# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:45:04 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: 3-(ethyldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCSSC[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
 SCS  SCS  3-(ethyldisulfanyl)-L-alanine  L-peptide  20  10  .  2012-08-28  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_SCS
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
 SCS  N    N  NH2    0  -0.815  13.3922  20.5106  16.2241
 SCS  CA   C  CH1    0  -0.203  14.3263  21.4503  15.6210
 SCS  C    C  C      0   0.397  15.1128  22.3093  16.6566
 SCS  O    O  O      0  -0.590  14.8373  22.1363  17.8594
 SCS  CB   C  CH2    0  -0.556  13.6587  22.3416  14.5809
 SCS  SG   S  S2     0  -0.080  12.4554  23.4517  15.4009
 SCS  SD   S  S2     0  -0.055  11.5511  24.3588  13.8018
 SCS  CE   C  CH3    0  -0.640   9.1326  23.1004  14.4323
 SCS  CZ   C  CH2    0  -0.554  10.2104  23.1999  13.3736
 SCS  OXT  O  OC    -1  -0.599  15.9608  23.0842  16.1777
 SCS  HN   H  HNH2   0   0.336  13.4735  20.6187  17.2290
 SCS  H2   H  HNH2   0   0.333  12.4372  20.7581  15.9964
 SCS  H3   H  HCH2   0   0.273  14.4007  22.9468  14.0653
 SCS  H4   H  HCH2   0   0.273  13.1223  21.7413  13.8436
 SCS  H5   H  HCH3   0   0.238   8.3602  22.3970  14.1179
 SCS  H6   H  HCH3   0   0.231   9.5419  22.7419  15.3769
 SCS  H7   H  HCH3   0   0.231   8.6605  24.0664  14.6078
 SCS  H8   H  HCH2   0   0.277   9.8087  23.5965  12.4380
 SCS  H9   H  HCH2   0   0.273  10.6494  22.2274  13.1493
 SCS  H11  H  HCH1   0   0.230  15.0903  20.8937  15.0585

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
 SCS  N   CA   single  1.458  0.019  1.458
 SCS  N   HN   single  0.890  0.020  1.040
 SCS  N   H2   single  0.890  0.020  1.040
 SCS  CA  C    single  1.525  0.021  1.525
 SCS  CA  CB   single  1.530  0.020  1.530
 SCS  C   O    deloc   1.231  0.020  1.231
 SCS  C   OXT  deloc   1.245  0.020  1.245
 SCS  CB  SG   single  1.831  0.020  1.831
 SCS  CB  H3   single  0.970  0.020  1.090
 SCS  CB  H4   single  0.970  0.020  1.090
 SCS  SG  SD   single  2.049  0.020  2.049
 SCS  SD  CZ   single  1.823  0.020  1.823
 SCS  CE  CZ   single  1.514  0.020  1.514
 SCS  CE  H5   single  0.970  0.020  1.090
 SCS  CE  H6   single  0.970  0.020  1.090
 SCS  CE  H7   single  0.970  0.020  1.090
 SCS  CZ  H8   single  0.970  0.020  1.090
 SCS  CZ  H9   single  0.970  0.020  1.090
 SCS  CA  H11  single  0.970  0.020  1.090

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
 SCS  H2   N   HN  105.81  3.000
 SCS  H2   N   CA  110.75  3.000
 SCS  HN   N   CA  106.88  3.000
 SCS  H11  CA  CB  104.55  3.000
 SCS  H11  CA  C   105.56  3.000
 SCS  CB   CA  C   110.10  1.900
 SCS  H11  CA  N   109.32  3.000
 SCS  CB   CA  N   110.50  1.700
 SCS  C    CA  N   111.00  2.800
 SCS  OXT  C   O   127.49  3.000
 SCS  OXT  C   CA  115.55  3.000
 SCS  O    C   CA  120.80  1.700
 SCS  H4   CB  H3  108.73  3.000
 SCS  H4   CB  SG  108.24  3.000
 SCS  H3   CB  SG  108.86  3.000
 SCS  H4   CB  CA  110.77  3.000
 SCS  H3   CB  CA  110.50  3.000
 SCS  SG   CB  CA  109.68  3.000
 SCS  SD   SG  CB  102.06  3.000
 SCS  CZ   SD  SG  103.09  3.000
 SCS  H7   CE  H6  108.35  3.000
 SCS  H7   CE  H5  108.14  3.000
 SCS  H6   CE  H5  107.67  3.000
 SCS  H7   CE  CZ  111.27  3.000
 SCS  H6   CE  CZ  111.12  3.000
 SCS  H5   CE  CZ  110.17  3.000
 SCS  H9   CZ  H8  107.19  3.000
 SCS  H9   CZ  CE  111.83  3.000
 SCS  H8   CZ  CE  111.16  3.000
 SCS  H9   CZ  SD  108.61  3.000
 SCS  H8   CZ  SD  103.93  3.000
 SCS  CE   CZ  SD  113.64  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
 SCS  Var_01  CE  CZ  SD  SG   66.80  30.0  3
 SCS  Var_02  H3  CB  SG  SD   65.56  30.0  1
 SCS  Var_03  H5  CE  CZ  SD  179.82  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
 SCS  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
 SCS  plan-1  CA   0.020
 SCS  plan-1  C    0.020
 SCS  plan-1  O    0.020
 SCS  plan-1  OXT  0.020

