# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:56:18 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (S)-{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)c(Cn2c3ccccc3nc2[C@@H](O)c4ccncc4)c1
#
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
 A6Y  A6Y  (S)-{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A6Y
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
 A6Y  C7   C  CR16  0  -0.313   2.8197   1.8165  -1.0650
 A6Y  C6   C  CR16  0  -0.274   3.1117   2.8200  -1.9729
 A6Y  C11  C  CR16  0  -0.378  -1.6414  -1.2702   1.7946
 A6Y  C5   C  CR16  0  -0.271   2.2389   3.8982  -2.1826
 A6Y  C4   C  CR16  0  -0.326   1.0454   4.0059  -1.4909
 A6Y  C3   C  CR56  0   0.163   0.7355   3.0049  -0.5724
 A6Y  N2   N  N     0  -0.511  -0.3596   2.8510   0.2453
 A6Y  C12  C  CR16  0  -0.031  -2.2335  -2.3532   1.1590
 A6Y  C20  C  CR16  0  -0.061  -3.1877  -1.0172  -0.4068
 A6Y  C28  C  CR16  0  -0.285   1.0752  -3.7136   0.2309
 A6Y  C26  C  CR6   0   0.066   1.1664  -1.3255   0.3574
 A6Y  C27  C  CR6   0   0.066   1.4708  -2.5733   0.9172
 A6Y  C29  C  CR16  0  -0.302   0.3979  -3.6337  -0.9780
 A6Y  C31  C  CR16  0  -0.315   0.4983  -1.2550  -0.8554
 A6Y  O22  O  OH1   0  -0.655  -2.0882   2.2131   2.1801
 A6Y  C9   C  CH1   0  -0.099  -1.1589   1.2139   1.8788
 A6Y  C10  C  CR6   0   0.204  -1.8297  -0.0023   1.2718
 A6Y  N19  N  N     0  -0.405  -2.9961  -2.2393   0.0820
 A6Y  C21  C  CR16  0  -0.350  -2.6297   0.1239   0.1421
 A6Y  C2   C  CR5   0   0.431  -0.1462   1.7496   0.9044
 A6Y  N3   N  NR5   0  -0.544   1.0300   1.1476   0.5877
 A6Y  C8   C  CR56  0   0.328   1.6207   1.9353  -0.3737
 A6Y  C25  C  CH3   0  -0.749   2.1930  -2.6857   2.2284
 A6Y  C30  C  CR6   0   0.115   0.1007  -2.4005  -1.5414
 A6Y  H1   H  HCR6  0   0.271   3.4952   0.9848  -0.9126
 A6Y  H2   H  HCR6  0   0.259   4.0344   2.7708  -2.5358
 A6Y  H3   H  HCR6  0   0.267  -1.0336  -1.4288   2.6769
 A6Y  H4   H  HCR6  0   0.256   2.5072   4.6600  -2.9026
 A6Y  H5   H  HCR6  0   0.259   0.3718   4.8369  -1.6550
 A6Y  H6   H  HCR6  0   0.259  -2.0801  -3.3545   1.5452
 A6Y  H7   H  HCR6  0   0.264  -3.8169  -0.9417  -1.2868
 A6Y  H10  H  HCR6  0   0.243   1.2972  -4.6871   0.6523
 A6Y  H11  H  HCR6  0   0.241   0.1008  -4.5446  -1.4843
 A6Y  H12  H  HCR6  0   0.238   0.2590  -0.2894  -1.2858
 A6Y  H13  H  HCH3  0   0.241  -0.1590  -1.5962  -3.5250
 A6Y  H14  H  HCH3  0   0.241  -0.7217  -3.2559  -3.3381
 A6Y  H15  H  HCH3  0   0.246  -1.6601  -1.9237  -2.6754
 A6Y  H16  H  HOH1  0   0.458  -1.9796   2.9213   1.5276
 A6Y  H17  H  HCH1  0   0.277  -0.6479   0.9076   2.8006
 A6Y  H18  H  HCR6  0   0.265  -2.8124   1.0867  -0.3180
 A6Y  H19  H  HCH3  0   0.242   1.6392  -2.2120   3.0430
 A6Y  H20  H  HCH3  0   0.257   2.3430  -3.7286   2.5029
 A6Y  H21  H  HCH3  0   0.246   3.1754  -2.2096   2.1961
 A6Y  C24  C  CH2   0  -0.377   1.5643  -0.0834   1.1196
 A6Y  C32  C  CH3   0  -0.728  -0.6448  -2.2906  -2.8385
 A6Y  H8   H  HCH2  0   0.280   1.2541  -0.1627   2.1635
 A6Y  H9   H  HCH2  0   0.296   2.6522   0.0147   1.1538

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
 A6Y  C20  C21  aromatic  1.384  0.020  1.384
 A6Y  C20  N19  aromatic  1.330  0.020  1.330
 A6Y  C21  C10  aromatic  1.390  0.020  1.390
 A6Y  N19  C12  aromatic  1.325  0.020  1.325
 A6Y  C10  C9   single    1.516  0.020  1.516
 A6Y  C10  C11  aromatic  1.384  0.020  1.384
 A6Y  C9   O22  single    1.397  0.020  1.397
 A6Y  C9   C2   single    1.504  0.020  1.504
 A6Y  N2   C2   aromatic  1.301  0.020  1.301
 A6Y  N2   C3   aromatic  1.375  0.020  1.375
 A6Y  C12  C11  aromatic  1.388  0.020  1.388
 A6Y  C2   N3   aromatic  1.359  0.020  1.359
 A6Y  C4   C3   aromatic  1.393  0.020  1.393
 A6Y  C4   C5   aromatic  1.384  0.020  1.384
 A6Y  C3   C8   aromatic  1.403  0.020  1.403
 A6Y  C5   C6   aromatic  1.403  0.020  1.403
 A6Y  N3   C8   aromatic  1.376  0.020  1.376
 A6Y  N3   C24  single    1.443  0.020  1.443
 A6Y  C8   C7   aromatic  1.389  0.020  1.389
 A6Y  C32  C30  single    1.500  0.020  1.500
 A6Y  C31  C30  aromatic  1.393  0.020  1.393
 A6Y  C31  C26  aromatic  1.386  0.020  1.386
 A6Y  C24  C26  single    1.511  0.020  1.511
 A6Y  C6   C7   aromatic  1.384  0.020  1.384
 A6Y  C30  C29  aromatic  1.388  0.020  1.388
 A6Y  C26  C27  aromatic  1.401  0.020  1.401
 A6Y  C29  C28  aromatic  1.388  0.020  1.388
 A6Y  C27  C28  aromatic  1.388  0.020  1.388
 A6Y  C27  C25  single    1.501  0.020  1.501
 A6Y  C7   H1   single    0.930  0.020  1.080
 A6Y  C6   H2   single    0.930  0.020  1.080
 A6Y  C11  H3   single    0.930  0.020  1.080
 A6Y  C5   H4   single    0.930  0.020  1.080
 A6Y  C4   H5   single    0.930  0.020  1.080
 A6Y  C12  H6   single    0.930  0.020  1.080
 A6Y  C20  H7   single    0.930  0.020  1.080
 A6Y  C24  H8   single    0.970  0.020  1.090
 A6Y  C24  H9   single    0.970  0.020  1.090
 A6Y  C28  H10  single    0.930  0.020  1.080
 A6Y  C29  H11  single    0.930  0.020  1.080
 A6Y  C31  H12  single    0.930  0.020  1.080
 A6Y  C32  H13  single    0.970  0.020  1.090
 A6Y  C32  H14  single    0.970  0.020  1.090
 A6Y  C32  H15  single    0.970  0.020  1.090
 A6Y  O22  H16  single    0.850  0.020  0.980
 A6Y  C9   H17  single    0.970  0.020  1.090
 A6Y  C21  H18  single    0.930  0.020  1.080
 A6Y  C25  H19  single    0.970  0.020  1.090
 A6Y  C25  H20  single    0.970  0.020  1.090
 A6Y  C25  H21  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
 A6Y  H1   C7   C8   122.30  3.000
 A6Y  H1   C7   C6   121.18  3.000
 A6Y  C8   C7   C6   116.52  3.000
 A6Y  H2   C6   C5   119.19  3.000
 A6Y  H2   C6   C7   119.22  3.000
 A6Y  C5   C6   C7   121.59  3.000
 A6Y  H3   C11  C10  121.21  3.000
 A6Y  H3   C11  C12  119.87  3.000
 A6Y  C10  C11  C12  118.92  3.000
 A6Y  H4   C5   C4   119.46  3.000
 A6Y  H4   C5   C6   119.09  3.000
 A6Y  C4   C5   C6   121.45  3.000
 A6Y  H5   C4   C3   120.87  3.000
 A6Y  H5   C4   C5   121.39  3.000
 A6Y  C3   C4   C5   117.74  3.000
 A6Y  C8   C3   N2   109.45  3.000
 A6Y  C8   C3   C4   120.06  3.000
 A6Y  N2   C3   C4   130.50  3.000
 A6Y  C2   N2   C3   105.38  3.000
 A6Y  H6   C12  N19  116.78  3.000
 A6Y  H6   C12  C11  119.81  3.000
 A6Y  N19  C12  C11  123.41  3.000
 A6Y  H7   C20  C21  119.90  3.000
 A6Y  H7   C20  N19  116.47  3.000
 A6Y  C21  C20  N19  123.63  3.000
 A6Y  H10  C28  C29  119.36  3.000
 A6Y  H10  C28  C27  119.16  3.000
 A6Y  C29  C28  C27  121.48  3.000
 A6Y  C31  C26  C27  119.96  3.000
 A6Y  C27  C26  C24  118.26  3.000
 A6Y  C31  C26  C24  121.77  3.000
 A6Y  C25  C27  C26  121.34  3.000
 A6Y  C25  C27  C28  120.48  3.000
 A6Y  C26  C27  C28  118.17  3.000
 A6Y  H11  C29  C30  119.90  3.000
 A6Y  H11  C29  C28  119.50  3.000
 A6Y  C30  C29  C28  120.61  3.000
 A6Y  H12  C31  C30  118.29  3.000
 A6Y  H12  C31  C26  119.94  3.000
 A6Y  C30  C31  C26  121.77  3.000
 A6Y  H16  O22  C9   107.62  3.000
 A6Y  H17  C9   C2   109.27  3.000
 A6Y  H17  C9   C10  108.57  3.000
 A6Y  C2   C9   C10  108.92  3.000
 A6Y  H17  C9   O22  109.15  3.000
 A6Y  C2   C9   O22  109.44  3.000
 A6Y  C10  C9   O22  111.45  3.000
 A6Y  C21  C10  C9   120.49  3.000
 A6Y  C9   C10  C11  121.56  3.000
 A6Y  C21  C10  C11  117.93  3.000
 A6Y  C20  N19  C12  117.44  3.000
 A6Y  H18  C21  C10  121.55  3.000
 A6Y  H18  C21  C20  119.78  3.000
 A6Y  C10  C21  C20  118.66  3.000
 A6Y  N3   C2   C9   125.18  3.000
 A6Y  N3   C2   N2   113.51  3.000
 A6Y  C9   C2   N2   121.28  3.000
 A6Y  C8   N3   C2   106.31  3.000
 A6Y  C8   N3   C24  125.93  3.000
 A6Y  C2   N3   C24  127.76  3.000
 A6Y  N3   C8   C3   105.35  3.000
 A6Y  N3   C8   C7   132.01  3.000
 A6Y  C3   C8   C7   122.65  3.000
 A6Y  H21  C25  H20  107.52  3.000
 A6Y  H21  C25  H19  106.80  3.000
 A6Y  H20  C25  H19  107.28  3.000
 A6Y  H21  C25  C27  111.98  3.000
 A6Y  H20  C25  C27  110.99  3.000
 A6Y  H19  C25  C27  112.01  3.000
 A6Y  C32  C30  C31  120.49  3.000
 A6Y  C31  C30  C29  118.00  3.000
 A6Y  C32  C30  C29  121.50  3.000
 A6Y  H9   C24  H8   105.04  3.000
 A6Y  H9   C24  N3   107.66  3.000
 A6Y  H8   C24  N3   108.00  3.000
 A6Y  H9   C24  C26  110.59  3.000
 A6Y  H8   C24  C26  110.36  3.000
 A6Y  N3   C24  C26  114.69  3.000
 A6Y  H15  C32  H14  107.49  3.000
 A6Y  H15  C32  H13  107.12  3.000
 A6Y  H14  C32  H13  107.87  3.000
 A6Y  H15  C32  C30  110.95  3.000
 A6Y  H14  C32  C30  111.51  3.000
 A6Y  H13  C32  C30  111.68  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
 A6Y  CONST_01  N2   C3   C8   C7    180.00   0.0  0
 A6Y  CONST_02  C4   C3   C8   C7      0.00   0.0  0
 A6Y  CONST_03  C2   N3   C8   C7    180.00   0.0  0
 A6Y  CONST_04  C4   C5   C6   C7      0.00   0.0  0
 A6Y  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 A6Y  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 A6Y  CONST_07  N3   C8   C7   C6    180.00   0.0  0
 A6Y  CONST_08  C20  C21  C10  C11     0.00   0.0  0
 A6Y  CONST_09  C20  N19  C12  C11     0.00   0.0  0
 A6Y  CONST_10  N2   C3   C4   C5    180.00   0.0  0
 A6Y  CONST_11  C8   C3   C4   C5      0.00   0.0  0
 A6Y  CONST_12  C8   C7   C6   C5      0.00   0.0  0
 A6Y  CONST_13  C2   N2   C3   C4    180.00   0.0  0
 A6Y  CONST_14  N3   C8   C3   C4    180.00   0.0  0
 A6Y  CONST_15  N3   C2   N2   C3      0.00   0.0  0
 A6Y  CONST_16  C2   N3   C8   C3      0.00   0.0  0
 A6Y  CONST_17  C8   N3   C2   N2      0.00   0.0  0
 A6Y  CONST_18  N3   C8   C3   N2      0.00   0.0  0
 A6Y  CONST_19  C21  C20  N19  C12     0.00   0.0  0
 A6Y  CONST_20  C21  C10  C11  C12     0.00   0.0  0
 A6Y  CONST_21  C31  C30  C29  C28     0.00   0.0  0
 A6Y  CONST_22  C31  C26  C27  C28     0.00   0.0  0
 A6Y  CONST_23  C29  C30  C31  C26     0.00   0.0  0
 A6Y  CONST_24  C29  C28  C27  C26     0.00   0.0  0
 A6Y  CONST_25  C30  C31  C26  C27     0.00   0.0  0
 A6Y  CONST_26  C30  C29  C28  C27     0.00   0.0  0
 A6Y  CONST_27  N19  C20  C21  C10     0.00   0.0  0
 A6Y  CONST_28  N19  C12  C11  C10     0.00   0.0  0
 A6Y  CONST_29  C8   C3   N2   C2      0.00   0.0  0
 A6Y  CONST_30  C24  N3   C8   C7      0.00   0.0  0
 A6Y  CONST_31  C9   C2   N2   C3    180.00   0.0  0
 A6Y  CONST_32  C24  N3   C8   C3    180.00   0.0  0
 A6Y  CONST_33  C24  N3   C2   N2    180.00   0.0  0
 A6Y  CONST_34  C9   C10  C11  C12   180.00   0.0  0
 A6Y  CONST_35  C9   C10  C21  C20   180.00   0.0  0
 A6Y  CONST_36  C30  C31  C26  C24   180.00   0.0  0
 A6Y  CONST_37  C28  C27  C26  C24   180.00   0.0  0
 A6Y  CONST_38  C32  C30  C29  C28   180.00   0.0  0
 A6Y  CONST_39  C32  C30  C31  C26   180.00   0.0  0
 A6Y  CONST_40  C25  C27  C28  C29   180.00   0.0  0
 A6Y  CONST_41  C25  C27  C26  C31   180.00   0.0  0
 A6Y  CONST_42  C8   N3   C2   C9    180.00   0.0  0
 A6Y  CONST_43  H4   C5   C6   C7    180.00   0.0  0
 A6Y  CONST_44  H5   C4   C5   C6    180.00   0.0  0
 A6Y  CONST_45  H18  C21  C10  C11   180.00   0.0  0
 A6Y  CONST_46  H1   C7   C6   C5    180.00   0.0  0
 A6Y  CONST_47  H2   C6   C5   C4    180.00   0.0  0
 A6Y  CONST_48  H7   C20  N19  C12   180.00   0.0  0
 A6Y  CONST_49  H6   C12  N19  C20   180.00   0.0  0
 A6Y  CONST_50  H10  C28  C27  C26   180.00   0.0  0
 A6Y  CONST_51  H12  C31  C26  C27   180.00   0.0  0
 A6Y  CONST_52  H11  C29  C28  C27   180.00   0.0  0
 A6Y  CONST_53  H3   C11  C12  N19   180.00   0.0  0
 A6Y  Var_01    C2   N3   C24  C26    89.85  30.0  2
 A6Y  Var_02    N3   C24  C26  C27  -170.51  30.0  1
 A6Y  Var_03    H19  C25  C27  C28  -119.20  30.0  2
 A6Y  Var_04    H13  C32  C30  C29  -132.25  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
 A6Y  chir_01  C9  C10  O22  C2  positiv

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
 A6Y  plan-1  C11  0.020
 A6Y  plan-1  C12  0.020
 A6Y  plan-1  C20  0.020
 A6Y  plan-1  C9   0.020
 A6Y  plan-1  C10  0.020
 A6Y  plan-1  N19  0.020
 A6Y  plan-1  C21  0.020
 A6Y  plan-1  H3   0.020
 A6Y  plan-1  H6   0.020
 A6Y  plan-1  H7   0.020
 A6Y  plan-1  H18  0.020
 A6Y  plan-2  C28  0.020
 A6Y  plan-2  C26  0.020
 A6Y  plan-2  C27  0.020
 A6Y  plan-2  C29  0.020
 A6Y  plan-2  C31  0.020
 A6Y  plan-2  C25  0.020
 A6Y  plan-2  C30  0.020
 A6Y  plan-2  H10  0.020
 A6Y  plan-2  H11  0.020
 A6Y  plan-2  H12  0.020
 A6Y  plan-2  C24  0.020
 A6Y  plan-2  C32  0.020
 A6Y  plan-3  C7   0.020
 A6Y  plan-3  C6   0.020
 A6Y  plan-3  C5   0.020
 A6Y  plan-3  C4   0.020
 A6Y  plan-3  C3   0.020
 A6Y  plan-3  N2   0.020
 A6Y  plan-3  C9   0.020
 A6Y  plan-3  C2   0.020
 A6Y  plan-3  N3   0.020
 A6Y  plan-3  C8   0.020
 A6Y  plan-3  H1   0.020
 A6Y  plan-3  H2   0.020
 A6Y  plan-3  H4   0.020
 A6Y  plan-3  H5   0.020
 A6Y  plan-3  C24  0.020

