# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:34:10 2021
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CC(=O)NC[C@@H]2CCCO2)cc1
#
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
 WLY  WLY  2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide  ligand  36  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WLY
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
 WLY  C10  C  CH2   0  -0.318  -31.5826   -5.8680  -19.3245
 WLY  C13  C  CH2   0  -0.497  -32.8224   -8.9188  -21.0687
 WLY  C17  C  CR16  0  -0.278  -28.0575   -9.5126  -21.3684
 WLY  C02  C  CR6   0   0.086  -27.2486   -8.7293  -22.1915
 WLY  C03  C  CR16  0  -0.287  -26.7689   -7.5278  -21.6788
 WLY  C04  C  CR16  0  -0.276  -27.0935   -7.1153  -20.3925
 WLY  C05  C  CR6   0   0.037  -27.9058   -7.8953  -19.5761
 WLY  C06  C  CH2   0  -0.631  -28.3002   -7.4437  -18.1992
 WLY  C07  C  C     0   0.539  -29.7024   -6.8590  -18.0723
 WLY  C11  C  CR15  0   0.058  -32.4634   -6.7354  -20.2119
 WLY  C12  C  CH2   0  -0.491  -32.6357   -8.1782  -19.7500
 WLY  C14  C  CH2   0  -0.158  -31.8789   -8.1495  -21.9819
 WLY  C16  C  CR16  0  -0.264  -28.3808   -9.1032  -20.0849
 WLY  N09  N  NH1   0  -0.620  -30.2466   -6.3965  -19.2074
 WLY  O08  O  O     0  -0.506  -30.2537   -6.7997  -16.9817
 WLY  O15  O  O     0  -0.513  -31.8905   -6.8065  -21.5147
 WLY  H1   H  HCH2  0   0.255  -31.5386   -4.8547  -19.7317
 WLY  H2   H  HCH2  0   0.254  -32.0267   -5.7943  -18.3331
 WLY  H3   H  HCH2  0   0.237  -33.8547   -8.8371  -21.4158
 WLY  H4   H  HCH2  0   0.248  -32.5709   -9.9773  -21.0087
 WLY  H6   H  HCH3  0   0.248  -27.7226   -8.8586  -24.2823
 WLY  H7   H  HCH3  0   0.243  -26.0048   -8.7013  -23.9497
 WLY  H8   H  HCH3  0   0.244  -26.8252  -10.2386  -23.6721
 WLY  H9   H  HCR6  0   0.248  -26.1286   -6.9028  -22.2901
 WLY  H10  H  HCR6  0   0.253  -26.7058   -6.1732  -20.0222
 WLY  H11  H  HCH2  0   0.280  -28.2421   -8.2728  -17.4918
 WLY  H12  H  HCH2  0   0.289  -27.6063   -6.6809  -17.8342
 WLY  H13  H  HCR5  0   0.222  -33.4449   -6.2470  -20.2784
 WLY  H14  H  HCH2  0   0.252  -33.4737   -8.2877  -19.0623
 WLY  H15  H  HCH2  0   0.235  -31.7363   -8.5378  -19.2436
 WLY  H16  H  HCH2  0   0.223  -32.1870   -8.1690  -23.0299
 WLY  H17  H  HCH2  0   0.206  -30.8629   -8.5577  -21.9235
 WLY  H18  H  HCR6  0   0.251  -29.0133   -9.7330  -19.4694
 WLY  H19  H  HNH1  0   0.404  -29.7277   -6.5019  -20.0647
 WLY  H5   H  HCR6  0   0.248  -28.4407  -10.4578  -21.7350
 WLY  C01  C  CH3   0  -0.721  -26.9285   -9.1565  -23.5942

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
 WLY  C01  C02  single    1.501  0.020  1.501
 WLY  C02  C17  aromatic  1.395  0.020  1.395
 WLY  C02  C03  aromatic  1.392  0.020  1.392
 WLY  C17  C16  aromatic  1.385  0.020  1.385
 WLY  O15  C14  single    1.422  0.020  1.422
 WLY  O15  C11  single    1.425  0.020  1.425
 WLY  C14  C13  single    1.522  0.020  1.522
 WLY  C03  C04  aromatic  1.389  0.020  1.389
 WLY  C16  C05  aromatic  1.394  0.020  1.394
 WLY  C13  C12  single    1.524  0.020  1.524
 WLY  C11  C10  single    1.522  0.020  1.522
 WLY  C11  C12  single    1.525  0.020  1.525
 WLY  C04  C05  aromatic  1.391  0.020  1.391
 WLY  C05  C06  single    1.502  0.020  1.502
 WLY  C10  N09  single    1.442  0.020  1.442
 WLY  N09  C07  single    1.341  0.020  1.341
 WLY  C07  C06  single    1.524  0.020  1.524
 WLY  C07  O08  double    1.223  0.020  1.223
 WLY  C10  H1   single    0.970  0.020  1.090
 WLY  C10  H2   single    0.970  0.020  1.090
 WLY  C13  H3   single    0.970  0.020  1.090
 WLY  C13  H4   single    0.970  0.020  1.090
 WLY  C17  H5   single    0.930  0.020  1.080
 WLY  C01  H6   single    0.970  0.020  1.090
 WLY  C01  H7   single    0.970  0.020  1.090
 WLY  C01  H8   single    0.970  0.020  1.090
 WLY  C03  H9   single    0.930  0.020  1.080
 WLY  C04  H10  single    0.930  0.020  1.080
 WLY  C06  H11  single    0.970  0.020  1.090
 WLY  C06  H12  single    0.970  0.020  1.090
 WLY  C11  H13  single    0.970  0.020  1.090
 WLY  C12  H14  single    0.970  0.020  1.090
 WLY  C12  H15  single    0.970  0.020  1.090
 WLY  C14  H16  single    0.970  0.020  1.090
 WLY  C14  H17  single    0.970  0.020  1.090
 WLY  C16  H18  single    0.930  0.020  1.080
 WLY  N09  H19  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
 WLY  H2   C10  H1   107.03  3.000
 WLY  H2   C10  N09  109.20  3.000
 WLY  H1   C10  N09  109.44  3.000
 WLY  H2   C10  C11  109.48  3.000
 WLY  H1   C10  C11  109.54  3.000
 WLY  N09  C10  C11  112.01  3.000
 WLY  H4   C13  H3   107.96  3.000
 WLY  H4   C13  C14  112.39  3.000
 WLY  H3   C13  C14  110.95  3.000
 WLY  H4   C13  C12  113.34  3.000
 WLY  H3   C13  C12  110.76  3.000
 WLY  C14  C13  C12  101.40  3.000
 WLY  H5   C17  C16  119.25  3.000
 WLY  H5   C17  C02  119.69  3.000
 WLY  C16  C17  C02  121.07  3.000
 WLY  C03  C02  C01  121.10  3.000
 WLY  C03  C02  C17  117.87  3.000
 WLY  C01  C02  C17  121.02  3.000
 WLY  H9   C03  C04  119.28  3.000
 WLY  H9   C03  C02  119.59  3.000
 WLY  C04  C03  C02  121.13  3.000
 WLY  H10  C04  C05  119.71  3.000
 WLY  H10  C04  C03  119.40  3.000
 WLY  C05  C04  C03  120.89  3.000
 WLY  C16  C05  C06  120.37  3.000
 WLY  C06  C05  C04  121.53  3.000
 WLY  C16  C05  C04  118.07  3.000
 WLY  H12  C06  H11  106.24  3.000
 WLY  H12  C06  C07  106.75  3.000
 WLY  H11  C06  C07  106.64  3.000
 WLY  H12  C06  C05  110.43  3.000
 WLY  H11  C06  C05  110.60  3.000
 WLY  C07  C06  C05  115.67  3.000
 WLY  O08  C07  N09  123.71  3.000
 WLY  O08  C07  C06  120.48  3.000
 WLY  N09  C07  C06  115.79  3.000
 WLY  H13  C11  O15  109.04  3.000
 WLY  H13  C11  C12  109.76  3.000
 WLY  O15  C11  C12  105.98  3.000
 WLY  H13  C11  C10  107.39  3.000
 WLY  C12  C11  C10  115.35  3.000
 WLY  O15  C11  C10  109.20  3.000
 WLY  H15  C12  H14  107.90  3.000
 WLY  H15  C12  C11  111.02  3.000
 WLY  H14  C12  C11  111.92  3.000
 WLY  H15  C12  C13  109.99  3.000
 WLY  H14  C12  C13  113.77  3.000
 WLY  C11  C12  C13  102.21  3.000
 WLY  H17  C14  H16  107.81  3.000
 WLY  H17  C14  O15  109.98  3.000
 WLY  H16  C14  O15  109.25  3.000
 WLY  H17  C14  C13  110.75  3.000
 WLY  H16  C14  C13  113.06  3.000
 WLY  O15  C14  C13  105.97  3.000
 WLY  H18  C16  C05  119.66  3.000
 WLY  H18  C16  C17  119.37  3.000
 WLY  C05  C16  C17  120.97  3.000
 WLY  H19  N09  C07  118.36  3.000
 WLY  H19  N09  C10  116.52  3.000
 WLY  C07  N09  C10  124.84  3.000
 WLY  C14  O15  C11  110.53  3.000
 WLY  H8   C01  H7   108.14  3.000
 WLY  H8   C01  H6   107.14  3.000
 WLY  H7   C01  H6   107.27  3.000
 WLY  H8   C01  C02  111.70  3.000
 WLY  H7   C01  C02  111.52  3.000
 WLY  H6   C01  C02  110.86  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
 WLY  CONST_01  C04  C03  C02  C17     0.00   0.0  0
 WLY  CONST_02  C04  C05  C16  C17     0.00   0.0  0
 WLY  CONST_03  C05  C16  C17  C02     0.00   0.0  0
 WLY  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 WLY  CONST_05  C16  C17  C02  C03     0.00   0.0  0
 WLY  CONST_06  C16  C05  C04  C03     0.00   0.0  0
 WLY  CONST_07  C06  C05  C16  C17   180.00   0.0  0
 WLY  CONST_08  C16  C17  C02  C01   180.00   0.0  0
 WLY  CONST_09  C04  C03  C02  C01   180.00   0.0  0
 WLY  CONST_10  C06  C05  C04  C03   180.00   0.0  0
 WLY  CONST_11  H9   C03  C02  C17   180.00   0.0  0
 WLY  CONST_12  H18  C16  C17  C02   180.00   0.0  0
 WLY  CONST_13  H10  C04  C03  C02   180.00   0.0  0
 WLY  CONST_14  H5   C17  C02  C03   180.00   0.0  0
 WLY  CONST_15  C06  C07  N09  C10   180.00   0.0  0
 WLY  CONST_16  O08  C07  N09  C10     0.00   0.0  0
 WLY  CONST_17  H19  N09  C07  C06     0.00   0.0  0
 WLY  Var_01    C14  C13  C12  C11    36.31  30.0  1
 WLY  Var_02    O15  C14  C13  C12   -32.29  30.0  1
 WLY  Var_03    H16  C14  O15  C11   137.21  30.0  1
 WLY  Var_04    C07  C06  C05  C04   100.83  30.0  2
 WLY  Var_05    H6   C01  C02  C17    84.26  30.0  2
 WLY  Var_06    N09  C07  C06  C05   -21.66  30.0  1
 WLY  Var_07    C11  C10  N09  C07  -114.68  30.0  1

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
 WLY  chir_01  C11  O15  C10  C12  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
 WLY  plan-1  C17  0.020
 WLY  plan-1  C02  0.020
 WLY  plan-1  C03  0.020
 WLY  plan-1  C04  0.020
 WLY  plan-1  C05  0.020
 WLY  plan-1  C06  0.020
 WLY  plan-1  C16  0.020
 WLY  plan-1  H9   0.020
 WLY  plan-1  H10  0.020
 WLY  plan-1  H18  0.020
 WLY  plan-1  H5   0.020
 WLY  plan-1  C01  0.020
 WLY  plan-2  C10  0.020
 WLY  plan-2  C06  0.020
 WLY  plan-2  C07  0.020
 WLY  plan-2  N09  0.020
 WLY  plan-2  O08  0.020
 WLY  plan-2  H19  0.020

