# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:22:22 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  20  13  .  2022-07-25  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_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  -0.714   1.3618   1.2808  -1.1185
 J8W  CA   C  CH1    0  -0.219   1.9399   0.7178   0.0826
 J8W  CB   C  CH2    0  -0.228   1.1957  -0.4961   0.6445
 J8W  OG   O  O2     0  -0.445  -0.1523  -0.1371   0.9783
 J8W  C    C  C      0   0.385   3.4106   0.2792  -0.1362
 J8W  O    O  O      0  -0.686   3.8060   0.1589  -1.3100
 J8W  C1   C  CH2    0  -0.787  -2.4621   0.0499   0.6654
 J8W  C2   C  C      0   0.603  -1.1734  -0.5881   0.2534
 J8W  C3   C  C      0   0.383  -2.7233   1.3466  -0.1509
 J8W  O7   O  O      0  -0.539  -1.0694  -1.4022  -0.6329
 J8W  O8   O  OC    -1  -0.695  -3.7403   1.9819   0.1632
 J8W  O9   O  O      0  -0.340  -1.9074   1.6211  -1.0530
 J8W  H1   H  HNH2   0   0.318   1.5942   0.6910  -1.9064
 J8W  H2   H  HNH2   0   0.329   0.3507   1.3385  -1.0617
 J8W  H4   H  HCH1   0   0.251   1.9435   1.4871   0.8645
 J8W  H5   H  HCH2   0   0.283   1.2005  -1.3222  -0.0685
 J8W  H6   H  HCH2   0   0.224   1.6593  -0.8334   1.5710
 J8W  H8   H  HCH2   0   0.238  -3.2804  -0.6491   0.4801
 J8W  H9   H  HCH2   0   0.221  -2.4706   0.2893   1.7298
 J8W  OXT  O  OC    -1  -0.582   4.0626   0.0478   0.9014

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    deloc   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  1.434  0.020  1.434
 J8W  OG  C2   single  1.331  0.020  1.331
 J8W  C2  O7   double  1.208  0.020  1.208
 J8W  C2  C1   single  1.496  0.020  1.496
 J8W  O9  C3   deloc   1.247  0.020  1.247
 J8W  C3  C1   single  1.554  0.020  1.554
 J8W  C3  O8   deloc   1.240  0.020  1.240
 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  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
 J8W  H2   N   H1  107.82  3.000
 J8W  H2   N   CA  111.95  3.000
 J8W  H1   N   CA  109.15  3.000
 J8W  H4   CA  C   107.21  3.000
 J8W  H4   CA  CB  107.23  3.000
 J8W  C    CA  CB  110.10  1.900
 J8W  H4   CA  N   108.67  3.000
 J8W  CB   CA  N   110.50  1.700
 J8W  C    CA  N   111.00  2.800
 J8W  H6   CB  H5  108.62  3.000
 J8W  H6   CB  OG  106.23  3.000
 J8W  H5   CB  OG  110.22  3.000
 J8W  H6   CB  CA  110.54  3.000
 J8W  H5   CB  CA  111.00  3.000
 J8W  OG   CB  CA  110.12  3.000
 J8W  C2   OG  CB  120.62  3.000
 J8W  OXT  C   O   126.92  3.000
 J8W  OXT  C   CA  115.54  3.000
 J8W  O    C   CA  120.80  1.700
 J8W  H9   C1  H8  107.47  3.000
 J8W  H9   C1  C3  109.15  3.000
 J8W  H8   C1  C3  108.60  3.000
 J8W  H9   C1  C2  111.65  3.000
 J8W  H8   C1  C2  109.01  3.000
 J8W  C3   C1  C2  110.85  3.000
 J8W  O7   C2  C1  124.31  3.000
 J8W  C1   C2  OG  111.49  3.000
 J8W  O7   C2  OG  124.20  3.000
 J8W  O9   C3  O8  127.40  3.000
 J8W  O8   C3  C1  115.62  3.000
 J8W  O9   C3  C1  116.97  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  Var_01  O7  C2  OG  CB    6.93  30.0  3
 J8W  Var_02  C3  C1  C2  OG   90.12  30.0  3
 J8W  Var_03  O9  C3  C1  C2    4.23  30.0  2
 J8W  Var_04  H5  CB  OG  C2  -13.53  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-2  C1   0.020
 J8W  plan-2  C3   0.020
 J8W  plan-2  O8   0.020
 J8W  plan-2  O9   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

