# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:45:17 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@H](NC(=O)Cc2ccccc2)C(=O)N1
#
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
 JOT  JOT  ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide  ligand  29  17  .  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_JOT
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
 JOT  C4   C  C     0   0.573  -3.0150  -0.8681  -0.4206
 JOT  C5   C  C     0   0.572   0.2972  -0.1325  -0.2006
 JOT  C6   C  CH2   0  -0.692   1.3810   0.2172  -1.2062
 JOT  C11  C  CR16  0  -0.242   4.6084   1.2997   0.4647
 JOT  C7   C  CR6   0   0.147   2.7521   0.1751  -0.5993
 JOT  C8   C  CR16  0  -0.300   3.4425  -1.0283  -0.4857
 JOT  C9   C  CR16  0  -0.244   4.7021  -1.0703   0.0956
 JOT  C10  C  CR16  0  -0.269   5.2886   0.0944   0.5749
 JOT  C12  C  CR16  0  -0.297   3.3485   1.3372  -0.1189
 JOT  N1   N  NH1   0  -0.679  -4.2980  -0.4455  -0.1875
 JOT  N2   N  NH1   0  -0.634  -0.9088   0.4078  -0.4769
 JOT  C3   C  CH1   0  -0.228  -2.0887   0.1231   0.2776
 JOT  C1   C  C     0   0.549  -4.3890   0.7871   0.4202
 JOT  C2   C  CH2   0  -0.599  -2.9866   1.3229   0.5696
 JOT  O1   O  O     0  -0.419  -5.4207   1.3216   0.7378
 JOT  O2   O  O     0  -0.407  -2.6926  -1.8478  -1.0401
 JOT  O3   O  O     0  -0.473   0.5005  -0.8509   0.7616
 JOT  H1   H  HCH2  0   0.302   1.3039  -0.5103  -2.0205
 JOT  H2   H  HCH2  0   0.283   1.1828   1.1951  -1.6497
 JOT  H4   H  HCR6  0   0.250   2.9959  -1.9410  -0.8612
 JOT  H5   H  HCR6  0   0.255   5.2268  -2.0137   0.1758
 JOT  H6   H  HCR6  0   0.255   6.2708   0.0622   1.0288
 JOT  H7   H  HCR6  0   0.250   2.8258   2.2826  -0.2057
 JOT  H8   H  HNH1  0   0.428  -5.1133  -0.9795  -0.4626
 JOT  H9   H  HNH1  0   0.412  -1.0077   0.9691  -1.3090
 JOT  H10  H  HCH1  0   0.331  -1.7872  -0.3506   1.2147
 JOT  H11  H  HCH2  0   0.311  -2.8329   1.7559   1.5561
 JOT  H12  H  HCH2  0   0.312  -2.8476   2.1179  -0.1680
 JOT  H3   H  HCR6  0   0.255   5.0588   2.2138   0.8297

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
 JOT  O1   C1   double    1.205  0.020  1.205
 JOT  N1   C1   single    1.377  0.020  1.377
 JOT  N1   C4   single    1.371  0.020  1.371
 JOT  C1   C2   single    1.509  0.020  1.509
 JOT  C4   O2   double    1.203  0.020  1.203
 JOT  C4   C3   single    1.526  0.020  1.526
 JOT  C2   C3   single    1.527  0.020  1.527
 JOT  C3   N2   single    1.429  0.020  1.429
 JOT  O3   C5   double    1.218  0.020  1.218
 JOT  N2   C5   single    1.350  0.020  1.350
 JOT  C5   C6   single    1.519  0.020  1.519
 JOT  C6   C7   single    1.500  0.020  1.500
 JOT  C7   C8   aromatic  1.392  0.020  1.392
 JOT  C7   C12  aromatic  1.392  0.020  1.392
 JOT  C8   C9   aromatic  1.388  0.020  1.388
 JOT  C12  C11  aromatic  1.389  0.020  1.389
 JOT  C9   C10  aromatic  1.389  0.020  1.389
 JOT  C11  C10  aromatic  1.388  0.020  1.388
 JOT  C6   H1   single    0.970  0.020  1.090
 JOT  C6   H2   single    0.970  0.020  1.090
 JOT  C11  H3   single    0.930  0.020  1.080
 JOT  C8   H4   single    0.930  0.020  1.080
 JOT  C9   H5   single    0.930  0.020  1.080
 JOT  C10  H6   single    0.930  0.020  1.080
 JOT  C12  H7   single    0.930  0.020  1.080
 JOT  N1   H8   single    0.860  0.020  1.020
 JOT  N2   H9   single    0.860  0.020  1.020
 JOT  C3   H10  single    0.970  0.020  1.090
 JOT  C2   H11  single    0.970  0.020  1.090
 JOT  C2   H12  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
 JOT  O2   C4   C3   127.01  3.000
 JOT  C3   C4   N1   106.86  3.000
 JOT  O2   C4   N1   126.12  3.000
 JOT  O3   C5   N2   123.15  3.000
 JOT  N2   C5   C6   114.18  3.000
 JOT  O3   C5   C6   122.66  3.000
 JOT  H2   C6   H1   106.27  3.000
 JOT  H2   C6   C7   110.82  3.000
 JOT  H1   C6   C7   110.29  3.000
 JOT  H2   C6   C5   110.21  3.000
 JOT  H1   C6   C5   106.80  3.000
 JOT  C7   C6   C5   112.20  3.000
 JOT  H3   C11  C12  119.75  3.000
 JOT  H3   C11  C10  120.17  3.000
 JOT  C12  C11  C10  120.08  3.000
 JOT  C12  C7   C8   118.76  3.000
 JOT  C12  C7   C6   120.52  3.000
 JOT  C8   C7   C6   120.71  3.000
 JOT  H4   C8   C9   119.59  3.000
 JOT  H4   C8   C7   119.71  3.000
 JOT  C9   C8   C7   120.69  3.000
 JOT  H5   C9   C10  120.03  3.000
 JOT  H5   C9   C8   119.82  3.000
 JOT  C10  C9   C8   120.15  3.000
 JOT  H6   C10  C9   120.18  3.000
 JOT  H6   C10  C11  120.24  3.000
 JOT  C9   C10  C11  119.58  3.000
 JOT  H7   C12  C7   119.61  3.000
 JOT  H7   C12  C11  119.65  3.000
 JOT  C7   C12  C11  120.74  3.000
 JOT  H8   N1   C1   122.59  3.000
 JOT  H8   N1   C4   123.01  3.000
 JOT  C1   N1   C4   114.38  3.000
 JOT  H9   N2   C3   117.74  3.000
 JOT  H9   N2   C5   118.63  3.000
 JOT  C3   N2   C5   123.35  3.000
 JOT  H10  C3   C2   109.82  3.000
 JOT  H10  C3   N2   108.14  3.000
 JOT  C2   C3   N2   115.46  3.000
 JOT  H10  C3   C4   106.17  3.000
 JOT  N2   C3   C4   112.89  3.000
 JOT  C2   C3   C4   103.95  3.000
 JOT  O1   C1   C2   127.77  3.000
 JOT  C2   C1   N1   107.47  3.000
 JOT  O1   C1   N1   124.75  3.000
 JOT  H12  C2   H11  107.72  3.000
 JOT  H12  C2   C1   108.03  3.000
 JOT  H11  C2   C1   111.24  3.000
 JOT  H12  C2   C3   111.57  3.000
 JOT  H11  C2   C3   113.77  3.000
 JOT  C1   C2   C3   104.39  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
 JOT  CONST_01  C8   C7   C12  C11    0.00   0.0  0
 JOT  CONST_02  C8   C9   C10  C11    0.00   0.0  0
 JOT  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 JOT  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 JOT  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 JOT  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 JOT  CONST_07  C1   N1   C4   C3     0.00   0.0  0
 JOT  CONST_08  C9   C8   C7   C6   180.00   0.0  0
 JOT  CONST_09  C11  C12  C7   C6   180.00   0.0  0
 JOT  CONST_10  O2   C4   N1   C1   180.00   0.0  0
 JOT  CONST_11  H5   C9   C10  C11  180.00   0.0  0
 JOT  CONST_12  H3   C11  C12  C7   180.00   0.0  0
 JOT  CONST_13  H7   C12  C7   C8   180.00   0.0  0
 JOT  CONST_14  H6   C10  C9   C8   180.00   0.0  0
 JOT  CONST_15  H4   C8   C9   C10  180.00   0.0  0
 JOT  CONST_16  H8   N1   C4   C3   180.00   0.0  0
 JOT  CONST_17  C3   N2   C5   C6   180.00   0.0  0
 JOT  CONST_18  O3   C5   N2   C3     0.00   0.0  0
 JOT  CONST_19  H9   N2   C5   C6     0.00   0.0  0
 JOT  Var_01    C2   C1   N1   C4     3.08  30.0  1
 JOT  Var_02    C3   C2   C1   N1   -12.75  30.0  1
 JOT  Var_03    C8   C7   C6   C5    83.36  30.0  2
 JOT  Var_04    O3   C5   C6   C7   -27.31  30.0  2

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
 JOT  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
 JOT  plan-1  C6   0.020
 JOT  plan-1  C11  0.020
 JOT  plan-1  C7   0.020
 JOT  plan-1  C8   0.020
 JOT  plan-1  C9   0.020
 JOT  plan-1  C10  0.020
 JOT  plan-1  C12  0.020
 JOT  plan-1  H4   0.020
 JOT  plan-1  H5   0.020
 JOT  plan-1  H6   0.020
 JOT  plan-1  H7   0.020
 JOT  plan-1  H3   0.020
 JOT  plan-2  C5   0.020
 JOT  plan-2  C6   0.020
 JOT  plan-2  N2   0.020
 JOT  plan-2  C3   0.020
 JOT  plan-2  O3   0.020
 JOT  plan-2  H9   0.020
 JOT  plan-3  N1   0.020
 JOT  plan-3  C1   0.020
 JOT  plan-3  C2   0.020
 JOT  plan-3  O1   0.020
 JOT  plan-4  C4   0.020
 JOT  plan-4  N1   0.020
 JOT  plan-4  C3   0.020
 JOT  plan-4  C1   0.020
 JOT  plan-4  O2   0.020
 JOT  plan-4  H8   0.020

