# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:52:30 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: [(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@H](NC(=O)OC[C@@H]2CCCN2)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
 JON  JON  '[(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate'  ligand  32  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_JON
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
 JON  C4   C  CR15  0  -0.135   3.5040   0.2387   0.6086
 JON  C5   C  CR5   0   0.573  -3.1439   0.8350   0.5179
 JON  C6   C  CR5   0   0.549  -4.5576  -0.8928  -0.0727
 JON  C7   C  CH2   0  -0.599  -3.1988  -1.3027  -0.5830
 JON  C8   C  CH2   0  -0.483   4.8246   0.9427   0.2088
 JON  C9   C  CH2   0  -0.454   5.8536  -0.1848   0.1765
 JON  C10  C  CH2   0  -0.315   4.9919  -1.3783  -0.2281
 JON  N1   N  NH1   0  -0.658  -1.0027  -0.2713   0.0150
 JON  N2   N  NR15  0  -0.678  -4.4114   0.3164   0.5703
 JON  C3   C  CH2   0  -0.148   2.3799   0.7073  -0.2896
 JON  N3   N  NR15  0  -0.591   3.7281  -1.2061   0.4825
 JON  C1   C  CR15  0  -0.231  -2.3396  -0.0492  -0.4317
 JON  C2   C  C     0   0.758   0.0511   0.4066  -0.4952
 JON  O1   O  O2    0  -0.480   1.1646   0.1102   0.1678
 JON  O2   O  O     0  -0.514  -0.0049   1.1669  -1.4390
 JON  O4   O  O     0  -0.410  -2.7520   1.8128   1.0995
 JON  H1   H  HCR5  0   0.246   3.2458   0.4764   1.6438
 JON  H2   H  HCH2  0   0.312  -2.8335  -2.1202   0.0443
 JON  H3   H  HCH2  0   0.311  -3.2570  -1.6726  -1.6049
 JON  H4   H  HCH2  0   0.232   4.7336   1.3912  -0.7857
 JON  H5   H  HCH2  0   0.247   5.0833   1.7468   0.8974
 JON  H6   H  HCH2  0   0.232   6.6779   0.0096  -0.5108
 JON  H7   H  HCH2  0   0.224   6.2777  -0.3510   1.1700
 JON  H8   H  HCH2  0   0.216   4.8170  -1.3609  -1.3089
 JON  H9   H  HCH2  0   0.237   5.4346  -2.3458   0.0102
 JON  H10  H  HNH1  0   0.408  -0.8643  -0.8271   0.8458
 JON  H11  H  HNR5  0   0.428  -5.1693   0.7619   1.0727
 JON  H12  H  HCH2  0   0.233   2.3000   1.7971  -0.2545
 JON  H13  H  HCH2  0   0.227   2.5778   0.4137  -1.3245
 JON  H14  H  HNR5  0   0.350   3.8242  -1.6010   1.4080
 JON  H16  H  HCR5  0   0.332  -2.2998   0.4824  -1.3855
 JON  O3   O  O     0  -0.419  -5.5949  -1.4979  -0.1688

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
 JON  O3   C6   double  1.205  0.020  1.205
 JON  N2   C6   single  1.377  0.020  1.377
 JON  N2   C5   single  1.370  0.020  1.370
 JON  C6   C7   single  1.508  0.020  1.508
 JON  C5   O4   double  1.203  0.020  1.203
 JON  C5   C1   single  1.527  0.020  1.527
 JON  C7   C1   single  1.527  0.020  1.527
 JON  C1   N1   single  1.427  0.020  1.427
 JON  O2   C2   double  1.213  0.020  1.213
 JON  N1   C2   single  1.353  0.020  1.353
 JON  C2   O1   single  1.329  0.020  1.329
 JON  O1   C3   single  1.429  0.020  1.429
 JON  C3   C4   single  1.513  0.020  1.513
 JON  C4   N3   single  1.468  0.020  1.468
 JON  C4   C8   single  1.549  0.020  1.549
 JON  N3   C10  single  1.460  0.020  1.460
 JON  C8   C9   single  1.527  0.020  1.527
 JON  C10  C9   single  1.527  0.020  1.527
 JON  C4   H1   single  0.970  0.020  1.090
 JON  C7   H2   single  0.970  0.020  1.090
 JON  C7   H3   single  0.970  0.020  1.090
 JON  C8   H4   single  0.970  0.020  1.090
 JON  C8   H5   single  0.970  0.020  1.090
 JON  C9   H6   single  0.970  0.020  1.090
 JON  C9   H7   single  0.970  0.020  1.090
 JON  C10  H8   single  0.970  0.020  1.090
 JON  C10  H9   single  0.970  0.020  1.090
 JON  N1   H10  single  0.860  0.020  1.020
 JON  N2   H11  single  0.860  0.020  1.020
 JON  C3   H12  single  0.970  0.020  1.090
 JON  C3   H13  single  0.970  0.020  1.090
 JON  N3   H14  single  0.890  0.020  1.040
 JON  C1   H16  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
 JON  H1   C4   N3   109.36  3.000
 JON  H1   C4   C3   108.62  3.000
 JON  N3   C4   C3   111.55  3.000
 JON  H1   C4   C8   110.31  3.000
 JON  N3   C4   C8   107.16  3.000
 JON  C3   C4   C8   109.84  3.000
 JON  O4   C5   C1   126.85  3.000
 JON  C1   C5   N2   106.97  3.000
 JON  O4   C5   N2   126.18  3.000
 JON  O3   C6   N2   124.72  3.000
 JON  N2   C6   C7   107.51  3.000
 JON  O3   C6   C7   127.75  3.000
 JON  H3   C7   H2   107.60  3.000
 JON  H3   C7   C1   113.71  3.000
 JON  H2   C7   C1   111.65  3.000
 JON  H3   C7   C6   111.21  3.000
 JON  H2   C7   C6   108.07  3.000
 JON  C1   C7   C6   104.50  3.000
 JON  H5   C8   H4   106.95  3.000
 JON  H5   C8   C9   113.46  3.000
 JON  H4   C8   C9   109.84  3.000
 JON  H5   C8   C4   112.00  3.000
 JON  H4   C8   C4   110.48  3.000
 JON  C9   C8   C4   104.15  3.000
 JON  H7   C9   H6   107.86  3.000
 JON  H7   C9   C10  109.94  3.000
 JON  H6   C9   C10  113.51  3.000
 JON  H7   C9   C8   110.77  3.000
 JON  H6   C9   C8   113.02  3.000
 JON  C10  C9   C8   101.68  3.000
 JON  H9   C10  H8   107.14  3.000
 JON  H9   C10  N3   110.47  3.000
 JON  H8   C10  N3   109.89  3.000
 JON  H9   C10  C9   113.99  3.000
 JON  H8   C10  C9   109.84  3.000
 JON  N3   C10  C9   105.51  3.000
 JON  H10  N1   C2   118.66  3.000
 JON  H10  N1   C1   118.16  3.000
 JON  C2   N1   C1   122.26  3.000
 JON  H11  N2   C6   122.58  3.000
 JON  H11  N2   C5   123.00  3.000
 JON  C6   N2   C5   114.37  3.000
 JON  H13  C3   H12  108.13  3.000
 JON  H13  C3   O1   110.15  3.000
 JON  H12  C3   O1   110.12  3.000
 JON  H13  C3   C4   110.13  3.000
 JON  H12  C3   C4   110.11  3.000
 JON  O1   C3   C4   108.20  3.000
 JON  H14  N3   C10  108.49  3.000
 JON  H14  N3   C4   108.69  3.000
 JON  C10  N3   C4   106.86  3.000
 JON  H16  C1   N1   108.35  3.000
 JON  H16  C1   C7   109.47  3.000
 JON  N1   C1   C7   115.49  3.000
 JON  H16  C1   C5   106.28  3.000
 JON  N1   C1   C5   112.90  3.000
 JON  C7   C1   C5   103.92  3.000
 JON  O2   C2   O1   124.49  3.000
 JON  O1   C2   N1   110.65  3.000
 JON  O2   C2   N1   124.85  3.000
 JON  C2   O1   C3   117.35  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
 JON  CONST_01  C1   C5   N2  C6    0.00   0.0  0
 JON  CONST_02  O4   C5   N2  C6  180.00   0.0  0
 JON  CONST_03  H11  N2   C5  C1  180.00   0.0  0
 JON  Var_01    C9   C10  N3  C4   31.79  30.0  1
 JON  Var_02    C7   C6   N2  C5    3.08  30.0  1
 JON  Var_03    N3   C10  C9  C8  -38.85  30.0  1
 JON  Var_04    C1   C7   C6  N2  -12.37  30.0  1
 JON  Var_05    O2   C2   N1  C1   -6.69  30.0  2
 JON  Var_06    H12  C3   O1  C2   59.32  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
 JON  chir_01  C4  C3  N3  C8  negativ
 JON  chir_02  C1  N1  C7  C5  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
 JON  plan-1  C6   0.020
 JON  plan-1  C7   0.020
 JON  plan-1  N2   0.020
 JON  plan-1  O3   0.020
 JON  plan-2  C5   0.020
 JON  plan-2  C6   0.020
 JON  plan-2  N2   0.020
 JON  plan-2  C1   0.020
 JON  plan-2  O4   0.020
 JON  plan-2  H11  0.020
 JON  plan-3  N1   0.020
 JON  plan-3  C2   0.020
 JON  plan-3  O1   0.020
 JON  plan-3  O2   0.020

