# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:50:16 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[[(5~{S})-5-[(1~{S})-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]-4,5-dihydro-1,2-oxazol-3-yl]sulfanyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC1=NO[C@@H](C1)[C@H](N)C(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
 8JB  8JB  '(2~{R})-2-azanyl-3-[[(5~{S})-5-[(1~{S})-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]-4,5-dihydro-1,2-oxazol-3-yl]sulfanyl]propanoic acid'  L-peptide  28  17  .  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_8JB
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
 8JB  O3   O  O      0  -0.420  51.0678  64.7291  16.3844
 8JB  C4   C  CH2    0  -0.550  51.6361  66.2907  14.7406
 8JB  C5   C  CR15   0   0.027  51.5495  66.0822  16.2486
 8JB  N2   N  N      0  -0.144  50.4999  64.3162  15.1894
 8JB  N3   N  NH2    0  -0.795  50.7408  66.7751  18.4254
 8JB  C    C  C      0   0.430  48.3919  63.9653  10.2376
 8JB  O    O  O      0  -0.593  47.5791  63.5550   9.3894
 8JB  CA   C  CH1    0  -0.203  48.0589  63.6918  11.7217
 8JB  N    N  NH2    0  -0.808  47.2592  62.4869  11.8583
 8JB  CB   C  CH2    0  -0.544  49.3183  63.5292  12.5650
 8JB  C3   C  CR5    0   0.066  50.7804  65.1540  14.2756
 8JB  C2   C  CH1    0  -0.217  50.6337  67.0523  16.9989
 8JB  C1   C  C      0   0.389  49.1831  67.0321  16.4394
 8JB  O2   O  OC    -1  -0.594  48.3409  66.3823  17.0875
 8JB  O1   O  O      0  -0.605  48.9869  67.6674  15.3825
 8JB  H1   H  HCH2   0   0.276  52.6522  66.1743  14.3550
 8JB  H2   H  HCH2   0   0.277  51.2579  67.2579  14.4171
 8JB  H3   H  HCR5   0   0.241  52.5341  66.1153  16.7209
 8JB  H4   H  HNH2   0   0.337  50.3620  67.5647  18.9345
 8JB  H5   H  HNH2   0   0.327  50.1016  66.0156  18.6320
 8JB  H7   H  HCH1   0   0.214  47.5323  64.5896  12.0885
 8JB  H8   H  HNH2   0   0.336  46.6881  62.5380  12.6912
 8JB  H9   H  HNH2   0   0.338  46.6307  62.4385  11.0666
 8JB  H11  H  HCH2   0   0.275  49.0503  63.2917  13.5939
 8JB  H12  H  HCH2   0   0.261  49.9360  62.7166  12.1811
 8JB  H13  H  HCH1   0   0.222  51.0536  68.0475  16.8174
 8JB  S    S  S2     0   0.043  50.3031  65.0612  12.6034
 8JB  O4   O  OC    -1  -0.587  49.4394  64.6098  10.0277

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
 8JB  O   C    deloc   1.231  0.020  1.231
 8JB  N   CA   single  1.458  0.019  1.458
 8JB  C   CA   single  1.525  0.021  1.525
 8JB  CA  CB   single  1.530  0.020  1.530
 8JB  CB  S    single  1.822  0.020  1.822
 8JB  S   C3   single  1.741  0.020  1.741
 8JB  C3  C4   single  1.497  0.020  1.497
 8JB  C3  N2   double  1.271  0.020  1.271
 8JB  C4  C5   single  1.525  0.020  1.525
 8JB  N2  O3   single  1.386  0.020  1.386
 8JB  O3  C5   single  1.443  0.020  1.443
 8JB  C5  C2   single  1.531  0.020  1.531
 8JB  O1  C1   deloc   1.249  0.020  1.249
 8JB  C2  C1   single  1.555  0.020  1.555
 8JB  C2  N3   single  1.457  0.020  1.457
 8JB  C1  O2   deloc   1.246  0.020  1.246
 8JB  C   O4   deloc   1.248  0.020  1.248
 8JB  C4  H1   single  0.970  0.020  1.090
 8JB  C4  H2   single  0.970  0.020  1.090
 8JB  C5  H3   single  0.970  0.020  1.090
 8JB  N3  H4   single  0.890  0.020  1.040
 8JB  N3  H5   single  0.890  0.020  1.040
 8JB  CA  H7   single  0.970  0.020  1.090
 8JB  N   H8   single  0.890  0.020  1.040
 8JB  N   H9   single  0.890  0.020  1.040
 8JB  CB  H11  single  0.970  0.020  1.090
 8JB  CB  H12  single  0.970  0.020  1.090
 8JB  C2  H13  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
 8JB  N2   O3  C5   109.58  3.000
 8JB  H2   C4  H1   108.24  3.000
 8JB  H2   C4  C3   112.59  3.000
 8JB  H1   C4  C3   109.94  3.000
 8JB  H2   C4  C5   113.33  3.000
 8JB  H1   C4  C5   112.78  3.000
 8JB  C3   C4  C5    99.84  3.000
 8JB  H3   C5  C2   107.94  3.000
 8JB  H3   C5  C4   111.85  3.000
 8JB  C2   C5  C4   115.60  3.000
 8JB  H3   C5  O3   106.78  3.000
 8JB  C2   C5  O3   110.40  3.000
 8JB  C4   C5  O3   103.91  3.000
 8JB  C3   N2  O3   109.45  3.000
 8JB  H5   N3  H4   104.22  3.000
 8JB  H5   N3  C2   107.19  3.000
 8JB  H4   N3  C2   108.44  3.000
 8JB  O4   C   CA   115.71  3.000
 8JB  O4   C   O    127.16  3.000
 8JB  CA   C   O    120.80  1.700
 8JB  H7   CA  CB   107.29  3.000
 8JB  H7   CA  N    112.39  3.000
 8JB  CB   CA  N    110.50  1.700
 8JB  H7   CA  C    106.14  3.000
 8JB  CB   CA  C    110.10  1.900
 8JB  N    CA  C    111.00  2.800
 8JB  H9   N   H8   107.22  3.000
 8JB  H9   N   CA   107.94  3.000
 8JB  H8   N   CA   110.27  3.000
 8JB  H12  CB  H11  108.02  3.000
 8JB  H12  CB  S    109.14  3.000
 8JB  H11  CB  S    107.24  3.000
 8JB  H12  CB  CA   110.66  3.000
 8JB  H11  CB  CA   110.03  3.000
 8JB  S    CB  CA   111.63  3.000
 8JB  S    C3  N2   126.49  3.000
 8JB  N2   C3  C4   113.79  3.000
 8JB  S    C3  C4   119.70  3.000
 8JB  H13  C2  C1   108.05  3.000
 8JB  H13  C2  N3   107.87  3.000
 8JB  C1   C2  N3   114.73  3.000
 8JB  H13  C2  C5   105.38  3.000
 8JB  N3   C2  C5   108.38  3.000
 8JB  C1   C2  C5   111.94  3.000
 8JB  O1   C1  O2   126.84  3.000
 8JB  O2   C1  C2   116.76  3.000
 8JB  O1   C1  C2   116.39  3.000
 8JB  C3   S   CB   102.31  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
 8JB  Var_01  C4   C3  N2  O3    1.04  30.0  1
 8JB  Var_02  N2   C3  C4  C5  -11.78  30.0  1
 8JB  Var_03  H11  CB  S   C3   17.27  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
 8JB  chir_01  C5  C4  O3  C2  positiv
 8JB  chir_02  CA  N   C   CB  positiv
 8JB  chir_03  C2  N3  C5  C1  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
 8JB  plan-1  C   0.020
 8JB  plan-1  O   0.020
 8JB  plan-1  CA  0.020
 8JB  plan-1  O4  0.020
 8JB  plan-2  C2  0.020
 8JB  plan-2  C1  0.020
 8JB  plan-2  O2  0.020
 8JB  plan-2  O1  0.020

