# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 03:05:06 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C#N)c(S[C@@H](C(N)=O)c2ccccc2)nc(N3CCC(N)CC3)c1C#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
 UXM  UXM  (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide  ligand  54  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UXM
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
 UXM  C10  C  C     0   0.569  -43.5642  -12.9151  27.0175
 UXM  C13  C  CR6   0   0.146  -41.2479  -12.0146  26.8146
 UXM  C01  C  CH3   0  -0.659  -45.1203   -6.7891  31.6394
 UXM  C03  C  CR6   0   0.341  -45.6759   -8.7579  30.2043
 UXM  C04  C  CR6   0  -0.103  -44.8239   -8.8523  29.1048
 UXM  C05  C  CSP   0  -0.030  -44.4542   -7.7090  28.3546
 UXM  C07  C  CR6   0   0.121  -44.2724  -10.1137  28.8009
 UXM  C09  C  CH1   0  -0.585  -42.5459  -11.9230  27.5808
 UXM  C14  C  CR16  0  -0.304  -40.0633  -12.2795  27.4930
 UXM  C15  C  CR16  0  -0.237  -38.8627  -12.3665  26.8018
 UXM  C16  C  CR16  0  -0.258  -38.8373  -12.1844  25.4259
 UXM  C17  C  CR16  0  -0.237  -40.0168  -11.9153  24.7440
 UXM  C18  C  CR16  0  -0.268  -41.2173  -11.8301  25.4340
 UXM  C20  C  CR6   0   0.607  -45.5431  -11.1910  30.3842
 UXM  C22  C  CH2   0  -0.316  -47.2093  -12.5395  31.6011
 UXM  C23  C  CH2   0  -0.490  -47.8534  -13.8873  31.2781
 UXM  C24  C  CH1   0  -0.049  -47.7217  -14.1891  29.7925
 UXM  C26  C  CH2   0  -0.455  -46.2366  -14.3755  29.4531
 UXM  C27  C  CH2   0  -0.343  -45.3445  -13.6231  30.4380
 UXM  C28  C  CR6   0  -0.219  -46.0018   -9.9315  30.8855
 UXM  C29  C  CSP   0   0.016  -46.6577   -9.7991  32.1365
 UXM  N06  N  NS    0  -0.237  -44.1487   -6.7877  27.7300
 UXM  N11  N  NH2   0  -0.799  -44.5144  -12.4376  26.2110
 UXM  N19  N  N     0  -0.492  -44.6297  -11.2139  29.3997
 UXM  N21  N  NT    0  -0.479  -45.9660  -12.3690  30.8480
 UXM  N25  N  NH2   0  -0.800  -48.4720  -15.3863  29.4467
 UXM  N30  N  NS    0  -0.248  -47.1466   -9.6343  33.1691
 UXM  O12  O  O     0  -0.471  -43.4231  -14.0955  27.2891
 UXM  S08  S  S2    0   0.115  -43.0289  -10.1690  27.5643
 UXM  H1   H  HCH3  0   0.250  -45.4817   -5.8199  31.9802
 UXM  H2   H  HCH3  0   0.241  -44.9554   -7.4132  32.5170
 UXM  H3   H  HCH3  0   0.240  -44.1599   -6.6351  31.1479
 UXM  H4   H  HCH2  0   0.277  -46.3023   -6.7571  29.8357
 UXM  H5   H  HCH2  0   0.276  -47.1052   -7.5113  31.1884
 UXM  H6   H  HCH1  0   0.347  -42.3749  -12.2048  28.6204
 UXM  H7   H  HCR6  0   0.261  -40.0796  -12.4212  28.5667
 UXM  H8   H  HCR6  0   0.260  -37.9479  -12.5780  27.3399
 UXM  H9   H  HCR6  0   0.260  -37.9017  -12.2523  24.8863
 UXM  H10  H  HCR6  0   0.261  -40.0035  -11.7727  23.6714
 UXM  H11  H  HCR6  0   0.260  -42.1308  -11.6248  24.8887
 UXM  H12  H  HCH2  0   0.264  -47.9038  -11.7518  31.3062
 UXM  H13  H  HCH2  0   0.268  -47.0349  -12.4502  32.6751
 UXM  H14  H  HCH2  0   0.261  -48.9027  -13.8300  31.5757
 UXM  H15  H  HCH2  0   0.241  -47.4064  -14.6949  31.8632
 UXM  H16  H  HCH1  0   0.206  -48.0840  -13.3018  29.2489
 UXM  H17  H  HCH2  0   0.234  -45.9848  -15.4375  29.5092
 UXM  H18  H  HCH2  0   0.246  -46.0380  -14.0488  28.4316
 UXM  H19  H  HCH2  0   0.266  -45.1947  -14.2139  31.3440
 UXM  H20  H  HCH2  0   0.287  -44.3635  -13.4317  30.0181
 UXM  H21  H  HNH2  0   0.409  -45.1810  -13.0674  25.7935
 UXM  H22  H  HNH2  0   0.413  -44.6079  -11.4566  26.0058
 UXM  H23  H  HNH2  0   0.342  -49.4632  -15.2009  29.5465
 UXM  H24  H  HNH2  0   0.344  -48.3347  -15.5957  28.4648
 UXM  C02  C  CH2   0  -0.550  -46.1410   -7.4183  30.6885

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
 UXM  C17  C16  aromatic  1.389  0.020  1.389
 UXM  C17  C18  aromatic  1.387  0.020  1.387
 UXM  C16  C15  aromatic  1.388  0.020  1.388
 UXM  C18  C13  aromatic  1.393  0.020  1.393
 UXM  O12  C10  double    1.219  0.020  1.219
 UXM  C15  C14  aromatic  1.388  0.020  1.388
 UXM  C13  C14  aromatic  1.391  0.020  1.391
 UXM  C13  C09  single    1.510  0.020  1.510
 UXM  N11  C10  single    1.335  0.020  1.335
 UXM  C10  C09  single    1.529  0.020  1.529
 UXM  C09  S08  single    1.819  0.020  1.819
 UXM  S08  C07  single    1.755  0.020  1.755
 UXM  N06  C05  triple    1.154  0.020  1.154
 UXM  C05  C04  single    1.417  0.020  1.417
 UXM  C07  C04  aromatic  1.410  0.020  1.410
 UXM  C07  N19  aromatic  1.303  0.020  1.303
 UXM  C04  C03  aromatic  1.394  0.020  1.394
 UXM  N25  C24  single    1.455  0.020  1.455
 UXM  N19  C20  aromatic  1.343  0.020  1.343
 UXM  C24  C26  single    1.535  0.020  1.535
 UXM  C24  C23  single    1.522  0.020  1.522
 UXM  C26  C27  single    1.527  0.020  1.527
 UXM  C03  C02  single    1.498  0.020  1.498
 UXM  C03  C28  aromatic  1.396  0.020  1.396
 UXM  C20  C28  aromatic  1.431  0.020  1.431
 UXM  C20  N21  single    1.335  0.020  1.335
 UXM  C23  C22  single    1.528  0.020  1.528
 UXM  C27  N21  single    1.459  0.020  1.459
 UXM  C02  C01  single    1.530  0.020  1.530
 UXM  C22  N21  single    1.464  0.020  1.464
 UXM  C28  C29  single    1.419  0.020  1.419
 UXM  C29  N30  triple    1.154  0.020  1.154
 UXM  C01  H1   single    0.970  0.020  1.090
 UXM  C01  H2   single    0.970  0.020  1.090
 UXM  C01  H3   single    0.970  0.020  1.090
 UXM  C02  H4   single    0.970  0.020  1.090
 UXM  C02  H5   single    0.970  0.020  1.090
 UXM  C09  H6   single    0.970  0.020  1.090
 UXM  C14  H7   single    0.930  0.020  1.080
 UXM  C15  H8   single    0.930  0.020  1.080
 UXM  C16  H9   single    0.930  0.020  1.080
 UXM  C17  H10  single    0.930  0.020  1.080
 UXM  C18  H11  single    0.930  0.020  1.080
 UXM  C22  H12  single    0.970  0.020  1.090
 UXM  C22  H13  single    0.970  0.020  1.090
 UXM  C23  H14  single    0.970  0.020  1.090
 UXM  C23  H15  single    0.970  0.020  1.090
 UXM  C24  H16  single    0.970  0.020  1.090
 UXM  C26  H17  single    0.970  0.020  1.090
 UXM  C26  H18  single    0.970  0.020  1.090
 UXM  C27  H19  single    0.970  0.020  1.090
 UXM  C27  H20  single    0.970  0.020  1.090
 UXM  N11  H21  single    0.860  0.020  1.020
 UXM  N11  H22  single    0.860  0.020  1.020
 UXM  N25  H23  single    0.890  0.020  1.040
 UXM  N25  H24  single    0.890  0.020  1.040

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
 UXM  O12  C10  N11  124.28  3.000
 UXM  N11  C10  C09  117.68  3.000
 UXM  O12  C10  C09  117.96  3.000
 UXM  C18  C13  C14  119.33  3.000
 UXM  C14  C13  C09  119.76  3.000
 UXM  C18  C13  C09  120.91  3.000
 UXM  H3   C01  H2   108.11  3.000
 UXM  H3   C01  H1   107.92  3.000
 UXM  H2   C01  H1   107.94  3.000
 UXM  H3   C01  C02  111.45  3.000
 UXM  H2   C01  C02  111.47  3.000
 UXM  H1   C01  C02  109.82  3.000
 UXM  C28  C03  C04  118.08  3.000
 UXM  C28  C03  C02  121.44  3.000
 UXM  C04  C03  C02  120.33  3.000
 UXM  C07  C04  C05  120.39  3.000
 UXM  C07  C04  C03  118.01  3.000
 UXM  C05  C04  C03  121.50  3.000
 UXM  N06  C05  C04  180.00  3.000
 UXM  S08  C07  N19  119.46  3.000
 UXM  N19  C07  C04  123.32  3.000
 UXM  S08  C07  C04  117.21  3.000
 UXM  H6   C09  S08  107.42  3.000
 UXM  H6   C09  C13  109.46  3.000
 UXM  S08  C09  C13  106.38  3.000
 UXM  H6   C09  C10  106.74  3.000
 UXM  S08  C09  C10  116.45  3.000
 UXM  C13  C09  C10  110.25  3.000
 UXM  H7   C14  C15  119.90  3.000
 UXM  H7   C14  C13  119.72  3.000
 UXM  C15  C14  C13  120.39  3.000
 UXM  H8   C15  C16  120.20  3.000
 UXM  H8   C15  C14  119.72  3.000
 UXM  C16  C15  C14  120.08  3.000
 UXM  H9   C16  C17  120.10  3.000
 UXM  H9   C16  C15  120.12  3.000
 UXM  C17  C16  C15  119.77  3.000
 UXM  H10  C17  C18  119.71  3.000
 UXM  H10  C17  C16  120.12  3.000
 UXM  C18  C17  C16  120.17  3.000
 UXM  H11  C18  C17  119.40  3.000
 UXM  H11  C18  C13  120.35  3.000
 UXM  C17  C18  C13  120.25  3.000
 UXM  N21  C20  N19  117.07  3.000
 UXM  N21  C20  C28  123.60  3.000
 UXM  N19  C20  C28  119.33  3.000
 UXM  H13  C22  H12  107.98  3.000
 UXM  H13  C22  N21  111.16  3.000
 UXM  H12  C22  N21  108.52  3.000
 UXM  H13  C22  C23  110.33  3.000
 UXM  H12  C22  C23  108.14  3.000
 UXM  N21  C22  C23  110.61  3.000
 UXM  H15  C23  H14  106.61  3.000
 UXM  H15  C23  C24  109.92  3.000
 UXM  H14  C23  C24  111.07  3.000
 UXM  H15  C23  C22  111.48  3.000
 UXM  H14  C23  C22  107.52  3.000
 UXM  C24  C23  C22  110.17  3.000
 UXM  H16  C24  N25  112.08  3.000
 UXM  H16  C24  C26  107.87  3.000
 UXM  N25  C24  C26  110.28  3.000
 UXM  H16  C24  C23  107.07  3.000
 UXM  C26  C24  C23  108.89  3.000
 UXM  N25  C24  C23  110.53  3.000
 UXM  H18  C26  H17  107.29  3.000
 UXM  H18  C26  C27  110.49  3.000
 UXM  H17  C26  C27  108.13  3.000
 UXM  H18  C26  C24  110.29  3.000
 UXM  H17  C26  C24  109.24  3.000
 UXM  C27  C26  C24  111.27  3.000
 UXM  H20  C27  H19  107.02  3.000
 UXM  H20  C27  N21  110.04  3.000
 UXM  H19  C27  N21  106.88  3.000
 UXM  H20  C27  C26  111.46  3.000
 UXM  H19  C27  C26  110.41  3.000
 UXM  N21  C27  C26  110.86  3.000
 UXM  C29  C28  C20  122.63  3.000
 UXM  C29  C28  C03  117.38  3.000
 UXM  C20  C28  C03  119.62  3.000
 UXM  N30  C29  C28  180.00  3.000
 UXM  H22  N11  H21  117.59  3.000
 UXM  H22  N11  C10  122.54  3.000
 UXM  H21  N11  C10  119.86  3.000
 UXM  C20  N19  C07  120.60  3.000
 UXM  C27  N21  C22  113.98  3.000
 UXM  C22  N21  C20  123.42  3.000
 UXM  C27  N21  C20  121.75  3.000
 UXM  H24  N25  H23  105.42  3.000
 UXM  H24  N25  C24  109.30  3.000
 UXM  H23  N25  C24  109.30  3.000
 UXM  C09  S08  C07  102.25  3.000
 UXM  H5   C02  H4   106.22  3.000
 UXM  H5   C02  C03  110.27  3.000
 UXM  H4   C02  C03  109.58  3.000
 UXM  H5   C02  C01  109.88  3.000
 UXM  H4   C02  C01  109.58  3.000
 UXM  C03  C02  C01  111.18  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
 UXM  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 UXM  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 UXM  CONST_03  N19  C07  C04  C03     0.00   0.0  0
 UXM  CONST_04  N19  C20  C28  C03     0.00   0.0  0
 UXM  CONST_05  C20  N19  C07  C04     0.00   0.0  0
 UXM  CONST_06  C20  C28  C03  C04     0.00   0.0  0
 UXM  CONST_07  C28  C03  C04  C07     0.00   0.0  0
 UXM  CONST_08  C28  C20  N19  C07     0.00   0.0  0
 UXM  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 UXM  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 UXM  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 UXM  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 UXM  CONST_13  N21  C20  C28  C03   180.00   0.0  0
 UXM  CONST_14  N21  C20  N19  C07   180.00   0.0  0
 UXM  CONST_15  C07  C04  C03  C02   180.00   0.0  0
 UXM  CONST_16  C20  C28  C03  C02   180.00   0.0  0
 UXM  CONST_17  S08  C07  C04  C03   180.00   0.0  0
 UXM  CONST_18  C29  C28  C03  C04   180.00   0.0  0
 UXM  CONST_19  N19  C07  C04  C05   180.00   0.0  0
 UXM  CONST_20  C28  C03  C04  C05   180.00   0.0  0
 UXM  CONST_21  C17  C18  C13  C09   180.00   0.0  0
 UXM  CONST_22  C15  C14  C13  C09   180.00   0.0  0
 UXM  CONST_23  S08  C07  N19  C20   180.00   0.0  0
 UXM  CONST_26  H10  C17  C18  C13   180.00   0.0  0
 UXM  CONST_27  H8   C15  C14  C13   180.00   0.0  0
 UXM  CONST_28  H9   C16  C15  C14   180.00   0.0  0
 UXM  CONST_29  H11  C18  C13  C14   180.00   0.0  0
 UXM  CONST_30  H7   C14  C15  C16   180.00   0.0  0
 UXM  CONST_31  H21  N11  C10  C09   180.00   0.0  0
 UXM  CONST_32  H22  N11  C10  C09     0.00   0.0  0
 UXM  Var_01    C26  C27  N21  C20  -105.21  30.0  1
 UXM  Var_02    C23  C22  N21  C20   145.59  30.0  1
 UXM  Var_03    N19  C20  N21  C22  -160.88  30.0  1
 UXM  Var_04    N21  C27  C26  C24   -35.59  30.0  1
 UXM  Var_05    N21  C22  C23  C24   -39.89  30.0  1
 UXM  Var_06    C04  C03  C02  C01   -84.86  30.0  2
 UXM  Var_07    N19  C07  S08  C09    -2.68  30.0  2
 UXM  Var_08    H1   C01  C02  C03  -179.79  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
 UXM  chir_01  C09  C13  C10  S08  positiv
 UXM  chir_02  C24  N25  C26  C23  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
 UXM  plan-1  C03  0.020
 UXM  plan-1  C04  0.020
 UXM  plan-1  C05  0.020
 UXM  plan-1  C07  0.020
 UXM  plan-1  C20  0.020
 UXM  plan-1  C28  0.020
 UXM  plan-1  C29  0.020
 UXM  plan-1  N06  0.020
 UXM  plan-1  N19  0.020
 UXM  plan-1  N21  0.020
 UXM  plan-1  N30  0.020
 UXM  plan-1  S08  0.020
 UXM  plan-1  C02  0.020
 UXM  plan-2  C13  0.020
 UXM  plan-2  C09  0.020
 UXM  plan-2  C14  0.020
 UXM  plan-2  C15  0.020
 UXM  plan-2  C16  0.020
 UXM  plan-2  C17  0.020
 UXM  plan-2  C18  0.020
 UXM  plan-2  H7   0.020
 UXM  plan-2  H8   0.020
 UXM  plan-2  H9   0.020
 UXM  plan-2  H10  0.020
 UXM  plan-2  H11  0.020
 UXM  plan-3  C10  0.020
 UXM  plan-3  C09  0.020
 UXM  plan-3  N11  0.020
 UXM  plan-3  O12  0.020
 UXM  plan-3  H21  0.020
 UXM  plan-3  H22  0.020

