# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:49:32 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (3R)-3-(oxaloamino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(O)=O)NC(=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
 8S6  8S6  "(3R)-3-(oxaloamino)butanoic acid"  ligand  19  12  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8S6
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
 8S6  C1   C  CH3    0  -0.664  34.9875  47.0670   2.3799
 8S6  C2   C  CH1    0  -0.064  33.7635  46.6243   1.5886
 8S6  C4   C  C      0   0.342  31.3843  47.1738   2.0197
 8S6  C6   C  C      0   0.328  30.4283  48.3882   2.2592
 8S6  C9   C  CH2    0  -0.545  34.0519  46.5441   0.0894
 8S6  C10  C  C      0   0.399  35.1194  45.4987  -0.2948
 8S6  N3   N  NH1    0  -0.608  32.6648  47.5308   1.8636
 8S6  O5   O  O      0  -0.505  30.9828  46.0170   1.9896
 8S6  O7   O  O      0  -0.574  29.2483  48.1000   2.4929
 8S6  O8   O  OC    -1  -0.586  30.9549  49.5147   2.1866
 8S6  O11  O  OC    -1  -0.612  35.0575  44.3996   0.2958
 8S6  O12  O  O      0  -0.609  35.9343  45.8252  -1.1799
 8S6  H1   H  HCH3   0   0.230  34.7774  47.0975   3.4496
 8S6  H2   H  HCH3   0   0.231  35.8172  46.3795   2.2214
 8S6  H3   H  HCH3   0   0.216  35.3168  48.0626   2.0721
 8S6  H4   H  HCH1   0   0.220  33.4584  45.6367   1.9344
 8S6  H5   H  HCH2   0   0.196  34.3372  47.5342  -0.2783
 8S6  H6   H  HCH2   0   0.227  33.1204  46.2801  -0.4252
 8S6  H7   H  HNH1   0   0.379  32.8385  48.5251   1.8619

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
 8S6  O12  C10  deloc   1.247  0.020  1.247
 8S6  C10  C9   single  1.543  0.020  1.543
 8S6  C10  O11  deloc   1.249  0.020  1.249
 8S6  C9   C2   single  1.529  0.020  1.529
 8S6  O7   C6   deloc   1.237  0.020  1.237
 8S6  C2   N3   single  1.451  0.020  1.451
 8S6  C2   C1   single  1.523  0.020  1.523
 8S6  O5   C4   double  1.225  0.020  1.225
 8S6  N3   C4   single  1.339  0.020  1.339
 8S6  C4   C6   single  1.564  0.020  1.564
 8S6  C6   O8   deloc   1.246  0.020  1.246
 8S6  C1   H1   single  0.970  0.020  1.090
 8S6  C1   H2   single  0.970  0.020  1.090
 8S6  C1   H3   single  0.970  0.020  1.090
 8S6  C2   H4   single  0.970  0.020  1.090
 8S6  C9   H5   single  0.970  0.020  1.090
 8S6  C9   H6   single  0.970  0.020  1.090
 8S6  N3   H7   single  0.860  0.020  1.020

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
 8S6  H3   C1   H2   107.73  3.000
 8S6  H3   C1   H1   107.99  3.000
 8S6  H2   C1   H1   107.88  3.000
 8S6  H3   C1   C2   111.14  3.000
 8S6  H2   C1   C2   110.68  3.000
 8S6  H1   C1   C2   111.28  3.000
 8S6  H4   C2   N3   107.10  3.000
 8S6  H4   C2   C9   108.44  3.000
 8S6  N3   C2   C9   111.19  3.000
 8S6  H4   C2   C1   108.87  3.000
 8S6  N3   C2   C1   109.18  3.000
 8S6  C9   C2   C1   111.91  3.000
 8S6  O5   C4   N3   124.24  3.000
 8S6  N3   C4   C6   113.30  3.000
 8S6  O5   C4   C6   122.46  3.000
 8S6  O8   C6   O7   128.68  3.000
 8S6  O8   C6   C4   115.77  3.000
 8S6  O7   C6   C4   115.54  3.000
 8S6  H6   C9   H5   106.36  3.000
 8S6  H6   C9   C10  107.93  3.000
 8S6  H5   C9   C10  110.43  3.000
 8S6  H6   C9   C2   108.21  3.000
 8S6  H5   C9   C2   109.35  3.000
 8S6  C10  C9   C2   114.23  3.000
 8S6  O12  C10  O11  126.76  3.000
 8S6  O11  C10  C9   116.37  3.000
 8S6  O12  C10  C9   116.85  3.000
 8S6  H7   N3   C4   115.31  3.000
 8S6  H7   N3   C2   119.01  3.000
 8S6  C4   N3   C2   125.45  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
 8S6  CONST_01  O5   C4   N3   C2      0.00   0.0  0
 8S6  CONST_02  C6   C4   N3   C2    180.00   0.0  0
 8S6  CONST_03  H7   N3   C4   C6      0.00   0.0  0
 8S6  CONST_04  H7   N3   C4   O5    180.00   0.0  0
 8S6  Var_01    O12  C10  C9   C2   -139.70  30.0  2
 8S6  Var_02    O11  C10  C9   C2     41.80  30.0  2
 8S6  Var_03    O7   C6   C4   N3   -175.62  30.0  2
 8S6  Var_04    O8   C6   C4   N3      4.53  30.0  2
 8S6  Var_05    O7   C6   C4   O5      3.96  30.0  2
 8S6  Var_06    O8   C6   C4   O5   -175.90  30.0  2
 8S6  Var_07    H5   C9   C10  O11   165.54  30.0  3
 8S6  Var_08    H6   C9   C10  O11   -78.58  30.0  3
 8S6  Var_09    H5   C9   C10  O12   -15.96  30.0  3
 8S6  Var_10    H6   C9   C10  O12    99.91  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
 8S6  chir_01  C2  C9  N3  C1  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
 8S6  plan-1  C2   0.020
 8S6  plan-1  C4   0.020
 8S6  plan-1  C6   0.020
 8S6  plan-1  N3   0.020
 8S6  plan-1  O5   0.020
 8S6  plan-1  H7   0.020
 8S6  plan-2  C4   0.020
 8S6  plan-2  C6   0.020
 8S6  plan-2  O7   0.020
 8S6  plan-2  O8   0.020
 8S6  plan-3  C9   0.020
 8S6  plan-3  C10  0.020
 8S6  plan-3  O11  0.020
 8S6  plan-3  O12  0.020

