# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:02:00 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (3S)-3-[(2R)-2-amino-5-oxohexyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CC[C@@H](N)C[C@@H]1CCNC1=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
 Z0A  Z0A  (3S)-3-[(2R)-2-amino-5-oxohexyl]pyrrolidin-2-one  ligand  32  14  .  2021-08-25  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Z0A
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
 Z0A  N1   N  NH2   0  -0.778  -0.0267   1.0102  -0.8092
 Z0A  C1   C  CH1   0  -0.103   0.2444   0.0477   0.2509
 Z0A  C2   C  CH2   0  -0.401  -0.8568  -1.0107   0.2331
 Z0A  C3   C  CH1   0  -0.397  -2.1844  -0.6247   0.9043
 Z0A  C4   C  CH2   0  -0.424   1.6214  -0.6223   0.1571
 Z0A  C5   C  C     0   0.564  -2.6593   0.7836   0.5699
 Z0A  O1   O  O     0  -0.503  -2.3284   1.8187   1.1244
 Z0A  N2   N  NH1   0  -0.624  -3.5650   0.6729  -0.4186
 Z0A  C6   C  CH2   0  -0.256  -3.8603  -0.6856  -0.8174
 Z0A  C7   C  CH2   0  -0.474  -3.3338  -1.4886   0.3770
 Z0A  C8   C  CH2   0  -0.567   2.7608   0.3819   0.1569
 Z0A  C9   C  C     0   0.394   4.1451  -0.2130   0.1171
 Z0A  C10  C  CH3   0  -0.767   5.2768   0.7795   0.1315
 Z0A  O2   O  O     0  -0.408   4.3378  -1.4078   0.0710
 Z0A  H1   H  HNH2  0   0.346   0.5554   1.8315  -0.7041
 Z0A  H2   H  HCH1  0   0.225   0.2007   0.5942   1.1998
 Z0A  H3   H  HCH2  0   0.223  -1.0387  -1.2913  -0.8107
 Z0A  H4   H  HCH2  0   0.238  -0.5097  -1.9211   0.7291
 Z0A  H5   H  HCH1  0   0.263  -2.0647  -0.7061   1.9868
 Z0A  H6   H  HCH2  0   0.226   1.7375  -1.3104   0.9984
 Z0A  H7   H  HCH2  0   0.220   1.6604  -1.2341  -0.7511
 Z0A  H8   H  HNH1  0   0.390  -3.9848   1.4764  -0.8583
 Z0A  H9   H  HCH2  0   0.250  -4.9299  -0.8253  -0.9734
 Z0A  H10  H  HCH2  0   0.229  -3.3529  -0.9533  -1.7493
 Z0A  H11  H  HCH2  0   0.249  -3.0178  -2.4932   0.0964
 Z0A  H12  H  HCH2  0   0.252  -4.1192  -1.5819   1.1296
 Z0A  H13  H  HCH2  0   0.258   2.6817   1.0653  -0.6960
 Z0A  H14  H  HCH2  0   0.264   2.7027   1.0313   1.0390
 Z0A  H15  H  HCH3  0   0.262   5.2121   1.4104   1.0195
 Z0A  H16  H  HCH3  0   0.257   6.2454   0.2844   0.1136
 Z0A  H17  H  HCH3  0   0.263   5.1991   1.4449  -0.7302
 Z0A  H18  H  HNH2  0   0.332   0.2192   0.6019  -1.7050

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
 Z0A  N1   C1   single  1.457  0.020  1.457
 Z0A  N1   H1   single  0.890  0.020  1.040
 Z0A  C1   C2   single  1.528  0.020  1.528
 Z0A  C1   C4   single  1.534  0.020  1.534
 Z0A  C1   H2   single  0.970  0.020  1.090
 Z0A  C2   C3   single  1.537  0.020  1.537
 Z0A  C2   H3   single  0.970  0.020  1.090
 Z0A  C2   H4   single  0.970  0.020  1.090
 Z0A  C3   C5   single  1.523  0.020  1.523
 Z0A  C3   C7   single  1.531  0.020  1.531
 Z0A  C3   H5   single  0.970  0.020  1.090
 Z0A  C4   C8   single  1.519  0.020  1.519
 Z0A  C4   H6   single  0.970  0.020  1.090
 Z0A  C4   H7   single  0.970  0.020  1.090
 Z0A  C5   O1   double  1.220  0.020  1.220
 Z0A  C5   N2   single  1.345  0.020  1.345
 Z0A  N2   C6   single  1.446  0.020  1.446
 Z0A  N2   H8   single  0.860  0.020  1.020
 Z0A  C6   C7   single  1.532  0.020  1.532
 Z0A  C6   H9   single  0.970  0.020  1.090
 Z0A  C6   H10  single  0.970  0.020  1.090
 Z0A  C7   H11  single  0.970  0.020  1.090
 Z0A  C7   H12  single  0.970  0.020  1.090
 Z0A  C8   C9   single  1.507  0.020  1.507
 Z0A  C8   H13  single  0.970  0.020  1.090
 Z0A  C8   H14  single  0.970  0.020  1.090
 Z0A  C9   C10  single  1.505  0.020  1.505
 Z0A  C9   O2   double  1.211  0.020  1.211
 Z0A  C10  H15  single  0.970  0.020  1.090
 Z0A  C10  H16  single  0.970  0.020  1.090
 Z0A  C10  H17  single  0.970  0.020  1.090
 Z0A  N1   H18  single  0.890  0.020  1.040

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
 Z0A  H18  N1   H1   106.19  3.000
 Z0A  H18  N1   C1   109.35  3.000
 Z0A  H1   N1   C1   110.70  3.000
 Z0A  H2   C1   C4   107.85  3.000
 Z0A  H2   C1   C2   109.08  3.000
 Z0A  C4   C1   C2   110.10  3.000
 Z0A  H2   C1   N1   107.04  3.000
 Z0A  C4   C1   N1   114.26  3.000
 Z0A  C2   C1   N1   108.36  3.000
 Z0A  H4   C2   H3   105.76  3.000
 Z0A  H4   C2   C3   106.57  3.000
 Z0A  H3   C2   C3   109.69  3.000
 Z0A  H4   C2   C1   110.05  3.000
 Z0A  H3   C2   C1   107.95  3.000
 Z0A  C3   C2   C1   116.33  3.000
 Z0A  H5   C3   C7   112.43  3.000
 Z0A  H5   C3   C5   108.70  3.000
 Z0A  C7   C3   C5   102.24  3.000
 Z0A  H5   C3   C2   108.63  3.000
 Z0A  C7   C3   C2   110.87  3.000
 Z0A  C5   C3   C2   113.93  3.000
 Z0A  H7   C4   H6   106.42  3.000
 Z0A  H7   C4   C8   110.02  3.000
 Z0A  H6   C4   C8   109.67  3.000
 Z0A  H7   C4   C1   109.06  3.000
 Z0A  H6   C4   C1   108.86  3.000
 Z0A  C8   C4   C1   112.62  3.000
 Z0A  N2   C5   O1   125.90  3.000
 Z0A  N2   C5   C3   107.16  3.000
 Z0A  O1   C5   C3   126.88  3.000
 Z0A  H8   N2   C6   122.93  3.000
 Z0A  H8   N2   C5   122.38  3.000
 Z0A  C6   N2   C5   114.67  3.000
 Z0A  H10  C6   H9   107.57  3.000
 Z0A  H10  C6   C7   112.10  3.000
 Z0A  H9   C6   C7   112.42  3.000
 Z0A  H10  C6   N2   111.71  3.000
 Z0A  H9   C6   N2   111.12  3.000
 Z0A  C7   C6   N2   101.95  3.000
 Z0A  H12  C7   H11  107.89  3.000
 Z0A  H12  C7   C6   109.57  3.000
 Z0A  H11  C7   C6   112.46  3.000
 Z0A  H12  C7   C3   110.53  3.000
 Z0A  H11  C7   C3   113.02  3.000
 Z0A  C6   C7   C3   103.33  3.000
 Z0A  H14  C8   H13  104.64  3.000
 Z0A  H14  C8   C9   107.68  3.000
 Z0A  H13  C8   C9   106.98  3.000
 Z0A  H14  C8   C4   110.58  3.000
 Z0A  H13  C8   C4   110.99  3.000
 Z0A  C9   C8   C4   115.34  3.000
 Z0A  O2   C9   C10  122.08  3.000
 Z0A  O2   C9   C8   122.45  3.000
 Z0A  C10  C9   C8   115.47  3.000
 Z0A  H17  C10  H16  109.14  3.000
 Z0A  H17  C10  H15  106.60  3.000
 Z0A  H16  C10  H15  109.22  3.000
 Z0A  H17  C10  C9   109.93  3.000
 Z0A  H16  C10  C9   111.66  3.000
 Z0A  H15  C10  C9   110.14  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
 Z0A  CONST_01  C6   N2   C5  C3     0.00   0.0  0
 Z0A  CONST_02  C6   N2   C5  O1   180.00   0.0  0
 Z0A  CONST_03  H8   N2   C5  C3   180.00   0.0  0
 Z0A  Var_01    N2   C6   C7  C3   -29.83  30.0  1
 Z0A  Var_02    C7   C6   N2  C5    17.62  30.0  1
 Z0A  Var_03    C9   C8   C4  C1   177.87  30.0  3
 Z0A  Var_04    C10  C9   C8  C4  -179.38  30.0  3
 Z0A  Var_05    H15  C10  C9  C8    57.76  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
 Z0A  chir_01  C1  N1  C2  C4  negativ
 Z0A  chir_02  C3  C7  C5  C2  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
 Z0A  plan-1  C8   0.020
 Z0A  plan-1  C9   0.020
 Z0A  plan-1  C10  0.020
 Z0A  plan-1  O2   0.020
 Z0A  plan-2  C3   0.020
 Z0A  plan-2  C5   0.020
 Z0A  plan-2  O1   0.020
 Z0A  plan-2  N2   0.020
 Z0A  plan-2  C6   0.020
 Z0A  plan-2  H8   0.020

