# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:33:55 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](COc1ccc(Cl)cc1Cl)CN2C(=N)N(CCN3CCCCC3)c4ccccc24
#
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
 768  768  (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol  ligand  59  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_768
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
 768  O1    O   OH1   0  -0.647  -1.1809   1.6597   0.7478
 768  C16   C   CH1   0  -0.013  -1.1497   0.5493  -0.1102
 768  C17   C   CH2   0  -0.203  -2.4950   0.2571  -0.7499
 768  O2    O   O2    0  -0.450  -3.4159  -0.0286   0.2873
 768  C18   C   CR6   0   0.478  -4.6769  -0.3295  -0.0382
 768  C19   C   CR16  0  -0.394  -5.1742  -0.3957  -1.3366
 768  C20   C   CR16  0  -0.193  -6.5024  -0.7206  -1.5747
 768  C21   C   CR6   0  -0.073  -7.3457  -0.9823  -0.5114
 768  CL1   CL  CL    0  -0.125  -9.0044  -1.3885  -0.8003
 768  C22   C   CR16  0  -0.162  -6.8793  -0.9229   0.7937
 768  C23   C   CR6   0  -0.166  -5.5550  -0.5990   1.0176
 768  CL2   CL  CL    0  -0.098  -4.9591  -0.5261   2.6358
 768  C15   C   CH2   0  -0.341  -0.0926   0.6926  -1.2047
 768  N3    N   NR5   0  -0.581   1.2106   0.9678  -0.6671
 768  C14   C   CR5   0   0.615   2.0595  -0.0170  -0.2076
 768  N4    N   N     0  -0.718   1.7745  -1.2615  -0.2426
 768  C13   C   CR56  0   0.344   1.7830   2.2089  -0.4939
 768  C12   C   CR16  0  -0.337   1.3347   3.4822  -0.7844
 768  C11   C   CR16  0  -0.278   2.1900   4.5492  -0.5037
 768  C10   C   CR16  0  -0.278   3.4468   4.3388   0.0487
 768  C9    C   CR16  0  -0.333   3.8975   3.0508   0.3436
 768  C8    C   CR56  0   0.331   3.0479   1.9984   0.0681
 768  N2    N   NR5   0  -0.586   3.1851   0.6374   0.2548
 768  C7    C   CH2   0  -0.362   4.3653  -0.0345   0.7369
 768  C6    C   CH2   0  -0.263   5.2855  -0.4492  -0.4103
 768  N1    N   NT    0  -0.422   6.4521  -1.1648   0.0592
 768  C5    C   CH2   0  -0.279   7.5254  -1.1293  -0.9232
 768  C4    C   CH2   0  -0.439   8.7920  -1.7769  -0.3855
 768  C3    C   CH2   0  -0.439   8.5199  -3.2090   0.0565
 768  C2    C   CH2   0  -0.436   7.3515  -3.2341   1.0329
 768  C1    C   CH2   0  -0.289   6.1391  -2.5355   0.4360
 768  HO1   H   HOH1  0   0.446  -1.4857   2.4323   0.2597
 768  H16   H   HCH1  0   0.254  -0.8719  -0.3046   0.5143
 768  H17   H   HCH2  0   0.238  -2.8359   1.1180  -1.3394
 768  H17A  H   HCH2  0   0.244  -2.4020  -0.5973  -1.4293
 768  H19   H   HCR6  0   0.301  -4.5351  -0.1990  -2.1862
 768  H20   H   HCR6  0   0.289  -6.8648  -0.7685  -2.5922
 768  H22   H   HCR6  0   0.301  -7.5358  -1.1251   1.6288
 768  H15   H   HCH2  0   0.274  -0.0385  -0.2269  -1.7891
 768  H15A  H   HCH2  0   0.268  -0.3526   1.4964  -1.8981
 768  HN4   H   H     0   0.331   2.5283  -1.8353   0.1141
 768  H12   H   HCR6  0   0.262   0.3586   3.6597  -1.2166
 768  H11   H   HCR6  0   0.253   1.8611   5.5569  -0.7197
 768  H10   H   HCR6  0   0.252   4.0898   5.1840   0.2551
 768  H9    H   HCR6  0   0.267   4.8798   2.8915   0.7693
 768  H7    H   HCH2  0   0.275   4.8930   0.6341   1.4172
 768  H7A   H   HCH2  0   0.260   4.0515  -0.8907   1.3365
 768  H6    H   HCH2  0   0.202   4.7112  -1.0287  -1.1538
 768  H6A   H   HCH2  0   0.243   5.6167   0.4600  -0.9190
 768  H5    H   HCH2  0   0.186   7.2281  -1.6367  -1.8584
 768  H5A   H   HCH2  0   0.235   7.7242  -0.0866  -1.1817
 768  H4    H   HCH2  0   0.231   9.5647  -1.7478  -1.1568
 768  H4A   H   HCH2  0   0.215   9.1622  -1.1909   0.4618
 768  H3    H   HCH2  0   0.211   8.2722  -3.8190  -0.8189
 768  H3A   H   HCH2  0   0.231   9.4111  -3.6524   0.5059
 768  H2    H   HCH2  0   0.231   7.0823  -4.2598   1.2941
 768  H2A   H   HCH2  0   0.216   7.6327  -2.7305   1.9626
 768  H1    H   HCH2  0   0.235   5.3279  -2.5363   1.1665
 768  H1A   H   HCH2  0   0.188   5.7779  -3.1110  -0.4357

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
 768  O1   C16   single    1.404  0.020  1.404
 768  C16  C17   single    1.518  0.020  1.518
 768  C16  C15   single    1.528  0.020  1.528
 768  C17  O2    single    1.416  0.020  1.416
 768  O2   C18   single    1.337  0.020  1.337
 768  C18  C19   aromatic  1.392  0.020  1.392
 768  C18  C23   aromatic  1.399  0.020  1.399
 768  C19  C20   aromatic  1.388  0.020  1.388
 768  C20  C21   aromatic  1.382  0.020  1.382
 768  C21  CL1   single    1.732  0.020  1.732
 768  C21  C22   aromatic  1.387  0.020  1.387
 768  C22  C23   aromatic  1.382  0.020  1.382
 768  C23  CL2   single    1.726  0.020  1.726
 768  C15  N3    single    1.436  0.020  1.436
 768  N3   C14   single    1.379  0.020  1.379
 768  N3   C13   single    1.378  0.020  1.378
 768  C14  N4    double    1.277  0.020  1.277
 768  C14  N2    single    1.382  0.020  1.382
 768  C13  C12   aromatic  1.381  0.020  1.381
 768  C13  C8    aromatic  1.400  0.020  1.400
 768  C12  C11   aromatic  1.396  0.020  1.396
 768  C11  C10   aromatic  1.389  0.020  1.389
 768  C10  C9    aromatic  1.396  0.020  1.396
 768  C9   C8    aromatic  1.380  0.020  1.380
 768  C8   N2    single    1.381  0.020  1.381
 768  N2   C7    single    1.441  0.020  1.441
 768  C7   C6    single    1.528  0.020  1.528
 768  C6   N1    single    1.447  0.020  1.447
 768  N1   C5    single    1.455  0.020  1.455
 768  N1   C1    single    1.456  0.020  1.456
 768  C5   C4    single    1.521  0.020  1.521
 768  C4   C3    single    1.523  0.020  1.523
 768  C3   C2    single    1.523  0.020  1.523
 768  C2   C1    single    1.521  0.020  1.521
 768  O1   HO1   single    0.850  0.020  0.980
 768  C16  H16   single    0.970  0.020  1.090
 768  C17  H17   single    0.970  0.020  1.090
 768  C17  H17A  single    0.970  0.020  1.090
 768  C19  H19   single    0.930  0.020  1.080
 768  C20  H20   single    0.930  0.020  1.080
 768  C22  H22   single    0.930  0.020  1.080
 768  C15  H15   single    0.970  0.020  1.090
 768  C15  H15A  single    0.970  0.020  1.090
 768  N4   HN4   single    0.890  0.020  1.040
 768  C12  H12   single    0.930  0.020  1.080
 768  C11  H11   single    0.930  0.020  1.080
 768  C10  H10   single    0.930  0.020  1.080
 768  C9   H9    single    0.930  0.020  1.080
 768  C7   H7    single    0.970  0.020  1.090
 768  C7   H7A   single    0.970  0.020  1.090
 768  C6   H6    single    0.970  0.020  1.090
 768  C6   H6A   single    0.970  0.020  1.090
 768  C5   H5    single    0.970  0.020  1.090
 768  C5   H5A   single    0.970  0.020  1.090
 768  C4   H4    single    0.970  0.020  1.090
 768  C4   H4A   single    0.970  0.020  1.090
 768  C3   H3    single    0.970  0.020  1.090
 768  C3   H3A   single    0.970  0.020  1.090
 768  C2   H2    single    0.970  0.020  1.090
 768  C2   H2A   single    0.970  0.020  1.090
 768  C1   H1    single    0.970  0.020  1.090
 768  C1   H1A   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
 768  HO1   O1   C16  109.37  3.000
 768  H16   C16  C15  107.84  3.000
 768  H16   C16  C17  108.38  3.000
 768  C15   C16  C17  109.22  3.000
 768  H16   C16  O1   105.92  3.000
 768  C15   C16  O1   112.27  3.000
 768  C17   C16  O1   112.97  3.000
 768  H17A  C17  H17  107.76  3.000
 768  H17A  C17  O2   110.61  3.000
 768  H17   C17  O2   110.46  3.000
 768  H17A  C17  C16  109.65  3.000
 768  H17   C17  C16  110.52  3.000
 768  O2    C17  C16  107.85  3.000
 768  C18   O2   C17  118.72  3.000
 768  C23   C18  C19  118.06  3.000
 768  C23   C18  O2   116.85  3.000
 768  C19   C18  O2   125.09  3.000
 768  H19   C19  C20  118.26  3.000
 768  H19   C19  C18  120.88  3.000
 768  C20   C19  C18  120.86  3.000
 768  H20   C20  C21  120.74  3.000
 768  H20   C20  C19  119.51  3.000
 768  C21   C20  C19  119.75  3.000
 768  C22   C21  CL1  119.27  3.000
 768  C22   C21  C20  120.70  3.000
 768  CL1   C21  C20  120.03  3.000
 768  H22   C22  C23  120.04  3.000
 768  H22   C22  C21  120.96  3.000
 768  C23   C22  C21  119.00  3.000
 768  CL2   C23  C22  119.53  3.000
 768  CL2   C23  C18  118.85  3.000
 768  C22   C23  C18  121.62  3.000
 768  H15A  C15  H15  106.97  3.000
 768  H15A  C15  N3   108.21  3.000
 768  H15   C15  N3   108.49  3.000
 768  H15A  C15  C16  111.02  3.000
 768  H15   C15  C16  109.81  3.000
 768  N3    C15  C16  112.18  3.000
 768  C13   N3   C14  110.23  3.000
 768  C13   N3   C15  126.63  3.000
 768  C14   N3   C15  123.12  3.000
 768  N2    C14  N4   130.72  3.000
 768  N2    C14  N3   105.95  3.000
 768  N4    C14  N3   123.33  3.000
 768  HN4   N4   C14  112.12  3.000
 768  C8    C13  C12  121.09  3.000
 768  C8    C13  N3   106.88  3.000
 768  C12   C13  N3   132.03  3.000
 768  H12   C12  C11  120.50  3.000
 768  H12   C12  C13  121.87  3.000
 768  C11   C12  C13  117.63  3.000
 768  H11   C11  C10  119.72  3.000
 768  H11   C11  C12  119.05  3.000
 768  C10   C11  C12  121.23  3.000
 768  H10   C10  C9   119.25  3.000
 768  H10   C10  C11  119.69  3.000
 768  C9    C10  C11  121.06  3.000
 768  H9    C9   C8   121.65  3.000
 768  H9    C9   C10  120.79  3.000
 768  C8    C9   C10  117.55  3.000
 768  N2    C8   C9   131.57  3.000
 768  N2    C8   C13  106.99  3.000
 768  C9    C8   C13  121.44  3.000
 768  C7    N2   C8   125.89  3.000
 768  C7    N2   C14  123.94  3.000
 768  C8    N2   C14  109.92  3.000
 768  H7A   C7   H7   106.11  3.000
 768  H7A   C7   C6   111.88  3.000
 768  H7    C7   C6   110.08  3.000
 768  H7A   C7   N2   108.31  3.000
 768  H7    C7   N2   108.62  3.000
 768  C6    C7   N2   111.63  3.000
 768  H6A   C6   H6   106.31  3.000
 768  H6A   C6   N1   108.55  3.000
 768  H6    C6   N1   112.23  3.000
 768  H6A   C6   C7   107.83  3.000
 768  H6    C6   C7   109.56  3.000
 768  N1    C6   C7   112.10  3.000
 768  C1    N1   C5   110.87  3.000
 768  C1    N1   C6   112.11  3.000
 768  C5    N1   C6   111.31  3.000
 768  H5A   C5   H5   106.68  3.000
 768  H5A   C5   C4   109.79  3.000
 768  H5    C5   C4   109.14  3.000
 768  H5A   C5   N1   108.49  3.000
 768  H5    C5   N1   111.21  3.000
 768  C4    C5   N1   111.42  3.000
 768  H4A   C4   H4   107.05  3.000
 768  H4A   C4   C3   109.82  3.000
 768  H4    C4   C3   110.87  3.000
 768  H4A   C4   C5   109.11  3.000
 768  H4    C4   C5   109.16  3.000
 768  C3    C4   C5   110.74  3.000
 768  H3A   C3   H3   106.70  3.000
 768  H3A   C3   C2   110.83  3.000
 768  H3    C3   C2   109.25  3.000
 768  H3A   C3   C4   110.81  3.000
 768  H3    C3   C4   109.39  3.000
 768  C2    C3   C4   109.79  3.000
 768  H2A   C2   H2   107.00  3.000
 768  H2A   C2   C1   109.08  3.000
 768  H2    C2   C1   109.19  3.000
 768  H2A   C2   C3   109.88  3.000
 768  H2    C2   C3   110.98  3.000
 768  C1    C2   C3   110.63  3.000
 768  H1A   C1   H1   106.52  3.000
 768  H1A   C1   C2   109.32  3.000
 768  H1    C1   C2   109.23  3.000
 768  H1A   C1   N1   110.88  3.000
 768  H1    C1   N1   109.50  3.000
 768  C2    C1   N1   111.27  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
 768  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 768  CONST_02  C21  C22  C23  C18     0.00   0.0  0
 768  CONST_03  C22  C23  C18  C19     0.00   0.0  0
 768  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 768  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 768  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 768  CONST_07  C10  C11  C12  C13     0.00   0.0  0
 768  CONST_08  C10  C9   C8   C13     0.00   0.0  0
 768  CONST_09  C9   C8   C13  C12     0.00   0.0  0
 768  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 768  CONST_11  C8   C13  C12  C11     0.00   0.0  0
 768  CONST_12  C8   C9   C10  C11     0.00   0.0  0
 768  CONST_13  C8   N2   C14  N3      0.00   0.0  0
 768  CONST_14  N2   C8   C13  N3      0.00   0.0  0
 768  CONST_15  C8   C13  N3   C14     0.00   0.0  0
 768  CONST_16  C13  C8   N2   C14     0.00   0.0  0
 768  CONST_17  N2   C14  N3   C13     0.00   0.0  0
 768  CONST_18  C20  C19  C18  O2    180.00   0.0  0
 768  CONST_19  C22  C23  C18  O2    180.00   0.0  0
 768  CONST_20  CL2  C23  C18  C19   180.00   0.0  0
 768  CONST_21  CL1  C21  C20  C19   180.00   0.0  0
 768  CONST_22  CL2  C23  C22  C21   180.00   0.0  0
 768  CONST_23  C23  C22  C21  CL1   180.00   0.0  0
 768  CONST_24  N2   C14  N3   C15   180.00   0.0  0
 768  CONST_25  C8   C13  N3   C15   180.00   0.0  0
 768  CONST_26  C7   N2   C14  N3    180.00   0.0  0
 768  CONST_27  C13  N3   C14  N4    180.00   0.0  0
 768  CONST_28  C8   N2   C14  N4    180.00   0.0  0
 768  CONST_29  C7   N2   C8   C13   180.00   0.0  0
 768  CONST_30  H20  C20  C19  C18   180.00   0.0  0
 768  CONST_31  H22  C22  C23  C18   180.00   0.0  0
 768  CONST_32  H19  C19  C20  C21   180.00   0.0  0
 768  CONST_33  H12  C12  C13  N3      0.00   0.0  0
 768  CONST_34  H11  C11  C12  C13   180.00   0.0  0
 768  CONST_35  H9   C9   C8   C13   180.00   0.0  0
 768  CONST_36  H10  C10  C11  C12   180.00   0.0  0
 768  CONST_37  N4   C14  N3   C15     0.00   0.0  0
 768  CONST_38  C7   N2   C14  N4      0.00   0.0  0
 768  CONST_39  HN4  N4   C14  N3    180.00   0.0  0
 768  Var_01    C3   C4   C5   N1     56.55  30.0  1
 768  Var_02    C3   C2   C1   N1    -57.06  30.0  1
 768  Var_03    C2   C1   N1   C5     59.58  30.0  1
 768  Var_04    C2   C3   C4   C5    -53.35  30.0  1
 768  Var_05    C1   N1   C5   C4    -59.35  30.0  1
 768  Var_06    C1   C2   C3   C4     53.60  30.0  1
 768  Var_07    C14  N3   C15  C16    83.63  30.0  3
 768  Var_08    C19  C18  O2   C17     0.39  30.0  2
 768  Var_09    C6   C7   N2   C14    82.93  30.0  3
 768  Var_10    N1   C6   C7   N2   -178.05  30.0  3
 768  Var_11    C5   N1   C6   C7   -159.31  30.0  3
 768  Var_12    H17  C17  O2   C18    59.64  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 768  chir_01  C16  O1  C17  C15  negativ

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
 768  plan-1  O2   0.020
 768  plan-1  C18  0.020
 768  plan-1  C19  0.020
 768  plan-1  C20  0.020
 768  plan-1  C21  0.020
 768  plan-1  CL1  0.020
 768  plan-1  C22  0.020
 768  plan-1  C23  0.020
 768  plan-1  CL2  0.020
 768  plan-1  H19  0.020
 768  plan-1  H20  0.020
 768  plan-1  H22  0.020
 768  plan-2  C15  0.020
 768  plan-2  N3   0.020
 768  plan-2  C14  0.020
 768  plan-2  N4   0.020
 768  plan-2  C13  0.020
 768  plan-2  C12  0.020
 768  plan-2  C11  0.020
 768  plan-2  C10  0.020
 768  plan-2  C9   0.020
 768  plan-2  C8   0.020
 768  plan-2  N2   0.020
 768  plan-2  C7   0.020
 768  plan-2  HN4  0.020
 768  plan-2  H12  0.020
 768  plan-2  H11  0.020
 768  plan-2  H10  0.020
 768  plan-2  H9   0.020

