# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:26:56 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)-~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(CNCCc2[nH]c3ccccc3n2)ccc1c4ccccc4
#
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
 AWN  AWN  2-(1~{H}-benzimidazol-2-yl)-~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]ethanamine  ligand  46  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AWN
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
 AWN  C8   C   CR16  0  -0.307   -8.0771   0.8099  -1.0444
 AWN  C5   C   CH2   0  -0.569   -3.1485   0.4574  -0.6610
 AWN  C4   C   CH2   0  -0.247   -2.3199   0.1917   0.5881
 AWN  C2   C   CR6   0   0.069    1.3938   0.2093   1.0626
 AWN  N1   N   NR15  0  -0.705   -5.5522   0.9402  -1.0936
 AWN  C6   C   CR5   0   0.478   -4.6017   0.2168  -0.4463
 AWN  C    C   CR6   0  -0.107    3.2017  -0.4419  -0.3868
 AWN  C15  C   CR6   0   0.139    4.1243   0.3109   0.3418
 AWN  C16  C   CR6   0   0.061    5.5598   0.3991  -0.0036
 AWN  C21  C   CR16  0  -0.284    6.3689  -0.7362  -0.0292
 AWN  C20  C   CR16  0  -0.244    7.7219  -0.6293  -0.3149
 AWN  C19  C   CR16  0  -0.263    8.2843   0.6127  -0.5830
 AWN  C18  C   CR16  0  -0.242    7.4863   1.7480  -0.5590
 AWN  C17  C   CR16  0  -0.292    6.1328   1.6416  -0.2679
 AWN  C14  C   CR16  0  -0.296    3.6335   1.0186   1.4370
 AWN  C13  C   CR16  0  -0.289    2.2947   0.9715   1.7948
 AWN  C1   C   CR16  0  -0.225    1.8619  -0.4934  -0.0435
 AWN  C3   C   CH2   0  -0.319   -0.0608   0.1327   1.4423
 AWN  N    N   NH1   0  -0.599   -0.9132   0.3785   0.2961
 AWN  N2   N   N     0  -0.482   -5.1136  -0.6975   0.3337
 AWN  C12  C   CR56  0   0.133   -6.4764  -0.5754   0.1939
 AWN  C7   C   CR56  0   0.324   -6.7750   0.4585  -0.7096
 AWN  C11  C   CR16  0  -0.339   -7.5124  -1.2935   0.7902
 AWN  C10  C   CR16  0  -0.271   -8.8131  -0.9523   0.4614
 AWN  C9   C   CR16  0  -0.281   -9.0913   0.0841  -0.4421
 AWN  H1   H   HCR6  0   0.265   -8.2913   1.6113  -1.7395
 AWN  H2   H   HCH2  0   0.259   -2.9990   1.4872  -0.9966
 AWN  H3   H   HCH2  0   0.272   -2.7940  -0.1853  -1.4730
 AWN  H4   H   HCH2  0   0.204   -2.6794   0.8305   1.4089
 AWN  H5   H   HCH2  0   0.232   -2.4703  -0.8405   0.9122
 AWN  H6   H   HNR5  0   0.417   -5.3815   1.7002  -1.7333
 AWN  H7   H   HCR6  0   0.255    5.9435  -1.7069   0.1909
 AWN  H8   H   HCR6  0   0.258    8.3401  -1.5176  -0.3250
 AWN  H9   H   HCR6  0   0.258    9.3402   0.6942  -0.8062
 AWN  H10  H   HCR6  0   0.258    7.9151   2.7191  -0.7693
 AWN  H11  H   HCR6  0   0.255    5.5132   2.5299  -0.2560
 AWN  H12  H   HCR6  0   0.261    4.3222   1.6151   2.0221
 AWN  H13  H   HCR6  0   0.257    1.9517   1.5339   2.6546
 AWN  H14  H   HCR6  0   0.269    1.1721  -1.0749  -0.6409
 AWN  H15  H   HCH2  0   0.245   -0.2811  -0.8733   1.8136
 AWN  H16  H   HCH2  0   0.222   -0.2523   0.8170   2.2816
 AWN  H17  H   HNH1  0   0.346   -0.7599   1.3279  -0.0249
 AWN  H20  H   HCR6  0   0.252   -7.3042  -2.0954   1.4871
 AWN  H21  H   HCR6  0   0.251   -9.6352  -1.4961   0.9082
 AWN  H22  H   HCR6  0   0.253  -10.1214   0.3218  -0.6729
 AWN  CL   CL  CL    0  -0.132    3.7099  -1.3148  -1.8001

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
 AWN  CL   C    single    1.737  0.020  1.737
 AWN  C20  C21  aromatic  1.387  0.020  1.387
 AWN  C20  C19  aromatic  1.390  0.020  1.390
 AWN  C21  C16  aromatic  1.394  0.020  1.394
 AWN  C19  C18  aromatic  1.388  0.020  1.388
 AWN  C    C1   aromatic  1.384  0.020  1.384
 AWN  C    C15  aromatic  1.396  0.020  1.396
 AWN  C16  C15  single    1.479  0.020  1.479
 AWN  C16  C17  aromatic  1.394  0.020  1.394
 AWN  C1   C2   aromatic  1.392  0.020  1.392
 AWN  C18  C17  aromatic  1.389  0.020  1.389
 AWN  C15  C14  aromatic  1.393  0.020  1.393
 AWN  C2   C3   single    1.505  0.020  1.505
 AWN  C2   C13  aromatic  1.389  0.020  1.389
 AWN  C14  C13  aromatic  1.387  0.020  1.387
 AWN  N    C3   single    1.449  0.020  1.449
 AWN  N    C4   single    1.449  0.020  1.449
 AWN  C4   C5   single    1.522  0.020  1.522
 AWN  C5   C6   single    1.489  0.020  1.489
 AWN  C6   N1   aromatic  1.359  0.020  1.359
 AWN  C6   N2   aromatic  1.306  0.020  1.306
 AWN  N1   C7   aromatic  1.369  0.020  1.369
 AWN  N2   C12  aromatic  1.375  0.020  1.375
 AWN  C7   C12  aromatic  1.405  0.020  1.405
 AWN  C7   C8   aromatic  1.390  0.020  1.390
 AWN  C12  C11  aromatic  1.394  0.020  1.394
 AWN  C8   C9   aromatic  1.385  0.020  1.385
 AWN  C11  C10  aromatic  1.384  0.020  1.384
 AWN  C9   C10  aromatic  1.403  0.020  1.403
 AWN  C8   H1   single    0.930  0.020  1.080
 AWN  C5   H2   single    0.970  0.020  1.090
 AWN  C5   H3   single    0.970  0.020  1.090
 AWN  C4   H4   single    0.970  0.020  1.090
 AWN  C4   H5   single    0.970  0.020  1.090
 AWN  N1   H6   single    0.860  0.020  1.020
 AWN  C21  H7   single    0.930  0.020  1.080
 AWN  C20  H8   single    0.930  0.020  1.080
 AWN  C19  H9   single    0.930  0.020  1.080
 AWN  C18  H10  single    0.930  0.020  1.080
 AWN  C17  H11  single    0.930  0.020  1.080
 AWN  C14  H12  single    0.930  0.020  1.080
 AWN  C13  H13  single    0.930  0.020  1.080
 AWN  C1   H14  single    0.930  0.020  1.080
 AWN  C3   H15  single    0.970  0.020  1.090
 AWN  C3   H16  single    0.970  0.020  1.090
 AWN  N    H17  single    0.890  0.020  1.040
 AWN  C11  H20  single    0.930  0.020  1.080
 AWN  C10  H21  single    0.930  0.020  1.080
 AWN  C9   H22  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
 AWN  H1   C8   C9   121.50  3.000
 AWN  H1   C8   C7   121.83  3.000
 AWN  C9   C8   C7   116.67  3.000
 AWN  H3   C5   H2   106.32  3.000
 AWN  H3   C5   C6   109.16  3.000
 AWN  H2   C5   C6   109.26  3.000
 AWN  H3   C5   C4   109.27  3.000
 AWN  H2   C5   C4   109.99  3.000
 AWN  C6   C5   C4   112.63  3.000
 AWN  H5   C4   H4   106.40  3.000
 AWN  H5   C4   N    108.38  3.000
 AWN  H4   C4   N    113.12  3.000
 AWN  H5   C4   C5   109.48  3.000
 AWN  H4   C4   C5   109.45  3.000
 AWN  N    C4   C5   109.91  3.000
 AWN  C3   C2   C1   119.99  3.000
 AWN  C3   C2   C13  121.46  3.000
 AWN  C1   C2   C13  118.55  3.000
 AWN  H6   N1   C7   126.47  3.000
 AWN  H6   N1   C6   125.83  3.000
 AWN  C7   N1   C6   107.69  3.000
 AWN  N2   C6   N1   112.52  3.000
 AWN  N2   C6   C5   125.58  3.000
 AWN  N1   C6   C5   121.89  3.000
 AWN  C1   C    C15  122.03  3.000
 AWN  C15  C    CL   120.15  3.000
 AWN  C1   C    CL   117.79  3.000
 AWN  C14  C15  C16  119.68  3.000
 AWN  C14  C15  C    116.84  3.000
 AWN  C16  C15  C    123.48  3.000
 AWN  C17  C16  C21  118.94  3.000
 AWN  C17  C16  C15  119.77  3.000
 AWN  C21  C16  C15  121.26  3.000
 AWN  H7   C21  C20  119.63  3.000
 AWN  H7   C21  C16  119.89  3.000
 AWN  C20  C21  C16  120.47  3.000
 AWN  H8   C20  C19  120.04  3.000
 AWN  H8   C20  C21  119.73  3.000
 AWN  C19  C20  C21  120.23  3.000
 AWN  H9   C19  C18  120.19  3.000
 AWN  H9   C19  C20  120.13  3.000
 AWN  C18  C19  C20  119.67  3.000
 AWN  H10  C18  C17  119.72  3.000
 AWN  H10  C18  C19  120.19  3.000
 AWN  C17  C18  C19  120.10  3.000
 AWN  H11  C17  C18  119.81  3.000
 AWN  H11  C17  C16  119.60  3.000
 AWN  C18  C17  C16  120.59  3.000
 AWN  H12  C14  C13  119.56  3.000
 AWN  H12  C14  C15  118.72  3.000
 AWN  C13  C14  C15  121.71  3.000
 AWN  H13  C13  C14  119.54  3.000
 AWN  H13  C13  C2   119.87  3.000
 AWN  C14  C13  C2   120.60  3.000
 AWN  H14  C1   C    120.01  3.000
 AWN  H14  C1   C2   119.71  3.000
 AWN  C    C1   C2   120.27  3.000
 AWN  H16  C3   H15  106.13  3.000
 AWN  H16  C3   N    113.31  3.000
 AWN  H15  C3   N    107.80  3.000
 AWN  H16  C3   C2   109.22  3.000
 AWN  H15  C3   C2   109.07  3.000
 AWN  N    C3   C2   111.12  3.000
 AWN  H17  N    C3   108.68  3.000
 AWN  H17  N    C4   109.35  3.000
 AWN  C3   N    C4   112.94  3.000
 AWN  C12  N2   C6   105.39  3.000
 AWN  C11  C12  C7   119.74  3.000
 AWN  C11  C12  N2   130.31  3.000
 AWN  C7   C12  N2   109.95  3.000
 AWN  C12  C7   N1   104.44  3.000
 AWN  C12  C7   C8   122.69  3.000
 AWN  N1   C7   C8   132.87  3.000
 AWN  H20  C11  C10  121.07  3.000
 AWN  H20  C11  C12  120.93  3.000
 AWN  C10  C11  C12  118.00  3.000
 AWN  H21  C10  C9   119.11  3.000
 AWN  H21  C10  C11  119.46  3.000
 AWN  C9   C10  C11  121.43  3.000
 AWN  H22  C9   C10  119.24  3.000
 AWN  H22  C9   C8   119.29  3.000
 AWN  C10  C9   C8   121.47  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
 AWN  CONST_01  C6   N1   C7   C8    180.00   0.0  0
 AWN  CONST_02  N2   C12  C7   C8    180.00   0.0  0
 AWN  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 AWN  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 AWN  CONST_05  C15  C    C1   C2      0.00   0.0  0
 AWN  CONST_06  C15  C14  C13  C2      0.00   0.0  0
 AWN  CONST_07  C12  N2   C6   N1      0.00   0.0  0
 AWN  CONST_08  N2   C12  C7   N1      0.00   0.0  0
 AWN  CONST_09  C11  C12  C7   N1    180.00   0.0  0
 AWN  CONST_10  C9   C8   C7   N1    180.00   0.0  0
 AWN  CONST_11  C12  C7   N1   C6      0.00   0.0  0
 AWN  CONST_12  C7   C12  N2   C6      0.00   0.0  0
 AWN  CONST_13  C11  C12  N2   C6    180.00   0.0  0
 AWN  CONST_14  C13  C2   C1   C       0.00   0.0  0
 AWN  CONST_17  C13  C14  C15  C       0.00   0.0  0
 AWN  CONST_18  C20  C21  C16  C15   180.00   0.0  0
 AWN  CONST_19  C18  C17  C16  C15   180.00   0.0  0
 AWN  CONST_20  C19  C20  C21  C16     0.00   0.0  0
 AWN  CONST_21  C1   C    C15  C16   180.00   0.0  0
 AWN  CONST_22  C13  C14  C15  C16   180.00   0.0  0
 AWN  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 AWN  CONST_24  C18  C19  C20  C21     0.00   0.0  0
 AWN  CONST_26  C18  C17  C16  C21     0.00   0.0  0
 AWN  CONST_27  C17  C16  C21  C20     0.00   0.0  0
 AWN  CONST_28  C17  C18  C19  C20     0.00   0.0  0
 AWN  CONST_30  C1   C    C15  C14     0.00   0.0  0
 AWN  CONST_31  C1   C2   C13  C14     0.00   0.0  0
 AWN  CONST_32  C7   N1   C6   N2      0.00   0.0  0
 AWN  CONST_33  C10  C11  C12  N2    180.00   0.0  0
 AWN  CONST_34  C9   C8   C7   C12     0.00   0.0  0
 AWN  CONST_35  C9   C10  C11  C12     0.00   0.0  0
 AWN  CONST_36  C10  C11  C12  C7      0.00   0.0  0
 AWN  CONST_37  C10  C9   C8   C7      0.00   0.0  0
 AWN  CONST_38  C7   N1   C6   C5    180.00   0.0  0
 AWN  CONST_39  C12  N2   C6   C5    180.00   0.0  0
 AWN  CONST_40  CL   C    C1   C2    180.00   0.0  0
 AWN  CONST_41  C16  C15  C    CL      0.00   0.0  0
 AWN  CONST_42  C14  C15  C    CL    180.00   0.0  0
 AWN  CONST_43  C3   C2   C1   C     180.00   0.0  0
 AWN  CONST_44  C3   C2   C13  C14   180.00   0.0  0
 AWN  CONST_45  H6   N1   C7   C8      0.00   0.0  0
 AWN  CONST_46  H21  C10  C9   C8    180.00   0.0  0
 AWN  CONST_47  H12  C14  C13  C2    180.00   0.0  0
 AWN  CONST_48  H1   C8   C7   N1      0.00   0.0  0
 AWN  CONST_49  H14  C1   C    C15   180.00   0.0  0
 AWN  CONST_50  H7   C21  C16  C15     0.00   0.0  0
 AWN  CONST_51  H11  C17  C16  C15     0.00   0.0  0
 AWN  CONST_52  H13  C13  C14  C15   180.00   0.0  0
 AWN  CONST_53  H8   C20  C21  C16   180.00   0.0  0
 AWN  CONST_54  H10  C18  C17  C16   180.00   0.0  0
 AWN  CONST_55  H9   C19  C20  C21   180.00   0.0  0
 AWN  CONST_56  H20  C11  C12  N2      0.00   0.0  0
 AWN  CONST_57  H22  C9   C8   C7    180.00   0.0  0
 AWN  Var_01    N1   C6   C5   C4    147.56  30.0  2
 AWN  Var_02    N    C3   C2   C13   130.55  30.0  2
 AWN  Var_03    C2   C3   N    C4    174.59  30.0  3
 AWN  Var_04    N    C4   C5   C6    177.16  30.0  1
 AWN  Var_05    C3   N    C4   C5   -179.62  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
 AWN  plan-1  C2   0.020
 AWN  plan-1  C    0.020
 AWN  plan-1  C15  0.020
 AWN  plan-1  C16  0.020
 AWN  plan-1  C14  0.020
 AWN  plan-1  C13  0.020
 AWN  plan-1  C1   0.020
 AWN  plan-1  C3   0.020
 AWN  plan-1  H12  0.020
 AWN  plan-1  H13  0.020
 AWN  plan-1  H14  0.020
 AWN  plan-1  CL   0.020
 AWN  plan-2  C15  0.020
 AWN  plan-2  C16  0.020
 AWN  plan-2  C21  0.020
 AWN  plan-2  C20  0.020
 AWN  plan-2  C19  0.020
 AWN  plan-2  C18  0.020
 AWN  plan-2  C17  0.020
 AWN  plan-2  H7   0.020
 AWN  plan-2  H8   0.020
 AWN  plan-2  H9   0.020
 AWN  plan-2  H10  0.020
 AWN  plan-2  H11  0.020
 AWN  plan-3  C8   0.020
 AWN  plan-3  C5   0.020
 AWN  plan-3  N1   0.020
 AWN  plan-3  C6   0.020
 AWN  plan-3  N2   0.020
 AWN  plan-3  C12  0.020
 AWN  plan-3  C7   0.020
 AWN  plan-3  C11  0.020
 AWN  plan-3  C10  0.020
 AWN  plan-3  C9   0.020
 AWN  plan-3  H1   0.020
 AWN  plan-3  H6   0.020
 AWN  plan-3  H20  0.020
 AWN  plan-3  H21  0.020
 AWN  plan-3  H22  0.020

