# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 05:41:42 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[3,4-bis(oxidanylidene)cyclohexa-1,5-dien-1-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=O)C(=O)C=C1)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
 G1X  G1X  '(2~{S})-2-azanyl-3-[3,4-bis(oxidanylidene)cyclohexa-1,5-dien-1-yl]propanoic acid'  L-peptide  22  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G1X
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
 G1X  N    N  NH2    0  -0.778  -15.0625  -18.5108  23.8653
 G1X  CA   C  CH1    0  -0.217  -16.2291  -18.1816  23.0616
 G1X  C    C  C      0   0.398  -17.5438  -18.9223  23.4387
 G1X  O    O  O      0  -0.605  -18.4760  -18.8415  22.6140
 G1X  CB   C  CH2    0  -0.529  -15.8937  -18.3570  21.5732
 G1X  CG   C  CR6    0   0.189  -14.6911  -17.5530  21.2005
 G1X  CD1  C  CR16   0  -0.213  -13.3666  -18.1473  21.4187
 G1X  CD2  C  CR16   0  -0.433  -14.8044  -16.3048  20.7076
 G1X  CE1  C  CR16   0  -0.352  -12.2191  -17.5046  21.1656
 G1X  CE2  C  CR6    0   0.317  -13.6311  -15.5041  20.4049
 G1X  CZ   C  CR6    0   0.300  -12.2449  -16.1374  20.6598
 G1X  OE2  O  O      0  -0.368  -13.6796  -14.3754  19.9681
 G1X  OZ   O  O      0  -0.357  -11.2513  -15.4883  20.4279
 G1X  H    H  HNH2   0   0.341  -15.2893  -18.3569  24.8399
 G1X  H2   H  HNH2   0   0.330  -14.8911  -19.5086  23.7985
 G1X  HA   H  HCH1   0   0.234  -16.4255  -17.1113  23.2110
 G1X  HB2  H  HCH2   0   0.260  -16.7501  -18.0465  20.9783
 G1X  HB3  H  HCH2   0   0.248  -15.7116  -19.4157  21.3608
 G1X  HD1  H  HCR6   0   0.279  -13.3394  -19.1672  21.7788
 G1X  HD2  H  HCR6   0   0.271  -15.7775  -15.8608  20.5314
 G1X  HE1  H  HCR6   0   0.282  -11.2580  -17.9757  21.3275
 G1X  OXT  O  OC    -1  -0.595  -17.5640  -19.4972  24.5432

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
 G1X  OE2  CE2  double  1.211  0.020  1.211
 G1X  OZ   CZ   double  1.209  0.020  1.209
 G1X  CE2  CZ   single  1.545  0.020  1.545
 G1X  CE2  CD2  single  1.452  0.020  1.452
 G1X  CZ   CE1  single  1.458  0.020  1.458
 G1X  CD2  CG   double  1.347  0.020  1.347
 G1X  CE1  CD1  double  1.339  0.020  1.339
 G1X  CG   CD1  single  1.468  0.020  1.468
 G1X  CG   CB   single  1.494  0.020  1.494
 G1X  CB   CA   single  1.530  0.020  1.530
 G1X  O    C    deloc   1.231  0.020  1.231
 G1X  CA   C    single  1.525  0.021  1.525
 G1X  CA   N    single  1.458  0.019  1.458
 G1X  N    H    single  0.860  0.020  0.860
 G1X  N    H2   single  0.890  0.020  1.040
 G1X  CA   HA   single  0.970  0.020  0.970
 G1X  CB   HB2  single  0.970  0.020  1.090
 G1X  CB   HB3  single  0.970  0.020  1.090
 G1X  CD1  HD1  single  0.930  0.020  1.080
 G1X  CD2  HD2  single  0.930  0.020  1.080
 G1X  CE1  HE1  single  0.930  0.020  1.080
 G1X  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
 G1X  H2   N    H    104.52  3.000
 G1X  H2   N    CA   108.77  3.000
 G1X  H    N    CA   114.00  3.000
 G1X  HA   CA   CB   109.00  3.000
 G1X  HA   CA   C    109.00  3.000
 G1X  CB   CA   C    110.10  1.900
 G1X  HA   CA   N    110.00  3.000
 G1X  C    CA   N    111.00  2.800
 G1X  CB   CA   N    110.50  1.700
 G1X  OXT  C    O    127.17  3.000
 G1X  OXT  C    CA   116.65  3.000
 G1X  O    C    CA   120.80  1.700
 G1X  HB3  CB   HB2  107.50  3.000
 G1X  HB3  CB   CG   109.76  3.000
 G1X  HB2  CB   CG   110.10  3.000
 G1X  HB3  CB   CA   109.56  3.000
 G1X  HB2  CB   CA   108.99  3.000
 G1X  CG   CB   CA   110.87  3.000
 G1X  CD2  CG   CD1  120.36  3.000
 G1X  CD1  CG   CB   118.12  3.000
 G1X  CD2  CG   CB   121.50  3.000
 G1X  HD1  CD1  CE1  119.59  3.000
 G1X  HD1  CD1  CG   116.99  3.000
 G1X  CE1  CD1  CG   123.40  3.000
 G1X  HD2  CD2  CE2  117.74  3.000
 G1X  HD2  CD2  CG   120.97  3.000
 G1X  CE2  CD2  CG   121.29  3.000
 G1X  HE1  CE1  CZ   118.41  3.000
 G1X  HE1  CE1  CD1  121.56  3.000
 G1X  CZ   CE1  CD1  120.03  3.000
 G1X  OE2  CE2  CZ   118.51  3.000
 G1X  CZ   CE2  CD2  117.67  3.000
 G1X  OE2  CE2  CD2  123.82  3.000
 G1X  OZ   CZ   CE2  119.04  3.000
 G1X  CE2  CZ   CE1  117.22  3.000
 G1X  OZ   CZ   CE1  123.73  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
 G1X  Var_01  CD2  CG  CB  CA  -93.19  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
 G1X  chir_01  CA  CB  C  N  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
 G1X  plan-1  CB   0.020
 G1X  plan-1  CG   0.020
 G1X  plan-1  CD1  0.020
 G1X  plan-1  CD2  0.020
 G1X  plan-1  CE1  0.020
 G1X  plan-1  CE2  0.020
 G1X  plan-1  CZ   0.020
 G1X  plan-1  OE2  0.020
 G1X  plan-1  OZ   0.020
 G1X  plan-1  HD1  0.020
 G1X  plan-1  HD2  0.020
 G1X  plan-1  HE1  0.020
 G1X  plan-2  CA   0.020
 G1X  plan-2  C    0.020
 G1X  plan-2  O    0.020
 G1X  plan-2  OXT  0.020

