# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:46:44 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-5-azanyl-2-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N[C@@H](CCCN)C(O)=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
 AQQ  AQQ  '(2~{S})-5-azanyl-2-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]pentanoic acid'  ligand  30  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AQQ
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
 AQQ  O    O  O     0  -0.437   2.4687  -1.6945   1.3927
 AQQ  C    C  C     0   0.543   2.7001  -1.1365   0.3508
 AQQ  CA   C  CH1   0  -0.213   1.6604  -0.4660  -0.5240
 AQQ  CB   C  CH3   0  -0.671   1.4260  -1.3296  -1.7729
 AQQ  N    N  NH1   0  -0.604   0.4733  -0.2114   0.2625
 AQQ  CAN  C  CH1   0  -0.178  -0.4621   0.7172  -0.3202
 AQQ  CAL  C  C     0   0.545   0.0392   2.1398  -0.1241
 AQQ  OAF  O  OH1   0  -0.595  -0.5946   2.9881  -0.9273
 AQQ  OAD  O  O     0  -0.432   0.8833   2.4793   0.6639
 AQQ  CAI  C  CH2   0  -0.452  -1.8443   0.5860   0.3363
 AQQ  CAH  C  CH2   0  -0.444  -2.5244  -0.7482   0.0451
 AQQ  CAG  C  CH2   0  -0.271  -3.9752  -0.7528   0.5027
 AQQ  NAB  N  NH2   0  -0.801  -4.6001  -2.0375   0.2265
 AQQ  OXT  O  OH1   0  -0.594   3.9099  -1.0735  -0.1928
 AQQ  H1   H  HCH1  0   0.277   2.0766   0.4939  -0.8428
 AQQ  H2   H  HCH3  0   0.246   2.3340  -1.4439  -2.3634
 AQQ  H3   H  HCH3  0   0.234   1.0679  -2.3225  -1.4961
 AQQ  H4   H  HCH3  0   0.248   0.6753  -0.8688  -2.4150
 AQQ  H5   H  HNH1  0   0.359   0.0151  -1.0839   0.4886
 AQQ  H7   H  HCH1  0   0.245  -0.6071   0.5729  -1.4027
 AQQ  H8   H  HOH1  0   0.481  -0.2961   3.8936  -0.7552
 AQQ  H9   H  HCH2  0   0.241  -1.7444   0.7345   1.4155
 AQQ  H10  H  HCH2  0   0.247  -2.4827   1.3895  -0.0373
 AQQ  H11  H  HCH2  0   0.226  -2.4865  -0.9554  -1.0286
 AQQ  H12  H  HCH2  0   0.221  -1.9984  -1.5705   0.5414
 AQQ  H13  H  HCH2  0   0.192  -4.0171  -0.4608   1.5623
 AQQ  H14  H  HCH2  0   0.217  -4.5199   0.0190  -0.0480
 AQQ  H15  H  HNH2  0   0.339  -4.1944  -2.7431   0.8292
 AQQ  H16  H  HNH2  0   0.347  -5.5795  -1.9978   0.4777
 AQQ  H18  H  HOH1  0   0.482   4.5474  -1.5563   0.3544

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
 AQQ  CB   CA   single  1.536  0.020  1.536
 AQQ  O    C    double  1.204  0.020  1.204
 AQQ  C    OXT  single  1.328  0.020  1.328
 AQQ  C    CA   single  1.515  0.020  1.515
 AQQ  CA   N    single  1.447  0.020  1.447
 AQQ  N    CAN  single  1.441  0.020  1.441
 AQQ  OAD  CAL  double  1.204  0.020  1.204
 AQQ  CAN  CAL  single  1.521  0.020  1.521
 AQQ  CAN  CAI  single  1.536  0.020  1.536
 AQQ  CAL  OAF  single  1.329  0.020  1.329
 AQQ  CAI  CAH  single  1.526  0.020  1.526
 AQQ  CAH  CAG  single  1.521  0.020  1.521
 AQQ  CAG  NAB  single  1.455  0.020  1.455
 AQQ  CA   H1   single  0.970  0.020  1.090
 AQQ  CB   H2   single  0.970  0.020  1.090
 AQQ  CB   H3   single  0.970  0.020  1.090
 AQQ  CB   H4   single  0.970  0.020  1.090
 AQQ  N    H5   single  0.890  0.020  1.040
 AQQ  CAN  H7   single  0.970  0.020  1.090
 AQQ  OAF  H8   single  0.850  0.020  0.980
 AQQ  CAI  H9   single  0.970  0.020  1.090
 AQQ  CAI  H10  single  0.970  0.020  1.090
 AQQ  CAH  H11  single  0.970  0.020  1.090
 AQQ  CAH  H12  single  0.970  0.020  1.090
 AQQ  CAG  H13  single  0.970  0.020  1.090
 AQQ  CAG  H14  single  0.970  0.020  1.090
 AQQ  NAB  H15  single  0.890  0.020  1.040
 AQQ  NAB  H16  single  0.890  0.020  1.040
 AQQ  OXT  H18  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
 AQQ  OXT  C    CA   111.58  3.000
 AQQ  CA   C    O    124.93  3.000
 AQQ  OXT  C    O    123.45  3.000
 AQQ  H1   CA   N    108.44  3.000
 AQQ  H1   CA   CB   108.32  3.000
 AQQ  N    CA   CB   114.56  3.000
 AQQ  H1   CA   C    107.19  3.000
 AQQ  N    CA   C    109.09  3.000
 AQQ  CB   CA   C    108.98  3.000
 AQQ  H4   CB   H3   107.95  3.000
 AQQ  H4   CB   H2   107.41  3.000
 AQQ  H3   CB   H2   108.40  3.000
 AQQ  H4   CB   CA   110.26  3.000
 AQQ  H3   CB   CA   110.81  3.000
 AQQ  H2   CB   CA   111.87  3.000
 AQQ  H5   N    CAN  110.63  3.000
 AQQ  H5   N    CA   109.97  3.000
 AQQ  CAN  N    CA   115.23  3.000
 AQQ  H7   CAN  CAI  106.88  3.000
 AQQ  H7   CAN  CAL  107.01  3.000
 AQQ  CAI  CAN  CAL  108.75  3.000
 AQQ  H7   CAN  N    113.47  3.000
 AQQ  CAI  CAN  N    110.87  3.000
 AQQ  CAL  CAN  N    109.67  3.000
 AQQ  OAD  CAL  OAF  123.37  3.000
 AQQ  OAF  CAL  CAN  111.21  3.000
 AQQ  OAD  CAL  CAN  125.40  3.000
 AQQ  H8   OAF  CAL  110.02  3.000
 AQQ  H10  CAI  H9   106.92  3.000
 AQQ  H10  CAI  CAH  108.52  3.000
 AQQ  H9   CAI  CAH  110.35  3.000
 AQQ  H10  CAI  CAN  108.48  3.000
 AQQ  H9   CAI  CAN  109.14  3.000
 AQQ  CAH  CAI  CAN  113.22  3.000
 AQQ  H12  CAH  H11  106.61  3.000
 AQQ  H12  CAH  CAG  108.63  3.000
 AQQ  H11  CAH  CAG  109.13  3.000
 AQQ  H12  CAH  CAI  110.86  3.000
 AQQ  H11  CAH  CAI  109.73  3.000
 AQQ  CAG  CAH  CAI  111.74  3.000
 AQQ  H14  CAG  H13  106.19  3.000
 AQQ  H14  CAG  NAB  108.28  3.000
 AQQ  H13  CAG  NAB  113.64  3.000
 AQQ  H14  CAG  CAH  108.75  3.000
 AQQ  H13  CAG  CAH  108.98  3.000
 AQQ  NAB  CAG  CAH  110.80  3.000
 AQQ  H16  NAB  H15  105.51  3.000
 AQQ  H16  NAB  CAG  109.50  3.000
 AQQ  H15  NAB  CAG  109.28  3.000
 AQQ  H18  OXT  C    110.15  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
 AQQ  CONST_01  H18  OXT  C    O       0.00   0.0  0
 AQQ  CONST_02  H8   OAF  CAL  CAN   180.00   0.0  0
 AQQ  Var_01    CAG  CAH  CAI  CAN  -170.17  30.0  3
 AQQ  Var_02    NAB  CAG  CAH  CAI  -179.48  30.0  3
 AQQ  Var_03    H15  NAB  CAG  CAH    68.87  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
 AQQ  chir_01  CA   CB  C    N    positiv
 AQQ  chir_02  CAN  N   CAL  CAI  positiv

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
 AQQ  plan-1  O    0.020
 AQQ  plan-1  C    0.020
 AQQ  plan-1  CA   0.020
 AQQ  plan-1  OXT  0.020
 AQQ  plan-1  H18  0.020
 AQQ  plan-2  CAN  0.020
 AQQ  plan-2  CAL  0.020
 AQQ  plan-2  OAF  0.020
 AQQ  plan-2  OAD  0.020
 AQQ  plan-2  H8   0.020

