# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:58:27 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: 3-(pyridin-4-yldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSc1ccncc1)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
 4GJ  4GJ  3-(pyridin-4-yldisulfanyl)-L-alanine  L-peptide  23  14  .  2016-04-22  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_4GJ
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
 4GJ  N5   N  N      0  -0.411  11.3354  37.5680  26.2992
 4GJ  C1   C  CR16   0  -0.318  11.5170  35.7818  27.8903
 4GJ  C2   C  CR6    0  -0.021  12.3342  35.0602  27.0304
 4GJ  C3   C  CR16   0  -0.340  12.6394  35.6241  25.7925
 4GJ  C4   C  CR16   0  -0.056  12.1180  36.8685  25.4840
 4GJ  C6   C  CR16   0  -0.057  11.0505  37.0195  27.4738
 4GJ  S2   S  S2     0   0.035  13.0666  33.4903  27.3795
 4GJ  N    N  NH2    0  -0.802  15.2234  32.9551  31.8035
 4GJ  CA   C  CH1    0  -0.156  14.4929  32.4147  30.6652
 4GJ  C    C  C      0   0.399  15.3938  32.2537  29.4147
 4GJ  O    O  O      0  -0.603  14.9877  31.4293  28.5718
 4GJ  CB   C  CH2    0  -0.564  13.3446  33.3912  30.3961
 4GJ  SG   S  S2     0  -0.032  12.1682  32.8725  29.1105
 4GJ  H1   H  HCR6   0   0.274  11.2396  35.3967  28.8619
 4GJ  H3   H  HCR6   0   0.280  13.2671  35.1111  25.0746
 4GJ  H4   H  HCR6   0   0.265  12.3457  37.3186  24.5239
 4GJ  H6   H  HCR6   0   0.265  10.4113  37.5944  28.1354
 4GJ  HA   H  HCH1   0   0.197  14.0456  31.4326  30.8731
 4GJ  HB2  H  HCH2   0   0.277  13.7220  34.3848  30.1512
 4GJ  HB3  H  HCH2   0   0.282  12.7276  33.4893  31.2943
 4GJ  OXT  O  OC    -1  -0.593  16.4172  32.9581  29.3492
 4GJ  H    H  HNH2   0   0.336  14.7230  32.7412  32.6572
 4GJ  H2   H  HNH2   0   0.340  16.1252  32.5037  31.8790

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
 4GJ  C4  C3   aromatic  1.384  0.020  1.384
 4GJ  C4  N5   aromatic  1.329  0.020  1.329
 4GJ  C3  C2   aromatic  1.394  0.020  1.394
 4GJ  N5  C6   aromatic  1.327  0.020  1.327
 4GJ  C2  S2   single    1.767  0.020  1.767
 4GJ  C2  C1   aromatic  1.389  0.020  1.389
 4GJ  S2  SG   single    2.046  0.020  2.046
 4GJ  C6  C1   aromatic  1.387  0.020  1.387
 4GJ  O   C    deloc     1.231  0.020  1.231
 4GJ  C   CA   single    1.525  0.021  1.525
 4GJ  SG  CB   single    1.818  0.020  1.818
 4GJ  CB  CA   single    1.530  0.020  1.530
 4GJ  CA  N    single    1.458  0.019  1.458
 4GJ  C1  H1   single    0.930  0.020  1.080
 4GJ  C3  H3   single    0.930  0.020  1.080
 4GJ  C4  H4   single    0.930  0.020  1.080
 4GJ  C6  H6   single    0.930  0.020  1.080
 4GJ  N   H    single    0.860  0.020  0.860
 4GJ  N   H2   single    0.890  0.020  1.040
 4GJ  CA  HA   single    0.970  0.020  0.970
 4GJ  CB  HB2  single    0.970  0.020  1.090
 4GJ  CB  HB3  single    0.970  0.020  1.090
 4GJ  C   OXT  deloc     1.244  0.020  1.244

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
 4GJ  C6   N5  C4   116.85  3.000
 4GJ  H1   C1  C6   120.10  3.000
 4GJ  H1   C1  C2   121.49  3.000
 4GJ  C6   C1  C2   118.41  3.000
 4GJ  S2   C2  C3   116.36  3.000
 4GJ  S2   C2  C1   125.68  3.000
 4GJ  C3   C2  C1   117.94  3.000
 4GJ  H3   C3  C4   119.77  3.000
 4GJ  H3   C3  C2   121.60  3.000
 4GJ  C4   C3  C2   118.63  3.000
 4GJ  H4   C4  C3   119.43  3.000
 4GJ  H4   C4  N5   116.63  3.000
 4GJ  C3   C4  N5   123.94  3.000
 4GJ  H6   C6  C1   119.21  3.000
 4GJ  H6   C6  N5   116.56  3.000
 4GJ  C1   C6  N5   124.22  3.000
 4GJ  SG   S2  C2   104.68  3.000
 4GJ  H2   N   H    106.47  3.000
 4GJ  H2   N   CA   109.88  3.000
 4GJ  H    N   CA   114.00  3.000
 4GJ  HA   CA  CB   109.00  3.000
 4GJ  HA   CA  C    109.00  3.000
 4GJ  CB   CA  C    110.10  1.900
 4GJ  HA   CA  N    110.00  3.000
 4GJ  CB   CA  N    110.50  1.700
 4GJ  C    CA  N    111.00  2.800
 4GJ  OXT  C   O    127.35  3.000
 4GJ  OXT  C   CA   117.51  3.000
 4GJ  O    C   CA   120.80  1.700
 4GJ  HB3  CB  HB2  107.32  3.000
 4GJ  HB3  CB  SG   103.96  3.000
 4GJ  HB2  CB  SG   108.96  3.000
 4GJ  HB3  CB  CA   109.62  3.000
 4GJ  HB2  CB  CA   111.16  3.000
 4GJ  SG   CB  CA   115.31  3.000
 4GJ  CB   SG  S2   103.18  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
 4GJ  CONST_01  C2  C3  C4  N5    0.00   0.0  0
 4GJ  CONST_02  C2  C1  C6  N5    0.00   0.0  0
 4GJ  CONST_03  C4  C3  C2  C1    0.00   0.0  0
 4GJ  CONST_04  C4  N5  C6  C1    0.00   0.0  0
 4GJ  CONST_05  C6  N5  C4  C3    0.00   0.0  0
 4GJ  CONST_06  C6  C1  C2  C3    0.00   0.0  0
 4GJ  CONST_07  S2  C2  C3  C4  180.00   0.0  0
 4GJ  CONST_08  S2  C2  C1  C6  180.00   0.0  0
 4GJ  CONST_09  H3  C3  C4  N5  180.00   0.0  0
 4GJ  CONST_10  H1  C1  C6  N5  180.00   0.0  0
 4GJ  CONST_11  H4  C4  C3  C2  180.00   0.0  0
 4GJ  CONST_12  H6  C6  C1  C2  180.00   0.0  0
 4GJ  Var_01    CA  CB  SG  S2  -84.42  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
 4GJ  chir_01  CA  C  CB  N  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
 4GJ  plan-1  N5   0.020
 4GJ  plan-1  C1   0.020
 4GJ  plan-1  C2   0.020
 4GJ  plan-1  C3   0.020
 4GJ  plan-1  C4   0.020
 4GJ  plan-1  C6   0.020
 4GJ  plan-1  S2   0.020
 4GJ  plan-1  H1   0.020
 4GJ  plan-1  H3   0.020
 4GJ  plan-1  H4   0.020
 4GJ  plan-1  H6   0.020
 4GJ  plan-2  CA   0.020
 4GJ  plan-2  C    0.020
 4GJ  plan-2  O    0.020
 4GJ  plan-2  OXT  0.020

