# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:46:42 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S})-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
 J8W  J8W  '(2~{S})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid'  L-peptide  22  13  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J8W
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
 J8W  N    N  NH2   0  -0.769   1.7210   1.6897  -0.8643
 J8W  CA   C  CH1   0  -0.305   2.0485   0.6858   0.1173
 J8W  CB   C  CH2   0  -0.150   1.0601  -0.4815   0.2096
 J8W  OG   O  O2    0  -0.524  -0.2025   0.0934   0.5544
 J8W  C    C  C     0   0.560   3.4391   0.1399  -0.1573
 J8W  O    O  O     0  -0.377   4.0960   0.3989  -1.1302
 J8W  C1   C  CH2   0  -0.721  -2.5068   0.0501   0.9618
 J8W  C2   C  C     0   0.637  -1.2492  -0.7110   0.6343
 J8W  C3   C  C     0   0.554  -3.1559   0.5405  -0.3084
 J8W  O7   O  O     0  -0.411  -1.2029  -1.9011   0.4631
 J8W  O8   O  OH1   0  -0.644  -4.2804   1.1914  -0.0558
 J8W  O9   O  O     0  -0.344  -2.7108   0.3592  -1.4115
 J8W  H1   H  HNH2  0   0.353   1.6101   1.2713  -1.7800
 J8W  H2   H  HNH2  0   0.345   0.8344   2.1169  -0.6326
 J8W  H4   H  HCH1  0   0.270   2.0878   1.1692   1.1002
 J8W  H5   H  HCH2  0   0.291   0.9893  -0.9936  -0.7544
 J8W  H6   H  HCH2  0   0.224   1.3538  -1.2082   0.9681
 J8W  H8   H  HCH2  0   0.353  -3.2018  -0.6033   1.4920
 J8W  H9   H  HCH2  0   0.347  -2.3000   0.9022   1.6124
 J8W  H10  H  HOH1  0   0.470  -4.6864   1.4892  -0.8839
 J8W  OXT  O  OH1   0  -0.629   3.8447  -0.6744   0.8092
 J8W  H3   H  HOH1  0   0.469   4.7240  -1.0238   0.6000

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
 J8W  N    CA   single  1.458  0.019  1.458
 J8W  O    C    double  1.231  0.020  1.231
 J8W  CA   C    single  1.525  0.021  1.525
 J8W  CA   CB   single  1.530  0.020  1.530
 J8W  CB   OG   single  1.429  0.020  1.429
 J8W  OG   C2   single  1.323  0.020  1.323
 J8W  C2   O7   double  1.203  0.020  1.203
 J8W  C2   C1   single  1.506  0.020  1.506
 J8W  O9   C3   double  1.203  0.020  1.203
 J8W  C3   C1   single  1.508  0.020  1.508
 J8W  C3   O8   single  1.324  0.020  1.324
 J8W  N    H1   single  0.890  0.020  1.040
 J8W  N    H2   single  0.890  0.020  1.040
 J8W  CA   H4   single  0.970  0.020  1.090
 J8W  CB   H5   single  0.970  0.020  1.090
 J8W  CB   H6   single  0.970  0.020  1.090
 J8W  C1   H8   single  0.970  0.020  1.090
 J8W  C1   H9   single  0.970  0.020  1.090
 J8W  O8   H10  single  0.850  0.020  0.980
 J8W  C    OXT  single  1.327  0.020  1.327
 J8W  OXT  H3   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
 J8W  H2   N    H1  106.61  3.000
 J8W  H2   N    CA  109.72  3.000
 J8W  H1   N    CA  110.66  3.000
 J8W  H4   CA   C   106.73  3.000
 J8W  H4   CA   CB  107.77  3.000
 J8W  C    CA   CB  110.10  1.900
 J8W  H4   CA   N   108.15  3.000
 J8W  CB   CA   N   110.50  1.700
 J8W  C    CA   N   111.00  2.800
 J8W  H6   CB   H5  108.56  3.000
 J8W  H6   CB   OG  109.76  3.000
 J8W  H5   CB   OG  110.11  3.000
 J8W  H6   CB   CA  112.06  3.000
 J8W  H5   CB   CA  110.20  3.000
 J8W  OG   CB   CA  106.14  3.000
 J8W  C2   OG   CB  117.97  3.000
 J8W  OXT  C    O   123.68  3.000
 J8W  OXT  C    CA  111.63  3.000
 J8W  O    C    CA  120.80  1.700
 J8W  H9   C1   H8  107.35  3.000
 J8W  H9   C1   C3  109.24  3.000
 J8W  H8   C1   C3  109.25  3.000
 J8W  H9   C1   C2  111.46  3.000
 J8W  H8   C1   C2  109.56  3.000
 J8W  C3   C1   C2  109.91  3.000
 J8W  O7   C2   C1  124.26  3.000
 J8W  C1   C2   OG  111.51  3.000
 J8W  O7   C2   OG  124.23  3.000
 J8W  O9   C3   O8  124.29  3.000
 J8W  O8   C3   C1  111.39  3.000
 J8W  O9   C3   C1  124.32  3.000
 J8W  H10  O8   C3  110.12  3.000
 J8W  H3   OXT  C   109.96  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
 J8W  CONST_01  H3   OXT  C   CA  180.00   0.0  0
 J8W  CONST_02  H10  O8   C3  C1  180.00   0.0  0
 J8W  Var_01    O7   C2   OG  CB    1.65  30.0  3
 J8W  Var_02    C3   C1   C2  OG   87.84  30.0  3
 J8W  Var_03    O9   C3   C1  C2   -1.03  30.0  2
 J8W  Var_04    H5   CB   OG  C2   57.64  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
 J8W  chir_01  CA  N  C  CB  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
 J8W  plan-1  CA   0.020
 J8W  plan-1  C    0.020
 J8W  plan-1  O    0.020
 J8W  plan-1  OXT  0.020
 J8W  plan-1  H3   0.020
 J8W  plan-2  C1   0.020
 J8W  plan-2  C3   0.020
 J8W  plan-2  O8   0.020
 J8W  plan-2  O9   0.020
 J8W  plan-2  H10  0.020
 J8W  plan-3  OG   0.020
 J8W  plan-3  C1   0.020
 J8W  plan-3  C2   0.020
 J8W  plan-3  O7   0.020

