# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:59:28 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc(NC(=O)Cc2ccccc2)n1)N3CC[C@@](C#N)(C4CC4)C3=O
#
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
 JE6  JE6  "~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide"
  ligand  50  28  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JE6
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
 JE6  C4   C  CR16  0  -0.493   2.6000  18.0138  -11.1643
 JE6  C14  C  CH2   0  -0.313   1.4116  20.0548   -9.5928
 JE6  C5   C  CR6   0   0.494   3.0938  17.0739  -12.0597
 JE6  C6   C  C     0   0.537   1.5799  15.1729  -11.5056
 JE6  C11  C  CR16  0  -0.264  -0.5282  13.8687  -15.8823
 JE6  C7   C  CH2   0  -0.650   1.2989  13.7610  -11.9880
 JE6  C8   C  CR6   0   0.112   0.6597  13.7806  -13.3545
 JE6  C9   C  CR16  0  -0.313   1.3815  13.4225  -14.4889
 JE6  C10  C  CR16  0  -0.237   0.7924  13.4653  -15.7464
 JE6  C12  C  CR16  0  -0.238  -1.2567  14.2275  -14.7544
 JE6  C13  C  CR16  0  -0.281  -0.6664  14.1841  -13.4999
 JE6  C3   C  CR6   0   0.506   3.1921  19.2763  -11.1544
 JE6  C1   C  CR6   0   0.244   4.6498  18.5232  -12.8910
 JE6  C15  C  CH2   0  -0.438   1.1362  21.4215   -8.9809
 JE6  C16  C  CT    0  -0.366   2.5438  21.9505   -8.6868
 JE6  C17  C  CSP   0   0.138   2.6300  23.4001   -8.7833
 JE6  C18  C  CH1   0  -0.208   3.0783  21.4476   -7.3503
 JE6  C19  C  CH2   0  -0.488   2.8792  22.2194   -6.0859
 JE6  C2   C  CR16  0  -0.395   4.2343  19.5393  -12.0391
 JE6  C20  C  CH2   0  -0.483   4.2510  22.0810   -6.6765
 JE6  C21  C  C     0   0.623   3.3888  21.3134   -9.7996
 JE6  O1   O  O     0  -0.418   4.4807  21.7008  -10.1368
 JE6  N    N  NH1   0  -0.705   2.6012  15.7779  -12.1727
 JE6  C    C  CH3   0  -0.728   5.7666  18.7714  -13.8595
 JE6  O    O  O     0  -0.445   0.9317  15.7053  -10.6264
 JE6  N1   N  N     0  -0.475   4.0949  17.3180  -12.8983
 JE6  N2   N  NT    0  -0.584   2.6992  20.2321  -10.2627
 JE6  N3   N  NS    0  -0.238   2.6845  24.5458   -8.8599
 JE6  H1   H  HCR6  0   0.310   1.7969  17.7593  -10.4952
 JE6  H2   H  HCH2  0   0.289   0.6450  19.7725  -10.3129
 JE6  H3   H  HCH2  0   0.273   1.4757  19.2725   -8.8334
 JE6  H5   H  HCH2  0   0.290   0.6387  13.2872  -11.2619
 JE6  H6   H  HCH2  0   0.293   2.2273  13.1857  -12.0149
 JE6  H7   H  HCR6  0   0.255   2.4117  13.0998  -14.3898
 JE6  H8   H  HCR6  0   0.256   1.3662  13.1798  -16.6187
 JE6  H9   H  HCR6  0   0.256  -2.2886  14.5393  -14.8520
 JE6  H10  H  HCR6  0   0.253  -1.2419  14.4617  -12.6245
 JE6  H11  H  HCH2  0   0.288   0.6313  22.0590   -9.7070
 JE6  H12  H  HCH2  0   0.291   0.5219  21.3647   -8.0848
 JE6  H13  H  HCH1  0   0.294   3.0032  20.3684   -7.2639
 JE6  H14  H  HCH2  0   0.260   2.4021  23.1905   -6.1377
 JE6  H15  H  HCH2  0   0.268   2.6384  21.6569   -5.1938
 JE6  H16  H  HCR6  0   0.280   4.7168  20.5009  -12.0900
 JE6  H17  H  HCH2  0   0.267   4.9622  21.4262   -6.1909
 JE6  H18  H  HCH2  0   0.260   4.6970  22.9598   -7.1258
 JE6  H19  H  HNH1  0   0.411   3.0824  15.2346  -12.8761
 JE6  H20  H  HCH3  0   0.250   6.0190  17.8628  -14.4016
 JE6  H21  H  HCH3  0   0.254   5.4895  19.5367  -14.5862
 JE6  H22  H  HCH3  0   0.252   6.6592  19.1277  -13.3442
 JE6  H4   H  HCR6  0   0.256  -0.9904  13.8998  -16.8604

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
 JE6  C11  C10  aromatic  1.388  0.020  1.388
 JE6  C11  C12  aromatic  1.390  0.020  1.390
 JE6  C10  C9   aromatic  1.389  0.020  1.389
 JE6  C12  C13  aromatic  1.387  0.020  1.387
 JE6  C9   C8   aromatic  1.391  0.020  1.391
 JE6  C13  C8   aromatic  1.394  0.020  1.394
 JE6  C    C1   single    1.499  0.020  1.499
 JE6  C8   C7   single    1.509  0.020  1.509
 JE6  N1   C1   aromatic  1.327  0.020  1.327
 JE6  N1   C5   aromatic  1.329  0.020  1.329
 JE6  C1   C2   aromatic  1.390  0.020  1.390
 JE6  N    C5   single    1.391  0.020  1.391
 JE6  N    C6   single    1.362  0.020  1.362
 JE6  C5   C4   aromatic  1.389  0.020  1.389
 JE6  C7   C6   single    1.518  0.020  1.518
 JE6  C6   O    double    1.215  0.020  1.215
 JE6  C2   C3   aromatic  1.392  0.020  1.392
 JE6  C4   C3   aromatic  1.394  0.020  1.394
 JE6  C3   N2   single    1.397  0.020  1.397
 JE6  O1   C21  double    1.207  0.020  1.207
 JE6  N2   C21  single    1.363  0.020  1.363
 JE6  N2   C14  single    1.462  0.020  1.462
 JE6  C21  C16  single    1.536  0.020  1.536
 JE6  C14  C15  single    1.523  0.020  1.523
 JE6  C15  C16  single    1.532  0.020  1.532
 JE6  C16  C17  single    1.455  0.020  1.455
 JE6  C16  C18  single    1.525  0.020  1.525
 JE6  C17  N3   triple    1.150  0.020  1.150
 JE6  C18  C20  single    1.493  0.020  1.493
 JE6  C18  C19  single    1.495  0.020  1.495
 JE6  C20  C19  single    1.500  0.020  1.500
 JE6  C4   H1   single    0.930  0.020  1.080
 JE6  C14  H2   single    0.970  0.020  1.090
 JE6  C14  H3   single    0.970  0.020  1.090
 JE6  C11  H4   single    0.930  0.020  1.080
 JE6  C7   H5   single    0.970  0.020  1.090
 JE6  C7   H6   single    0.970  0.020  1.090
 JE6  C9   H7   single    0.930  0.020  1.080
 JE6  C10  H8   single    0.930  0.020  1.080
 JE6  C12  H9   single    0.930  0.020  1.080
 JE6  C13  H10  single    0.930  0.020  1.080
 JE6  C15  H11  single    0.970  0.020  1.090
 JE6  C15  H12  single    0.970  0.020  1.090
 JE6  C18  H13  single    0.970  0.020  1.090
 JE6  C19  H14  single    0.970  0.020  1.090
 JE6  C19  H15  single    0.970  0.020  1.090
 JE6  C2   H16  single    0.930  0.020  1.080
 JE6  C20  H17  single    0.970  0.020  1.090
 JE6  C20  H18  single    0.970  0.020  1.090
 JE6  N    H19  single    0.860  0.020  1.020
 JE6  C    H20  single    0.970  0.020  1.090
 JE6  C    H21  single    0.970  0.020  1.090
 JE6  C    H22  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
 JE6  H1   C4   C3   121.78  3.000
 JE6  H1   C4   C5   120.42  3.000
 JE6  C3   C4   C5   117.80  3.000
 JE6  H3   C14  H2   108.39  3.000
 JE6  H3   C14  N2   110.72  3.000
 JE6  H2   C14  N2   110.39  3.000
 JE6  H3   C14  C15  111.97  3.000
 JE6  H2   C14  C15  111.79  3.000
 JE6  N2   C14  C15  103.56  3.000
 JE6  N1   C5   N    112.76  3.000
 JE6  N    C5   C4   123.85  3.000
 JE6  N1   C5   C4   123.40  3.000
 JE6  O    C6   N    124.05  3.000
 JE6  O    C6   C7   122.59  3.000
 JE6  N    C6   C7   113.35  3.000
 JE6  H4   C11  C12  120.15  3.000
 JE6  H4   C11  C10  120.22  3.000
 JE6  C12  C11  C10  119.63  3.000
 JE6  H6   C7   H5   107.60  3.000
 JE6  H6   C7   C8   110.15  3.000
 JE6  H5   C7   C8   110.64  3.000
 JE6  H6   C7   C6   109.89  3.000
 JE6  H5   C7   C6   107.74  3.000
 JE6  C8   C7   C6   110.74  3.000
 JE6  C13  C8   C9   118.88  3.000
 JE6  C13  C8   C7   120.09  3.000
 JE6  C9   C8   C7   121.02  3.000
 JE6  H7   C9   C10  119.66  3.000
 JE6  H7   C9   C8   119.67  3.000
 JE6  C10  C9   C8   120.67  3.000
 JE6  H8   C10  C9   119.77  3.000
 JE6  H8   C10  C11  120.15  3.000
 JE6  C9   C10  C11  120.08  3.000
 JE6  H9   C12  C13  119.75  3.000
 JE6  H9   C12  C11  120.06  3.000
 JE6  C13  C12  C11  120.19  3.000
 JE6  H10  C13  C12  119.77  3.000
 JE6  H10  C13  C8   119.68  3.000
 JE6  C12  C13  C8   120.55  3.000
 JE6  N2   C3   C2   122.72  3.000
 JE6  N2   C3   C4   118.30  3.000
 JE6  C2   C3   C4   118.97  3.000
 JE6  N1   C1   C    117.29  3.000
 JE6  N1   C1   C2   122.86  3.000
 JE6  C    C1   C2   119.86  3.000
 JE6  H12  C15  H11  108.52  3.000
 JE6  H12  C15  C16  112.25  3.000
 JE6  H11  C15  C16  110.57  3.000
 JE6  H12  C15  C14  112.73  3.000
 JE6  H11  C15  C14  109.94  3.000
 JE6  C16  C15  C14  102.76  3.000
 JE6  C21  C16  C18  107.79  3.000
 JE6  C18  C16  C17  111.46  3.000
 JE6  C21  C16  C17  109.42  3.000
 JE6  C18  C16  C15  112.11  3.000
 JE6  C17  C16  C15  112.68  3.000
 JE6  C21  C16  C15  102.90  3.000
 JE6  N3   C17  C16  180.00  3.000
 JE6  H13  C18  C20  116.11  3.000
 JE6  H13  C18  C19  115.91  3.000
 JE6  C20  C18  C19   60.26  3.000
 JE6  H13  C18  C16  111.93  3.000
 JE6  C19  C18  C16  121.63  3.000
 JE6  C20  C18  C16  122.06  3.000
 JE6  H15  C19  H14  114.05  3.000
 JE6  H15  C19  C20  118.71  3.000
 JE6  H14  C19  C20  117.82  3.000
 JE6  H15  C19  C18  117.30  3.000
 JE6  H14  C19  C18  118.76  3.000
 JE6  C20  C19  C18   59.83  3.000
 JE6  H16  C2   C1   119.34  3.000
 JE6  H16  C2   C3   122.28  3.000
 JE6  C1   C2   C3   118.38  3.000
 JE6  H18  C20  H17  114.00  3.000
 JE6  H18  C20  C19  117.71  3.000
 JE6  H17  C20  C19  118.70  3.000
 JE6  H18  C20  C18  118.71  3.000
 JE6  H17  C20  C18  117.52  3.000
 JE6  C19  C20  C18   59.91  3.000
 JE6  N2   C21  O1   128.12  3.000
 JE6  N2   C21  C16  107.27  3.000
 JE6  O1   C21  C16  124.56  3.000
 JE6  H19  N    C6   117.33  3.000
 JE6  H19  N    C5   112.88  3.000
 JE6  C6   N    C5   129.78  3.000
 JE6  H22  C    H21  107.06  3.000
 JE6  H22  C    H20  108.58  3.000
 JE6  H21  C    H20  108.23  3.000
 JE6  H22  C    C1   111.01  3.000
 JE6  H21  C    C1   110.93  3.000
 JE6  H20  C    C1   110.89  3.000
 JE6  C1   N1   C5   118.59  3.000
 JE6  C21  N2   C3   125.52  3.000
 JE6  C21  N2   C14  112.70  3.000
 JE6  C3   N2   C14  121.34  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
 JE6  CONST_01  C1   N1   C5   C4      0.00   0.0  0
 JE6  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 JE6  CONST_03  C2   C1   N1   C5      0.00   0.0  0
 JE6  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 JE6  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 JE6  CONST_06  C8   C13  C12  C11     0.00   0.0  0
 JE6  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 JE6  CONST_08  C12  C13  C8   C9      0.00   0.0  0
 JE6  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 JE6  CONST_10  C13  C8   C9   C10     0.00   0.0  0
 JE6  CONST_11  N1   C1   C2   C3      0.00   0.0  0
 JE6  CONST_12  N1   C5   C4   C3      0.00   0.0  0
 JE6  CONST_13  N2   C3   C4   C5    180.00   0.0  0
 JE6  CONST_14  N2   C3   C2   C1    180.00   0.0  0
 JE6  CONST_15  C16  C21  N2   C14     0.00   0.0  0
 JE6  CONST_16  C16  C21  N2   C3    180.00   0.0  0
 JE6  CONST_17  C    C1   N1   C5    180.00   0.0  0
 JE6  CONST_18  C10  C9   C8   C7    180.00   0.0  0
 JE6  CONST_19  C12  C13  C8   C7    180.00   0.0  0
 JE6  CONST_20  C    C1   C2   C3    180.00   0.0  0
 JE6  CONST_21  N    C5   C4   C3    180.00   0.0  0
 JE6  CONST_22  N    C5   N1   C1    180.00   0.0  0
 JE6  CONST_23  O1   C21  N2   C14   180.00   0.0  0
 JE6  CONST_24  O1   C21  N2   C3      0.00   0.0  0
 JE6  CONST_25  H16  C2   C3   C4    180.00   0.0  0
 JE6  CONST_26  H7   C9   C10  C11   180.00   0.0  0
 JE6  CONST_27  H10  C13  C12  C11   180.00   0.0  0
 JE6  CONST_28  H8   C10  C9   C8    180.00   0.0  0
 JE6  CONST_29  H9   C12  C13  C8    180.00   0.0  0
 JE6  CONST_30  H4   C11  C10  C9    180.00   0.0  0
 JE6  CONST_31  H10  C13  C8   C9    180.00   0.0  0
 JE6  CONST_32  H9   C12  C11  C10   180.00   0.0  0
 JE6  CONST_33  H8   C10  C11  C12   180.00   0.0  0
 JE6  CONST_34  H4   C11  C12  C13   180.00   0.0  0
 JE6  CONST_35  H7   C9   C8   C13   180.00   0.0  0
 JE6  CONST_36  H1   C4   C3   C2    180.00   0.0  0
 JE6  CONST_37  H16  C2   C1   N1    180.00   0.0  0
 JE6  CONST_38  H1   C4   C5   N1    180.00   0.0  0
 JE6  CONST_39  H16  C2   C3   N2      0.00   0.0  0
 JE6  CONST_40  H1   C4   C3   N2      0.00   0.0  0
 JE6  CONST_41  C6   N    C5   C4      0.00   0.0  0
 JE6  CONST_42  N1   C5   N    C6    180.00   0.0  0
 JE6  CONST_43  H19  N    C5   C4    180.00   0.0  0
 JE6  CONST_44  H19  N    C5   N1      0.00   0.0  0
 JE6  CONST_45  C7   C6   N    C5    180.00   0.0  0
 JE6  CONST_46  O    C6   N    C5      0.00   0.0  0
 JE6  CONST_47  H19  N    C6   C7      0.00   0.0  0
 JE6  CONST_48  H19  N    C6   O     180.00   0.0  0
 JE6  Var_01    C21  N2   C3   C4    157.00  30.0  2
 JE6  Var_02    C14  N2   C3   C4    -14.80  30.0  2
 JE6  Var_03    C2   C3   N2   C14   164.41  30.0  3
 JE6  Var_04    C15  C14  N2   C3   -168.13  30.0  1
 JE6  Var_05    C21  N2   C14  C15    19.10  30.0  1
 JE6  Var_06    N2   C14  C15  C16   -30.76  30.0  1
 JE6  Var_07    C19  C20  C18  C16   110.79  30.0  1
 JE6  Var_08    C21  N2   C3   C2    -23.79  30.0  2
 JE6  Var_09    H2   C14  N2   C3    -48.32  30.0  1
 JE6  Var_10    H3   C14  N2   C3     71.70  30.0  1
 JE6  Var_11    H2   C14  C15  C16  -149.60  30.0  1
 JE6  Var_12    H3   C14  C15  C16    88.56  30.0  1
 JE6  Var_13    H17  C20  C18  C16  -140.30  30.0  1
 JE6  Var_14    H18  C20  C18  C16     3.60  30.0  1
 JE6  Var_15    H14  C19  C18  C16    -4.22  30.0  1
 JE6  Var_16    H15  C19  C18  C16   139.55  30.0  1
 JE6  Var_17    H14  C19  C20  C18  -108.82  30.0  1
 JE6  Var_18    H15  C19  C20  C18   106.65  30.0  1
 JE6  Var_19    H17  C20  C19  C18  -106.95  30.0  1
 JE6  Var_20    H18  C20  C19  C18   108.82  30.0  1
 JE6  Var_21    H13  C18  C20  C19  -106.28  30.0  1
 JE6  Var_22    H2   C14  N2   C21   138.91  30.0  1
 JE6  Var_23    H3   C14  N2   C21  -101.07  30.0  1
 JE6  Var_24    H11  C15  C14  N2     86.98  30.0  1
 JE6  Var_25    H12  C15  C14  N2   -151.81  30.0  1
 JE6  Var_26    C9   C8   C7   C6    105.92  30.0  2
 JE6  Var_27    C13  C8   C7   C6    -72.93  30.0  2
 JE6  Var_28    H5   C7   C8   C9   -134.68  30.0  2
 JE6  Var_29    H6   C7   C8   C9    -15.84  30.0  2
 JE6  Var_30    H5   C7   C8   C13    46.46  30.0  2
 JE6  Var_31    H6   C7   C8   C13   165.30  30.0  2
 JE6  Var_32    H20  C    C1   C2    175.96  30.0  2
 JE6  Var_33    H21  C    C1   C2    -63.74  30.0  2
 JE6  Var_34    H22  C    C1   C2     55.17  30.0  2
 JE6  Var_35    H20  C    C1   N1     -4.33  30.0  2
 JE6  Var_36    H21  C    C1   N1    115.97  30.0  2
 JE6  Var_37    H22  C    C1   N1   -125.12  30.0  2
 JE6  Var_38    N    C6   C7   C8    -71.52  30.0  3
 JE6  Var_39    O    C6   C7   C8    107.19  30.0  3
 JE6  Var_40    H5   C7   C6   N     167.36  30.0  1
 JE6  Var_41    H6   C7   C6   N      50.40  30.0  1
 JE6  Var_42    H5   C7   C6   O     -13.93  30.0  1
 JE6  Var_43    H6   C7   C6   O    -130.89  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
 JE6  chir_01  C16  C15  C21  C18  positiv
 JE6  chir_02  C18  C16  C20  C19  both

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
 JE6  plan-1  C11  0.020
 JE6  plan-1  C7   0.020
 JE6  plan-1  C8   0.020
 JE6  plan-1  C9   0.020
 JE6  plan-1  C10  0.020
 JE6  plan-1  C12  0.020
 JE6  plan-1  C13  0.020
 JE6  plan-1  H7   0.020
 JE6  plan-1  H8   0.020
 JE6  plan-1  H9   0.020
 JE6  plan-1  H10  0.020
 JE6  plan-1  H4   0.020
 JE6  plan-2  C4   0.020
 JE6  plan-2  C5   0.020
 JE6  plan-2  C3   0.020
 JE6  plan-2  C1   0.020
 JE6  plan-2  C2   0.020
 JE6  plan-2  N    0.020
 JE6  plan-2  C    0.020
 JE6  plan-2  N1   0.020
 JE6  plan-2  N2   0.020
 JE6  plan-2  H1   0.020
 JE6  plan-2  H16  0.020
 JE6  plan-3  C5   0.020
 JE6  plan-3  C6   0.020
 JE6  plan-3  C7   0.020
 JE6  plan-3  N    0.020
 JE6  plan-3  O    0.020
 JE6  plan-3  H19  0.020
 JE6  plan-4  C14  0.020
 JE6  plan-4  C3   0.020
 JE6  plan-4  C16  0.020
 JE6  plan-4  C21  0.020
 JE6  plan-4  O1   0.020
 JE6  plan-4  N2   0.020

