# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:04:11 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(7-methyl-1~{H}-benzimidazol-2-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4c(C)cccc4n3)cc2Cl
#
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
 AWK  AWK  ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(7-methyl-1~{H}-benzimidazol-2-yl)ethanamine  ligand  55  29  .  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_AWK
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
 AWK  C1   C   CH2   0  -0.518  -6.1891  -1.5187  -1.3071
 AWK  N1   N   NR15  0  -0.709   5.7117   0.6703   0.8779
 AWK  C2   C   CR6   0   0.110  -6.4585  -0.6001  -0.1457
 AWK  N2   N   N     0  -0.484   5.1485  -0.7750  -0.7036
 AWK  C3   C   CR6   0   0.022  -5.4470   0.1629   0.4500
 AWK  C4   C   CR16  0  -0.271  -5.7360   0.9524   1.5606
 AWK  C5   C   CR16  0  -0.262  -7.0175   0.9996   2.0893
 AWK  C6   C   CR16  0  -0.248  -8.0253   0.2480   1.5026
 AWK  C24  C   CR6   0  -0.097  -3.6381   0.8206  -1.1841
 AWK  C8   C   CR6   0   0.103  -4.0511   0.1290  -0.0513
 AWK  C7   C   CR16  0  -0.303  -7.7397  -0.5423   0.3987
 AWK  C    C   CH3   0  -0.654  -5.7195  -2.8984  -0.8499
 AWK  C23  C   CR16  0  -0.261  -2.3222   0.7930  -1.6244
 AWK  C11  C   CR6   0   0.077  -1.3686   0.0616  -0.9298
 AWK  C10  C   CR16  0  -0.267  -1.7599  -0.6261   0.2163
 AWK  C9   C   CR16  0  -0.287  -3.0766  -0.5910   0.6406
 AWK  C12  C   CH2   0  -0.320   0.0569   0.0083  -1.4114
 AWK  N    N   NH1   0  -0.599   0.9829   0.2840  -0.3321
 AWK  C13  C   CH2   0  -0.247   2.3678   0.0863  -0.7091
 AWK  C14  C   CH2   0  -0.567   3.2738   0.3477   0.4852
 AWK  C15  C   CR5   0   0.475   4.7061   0.0693   0.1898
 AWK  C22  C   CR56  0   0.137   6.5195  -0.7336  -0.6009
 AWK  C16  C   CR56  0   0.302   6.8971   0.1758   0.3981
 AWK  C21  C   CR16  0  -0.354   7.4989  -1.4286  -1.3113
 AWK  C20  C   CR16  0  -0.260   8.8198  -1.1821  -0.9859
 AWK  C19  C   CR16  0  -0.341   9.1713  -0.2676   0.0193
 AWK  C17  C   CR6   0   0.052   8.2221   0.4405   0.7422
 AWK  C18  C   CH3   0  -0.734   8.5754   1.4213   1.8174
 AWK  H1   H   HCH2  0   0.243  -7.1045  -1.6259  -1.8934
 AWK  H2   H   HCH2  0   0.239  -5.4463  -1.0852  -1.9777
 AWK  H3   H   HNR5  0   0.417   5.5973   1.3569   1.6066
 AWK  H5   H   HCR6  0   0.249  -4.9468   1.5412   2.0118
 AWK  H6   H   HCR6  0   0.255  -7.2246   1.6197   2.9517
 AWK  H7   H   HCR6  0   0.254  -9.0310   0.2759   1.9016
 AWK  H8   H   HCR6  0   0.247  -8.5282  -1.1327  -0.0538
 AWK  H9   H   HCH3  0   0.227  -4.7897  -2.8337  -0.2833
 AWK  H10  H   HCH3  0   0.226  -6.4660  -3.3761  -0.2142
 AWK  H11  H   HCH3  0   0.232  -5.5416  -3.5505  -1.7056
 AWK  H12  H   HCR6  0   0.272  -2.0386   1.3489  -2.5094
 AWK  H13  H   HCR6  0   0.253  -1.0291  -1.1926   0.7786
 AWK  H14  H   HCR6  0   0.258  -3.3684  -1.1360   1.5297
 AWK  H15  H   HCH2  0   0.245   0.2691  -0.9997  -1.7823
 AWK  H16  H   HCH2  0   0.220   0.1759   0.6813  -2.2732
 AWK  H17  H   HNH1  0   0.346   0.8503   1.2398  -0.0219
 AWK  H19  H   HCH2  0   0.231   2.4905  -0.9486  -1.0358
 AWK  H20  H   HCH2  0   0.203   2.6820   0.7171  -1.5541
 AWK  H21  H   HCH2  0   0.259   3.1684   1.3839   0.8185
 AWK  H22  H   HCH2  0   0.271   2.9515  -0.2777   1.3240
 AWK  H23  H   HCR6  0   0.249   7.2324  -2.1344  -2.0875
 AWK  H24  H   HCR6  0   0.248   9.6059  -1.7049  -1.5154
 AWK  H25  H   HCR6  0   0.245  10.2202  -0.1084   0.2397
 AWK  H26  H   HCH3  0   0.247   8.1496   1.1295   2.7794
 AWK  H27  H   HCH3  0   0.252   9.6545   1.4963   1.9414
 AWK  H28  H   HCH3  0   0.247   8.1967   2.4192   1.5881
 AWK  CL   CL  CL    0  -0.128  -4.7846   1.7676  -2.0787

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
 AWK  C5   C6   aromatic  1.387  0.020  1.387
 AWK  C5   C4   aromatic  1.387  0.020  1.387
 AWK  C6   C7   aromatic  1.387  0.020  1.387
 AWK  C4   C3   aromatic  1.393  0.020  1.393
 AWK  C7   C2   aromatic  1.393  0.020  1.393
 AWK  C9   C10  aromatic  1.384  0.020  1.384
 AWK  C9   C8   aromatic  1.395  0.020  1.395
 AWK  C3   C2   aromatic  1.400  0.020  1.400
 AWK  C3   C8   single    1.484  0.020  1.484
 AWK  C2   C1   single    1.505  0.020  1.505
 AWK  C10  C11  aromatic  1.393  0.020  1.393
 AWK  C8   C24  aromatic  1.390  0.020  1.390
 AWK  C    C1   single    1.527  0.020  1.527
 AWK  C11  C12  single    1.506  0.020  1.506
 AWK  C11  C23  aromatic  1.388  0.020  1.388
 AWK  C24  C23  aromatic  1.388  0.020  1.388
 AWK  C24  CL   single    1.735  0.020  1.735
 AWK  C12  N    single    1.449  0.020  1.449
 AWK  N    C13  single    1.449  0.020  1.449
 AWK  C13  C14  single    1.522  0.020  1.522
 AWK  C14  C15  single    1.489  0.020  1.489
 AWK  C15  N2   aromatic  1.306  0.020  1.306
 AWK  C15  N1   aromatic  1.359  0.020  1.359
 AWK  N2   C22  aromatic  1.375  0.020  1.375
 AWK  N1   C16  aromatic  1.371  0.020  1.371
 AWK  C22  C16  aromatic  1.403  0.020  1.403
 AWK  C22  C21  aromatic  1.395  0.020  1.395
 AWK  C16  C17  aromatic  1.394  0.020  1.394
 AWK  C21  C20  aromatic  1.383  0.020  1.383
 AWK  C17  C18  single    1.498  0.020  1.498
 AWK  C17  C19  aromatic  1.387  0.020  1.387
 AWK  C20  C19  aromatic  1.404  0.020  1.404
 AWK  C1   H1   single    0.970  0.020  1.090
 AWK  C1   H2   single    0.970  0.020  1.090
 AWK  N1   H3   single    0.860  0.020  1.020
 AWK  C4   H5   single    0.930  0.020  1.080
 AWK  C5   H6   single    0.930  0.020  1.080
 AWK  C6   H7   single    0.930  0.020  1.080
 AWK  C7   H8   single    0.930  0.020  1.080
 AWK  C    H9   single    0.970  0.020  1.090
 AWK  C    H10  single    0.970  0.020  1.090
 AWK  C    H11  single    0.970  0.020  1.090
 AWK  C23  H12  single    0.930  0.020  1.080
 AWK  C10  H13  single    0.930  0.020  1.080
 AWK  C9   H14  single    0.930  0.020  1.080
 AWK  C12  H15  single    0.970  0.020  1.090
 AWK  C12  H16  single    0.970  0.020  1.090
 AWK  N    H17  single    0.890  0.020  1.040
 AWK  C13  H19  single    0.970  0.020  1.090
 AWK  C13  H20  single    0.970  0.020  1.090
 AWK  C14  H21  single    0.970  0.020  1.090
 AWK  C14  H22  single    0.970  0.020  1.090
 AWK  C21  H23  single    0.930  0.020  1.080
 AWK  C20  H24  single    0.930  0.020  1.080
 AWK  C19  H25  single    0.930  0.020  1.080
 AWK  C18  H26  single    0.970  0.020  1.090
 AWK  C18  H27  single    0.970  0.020  1.090
 AWK  C18  H28  single    0.970  0.020  1.090

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
 AWK  H2   C1   H1   106.24  3.000
 AWK  H2   C1   C    109.49  3.000
 AWK  H1   C1   C    109.25  3.000
 AWK  H2   C1   C2   110.72  3.000
 AWK  H1   C1   C2   108.91  3.000
 AWK  C    C1   C2   112.05  3.000
 AWK  H3   N1   C16  126.65  3.000
 AWK  H3   N1   C15  125.70  3.000
 AWK  C16  N1   C15  107.65  3.000
 AWK  C7   C2   C3   118.39  3.000
 AWK  C3   C2   C1   122.11  3.000
 AWK  C7   C2   C1   119.43  3.000
 AWK  C22  N2   C15  105.49  3.000
 AWK  C8   C3   C4   118.53  3.000
 AWK  C8   C3   C2   121.57  3.000
 AWK  C4   C3   C2   119.88  3.000
 AWK  H5   C4   C5   119.73  3.000
 AWK  H5   C4   C3   119.28  3.000
 AWK  C5   C4   C3   120.99  3.000
 AWK  H6   C5   C6   120.57  3.000
 AWK  H6   C5   C4   120.00  3.000
 AWK  C6   C5   C4   119.43  3.000
 AWK  H7   C6   C7   119.96  3.000
 AWK  H7   C6   C5   120.33  3.000
 AWK  C7   C6   C5   119.71  3.000
 AWK  C23  C24  C8   122.03  3.000
 AWK  C23  C24  CL   118.27  3.000
 AWK  C8   C24  CL   119.69  3.000
 AWK  C9   C8   C24  116.96  3.000
 AWK  C24  C8   C3   122.93  3.000
 AWK  C9   C8   C3   120.09  3.000
 AWK  H8   C7   C6   119.52  3.000
 AWK  H8   C7   C2   118.90  3.000
 AWK  C6   C7   C2   121.59  3.000
 AWK  H11  C    H10  107.89  3.000
 AWK  H11  C    H9   107.70  3.000
 AWK  H10  C    H9   107.86  3.000
 AWK  H11  C    C1   110.82  3.000
 AWK  H10  C    C1   111.08  3.000
 AWK  H9   C    C1   111.35  3.000
 AWK  H12  C23  C11  119.97  3.000
 AWK  H12  C23  C24  119.82  3.000
 AWK  C11  C23  C24  120.21  3.000
 AWK  C12  C11  C10  120.79  3.000
 AWK  C12  C11  C23  120.60  3.000
 AWK  C10  C11  C23  118.61  3.000
 AWK  H13  C10  C9   119.77  3.000
 AWK  H13  C10  C11  119.76  3.000
 AWK  C9   C10  C11  120.48  3.000
 AWK  H14  C9   C10  119.69  3.000
 AWK  H14  C9   C8   118.60  3.000
 AWK  C10  C9   C8   121.71  3.000
 AWK  H16  C12  H15  106.07  3.000
 AWK  H16  C12  N    113.46  3.000
 AWK  H15  C12  N    107.68  3.000
 AWK  H16  C12  C11  109.36  3.000
 AWK  H15  C12  C11  108.93  3.000
 AWK  N    C12  C11  111.11  3.000
 AWK  H17  N    C13  109.47  3.000
 AWK  H17  N    C12  108.90  3.000
 AWK  C13  N    C12  113.03  3.000
 AWK  H20  C13  H19  106.34  3.000
 AWK  H20  C13  C14  109.53  3.000
 AWK  H19  C13  C14  109.30  3.000
 AWK  H20  C13  N    113.24  3.000
 AWK  H19  C13  N    108.33  3.000
 AWK  C14  C13  N    109.97  3.000
 AWK  H22  C14  H21  106.22  3.000
 AWK  H22  C14  C15  109.18  3.000
 AWK  H21  C14  C15  109.30  3.000
 AWK  H22  C14  C13  109.14  3.000
 AWK  H21  C14  C13  110.15  3.000
 AWK  C15  C14  C13  112.64  3.000
 AWK  C14  C15  N2   125.62  3.000
 AWK  N2   C15  N1   112.43  3.000
 AWK  C14  C15  N1   121.93  3.000
 AWK  C21  C22  C16  119.77  3.000
 AWK  C21  C22  N2   130.29  3.000
 AWK  C16  C22  N2   109.94  3.000
 AWK  C17  C16  C22  123.68  3.000
 AWK  C17  C16  N1   131.82  3.000
 AWK  C22  C16  N1   104.49  3.000
 AWK  H23  C21  C20  121.35  3.000
 AWK  H23  C21  C22  121.13  3.000
 AWK  C20  C21  C22  117.52  3.000
 AWK  H24  C20  C19  118.89  3.000
 AWK  H24  C20  C21  119.51  3.000
 AWK  C19  C20  C21  121.59  3.000
 AWK  H25  C19  C17  118.77  3.000
 AWK  H25  C19  C20  118.93  3.000
 AWK  C17  C19  C20  122.30  3.000
 AWK  C18  C17  C19  123.15  3.000
 AWK  C19  C17  C16  115.13  3.000
 AWK  C18  C17  C16  121.71  3.000
 AWK  H28  C18  H27  107.74  3.000
 AWK  H28  C18  H26  107.10  3.000
 AWK  H27  C18  H26  107.73  3.000
 AWK  H28  C18  C17  111.47  3.000
 AWK  H27  C18  C17  111.14  3.000
 AWK  H26  C18  C17  111.44  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
 AWK  CONST_01  C22  N2   C15  N1      0.00   0.0  0
 AWK  CONST_02  N2   C22  C16  N1      0.00   0.0  0
 AWK  CONST_03  C21  C22  C16  N1    180.00   0.0  0
 AWK  CONST_04  C19  C17  C16  N1    180.00   0.0  0
 AWK  CONST_05  C5   C6   C7   C2      0.00   0.0  0
 AWK  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 AWK  CONST_09  C16  N1   C15  N2      0.00   0.0  0
 AWK  CONST_10  C17  C16  C22  N2    180.00   0.0  0
 AWK  CONST_11  C20  C21  C22  N2    180.00   0.0  0
 AWK  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 AWK  CONST_13  C6   C7   C2   C3      0.00   0.0  0
 AWK  CONST_14  C10  C9   C8   C3    180.00   0.0  0
 AWK  CONST_15  C23  C24  C8   C3    180.00   0.0  0
 AWK  CONST_16  C7   C6   C5   C4      0.00   0.0  0
 AWK  CONST_17  C7   C2   C3   C4      0.00   0.0  0
 AWK  CONST_20  C8   C3   C4   C5    180.00   0.0  0
 AWK  CONST_21  C10  C9   C8   C24     0.00   0.0  0
 AWK  CONST_22  C10  C11  C23  C24     0.00   0.0  0
 AWK  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 AWK  CONST_24  C7   C2   C3   C8    180.00   0.0  0
 AWK  CONST_25  C11  C23  C24  C8      0.00   0.0  0
 AWK  CONST_26  C9   C10  C11  C23     0.00   0.0  0
 AWK  CONST_27  C9   C8   C24  C23     0.00   0.0  0
 AWK  CONST_28  C16  C22  N2   C15     0.00   0.0  0
 AWK  CONST_29  C21  C22  N2   C15   180.00   0.0  0
 AWK  CONST_30  C22  C16  N1   C15     0.00   0.0  0
 AWK  CONST_31  C17  C16  N1   C15   180.00   0.0  0
 AWK  CONST_32  C19  C17  C16  C22     0.00   0.0  0
 AWK  CONST_33  C19  C20  C21  C22     0.00   0.0  0
 AWK  CONST_34  C20  C21  C22  C16     0.00   0.0  0
 AWK  CONST_35  C20  C19  C17  C16     0.00   0.0  0
 AWK  CONST_36  C17  C16  C22  C21     0.00   0.0  0
 AWK  CONST_37  C17  C19  C20  C21     0.00   0.0  0
 AWK  CONST_38  C6   C7   C2   C1    180.00   0.0  0
 AWK  CONST_39  C4   C3   C2   C1    180.00   0.0  0
 AWK  CONST_40  C8   C3   C2   C1      0.00   0.0  0
 AWK  CONST_41  C18  C17  C16  N1      0.00   0.0  0
 AWK  CONST_42  CL   C24  C8   C3      0.00   0.0  0
 AWK  CONST_43  C9   C8   C24  CL    180.00   0.0  0
 AWK  CONST_44  C11  C23  C24  CL    180.00   0.0  0
 AWK  CONST_45  C12  C11  C23  C24   180.00   0.0  0
 AWK  CONST_46  C12  C11  C10  C9    180.00   0.0  0
 AWK  CONST_47  C22  N2   C15  C14   180.00   0.0  0
 AWK  CONST_48  C16  N1   C15  C14   180.00   0.0  0
 AWK  CONST_49  C18  C17  C16  C22   180.00   0.0  0
 AWK  CONST_50  C18  C17  C19  C20   180.00   0.0  0
 AWK  CONST_51  H7   C6   C7   C2    180.00   0.0  0
 AWK  CONST_52  H5   C4   C3   C2    180.00   0.0  0
 AWK  CONST_53  H3   N1   C15  N2    180.00   0.0  0
 AWK  CONST_54  H23  C21  C22  N2      0.00   0.0  0
 AWK  CONST_55  H6   C5   C4   C3    180.00   0.0  0
 AWK  CONST_56  H8   C7   C2   C3    180.00   0.0  0
 AWK  CONST_57  H14  C9   C8   C3      0.00   0.0  0
 AWK  CONST_58  H13  C10  C9   C8    180.00   0.0  0
 AWK  CONST_59  H12  C23  C24  C8    180.00   0.0  0
 AWK  CONST_60  H24  C20  C21  C22   180.00   0.0  0
 AWK  CONST_61  H25  C19  C17  C16   180.00   0.0  0
 AWK  Var_01    C13  C14  C15  N1    155.11  30.0  1
 AWK  Var_02    C    C1   C2   C3     85.85  30.0  2
 AWK  Var_03    N    C12  C11  C23   131.15  30.0  2
 AWK  Var_04    H26  C18  C17  C16    59.98  30.0  2
 AWK  Var_05    C13  N    C12  C11   173.02  30.0  3
 AWK  Var_06    C15  C14  C13  N     176.00  30.0  3
 AWK  Var_07    H9   C    C1   C2    -60.80  30.0  3
 AWK  Var_08    C14  C13  N    C12  -178.06  30.0  3

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
 AWK  plan-1  C1   0.020
 AWK  plan-1  C2   0.020
 AWK  plan-1  C3   0.020
 AWK  plan-1  C4   0.020
 AWK  plan-1  C5   0.020
 AWK  plan-1  C6   0.020
 AWK  plan-1  C8   0.020
 AWK  plan-1  C7   0.020
 AWK  plan-1  H5   0.020
 AWK  plan-1  H6   0.020
 AWK  plan-1  H7   0.020
 AWK  plan-1  H8   0.020
 AWK  plan-2  C3   0.020
 AWK  plan-2  C24  0.020
 AWK  plan-2  C8   0.020
 AWK  plan-2  C23  0.020
 AWK  plan-2  C11  0.020
 AWK  plan-2  C10  0.020
 AWK  plan-2  C9   0.020
 AWK  plan-2  C12  0.020
 AWK  plan-2  H12  0.020
 AWK  plan-2  H13  0.020
 AWK  plan-2  H14  0.020
 AWK  plan-2  CL   0.020
 AWK  plan-3  N1   0.020
 AWK  plan-3  N2   0.020
 AWK  plan-3  C14  0.020
 AWK  plan-3  C15  0.020
 AWK  plan-3  C22  0.020
 AWK  plan-3  C16  0.020
 AWK  plan-3  C21  0.020
 AWK  plan-3  C20  0.020
 AWK  plan-3  C19  0.020
 AWK  plan-3  C17  0.020
 AWK  plan-3  C18  0.020
 AWK  plan-3  H3   0.020
 AWK  plan-3  H23  0.020
 AWK  plan-3  H24  0.020
 AWK  plan-3  H25  0.020

