# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:05:50 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: (2E,4E)-5-(2H-1,3-benzodioxol-5-yl)-1-(piperidin-1-yl)penta-2,4-dien-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(/C=C/C=C/c1ccc2OCOc2c1)N3CCCCC3
#
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
 AYR  AYR  (2E,4E)-5-(2H-1,3-benzodioxol-5-yl)-1-(piperidin-1-yl)penta-2,4-dien-1-one  ligand  40  21  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AYR
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
 AYR  C1   C  C1    0  -0.288  26.4577  -22.5530  21.0965
 AYR  C2   C  CR6   0   0.137  25.0510  -22.6364  21.4675
 AYR  C3   C  CR16  0  -0.338  24.6206  -22.6704  22.7959
 AYR  C4   C  CR16  0  -0.317  23.2711  -22.7624  23.1349
 AYR  C5   C  CR56  0   0.293  22.3683  -22.8198  22.0988
 AYR  C6   C  CR56  0   0.317  22.7786  -22.7833  20.7758
 AYR  C7   C  CR16  0  -0.400  24.0999  -22.6920  20.4275
 AYR  O8   O  O     0  -0.481  21.0202  -22.8950  22.1516
 AYR  C9   C  CH2   0   0.069  20.5780  -23.0864  20.8120
 AYR  O10  O  O     0  -0.486  21.6925  -22.8314  19.9678
 AYR  C11  C  C1    0  -0.256  27.5179  -22.5370  21.9235
 AYR  C12  C  C1    0  -0.170  28.8700  -22.4671  21.4315
 AYR  C13  C  C1    0  -0.434  29.9509  -22.4659  22.2278
 AYR  C14  C  C     0   0.558  31.3132  -22.4307  21.6506
 AYR  O15  O  O     0  -0.515  31.4718  -22.5328  20.4345
 AYR  N16  N  NT    0  -0.470  32.3660  -22.3246  22.4962
 AYR  C17  C  CH2   0  -0.316  32.3163  -21.9524  23.9024
 AYR  C18  C  CH2   0  -0.427  32.9082  -20.5616  24.1112
 AYR  C19  C  CH2   0  -0.445  34.3227  -20.4749  23.5490
 AYR  C20  C  CH2   0  -0.433  34.3592  -20.9461  22.0991
 AYR  C21  C  CH2   0  -0.315  33.7224  -22.3242  21.9679
 AYR  H1   H  H     0   0.257  26.6509  -22.5053  20.0282
 AYR  H2   H  HCR6  0   0.261  25.3448  -22.6273  23.5981
 AYR  H3   H  HCR6  0   0.278  22.9541  -22.7866  24.1686
 AYR  H4   H  HCR6  0   0.274  24.4084  -22.6617  19.3901
 AYR  H5   H  HCH2  0   0.247  19.7742  -22.3859  20.5858
 AYR  H6   H  H     0   0.259  27.3861  -22.5855  22.9999
 AYR  H7   H  H     0   0.259  29.0008  -22.4191  20.3549
 AYR  H8   H  H     0   0.265  29.8041  -22.5213  23.2976
 AYR  H9   H  HCH2  0   0.265  31.3019  -21.9862  24.2853
 AYR  H10  H  HCH2  0   0.239  32.8932  -22.6893  24.4709
 AYR  H11  H  HCH2  0   0.239  32.9027  -20.3318  25.1789
 AYR  H12  H  HCH2  0   0.224  32.2636  -19.8252  23.6220
 AYR  H13  H  HCH2  0   0.217  34.9874  -21.1056  24.1485
 AYR  H14  H  HCH2  0   0.238  34.7020  -19.4544  23.6318
 AYR  H15  H  HCH2  0   0.236  35.3878  -20.9917  21.7347
 AYR  H16  H  HCH2  0   0.224  33.8236  -20.2388  21.4588
 AYR  H17  H  HCH2  0   0.262  33.7086  -22.6561  20.9342
 AYR  H18  H  HCH2  0   0.236  34.3057  -23.0535  22.5406
 AYR  H19  H  HCH2  0   0.237  20.2375  -24.1184  20.6794

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
 AYR  C7   C6   aromatic  1.370  0.020  1.370
 AYR  C7   C2   aromatic  1.410  0.020  1.410
 AYR  O15  C14  double    1.231  0.020  1.231
 AYR  O10  C6   single    1.355  0.020  1.355
 AYR  O10  C9   single    1.421  0.020  1.421
 AYR  C1   C2   single    1.457  0.020  1.457
 AYR  C1   C11  double    1.345  0.020  1.345
 AYR  C6   C5   aromatic  1.386  0.020  1.386
 AYR  C2   C3   aromatic  1.397  0.020  1.397
 AYR  C12  C11  single    1.440  0.020  1.440
 AYR  C12  C13  double    1.343  0.020  1.343
 AYR  C9   O8   single    1.424  0.020  1.424
 AYR  C14  C13  single    1.480  0.020  1.480
 AYR  C14  N16  single    1.355  0.020  1.355
 AYR  C21  C20  single    1.524  0.020  1.524
 AYR  C21  N16  single    1.456  0.020  1.456
 AYR  C5   O8   single    1.351  0.020  1.351
 AYR  C5   C4   aromatic  1.375  0.020  1.375
 AYR  C3   C4   aromatic  1.395  0.020  1.395
 AYR  C20  C19  single    1.525  0.020  1.525
 AYR  N16  C17  single    1.456  0.020  1.456
 AYR  C19  C18  single    1.525  0.020  1.525
 AYR  C17  C18  single    1.526  0.020  1.526
 AYR  C1   H1   single    0.930  0.020  1.080
 AYR  C3   H2   single    0.930  0.020  1.080
 AYR  C4   H3   single    0.930  0.020  1.080
 AYR  C7   H4   single    0.930  0.020  1.080
 AYR  C9   H5   single    0.970  0.020  1.090
 AYR  C11  H6   single    0.930  0.020  1.080
 AYR  C12  H7   single    0.930  0.020  1.080
 AYR  C13  H8   single    0.930  0.020  1.080
 AYR  C17  H9   single    0.970  0.020  1.090
 AYR  C17  H10  single    0.970  0.020  1.090
 AYR  C18  H11  single    0.970  0.020  1.090
 AYR  C18  H12  single    0.970  0.020  1.090
 AYR  C19  H13  single    0.970  0.020  1.090
 AYR  C19  H14  single    0.970  0.020  1.090
 AYR  C20  H15  single    0.970  0.020  1.090
 AYR  C20  H16  single    0.970  0.020  1.090
 AYR  C21  H17  single    0.970  0.020  1.090
 AYR  C21  H18  single    0.970  0.020  1.090
 AYR  C9   H19  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
 AYR  H1   C1   C11  117.64  3.000
 AYR  H1   C1   C2   115.12  3.000
 AYR  C11  C1   C2   127.24  3.000
 AYR  C7   C2   C3   119.51  3.000
 AYR  C3   C2   C1   122.75  3.000
 AYR  C7   C2   C1   117.74  3.000
 AYR  H2   C3   C4   118.05  3.000
 AYR  H2   C3   C2   119.88  3.000
 AYR  C4   C3   C2   122.07  3.000
 AYR  H3   C4   C5   121.78  3.000
 AYR  H3   C4   C3   121.16  3.000
 AYR  C5   C4   C3   117.05  3.000
 AYR  O8   C5   C6   109.52  3.000
 AYR  O8   C5   C4   128.88  3.000
 AYR  C6   C5   C4   121.59  3.000
 AYR  O10  C6   C7   128.62  3.000
 AYR  O10  C6   C5   109.35  3.000
 AYR  C7   C6   C5   122.02  3.000
 AYR  H4   C7   C6   121.36  3.000
 AYR  H4   C7   C2   120.89  3.000
 AYR  C6   C7   C2   117.75  3.000
 AYR  C9   O8   C5   106.30  3.000
 AYR  H19  C9   H5   110.57  3.000
 AYR  H19  C9   O10  109.94  3.000
 AYR  H5   C9   O10  109.86  3.000
 AYR  H19  C9   O8   109.71  3.000
 AYR  H5   C9   O8   109.76  3.000
 AYR  O10  C9   O8   106.93  3.000
 AYR  C9   O10  C6   106.31  3.000
 AYR  H6   C11  C12  117.06  3.000
 AYR  H6   C11  C1   120.90  3.000
 AYR  C12  C11  C1   122.04  3.000
 AYR  H7   C12  C13  119.42  3.000
 AYR  H7   C12  C11  117.00  3.000
 AYR  C13  C12  C11  123.58  3.000
 AYR  H8   C13  C14  120.80  3.000
 AYR  H8   C13  C12  118.52  3.000
 AYR  C14  C13  C12  120.65  3.000
 AYR  N16  C14  O15  121.55  3.000
 AYR  N16  C14  C13  118.28  3.000
 AYR  O15  C14  C13  120.14  3.000
 AYR  C21  N16  C17  112.48  3.000
 AYR  C17  N16  C14  126.63  3.000
 AYR  C21  N16  C14  119.85  3.000
 AYR  H10  C17  H9   106.76  3.000
 AYR  H10  C17  C18  109.75  3.000
 AYR  H9   C17  C18  110.06  3.000
 AYR  H10  C17  N16  108.15  3.000
 AYR  H9   C17  N16  111.41  3.000
 AYR  C18  C17  N16  110.61  3.000
 AYR  H12  C18  H11  107.01  3.000
 AYR  H12  C18  C19  110.08  3.000
 AYR  H11  C18  C19  110.69  3.000
 AYR  H12  C18  C17  108.89  3.000
 AYR  H11  C18  C17  108.88  3.000
 AYR  C19  C18  C17  111.18  3.000
 AYR  H14  C19  H13  106.61  3.000
 AYR  H14  C19  C20  110.65  3.000
 AYR  H13  C19  C20  109.15  3.000
 AYR  H14  C19  C18  110.34  3.000
 AYR  H13  C19  C18  109.18  3.000
 AYR  C20  C19  C18  110.81  3.000
 AYR  H16  C20  H15  107.02  3.000
 AYR  H16  C20  C21  109.25  3.000
 AYR  H15  C20  C21  109.09  3.000
 AYR  H16  C20  C19  110.18  3.000
 AYR  H15  C20  C19  110.65  3.000
 AYR  C21  C20  C19  110.57  3.000
 AYR  H18  C21  H17  107.51  3.000
 AYR  H18  C21  C20  109.54  3.000
 AYR  H17  C21  C20  111.33  3.000
 AYR  H18  C21  N16  107.84  3.000
 AYR  H17  C21  N16  109.49  3.000
 AYR  C20  C21  N16  111.00  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
 AYR  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 AYR  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 AYR  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 AYR  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 AYR  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 AYR  CONST_06  C7   C2   C3   C4      0.00   0.0  0
 AYR  CONST_07  C6   C7   C2   C1    180.00   0.0  0
 AYR  CONST_08  C4   C3   C2   C1    180.00   0.0  0
 AYR  CONST_09  H3   C4   C3   C2    180.00   0.0  0
 AYR  CONST_10  H4   C7   C2   C3    180.00   0.0  0
 AYR  CONST_11  H2   C3   C4   C5    180.00   0.0  0
 AYR  CONST_12  C21  N16  C14  C13   180.00   0.0  0
 AYR  CONST_13  C17  N16  C14  C13     0.00   0.0  0
 AYR  CONST_14  C21  N16  C14  O15     0.00   0.0  0
 AYR  CONST_15  C17  N16  C14  O15   180.00   0.0  0
 AYR  Var_01    O10  C9   O8   C5    -12.24  30.0  1
 AYR  Var_02    O8   C9   O10  C6     12.34  30.0  1
 AYR  Var_03    C19  C20  C21  N16    55.65  30.0  1
 AYR  Var_04    C19  C18  C17  N16   -55.00  30.0  1
 AYR  Var_05    C20  C21  N16  C17   -59.54  30.0  1
 AYR  Var_06    C20  C19  C18  C17    52.48  30.0  1
 AYR  Var_07    C21  C20  C19  C18   -52.54  30.0  1
 AYR  Var_08    C21  N16  C17  C18    58.90  30.0  1
 AYR  Var_09    C11  C1   C2   C3      2.09  30.0  2
 AYR  Var_10    C12  C11  C1   C2    179.25   0.0  2
 AYR  Var_11    N16  C14  C13  C12   174.89  30.0  2
 AYR  Var_12    C14  C13  C12  C11   178.25   0.0  2
 AYR  Var_13    C13  C12  C11  C1   -179.15  30.0  1

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
 AYR  plan-1  C13  0.020
 AYR  plan-1  C14  0.020
 AYR  plan-1  O15  0.020
 AYR  plan-1  N16  0.020
 AYR  plan-1  C17  0.020
 AYR  plan-1  C21  0.020
 AYR  plan-2  C1   0.020
 AYR  plan-2  C2   0.020
 AYR  plan-2  C3   0.020
 AYR  plan-2  C4   0.020
 AYR  plan-2  C5   0.020
 AYR  plan-2  C6   0.020
 AYR  plan-2  C7   0.020
 AYR  plan-2  O8   0.020
 AYR  plan-2  O10  0.020
 AYR  plan-2  H2   0.020
 AYR  plan-2  H3   0.020
 AYR  plan-2  H4   0.020
 AYR  plan-3  C1   0.020
 AYR  plan-3  C2   0.020
 AYR  plan-3  C11  0.020
 AYR  plan-3  C12  0.020
 AYR  plan-3  H1   0.020
 AYR  plan-3  H6   0.020
 AYR  plan-4  C11  0.020
 AYR  plan-4  C12  0.020
 AYR  plan-4  C13  0.020
 AYR  plan-4  C14  0.020
 AYR  plan-4  H7   0.020
 AYR  plan-4  H8   0.020

