# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 19:11:40 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  25  14  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.654   0.0013  -1.3169  -1.7934
 CEM  C2    C  CH1   0   0.016   0.1746   0.0739  -1.6680
 CEM  C3    C  CH1   0  -0.244   0.9777   0.4274  -0.4043
 CEM  N4    N  NH1   0  -0.599   0.2681   0.1179   0.8064
 CEM  C5    C  C1    0   0.065  -0.0787   1.0393   1.7125
 CEM  C6    C  C1    0  -0.473  -0.7373   0.8730   2.8965
 CEM  C7    C  C1    0   0.139  -1.2027  -0.3831   3.3991
 CEM  O8    O  O     0  -0.456  -1.7940  -0.5426   4.4572
 CEM  C9    C  CH2   0  -0.595  -1.1529   0.8173  -1.7206
 CEM  C10   C  C1    0   0.195  -1.8668   0.5146  -3.0059
 CEM  O11   O  O     0  -0.371  -3.0329   0.2253  -3.0911
 CEM  C12   C  C     0   0.568   2.3491  -0.2349  -0.4891
 CEM  O13   O  O     0  -0.434   3.0655  -0.1007  -1.4472
 CEM  O14   O  OH1   0  -0.575   2.6581  -0.9404   0.5812
 CEM  HO1   H  HOH1  0   0.455  -0.7037  -1.6134  -1.2070
 CEM  H2    H  HCH1  0   0.273   0.7774   0.3843  -2.5249
 CEM  H3    H  HCH1  0   0.320   1.1615   1.5057  -0.4212
 CEM  HN4   H  HNH1  0   0.407   0.0695  -0.8534   0.9926
 CEM  H5    H  H     0   0.299   0.2121   2.0482   1.4412
 CEM  H6    H  H     0   0.258  -0.9182   1.7633   3.4842
 CEM  H7    H  H     0   0.160  -1.0018  -1.2641   2.7604
 CEM  H91   H  HCH2  0   0.272  -1.7966   0.5867  -0.8687
 CEM  H92   H  HCH2  0   0.292  -0.9574   1.8958  -1.7075
 CEM  H10   H  H     0   0.193  -1.2364   0.5968  -3.9102
 CEM  HO14  H  HOH1  0   0.491   3.5374  -1.3365   0.4780

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  1.407  0.020  1.407
 CEM  O1   HO1   single  0.850  0.020  0.980
 CEM  C2   C3    single  1.538  0.020  1.538
 CEM  C2   C9    single  1.522  0.020  1.522
 CEM  C2   H2    single  0.970  0.020  1.090
 CEM  C3   N4    single  1.437  0.020  1.437
 CEM  C3   C12   single  1.525  0.020  1.525
 CEM  C3   H3    single  0.970  0.020  1.090
 CEM  N4   C5    single  1.338  0.020  1.338
 CEM  N4   HN4   single  0.860  0.020  1.020
 CEM  C5   C6    double  1.365  0.020  1.365
 CEM  C5   H5    single  0.930  0.020  1.080
 CEM  C6   C7    single  1.431  0.020  1.431
 CEM  C6   H6    single  0.930  0.020  1.080
 CEM  C7   O8    double  1.223  0.020  1.223
 CEM  C7   H7    single  0.930  0.020  1.080
 CEM  C9   C10   single  1.501  0.020  1.501
 CEM  C9   H91   single  0.970  0.020  1.090
 CEM  C9   H92   single  0.970  0.020  1.090
 CEM  C10  O11   double  1.204  0.020  1.204
 CEM  C10  H10   single  0.930  0.020  1.080
 CEM  C12  O13   double  1.204  0.020  1.204
 CEM  C12  O14   single  1.319  0.020  1.319
 CEM  O14  HO14  single  0.850  0.020  0.980

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   109.87  3.000
 CEM  H2    C2   C9   108.37  3.000
 CEM  H2    C2   C3   106.91  3.000
 CEM  C9    C2   C3   111.80  3.000
 CEM  H2    C2   O1   106.19  3.000
 CEM  C9    C2   O1   111.85  3.000
 CEM  C3    C2   O1   111.39  3.000
 CEM  H3    C3   C12  106.03  3.000
 CEM  H3    C3   N4   107.95  3.000
 CEM  C12   C3   N4   113.41  3.000
 CEM  H3    C3   C2   107.55  3.000
 CEM  C12   C3   C2   108.90  3.000
 CEM  N4    C3   C2   112.63  3.000
 CEM  HN4   N4   C5   119.15  3.000
 CEM  HN4   N4   C3   117.39  3.000
 CEM  C5    N4   C3   123.38  3.000
 CEM  H5    C5   C6   117.37  3.000
 CEM  H5    C5   N4   113.69  3.000
 CEM  C6    C5   N4   128.94  3.000
 CEM  H6    C6   C7   118.50  3.000
 CEM  H6    C6   C5   116.84  3.000
 CEM  C7    C6   C5   124.65  3.000
 CEM  H7    C7   O8   118.92  3.000
 CEM  H7    C7   C6   115.92  3.000
 CEM  O8    C7   C6   125.16  3.000
 CEM  H92   C9   H91  107.67  3.000
 CEM  H92   C9   C10  107.07  3.000
 CEM  H91   C9   C10  110.18  3.000
 CEM  H92   C9   C2   108.93  3.000
 CEM  H91   C9   C2   112.57  3.000
 CEM  C10   C9   C2   110.24  3.000
 CEM  H10   C10  O11  120.80  3.000
 CEM  H10   C10  C9   114.47  3.000
 CEM  O11   C10  C9   124.71  3.000
 CEM  O14   C12  O13  124.49  3.000
 CEM  O14   C12  C3   113.45  3.000
 CEM  O13   C12  C3   122.06  3.000
 CEM  HO14  O14  C12  110.16  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  CONST_01  HO14  O14  C12  C3   180.00   0.0  0
 CEM  Var_01    C7    C6   C5   N4    -0.34   0.0  2
 CEM  Var_02    O11   C10  C9   C2   133.65  30.0  3
 CEM  Var_03    C6    C5   N4   C3  -179.36  30.0  2
 CEM  Var_04    O8    C7   C6   C5  -179.95  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-1  HO14  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

