# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:37:47 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2~{S})-2-azanyl-2-[(3~{R})-oxolan-3-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H]1CCOC1)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
 8YR  8YR  '(2~{S})-2-azanyl-2-[(3~{R})-oxolan-3-yl]ethanoic acid'  L-peptide  20  10  .  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
;

data_comp_8YR
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
 8YR  CA   C  CH1    0  -0.193  19.8903  25.5710  16.2936
 8YR  N    N  NH2    0  -0.791  21.2415  25.3339  16.7944
 8YR  CB   C  CH1    0  -0.296  19.9785  25.9743  14.8245
 8YR  CG2  C  CH2    0  -0.485  18.6764  26.4531  14.1876
 8YR  CG1  C  CH2    0  -0.108  20.8800  27.1809  14.5811
 8YR  C    C  C      0   0.392  18.9254  24.3683  16.4373
 8YR  CD2  C  CH2    0  -0.148  19.1802  27.2520  12.9945
 8YR  O    O  O      0  -0.606  19.4311  23.2357  16.2928
 8YR  OD1  O  O2     0  -0.504  20.4483  27.7747  13.3657
 8YR  H8   H  HCH1   0   0.198  19.4777  26.4232  16.8456
 8YR  H9   H  HNH2   0   0.335  21.1974  25.2031  17.7986
 8YR  H10  H  HCH1   0   0.225  20.3599  25.1201  14.2498
 8YR  H12  H  HCH2   0   0.224  18.1299  27.0937  14.8849
 8YR  H13  H  HCH2   0   0.242  18.0114  25.6439  13.8895
 8YR  H16  H  HCH2   0   0.211  21.9352  26.9142  14.4969
 8YR  H17  H  HCH2   0   0.183  20.7827  27.8959  15.4099
 8YR  H20  H  HCH2   0   0.195  19.2871  26.6080  12.1132
 8YR  H21  H  HCH2   0   0.212  18.5102  28.0723  12.7220
 8YR  OXT  O  OC    -1  -0.608  17.7238  24.6301  16.6493
 8YR  H2   H  HNH2   0   0.323  21.5432  24.4351  16.4328

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
 8YR  CD2  CG2  single  1.522  0.020  1.522
 8YR  CD2  OD1  single  1.421  0.020  1.421
 8YR  CG2  CB   single  1.527  0.020  1.527
 8YR  OD1  CG1  single  1.420  0.020  1.420
 8YR  CG1  CB   single  1.526  0.020  1.526
 8YR  CB   CA   single  1.521  0.033  1.521
 8YR  O    C    deloc   1.231  0.020  1.231
 8YR  CA   C    single  1.525  0.021  1.525
 8YR  CA   N    single  1.458  0.019  1.458
 8YR  CA   H8   single  0.970  0.020  1.090
 8YR  N    H9   single  0.890  0.020  1.040
 8YR  CB   H10  single  0.970  0.020  1.090
 8YR  CG2  H12  single  0.970  0.020  1.090
 8YR  CG2  H13  single  0.970  0.020  1.090
 8YR  CG1  H16  single  0.970  0.020  1.090
 8YR  CG1  H17  single  0.970  0.020  1.090
 8YR  CD2  H20  single  0.970  0.020  1.090
 8YR  CD2  H21  single  0.970  0.020  1.090
 8YR  C    OXT  deloc   1.248  0.020  1.248
 8YR  N    H2   single  0.890  0.020  1.040

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
 8YR  H8   CA   C    108.81  3.000
 8YR  H8   CA   CB   107.53  3.000
 8YR  C    CA   CB   110.50  1.500
 8YR  H8   CA   N    107.57  3.000
 8YR  C    CA   N    111.00  2.800
 8YR  CB   CA   N    110.40  1.500
 8YR  H2   N    H9   104.57  3.000
 8YR  H2   N    CA   107.26  3.000
 8YR  H9   N    CA   108.69  3.000
 8YR  H10  CB   CG1  109.06  3.000
 8YR  H10  CB   CG2  108.78  3.000
 8YR  CG1  CB   CG2  100.91  3.000
 8YR  H10  CB   CA   108.57  3.000
 8YR  CG1  CB   CA   113.37  3.000
 8YR  CG2  CB   CA   115.80  3.000
 8YR  H13  CG2  H12  107.74  3.000
 8YR  H13  CG2  CD2  112.19  3.000
 8YR  H12  CG2  CD2  110.98  3.000
 8YR  H13  CG2  CB   113.70  3.000
 8YR  H12  CG2  CB   110.12  3.000
 8YR  CD2  CG2  CB   102.09  3.000
 8YR  H17  CG1  H16  107.62  3.000
 8YR  H17  CG1  OD1  110.28  3.000
 8YR  H16  CG1  OD1  109.27  3.000
 8YR  H17  CG1  CB   110.00  3.000
 8YR  H16  CG1  CB   112.97  3.000
 8YR  OD1  CG1  CB   106.72  3.000
 8YR  OXT  C    O    126.86  3.000
 8YR  OXT  C    CA   120.80  1.700
 8YR  O    C    CA   120.80  1.700
 8YR  H21  CD2  H20  107.45  3.000
 8YR  H21  CD2  OD1  109.63  3.000
 8YR  H20  CD2  OD1  109.81  3.000
 8YR  H21  CD2  CG2  112.73  3.000
 8YR  H20  CD2  CG2  110.73  3.000
 8YR  OD1  CD2  CG2  106.49  3.000
 8YR  CD2  OD1  CG1  109.94  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
 8YR  Var_01  OD1  CD2  CG2  CB  -29.73  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
 8YR  chir_01  CA  CB  C    N    negativ
 8YR  chir_02  CB  CA  CG1  CG2  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
 8YR  plan-1  CA   0.020
 8YR  plan-1  C    0.020
 8YR  plan-1  O    0.020
 8YR  plan-1  OXT  0.020

