# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:33:41 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cccc(Oc2cc(nc(n2)c3ccncc3)[C@@H]4CCCNC4)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
 OWB  OWB  ~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide  ligand  52  29  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OWB
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
 OWB  C1   C  CR16  0  -0.244  92.4471  89.2605  -2.0842
 OWB  C2   C  CR16  0  -0.317  91.2639  88.6210  -2.4260
 OWB  C4   C  CR16  0  -0.400  92.0490  86.6463  -1.2923
 OWB  C5   C  CR6   0   0.307  93.2156  87.3113  -0.9741
 OWB  C6   C  CR16  0  -0.312  93.4394  88.6230  -1.3562
 OWB  C13  C  CR16  0  -0.470  93.3606  87.4608   1.8134
 OWB  C14  C  CR6   0   0.363  93.5801  87.4606   3.1838
 OWB  C16  C  CR6   0   0.397  95.3862  86.1147   2.8966
 OWB  C18  C  CR6   0   0.084  96.5086  85.3581   3.4982
 OWB  C19  C  CR16  0  -0.351  96.7544  85.4058   4.8668
 OWB  C23  C  CR16  0  -0.350  97.3512  84.5745   2.7161
 OWB  C24  C  CH1   0  -0.367  92.6904  88.2267   4.1168
 OWB  C25  C  CH2   0  -0.267  92.7943  89.7355   3.8616
 OWB  C27  C  CH2   0  -0.294  90.5655  90.1144   4.6823
 OWB  C28  C  CH2   0  -0.435  90.3584  88.6308   4.9482
 OWB  C29  C  CH2   0  -0.428  91.2244  87.7909   4.0155
 OWB  C3   C  CR6   0   0.392  91.0566  87.2972  -2.0313
 OWB  N7   N  NH1   0  -0.735  89.9105  86.5569  -2.3155
 OWB  C8   C  C     0   0.505  88.8205  86.8947  -3.0612
 OWB  C9   C  CH3   0  -0.791  87.7997  85.7895  -3.1548
 OWB  O10  O  O     0  -0.462  88.6832  87.9724  -3.6086
 OWB  O11  O  O2    0  -0.478  94.1970  86.6246  -0.2878
 OWB  C12  C  CR6   0   0.548  94.2583  86.7277   1.0467
 OWB  N15  N  N     0  -0.455  94.5970  86.7870   3.7198
 OWB  N17  N  N     0  -0.451  95.2598  86.0578   1.5791
 OWB  C20  C  CR16  0  -0.057  97.8163  84.6785   5.3802
 OWB  N21  N  N     0  -0.400  98.6222  83.9286   4.6372
 OWB  C22  C  CR16  0  -0.058  98.3839  83.8851   3.3315
 OWB  N26  N  NH1   0  -0.596  91.9732  90.4450   4.8203
 OWB  H1   H  HCR6  0   0.270  92.5961  90.2850  -2.3980
 OWB  H2   H  HCR6  0   0.287  90.5205  89.1529  -2.9945
 OWB  H3   H  HCR6  0   0.290  91.9115  85.6194  -0.9735
 OWB  H4   H  HCR6  0   0.280  94.3612  89.1276  -1.0985
 OWB  H5   H  HCR6  0   0.291  92.5338  88.0021   1.3773
 OWB  H6   H  HCR6  0   0.271  96.1337  85.9989   5.5228
 OWB  H7   H  HCR6  0   0.270  97.2088  84.4969   1.6477
 OWB  H8   H  HCH1  0   0.256  93.0463  88.0323   5.1326
 OWB  H9   H  HCH2  0   0.244  93.8312  90.0611   3.9703
 OWB  H10  H  HCH2  0   0.192  92.4982  89.9392   2.8187
 OWB  H11  H  HCH2  0   0.188  90.1740  90.3533   3.6792
 OWB  H12  H  HCH2  0   0.234  89.9938  90.7095   5.3969
 OWB  H13  H  HCH2  0   0.235  89.3053  88.3735   4.8176
 OWB  H14  H  HCH2  0   0.220  90.6180  88.4115   5.9879
 OWB  H15  H  HCH2  0   0.247  91.1287  86.7285   4.2502
 OWB  H16  H  HCH2  0   0.220  90.8746  87.9192   2.9855
 OWB  H17  H  HNH1  0   0.421  89.8998  85.6274  -1.9232
 OWB  H18  H  HCH3  0   0.269  86.9016  86.1496  -3.6487
 OWB  H19  H  HCH3  0   0.276  88.1997  84.9523  -3.7295
 OWB  H20  H  HCH3  0   0.269  87.5337  85.4101  -2.1679
 OWB  H21  H  HCR6  0   0.267  98.0228  84.7055   6.4442
 OWB  H22  H  HCR6  0   0.268  99.0485  83.2684   2.7370
 OWB  H23  H  HNH1  0   0.355  92.1051  91.4405   4.7004

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
 OWB  C1   C2   aromatic  1.388  0.020  1.388
 OWB  C1   C6   aromatic  1.386  0.020  1.386
 OWB  C2   C3   aromatic  1.397  0.020  1.397
 OWB  O10  C8   double    1.216  0.020  1.216
 OWB  C6   C5   aromatic  1.384  0.020  1.384
 OWB  C8   N7   single    1.363  0.020  1.363
 OWB  C8   C9   single    1.507  0.020  1.507
 OWB  C3   N7   single    1.394  0.020  1.394
 OWB  C3   C4   aromatic  1.398  0.020  1.398
 OWB  C5   C4   aromatic  1.380  0.020  1.380
 OWB  C5   O11  single    1.380  0.020  1.380
 OWB  O11  C12  single    1.340  0.020  1.340
 OWB  C12  N17  aromatic  1.317  0.020  1.317
 OWB  C12  C13  aromatic  1.390  0.020  1.390
 OWB  N17  C16  aromatic  1.325  0.020  1.325
 OWB  C13  C14  aromatic  1.388  0.020  1.388
 OWB  C16  C18  single    1.481  0.020  1.481
 OWB  C16  N15  aromatic  1.324  0.020  1.324
 OWB  C14  C24  single    1.500  0.020  1.500
 OWB  C14  N15  aromatic  1.332  0.020  1.332
 OWB  C29  C28  single    1.525  0.020  1.525
 OWB  C29  C24  single    1.533  0.020  1.533
 OWB  C23  C18  aromatic  1.391  0.020  1.391
 OWB  C23  C22  aromatic  1.386  0.020  1.386
 OWB  C27  C28  single    1.521  0.020  1.521
 OWB  C27  N26  single    1.453  0.020  1.453
 OWB  C24  C25  single    1.534  0.020  1.534
 OWB  C18  C19  aromatic  1.391  0.020  1.391
 OWB  C25  N26  single    1.448  0.020  1.448
 OWB  C22  N21  aromatic  1.328  0.020  1.328
 OWB  C19  C20  aromatic  1.386  0.020  1.386
 OWB  N21  C20  aromatic  1.328  0.020  1.328
 OWB  C1   H1   single    0.930  0.020  1.080
 OWB  C2   H2   single    0.930  0.020  1.080
 OWB  C4   H3   single    0.930  0.020  1.080
 OWB  C6   H4   single    0.930  0.020  1.080
 OWB  C13  H5   single    0.930  0.020  1.080
 OWB  C19  H6   single    0.930  0.020  1.080
 OWB  C23  H7   single    0.930  0.020  1.080
 OWB  C24  H8   single    0.970  0.020  1.090
 OWB  C25  H9   single    0.970  0.020  1.090
 OWB  C25  H10  single    0.970  0.020  1.090
 OWB  C27  H11  single    0.970  0.020  1.090
 OWB  C27  H12  single    0.970  0.020  1.090
 OWB  C28  H13  single    0.970  0.020  1.090
 OWB  C28  H14  single    0.970  0.020  1.090
 OWB  C29  H15  single    0.970  0.020  1.090
 OWB  C29  H16  single    0.970  0.020  1.090
 OWB  N7   H17  single    0.860  0.020  1.020
 OWB  C9   H18  single    0.970  0.020  1.090
 OWB  C9   H19  single    0.970  0.020  1.090
 OWB  C9   H20  single    0.970  0.020  1.090
 OWB  C20  H21  single    0.930  0.020  1.080
 OWB  C22  H22  single    0.930  0.020  1.080
 OWB  N26  H23  single    0.890  0.020  1.040

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
 OWB  H1   C1   C6   119.29  3.000
 OWB  H1   C1   C2   118.84  3.000
 OWB  C6   C1   C2   121.86  3.000
 OWB  H2   C2   C3   121.00  3.000
 OWB  H2   C2   C1   119.42  3.000
 OWB  C3   C2   C1   119.58  3.000
 OWB  H3   C4   C3   120.43  3.000
 OWB  H3   C4   C5   119.73  3.000
 OWB  C3   C4   C5   119.84  3.000
 OWB  O11  C5   C6   119.58  3.000
 OWB  O11  C5   C4   118.41  3.000
 OWB  C6   C5   C4   121.98  3.000
 OWB  H4   C6   C5   120.92  3.000
 OWB  H4   C6   C1   121.37  3.000
 OWB  C5   C6   C1   117.71  3.000
 OWB  H5   C13  C12  122.41  3.000
 OWB  H5   C13  C14  121.32  3.000
 OWB  C12  C13  C14  116.27  3.000
 OWB  N15  C14  C24  117.44  3.000
 OWB  N15  C14  C13  121.20  3.000
 OWB  C24  C14  C13  121.36  3.000
 OWB  N17  C16  N15  125.68  3.000
 OWB  N15  C16  C18  117.30  3.000
 OWB  N17  C16  C18  117.02  3.000
 OWB  C23  C18  C19  117.73  3.000
 OWB  C19  C18  C16  121.06  3.000
 OWB  C23  C18  C16  121.22  3.000
 OWB  H6   C19  C20  120.23  3.000
 OWB  H6   C19  C18  120.97  3.000
 OWB  C20  C19  C18  118.80  3.000
 OWB  H7   C23  C22  120.10  3.000
 OWB  H7   C23  C18  121.09  3.000
 OWB  C22  C23  C18  118.81  3.000
 OWB  H8   C24  C29  108.79  3.000
 OWB  H8   C24  C25  107.90  3.000
 OWB  C29  C24  C25  109.48  3.000
 OWB  H8   C24  C14  107.09  3.000
 OWB  C25  C24  C14  111.03  3.000
 OWB  C29  C24  C14  112.40  3.000
 OWB  H10  C25  H9   107.09  3.000
 OWB  H10  C25  N26  112.54  3.000
 OWB  H9   C25  N26  109.05  3.000
 OWB  H10  C25  C24  108.71  3.000
 OWB  H9   C25  C24  109.94  3.000
 OWB  N26  C25  C24  109.48  3.000
 OWB  H12  C27  H11  106.94  3.000
 OWB  H12  C27  N26  108.74  3.000
 OWB  H11  C27  N26  112.40  3.000
 OWB  H12  C27  C28  110.23  3.000
 OWB  H11  C27  C28  108.77  3.000
 OWB  N26  C27  C28  109.71  3.000
 OWB  H14  C28  H13  107.18  3.000
 OWB  H14  C28  C29  109.64  3.000
 OWB  H13  C28  C29  110.16  3.000
 OWB  H14  C28  C27  109.23  3.000
 OWB  H13  C28  C27  109.89  3.000
 OWB  C29  C28  C27  110.66  3.000
 OWB  H16  C29  H15  106.74  3.000
 OWB  H16  C29  C28  109.23  3.000
 OWB  H15  C29  C28  110.77  3.000
 OWB  H16  C29  C24  109.53  3.000
 OWB  H15  C29  C24  110.25  3.000
 OWB  C28  C29  C24  110.25  3.000
 OWB  N7   C3   C4   116.37  3.000
 OWB  C4   C3   C2   119.03  3.000
 OWB  N7   C3   C2   124.60  3.000
 OWB  H17  N7   C8   115.62  3.000
 OWB  H17  N7   C3   114.76  3.000
 OWB  C8   N7   C3   129.61  3.000
 OWB  O10  C8   C9   123.03  3.000
 OWB  C9   C8   N7   113.19  3.000
 OWB  O10  C8   N7   123.77  3.000
 OWB  H20  C9   H19  107.40  3.000
 OWB  H20  C9   H18  108.98  3.000
 OWB  H19  C9   H18  108.53  3.000
 OWB  H20  C9   C8   111.35  3.000
 OWB  H19  C9   C8   110.30  3.000
 OWB  H18  C9   C8   110.18  3.000
 OWB  C12  O11  C5   119.30  3.000
 OWB  N17  C12  O11  113.47  3.000
 OWB  N17  C12  C13  122.44  3.000
 OWB  O11  C12  C13  124.10  3.000
 OWB  C16  N15  C14  117.50  3.000
 OWB  C12  N17  C16  116.92  3.000
 OWB  H21  C20  N21  116.59  3.000
 OWB  H21  C20  C19  119.76  3.000
 OWB  N21  C20  C19  123.65  3.000
 OWB  C22  N21  C20  117.36  3.000
 OWB  H22  C22  N21  116.60  3.000
 OWB  H22  C22  C23  119.76  3.000
 OWB  N21  C22  C23  123.64  3.000
 OWB  H23  N26  C27  109.82  3.000
 OWB  H23  N26  C25  109.26  3.000
 OWB  C27  N26  C25  112.03  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
 OWB  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 OWB  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 OWB  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 OWB  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 OWB  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 OWB  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 OWB  CONST_07  C16  N17  C12  C13     0.00   0.0  0
 OWB  CONST_08  C16  N15  C14  C13     0.00   0.0  0
 OWB  CONST_09  N17  C12  C13  C14     0.00   0.0  0
 OWB  CONST_10  N17  C16  N15  C14     0.00   0.0  0
 OWB  CONST_11  C18  C16  N15  C14   180.00   0.0  0
 OWB  CONST_12  C22  C23  C18  C16   180.00   0.0  0
 OWB  CONST_13  C20  C19  C18  C16   180.00   0.0  0
 OWB  CONST_14  C12  N17  C16  C18   180.00   0.0  0
 OWB  CONST_15  N21  C22  C23  C18     0.00   0.0  0
 OWB  CONST_16  N21  C20  C19  C18     0.00   0.0  0
 OWB  CONST_17  N17  C16  C18  C19   180.00   0.0  0
 OWB  CONST_18  N15  C16  C18  C19     0.00   0.0  0
 OWB  CONST_19  C22  C23  C18  C19     0.00   0.0  0
 OWB  CONST_20  C22  N21  C20  C19     0.00   0.0  0
 OWB  CONST_21  N17  C16  C18  C23     0.00   0.0  0
 OWB  CONST_22  N15  C16  C18  C23   180.00   0.0  0
 OWB  CONST_23  C20  C19  C18  C23     0.00   0.0  0
 OWB  CONST_24  C20  N21  C22  C23     0.00   0.0  0
 OWB  CONST_25  N15  C16  N17  C12     0.00   0.0  0
 OWB  CONST_26  N15  C14  C13  C12     0.00   0.0  0
 OWB  CONST_27  C24  C14  N15  C16   180.00   0.0  0
 OWB  CONST_28  C12  C13  C14  C24   180.00   0.0  0
 OWB  CONST_29  N7   C3   C2   C1    180.00   0.0  0
 OWB  CONST_30  O11  C5   C6   C1    180.00   0.0  0
 OWB  CONST_31  N7   C3   C4   C5    180.00   0.0  0
 OWB  CONST_32  O11  C12  C13  C14   180.00   0.0  0
 OWB  CONST_33  O11  C12  N17  C16   180.00   0.0  0
 OWB  CONST_34  O11  C5   C4   C3    180.00   0.0  0
 OWB  CONST_35  H4   C6   C1   C2    180.00   0.0  0
 OWB  CONST_36  H3   C4   C3   C2    180.00   0.0  0
 OWB  CONST_37  H2   C2   C3   C4    180.00   0.0  0
 OWB  CONST_38  H1   C1   C6   C5    180.00   0.0  0
 OWB  CONST_39  H7   C23  C18  C16     0.00   0.0  0
 OWB  CONST_40  H6   C19  C18  C16     0.00   0.0  0
 OWB  CONST_41  H22  C22  C23  C18   180.00   0.0  0
 OWB  CONST_42  H21  C20  C19  C18   180.00   0.0  0
 OWB  CONST_43  H5   C13  C14  C24     0.00   0.0  0
 OWB  CONST_44  C8   N7   C3   C2      0.00   0.0  0
 OWB  CONST_45  C8   N7   C3   C4    180.00   0.0  0
 OWB  CONST_46  H17  N7   C3   C2    180.00   0.0  0
 OWB  CONST_47  O10  C8   N7   C3      0.00   0.0  0
 OWB  CONST_48  C9   C8   N7   C3    180.00   0.0  0
 OWB  Var_01    C27  C28  C29  C24    53.83  30.0  1
 OWB  Var_02    C27  N26  C25  C24   -62.85  30.0  1
 OWB  Var_03    C28  C27  N26  C25    61.87  30.0  1
 OWB  Var_04    N26  C27  C28  C29   -56.52  30.0  1
 OWB  Var_05    N17  C12  O11  C5   -178.14  30.0  2
 OWB  Var_06    H18  C9   C8   N7    172.83  30.0  3

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
 OWB  chir_01  C24  C14  C29  C25  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
 OWB  plan-1  C1   0.020
 OWB  plan-1  C2   0.020
 OWB  plan-1  C4   0.020
 OWB  plan-1  C5   0.020
 OWB  plan-1  C6   0.020
 OWB  plan-1  C3   0.020
 OWB  plan-1  N7   0.020
 OWB  plan-1  O11  0.020
 OWB  plan-1  H1   0.020
 OWB  plan-1  H2   0.020
 OWB  plan-1  H3   0.020
 OWB  plan-1  H4   0.020
 OWB  plan-2  C16  0.020
 OWB  plan-2  C18  0.020
 OWB  plan-2  C19  0.020
 OWB  plan-2  C23  0.020
 OWB  plan-2  C20  0.020
 OWB  plan-2  N21  0.020
 OWB  plan-2  C22  0.020
 OWB  plan-2  H6   0.020
 OWB  plan-2  H7   0.020
 OWB  plan-2  H21  0.020
 OWB  plan-2  H22  0.020
 OWB  plan-3  C13  0.020
 OWB  plan-3  C14  0.020
 OWB  plan-3  C16  0.020
 OWB  plan-3  C18  0.020
 OWB  plan-3  C24  0.020
 OWB  plan-3  O11  0.020
 OWB  plan-3  C12  0.020
 OWB  plan-3  N15  0.020
 OWB  plan-3  N17  0.020
 OWB  plan-3  H5   0.020
 OWB  plan-4  C3   0.020
 OWB  plan-4  N7   0.020
 OWB  plan-4  C8   0.020
 OWB  plan-4  C9   0.020
 OWB  plan-4  O10  0.020
 OWB  plan-4  H17  0.020

