# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:13:21 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (1~{R})-2-[2-azanylidene-3-[(2-methylphenyl)methyl]benzimidazol-1-yl]-1-(3,4-dichlorophenyl)ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1CN2C(=N)N(C[C@H](O)c3ccc(Cl)c(Cl)c3)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
 5PZ  5PZ  (1~{R})-2-[2-azanylidene-3-[(2-methylphenyl)methyl]benzimidazol-1-yl]-1-(3,4-dichlorophenyl)ethanol  ligand  50  29  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5PZ
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
 5PZ  C10  C   CR5   0   0.694  -1.4733   0.3665   0.6314
 5PZ  N12  N   NR5   0  -0.593  -0.6361  -0.6258   0.1808
 5PZ  C13  C   CH2   0  -0.363   0.7382  -0.3928  -0.2023
 5PZ  C17  C   CR16  0  -0.295   3.6936  -1.5685   0.3423
 5PZ  C21  C   CR6   0   0.025   5.1088   0.6743  -0.4292
 5PZ  C24  C   CR56  0   0.344  -1.3465  -1.7993   0.0137
 5PZ  C26  C   CR16  0  -0.272  -1.9534  -4.0402  -0.4748
 5PZ  C28  C   CR16  0  -0.322  -3.6556  -2.4886   0.2835
 5PZ  C02  C   CR6   0   0.082  -6.0083   1.5827   0.3229
 5PZ  C03  C   CR16  0  -0.299  -6.7949   2.0603  -0.7205
 5PZ  C04  C   CR16  0  -0.253  -6.3754   1.9710  -2.0414
 5PZ  C05  C   CR16  0  -0.259  -5.1475   1.3990  -2.3310
 5PZ  C06  C   CR16  0  -0.286  -4.3493   0.9208  -1.2994
 5PZ  C07  C   CR6   0   0.052  -4.7668   1.0049   0.0228
 5PZ  C08  C   CH2   0  -0.386  -3.9084   0.4994   1.1598
 5PZ  N09  N   NR5   0  -0.594  -2.7228  -0.1949   0.7409
 5PZ  N11  N   N     0  -0.782  -1.0580   1.5526   0.8874
 5PZ  C14  C   CH1   0   0.009   1.6918  -0.1863   0.9852
 5PZ  O15  O   OH1   0  -0.698   1.5193   1.0510   1.6111
 5PZ  C16  C   CR6   0   0.079   3.1095  -0.3130   0.4758
 5PZ  C18  C   CR16  0  -0.201   4.9695  -1.7073  -0.1748
 5PZ  C19  C   CR6   0  -0.016   5.6833  -0.5835  -0.5648
 5PZ  CL1  CL  CL    0  -0.100   7.2727  -0.7637  -1.2045
 5PZ  C23  C   CR16  0  -0.271   3.8292   0.8086   0.0888
 5PZ  C25  C   CR16  0  -0.327  -0.9643  -3.0589  -0.4031
 5PZ  C27  C   CR16  0  -0.277  -3.2728  -3.7617  -0.1394
 5PZ  C29  C   CR56  0   0.328  -2.6724  -1.5239   0.3585
 5PZ  H1   H   HCH2  0   0.283   1.0611  -1.2527  -0.7869
 5PZ  H2   H   HCH2  0   0.279   0.7872   0.4768  -0.8641
 5PZ  H3   H   HCR6  0   0.266   3.1531  -2.4557   0.6497
 5PZ  H4   H   HCR6  0   0.258  -1.6813  -5.0362  -0.7970
 5PZ  H5   H   HCR6  0   0.269  -4.6857  -2.2731   0.5357
 5PZ  H6   H   HCH3  0   0.247  -5.7698   2.1993   2.3816
 5PZ  H7   H   HCH3  0   0.258  -7.4293   2.2294   1.7974
 5PZ  H8   H   HCH3  0   0.249  -6.6559   0.6976   2.1814
 5PZ  H9   H   HCR6  0   0.249  -7.7532   2.5115  -0.4918
 5PZ  H10  H   HCR6  0   0.254  -7.0062   2.3472  -2.8368
 5PZ  H11  H   HCR6  0   0.255  -4.8051   1.3230  -3.3547
 5PZ  H12  H   HCR6  0   0.249  -3.3926   0.4785  -1.5458
 5PZ  H13  H   HCH2  0   0.283  -3.6125   1.3295   1.8070
 5PZ  H14  H   HCH2  0   0.284  -4.4827  -0.1713   1.8045
 5PZ  H15  H   H     0   0.355  -1.7837   2.1853   1.1947
 5PZ  H17  H   HCH1  0   0.230   1.5141  -1.0132   1.6907
 5PZ  H18  H   HOH1  0   0.462   0.6160   1.3952   1.4073
 5PZ  H19  H   HCR6  0   0.289   5.4156  -2.6874  -0.2736
 5PZ  H20  H   HCR6  0   0.280   3.4011   1.7957   0.1948
 5PZ  H21  H   HCR6  0   0.269   0.0604  -3.2892  -0.6630
 5PZ  H22  H   HCR6  0   0.258  -4.0195  -4.5410  -0.2076
 5PZ  CL2  CL  CL    0  -0.100   5.9784   2.0874  -0.8976
 5PZ  C01  C   CH3   0  -0.746  -6.4888   1.6838   1.7416

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
 5PZ  C18  C17  aromatic  1.384  0.020  1.384
 5PZ  C18  C19  aromatic  1.387  0.020  1.387
 5PZ  C17  C16  aromatic  1.391  0.020  1.391
 5PZ  CL1  C19  single    1.723  0.020  1.723
 5PZ  C19  C21  aromatic  1.389  0.020  1.389
 5PZ  C26  C25  aromatic  1.395  0.020  1.395
 5PZ  C26  C27  aromatic  1.390  0.020  1.390
 5PZ  C16  C14  single    1.512  0.020  1.512
 5PZ  C16  C23  aromatic  1.388  0.020  1.388
 5PZ  C25  C24  aromatic  1.381  0.020  1.381
 5PZ  C14  O15  single    1.397  0.020  1.397
 5PZ  C14  C13  single    1.537  0.020  1.537
 5PZ  C21  C23  aromatic  1.387  0.020  1.387
 5PZ  C21  CL2  single    1.724  0.020  1.724
 5PZ  C27  C28  aromatic  1.395  0.020  1.395
 5PZ  C24  C29  aromatic  1.397  0.020  1.397
 5PZ  C24  N12  single    1.382  0.020  1.382
 5PZ  C28  C29  aromatic  1.379  0.020  1.379
 5PZ  C13  N12  single    1.446  0.020  1.446
 5PZ  C29  N09  single    1.384  0.020  1.384
 5PZ  N12  C10  single    1.374  0.020  1.374
 5PZ  C01  C02  single    1.501  0.020  1.501
 5PZ  C03  C04  aromatic  1.389  0.020  1.389
 5PZ  C03  C02  aromatic  1.391  0.020  1.391
 5PZ  C04  C05  aromatic  1.385  0.020  1.385
 5PZ  C02  C07  aromatic  1.402  0.020  1.402
 5PZ  C10  N09  single    1.374  0.020  1.374
 5PZ  C10  N11  double    1.282  0.020  1.282
 5PZ  N09  C08  single    1.436  0.020  1.436
 5PZ  C07  C06  aromatic  1.389  0.020  1.389
 5PZ  C07  C08  single    1.512  0.020  1.512
 5PZ  C05  C06  aromatic  1.389  0.020  1.389
 5PZ  C13  H1   single    0.970  0.020  1.090
 5PZ  C13  H2   single    0.970  0.020  1.090
 5PZ  C17  H3   single    0.930  0.020  1.080
 5PZ  C26  H4   single    0.930  0.020  1.080
 5PZ  C28  H5   single    0.930  0.020  1.080
 5PZ  C01  H6   single    0.970  0.020  1.090
 5PZ  C01  H7   single    0.970  0.020  1.090
 5PZ  C01  H8   single    0.970  0.020  1.090
 5PZ  C03  H9   single    0.930  0.020  1.080
 5PZ  C04  H10  single    0.930  0.020  1.080
 5PZ  C05  H11  single    0.930  0.020  1.080
 5PZ  C06  H12  single    0.930  0.020  1.080
 5PZ  C08  H13  single    0.970  0.020  1.090
 5PZ  C08  H14  single    0.970  0.020  1.090
 5PZ  N11  H15  single    0.890  0.020  1.040
 5PZ  C14  H17  single    0.970  0.020  1.090
 5PZ  O15  H18  single    0.850  0.020  0.980
 5PZ  C18  H19  single    0.930  0.020  1.080
 5PZ  C23  H20  single    0.930  0.020  1.080
 5PZ  C25  H21  single    0.930  0.020  1.080
 5PZ  C27  H22  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
 5PZ  N11  C10  N09  131.02  3.000
 5PZ  N11  C10  N12  122.41  3.000
 5PZ  N09  C10  N12  106.56  3.000
 5PZ  C24  N12  C13  126.40  3.000
 5PZ  C13  N12  C10  123.34  3.000
 5PZ  C24  N12  C10  109.86  3.000
 5PZ  H2   C13  H1   106.84  3.000
 5PZ  H2   C13  C14  109.44  3.000
 5PZ  H1   C13  C14  109.69  3.000
 5PZ  H2   C13  N12  109.34  3.000
 5PZ  H1   C13  N12  107.28  3.000
 5PZ  C14  C13  N12  114.00  3.000
 5PZ  H3   C17  C18  118.94  3.000
 5PZ  H3   C17  C16  120.16  3.000
 5PZ  C18  C17  C16  120.90  3.000
 5PZ  C23  C21  CL2  119.17  3.000
 5PZ  CL2  C21  C19  120.46  3.000
 5PZ  C23  C21  C19  120.37  3.000
 5PZ  C29  C24  C25  121.13  3.000
 5PZ  C29  C24  N12  106.89  3.000
 5PZ  C25  C24  N12  131.99  3.000
 5PZ  H4   C26  C27  119.69  3.000
 5PZ  H4   C26  C25  118.99  3.000
 5PZ  C27  C26  C25  121.32  3.000
 5PZ  H5   C28  C29  121.77  3.000
 5PZ  H5   C28  C27  120.90  3.000
 5PZ  C29  C28  C27  117.33  3.000
 5PZ  C07  C02  C03  118.79  3.000
 5PZ  C07  C02  C01  120.90  3.000
 5PZ  C03  C02  C01  120.31  3.000
 5PZ  H9   C03  C04  119.64  3.000
 5PZ  H9   C03  C02  118.99  3.000
 5PZ  C04  C03  C02  121.37  3.000
 5PZ  H10  C04  C05  120.43  3.000
 5PZ  H10  C04  C03  120.03  3.000
 5PZ  C05  C04  C03  119.54  3.000
 5PZ  H11  C05  C06  119.77  3.000
 5PZ  H11  C05  C04  120.48  3.000
 5PZ  C06  C05  C04  119.75  3.000
 5PZ  H12  C06  C07  120.47  3.000
 5PZ  H12  C06  C05  118.65  3.000
 5PZ  C07  C06  C05  120.88  3.000
 5PZ  C08  C07  C06  121.67  3.000
 5PZ  C08  C07  C02  118.67  3.000
 5PZ  C06  C07  C02  119.67  3.000
 5PZ  H14  C08  H13  105.00  3.000
 5PZ  H14  C08  N09  108.00  3.000
 5PZ  H13  C08  N09  108.44  3.000
 5PZ  H14  C08  C07  110.51  3.000
 5PZ  H13  C08  C07  110.19  3.000
 5PZ  N09  C08  C07  114.27  3.000
 5PZ  C29  N09  C08  125.09  3.000
 5PZ  C08  N09  C10  125.19  3.000
 5PZ  C29  N09  C10  109.71  3.000
 5PZ  H15  N11  C10  114.03  3.000
 5PZ  H17  C14  C16  107.72  3.000
 5PZ  H17  C14  O15  110.97  3.000
 5PZ  C16  C14  O15  109.93  3.000
 5PZ  H17  C14  C13  107.10  3.000
 5PZ  O15  C14  C13  112.85  3.000
 5PZ  C16  C14  C13  108.07  3.000
 5PZ  H18  O15  C14  109.21  3.000
 5PZ  C23  C16  C14  120.84  3.000
 5PZ  C23  C16  C17  119.01  3.000
 5PZ  C14  C16  C17  120.11  3.000
 5PZ  H19  C18  C19  119.76  3.000
 5PZ  H19  C18  C17  120.36  3.000
 5PZ  C19  C18  C17  119.88  3.000
 5PZ  CL1  C19  C18  119.63  3.000
 5PZ  CL1  C19  C21  120.82  3.000
 5PZ  C18  C19  C21  119.55  3.000
 5PZ  H20  C23  C16  120.35  3.000
 5PZ  H20  C23  C21  119.36  3.000
 5PZ  C16  C23  C21  120.29  3.000
 5PZ  H21  C25  C26  120.62  3.000
 5PZ  H21  C25  C24  121.93  3.000
 5PZ  C26  C25  C24  117.45  3.000
 5PZ  H22  C27  C28  119.16  3.000
 5PZ  H22  C27  C26  119.74  3.000
 5PZ  C28  C27  C26  121.10  3.000
 5PZ  N09  C29  C28  131.35  3.000
 5PZ  N09  C29  C24  106.98  3.000
 5PZ  C28  C29  C24  121.67  3.000
 5PZ  H8   C01  H7   107.43  3.000
 5PZ  H8   C01  H6   106.91  3.000
 5PZ  H7   C01  H6   107.58  3.000
 5PZ  H8   C01  C02  111.63  3.000
 5PZ  H7   C01  C02  111.02  3.000
 5PZ  H6   C01  C02  112.02  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
 5PZ  CONST_01  C21  C19  C18  C17     0.00   0.0  0
 5PZ  CONST_02  C21  C23  C16  C17     0.00   0.0  0
 5PZ  CONST_03  C27  C26  C25  C24     0.00   0.0  0
 5PZ  CONST_04  C27  C28  C29  C24     0.00   0.0  0
 5PZ  CONST_05  C29  C24  C25  C26     0.00   0.0  0
 5PZ  CONST_06  C29  C28  C27  C26     0.00   0.0  0
 5PZ  CONST_07  C25  C26  C27  C28     0.00   0.0  0
 5PZ  CONST_08  C25  C24  C29  C28     0.00   0.0  0
 5PZ  CONST_09  C05  C04  C03  C02     0.00   0.0  0
 5PZ  CONST_10  C05  C06  C07  C02     0.00   0.0  0
 5PZ  CONST_11  C06  C05  C04  C03     0.00   0.0  0
 5PZ  CONST_12  C06  C07  C02  C03     0.00   0.0  0
 5PZ  CONST_13  C07  C02  C03  C04     0.00   0.0  0
 5PZ  CONST_14  C07  C06  C05  C04     0.00   0.0  0
 5PZ  CONST_15  C19  C18  C17  C16     0.00   0.0  0
 5PZ  CONST_16  C19  C21  C23  C16     0.00   0.0  0
 5PZ  CONST_17  C23  C16  C17  C18     0.00   0.0  0
 5PZ  CONST_18  C23  C21  C19  C18     0.00   0.0  0
 5PZ  CONST_19  C29  C24  N12  C10     0.00   0.0  0
 5PZ  CONST_20  C24  C29  N09  C10     0.00   0.0  0
 5PZ  CONST_21  N09  C29  C24  N12     0.00   0.0  0
 5PZ  CONST_22  C29  N09  C10  N12     0.00   0.0  0
 5PZ  CONST_23  N09  C10  N12  C24     0.00   0.0  0
 5PZ  CONST_24  CL1  C19  C18  C17   180.00   0.0  0
 5PZ  CONST_25  C14  C16  C23  C21   180.00   0.0  0
 5PZ  CONST_26  C04  C03  C02  C01   180.00   0.0  0
 5PZ  CONST_27  C06  C07  C02  C01   180.00   0.0  0
 5PZ  CONST_28  C08  C07  C02  C03   180.00   0.0  0
 5PZ  CONST_29  C08  C07  C06  C05   180.00   0.0  0
 5PZ  CONST_30  C18  C17  C16  C14   180.00   0.0  0
 5PZ  CONST_31  CL2  C21  C23  C16   180.00   0.0  0
 5PZ  CONST_32  CL2  C21  C19  C18   180.00   0.0  0
 5PZ  CONST_33  C23  C21  C19  CL1   180.00   0.0  0
 5PZ  CONST_34  C08  N09  C10  N12   180.00   0.0  0
 5PZ  CONST_35  C29  C24  N12  C13   180.00   0.0  0
 5PZ  CONST_36  N09  C10  N12  C13   180.00   0.0  0
 5PZ  CONST_37  C08  N09  C29  C24   180.00   0.0  0
 5PZ  CONST_38  N11  C10  N12  C24   180.00   0.0  0
 5PZ  CONST_39  C29  N09  C10  N11   180.00   0.0  0
 5PZ  CONST_40  H21  C25  C24  N12     0.00   0.0  0
 5PZ  CONST_41  H20  C23  C16  C17   180.00   0.0  0
 5PZ  CONST_42  H19  C18  C19  C21   180.00   0.0  0
 5PZ  CONST_43  H4   C26  C25  C24   180.00   0.0  0
 5PZ  CONST_44  H5   C28  C29  C24   180.00   0.0  0
 5PZ  CONST_45  H10  C04  C03  C02   180.00   0.0  0
 5PZ  CONST_46  H12  C06  C07  C02   180.00   0.0  0
 5PZ  CONST_47  H11  C05  C04  C03   180.00   0.0  0
 5PZ  CONST_48  H9   C03  C04  C05   180.00   0.0  0
 5PZ  CONST_49  H3   C17  C18  C19   180.00   0.0  0
 5PZ  CONST_50  H22  C27  C26  C25   180.00   0.0  0
 5PZ  CONST_51  N11  C10  N12  C13     0.00   0.0  0
 5PZ  CONST_52  N11  C10  N09  C08     0.00   0.0  0
 5PZ  CONST_53  H15  N11  C10  N12   180.00   0.0  0
 5PZ  Var_01    C07  C08  N09  C10    96.39  30.0  3
 5PZ  Var_02    N09  C08  C07  C02   173.98  30.0  2
 5PZ  Var_03    C14  C13  N12  C10    75.12  30.0  2
 5PZ  Var_04    H6   C01  C02  C03  -125.14  30.0  2

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
 5PZ  chir_01  C14  C16  O15  C13  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
 5PZ  plan-1  C02  0.020
 5PZ  plan-1  C03  0.020
 5PZ  plan-1  C04  0.020
 5PZ  plan-1  C05  0.020
 5PZ  plan-1  C06  0.020
 5PZ  plan-1  C07  0.020
 5PZ  plan-1  C08  0.020
 5PZ  plan-1  H9   0.020
 5PZ  plan-1  H10  0.020
 5PZ  plan-1  H11  0.020
 5PZ  plan-1  H12  0.020
 5PZ  plan-1  C01  0.020
 5PZ  plan-2  C17  0.020
 5PZ  plan-2  C21  0.020
 5PZ  plan-2  C14  0.020
 5PZ  plan-2  C16  0.020
 5PZ  plan-2  C18  0.020
 5PZ  plan-2  C19  0.020
 5PZ  plan-2  CL1  0.020
 5PZ  plan-2  C23  0.020
 5PZ  plan-2  H3   0.020
 5PZ  plan-2  H19  0.020
 5PZ  plan-2  H20  0.020
 5PZ  plan-2  CL2  0.020
 5PZ  plan-3  C10  0.020
 5PZ  plan-3  N12  0.020
 5PZ  plan-3  C13  0.020
 5PZ  plan-3  C24  0.020
 5PZ  plan-3  C26  0.020
 5PZ  plan-3  C28  0.020
 5PZ  plan-3  C08  0.020
 5PZ  plan-3  N09  0.020
 5PZ  plan-3  N11  0.020
 5PZ  plan-3  C25  0.020
 5PZ  plan-3  C27  0.020
 5PZ  plan-3  C29  0.020
 5PZ  plan-3  H4   0.020
 5PZ  plan-3  H5   0.020
 5PZ  plan-3  H15  0.020
 5PZ  plan-3  H21  0.020
 5PZ  plan-3  H22  0.020

