# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 09:40:38 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (2~{R})-2-azanyl-3-(4-ethanoylsulfanyl-1~{H}-imidazol-5-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Sc1nc[nH]c1C[C@@H](N)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
 SNK  SNK  "(2~{R})-2-azanyl-3-(4-ethanoylsulfanyl-1~{H}-imidazol-5-yl)propanoic acid"  L-peptide  25  15  .  2022-09-22  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_SNK
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
 SNK  N    N  NH2    0  .  226.9262  203.1080  223.4770
 SNK  CA   C  CH1    0  .  227.6914  203.5875  222.3563
 SNK  C    C  C      0  .  227.4566  202.9297  220.9455
 SNK  O    O  O      0  .  227.1768  203.8279  219.8492
 SNK  CB   C  CH2    0  .  227.7287  205.2304  222.4829
 SNK  CG   C  CR5    0  .  228.4775  205.8284  223.4934
 SNK  ND1  N  NR15   0  .  229.7155  205.2538  223.9908
 SNK  CD2  C  CR5    0  .  228.2478  206.7034  224.5909
 SNK  CE1  C  CR15   0  .  230.2294  205.8107  225.0837
 SNK  NE2  N  N      0  .  229.3419  206.8097  225.4174
 SNK  C01  C  CH3    0  .  227.0899  209.8844  226.8346
 SNK  C02  C  C      0  .  227.2413  209.6667  225.4212
 SNK  O03  O  O      0  .  227.5956  210.4328  224.7509
 SNK  S04  S  S2     0  .  226.9037  207.9101  224.6809
 SNK  H1   H  HNH2   0  .  226.9752  203.5626  224.3973
 SNK  H2   H  HNH2   0  .  225.7991  203.3243  223.2422
 SNK  H4   H  HCH1   0  .  228.6519  203.3052  222.5025
 SNK  H6   H  HCH2   0  .  228.2177  205.5434  221.4539
 SNK  H7   H  HCH2   0  .  226.6532  205.6513  222.3340
 SNK  H8   H  HNR5   0  .  230.1668  204.4627  223.4101
 SNK  H9   H  HCR5   0  .  231.0927  205.7246  225.4859
 SNK  H11  H  HCH3   0  .  227.4207  210.9538  227.1188
 SNK  H12  H  HCH3   0  .  226.1476  209.6907  227.2779
 SNK  H13  H  HCH3   0  .  227.8929  209.2385  227.4149
 SNK  O1   O  OC    -1  .  227.3439  201.7647  220.8191

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
 SNK  O    C    deloc     1.231  0.020  1.231
 SNK  C    CA   single    1.525  0.021  1.525
 SNK  CA   CB   single    1.530  0.020  1.530
 SNK  CA   N    single    1.458  0.019  1.458
 SNK  CB   CG   single    1.393  0.020  1.393
 SNK  CG   ND1  aromatic  1.453  0.020  1.453
 SNK  CG   CD2  aromatic  1.422  0.020  1.422
 SNK  ND1  CE1  aromatic  1.330  0.020  1.330
 SNK  CD2  S04  single    1.809  0.020  1.809
 SNK  CD2  NE2  aromatic  1.375  0.020  1.375
 SNK  O03  C02  double    1.078  0.020  1.078
 SNK  S04  C02  single    1.936  0.020  1.936
 SNK  CE1  NE2  aromatic  1.377  0.020  1.377
 SNK  C02  C01  single    1.438  0.020  1.438
 SNK  N    H1   single    0.890  0.020  1.040
 SNK  N    H2   single    0.890  0.020  1.040
 SNK  CA   H4   single    0.970  0.020  1.090
 SNK  CB   H6   single    0.970  0.020  1.090
 SNK  CB   H7   single    0.970  0.020  1.090
 SNK  ND1  H8   single    0.860  0.020  1.020
 SNK  CE1  H9   single    0.930  0.020  1.080
 SNK  C01  H11  single    0.970  0.020  1.090
 SNK  C01  H12  single    0.970  0.020  1.090
 SNK  C01  H13  single    0.970  0.020  1.090
 SNK  C    O1   deloc     1.177  0.020  1.177

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
 SNK  H2   N    H1    98.27  3.000
 SNK  H2   N    CA   107.10  3.000
 SNK  H1   N    CA   121.64  3.000
 SNK  H4   CA   CB   104.21  3.000
 SNK  H4   CA   C     98.89  3.000
 SNK  CB   CA   C    110.10  1.900
 SNK  H4   CA   N    107.42  3.000
 SNK  CB   CA   N    110.50  1.700
 SNK  C    CA   N    111.00  2.800
 SNK  O1   C    O    121.02  3.000
 SNK  O1   C    CA   121.60  3.000
 SNK  O    C    CA   120.80  1.700
 SNK  H7   CB   H6   100.08  3.000
 SNK  H7   CB   CG   115.73  3.000
 SNK  H6   CB   CG   107.20  3.000
 SNK  H7   CB   CA   109.24  3.000
 SNK  H6   CB   CA   101.92  3.000
 SNK  CG   CB   CA   119.73  3.000
 SNK  CD2  CG   ND1   96.70  3.000
 SNK  CD2  CG   CB   137.50  3.000
 SNK  ND1  CG   CB   122.47  3.000
 SNK  H8   ND1  CE1  125.94  3.000
 SNK  H8   ND1  CG   117.50  3.000
 SNK  CE1  ND1  CG   116.43  3.000
 SNK  S04  CD2  NE2  120.65  3.000
 SNK  NE2  CD2  CG   112.51  3.000
 SNK  S04  CD2  CG   124.68  3.000
 SNK  H9   CE1  NE2  123.03  3.000
 SNK  H9   CE1  ND1  131.06  3.000
 SNK  NE2  CE1  ND1  104.70  3.000
 SNK  CE1  NE2  CD2  108.12  3.000
 SNK  H13  C01  H12  107.38  3.000
 SNK  H13  C01  H11  100.98  3.000
 SNK  H12  C01  H11  108.73  3.000
 SNK  H13  C01  C02  109.15  3.000
 SNK  H12  C01  C02  118.51  3.000
 SNK  H11  C01  C02  110.60  3.000
 SNK  S04  C02  O03  117.67  3.000
 SNK  S04  C02  C01  119.66  3.000
 SNK  O03  C02  C01  122.57  3.000
 SNK  C02  S04  CD2  119.66  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
 SNK  CONST_01  NE2  CE1  ND1  CG      0.00   0.0  0
 SNK  CONST_02  CE1  NE2  CD2  CG      0.00   0.0  0
 SNK  CONST_03  NE2  CD2  CG   ND1     0.00   0.0  0
 SNK  CONST_04  CD2  NE2  CE1  ND1     0.00   0.0  0
 SNK  CONST_05  CE1  ND1  CG   CD2     0.00   0.0  0
 SNK  CONST_06  CE1  ND1  CG   CB    180.00   0.0  0
 SNK  CONST_07  NE2  CD2  CG   CB    180.00   0.0  0
 SNK  CONST_08  S04  CD2  CG   ND1   180.00   0.0  0
 SNK  CONST_09  S04  CD2  NE2  CE1   180.00   0.0  0
 SNK  CONST_10  H9   CE1  ND1  CG    180.00   0.0  0
 SNK  CONST_11  H8   ND1  CG   CD2   180.00   0.0  0
 SNK  CONST_12  H9   CE1  NE2  CD2   180.00   0.0  0
 SNK  CONST_13  H8   ND1  CE1  NE2   180.00   0.0  0
 SNK  Var_01    ND1  CG   CB   CA     32.94  30.0  2
 SNK  Var_02    CD2  CG   CB   CA   -121.12  30.0  2
 SNK  Var_03    C02  S04  CD2  CG   -139.53  30.0  2
 SNK  Var_04    C02  S04  CD2  NE2    22.45  30.0  2
 SNK  Var_05    H6   CB   CG   ND1   -82.27  30.0  2
 SNK  Var_06    H7   CB   CG   ND1   167.09  30.0  2
 SNK  Var_07    H6   CB   CG   CD2   123.67  30.0  2
 SNK  Var_08    H7   CB   CG   CD2    13.03  30.0  2
 SNK  Var_09    O03  C02  S04  CD2    87.70  30.0  3
 SNK  Var_10    C01  C02  S04  CD2   -88.73  30.0  3
 SNK  Var_11    H11  C01  C02  O03    -1.39  30.0  3
 SNK  Var_12    H12  C01  C02  O03   125.09  30.0  3
 SNK  Var_13    H13  C01  C02  O03  -111.64  30.0  3
 SNK  Var_14    H11  C01  C02  S04   174.86  30.0  3
 SNK  Var_15    H12  C01  C02  S04   -58.66  30.0  3
 SNK  Var_16    H13  C01  C02  S04    64.61  30.0  3

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
 SNK  chir_01  CA  C  CB  N  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
 SNK  plan-1  CB   0.020
 SNK  plan-1  CG   0.020
 SNK  plan-1  ND1  0.020
 SNK  plan-1  CD2  0.020
 SNK  plan-1  CE1  0.020
 SNK  plan-1  NE2  0.020
 SNK  plan-1  S04  0.020
 SNK  plan-1  H8   0.020
 SNK  plan-1  H9   0.020
 SNK  plan-2  CA   0.020
 SNK  plan-2  C    0.020
 SNK  plan-2  O    0.020
 SNK  plan-2  O1   0.020
 SNK  plan-3  C01  0.020
 SNK  plan-3  C02  0.020
 SNK  plan-3  O03  0.020
 SNK  plan-3  S04  0.020

