# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:24:25 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-phenyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCc1ccccc1)N[C@H]2CC(=O)NC2=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
 JOK  JOK  ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-phenyl-propanamide  ligand  32  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JOK
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
 JOK  C4   C  C     0   0.573  -3.3651   1.0011   0.1386
 JOK  C5   C  C     0   0.575  -0.2704  -0.1391  -0.8460
 JOK  C6   C  CH2   0  -0.581   1.0909  -0.3736  -0.2291
 JOK  C11  C  CR16  0  -0.273   6.0167  -0.4870   0.8456
 JOK  C7   C  CH2   0  -0.507   2.1880   0.4714  -0.8736
 JOK  C8   C  CR6   0   0.128   3.5352   0.1538  -0.2860
 JOK  C9   C  CR16  0  -0.306   3.9526   0.7495   0.9029
 JOK  C10  C  CR16  0  -0.239   5.1817   0.4340   1.4658
 JOK  C12  C  CR16  0  -0.239   5.6115  -1.0880  -0.3388
 JOK  C13  C  CR16  0  -0.313   4.3805  -0.7688  -0.8975
 JOK  N1   N  NH1   0  -0.679  -4.6343   0.6311   0.5024
 JOK  N2   N  NH1   0  -0.639  -1.3099  -0.3451  -0.0084
 JOK  C3   C  CH1   0  -0.231  -2.6778  -0.2459  -0.4084
 JOK  C1   C  C     0   0.549  -4.8716  -0.7240   0.4415
 JOK  C2   C  CH2   0  -0.598  -3.5798  -1.3925   0.0443
 JOK  O1   O  O     0  -0.420  -5.9275  -1.2483   0.6896
 JOK  O2   O  O     0  -0.408  -2.8994   2.1077   0.2197
 JOK  O3   O  O     0  -0.488  -0.4167   0.1708  -2.0171
 JOK  H1   H  HCH2  0   0.266   1.0606  -0.1977   0.8489
 JOK  H2   H  HCH2  0   0.284   1.3220  -1.4366  -0.3560
 JOK  H4   H  HCH2  0   0.253   2.2019   0.2910  -1.9493
 JOK  H5   H  HCH2  0   0.253   1.9620   1.5308  -0.7311
 JOK  H6   H  HCR6  0   0.246   3.3091   1.4720   1.3916
 JOK  H7   H  HCR6  0   0.253   5.4893   0.9103   2.3881
 JOK  H8   H  HCR6  0   0.253   6.2560  -1.8043  -0.8320
 JOK  H9   H  HCR6  0   0.247   4.0760  -1.2399  -1.8252
 JOK  H10  H  HNH1  0   0.428  -5.3319   1.2936   0.8188
 JOK  H11  H  HNH1  0   0.409  -1.1188  -0.5559   0.9587
 JOK  H12  H  HCH1  0   0.329  -2.7072  -0.1592  -1.4975
 JOK  H13  H  HCH2  0   0.310  -3.7465  -2.1465  -0.7227
 JOK  H14  H  HCH2  0   0.311  -3.1724  -1.9017   0.9227
 JOK  H3   H  HCR6  0   0.253   6.9773  -0.7318   1.2804

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
 JOK  O1   C1   double    1.205  0.020  1.205
 JOK  N1   C1   single    1.377  0.020  1.377
 JOK  N1   C4   single    1.371  0.020  1.371
 JOK  C1   C2   single    1.508  0.020  1.508
 JOK  C4   C3   single    1.525  0.020  1.525
 JOK  C4   O2   double    1.203  0.020  1.203
 JOK  C2   C3   single    1.528  0.020  1.528
 JOK  C3   N2   single    1.429  0.020  1.429
 JOK  O3   C5   double    1.220  0.020  1.220
 JOK  N2   C5   single    1.351  0.020  1.351
 JOK  C5   C6   single    1.513  0.020  1.513
 JOK  C9   C10  aromatic  1.388  0.020  1.388
 JOK  C9   C8   aromatic  1.394  0.020  1.394
 JOK  C6   C7   single    1.527  0.020  1.527
 JOK  C10  C11  aromatic  1.389  0.020  1.389
 JOK  C7   C8   single    1.504  0.020  1.504
 JOK  C8   C13  aromatic  1.393  0.020  1.393
 JOK  C11  C12  aromatic  1.389  0.020  1.389
 JOK  C13  C12  aromatic  1.389  0.020  1.389
 JOK  C6   H1   single    0.970  0.020  1.090
 JOK  C6   H2   single    0.970  0.020  1.090
 JOK  C11  H3   single    0.930  0.020  1.080
 JOK  C7   H4   single    0.970  0.020  1.090
 JOK  C7   H5   single    0.970  0.020  1.090
 JOK  C9   H6   single    0.930  0.020  1.080
 JOK  C10  H7   single    0.930  0.020  1.080
 JOK  C12  H8   single    0.930  0.020  1.080
 JOK  C13  H9   single    0.930  0.020  1.080
 JOK  N1   H10  single    0.860  0.020  1.020
 JOK  N2   H11  single    0.860  0.020  1.020
 JOK  C3   H12  single    0.970  0.020  1.090
 JOK  C2   H13  single    0.970  0.020  1.090
 JOK  C2   H14  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
 JOK  O2   C4   C3   126.99  3.000
 JOK  O2   C4   N1   126.05  3.000
 JOK  C3   C4   N1   106.95  3.000
 JOK  O3   C5   N2   122.79  3.000
 JOK  N2   C5   C6   114.58  3.000
 JOK  O3   C5   C6   122.59  3.000
 JOK  H2   C6   H1   106.04  3.000
 JOK  H2   C6   C7   109.66  3.000
 JOK  H1   C6   C7   110.31  3.000
 JOK  H2   C6   C5   107.05  3.000
 JOK  H1   C6   C5   110.63  3.000
 JOK  C7   C6   C5   112.86  3.000
 JOK  H3   C11  C12  120.25  3.000
 JOK  H3   C11  C10  120.26  3.000
 JOK  C12  C11  C10  119.49  3.000
 JOK  H5   C7   H4   106.96  3.000
 JOK  H5   C7   C8   109.83  3.000
 JOK  H4   C7   C8   109.82  3.000
 JOK  H5   C7   C6   109.43  3.000
 JOK  H4   C7   C6   109.50  3.000
 JOK  C8   C7   C6   111.21  3.000
 JOK  C13  C8   C9   118.42  3.000
 JOK  C13  C8   C7   120.80  3.000
 JOK  C9   C8   C7   120.76  3.000
 JOK  H6   C9   C10  119.62  3.000
 JOK  H6   C9   C8   119.45  3.000
 JOK  C10  C9   C8   120.93  3.000
 JOK  H7   C10  C9   119.81  3.000
 JOK  H7   C10  C11  120.08  3.000
 JOK  C9   C10  C11  120.11  3.000
 JOK  H8   C12  C13  119.77  3.000
 JOK  H8   C12  C11  120.08  3.000
 JOK  C13  C12  C11  120.15  3.000
 JOK  H9   C13  C12  119.56  3.000
 JOK  H9   C13  C8   119.55  3.000
 JOK  C12  C13  C8   120.90  3.000
 JOK  H10  N1   C1   122.61  3.000
 JOK  H10  N1   C4   122.95  3.000
 JOK  C1   N1   C4   114.42  3.000
 JOK  H11  N2   C3   117.69  3.000
 JOK  H11  N2   C5   118.74  3.000
 JOK  C3   N2   C5   123.55  3.000
 JOK  H12  C3   C2   109.81  3.000
 JOK  H12  C3   N2   108.08  3.000
 JOK  C2   C3   N2   115.49  3.000
 JOK  H12  C3   C4   106.28  3.000
 JOK  N2   C3   C4   112.82  3.000
 JOK  C2   C3   C4   103.96  3.000
 JOK  O1   C1   C2   127.75  3.000
 JOK  C2   C1   N1   107.47  3.000
 JOK  O1   C1   N1   124.77  3.000
 JOK  H14  C2   H13  107.48  3.000
 JOK  H14  C2   C1   108.30  3.000
 JOK  H13  C2   C1   111.20  3.000
 JOK  H14  C2   C3   111.55  3.000
 JOK  H13  C2   C3   113.68  3.000
 JOK  C1   C2   C3   104.55  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
 JOK  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 JOK  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 JOK  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 JOK  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 JOK  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 JOK  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 JOK  CONST_07  C1   N1   C4   C3      0.00   0.0  0
 JOK  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 JOK  CONST_09  C12  C13  C8   C7    180.00   0.0  0
 JOK  CONST_10  O2   C4   N1   C1    180.00   0.0  0
 JOK  CONST_11  H6   C9   C10  C11   180.00   0.0  0
 JOK  CONST_12  H9   C13  C12  C11   180.00   0.0  0
 JOK  CONST_13  H7   C10  C9   C8    180.00   0.0  0
 JOK  CONST_14  H8   C12  C13  C8    180.00   0.0  0
 JOK  CONST_15  H3   C11  C10  C9    180.00   0.0  0
 JOK  CONST_16  H10  N1   C4   C3    180.00   0.0  0
 JOK  CONST_17  C3   N2   C5   C6    180.00   0.0  0
 JOK  CONST_18  O3   C5   N2   C3      0.00   0.0  0
 JOK  CONST_19  H11  N2   C5   C6      0.00   0.0  0
 JOK  Var_01    C2   C1   N1   C4      2.95  30.0  1
 JOK  Var_02    C3   C2   C1   N1    -12.10  30.0  1
 JOK  Var_03    C9   C8   C7   C6    -83.31  30.0  2
 JOK  Var_04    C8   C7   C6   C5   -176.83  30.0  3
 JOK  Var_05    O3   C5   C6   C7     30.55  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
 JOK  chir_01  C3  C4  C2  N2  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
 JOK  plan-1  C11  0.020
 JOK  plan-1  C7   0.020
 JOK  plan-1  C8   0.020
 JOK  plan-1  C9   0.020
 JOK  plan-1  C10  0.020
 JOK  plan-1  C12  0.020
 JOK  plan-1  C13  0.020
 JOK  plan-1  H6   0.020
 JOK  plan-1  H7   0.020
 JOK  plan-1  H8   0.020
 JOK  plan-1  H9   0.020
 JOK  plan-1  H3   0.020
 JOK  plan-2  C5   0.020
 JOK  plan-2  C6   0.020
 JOK  plan-2  N2   0.020
 JOK  plan-2  C3   0.020
 JOK  plan-2  O3   0.020
 JOK  plan-2  H11  0.020
 JOK  plan-3  N1   0.020
 JOK  plan-3  C1   0.020
 JOK  plan-3  C2   0.020
 JOK  plan-3  O1   0.020
 JOK  plan-4  C4   0.020
 JOK  plan-4  N1   0.020
 JOK  plan-4  C3   0.020
 JOK  plan-4  C1   0.020
 JOK  plan-4  O2   0.020
 JOK  plan-4  H10  0.020

