# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 14:50:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)ethyl-[[3,5-bis(chloranyl)-4-phenyl-phenyl]methyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(C[NH2+]CCc2[nH]c3ccccc3n2)cc(Cl)c1c4ccccc4
#
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
 AU2  AU2  2-(1~{H}-benzimidazol-2-yl)ethyl-[[3,5-bis(chloranyl)-4-phenyl-phenyl]methyl]azanium  ligand  47  27  .  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_AU2
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
 AU2  C1   C   CR16  0  -0.210  -1.7743   0.9994  -1.1256
 AU2  C2   C   CR6   0   0.043  -1.0726  -0.1904  -0.9921
 AU2  C3   C   CH2   0  -0.381   0.3769  -0.2568  -1.3656
 AU2  C4   C   CH2   0  -0.282   2.6884   0.0030  -0.4719
 AU2  C5   C   CH2   0  -0.589   3.4858   0.4131   0.7538
 AU2  C6   C   CR5   0   0.486   4.9444   0.2350   0.5080
 AU2  C7   C   CR56  0   0.327   7.0992   0.6543   0.5961
 AU2  N1   N   NR15  0  -0.704   5.8651   1.1182   0.9670
 AU2  N2   N   N     0  -0.476   5.4779  -0.7664  -0.1358
 AU2  C9   C   CR16  0  -0.279   9.4193   0.3852   0.2579
 AU2  C8   C   CR16  0  -0.305   8.3872   1.1399   0.7881
 AU2  CL1  CL  CL    0  -0.100  -3.7932  -2.6438   0.5440
 AU2  C14  C   CR6   0  -0.119  -3.0361  -1.2335  -0.1031
 AU2  C15  C   CR6   0   0.232  -3.7731  -0.0563  -0.2222
 AU2  C16  C   CR6   0   0.048  -5.1955   0.0150   0.1816
 AU2  C21  C   CR16  0  -0.268  -5.5468   0.5817   1.4024
 AU2  C20  C   CR16  0  -0.244  -6.8803   0.6491   1.7802
 AU2  C19  C   CR16  0  -0.258  -7.8687   0.1543   0.9391
 AU2  C18  C   CR16  0  -0.243  -7.5202  -0.4104  -0.2808
 AU2  C17  C   CR16  0  -0.268  -6.1867  -0.4819  -0.6585
 AU2  C    C   CR6   0  -0.118  -3.1042   1.0503  -0.7433
 AU2  CL   CL  CL    0  -0.100  -3.9582   2.5386  -0.9364
 AU2  C13  C   CR16  0  -0.208  -1.7063  -1.3140  -0.4803
 AU2  N    N   NT2   1  -0.668   1.2309   0.0839  -0.1881
 AU2  C12  C   CR56  0   0.136   6.8337  -0.5367  -0.1001
 AU2  C11  C   CR16  0  -0.335   7.8881  -1.2829  -0.6261
 AU2  C10  C   CR16  0  -0.270   9.1741  -0.8092  -0.4373
 AU2  H1   H   HCR6  0   0.294  -1.2926   1.8787  -1.5329
 AU2  H2   H   HCH2  0   0.327   0.6646  -1.2561  -1.6857
 AU2  H3   H   HCH2  0   0.328   0.6274   0.4515  -2.1528
 AU2  H4   H   HCH2  0   0.310   2.8881   0.6621  -1.3143
 AU2  H5   H   HCH2  0   0.308   2.9012  -1.0223  -0.7646
 AU2  H6   H   HCH2  0   0.292   3.2786   1.4533   1.0112
 AU2  H7   H   HCH2  0   0.302   3.1907  -0.1938   1.6157
 AU2  H8   H   HNR5  0   0.421   5.6703   1.9641   1.4796
 AU2  H10  H   HCR6  0   0.256  10.4395   0.7236   0.3824
 AU2  H11  H   HCR6  0   0.267   8.5782   2.0605   1.3236
 AU2  H12  H   HCR6  0   0.258  -4.7770   0.9682   2.0589
 AU2  H13  H   HCR6  0   0.261  -7.1480   1.0898   2.7316
 AU2  H14  H   HCR6  0   0.261  -8.9086   0.2094   1.2341
 AU2  H15  H   HCR6  0   0.261  -8.2868  -0.7957  -0.9404
 AU2  H16  H   HCR6  0   0.259  -5.9147  -0.9225  -1.6093
 AU2  H17  H   HCR6  0   0.294  -1.1686  -2.2478  -0.3791
 AU2  H18  H   HNT2  0   0.474   0.9956   1.0241   0.1363
 AU2  H19  H   HNT2  0   0.474   1.0011  -0.5404   0.5884
 AU2  H20  H   HCR6  0   0.254   7.7017  -2.2032  -1.1646
 AU2  H21  H   HCR6  0   0.253  10.0118  -1.3691  -0.8320

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
 AU2  C11  C10  aromatic  1.383  0.020  1.383
 AU2  C11  C12  aromatic  1.395  0.020  1.395
 AU2  C10  C9   aromatic  1.403  0.020  1.403
 AU2  N2   C12  aromatic  1.376  0.020  1.376
 AU2  N2   C6   aromatic  1.305  0.020  1.305
 AU2  C12  C7   aromatic  1.405  0.020  1.405
 AU2  C9   C8   aromatic  1.384  0.020  1.384
 AU2  C6   C5   single    1.490  0.020  1.490
 AU2  C6   N1   aromatic  1.356  0.020  1.356
 AU2  C7   C8   aromatic  1.390  0.020  1.390
 AU2  C7   N1   aromatic  1.370  0.020  1.370
 AU2  C5   C4   single    1.519  0.020  1.519
 AU2  C4   N    single    1.487  0.020  1.487
 AU2  N    C3   single    1.494  0.020  1.494
 AU2  CL1  C14  single    1.727  0.020  1.727
 AU2  C13  C14  aromatic  1.385  0.020  1.385
 AU2  C13  C2   aromatic  1.388  0.020  1.388
 AU2  C17  C18  aromatic  1.388  0.020  1.388
 AU2  C17  C16  aromatic  1.391  0.020  1.391
 AU2  C3   C2   single    1.498  0.020  1.498
 AU2  C14  C15  aromatic  1.394  0.020  1.394
 AU2  C2   C1   aromatic  1.388  0.020  1.388
 AU2  C18  C19  aromatic  1.389  0.020  1.389
 AU2  C15  C    aromatic  1.394  0.020  1.394
 AU2  C15  C16  single    1.480  0.020  1.480
 AU2  C1   C    aromatic  1.385  0.020  1.385
 AU2  C    CL   single    1.727  0.020  1.727
 AU2  C16  C21  aromatic  1.391  0.020  1.391
 AU2  C19  C20  aromatic  1.389  0.020  1.389
 AU2  C21  C20  aromatic  1.388  0.020  1.388
 AU2  C1   H1   single    0.930  0.020  1.080
 AU2  C3   H2   single    0.970  0.020  1.090
 AU2  C3   H3   single    0.970  0.020  1.090
 AU2  C4   H4   single    0.970  0.020  1.090
 AU2  C4   H5   single    0.970  0.020  1.090
 AU2  C5   H6   single    0.970  0.020  1.090
 AU2  C5   H7   single    0.970  0.020  1.090
 AU2  N1   H8   single    0.860  0.020  1.020
 AU2  C9   H10  single    0.930  0.020  1.080
 AU2  C8   H11  single    0.930  0.020  1.080
 AU2  C21  H12  single    0.930  0.020  1.080
 AU2  C20  H13  single    0.930  0.020  1.080
 AU2  C19  H14  single    0.930  0.020  1.080
 AU2  C18  H15  single    0.930  0.020  1.080
 AU2  C17  H16  single    0.930  0.020  1.080
 AU2  C13  H17  single    0.930  0.020  1.080
 AU2  N    H18  single    0.890  0.020  1.040
 AU2  N    H19  single    0.890  0.020  1.040
 AU2  C11  H20  single    0.930  0.020  1.080
 AU2  C10  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
 AU2  H1   C1   C    120.11  3.000
 AU2  H1   C1   C2   120.51  3.000
 AU2  C    C1   C2   119.38  3.000
 AU2  C13  C2   C3   119.85  3.000
 AU2  C3   C2   C1   120.22  3.000
 AU2  C13  C2   C1   119.91  3.000
 AU2  H3   C3   H2   108.91  3.000
 AU2  H3   C3   N    106.87  3.000
 AU2  H2   C3   N    106.87  3.000
 AU2  H3   C3   C2   111.97  3.000
 AU2  H2   C3   C2   111.71  3.000
 AU2  N    C3   C2   110.27  3.000
 AU2  H5   C4   H4   109.08  3.000
 AU2  H5   C4   N    107.12  3.000
 AU2  H4   C4   N    107.14  3.000
 AU2  H5   C4   C5   111.66  3.000
 AU2  H4   C4   C5   111.40  3.000
 AU2  N    C4   C5   110.24  3.000
 AU2  H7   C5   H6   106.95  3.000
 AU2  H7   C5   C6   109.12  3.000
 AU2  H6   C5   C6   109.80  3.000
 AU2  H7   C5   C4   110.13  3.000
 AU2  H6   C5   C4   110.36  3.000
 AU2  C6   C5   C4   110.40  3.000
 AU2  N2   C6   N1   112.91  3.000
 AU2  N1   C6   C5   122.08  3.000
 AU2  N2   C6   C5   125.00  3.000
 AU2  C12  C7   C8   122.67  3.000
 AU2  C8   C7   N1   132.79  3.000
 AU2  C12  C7   N1   104.54  3.000
 AU2  H8   N1   C7   126.58  3.000
 AU2  H8   N1   C6   125.98  3.000
 AU2  C7   N1   C6   107.43  3.000
 AU2  C12  N2   C6   105.20  3.000
 AU2  H10  C9   C10  119.21  3.000
 AU2  H10  C9   C8   119.23  3.000
 AU2  C10  C9   C8   121.56  3.000
 AU2  H11  C8   C9   121.46  3.000
 AU2  H11  C8   C7   121.95  3.000
 AU2  C9   C8   C7   116.59  3.000
 AU2  C13  C14  C15  122.25  3.000
 AU2  C15  C14  CL1  119.34  3.000
 AU2  C13  C14  CL1  118.41  3.000
 AU2  C    C15  C16  121.65  3.000
 AU2  C16  C15  C14  121.70  3.000
 AU2  C    C15  C14  116.65  3.000
 AU2  C17  C16  C21  119.71  3.000
 AU2  C21  C16  C15  120.11  3.000
 AU2  C17  C16  C15  120.18  3.000
 AU2  H12  C21  C20  120.04  3.000
 AU2  H12  C21  C16  119.86  3.000
 AU2  C20  C21  C16  120.09  3.000
 AU2  H13  C20  C19  120.10  3.000
 AU2  H13  C20  C21  119.79  3.000
 AU2  C19  C20  C21  120.11  3.000
 AU2  H14  C19  C18  120.08  3.000
 AU2  H14  C19  C20  120.04  3.000
 AU2  C18  C19  C20  119.89  3.000
 AU2  H15  C18  C17  119.77  3.000
 AU2  H15  C18  C19  120.16  3.000
 AU2  C17  C18  C19  120.07  3.000
 AU2  H16  C17  C18  120.09  3.000
 AU2  H16  C17  C16  119.79  3.000
 AU2  C18  C17  C16  120.13  3.000
 AU2  CL   C    C15  119.25  3.000
 AU2  CL   C    C1   118.41  3.000
 AU2  C15  C    C1   122.33  3.000
 AU2  H17  C13  C14  120.13  3.000
 AU2  H17  C13  C2   120.40  3.000
 AU2  C14  C13  C2   119.47  3.000
 AU2  H19  N    H18  105.59  3.000
 AU2  H19  N    C4   109.39  3.000
 AU2  H18  N    C4   109.65  3.000
 AU2  H19  N    C3   109.32  3.000
 AU2  H18  N    C3   109.17  3.000
 AU2  C4   N    C3   113.42  3.000
 AU2  C11  C12  N2   130.24  3.000
 AU2  N2   C12  C7   109.92  3.000
 AU2  C11  C12  C7   119.84  3.000
 AU2  H20  C11  C10  121.27  3.000
 AU2  H20  C11  C12  120.82  3.000
 AU2  C10  C11  C12  117.91  3.000
 AU2  H21  C10  C11  119.51  3.000
 AU2  H21  C10  C9   119.06  3.000
 AU2  C11  C10  C9   121.43  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
 AU2  CONST_01  C14  C13  C2   C1     0.00   0.0  0
 AU2  CONST_02  C14  C15  C    C1     0.00   0.0  0
 AU2  CONST_03  C16  C15  C    C1   180.00   0.0  0
 AU2  CONST_04  C15  C14  C13  C2     0.00   0.0  0
 AU2  CONST_05  C15  C    C1   C2     0.00   0.0  0
 AU2  CONST_06  C11  C12  N2   C6   180.00   0.0  0
 AU2  CONST_07  C7   C12  N2   C6     0.00   0.0  0
 AU2  CONST_08  C12  C7   N1   C6     0.00   0.0  0
 AU2  CONST_09  C8   C7   N1   C6   180.00   0.0  0
 AU2  CONST_10  C10  C11  C12  C7     0.00   0.0  0
 AU2  CONST_11  C10  C9   C8   C7     0.00   0.0  0
 AU2  CONST_12  N2   C6   N1   C7     0.00   0.0  0
 AU2  CONST_13  C12  N2   C6   N1     0.00   0.0  0
 AU2  CONST_14  C11  C12  C7   N1   180.00   0.0  0
 AU2  CONST_15  N2   C12  C7   N1     0.00   0.0  0
 AU2  CONST_16  C9   C8   C7   N1   180.00   0.0  0
 AU2  CONST_17  C10  C11  C12  N2   180.00   0.0  0
 AU2  CONST_18  C8   C7   C12  N2   180.00   0.0  0
 AU2  CONST_19  C12  C11  C10  C9     0.00   0.0  0
 AU2  CONST_20  C12  C7   C8   C9     0.00   0.0  0
 AU2  CONST_21  C11  C10  C9   C8     0.00   0.0  0
 AU2  CONST_22  C11  C12  C7   C8     0.00   0.0  0
 AU2  CONST_25  C18  C17  C16  C15  180.00   0.0  0
 AU2  CONST_26  C20  C21  C16  C15  180.00   0.0  0
 AU2  CONST_27  C19  C18  C17  C16    0.00   0.0  0
 AU2  CONST_28  C13  C14  C15  C16  180.00   0.0  0
 AU2  CONST_29  C19  C20  C21  C16    0.00   0.0  0
 AU2  CONST_30  C18  C17  C16  C21    0.00   0.0  0
 AU2  CONST_32  C18  C19  C20  C21    0.00   0.0  0
 AU2  CONST_33  C17  C18  C19  C20    0.00   0.0  0
 AU2  CONST_34  C17  C16  C21  C20    0.00   0.0  0
 AU2  CONST_36  C13  C14  C15  C      0.00   0.0  0
 AU2  CONST_37  C13  C2   C1   C      0.00   0.0  0
 AU2  CONST_38  CL1  C14  C13  C2   180.00   0.0  0
 AU2  CONST_39  CL   C    C1   C2   180.00   0.0  0
 AU2  CONST_40  C14  C13  C2   C3   180.00   0.0  0
 AU2  CONST_41  C    C1   C2   C3   180.00   0.0  0
 AU2  CONST_42  C12  N2   C6   C5   180.00   0.0  0
 AU2  CONST_43  C7   N1   C6   C5   180.00   0.0  0
 AU2  CONST_44  C    C15  C14  CL1  180.00   0.0  0
 AU2  CONST_45  C16  C15  C14  CL1    0.00   0.0  0
 AU2  CONST_46  CL   C    C15  C14  180.00   0.0  0
 AU2  CONST_47  CL   C    C15  C16    0.00   0.0  0
 AU2  CONST_48  H17  C13  C2   C1   180.00   0.0  0
 AU2  CONST_49  H20  C11  C12  C7   180.00   0.0  0
 AU2  CONST_50  H10  C9   C8   C7   180.00   0.0  0
 AU2  CONST_51  H11  C8   C7   N1     0.00   0.0  0
 AU2  CONST_52  H8   N1   C6   N2   180.00   0.0  0
 AU2  CONST_53  H21  C10  C9   C8   180.00   0.0  0
 AU2  CONST_54  H1   C1   C    C15  180.00   0.0  0
 AU2  CONST_55  H16  C17  C16  C15    0.00   0.0  0
 AU2  CONST_56  H12  C21  C16  C15    0.00   0.0  0
 AU2  CONST_57  H15  C18  C17  C16  180.00   0.0  0
 AU2  CONST_58  H13  C20  C21  C16  180.00   0.0  0
 AU2  CONST_59  H14  C19  C20  C21  180.00   0.0  0
 AU2  Var_01    N    C3   C2   C1    89.65  30.0  2
 AU2  Var_02    N2   C6   C5   C4   -39.69  30.0  2
 AU2  Var_03    C4   N    C3   C2   178.42  30.0  1
 AU2  Var_04    N    C4   C5   C6   175.72  30.0  3
 AU2  Var_05    C5   C4   N    C3   177.86  30.0  1

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
 AU2  plan-1  C15  0.020
 AU2  plan-1  C16  0.020
 AU2  plan-1  C21  0.020
 AU2  plan-1  C20  0.020
 AU2  plan-1  C19  0.020
 AU2  plan-1  C18  0.020
 AU2  plan-1  C17  0.020
 AU2  plan-1  H12  0.020
 AU2  plan-1  H13  0.020
 AU2  plan-1  H14  0.020
 AU2  plan-1  H15  0.020
 AU2  plan-1  H16  0.020
 AU2  plan-2  C1   0.020
 AU2  plan-2  C2   0.020
 AU2  plan-2  C3   0.020
 AU2  plan-2  CL1  0.020
 AU2  plan-2  C14  0.020
 AU2  plan-2  C15  0.020
 AU2  plan-2  C16  0.020
 AU2  plan-2  C    0.020
 AU2  plan-2  CL   0.020
 AU2  plan-2  C13  0.020
 AU2  plan-2  H1   0.020
 AU2  plan-2  H17  0.020
 AU2  plan-3  C5   0.020
 AU2  plan-3  C6   0.020
 AU2  plan-3  C7   0.020
 AU2  plan-3  N1   0.020
 AU2  plan-3  N2   0.020
 AU2  plan-3  C9   0.020
 AU2  plan-3  C8   0.020
 AU2  plan-3  C12  0.020
 AU2  plan-3  C11  0.020
 AU2  plan-3  C10  0.020
 AU2  plan-3  H8   0.020
 AU2  plan-3  H10  0.020
 AU2  plan-3  H11  0.020
 AU2  plan-3  H20  0.020
 AU2  plan-3  H21  0.020

