# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:18:52 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(c(CCC3=COc4ccccc4C3=O)nc2c1)c5ccccc5
#
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
 DKU  DKU  3-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]chromen-4-one  ligand  49  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DKU
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
 DKU  C12  C  CH2   0  -0.513  -0.6879   1.3503  -0.5112
 DKU  C13  C  CH2   0  -0.542   0.0630   0.7596   0.6934
 DKU  C14  C  CR5   0   0.447   1.5345   0.7527   0.4636
 DKU  C20  C  CR16  0  -0.311   5.8931   0.0472  -0.3636
 DKU  C10  C  CR6   0   0.427  -2.9038   0.0744  -0.5291
 DKU  C5   C  CR66  0  -0.120  -4.3475   0.1638  -0.2745
 DKU  C6   C  CR16  0  -0.288  -5.1885  -0.9457  -0.4244
 DKU  C1   C  CR16  0  -0.248  -6.5401  -0.8377  -0.1848
 DKU  C2   C  CR16  0  -0.247  -7.0820   0.3893   0.2115
 DKU  C3   C  CR16  0  -0.326  -6.2774   1.4980   0.3673
 DKU  C4   C  CR66  0   0.368  -4.9121   1.3737   0.1218
 DKU  O7   O  O     0  -0.427  -4.1561   2.4816   0.2827
 DKU  C8   C  CR16  0   0.029  -2.8409   2.4172   0.0638
 DKU  C9   C  CR6   0  -0.153  -2.1719   1.3152  -0.3184
 DKU  N18  N  N     0  -0.473   2.2735   1.8274   0.4438
 DKU  C17  C  CR56  0   0.147   3.5519   1.3977   0.1847
 DKU  C22  C  CR16  0  -0.389   4.7341   2.1265   0.0481
 DKU  C21  C  CR6   0   0.083   5.9116   1.4494  -0.2259
 DKU  C29  C  CH3   0  -0.724   7.2092   2.1907  -0.3847
 DKU  C19  C  CR16  0  -0.286   4.7348  -0.6965  -0.2317
 DKU  C16  C  CR56  0   0.302   3.5692   0.0054   0.0493
 DKU  N15  N  NR5   0  -0.639   2.2592  -0.3876   0.2277
 DKU  C23  C  CR6   0   0.269   1.7912  -1.7227   0.1955
 DKU  C28  C  CR16  0  -0.276   2.3040  -2.6474   1.0983
 DKU  C27  C  CR16  0  -0.257   1.8594  -3.9605   1.0606
 DKU  C26  C  CR16  0  -0.251   0.8944  -4.3461   0.1386
 DKU  C25  C  CR16  0  -0.253   0.3798  -3.4152  -0.7530
 DKU  C24  C  CR16  0  -0.254   0.8360  -2.1050  -0.7369
 DKU  H1   H  HCH2  0   0.267  -0.3579   2.3790  -0.6644
 DKU  H2   H  HCH2  0   0.266  -0.4240   0.7998  -1.4167
 DKU  H3   H  HCH2  0   0.280  -0.1428   1.3713   1.5737
 DKU  H4   H  HCH2  0   0.278  -0.2973  -0.2456   0.9102
 DKU  H5   H  HCR6  0   0.247   6.8206  -0.4679  -0.5838
 DKU  H6   H  HCR6  0   0.270  -4.7605  -1.8901  -0.7329
 DKU  H7   H  HCR6  0   0.269  -7.1847  -1.6978  -0.3032
 DKU  H8   H  HCR6  0   0.276  -8.1441   0.4742   0.3981
 DKU  H9   H  HCR6  0   0.285  -6.6880   2.4512   0.6735
 DKU  H10  H  HCR6  0   0.305  -2.3626   3.3742   0.2297
 DKU  H11  H  HCR6  0   0.246   4.7265   3.2052   0.1500
 DKU  H12  H  HCH3  0   0.243   7.6314   2.0433  -1.3802
 DKU  H13  H  HCH3  0   0.242   7.0769   3.2616  -0.2356
 DKU  H14  H  HCH3  0   0.242   7.9559   1.8443   0.3318
 DKU  H15  H  HCR6  0   0.266   4.7471  -1.7730  -0.3426
 DKU  H16  H  HCR6  0   0.277   3.0392  -2.3416   1.8318
 DKU  H17  H  HCR6  0   0.266   2.2609  -4.6798   1.7620
 DKU  H18  H  HCR6  0   0.263   0.5425  -5.3690   0.1187
 DKU  H19  H  HCR6  0   0.264  -0.3734  -3.7075  -1.4724
 DKU  H20  H  HCR6  0   0.274   0.4423  -1.3862  -1.4426
 DKU  O11  O  O     0  -0.419  -2.3654  -0.9612  -0.8950

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
 DKU  C29  C21  single    1.503  0.020  1.503
 DKU  C20  C21  aromatic  1.409  0.020  1.409
 DKU  C20  C19  aromatic  1.383  0.020  1.383
 DKU  C21  C22  aromatic  1.386  0.020  1.386
 DKU  C19  C16  aromatic  1.389  0.020  1.389
 DKU  C22  C17  aromatic  1.395  0.020  1.395
 DKU  C16  C17  aromatic  1.399  0.020  1.399
 DKU  C16  N15  aromatic  1.379  0.020  1.379
 DKU  C25  C24  aromatic  1.387  0.020  1.387
 DKU  C25  C26  aromatic  1.388  0.020  1.388
 DKU  C24  C23  aromatic  1.389  0.020  1.389
 DKU  C17  N18  aromatic  1.373  0.020  1.373
 DKU  C26  C27  aromatic  1.389  0.020  1.389
 DKU  C23  N15  single    1.415  0.020  1.415
 DKU  C23  C28  aromatic  1.390  0.020  1.390
 DKU  N15  C14  aromatic  1.372  0.020  1.372
 DKU  C27  C28  aromatic  1.387  0.020  1.387
 DKU  N18  C14  aromatic  1.304  0.020  1.304
 DKU  C14  C13  single    1.489  0.020  1.489
 DKU  C13  C12  single    1.537  0.020  1.537
 DKU  C12  C9   single    1.497  0.020  1.497
 DKU  C8   C9   double    1.345  0.020  1.345
 DKU  C8   O7   single    1.335  0.020  1.335
 DKU  C9   C10  single    1.456  0.020  1.456
 DKU  O7   C4   single    1.351  0.020  1.351
 DKU  C10  O11  double    1.223  0.020  1.223
 DKU  C10  C5   single    1.469  0.020  1.469
 DKU  C4   C5   aromatic  1.393  0.020  1.393
 DKU  C4   C3   aromatic  1.393  0.020  1.393
 DKU  C5   C6   aromatic  1.400  0.020  1.400
 DKU  C3   C2   aromatic  1.379  0.020  1.379
 DKU  C6   C1   aromatic  1.377  0.020  1.377
 DKU  C2   C1   aromatic  1.399  0.020  1.399
 DKU  C12  H1   single    0.970  0.020  1.090
 DKU  C12  H2   single    0.970  0.020  1.090
 DKU  C13  H3   single    0.970  0.020  1.090
 DKU  C13  H4   single    0.970  0.020  1.090
 DKU  C20  H5   single    0.930  0.020  1.080
 DKU  C6   H6   single    0.930  0.020  1.080
 DKU  C1   H7   single    0.930  0.020  1.080
 DKU  C2   H8   single    0.930  0.020  1.080
 DKU  C3   H9   single    0.930  0.020  1.080
 DKU  C8   H10  single    0.930  0.020  1.080
 DKU  C22  H11  single    0.930  0.020  1.080
 DKU  C29  H12  single    0.970  0.020  1.090
 DKU  C29  H13  single    0.970  0.020  1.090
 DKU  C29  H14  single    0.970  0.020  1.090
 DKU  C19  H15  single    0.930  0.020  1.080
 DKU  C28  H16  single    0.930  0.020  1.080
 DKU  C27  H17  single    0.930  0.020  1.080
 DKU  C26  H18  single    0.930  0.020  1.080
 DKU  C25  H19  single    0.930  0.020  1.080
 DKU  C24  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
 DKU  H2   C12  H1   106.60  3.000
 DKU  H2   C12  C9   109.54  3.000
 DKU  H1   C12  C9   109.87  3.000
 DKU  H2   C12  C13  109.76  3.000
 DKU  H1   C12  C13  108.94  3.000
 DKU  C9   C12  C13  111.98  3.000
 DKU  H4   C13  H3   107.11  3.000
 DKU  H4   C13  C14  110.67  3.000
 DKU  H3   C13  C14  108.26  3.000
 DKU  H4   C13  C12  110.41  3.000
 DKU  H3   C13  C12  108.94  3.000
 DKU  C14  C13  C12  111.31  3.000
 DKU  N15  C14  N18  112.52  3.000
 DKU  N18  C14  C13  123.93  3.000
 DKU  N15  C14  C13  123.54  3.000
 DKU  H5   C20  C19  118.73  3.000
 DKU  H5   C20  C21  118.80  3.000
 DKU  C19  C20  C21  122.47  3.000
 DKU  C9   C10  C5   114.66  3.000
 DKU  C5   C10  O11  122.42  3.000
 DKU  C9   C10  O11  122.93  3.000
 DKU  C4   C5   C6   118.38  3.000
 DKU  C6   C5   C10  121.57  3.000
 DKU  C4   C5   C10  120.05  3.000
 DKU  H6   C6   C1   120.43  3.000
 DKU  H6   C6   C5   118.99  3.000
 DKU  C1   C6   C5   120.58  3.000
 DKU  H7   C1   C2   119.86  3.000
 DKU  H7   C1   C6   120.24  3.000
 DKU  C2   C1   C6   119.90  3.000
 DKU  H8   C2   C3   119.37  3.000
 DKU  H8   C2   C1   119.87  3.000
 DKU  C3   C2   C1   120.76  3.000
 DKU  H9   C3   C4   120.03  3.000
 DKU  H9   C3   C2   121.26  3.000
 DKU  C4   C3   C2   118.71  3.000
 DKU  O7   C4   C3   117.03  3.000
 DKU  C3   C4   C5   121.67  3.000
 DKU  O7   C4   C5   121.30  3.000
 DKU  C8   O7   C4   119.49  3.000
 DKU  H10  C8   C9   123.24  3.000
 DKU  H10  C8   O7   111.56  3.000
 DKU  C9   C8   O7   125.20  3.000
 DKU  C8   C9   C10  119.30  3.000
 DKU  C10  C9   C12  119.98  3.000
 DKU  C8   C9   C12  120.71  3.000
 DKU  C17  N18  C14  105.81  3.000
 DKU  C16  C17  C22  119.99  3.000
 DKU  C16  C17  N18  109.94  3.000
 DKU  C22  C17  N18  130.07  3.000
 DKU  H11  C22  C21  120.73  3.000
 DKU  H11  C22  C17  120.32  3.000
 DKU  C21  C22  C17  118.95  3.000
 DKU  C29  C21  C22  120.90  3.000
 DKU  C22  C21  C20  119.63  3.000
 DKU  C29  C21  C20  119.47  3.000
 DKU  H14  C29  H13  107.77  3.000
 DKU  H14  C29  H12  106.94  3.000
 DKU  H13  C29  H12  107.74  3.000
 DKU  H14  C29  C21  111.40  3.000
 DKU  H13  C29  C21  111.45  3.000
 DKU  H12  C29  C21  111.33  3.000
 DKU  H15  C19  C16  122.19  3.000
 DKU  H15  C19  C20  121.04  3.000
 DKU  C16  C19  C20  116.76  3.000
 DKU  N15  C16  C19  132.77  3.000
 DKU  N15  C16  C17  105.03  3.000
 DKU  C19  C16  C17  122.19  3.000
 DKU  C23  N15  C16  125.45  3.000
 DKU  C23  N15  C14  127.84  3.000
 DKU  C16  N15  C14  106.69  3.000
 DKU  C24  C23  C28  120.44  3.000
 DKU  C28  C23  N15  119.39  3.000
 DKU  C24  C23  N15  120.17  3.000
 DKU  H16  C28  C27  120.23  3.000
 DKU  H16  C28  C23  120.17  3.000
 DKU  C27  C28  C23  119.60  3.000
 DKU  H17  C27  C26  120.23  3.000
 DKU  H17  C27  C28  119.54  3.000
 DKU  C26  C27  C28  120.23  3.000
 DKU  H18  C26  C25  120.11  3.000
 DKU  H18  C26  C27  120.04  3.000
 DKU  C25  C26  C27  119.85  3.000
 DKU  H19  C25  C24  119.46  3.000
 DKU  H19  C25  C26  120.27  3.000
 DKU  C24  C25  C26  120.27  3.000
 DKU  H20  C24  C25  120.02  3.000
 DKU  H20  C24  C23  120.37  3.000
 DKU  C25  C24  C23  119.60  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
 DKU  CONST_01  C19  C16  N15  C14   180.00   0.0  0
 DKU  CONST_02  C17  C16  N15  C14     0.00   0.0  0
 DKU  CONST_05  C22  C17  N18  C14   180.00   0.0  0
 DKU  CONST_06  C16  C17  N18  C14     0.00   0.0  0
 DKU  CONST_07  C17  C22  C21  C20     0.00   0.0  0
 DKU  CONST_08  C17  C16  C19  C20     0.00   0.0  0
 DKU  CONST_09  N15  C16  C19  C20   180.00   0.0  0
 DKU  CONST_10  C2   C3   C4   C5      0.00   0.0  0
 DKU  CONST_11  C2   C1   C6   C5      0.00   0.0  0
 DKU  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 DKU  CONST_13  C3   C2   C1   C6      0.00   0.0  0
 DKU  CONST_14  C4   C5   C6   C1      0.00   0.0  0
 DKU  CONST_15  C4   C3   C2   C1      0.00   0.0  0
 DKU  CONST_16  C21  C22  C17  N18   180.00   0.0  0
 DKU  CONST_17  C19  C16  C17  N18   180.00   0.0  0
 DKU  CONST_18  N15  C16  C17  N18     0.00   0.0  0
 DKU  CONST_19  C16  N15  C14  N18     0.00   0.0  0
 DKU  CONST_20  C23  N15  C14  N18   180.00   0.0  0
 DKU  CONST_21  C23  N15  C16  C17   180.00   0.0  0
 DKU  CONST_22  N15  C14  N18  C17     0.00   0.0  0
 DKU  CONST_23  C19  C20  C21  C22     0.00   0.0  0
 DKU  CONST_24  C19  C16  C17  C22     0.00   0.0  0
 DKU  CONST_25  N15  C16  C17  C22   180.00   0.0  0
 DKU  CONST_26  C16  C19  C20  C21     0.00   0.0  0
 DKU  CONST_27  C16  C17  C22  C21     0.00   0.0  0
 DKU  CONST_28  C23  N15  C16  C19     0.00   0.0  0
 DKU  CONST_31  C25  C24  C23  N15   180.00   0.0  0
 DKU  CONST_32  C27  C28  C23  N15   180.00   0.0  0
 DKU  CONST_33  C26  C25  C24  C23     0.00   0.0  0
 DKU  CONST_34  C26  C27  C28  C23     0.00   0.0  0
 DKU  CONST_35  C25  C24  C23  C28     0.00   0.0  0
 DKU  CONST_36  C25  C26  C27  C28     0.00   0.0  0
 DKU  CONST_37  C24  C25  C26  C27     0.00   0.0  0
 DKU  CONST_38  C24  C23  C28  C27     0.00   0.0  0
 DKU  CONST_39  C16  N15  C14  C13   180.00   0.0  0
 DKU  CONST_40  C23  N15  C14  C13     0.00   0.0  0
 DKU  CONST_41  C17  N18  C14  C13   180.00   0.0  0
 DKU  CONST_42  C29  C21  C22  C17   180.00   0.0  0
 DKU  CONST_43  C19  C20  C21  C29   180.00   0.0  0
 DKU  CONST_44  H11  C22  C21  C20   180.00   0.0  0
 DKU  CONST_45  H6   C6   C5   C10     0.00   0.0  0
 DKU  CONST_46  H9   C3   C4   C5    180.00   0.0  0
 DKU  CONST_47  H7   C1   C6   C5    180.00   0.0  0
 DKU  CONST_48  H8   C2   C1   C6    180.00   0.0  0
 DKU  CONST_49  H15  C19  C16  C17   180.00   0.0  0
 DKU  CONST_50  H5   C20  C21  C22   180.00   0.0  0
 DKU  CONST_51  H20  C24  C23  N15     0.00   0.0  0
 DKU  CONST_52  H16  C28  C23  N15     0.00   0.0  0
 DKU  CONST_53  H19  C25  C24  C23   180.00   0.0  0
 DKU  CONST_54  H17  C27  C28  C23   180.00   0.0  0
 DKU  CONST_55  H18  C26  C27  C28   180.00   0.0  0
 DKU  Var_01    O7   C8   C9   C10     0.40  30.0  1
 DKU  Var_02    C8   C9   C10  C5     -0.74  30.0  1
 DKU  Var_03    C9   C10  C5   C6   -179.61  30.0  1
 DKU  Var_04    C9   C8   O7   C4      0.15  30.0  1
 DKU  Var_05    N15  C14  C13  C12  -108.15  30.0  2
 DKU  Var_06    C9   C12  C13  C14   177.77  30.0  3
 DKU  Var_07    H12  C29  C21  C20    60.66  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
 DKU  plan-1  N15  0.020
 DKU  plan-1  C23  0.020
 DKU  plan-1  C28  0.020
 DKU  plan-1  C27  0.020
 DKU  plan-1  C26  0.020
 DKU  plan-1  C25  0.020
 DKU  plan-1  C24  0.020
 DKU  plan-1  H16  0.020
 DKU  plan-1  H17  0.020
 DKU  plan-1  H18  0.020
 DKU  plan-1  H19  0.020
 DKU  plan-1  H20  0.020
 DKU  plan-2  C13  0.020
 DKU  plan-2  C14  0.020
 DKU  plan-2  C20  0.020
 DKU  plan-2  N18  0.020
 DKU  plan-2  C17  0.020
 DKU  plan-2  C22  0.020
 DKU  plan-2  C21  0.020
 DKU  plan-2  C29  0.020
 DKU  plan-2  C19  0.020
 DKU  plan-2  C16  0.020
 DKU  plan-2  N15  0.020
 DKU  plan-2  C23  0.020
 DKU  plan-2  H5   0.020
 DKU  plan-2  H11  0.020
 DKU  plan-2  H15  0.020
 DKU  plan-3  C10  0.020
 DKU  plan-3  C5   0.020
 DKU  plan-3  C6   0.020
 DKU  plan-3  C1   0.020
 DKU  plan-3  C2   0.020
 DKU  plan-3  C3   0.020
 DKU  plan-3  C4   0.020
 DKU  plan-3  O7   0.020
 DKU  plan-3  H6   0.020
 DKU  plan-3  H7   0.020
 DKU  plan-3  H8   0.020
 DKU  plan-3  H9   0.020
 DKU  plan-4  C10  0.020
 DKU  plan-4  C5   0.020
 DKU  plan-4  C9   0.020
 DKU  plan-4  O11  0.020

