# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:33:09 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-4-[1-(carboxymethyl)hydrazinyl]-2-hydroxy-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NN(CC(O)=O)C(=O)C[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
 MY0  MY0  '(2S)-4-[1-(carboxymethyl)hydrazinyl]-2-hydroxy-4-oxobutanoic acid'  peptide  22  14  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MY0
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
 MY0  N    N  NH2    0  -0.645   1.1810   1.8062  -0.8800
 MY0  N5   N  NT     0  -0.328   1.3243   0.9549   0.2086
 MY0  O    O  O      0  -0.610  -4.1393  -0.7592  -0.8995
 MY0  O4   O  O      0  -0.511   0.3869  -0.6489   1.4703
 MY0  O7   O  OC    -1  -0.618   4.5967  -0.5748   0.0904
 MY0  O8   O  O      0  -0.598   2.8429  -0.7301  -1.2843
 MY0  O2   O  OH1    0  -0.698  -1.9165  -1.7393  -0.1578
 MY0  C3   C  CH2    0  -0.574  -1.0679   0.5205  -0.0380
 MY0  C5   C  CH2    0  -0.453   2.6637   0.6516   0.6558
 MY0  C    C  C      0   0.395  -3.5359   0.0419  -0.1486
 MY0  C4   C  C      0   0.568   0.2694   0.2056   0.6011
 MY0  C6   C  C      0   0.407   3.4343  -0.3128  -0.2726
 MY0  C2   C  CH1    0  -0.079  -2.1633  -0.4561   0.3609
 MY0  H    H  HNH2   0   0.361   1.5796   2.7067  -0.6423
 MY0  HO2  H  HOH1   0   0.423  -2.7095  -1.8856  -0.7077
 MY0  H3   H  HCH2   0   0.257  -1.3571   1.5355   0.2453
 MY0  H3A  H  HCH2   0   0.251  -0.9695   0.5365  -1.1253
 MY0  H5   H  HCH2   0   0.245   3.2166   1.5928   0.7342
 MY0  H5A  H  HCH2   0   0.251   2.6261   0.2339   1.6615
 MY0  H20  H  HCH1   0   0.196  -2.2211  -0.4975   1.4579
 MY0  H2   H  HNH2   0   0.357   1.7170   1.4229  -1.6515
 MY0  OXT  O  OC    -1  -0.596  -3.9214   1.1610   0.2233

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
 MY0  N   N5   single  1.389  0.020  1.389
 MY0  N   H    single  0.860  0.020  0.860
 MY0  N5  C4   single  1.352  0.020  1.352
 MY0  O   C    deloc   1.231  0.020  1.231
 MY0  O7  C6   deloc   1.246  0.020  1.246
 MY0  O8  C6   deloc   1.244  0.020  1.244
 MY0  O2  C2   single  1.406  0.020  1.406
 MY0  O2  HO2  single  0.850  0.020  0.980
 MY0  C3  C4   single  1.515  0.020  1.515
 MY0  C3  C2   single  1.521  0.020  1.521
 MY0  C3  H3   single  0.970  0.020  1.090
 MY0  C3  H3A  single  0.970  0.020  1.090
 MY0  C5  N5   single  1.444  0.020  1.444
 MY0  C5  H5   single  0.970  0.020  1.090
 MY0  C5  H5A  single  0.970  0.020  1.090
 MY0  C4  O4   double  1.225  0.020  1.225
 MY0  C6  C5   single  1.545  0.020  1.545
 MY0  C2  C    single  1.547  0.020  1.547
 MY0  C2  H20  single  0.970  0.020  1.090
 MY0  N   H2   single  0.890  0.020  1.040
 MY0  C   OXT  deloc   1.241  0.020  1.241

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
 MY0  H2   N   H   107.84  3.000
 MY0  H2   N   N5  108.05  3.000
 MY0  H    N   N5  108.68  3.000
 MY0  C4   N5  C5  121.15  3.000
 MY0  C5   N5  N   117.83  3.000
 MY0  C4   N5  N   119.11  3.000
 MY0  HO2  O2  C2  101.67  3.000
 MY0  H3A  C3  H3  105.57  3.000
 MY0  H3A  C3  C2  109.61  3.000
 MY0  H3   C3  C2  109.74  3.000
 MY0  H3A  C3  C4  110.09  3.000
 MY0  H3   C3  C4  108.49  3.000
 MY0  C2   C3  C4  113.05  3.000
 MY0  H5A  C5  H5  106.32  3.000
 MY0  H5A  C5  C6  109.43  3.000
 MY0  H5   C5  C6  109.14  3.000
 MY0  C6   C5  N5  114.06  3.000
 MY0  H5A  C5  N5  109.53  3.000
 MY0  H5   C5  N5  108.07  3.000
 MY0  OXT  C   C2  117.88  3.000
 MY0  OXT  C   O   127.35  3.000
 MY0  C2   C   O   114.77  3.000
 MY0  C3   C4  O4  121.94  3.000
 MY0  O4   C4  N5  121.19  3.000
 MY0  C3   C4  N5  116.81  3.000
 MY0  C5   C6  O8  117.46  3.000
 MY0  C5   C6  O7  114.94  3.000
 MY0  O8   C6  O7  127.59  3.000
 MY0  H20  C2  C   107.11  3.000
 MY0  H20  C2  C3  108.90  3.000
 MY0  C    C2  C3  110.24  3.000
 MY0  H20  C2  O2  110.06  3.000
 MY0  C    C2  O2  109.15  3.000
 MY0  C3   C2  O2  111.28  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
 MY0  CONST_01  C3  C4  N5  N     0.00   0.0  0
 MY0  CONST_02  O4  C4  N5  N   180.00   0.0  0
 MY0  CONST_03  C5  N5  C4  O4    0.00   0.0  0
 MY0  CONST_04  C5  N5  C4  C3  180.00   0.0  0
 MY0  Var_01    C6  C5  N5  N   -73.66  30.0  2
 MY0  Var_02    C2  C3  C4  N5  174.40  30.0  1
 MY0  Var_03    O7  C6  C5  N5  179.29  30.0  3
 MY0  Var_04    H   N   N5  C5  -61.45  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
 MY0  chir_01  C2  O2  C3  C  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
 MY0  plan-1  N    0.020
 MY0  plan-1  N5   0.020
 MY0  plan-1  O4   0.020
 MY0  plan-1  C3   0.020
 MY0  plan-1  C5   0.020
 MY0  plan-1  C4   0.020
 MY0  plan-2  O    0.020
 MY0  plan-2  C    0.020
 MY0  plan-2  C2   0.020
 MY0  plan-2  OXT  0.020
 MY0  plan-3  O7   0.020
 MY0  plan-3  O8   0.020
 MY0  plan-3  C5   0.020
 MY0  plan-3  C6   0.020

