# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 16:46:07 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]-~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4cc(Cl)c(Cl)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
 AT8  AT8  2-[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]-~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]ethanamine  ligand  52  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_AT8
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
 AT8  CL2  CL  CL    0  -0.128   5.9349   1.9292   1.8400
 AT8  C23  C   CR6   0  -0.096   4.8624   0.8641   0.9874
 AT8  C8   C   CR6   0   0.104   5.3576   0.0629  -0.0346
 AT8  C7   C   CR6   0   0.021   6.7839   0.0730  -0.4423
 AT8  C6   C   CR16  0  -0.270   7.1392   0.7416  -1.6112
 AT8  C5   C   CR16  0  -0.262   8.4553   0.7628  -2.0491
 AT8  C4   C   CR16  0  -0.248   9.4302   0.1083  -1.3102
 AT8  C3   C   CR16  0  -0.303   9.0786  -0.5617  -0.1474
 AT8  C2   C   CR6   0   0.110   7.7617  -0.5934   0.3064
 AT8  C1   C   CH2   0  -0.520   7.4210  -1.3915   1.5360
 AT8  C    C   CH3   0  -0.654   6.9994  -2.8185   1.1906
 AT8  C22  C   CR16  0  -0.261   3.5223   0.8514   1.3486
 AT8  C11  C   CR6   0   0.078   2.6280   0.0260   0.6814
 AT8  C10  C   CR16  0  -0.267   3.1016  -0.7687  -0.3600
 AT8  C9   C   CR16  0  -0.287   4.4416  -0.7492  -0.7042
 AT8  C12  C   CH2   0  -0.324   1.1757  -0.0083   1.0739
 AT8  N    N   NH1   0  -0.597   0.3215   0.2271  -0.0739
 AT8  C13  C   CH2   0  -0.249  -1.0862   0.0981   0.2416
 AT8  C14  C   CH2   0  -0.572  -1.9268   0.3436  -1.0059
 AT8  C15  C   CR5   0   0.483  -3.3805   0.1633  -0.7457
 AT8  N2   N   NR15  0  -0.706  -4.3127   1.0322  -1.2175
 AT8  C21  C   CR56  0   0.342  -5.5381   0.5785  -0.8207
 AT8  C16  C   CR56  0   0.144  -5.2618  -0.5928  -0.0968
 AT8  N1   N   N     0  -0.473  -3.9106  -0.8221  -0.0696
 AT8  C20  C   CR16  0  -0.267  -6.8245   1.0571  -1.0093
 AT8  C19  C   CR6   0  -0.026  -7.8502   0.3202  -0.4451
 AT8  CL1  CL  CL    0  -0.103  -9.4737   0.8707  -0.6464
 AT8  C18  C   CR6   0  -0.013  -7.5932  -0.8550   0.2816
 AT8  CL   CL  CL    0  -0.107  -8.9067  -1.7419   0.9701
 AT8  C17  C   CR16  0  -0.303  -6.3054  -1.3224   0.4632
 AT8  H1   H   HCR6  0   0.249   6.3745   1.2562  -2.1801
 AT8  H2   H   HCR6  0   0.255   8.7155   1.2883  -2.9586
 AT8  H3   H   HCR6  0   0.254  10.4620   0.1181  -1.6372
 AT8  H4   H   HCR6  0   0.248   9.8430  -1.0765   0.4233
 AT8  H5   H   HCH2  0   0.244   8.2910  -1.4197   2.1956
 AT8  H6   H   HCH2  0   0.239   6.6245  -0.9087   2.1042
 AT8  H7   H   HCH3  0   0.227   6.1145  -2.8250   0.5526
 AT8  H8   H   HCH3  0   0.226   7.7953  -3.3470   0.6645
 AT8  H9   H   HCH3  0   0.232   6.7622  -3.3820   2.0936
 AT8  H10  H   HCR6  0   0.273   3.1737   1.4904   2.1503
 AT8  H11  H   HCR6  0   0.253   2.4172  -1.4090  -0.9011
 AT8  H12  H   HCR6  0   0.258   4.7992  -1.3782  -1.5098
 AT8  H13  H   HCH2  0   0.245   0.9366  -0.9999   1.4710
 AT8  H14  H   HCH2  0   0.221   1.0020   0.7012   1.8963
 AT8  H15  H   HNH1  0   0.346   0.5021   1.1604  -0.4263
 AT8  H17  H   HCH2  0   0.234  -1.2671  -0.9162   0.6046
 AT8  H18  H   HCH2  0   0.207  -1.4136   0.7791   1.0417
 AT8  H19  H   HCH2  0   0.263  -1.7482   1.3524  -1.3854
 AT8  H20  H   HCH2  0   0.275  -1.6156  -0.3477  -1.7944
 AT8  H21  H   HNR5  0   0.425  -4.1256   1.8649  -1.7546
 AT8  H23  H   HCR6  0   0.297  -7.0263   1.9607  -1.5659
 AT8  H24  H   HCR6  0   0.285  -6.1185  -2.2279   1.0244

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
 AT8  C5   C6   aromatic  1.387  0.020  1.387
 AT8  C5   C4   aromatic  1.387  0.020  1.387
 AT8  C6   C7   aromatic  1.393  0.020  1.393
 AT8  C4   C3   aromatic  1.387  0.020  1.387
 AT8  C9   C10  aromatic  1.384  0.020  1.384
 AT8  C9   C8   aromatic  1.395  0.020  1.395
 AT8  C7   C2   aromatic  1.400  0.020  1.400
 AT8  C7   C8   single    1.483  0.020  1.483
 AT8  C3   C2   aromatic  1.393  0.020  1.393
 AT8  C10  C11  aromatic  1.393  0.020  1.393
 AT8  C2   C1   single    1.505  0.020  1.505
 AT8  C8   C23  aromatic  1.390  0.020  1.390
 AT8  C    C1   single    1.528  0.020  1.528
 AT8  C11  C12  single    1.505  0.020  1.505
 AT8  C11  C22  aromatic  1.388  0.020  1.388
 AT8  C23  C22  aromatic  1.388  0.020  1.388
 AT8  C23  CL2  single    1.735  0.020  1.735
 AT8  C12  N    single    1.450  0.020  1.450
 AT8  N    C13  single    1.448  0.020  1.448
 AT8  C13  C14  single    1.524  0.020  1.524
 AT8  C14  C15  single    1.488  0.020  1.488
 AT8  C15  N2   aromatic  1.359  0.020  1.359
 AT8  C15  N1   aromatic  1.307  0.020  1.307
 AT8  N2   C21  aromatic  1.366  0.020  1.366
 AT8  N1   C16  aromatic  1.371  0.020  1.371
 AT8  C21  C16  aromatic  1.404  0.020  1.404
 AT8  C21  C20  aromatic  1.385  0.020  1.385
 AT8  C16  C17  aromatic  1.391  0.020  1.391
 AT8  C20  C19  aromatic  1.383  0.020  1.383
 AT8  C17  C18  aromatic  1.382  0.020  1.382
 AT8  C19  C18  aromatic  1.405  0.020  1.405
 AT8  C19  CL1  single    1.726  0.020  1.726
 AT8  C18  CL   single    1.728  0.020  1.728
 AT8  C6   H1   single    0.930  0.020  1.080
 AT8  C5   H2   single    0.930  0.020  1.080
 AT8  C4   H3   single    0.930  0.020  1.080
 AT8  C3   H4   single    0.930  0.020  1.080
 AT8  C1   H5   single    0.970  0.020  1.090
 AT8  C1   H6   single    0.970  0.020  1.090
 AT8  C    H7   single    0.970  0.020  1.090
 AT8  C    H8   single    0.970  0.020  1.090
 AT8  C    H9   single    0.970  0.020  1.090
 AT8  C22  H10  single    0.930  0.020  1.080
 AT8  C10  H11  single    0.930  0.020  1.080
 AT8  C9   H12  single    0.930  0.020  1.080
 AT8  C12  H13  single    0.970  0.020  1.090
 AT8  C12  H14  single    0.970  0.020  1.090
 AT8  N    H15  single    0.890  0.020  1.040
 AT8  C13  H17  single    0.970  0.020  1.090
 AT8  C13  H18  single    0.970  0.020  1.090
 AT8  C14  H19  single    0.970  0.020  1.090
 AT8  C14  H20  single    0.970  0.020  1.090
 AT8  N2   H21  single    0.860  0.020  1.020
 AT8  C20  H23  single    0.930  0.020  1.080
 AT8  C17  H24  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
 AT8  C22  C23  C8   122.01  3.000
 AT8  C22  C23  CL2  118.32  3.000
 AT8  C8   C23  CL2  119.66  3.000
 AT8  C9   C8   C7   120.21  3.000
 AT8  C7   C8   C23  122.74  3.000
 AT8  C9   C8   C23  117.03  3.000
 AT8  C2   C7   C6   119.94  3.000
 AT8  C2   C7   C8   121.41  3.000
 AT8  C6   C7   C8   118.64  3.000
 AT8  H1   C6   C5   119.78  3.000
 AT8  H1   C6   C7   119.26  3.000
 AT8  C5   C6   C7   120.95  3.000
 AT8  H2   C5   C4   120.51  3.000
 AT8  H2   C5   C6   120.06  3.000
 AT8  C4   C5   C6   119.43  3.000
 AT8  H3   C4   C3   119.94  3.000
 AT8  H3   C4   C5   120.31  3.000
 AT8  C3   C4   C5   119.75  3.000
 AT8  H4   C3   C2   118.96  3.000
 AT8  H4   C3   C4   119.47  3.000
 AT8  C2   C3   C4   121.57  3.000
 AT8  C1   C2   C3   119.48  3.000
 AT8  C1   C2   C7   122.08  3.000
 AT8  C3   C2   C7   118.37  3.000
 AT8  H6   C1   H5   106.17  3.000
 AT8  H6   C1   C    109.25  3.000
 AT8  H5   C1   C    109.41  3.000
 AT8  H6   C1   C2   110.86  3.000
 AT8  H5   C1   C2   109.07  3.000
 AT8  C    C1   C2   111.91  3.000
 AT8  H9   C    H8   107.93  3.000
 AT8  H9   C    H7   107.74  3.000
 AT8  H8   C    H7   107.88  3.000
 AT8  H9   C    C1   110.82  3.000
 AT8  H8   C    C1   111.12  3.000
 AT8  H7   C    C1   111.20  3.000
 AT8  H10  C22  C11  119.97  3.000
 AT8  H10  C22  C23  119.87  3.000
 AT8  C11  C22  C23  120.16  3.000
 AT8  C12  C11  C10  120.68  3.000
 AT8  C12  C11  C22  120.66  3.000
 AT8  C10  C11  C22  118.66  3.000
 AT8  H11  C10  C9   119.77  3.000
 AT8  H11  C10  C11  119.75  3.000
 AT8  C9   C10  C11  120.48  3.000
 AT8  H12  C9   C10  119.79  3.000
 AT8  H12  C9   C8   118.57  3.000
 AT8  C10  C9   C8   121.64  3.000
 AT8  H14  C12  H13  106.18  3.000
 AT8  H14  C12  N    113.22  3.000
 AT8  H13  C12  N    107.79  3.000
 AT8  H14  C12  C11  109.43  3.000
 AT8  H13  C12  C11  109.03  3.000
 AT8  N    C12  C11  111.00  3.000
 AT8  H15  N    C13  109.32  3.000
 AT8  H15  N    C12  108.64  3.000
 AT8  C13  N    C12  112.68  3.000
 AT8  H18  C13  H17  106.48  3.000
 AT8  H18  C13  C14  109.35  3.000
 AT8  H17  C13  C14  109.28  3.000
 AT8  H18  C13  N    113.10  3.000
 AT8  H17  C13  N    108.42  3.000
 AT8  C14  C13  N    110.08  3.000
 AT8  H20  C14  H19  106.66  3.000
 AT8  H20  C14  C15  109.11  3.000
 AT8  H19  C14  C15  109.41  3.000
 AT8  H20  C14  C13  109.35  3.000
 AT8  H19  C14  C13  110.06  3.000
 AT8  C15  C14  C13  112.10  3.000
 AT8  N1   C15  N2   112.54  3.000
 AT8  N1   C15  C14  125.31  3.000
 AT8  N2   C15  C14  122.15  3.000
 AT8  H21  N2   C21  126.56  3.000
 AT8  H21  N2   C15  125.85  3.000
 AT8  C21  N2   C15  107.59  3.000
 AT8  C20  C21  C16  122.75  3.000
 AT8  C20  C21  N2   132.75  3.000
 AT8  C16  C21  N2   104.50  3.000
 AT8  C17  C16  N1   130.08  3.000
 AT8  C17  C16  C21  119.83  3.000
 AT8  N1   C16  C21  110.10  3.000
 AT8  C16  N1   C15  105.27  3.000
 AT8  H23  C20  C19  121.15  3.000
 AT8  H23  C20  C21  122.17  3.000
 AT8  C19  C20  C21  116.67  3.000
 AT8  C18  C19  CL1  119.93  3.000
 AT8  CL1  C19  C20  118.68  3.000
 AT8  C18  C19  C20  121.39  3.000
 AT8  C17  C18  CL   118.84  3.000
 AT8  CL   C18  C19  119.75  3.000
 AT8  C17  C18  C19  121.41  3.000
 AT8  H24  C17  C18  120.83  3.000
 AT8  H24  C17  C16  121.22  3.000
 AT8  C18  C17  C16  117.95  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
 AT8  CONST_01  C10  C9   C8   C23     0.00   0.0  0
 AT8  CONST_04  C10  C11  C22  C23     0.00   0.0  0
 AT8  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 AT8  CONST_06  C5   C6   C7   C8    180.00   0.0  0
 AT8  CONST_07  C3   C2   C7   C8    180.00   0.0  0
 AT8  CONST_08  C11  C22  C23  C8      0.00   0.0  0
 AT8  CONST_09  C4   C5   C6   C7      0.00   0.0  0
 AT8  CONST_10  C4   C3   C2   C7      0.00   0.0  0
 AT8  CONST_11  C10  C9   C8   C7    180.00   0.0  0
 AT8  CONST_12  C22  C23  C8   C7    180.00   0.0  0
 AT8  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 AT8  CONST_14  C3   C2   C7   C6      0.00   0.0  0
 AT8  CONST_16  C2   C7   C6   C5      0.00   0.0  0
 AT8  CONST_17  C2   C3   C4   C5      0.00   0.0  0
 AT8  CONST_19  C9   C10  C11  C22     0.00   0.0  0
 AT8  CONST_20  C9   C8   C23  C22     0.00   0.0  0
 AT8  CONST_21  C16  C21  N2   C15     0.00   0.0  0
 AT8  CONST_22  C20  C21  N2   C15   180.00   0.0  0
 AT8  CONST_23  C21  C16  N1   C15     0.00   0.0  0
 AT8  CONST_24  C17  C16  N1   C15   180.00   0.0  0
 AT8  CONST_25  C16  N1   C15  N2      0.00   0.0  0
 AT8  CONST_26  N1   C16  C21  N2      0.00   0.0  0
 AT8  CONST_27  C17  C16  C21  N2    180.00   0.0  0
 AT8  CONST_28  C19  C20  C21  N2    180.00   0.0  0
 AT8  CONST_29  N1   C15  N2   C21     0.00   0.0  0
 AT8  CONST_30  C18  C17  C16  C21     0.00   0.0  0
 AT8  CONST_31  C18  C19  C20  C21     0.00   0.0  0
 AT8  CONST_32  C19  C20  C21  C16     0.00   0.0  0
 AT8  CONST_33  C19  C18  C17  C16     0.00   0.0  0
 AT8  CONST_34  C20  C21  C16  N1    180.00   0.0  0
 AT8  CONST_35  C18  C17  C16  N1    180.00   0.0  0
 AT8  CONST_36  C17  C16  C21  C20     0.00   0.0  0
 AT8  CONST_37  C17  C18  C19  C20     0.00   0.0  0
 AT8  CONST_38  C9   C8   C23  CL2   180.00   0.0  0
 AT8  CONST_39  C7   C8   C23  CL2     0.00   0.0  0
 AT8  CONST_40  C11  C22  C23  CL2   180.00   0.0  0
 AT8  CONST_41  C12  C11  C22  C23   180.00   0.0  0
 AT8  CONST_42  C1   C2   C7   C8      0.00   0.0  0
 AT8  CONST_43  C1   C2   C7   C6    180.00   0.0  0
 AT8  CONST_44  C1   C2   C3   C4    180.00   0.0  0
 AT8  CONST_45  C12  C11  C10  C9    180.00   0.0  0
 AT8  CONST_46  C21  N2   C15  C14   180.00   0.0  0
 AT8  CONST_47  C16  N1   C15  C14   180.00   0.0  0
 AT8  CONST_48  CL1  C19  C20  C21   180.00   0.0  0
 AT8  CONST_49  CL   C18  C17  C16   180.00   0.0  0
 AT8  CONST_50  CL   C18  C19  C20   180.00   0.0  0
 AT8  CONST_51  C17  C18  C19  CL1   180.00   0.0  0
 AT8  CONST_52  H12  C9   C8   C23   180.00   0.0  0
 AT8  CONST_53  H11  C10  C9   C8    180.00   0.0  0
 AT8  CONST_54  H1   C6   C7   C8      0.00   0.0  0
 AT8  CONST_55  H10  C22  C23  C8    180.00   0.0  0
 AT8  CONST_56  H2   C5   C6   C7    180.00   0.0  0
 AT8  CONST_57  H4   C3   C2   C7    180.00   0.0  0
 AT8  CONST_58  H3   C4   C5   C6    180.00   0.0  0
 AT8  CONST_59  H23  C20  C21  N2      0.00   0.0  0
 AT8  CONST_60  H24  C17  C16  C21   180.00   0.0  0
 AT8  CONST_61  H21  N2   C21  C16   180.00   0.0  0
 AT8  Var_01    C    C1   C2   C7     85.09  30.0  2
 AT8  Var_02    N    C12  C11  C22   126.78  30.0  2
 AT8  Var_03    N2   C15  C14  C13   136.10  30.0  2
 AT8  Var_04    C13  N    C12  C11   175.45  30.0  3
 AT8  Var_05    C15  C14  C13  N     177.50  30.0  3
 AT8  Var_06    H7   C    C1   C2    -60.50  30.0  3
 AT8  Var_07    C14  C13  N    C12  -179.46  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
 AT8  plan-1  C8   0.020
 AT8  plan-1  C7   0.020
 AT8  plan-1  C6   0.020
 AT8  plan-1  C5   0.020
 AT8  plan-1  C4   0.020
 AT8  plan-1  C3   0.020
 AT8  plan-1  C2   0.020
 AT8  plan-1  C1   0.020
 AT8  plan-1  H1   0.020
 AT8  plan-1  H2   0.020
 AT8  plan-1  H3   0.020
 AT8  plan-1  H4   0.020
 AT8  plan-2  CL2  0.020
 AT8  plan-2  C23  0.020
 AT8  plan-2  C8   0.020
 AT8  plan-2  C7   0.020
 AT8  plan-2  C22  0.020
 AT8  plan-2  C11  0.020
 AT8  plan-2  C10  0.020
 AT8  plan-2  C9   0.020
 AT8  plan-2  C12  0.020
 AT8  plan-2  H10  0.020
 AT8  plan-2  H11  0.020
 AT8  plan-2  H12  0.020
 AT8  plan-3  C14  0.020
 AT8  plan-3  C15  0.020
 AT8  plan-3  N2   0.020
 AT8  plan-3  C21  0.020
 AT8  plan-3  C16  0.020
 AT8  plan-3  N1   0.020
 AT8  plan-3  C20  0.020
 AT8  plan-3  C19  0.020
 AT8  plan-3  CL1  0.020
 AT8  plan-3  C18  0.020
 AT8  plan-3  CL   0.020
 AT8  plan-3  C17  0.020
 AT8  plan-3  H21  0.020
 AT8  plan-3  H23  0.020
 AT8  plan-3  H24  0.020

