# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:53:24 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[3,5-bis(chloranyl)-4-(2-ethylphenyl)phenyl]methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2c(Cl)cc(CNCCc3[nH]c4ccccc4n3)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
 AUW  AUW  2-(1~{H}-benzimidazol-2-yl)-~{N}-[[3,5-bis(chloranyl)-4-(2-ethylphenyl)phenyl]methyl]ethanamine  ligand  52  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_AUW
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
 AUW  C2   C   CR6   0   0.121  -5.5491  -0.1756  -0.9062
 AUW  C1   C   CH2   0  -0.525  -4.9000   0.2473  -2.1961
 AUW  C23  C   CR6   0  -0.116  -2.3920  -0.9043   0.3351
 AUW  C8   C   CR6   0   0.192  -3.3947   0.0648   0.3609
 AUW  C7   C   CR6   0   0.022  -4.8336  -0.2835   0.2904
 AUW  C6   C   CR16  0  -0.258  -5.4703  -0.7134   1.4516
 AUW  C5   C   CR16  0  -0.265  -6.8165  -1.0432   1.4427
 AUW  C4   C   CR16  0  -0.245  -7.5347  -0.9424   0.2592
 AUW  C3   C   CR16  0  -0.304  -6.9013  -0.5130  -0.8972
 AUW  C    C   CH3   0  -0.650  -4.3263  -0.9387  -2.9704
 AUW  C22  C   CR16  0  -0.224  -1.0467  -0.5926   0.4179
 AUW  C11  C   CR6   0   0.051  -0.6522   0.7341   0.5445
 AUW  C10  C   CR16  0  -0.244  -1.6232   1.7254   0.5752
 AUW  C9   C   CR6   0  -0.115  -2.9629   1.3826   0.4900
 AUW  CL   CL  CL    0  -0.112  -4.1403   2.6513   0.5383
 AUW  C12  C   CH2   0  -0.311   0.8055   1.0867   0.6889
 AUW  N    N   NH1   0  -0.599   1.6402   0.2658  -0.1619
 AUW  C13  C   CH2   0  -0.253   3.0554   0.4203   0.1048
 AUW  C14  C   CH2   0  -0.555   3.8587  -0.5494  -0.7621
 AUW  C15  C   CR5   0   0.430   5.3198  -0.4619  -0.4994
 AUW  N2   N   NR15  0  -0.693   5.8738  -0.9647   0.6370
 AUW  C21  C   CR56  0   0.334   7.2178  -0.7088   0.5922
 AUW  C16  C   CR56  0   0.133   7.4056  -0.0297  -0.6237
 AUW  N1   N   N     0  -0.474   6.2021   0.1072  -1.2761
 AUW  C20  C   CR16  0  -0.309   8.2643  -0.9940   1.4609
 AUW  C19  C   CR16  0  -0.280   9.5254  -0.5723   1.0742
 AUW  C18  C   CR16  0  -0.272   9.7323   0.1080  -0.1353
 AUW  C17  C   CR16  0  -0.337   8.6837   0.3869  -0.9945
 AUW  H1   H   HCH2  0   0.246  -5.6411   0.7574  -2.8154
 AUW  H2   H   HCH2  0   0.241  -4.1078   0.9744  -2.0100
 AUW  H3   H   HCR6  0   0.251  -4.9035  -0.7839   2.3720
 AUW  H4   H   HCR6  0   0.256  -7.3000  -1.3722   2.3531
 AUW  H5   H   HCR6  0   0.255  -8.5875  -1.1924   0.2361
 AUW  H6   H   HCR6  0   0.249  -7.4702  -0.4311  -1.8163
 AUW  H7   H   HCH3  0   0.226  -5.1012  -1.6754  -3.1856
 AUW  H8   H   HCH3  0   0.232  -3.9010  -0.6110  -3.9192
 AUW  H9   H   HCH3  0   0.221  -3.5400  -1.4400  -2.4060
 AUW  H10  H   HCR6  0   0.275  -0.3014  -1.3753   0.3837
 AUW  H11  H   HCR6  0   0.278  -1.3374   2.7650   0.6691
 AUW  H12  H   HCH2  0   0.227   0.9357   2.1656   0.5231
 AUW  H13  H   HCH2  0   0.253   1.1013   0.9042   1.7272
 AUW  H14  H   HNH1  0   0.350   1.4539   0.4984  -1.1307
 AUW  H16  H   HCH2  0   0.212   3.4187   1.4450  -0.0625
 AUW  H17  H   HCH2  0   0.231   3.2272   0.1974   1.1613
 AUW  H18  H   HCH2  0   0.263   3.5076  -1.5673  -0.5760
 AUW  H19  H   HCH2  0   0.265   3.6918  -0.3309  -1.8178
 AUW  H20  H   HNR5  0   0.418   5.3845  -1.4641   1.3630
 AUW  H22  H   HCR6  0   0.264   8.1059  -1.5211   2.3927
 AUW  H23  H   HCR6  0   0.254  10.3714  -0.7724   1.7187
 AUW  H24  H   HCR6  0   0.252  10.7351   0.4179  -0.3992
 AUW  H25  H   HCR6  0   0.252   8.8479   0.9118  -1.9270
 AUW  CL1  CL  CL    0  -0.113  -2.8362  -2.5730   0.1928

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
 AUW  C17  C18  aromatic  1.384  0.020  1.384
 AUW  C17  C16  aromatic  1.394  0.020  1.394
 AUW  C    C1   single    1.528  0.020  1.528
 AUW  C18  C19  aromatic  1.403  0.020  1.403
 AUW  N1   C16  aromatic  1.376  0.020  1.376
 AUW  N1   C15  aromatic  1.306  0.020  1.306
 AUW  C16  C21  aromatic  1.405  0.020  1.405
 AUW  C19  C20  aromatic  1.385  0.020  1.385
 AUW  C15  C14  single    1.487  0.020  1.487
 AUW  C15  N2   aromatic  1.361  0.020  1.361
 AUW  C14  C13  single    1.529  0.020  1.529
 AUW  C21  C20  aromatic  1.390  0.020  1.390
 AUW  C21  N2   aromatic  1.369  0.020  1.369
 AUW  C1   C2   single    1.505  0.020  1.505
 AUW  C13  N    single    1.448  0.020  1.448
 AUW  N    C12  single    1.447  0.020  1.447
 AUW  C2   C3   aromatic  1.394  0.020  1.394
 AUW  C2   C7   aromatic  1.398  0.020  1.398
 AUW  C12  C11  single    1.507  0.020  1.507
 AUW  C10  C11  aromatic  1.388  0.020  1.388
 AUW  C10  C9   aromatic  1.385  0.020  1.385
 AUW  CL   C9   single    1.732  0.020  1.732
 AUW  C11  C22  aromatic  1.390  0.020  1.390
 AUW  C9   C8   aromatic  1.393  0.020  1.393
 AUW  C3   C4   aromatic  1.387  0.020  1.387
 AUW  C22  C23  aromatic  1.383  0.020  1.383
 AUW  C8   C23  aromatic  1.395  0.020  1.395
 AUW  C8   C7   single    1.482  0.020  1.482
 AUW  C23  CL1  single    1.733  0.020  1.733
 AUW  C7   C6   aromatic  1.392  0.020  1.392
 AUW  C4   C5   aromatic  1.388  0.020  1.388
 AUW  C6   C5   aromatic  1.386  0.020  1.386
 AUW  C1   H1   single    0.970  0.020  1.090
 AUW  C1   H2   single    0.970  0.020  1.090
 AUW  C6   H3   single    0.930  0.020  1.080
 AUW  C5   H4   single    0.930  0.020  1.080
 AUW  C4   H5   single    0.930  0.020  1.080
 AUW  C3   H6   single    0.930  0.020  1.080
 AUW  C    H7   single    0.970  0.020  1.090
 AUW  C    H8   single    0.970  0.020  1.090
 AUW  C    H9   single    0.970  0.020  1.090
 AUW  C22  H10  single    0.930  0.020  1.080
 AUW  C10  H11  single    0.930  0.020  1.080
 AUW  C12  H12  single    0.970  0.020  1.090
 AUW  C12  H13  single    0.970  0.020  1.090
 AUW  N    H14  single    0.890  0.020  1.040
 AUW  C13  H16  single    0.970  0.020  1.090
 AUW  C13  H17  single    0.970  0.020  1.090
 AUW  C14  H18  single    0.970  0.020  1.090
 AUW  C14  H19  single    0.970  0.020  1.090
 AUW  N2   H20  single    0.860  0.020  1.020
 AUW  C20  H22  single    0.930  0.020  1.080
 AUW  C19  H23  single    0.930  0.020  1.080
 AUW  C18  H24  single    0.930  0.020  1.080
 AUW  C17  H25  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
 AUW  C3   C2   C7   118.18  3.000
 AUW  C7   C2   C1   122.31  3.000
 AUW  C3   C2   C1   119.48  3.000
 AUW  H2   C1   H1   106.15  3.000
 AUW  H2   C1   C    109.33  3.000
 AUW  H1   C1   C    109.26  3.000
 AUW  H2   C1   C2   110.74  3.000
 AUW  H1   C1   C2   108.94  3.000
 AUW  C    C1   C2   112.22  3.000
 AUW  C22  C23  C8   122.78  3.000
 AUW  C8   C23  CL1  119.11  3.000
 AUW  C22  C23  CL1  118.11  3.000
 AUW  C9   C8   C7   121.85  3.000
 AUW  C7   C8   C23  122.26  3.000
 AUW  C9   C8   C23  115.87  3.000
 AUW  C6   C7   C8   118.48  3.000
 AUW  C6   C7   C2   120.23  3.000
 AUW  C8   C7   C2   121.28  3.000
 AUW  H3   C6   C5   119.88  3.000
 AUW  H3   C6   C7   119.30  3.000
 AUW  C5   C6   C7   120.81  3.000
 AUW  H4   C5   C4   120.55  3.000
 AUW  H4   C5   C6   120.06  3.000
 AUW  C4   C5   C6   119.39  3.000
 AUW  H5   C4   C3   119.87  3.000
 AUW  H5   C4   C5   120.31  3.000
 AUW  C3   C4   C5   119.82  3.000
 AUW  H6   C3   C4   119.39  3.000
 AUW  H6   C3   C2   119.04  3.000
 AUW  C4   C3   C2   121.57  3.000
 AUW  H9   C    H8   107.91  3.000
 AUW  H9   C    H7   107.70  3.000
 AUW  H8   C    H7   107.96  3.000
 AUW  H9   C    C1   111.44  3.000
 AUW  H8   C    C1   110.74  3.000
 AUW  H7   C    C1   110.95  3.000
 AUW  H10  C22  C11  119.88  3.000
 AUW  H10  C22  C23  120.35  3.000
 AUW  C11  C22  C23  119.77  3.000
 AUW  C12  C11  C10  120.50  3.000
 AUW  C10  C11  C22  119.03  3.000
 AUW  C12  C11  C22  120.44  3.000
 AUW  H11  C10  C9   119.89  3.000
 AUW  H11  C10  C11  120.22  3.000
 AUW  C9   C10  C11  119.89  3.000
 AUW  CL   C9   C10  118.33  3.000
 AUW  CL   C9   C8   119.02  3.000
 AUW  C10  C9   C8   122.66  3.000
 AUW  H13  C12  H12  105.94  3.000
 AUW  H13  C12  N    107.88  3.000
 AUW  H12  C12  N    113.57  3.000
 AUW  H13  C12  C11  108.25  3.000
 AUW  H12  C12  C11  109.26  3.000
 AUW  N    C12  C11  111.65  3.000
 AUW  H14  N    C13  109.33  3.000
 AUW  H14  N    C12  109.01  3.000
 AUW  C13  N    C12  113.25  3.000
 AUW  H17  C13  H16  106.56  3.000
 AUW  H17  C13  C14  109.64  3.000
 AUW  H16  C13  C14  109.33  3.000
 AUW  H17  C13  N    108.04  3.000
 AUW  H16  C13  N    113.21  3.000
 AUW  C14  C13  N    109.96  3.000
 AUW  H19  C14  H18  107.60  3.000
 AUW  H19  C14  C15  108.02  3.000
 AUW  H18  C14  C15  109.90  3.000
 AUW  H19  C14  C13  109.96  3.000
 AUW  H18  C14  C13  108.99  3.000
 AUW  C15  C14  C13  112.26  3.000
 AUW  N1   C15  N2   112.50  3.000
 AUW  N2   C15  C14  121.73  3.000
 AUW  N1   C15  C14  125.76  3.000
 AUW  H20  N2   C21  126.36  3.000
 AUW  H20  N2   C15  125.95  3.000
 AUW  C21  N2   C15  107.66  3.000
 AUW  C20  C21  C16  122.64  3.000
 AUW  C20  C21  N2   132.89  3.000
 AUW  C16  C21  N2   104.47  3.000
 AUW  C17  C16  N1   130.24  3.000
 AUW  N1   C16  C21  109.97  3.000
 AUW  C17  C16  C21  119.80  3.000
 AUW  C16  N1   C15  105.40  3.000
 AUW  H22  C20  C19  121.47  3.000
 AUW  H22  C20  C21  121.87  3.000
 AUW  C19  C20  C21  116.66  3.000
 AUW  H23  C19  C18  119.19  3.000
 AUW  H23  C19  C20  119.29  3.000
 AUW  C18  C19  C20  121.51  3.000
 AUW  H24  C18  C17  119.53  3.000
 AUW  H24  C18  C19  119.06  3.000
 AUW  C17  C18  C19  121.41  3.000
 AUW  H25  C17  C18  121.16  3.000
 AUW  H25  C17  C16  120.86  3.000
 AUW  C18  C17  C16  117.98  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
 AUW  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 AUW  CONST_04  C5   C6   C7   C2      0.00   0.0  0
 AUW  CONST_05  C10  C11  C22  C23     0.00   0.0  0
 AUW  CONST_06  C10  C9   C8   C23     0.00   0.0  0
 AUW  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 AUW  CONST_09  C11  C22  C23  C8      0.00   0.0  0
 AUW  CONST_10  C3   C2   C7   C8    180.00   0.0  0
 AUW  CONST_11  C5   C6   C7   C8    180.00   0.0  0
 AUW  CONST_12  C4   C3   C2   C7      0.00   0.0  0
 AUW  CONST_13  C10  C9   C8   C7    180.00   0.0  0
 AUW  CONST_14  C22  C23  C8   C7    180.00   0.0  0
 AUW  CONST_15  C4   C5   C6   C7      0.00   0.0  0
 AUW  CONST_16  C3   C2   C7   C6      0.00   0.0  0
 AUW  CONST_18  C3   C4   C5   C6      0.00   0.0  0
 AUW  CONST_19  C9   C10  C11  C22     0.00   0.0  0
 AUW  CONST_20  C9   C8   C23  C22     0.00   0.0  0
 AUW  CONST_21  C17  C16  N1   C15   180.00   0.0  0
 AUW  CONST_22  C21  C16  N1   C15     0.00   0.0  0
 AUW  CONST_23  C16  C21  N2   C15     0.00   0.0  0
 AUW  CONST_24  C20  C21  N2   C15   180.00   0.0  0
 AUW  CONST_25  C16  N1   C15  N2      0.00   0.0  0
 AUW  CONST_26  C17  C16  C21  N2    180.00   0.0  0
 AUW  CONST_27  N1   C16  C21  N2      0.00   0.0  0
 AUW  CONST_28  C19  C20  C21  N2    180.00   0.0  0
 AUW  CONST_29  C18  C17  C16  C21     0.00   0.0  0
 AUW  CONST_30  C18  C19  C20  C21     0.00   0.0  0
 AUW  CONST_31  N1   C15  N2   C21     0.00   0.0  0
 AUW  CONST_32  C19  C18  C17  C16     0.00   0.0  0
 AUW  CONST_33  C19  C20  C21  C16     0.00   0.0  0
 AUW  CONST_34  C18  C17  C16  N1    180.00   0.0  0
 AUW  CONST_35  C20  C21  C16  N1    180.00   0.0  0
 AUW  CONST_36  C17  C18  C19  C20     0.00   0.0  0
 AUW  CONST_37  C17  C16  C21  C20     0.00   0.0  0
 AUW  CONST_38  C4   C3   C2   C1    180.00   0.0  0
 AUW  CONST_39  C8   C7   C2   C1      0.00   0.0  0
 AUW  CONST_40  C6   C7   C2   C1    180.00   0.0  0
 AUW  CONST_41  C11  C22  C23  CL1   180.00   0.0  0
 AUW  CONST_42  C9   C8   C23  CL1   180.00   0.0  0
 AUW  CONST_43  C7   C8   C23  CL1     0.00   0.0  0
 AUW  CONST_44  C12  C11  C22  C23   180.00   0.0  0
 AUW  CONST_45  CL   C9   C8   C23   180.00   0.0  0
 AUW  CONST_46  CL   C9   C8   C7      0.00   0.0  0
 AUW  CONST_47  CL   C9   C10  C11   180.00   0.0  0
 AUW  CONST_48  C12  C11  C10  C9    180.00   0.0  0
 AUW  CONST_49  C16  N1   C15  C14   180.00   0.0  0
 AUW  CONST_50  C21  N2   C15  C14   180.00   0.0  0
 AUW  CONST_51  H5   C4   C3   C2    180.00   0.0  0
 AUW  CONST_52  H3   C6   C7   C2    180.00   0.0  0
 AUW  CONST_53  H11  C10  C9   C8    180.00   0.0  0
 AUW  CONST_54  H10  C22  C23  C8    180.00   0.0  0
 AUW  CONST_55  H6   C3   C2   C7    180.00   0.0  0
 AUW  CONST_56  H4   C5   C6   C7    180.00   0.0  0
 AUW  CONST_57  H22  C20  C21  N2      0.00   0.0  0
 AUW  CONST_58  H25  C17  C16  C21   180.00   0.0  0
 AUW  CONST_59  H23  C19  C20  C21   180.00   0.0  0
 AUW  CONST_60  H24  C18  C17  C16   180.00   0.0  0
 AUW  CONST_61  H20  N2   C21  C16   180.00   0.0  0
 AUW  Var_01    C    C1   C2   C7     88.49  30.0  3
 AUW  Var_02    N    C12  C11  C22    39.50  30.0  2
 AUW  Var_03    N1   C15  C14  C13  -105.01  30.0  2
 AUW  Var_04    C13  N    C12  C11  -170.52  30.0  1
 AUW  Var_05    C15  C14  C13  N    -178.30  30.0  1
 AUW  Var_06    H7   C    C1   C2     57.67  30.0  3
 AUW  Var_07    C14  C13  N    C12   175.98  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
 AUW  plan-1  C2   0.020
 AUW  plan-1  C1   0.020
 AUW  plan-1  C8   0.020
 AUW  plan-1  C7   0.020
 AUW  plan-1  C6   0.020
 AUW  plan-1  C5   0.020
 AUW  plan-1  C4   0.020
 AUW  plan-1  C3   0.020
 AUW  plan-1  H3   0.020
 AUW  plan-1  H4   0.020
 AUW  plan-1  H5   0.020
 AUW  plan-1  H6   0.020
 AUW  plan-2  C23  0.020
 AUW  plan-2  C8   0.020
 AUW  plan-2  C7   0.020
 AUW  plan-2  C22  0.020
 AUW  plan-2  C11  0.020
 AUW  plan-2  C10  0.020
 AUW  plan-2  C9   0.020
 AUW  plan-2  CL   0.020
 AUW  plan-2  C12  0.020
 AUW  plan-2  H10  0.020
 AUW  plan-2  H11  0.020
 AUW  plan-2  CL1  0.020
 AUW  plan-3  C14  0.020
 AUW  plan-3  C15  0.020
 AUW  plan-3  N2   0.020
 AUW  plan-3  C21  0.020
 AUW  plan-3  C16  0.020
 AUW  plan-3  N1   0.020
 AUW  plan-3  C20  0.020
 AUW  plan-3  C19  0.020
 AUW  plan-3  C18  0.020
 AUW  plan-3  C17  0.020
 AUW  plan-3  H20  0.020
 AUW  plan-3  H22  0.020
 AUW  plan-3  H23  0.020
 AUW  plan-3  H24  0.020
 AUW  plan-3  H25  0.020

