# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:00:00 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-methyl-but-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CC(=O)N[C@H]1CC(=O)NC1=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
 JPQ  JPQ  ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-methyl-but-2-enamide  ligand  26  14  .  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_JPQ
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
 JPQ  C4   C  CR15  0  -0.223  -1.2186  -0.0748  -0.4262
 JPQ  C5   C  C     0   0.560   1.2309   0.0391  -0.3701
 JPQ  C6   C  C1    0  -0.444   2.4027  -0.5039   0.3423
 JPQ  C7   C  C     0   0.145   3.6953  -0.2705   0.0694
 JPQ  C8   C  CH3   0  -0.713   4.7494  -0.8861   0.9373
 JPQ  C9   C  CH3   0  -0.725   4.2293   0.5873  -1.0352
 JPQ  N1   N  NR15  0  -0.679  -3.2621   0.5072   0.5351
 JPQ  N2   N  NH1   0  -0.655   0.0567  -0.4869   0.0650
 JPQ  C3   C  CH2   0  -0.600  -2.2235  -1.2020  -0.6573
 JPQ  O1   O  O     0  -0.409  -1.4545   1.7806   1.1513
 JPQ  C1   C  CR5   0   0.571  -1.9405   0.8720   0.5297
 JPQ  C2   C  CR5   0   0.549  -3.5351  -0.6535  -0.1535
 JPQ  O2   O  O     0  -0.421  -4.6335  -1.1297  -0.2884
 JPQ  O3   O  O     0  -0.490   1.2711   0.8726  -1.2660
 JPQ  H1   H  HCR5  0   0.327  -1.0637   0.4824  -1.3534
 JPQ  H2   H  H     0   0.252   2.1816  -1.1561   1.1815
 JPQ  H3   H  HCH3  0   0.249   5.4107  -1.5208   0.3434
 JPQ  H4   H  HCH3  0   0.250   5.3797  -0.1083   1.3753
 JPQ  H5   H  HCH3  0   0.246   4.3307  -1.4826   1.7461
 JPQ  H6   H  HCH3  0   0.260   3.5363   0.7191  -1.8580
 JPQ  H7   H  HCH3  0   0.253   4.4750   1.5775  -0.6421
 JPQ  H8   H  HCH3  0   0.239   5.1607   0.1661  -1.4161
 JPQ  H9   H  HNR5  0   0.427  -3.9746   1.0265   1.0329
 JPQ  H10  H  HNH1  0   0.408   0.0704  -1.1328   0.8388
 JPQ  H11  H  HCH2  0   0.310  -2.3021  -1.5109  -1.6980
 JPQ  H12  H  HCH2  0   0.311  -1.9760  -2.0892  -0.0684

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
 JPQ  O1  C1   double  1.203  0.020  1.203
 JPQ  N1  C1   single  1.371  0.020  1.371
 JPQ  N1  C2   single  1.377  0.020  1.377
 JPQ  C1  C4   single  1.527  0.020  1.527
 JPQ  C2  O2   double  1.205  0.020  1.205
 JPQ  C2  C3   single  1.508  0.020  1.508
 JPQ  N2  C4   single  1.427  0.020  1.427
 JPQ  N2  C5   single  1.358  0.020  1.358
 JPQ  C4  C3   single  1.528  0.020  1.528
 JPQ  C6  C5   single  1.475  0.020  1.475
 JPQ  C6  C7   double  1.342  0.020  1.342
 JPQ  C5  O3   double  1.224  0.020  1.224
 JPQ  C8  C7   single  1.498  0.020  1.498
 JPQ  C7  C9   single  1.497  0.020  1.497
 JPQ  C4  H1   single  0.970  0.020  1.090
 JPQ  C6  H2   single  0.930  0.020  1.080
 JPQ  C8  H3   single  0.970  0.020  1.090
 JPQ  C8  H4   single  0.970  0.020  1.090
 JPQ  C8  H5   single  0.970  0.020  1.090
 JPQ  C9  H6   single  0.970  0.020  1.090
 JPQ  C9  H7   single  0.970  0.020  1.090
 JPQ  C9  H8   single  0.970  0.020  1.090
 JPQ  N1  H9   single  0.860  0.020  1.020
 JPQ  N2  H10  single  0.860  0.020  1.020
 JPQ  C3  H11  single  0.970  0.020  1.090
 JPQ  C3  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
 JPQ  H1   C4  C1   106.38  3.000
 JPQ  H1   C4  C3   109.94  3.000
 JPQ  C1   C4  C3   103.96  3.000
 JPQ  H1   C4  N2   108.21  3.000
 JPQ  C3   C4  N2   115.26  3.000
 JPQ  C1   C4  N2   112.70  3.000
 JPQ  O3   C5  N2   121.76  3.000
 JPQ  O3   C5  C6   125.31  3.000
 JPQ  N2   C5  C6   112.93  3.000
 JPQ  H2   C6  C7   117.26  3.000
 JPQ  H2   C6  C5   115.64  3.000
 JPQ  C7   C6  C5   127.09  3.000
 JPQ  C9   C7  C8   114.33  3.000
 JPQ  C9   C7  C6   126.41  3.000
 JPQ  C8   C7  C6   119.25  3.000
 JPQ  H5   C8  H4   108.31  3.000
 JPQ  H5   C8  H3   108.57  3.000
 JPQ  H4   C8  H3   106.41  3.000
 JPQ  H5   C8  C7   112.64  3.000
 JPQ  H4   C8  C7   110.22  3.000
 JPQ  H3   C8  C7   110.48  3.000
 JPQ  H8   C9  H7   106.46  3.000
 JPQ  H8   C9  H6   109.14  3.000
 JPQ  H7   C9  H6   107.85  3.000
 JPQ  H8   C9  C7   109.94  3.000
 JPQ  H7   C9  C7   109.50  3.000
 JPQ  H6   C9  C7   113.69  3.000
 JPQ  H9   N1  C2   122.60  3.000
 JPQ  H9   N1  C1   122.94  3.000
 JPQ  C2   N1  C1   114.42  3.000
 JPQ  H10  N2  C5   118.83  3.000
 JPQ  H10  N2  C4   117.47  3.000
 JPQ  C5   N2  C4   123.40  3.000
 JPQ  H12  C3  H11  107.52  3.000
 JPQ  H12  C3  C2   108.19  3.000
 JPQ  H11  C3  C2   111.09  3.000
 JPQ  H12  C3  C4   111.61  3.000
 JPQ  H11  C3  C4   113.68  3.000
 JPQ  C2   C3  C4   104.66  3.000
 JPQ  O1   C1  N1   126.03  3.000
 JPQ  N1   C1  C4   107.05  3.000
 JPQ  O1   C1  C4   126.92  3.000
 JPQ  O2   C2  C3   127.71  3.000
 JPQ  C3   C2  N1   107.53  3.000
 JPQ  O2   C2  N1   124.74  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
 JPQ  CONST_01  C2   N1  C1  C4    0.00   0.0  0
 JPQ  CONST_02  C2   N1  C1  O1  180.00   0.0  0
 JPQ  CONST_03  H9   N1  C1  C4  180.00   0.0  0
 JPQ  CONST_04  C6   C5  N2  C4  180.00   0.0  0
 JPQ  CONST_05  O3   C5  N2  C4    0.00   0.0  0
 JPQ  CONST_06  C8   C7  C6  C5  180.00   0.0  0
 JPQ  CONST_07  C9   C7  C6  C5    0.00   0.0  0
 JPQ  CONST_08  H10  N2  C5  C6    0.00   0.0  0
 JPQ  CONST_09  H2   C6  C7  C8    0.00   0.0  0
 JPQ  Var_01    N1   C2  C3  C4  -11.40  30.0  1
 JPQ  Var_02    C1   N1  C2  C3    2.66  30.0  1
 JPQ  Var_03    N2   C5  C6  C7  173.98  30.0  2
 JPQ  Var_04    H3   C8  C7  C6  121.08  30.0  3
 JPQ  Var_05    H6   C9  C7  C6  -22.90  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
 JPQ  chir_01  C4  C1  N2  C3  negativ

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
 JPQ  plan-1  C4   0.020
 JPQ  plan-1  C5   0.020
 JPQ  plan-1  C6   0.020
 JPQ  plan-1  N2   0.020
 JPQ  plan-1  O3   0.020
 JPQ  plan-1  H10  0.020
 JPQ  plan-2  N1   0.020
 JPQ  plan-2  C3   0.020
 JPQ  plan-2  C2   0.020
 JPQ  plan-2  O2   0.020
 JPQ  plan-3  C4   0.020
 JPQ  plan-3  N1   0.020
 JPQ  plan-3  O1   0.020
 JPQ  plan-3  C1   0.020
 JPQ  plan-3  C2   0.020
 JPQ  plan-3  H9   0.020
 JPQ  plan-4  C5   0.020
 JPQ  plan-4  C6   0.020
 JPQ  plan-4  C7   0.020
 JPQ  plan-4  C8   0.020
 JPQ  plan-4  C9   0.020
 JPQ  plan-4  H2   0.020

