# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 03:34:58 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](NC(=O)/C=C/c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCCNC2=O)C=O
#
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
 H60  H60  "(2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide"
  ligand  61  30  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H60
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
 H60  C20  C  C     0   0.589  -10.9979  11.6139  69.6916
 H60  O29  O  O     0  -0.490  -11.4204  11.5944  68.5408
 H60  C21  C  C1    0  -0.425  -10.5001  10.4117  70.3938
 H60  C22  C  C1    0  -0.227  -10.4180   9.2393  69.7577
 H60  C23  C  CR6   0   0.149   -9.9464   7.9695  70.3016
 H60  C24  C  CR16  0  -0.315   -9.5802   7.7974  71.6409
 H60  C25  C  CR16  0  -0.231   -9.1384   6.5680  72.0974
 H60  C26  C  CR16  0  -0.259   -9.0509   5.4849  71.2282
 H60  C27  C  CR16  0  -0.239   -9.4127   5.6404  69.8977
 H60  C28  C  CR16  0  -0.305   -9.8587   6.8719  69.4415
 H60  N19  N  NH1   0  -0.662  -10.9681  12.7495  70.4165
 H60  C14  C  CH1   0  -0.191  -11.3454  14.0094  69.8349
 H60  C13  C  C     0   0.564  -10.3820  14.3763  68.7027
 H60  O30  O  O     0  -0.469   -9.1992  14.0909  68.7434
 H60  C15  C  CH2   0  -0.457  -11.3473  15.1162  70.8897
 H60  C16  C  CH2   0  -0.422  -12.3891  14.8991  71.9841
 H60  C17  C  CH2   0  -0.428  -12.5622  16.1090  72.8978
 H60  C18  C  CH3   0  -0.667  -11.3150  16.4699  73.6944
 H60  C07  C  CH2   0  -0.469   -8.8861  12.7727  63.7663
 H60  C03  C  CH1   0  -0.221  -10.2541  15.4835  66.5041
 H60  C06  C  CH2   0  -0.457   -9.4184  12.7243  65.1880
 H60  C10  C  C     0   0.533  -11.7384  12.8208  64.1554
 H60  C04  C  CH2   0  -0.436  -10.8431  14.8569  65.2449
 H60  C02  C  C1    0   0.194  -10.2204  16.9973  66.4555
 H60  C05  C  CH1   0  -0.383  -10.8234  13.3211  65.2631
 H60  C08  C  CH2   0  -0.260   -9.7708  11.9283  62.8732
 H60  N12  N  NH1   0  -0.641  -10.9506  15.0757  67.6996
 H60  N09  N  NH1   0  -0.621  -11.1742  12.2312  63.0887
 H60  H6   H  H     0   0.271  -10.2015  10.5226  71.4306
 H60  H8   H  H     0   0.261  -10.7247   9.2090  68.7163
 H60  H10  H  HCR6  0   0.256   -9.6422   8.6248  72.3363
 H60  H30  H  HCR6  0   0.260   -8.8611   6.4510  73.1369
 H60  H11  H  HCR6  0   0.261   -8.7038   4.5257  71.5897
 H60  H31  H  HCR6  0   0.260   -9.3498   4.8035  69.2146
 H60  H12  H  HCR6  0   0.259  -10.1425   6.9890  68.4023
 H60  H33  H  HNH1  0   0.406  -10.5121  12.7496  71.3158
 H60  H24  H  HCH1  0   0.270  -12.3584  13.9224  69.4273
 H60  H2   H  HCH2  0   0.246  -10.3439  15.2057  71.3163
 H60  H3   H  HCH2  0   0.249  -11.5544  16.0632  70.3840
 H60  H25  H  HCH2  0   0.228  -13.3503  14.6682  71.5150
 H60  H26  H  HCH2  0   0.222  -12.1275  14.0272  72.5910
 H60  H4   H  HCH2  0   0.215  -12.8800  16.9697  72.3015
 H60  H5   H  HCH2  0   0.225  -13.3815  15.9041  73.5918
 H60  H27  H  HCH3  0   0.229  -11.5174  17.2826  74.3928
 H60  H28  H  HCH3  0   0.216  -10.9606  15.6166  74.2761
 H60  H29  H  HCH3  0   0.222  -10.4955  16.7939  73.0518
 H60  H20  H  HCH2  0   0.251   -7.8659  12.3907  63.7166
 H60  H21  H  HCH2  0   0.237   -8.8565  13.8030  63.4022
 H60  H14  H  HCH1  0   0.299   -9.2079  15.1826  66.6317
 H60  H18  H  HCH2  0   0.240   -9.4516  11.6839  65.5246
 H60  H19  H  HCH2  0   0.249   -8.7448  13.2378  65.8757
 H60  H15  H  HCH2  0   0.255  -10.2966  15.2323  64.3769
 H60  H16  H  HCH2  0   0.255  -11.8747  15.2010  65.1346
 H60  H13  H  H     0   0.209  -10.0181  17.4665  67.4362
 H60  H17  H  HCH1  0   0.279  -11.2962  12.9891  66.1917
 H60  H22  H  HCH2  0   0.232   -9.5877  10.8670  63.0696
 H60  H23  H  HCH2  0   0.250   -9.5412  12.1027  61.8212
 H60  H1   H  HNH1  0   0.408  -11.9503  15.2161  67.7172
 H60  H32  H  HNH1  0   0.390  -11.8210  11.8907  62.3919
 H60  O01  O  O     0  -0.359  -10.3838  17.6566  65.4638
 H60  O11  O  O     0  -0.504  -12.9521  12.9783  64.2331

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
 H60  N09  C10  single    1.343  0.020  1.343
 H60  N09  C08  single    1.452  0.020  1.452
 H60  O11  C10  double    1.226  0.020  1.226
 H60  C10  C05  single    1.521  0.020  1.521
 H60  C08  C07  single    1.514  0.020  1.514
 H60  C07  C06  single    1.519  0.020  1.519
 H60  O01  C02  double    1.202  0.020  1.202
 H60  C04  C05  single    1.536  0.020  1.536
 H60  C04  C03  single    1.525  0.020  1.525
 H60  C05  C06  single    1.528  0.020  1.528
 H60  C02  C03  single    1.515  0.020  1.515
 H60  C03  N12  single    1.442  0.020  1.442
 H60  N12  C13  single    1.349  0.020  1.349
 H60  O29  C20  double    1.226  0.020  1.226
 H60  O30  C13  double    1.217  0.020  1.217
 H60  C13  C14  single    1.531  0.020  1.531
 H60  C22  C23  single    1.460  0.020  1.460
 H60  C22  C21  double    1.336  0.020  1.336
 H60  C28  C23  aromatic  1.397  0.020  1.397
 H60  C28  C27  aromatic  1.387  0.020  1.387
 H60  C20  C21  single    1.479  0.020  1.479
 H60  C20  N19  single    1.348  0.020  1.348
 H60  C14  N19  single    1.438  0.020  1.438
 H60  C14  C15  single    1.529  0.020  1.529
 H60  C23  C24  aromatic  1.399  0.020  1.399
 H60  C27  C26  aromatic  1.388  0.020  1.388
 H60  C15  C16  single    1.527  0.020  1.527
 H60  C24  C25  aromatic  1.384  0.020  1.384
 H60  C26  C25  aromatic  1.391  0.020  1.391
 H60  C16  C17  single    1.526  0.020  1.526
 H60  C17  C18  single    1.523  0.020  1.523
 H60  N12  H1   single    0.860  0.020  1.020
 H60  C15  H2   single    0.970  0.020  1.090
 H60  C15  H3   single    0.970  0.020  1.090
 H60  C17  H4   single    0.970  0.020  1.090
 H60  C17  H5   single    0.970  0.020  1.090
 H60  C21  H6   single    0.930  0.020  1.080
 H60  C22  H8   single    0.930  0.020  1.080
 H60  C24  H10  single    0.930  0.020  1.080
 H60  C26  H11  single    0.930  0.020  1.080
 H60  C28  H12  single    0.930  0.020  1.080
 H60  C02  H13  single    0.930  0.020  1.080
 H60  C03  H14  single    0.970  0.020  1.090
 H60  C04  H15  single    0.970  0.020  1.090
 H60  C04  H16  single    0.970  0.020  1.090
 H60  C05  H17  single    0.970  0.020  1.090
 H60  C06  H18  single    0.970  0.020  1.090
 H60  C06  H19  single    0.970  0.020  1.090
 H60  C07  H20  single    0.970  0.020  1.090
 H60  C07  H21  single    0.970  0.020  1.090
 H60  C08  H22  single    0.970  0.020  1.090
 H60  C08  H23  single    0.970  0.020  1.090
 H60  C14  H24  single    0.970  0.020  1.090
 H60  C16  H25  single    0.970  0.020  1.090
 H60  C16  H26  single    0.970  0.020  1.090
 H60  C18  H27  single    0.970  0.020  1.090
 H60  C18  H28  single    0.970  0.020  1.090
 H60  C18  H29  single    0.970  0.020  1.090
 H60  C25  H30  single    0.930  0.020  1.080
 H60  C27  H31  single    0.930  0.020  1.080
 H60  N09  H32  single    0.860  0.020  1.020
 H60  N19  H33  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
 H60  N19  C20  C21  114.97  3.000
 H60  N19  C20  O29  121.73  3.000
 H60  C21  C20  O29  123.29  3.000
 H60  H6   C21  C22  121.85  3.000
 H60  H6   C21  C20  117.62  3.000
 H60  C22  C21  C20  120.53  3.000
 H60  H8   C22  C23  115.10  3.000
 H60  H8   C22  C21  117.62  3.000
 H60  C23  C22  C21  127.28  3.000
 H60  C28  C23  C24  118.44  3.000
 H60  C24  C23  C22  123.25  3.000
 H60  C28  C23  C22  118.31  3.000
 H60  H10  C24  C25  119.04  3.000
 H60  H10  C24  C23  120.39  3.000
 H60  C25  C24  C23  120.57  3.000
 H60  H30  C25  C26  119.98  3.000
 H60  H30  C25  C24  119.65  3.000
 H60  C26  C25  C24  120.37  3.000
 H60  H11  C26  C27  120.21  3.000
 H60  H11  C26  C25  120.09  3.000
 H60  C27  C26  C25  119.69  3.000
 H60  H31  C27  C28  119.85  3.000
 H60  H31  C27  C26  120.23  3.000
 H60  C28  C27  C26  119.92  3.000
 H60  H12  C28  C27  119.71  3.000
 H60  H12  C28  C23  119.28  3.000
 H60  C27  C28  C23  121.01  3.000
 H60  H33  N19  C14  118.64  3.000
 H60  H33  N19  C20  119.33  3.000
 H60  C14  N19  C20  120.99  3.000
 H60  H24  C14  C15  108.25  3.000
 H60  H24  C14  C13  109.01  3.000
 H60  C15  C14  C13  109.72  3.000
 H60  H24  C14  N19  108.88  3.000
 H60  C15  C14  N19  110.82  3.000
 H60  C13  C14  N19  110.11  3.000
 H60  N12  C13  O30  123.78  3.000
 H60  O30  C13  C14  122.03  3.000
 H60  N12  C13  C14  114.14  3.000
 H60  H3   C15  H2   106.46  3.000
 H60  H3   C15  C16  109.00  3.000
 H60  H2   C15  C16  110.98  3.000
 H60  H3   C15  C14  107.94  3.000
 H60  H2   C15  C14  109.10  3.000
 H60  C16  C15  C14  113.11  3.000
 H60  H26  C16  H25  106.24  3.000
 H60  H26  C16  C17  109.08  3.000
 H60  H25  C16  C17  108.93  3.000
 H60  H26  C16  C15  110.35  3.000
 H60  H25  C16  C15  108.79  3.000
 H60  C17  C16  C15  113.20  3.000
 H60  H5   C17  H4   106.01  3.000
 H60  H5   C17  C18  109.03  3.000
 H60  H4   C17  C18  109.66  3.000
 H60  H5   C17  C16  108.46  3.000
 H60  H4   C17  C16  109.29  3.000
 H60  C18  C17  C16  114.08  3.000
 H60  H29  C18  H28  107.59  3.000
 H60  H29  C18  H27  107.19  3.000
 H60  H28  C18  H27  107.55  3.000
 H60  H29  C18  C17  112.18  3.000
 H60  H28  C18  C17  111.05  3.000
 H60  H27  C18  C17  111.07  3.000
 H60  H21  C07  H20  106.83  3.000
 H60  H21  C07  C08  110.18  3.000
 H60  H20  C07  C08  108.92  3.000
 H60  H21  C07  C06  110.57  3.000
 H60  H20  C07  C06  111.06  3.000
 H60  C08  C07  C06  109.24  3.000
 H60  H14  C03  N12  106.67  3.000
 H60  H14  C03  C02  104.88  3.000
 H60  N12  C03  C02  108.65  3.000
 H60  H14  C03  C04  110.61  3.000
 H60  N12  C03  C04  112.44  3.000
 H60  C02  C03  C04  113.13  3.000
 H60  H19  C06  H18  105.80  3.000
 H60  H19  C06  C05  110.66  3.000
 H60  H18  C06  C05  109.17  3.000
 H60  H19  C06  C07  111.01  3.000
 H60  H18  C06  C07  109.21  3.000
 H60  C05  C06  C07  110.84  3.000
 H60  O11  C10  N09  121.50  3.000
 H60  O11  C10  C05  120.45  3.000
 H60  N09  C10  C05  118.03  3.000
 H60  H16  C04  H15  106.49  3.000
 H60  H16  C04  C05  109.15  3.000
 H60  H15  C04  C05  110.28  3.000
 H60  H16  C04  C03  108.57  3.000
 H60  H15  C04  C03  108.77  3.000
 H60  C05  C04  C03  113.34  3.000
 H60  H13  C02  O01  121.59  3.000
 H60  H13  C02  C03  113.56  3.000
 H60  O01  C02  C03  124.85  3.000
 H60  H17  C05  C04  107.94  3.000
 H60  H17  C05  C10  104.97  3.000
 H60  C04  C05  C10  108.21  3.000
 H60  H17  C05  C06  108.70  3.000
 H60  C04  C05  C06  113.68  3.000
 H60  C10  C05  C06  112.87  3.000
 H60  H23  C08  H22  107.03  3.000
 H60  H23  C08  N09  108.26  3.000
 H60  H22  C08  N09  109.71  3.000
 H60  H23  C08  C07  110.89  3.000
 H60  H22  C08  C07  109.70  3.000
 H60  N09  C08  C07  111.15  3.000
 H60  H1   N12  C03  116.95  3.000
 H60  H1   N12  C13  118.47  3.000
 H60  C03  N12  C13  124.02  3.000
 H60  H32  N09  C08  116.51  3.000
 H60  H32  N09  C10  115.28  3.000
 H60  C08  N09  C10  128.00  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
 H60  CONST_01  C26  C27  C28  C23     0.00   0.0  0
 H60  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 H60  CONST_03  C27  C28  C23  C24     0.00   0.0  0
 H60  CONST_04  C27  C26  C25  C24     0.00   0.0  0
 H60  CONST_05  C28  C23  C24  C25     0.00   0.0  0
 H60  CONST_06  C28  C27  C26  C25     0.00   0.0  0
 H60  CONST_07  C08  N09  C10  C05     0.00   0.0  0
 H60  CONST_08  C27  C28  C23  C22   180.00   0.0  0
 H60  CONST_09  C25  C24  C23  C22   180.00   0.0  0
 H60  CONST_10  O11  C10  N09  C08   180.00   0.0  0
 H60  CONST_11  H31  C27  C28  C23   180.00   0.0  0
 H60  CONST_12  H30  C25  C24  C23   180.00   0.0  0
 H60  CONST_13  H12  C28  C23  C24   180.00   0.0  0
 H60  CONST_14  H11  C26  C25  C24   180.00   0.0  0
 H60  CONST_15  H31  C27  C26  C25   180.00   0.0  0
 H60  CONST_16  H12  C28  C27  C26   180.00   0.0  0
 H60  CONST_17  H10  C24  C25  C26   180.00   0.0  0
 H60  CONST_18  H30  C25  C26  C27   180.00   0.0  0
 H60  CONST_19  H10  C24  C23  C28   180.00   0.0  0
 H60  CONST_20  H11  C26  C27  C28   180.00   0.0  0
 H60  CONST_21  H32  N09  C10  C05   180.00   0.0  0
 H60  CONST_22  H32  N09  C10  O11     0.00   0.0  0
 H60  CONST_23  C14  N19  C20  O29     0.00   0.0  0
 H60  CONST_24  C14  N19  C20  C21   180.00   0.0  0
 H60  CONST_25  C03  N12  C13  C14   180.00   0.0  0
 H60  CONST_26  C03  N12  C13  O30     0.00   0.0  0
 H60  CONST_27  H33  N19  C20  O29   180.00   0.0  0
 H60  CONST_28  H33  N19  C20  C21     0.00   0.0  0
 H60  CONST_29  H1   N12  C13  C14     0.00   0.0  0
 H60  CONST_30  H1   N12  C13  O30   180.00   0.0  0
 H60  Var_01    C10  N09  C08  C07   -20.17  30.0  1
 H60  Var_02    N09  C08  C07  C06    47.93  30.0  1
 H60  Var_03    C08  C07  C06  C05   -62.50  30.0  1
 H60  Var_04    H32  N09  C08  C07   165.51  30.0  1
 H60  Var_05    H22  C08  C07  C06   -73.58  30.0  1
 H60  Var_06    H23  C08  C07  C06   168.41  30.0  1
 H60  Var_07    H22  C08  N09  C10   101.32  30.0  1
 H60  Var_08    H23  C08  N09  C10  -142.20  30.0  1
 H60  Var_09    H20  C07  C06  C05   177.34  30.0  1
 H60  Var_10    H21  C07  C06  C05    58.92  30.0  1
 H60  Var_11    H18  C06  C07  C08    57.81  30.0  1
 H60  Var_12    H19  C06  C07  C08   174.09  30.0  1
 H60  Var_13    H20  C07  C08  N09   169.40  30.0  1
 H60  Var_14    H21  C07  C08  N09   -73.72  30.0  1
 H60  Var_15    C28  C23  C22  C21  -175.97  30.0  2
 H60  Var_16    C24  C23  C22  C21     4.13  30.0  2
 H60  Var_17    H8   C22  C23  C24  -176.38  30.0  3
 H60  Var_18    H8   C22  C23  C28     3.53  30.0  3
 H60  Var_19    C23  C22  C21  C20   179.72   0.0  2
 H60  Var_20    H6   C21  C22  C23     0.19   0.0  2
 H60  Var_21    C22  C21  C20  O29     3.95  30.0  2
 H60  Var_22    N19  C20  C21  C22  -176.66  30.0  2
 H60  Var_23    C17  C16  C15  C14  -170.00  30.0  3
 H60  Var_24    C18  C17  C16  C15   -63.20  30.0  3
 H60  Var_25    H8   C22  C21  C20     0.23   0.0  2
 H60  Var_26    H6   C21  C20  O29  -176.51  30.0  2
 H60  Var_27    H6   C21  C20  N19     2.88  30.0  2
 H60  Var_28    H25  C16  C15  C14   -48.77  30.0  3
 H60  Var_29    H26  C16  C15  C14    67.42  30.0  3
 H60  Var_30    H4   C17  C16  C15    59.94  30.0  3
 H60  Var_31    H5   C17  C16  C15   175.08  30.0  3
 H60  Var_32    H27  C18  C17  C16  -175.01  30.0  3
 H60  Var_33    H28  C18  C17  C16   -55.38  30.0  3
 H60  Var_34    H29  C18  C17  C16    65.06  30.0  3
 H60  Var_35    H2   C15  C16  C17    67.00  30.0  1
 H60  Var_36    H3   C15  C16  C17   -49.93  30.0  1
 H60  Var_37    H25  C16  C17  C18   175.64  30.0  2
 H60  Var_38    H26  C16  C17  C18    60.08  30.0  2
 H60  Var_39    H8   C22  C21  H6   -179.29   0.0  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
 H60  chir_01  C14  C13  N19  C15  negativ
 H60  chir_02  C03  N12  C02  C04  positiv
 H60  chir_03  C05  C10  C04  C06  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
 H60  plan-1  C22  0.020
 H60  plan-1  C23  0.020
 H60  plan-1  C24  0.020
 H60  plan-1  C25  0.020
 H60  plan-1  C26  0.020
 H60  plan-1  C27  0.020
 H60  plan-1  C28  0.020
 H60  plan-1  H10  0.020
 H60  plan-1  H30  0.020
 H60  plan-1  H11  0.020
 H60  plan-1  H31  0.020
 H60  plan-1  H12  0.020
 H60  plan-2  C20  0.020
 H60  plan-2  C21  0.020
 H60  plan-2  C22  0.020
 H60  plan-2  C23  0.020
 H60  plan-2  H6   0.020
 H60  plan-2  H8   0.020
 H60  plan-3  C20  0.020
 H60  plan-3  O29  0.020
 H60  plan-3  C21  0.020
 H60  plan-3  N19  0.020
 H60  plan-3  C14  0.020
 H60  plan-3  H33  0.020
 H60  plan-4  C14  0.020
 H60  plan-4  C13  0.020
 H60  plan-4  O30  0.020
 H60  plan-4  C03  0.020
 H60  plan-4  N12  0.020
 H60  plan-4  H1   0.020
 H60  plan-5  C10  0.020
 H60  plan-5  C05  0.020
 H60  plan-5  C08  0.020
 H60  plan-5  N09  0.020
 H60  plan-5  H32  0.020
 H60  plan-5  O11  0.020
 H60  plan-6  C03  0.020
 H60  plan-6  C02  0.020
 H60  plan-6  H13  0.020
 H60  plan-6  O01  0.020

