# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:37:00 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-[4-(4-chlorophenoxy)phenyl]-1H-benzimidazole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc2nc([nH]c2c1)c3ccc(Oc4ccc(Cl)cc4)cc3
#
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
 RU5  RU5  2-[4-(4-chlorophenoxy)phenyl]-1H-benzimidazole-6-carboxamide  ligand  40  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RU5
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
 RU5  C1    C   C     0   0.493  -7.3888   1.1987  -0.6113
 RU5  N1    N   NH2   0  -0.818  -8.4309   1.2749   0.2333
 RU5  O1    O   O2    0  -0.503   3.6376  -1.7775  -0.1565
 RU5  C2    C   CR6   0  -0.067  -6.1791   0.4743  -0.1162
 RU5  C3    C   CR16  0  -0.340  -4.9754   0.7360  -0.7594
 RU5  N3    N   NR15  0  -0.733  -2.5389   0.0989  -0.6698
 RU5  C4    C   CR56  0   0.366  -3.8545   0.0699  -0.2955
 RU5  N4    N   N     0  -0.480  -2.6524  -1.3606   0.9987
 RU5  C5    C   CR5   0   0.486  -1.8666  -0.7715   0.1306
 RU5  C6    C   CR56  0   0.160  -3.9007  -0.8568   0.7608
 RU5  C7    C   CR16  0  -0.328  -5.1177  -1.1261   1.3861
 RU5  C8    C   CR16  0  -0.293  -6.2391  -0.4547   0.9413
 RU5  C9    C   CR6   0   0.007  -0.4303  -1.0043   0.0279
 RU5  CLA   CL  CL    0  -0.130   7.8174   2.3234  -0.0735
 RU5  C10   C   CR16  0  -0.281   0.1372  -2.0845   0.7052
 RU5  C11   C   CR16  0  -0.316   1.4979  -2.3197   0.6477
 RU5  C12   C   CR6   0   0.339   2.3103  -1.4737  -0.0979
 RU5  C13   C   CR16  0  -0.322   1.7641  -0.3987  -0.7895
 RU5  C14   C   CR16  0  -0.309   0.4009  -0.1695  -0.7189
 RU5  C15   C   CR6   0   0.345   4.5680  -0.7773  -0.1403
 RU5  C16   C   CR16  0  -0.334   4.4593   0.3156   0.7115
 RU5  C17   C   CR16  0  -0.217   5.4607   1.2739   0.7282
 RU5  C18   C   CR6   0  -0.053   6.5641   1.1252  -0.0983
 RU5  C19   C   CR16  0  -0.195   6.6811   0.0322  -0.9419
 RU5  C20   C   CR16  0  -0.317   5.6732  -0.9194  -0.9667
 RU5  OAB   O   O     0  -0.485  -7.4167   1.6910  -1.7320
 RU5  HN1   H   HNH2  0   0.410  -8.3584   1.0326   1.2056
 RU5  HN1A  H   HNH2  0   0.404  -9.2460   1.7996  -0.0399
 RU5  H3    H   HCR6  0   0.273  -4.9214   1.4396  -1.5791
 RU5  HN3   H   HNR5  0   0.423  -2.1564   0.6322  -1.4341
 RU5  H7    H   HCR6  0   0.262  -5.1820  -1.8443   2.1926
 RU5  H8    H   HCR6  0   0.255  -7.1872  -0.6808   1.4113
 RU5  H10   H   HCR6  0   0.265  -0.4943  -2.7417   1.2875
 RU5  H11   H   HCR6  0   0.281   1.9323  -3.1590   1.1750
 RU5  H13   H   HCR6  0   0.320   2.3874   0.2610  -1.3786
 RU5  H14   H   HCR6  0   0.273   0.0045   0.6846  -1.2524
 RU5  H16   H   HCR6  0   0.319   3.6038   0.4304   1.3643
 RU5  H17   H   HCR6  0   0.307   5.3792   2.1260   1.3887
 RU5  H19   H   HCR6  0   0.275   7.5477  -0.0762  -1.5769
 RU5  H20   H   HCR6  0   0.257   5.7503  -1.7734  -1.6265

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
 RU5  C1   N1    single    1.344  0.020  1.344
 RU5  C1   C2    single    1.494  0.020  1.494
 RU5  C1   OAB   double    1.224  0.020  1.224
 RU5  O1   C12   single    1.363  0.020  1.363
 RU5  O1   C15   single    1.366  0.020  1.366
 RU5  C2   C3    aromatic  1.390  0.020  1.390
 RU5  C2   C8    aromatic  1.409  0.020  1.409
 RU5  C3   C4    aromatic  1.384  0.020  1.384
 RU5  N3   C4    aromatic  1.368  0.020  1.368
 RU5  N3   C5    aromatic  1.360  0.020  1.360
 RU5  C4   C6    aromatic  1.406  0.020  1.406
 RU5  N4   C5    aromatic  1.311  0.020  1.311
 RU5  N4   C6    aromatic  1.367  0.020  1.367
 RU5  C5   C9    single    1.459  0.020  1.459
 RU5  C6   C7    aromatic  1.395  0.020  1.395
 RU5  C7   C8    aromatic  1.381  0.020  1.381
 RU5  C9   C10   aromatic  1.396  0.020  1.396
 RU5  C9   C14   aromatic  1.395  0.020  1.395
 RU5  CLA  C18   single    1.734  0.020  1.734
 RU5  C10  C11   aromatic  1.382  0.020  1.382
 RU5  C11  C12   aromatic  1.390  0.020  1.390
 RU5  C12  C13   aromatic  1.390  0.020  1.390
 RU5  C13  C14   aromatic  1.384  0.020  1.384
 RU5  C15  C16   aromatic  1.390  0.020  1.390
 RU5  C15  C20   aromatic  1.387  0.020  1.387
 RU5  C16  C17   aromatic  1.386  0.020  1.386
 RU5  C17  C18   aromatic  1.387  0.020  1.387
 RU5  C18  C19   aromatic  1.386  0.020  1.386
 RU5  C19  C20   aromatic  1.386  0.020  1.386
 RU5  N1   HN1   single    0.860  0.020  1.020
 RU5  N1   HN1A  single    0.860  0.020  1.020
 RU5  C3   H3    single    0.930  0.020  1.080
 RU5  N3   HN3   single    0.860  0.020  1.020
 RU5  C7   H7    single    0.930  0.020  1.080
 RU5  C8   H8    single    0.930  0.020  1.080
 RU5  C10  H10   single    0.930  0.020  1.080
 RU5  C11  H11   single    0.930  0.020  1.080
 RU5  C13  H13   single    0.930  0.020  1.080
 RU5  C14  H14   single    0.930  0.020  1.080
 RU5  C16  H16   single    0.930  0.020  1.080
 RU5  C17  H17   single    0.930  0.020  1.080
 RU5  C19  H19   single    0.930  0.020  1.080
 RU5  C20  H20   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
 RU5  OAB   C1   C2   121.10  3.000
 RU5  OAB   C1   N1   122.34  3.000
 RU5  C2    C1   N1   116.56  3.000
 RU5  HN1A  N1   HN1  116.52  3.000
 RU5  HN1A  N1   C1   119.13  3.000
 RU5  HN1   N1   C1   122.60  3.000
 RU5  C15   O1   C12  119.97  3.000
 RU5  C8    C2   C3   120.56  3.000
 RU5  C8    C2   C1   122.27  3.000
 RU5  C3    C2   C1   117.16  3.000
 RU5  H3    C3   C4   121.78  3.000
 RU5  H3    C3   C2   121.10  3.000
 RU5  C4    C3   C2   117.11  3.000
 RU5  HN3   N3   C5   126.69  3.000
 RU5  HN3   N3   C4   125.73  3.000
 RU5  C5    N3   C4   107.50  3.000
 RU5  C6    C4   N3   104.54  3.000
 RU5  C6    C4   C3   122.85  3.000
 RU5  N3    C4   C3   132.61  3.000
 RU5  C6    N4   C5   105.46  3.000
 RU5  C9    C5   N4   124.42  3.000
 RU5  C9    C5   N3   123.19  3.000
 RU5  N4    C5   N3   112.39  3.000
 RU5  C7    C6   N4   130.37  3.000
 RU5  C7    C6   C4   119.53  3.000
 RU5  N4    C6   C4   110.10  3.000
 RU5  H7    C7   C8   120.98  3.000
 RU5  H7    C7   C6   120.96  3.000
 RU5  C8    C7   C6   118.06  3.000
 RU5  H8    C8   C7   118.05  3.000
 RU5  H8    C8   C2   120.07  3.000
 RU5  C7    C8   C2   121.86  3.000
 RU5  C14   C9   C10  118.74  3.000
 RU5  C14   C9   C5   121.94  3.000
 RU5  C10   C9   C5   119.32  3.000
 RU5  H10   C10  C11  119.59  3.000
 RU5  H10   C10  C9   119.62  3.000
 RU5  C11   C10  C9   120.79  3.000
 RU5  H11   C11  C12  119.92  3.000
 RU5  H11   C11  C10  120.46  3.000
 RU5  C12   C11  C10  119.62  3.000
 RU5  C13   C12  C11  120.53  3.000
 RU5  C13   C12  O1   122.25  3.000
 RU5  C11   C12  O1   117.17  3.000
 RU5  H13   C13  C14  119.62  3.000
 RU5  H13   C13  C12  121.07  3.000
 RU5  C14   C13  C12  119.32  3.000
 RU5  H14   C14  C13  117.79  3.000
 RU5  H14   C14  C9   121.20  3.000
 RU5  C13   C14  C9   121.01  3.000
 RU5  C20   C15  C16  120.53  3.000
 RU5  C20   C15  O1   117.42  3.000
 RU5  C16   C15  O1   121.99  3.000
 RU5  H16   C16  C17  119.38  3.000
 RU5  H16   C16  C15  120.99  3.000
 RU5  C17   C16  C15  119.64  3.000
 RU5  H17   C17  C18  120.57  3.000
 RU5  H17   C17  C16  119.85  3.000
 RU5  C18   C17  C16  119.58  3.000
 RU5  C19   C18  C17  120.97  3.000
 RU5  C19   C18  CLA  119.52  3.000
 RU5  C17   C18  CLA  119.51  3.000
 RU5  H19   C19  C20  120.27  3.000
 RU5  H19   C19  C18  120.33  3.000
 RU5  C20   C19  C18  119.40  3.000
 RU5  H20   C20  C19  120.06  3.000
 RU5  H20   C20  C15  120.06  3.000
 RU5  C19   C20  C15  119.88  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
 RU5  CONST_01  N3    C4   C3   C2    180.00   0.0  0
 RU5  CONST_02  C6    C4   C3   C2      0.00   0.0  0
 RU5  CONST_03  C6    C7   C8   C2      0.00   0.0  0
 RU5  CONST_04  C7    C8   C2   C3      0.00   0.0  0
 RU5  CONST_05  C5    N3   C4   C3    180.00   0.0  0
 RU5  CONST_06  N4    C6   C4   C3    180.00   0.0  0
 RU5  CONST_07  C7    C6   C4   C3      0.00   0.0  0
 RU5  CONST_08  N4    C6   C4   N3      0.00   0.0  0
 RU5  CONST_09  C7    C6   C4   N3    180.00   0.0  0
 RU5  CONST_10  C6    N4   C5   N3      0.00   0.0  0
 RU5  CONST_11  C10   C9   C5   N3    180.00   0.0  0
 RU5  CONST_12  C14   C9   C5   N3      0.00   0.0  0
 RU5  CONST_13  C8    C2   C3   C4      0.00   0.0  0
 RU5  CONST_14  N4    C5   N3   C4      0.00   0.0  0
 RU5  CONST_15  C9    C5   N3   C4    180.00   0.0  0
 RU5  CONST_16  C5    N4   C6   C4      0.00   0.0  0
 RU5  CONST_17  C8    C7   C6   C4      0.00   0.0  0
 RU5  CONST_18  C10   C9   C5   N4      0.00   0.0  0
 RU5  CONST_19  C14   C9   C5   N4    180.00   0.0  0
 RU5  CONST_20  C8    C7   C6   N4    180.00   0.0  0
 RU5  CONST_21  C6    C4   N3   C5      0.00   0.0  0
 RU5  CONST_22  C7    C6   N4   C5    180.00   0.0  0
 RU5  CONST_23  C11   C10  C9   C5    180.00   0.0  0
 RU5  CONST_24  C13   C14  C9   C5    180.00   0.0  0
 RU5  CONST_25  C9    C5   N4   C6    180.00   0.0  0
 RU5  CONST_26  C12   C11  C10  C9      0.00   0.0  0
 RU5  CONST_27  C12   C13  C14  C9      0.00   0.0  0
 RU5  CONST_28  C13   C14  C9   C10     0.00   0.0  0
 RU5  CONST_29  C13   C12  C11  C10     0.00   0.0  0
 RU5  CONST_30  C14   C9   C10  C11     0.00   0.0  0
 RU5  CONST_31  C14   C13  C12  C11     0.00   0.0  0
 RU5  CONST_32  C18   C17  C16  C15     0.00   0.0  0
 RU5  CONST_33  C18   C19  C20  C15     0.00   0.0  0
 RU5  CONST_34  C19   C20  C15  C16     0.00   0.0  0
 RU5  CONST_35  C19   C18  C17  C16     0.00   0.0  0
 RU5  CONST_36  C20   C15  C16  C17     0.00   0.0  0
 RU5  CONST_37  C20   C19  C18  C17     0.00   0.0  0
 RU5  CONST_38  C4    C3   C2   C1    180.00   0.0  0
 RU5  CONST_39  C7    C8   C2   C1    180.00   0.0  0
 RU5  CONST_40  C10   C11  C12  O1    180.00   0.0  0
 RU5  CONST_41  C14   C13  C12  O1    180.00   0.0  0
 RU5  CONST_42  C17   C16  C15  O1    180.00   0.0  0
 RU5  CONST_43  C19   C20  C15  O1    180.00   0.0  0
 RU5  CONST_44  C16   C17  C18  CLA   180.00   0.0  0
 RU5  CONST_45  C20   C19  C18  CLA   180.00   0.0  0
 RU5  CONST_46  H7    C7   C8   C2    180.00   0.0  0
 RU5  CONST_47  H8    C8   C2   C3    180.00   0.0  0
 RU5  CONST_48  HN3   N3   C4   C3      0.00   0.0  0
 RU5  CONST_49  H3    C3   C4   N3      0.00   0.0  0
 RU5  CONST_50  H10   C10  C9   C5      0.00   0.0  0
 RU5  CONST_51  H14   C14  C9   C5      0.00   0.0  0
 RU5  CONST_52  H11   C11  C10  C9    180.00   0.0  0
 RU5  CONST_53  H13   C13  C14  C9    180.00   0.0  0
 RU5  CONST_54  H17   C17  C16  C15   180.00   0.0  0
 RU5  CONST_55  H19   C19  C20  C15   180.00   0.0  0
 RU5  CONST_56  H20   C20  C15  C16   180.00   0.0  0
 RU5  CONST_57  H16   C16  C17  C18   180.00   0.0  0
 RU5  CONST_58  HN1   N1   C1   C2      0.00   0.0  0
 RU5  CONST_59  HN1A  N1   C1   C2    180.00   0.0  0
 RU5  Var_01    C16   C15  O1   C12    42.42  30.0  2
 RU5  Var_02    C3    C2   C1   N1   -160.04  30.0  2

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
 RU5  plan-1  O1    0.020
 RU5  plan-1  C5    0.020
 RU5  plan-1  C9    0.020
 RU5  plan-1  C10   0.020
 RU5  plan-1  C11   0.020
 RU5  plan-1  C12   0.020
 RU5  plan-1  C13   0.020
 RU5  plan-1  C14   0.020
 RU5  plan-1  H10   0.020
 RU5  plan-1  H11   0.020
 RU5  plan-1  H13   0.020
 RU5  plan-1  H14   0.020
 RU5  plan-2  O1    0.020
 RU5  plan-2  CLA   0.020
 RU5  plan-2  C15   0.020
 RU5  plan-2  C16   0.020
 RU5  plan-2  C17   0.020
 RU5  plan-2  C18   0.020
 RU5  plan-2  C19   0.020
 RU5  plan-2  C20   0.020
 RU5  plan-2  H16   0.020
 RU5  plan-2  H17   0.020
 RU5  plan-2  H19   0.020
 RU5  plan-2  H20   0.020
 RU5  plan-3  C1    0.020
 RU5  plan-3  C2    0.020
 RU5  plan-3  C3    0.020
 RU5  plan-3  N3    0.020
 RU5  plan-3  C4    0.020
 RU5  plan-3  N4    0.020
 RU5  plan-3  C5    0.020
 RU5  plan-3  C6    0.020
 RU5  plan-3  C7    0.020
 RU5  plan-3  C8    0.020
 RU5  plan-3  C9    0.020
 RU5  plan-3  H3    0.020
 RU5  plan-3  HN3   0.020
 RU5  plan-3  H7    0.020
 RU5  plan-3  H8    0.020
 RU5  plan-4  C1    0.020
 RU5  plan-4  N1    0.020
 RU5  plan-4  C2    0.020
 RU5  plan-4  OAB   0.020
 RU5  plan-4  HN1   0.020
 RU5  plan-4  HN1A  0.020

