# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:44:48 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[4-(aminomethyl)-4-methylpiperidin-1-yl]-5-{[2-(trifluoromethyl)pyridin-3-yl]sulfanyl}pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(CN)CCN(CC1)C2=NC=C(Sc3cccnc3C(F)(F)F)C(=O)N2
#
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
 JE1  JE1  2-[4-(aminomethyl)-4-methylpiperidin-1-yl]-5-{[2-(trifluoromethyl)pyridin-3-yl]sulfanyl}pyrimidin-4(3H)-one  ligand  47  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JE1
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
 JE1  C1   C  CR6   0   0.590   0.0280  -0.6905   1.2819
 JE1  C2   C  CR6   0  -0.448   0.6280  -1.1372   0.0568
 JE1  C3   C  CR16  0   0.023  -0.1845  -1.6526  -0.9221
 JE1  O1   O  O     0  -0.458   0.5936  -0.1983   2.2412
 JE1  C11  C  CH2   0  -0.260  -5.9030   1.6741  -0.8435
 JE1  C12  C  CR6   0  -0.142   2.7138   0.5998  -0.3831
 JE1  C13  C  CR16  0  -0.116   1.7235   1.5226  -0.7063
 JE1  C14  C  CR16  0  -0.305   2.0617   2.8477  -0.9035
 JE1  C15  C  CR16  0  -0.080   3.3903   3.2246  -0.7771
 JE1  C16  C  CR6   0  -0.041   4.0196   1.0909  -0.2845
 JE1  C17  C  CT    0   1.043   5.1677   0.1819   0.0765
 JE1  C10  C  CH3   0  -0.650  -6.9446  -0.4140   0.0608
 JE1  C4   C  CR6   0   0.803  -2.0891  -1.3768   0.2803
 JE1  C5   C  CH2   0  -0.335  -4.2444  -1.8080  -0.7423
 JE1  C6   C  CH2   0  -0.417  -4.8274  -0.5150  -1.2973
 JE1  C7   C  CT    0  -0.097  -5.6221   0.2861  -0.2533
 JE1  C8   C  CH2   0  -0.421  -4.7739   0.4322   1.0225
 JE1  C9   C  CH2   0  -0.371  -4.1915  -0.8967   1.4880
 JE1  F1   F  F     0  -0.292   6.3429   0.7861  -0.0412
 JE1  F2   F  F     0  -0.313   5.0665  -0.2563   1.3387
 JE1  F3   F  F     0  -0.316   5.1955  -0.9056  -0.7092
 JE1  N1   N  NR16  0  -0.735  -1.3571  -0.8469   1.2946
 JE1  N2   N  N     0  -0.505  -1.5058  -1.7854  -0.8361
 JE1  N3   N  NT    0  -0.467  -3.4124  -1.5043   0.4179
 JE1  N4   N  NH2   0  -0.801  -6.6436   2.5362   0.0627
 JE1  N5   N  N     0  -0.408   4.3428   2.3571  -0.4768
 JE1  S1   S  S2    0   0.112   2.3616  -1.1152  -0.1182
 JE1  H2   H  HCR6  0   0.285   0.2609  -1.9897  -1.8526
 JE1  H3   H  HCH2  0   0.199  -4.9443   2.1078  -1.1666
 JE1  H4   H  HCH2  0   0.222  -6.4999   1.5458  -1.7517
 JE1  H5   H  HCR6  0   0.287   0.6940   1.2071  -0.8094
 JE1  H6   H  HCR6  0   0.285   1.3048   3.5777  -1.1545
 JE1  H7   H  HCR6  0   0.277   3.6940   4.2539  -0.9223
 JE1  H8   H  HCH3  0   0.225  -6.8078  -1.4068   0.4926
 JE1  H9   H  HCH3  0   0.233  -7.5311   0.1770   0.7633
 JE1  H10  H  HCH3  0   0.223  -7.5369  -0.5377  -0.8484
 JE1  H11  H  HCH2  0   0.258  -5.0304  -2.4901  -0.4130
 JE1  H12  H  HCH2  0   0.284  -3.6538  -2.3248  -1.4913
 JE1  H13  H  HCH2  0   0.232  -4.0001   0.0933  -1.6791
 JE1  H14  H  HCH2  0   0.242  -5.4662  -0.7492  -2.1537
 JE1  H15  H  HCH2  0   0.237  -3.9526   1.1360   0.8447
 JE1  H16  H  HCH2  0   0.249  -5.3763   0.8511   1.8324
 JE1  H17  H  HCH2  0   0.270  -3.6113  -0.7769   2.4006
 JE1  H18  H  HCH2  0   0.277  -4.9868  -1.5998   1.7437
 JE1  H19  H  HNH2  0   0.343  -6.0258   2.8946   0.7802
 JE1  H20  H  HNH2  0   0.350  -6.9685   3.3497  -0.4429
 JE1  H1   H  HNR6  0   0.430  -1.8106  -0.5188   2.1362

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
 JE1  C10  C7   single    1.529  0.020  1.529
 JE1  C9   N3   single    1.457  0.020  1.457
 JE1  C9   C8   single    1.524  0.020  1.524
 JE1  N3   C5   single    1.460  0.020  1.460
 JE1  N3   C4   single    1.337  0.020  1.337
 JE1  C8   C7   single    1.539  0.020  1.539
 JE1  C5   C6   single    1.523  0.020  1.523
 JE1  C7   C6   single    1.537  0.020  1.537
 JE1  C7   C11  single    1.534  0.020  1.534
 JE1  N1   C4   single    1.358  0.020  1.358
 JE1  N1   C1   single    1.394  0.020  1.394
 JE1  C4   N2   double    1.324  0.020  1.324
 JE1  C14  C13  aromatic  1.382  0.020  1.382
 JE1  C14  C15  aromatic  1.387  0.020  1.387
 JE1  C11  N4   single    1.454  0.020  1.454
 JE1  O1   C1   double    1.218  0.020  1.218
 JE1  C1   C2   single    1.435  0.020  1.435
 JE1  N2   C3   single    1.331  0.020  1.331
 JE1  C13  C12  aromatic  1.392  0.020  1.392
 JE1  C15  N5   aromatic  1.323  0.020  1.323
 JE1  C3   C2   double    1.373  0.020  1.373
 JE1  C2   S1   single    1.743  0.020  1.743
 JE1  N5   C16  aromatic  1.321  0.020  1.321
 JE1  C12  C16  aromatic  1.399  0.020  1.399
 JE1  C12  S1   single    1.771  0.020  1.771
 JE1  C16  C17  single    1.508  0.020  1.508
 JE1  C17  F3   single    1.342  0.020  1.342
 JE1  C17  F1   single    1.327  0.020  1.327
 JE1  C17  F2   single    1.340  0.020  1.340
 JE1  C3   H2   single    0.930  0.020  1.080
 JE1  C11  H3   single    0.970  0.020  1.090
 JE1  C11  H4   single    0.970  0.020  1.090
 JE1  C13  H5   single    0.930  0.020  1.080
 JE1  C14  H6   single    0.930  0.020  1.080
 JE1  C15  H7   single    0.930  0.020  1.080
 JE1  C10  H8   single    0.970  0.020  1.090
 JE1  C10  H9   single    0.970  0.020  1.090
 JE1  C10  H10  single    0.970  0.020  1.090
 JE1  C5   H11  single    0.970  0.020  1.090
 JE1  C5   H12  single    0.970  0.020  1.090
 JE1  C6   H13  single    0.970  0.020  1.090
 JE1  C6   H14  single    0.970  0.020  1.090
 JE1  C8   H15  single    0.970  0.020  1.090
 JE1  C8   H16  single    0.970  0.020  1.090
 JE1  C9   H17  single    0.970  0.020  1.090
 JE1  C9   H18  single    0.970  0.020  1.090
 JE1  N4   H19  single    0.890  0.020  1.040
 JE1  N4   H20  single    0.890  0.020  1.040
 JE1  N1   H1   single    0.860  0.020  1.020

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
 JE1  N1   C1   O1   119.99  3.000
 JE1  O1   C1   C2   127.16  3.000
 JE1  N1   C1   C2   112.84  3.000
 JE1  S1   C2   C3   121.47  3.000
 JE1  S1   C2   C1   119.85  3.000
 JE1  C3   C2   C1   118.56  3.000
 JE1  H2   C3   N2   115.59  3.000
 JE1  H2   C3   C2   119.02  3.000
 JE1  N2   C3   C2   125.39  3.000
 JE1  H4   C11  H3   106.12  3.000
 JE1  H4   C11  N4   108.00  3.000
 JE1  H3   C11  N4   113.14  3.000
 JE1  H4   C11  C7   108.24  3.000
 JE1  H3   C11  C7   108.05  3.000
 JE1  N4   C11  C7   112.96  3.000
 JE1  S1   C12  C16  121.02  3.000
 JE1  S1   C12  C13  122.37  3.000
 JE1  C16  C12  C13  116.61  3.000
 JE1  H5   C13  C14  119.94  3.000
 JE1  H5   C13  C12  120.40  3.000
 JE1  C14  C13  C12  119.66  3.000
 JE1  H6   C14  C15  120.55  3.000
 JE1  H6   C14  C13  120.62  3.000
 JE1  C15  C14  C13  118.83  3.000
 JE1  H7   C15  N5   116.85  3.000
 JE1  H7   C15  C14  120.99  3.000
 JE1  N5   C15  C14  122.16  3.000
 JE1  N5   C16  C17  115.23  3.000
 JE1  C17  C16  C12  121.06  3.000
 JE1  N5   C16  C12  123.70  3.000
 JE1  F3   C17  F2   106.74  3.000
 JE1  F2   C17  F1   107.42  3.000
 JE1  F3   C17  F1   107.39  3.000
 JE1  F2   C17  C16  111.41  3.000
 JE1  F1   C17  C16  112.25  3.000
 JE1  F3   C17  C16  111.35  3.000
 JE1  H10  C10  H9   107.83  3.000
 JE1  H10  C10  H8   107.12  3.000
 JE1  H9   C10  H8   107.82  3.000
 JE1  H10  C10  C7   110.48  3.000
 JE1  H9   C10  C7   110.47  3.000
 JE1  H8   C10  C7   112.92  3.000
 JE1  N3   C4   N2   119.57  3.000
 JE1  N2   C4   N1   120.83  3.000
 JE1  N3   C4   N1   119.59  3.000
 JE1  H12  C5   H11  107.62  3.000
 JE1  H12  C5   N3   109.73  3.000
 JE1  H11  C5   N3   107.50  3.000
 JE1  H12  C5   C6   111.18  3.000
 JE1  H11  C5   C6   111.39  3.000
 JE1  N3   C5   C6   109.34  3.000
 JE1  H14  C6   H13  106.68  3.000
 JE1  H14  C6   C7   109.96  3.000
 JE1  H13  C6   C7   109.74  3.000
 JE1  H14  C6   C5   109.09  3.000
 JE1  H13  C6   C5   108.01  3.000
 JE1  C7   C6   C5   113.13  3.000
 JE1  C8   C7   C6   109.12  3.000
 JE1  C6   C7   C10  110.37  3.000
 JE1  C8   C7   C10  110.48  3.000
 JE1  C6   C7   C11  107.75  3.000
 JE1  C8   C7   C11  109.51  3.000
 JE1  C10  C7   C11  109.57  3.000
 JE1  H16  C8   H15  106.68  3.000
 JE1  H16  C8   C9   108.58  3.000
 JE1  H15  C8   C9   108.86  3.000
 JE1  H16  C8   C7   110.30  3.000
 JE1  H15  C8   C7   109.84  3.000
 JE1  C9   C8   C7   112.40  3.000
 JE1  H18  C9   H17  105.24  3.000
 JE1  H18  C9   N3   107.04  3.000
 JE1  H17  C9   N3   112.14  3.000
 JE1  H18  C9   C8   110.78  3.000
 JE1  H17  C9   C8   111.35  3.000
 JE1  N3   C9   C8   110.11  3.000
 JE1  H1   N1   C4   120.43  3.000
 JE1  H1   N1   C1   114.65  3.000
 JE1  C4   N1   C1   124.91  3.000
 JE1  C4   N2   C3   117.45  3.000
 JE1  C9   N3   C5   111.46  3.000
 JE1  C5   N3   C4   120.16  3.000
 JE1  C9   N3   C4   124.43  3.000
 JE1  H20  N4   H19  105.41  3.000
 JE1  H20  N4   C11  109.21  3.000
 JE1  H19  N4   C11  109.93  3.000
 JE1  C16  N5   C15  119.04  3.000
 JE1  C12  S1   C2   103.01  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
 JE1  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 JE1  CONST_02  C15  N5   C16  C12    0.00   0.0  0
 JE1  CONST_03  N5   C15  C14  C13    0.00   0.0  0
 JE1  CONST_04  N5   C16  C12  C13    0.00   0.0  0
 JE1  CONST_05  C16  C12  C13  C14    0.00   0.0  0
 JE1  CONST_06  C16  N5   C15  C14    0.00   0.0  0
 JE1  CONST_07  N3   C4   N1   C1   180.00   0.0  0
 JE1  CONST_08  N2   C4   N1   C1     0.00   0.0  0
 JE1  CONST_09  C4   N1   C1   C2     0.00   0.0  0
 JE1  CONST_10  N3   C4   N2   C3   180.00   0.0  0
 JE1  CONST_11  N1   C4   N2   C3     0.00   0.0  0
 JE1  CONST_12  N1   C4   N3   C5   180.00   0.0  0
 JE1  CONST_13  N2   C4   N3   C5     0.00   0.0  0
 JE1  CONST_14  N1   C4   N3   C9     0.00   0.0  0
 JE1  CONST_15  N2   C4   N3   C9   180.00   0.0  0
 JE1  CONST_16  C17  C16  C12  C13  180.00   0.0  0
 JE1  CONST_17  S1   C12  C13  C14  180.00   0.0  0
 JE1  CONST_18  C17  C16  N5   C15  180.00   0.0  0
 JE1  CONST_19  S1   C12  C16  N5   180.00   0.0  0
 JE1  CONST_20  C4   N1   C1   O1   180.00   0.0  0
 JE1  CONST_21  H6   C14  C13  C12  180.00   0.0  0
 JE1  CONST_22  H7   C15  C14  C13  180.00   0.0  0
 JE1  CONST_23  H5   C13  C14  C15  180.00   0.0  0
 JE1  CONST_24  H1   N1   C1   C2   180.00   0.0  0
 JE1  Var_01    C8   C9   N3   C4    95.14  30.0  1
 JE1  Var_02    C6   C5   N3   C4   -96.63  30.0  1
 JE1  Var_03    N3   C9   C8   C7    56.05  30.0  1
 JE1  Var_04    N3   C5   C6   C7   -56.12  30.0  1
 JE1  Var_05    C13  C12  S1   C2   -14.47  30.0  2
 JE1  Var_06    F3   C17  C16  C12   51.71  30.0  2
 JE1  Var_07    H19  N4   C11  C7    76.84  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
 JE1  chir_01  C7  C8  C6  C11  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
 JE1  plan-1  C12  0.020
 JE1  plan-1  C13  0.020
 JE1  plan-1  C14  0.020
 JE1  plan-1  C15  0.020
 JE1  plan-1  C16  0.020
 JE1  plan-1  C17  0.020
 JE1  plan-1  N5   0.020
 JE1  plan-1  S1   0.020
 JE1  plan-1  H5   0.020
 JE1  plan-1  H6   0.020
 JE1  plan-1  H7   0.020
 JE1  plan-2  C1   0.020
 JE1  plan-2  C2   0.020
 JE1  plan-2  C3   0.020
 JE1  plan-2  O1   0.020
 JE1  plan-2  C4   0.020
 JE1  plan-2  C5   0.020
 JE1  plan-2  C9   0.020
 JE1  plan-2  N1   0.020
 JE1  plan-2  N2   0.020
 JE1  plan-2  N3   0.020
 JE1  plan-2  S1   0.020
 JE1  plan-2  H2   0.020
 JE1  plan-2  H1   0.020

