# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:08:32 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (3S)-3-amino-5-chloro-4-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)C(=O)CCl
#
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
 AKL  AKL  '(3S)-3-amino-5-chloro-4-oxopentanoic acid'  L-peptide  17  10  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AKL
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
 AKL  N    N   NH2    0  -0.784  4.0079  -0.7386  -1.3772
 AKL  CA   C   CH1    0  -0.171  3.5841  -0.3898  -0.0279
 AKL  CB   C   CH2    0  -0.588  4.5694   0.5564   0.6349
 AKL  CG   C   C      0   0.445  4.0412   1.0041   2.0001
 AKL  OD2  O   OC    -1  -0.605  4.8384   1.5090   2.8075
 AKL  OD1  O   O      0  -0.580  2.8111   0.8279   2.1817
 AKL  C    C   C      0   0.411  2.2109   0.2751  -0.0302
 AKL  O    O   O      0  -0.446  2.0390   1.3300  -0.6097
 AKL  CM   C   CH2    0  -0.530  0.9510  -0.4576   0.3976
 AKL  CL1  CL  CL     0  -0.162  1.1719  -1.8927   1.4382
 AKL  H    H   HNH2   0   0.339  3.9514   0.0754  -1.9780
 AKL  H2   H   HNH2   0   0.348  3.3876  -1.4324  -1.7763
 AKL  HA   H   HCH1   0   0.237  3.5493  -1.3132   0.5502
 AKL  HB2  H   HCH2   0   0.241  5.5477   0.0799   0.7290
 AKL  HB3  H   HCH2   0   0.236  4.7192   1.4420   0.0057
 AKL  HM1  H   HCH2   0   0.301  0.4381  -0.8006  -0.5020
 AKL  HM2  H   HCH2   0   0.305  0.2942   0.2330   0.9208

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
 AKL  N   CA   single  1.458  0.019  1.458
 AKL  N   H    single  0.860  0.020  0.860
 AKL  N   H2   single  0.890  0.020  1.040
 AKL  CA  CB   single  1.530  0.020  1.530
 AKL  CA  C    single  1.525  0.021  1.525
 AKL  CA  HA   single  0.970  0.020  0.970
 AKL  CB  CG   single  1.531  0.020  1.531
 AKL  CB  HB2  single  0.970  0.020  1.090
 AKL  CB  HB3  single  0.970  0.020  1.090
 AKL  CG  OD2  deloc   1.242  0.020  1.242
 AKL  CG  OD1  deloc   1.256  0.020  1.256
 AKL  C   O    double  1.231  0.020  1.231
 AKL  C   CM   single  1.519  0.020  1.519
 AKL  CM  CL1  single  1.786  0.020  1.786
 AKL  CM  HM1  single  0.970  0.020  1.090
 AKL  CM  HM2  single  0.970  0.020  1.090

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
 AKL  H2   N   H    106.41  3.000
 AKL  H2   N   CA   110.54  3.000
 AKL  H    N   CA   114.00  3.000
 AKL  HA   CA  C    109.00  3.000
 AKL  HA   CA  CB   109.00  3.000
 AKL  C    CA  CB   110.10  1.900
 AKL  HA   CA  N    110.00  3.000
 AKL  C    CA  N    111.00  2.800
 AKL  CB   CA  N    110.50  1.700
 AKL  HB3  CB  HB2  106.23  3.000
 AKL  HB3  CB  CG   108.82  3.000
 AKL  HB2  CB  CG   111.09  3.000
 AKL  HB3  CB  CA   109.97  3.000
 AKL  HB2  CB  CA   110.30  3.000
 AKL  CG   CB  CA   110.34  3.000
 AKL  OD1  CG  OD2  126.29  3.000
 AKL  OD1  CG  CB   115.20  3.000
 AKL  OD2  CG  CB   118.50  3.000
 AKL  CM   C   O    115.82  3.000
 AKL  CM   C   CA   122.40  3.000
 AKL  O    C   CA   120.80  1.700
 AKL  HM2  CM  HM1  108.21  3.000
 AKL  HM2  CM  CL1  107.74  3.000
 AKL  HM1  CM  CL1  106.62  3.000
 AKL  HM2  CM  C    109.28  3.000
 AKL  HM1  CM  C    108.02  3.000
 AKL  CL1  CM  C    116.68  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
 AKL  Var_01  OD2  CG  CB  CA  162.96  30.0  3
 AKL  Var_02  CL1  CM  C   CA   21.29  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
 AKL  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
 AKL  plan-1  CA   0.020
 AKL  plan-1  C    0.020
 AKL  plan-1  O    0.020
 AKL  plan-1  CM   0.020
 AKL  plan-2  CB   0.020
 AKL  plan-2  CG   0.020
 AKL  plan-2  OD2  0.020
 AKL  plan-2  OD1  0.020

