# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:56:08 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-[4-(4-cyano-3-methylphenoxy)phenyl]-N-methyl-N-[2-(5-methyl-1,2,4-oxadiazol-3-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCc1noc(C)n1)C(=O)Cc2ccc(Oc3ccc(C#N)c(C)c3)cc2
#
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
 ONY  ONY  2-[4-(4-cyano-3-methylphenoxy)phenyl]-N-methyl-N-[2-(5-methyl-1,2,4-oxadiazol-3-yl)ethyl]acetamide  ligand  51  29  .  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_ONY
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
 ONY  C01  C  CH3   0  -0.529  21.9482   -2.2081   1.9613
 ONY  C03  C  CH2   0  -0.333  21.8254   -2.6741  -0.4675
 ONY  C04  C  CH2   0  -0.542  23.3008   -2.8389  -0.8479
 ONY  C05  C  CR5   0   0.327  23.5600   -2.3810  -2.2356
 ONY  C08  C  CR5   0   0.502  23.6784   -1.1441  -3.9020
 ONY  C10  C  CH3   0  -0.757  23.6700   -0.0602  -4.9057
 ONY  C11  C  C     0   0.570  21.1784   -4.3617   1.2132
 ONY  C13  C  CH2   0  -0.717  20.8341   -5.3053   0.0667
 ONY  C14  C  CR6   0   0.187  20.5156   -6.6845   0.5598
 ONY  C15  C  CR16  0  -0.306  19.2045   -7.0625   0.8280
 ONY  C16  C  CR16  0  -0.284  18.9064   -8.3370   1.2866
 ONY  C17  C  CR6   0   0.280  19.9369   -9.2427   1.4789
 ONY  C18  C  CR16  0  -0.289  21.2515   -8.8922   1.2204
 ONY  C19  C  CR16  0  -0.302  21.5303   -7.6145   0.7579
 ONY  C21  C  CR6   0   0.408  19.4752  -10.7858   3.1995
 ONY  C22  C  CR16  0  -0.355  19.6517   -9.8372   4.2028
 ONY  C23  C  CR16  0  -0.222  19.4500  -10.2137   5.5171
 ONY  C24  C  CR6   0  -0.043  19.0767  -11.5176   5.8349
 ONY  C25  C  CR6   0   0.153  18.8998  -12.4807   4.8268
 ONY  C26  C  CR16  0  -0.388  19.1047  -12.0929   3.5155
 ONY  C27  C  CH3   0  -0.745  18.4918  -13.8819   5.1621
 ONY  C28  C  CSP   0   0.026  18.8728  -11.8730   7.1983
 ONY  N02  N  NT    0  -0.450  21.5618   -3.1072   0.8884
 ONY  N06  N  N     0  -0.151  24.0029   -3.1648  -3.1678
 ONY  N09  N  N     0  -0.457  23.3398   -1.0997  -2.6561
 ONY  N29  N  NS    0  -0.259  18.7056  -12.1644   8.3018
 ONY  O07  O  O     0  -0.328  24.0856   -2.3524  -4.2686
 ONY  O12  O  O     0  -0.482  21.0905   -4.7225   2.3763
 ONY  O20  O  O2    0  -0.504  19.6499  -10.5276   1.8860
 ONY  H1   H  HCH3  0   0.253  21.1843   -2.1702   2.7355
 ONY  H2   H  HCH3  0   0.241  22.8923   -2.5001   2.4250
 ONY  H3   H  HCH3  0   0.248  22.0660   -1.2072   1.5531
 ONY  H4   H  HCH2  0   0.278  21.5363   -1.6258  -0.5548
 ONY  H5   H  HCH2  0   0.283  21.1948   -3.2194  -1.1671
 ONY  H6   H  HCH2  0   0.268  23.6044   -3.8825  -0.7507
 ONY  H7   H  HCH2  0   0.283  23.9225   -2.2557  -0.1641
 ONY  H8   H  HCH3  0   0.282  23.0896   -0.3486  -5.7817
 ONY  H9   H  HCH3  0   0.278  23.2359    0.8364  -4.4736
 ONY  H10  H  HCH3  0   0.284  24.6840    0.1643  -5.2374
 ONY  H11  H  HCH2  0   0.286  21.6615   -5.3505  -0.6462
 ONY  H12  H  HCH2  0   0.301  19.9837   -4.8968  -0.4862
 ONY  H13  H  HCR6  0   0.258  18.3980   -6.3560   0.6731
 ONY  H14  H  HCR6  0   0.276  17.8816   -8.6245   1.4854
 ONY  H15  H  HCR6  0   0.274  22.0476   -9.6107   1.3678
 ONY  H16  H  HCR6  0   0.257  22.5577   -7.3428   0.5480
 ONY  H17  H  HCR6  0   0.291  19.9420   -8.8205   3.9780
 ONY  H18  H  HCR6  0   0.285  19.5844   -9.4853   6.3052
 ONY  H19  H  HCR6  0   0.277  18.9782  -12.8121   2.7157
 ONY  H20  H  HCH3  0   0.259  19.1803  -14.3369   5.8754
 ONY  H21  H  HCH3  0   0.262  17.4988  -13.9015   5.6143
 ONY  H22  H  HCH3  0   0.264  18.4672  -14.5080   4.2730

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
 ONY  C10  C08  single    1.477  0.020  1.477
 ONY  C08  O07  aromatic  1.327  0.020  1.327
 ONY  C08  N09  aromatic  1.292  0.020  1.292
 ONY  O07  N06  aromatic  1.371  0.020  1.371
 ONY  N09  C05  aromatic  1.366  0.020  1.366
 ONY  N06  C05  aromatic  1.296  0.020  1.296
 ONY  C05  C04  single    1.484  0.020  1.484
 ONY  C04  C03  single    1.533  0.020  1.533
 ONY  C03  N02  single    1.448  0.020  1.448
 ONY  C13  C14  single    1.499  0.020  1.499
 ONY  C13  C11  single    1.524  0.020  1.524
 ONY  C15  C16  aromatic  1.387  0.020  1.387
 ONY  C15  C14  aromatic  1.391  0.020  1.391
 ONY  C16  C17  aromatic  1.385  0.020  1.385
 ONY  C14  C19  aromatic  1.391  0.020  1.391
 ONY  C17  O20  single    1.378  0.020  1.378
 ONY  C17  C18  aromatic  1.385  0.020  1.385
 ONY  C19  C18  aromatic  1.387  0.020  1.387
 ONY  O20  C21  single    1.350  0.020  1.350
 ONY  N02  C11  single    1.351  0.020  1.351
 ONY  N02  C01  single    1.452  0.020  1.452
 ONY  C11  O12  double    1.221  0.020  1.221
 ONY  C21  C26  aromatic  1.395  0.020  1.395
 ONY  C21  C22  aromatic  1.392  0.020  1.392
 ONY  C26  C25  aromatic  1.383  0.020  1.383
 ONY  C22  C23  aromatic  1.382  0.020  1.382
 ONY  C25  C27  single    1.497  0.020  1.497
 ONY  C25  C24  aromatic  1.405  0.020  1.405
 ONY  C23  C24  aromatic  1.393  0.020  1.393
 ONY  C24  C28  single    1.424  0.020  1.424
 ONY  C28  N29  triple    1.153  0.020  1.153
 ONY  C01  H1   single    0.970  0.020  1.090
 ONY  C01  H2   single    0.970  0.020  1.090
 ONY  C01  H3   single    0.970  0.020  1.090
 ONY  C03  H4   single    0.970  0.020  1.090
 ONY  C03  H5   single    0.970  0.020  1.090
 ONY  C04  H6   single    0.970  0.020  1.090
 ONY  C04  H7   single    0.970  0.020  1.090
 ONY  C10  H8   single    0.970  0.020  1.090
 ONY  C10  H9   single    0.970  0.020  1.090
 ONY  C10  H10  single    0.970  0.020  1.090
 ONY  C13  H11  single    0.970  0.020  1.090
 ONY  C13  H12  single    0.970  0.020  1.090
 ONY  C15  H13  single    0.930  0.020  1.080
 ONY  C16  H14  single    0.930  0.020  1.080
 ONY  C18  H15  single    0.930  0.020  1.080
 ONY  C19  H16  single    0.930  0.020  1.080
 ONY  C22  H17  single    0.930  0.020  1.080
 ONY  C23  H18  single    0.930  0.020  1.080
 ONY  C26  H19  single    0.930  0.020  1.080
 ONY  C27  H20  single    0.970  0.020  1.090
 ONY  C27  H21  single    0.970  0.020  1.090
 ONY  C27  H22  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
 ONY  H3   C01  H2   108.18  3.000
 ONY  H3   C01  H1   108.13  3.000
 ONY  H2   C01  H1   108.31  3.000
 ONY  H3   C01  N02  108.75  3.000
 ONY  H2   C01  N02  112.23  3.000
 ONY  H1   C01  N02  111.13  3.000
 ONY  H5   C03  H4   106.05  3.000
 ONY  H5   C03  N02  110.28  3.000
 ONY  H4   C03  N02  108.31  3.000
 ONY  H5   C03  C04  110.14  3.000
 ONY  H4   C03  C04  109.80  3.000
 ONY  N02  C03  C04  112.06  3.000
 ONY  H7   C04  H6   107.24  3.000
 ONY  H7   C04  C05  108.73  3.000
 ONY  H6   C04  C05  109.25  3.000
 ONY  H7   C04  C03  109.57  3.000
 ONY  H6   C04  C03  110.40  3.000
 ONY  C05  C04  C03  111.53  3.000
 ONY  N09  C05  N06  113.63  3.000
 ONY  N06  C05  C04  123.07  3.000
 ONY  N09  C05  C04  123.30  3.000
 ONY  O07  C08  N09  112.23  3.000
 ONY  N09  C08  C10  128.94  3.000
 ONY  O07  C08  C10  118.83  3.000
 ONY  H10  C10  H9   108.84  3.000
 ONY  H10  C10  H8   107.77  3.000
 ONY  H9   C10  H8   109.00  3.000
 ONY  H10  C10  C08  110.64  3.000
 ONY  H9   C10  C08  109.75  3.000
 ONY  H8   C10  C08  110.80  3.000
 ONY  O12  C11  N02  121.58  3.000
 ONY  O12  C11  C13  121.15  3.000
 ONY  N02  C11  C13  117.26  3.000
 ONY  H12  C13  H11  105.92  3.000
 ONY  H12  C13  C14  110.17  3.000
 ONY  H11  C13  C14  109.71  3.000
 ONY  H12  C13  C11  108.95  3.000
 ONY  H11  C13  C11  110.19  3.000
 ONY  C14  C13  C11  111.73  3.000
 ONY  C19  C14  C15  118.60  3.000
 ONY  C19  C14  C13  120.48  3.000
 ONY  C15  C14  C13  120.92  3.000
 ONY  H13  C15  C16  119.11  3.000
 ONY  H13  C15  C14  119.81  3.000
 ONY  C16  C15  C14  121.08  3.000
 ONY  H14  C16  C17  120.33  3.000
 ONY  H14  C16  C15  120.54  3.000
 ONY  C17  C16  C15  119.13  3.000
 ONY  O20  C17  C18  119.27  3.000
 ONY  C18  C17  C16  120.98  3.000
 ONY  O20  C17  C16  119.71  3.000
 ONY  H15  C18  C19  120.60  3.000
 ONY  H15  C18  C17  120.31  3.000
 ONY  C19  C18  C17  119.09  3.000
 ONY  H16  C19  C18  119.10  3.000
 ONY  H16  C19  C14  119.78  3.000
 ONY  C18  C19  C14  121.12  3.000
 ONY  O20  C21  C26  115.72  3.000
 ONY  C26  C21  C22  120.60  3.000
 ONY  O20  C21  C22  123.68  3.000
 ONY  H17  C22  C23  119.55  3.000
 ONY  H17  C22  C21  121.68  3.000
 ONY  C23  C22  C21  118.77  3.000
 ONY  H18  C23  C24  119.83  3.000
 ONY  H18  C23  C22  119.43  3.000
 ONY  C24  C23  C22  120.74  3.000
 ONY  C28  C24  C25  119.85  3.000
 ONY  C28  C24  C23  119.38  3.000
 ONY  C25  C24  C23  120.77  3.000
 ONY  C27  C25  C26  121.01  3.000
 ONY  C27  C25  C24  121.00  3.000
 ONY  C26  C25  C24  118.00  3.000
 ONY  H19  C26  C25  119.79  3.000
 ONY  H19  C26  C21  119.08  3.000
 ONY  C25  C26  C21  121.13  3.000
 ONY  H22  C27  H21  107.93  3.000
 ONY  H22  C27  H20  107.98  3.000
 ONY  H21  C27  H20  107.21  3.000
 ONY  H22  C27  C25  111.20  3.000
 ONY  H21  C27  C25  110.95  3.000
 ONY  H20  C27  C25  111.39  3.000
 ONY  N29  C28  C24  180.00  3.000
 ONY  C11  N02  C03  123.68  3.000
 ONY  C11  N02  C01  118.21  3.000
 ONY  C03  N02  C01  117.28  3.000
 ONY  O07  N06  C05  103.88  3.000
 ONY  C08  N09  C05  102.84  3.000
 ONY  N06  O07  C08  107.42  3.000
 ONY  C21  O20  C17  119.52  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
 ONY  CONST_01  O07  C08  N09  C05     0.00   0.0  0
 ONY  CONST_02  C08  O07  N06  C05     0.00   0.0  0
 ONY  CONST_03  N06  C05  N09  C08     0.00   0.0  0
 ONY  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 ONY  CONST_05  C17  C18  C19  C14     0.00   0.0  0
 ONY  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 ONY  CONST_07  C18  C19  C14  C15     0.00   0.0  0
 ONY  CONST_08  C19  C14  C15  C16     0.00   0.0  0
 ONY  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 ONY  CONST_10  C24  C25  C26  C21     0.00   0.0  0
 ONY  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 ONY  CONST_12  C25  C26  C21  C22     0.00   0.0  0
 ONY  CONST_13  C25  C24  C23  C22     0.00   0.0  0
 ONY  CONST_14  C26  C21  C22  C23     0.00   0.0  0
 ONY  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 ONY  CONST_16  N09  C08  O07  N06     0.00   0.0  0
 ONY  CONST_17  O07  N06  C05  N09     0.00   0.0  0
 ONY  CONST_18  C08  N09  C05  C04   180.00   0.0  0
 ONY  CONST_19  O07  N06  C05  C04   180.00   0.0  0
 ONY  CONST_20  C10  C08  N09  C05   180.00   0.0  0
 ONY  CONST_21  N06  O07  C08  C10   180.00   0.0  0
 ONY  CONST_22  C16  C15  C14  C13   180.00   0.0  0
 ONY  CONST_23  C18  C19  C14  C13   180.00   0.0  0
 ONY  CONST_24  O20  C17  C16  C15   180.00   0.0  0
 ONY  CONST_25  O20  C17  C18  C19   180.00   0.0  0
 ONY  CONST_26  C27  C25  C26  C21   180.00   0.0  0
 ONY  CONST_27  C28  C24  C23  C22   180.00   0.0  0
 ONY  CONST_28  O20  C21  C22  C23   180.00   0.0  0
 ONY  CONST_29  C27  C25  C24  C23   180.00   0.0  0
 ONY  CONST_30  O20  C21  C26  C25   180.00   0.0  0
 ONY  CONST_31  C28  C24  C25  C26   180.00   0.0  0
 ONY  CONST_32  H14  C16  C15  C14   180.00   0.0  0
 ONY  CONST_33  H15  C18  C19  C14   180.00   0.0  0
 ONY  CONST_34  H16  C19  C14  C15   180.00   0.0  0
 ONY  CONST_35  H13  C15  C16  C17   180.00   0.0  0
 ONY  CONST_36  H18  C23  C22  C21   180.00   0.0  0
 ONY  CONST_37  H19  C26  C21  C22   180.00   0.0  0
 ONY  CONST_38  H17  C22  C23  C24   180.00   0.0  0
 ONY  CONST_39  C13  C11  N02  C01   180.00   0.0  0
 ONY  CONST_40  O12  C11  N02  C01     0.00   0.0  0
 ONY  CONST_41  C13  C11  N02  C03     0.00   0.0  0
 ONY  CONST_42  O12  C11  N02  C03   180.00   0.0  0
 ONY  Var_01    C26  C21  O20  C17   176.08  30.0  2
 ONY  Var_02    N09  C05  C04  C03    60.65  30.0  2
 ONY  Var_03    C15  C14  C13  C11    93.31  30.0  2
 ONY  Var_04    H20  C27  C25  C24   -55.64  30.0  2
 ONY  Var_05    H8   C10  C08  N09  -125.44  30.0  2
 ONY  Var_06    N02  C03  C04  C05  -179.52  30.0  3
 ONY  Var_07    N02  C11  C13  C14   176.17  30.0  3
 ONY  Var_08    C04  C03  N02  C01    77.50  30.0  1
 ONY  Var_09    H1   C01  N02  C03   138.25  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
 ONY  plan-1  C04  0.020
 ONY  plan-1  C05  0.020
 ONY  plan-1  C08  0.020
 ONY  plan-1  C10  0.020
 ONY  plan-1  N06  0.020
 ONY  plan-1  N09  0.020
 ONY  plan-1  O07  0.020
 ONY  plan-2  C13  0.020
 ONY  plan-2  C14  0.020
 ONY  plan-2  C15  0.020
 ONY  plan-2  C16  0.020
 ONY  plan-2  C17  0.020
 ONY  plan-2  C18  0.020
 ONY  plan-2  C19  0.020
 ONY  plan-2  O20  0.020
 ONY  plan-2  H13  0.020
 ONY  plan-2  H14  0.020
 ONY  plan-2  H15  0.020
 ONY  plan-2  H16  0.020
 ONY  plan-3  C21  0.020
 ONY  plan-3  C22  0.020
 ONY  plan-3  C23  0.020
 ONY  plan-3  C24  0.020
 ONY  plan-3  C25  0.020
 ONY  plan-3  C26  0.020
 ONY  plan-3  C27  0.020
 ONY  plan-3  C28  0.020
 ONY  plan-3  N29  0.020
 ONY  plan-3  O20  0.020
 ONY  plan-3  H17  0.020
 ONY  plan-3  H18  0.020
 ONY  plan-3  H19  0.020
 ONY  plan-4  C01  0.020
 ONY  plan-4  C03  0.020
 ONY  plan-4  C11  0.020
 ONY  plan-4  C13  0.020
 ONY  plan-4  N02  0.020
 ONY  plan-4  O12  0.020

