# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:47:02 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-[(1S)-2-{[(1R)-2-(benzyloxy)-1-cyano-1-methylethyl]amino}-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](COCc1ccccc1)(NC(=O)[C@H](CC2CCCCC2)NC(=O)N3CCOCC3)C#N
#
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
 Y15  Y15  N-[(1S)-2-{[(1R)-2-(benzyloxy)-1-cyano-1-methylethyl]amino}-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide  ligand  69  33  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y15
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
 Y15  C01   C  C     0   0.757   4.3004  -0.3646   0.6114
 Y15  C02   C  CH2   0  -0.335   5.4127  -1.9737  -0.9351
 Y15  C03   C  CH2   0  -0.180   6.2886  -3.1912  -0.6854
 Y15  C04   C  CH2   0  -0.190   7.4731  -2.1159   0.9870
 Y15  C05   C  CH2   0  -0.308   6.6715  -0.8421   0.8112
 Y15  O06   O  O     0  -0.544   4.3369   0.3736   1.5908
 Y15  O07   O  O2    0  -0.482   7.5691  -2.8374  -0.2214
 Y15  N08   N  NT    0  -0.514   5.3630  -1.1473   0.2571
 Y15  N09   N  NH1   0  -0.694   3.1751  -0.4794  -0.1509
 Y15  C10   C  CH1   0  -0.193   2.0387   0.3800   0.0878
 Y15  C11   C  CH2   0  -0.411   2.1940   1.7398  -0.6086
 Y15  C12   C  CH1   0  -0.251   1.0164   2.7044  -0.4817
 Y15  C13   C  CH2   0  -0.421   0.7205   3.1052   0.9643
 Y15  C14   C  CH2   0  -0.428  -0.4260   4.1089   1.0509
 Y15  C15   C  CH2   0  -0.430  -0.1552   5.3450   0.2007
 Y15  C16   C  CH2   0  -0.432   0.1438   4.9608  -1.2442
 Y15  C17   C  CH2   0  -0.411   1.2841   3.9521  -1.3250
 Y15  C18   C  C     0   0.576   0.8057  -0.3285  -0.4527
 Y15  O19   O  O     0  -0.470   0.7876  -0.8228  -1.5671
 Y15  C20   C  CH2   0  -0.139  -2.5618  -0.3254   1.0334
 Y15  C21   C  CH3   0  -0.630  -1.5472  -2.4033  -0.0052
 Y15  N22   N  NH1   0  -0.673  -0.2684  -0.3120   0.3577
 Y15  O23   O  O2    0  -0.477  -3.8296  -0.7725   0.6762
 Y15  C24   C  CH2   0  -0.190  -4.8645  -0.1874   1.4357
 Y15  C25   C  CR6   0   0.062  -6.1873  -0.6050   0.8629
 Y15  C26   C  CR16  0  -0.306  -7.2161  -1.0272   1.6975
 Y15  C27   C  CR16  0  -0.241  -8.4546  -1.3783   1.1736
 Y15  C28   C  CR16  0  -0.266  -8.6714  -1.3199  -0.1955
 Y15  C29   C  CR16  0  -0.241  -7.6455  -0.9042  -1.0368
 Y15  C30   C  CR16  0  -0.287  -6.4125  -0.5469  -0.5117
 Y15  C31   C  CSP   0   0.154  -1.9732  -0.3658  -1.3147
 Y15  N32   N  NS    0  -0.259  -2.3598   0.0321  -2.3212
 Y15  C33   C  CT    0  -0.001  -1.5573  -0.8734   0.0066
 Y15  H021  H  HCH2  0   0.243   5.7955  -1.4049  -1.7912
 Y15  H022  H  HCH2  0   0.256   4.4226  -2.3461  -1.1941
 Y15  H031  H  HCH2  0   0.209   5.7865  -3.8502   0.0364
 Y15  H032  H  HCH2  0   0.247   6.4134  -3.7425  -1.6181
 Y15  H041  H  HCH2  0   0.244   8.4870  -1.8710   1.3058
 Y15  H042  H  HCH2  0   0.208   7.0105  -2.7358   1.7681
 Y15  H051  H  HCH2  0   0.265   6.5599  -0.3539   1.7759
 Y15  H052  H  HCH2  0   0.233   7.2106  -0.1541   0.1477
 Y15  HN09  H  HNH1  0   0.399   3.2383  -0.8484  -1.0863
 Y15  H10   H  HCH1  0   0.275   1.9481   0.5231   1.1650
 Y15  H111  H  HCH2  0   0.242   3.0931   2.2127  -0.2034
 Y15  H112  H  HCH2  0   0.233   2.3914   1.5550  -1.6693
 Y15  H12   H  HCH1  0   0.212   0.1166   2.2239  -0.8908
 Y15  H131  H  HCH2  0   0.216   0.4802   2.2316   1.5768
 Y15  H132  H  HCH2  0   0.214   1.6242   3.5445   1.4033
 Y15  H141  H  HCH2  0   0.208  -1.3516   3.6310   0.7096
 Y15  H142  H  HCH2  0   0.228  -0.5937   4.3936   2.0923
 Y15  H151  H  HCH2  0   0.227  -1.0069   6.0281   0.2449
 Y15  H152  H  HCH2  0   0.208   0.7010   5.8879   0.6159
 Y15  H161  H  HCH2  0   0.209  -0.7549   4.5276  -1.6970
 Y15  H162  H  HCH2  0   0.227   0.3890   5.8493  -1.8315
 Y15  H171  H  HCH2  0   0.208   2.2121   4.4212  -0.9762
 Y15  H172  H  HCH2  0   0.227   1.4572   3.6614  -2.3649
 Y15  H201  H  HCH2  0   0.236  -2.5063   0.7727   1.0431
 Y15  H202  H  HCH2  0   0.250  -2.2624  -0.6824   2.0292
 Y15  H211  H  HCH3  0   0.256  -1.2801  -2.7611   0.9891
 Y15  H212  H  HCH3  0   0.258  -2.5270  -2.7990  -0.2650
 Y15  H213  H  HCH3  0   0.262  -0.8213  -2.7828  -0.7198
 Y15  HN22  H  HNH1  0   0.421  -0.1602   0.0308   1.2999
 Y15  H241  H  HCH2  0   0.232  -4.7926  -0.4843   2.4896
 Y15  H242  H  HCH2  0   0.229  -4.7751   0.9075   1.4082
 Y15  H26   H  HCR6  0   0.253  -7.0514  -1.0856   2.7671
 Y15  H27   H  HCR6  0   0.256  -9.2462  -1.7045   1.8359
 Y15  H28   H  HCR6  0   0.257  -9.6328  -1.5994  -0.6065
 Y15  H29   H  HCR6  0   0.256  -7.8077  -0.8573  -2.1061
 Y15  H30   H  HCR6  0   0.250  -5.6216  -0.2234  -1.1774

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
 Y15  C04  O07   single    1.411  0.020  1.411
 Y15  C04  C05   single    1.515  0.020  1.515
 Y15  O07  C03   single    1.407  0.020  1.407
 Y15  C05  N08   single    1.453  0.020  1.453
 Y15  C03  C02   single    1.520  0.020  1.520
 Y15  C14  C13   single    1.526  0.020  1.526
 Y15  C14  C15   single    1.524  0.020  1.524
 Y15  C13  C12   single    1.529  0.020  1.529
 Y15  N08  C02   single    1.451  0.020  1.451
 Y15  N08  C01   single    1.367  0.020  1.367
 Y15  C12  C11   single    1.528  0.020  1.528
 Y15  C12  C17   single    1.530  0.020  1.530
 Y15  C15  C16   single    1.525  0.020  1.525
 Y15  N09  C01   single    1.364  0.020  1.364
 Y15  N09  C10   single    1.445  0.020  1.445
 Y15  C11  C10   single    1.536  0.020  1.536
 Y15  C16  C17   single    1.525  0.020  1.525
 Y15  C01  O06   double    1.227  0.020  1.227
 Y15  O19  C18   double    1.219  0.020  1.219
 Y15  C10  C18   single    1.521  0.020  1.521
 Y15  C18  N22   single    1.346  0.020  1.346
 Y15  N22  C33   single    1.449  0.020  1.449
 Y15  C31  N32   triple    1.149  0.020  1.149
 Y15  C31  C33   single    1.475  0.020  1.475
 Y15  C21  C33   single    1.530  0.020  1.530
 Y15  C33  C20   single    1.537  0.020  1.537
 Y15  C20  O23   single    1.391  0.020  1.391
 Y15  O23  C24   single    1.411  0.020  1.411
 Y15  C24  C25   single    1.501  0.020  1.501
 Y15  C30  C25   aromatic  1.394  0.020  1.394
 Y15  C30  C29   aromatic  1.387  0.020  1.387
 Y15  C25  C26   aromatic  1.390  0.020  1.390
 Y15  C29  C28   aromatic  1.390  0.020  1.390
 Y15  C26  C27   aromatic  1.390  0.020  1.390
 Y15  C28  C27   aromatic  1.387  0.020  1.387
 Y15  C02  H021  single    0.970  0.020  1.090
 Y15  C02  H022  single    0.970  0.020  1.090
 Y15  C03  H031  single    0.970  0.020  1.090
 Y15  C03  H032  single    0.970  0.020  1.090
 Y15  C04  H041  single    0.970  0.020  1.090
 Y15  C04  H042  single    0.970  0.020  1.090
 Y15  C05  H051  single    0.970  0.020  1.090
 Y15  C05  H052  single    0.970  0.020  1.090
 Y15  N09  HN09  single    0.890  0.020  1.040
 Y15  C10  H10   single    0.970  0.020  1.090
 Y15  C11  H111  single    0.970  0.020  1.090
 Y15  C11  H112  single    0.970  0.020  1.090
 Y15  C12  H12   single    0.970  0.020  1.090
 Y15  C13  H131  single    0.970  0.020  1.090
 Y15  C13  H132  single    0.970  0.020  1.090
 Y15  C14  H141  single    0.970  0.020  1.090
 Y15  C14  H142  single    0.970  0.020  1.090
 Y15  C15  H151  single    0.970  0.020  1.090
 Y15  C15  H152  single    0.970  0.020  1.090
 Y15  C16  H161  single    0.970  0.020  1.090
 Y15  C16  H162  single    0.970  0.020  1.090
 Y15  C17  H171  single    0.970  0.020  1.090
 Y15  C17  H172  single    0.970  0.020  1.090
 Y15  C20  H201  single    0.970  0.020  1.090
 Y15  C20  H202  single    0.970  0.020  1.090
 Y15  C21  H211  single    0.970  0.020  1.090
 Y15  C21  H212  single    0.970  0.020  1.090
 Y15  C21  H213  single    0.970  0.020  1.090
 Y15  N22  HN22  single    0.860  0.020  1.020
 Y15  C24  H241  single    0.970  0.020  1.090
 Y15  C24  H242  single    0.970  0.020  1.090
 Y15  C26  H26   single    0.930  0.020  1.080
 Y15  C27  H27   single    0.930  0.020  1.080
 Y15  C28  H28   single    0.930  0.020  1.080
 Y15  C29  H29   single    0.930  0.020  1.080
 Y15  C30  H30   single    0.930  0.020  1.080

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
 Y15  N09   C01  N08   116.64  3.000
 Y15  N09   C01  O06   121.42  3.000
 Y15  N08   C01  O06   121.90  3.000
 Y15  H022  C02  H021  108.00  3.000
 Y15  H022  C02  N08   111.03  3.000
 Y15  H021  C02  N08   110.96  3.000
 Y15  H022  C02  C03   106.79  3.000
 Y15  H021  C02  C03   110.03  3.000
 Y15  N08   C02  C03   109.92  3.000
 Y15  H032  C03  H031  108.12  3.000
 Y15  H032  C03  O07   107.76  3.000
 Y15  H031  C03  O07   110.49  3.000
 Y15  H032  C03  C02   109.28  3.000
 Y15  H031  C03  C02   108.96  3.000
 Y15  O07   C03  C02   112.15  3.000
 Y15  H042  C04  H041  108.06  3.000
 Y15  H042  C04  O07   110.42  3.000
 Y15  H041  C04  O07   107.57  3.000
 Y15  H042  C04  C05   109.50  3.000
 Y15  H041  C04  C05   109.69  3.000
 Y15  O07   C04  C05   111.51  3.000
 Y15  H052  C05  H051  107.79  3.000
 Y15  H052  C05  N08   110.08  3.000
 Y15  H051  C05  N08   109.89  3.000
 Y15  H052  C05  C04   109.71  3.000
 Y15  H051  C05  C04   109.21  3.000
 Y15  N08   C05  C04   110.12  3.000
 Y15  C04   O07  C03   110.43  3.000
 Y15  C05   N08  C02   113.70  3.000
 Y15  C02   N08  C01   124.45  3.000
 Y15  C05   N08  C01   118.74  3.000
 Y15  HN09  N09  C10   114.88  3.000
 Y15  HN09  N09  C01   119.86  3.000
 Y15  C10   N09  C01   120.43  3.000
 Y15  H10   C10  C18   110.17  3.000
 Y15  H10   C10  C11   109.89  3.000
 Y15  C18   C10  C11   109.46  3.000
 Y15  H10   C10  N09   107.86  3.000
 Y15  C18   C10  N09   107.56  3.000
 Y15  C11   C10  N09   111.86  3.000
 Y15  H112  C11  H111  106.48  3.000
 Y15  H112  C11  C12   109.04  3.000
 Y15  H111  C11  C12   109.27  3.000
 Y15  H112  C11  C10   107.95  3.000
 Y15  H111  C11  C10   107.34  3.000
 Y15  C12   C11  C10   116.33  3.000
 Y15  H12   C12  C17   107.14  3.000
 Y15  H12   C12  C13   107.94  3.000
 Y15  C17   C12  C13   109.96  3.000
 Y15  H12   C12  C11   108.91  3.000
 Y15  C17   C12  C11   109.54  3.000
 Y15  C13   C12  C11   113.15  3.000
 Y15  H132  C13  H131  106.08  3.000
 Y15  H132  C13  C14   109.44  3.000
 Y15  H131  C13  C14   109.18  3.000
 Y15  H132  C13  C12   108.90  3.000
 Y15  H131  C13  C12   111.26  3.000
 Y15  C14   C13  C12   111.80  3.000
 Y15  H142  C14  H141  106.31  3.000
 Y15  H142  C14  C15   110.34  3.000
 Y15  H141  C14  C15   109.26  3.000
 Y15  H142  C14  C13   109.92  3.000
 Y15  H141  C14  C13   109.27  3.000
 Y15  C15   C14  C13   111.60  3.000
 Y15  H152  C15  H151  106.50  3.000
 Y15  H152  C15  C16   109.32  3.000
 Y15  H151  C15  C16   110.41  3.000
 Y15  H152  C15  C14   109.23  3.000
 Y15  H151  C15  C14   110.23  3.000
 Y15  C16   C15  C14   111.04  3.000
 Y15  H162  C16  H161  106.46  3.000
 Y15  H162  C16  C17   109.98  3.000
 Y15  H161  C16  C17   109.27  3.000
 Y15  H162  C16  C15   110.39  3.000
 Y15  H161  C16  C15   109.29  3.000
 Y15  C17   C16  C15   111.32  3.000
 Y15  H172  C17  H171  106.39  3.000
 Y15  H172  C17  C16   110.16  3.000
 Y15  H171  C17  C16   109.46  3.000
 Y15  H172  C17  C12   109.58  3.000
 Y15  H171  C17  C12   108.76  3.000
 Y15  C16   C17  C12   112.31  3.000
 Y15  N22   C18  O19   122.92  3.000
 Y15  N22   C18  C10   115.29  3.000
 Y15  O19   C18  C10   121.71  3.000
 Y15  H202  C20  H201  107.62  3.000
 Y15  H202  C20  C33   108.13  3.000
 Y15  H201  C20  C33   109.20  3.000
 Y15  H202  C20  O23   112.11  3.000
 Y15  H201  C20  O23   111.67  3.000
 Y15  C33   C20  O23   108.02  3.000
 Y15  H213  C21  H212  108.51  3.000
 Y15  H213  C21  H211  108.75  3.000
 Y15  H212  C21  H211  108.61  3.000
 Y15  H213  C21  C33   111.01  3.000
 Y15  H212  C21  C33   111.07  3.000
 Y15  H211  C21  C33   108.83  3.000
 Y15  HN22  N22  C33   116.97  3.000
 Y15  HN22  N22  C18   118.76  3.000
 Y15  C33   N22  C18   124.01  3.000
 Y15  C24   O23  C20   113.39  3.000
 Y15  H242  C24  H241  106.76  3.000
 Y15  H242  C24  C25   109.84  3.000
 Y15  H241  C24  C25   110.43  3.000
 Y15  H242  C24  O23   109.88  3.000
 Y15  H241  C24  O23   110.90  3.000
 Y15  C25   C24  O23   109.00  3.000
 Y15  C30   C25  C26   119.01  3.000
 Y15  C26   C25  C24   120.50  3.000
 Y15  C30   C25  C24   120.47  3.000
 Y15  H26   C26  C27   119.59  3.000
 Y15  H26   C26  C25   119.76  3.000
 Y15  C27   C26  C25   120.65  3.000
 Y15  H27   C27  C28   120.15  3.000
 Y15  H27   C27  C26   119.81  3.000
 Y15  C28   C27  C26   120.04  3.000
 Y15  H28   C28  C29   120.19  3.000
 Y15  H28   C28  C27   120.18  3.000
 Y15  C29   C28  C27   119.63  3.000
 Y15  H29   C29  C30   119.73  3.000
 Y15  H29   C29  C28   120.01  3.000
 Y15  C30   C29  C28   120.26  3.000
 Y15  H30   C30  C29   119.56  3.000
 Y15  H30   C30  C25   120.03  3.000
 Y15  C29   C30  C25   120.41  3.000
 Y15  C33   C31  N32   180.00  3.000
 Y15  C31   C33  N22   109.54  3.000
 Y15  C31   C33  C21   109.82  3.000
 Y15  N22   C33  C21   112.55  3.000
 Y15  C21   C33  C20   111.46  3.000
 Y15  C31   C33  C20   106.94  3.000
 Y15  N22   C33  C20   106.33  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
 Y15  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 Y15  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 Y15  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 Y15  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 Y15  CONST_05  C30   C25  C26  C27     0.00   0.0  0
 Y15  CONST_06  C30   C29  C28  C27     0.00   0.0  0
 Y15  CONST_07  C29   C30  C25  C24   180.00   0.0  0
 Y15  CONST_08  C27   C26  C25  C24   180.00   0.0  0
 Y15  CONST_09  H29   C29  C30  C25   180.00   0.0  0
 Y15  CONST_10  H27   C27  C26  C25   180.00   0.0  0
 Y15  CONST_11  H30   C30  C25  C26   180.00   0.0  0
 Y15  CONST_12  H28   C28  C27  C26   180.00   0.0  0
 Y15  CONST_13  H26   C26  C27  C28   180.00   0.0  0
 Y15  CONST_14  O06   C01  N08  C02   180.00   0.0  0
 Y15  CONST_16  N09   C01  N08  C02     0.00   0.0  0
 Y15  CONST_17  N09   C01  N08  C05   180.00   0.0  0
 Y15  CONST_18  C10   N09  C01  N08   180.00   0.0  0
 Y15  CONST_20  C10   N09  C01  O06     0.00   0.0  0
 Y15  CONST_21  C33   N22  C18  C10   180.00   0.0  0
 Y15  CONST_22  C33   N22  C18  O19     0.00   0.0  0
 Y15  CONST_23  HN22  N22  C18  C10     0.00   0.0  0
 Y15  Var_01    C04   C05  N08  C02   -51.12  30.0  1
 Y15  Var_02    C05   C04  O07  C03   -59.98  30.0  1
 Y15  Var_03    C05   N08  C02  C03    50.29  30.0  1
 Y15  Var_04    N08   C05  C04  O07    55.18  30.0  1
 Y15  Var_05    N08   C02  C03  O07   -54.04  30.0  1
 Y15  Var_06    C15   C14  C13  C12   -55.75  30.0  1
 Y15  Var_07    C15   C16  C17  C12    55.41  30.0  1
 Y15  Var_08    C16   C15  C14  C13    54.90  30.0  1
 Y15  Var_09    C17   C16  C15  C14   -54.52  30.0  1
 Y15  Var_10    H031  C03  O07  C04   -62.21  30.0  1
 Y15  Var_11    C30   C25  C24  O23   -46.58  30.0  2
 Y15  Var_12    C25   C24  O23  C20   173.12  30.0  3
 Y15  Var_13    C33   C20  O23  C24  -171.81  30.0  1

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
 Y15  chir_01  C10  N09  C11  C18  negativ
 Y15  chir_02  C12  C13  C11  C17  positiv
 Y15  chir_03  C33  C31  C21  C20  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
 Y15  plan-1  C01   0.020
 Y15  plan-1  C02   0.020
 Y15  plan-1  C05   0.020
 Y15  plan-1  O06   0.020
 Y15  plan-1  N08   0.020
 Y15  plan-1  N09   0.020
 Y15  plan-1  C10   0.020
 Y15  plan-1  HN09  0.020
 Y15  plan-2  C24   0.020
 Y15  plan-2  C25   0.020
 Y15  plan-2  C26   0.020
 Y15  plan-2  C27   0.020
 Y15  plan-2  C28   0.020
 Y15  plan-2  C29   0.020
 Y15  plan-2  C30   0.020
 Y15  plan-2  H26   0.020
 Y15  plan-2  H27   0.020
 Y15  plan-2  H28   0.020
 Y15  plan-2  H29   0.020
 Y15  plan-2  H30   0.020
 Y15  plan-3  C10   0.020
 Y15  plan-3  C18   0.020
 Y15  plan-3  O19   0.020
 Y15  plan-3  N22   0.020
 Y15  plan-3  C33   0.020
 Y15  plan-3  HN22  0.020

