# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 16:21:36 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  27  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 PERFECT
;

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  -0.437   2.4164  -2.1406   0.7052
 AQK  CAK  C  C     0   0.521   2.7333  -1.3039  -0.0999
 AQK  OAD  O  OH1   0  -0.596   3.9025  -1.2933  -0.7301
 AQK  CAI  C  CH2   0  -0.386   1.8836  -0.1281  -0.5121
 AQK  N    N  NH1   0  -0.580   0.5879  -0.1778   0.1133
 AQK  CA   C  CH1   0  -0.195  -0.3467   0.8097  -0.3576
 AQK  C    C  C     0   0.531   0.0427   2.2361   0.0140
 AQK  O    O  O     0  -0.441   0.7704   2.5229   0.9320
 AQK  CB   C  CH2   0  -0.443  -1.7540   0.5305   0.1900
 AQK  CAG  C  CH2   0  -0.418  -2.2785  -0.8444  -0.1986
 AQK  CAF  C  CH2   0  -0.274  -3.7092  -1.0622   0.2712
 AQK  NAA  N  NH2   0  -0.801  -4.1744  -2.3939  -0.0894
 AQK  OXT  O  OH1   0  -0.591  -0.5390   3.1363  -0.7680
 AQK  H1   H  HOH1  0   0.483   4.4438  -2.0413  -0.4374
 AQK  H2   H  HCH2  0   0.252   2.4655   0.7834  -0.3107
 AQK  H3   H  HCH2  0   0.277   1.7593  -0.1670  -1.5988
 AQK  H4   H  HNH1  0   0.350   0.6728  -0.1338   1.1212
 AQK  H6   H  HCH1  0   0.268  -0.3915   0.7467  -1.4504
 AQK  H7   H  HCH2  0   0.232  -1.7429   0.6309   1.2808
 AQK  H8   H  HCH2  0   0.243  -2.4362   1.2985  -0.1834
 AQK  H9   H  HCH2  0   0.215  -2.2358  -0.9636  -1.2857
 AQK  H10  H  HCH2  0   0.225  -1.6321  -1.6161   0.2262
 AQK  H11  H  HCH2  0   0.188  -3.7669  -0.8557   1.3504
 AQK  H12  H  HCH2  0   0.212  -4.3617  -0.3304  -0.2132
 AQK  H13  H  HNH2  0   0.337  -3.6659  -3.0819   0.4528
 AQK  H14  H  HNH2  0   0.345  -5.1435  -2.4985   0.1829
 AQK  H16  H  HOH1  0   0.481  -0.3097   4.0323  -0.4776

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  1.456  0.020  1.456
 AQK  CAF  CAG  single  1.522  0.020  1.522
 AQK  CAG  CB   single  1.522  0.020  1.522
 AQK  CB   CA   single  1.536  0.020  1.536
 AQK  O    C    double  1.206  0.020  1.206
 AQK  C    CA   single  1.525  0.020  1.525
 AQK  C    OXT  single  1.327  0.020  1.327
 AQK  CA   N    single  1.439  0.020  1.439
 AQK  N    CAI  single  1.440  0.020  1.440
 AQK  CAI  CAK  single  1.508  0.020  1.508
 AQK  OAB  CAK  double  1.204  0.020  1.204
 AQK  CAK  OAD  single  1.328  0.020  1.328
 AQK  OAD  H1   single  0.850  0.020  0.980
 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
 AQK  OXT  H16  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
 AQK  CAI  CAK  OAD  111.10  3.000
 AQK  OAD  CAK  OAB  123.69  3.000
 AQK  CAI  CAK  OAB  125.20  3.000
 AQK  H1   OAD  CAK  110.02  3.000
 AQK  H3   CAI  H2   105.74  3.000
 AQK  H3   CAI  N    109.14  3.000
 AQK  H2   CAI  N    115.16  3.000
 AQK  H3   CAI  CAK  107.92  3.000
 AQK  H2   CAI  CAK  107.33  3.000
 AQK  N    CAI  CAK  111.19  3.000
 AQK  H4   N    CA   110.51  3.000
 AQK  H4   N    CAI  110.83  3.000
 AQK  CA   N    CAI  114.75  3.000
 AQK  H6   CA   CB   107.92  3.000
 AQK  H6   CA   C    107.90  3.000
 AQK  CB   CA   C    108.49  3.000
 AQK  H6   CA   N    108.28  3.000
 AQK  C    CA   N    113.35  3.000
 AQK  CB   CA   N    110.72  3.000
 AQK  OXT  C    O    123.50  3.000
 AQK  OXT  C    CA   112.28  3.000
 AQK  O    C    CA   124.20  3.000
 AQK  H8   CB   H7   106.39  3.000
 AQK  H8   CB   CAG  109.42  3.000
 AQK  H7   CB   CAG  109.91  3.000
 AQK  H8   CB   CA   108.81  3.000
 AQK  H7   CB   CA   109.21  3.000
 AQK  CAG  CB   CA   112.89  3.000
 AQK  H10  CAG  H9   106.63  3.000
 AQK  H10  CAG  CAF  109.58  3.000
 AQK  H9   CAG  CAF  109.13  3.000
 AQK  H10  CAG  CB   109.57  3.000
 AQK  H9   CAG  CB   109.79  3.000
 AQK  CAF  CAG  CB   112.00  3.000
 AQK  H12  CAF  H11  106.12  3.000
 AQK  H12  CAF  NAA  108.16  3.000
 AQK  H11  CAF  NAA  113.45  3.000
 AQK  H12  CAF  CAG  109.18  3.000
 AQK  H11  CAF  CAG  108.98  3.000
 AQK  NAA  CAF  CAG  110.78  3.000
 AQK  H14  NAA  H13  105.45  3.000
 AQK  H14  NAA  CAF  109.50  3.000
 AQK  H13  NAA  CAF  109.17  3.000
 AQK  H16  OXT  C    110.29  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  CONST_01  H1   OAD  CAK  OAB     0.00   0.0  0
 AQK  CONST_02  H16  OXT  C    CA    180.00   0.0  0
 AQK  Var_01    N    CAI  CAK  OAB    -4.10  30.0  1
 AQK  Var_02    CA   N    CAI  CAK  -172.32  30.0  1
 AQK  Var_03    CAF  CAG  CB   CA   -176.03  30.0  1
 AQK  Var_04    NAA  CAF  CAG  CB   -178.82  30.0  2
 AQK  Var_05    H13  NAA  CAF  CAG    68.34  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-1  H1   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
 AQK  plan-2  H16  0.020

