# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:36:53 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-[(1S)-2-[(4-cyano-1-methylpiperidin-4-yl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)(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
 Y11  Y11  N-[(1S)-2-[(4-cyano-1-methylpiperidin-4-yl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide  ligand  64  29  .  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_Y11
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
 Y11  C01   C  C     0   0.764   1.4726   1.0757  -0.9721
 Y11  C02   C  CH2   0  -0.311   2.5629   2.8984  -2.1300
 Y11  C03   C  CH2   0  -0.190   3.9916   3.2156  -2.5258
 Y11  C04   C  CH2   0  -0.179   4.7855   2.6413  -0.4262
 Y11  C05   C  CH2   0  -0.335   3.3904   2.2887   0.0609
 Y11  O06   O  O     0  -0.536   0.6047   1.0336  -1.8379
 Y11  O07   O  O2    0  -0.481   4.7611   3.6358  -1.4212
 Y11  N08   N  NT    0  -0.517   2.5552   1.9071  -1.0660
 Y11  N09   N  NH1   0  -0.686   1.4164   0.2365   0.0993
 Y11  C10   C  CH1   0  -0.201   0.2206  -0.5228   0.3259
 Y11  C11   C  CH2   0  -0.451   0.3886  -1.4503   1.5330
 Y11  C12   C  CH1   0  -0.229   1.5589  -2.4295   1.4458
 Y11  C13   C  CH2   0  -0.413   1.5790  -3.3092   2.6973
 Y11  C14   C  CH2   0  -0.433   2.7220  -4.3176   2.6736
 Y11  C15   C  CH2   0  -0.430   2.6685  -5.1819   1.4183
 Y11  C16   C  CH2   0  -0.429   2.6532  -4.3143   0.1643
 Y11  C17   C  CH2   0  -0.428   1.5121  -3.3013   0.1920
 Y11  C18   C  C     0   0.586  -0.9663   0.4065   0.5832
 Y11  O19   O  O     0  -0.470  -0.8383   1.5147   1.0693
 Y11  N20   N  NH1   0  -0.670  -2.1678  -0.1310   0.2956
 Y11  C21   C  CH2   0  -0.415  -3.6444   1.7399  -0.4112
 Y11  C22   C  CH2   0  -0.285  -3.8096   1.2662  -1.8451
 Y11  C23   C  CH2   0  -0.291  -4.7170  -0.8352  -1.1464
 Y11  C24   C  CH2   0  -0.458  -4.5737  -0.4613   0.3212
 Y11  N25   N  NT    0  -0.410  -4.9183   0.3400  -1.9654
 Y11  C26   C  CH3   0  -0.519  -5.1767  -0.0096  -3.3435
 Y11  C27   C  CSP   0   0.147  -3.4801   1.0034   1.9307
 Y11  N28   N  NS    0  -0.260  -3.5953   1.3555   3.0194
 Y11  C29   C  CT    0   0.016  -3.4274   0.5430   0.5319
 Y11  H022  H  HCH2  0   0.265   2.0324   2.5153  -2.9982
 Y11  H031  H  HCH2  0   0.207   4.4438   2.3301  -2.9940
 Y11  H032  H  HCH2  0   0.244   3.9980   4.0242  -3.2574
 Y11  H041  H  HCH2  0   0.246   5.3746   3.0227   0.4088
 Y11  H042  H  HCH2  0   0.209   5.2758   1.7310  -0.7995
 Y11  H051  H  HCH2  0   0.255   3.5039   1.4807   0.7813
 Y11  H052  H  HCH2  0   0.244   2.9500   3.1424   0.5902
 Y11  HN09  H  HNH1  0   0.397   2.0237   0.3713   0.8883
 Y11  H10   H  HCH1  0   0.273   0.0058  -1.1286  -0.5587
 Y11  H111  H  HCH2  0   0.248   0.4938  -0.8439   2.4391
 Y11  H112  H  HCH2  0   0.245  -0.5384  -2.0192   1.6519
 Y11  H12   H  HCH1  0   0.215   2.4960  -1.8579   1.4256
 Y11  H131  H  HCH2  0   0.227   1.6436  -2.6821   3.5913
 Y11  H132  H  HCH2  0   0.207   0.6247  -3.8461   2.7626
 Y11  H141  H  HCH2  0   0.209   3.6784  -3.7838   2.7035
 Y11  H142  H  HCH2  0   0.226   2.6873  -4.9427   3.5693
 Y11  H151  H  HCH2  0   0.226   3.5180  -5.8687   1.3930
 Y11  H152  H  HCH2  0   0.208   1.7660  -5.8024   1.4425
 Y11  H161  H  HCH2  0   0.209   3.6057  -3.7781   0.0884
 Y11  H162  H  HCH2  0   0.227   2.5765  -4.9379  -0.7297
 Y11  H171  H  HCH2  0   0.208   0.5510  -3.8296   0.1607
 Y11  H172  H  HCH2  0   0.233   1.5571  -2.6814  -0.7072
 Y11  HN20  H  HNH1  0   0.411  -2.2035  -1.0556  -0.1044
 Y11  H211  H  HCH2  0   0.269  -2.8094   2.4343  -0.3361
 Y11  H212  H  HCH2  0   0.253  -4.5457   2.2698  -0.0954
 Y11  H221  H  HCH2  0   0.251  -4.0088   2.1359  -2.4749
 Y11  H222  H  HCH2  0   0.203  -2.8633   0.8276  -2.2060
 Y11  H231  H  HCH2  0   0.198  -3.8496  -1.4310  -1.4838
 Y11  H232  H  HCH2  0   0.259  -5.5848  -1.4906  -1.2460
 Y11  H241  H  HCH2  0   0.271  -5.5016  -0.0025   0.6650
 Y11  H242  H  HCH2  0   0.276  -4.4033  -1.3540   0.9261
 Y11  H261  H  HCH3  0   0.235  -6.0444  -0.6682  -3.4045
 Y11  H262  H  HCH3  0   0.235  -5.3985   0.8888  -3.9212
 Y11  H263  H  HCH3  0   0.195  -4.3317  -0.5214  -3.8289
 Y11  H021  H  HCH2  0   0.232   2.0521   3.8140  -1.8049

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
 Y11  C15  C14   single  1.525  0.020  1.525
 Y11  C15  C16   single  1.525  0.020  1.525
 Y11  C14  C13   single  1.524  0.020  1.524
 Y11  C13  C12   single  1.530  0.020  1.530
 Y11  C16  C17   single  1.526  0.020  1.526
 Y11  C17  C12   single  1.528  0.020  1.528
 Y11  C12  C11   single  1.528  0.020  1.528
 Y11  C11  C10   single  1.532  0.020  1.532
 Y11  C27  N28   triple  1.150  0.020  1.150
 Y11  C27  C29   single  1.474  0.020  1.474
 Y11  C10  C18   single  1.529  0.020  1.529
 Y11  C10  N09   single  1.435  0.020  1.435
 Y11  N20  C18   single  1.347  0.020  1.347
 Y11  N20  C29   single  1.448  0.020  1.448
 Y11  C24  C29   single  1.538  0.020  1.538
 Y11  C24  C23   single  1.521  0.020  1.521
 Y11  C18  O19   double  1.217  0.020  1.217
 Y11  C29  C21   single  1.539  0.020  1.539
 Y11  N09  C01   single  1.362  0.020  1.362
 Y11  C23  N25   single  1.447  0.020  1.447
 Y11  C21  C22   single  1.519  0.020  1.519
 Y11  C01  O06   double  1.227  0.020  1.227
 Y11  C01  N08   single  1.368  0.020  1.368
 Y11  N25  C22   single  1.450  0.020  1.450
 Y11  N25  C26   single  1.445  0.020  1.445
 Y11  C05  N08   single  1.454  0.020  1.454
 Y11  C05  C04   single  1.519  0.020  1.519
 Y11  N08  C02   single  1.454  0.020  1.454
 Y11  C04  O07   single  1.407  0.020  1.407
 Y11  C02  C03   single  1.516  0.020  1.516
 Y11  O07  C03   single  1.410  0.020  1.410
 Y11  C02  H021  single  0.970  0.020  1.090
 Y11  C02  H022  single  0.970  0.020  1.090
 Y11  C03  H031  single  0.970  0.020  1.090
 Y11  C03  H032  single  0.970  0.020  1.090
 Y11  C04  H041  single  0.970  0.020  1.090
 Y11  C04  H042  single  0.970  0.020  1.090
 Y11  C05  H051  single  0.970  0.020  1.090
 Y11  C05  H052  single  0.970  0.020  1.090
 Y11  N09  HN09  single  0.890  0.020  1.040
 Y11  C10  H10   single  0.970  0.020  1.090
 Y11  C11  H111  single  0.970  0.020  1.090
 Y11  C11  H112  single  0.970  0.020  1.090
 Y11  C12  H12   single  0.970  0.020  1.090
 Y11  C13  H131  single  0.970  0.020  1.090
 Y11  C13  H132  single  0.970  0.020  1.090
 Y11  C14  H141  single  0.970  0.020  1.090
 Y11  C14  H142  single  0.970  0.020  1.090
 Y11  C15  H151  single  0.970  0.020  1.090
 Y11  C15  H152  single  0.970  0.020  1.090
 Y11  C16  H161  single  0.970  0.020  1.090
 Y11  C16  H162  single  0.970  0.020  1.090
 Y11  C17  H171  single  0.970  0.020  1.090
 Y11  C17  H172  single  0.970  0.020  1.090
 Y11  N20  HN20  single  0.860  0.020  1.020
 Y11  C21  H211  single  0.970  0.020  1.090
 Y11  C21  H212  single  0.970  0.020  1.090
 Y11  C22  H221  single  0.970  0.020  1.090
 Y11  C22  H222  single  0.970  0.020  1.090
 Y11  C23  H231  single  0.970  0.020  1.090
 Y11  C23  H232  single  0.970  0.020  1.090
 Y11  C24  H241  single  0.970  0.020  1.090
 Y11  C24  H242  single  0.970  0.020  1.090
 Y11  C26  H261  single  0.970  0.020  1.090
 Y11  C26  H262  single  0.970  0.020  1.090
 Y11  C26  H263  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
 Y11  N09   C01  N08   117.45  3.000
 Y11  N08   C01  O06   122.15  3.000
 Y11  N09   C01  O06   120.32  3.000
 Y11  H022  C02  H021  107.66  3.000
 Y11  H022  C02  N08   109.97  3.000
 Y11  H021  C02  N08   110.45  3.000
 Y11  H022  C02  C03   108.97  3.000
 Y11  H021  C02  C03   109.96  3.000
 Y11  N08   C02  C03   109.79  3.000
 Y11  H032  C03  H031  108.01  3.000
 Y11  H032  C03  O07   107.54  3.000
 Y11  H031  C03  O07   110.44  3.000
 Y11  H032  C03  C02   109.62  3.000
 Y11  H031  C03  C02   109.29  3.000
 Y11  O07   C03  C02   111.84  3.000
 Y11  H042  C04  H041  107.97  3.000
 Y11  H042  C04  O07   110.66  3.000
 Y11  H041  C04  O07   107.67  3.000
 Y11  H042  C04  C05   109.05  3.000
 Y11  H041  C04  C05   109.37  3.000
 Y11  O07   C04  C05   112.01  3.000
 Y11  H052  C05  H051  107.47  3.000
 Y11  H052  C05  N08   110.35  3.000
 Y11  H051  C05  N08   112.22  3.000
 Y11  H052  C05  C04   110.05  3.000
 Y11  H051  C05  C04   106.78  3.000
 Y11  N08   C05  C04   109.88  3.000
 Y11  C04   O07  C03   110.66  3.000
 Y11  C05   N08  C02   112.66  3.000
 Y11  C02   N08  C01   117.95  3.000
 Y11  C05   N08  C01   124.12  3.000
 Y11  HN09  N09  C10   116.79  3.000
 Y11  HN09  N09  C01   120.67  3.000
 Y11  C10   N09  C01   119.00  3.000
 Y11  H10   C10  C18   108.68  3.000
 Y11  H10   C10  C11   108.89  3.000
 Y11  C18   C10  C11   108.69  3.000
 Y11  H10   C10  N09   109.22  3.000
 Y11  C18   C10  N09   110.60  3.000
 Y11  C11   C10  N09   110.71  3.000
 Y11  H112  C11  H111  106.22  3.000
 Y11  H112  C11  C12   108.77  3.000
 Y11  H111  C11  C12   109.17  3.000
 Y11  H112  C11  C10   107.91  3.000
 Y11  H111  C11  C10   109.11  3.000
 Y11  C12   C11  C10   115.28  3.000
 Y11  H12   C12  C17   107.94  3.000
 Y11  H12   C12  C13   107.66  3.000
 Y11  C17   C12  C13   110.10  3.000
 Y11  H12   C12  C11   108.72  3.000
 Y11  C17   C12  C11   112.89  3.000
 Y11  C13   C12  C11   109.38  3.000
 Y11  H132  C13  H131  106.46  3.000
 Y11  H132  C13  C14   109.24  3.000
 Y11  H131  C13  C14   110.35  3.000
 Y11  H132  C13  C12   108.58  3.000
 Y11  H131  C13  C12   109.85  3.000
 Y11  C14   C13  C12   112.18  3.000
 Y11  H142  C14  H141  106.50  3.000
 Y11  H142  C14  C15   110.45  3.000
 Y11  H141  C14  C15   109.22  3.000
 Y11  H142  C14  C13   109.99  3.000
 Y11  H141  C14  C13   109.38  3.000
 Y11  C15   C14  C13   111.19  3.000
 Y11  H152  C15  H151  106.55  3.000
 Y11  H152  C15  C16   109.40  3.000
 Y11  H151  C15  C16   110.27  3.000
 Y11  H152  C15  C14   109.38  3.000
 Y11  H151  C15  C14   110.36  3.000
 Y11  C16   C15  C14   110.78  3.000
 Y11  H162  C16  H161  106.47  3.000
 Y11  H162  C16  C17   109.95  3.000
 Y11  H161  C16  C17   109.05  3.000
 Y11  H162  C16  C15   110.41  3.000
 Y11  H161  C16  C15   109.07  3.000
 Y11  C17   C16  C15   111.73  3.000
 Y11  H172  C17  H171  106.60  3.000
 Y11  H172  C17  C16   109.32  3.000
 Y11  H171  C17  C16   109.57  3.000
 Y11  H172  C17  C12   110.50  3.000
 Y11  H171  C17  C12   108.96  3.000
 Y11  C16   C17  C12   111.76  3.000
 Y11  N20   C18  O19   122.85  3.000
 Y11  O19   C18  C10   122.62  3.000
 Y11  N20   C18  C10   114.44  3.000
 Y11  HN20  N20  C29   117.44  3.000
 Y11  HN20  N20  C18   118.83  3.000
 Y11  C29   N20  C18   123.73  3.000
 Y11  H212  C21  H211  107.67  3.000
 Y11  H212  C21  C29   108.45  3.000
 Y11  H211  C21  C29   110.22  3.000
 Y11  H212  C21  C22   109.54  3.000
 Y11  H211  C21  C22   110.33  3.000
 Y11  C29   C21  C22   110.56  3.000
 Y11  H222  C22  H221  106.52  3.000
 Y11  H222  C22  N25   112.01  3.000
 Y11  H221  C22  N25   108.75  3.000
 Y11  H222  C22  C21   109.83  3.000
 Y11  H221  C22  C21   108.41  3.000
 Y11  N25   C22  C21   111.14  3.000
 Y11  H232  C23  H231  105.80  3.000
 Y11  H232  C23  N25   108.99  3.000
 Y11  H231  C23  N25   111.99  3.000
 Y11  H232  C23  C24   108.08  3.000
 Y11  H231  C23  C24   110.68  3.000
 Y11  N25   C23  C24   111.08  3.000
 Y11  H242  C24  H241  107.58  3.000
 Y11  H242  C24  C29   109.98  3.000
 Y11  H241  C24  C29   108.43  3.000
 Y11  H242  C24  C23   110.38  3.000
 Y11  H241  C24  C23   109.10  3.000
 Y11  C29   C24  C23   111.27  3.000
 Y11  C26   N25  C23   111.61  3.000
 Y11  C26   N25  C22   111.74  3.000
 Y11  C23   N25  C22   111.45  3.000
 Y11  H263  C26  H262  107.78  3.000
 Y11  H263  C26  H261  107.78  3.000
 Y11  H262  C26  H261  107.81  3.000
 Y11  H263  C26  N25   113.32  3.000
 Y11  H262  C26  N25   110.00  3.000
 Y11  H261  C26  N25   109.98  3.000
 Y11  C29   C27  N28   180.00  3.000
 Y11  C27   C29  C24   107.89  3.000
 Y11  C24   C29  C21   108.58  3.000
 Y11  C27   C29  C21   109.49  3.000
 Y11  C21   C29  N20   112.62  3.000
 Y11  C24   C29  N20   108.78  3.000
 Y11  C27   C29  N20   109.36  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
 Y11  CONST_01  O06   C01  N08  C02     0.00   0.0  0
 Y11  CONST_03  N09   C01  N08  C02   180.00   0.0  0
 Y11  CONST_05  C29   N20  C18  C10   180.00   0.0  0
 Y11  CONST_06  C29   N20  C18  O19     0.00   0.0  0
 Y11  CONST_07  C10   N09  C01  N08   180.00   0.0  0
 Y11  CONST_08  HN09  N09  C01  N08     0.00   0.0  0
 Y11  CONST_09  C10   N09  C01  O06     0.00   0.0  0
 Y11  CONST_10  HN20  N20  C18  C10     0.00   0.0  0
 Y11  Var_01    C04   C05  N08  C02   -52.47  30.0  1
 Y11  Var_02    C05   N08  C02  C03    52.84  30.0  1
 Y11  Var_03    C05   C04  O07  C03   -58.65  30.0  1
 Y11  Var_04    N08   C05  C04  O07    55.00  30.0  1
 Y11  Var_05    N08   C02  C03  O07   -55.63  30.0  1
 Y11  Var_06    C15   C14  C13  C12   -55.88  30.0  1
 Y11  Var_07    C15   C16  C17  C12    55.57  30.0  1
 Y11  Var_08    C16   C15  C14  C13    55.06  30.0  1
 Y11  Var_09    C17   C16  C15  C14   -55.16  30.0  1
 Y11  Var_10    C23   N25  C22  C21   -60.45  30.0  1
 Y11  Var_11    C24   C23  N25  C22    59.51  30.0  1
 Y11  Var_12    C29   C24  C23  N25   -56.53  30.0  1
 Y11  Var_13    C29   C21  C22  N25    57.84  30.0  1
 Y11  Var_14    H261  C26  N25  C22  -177.29  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
 Y11  chir_01  C10  C11  C18  N09  negativ
 Y11  chir_02  C12  C11  C17  C13  positiv
 Y11  chir_03  C29  C27  C24  C21  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
 Y11  plan-1  C01   0.020
 Y11  plan-1  C02   0.020
 Y11  plan-1  C05   0.020
 Y11  plan-1  O06   0.020
 Y11  plan-1  N08   0.020
 Y11  plan-1  N09   0.020
 Y11  plan-1  C10   0.020
 Y11  plan-1  HN09  0.020
 Y11  plan-2  C10   0.020
 Y11  plan-2  C18   0.020
 Y11  plan-2  O19   0.020
 Y11  plan-2  N20   0.020
 Y11  plan-2  C29   0.020
 Y11  plan-2  HN20  0.020

