# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:42:41 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[[1-cyclopentyl-5-[1-(oxetan-3-yl)piperidin-4-yl]pyrazol-3-yl]amino]pyridine-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccnc(Nc2cc(C3CCN(CC3)C4COC4)n(n2)C5CCCC5)c1
#
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
 50F  50F  2-[[1-cyclopentyl-5-[1-(oxetan-3-yl)piperidin-4-yl]pyrazol-3-yl]amino]pyridine-4-carbonitrile  ligand  57  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_50F
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
 50F  C4   C  CR6   0   0.569  -3.7639   0.6614  -0.0658
 50F  C5   C  CR16  0  -0.415  -5.1577   0.6680   0.1409
 50F  C6   C  CR6   0   0.121  -5.8071   1.8824   0.0913
 50F  C11  C  CR15  0  -0.604  -0.6660   0.0869  -0.3714
 50F  C7   C  CSP   0   0.069  -7.2218   1.9321   0.2995
 50F  C10  C  CR5   0   0.482  -1.7543  -0.7759  -0.1523
 50F  C12  C  CR5   0   0.532   0.4322  -0.7535  -0.4042
 50F  N3   N  N     0  -0.459  -3.0817   1.7747  -0.3016
 50F  C1   C  CR16  0  -0.367  -5.0957   3.0609  -0.1577
 50F  C2   C  CR16  0  -0.027  -3.7358   2.9312  -0.3442
 50F  N8   N  NS    0  -0.236  -8.3594   1.9762   0.4688
 50F  N9   N  NH1   0  -0.765  -3.1096  -0.5280  -0.0199
 50F  N13  N  NR5   0  -0.361  -0.0352  -2.0036  -0.2202
 50F  N14  N  N     0  -0.335  -1.3619  -2.0328  -0.0618
 50F  C15  C  CH1   0  -0.093   0.7030  -3.2485  -0.1123
 50F  C16  C  CH2   0  -0.451   0.5223  -3.9209   1.2679
 50F  C17  C  CH2   0  -0.440  -0.3773  -5.1267   1.0100
 50F  C18  C  CH2   0  -0.451   0.0775  -5.5993  -0.3679
 50F  C19  C  CH2   0  -0.450   0.2421  -4.2958  -1.1513
 50F  C20  C  CH1   0  -0.375   1.8804  -0.4145  -0.5498
 50F  C21  C  CH2   0  -0.426   2.5987  -0.4155   0.8051
 50F  C22  C  CH2   0  -0.288   4.0554  -0.0127   0.6475
 50F  N23  N  NT    0  -0.426   4.1722   1.2879   0.0115
 50F  C24  C  CH2   0  -0.290   3.5618   1.2830  -1.3069
 50F  C25  C  CH2   0  -0.422   2.0833   0.9403  -1.2246
 50F  C26  C  C     0  -0.176   5.5466   1.7099  -0.0528
 50F  C27  C  C     0  -0.140   5.7890   3.1829  -0.3999
 50F  O28  O  O     0  -0.514   6.5095   3.3985   0.8199
 50F  C29  C  C     0  -0.140   6.2022   2.0776   1.2824
 50F  H1   H  HCR6  0   0.300  -5.6974  -0.2490   0.3355
 50F  H3   H  HCR6  0   0.286  -5.5834   4.0231  -0.1996
 50F  H4   H  HCR6  0   0.274  -3.1328   3.8098  -0.5413
 50F  H5   H  HNH1  0   0.410  -3.6691  -1.3482   0.1572
 50F  H6   H  HCH1  0   0.275   1.7493  -2.9975  -0.2726
 50F  H7   H  HCH2  0   0.237   1.4974  -4.2589   1.6254
 50F  H8   H  HCH2  0   0.245   0.1256  -3.2299   2.0118
 50F  H9   H  HCH2  0   0.233  -0.2906  -5.8930   1.7812
 50F  H10  H  HCH2  0   0.223  -1.4227  -4.8114   0.9681
 50F  H11  H  HCH2  0   0.222   1.0351  -6.1207  -0.2834
 50F  H12  H  HCH2  0   0.235  -0.6235  -6.2855  -0.8450
 50F  H13  H  HCH2  0   0.243  -0.7200  -3.9955  -1.5689
 50F  H14  H  HCH2  0   0.244   0.9453  -4.3780  -1.9802
 50F  H15  H  HCH1  0   0.253   2.3580  -1.1676  -1.1888
 50F  H16  H  HCH2  0   0.233   2.0952   0.2807   1.4815
 50F  H17  H  HCH2  0   0.242   2.5530  -1.4029   1.2704
 50F  H18  H  HCH2  0   0.246   4.5257   0.0300   1.6327
 50F  H19  H  HCH2  0   0.196   4.5902  -0.7906   0.0738
 50F  H21  H  HCH2  0   0.245   3.6771   2.2734  -1.7536
 50F  H22  H  HCH2  0   0.196   4.0680   0.5712  -1.9833
 50F  H23  H  HCH2  0   0.244   1.6603   0.9300  -2.2307
 50F  H24  H  HCH2  0   0.228   1.5668   1.7218  -0.6609
 50F  H25  H  H     0   0.233   6.1651   1.0262  -0.6559
 50F  H26  H  H     0   0.223   6.3989   3.3784  -1.2851
 50F  H27  H  H     0   0.209   4.8744   3.7827  -0.4552
 50F  H28  H  H     0   0.209   5.5084   2.0848   2.1296
 50F  H29  H  H     0   0.223   7.0960   1.5132   1.5589
 50F  H2   H  HCR5  0   0.269  -0.6790   1.1540  -0.4883

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
 50F  C29  O28  single    1.433  0.020  1.433
 50F  C29  C26  single    1.532  0.020  1.532
 50F  O28  C27  single    1.433  0.020  1.433
 50F  C22  C21  single    1.520  0.020  1.520
 50F  C22  N23  single    1.453  0.020  1.453
 50F  C26  C27  single    1.533  0.020  1.533
 50F  C26  N23  single    1.439  0.020  1.439
 50F  C21  C20  single    1.533  0.020  1.533
 50F  N23  C24  single    1.453  0.020  1.453
 50F  C16  C17  single    1.526  0.020  1.526
 50F  C16  C15  single    1.546  0.020  1.546
 50F  C20  C12  single    1.494  0.020  1.494
 50F  C20  C25  single    1.527  0.020  1.527
 50F  C17  C18  single    1.526  0.020  1.526
 50F  C24  C25  single    1.520  0.020  1.520
 50F  C12  N13  aromatic  1.347  0.020  1.347
 50F  C12  C11  aromatic  1.383  0.020  1.383
 50F  C15  N13  single    1.451  0.020  1.451
 50F  C15  C19  single    1.546  0.020  1.546
 50F  N13  N14  aromatic  1.336  0.020  1.336
 50F  C11  C10  aromatic  1.406  0.020  1.406
 50F  N14  C10  aromatic  1.320  0.020  1.320
 50F  C10  N9   single    1.384  0.020  1.384
 50F  C18  C19  single    1.530  0.020  1.530
 50F  N9   C4   single    1.358  0.020  1.358
 50F  C4   N3   aromatic  1.327  0.020  1.327
 50F  C4   C5   aromatic  1.409  0.020  1.409
 50F  N3   C2   aromatic  1.329  0.020  1.329
 50F  C5   C6   aromatic  1.378  0.020  1.378
 50F  C2   C1   aromatic  1.379  0.020  1.379
 50F  C6   C1   aromatic  1.399  0.020  1.399
 50F  C6   C7   single    1.431  0.020  1.431
 50F  C7   N8   triple    1.151  0.020  1.151
 50F  C5   H1   single    0.930  0.020  1.080
 50F  C11  H2   single    0.930  0.020  1.080
 50F  C1   H3   single    0.930  0.020  1.080
 50F  C2   H4   single    0.930  0.020  1.080
 50F  N9   H5   single    0.860  0.020  1.020
 50F  C15  H6   single    0.970  0.020  1.090
 50F  C16  H7   single    0.970  0.020  1.090
 50F  C16  H8   single    0.970  0.020  1.090
 50F  C17  H9   single    0.970  0.020  1.090
 50F  C17  H10  single    0.970  0.020  1.090
 50F  C18  H11  single    0.970  0.020  1.090
 50F  C18  H12  single    0.970  0.020  1.090
 50F  C19  H13  single    0.970  0.020  1.090
 50F  C19  H14  single    0.970  0.020  1.090
 50F  C20  H15  single    0.970  0.020  1.090
 50F  C21  H16  single    0.970  0.020  1.090
 50F  C21  H17  single    0.970  0.020  1.090
 50F  C22  H18  single    0.970  0.020  1.090
 50F  C22  H19  single    0.970  0.020  1.090
 50F  C24  H21  single    0.970  0.020  1.090
 50F  C24  H22  single    0.970  0.020  1.090
 50F  C25  H23  single    0.970  0.020  1.090
 50F  C25  H24  single    0.970  0.020  1.090
 50F  C26  H25  single    0.970  0.020  1.090
 50F  C27  H26  single    0.970  0.020  1.090
 50F  C27  H27  single    0.970  0.020  1.090
 50F  C29  H28  single    0.970  0.020  1.090
 50F  C29  H29  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
 50F  N9   C4   N3   119.54  3.000
 50F  N3   C4   C5   122.05  3.000
 50F  N9   C4   C5   118.40  3.000
 50F  H1   C5   C6   121.22  3.000
 50F  H1   C5   C4   121.06  3.000
 50F  C6   C5   C4   117.72  3.000
 50F  C1   C6   C7   119.96  3.000
 50F  C7   C6   C5   119.44  3.000
 50F  C1   C6   C5   120.60  3.000
 50F  H2   C11  C12  127.65  3.000
 50F  H2   C11  C10  128.14  3.000
 50F  C12  C11  C10  104.21  3.000
 50F  N8   C7   C6   180.00  3.000
 50F  N14  C10  N9   117.07  3.000
 50F  N9   C10  C11  131.52  3.000
 50F  N14  C10  C11  111.41  3.000
 50F  C20  C12  N13  124.05  3.000
 50F  N13  C12  C11  106.56  3.000
 50F  C20  C12  C11  129.34  3.000
 50F  C2   N3   C4   118.86  3.000
 50F  H3   C1   C2   121.61  3.000
 50F  H3   C1   C6   121.87  3.000
 50F  C2   C1   C6   116.51  3.000
 50F  H4   C2   C1   119.81  3.000
 50F  H4   C2   N3   115.94  3.000
 50F  C1   C2   N3   124.25  3.000
 50F  H5   N9   C10  114.48  3.000
 50F  H5   N9   C4   116.80  3.000
 50F  C10  N9   C4   128.70  3.000
 50F  C15  N13  N14  118.52  3.000
 50F  N14  N13  C12  112.39  3.000
 50F  C15  N13  C12  129.02  3.000
 50F  N13  N14  C10  105.44  3.000
 50F  H6   C15  C19  110.13  3.000
 50F  H6   C15  C16  110.14  3.000
 50F  C19  C15  C16  105.70  3.000
 50F  H6   C15  N13  106.28  3.000
 50F  C19  C15  N13  112.31  3.000
 50F  C16  C15  N13  112.33  3.000
 50F  H8   C16  H7   107.32  3.000
 50F  H8   C16  C17  113.68  3.000
 50F  H7   C16  C17  109.70  3.000
 50F  H8   C16  C15  112.09  3.000
 50F  H7   C16  C15  108.81  3.000
 50F  C17  C16  C15  105.17  3.000
 50F  H10  C17  H9   107.81  3.000
 50F  H10  C17  C18  109.87  3.000
 50F  H9   C17  C18  113.40  3.000
 50F  H10  C17  C16  110.02  3.000
 50F  H9   C17  C16  112.87  3.000
 50F  C18  C17  C16  102.80  3.000
 50F  H12  C18  H11  107.25  3.000
 50F  H12  C18  C19  112.41  3.000
 50F  H11  C18  C19  110.59  3.000
 50F  H12  C18  C17  113.47  3.000
 50F  H11  C18  C17  109.81  3.000
 50F  C19  C18  C17  103.33  3.000
 50F  H14  C19  H13  107.37  3.000
 50F  H14  C19  C18  113.24  3.000
 50F  H13  C19  C18  109.61  3.000
 50F  H14  C19  C15  111.71  3.000
 50F  H13  C19  C15  109.50  3.000
 50F  C18  C19  C15  105.38  3.000
 50F  H15  C20  C25  107.08  3.000
 50F  H15  C20  C21  108.07  3.000
 50F  C25  C20  C21  109.19  3.000
 50F  H15  C20  C12  108.84  3.000
 50F  C25  C20  C12  111.90  3.000
 50F  C21  C20  C12  111.57  3.000
 50F  H17  C21  H16  107.02  3.000
 50F  H17  C21  C22  108.90  3.000
 50F  H16  C21  C22  109.68  3.000
 50F  H17  C21  C20  110.93  3.000
 50F  H16  C21  C20  109.30  3.000
 50F  C22  C21  C20  110.93  3.000
 50F  H19  C22  H18  106.71  3.000
 50F  H19  C22  N23  111.36  3.000
 50F  H18  C22  N23  108.98  3.000
 50F  H19  C22  C21  109.35  3.000
 50F  H18  C22  C21  109.23  3.000
 50F  N23  C22  C21  111.09  3.000
 50F  C26  N23  C24  111.21  3.000
 50F  C24  N23  C22  111.13  3.000
 50F  C26  N23  C22  111.03  3.000
 50F  H22  C24  H21  106.58  3.000
 50F  H22  C24  C25  109.49  3.000
 50F  H21  C24  C25  109.22  3.000
 50F  H22  C24  N23  111.42  3.000
 50F  H21  C24  N23  108.88  3.000
 50F  C25  C24  N23  111.12  3.000
 50F  H24  C25  H23  107.39  3.000
 50F  H24  C25  C24  109.04  3.000
 50F  H23  C25  C24  109.22  3.000
 50F  H24  C25  C20  110.09  3.000
 50F  H23  C25  C20  110.33  3.000
 50F  C24  C25  C20  110.69  3.000
 50F  H25  C26  C29  112.69  3.000
 50F  H25  C26  C27  112.56  3.000
 50F  C29  C26  C27   84.20  3.000
 50F  H25  C26  N23  112.25  3.000
 50F  C27  C26  N23  116.29  3.000
 50F  C29  C26  N23  116.11  3.000
 50F  H27  C27  H26  109.10  3.000
 50F  H27  C27  O28  112.36  3.000
 50F  H26  C27  O28  112.45  3.000
 50F  H27  C27  C26  113.95  3.000
 50F  H26  C27  C26  116.34  3.000
 50F  O28  C27  C26   91.80  3.000
 50F  C29  O28  C27   91.61  3.000
 50F  H29  C29  H28  109.02  3.000
 50F  H29  C29  O28  112.48  3.000
 50F  H28  C29  O28  112.31  3.000
 50F  H29  C29  C26  116.53  3.000
 50F  H28  C29  C26  113.87  3.000
 50F  O28  C29  C26   91.82  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
 50F  CONST_01  C1   C2   N3   C4      0.00   0.0  0
 50F  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 50F  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 50F  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 50F  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 50F  CONST_06  N3   C2   C1   C6      0.00   0.0  0
 50F  CONST_07  N14  N13  C12  C11     0.00   0.0  0
 50F  CONST_08  N13  N14  C10  C11     0.00   0.0  0
 50F  CONST_09  N13  C12  C11  C10     0.00   0.0  0
 50F  CONST_10  C12  N13  N14  C10     0.00   0.0  0
 50F  CONST_11  N14  C10  C11  C12     0.00   0.0  0
 50F  CONST_12  C15  N13  C12  C11   180.00   0.0  0
 50F  CONST_13  C20  C12  C11  C10   180.00   0.0  0
 50F  CONST_14  C15  N13  N14  C10   180.00   0.0  0
 50F  CONST_15  C20  C12  N13  N14   180.00   0.0  0
 50F  CONST_16  C20  C12  N13  C15     0.00   0.0  0
 50F  CONST_17  C7   C6   C5   C4    180.00   0.0  0
 50F  CONST_18  N9   C4   C5   C6    180.00   0.0  0
 50F  CONST_19  C2   C1   C6   C7    180.00   0.0  0
 50F  CONST_20  N9   C10  C11  C12   180.00   0.0  0
 50F  CONST_21  N9   C4   N3   C2    180.00   0.0  0
 50F  CONST_22  N13  N14  C10  N9    180.00   0.0  0
 50F  CONST_23  H4   C2   N3   C4    180.00   0.0  0
 50F  CONST_24  H3   C1   C6   C5    180.00   0.0  0
 50F  CONST_25  H1   C5   C4   N3    180.00   0.0  0
 50F  CONST_26  H2   C11  C12  N13   180.00   0.0  0
 50F  Var_01    C18  C17  C16  C15    35.71  30.0  1
 50F  Var_02    C17  C18  C19  C15    32.74  30.0  1
 50F  Var_03    C19  C18  C17  C16   -42.36  30.0  1
 50F  Var_04    N23  C22  C21  C20    56.71  30.0  1
 50F  Var_05    N23  C24  C25  C20   -57.45  30.0  1
 50F  Var_06    C26  N23  C22  C21   175.98  30.0  1
 50F  Var_07    C25  C24  N23  C22    60.10  30.0  1
 50F  Var_08    C11  C10  N9   C4     -0.21  30.0  2
 50F  Var_09    C10  N9   C4   C5   -177.94  30.0  2
 50F  Var_10    H28  C29  O28  C27  -110.93  30.0  1
 50F  Var_11    H26  C27  O28  C29  -125.42  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
 50F  chir_01  C15  C16  N13  C19  positiv
 50F  chir_02  C20  C25  C12  C21  positiv
 50F  chir_03  C26  N23  C29  C27  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
 50F  plan-1  C11  0.020
 50F  plan-1  C10  0.020
 50F  plan-1  C12  0.020
 50F  plan-1  N9   0.020
 50F  plan-1  N13  0.020
 50F  plan-1  N14  0.020
 50F  plan-1  C15  0.020
 50F  plan-1  C20  0.020
 50F  plan-1  H2   0.020
 50F  plan-2  C4   0.020
 50F  plan-2  C5   0.020
 50F  plan-2  C6   0.020
 50F  plan-2  C7   0.020
 50F  plan-2  N3   0.020
 50F  plan-2  C1   0.020
 50F  plan-2  C2   0.020
 50F  plan-2  N8   0.020
 50F  plan-2  N9   0.020
 50F  plan-2  H1   0.020
 50F  plan-2  H3   0.020
 50F  plan-2  H4   0.020

