# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:33:07 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: O-(benzylsulfonyl)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[S](=O)(=O)Cc1ccccc1)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
 SEB  SEB  O-(benzylsulfonyl)-L-serine  L-peptide  29  17  .  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_SEB
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
 SEB  C    C  C      0   0.407  16.3772  22.1439  -3.4901
 SEB  N    N  NH2    0  -0.791  14.6060  22.3615  -1.7482
 SEB  CI2  C  CR16   0  -0.238  21.7986  22.6038  -0.9547
 SEB  CH2  C  CR16   0  -0.284  20.6164  23.0114  -0.3533
 SEB  CJ   C  CR16   0  -0.258  22.4728  21.4879  -0.4769
 SEB  CI1  C  CR16   0  -0.240  21.9630  20.7845   0.6072
 SEB  CH1  C  CR16   0  -0.275  20.7812  21.1925   1.2074
 SEB  CZ   C  CR6    0   0.119  20.1008  22.3102   0.7325
 SEB  CE   C  CH2    0  -0.732  18.8253  22.7470   1.3770
 SEB  OD2  O  OS     0  -0.638  17.6599  20.4204   0.8296
 SEB  OD1  O  OS     0  -0.647  16.2162  22.3933   1.3654
 SEB  SD   S  S      0   1.444  17.4084  21.8429   0.7470
 SEB  OG   O  OC2    0  -0.578  17.4343  22.1608  -0.8108
 SEB  CB   C  CH2    0  -0.209  16.8553  23.3753  -1.3544
 SEB  CA   C  CH1    0  -0.231  15.7626  22.9977  -2.3436
 SEB  O    O  O      0  -0.608  17.3044  22.6928  -4.1162
 SEB  OXT  O  OC    -1  -0.587  15.9095  21.0064  -3.6695
 SEB  H    H  HNH2   0   0.333  14.3735  22.7924  -0.8623
 SEB  H2   H  HNH2   0   0.332  14.8126  21.3887  -1.5655
 SEB  HJ   H  HCR6   0   0.259  23.3959  21.1705  -0.9443
 SEB  HI1  H  HCR6   0   0.258  22.4877  19.9171   0.9862
 SEB  HH1  H  HCR6   0   0.258  20.3917  20.6455   2.0571
 SEB  HE3  H  HCH2   0   0.334  18.8177  22.5582   2.4530
 SEB  HE2  H  HCH2   0   0.329  18.6168  23.8068   1.2188
 SEB  HB3  H  HCH2   0   0.248  16.4586  23.9998  -0.5509
 SEB  HB2  H  HCH2   0   0.248  17.6640  23.9173  -1.8421
 SEB  HA   H  HCH1   0   0.229  15.4508  23.9520  -2.7879
 SEB  HI2  H  HCR6   0   0.259  22.1930  23.1593  -1.7952
 SEB  HH2  H  HCR6   0   0.260  20.0965  23.8872  -0.7230

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
 SEB  C    CA   single    1.525  0.021  1.525
 SEB  C    O    deloc     1.231  0.020  1.231
 SEB  C    OXT  deloc     1.243  0.020  1.243
 SEB  N    CA   single    1.458  0.019  1.458
 SEB  N    H    single    0.860  0.020  0.860
 SEB  N    H2   single    0.890  0.020  1.040
 SEB  CI2  CH2  aromatic  1.388  0.020  1.388
 SEB  CI2  CJ   aromatic  1.389  0.020  1.389
 SEB  CI2  HI2  single    0.930  0.020  1.080
 SEB  CH2  CZ   aromatic  1.392  0.020  1.392
 SEB  CH2  HH2  single    0.930  0.020  1.080
 SEB  CJ   CI1  aromatic  1.389  0.020  1.389
 SEB  CJ   HJ   single    0.930  0.020  1.080
 SEB  CI1  CH1  aromatic  1.387  0.020  1.387
 SEB  CI1  HI1  single    0.930  0.020  1.080
 SEB  CH1  CZ   aromatic  1.392  0.020  1.392
 SEB  CH1  HH1  single    0.930  0.020  1.080
 SEB  CZ   CE   single    1.494  0.020  1.494
 SEB  CE   SD   single    1.795  0.020  1.795
 SEB  CE   HE3  single    0.970  0.020  1.090
 SEB  CE   HE2  single    0.970  0.020  1.090
 SEB  OD2  SD   deloc     1.447  0.020  1.447
 SEB  OD1  SD   deloc     1.451  0.020  1.451
 SEB  SD   OG   single    1.590  0.020  1.590
 SEB  OG   CB   single    1.451  0.020  1.451
 SEB  CB   CA   single    1.530  0.020  1.530
 SEB  CB   HB3  single    0.970  0.020  1.090
 SEB  CB   HB2  single    0.970  0.020  1.090
 SEB  CA   HA   single    0.970  0.020  0.970

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
 SEB  OXT  C    O    127.62  3.000
 SEB  OXT  C    CA   117.39  3.000
 SEB  O    C    CA   120.80  1.700
 SEB  H2   N    H    107.35  3.000
 SEB  H2   N    CA   109.50  3.000
 SEB  H    N    CA   114.00  3.000
 SEB  HI2  CI2  CJ   120.20  3.000
 SEB  HI2  CI2  CH2  119.76  3.000
 SEB  CJ   CI2  CH2  120.03  3.000
 SEB  HH2  CH2  CZ   119.71  3.000
 SEB  HH2  CH2  CI2  119.89  3.000
 SEB  CZ   CH2  CI2  120.39  3.000
 SEB  HJ   CJ   CI1  120.11  3.000
 SEB  HJ   CJ   CI2  120.07  3.000
 SEB  CI1  CJ   CI2  119.82  3.000
 SEB  HI1  CI1  CH1  119.83  3.000
 SEB  HI1  CI1  CJ   120.07  3.000
 SEB  CH1  CI1  CJ   120.10  3.000
 SEB  HH1  CH1  CZ   119.83  3.000
 SEB  HH1  CH1  CI1  119.83  3.000
 SEB  CZ   CH1  CI1  120.34  3.000
 SEB  CE   CZ   CH1  120.32  3.000
 SEB  CE   CZ   CH2  120.37  3.000
 SEB  CH1  CZ   CH2  119.32  3.000
 SEB  HE2  CE   HE3  108.01  3.000
 SEB  HE2  CE   SD   106.70  3.000
 SEB  HE3  CE   SD   104.66  3.000
 SEB  HE2  CE   CZ   112.61  3.000
 SEB  HE3  CE   CZ   112.35  3.000
 SEB  SD   CE   CZ   112.04  3.000
 SEB  OG   SD   OD1  110.79  3.000
 SEB  OG   SD   OD2  104.46  3.000
 SEB  OD1  SD   OD2  119.42  3.000
 SEB  OG   SD   CE   103.31  3.000
 SEB  OD1  SD   CE   107.93  3.000
 SEB  OD2  SD   CE   109.75  3.000
 SEB  CB   OG   SD   121.86  3.000
 SEB  HB2  CB   HB3  108.34  3.000
 SEB  HB2  CB   CA   111.45  3.000
 SEB  HB3  CB   CA   111.05  3.000
 SEB  HB2  CB   OG   106.74  3.000
 SEB  HB3  CB   OG   110.36  3.000
 SEB  CA   CB   OG   108.81  3.000
 SEB  HA   CA   CB   109.00  3.000
 SEB  HA   CA   N    110.00  3.000
 SEB  CB   CA   N    110.50  1.700
 SEB  HA   CA   C    109.00  3.000
 SEB  CB   CA   C    110.10  1.900
 SEB  N    CA   C    111.00  2.800

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
 SEB  CONST_01  CH1  CZ   CH2  CI2     0.00   0.0  0
 SEB  CONST_02  CH1  CI1  CJ   CI2     0.00   0.0  0
 SEB  CONST_03  CI1  CJ   CI2  CH2     0.00   0.0  0
 SEB  CONST_04  CI1  CH1  CZ   CH2     0.00   0.0  0
 SEB  CONST_05  CZ   CH2  CI2  CJ      0.00   0.0  0
 SEB  CONST_06  CZ   CH1  CI1  CJ      0.00   0.0  0
 SEB  CONST_07  CE   CZ   CH2  CI2   180.00   0.0  0
 SEB  CONST_08  CE   CZ   CH1  CI1   180.00   0.0  0
 SEB  CONST_09  HI1  CI1  CJ   CI2   180.00   0.0  0
 SEB  CONST_10  HJ   CJ   CI2  CH2   180.00   0.0  0
 SEB  CONST_11  HH1  CH1  CZ   CH2   180.00   0.0  0
 SEB  CONST_12  HH2  CH2  CI2  CJ    180.00   0.0  0
 SEB  CONST_13  HI2  CI2  CJ   CI1   180.00   0.0  0
 SEB  Var_01    SD   CE   CZ   CH2    95.94  30.0  2
 SEB  Var_02    OD2  SD   CE   CZ     51.94  30.0  3
 SEB  Var_03    CA   CB   OG   SD   -120.29  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
 SEB  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
 SEB  plan-1  CI2  0.020
 SEB  plan-1  CH2  0.020
 SEB  plan-1  CJ   0.020
 SEB  plan-1  CI1  0.020
 SEB  plan-1  CH1  0.020
 SEB  plan-1  CZ   0.020
 SEB  plan-1  CE   0.020
 SEB  plan-1  HJ   0.020
 SEB  plan-1  HI1  0.020
 SEB  plan-1  HH1  0.020
 SEB  plan-1  HI2  0.020
 SEB  plan-1  HH2  0.020
 SEB  plan-2  C    0.020
 SEB  plan-2  CA   0.020
 SEB  plan-2  O    0.020
 SEB  plan-2  OXT  0.020

