659
 FV4  H15  H   HCH2  0   0.224   2.4293   3.8186  -1.0252
 FV4  H16  H   HCH2  0   0.253   2.3491   2.2415  -1.8177
 FV4  H17  H   HCH2  0   0.200   3.7944   1.5018   1.9083
 FV4  H18  H   HCH2  0   0.242   3.9030   3.0799   2.6997
 FV4  H19  H   HCR6  0   0.251   2.2117  -0.4842  -0.2704
 FV4  H20  H   HCH3  0   0.252   2.5883  -2.9001  -2.7423
 FV4  H21  H   HCH3  0   0.246   3.4982  -1.6954  -1.8369
 FV4  H22  H   HCH3  0   0.252   3.6967  -3.4063  -1.4773
 FV4  H23  H   HCR6  0   0.259  -0.9976  -2.3363   1.8645
 FV4  F    F   F     0  -0.310   1.3018  -4.7851  -1.0865
 FV4  C    C   CH3   0  -0.718  -0.7936  -4.8223   0.7637

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
 FV4  C18  C17  single    1.499  0.020  1.499
 FV4  N3   C13  single    1.450  0.020  1.450
 FV4  N3   C14  single    1.450  0.020  1.450
 FV4  C13  C12  single    1.518  0.020  1.518
 FV4  F    C19  single    1.347  0.020  1.347
 FV4  C17  C19  aromatic  1.388  0.020  1.388
 FV4  C17  C16  aromatic  1.389  0.020  1.389
 FV4  C19  C1   aromatic  1.384  0.020  1.384
 FV4  C14  C15  single    1.516  0.020  1.516
 FV4  C16  C3   aromatic  1.391  0.020  1.391
 FV4  C12  N2   single    1.456  0.020  1.456
 FV4  C1   C    single    1.499  0.020  1.499
 FV4  C1   C2   aromatic  1.393  0.020  1.393
 FV4  C3   C2   aromatic  1.387  0.020  1.387
 FV4  C3   C4   single    1.507  0.020  1.507
 FV4  N2   C15  single    1.464  0.020  1.464
 FV4  N2   C5   single    1.369  0.020  1.369
 FV4  C4   N    single    1.453  0.020  1.453
 FV4  C5   N    aromatic  1.375  0.020  1.375
 FV4  C5   N1   aromatic  1.306  0.020  1.306
 FV4  N    C11  aromatic  1.374  0.020  1.374
 FV4  N1   C6   aromatic  1.373  0.020  1.373
 FV4  C11  C6   aromatic  1.404  0.020  1.404
 FV4  C11  C10  aromatic  1.386  0.020  1.386
 FV4  C6   C7   aromatic  1.390  0.020  1.390
 FV4  C10  C9   aromatic  1.386  0.020  1.386
 FV4  C7   C8   aromatic  1.386  0.020  1.386
 FV4  C9   C8   aromatic  1.396  0.020  1.396
 FV4  C9   CL   single    1.738  0.020  1.738
 FV4  N3   H1   single    0.890  0.020  1.040
 FV4  C4   H3   single    0.970  0.020  1.090
 FV4  C4   H4   single    0.970  0.020  1.090
 FV4  C7   H5   single    0.930  0.020  1.080
 FV4  C8   H6   single    0.930  0.020  1.080
 FV4  C10  H7   single    0.930  0.020  1.080
 FV4  C13  H8   single    0.970  0.020  1.090
 FV4  C13  H9   single    0.970  0.020  1.090
 FV4  C15  H10  single    0.970  0.020  1.090
 FV4  C15  H11  single    0.970  0.020  1.090
 FV4  C    H12  single    0.970  0.020  1.090
 FV4  C    H13  single    0.970  0.020  1.090
 FV4  C    H14  single    0.970  0.020  1.090
 FV4  C12  H15  single    0.970  0.020  1.090
 FV4  C12  H16  single    0.970  0.020  1.090
 FV4  C14  H17  single    0.970  0.020  1.090
 FV4  C14  H18  single    0.970  0.020  1.090
 FV4  C16  H19  single    0.930  0.020  1.080
 FV4  C18  H20  single    0.970  0.020  1.090
 FV4  C18  H21  single    0.970  0.020  1.090
 FV4  C18  H22  single    0.970  0.020  1.090
 FV4  C2   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
 FV4  C6   N1   C5   105.22  3.000
 FV4  H1   N3   C14  109.86  3.000
 FV4  H1   N3   C13  109.88  3.000
 FV4  C14  N3   C13  111.23  3.000
 FV4  H4   C4   H3   106.48  3.000
 FV4  H4   C4   C3   110.86  3.000
 FV4  H3   C4   C3   110.09  3.000
 FV4  H4   C4   N    108.33  3.000
 FV4  H3   C4   N    108.89  3.000
 FV4  C3   C4   N    112.01  3.000
 FV4  N2   C5   N    120.94  3.000
 FV4  N    C5   N1   113.25  3.000
 FV4  N2   C5   N1   125.76  3.000
 FV4  C11  C6   C7   119.71  3.000
 FV4  C7   C6   N1   130.29  3.000
 FV4  C11  C6   N1   110.00  3.000
 FV4  H5   C7   C8   120.46  3.000
 FV4  H5   C7   C6   121.02  3.000
 FV4  C8   C7   C6   118.53  3.000
 FV4  H6   C8   C9   119.75  3.000
 FV4  H6   C8   C7   120.00  3.000
 FV4  C9   C8   C7   120.25  3.000
 FV4  H7   C10  C9   121.31  3.000
 FV4  H7   C10  C11  122.80  3.000
 FV4  C9   C10  C11  115.89  3.000
 FV4  H9   C13  H8   107.35  3.000
 FV4  H9   C13  C12  108.52  3.000
 FV4  H8   C13  C12  108.94  3.000
 FV4  H9   C13  N3   112.88  3.000
 FV4  H8   C13  N3   109.34  3.000
 FV4  C12  C13  N3   109.71  3.000
 FV4  H11  C15  H10  107.18  3.000
 FV4  H11  C15  N2   110.03  3.000
 FV4  H10  C15  N2   110.73  3.000
 FV4  H11  C15  C14  109.87  3.000
 FV4  H10  C15  C14  110.03  3.000
 FV4  N2   C15  C14  108.99  3.000
 FV4  C19  C17  C18  121.23  3.000
 FV4  C19  C17  C16  116.82  3.000
 FV4  C18  C17  C16  121.95  3.000
 FV4  C11  N    C5   106.12  3.000
 FV4  C11  N    C4   124.12  3.000
 FV4  C5   N    C4   127.44  3.000
 FV4  C2   C1   C19  116.76  3.000
 FV4  C2   C1   C    122.00  3.000
 FV4  C19  C1   C    121.25  3.000
 FV4  N    C11  C10  131.74  3.000
 FV4  C10  C11  C6   122.85  3.000
 FV4  N    C11  C6   105.41  3.000
 FV4  H16  C12  H15  107.80  3.000
 FV4  H16  C12  N2   109.22  3.000
 FV4  H15  C12  N2   111.38  3.000
 FV4  H16  C12  C13  109.91  3.000
 FV4  H15  C12  C13  109.83  3.000
 FV4  N2   C12  C13  108.69  3.000
 FV4  H18  C14  H17  107.50  3.000
 FV4  H18  C14  C15  109.17  3.000
 FV4  H17  C14  C15  108.46  3.000
 FV4  H18  C14  N3   109.34  3.000
 FV4  H17  C14  N3   113.04  3.000
 FV4  C15  C14  N3   109.26  3.000
 FV4  H19  C16  C3   119.59  3.000
 FV4  H19  C16  C17  118.90  3.000
 FV4  C3   C16  C17  121.50  3.000
 FV4  H22  C18  H21  107.67  3.000
 FV4  H22  C18  H20  107.25  3.000
 FV4  H21  C18  H20  107.74  3.000
 FV4  H22  C18  C17  111.84  3.000
 FV4  H21  C18  C17  110.46  3.000
 FV4  H20  C18  C17  111.67  3.000
 FV4  F    C19  C1   117.99  3.000
 FV4  C1   C19  C17  124.21  3.000
 FV4  F    C19  C17  117.80  3.000
 FV4  H23  C2   C3   119.79  3.000
 FV4  H23  C2   C1   118.67  3.000
 FV4  C3   C2   C1   121.54  3.000
 FV4  C2   C3   C16  119.17  3.000
 FV4  C2   C3   C4   120.91  3.000
 FV4  C16  C3   C4   119.92  3.000
 FV4  CL   C9   C10  118.56  3.000
 FV4  CL   C9   C8   118.66  3.000
 FV4  C10  C9   C8   122.78  3.000
 FV4  C12  N2   C15  111.74  3.000
 FV4  C15  N2   C5   118.07  3.000
 FV4  C12  N2   C5   116.38  3.000
 FV4  H14  C    H13  107.61  3.000
 FV4  H14  C    H12  107.78  3.000
 FV4  H13  C    H12  107.26  3.000
 FV4  H14  C    C1   110.55  3.000
 FV4  H13  C    C1   111.59  3.000
 FV4  H12  C    C1   111.84  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
 FV4  CONST_01  C11  N    C5   N1      0.00   0.0  0
 FV4  CONST_02  N    C11  C6   N1      0.00   0.0  0
 FV4  CONST_03  C10  C11  C6   N1    180.00   0.0  0
 FV4  CONST_04  C8   C7   C6   N1    180.00   0.0  0
 FV4  CONST_05  C6   C11  N    C5      0.00   0.0  0
 FV4  CONST_06  C10  C11  N    C5    180.00   0.0  0
 FV4  CONST_07  C11  C6   N1   C5      0.00   0.0  0
 FV4  CONST_08  C7   C6   N1   C5    180.00   0.0  0
 FV4  CONST_09  N    C5   N1   C6      0.00   0.0  0
 FV4  CONST_10  C9   C10  C11  C6      0.00   0.0  0
 FV4  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 FV4  CONST_12  N    C11  C6   C7    180.00   0.0  0
 FV4  CONST_13  C10  C11  C6   C7      0.00   0.0  0
 FV4  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 FV4  CONST_15  C11  C6   C7   C8      0.00   0.0  0
 FV4  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 FV4  CONST_17  C2   C1   C19  C17     0.00   0.0  0
 FV4  CONST_18  C2   C3   C16  C17     0.00   0.0  0
 FV4  CONST_19  C9   C10  C11  N     180.00   0.0  0
 FV4  CONST_20  C16  C17  C19  C1      0.00   0.0  0
 FV4  CONST_21  C16  C3   C2   C1      0.00   0.0  0
 FV4  CONST_22  C3   C16  C17  C19     0.00   0.0  0
 FV4  CONST_23  C3   C2   C1   C19     0.00   0.0  0
 FV4  CONST_24  N2   C5   N1   C6    180.00   0.0  0
 FV4  CONST_25  N2   C5   N    C11   180.00   0.0  0
 FV4  CONST_27  C17  C16  C3   C4    180.00   0.0  0
 FV4  CONST_28  C1   C2   C3   C4    180.00   0.0  0
 FV4  CONST_29  N2   C5   N    C4      0.00   0.0  0
 FV4  CONST_32  CL   C9   C8   C7    180.00   0.0  0
 FV4  CONST_33  C    C1   C19  C17   180.00   0.0  0
 FV4  CONST_34  C3   C2   C1   C     180.00   0.0  0
 FV4  CONST_35  C18  C17  C19  C1    180.00   0.0  0
 FV4  CONST_36  CL   C9   C10  C11   180.00   0.0  0
 FV4  CONST_37  F    C19  C17  C16   180.00   0.0  0
 FV4  CONST_38  C3   C16  C17  C18   180.00   0.0  0
 FV4  CONST_39  F    C19  C1   C2    180.00   0.0  0
 FV4  CONST_40  H5   C7   C6   N1      0.00   0.0  0
 FV4  CONST_41  H7   C10  C11  C6    180.00   0.0  0
 FV4  CONST_42  H6   C8   C7   C6    180.00   0.0  0
 FV4  CONST_43  H23  C2   C3   C16   180.00   0.0  0
 FV4  CONST_44  H19  C16  C17  C19   180.00   0.0  0
 FV4  Var_01    C12  N2   C5   N1    -20.56  30.0  2
 FV4  Var_02    N2   C12  C13  N3    -57.86  30.0  1
 FV4  Var_03    N2   C15  C14  N3     57.96  30.0  1
 FV4  Var_04    C13  C12  N2   C5   -161.61  30.0  1
 FV4  Var_05    C14  C15  N2   C5    162.02  30.0  1
 FV4  Var_06    C15  C14  N3   C13   -59.78  30.0  1
 FV4  Var_07    C14  N3   C13  C12    59.88  30.0  1
 FV4  Var_08    C3   C4   N    C5    -90.57  30.0  2
 FV4  Var_09    C16  C3   C4   N      68.26  30.0  2
 FV4  Var_10    H20  C18  C17  C16  -118.82  30.0  2
 FV4  Var_11    H12  C    C1   C19   -56.25  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
 FV4  plan-1  C4   0.020
 FV4  plan-1  C17  0.020
 FV4  plan-1  C1   0.020
 FV4  plan-1  C16  0.020
 FV4  plan-1  C18  0.020
 FV4  plan-1  C19  0.020
 FV4  plan-1  C2   0.020
 FV4  plan-1  C3   0.020
 FV4  plan-1  H19  0.020
 FV4  plan-1  H23  0.020
 FV4  plan-1  F    0.020
 FV4  plan-1  C    0.020
 FV4  plan-2  N1   0.020
 FV4  plan-2  C4   0.020
 FV4  plan-2  C5   0.020
 FV4  plan-2  C6   0.020
 FV4  plan-2  C7   0.020
 FV4  plan-2  C8   0.020
 FV4  plan-2  C10  0.020
 FV4  plan-2  N    0.020
 FV4  plan-2  C11  0.020
 FV4  plan-2  C9   0.020
 FV4  plan-2  N2   0.020
 FV4  plan-2  CL   0.020
 FV4  plan-2  H5   0.020
 FV4  plan-2  H6   0.020
 FV4  plan-2  H7   0.020

