# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:00:42 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[C@H](NCC(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
 AQK  AQK  '(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic acid'  ligand  25  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AQK
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
 AQK  OAB  O  O      0  -0.610   2.7423  -1.5061   1.1310
 AQK  CAK  C  C      0   0.381   2.9146  -1.1140  -0.0395
 AQK  OAD  O  OC    -1  -0.632   3.9097  -1.3381  -0.7603
 AQK  CAI  C  CH2    0  -0.400   1.8263  -0.2248  -0.6640
 AQK  N    N  NH1    0  -0.584   0.5741  -0.2525   0.0557
 AQK  CA   C  CH1    0  -0.177  -0.3573   0.7727  -0.3649
 AQK  C    C  C      0   0.387   0.0363   2.2177   0.0331
 AQK  O    O  O      0  -0.611   0.7752   2.3547   1.0291
 AQK  CB   C  CH2    0  -0.429  -1.7567   0.4788   0.1882
 AQK  CAG  C  CH2    0  -0.414  -2.3231  -0.8617  -0.2576
 AQK  CAF  C  CH2    0  -0.272  -3.7220  -1.1180   0.2817
 AQK  NAA  N  NH2    0  -0.801  -4.2166  -2.4199  -0.1464
 AQK  OXT  O  OC    -1  -0.624  -0.4619   3.1376  -0.6505
 AQK  H2   H  HCH2   0   0.186   2.2575   0.7884  -0.7493
 AQK  H3   H  HCH2   0   0.204   1.6571  -0.5533  -1.6954
 AQK  H4   H  HNH1   0   0.313   0.7801  -0.1195   1.0382
 AQK  H6   H  HCH1   0   0.192  -0.4252   0.7319  -1.4593
 AQK  H7   H  HCH2   0   0.202  -1.7240   0.5173   1.2840
 AQK  H8   H  HCH2   0   0.212  -2.4313   1.2811  -0.1255
 AQK  H9   H  HCH2   0   0.202  -2.3495  -0.9046  -1.3516
 AQK  H10  H  HCH2   0   0.211  -1.6516  -1.6611   0.0671
 AQK  H11  H  HCH2   0   0.182  -3.7112  -0.9930   1.3751
 AQK  H12  H  HCH2   0   0.206  -4.4023  -0.3524  -0.1030
 AQK  H13  H  HNH2   0   0.335  -3.6582  -3.1445   0.2883
 AQK  H14  H  HNH2   0   0.343  -5.1566  -2.5577   0.2026

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
 AQK  NAA  CAF  single  1.457  0.020  1.457
 AQK  CAF  CAG  single  1.521  0.020  1.521
 AQK  CAG  CB   single  1.522  0.020  1.522
 AQK  CB   CA   single  1.533  0.020  1.533
 AQK  O    C    deloc   1.248  0.020  1.248
 AQK  C    CA   single  1.550  0.020  1.550
 AQK  C    OXT  deloc   1.250  0.020  1.250
 AQK  CA   N    single  1.448  0.020  1.448
 AQK  N    CAI  single  1.445  0.020  1.445
 AQK  CAI  CAK  single  1.538  0.020  1.538
 AQK  OAB  CAK  deloc   1.246  0.020  1.246
 AQK  CAK  OAD  deloc   1.249  0.020  1.249
 AQK  CAI  H2   single  0.970  0.020  1.090
 AQK  CAI  H3   single  0.970  0.020  1.090
 AQK  N    H4   single  0.890  0.020  1.040
 AQK  CA   H6   single  0.970  0.020  1.090
 AQK  CB   H7   single  0.970  0.020  1.090
 AQK  CB   H8   single  0.970  0.020  1.090
 AQK  CAG  H9   single  0.970  0.020  1.090
 AQK  CAG  H10  single  0.970  0.020  1.090
 AQK  CAF  H11  single  0.970  0.020  1.090
 AQK  CAF  H12  single  0.970  0.020  1.090
 AQK  NAA  H13  single  0.890  0.020  1.040
 AQK  NAA  H14  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
 AQK  CAI  CAK  OAD  115.67  3.000
 AQK  OAD  CAK  OAB  126.56  3.000
 AQK  CAI  CAK  OAB  117.74  3.000
 AQK  H3   CAI  H2   105.23  3.000
 AQK  H3   CAI  N    109.23  3.000
 AQK  H2   CAI  N    113.24  3.000
 AQK  H3   CAI  CAK  108.56  3.000
 AQK  H2   CAI  CAK  106.59  3.000
 AQK  N    CAI  CAK  113.58  3.000
 AQK  H4   N    CA   108.65  3.000
 AQK  H4   N    CAI  107.73  3.000
 AQK  CA   N    CAI  113.54  3.000
 AQK  H6   CA   CB   107.23  3.000
 AQK  H6   CA   C    107.86  3.000
 AQK  CB   CA   C    108.54  3.000
 AQK  H6   CA   N    107.65  3.000
 AQK  C    CA   N    114.98  3.000
 AQK  CB   CA   N    110.28  3.000
 AQK  OXT  C    O    126.30  3.000
 AQK  OXT  C    CA   116.40  3.000
 AQK  O    C    CA   117.24  3.000
 AQK  H8   CB   H7   106.21  3.000
 AQK  H8   CB   CAG  109.41  3.000
 AQK  H7   CB   CAG  109.54  3.000
 AQK  H8   CB   CA   108.59  3.000
 AQK  H7   CB   CA   109.06  3.000
 AQK  CAG  CB   CA   113.76  3.000
 AQK  H10  CAG  H9   106.42  3.000
 AQK  H10  CAG  CAF  109.65  3.000
 AQK  H9   CAG  CAF  108.99  3.000
 AQK  H10  CAG  CB   109.18  3.000
 AQK  H9   CAG  CB   109.64  3.000
 AQK  CAF  CAG  CB   112.76  3.000
 AQK  H12  CAF  H11  106.01  3.000
 AQK  H12  CAF  NAA  108.11  3.000
 AQK  H11  CAF  NAA  113.38  3.000
 AQK  H12  CAF  CAG  109.22  3.000
 AQK  H11  CAF  CAG  108.91  3.000
 AQK  NAA  CAF  CAG  111.02  3.000
 AQK  H14  NAA  H13  105.46  3.000
 AQK  H14  NAA  CAF  109.61  3.000
 AQK  H13  NAA  CAF  109.02  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
 AQK  Var_01  N    CAI  CAK  OAB   -15.96  30.0  2
 AQK  Var_02  CA   N    CAI  CAK   168.39  30.0  1
 AQK  Var_03  CAF  CAG  CB   CA   -178.88  30.0  1
 AQK  Var_04  NAA  CAF  CAG  CB   -178.92  30.0  1
 AQK  Var_05  H13  NAA  CAF  CAG    66.55  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
 AQK  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
 AQK  plan-1  OAB  0.020
 AQK  plan-1  CAK  0.020
 AQK  plan-1  OAD  0.020
 AQK  plan-1  CAI  0.020
 AQK  plan-2  CA   0.020
 AQK  plan-2  C    0.020
 AQK  plan-2  O    0.020
 AQK  plan-2  OXT  0.020

