# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:14:27 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(2-sulfanylethanoylamino)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CNC(=O)CS)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
 7O5  7O5  '(2~{S})-2-azanyl-3-(2-sulfanylethanoylamino)propanoic acid'  L-peptide  21  11  .  2022-09-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7O5
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
 7O5  C    C  C     0   0.543   -8.7540  22.0747  -5.3387
 7O5  CB   C  CH2   0  -0.274  -10.7080  20.8924  -4.3414
 7O5  CA   C  CH1   0  -0.215   -9.4869  20.7499  -5.2683
 7O5  N    N  NH2   0  -0.790   -8.5981  19.7288  -4.7642
 7O5  O    O  O     0  -0.431   -7.6177  22.2546  -4.9855
 7O5  S1G  S  S2    0  -0.210  -10.9393  16.2975  -3.9703
 7O5  C1S  C  CH2   0  -0.695  -12.1230  17.5313  -3.3371
 7O5  C2S  C  C     0   0.539  -11.4233  18.8592  -3.1396
 7O5  O2S  O  O     0  -0.478  -10.8734  19.1455  -2.0896
 7O5  H2   H  HCH2  0   0.263  -10.3851  21.1948  -3.3465
 7O5  H3   H  HCH2  0   0.267  -11.3820  21.6566  -4.7268
 7O5  H4   H  HCH1  0   0.260   -9.8647  20.5481  -6.2838
 7O5  H5   H  HNH2  0   0.344   -9.0798  18.8386  -4.7715
 7O5  H6   H  HNH2  0   0.356   -7.8096  19.6153  -5.3881
 7O5  H8   H  HSH1  0   0.229  -10.9364  16.6989  -5.2467
 7O5  H9   H  HCH2  0   0.306  -12.9821  17.5923  -4.0042
 7O5  H10  H  HCH2  0   0.316  -12.4635  17.1539  -2.3748
 7O5  H11  H  HNH1  0   0.407  -11.9512  19.3493  -5.0387
 7O5  OXT  O  OH1   0  -0.595   -9.5229  23.0281  -5.8513
 7O5  HXT  H  HOH1  0   0.484   -9.0404  23.8682  -5.8752
 7O5  NS   N  NH1   0  -0.626  -11.4265  19.6479  -4.2310

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
 7O5  CA   N    single  1.458  0.019  1.458
 7O5  CA   C    single  1.525  0.021  1.525
 7O5  CA   CB   single  1.521  0.033  1.521
 7O5  C    O    double  1.231  0.020  1.231
 7O5  NS   CB   single  1.441  0.020  1.441
 7O5  NS   C2S  single  1.347  0.020  1.347
 7O5  S1G  C1S  single  1.823  0.020  1.823
 7O5  C2S  C1S  single  1.514  0.020  1.514
 7O5  C2S  O2S  double  1.219  0.020  1.219
 7O5  CB   H2   single  0.970  0.020  1.090
 7O5  CB   H3   single  0.970  0.020  1.090
 7O5  CA   H4   single  0.970  0.020  1.090
 7O5  N    H5   single  0.890  0.020  1.040
 7O5  N    H6   single  0.890  0.020  1.040
 7O5  S1G  H8   single  1.200  0.020  1.300
 7O5  C1S  H9   single  0.970  0.020  1.090
 7O5  C1S  H10  single  0.970  0.020  1.090
 7O5  NS   H11  single  0.860  0.020  1.020
 7O5  C    OXT  single  1.328  0.020  1.328
 7O5  OXT  HXT  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
 7O5  OXT  C    O    123.56  3.000
 7O5  OXT  C    CA   111.44  3.000
 7O5  O    C    CA   120.80  1.700
 7O5  H3   CB   H2   108.17  3.000
 7O5  H3   CB   NS   108.93  3.000
 7O5  H2   CB   NS   108.52  3.000
 7O5  H3   CB   CA   110.04  3.000
 7O5  H2   CB   CA   109.91  3.000
 7O5  NS   CB   CA   111.20  3.000
 7O5  H4   CA   N    113.76  3.000
 7O5  H4   CA   CB   107.44  3.000
 7O5  N    CA   CB   110.40  1.500
 7O5  H4   CA   C    106.44  3.000
 7O5  CB   CA   C    110.50  1.500
 7O5  N    CA   C    111.00  2.800
 7O5  H6   N    H5   105.53  3.000
 7O5  H6   N    CA   110.09  3.000
 7O5  H5   N    CA   109.05  3.000
 7O5  H8   S1G  C1S   97.45  3.000
 7O5  H10  C1S  H9   108.31  3.000
 7O5  H10  C1S  C2S  109.48  3.000
 7O5  H9   C1S  C2S  113.28  3.000
 7O5  H10  C1S  S1G  105.99  3.000
 7O5  H9   C1S  S1G  109.70  3.000
 7O5  C2S  C1S  S1G  109.80  3.000
 7O5  NS   C2S  O2S  124.16  3.000
 7O5  O2S  C2S  C1S  121.78  3.000
 7O5  NS   C2S  C1S  114.01  3.000
 7O5  HXT  OXT  C    110.10  3.000
 7O5  H11  NS   C2S  118.49  3.000
 7O5  H11  NS   CB   116.98  3.000
 7O5  C2S  NS   CB   124.52  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
 7O5  CONST_01  C1S  C2S  NS   CB   180.00   0.0  0
 7O5  CONST_02  O2S  C2S  NS   CB     0.00   0.0  0
 7O5  CONST_03  H11  NS   C2S  C1S    0.00   0.0  0
 7O5  CONST_04  HXT  OXT  C    CA   180.00   0.0  0
 7O5  Var_01    C2S  NS   CB   CA   107.19  30.0  1
 7O5  Var_02    NS   C2S  C1S  S1G   88.57  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
 7O5  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
 7O5  plan-1  CB   0.020
 7O5  plan-1  C1S  0.020
 7O5  plan-1  C2S  0.020
 7O5  plan-1  O2S  0.020
 7O5  plan-1  H11  0.020
 7O5  plan-1  NS   0.020
 7O5  plan-2  C    0.020
 7O5  plan-2  CA   0.020
 7O5  plan-2  O    0.020
 7O5  plan-2  OXT  0.020
 7O5  plan-2  HXT  0.020

