# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 03:17:15 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (3S)-3-hydroxy-5-oxo-N-[(1Z)-3-oxoprop-1-en-1-yl]-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC=O)[C@@H](N\C=C/C=O)C(O)=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
 CEM  CEM  (3S)-3-hydroxy-5-oxo-N-[(1Z)-3-oxoprop-1-en-1-yl]-D-norvaline  ligand  24  14  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CEM
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
 CEM  O1   O  OH1    0  -0.660  -0.1517  -1.2513  -1.7069
 CEM  C2   C  CH1    0   0.030   0.1807   0.1164  -1.6308
 CEM  C3   C  CH1    0  -0.268   1.0407   0.4192  -0.3979
 CEM  N4   N  NH1    0  -0.595   0.3560   0.1066   0.8365
 CEM  C5   C  C1     0   0.058  -0.3877   0.9641   1.5296
 CEM  C6   C  C1     0  -0.481  -1.0069   0.7841   2.7406
 CEM  C7   C  C1     0   0.133  -0.9750  -0.4285   3.4897
 CEM  O8   O  O      0  -0.471  -1.5231  -0.6116   4.5704
 CEM  C9   C  CH2    0  -0.593  -1.0752   0.9803  -1.7252
 CEM  C10  C  C1     0   0.198  -1.8260   0.6527  -2.9802
 CEM  O11  O  O      0  -0.378  -3.0076   0.4219  -3.0402
 CEM  C12  C  C      0   0.443   2.3582  -0.4020  -0.4818
 CEM  O13  O  O      0  -0.595   3.0672  -0.1622  -1.4718
 CEM  O14  O  OC    -1  -0.587   2.5727  -1.2156   0.4346
 CEM  HO1  H  HOH1   0   0.444  -0.6925  -1.4773  -0.9413
 CEM  H2   H  HCH1   0   0.251   0.8043   0.3249  -2.5035
 CEM  H3   H  HCH1   0   0.263   1.2967   1.4835  -0.4122
 CEM  HN4  H  HNH1   0   0.394   0.6695  -0.7583   1.2583
 CEM  H5   H  H      0   0.286  -0.5069   1.9330   1.0554
 CEM  H6   H  H      0   0.248  -1.5622   1.6235   3.1380
 CEM  H7   H  H      0   0.154  -0.4039  -1.2597   3.0327
 CEM  H91  H  HCH2   0   0.260  -1.7353   0.8634  -0.8625
 CEM  H92  H  HCH2   0   0.280  -0.7817   2.0348  -1.7868
 CEM  H10  H  H      0   0.185  -1.2048   0.6495  -3.8953

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
 CEM  O1   C2   single  1.410  0.020  1.410
 CEM  O1   HO1  single  0.850  0.020  0.980
 CEM  C2   C3   single  1.533  0.020  1.533
 CEM  C2   C9   single  1.527  0.020  1.527
 CEM  C2   H2   single  0.970  0.020  1.090
 CEM  C3   N4   single  1.446  0.020  1.446
 CEM  C3   C12  single  1.555  0.020  1.555
 CEM  C3   H3   single  0.970  0.020  1.090
 CEM  N4   C5   single  1.330  0.020  1.330
 CEM  N4   HN4  single  0.860  0.020  1.020
 CEM  C5   C6   double  1.372  0.020  1.372
 CEM  C5   H5   single  0.930  0.020  1.080
 CEM  C6   C7   single  1.426  0.020  1.426
 CEM  C6   H6   single  0.930  0.020  1.080
 CEM  C7   O8   double  1.225  0.020  1.225
 CEM  C7   H7   single  0.930  0.020  1.080
 CEM  C9   C10  single  1.499  0.020  1.499
 CEM  C9   H91  single  0.970  0.020  1.090
 CEM  C9   H92  single  0.970  0.020  1.090
 CEM  C10  O11  double  1.205  0.020  1.205
 CEM  C10  H10  single  0.930  0.020  1.080
 CEM  C12  O13  deloc   1.241  0.020  1.241
 CEM  C12  O14  deloc   1.244  0.020  1.244

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
 CEM  HO1  O1   C2   108.47  3.000
 CEM  H2   C2   C9   108.18  3.000
 CEM  H2   C2   C3   106.52  3.000
 CEM  C9   C2   C3   113.53  3.000
 CEM  H2   C2   O1   106.06  3.000
 CEM  C9   C2   O1   110.59  3.000
 CEM  C3   C2   O1   111.55  3.000
 CEM  H3   C3   C12  108.34  3.000
 CEM  H3   C3   N4   109.39  3.000
 CEM  C12  C3   N4   109.47  3.000
 CEM  H3   C3   C2   108.22  3.000
 CEM  C12  C3   C2   109.12  3.000
 CEM  N4   C3   C2   112.22  3.000
 CEM  HN4  N4   C5   120.47  3.000
 CEM  HN4  N4   C3   113.19  3.000
 CEM  C5   N4   C3   124.78  3.000
 CEM  H5   C5   C6   116.95  3.000
 CEM  H5   C5   N4   114.16  3.000
 CEM  C6   C5   N4   128.88  3.000
 CEM  H6   C6   C7   118.58  3.000
 CEM  H6   C6   C5   117.00  3.000
 CEM  C7   C6   C5   124.42  3.000
 CEM  H7   C7   O8   118.85  3.000
 CEM  H7   C7   C6   115.67  3.000
 CEM  O8   C7   C6   125.48  3.000
 CEM  H92  C9   H91  108.00  3.000
 CEM  H92  C9   C10  107.30  3.000
 CEM  H91  C9   C10  109.59  3.000
 CEM  H92  C9   C2   109.11  3.000
 CEM  H91  C9   C2   112.79  3.000
 CEM  C10  C9   C2   109.88  3.000
 CEM  H10  C10  O11  120.58  3.000
 CEM  H10  C10  C9   114.34  3.000
 CEM  O11  C10  C9   125.07  3.000
 CEM  O14  C12  O13  127.98  3.000
 CEM  O14  C12  C3   116.86  3.000
 CEM  O13  C12  C3   115.16  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
 CEM  Var_01  C7   C6   C5  N4    -1.25   0.0  2
 CEM  Var_02  O11  C10  C9  C2   131.05  30.0  3
 CEM  Var_03  C6   C5   N4  C3  -175.82  30.0  2
 CEM  Var_04  O8   C7   C6  C5  -179.81  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
 CEM  chir_01  C2  O1  C3  C9   positiv
 CEM  chir_02  C3  N4  C2  C12  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
 CEM  plan-1  C3   0.020
 CEM  plan-1  C12  0.020
 CEM  plan-1  O13  0.020
 CEM  plan-1  O14  0.020
 CEM  plan-2  N4   0.020
 CEM  plan-2  C5   0.020
 CEM  plan-2  C6   0.020
 CEM  plan-2  C7   0.020
 CEM  plan-2  H5   0.020
 CEM  plan-2  H6   0.020
 CEM  plan-3  C6   0.020
 CEM  plan-3  C7   0.020
 CEM  plan-3  O8   0.020
 CEM  plan-3  H7   0.020
 CEM  plan-4  C9   0.020
 CEM  plan-4  C10  0.020
 CEM  plan-4  O11  0.020
 CEM  plan-4  H10  0.020

