# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 13:06:47 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-(2-chloranyl-6-methoxy-benzimidazol-1-yl)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc(Cl)n(c3ccc(C=O)cc3)c2c1
#
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
 UOT  UOT  4-(2-chloranyl-6-methoxy-benzimidazol-1-yl)benzaldehyde  ligand  31  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UOT
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
 UOT  C10  C   CR6   0   0.386  -13.9347  -18.8613   0.3260
 UOT  C12  C   CH3   0  -0.436  -12.6167  -16.8896   0.5231
 UOT  C13  C   CR16  0  -0.389  -13.2123  -19.2998  -0.7993
 UOT  C14  C   CR16  0  -0.311  -13.5351  -20.4833  -1.4420
 UOT  C15  C   CR56  0   0.133  -14.5972  -21.2347  -0.9579
 UOT  C17  C   CR5   0   0.363  -16.0875  -22.6798  -0.5867
 UOT  C03  C   CR6   0  -0.006  -19.1535  -21.6508   3.4135
 UOT  C04  C   CR16  0  -0.276  -19.1317  -20.6579   2.4396
 UOT  C05  C   CR16  0  -0.247  -18.1854  -20.6896   1.4289
 UOT  C06  C   CR6   0   0.289  -17.2536  -21.7177   1.4055
 UOT  C08  C   CR56  0   0.363  -15.3076  -20.7752   0.1592
 UOT  C09  C   CR16  0  -0.401  -15.0028  -19.6024   0.8256
 UOT  C19  C   CR16  0  -0.247  -17.2571  -22.7102   2.3811
 UOT  C20  C   CR16  0  -0.264  -18.2123  -22.6787   3.3785
 UOT  N07  N   NR5   0  -0.629  -16.2731  -21.7358   0.3885
 UOT  N16  N   N     0  -0.428  -15.1207  -22.4343  -1.3980
 UOT  O11  O   O2    0  -0.471  -13.6562  -17.7237   0.9917
 UOT  CL1  CL  CL    0  -0.059  -17.1135  -24.0288  -0.6865
 UOT  H1   H   HCH3  0   0.259  -12.5835  -16.0344   1.1939
 UOT  H2   H   HCH3  0   0.228  -11.6453  -17.3902   0.5462
 UOT  H3   H   HCH3  0   0.228  -12.8042  -16.5312  -0.4926
 UOT  H4   H   HCR6  0   0.280  -12.3854  -18.7179  -1.1814
 UOT  H5   H   HCR6  0   0.266  -12.9678  -20.8110  -2.3030
 UOT  H6   H   H     0   0.203  -20.8639  -20.7270   4.3948
 UOT  H9   H   HCR6  0   0.281  -19.8618  -19.8579   2.4641
 UOT  H10  H   HCR6  0   0.289  -18.1750  -19.9269   0.6613
 UOT  H11  H   HCR6  0   0.279  -15.5565  -19.2614   1.6910
 UOT  H12  H   HCR6  0   0.288  -16.5122  -23.4947   2.3623
 UOT  H13  H   HCR6  0   0.277  -18.2195  -23.4491   4.1383
 UOT  O1   O   O     0  -0.366  -20.2858  -22.3971   5.3623
 UOT  C02  C   C1    0   0.121  -20.1783  -21.5895   4.4717

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
 UOT  N16  C15  aromatic  1.381  0.020  1.381
 UOT  N16  C17  aromatic  1.286  0.020  1.286
 UOT  C14  C15  aromatic  1.388  0.020  1.388
 UOT  C14  C13  aromatic  1.385  0.020  1.385
 UOT  CL1  C17  single    1.698  0.020  1.698
 UOT  C15  C08  aromatic  1.401  0.020  1.401
 UOT  C17  N07  aromatic  1.370  0.020  1.370
 UOT  C13  C10  aromatic  1.407  0.020  1.407
 UOT  C08  N07  aromatic  1.381  0.020  1.381
 UOT  C08  C09  aromatic  1.383  0.020  1.383
 UOT  N07  C06  single    1.413  0.020  1.413
 UOT  C10  C09  aromatic  1.393  0.020  1.393
 UOT  C10  O11  single    1.347  0.020  1.347
 UOT  C12  O11  single    1.413  0.020  1.413
 UOT  C05  C06  aromatic  1.388  0.020  1.388
 UOT  C05  C04  aromatic  1.385  0.020  1.385
 UOT  C06  C19  aromatic  1.392  0.020  1.392
 UOT  C04  C03  aromatic  1.391  0.020  1.391
 UOT  C19  C20  aromatic  1.381  0.020  1.381
 UOT  C03  C20  aromatic  1.394  0.020  1.394
 UOT  C03  C02  single    1.474  0.020  1.474
 UOT  C12  H1   single    0.970  0.020  1.090
 UOT  C12  H2   single    0.970  0.020  1.090
 UOT  C12  H3   single    0.970  0.020  1.090
 UOT  C13  H4   single    0.930  0.020  1.080
 UOT  C14  H5   single    0.930  0.020  1.080
 UOT  C02  H6   single    0.930  0.020  1.080
 UOT  C04  H9   single    0.930  0.020  1.080
 UOT  C05  H10  single    0.930  0.020  1.080
 UOT  C09  H11  single    0.930  0.020  1.080
 UOT  C19  H12  single    0.930  0.020  1.080
 UOT  C20  H13  single    0.930  0.020  1.080
 UOT  C02  O1   double    1.207  0.020  1.207

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
 UOT  O11  C10  C09  115.50  3.000
 UOT  O11  C10  C13  123.51  3.000
 UOT  C09  C10  C13  120.98  3.000
 UOT  H3   C12  H2   108.79  3.000
 UOT  H3   C12  H1   108.69  3.000
 UOT  H2   C12  H1   108.67  3.000
 UOT  H3   C12  O11  112.06  3.000
 UOT  H2   C12  O11  112.12  3.000
 UOT  H1   C12  O11  106.39  3.000
 UOT  H4   C13  C14  118.31  3.000
 UOT  H4   C13  C10  120.51  3.000
 UOT  C14  C13  C10  121.18  3.000
 UOT  H5   C14  C15  120.99  3.000
 UOT  H5   C14  C13  120.39  3.000
 UOT  C15  C14  C13  118.62  3.000
 UOT  N16  C15  C08  110.29  3.000
 UOT  C08  C15  C14  119.24  3.000
 UOT  N16  C15  C14  130.47  3.000
 UOT  CL1  C17  N16  124.69  3.000
 UOT  CL1  C17  N07  120.50  3.000
 UOT  N16  C17  N07  114.80  3.000
 UOT  C20  C03  C04  119.88  3.000
 UOT  C20  C03  C02  121.19  3.000
 UOT  C04  C03  C02  118.93  3.000
 UOT  H9   C04  C05  119.59  3.000
 UOT  H9   C04  C03  120.05  3.000
 UOT  C05  C04  C03  120.36  3.000
 UOT  H10  C05  C06  120.25  3.000
 UOT  H10  C05  C04  120.54  3.000
 UOT  C06  C05  C04  119.21  3.000
 UOT  N07  C06  C19  119.81  3.000
 UOT  C19  C06  C05  120.99  3.000
 UOT  N07  C06  C05  119.18  3.000
 UOT  N07  C08  C09  131.60  3.000
 UOT  C09  C08  C15  123.40  3.000
 UOT  N07  C08  C15  104.99  3.000
 UOT  H11  C09  C08  122.66  3.000
 UOT  H11  C09  C10  120.76  3.000
 UOT  C08  C09  C10  116.58  3.000
 UOT  H12  C19  C20  120.34  3.000
 UOT  H12  C19  C06  120.21  3.000
 UOT  C20  C19  C06  119.45  3.000
 UOT  H13  C20  C19  119.69  3.000
 UOT  H13  C20  C03  120.19  3.000
 UOT  C19  C20  C03  120.12  3.000
 UOT  C08  N07  C06  126.56  3.000
 UOT  C06  N07  C17  127.98  3.000
 UOT  C08  N07  C17  105.45  3.000
 UOT  C17  N16  C15  104.47  3.000
 UOT  C12  O11  C10  119.13  3.000
 UOT  O1   C02  H6   121.24  3.000
 UOT  O1   C02  C03  124.31  3.000
 UOT  H6   C02  C03  114.45  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
 UOT  CONST_01  C15  C14  C13  C10     0.00   0.0  0
 UOT  CONST_02  C15  C08  C09  C10     0.00   0.0  0
 UOT  CONST_03  N07  C08  C09  C10   180.00   0.0  0
 UOT  CONST_04  N16  C15  C14  C13   180.00   0.0  0
 UOT  CONST_05  C08  C15  C14  C13     0.00   0.0  0
 UOT  CONST_06  C08  C09  C10  C13     0.00   0.0  0
 UOT  CONST_07  C17  N16  C15  C14   180.00   0.0  0
 UOT  CONST_08  N07  C08  C15  C14   180.00   0.0  0
 UOT  CONST_09  C09  C08  C15  C14     0.00   0.0  0
 UOT  CONST_10  C09  C10  C13  C14     0.00   0.0  0
 UOT  CONST_11  N07  C17  N16  C15     0.00   0.0  0
 UOT  CONST_12  C17  N07  C08  C15     0.00   0.0  0
 UOT  CONST_13  C06  N07  C08  C15   180.00   0.0  0
 UOT  CONST_14  C08  C15  N16  C17     0.00   0.0  0
 UOT  CONST_15  C09  C08  N07  C17   180.00   0.0  0
 UOT  CONST_18  C06  C05  C04  C03     0.00   0.0  0
 UOT  CONST_19  C06  C19  C20  C03     0.00   0.0  0
 UOT  CONST_20  N07  C06  C05  C04   180.00   0.0  0
 UOT  CONST_21  C19  C06  C05  C04     0.00   0.0  0
 UOT  CONST_22  C19  C20  C03  C04     0.00   0.0  0
 UOT  CONST_24  C20  C19  C06  C05     0.00   0.0  0
 UOT  CONST_25  C20  C03  C04  C05     0.00   0.0  0
 UOT  CONST_26  N16  C17  N07  C06   180.00   0.0  0
 UOT  CONST_27  C09  C08  N07  C06     0.00   0.0  0
 UOT  CONST_28  N16  C17  N07  C08     0.00   0.0  0
 UOT  CONST_30  N16  C15  C08  C09   180.00   0.0  0
 UOT  CONST_31  N07  C06  C19  C20   180.00   0.0  0
 UOT  CONST_32  N16  C15  C08  N07     0.00   0.0  0
 UOT  CONST_33  O11  C10  C13  C14   180.00   0.0  0
 UOT  CONST_34  CL1  C17  N16  C15   180.00   0.0  0
 UOT  CONST_35  C05  C04  C03  C02   180.00   0.0  0
 UOT  CONST_36  C19  C20  C03  C02   180.00   0.0  0
 UOT  CONST_37  CL1  C17  N07  C06     0.00   0.0  0
 UOT  CONST_38  CL1  C17  N07  C08   180.00   0.0  0
 UOT  CONST_39  O11  C10  C09  C08   180.00   0.0  0
 UOT  CONST_40  H5   C14  C13  C10   180.00   0.0  0
 UOT  CONST_41  H11  C09  C10  C13   180.00   0.0  0
 UOT  CONST_42  H4   C13  C14  C15   180.00   0.0  0
 UOT  CONST_43  H10  C05  C04  C03   180.00   0.0  0
 UOT  CONST_44  H12  C19  C20  C03   180.00   0.0  0
 UOT  CONST_45  H13  C20  C03  C04   180.00   0.0  0
 UOT  CONST_46  H9   C04  C05  C06   180.00   0.0  0
 UOT  Var_01    C13  C10  O11  C12     2.28  30.0  2
 UOT  Var_02    O1   C02  C03  C04  -179.98  30.0  2
 UOT  Var_03    H1   C12  O11  C10   179.01  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
 UOT  plan-1  C03  0.020
 UOT  plan-1  C04  0.020
 UOT  plan-1  C05  0.020
 UOT  plan-1  C06  0.020
 UOT  plan-1  C19  0.020
 UOT  plan-1  C20  0.020
 UOT  plan-1  N07  0.020
 UOT  plan-1  H9   0.020
 UOT  plan-1  H10  0.020
 UOT  plan-1  H12  0.020
 UOT  plan-1  H13  0.020
 UOT  plan-1  C02  0.020
 UOT  plan-2  C10  0.020
 UOT  plan-2  C13  0.020
 UOT  plan-2  C14  0.020
 UOT  plan-2  C15  0.020
 UOT  plan-2  C17  0.020
 UOT  plan-2  C06  0.020
 UOT  plan-2  C08  0.020
 UOT  plan-2  C09  0.020
 UOT  plan-2  N07  0.020
 UOT  plan-2  N16  0.020
 UOT  plan-2  O11  0.020
 UOT  plan-2  CL1  0.020
 UOT  plan-2  H4   0.020
 UOT  plan-2  H5   0.020
 UOT  plan-2  H11  0.020
 UOT  plan-3  C03  0.020
 UOT  plan-3  H6   0.020
 UOT  plan-3  O1   0.020
 UOT  plan-3  C02  0.020

