# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:59:10 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-[(2-aminophenyl)disulfanyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSc1ccccc1N)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
 CS1  CS1  3-[(2-aminophenyl)disulfanyl]-L-alanine  L-peptide  26  15  .  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_CS1
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
 CS1  O     O  O      0  -0.597  3.8113   7.1851   0.2403
 CS1  C     C  C      0   0.428  4.8111   7.9204   0.1719
 CS1  CA    C  CH1    0  -0.169  6.2010   7.2433   0.2592
 CS1  N     N  NH2    0  -0.791  6.9881   7.6625  -0.8939
 CS1  CB    C  CH2    0  -0.580  6.9173   7.5767   1.5701
 CS1  SG    S  S2     0  -0.058  6.1959   6.8624   3.0810
 CS1  SD    S  S2     0  -0.041  4.5690   8.0729   3.4988
 CS1  CE    C  C      0  -0.227  5.3049   9.5037   4.2242
 CS1  C5    C  C1     0  -0.221  5.5402  10.6133   3.4132
 CS1  C4    C  C1     0  -0.287  6.0751  11.7788   3.9331
 CS1  C3    C  C1     0  -0.244  6.3783  11.8253   5.2913
 CS1  C2    C  C1     0  -0.327  6.1530  10.7347   6.1090
 CS1  C1    C  C      0   0.364  5.6090   9.5446   5.5996
 CS1  N1    N  NH2    0  -0.849  5.3499   8.4934   6.4307
 CS1  OXT   O  OC    -1  -0.609  4.8297   9.1622   0.0262
 CS1  HA    H  HCH1   0   0.205  6.0744   6.1582   0.2121
 CS1  H     H  HNH2   0   0.330  7.0271   8.6746  -0.9045
 CS1  H2    H  HNH2   0   0.335  7.9434   7.3367  -0.8036
 CS1  HB2   H  HCH2   0   0.275  7.9259   7.1513   1.5558
 CS1  HB3   H  HCH2   0   0.268  7.0279   8.6555   1.7014
 CS1  H5    H  H      0   0.262  5.2989  10.5400   2.3597
 CS1  H4    H  H      0   0.248  6.2531  12.6337   3.2952
 CS1  H3    H  H      0   0.255  6.7981  12.7260   5.7213
 CS1  HC2   H  H      0   0.258  6.3957  10.7919   7.1637
 CS1  HN11  H  HNH2   0   0.382  5.2233   7.5852   6.0160
 CS1  HN12  H  HNH2   0   0.387  5.8364   8.4758   7.3115

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
 CS1  O   C     deloc     1.231  0.020  1.231
 CS1  C   OXT   deloc     1.250  0.020  1.250
 CS1  C   CA    single    1.525  0.021  1.525
 CS1  CA  N     single    1.458  0.019  1.458
 CS1  CA  CB    single    1.530  0.020  1.530
 CS1  CA  HA    single    0.970  0.020  0.970
 CS1  N   H     single    0.860  0.020  0.860
 CS1  N   H2    single    0.890  0.020  1.040
 CS1  CB  SG    single    1.820  0.020  1.820
 CS1  CB  HB2   single    0.970  0.020  1.090
 CS1  CB  HB3   single    0.970  0.020  1.090
 CS1  SG  SD    single    2.070  0.020  2.070
 CS1  SD  CE    single    1.765  0.020  1.765
 CS1  CE  C5    aromatic  1.394  0.020  1.394
 CS1  CE  C1    aromatic  1.409  0.020  1.409
 CS1  C5  C4    aromatic  1.384  0.020  1.384
 CS1  C5  H5    single    0.930  0.020  1.080
 CS1  C4  C3    aromatic  1.392  0.020  1.392
 CS1  C4  H4    single    0.930  0.020  1.080
 CS1  C3  C2    aromatic  1.382  0.020  1.382
 CS1  C3  H3    single    0.930  0.020  1.080
 CS1  C2  C1    aromatic  1.404  0.020  1.404
 CS1  C2  HC2   single    0.930  0.020  1.080
 CS1  C1  N1    single    1.365  0.020  1.365
 CS1  N1  HN11  single    0.890  0.020  1.040
 CS1  N1  HN12  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
 CS1  OXT   C   CA    115.30  3.000
 CS1  CA    C   O     120.80  1.700
 CS1  OXT   C   O     127.29  3.000
 CS1  HA    CA  CB    109.00  3.000
 CS1  HA    CA  N     110.00  3.000
 CS1  CB    CA  N     110.50  1.700
 CS1  HA    CA  C     109.00  3.000
 CS1  CB    CA  C     110.10  1.900
 CS1  N     CA  C     111.00  2.800
 CS1  H2    N   H     106.61  3.000
 CS1  H2    N   CA    110.24  3.000
 CS1  H     N   CA    114.00  3.000
 CS1  HB3   CB  HB2   106.99  3.000
 CS1  HB3   CB  SG    109.14  3.000
 CS1  HB2   CB  SG    102.91  3.000
 CS1  HB3   CB  CA    111.43  3.000
 CS1  HB2   CB  CA    109.59  3.000
 CS1  SG    CB  CA    116.10  3.000
 CS1  SD    SG  CB    104.45  3.000
 CS1  CE    SD  SG    103.25  3.000
 CS1  C1    CE  C5    120.54  3.000
 CS1  C1    CE  SD    120.98  3.000
 CS1  C5    CE  SD    118.45  3.000
 CS1  H5    C5  C4    120.56  3.000
 CS1  H5    C5  CE    118.31  3.000
 CS1  C4    C5  CE    121.13  3.000
 CS1  H4    C4  C3    120.87  3.000
 CS1  H4    C4  C5    120.52  3.000
 CS1  C3    C4  C5    118.61  3.000
 CS1  H3    C3  C2    119.00  3.000
 CS1  H3    C3  C4    119.98  3.000
 CS1  C2    C3  C4    121.03  3.000
 CS1  HC2   C2  C1    118.98  3.000
 CS1  HC2   C2  C3    119.86  3.000
 CS1  C1    C2  C3    121.16  3.000
 CS1  N1    C1  C2    120.36  3.000
 CS1  N1    C1  CE    122.07  3.000
 CS1  C2    C1  CE    117.53  3.000
 CS1  HN12  N1  HN11  113.93  3.000
 CS1  HN12  N1  C1    117.04  3.000
 CS1  HN11  N1  C1    117.91  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
 CS1  CONST_01  C3   C4  C5  CE    0.00   0.0  0
 CS1  CONST_02  C3   C2  C1  CE    0.00   0.0  0
 CS1  CONST_03  C2   C1  CE  C5    0.00   0.0  0
 CS1  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 CS1  CONST_05  C1   CE  C5  C4    0.00   0.0  0
 CS1  CONST_06  C1   C2  C3  C4    0.00   0.0  0
 CS1  CONST_07  C4   C5  CE  SD  180.00   0.0  0
 CS1  CONST_08  C2   C1  CE  SD  180.00   0.0  0
 CS1  CONST_09  N1   C1  CE  C5  180.00   0.0  0
 CS1  CONST_10  N1   C1  C2  C3  180.00   0.0  0
 CS1  CONST_11  H4   C4  C5  CE  180.00   0.0  0
 CS1  CONST_12  HC2  C2  C1  CE  180.00   0.0  0
 CS1  CONST_13  H3   C3  C4  C5  180.00   0.0  0
 CS1  CONST_14  H5   C5  C4  C3  180.00   0.0  0
 CS1  Var_01    C5   CE  SD  SG   97.12  30.0  2
 CS1  Var_02    HB2  CB  SG  SD  162.07  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
 CS1  chir_01  CA  C  N  CB  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
 CS1  plan-1  SD    0.020
 CS1  plan-1  CE    0.020
 CS1  plan-1  C5    0.020
 CS1  plan-1  C4    0.020
 CS1  plan-1  C3    0.020
 CS1  plan-1  C2    0.020
 CS1  plan-1  C1    0.020
 CS1  plan-1  N1    0.020
 CS1  plan-1  H5    0.020
 CS1  plan-1  H4    0.020
 CS1  plan-1  H3    0.020
 CS1  plan-1  HC2   0.020
 CS1  plan-2  C1    0.020
 CS1  plan-2  N1    0.020
 CS1  plan-2  HN11  0.020
 CS1  plan-2  HN12  0.020
 CS1  plan-3  O     0.020
 CS1  plan-3  C     0.020
 CS1  plan-3  CA    0.020
 CS1  plan-3  OXT   0.020

