# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:46:19 2020
#   Inital geometry file: a 164 line input string
#   Ligand name: "(3~{S})-3-[(1~{S},3~{a}~{S},4~{E},7~{a}~{S})-7~{a}-methyl-4-[(2~{Z})-2-[(5~{S})-2-methylidene-5-oxidanyl-cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-3-oxidanyl-~{N}-propan-2-yl-butanamide"
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)C[C@](C)(O)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C3/C[C@@H](O)CCC3=C
#
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
 AYK  AYK  "(3~{S})-3-[(1~{S},3~{a}~{S},4~{E},7~{a}~{S})-7~{a}-methyl-4-[(2~{Z})-2-[(5~{S})-2-methylidene-5-oxidanyl-cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-3-oxidanyl-~{N}-propan-2-yl-butanamide"
  ligand  71  30  .  2022-07-24  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_AYK
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
 AYK  C4   C  C     0   0.082   5.0847   0.1794  -0.5012
 AYK  C5   C  CH2   0  -0.534   6.4841   0.0460   0.0391
 AYK  C6   C  CH1   0   0.075   7.0142   1.3825   0.5654
 AYK  C7   C  C1    0  -0.302   4.0962  -0.6367  -0.0946
 AYK  C10  C  C1    0  -0.362   2.6994  -0.5586  -0.4778
 AYK  C11  C  C     0   0.153   1.7546  -1.4761  -0.2168
 AYK  C12  C  CH1   0  -0.244   0.3264  -1.3071  -0.6272
 AYK  C13  C  CT    0  -0.066  -0.6556  -1.4030   0.5693
 AYK  C14  C  CH2   0  -0.417  -0.4645  -2.7841   1.2062
 AYK  C15  C  CH2   0  -0.437   0.9883  -3.0298   1.6140
 AYK  C1   C  CH2   0  -0.463   6.9323   2.4432  -0.5191
 AYK  C2   C  CH2   0  -0.512   5.4964   2.5994  -1.0176
 AYK  C3   C  C     0   0.108   4.9199   1.2827  -1.4695
 AYK  O9   O  OH1   0  -0.674   8.3593   1.2842   0.9820
 AYK  C16  C  CH2   0  -0.504   1.9785  -2.7974   0.4670
 AYK  C17  C  CH1   0  -0.191  -1.9931  -1.1914  -0.1850
 AYK  C18  C  CH2   0  -0.462  -1.6585  -0.1277  -1.2710
 AYK  C19  C  CH2   0  -0.450  -0.1243  -0.0668  -1.3782
 AYK  C20  C  CT    0   0.210  -3.3038  -0.9062   0.5861
 AYK  C21  C  CH2   0  -0.607  -4.4578  -0.9441  -0.4552
 AYK  C22  C  CH3   0  -0.674  -3.5554  -1.9395   1.6776
 AYK  C23  C  C     0   0.560  -5.7549  -0.3745   0.0775
 AYK  O24  O  OH1   0  -0.668  -3.3037   0.3478   1.2436
 AYK  N25  N  NH1   0  -0.620  -6.0462   0.8656  -0.3471
 AYK  C26  C  CH1   0  -0.083  -7.2436   1.5963   0.0338
 AYK  C27  C  CH3   0  -0.674  -6.9634   3.0889  -0.0554
 AYK  C28  C  CH3   0  -0.648  -8.4383   1.1960  -0.8253
 AYK  C30  C  CH3   0  -0.660  -0.3715  -0.2965   1.5882
 AYK  O31  O  O     0  -0.509  -6.4823  -0.9946   0.8454
 AYK  H1   H  HCH2  0   0.244   6.5151  -0.7100   0.8285
 AYK  H2   H  HCH2  0   0.236   7.1544  -0.2909  -0.7616
 AYK  H3   H  HCH1  0   0.197   6.3743   1.6971   1.4045
 AYK  H4   H  H     0   0.233   4.3693  -1.4122   0.6148
 AYK  H5   H  H     0   0.239   3.9771   0.1615  -2.9940
 AYK  H6   H  H     0   0.236   4.2794   1.9425  -3.3686
 AYK  H7   H  H     0   0.236   2.4024   0.3317  -1.0217
 AYK  H8   H  HCH1  0   0.232   0.0899  -2.1719  -1.2689
 AYK  H9   H  HCH2  0   0.233  -1.1071  -2.9146   2.0775
 AYK  H10  H  HCH2  0   0.212  -0.7680  -3.5482   0.4807
 AYK  H11  H  HCH2  0   0.223   1.2566  -2.3885   2.4578
 AYK  H12  H  HCH2  0   0.234   1.0944  -4.0561   1.9731
 AYK  H13  H  HCH2  0   0.244   7.2962   3.3998  -0.1367
 AYK  H14  H  HCH2  0   0.226   7.5821   2.1582  -1.3533
 AYK  H15  H  HCH2  0   0.239   4.8787   2.9909  -0.2015
 AYK  H16  H  HCH2  0   0.249   5.4524   3.3313  -1.8255
 AYK  H17  H  HOH1  0   0.448   8.4045   0.6643   1.7168
 AYK  H18  H  HCH2  0   0.232   1.8323  -3.5873  -0.2799
 AYK  H19  H  HCH2  0   0.244   2.9995  -2.9092   0.8320
 AYK  H20  H  HCH1  0   0.228  -2.1812  -2.1343  -0.7144
 AYK  H21  H  HCH2  0   0.245  -2.1031  -0.4098  -2.2257
 AYK  H22  H  HCH2  0   0.214  -2.0603   0.8622  -1.0377
 AYK  H23  H  HCH2  0   0.226   0.2621   0.8393  -0.9078
 AYK  H24  H  HCH2  0   0.239   0.2198  -0.0585  -2.4134
 AYK  H25  H  HCH2  0   0.266  -4.1609  -0.4004  -1.3555
 AYK  H26  H  HCH2  0   0.266  -4.6334  -1.9773  -0.7626
 AYK  H27  H  HCH3  0   0.235  -2.8319  -1.8429   2.4858
 AYK  H28  H  HCH3  0   0.250  -4.5496  -1.8219   2.1045
 AYK  H29  H  HCH3  0   0.223  -3.4826  -2.9501   1.2755
 AYK  H30  H  HOH1  0   0.438  -3.0749   1.0411   0.6168
 AYK  H31  H  HNH1  0   0.390  -5.4389   1.2985  -1.0244
 AYK  H32  H  HCH1  0   0.239  -7.4615   1.3444   1.0736
 AYK  H33  H  HCH3  0   0.225  -6.7160   3.3832  -1.0781
 AYK  H34  H  HCH3  0   0.239  -7.8430   3.6568   0.2466
 AYK  H35  H  HCH3  0   0.239  -6.1357   3.3774   0.5930
 AYK  H36  H  HCH3  0   0.235  -8.6281   0.1248  -0.7600
 AYK  H37  H  HCH3  0   0.227  -9.3381   1.7169  -0.4947
 AYK  H38  H  HCH3  0   0.219  -8.2674   1.4509  -1.8729
 AYK  H39  H  HCH3  0   0.230  -1.0114  -0.3917   2.4655
 AYK  H40  H  HCH3  0   0.227   0.6643  -0.3310   1.9276
 AYK  H41  H  HCH3  0   0.226  -0.5381   0.7005   1.1802
 AYK  C8   C  C2    0  -0.589   4.3603   1.1199  -2.6685

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
 AYK  C27  C26  single  1.521  0.020  1.521
 AYK  C28  C26  single  1.525  0.020  1.525
 AYK  C26  N25  single  1.453  0.020  1.453
 AYK  N25  C23  single  1.343  0.020  1.343
 AYK  C23  O31  double  1.226  0.020  1.226
 AYK  C23  C21  single  1.513  0.020  1.513
 AYK  O24  C20  single  1.416  0.020  1.416
 AYK  C21  C20  single  1.555  0.020  1.555
 AYK  C30  C13  single  1.531  0.020  1.531
 AYK  C15  C14  single  1.529  0.020  1.529
 AYK  C15  C16  single  1.533  0.020  1.533
 AYK  C8   C3   double  1.333  0.020  1.333
 AYK  C20  C22  single  1.524  0.020  1.524
 AYK  C20  C17  single  1.547  0.020  1.547
 AYK  C14  C13  single  1.533  0.020  1.533
 AYK  C13  C17  single  1.550  0.020  1.550
 AYK  C13  C12  single  1.551  0.020  1.551
 AYK  C3   C4   single  1.477  0.020  1.477
 AYK  C3   C2   single  1.507  0.020  1.507
 AYK  C1   C2   single  1.528  0.020  1.528
 AYK  C1   C6   single  1.519  0.020  1.519
 AYK  C5   C4   single  1.506  0.020  1.506
 AYK  C5   C6   single  1.531  0.020  1.531
 AYK  C4   C7   double  1.345  0.020  1.345
 AYK  C17  C18  single  1.557  0.020  1.557
 AYK  C7   C10  single  1.451  0.020  1.451
 AYK  C6   O9   single  1.412  0.020  1.412
 AYK  C16  C11  single  1.504  0.020  1.504
 AYK  C10  C11  double  1.343  0.020  1.343
 AYK  C11  C12  single  1.496  0.020  1.496
 AYK  C12  C19  single  1.518  0.020  1.518
 AYK  C18  C19  single  1.539  0.020  1.539
 AYK  C5   H1   single  0.970  0.020  1.090
 AYK  C5   H2   single  0.970  0.020  1.090
 AYK  C6   H3   single  0.970  0.020  1.090
 AYK  C7   H4   single  0.930  0.020  1.080
 AYK  C8   H5   single  0.930  0.020  1.080
 AYK  C8   H6   single  0.930  0.020  1.080
 AYK  C10  H7   single  0.930  0.020  1.080
 AYK  C12  H8   single  0.970  0.020  1.090
 AYK  C14  H9   single  0.970  0.020  1.090
 AYK  C14  H10  single  0.970  0.020  1.090
 AYK  C15  H11  single  0.970  0.020  1.090
 AYK  C15  H12  single  0.970  0.020  1.090
 AYK  C1   H13  single  0.970  0.020  1.090
 AYK  C1   H14  single  0.970  0.020  1.090
 AYK  C2   H15  single  0.970  0.020  1.090
 AYK  C2   H16  single  0.970  0.020  1.090
 AYK  O9   H17  single  0.850  0.020  0.980
 AYK  C16  H18  single  0.970  0.020  1.090
 AYK  C16  H19  single  0.970  0.020  1.090
 AYK  C17  H20  single  0.970  0.020  1.090
 AYK  C18  H21  single  0.970  0.020  1.090
 AYK  C18  H22  single  0.970  0.020  1.090
 AYK  C19  H23  single  0.970  0.020  1.090
 AYK  C19  H24  single  0.970  0.020  1.090
 AYK  C21  H25  single  0.970  0.020  1.090
 AYK  C21  H26  single  0.970  0.020  1.090
 AYK  C22  H27  single  0.970  0.020  1.090
 AYK  C22  H28  single  0.970  0.020  1.090
 AYK  C22  H29  single  0.970  0.020  1.090
 AYK  O24  H30  single  0.850  0.020  0.980
 AYK  N25  H31  single  0.860  0.020  1.020
 AYK  C26  H32  single  0.970  0.020  1.090
 AYK  C27  H33  single  0.970  0.020  1.090
 AYK  C27  H34  single  0.970  0.020  1.090
 AYK  C27  H35  single  0.970  0.020  1.090
 AYK  C28  H36  single  0.970  0.020  1.090
 AYK  C28  H37  single  0.970  0.020  1.090
 AYK  C28  H38  single  0.970  0.020  1.090
 AYK  C30  H39  single  0.970  0.020  1.090
 AYK  C30  H40  single  0.970  0.020  1.090
 AYK  C30  H41  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
 AYK  C3   C4   C7   124.72  3.000
 AYK  C7   C4   C5   121.39  3.000
 AYK  C3   C4   C5   113.89  3.000
 AYK  H2   C5   H1   107.28  3.000
 AYK  H2   C5   C6   107.90  3.000
 AYK  H1   C5   C6   110.22  3.000
 AYK  H2   C5   C4   109.45  3.000
 AYK  H1   C5   C4   110.28  3.000
 AYK  C6   C5   C4   111.58  3.000
 AYK  H3   C6   O9   110.41  3.000
 AYK  H3   C6   C1   108.25  3.000
 AYK  O9   C6   C1   108.10  3.000
 AYK  H3   C6   C5   108.07  3.000
 AYK  O9   C6   C5   111.75  3.000
 AYK  C1   C6   C5   110.21  3.000
 AYK  H4   C7   C10  116.95  3.000
 AYK  H4   C7   C4   116.49  3.000
 AYK  C10  C7   C4   126.53  3.000
 AYK  H7   C10  C11  117.75  3.000
 AYK  H7   C10  C7   116.12  3.000
 AYK  C11  C10  C7   126.12  3.000
 AYK  C16  C11  C12  111.47  3.000
 AYK  C12  C11  C10  122.78  3.000
 AYK  C16  C11  C10  125.72  3.000
 AYK  H8   C12  C19  106.80  3.000
 AYK  H8   C12  C13  105.35  3.000
 AYK  C19  C12  C13  104.13  3.000
 AYK  H8   C12  C11  106.02  3.000
 AYK  C19  C12  C11  120.76  3.000
 AYK  C13  C12  C11  112.71  3.000
 AYK  C30  C13  C17  112.67  3.000
 AYK  C17  C13  C14  115.64  3.000
 AYK  C30  C13  C14  110.58  3.000
 AYK  C17  C13  C12   99.36  3.000
 AYK  C14  C13  C12  107.30  3.000
 AYK  C30  C13  C12  110.57  3.000
 AYK  H10  C14  H9   106.39  3.000
 AYK  H10  C14  C15  109.11  3.000
 AYK  H9   C14  C15  109.13  3.000
 AYK  H10  C14  C13  108.57  3.000
 AYK  H9   C14  C13  111.49  3.000
 AYK  C15  C14  C13  111.97  3.000
 AYK  H12  C15  H11  105.87  3.000
 AYK  H12  C15  C16  109.01  3.000
 AYK  H11  C15  C16  109.27  3.000
 AYK  H12  C15  C14  109.33  3.000
 AYK  H11  C15  C14  110.17  3.000
 AYK  C16  C15  C14  112.95  3.000
 AYK  H14  C1   H13  107.27  3.000
 AYK  H14  C1   C2   109.61  3.000
 AYK  H13  C1   C2   109.74  3.000
 AYK  H14  C1   C6   109.27  3.000
 AYK  H13  C1   C6   110.09  3.000
 AYK  C2   C1   C6   110.79  3.000
 AYK  H16  C2   H15  106.80  3.000
 AYK  H16  C2   C3   110.41  3.000
 AYK  H15  C2   C3   108.66  3.000
 AYK  H16  C2   C1   110.37  3.000
 AYK  H15  C2   C1   108.86  3.000
 AYK  C3   C2   C1   111.60  3.000
 AYK  C2   C3   C8   122.48  3.000
 AYK  C2   C3   C4   114.42  3.000
 AYK  C8   C3   C4   123.03  3.000
 AYK  H17  O9   C6   108.36  3.000
 AYK  H19  C16  H18  106.20  3.000
 AYK  H19  C16  C15  109.81  3.000
 AYK  H18  C16  C15  108.31  3.000
 AYK  H19  C16  C11  112.44  3.000
 AYK  H18  C16  C11  107.65  3.000
 AYK  C15  C16  C11  112.15  3.000
 AYK  H20  C17  C20  104.69  3.000
 AYK  H20  C17  C18  106.70  3.000
 AYK  C20  C17  C18  113.82  3.000
 AYK  H20  C17  C13  105.38  3.000
 AYK  C18  C17  C13  104.32  3.000
 AYK  C20  C17  C13  120.91  3.000
 AYK  H22  C18  H21  105.74  3.000
 AYK  H22  C18  C19  110.20  3.000
 AYK  H21  C18  C19  110.84  3.000
 AYK  H22  C18  C17  113.00  3.000
 AYK  H21  C18  C17  110.27  3.000
 AYK  C19  C18  C17  106.85  3.000
 AYK  H24  C19  H23  106.92  3.000
 AYK  H24  C19  C18  112.38  3.000
 AYK  H23  C19  C18  110.83  3.000
 AYK  H24  C19  C12  112.45  3.000
 AYK  H23  C19  C12  111.09  3.000
 AYK  C18  C19  C12  103.25  3.000
 AYK  O24  C20  C22  105.54  3.000
 AYK  C22  C20  C21  109.91  3.000
 AYK  O24  C20  C21  109.43  3.000
 AYK  C22  C20  C17  111.83  3.000
 AYK  C21  C20  C17  106.89  3.000
 AYK  O24  C20  C17  113.24  3.000
 AYK  H26  C21  H25  106.41  3.000
 AYK  H26  C21  C23  108.50  3.000
 AYK  H25  C21  C23  109.61  3.000
 AYK  H26  C21  C20  109.32  3.000
 AYK  H25  C21  C20  109.75  3.000
 AYK  C23  C21  C20  113.03  3.000
 AYK  H29  C22  H28  107.81  3.000
 AYK  H29  C22  H27  108.16  3.000
 AYK  H28  C22  H27  107.82  3.000
 AYK  H29  C22  C20  110.70  3.000
 AYK  H28  C22  C20  111.01  3.000
 AYK  H27  C22  C20  111.21  3.000
 AYK  O31  C23  N25  122.44  3.000
 AYK  O31  C23  C21  122.59  3.000
 AYK  N25  C23  C21  114.97  3.000
 AYK  H30  O24  C20  109.61  3.000
 AYK  H31  N25  C26  117.18  3.000
 AYK  H31  N25  C23  118.60  3.000
 AYK  C26  N25  C23  124.06  3.000
 AYK  H32  C26  C28  108.64  3.000
 AYK  H32  C26  C27  108.60  3.000
 AYK  C28  C26  C27  111.64  3.000
 AYK  H32  C26  N25  107.34  3.000
 AYK  C28  C26  N25  111.46  3.000
 AYK  C27  C26  N25  109.03  3.000
 AYK  H35  C27  H34  108.06  3.000
 AYK  H35  C27  H33  108.27  3.000
 AYK  H34  C27  H33  107.57  3.000
 AYK  H35  C27  C26  111.38  3.000
 AYK  H34  C27  C26  110.27  3.000
 AYK  H33  C27  C26  111.16  3.000
 AYK  H38  C28  H37  107.97  3.000
 AYK  H38  C28  H36  108.32  3.000
 AYK  H37  C28  H36  107.90  3.000
 AYK  H38  C28  C26  110.89  3.000
 AYK  H37  C28  C26  110.50  3.000
 AYK  H36  C28  C26  111.14  3.000
 AYK  H41  C30  H40  106.89  3.000
 AYK  H41  C30  H39  106.95  3.000
 AYK  H40  C30  H39  107.72  3.000
 AYK  H41  C30  C13  112.56  3.000
 AYK  H40  C30  C13  111.13  3.000
 AYK  H39  C30  C13  111.32  3.000
 AYK  H6   C8   H5   116.84  3.000
 AYK  H6   C8   C3   121.33  3.000
 AYK  H5   C8   C3   121.82  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
 AYK  CONST_01  C26  N25  C23  C21  180.00   0.0  0
 AYK  CONST_02  O31  C23  N25  C26    0.00   0.0  0
 AYK  CONST_03  H31  N25  C23  C21    0.00   0.0  0
 AYK  Var_01    C1   C2   C3   C4    49.73  30.0  1
 AYK  Var_02    C2   C3   C4   C5   -48.36  30.0  1
 AYK  Var_03    C3   C2   C1   C6   -54.39  30.0  1
 AYK  Var_04    C3   C4   C5   C6    50.83  30.0  1
 AYK  Var_05    C14  C15  C16  C11   49.77  30.0  1
 AYK  Var_06    C15  C16  C11  C12  -51.85  30.0  1
 AYK  Var_07    C17  C18  C19  C12   13.48  30.0  1
 AYK  Var_08    C16  C15  C14  C13  -53.09  30.0  1
 AYK  Var_09    C11  C10  C7   C4   170.33  30.0  2
 AYK  Var_10    C10  C7   C4   C5   176.07  30.0  2
 AYK  Var_11    C16  C11  C10  C7    -3.21  30.0  2
 AYK  Var_12    H5   C8   C3   C4     1.04  30.0  2
 AYK  Var_13    N25  C23  C21  C20  102.82  30.0  2
 AYK  Var_14    C27  C26  N25  C23  153.70  30.0  2
 AYK  Var_15    H33  C27  C26  N25   61.98  30.0  3
 AYK  Var_16    H36  C28  C26  N25   57.46  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
 AYK  chir_01  C6   C1   C5   O9   negativ
 AYK  chir_02  C12  C13  C11  C19  positiv
 AYK  chir_03  C13  C14  C17  C12  positiv
 AYK  chir_04  C17  C18  C13  C20  negativ
 AYK  chir_05  C20  C21  C22  C17  negativ

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
 AYK  plan-1  C21  0.020
 AYK  plan-1  C23  0.020
 AYK  plan-1  N25  0.020
 AYK  plan-1  C26  0.020
 AYK  plan-1  O31  0.020
 AYK  plan-1  H31  0.020

