# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:15:30 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[2,5-bis(oxidanylidene)imidazol-4-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=NC(=O)NC1=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
 HOO  HOO  '(2~{S})-2-azanyl-3-[2,5-bis(oxidanylidene)imidazol-4-yl]propanoic acid'  L-peptide  19  13  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HOO
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
 HOO  C    C  C      0   0.407   8.0186  -10.0124  -11.2501
 HOO  O    O  O      0  -0.615   9.1046   -9.3935  -11.2189
 HOO  N    N  NH2    0  -0.803   6.6081  -10.5335  -13.2667
 HOO  CA   C  CH1    0  -0.240   7.7712  -10.9296  -12.4783
 HOO  CB   C  CH2    0  -0.533   8.9854  -10.9383  -13.3907
 HOO  CG   C  CR5    0   0.226  10.2203  -11.3419  -12.6959
 HOO  ND1  N  N      0  -0.359  10.3165  -12.2062  -11.7621
 HOO  CE1  C  CR5    0   0.566  11.6851  -12.3163  -11.4246
 HOO  OAG  O  O      0  -0.412  12.1279  -13.0495  -10.5860
 HOO  NE2  N  NR15   0  -0.659  12.4237  -11.4781  -12.2444
 HOO  CD2  C  CR5    0   0.486  11.5860  -10.7884  -13.0683
 HOO  OAM  O  O      0  -0.475  11.8519   -9.9724  -13.9113
 HOO  H7   H  HCH1   0   0.247   7.5681  -11.9384  -12.1060
 HOO  H8   H  HCH2   0   0.312   9.1437   -9.9320  -13.7841
 HOO  H9   H  HCH2   0   0.295   8.8332  -11.5899  -14.2584
 HOO  H10  H  HNR5   0   0.438  13.4278  -11.3757  -12.2017
 HOO  OXT  O  OC    -1  -0.567   7.0822   -9.9304  -10.4331
 HOO  H4   H  HNH2   0   0.353   5.7900  -10.5610  -12.6691
 HOO  H5   H  HNH2   0   0.333   6.7032   -9.5601  -13.5375

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
 HOO  OAM  CD2  double  1.203  0.020  1.203
 HOO  N    CA   single  1.458  0.019  1.458
 HOO  CB   CG   single  1.473  0.020  1.473
 HOO  CB   CA   single  1.530  0.020  1.530
 HOO  CD2  CG   single  1.520  0.020  1.520
 HOO  CD2  NE2  single  1.362  0.020  1.362
 HOO  CG   ND1  double  1.276  0.020  1.276
 HOO  NE2  CE1  single  1.386  0.020  1.386
 HOO  CA   C    single  1.525  0.021  1.525
 HOO  O    C    deloc   1.231  0.020  1.231
 HOO  ND1  CE1  single  1.414  0.020  1.414
 HOO  CE1  OAG  double  1.199  0.020  1.199
 HOO  N    H4   single  0.890  0.020  1.040
 HOO  N    H5   single  0.890  0.020  1.040
 HOO  CA   H7   single  0.970  0.020  1.090
 HOO  CB   H8   single  0.970  0.020  1.090
 HOO  CB   H9   single  0.970  0.020  1.090
 HOO  NE2  H10  single  0.860  0.020  1.020
 HOO  C    OXT  deloc   1.245  0.020  1.245

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
 HOO  OXT  C    CA   115.97  3.000
 HOO  OXT  C    O    127.16  3.000
 HOO  CA   C    O    120.80  1.700
 HOO  H5   N    H4   105.01  3.000
 HOO  H5   N    CA   109.24  3.000
 HOO  H4   N    CA   108.50  3.000
 HOO  H7   CA   CB   110.33  3.000
 HOO  H7   CA   N    106.62  3.000
 HOO  CB   CA   N    110.50  1.700
 HOO  H7   CA   C    107.76  3.000
 HOO  CB   CA   C    110.10  1.900
 HOO  N    CA   C    111.00  2.800
 HOO  H9   CB   H8   106.43  3.000
 HOO  H9   CB   CG   109.08  3.000
 HOO  H8   CB   CG   107.50  3.000
 HOO  H9   CB   CA   111.60  3.000
 HOO  H8   CB   CA   109.09  3.000
 HOO  CG   CB   CA   112.85  3.000
 HOO  CD2  CG   ND1  110.99  3.000
 HOO  ND1  CG   CB   126.43  3.000
 HOO  CD2  CG   CB   122.54  3.000
 HOO  CE1  ND1  CG   107.49  3.000
 HOO  NE2  CE1  OAG  125.94  3.000
 HOO  OAG  CE1  ND1  124.91  3.000
 HOO  NE2  CE1  ND1  109.12  3.000
 HOO  H10  NE2  CD2  125.83  3.000
 HOO  H10  NE2  CE1  124.48  3.000
 HOO  CD2  NE2  CE1  109.65  3.000
 HOO  OAM  CD2  NE2  129.14  3.000
 HOO  NE2  CD2  CG   102.71  3.000
 HOO  OAM  CD2  CG   128.12  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
 HOO  CONST_01  CE1  NE2  CD2  CG      0.00   0.0  0
 HOO  CONST_02  NE2  CE1  ND1  CG      0.00   0.0  0
 HOO  CONST_03  NE2  CD2  CG   ND1     0.00   0.0  0
 HOO  CONST_04  CD2  NE2  CE1  ND1     0.00   0.0  0
 HOO  CONST_05  CD2  CG   ND1  CE1     0.00   0.0  0
 HOO  CONST_06  OAG  CE1  ND1  CG    180.00   0.0  0
 HOO  CONST_07  CD2  NE2  CE1  OAG   180.00   0.0  0
 HOO  CONST_08  H10  NE2  CD2  CG    180.00   0.0  0
 HOO  Var_01    CD2  CG   CB   CA   -147.41  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
 HOO  chir_01  CA  N  CB  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
 HOO  plan-1  CB   0.020
 HOO  plan-1  CG   0.020
 HOO  plan-1  ND1  0.020
 HOO  plan-1  CE1  0.020
 HOO  plan-1  OAG  0.020
 HOO  plan-1  NE2  0.020
 HOO  plan-1  CD2  0.020
 HOO  plan-1  OAM  0.020
 HOO  plan-1  H10  0.020
 HOO  plan-2  C    0.020
 HOO  plan-2  O    0.020
 HOO  plan-2  CA   0.020
 HOO  plan-2  OXT  0.020

