# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 13:16:30 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(5-methoxy-1~{H}-benzimidazol-2-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4ccc(OC)cc4n3)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
 AQT  AQT  ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(5-methoxy-1~{H}-benzimidazol-2-yl)ethanamine  ligand  56  30  .  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_AQT
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
 AQT  N1   N   NR15  0  -0.694   -5.0409   1.3747  -0.6395
 AQT  C1   C   CH2   0  -0.520    6.4904  -1.5917   1.3577
 AQT  N2   N   N     0  -0.480   -4.8717  -0.8334  -0.7674
 AQT  C2   C   CR6   0   0.111    6.8756  -0.6932   0.2139
 AQT  C5   C   CR16  0  -0.262    7.6481   0.8564  -1.9925
 AQT  C6   C   CR16  0  -0.271    6.3269   0.8432  -1.5701
 AQT  C7   C   CR6   0   0.022    5.9321   0.0784  -0.4751
 AQT  C24  C   CR6   0  -0.096    4.0210   0.8043   1.0035
 AQT  C8   C   CR6   0   0.103    4.5012   0.0841  -0.0841
 AQT  C4   C   CR16  0  -0.248    8.5889   0.0966  -1.3126
 AQT  C3   C   CR16  0  -0.303    8.1983  -0.6685  -0.2232
 AQT  C    C   CH3   0  -0.654    6.0589  -2.9756   0.8761
 AQT  C23  C   CR16  0  -0.260    2.6757   0.8140   1.3438
 AQT  C11  C   CR6   0   0.073    1.7598   0.0930   0.5898
 AQT  C10  C   CR16  0  -0.267    2.2193  -0.6222  -0.5134
 AQT  C9   C   CR16  0  -0.287    3.5648  -0.6246  -0.8372
 AQT  C12  C   CH2   0  -0.319    0.3025   0.0784   0.9663
 AQT  N    N   NH1   0  -0.597   -0.5397   0.3304  -0.1863
 AQT  C13  C   CH2   0  -0.252   -1.9516   0.2224   0.1166
 AQT  C14  C   CH2   0  -0.556   -2.7831   0.4521  -1.1454
 AQT  C15  C   CR5   0   0.438   -4.2377   0.3069  -0.8697
 AQT  C22  C   CR56  0   0.151   -6.1676  -0.5017  -0.4521
 AQT  C16  C   CR56  0   0.316   -6.2978   0.8948  -0.3668
 AQT  C21  C   CR16  0  -0.445   -7.2673  -1.3238  -0.2282
 AQT  C19  C   CR6   0   0.378   -8.4827  -0.7251   0.0817
 AQT  O    O   O2    0  -0.481   -9.5199  -1.5691   0.2949
 AQT  C20  C   CH3   0  -0.435  -10.7777  -1.0284   0.6366
 AQT  C18  C   CR16  0  -0.402   -8.5979   0.6742   0.1630
 AQT  C17  C   CR16  0  -0.295   -7.5053   1.4989  -0.0622
 AQT  H1   H   HNR5  0   0.417   -4.7612   2.3420  -0.6754
 AQT  H2   H   HCH2  0   0.244    7.3406  -1.6944   2.0357
 AQT  H3   H   HCH2  0   0.240    5.6853  -1.1481   1.9447
 AQT  H5   H   HCR6  0   0.255    7.9385   1.4569  -2.8448
 AQT  H6   H   HCR6  0   0.249    5.5896   1.4404  -2.0926
 AQT  H7   H   HCR6  0   0.254    9.6242   0.0980  -1.6285
 AQT  H8   H   HCR6  0   0.248    8.9352  -1.2660   0.3010
 AQT  H9   H   HCH3  0   0.226    6.8633  -3.4705   0.3306
 AQT  H10  H   HCH3  0   0.232    5.7848  -3.6112   1.7189
 AQT  H11  H   HCH3  0   0.226    5.1951  -2.9124   0.2131
 AQT  H12  H   HCR6  0   0.272    2.3403   1.3901   2.1972
 AQT  H13  H   HCR6  0   0.253    1.5189  -1.1796  -1.1214
 AQT  H14  H   HCR6  0   0.258    3.9093  -1.1895  -1.6945
 AQT  H15  H   HCH2  0   0.246    0.0473  -0.9122   1.3566
 AQT  H16  H   HCH2  0   0.221    0.1316   0.7846   1.7919
 AQT  H17  H   HNH1  0   0.347   -0.3438   1.2618  -0.5353
 AQT  H19  H   HCH2  0   0.234   -2.1482  -0.7847   0.4935
 AQT  H20  H   HCH2  0   0.207   -2.2781   0.9201   0.9029
 AQT  H21  H   HCH2  0   0.260   -2.5807   1.4483  -1.5461
 AQT  H22  H   HCH2  0   0.265   -2.4905  -0.2719  -1.9070
 AQT  H23  H   HCR6  0   0.256   -7.1819  -2.4019  -0.2877
 AQT  H24  H   HCH3  0   0.257  -11.4499  -1.8721   0.7739
 AQT  H25  H   HCH3  0   0.224  -10.7420  -0.4573   1.5686
 AQT  H26  H   HCH3  0   0.224  -11.1799  -0.3863  -0.1522
 AQT  H27  H   HCR6  0   0.277   -9.5446   1.1364   0.4054
 AQT  H28  H   HCR6  0   0.269   -7.6090   2.5738   0.0035
 AQT  CL   CL  CL    0  -0.127    5.1198   1.7394   1.9675

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
 AQT  C5   C6   aromatic  1.387  0.020  1.387
 AQT  C5   C4   aromatic  1.387  0.020  1.387
 AQT  C6   C7   aromatic  1.393  0.020  1.393
 AQT  C4   C3   aromatic  1.387  0.020  1.387
 AQT  C9   C10  aromatic  1.384  0.020  1.384
 AQT  C9   C8   aromatic  1.395  0.020  1.395
 AQT  C7   C2   aromatic  1.400  0.020  1.400
 AQT  C7   C8   single    1.483  0.020  1.483
 AQT  C3   C2   aromatic  1.393  0.020  1.393
 AQT  C2   C1   single    1.505  0.020  1.505
 AQT  C10  C11  aromatic  1.393  0.020  1.393
 AQT  C8   C24  aromatic  1.390  0.020  1.390
 AQT  C    C1   single    1.528  0.020  1.528
 AQT  C11  C23  aromatic  1.388  0.020  1.388
 AQT  C11  C12  single    1.505  0.020  1.505
 AQT  C24  C23  aromatic  1.388  0.020  1.388
 AQT  C24  CL   single    1.735  0.020  1.735
 AQT  C12  N    single    1.450  0.020  1.450
 AQT  N    C13  single    1.448  0.020  1.448
 AQT  C13  C14  single    1.529  0.020  1.529
 AQT  C14  C15  single    1.488  0.020  1.488
 AQT  C15  N1   aromatic  1.356  0.020  1.356
 AQT  C15  N2   aromatic  1.309  0.020  1.309
 AQT  N1   C16  aromatic  1.373  0.020  1.373
 AQT  N2   C22  aromatic  1.374  0.020  1.374
 AQT  C16  C22  aromatic  1.405  0.020  1.405
 AQT  C16  C17  aromatic  1.384  0.020  1.384
 AQT  C22  C21  aromatic  1.391  0.020  1.391
 AQT  C17  C18  aromatic  1.387  0.020  1.387
 AQT  C21  C19  aromatic  1.390  0.020  1.390
 AQT  C18  C19  aromatic  1.406  0.020  1.406
 AQT  C19  O    single    1.354  0.020  1.354
 AQT  O    C20  single    1.411  0.020  1.411
 AQT  N1   H1   single    0.860  0.020  1.020
 AQT  C1   H2   single    0.970  0.020  1.090
 AQT  C1   H3   single    0.970  0.020  1.090
 AQT  C5   H5   single    0.930  0.020  1.080
 AQT  C6   H6   single    0.930  0.020  1.080
 AQT  C4   H7   single    0.930  0.020  1.080
 AQT  C3   H8   single    0.930  0.020  1.080
 AQT  C    H9   single    0.970  0.020  1.090
 AQT  C    H10  single    0.970  0.020  1.090
 AQT  C    H11  single    0.970  0.020  1.090
 AQT  C23  H12  single    0.930  0.020  1.080
 AQT  C10  H13  single    0.930  0.020  1.080
 AQT  C9   H14  single    0.930  0.020  1.080
 AQT  C12  H15  single    0.970  0.020  1.090
 AQT  C12  H16  single    0.970  0.020  1.090
 AQT  N    H17  single    0.890  0.020  1.040
 AQT  C13  H19  single    0.970  0.020  1.090
 AQT  C13  H20  single    0.970  0.020  1.090
 AQT  C14  H21  single    0.970  0.020  1.090
 AQT  C14  H22  single    0.970  0.020  1.090
 AQT  C21  H23  single    0.930  0.020  1.080
 AQT  C20  H24  single    0.970  0.020  1.090
 AQT  C20  H25  single    0.970  0.020  1.090
 AQT  C20  H26  single    0.970  0.020  1.090
 AQT  C18  H27  single    0.930  0.020  1.080
 AQT  C17  H28  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
 AQT  H1   N1   C16  126.65  3.000
 AQT  H1   N1   C15  125.85  3.000
 AQT  C16  N1   C15  107.50  3.000
 AQT  H3   C1   H2   106.19  3.000
 AQT  H3   C1   C    109.25  3.000
 AQT  H2   C1   C    109.29  3.000
 AQT  H3   C1   C2   110.81  3.000
 AQT  H2   C1   C2   109.19  3.000
 AQT  C    C1   C2   111.94  3.000
 AQT  C22  N2   C15  105.34  3.000
 AQT  C3   C2   C7   118.40  3.000
 AQT  C3   C2   C1   119.48  3.000
 AQT  C7   C2   C1   122.05  3.000
 AQT  H5   C5   C4   120.52  3.000
 AQT  H5   C5   C6   120.05  3.000
 AQT  C4   C5   C6   119.44  3.000
 AQT  H6   C6   C7   119.28  3.000
 AQT  H6   C6   C5   119.75  3.000
 AQT  C7   C6   C5   120.97  3.000
 AQT  C8   C7   C6   118.59  3.000
 AQT  C8   C7   C2   121.50  3.000
 AQT  C6   C7   C2   119.90  3.000
 AQT  C23  C24  C8   122.03  3.000
 AQT  C23  C24  CL   118.29  3.000
 AQT  C8   C24  CL   119.68  3.000
 AQT  C9   C8   C24  116.98  3.000
 AQT  C24  C8   C7   122.78  3.000
 AQT  C9   C8   C7   120.21  3.000
 AQT  H7   C4   C3   119.95  3.000
 AQT  H7   C4   C5   120.32  3.000
 AQT  C3   C4   C5   119.73  3.000
 AQT  H8   C3   C4   119.50  3.000
 AQT  H8   C3   C2   118.94  3.000
 AQT  C4   C3   C2   121.56  3.000
 AQT  H11  C    H10  107.72  3.000
 AQT  H11  C    H9   107.85  3.000
 AQT  H10  C    H9   107.91  3.000
 AQT  H11  C    C1   111.27  3.000
 AQT  H10  C    C1   110.81  3.000
 AQT  H9   C    C1   111.13  3.000
 AQT  H12  C23  C11  120.00  3.000
 AQT  H12  C23  C24  119.81  3.000
 AQT  C11  C23  C24  120.19  3.000
 AQT  C12  C11  C10  120.83  3.000
 AQT  C12  C11  C23  120.53  3.000
 AQT  C10  C11  C23  118.64  3.000
 AQT  H13  C10  C9   119.80  3.000
 AQT  H13  C10  C11  119.74  3.000
 AQT  C9   C10  C11  120.46  3.000
 AQT  H14  C9   C10  119.70  3.000
 AQT  H14  C9   C8   118.61  3.000
 AQT  C10  C9   C8   121.69  3.000
 AQT  H16  C12  H15  106.09  3.000
 AQT  H16  C12  N    113.27  3.000
 AQT  H15  C12  N    107.78  3.000
 AQT  H16  C12  C11  109.38  3.000
 AQT  H15  C12  C11  108.88  3.000
 AQT  N    C12  C11  111.22  3.000
 AQT  H17  N    C13  109.20  3.000
 AQT  H17  N    C12  108.74  3.000
 AQT  C13  N    C12  112.78  3.000
 AQT  H20  C13  H19  106.51  3.000
 AQT  H20  C13  C14  109.46  3.000
 AQT  H19  C13  C14  108.98  3.000
 AQT  H20  C13  N    113.04  3.000
 AQT  H19  C13  N    108.43  3.000
 AQT  C14  C13  N    110.28  3.000
 AQT  H22  C14  H21  107.42  3.000
 AQT  H22  C14  C15  109.08  3.000
 AQT  H21  C14  C15  109.75  3.000
 AQT  H22  C14  C13  109.32  3.000
 AQT  H21  C14  C13  109.82  3.000
 AQT  C15  C14  C13  111.36  3.000
 AQT  C14  C15  N2   124.98  3.000
 AQT  N2   C15  N1   112.70  3.000
 AQT  C14  C15  N1   122.26  3.000
 AQT  C21  C22  C16  120.29  3.000
 AQT  C21  C22  N2   129.77  3.000
 AQT  C16  C22  N2   109.95  3.000
 AQT  C17  C16  C22  121.87  3.000
 AQT  C17  C16  N1   133.62  3.000
 AQT  C22  C16  N1   104.51  3.000
 AQT  H23  C21  C19  120.67  3.000
 AQT  H23  C21  C22  121.13  3.000
 AQT  C19  C21  C22  118.20  3.000
 AQT  C18  C19  O    123.25  3.000
 AQT  O    C19  C21  115.87  3.000
 AQT  C18  C19  C21  120.88  3.000
 AQT  C20  O    C19  118.82  3.000
 AQT  H26  C20  H25  108.67  3.000
 AQT  H26  C20  H24  108.62  3.000
 AQT  H25  C20  H24  108.52  3.000
 AQT  H26  C20  O    112.22  3.000
 AQT  H25  C20  O    112.17  3.000
 AQT  H24  C20  O    106.52  3.000
 AQT  H27  C18  C17  118.16  3.000
 AQT  H27  C18  C19  120.67  3.000
 AQT  C17  C18  C19  121.17  3.000
 AQT  H28  C17  C18  120.35  3.000
 AQT  H28  C17  C16  122.05  3.000
 AQT  C18  C17  C16  117.60  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
 AQT  CONST_01  C22  N2   C15  N1      0.00   0.0  0
 AQT  CONST_02  N2   C22  C16  N1      0.00   0.0  0
 AQT  CONST_03  C21  C22  C16  N1    180.00   0.0  0
 AQT  CONST_04  C18  C17  C16  N1    180.00   0.0  0
 AQT  CONST_05  C16  N1   C15  N2      0.00   0.0  0
 AQT  CONST_06  C17  C16  C22  N2    180.00   0.0  0
 AQT  CONST_07  C19  C21  C22  N2    180.00   0.0  0
 AQT  CONST_08  C5   C6   C7   C2      0.00   0.0  0
 AQT  CONST_11  C5   C4   C3   C2      0.00   0.0  0
 AQT  CONST_12  C8   C7   C6   C5    180.00   0.0  0
 AQT  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 AQT  CONST_14  C3   C2   C7   C6      0.00   0.0  0
 AQT  CONST_17  C4   C5   C6   C7      0.00   0.0  0
 AQT  CONST_18  C4   C3   C2   C7      0.00   0.0  0
 AQT  CONST_19  C10  C9   C8   C7    180.00   0.0  0
 AQT  CONST_20  C23  C24  C8   C7    180.00   0.0  0
 AQT  CONST_21  C10  C9   C8   C24     0.00   0.0  0
 AQT  CONST_22  C10  C11  C23  C24     0.00   0.0  0
 AQT  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 AQT  CONST_24  C3   C2   C7   C8    180.00   0.0  0
 AQT  CONST_25  C11  C23  C24  C8      0.00   0.0  0
 AQT  CONST_26  C9   C10  C11  C23     0.00   0.0  0
 AQT  CONST_27  C9   C8   C24  C23     0.00   0.0  0
 AQT  CONST_28  C22  C16  N1   C15     0.00   0.0  0
 AQT  CONST_29  C17  C16  N1   C15   180.00   0.0  0
 AQT  CONST_30  C16  C22  N2   C15     0.00   0.0  0
 AQT  CONST_31  C21  C22  N2   C15   180.00   0.0  0
 AQT  CONST_32  C18  C17  C16  C22     0.00   0.0  0
 AQT  CONST_33  C18  C19  C21  C22     0.00   0.0  0
 AQT  CONST_34  C19  C21  C22  C16     0.00   0.0  0
 AQT  CONST_35  C19  C18  C17  C16     0.00   0.0  0
 AQT  CONST_36  C17  C16  C22  C21     0.00   0.0  0
 AQT  CONST_37  C17  C18  C19  C21     0.00   0.0  0
 AQT  CONST_38  C6   C7   C2   C1    180.00   0.0  0
 AQT  CONST_39  C8   C7   C2   C1      0.00   0.0  0
 AQT  CONST_40  C4   C3   C2   C1    180.00   0.0  0
 AQT  CONST_41  CL   C24  C8   C7      0.00   0.0  0
 AQT  CONST_42  C9   C8   C24  CL    180.00   0.0  0
 AQT  CONST_43  C11  C23  C24  CL    180.00   0.0  0
 AQT  CONST_44  C12  C11  C23  C24   180.00   0.0  0
 AQT  CONST_45  C12  C11  C10  C9    180.00   0.0  0
 AQT  CONST_46  C16  N1   C15  C14   180.00   0.0  0
 AQT  CONST_47  C22  N2   C15  C14   180.00   0.0  0
 AQT  CONST_48  O    C19  C21  C22   180.00   0.0  0
 AQT  CONST_49  C17  C18  C19  O     180.00   0.0  0
 AQT  CONST_50  H28  C17  C16  N1      0.00   0.0  0
 AQT  CONST_51  H1   N1   C15  N2    180.00   0.0  0
 AQT  CONST_52  H23  C21  C22  N2      0.00   0.0  0
 AQT  CONST_53  H6   C6   C7   C2    180.00   0.0  0
 AQT  CONST_54  H7   C4   C3   C2    180.00   0.0  0
 AQT  CONST_55  H8   C3   C4   C5    180.00   0.0  0
 AQT  CONST_56  H5   C5   C6   C7    180.00   0.0  0
 AQT  CONST_57  H14  C9   C8   C7      0.00   0.0  0
 AQT  CONST_58  H13  C10  C9   C8    180.00   0.0  0
 AQT  CONST_59  H12  C23  C24  C8    180.00   0.0  0
 AQT  CONST_60  H27  C18  C17  C16   180.00   0.0  0
 AQT  Var_01    C13  C14  C15  N1     97.74  30.0  2
 AQT  Var_02    C    C1   C2   C7     86.76  30.0  2
 AQT  Var_03    N    C12  C11  C23   132.35  30.0  2
 AQT  Var_04    C18  C19  O    C20    -1.02  30.0  1
 AQT  Var_05    C13  N    C12  C11   175.55  30.0  3
 AQT  Var_06    C15  C14  C13  N     178.33  30.0  3
 AQT  Var_07    H9   C    C1   C2     59.99  30.0  3
 AQT  Var_08    H24  C20  O    C19  -179.21  30.0  3
 AQT  Var_09    C14  C13  N    C12  -178.11  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
 AQT  plan-1  C1   0.020
 AQT  plan-1  C2   0.020
 AQT  plan-1  C5   0.020
 AQT  plan-1  C6   0.020
 AQT  plan-1  C7   0.020
 AQT  plan-1  C8   0.020
 AQT  plan-1  C4   0.020
 AQT  plan-1  C3   0.020
 AQT  plan-1  H5   0.020
 AQT  plan-1  H6   0.020
 AQT  plan-1  H7   0.020
 AQT  plan-1  H8   0.020
 AQT  plan-2  C7   0.020
 AQT  plan-2  C24  0.020
 AQT  plan-2  C8   0.020
 AQT  plan-2  C23  0.020
 AQT  plan-2  C11  0.020
 AQT  plan-2  C10  0.020
 AQT  plan-2  C9   0.020
 AQT  plan-2  C12  0.020
 AQT  plan-2  H12  0.020
 AQT  plan-2  H13  0.020
 AQT  plan-2  H14  0.020
 AQT  plan-2  CL   0.020
 AQT  plan-3  N1   0.020
 AQT  plan-3  N2   0.020
 AQT  plan-3  C14  0.020
 AQT  plan-3  C15  0.020
 AQT  plan-3  C22  0.020
 AQT  plan-3  C16  0.020
 AQT  plan-3  C21  0.020
 AQT  plan-3  C19  0.020
 AQT  plan-3  O    0.020
 AQT  plan-3  C18  0.020
 AQT  plan-3  C17  0.020
 AQT  plan-3  H1   0.020
 AQT  plan-3  H23  0.020
 AQT  plan-3  H27  0.020
 AQT  plan-3  H28  0.020

