# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:24:17 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H]1CC=NO1)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
 4UD  4UD  '(2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid'  L-peptide  18  10  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4UD
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
 4UD  C3   C  CR15  0  -0.070  -2.6198  -0.0245   0.3298
 4UD  C4   C  CR15  0   0.030  -0.5859   0.4871  -0.6092
 4UD  C5   C  CH2   0  -0.564  -1.8344   1.1778  -0.0745
 4UD  C6   C  CH1   0  -0.231   0.5824   0.5529   0.3813
 4UD  C8   C  C     0   0.538   1.6469  -0.4396  -0.0651
 4UD  O9   O  OH1   0  -0.582   1.7543  -1.4872   0.7362
 4UD  O10  O  O     0  -0.447   2.3240  -0.2778  -1.0511
 4UD  N7   N  NH2   0  -0.777   1.0566   1.9160   0.4402
 4UD  O2   O  O     0  -0.415  -0.9794  -0.8842  -0.7836
 4UD  N1   N  N     0  -0.088  -2.1356  -1.1234  -0.0707
 4UD  H1   H  HCR5  0   0.289  -3.5415  -0.0240   0.8946
 4UD  H3   H  HCR5  0   0.271  -0.2687   0.8679  -1.5826
 4UD  H4   H  HCH2  0   0.288  -2.3721   1.7513  -0.8335
 4UD  H5   H  HCH2  0   0.284  -1.6251   1.8534   0.7552
 4UD  H6   H  HCH1  0   0.275   0.2190   0.2704   1.3729
 4UD  H7   H  HOH1  0   0.481   2.4294  -2.0971   0.4005
 4UD  H8   H  HNH2  0   0.366   1.7191   2.0307   1.1957
 4UD  H9   H  HNH2  0   0.352   1.5402   2.1614  -0.4152

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
 4UD  C3   N1  double  1.266  0.020  1.266
 4UD  C3   C5  single  1.492  0.020  1.492
 4UD  N1   O2  single  1.379  0.020  1.379
 4UD  C5   C4  single  1.524  0.020  1.524
 4UD  O2   C4  single  1.437  0.020  1.437
 4UD  C4   C6  single  1.533  0.020  1.533
 4UD  C6   C8  single  1.522  0.020  1.522
 4UD  C6   N7  single  1.444  0.020  1.444
 4UD  O10  C8  double  1.207  0.020  1.207
 4UD  C8   O9  single  1.323  0.020  1.323
 4UD  C3   H1  single  0.930  0.020  1.080
 4UD  C4   H3  single  0.970  0.020  1.090
 4UD  C5   H4  single  0.970  0.020  1.090
 4UD  C5   H5  single  0.970  0.020  1.090
 4UD  C6   H6  single  0.970  0.020  1.090
 4UD  O9   H7  single  0.850  0.020  0.980
 4UD  N7   H8  single  0.890  0.020  1.040
 4UD  N7   H9  single  0.890  0.020  1.040

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
 4UD  H1   C3  N1  119.46  3.000
 4UD  H1   C3  C5  126.16  3.000
 4UD  N1   C3  C5  114.36  3.000
 4UD  H3   C4  O2  107.70  3.000
 4UD  H3   C4  C6  109.85  3.000
 4UD  O2   C4  C6  109.15  3.000
 4UD  H3   C4  C5  113.12  3.000
 4UD  C6   C4  C5  112.23  3.000
 4UD  O2   C4  C5  104.52  3.000
 4UD  H5   C5  H4  107.32  3.000
 4UD  H5   C5  C4  113.00  3.000
 4UD  H4   C5  C4  113.42  3.000
 4UD  H5   C5  C3  113.21  3.000
 4UD  H4   C5  C3  110.62  3.000
 4UD  C4   C5  C3   99.28  3.000
 4UD  H6   C6  N7  108.42  3.000
 4UD  H6   C6  C8  109.27  3.000
 4UD  N7   C6  C8  113.43  3.000
 4UD  H6   C6  C4  108.76  3.000
 4UD  N7   C6  C4  108.48  3.000
 4UD  C8   C6  C4  108.39  3.000
 4UD  O10  C8  O9  123.73  3.000
 4UD  O9   C8  C6  113.28  3.000
 4UD  O10  C8  C6  122.99  3.000
 4UD  H7   O9  C8  110.17  3.000
 4UD  H9   N7  H8  106.89  3.000
 4UD  H9   N7  C6  110.54  3.000
 4UD  H8   N7  C6  110.65  3.000
 4UD  N1   O2  C4  109.41  3.000
 4UD  O2   N1  C3  109.49  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
 4UD  CONST_01  H7  O9  C8  C6  180.00   0.0  0
 4UD  Var_01    N1  C3  C5  C4  -10.36  30.0  1

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
 4UD  chir_01  C4  C5  O2  C6  positiv
 4UD  chir_02  C6  N7  C4  C8  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
 4UD  plan-1  C6   0.020
 4UD  plan-1  C8   0.020
 4UD  plan-1  O9   0.020
 4UD  plan-1  O10  0.020
 4UD  plan-1  H7   0.020

