# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 15:24:17 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-methyl-5-(2-phenoxyphenyl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=CNC1=O)c2ccccc2Oc3ccccc3
#
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
 8NP  8NP  3-methyl-5-(2-phenoxyphenyl)pyridin-2(1H)-one  ligand  36  21  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8NP
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
 8NP  C4   C  CR16  0  -0.250   4.4074  -2.0060   0.9034
 8NP  C5   C  CR16  0  -0.259   1.5891   3.3823  -0.0063
 8NP  C6   C  CR16  0  -0.307  -0.6988   2.7097  -0.2360
 8NP  C7   C  CR16  0  -0.311   2.8809  -0.7472  -1.0500
 8NP  C8   C  CR16  0  -0.324   3.2230  -1.3730   1.2572
 8NP  C10  C  CR6   0  -0.006  -0.3715   1.3790   0.0287
 8NP  C13  C  CR16  0  -0.190  -2.6751   0.6066   0.6927
 8NP  C15  C  CR6   0  -0.046  -1.4305   0.3534   0.0504
 8NP  C17  C  CR6   0   0.521  -3.5369  -1.5724   0.0613
 8NP  C1   C  CR16  0  -0.263   4.8369  -2.0078  -0.4166
 8NP  C2   C  CR16  0  -0.256   0.2637   3.7062  -0.2595
 8NP  C3   C  CR16  0  -0.249   4.0711  -1.3747  -1.3880
 8NP  C9   C  CR16  0  -0.315   1.9421   2.0720   0.2772
 8NP  C11  C  CR6   0   0.333   2.4641  -0.7525   0.2760
 8NP  C12  C  CR6   0   0.296   0.9685   1.0807   0.2969
 8NP  C14  C  CR16  0   0.026  -1.3058  -0.8489  -0.5745
 8NP  C16  C  CR6   0  -0.133  -3.6980  -0.2913   0.7130
 8NP  C18  C  CH3   0  -0.709  -4.9882  -0.0303   1.4219
 8NP  N19  N  NR16  0  -0.659  -2.3185  -1.7422  -0.5603
 8NP  O20  O  O     0  -0.502  -4.3834  -2.4631   0.0310
 8NP  O21  O  O2    0  -0.512   1.2653  -0.2048   0.6452
 8NP  H1   H  HCR6  0   0.263   4.9974  -2.4943   1.6679
 8NP  H2   H  HCR6  0   0.264   2.3530   4.1481  -0.0154
 8NP  H3   H  HCR6  0   0.260  -1.7298   2.9632  -0.4505
 8NP  H4   H  HCR6  0   0.279   2.2837  -0.2634  -1.8132
 8NP  H5   H  HCR6  0   0.270   2.8867  -1.3651   2.2862
 8NP  H7   H  HCR6  0   0.259   5.7615  -2.4992  -0.6884
 8NP  H8   H  HCR6  0   0.259  -0.0201   4.7256  -0.4829
 8NP  H9   H  HCR6  0   0.264   4.3969  -1.3727  -2.4199
 8NP  H10  H  HCR6  0   0.279   2.9735   1.8285   0.4981
 8NP  H11  H  HCR6  0   0.299  -0.4352  -1.1503  -1.1377
 8NP  H13  H  HCH3  0   0.244  -5.8417  -0.3733   0.8376
 8NP  H14  H  HCH3  0   0.247  -5.0264  -0.5576   2.3777
 8NP  H15  H  HCH3  0   0.243  -5.1178   1.0321   1.6211
 8NP  H12  H  HNR6  0   0.423  -2.1826  -2.6171  -1.0494
 8NP  H6   H  HCR6  0   0.263  -2.8101   1.5586   1.1951

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
 8NP  C18  C16  single    1.495  0.020  1.495
 8NP  O20  C17  double    1.229  0.020  1.229
 8NP  C16  C17  single    1.446  0.020  1.446
 8NP  C16  C13  double    1.361  0.020  1.361
 8NP  C17  N19  single    1.378  0.020  1.378
 8NP  C13  C15  single    1.423  0.020  1.423
 8NP  N19  C14  single    1.350  0.020  1.350
 8NP  C6   C2   aromatic  1.386  0.020  1.386
 8NP  C6   C10  aromatic  1.396  0.020  1.396
 8NP  C15  C14  double    1.361  0.020  1.361
 8NP  C15  C10  single    1.474  0.020  1.474
 8NP  C2   C5   aromatic  1.388  0.020  1.388
 8NP  C10  C12  aromatic  1.399  0.020  1.399
 8NP  C5   C9   aromatic  1.386  0.020  1.386
 8NP  C12  C9   aromatic  1.390  0.020  1.390
 8NP  C12  O21  single    1.364  0.020  1.364
 8NP  O21  C11  single    1.369  0.020  1.369
 8NP  C11  C7   aromatic  1.390  0.020  1.390
 8NP  C11  C8   aromatic  1.387  0.020  1.387
 8NP  C7   C3   aromatic  1.387  0.020  1.387
 8NP  C8   C4   aromatic  1.389  0.020  1.389
 8NP  C3   C1   aromatic  1.390  0.020  1.390
 8NP  C4   C1   aromatic  1.388  0.020  1.388
 8NP  C4   H1   single    0.930  0.020  1.080
 8NP  C5   H2   single    0.930  0.020  1.080
 8NP  C6   H3   single    0.930  0.020  1.080
 8NP  C7   H4   single    0.930  0.020  1.080
 8NP  C8   H5   single    0.930  0.020  1.080
 8NP  C13  H6   single    0.930  0.020  1.080
 8NP  C1   H7   single    0.930  0.020  1.080
 8NP  C2   H8   single    0.930  0.020  1.080
 8NP  C3   H9   single    0.930  0.020  1.080
 8NP  C9   H10  single    0.930  0.020  1.080
 8NP  C14  H11  single    0.930  0.020  1.080
 8NP  C18  H13  single    0.970  0.020  1.090
 8NP  C18  H14  single    0.970  0.020  1.090
 8NP  C18  H15  single    0.970  0.020  1.090
 8NP  N19  H12  single    0.860  0.020  1.020

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
 8NP  H1   C4   C1   120.16  3.000
 8NP  H1   C4   C8   119.39  3.000
 8NP  C1   C4   C8   120.45  3.000
 8NP  H2   C5   C9   119.41  3.000
 8NP  H2   C5   C2   120.51  3.000
 8NP  C9   C5   C2   120.08  3.000
 8NP  H3   C6   C2   119.31  3.000
 8NP  H3   C6   C10  118.94  3.000
 8NP  C2   C6   C10  121.73  3.000
 8NP  H4   C7   C11  120.57  3.000
 8NP  H4   C7   C3   120.22  3.000
 8NP  C11  C7   C3   119.21  3.000
 8NP  H5   C8   C11  119.94  3.000
 8NP  H5   C8   C4   120.70  3.000
 8NP  C11  C8   C4   119.36  3.000
 8NP  C12  C10  C15  122.48  3.000
 8NP  C12  C10  C6   117.67  3.000
 8NP  C15  C10  C6   119.84  3.000
 8NP  H6   C13  C16  118.59  3.000
 8NP  H6   C13  C15  118.29  3.000
 8NP  C16  C13  C15  123.13  3.000
 8NP  C14  C15  C13  116.39  3.000
 8NP  C14  C15  C10  122.82  3.000
 8NP  C13  C15  C10  120.73  3.000
 8NP  O20  C17  N19  120.56  3.000
 8NP  N19  C17  C16  114.26  3.000
 8NP  O20  C17  C16  125.19  3.000
 8NP  H7   C1   C3   120.16  3.000
 8NP  H7   C1   C4   120.27  3.000
 8NP  C3   C1   C4   119.58  3.000
 8NP  H8   C2   C6   119.94  3.000
 8NP  H8   C2   C5   120.56  3.000
 8NP  C6   C2   C5   119.50  3.000
 8NP  H9   C3   C1   120.10  3.000
 8NP  H9   C3   C7   119.33  3.000
 8NP  C1   C3   C7   120.57  3.000
 8NP  H10  C9   C12  120.28  3.000
 8NP  H10  C9   C5   119.79  3.000
 8NP  C12  C9   C5   119.92  3.000
 8NP  O21  C11  C8   117.86  3.000
 8NP  C8   C11  C7   120.83  3.000
 8NP  O21  C11  C7   121.23  3.000
 8NP  O21  C12  C9   121.55  3.000
 8NP  O21  C12  C10  117.27  3.000
 8NP  C9   C12  C10  121.09  3.000
 8NP  H11  C14  N19  115.18  3.000
 8NP  H11  C14  C15  124.06  3.000
 8NP  N19  C14  C15  120.72  3.000
 8NP  C18  C16  C17  117.67  3.000
 8NP  C17  C16  C13  119.60  3.000
 8NP  C18  C16  C13  122.71  3.000
 8NP  H15  C18  H14  107.86  3.000
 8NP  H15  C18  H13  108.18  3.000
 8NP  H14  C18  H13  106.85  3.000
 8NP  H15  C18  C16  111.09  3.000
 8NP  H14  C18  C16  111.15  3.000
 8NP  H13  C18  C16  111.51  3.000
 8NP  H12  N19  C14  117.79  3.000
 8NP  H12  N19  C17  116.32  3.000
 8NP  C14  N19  C17  125.89  3.000
 8NP  C12  O21  C11  119.91  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
 8NP  CONST_01  C7   C11  C8   C4     0.00   0.0  0
 8NP  CONST_02  C7   C3   C1   C4     0.00   0.0  0
 8NP  CONST_03  C10  C6   C2   C5     0.00   0.0  0
 8NP  CONST_04  C10  C12  C9   C5     0.00   0.0  0
 8NP  CONST_05  C9   C5   C2   C6     0.00   0.0  0
 8NP  CONST_06  C9   C12  C10  C6     0.00   0.0  0
 8NP  CONST_07  C3   C7   C11  C8     0.00   0.0  0
 8NP  CONST_08  C3   C1   C4   C8     0.00   0.0  0
 8NP  CONST_09  C11  C7   C3   C1     0.00   0.0  0
 8NP  CONST_10  C11  C8   C4   C1     0.00   0.0  0
 8NP  CONST_11  C12  C10  C6   C2     0.00   0.0  0
 8NP  CONST_12  C12  C9   C5   C2     0.00   0.0  0
 8NP  CONST_13  C2   C6   C10  C15  180.00   0.0  0
 8NP  CONST_14  C9   C12  C10  C15  180.00   0.0  0
 8NP  CONST_15  C16  C17  N19  C14    0.00   0.0  0
 8NP  CONST_16  O21  C11  C8   C4   180.00   0.0  0
 8NP  CONST_17  O21  C12  C9   C5   180.00   0.0  0
 8NP  CONST_18  O21  C12  C10  C6   180.00   0.0  0
 8NP  CONST_19  O21  C12  C10  C15    0.00   0.0  0
 8NP  CONST_20  O21  C11  C7   C3   180.00   0.0  0
 8NP  CONST_21  O20  C17  N19  C14  180.00   0.0  0
 8NP  CONST_22  H9   C3   C1   C4   180.00   0.0  0
 8NP  CONST_23  H3   C6   C2   C5   180.00   0.0  0
 8NP  CONST_24  H2   C5   C2   C6   180.00   0.0  0
 8NP  CONST_25  H5   C8   C11  C7   180.00   0.0  0
 8NP  CONST_26  H7   C1   C3   C7   180.00   0.0  0
 8NP  CONST_27  H4   C7   C11  C8   180.00   0.0  0
 8NP  CONST_28  H8   C2   C6   C10  180.00   0.0  0
 8NP  CONST_29  H10  C9   C12  C10  180.00   0.0  0
 8NP  CONST_30  H1   C4   C1   C3   180.00   0.0  0
 8NP  CONST_31  H12  N19  C17  C16  180.00   0.0  0
 8NP  Var_01    C13  C15  C10  C6   -43.21  30.0  2
 8NP  Var_02    H13  C18  C16  C13  138.91  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
 8NP  plan-1  C5   0.020
 8NP  plan-1  C6   0.020
 8NP  plan-1  C10  0.020
 8NP  plan-1  C15  0.020
 8NP  plan-1  C2   0.020
 8NP  plan-1  C9   0.020
 8NP  plan-1  C12  0.020
 8NP  plan-1  O21  0.020
 8NP  plan-1  H2   0.020
 8NP  plan-1  H3   0.020
 8NP  plan-1  H8   0.020
 8NP  plan-1  H10  0.020
 8NP  plan-2  C4   0.020
 8NP  plan-2  C7   0.020
 8NP  plan-2  C8   0.020
 8NP  plan-2  C1   0.020
 8NP  plan-2  C3   0.020
 8NP  plan-2  C11  0.020
 8NP  plan-2  O21  0.020
 8NP  plan-2  H1   0.020
 8NP  plan-2  H4   0.020
 8NP  plan-2  H5   0.020
 8NP  plan-2  H7   0.020
 8NP  plan-2  H9   0.020
 8NP  plan-3  C10  0.020
 8NP  plan-3  C13  0.020
 8NP  plan-3  C15  0.020
 8NP  plan-3  C17  0.020
 8NP  plan-3  C14  0.020
 8NP  plan-3  C16  0.020
 8NP  plan-3  C18  0.020
 8NP  plan-3  N19  0.020
 8NP  plan-3  O20  0.020
 8NP  plan-3  H11  0.020
 8NP  plan-3  H12  0.020
 8NP  plan-3  H6   0.020

