# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:34:54 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC[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
 85F  85F  '(2~{R})-2-azanyl-3-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid'  L-peptide  23  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_85F
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
 85F  N    N  NH2    0  -0.811  27.3661  54.0181  46.3413
 85F  CA   C  CH1    0  -0.224  27.8554  55.2143  47.0099
 85F  CB   C  CH2    0  -0.515  27.8711  55.0166  48.5192
 85F  SG   S  S2     0  -0.062  26.2025  54.6177  49.1259
 85F  CD   C  CH2    0  -0.564  26.3950  54.9644  50.8978
 85F  CE   C  CH1    0  -0.209  27.4588  54.1448  51.6240
 85F  NZ2  N  NH2    0  -0.776  27.2544  52.7240  51.4074
 85F  CZ1  C  C      0   0.395  27.5249  54.6020  53.1124
 85F  OH1  O  OC    -1  -0.596  27.4179  53.7217  53.9862
 85F  OH2  O  O      0  -0.612  27.7046  55.8241  53.2953
 85F  C    C  C      0   0.425  29.2672  55.5997  46.4800
 85F  O    O  O     -1  -0.598  29.5675  55.1773  45.3463
 85F  OXT  O  OC     0  -0.599  29.9571  56.3315  47.2139
 85F  H1   H  HNH2   0   0.332  26.3560  54.0325  46.2862
 85F  H2   H  HNH2   0   0.335  27.7099  54.0421  45.3899
 85F  H4   H  HCH1   0   0.204  27.2168  56.0914  46.8052
 85F  H5   H  HCH2   0   0.238  28.5560  54.2084  48.7851
 85F  H6   H  HCH2   0   0.246  28.2036  55.9280  49.0147
 85F  H7   H  HCH2   0   0.259  26.6005  56.0255  51.0295
 85F  H8   H  HCH2   0   0.256  25.4088  54.7695  51.3311
 85F  H9   H  HCH1   0   0.224  28.4318  54.4057  51.1880
 85F  H10  H  HNH2   0   0.332  27.8887  52.2224  52.0172
 85F  H11  H  HNH2   0   0.321  26.3331  52.4762  51.7522

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
 85F  O    C    deloc   1.231  0.020  1.231
 85F  C    CA   single  1.525  0.021  1.525
 85F  C    OXT  deloc   1.245  0.020  1.245
 85F  N    CA   single  1.458  0.019  1.458
 85F  CA   CB   single  1.530  0.020  1.530
 85F  CB   SG   single  1.820  0.020  1.820
 85F  SG   CD   single  1.816  0.020  1.816
 85F  CD   CE   single  1.527  0.020  1.527
 85F  NZ2  CE   single  1.452  0.020  1.452
 85F  CE   CZ1  single  1.559  0.020  1.559
 85F  CZ1  OH2  deloc   1.249  0.020  1.249
 85F  CZ1  OH1  deloc   1.245  0.020  1.245
 85F  N    H1   single  0.890  0.020  1.040
 85F  N    H2   single  0.890  0.020  1.040
 85F  CA   H4   single  0.970  0.020  1.090
 85F  CB   H5   single  0.970  0.020  1.090
 85F  CB   H6   single  0.970  0.020  1.090
 85F  CD   H7   single  0.970  0.020  1.090
 85F  CD   H8   single  0.970  0.020  1.090
 85F  CE   H9   single  0.970  0.020  1.090
 85F  NZ2  H10  single  0.890  0.020  1.040
 85F  NZ2  H11  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
 85F  H2   N    H1   106.72  3.000
 85F  H2   N    CA   107.35  3.000
 85F  H1   N    CA   110.43  3.000
 85F  H4   CA   C    105.36  3.000
 85F  H4   CA   CB   107.03  3.000
 85F  C    CA   CB   110.10  1.900
 85F  H4   CA   N    111.92  3.000
 85F  CB   CA   N    110.50  1.700
 85F  C    CA   N    111.00  2.800
 85F  H6   CB   H5   108.47  3.000
 85F  H6   CB   SG   108.15  3.000
 85F  H5   CB   SG   109.37  3.000
 85F  H6   CB   CA   110.21  3.000
 85F  H5   CB   CA   110.12  3.000
 85F  SG   CB   CA   110.47  3.000
 85F  CD   SG   CB   100.74  3.000
 85F  H8   CD   H7   107.20  3.000
 85F  H8   CD   CE   110.11  3.000
 85F  H7   CD   CE   109.52  3.000
 85F  H8   CD   SG   104.88  3.000
 85F  H7   CD   SG   108.92  3.000
 85F  CE   CD   SG   115.82  3.000
 85F  H9   CE   CZ1  105.78  3.000
 85F  H9   CE   NZ2  107.35  3.000
 85F  CZ1  CE   NZ2  115.83  3.000
 85F  H9   CE   CD   107.52  3.000
 85F  CZ1  CE   CD   109.04  3.000
 85F  NZ2  CE   CD   110.88  3.000
 85F  H11  NZ2  H10  104.07  3.000
 85F  H11  NZ2  CE   108.43  3.000
 85F  H10  NZ2  CE   107.86  3.000
 85F  OH2  CZ1  OH1  126.98  3.000
 85F  OH1  CZ1  CE   117.34  3.000
 85F  OH2  CZ1  CE   115.67  3.000
 85F  OXT  C    O    127.00  3.000
 85F  OXT  C    CA   116.58  3.000
 85F  O    C    CA   120.80  1.700

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
 85F  Var_01  CE  CD  SG  CB  -59.88  30.0  3
 85F  Var_02  H5  CB  SG  CD   75.98  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
 85F  chir_01  CA  C    N   CB   negativ
 85F  chir_02  CE  NZ2  CD  CZ1  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
 85F  plan-1  CE   0.020
 85F  plan-1  CZ1  0.020
 85F  plan-1  OH1  0.020
 85F  plan-1  OH2  0.020
 85F  plan-2  CA   0.020
 85F  plan-2  C    0.020
 85F  plan-2  O    0.020
 85F  plan-2  OXT  0.020

