# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:50:24 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3S)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(tert-butoxymethyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC[C@@H]1N(CCNC1=O)C(=O)C[C@H](N)Cc2cc(F)c(F)cc2F
#
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
 8OL  8OL  (3S)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(tert-butoxymethyl)piperazin-2-one  ligand  54  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8OL
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
 8OL  C10   C  C     0   0.605  -1.0357   0.8620  -0.2543
 8OL  C13   C  CH1   0  -0.256  -3.4038   1.0591  -0.6946
 8OL  C17   C  CH2   0  -0.343  -2.6410   1.0821   1.6442
 8OL  C26   C  CH3   0  -0.677  -4.0669  -3.2110  -0.3342
 8OL  C28   C  CH3   0  -0.658  -5.7687  -2.4155   1.3101
 8OL  C01   C  CR6   0   0.399   6.3012  -0.8845  -0.4040
 8OL  C02   C  CR16  0  -0.553   5.8379   0.3402  -0.8366
 8OL  C03   C  CR6   0   0.531   4.6388   0.8001  -0.3258
 8OL  C04   C  CR6   0  -0.064   3.8843   0.0970   0.6018
 8OL  C05   C  CR16  0  -0.457   4.3849  -1.1369   1.0113
 8OL  C06   C  CR6   0   0.405   5.5777  -1.6200   0.5167
 8OL  C07   C  CH2   0  -0.517   2.5668   0.6069   1.1027
 8OL  C08   C  CH1   0  -0.081   1.4065   0.2864   0.1355
 8OL  C09   C  CH2   0  -0.612   0.1078   0.8006   0.7407
 8OL  N11   N  NT    0  -0.486  -2.2941   0.9713   0.2415
 8OL  O12   O  O     0  -0.496  -0.8313   0.8472  -1.4595
 8OL  C14   C  C     0   0.547  -4.5429   1.9571  -0.2241
 8OL  N15   N  NH1   0  -0.626  -4.4270   2.5605   0.9636
 8OL  C16   C  CH2   0  -0.256  -3.3217   2.4094   1.8842
 8OL  O18   O  O     0  -0.502  -5.5118   2.1177  -0.9544
 8OL  N19   N  NH2   0  -0.783   1.2553  -1.1234  -0.1729
 8OL  F20   F  F     0  -0.307   6.0464  -2.8058   0.9212
 8OL  F22   F  F     0  -0.306   4.1926   1.9907  -0.7540
 8OL  C23   C  CH2   0  -0.121  -3.9499  -0.3108  -1.0764
 8OL  O24   O  O2    0  -0.492  -4.5642  -0.8582   0.0579
 8OL  C25   C  CT    0   0.221  -5.1395  -2.1590  -0.0543
 8OL  C27   C  CH3   0  -0.683  -6.2187  -2.1947  -1.1358
 8OL  H131  H  HCH1  0   0.306  -3.0335   1.5229  -1.6121
 8OL  H171  H  HCH2  0   0.270  -3.3018   0.2616   1.9267
 8OL  H172  H  HCH2  0   0.281  -1.7596   1.0231   2.2730
 8OL  H1    H  HCH3  0   0.232  -4.5035  -4.2102  -0.3033
 8OL  H2    H  HCH3  0   0.231  -3.6132  -3.0914  -1.3194
 8OL  H3    H  HCH3  0   0.232  -3.2737  -3.1681   0.4142
 8OL  H4    H  HCH3  0   0.230  -5.0194  -2.3673   2.1022
 8OL  H5    H  HCH3  0   0.229  -6.5463  -1.6814   1.5286
 8OL  H6    H  HCH3  0   0.222  -6.2243  -3.4056   1.3377
 8OL  H021  H  HCR6  0   0.313   6.4005   0.9216  -1.5551
 8OL  H051  H  HCR6  0   0.296   3.8383  -1.7269   1.7364
 8OL  H072  H  HCH2  0   0.255   2.3567   0.1520   2.0747
 8OL  H071  H  HCH2  0   0.255   2.6136   1.6852   1.2676
 8OL  H7    H  HCH1  0   0.244   1.5969   0.8087  -0.8048
 8OL  H091  H  HCH2  0   0.282   0.2534   1.8065   1.1503
 8OL  H092  H  HCH2  0   0.264  -0.1442   0.1638   1.5923
 8OL  H8    H  HNH1  0   0.402  -5.1702   3.1942   1.2191
 8OL  H162  H  HCH2  0   0.261  -3.7072   2.4464   2.9028
 8OL  H161  H  HCH2  0   0.243  -2.6048   3.2272   1.7697
 8OL  H10   H  HNH2  0   0.351   2.0733  -1.4695  -0.6591
 8OL  H9    H  HNH2  0   0.337   1.1899  -1.6610   0.6849
 8OL  H232  H  HCH2  0   0.215  -4.6504  -0.1906  -1.9092
 8OL  H231  H  HCH2  0   0.221  -3.1156  -0.9233  -1.4368
 8OL  H12   H  HCH3  0   0.234  -6.7639  -3.1383  -1.0905
 8OL  H13   H  HCH3  0   0.233  -6.9373  -1.3854  -0.9949
 8OL  H14   H  HCH3  0   0.231  -5.8049  -2.1118  -2.1420
 8OL  F21   F  F     0  -0.301   7.4557  -1.3652  -0.8703

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
 8OL  C28  C25   single    1.524  0.020  1.524
 8OL  C27  C25   single    1.528  0.020  1.528
 8OL  C26  C25   single    1.528  0.020  1.528
 8OL  C25  O24   single    1.427  0.020  1.427
 8OL  O24  C23   single    1.401  0.020  1.401
 8OL  C23  C13   single    1.523  0.020  1.523
 8OL  F22  C03   single    1.342  0.020  1.342
 8OL  C16  C17   single    1.511  0.020  1.511
 8OL  C16  N15   single    1.446  0.020  1.446
 8OL  C13  C14   single    1.525  0.020  1.525
 8OL  C13  N11   single    1.454  0.020  1.454
 8OL  C07  C04   single    1.499  0.020  1.499
 8OL  C07  C08   single    1.544  0.020  1.544
 8OL  C03  C04   aromatic  1.387  0.020  1.387
 8OL  C03  C02   aromatic  1.382  0.020  1.382
 8OL  C04  C05   aromatic  1.393  0.020  1.393
 8OL  C02  C01   aromatic  1.379  0.020  1.379
 8OL  C17  N11   single    1.449  0.020  1.449
 8OL  N15  C14   single    1.337  0.020  1.337
 8OL  C14  O18   double    1.224  0.020  1.224
 8OL  N11  C10   single    1.357  0.020  1.357
 8OL  C05  C06   aromatic  1.379  0.020  1.379
 8OL  C01  C06   aromatic  1.383  0.020  1.383
 8OL  C01  F21   single    1.335  0.020  1.335
 8OL  C06  F20   single    1.338  0.020  1.338
 8OL  C10  C09   single    1.517  0.020  1.517
 8OL  C10  O12   double    1.223  0.020  1.223
 8OL  C09  C08   single    1.522  0.020  1.522
 8OL  C08  N19   single    1.451  0.020  1.451
 8OL  C13  H131  single    0.970  0.020  1.090
 8OL  C17  H171  single    0.970  0.020  1.090
 8OL  C17  H172  single    0.970  0.020  1.090
 8OL  C26  H1    single    0.970  0.020  1.090
 8OL  C26  H2    single    0.970  0.020  1.090
 8OL  C26  H3    single    0.970  0.020  1.090
 8OL  C28  H4    single    0.970  0.020  1.090
 8OL  C28  H5    single    0.970  0.020  1.090
 8OL  C28  H6    single    0.970  0.020  1.090
 8OL  C02  H021  single    0.930  0.020  1.080
 8OL  C05  H051  single    0.930  0.020  1.080
 8OL  C07  H072  single    0.970  0.020  1.090
 8OL  C07  H071  single    0.970  0.020  1.090
 8OL  C08  H7    single    0.970  0.020  1.090
 8OL  C09  H091  single    0.970  0.020  1.090
 8OL  C09  H092  single    0.970  0.020  1.090
 8OL  N15  H8    single    0.860  0.020  1.020
 8OL  C16  H162  single    0.970  0.020  1.090
 8OL  C16  H161  single    0.970  0.020  1.090
 8OL  N19  H10   single    0.890  0.020  1.040
 8OL  N19  H9    single    0.890  0.020  1.040
 8OL  C23  H232  single    0.970  0.020  1.090
 8OL  C23  H231  single    0.970  0.020  1.090
 8OL  C27  H12   single    0.970  0.020  1.090
 8OL  C27  H13   single    0.970  0.020  1.090
 8OL  C27  H14   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
 8OL  O12   C10  N11   121.08  3.000
 8OL  O12   C10  C09   121.34  3.000
 8OL  N11   C10  C09   117.56  3.000
 8OL  H131  C13  C23   107.02  3.000
 8OL  H131  C13  C14   105.21  3.000
 8OL  C23   C13  C14   109.82  3.000
 8OL  H131  C13  N11   107.90  3.000
 8OL  C14   C13  N11   114.01  3.000
 8OL  C23   C13  N11   112.37  3.000
 8OL  H172  C17  H171  107.54  3.000
 8OL  H172  C17  C16   108.77  3.000
 8OL  H171  C17  C16   110.29  3.000
 8OL  H172  C17  N11   111.26  3.000
 8OL  H171  C17  N11   109.77  3.000
 8OL  C16   C17  N11   109.20  3.000
 8OL  H3    C26  H2    108.21  3.000
 8OL  H3    C26  H1    107.91  3.000
 8OL  H2    C26  H1    107.00  3.000
 8OL  H3    C26  C25   110.94  3.000
 8OL  H2    C26  C25   112.44  3.000
 8OL  H1    C26  C25   110.15  3.000
 8OL  H6    C28  H5    107.94  3.000
 8OL  H6    C28  H4    107.98  3.000
 8OL  H5    C28  H4    108.31  3.000
 8OL  H6    C28  C25   110.37  3.000
 8OL  H5    C28  C25   111.11  3.000
 8OL  H4    C28  C25   111.03  3.000
 8OL  F21   C01  C06   119.58  3.000
 8OL  F21   C01  C02   120.06  3.000
 8OL  C06   C01  C02   120.36  3.000
 8OL  H021  C02  C03   121.18  3.000
 8OL  H021  C02  C01   120.71  3.000
 8OL  C03   C02  C01   118.11  3.000
 8OL  F22   C03  C04   118.84  3.000
 8OL  C04   C03  C02   123.39  3.000
 8OL  F22   C03  C02   117.77  3.000
 8OL  C07   C04  C05   121.26  3.000
 8OL  C05   C04  C03   116.75  3.000
 8OL  C07   C04  C03   121.95  3.000
 8OL  H051  C05  C06   119.08  3.000
 8OL  H051  C05  C04   119.87  3.000
 8OL  C06   C05  C04   121.05  3.000
 8OL  F20   C06  C05   120.35  3.000
 8OL  F20   C06  C01   119.31  3.000
 8OL  C05   C06  C01   120.34  3.000
 8OL  H071  C07  H072  106.55  3.000
 8OL  H071  C07  C08   109.38  3.000
 8OL  H072  C07  C08   109.03  3.000
 8OL  H071  C07  C04   110.41  3.000
 8OL  H072  C07  C04   108.93  3.000
 8OL  C08   C07  C04   112.37  3.000
 8OL  H7    C08  N19   107.44  3.000
 8OL  H7    C08  C09   109.23  3.000
 8OL  N19   C08  C09   108.89  3.000
 8OL  H7    C08  C07   108.00  3.000
 8OL  N19   C08  C07   114.40  3.000
 8OL  C09   C08  C07   108.78  3.000
 8OL  H092  C09  H091  105.92  3.000
 8OL  H092  C09  C08   108.05  3.000
 8OL  H091  C09  C08   110.20  3.000
 8OL  H092  C09  C10   111.15  3.000
 8OL  H091  C09  C10   107.95  3.000
 8OL  C08   C09  C10   113.33  3.000
 8OL  C17   N11  C13   115.83  3.000
 8OL  C17   N11  C10   125.58  3.000
 8OL  C13   N11  C10   118.51  3.000
 8OL  O18   C14  N15   122.64  3.000
 8OL  O18   C14  C13   118.98  3.000
 8OL  N15   C14  C13   118.36  3.000
 8OL  H8    N15  C16   117.84  3.000
 8OL  H8    N15  C14   116.38  3.000
 8OL  C16   N15  C14   125.76  3.000
 8OL  H161  C16  H162  107.72  3.000
 8OL  H161  C16  N15   110.86  3.000
 8OL  H162  C16  N15   108.73  3.000
 8OL  H161  C16  C17   110.18  3.000
 8OL  H162  C16  C17   109.74  3.000
 8OL  N15   C16  C17   109.57  3.000
 8OL  H9    N19  H10   106.08  3.000
 8OL  H9    N19  C08   109.99  3.000
 8OL  H10   N19  C08   110.48  3.000
 8OL  H231  C23  H232  107.35  3.000
 8OL  H231  C23  O24   112.43  3.000
 8OL  H232  C23  O24   112.22  3.000
 8OL  H231  C23  C13   108.18  3.000
 8OL  H232  C23  C13   108.74  3.000
 8OL  O24   C23  C13   107.79  3.000
 8OL  C25   O24  C23   117.98  3.000
 8OL  C27   C25  O24   111.20  3.000
 8OL  O24   C25  C28   104.44  3.000
 8OL  C27   C25  C28   109.76  3.000
 8OL  O24   C25  C26   111.04  3.000
 8OL  C27   C25  C26   110.49  3.000
 8OL  C28   C25  C26   109.74  3.000
 8OL  H14   C27  H13   108.20  3.000
 8OL  H14   C27  H12   107.07  3.000
 8OL  H13   C27  H12   107.88  3.000
 8OL  H14   C27  C25   112.52  3.000
 8OL  H13   C27  C25   110.88  3.000
 8OL  H12   C27  C25   110.11  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
 8OL  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 8OL  CONST_02  C04   C05  C06  C01    0.00   0.0  0
 8OL  CONST_03  C05   C04  C03  C02    0.00   0.0  0
 8OL  CONST_04  C05   C06  C01  C02    0.00   0.0  0
 8OL  CONST_05  C06   C05  C04  C03    0.00   0.0  0
 8OL  CONST_06  C06   C01  C02  C03    0.00   0.0  0
 8OL  CONST_07  C16   N15  C14  C13    0.00   0.0  0
 8OL  CONST_08  F22   C03  C02  C01  180.00   0.0  0
 8OL  CONST_09  C07   C04  C03  C02  180.00   0.0  0
 8OL  CONST_10  F20   C06  C01  C02  180.00   0.0  0
 8OL  CONST_11  F21   C01  C02  C03  180.00   0.0  0
 8OL  CONST_12  F20   C06  C05  C04  180.00   0.0  0
 8OL  CONST_13  F22   C03  C04  C05  180.00   0.0  0
 8OL  CONST_14  F21   C01  C06  C05  180.00   0.0  0
 8OL  CONST_15  C07   C04  C05  C06  180.00   0.0  0
 8OL  CONST_16  O18   C14  N15  C16  180.00   0.0  0
 8OL  CONST_17  H051  C05  C06  C01  180.00   0.0  0
 8OL  CONST_18  H021  C02  C03  C04  180.00   0.0  0
 8OL  CONST_19  H8    N15  C14  C13  180.00   0.0  0
 8OL  CONST_20  C09   C10  N11  C13  180.00   0.0  0
 8OL  CONST_21  O12   C10  N11  C13    0.00   0.0  0
 8OL  CONST_22  C09   C10  N11  C17    0.00   0.0  0
 8OL  CONST_23  O12   C10  N11  C17  180.00   0.0  0
 8OL  Var_01    C16   C17  N11  C13  -59.00  30.0  1
 8OL  Var_02    C14   N15  C16  C17  -24.77  30.0  1
 8OL  Var_03    N15   C16  C17  N11   53.02  30.0  1
 8OL  Var_04    C08   C07  C04  C03   82.21  30.0  2
 8OL  Var_05    N11   C10  C09  C08  163.47  30.0  3
 8OL  Var_06    C27   C25  O24  C23  -59.02  30.0  3
 8OL  Var_07    H4    C28  C25  C26   59.96  30.0  3
 8OL  Var_08    H12   C27  C25  C26   66.03  30.0  3
 8OL  Var_09    H1    C26  C25  C28   58.55  30.0  3
 8OL  Var_10    H232  C23  O24  C25   61.10  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
 8OL  chir_01  C13  C23  C14  N11  negativ
 8OL  chir_02  C08  N19  C07  C09  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
 8OL  plan-1  C01   0.020
 8OL  plan-1  C02   0.020
 8OL  plan-1  C03   0.020
 8OL  plan-1  C04   0.020
 8OL  plan-1  C05   0.020
 8OL  plan-1  C06   0.020
 8OL  plan-1  C07   0.020
 8OL  plan-1  F20   0.020
 8OL  plan-1  F22   0.020
 8OL  plan-1  H021  0.020
 8OL  plan-1  H051  0.020
 8OL  plan-1  F21   0.020
 8OL  plan-2  C10   0.020
 8OL  plan-2  C13   0.020
 8OL  plan-2  C17   0.020
 8OL  plan-2  C09   0.020
 8OL  plan-2  N11   0.020
 8OL  plan-2  O12   0.020
 8OL  plan-3  C13   0.020
 8OL  plan-3  C14   0.020
 8OL  plan-3  N15   0.020
 8OL  plan-3  C16   0.020
 8OL  plan-3  O18   0.020
 8OL  plan-3  H8    0.020

