# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:10:23 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S})-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-methyl-3-phenyl-3~{H}-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](c2ccccc2)c3cc(ccc3C1=O)c4c(C)onc4C
#
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
 5W4  5W4  (3~{S})-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-methyl-3-phenyl-3~{H}-isoindol-1-one  ligand  42  24  .  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_5W4
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
 5W4  C4   C  CR16  0  -0.319  -1.6141   1.8481   0.7129
 5W4  C14  C  CR16  0  -0.240   3.1519  -2.2965   1.4714
 5W4  C5   C  CR16  0  -0.282  -0.4182   2.5432   0.7882
 5W4  C6   C  CR56  0  -0.091   0.7006   1.9736   0.2041
 5W4  C11  C  CR16  0  -0.315   2.5564  -2.0483  -1.2238
 5W4  C7   C  CR5   0   0.531   2.0926   2.4671   0.1431
 5W4  C9   C  CR15  0  -0.185   1.9965   0.3856  -0.9547
 5W4  C10  C  CR6   0   0.159   2.4660  -0.9379  -0.3957
 5W4  C12  C  CR16  0  -0.240   2.9361  -3.2824  -0.7087
 5W4  C13  C  CR16  0  -0.263   3.2351  -3.4082   0.6395
 5W4  N1   N  N     0  -0.178  -5.1484  -0.5696  -0.2795
 5W4  C3   C  CR6   0   0.058  -1.6981   0.6101   0.0590
 5W4  O    O  O     0  -0.475   2.5282   3.5150   0.5882
 5W4  N    N  NR5   0  -0.493   2.7963   1.5131  -0.5159
 5W4  C15  C  CR16  0  -0.291   2.7675  -1.0682   0.9573
 5W4  C16  C  CR56  0   0.169   0.6306   0.7572  -0.4468
 5W4  C17  C  CR16  0  -0.383  -0.5588   0.0631  -0.5360
 5W4  C2   C  CR5   0  -0.185  -2.9676  -0.1170   0.0142
 5W4  C18  C  CR5   0   0.427  -3.1911  -1.4326   0.2816
 5W4  C19  C  CH3   0  -0.762  -2.3141  -2.5420   0.7187
 5W4  O1   O  O     0  -0.343  -4.4864  -1.6984   0.1106
 5W4  C1   C  CR5   0   0.253  -4.2608   0.3782  -0.3343
 5W4  C    C  CH3   0  -0.750  -4.6382   1.7549  -0.7500
 5W4  H1   H  HCR6  0   0.259  -2.4949   2.2586   1.1887
 5W4  H3   H  HCR6  0   0.264  -0.3629   3.4938   1.3028
 5W4  H4   H  HCR6  0   0.256   2.3310  -1.9493  -2.2791
 5W4  H5   H  HCH3  0   0.247   4.3308   1.7039  -1.9286
 5W4  H6   H  HCH3  0   0.260   4.6197   2.4838  -0.3663
 5W4  H7   H  HCH3  0   0.246   4.7318   0.7261  -0.5084
 5W4  H8   H  HCR5  0   0.296   1.9987   0.3306  -2.0503
 5W4  H9   H  HCR6  0   0.258   3.0024  -4.1407  -1.3645
 5W4  H10  H  HCR6  0   0.258   3.5351  -4.3662   1.0433
 5W4  H11  H  HCR6  0   0.256   2.7043  -0.2092   1.6154
 5W4  H12  H  HCR6  0   0.260  -0.6146  -0.8811  -1.0640
 5W4  H13  H  HCH3  0   0.277  -2.7479  -3.0728   1.5665
 5W4  H14  H  HCH3  0   0.275  -2.1619  -3.2656  -0.0839
 5W4  H15  H  HCH3  0   0.262  -1.3404  -2.1600   1.0170
 5W4  H16  H  HCH3  0   0.261  -4.5667   2.4536   0.0830
 5W4  H17  H  HCH3  0   0.260  -3.9747   2.1147  -1.5361
 5W4  H18  H  HCH3  0   0.266  -5.6603   1.7781  -1.1226
 5W4  C8   C  CH3   0  -0.519   4.1919   1.6099  -0.8501
 5W4  H2   H  HCR6  0   0.258   3.3859  -2.3890   2.5240

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
 5W4  C14  C13  aromatic  1.391  0.020  1.391
 5W4  C14  C15  aromatic  1.386  0.020  1.386
 5W4  C13  C12  aromatic  1.387  0.020  1.387
 5W4  C15  C10  aromatic  1.392  0.020  1.392
 5W4  C12  C11  aromatic  1.390  0.020  1.390
 5W4  C10  C11  aromatic  1.388  0.020  1.388
 5W4  C10  C9   single    1.511  0.020  1.511
 5W4  C8   N    single    1.438  0.020  1.438
 5W4  C9   N    single    1.450  0.020  1.450
 5W4  C9   C16  single    1.504  0.020  1.504
 5W4  N    C7   single    1.356  0.020  1.356
 5W4  C19  C18  single    1.480  0.020  1.480
 5W4  C16  C17  aromatic  1.380  0.020  1.380
 5W4  C16  C6   aromatic  1.381  0.020  1.381
 5W4  C17  C3   aromatic  1.397  0.020  1.397
 5W4  C18  O1   aromatic  1.333  0.020  1.333
 5W4  C18  C2   aromatic  1.361  0.020  1.361
 5W4  C7   C6   single    1.478  0.020  1.478
 5W4  C7   O    double    1.219  0.020  1.219
 5W4  O1   N1   aromatic  1.365  0.020  1.365
 5W4  C6   C5   aromatic  1.385  0.020  1.385
 5W4  C3   C2   single    1.464  0.020  1.464
 5W4  C3   C4   aromatic  1.403  0.020  1.403
 5W4  C2   C1   aromatic  1.428  0.020  1.428
 5W4  N1   C1   aromatic  1.300  0.020  1.300
 5W4  C1   C    single    1.487  0.020  1.487
 5W4  C5   C4   aromatic  1.385  0.020  1.385
 5W4  C4   H1   single    0.930  0.020  1.080
 5W4  C14  H2   single    0.930  0.020  1.080
 5W4  C5   H3   single    0.930  0.020  1.080
 5W4  C11  H4   single    0.930  0.020  1.080
 5W4  C8   H5   single    0.970  0.020  1.090
 5W4  C8   H6   single    0.970  0.020  1.090
 5W4  C8   H7   single    0.970  0.020  1.090
 5W4  C9   H8   single    0.970  0.020  1.090
 5W4  C12  H9   single    0.930  0.020  1.080
 5W4  C13  H10  single    0.930  0.020  1.080
 5W4  C15  H11  single    0.930  0.020  1.080
 5W4  C17  H12  single    0.930  0.020  1.080
 5W4  C19  H13  single    0.970  0.020  1.090
 5W4  C19  H14  single    0.970  0.020  1.090
 5W4  C19  H15  single    0.970  0.020  1.090
 5W4  C    H16  single    0.970  0.020  1.090
 5W4  C    H17  single    0.970  0.020  1.090
 5W4  C    H18  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
 5W4  H1   C4   C3   119.42  3.000
 5W4  H1   C4   C5   119.23  3.000
 5W4  C3   C4   C5   121.33  3.000
 5W4  H2   C14  C15  119.76  3.000
 5W4  H2   C14  C13  120.03  3.000
 5W4  C15  C14  C13  120.20  3.000
 5W4  H3   C5   C6   121.37  3.000
 5W4  H3   C5   C4   120.71  3.000
 5W4  C6   C5   C4   117.91  3.000
 5W4  C16  C6   C7   108.80  3.000
 5W4  C7   C6   C5   129.86  3.000
 5W4  C16  C6   C5   121.34  3.000
 5W4  H4   C11  C12  119.92  3.000
 5W4  H4   C11  C10  119.62  3.000
 5W4  C12  C11  C10  120.46  3.000
 5W4  N    C7   O    126.63  3.000
 5W4  O    C7   C6   127.47  3.000
 5W4  N    C7   C6   105.89  3.000
 5W4  H8   C9   C16  110.58  3.000
 5W4  H8   C9   N    109.88  3.000
 5W4  C16  C9   N    101.92  3.000
 5W4  H8   C9   C10  108.96  3.000
 5W4  C16  C9   C10  111.94  3.000
 5W4  N    C9   C10  113.43  3.000
 5W4  C15  C10  C9   120.57  3.000
 5W4  C9   C10  C11  120.00  3.000
 5W4  C15  C10  C11  119.39  3.000
 5W4  H9   C12  C13  120.27  3.000
 5W4  H9   C12  C11  119.76  3.000
 5W4  C13  C12  C11  119.98  3.000
 5W4  H10  C13  C12  120.19  3.000
 5W4  H10  C13  C14  120.07  3.000
 5W4  C12  C13  C14  119.74  3.000
 5W4  C1   N1   O1   106.49  3.000
 5W4  C2   C3   C17  119.99  3.000
 5W4  C2   C3   C4   120.31  3.000
 5W4  C17  C3   C4   119.69  3.000
 5W4  C9   N    C8   121.14  3.000
 5W4  C9   N    C7   114.06  3.000
 5W4  C8   N    C7   124.68  3.000
 5W4  H11  C15  C10  120.21  3.000
 5W4  H11  C15  C14  119.56  3.000
 5W4  C10  C15  C14  120.23  3.000
 5W4  C17  C16  C9   129.55  3.000
 5W4  C17  C16  C6   121.13  3.000
 5W4  C9   C16  C6   109.31  3.000
 5W4  H12  C17  C16  120.95  3.000
 5W4  H12  C17  C3   120.45  3.000
 5W4  C16  C17  C3   118.59  3.000
 5W4  C1   C2   C18  103.56  3.000
 5W4  C1   C2   C3   128.37  3.000
 5W4  C18  C2   C3   128.07  3.000
 5W4  O1   C18  C19  117.65  3.000
 5W4  O1   C18  C2   109.09  3.000
 5W4  C19  C18  C2   133.25  3.000
 5W4  H15  C19  H14  108.04  3.000
 5W4  H15  C19  H13  108.29  3.000
 5W4  H14  C19  H13  107.72  3.000
 5W4  H15  C19  C18  110.38  3.000
 5W4  H14  C19  C18  111.25  3.000
 5W4  H13  C19  C18  111.03  3.000
 5W4  C18  O1   N1   110.05  3.000
 5W4  C    C1   C2   128.26  3.000
 5W4  C    C1   N1   120.91  3.000
 5W4  C2   C1   N1   110.81  3.000
 5W4  H18  C    H17  108.53  3.000
 5W4  H18  C    H16  108.04  3.000
 5W4  H17  C    H16  107.45  3.000
 5W4  H18  C    C1   110.73  3.000
 5W4  H17  C    C1   110.66  3.000
 5W4  H16  C    C1   111.31  3.000
 5W4  H7   C8   H6   108.51  3.000
 5W4  H7   C8   H5   108.44  3.000
 5W4  H6   C8   H5   108.70  3.000
 5W4  H7   C8   N    110.67  3.000
 5W4  H6   C8   N    109.43  3.000
 5W4  H5   C8   N    111.03  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
 5W4  CONST_01  C16  C17  C3   C4      0.00   0.0  0
 5W4  CONST_04  C16  C6   C5   C4      0.00   0.0  0
 5W4  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 5W4  CONST_06  C11  C10  C15  C14     0.00   0.0  0
 5W4  CONST_07  C17  C16  C6   C5      0.00   0.0  0
 5W4  CONST_08  C17  C3   C4   C5      0.00   0.0  0
 5W4  CONST_09  C2   C3   C4   C5    180.00   0.0  0
 5W4  CONST_10  C3   C17  C16  C6      0.00   0.0  0
 5W4  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 5W4  CONST_12  C13  C14  C15  C10     0.00   0.0  0
 5W4  CONST_13  C13  C12  C11  C10     0.00   0.0  0
 5W4  CONST_14  C15  C14  C13  C12     0.00   0.0  0
 5W4  CONST_15  C15  C10  C11  C12     0.00   0.0  0
 5W4  CONST_16  C2   C18  O1   N1      0.00   0.0  0
 5W4  CONST_17  C18  C2   C1   N1      0.00   0.0  0
 5W4  CONST_18  C3   C2   C1   N1    180.00   0.0  0
 5W4  CONST_19  O1   C18  C2   C3    180.00   0.0  0
 5W4  CONST_20  C2   C3   C17  C16   180.00   0.0  0
 5W4  CONST_23  O1   N1   C1   C2      0.00   0.0  0
 5W4  CONST_24  C1   N1   O1   C18     0.00   0.0  0
 5W4  CONST_25  C1   C2   C18  O1      0.00   0.0  0
 5W4  CONST_26  C9   C10  C15  C14   180.00   0.0  0
 5W4  CONST_27  C12  C11  C10  C9    180.00   0.0  0
 5W4  CONST_28  C9   N    C7   C6      0.00   0.0  0
 5W4  CONST_29  C19  C18  O1   N1    180.00   0.0  0
 5W4  CONST_30  C19  C18  C2   C3      0.00   0.0  0
 5W4  CONST_31  C    C1   C2   C3      0.00   0.0  0
 5W4  CONST_32  C    C1   C2   C18   180.00   0.0  0
 5W4  CONST_33  C1   C2   C18  C19   180.00   0.0  0
 5W4  CONST_34  C    C1   N1   O1    180.00   0.0  0
 5W4  CONST_35  C8   N    C7   C6    180.00   0.0  0
 5W4  CONST_36  O    C7   N    C9    180.00   0.0  0
 5W4  CONST_37  H12  C17  C3   C4    180.00   0.0  0
 5W4  CONST_38  H9   C12  C13  C14   180.00   0.0  0
 5W4  CONST_39  H1   C4   C5   C6    180.00   0.0  0
 5W4  CONST_40  H10  C13  C12  C11   180.00   0.0  0
 5W4  CONST_41  H11  C15  C10  C11   180.00   0.0  0
 5W4  CONST_42  H3   C5   C6   C7      0.00   0.0  0
 5W4  CONST_43  H4   C11  C10  C9      0.00   0.0  0
 5W4  CONST_44  H2   C14  C15  C10   180.00   0.0  0
 5W4  CONST_45  O    C7   N    C8      0.00   0.0  0
 5W4  Var_01    H5   C8   N    C7   -111.51  30.0  3
 5W4  Var_02    H16  C    C1   N1    111.55  30.0  2
 5W4  Var_03    H13  C19  C18  C2    130.66  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
 5W4  chir_01  C9  C10  N  C16  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
 5W4  plan-1  N1   0.020
 5W4  plan-1  C3   0.020
 5W4  plan-1  C2   0.020
 5W4  plan-1  C18  0.020
 5W4  plan-1  C19  0.020
 5W4  plan-1  O1   0.020
 5W4  plan-1  C1   0.020
 5W4  plan-1  C    0.020
 5W4  plan-2  C14  0.020
 5W4  plan-2  C11  0.020
 5W4  plan-2  C9   0.020
 5W4  plan-2  C10  0.020
 5W4  plan-2  C12  0.020
 5W4  plan-2  C13  0.020
 5W4  plan-2  C15  0.020
 5W4  plan-2  H4   0.020
 5W4  plan-2  H9   0.020
 5W4  plan-2  H10  0.020
 5W4  plan-2  H11  0.020
 5W4  plan-2  H2   0.020
 5W4  plan-3  C4   0.020
 5W4  plan-3  C5   0.020
 5W4  plan-3  C6   0.020
 5W4  plan-3  C7   0.020
 5W4  plan-3  C9   0.020
 5W4  plan-3  C3   0.020
 5W4  plan-3  O    0.020
 5W4  plan-3  N    0.020
 5W4  plan-3  C16  0.020
 5W4  plan-3  C17  0.020
 5W4  plan-3  C2   0.020
 5W4  plan-3  H1   0.020
 5W4  plan-3  H3   0.020
 5W4  plan-3  H12  0.020
 5W4  plan-3  C8   0.020

