# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 23:35:34 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  24  14  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.639   1.1645   1.7913  -1.0674
 MY0  N5   N  NT    0  -0.346   1.3362   1.0009   0.0575
 MY0  O    O  O     0  -0.434  -4.0867  -0.5185  -0.9953
 MY0  O4   O  O     0  -0.489   0.4486  -0.4476   1.5176
 MY0  O7   O  OH1   0  -0.589   4.4630  -0.7615   0.3769
 MY0  O8   O  O     0  -0.433   2.7507  -1.0953  -1.0235
 MY0  O2   O  OH1   0  -0.648  -1.7110  -1.6907  -0.3436
 MY0  C3   C  CH2   0  -0.613  -1.0861   0.6296   0.0269
 MY0  C5   C  CH2   0  -0.440   2.6640   0.7324   0.5407
 MY0  C    C  C     0   0.508  -3.4718  -0.0796  -0.0580
 MY0  C4   C  C     0   0.601   0.2871   0.3259   0.5879
 MY0  C6   C  C     0   0.542   3.2737  -0.4792  -0.1327
 MY0  C2   C  CH1   0  -0.065  -2.0615  -0.5108   0.3135
 MY0  H    H  HNH2  0   0.376   1.5299   2.7181  -0.8876
 MY0  HO7  H  HOH1  0   0.485   4.8537  -1.5227  -0.0783
 MY0  HO2  H  HOH1  0   0.447  -1.7686  -1.5508  -1.2953
 MY0  H3   H  HCH2  0   0.294  -1.4273   1.5590   0.4923
 MY0  H3A  H  HCH2  0   0.285  -1.0412   0.8322  -1.0430
 MY0  H5   H  HCH2  0   0.310   3.2961   1.6015   0.3437
 MY0  H5A  H  HCH2  0   0.300   2.6657   0.5880   1.6217
 MY0  H20  H  HCH1  0   0.279  -2.0518  -0.7331   1.3835
 MY0  H2   H  HNH2  0   0.372   1.6749   1.3938  -1.8472
 MY0  HXT  H  HOH1  0   0.486  -4.8234   1.1262   0.4978
 MY0  OXT  O  OH1   0  -0.589  -3.9361   0.8458   0.7687

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  1.386  0.020  1.386
 MY0  N    H    single  0.860  0.020  0.860
 MY0  N5   C4   single  1.356  0.020  1.356
 MY0  O    C    double  1.231  0.020  1.231
 MY0  O7   C6   single  1.324  0.020  1.324
 MY0  O7   HO7  single  0.850  0.020  0.980
 MY0  O8   C6   double  1.203  0.020  1.203
 MY0  O2   C2   single  1.395  0.020  1.395
 MY0  O2   HO2  single  0.850  0.020  0.980
 MY0  C3   C4   single  1.514  0.020  1.514
 MY0  C3   C2   single  1.528  0.020  1.528
 MY0  C3   H3   single  0.970  0.020  1.090
 MY0  C3   H3A  single  0.970  0.020  1.090
 MY0  C5   N5   single  1.438  0.020  1.438
 MY0  C5   H5   single  0.970  0.020  1.090
 MY0  C5   H5A  single  0.970  0.020  1.090
 MY0  C4   O4   double  1.220  0.020  1.220
 MY0  C6   C5   single  1.514  0.020  1.514
 MY0  C2   C    single  1.521  0.020  1.521
 MY0  C2   H20  single  0.970  0.020  1.090
 MY0  N    H2   single  0.890  0.020  1.040
 MY0  C    OXT  single  1.325  0.020  1.325
 MY0  OXT  HXT  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
 MY0  H2   N    H   108.30  3.000
 MY0  H2   N    N5  109.79  3.000
 MY0  H    N    N5  109.47  3.000
 MY0  C4   N5   C5  119.35  3.000
 MY0  C5   N5   N   119.58  3.000
 MY0  C4   N5   N   120.39  3.000
 MY0  HO7  O7   C6  110.41  3.000
 MY0  HO2  O2   C2  109.11  3.000
 MY0  H3A  C3   H3  105.81  3.000
 MY0  H3A  C3   C2  110.45  3.000
 MY0  H3   C3   C2  110.80  3.000
 MY0  H3A  C3   C4  111.33  3.000
 MY0  H3   C3   C4  107.19  3.000
 MY0  C2   C3   C4  111.09  3.000
 MY0  H5A  C5   H5  106.45  3.000
 MY0  H5A  C5   C6  109.53  3.000
 MY0  H5   C5   C6  108.87  3.000
 MY0  C6   C5   N5  111.82  3.000
 MY0  H5A  C5   N5  111.05  3.000
 MY0  H5   C5   N5  108.96  3.000
 MY0  OXT  C    C2  111.75  3.000
 MY0  OXT  C    O   124.16  3.000
 MY0  C2   C    O   124.09  3.000
 MY0  C3   C4   O4  121.97  3.000
 MY0  O4   C4   N5  120.75  3.000
 MY0  C3   C4   N5  117.20  3.000
 MY0  C5   C6   O8  124.34  3.000
 MY0  C5   C6   O7  111.16  3.000
 MY0  O8   C6   O7  124.49  3.000
 MY0  H20  C2   C   107.76  3.000
 MY0  H20  C2   C3  109.26  3.000
 MY0  C    C2   C3  109.54  3.000
 MY0  H20  C2   O2  106.67  3.000
 MY0  C    C2   O2  110.96  3.000
 MY0  C3   C2   O2  112.49  3.000
 MY0  HXT  OXT  C   110.40  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  CONST_05  HXT  OXT  C   O      0.00   0.0  0
 MY0  CONST_06  HO7  O7   C6  O8     0.00   0.0  0
 MY0  Var_01    C6   C5   N5  N    -87.29  30.0  2
 MY0  Var_02    C2   C3   C4  N5   159.00  30.0  1
 MY0  Var_03    O7   C6   C5  N5  -176.31  30.0  1
 MY0  Var_04    H    N    N5  C5   -61.87  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  HXT  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
 MY0  plan-3  HO7  0.020

