# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:11:25 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{R})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](COC(=O)CC(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
 K5L  K5L  '(2~{R})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid'  L-peptide  20  13  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_K5L
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
 K5L  O    O  O      0  -0.592  21.2817  25.9920  62.2916
 K5L  C    C  C      0   0.399  21.9286  27.0356  62.4935
 K5L  CA   C  CH1    0  -0.245  23.1006  26.9603  63.5080
 K5L  N    N  NH2    0  -0.791  23.5102  25.5915  63.7614
 K5L  CB   C  CH2    0  -0.193  22.6596  27.7250  64.7581
 K5L  OAI  O  O2     0  -0.464  23.6638  27.7230  65.7800
 K5L  CAK  C  C      0   0.583  24.6114  28.6594  65.7495
 K5L  OAC  O  O      0  -0.465  24.6905  29.4975  64.8834
 K5L  CAG  C  CH2    0  -0.716  25.5245  28.5564  66.9278
 K5L  CAJ  C  C      0   0.432  24.9298  29.3040  68.1604
 K5L  OAE  O  O      0  -0.596  25.5636  29.1680  69.2180
 K5L  OAB  O  OC    -1  -0.590  23.8957  29.9652  67.9596
 K5L  H2   H  HCH1   0   0.219  23.9486  27.4963  63.0695
 K5L  H3   H  HNH2   0   0.331  24.1236  25.5517  64.5659
 K5L  H4   H  HNH2   0   0.326  22.6922  25.0403  63.9886
 K5L  H6   H  HCH2   0   0.225  22.3718  28.7465  64.5095
 K5L  H7   H  HCH2   0   0.233  21.8009  27.2264  65.2134
 K5L  H8   H  HCH2   0   0.254  25.7136  27.5141  67.1913
 K5L  H9   H  HCH2   0   0.259  26.4855  29.0098  66.6758
 K5L  OXT  O  OC    -1  -0.607  21.7212  28.1616  61.9998

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
 K5L  N    CA   single  1.458  0.019  1.458
 K5L  O    C    deloc   1.231  0.020  1.231
 K5L  C    CA   single  1.525  0.021  1.525
 K5L  CA   CB   single  1.530  0.020  1.530
 K5L  OAC  CAK  double  1.208  0.020  1.208
 K5L  CB   OAI  single  1.433  0.020  1.433
 K5L  OAI  CAK  single  1.333  0.020  1.333
 K5L  CAK  CAG  single  1.494  0.020  1.494
 K5L  CAG  CAJ  single  1.559  0.020  1.559
 K5L  OAE  CAJ  deloc   1.240  0.020  1.240
 K5L  CAJ  OAB  deloc   1.244  0.020  1.244
 K5L  CA   H2   single  0.970  0.020  1.090
 K5L  N    H3   single  0.890  0.020  1.040
 K5L  N    H4   single  0.890  0.020  1.040
 K5L  CB   H6   single  0.970  0.020  1.090
 K5L  CB   H7   single  0.970  0.020  1.090
 K5L  CAG  H8   single  0.970  0.020  1.090
 K5L  CAG  H9   single  0.970  0.020  1.090
 K5L  C    OXT  deloc   1.247  0.020  1.247

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
 K5L  OXT  C    CA   115.36  3.000
 K5L  OXT  C    O    127.35  3.000
 K5L  CA   C    O    120.80  1.700
 K5L  H2   CA   CB   107.80  3.000
 K5L  H2   CA   N    108.25  3.000
 K5L  CB   CA   N    110.50  1.700
 K5L  H2   CA   C    107.42  3.000
 K5L  CB   CA   C    110.10  1.900
 K5L  N    CA   C    111.00  2.800
 K5L  H4   N    H3   106.85  3.000
 K5L  H4   N    CA   108.95  3.000
 K5L  H3   N    CA   110.29  3.000
 K5L  H7   CB   H6   108.38  3.000
 K5L  H7   CB   OAI  104.66  3.000
 K5L  H6   CB   OAI  110.43  3.000
 K5L  H7   CB   CA   109.81  3.000
 K5L  H6   CB   CA   110.98  3.000
 K5L  OAI  CB   CA   112.33  3.000
 K5L  CAK  OAI  CB   118.76  3.000
 K5L  CAG  CAK  OAC  124.98  3.000
 K5L  CAG  CAK  OAI  111.59  3.000
 K5L  OAC  CAK  OAI  123.41  3.000
 K5L  H9   CAG  H8   107.44  3.000
 K5L  H9   CAG  CAJ  108.60  3.000
 K5L  H8   CAG  CAJ  109.45  3.000
 K5L  H9   CAG  CAK  109.10  3.000
 K5L  H8   CAG  CAK  111.22  3.000
 K5L  CAJ  CAG  CAK  110.93  3.000
 K5L  OAB  CAJ  OAE  128.37  3.000
 K5L  OAB  CAJ  CAG  116.38  3.000
 K5L  OAE  CAJ  CAG  115.25  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
 K5L  Var_01  OAC  CAK  OAI  CB    -1.85  30.0  3
 K5L  Var_02  CAJ  CAG  CAK  OAI  -84.46  30.0  3
 K5L  Var_03  OAE  CAJ  CAG  CAK  173.73  30.0  3
 K5L  Var_04  H6   CB   OAI  CAK  -38.39  30.0  1

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
 K5L  chir_01  CA  N  C  CB  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
 K5L  plan-1  O    0.020
 K5L  plan-1  C    0.020
 K5L  plan-1  CA   0.020
 K5L  plan-1  OXT  0.020
 K5L  plan-2  CAG  0.020
 K5L  plan-2  CAJ  0.020
 K5L  plan-2  OAE  0.020
 K5L  plan-2  OAB  0.020
 K5L  plan-3  OAI  0.020
 K5L  plan-3  CAK  0.020
 K5L  plan-3  OAC  0.020
 K5L  plan-3  CAG  0.020

