# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:53:02 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[4-(3-hydroxyphenoxy)phenyl]-1H-benzimidazole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc2nc([nH]c2c1)c3ccc(Oc4cccc(O)c4)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
 RU9  RU9  2-[4-(3-hydroxyphenoxy)phenyl]-1H-benzimidazole-6-carboxamide  ligand  41  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_RU9
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
 RU9  C1    C  C     0   0.494  -7.3248  -0.3022  -0.1184
 RU9  N1    N  NH2   0  -0.818  -8.2413   0.6768  -0.0598
 RU9  O1    O  O2    0  -0.507   4.0314  -1.3490   0.4462
 RU9  C2    C  CR6   0  -0.066  -5.9004   0.1234  -0.2756
 RU9  C3    C  CR16  0  -0.342  -4.9200  -0.7953   0.0803
 RU9  N3    N  NR15  0  -0.737  -2.4136  -1.0253   0.1977
 RU9  C4    C  CR56  0   0.365  -3.6019  -0.3999  -0.0644
 RU9  N4    N  N     0  -0.485  -1.8733   0.9745  -0.5992
 RU9  C5    C  CR5   0   0.493  -1.4151  -0.1637  -0.1358
 RU9  C6    C  CR56  0   0.163  -3.2346   0.8609  -0.5665
 RU9  C7    C  CR16  0  -0.329  -4.2264   1.7667  -0.9414
 RU9  C8    C  CR16  0  -0.293  -5.5450   1.3868  -0.7878
 RU9  C9    C  CR6   0  -0.001   0.0004  -0.4791   0.0162
 RU9  C10   C  CR16  0  -0.279   0.9504   0.5097  -0.2379
 RU9  C11   C  CR16  0  -0.320   2.3036   0.2599  -0.0984
 RU9  C12   C  CR6   0   0.361   2.7280  -1.0028   0.3059
 RU9  C13   C  CR16  0  -0.314   1.7947  -2.0046   0.5559
 RU9  C14   C  CR16  0  -0.292   0.4464  -1.7421   0.4088
 RU9  C15   C  CR6   0   0.327   4.9953  -0.3750   0.5318
 RU9  C16   C  CR16  0  -0.329   5.0460   0.4740   1.6269
 RU9  C17   C  CR16  0  -0.240   6.0774   1.4015   1.6896
 RU9  C18   C  CR16  0  -0.342   7.0375   1.4816   0.6938
 RU9  C19   C  CR6   0   0.371   6.9714   0.6148  -0.3955
 RU9  C20   C  CR16  0  -0.451   5.9374  -0.3152  -0.4820
 RU9  OAB   O  O     0  -0.487  -7.6257  -1.4874  -0.0478
 RU9  OAC   O  OH1   0  -0.629   7.9250   0.7146  -1.3390
 RU9  H11N  H  HNH2  0   0.412  -7.9969   1.6481   0.0185
 RU9  H12N  H  HNH2  0   0.404  -9.2133   0.4408   0.0558
 RU9  H3    H  HCR6  0   0.272  -5.1831  -1.7717   0.4644
 RU9  H8    H  HCR6  0   0.253  -6.3134   2.0827  -1.0984
 RU9  HA    H  HNR5  0   0.426  -2.3110  -1.9462   0.5933
 RU9  H7    H  HCR6  0   0.262  -3.9699   2.7368  -1.3457
 RU9  H10   H  HCR6  0   0.266   0.6248   1.4922  -0.5514
 RU9  H14   H  HCR6  0   0.253  -0.2494  -2.5471   0.6062
 RU9  H11   H  HCR6  0   0.287   3.0124   1.0505  -0.3051
 RU9  H13   H  HCR6  0   0.279   2.1281  -2.9869   0.8636
 RU9  H16   H  HCR6  0   0.276   4.3067   0.4105   2.4144
 RU9  H20   H  HCR6  0   0.286   5.8697  -0.9959  -1.3233
 RU9  H17   H  HCR6  0   0.267   6.1368   2.0720   2.5367
 RU9  H18   H  HCR6  0   0.268   7.8405   2.2045   0.7589
 RU9  HAC   H  HOH1  0   0.477   7.7719   0.0777  -2.0459

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
 RU9  C1   N1    single    1.342  0.020  1.342
 RU9  C1   C2    single    1.495  0.020  1.495
 RU9  C1   OAB   double    1.225  0.020  1.225
 RU9  O1   C12   single    1.356  0.020  1.356
 RU9  O1   C15   single    1.373  0.020  1.373
 RU9  C2   C3    aromatic  1.390  0.020  1.390
 RU9  C2   C8    aromatic  1.409  0.020  1.409
 RU9  C3   C4    aromatic  1.384  0.020  1.384
 RU9  N3   C4    aromatic  1.368  0.020  1.368
 RU9  N3   C5    aromatic  1.360  0.020  1.360
 RU9  C4   C6    aromatic  1.406  0.020  1.406
 RU9  N4   C5    aromatic  1.312  0.020  1.312
 RU9  N4   C6    aromatic  1.366  0.020  1.366
 RU9  C5   C9    single    1.458  0.020  1.458
 RU9  C6   C7    aromatic  1.394  0.020  1.394
 RU9  C7   C8    aromatic  1.381  0.020  1.381
 RU9  C9   C10   aromatic  1.395  0.020  1.395
 RU9  C9   C14   aromatic  1.396  0.020  1.396
 RU9  C10  C11   aromatic  1.383  0.020  1.383
 RU9  C11  C12   aromatic  1.392  0.020  1.392
 RU9  C12  C13   aromatic  1.392  0.020  1.392
 RU9  C13  C14   aromatic  1.381  0.020  1.381
 RU9  C15  C16   aromatic  1.387  0.020  1.387
 RU9  C15  C20   aromatic  1.385  0.020  1.385
 RU9  C16  C17   aromatic  1.389  0.020  1.389
 RU9  C17  C18   aromatic  1.386  0.020  1.386
 RU9  C18  C19   aromatic  1.394  0.020  1.394
 RU9  C19  C20   aromatic  1.393  0.020  1.393
 RU9  C19  OAC   single    1.345  0.020  1.345
 RU9  N1   H11N  single    0.860  0.020  1.020
 RU9  N1   H12N  single    0.860  0.020  1.020
 RU9  C3   H3    single    0.930  0.020  1.080
 RU9  C8   H8    single    0.930  0.020  1.080
 RU9  N3   HA    single    0.860  0.020  1.020
 RU9  C7   H7    single    0.930  0.020  1.080
 RU9  C10  H10   single    0.930  0.020  1.080
 RU9  C14  H14   single    0.930  0.020  1.080
 RU9  C11  H11   single    0.930  0.020  1.080
 RU9  C13  H13   single    0.930  0.020  1.080
 RU9  C16  H16   single    0.930  0.020  1.080
 RU9  C20  H20   single    0.930  0.020  1.080
 RU9  C17  H17   single    0.930  0.020  1.080
 RU9  C18  H18   single    0.930  0.020  1.080
 RU9  OAC  HAC   single    0.850  0.020  0.980

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
 RU9  OAB   C1   C2    121.04  3.000
 RU9  OAB   C1   N1    122.38  3.000
 RU9  C2    C1   N1    116.58  3.000
 RU9  H12N  N1   H11N  116.90  3.000
 RU9  H12N  N1   C1    119.55  3.000
 RU9  H11N  N1   C1    122.85  3.000
 RU9  C15   O1   C12   120.02  3.000
 RU9  C8    C2   C3    120.53  3.000
 RU9  C8    C2   C1    122.27  3.000
 RU9  C3    C2   C1    117.19  3.000
 RU9  H3    C3   C4    121.79  3.000
 RU9  H3    C3   C2    121.07  3.000
 RU9  C4    C3   C2    117.14  3.000
 RU9  HA    N3   C5    126.90  3.000
 RU9  HA    N3   C4    125.56  3.000
 RU9  C5    N3   C4    107.52  3.000
 RU9  C6    C4   N3    104.56  3.000
 RU9  C6    C4   C3    122.85  3.000
 RU9  N3    C4   C3    132.58  3.000
 RU9  C6    N4   C5    105.51  3.000
 RU9  C9    C5   N4    124.31  3.000
 RU9  C9    C5   N3    123.37  3.000
 RU9  N4    C5   N3    112.32  3.000
 RU9  C7    C6   N4    130.40  3.000
 RU9  C7    C6   C4    119.52  3.000
 RU9  N4    C6   C4    110.08  3.000
 RU9  H7    C7   C8    120.98  3.000
 RU9  H7    C7   C6    120.95  3.000
 RU9  C8    C7   C6    118.07  3.000
 RU9  H8    C8   C7    117.98  3.000
 RU9  H8    C8   C2    120.13  3.000
 RU9  C7    C8   C2    121.87  3.000
 RU9  C14   C9   C10   118.37  3.000
 RU9  C14   C9   C5    122.36  3.000
 RU9  C10   C9   C5    119.27  3.000
 RU9  H10   C10  C11   119.20  3.000
 RU9  H10   C10  C9    119.46  3.000
 RU9  C11   C10  C9    121.33  3.000
 RU9  H11   C11  C12   121.24  3.000
 RU9  H11   C11  C10   119.33  3.000
 RU9  C12   C11  C10   119.43  3.000
 RU9  C13   C12  C11   120.04  3.000
 RU9  C13   C12  O1    116.25  3.000
 RU9  C11   C12  O1    123.69  3.000
 RU9  H13   C13  C14   120.23  3.000
 RU9  H13   C13  C12   119.86  3.000
 RU9  C14   C13  C12   119.91  3.000
 RU9  H14   C14  C13   117.83  3.000
 RU9  H14   C14  C9    121.26  3.000
 RU9  C13   C14  C9    120.91  3.000
 RU9  C20   C15  C16   121.78  3.000
 RU9  C20   C15  O1    117.55  3.000
 RU9  C16   C15  O1    120.61  3.000
 RU9  H16   C16  C17   120.92  3.000
 RU9  H16   C16  C15   120.93  3.000
 RU9  C17   C16  C15   118.15  3.000
 RU9  H17   C17  C18   119.26  3.000
 RU9  H17   C17  C16   119.34  3.000
 RU9  C18   C17  C16   121.39  3.000
 RU9  H18   C18  C19   119.84  3.000
 RU9  H18   C18  C17   120.63  3.000
 RU9  C19   C18  C17   119.53  3.000
 RU9  OAC   C19  C20   122.14  3.000
 RU9  OAC   C19  C18   117.93  3.000
 RU9  C20   C19  C18   119.93  3.000
 RU9  H20   C20  C19   120.90  3.000
 RU9  H20   C20  C15   119.88  3.000
 RU9  C19   C20  C15   119.21  3.000
 RU9  HAC   OAC  C19   110.66  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
 RU9  CONST_01  N3    C4   C3   C2   180.00   0.0  0
 RU9  CONST_02  C6    C4   C3   C2     0.00   0.0  0
 RU9  CONST_03  C6    C7   C8   C2     0.00   0.0  0
 RU9  CONST_04  C7    C8   C2   C3     0.00   0.0  0
 RU9  CONST_05  C5    N3   C4   C3   180.00   0.0  0
 RU9  CONST_06  N4    C6   C4   C3   180.00   0.0  0
 RU9  CONST_07  C7    C6   C4   C3     0.00   0.0  0
 RU9  CONST_08  N4    C6   C4   N3     0.00   0.0  0
 RU9  CONST_09  C7    C6   C4   N3   180.00   0.0  0
 RU9  CONST_10  C6    N4   C5   N3     0.00   0.0  0
 RU9  CONST_11  C10   C9   C5   N3   180.00   0.0  0
 RU9  CONST_12  C14   C9   C5   N3     0.00   0.0  0
 RU9  CONST_13  C8    C2   C3   C4     0.00   0.0  0
 RU9  CONST_14  N4    C5   N3   C4     0.00   0.0  0
 RU9  CONST_15  C9    C5   N3   C4   180.00   0.0  0
 RU9  CONST_16  C5    N4   C6   C4     0.00   0.0  0
 RU9  CONST_17  C8    C7   C6   C4     0.00   0.0  0
 RU9  CONST_18  C10   C9   C5   N4     0.00   0.0  0
 RU9  CONST_19  C14   C9   C5   N4   180.00   0.0  0
 RU9  CONST_20  C8    C7   C6   N4   180.00   0.0  0
 RU9  CONST_21  C6    C4   N3   C5     0.00   0.0  0
 RU9  CONST_22  C7    C6   N4   C5   180.00   0.0  0
 RU9  CONST_23  C11   C10  C9   C5   180.00   0.0  0
 RU9  CONST_24  C13   C14  C9   C5   180.00   0.0  0
 RU9  CONST_25  C9    C5   N4   C6   180.00   0.0  0
 RU9  CONST_26  C12   C11  C10  C9     0.00   0.0  0
 RU9  CONST_27  C12   C13  C14  C9     0.00   0.0  0
 RU9  CONST_28  C13   C14  C9   C10    0.00   0.0  0
 RU9  CONST_29  C13   C12  C11  C10    0.00   0.0  0
 RU9  CONST_30  C14   C9   C10  C11    0.00   0.0  0
 RU9  CONST_31  C14   C13  C12  C11    0.00   0.0  0
 RU9  CONST_32  C18   C17  C16  C15    0.00   0.0  0
 RU9  CONST_33  C18   C19  C20  C15    0.00   0.0  0
 RU9  CONST_34  C19   C20  C15  C16    0.00   0.0  0
 RU9  CONST_35  C19   C18  C17  C16    0.00   0.0  0
 RU9  CONST_36  C20   C15  C16  C17    0.00   0.0  0
 RU9  CONST_37  C20   C19  C18  C17    0.00   0.0  0
 RU9  CONST_38  C4    C3   C2   C1   180.00   0.0  0
 RU9  CONST_39  C7    C8   C2   C1   180.00   0.0  0
 RU9  CONST_40  C10   C11  C12  O1   180.00   0.0  0
 RU9  CONST_41  C14   C13  C12  O1   180.00   0.0  0
 RU9  CONST_42  C17   C16  C15  O1   180.00   0.0  0
 RU9  CONST_43  C19   C20  C15  O1   180.00   0.0  0
 RU9  CONST_44  OAC   C19  C20  C15  180.00   0.0  0
 RU9  CONST_45  OAC   C19  C18  C17  180.00   0.0  0
 RU9  CONST_46  H7    C7   C8   C2   180.00   0.0  0
 RU9  CONST_47  H8    C8   C2   C3   180.00   0.0  0
 RU9  CONST_48  HA    N3   C4   C3     0.00   0.0  0
 RU9  CONST_49  H3    C3   C4   N3     0.00   0.0  0
 RU9  CONST_50  H10   C10  C9   C5     0.00   0.0  0
 RU9  CONST_51  H14   C14  C9   C5     0.00   0.0  0
 RU9  CONST_52  H11   C11  C10  C9   180.00   0.0  0
 RU9  CONST_53  H13   C13  C14  C9   180.00   0.0  0
 RU9  CONST_54  H17   C17  C16  C15  180.00   0.0  0
 RU9  CONST_55  H20   C20  C15  C16  180.00   0.0  0
 RU9  CONST_56  H18   C18  C17  C16  180.00   0.0  0
 RU9  CONST_57  H16   C16  C17  C18  180.00   0.0  0
 RU9  CONST_58  H11N  N1   C1   C2     0.00   0.0  0
 RU9  CONST_59  H12N  N1   C1   C2   180.00   0.0  0
 RU9  Var_01    C16   C15  O1   C12   66.75  30.0  2
 RU9  Var_02    C3    C2   C1   N1   160.11  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
 RU9  plan-1  O1    0.020
 RU9  plan-1  C5    0.020
 RU9  plan-1  C9    0.020
 RU9  plan-1  C10   0.020
 RU9  plan-1  C11   0.020
 RU9  plan-1  C12   0.020
 RU9  plan-1  C13   0.020
 RU9  plan-1  C14   0.020
 RU9  plan-1  H10   0.020
 RU9  plan-1  H14   0.020
 RU9  plan-1  H11   0.020
 RU9  plan-1  H13   0.020
 RU9  plan-2  O1    0.020
 RU9  plan-2  C15   0.020
 RU9  plan-2  C16   0.020
 RU9  plan-2  C17   0.020
 RU9  plan-2  C18   0.020
 RU9  plan-2  C19   0.020
 RU9  plan-2  C20   0.020
 RU9  plan-2  OAC   0.020
 RU9  plan-2  H16   0.020
 RU9  plan-2  H20   0.020
 RU9  plan-2  H17   0.020
 RU9  plan-2  H18   0.020
 RU9  plan-3  C1    0.020
 RU9  plan-3  C2    0.020
 RU9  plan-3  C3    0.020
 RU9  plan-3  N3    0.020
 RU9  plan-3  C4    0.020
 RU9  plan-3  N4    0.020
 RU9  plan-3  C5    0.020
 RU9  plan-3  C6    0.020
 RU9  plan-3  C7    0.020
 RU9  plan-3  C8    0.020
 RU9  plan-3  C9    0.020
 RU9  plan-3  H3    0.020
 RU9  plan-3  H8    0.020
 RU9  plan-3  HA    0.020
 RU9  plan-3  H7    0.020
 RU9  plan-4  C1    0.020
 RU9  plan-4  N1    0.020
 RU9  plan-4  C2    0.020
 RU9  plan-4  OAB   0.020
 RU9  plan-4  H11N  0.020
 RU9  plan-4  H12N  0.020

