# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:29:23 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (3~{R})-3-[[(1~{R})-1,2-bis(oxidanyl)-2-oxidanylidene-ethyl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(O)=O)N[C@H](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
 E79  E79  '(3~{R})-3-[[(1~{R})-1,2-bis(oxidanyl)-2-oxidanylidene-ethyl]amino]butanoic acid'  ligand  23  12  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E79
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
 E79  C1   C  CH3   0  -0.649   0.4424   2.3093   1.0502
 E79  C2   C  CH1   0  -0.081   0.8170   0.8905   0.6450
 E79  C4   C  CH1   0   0.088  -1.5586   0.2183   0.5103
 E79  C6   C  C     0   0.513  -2.4969  -0.4202  -0.5105
 E79  C9   C  CH2   0  -0.622   2.0577   0.9371  -0.2417
 E79  C10  C  C     0   0.498   2.6403  -0.4087  -0.5798
 E79  N3   N  NH1   0  -0.681  -0.2650   0.2475  -0.1000
 E79  O5   O  OH1   0  -0.614  -1.6640  -0.4316   1.7464
 E79  O7   O  O     0  -0.431  -2.8501  -1.5702  -0.4572
 E79  O8   O  OH1   0  -0.666  -2.8482   0.4233  -1.4651
 E79  O11  O  OH1   0  -0.677   3.7364  -0.2980  -1.3231
 E79  O12  O  O     0  -0.251   2.1963  -1.4728  -0.2255
 E79  H1   H  HCH3  0   0.194   0.1053   2.8875   0.1879
 E79  H2   H  HCH3  0   0.259  -0.3421   2.3339   1.8057
 E79  H3   H  HCH3  0   0.238   1.3071   2.8153   1.4787
 E79  H4   H  HCH1  0   0.281   1.0692   0.3331   1.5568
 E79  H5   H  HCH1  0   0.300  -1.8937   1.2412   0.6910
 E79  H6   H  HCH2  0   0.293   1.8339   1.4684  -1.1722
 E79  H7   H  HCH2  0   0.272   2.8411   1.5167   0.2549
 E79  H8   H  HNH1  0   0.363   0.0245  -0.6895  -0.3560
 E79  H10  H  HOH1  0   0.452  -1.5029  -1.3743   1.6252
 E79  H11  H  HOH1  0   0.461  -3.4098  -0.0273  -2.1122
 E79  H12  H  HOH1  0   0.461   4.0897  -1.1796  -1.5101

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
 E79  O7   C6   double  1.204  0.020  1.204
 E79  C6   C4   single  1.526  0.020  1.526
 E79  C6   O8   single  1.321  0.020  1.321
 E79  C1   C2   single  1.522  0.020  1.522
 E79  C4   N3   single  1.431  0.020  1.431
 E79  C4   O5   single  1.401  0.020  1.401
 E79  N3   C2   single  1.463  0.020  1.463
 E79  C2   C9   single  1.526  0.020  1.526
 E79  O12  C10  double  1.206  0.020  1.206
 E79  C9   C10  single  1.505  0.020  1.505
 E79  C10  O11  single  1.329  0.020  1.329
 E79  C1   H1   single  0.970  0.020  1.090
 E79  C1   H2   single  0.970  0.020  1.090
 E79  C1   H3   single  0.970  0.020  1.090
 E79  C2   H4   single  0.970  0.020  1.090
 E79  C4   H5   single  0.970  0.020  1.090
 E79  C9   H6   single  0.970  0.020  1.090
 E79  C9   H7   single  0.970  0.020  1.090
 E79  N3   H8   single  0.890  0.020  1.040
 E79  O5   H10  single  0.850  0.020  0.980
 E79  O8   H11  single  0.850  0.020  0.980
 E79  O11  H12  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
 E79  H3   C1   H2   106.75  3.000
 E79  H3   C1   H1   108.05  3.000
 E79  H2   C1   H1   108.26  3.000
 E79  H3   C1   C2   110.01  3.000
 E79  H2   C1   C2   112.51  3.000
 E79  H1   C1   C2   111.07  3.000
 E79  H4   C2   N3   111.70  3.000
 E79  H4   C2   C9   108.14  3.000
 E79  N3   C2   C9   108.60  3.000
 E79  H4   C2   C1   107.97  3.000
 E79  C9   C2   C1   109.05  3.000
 E79  N3   C2   C1   111.30  3.000
 E79  H5   C4   O5   105.40  3.000
 E79  H5   C4   N3   109.22  3.000
 E79  O5   C4   N3   117.00  3.000
 E79  H5   C4   C6   108.30  3.000
 E79  O5   C4   C6   110.48  3.000
 E79  N3   C4   C6   106.21  3.000
 E79  O8   C6   O7   124.31  3.000
 E79  O8   C6   C4   112.30  3.000
 E79  O7   C6   C4   123.38  3.000
 E79  H7   C9   H6   105.97  3.000
 E79  H7   C9   C10  107.37  3.000
 E79  H6   C9   C10  108.79  3.000
 E79  H7   C9   C2   109.56  3.000
 E79  H6   C9   C2   110.04  3.000
 E79  C10  C9   C2   114.71  3.000
 E79  O12  C10  O11  122.78  3.000
 E79  O11  C10  C9   111.74  3.000
 E79  O12  C10  C9   125.48  3.000
 E79  H8   N3   C4   110.31  3.000
 E79  H8   N3   C2   108.89  3.000
 E79  C4   N3   C2   117.43  3.000
 E79  H10  O5   C4   109.28  3.000
 E79  H11  O8   C6   109.88  3.000
 E79  H12  O11  C10  109.46  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
 E79  CONST_01  H11  O8   C6   C4  180.00   0.0  0
 E79  CONST_02  H12  O11  C10  C9  180.00   0.0  0
 E79  Var_01    O12  C10  C9   C2    1.09  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
 E79  chir_01  C2  C1  N3  C9  negativ
 E79  chir_02  C4  O5  N3  C6  negativ

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
 E79  plan-1  C4   0.020
 E79  plan-1  C6   0.020
 E79  plan-1  O7   0.020
 E79  plan-1  O8   0.020
 E79  plan-1  H11  0.020
 E79  plan-2  C9   0.020
 E79  plan-2  C10  0.020
 E79  plan-2  O11  0.020
 E79  plan-2  O12  0.020
 E79  plan-2  H12  0.020

