# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 19 18:22:56 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  21  12  .  2022-09-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.681  34.9713  47.0661   2.4080
 8S6  C2   C  CH1   0  -0.087  33.7258  46.5640   1.6946
 8S6  C4   C  C     0   0.447  31.3415  47.0602   1.9439
 8S6  C6   C  C     0   0.464  30.2896  48.1239   2.2987
 8S6  C9   C  CH2   0  -0.550  33.9160  46.4869   0.1725
 8S6  C10  C  C     0   0.527  35.0135  45.5573  -0.2714
 8S6  N3   N  NH1   0  -0.624  32.6163  47.4505   2.0053
 8S6  O5   O  O     0  -0.452  30.9594  45.9490   1.6345
 8S6  O7   O  O     0  -0.397  29.1212  47.9223   2.1321
 8S6  O8   O  OH1   0  -0.585  30.8161  49.2286   2.7932
 8S6  O11  O  OH1   0  -0.590  34.9364  44.3701   0.3241
 8S6  O12  O  O     0  -0.431  35.8566  45.8318  -1.0869
 8S6  H1   H  HCH3  0   0.254  34.8077  47.1144   3.4842
 8S6  H2   H  HCH3  0   0.250  35.8139  46.3981   2.2341
 8S6  H3   H  HCH3  0   0.237  35.2537  48.0602   2.0566
 8S6  H4   H  HCH1  0   0.265  33.4687  45.5753   2.0765
 8S6  H5   H  HCH2  0   0.269  34.1256  47.4799  -0.2264
 8S6  H6   H  HCH2  0   0.293  32.9861  46.1403  -0.2888
 8S6  H7   H  HNH1  0   0.417  32.8333  48.4104   2.2268
 8S6  H8   H  HOH1  0   0.496  30.1281  49.8815   3.0002
 8S6  H9   H  HOH1  0   0.480  35.6542  43.7958   0.0158

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  double  1.205  0.020  1.205
 8S6  C10  C9   single  1.505  0.020  1.505
 8S6  C10  O11  single  1.330  0.020  1.330
 8S6  C9   C2   single  1.536  0.020  1.536
 8S6  O7   C6   double  1.197  0.020  1.197
 8S6  C2   N3   single  1.454  0.020  1.454
 8S6  C2   C1   single  1.521  0.020  1.521
 8S6  O5   C4   double  1.215  0.020  1.215
 8S6  N3   C4   single  1.335  0.020  1.335
 8S6  C4   C6   single  1.537  0.020  1.537
 8S6  C6   O8   single  1.320  0.020  1.320
 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
 8S6  O8   H8   single  0.850  0.020  0.980
 8S6  O11  H9   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
 8S6  H3   C1   H2   107.88  3.000
 8S6  H3   C1   H1   108.44  3.000
 8S6  H2   C1   H1   107.52  3.000
 8S6  H3   C1   C2   111.20  3.000
 8S6  H2   C1   C2   110.87  3.000
 8S6  H1   C1   C2   110.80  3.000
 8S6  H4   C2   N3   107.33  3.000
 8S6  H4   C2   C9   109.31  3.000
 8S6  N3   C2   C9   109.69  3.000
 8S6  H4   C2   C1   109.15  3.000
 8S6  N3   C2   C1   108.88  3.000
 8S6  C9   C2   C1   112.34  3.000
 8S6  O5   C4   N3   125.41  3.000
 8S6  N3   C4   C6   116.14  3.000
 8S6  O5   C4   C6   118.45  3.000
 8S6  O8   C6   O7   125.61  3.000
 8S6  O8   C6   C4   113.11  3.000
 8S6  O7   C6   C4   121.27  3.000
 8S6  H6   C9   H5   107.31  3.000
 8S6  H6   C9   C10  107.44  3.000
 8S6  H5   C9   C10  108.33  3.000
 8S6  H6   C9   C2   109.17  3.000
 8S6  H5   C9   C2   109.91  3.000
 8S6  C10  C9   C2   114.43  3.000
 8S6  O12  C10  O11  123.16  3.000
 8S6  O11  C10  C9   112.14  3.000
 8S6  O12  C10  C9   124.69  3.000
 8S6  H7   N3   C4   119.59  3.000
 8S6  H7   N3   C2   117.58  3.000
 8S6  C4   N3   C2   122.74  3.000
 8S6  H8   O8   C6   111.11  3.000
 8S6  H9   O11  C10  110.08  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  CONST_05  H8   O8   C6   C4    180.00   0.0  0
 8S6  CONST_06  H9   O11  C10  C9    180.00   0.0  0
 8S6  CONST_07  H8   O8   C6   O7      0.00   0.0  0
 8S6  CONST_08  H9   O11  C10  O12     0.00   0.0  0
 8S6  Var_01    O12  C10  C9   C2   -133.02  30.0  2
 8S6  Var_02    O11  C10  C9   C2     48.23  30.0  2
 8S6  Var_03    O7   C6   C4   N3    171.60  30.0  2
 8S6  Var_04    O8   C6   C4   N3     -8.78  30.0  2
 8S6  Var_05    O7   C6   C4   O5     -8.40  30.0  2
 8S6  Var_06    O8   C6   C4   O5    171.23  30.0  2
 8S6  Var_07    H5   C9   C10  O11   171.22  30.0  3
 8S6  Var_08    H6   C9   C10  O11   -73.15  30.0  3
 8S6  Var_09    H5   C9   C10  O12   -10.03  30.0  3
 8S6  Var_10    H6   C9   C10  O12   105.60  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-2  H8   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
 8S6  plan-3  H9   0.020

