# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 16:05:17 2021
#   Inital geometry file: a 164 line input string
#   Ligand name: (2~{R},3~{R})-2-azanyl-1-[4-[[4-[2-[4-(hydroxymethyl)phenyl]ethynyl]phenyl]methyl]piperidin-1-yl]-4-methylsulfonyl-3-oxidanyl-butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)C[C@H](O)[C@@H](N)C(=O)N1CCC(CC1)Cc2ccc(cc2)C#Cc3ccc(CO)cc3
#
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
 FY9  FY9  (2~{R},3~{R})-2-azanyl-1-[4-[[4-[2-[4-(hydroxymethyl)phenyl]ethynyl]phenyl]methyl]piperidin-1-yl]-4-methylsulfonyl-3-oxidanyl-butan-1-one  ligand  66  34  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FY9
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
 FY9  C1   C  CR6   0   0.056  -3.5072   3.5707  33.4966
 FY9  C2   C  CR16  0  -0.290  -3.4804   2.3328  32.8597
 FY9  C3   C  CR16  0  -0.283  -2.3506   1.8975  32.1890
 FY9  C4   C  CR6   0  -0.122  -1.2109   2.7049  32.1329
 FY9  C5   C  CR16  0  -0.283  -1.2366   3.9513  32.7676
 FY9  C6   C  CR16  0  -0.280  -2.3702   4.3747  33.4394
 FY9  C7   C  CSP   0   0.129  -0.0499   2.2681  31.4372
 FY9  C8   C  CSP   0   0.134   0.9307   1.8923  30.8397
 FY9  C9   C  CR6   0  -0.126   2.0838   1.4502  30.1346
 FY9  C10  C  CR16  0  -0.281   3.2570   2.2128  30.1379
 FY9  C11  C  CR16  0  -0.299   4.3756   1.7743  29.4529
 FY9  C12  C  CR6   0   0.138   4.3661   0.5721  28.7448
 FY9  C13  C  CR16  0  -0.305   3.1950  -0.1823  28.7470
 FY9  C14  C  CR16  0  -0.282   2.0673   0.2439  29.4289
 FY9  C15  C  CH2   0  -0.505   5.5819   0.1328  27.9808
 FY9  C16  C  CH1   0  -0.242   5.7612   0.8785  26.6544
 FY9  C17  C  CH2   0  -0.421   7.1033   0.5292  26.0170
 FY9  C18  C  CH2   0  -0.332   7.2760   1.2085  24.6653
 FY9  N19  N  NT    0  -0.453   6.1719   0.8881  23.7765
 FY9  C20  C  CH2   0  -0.309   4.8807   1.2724  24.3258
 FY9  C21  C  CH2   0  -0.415   4.6358   0.5907  25.6651
 FY9  C22  C  CH2   0  -0.198  -4.7293   3.9975  34.2597
 FY9  O23  O  OH1   0  -0.666  -4.9063   5.3875  34.1368
 FY9  C24  C  C     0   0.569   6.2569   0.3388  22.5457
 FY9  C25  C  CH1   0  -0.266   7.6318  -0.1310  22.0553
 FY9  O26  O  O     0  -0.494   5.2770   0.1802  21.8323
 FY9  C27  C  CH1   0   0.033   7.9760  -1.4497  22.7870
 FY9  N28  N  NH2   0  -0.782   7.6021  -0.2177  20.6153
 FY9  C29  C  CH2   0  -0.646   9.4042  -1.8703  22.4471
 FY9  O30  O  OH1   0  -0.657   7.0330  -2.4148  22.4015
 FY9  S31  S  S     0   1.195   9.8217  -3.4370  23.2240
 FY9  C32  C  CH3   0  -0.791  11.5996  -3.4300  23.2537
 FY9  O33  O  OS    0  -0.680   9.3788  -4.5358  22.3668
 FY9  O34  O  OS    0  -0.685   9.3275  -3.4071  24.6034
 FY9  H1   H  HCR6  0   0.258  -4.3585   1.6985  32.8821
 FY9  H2   H  HCR6  0   0.259  -2.3511   0.9337  31.6969
 FY9  H3   H  HCR6  0   0.259  -0.3619   4.5878  32.7326
 FY9  H4   H  HCR6  0   0.257  -2.3631   5.3423  33.9234
 FY9  H5   H  HCR6  0   0.258   3.2879   3.1463  30.6845
 FY9  H6   H  HCR6  0   0.253   5.2769   2.3760  29.4733
 FY9  H7   H  HCR6  0   0.253   3.1625  -1.1203  28.2062
 FY9  H8   H  HCR6  0   0.258   1.1683  -0.3584  29.4170
 FY9  H9   H  HCH2  0   0.243   5.5296  -0.9417  27.7819
 FY9  H10  H  HCH2  0   0.251   6.4722   0.2935  28.5956
 FY9  H11  H  HCH1  0   0.230   5.7606   1.9565  26.8637
 FY9  H12  H  HCH2  0   0.225   7.1803  -0.5566  25.8924
 FY9  H13  H  HCH2  0   0.246   7.9245   0.8337  26.6704
 FY9  H14  H  HCH2  0   0.263   8.2308   0.9304  24.2292
 FY9  H15  H  HCH2  0   0.254   7.3058   2.2950  24.8036
 FY9  H16  H  HCH2  0   0.235   4.8656   2.3606  24.4561
 FY9  H17  H  HCH2  0   0.266   4.0985   1.0209  23.6160
 FY9  H18  H  HCH2  0   0.243   3.6767   0.9339  26.0595
 FY9  H19  H  HCH2  0   0.222   4.5478  -0.4903  25.5092
 FY9  H20  H  HCH2  0   0.214  -5.5974   3.4395  33.8860
 FY9  H21  H  HCH2  0   0.224  -4.6034   3.7037  35.3103
 FY9  H22  H  HOH1  0   0.460  -5.5720   5.6597  34.7747
 FY9  H23  H  HCH1  0   0.279   8.3981   0.6051  22.3095
 FY9  H24  H  HCH1  0   0.251   7.9387  -1.2737  23.8669
 FY9  H25  H  HNH2  0   0.357   8.5268  -0.4064  20.2527
 FY9  H26  H  HNH2  0   0.348   6.9976  -0.9685  20.3093
 FY9  H28  H  HCH2  0   0.302   9.5657  -2.0038  21.3764
 FY9  H29  H  HCH2  0   0.309  10.1113  -1.1257  22.8195
 FY9  H30  H  HOH1  0   0.460   6.8714  -3.0211  23.1301
 FY9  H31  H  HCH3  0   0.295  11.9519  -2.6070  23.8703
 FY9  H32  H  HCH3  0   0.312  11.9173  -4.3808  23.6791
 FY9  H33  H  HCH3  0   0.296  11.9754  -3.3341  22.2374

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
 FY9  N28  C25  single    1.443  0.020  1.443
 FY9  O30  C27  single    1.403  0.020  1.403
 FY9  C25  C24  single    1.533  0.020  1.533
 FY9  C25  C27  single    1.547  0.020  1.547
 FY9  O26  C24  double    1.222  0.020  1.222
 FY9  C24  N19  single    1.350  0.020  1.350
 FY9  C27  C29  single    1.527  0.020  1.527
 FY9  O33  S31  double    1.462  0.020  1.462
 FY9  N19  C20  single    1.455  0.020  1.455
 FY9  N19  C18  single    1.453  0.020  1.453
 FY9  C29  S31  single    1.798  0.020  1.798
 FY9  C20  C21  single    1.523  0.020  1.523
 FY9  C18  C17  single    1.523  0.020  1.523
 FY9  S31  O34  double    1.466  0.020  1.466
 FY9  S31  C32  single    1.778  0.020  1.778
 FY9  C21  C16  single    1.526  0.020  1.526
 FY9  C17  C16  single    1.526  0.020  1.526
 FY9  C16  C15  single    1.532  0.020  1.532
 FY9  C15  C12  single    1.502  0.020  1.502
 FY9  C12  C13  aromatic  1.393  0.020  1.393
 FY9  C12  C11  aromatic  1.395  0.020  1.395
 FY9  C13  C14  aromatic  1.385  0.020  1.385
 FY9  C11  C10  aromatic  1.383  0.020  1.383
 FY9  C14  C9   aromatic  1.398  0.020  1.398
 FY9  C9   C10  aromatic  1.399  0.020  1.399
 FY9  C9   C8   single    1.422  0.020  1.422
 FY9  C8   C7   triple    1.208  0.020  1.208
 FY9  C7   C4   single    1.422  0.020  1.422
 FY9  C3   C4   aromatic  1.398  0.020  1.398
 FY9  C3   C2   aromatic  1.384  0.020  1.384
 FY9  C4   C5   aromatic  1.399  0.020  1.399
 FY9  C2   C1   aromatic  1.392  0.020  1.392
 FY9  C5   C6   aromatic  1.384  0.020  1.384
 FY9  C1   C6   aromatic  1.394  0.020  1.394
 FY9  C1   C22  single    1.503  0.020  1.503
 FY9  C22  O23  single    1.407  0.020  1.407
 FY9  C2   H1   single    0.930  0.020  1.080
 FY9  C3   H2   single    0.930  0.020  1.080
 FY9  C5   H3   single    0.930  0.020  1.080
 FY9  C6   H4   single    0.930  0.020  1.080
 FY9  C10  H5   single    0.930  0.020  1.080
 FY9  C11  H6   single    0.930  0.020  1.080
 FY9  C13  H7   single    0.930  0.020  1.080
 FY9  C14  H8   single    0.930  0.020  1.080
 FY9  C15  H9   single    0.970  0.020  1.090
 FY9  C15  H10  single    0.970  0.020  1.090
 FY9  C16  H11  single    0.970  0.020  1.090
 FY9  C17  H12  single    0.970  0.020  1.090
 FY9  C17  H13  single    0.970  0.020  1.090
 FY9  C18  H14  single    0.970  0.020  1.090
 FY9  C18  H15  single    0.970  0.020  1.090
 FY9  C20  H16  single    0.970  0.020  1.090
 FY9  C20  H17  single    0.970  0.020  1.090
 FY9  C21  H18  single    0.970  0.020  1.090
 FY9  C21  H19  single    0.970  0.020  1.090
 FY9  C22  H20  single    0.970  0.020  1.090
 FY9  C22  H21  single    0.970  0.020  1.090
 FY9  O23  H22  single    0.850  0.020  0.980
 FY9  C25  H23  single    0.970  0.020  1.090
 FY9  C27  H24  single    0.970  0.020  1.090
 FY9  N28  H25  single    0.890  0.020  1.040
 FY9  N28  H26  single    0.890  0.020  1.040
 FY9  C29  H28  single    0.970  0.020  1.090
 FY9  C29  H29  single    0.970  0.020  1.090
 FY9  O30  H30  single    0.850  0.020  0.980
 FY9  C32  H31  single    0.970  0.020  1.090
 FY9  C32  H32  single    0.970  0.020  1.090
 FY9  C32  H33  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
 FY9  C22  C1   C6   121.36  3.000
 FY9  C22  C1   C2   120.03  3.000
 FY9  C6   C1   C2   118.58  3.000
 FY9  H1   C2   C3   119.17  3.000
 FY9  H1   C2   C1   119.70  3.000
 FY9  C3   C2   C1   121.13  3.000
 FY9  H2   C3   C4   119.78  3.000
 FY9  H2   C3   C2   120.01  3.000
 FY9  C4   C3   C2   120.21  3.000
 FY9  C7   C4   C5   120.70  3.000
 FY9  C5   C4   C3   118.78  3.000
 FY9  C7   C4   C3   120.51  3.000
 FY9  H3   C5   C6   119.84  3.000
 FY9  H3   C5   C4   119.64  3.000
 FY9  C6   C5   C4   120.52  3.000
 FY9  H4   C6   C5   119.04  3.000
 FY9  H4   C6   C1   120.19  3.000
 FY9  C5   C6   C1   120.77  3.000
 FY9  C8   C7   C4   180.00  3.000
 FY9  C9   C8   C7   180.00  3.000
 FY9  C14  C9   C10  118.79  3.000
 FY9  C10  C9   C8   120.61  3.000
 FY9  C14  C9   C8   120.60  3.000
 FY9  H5   C10  C11  120.04  3.000
 FY9  H5   C10  C9   119.69  3.000
 FY9  C11  C10  C9   120.27  3.000
 FY9  H6   C11  C12  119.58  3.000
 FY9  H6   C11  C10  119.16  3.000
 FY9  C12  C11  C10  121.26  3.000
 FY9  C15  C12  C13  121.53  3.000
 FY9  C13  C12  C11  118.14  3.000
 FY9  C15  C12  C11  120.31  3.000
 FY9  H7   C13  C14  119.20  3.000
 FY9  H7   C13  C12  119.56  3.000
 FY9  C14  C13  C12  121.24  3.000
 FY9  H8   C14  C13  119.98  3.000
 FY9  H8   C14  C9   119.72  3.000
 FY9  C13  C14  C9   120.30  3.000
 FY9  H10  C15  H9   106.59  3.000
 FY9  H10  C15  C16  108.65  3.000
 FY9  H9   C15  C16  109.04  3.000
 FY9  H10  C15  C12  109.27  3.000
 FY9  H9   C15  C12  109.95  3.000
 FY9  C16  C15  C12  113.13  3.000
 FY9  H11  C16  C21  107.96  3.000
 FY9  H11  C16  C17  107.74  3.000
 FY9  C21  C16  C17  109.55  3.000
 FY9  H11  C16  C15  108.22  3.000
 FY9  C17  C16  C15  110.68  3.000
 FY9  C21  C16  C15  112.53  3.000
 FY9  H13  C17  H12  106.93  3.000
 FY9  H13  C17  C18  108.74  3.000
 FY9  H12  C17  C18  109.47  3.000
 FY9  H13  C17  C16  110.32  3.000
 FY9  H12  C17  C16  109.64  3.000
 FY9  C18  C17  C16  111.62  3.000
 FY9  H15  C18  H14  106.31  3.000
 FY9  H15  C18  N19  108.45  3.000
 FY9  H14  C18  N19  111.47  3.000
 FY9  H15  C18  C17  109.48  3.000
 FY9  H14  C18  C17  110.00  3.000
 FY9  N19  C18  C17  111.00  3.000
 FY9  C24  N19  C20  120.49  3.000
 FY9  C20  N19  C18  112.65  3.000
 FY9  C24  N19  C18  126.82  3.000
 FY9  H17  C20  H16  107.33  3.000
 FY9  H17  C20  C21  110.82  3.000
 FY9  H16  C20  C21  109.74  3.000
 FY9  H17  C20  N19  109.35  3.000
 FY9  H16  C20  N19  108.63  3.000
 FY9  C21  C20  N19  110.89  3.000
 FY9  H19  C21  H18  106.90  3.000
 FY9  H19  C21  C20  109.24  3.000
 FY9  H18  C21  C20  108.55  3.000
 FY9  H19  C21  C16  109.73  3.000
 FY9  H18  C21  C16  110.75  3.000
 FY9  C20  C21  C16  111.54  3.000
 FY9  H21  C22  H20  106.28  3.000
 FY9  H21  C22  O23  111.25  3.000
 FY9  H20  C22  O23  111.91  3.000
 FY9  H21  C22  C1   108.45  3.000
 FY9  H20  C22  C1   109.03  3.000
 FY9  O23  C22  C1   109.80  3.000
 FY9  H22  O23  C22  107.99  3.000
 FY9  O26  C24  C25  119.49  3.000
 FY9  O26  C24  N19  122.30  3.000
 FY9  C25  C24  N19  118.20  3.000
 FY9  H23  C25  N28  106.68  3.000
 FY9  H23  C25  C27  107.95  3.000
 FY9  N28  C25  C27  115.18  3.000
 FY9  H23  C25  C24  110.37  3.000
 FY9  C27  C25  C24  108.03  3.000
 FY9  N28  C25  C24  108.61  3.000
 FY9  H24  C27  O30  111.02  3.000
 FY9  H24  C27  C29  107.19  3.000
 FY9  O30  C27  C29  112.21  3.000
 FY9  H24  C27  C25  108.78  3.000
 FY9  C29  C27  C25  109.73  3.000
 FY9  O30  C27  C25  107.87  3.000
 FY9  H26  N28  H25  107.44  3.000
 FY9  H26  N28  C25  111.03  3.000
 FY9  H25  N28  C25  110.51  3.000
 FY9  H29  C29  H28  108.80  3.000
 FY9  H29  C29  S31  107.24  3.000
 FY9  H28  C29  S31  106.44  3.000
 FY9  H29  C29  C27  109.99  3.000
 FY9  H28  C29  C27  112.99  3.000
 FY9  S31  C29  C27  111.16  3.000
 FY9  H30  O30  C27  109.78  3.000
 FY9  O34  S31  O33  117.71  3.000
 FY9  O34  S31  C32  108.74  3.000
 FY9  O33  S31  C32  108.40  3.000
 FY9  C32  S31  C29  103.65  3.000
 FY9  O34  S31  C29  108.09  3.000
 FY9  O33  S31  C29  109.34  3.000
 FY9  H33  C32  H32  109.94  3.000
 FY9  H33  C32  H31  110.56  3.000
 FY9  H32  C32  H31  110.17  3.000
 FY9  H33  C32  S31  109.28  3.000
 FY9  H32  C32  S31  107.14  3.000
 FY9  H31  C32  S31  109.67  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
 FY9  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 FY9  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 FY9  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 FY9  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 FY9  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 FY9  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 FY9  CONST_07  C12  C13  C14  C9      0.00   0.0  0
 FY9  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 FY9  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 FY9  CONST_10  C13  C14  C9   C10     0.00   0.0  0
 FY9  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 FY9  CONST_12  C14  C9   C10  C11     0.00   0.0  0
 FY9  CONST_13  C7   C4   C3   C2    180.00   0.0  0
 FY9  CONST_14  C22  C1   C2   C3    180.00   0.0  0
 FY9  CONST_15  C22  C1   C6   C5    180.00   0.0  0
 FY9  CONST_16  C7   C4   C5   C6    180.00   0.0  0
 FY9  CONST_17  C13  C14  C9   C8    180.00   0.0  0
 FY9  CONST_18  C11  C10  C9   C8    180.00   0.0  0
 FY9  CONST_19  C15  C12  C11  C10   180.00   0.0  0
 FY9  CONST_20  C15  C12  C13  C14   180.00   0.0  0
 FY9  CONST_21  H2   C3   C2   C1    180.00   0.0  0
 FY9  CONST_22  H3   C5   C6   C1    180.00   0.0  0
 FY9  CONST_23  H4   C6   C1   C2    180.00   0.0  0
 FY9  CONST_24  H1   C2   C3   C4    180.00   0.0  0
 FY9  CONST_25  H7   C13  C14  C9    180.00   0.0  0
 FY9  CONST_26  H6   C11  C10  C9    180.00   0.0  0
 FY9  CONST_27  H8   C14  C9   C10   180.00   0.0  0
 FY9  CONST_28  H5   C10  C11  C12   180.00   0.0  0
 FY9  CONST_29  C25  C24  N19  C18     0.00   0.0  0
 FY9  CONST_30  O26  C24  N19  C18   180.00   0.0  0
 FY9  CONST_31  C25  C24  N19  C20   180.00   0.0  0
 FY9  CONST_32  O26  C24  N19  C20     0.00   0.0  0
 FY9  Var_01    N19  C20  C21  C16    55.61  30.0  1
 FY9  Var_02    N19  C18  C17  C16   -55.29  30.0  1
 FY9  Var_03    C20  N19  C18  C17    58.04  30.0  1
 FY9  Var_04    C21  C20  N19  C18   -58.20  30.0  1
 FY9  Var_05    C16  C15  C12  C11   -76.96  30.0  2
 FY9  Var_06    O23  C22  C1   C2   -145.52  30.0  2
 FY9  Var_07    O33  S31  C29  C27    85.73  30.0  3
 FY9  Var_08    H31  C32  S31  C29    62.76  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
 FY9  chir_01  C16  C21  C17  C15  positiv
 FY9  chir_02  C25  N28  C24  C27  negativ
 FY9  chir_03  C27  O30  C25  C29  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
 FY9  plan-1  C1   0.020
 FY9  plan-1  C2   0.020
 FY9  plan-1  C3   0.020
 FY9  plan-1  C4   0.020
 FY9  plan-1  C5   0.020
 FY9  plan-1  C6   0.020
 FY9  plan-1  C7   0.020
 FY9  plan-1  C8   0.020
 FY9  plan-1  C22  0.020
 FY9  plan-1  H1   0.020
 FY9  plan-1  H2   0.020
 FY9  plan-1  H3   0.020
 FY9  plan-1  H4   0.020
 FY9  plan-2  C7   0.020
 FY9  plan-2  C8   0.020
 FY9  plan-2  C9   0.020
 FY9  plan-2  C10  0.020
 FY9  plan-2  C11  0.020
 FY9  plan-2  C12  0.020
 FY9  plan-2  C13  0.020
 FY9  plan-2  C14  0.020
 FY9  plan-2  C15  0.020
 FY9  plan-2  H5   0.020
 FY9  plan-2  H6   0.020
 FY9  plan-2  H7   0.020
 FY9  plan-2  H8   0.020
 FY9  plan-3  C18  0.020
 FY9  plan-3  N19  0.020
 FY9  plan-3  C20  0.020
 FY9  plan-3  C24  0.020
 FY9  plan-3  C25  0.020
 FY9  plan-3  O26  0.020

