# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:08:37 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: S-benzyl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCc1ccccc1)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
 BCS  BCS  'S-benzyl-L-cysteine      '  L-peptide  26  14  .  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_BCS
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
 BCS  N    N  NH2    0  -0.798  11.6205  7.5380  27.3083
 BCS  CA   C  CH1    0  -0.198  10.4526  6.9205  27.9082
 BCS  CB   C  CH2    0  -0.563  10.8525  5.6137  28.5799
 BCS  SG   S  S2     0  -0.035  11.5096  4.3615  27.4379
 BCS  CD   C  CH2    0  -0.665   9.9829  3.8420  26.5851
 BCS  CE   C  CR6    0   0.149   9.0252  3.1342  27.4929
 BCS  CZ1  C  CR16   0  -0.296   7.9359  3.8054  28.0420
 BCS  CZ2  C  CR16   0  -0.289   9.2250  1.7955  27.8289
 BCS  CT1  C  CR16   0  -0.243   7.0634  3.1555  28.9071
 BCS  CT2  C  CR16   0  -0.243   8.3534  1.1429  28.6869
 BCS  CH   C  CR16   0  -0.267   7.2688  1.8223  29.2312
 BCS  C    C  C      0   0.412   9.7572  7.8564  28.9344
 BCS  O    O  O      0  -0.592  10.1724  9.0261  29.0176
 BCS  OXT  O  OC    -1  -0.608   8.8097  7.3472  29.5672
 BCS  H    H  HNH2   0   0.333  11.3838  8.4750  27.0133
 BCS  H2   H  HNH2   0   0.329  11.8824  7.0241  26.4766
 BCS  HA   H  HCH1   0   0.203   9.6707  6.6884  27.1641
 BCS  HB2  H  HCH2   0   0.265  11.6565  5.7952  29.2971
 BCS  HB3  H  HCH2   0   0.267  10.0147  5.1817  29.1246
 BCS  HD2  H  HCH2   0   0.285   9.5174  4.7104  26.1169
 BCS  HD3  H  HCH2   0   0.294  10.3217  3.1851  25.7824
 BCS  HZ1  H  HCR6   0   0.252   7.7695  4.8477  27.7953
 BCS  HZ2  H  HCR6   0   0.249  10.0707  1.2610  27.4115
 BCS  HT1  H  HCR6   0   0.252   6.2228  3.6936  29.3263
 BCS  HT2  H  HCR6   0   0.252   8.5191  0.1017  28.9326
 BCS  HH   H  HCR6   0   0.252   6.5891  1.3132  29.9023

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
 BCS  N    CA   single    1.458  0.019  1.458
 BCS  N    H    single    0.860  0.020  0.860
 BCS  N    H2   single    0.890  0.020  1.040
 BCS  CA   CB   single    1.530  0.020  1.530
 BCS  CA   C    single    1.525  0.021  1.525
 BCS  CA   HA   single    0.970  0.020  0.970
 BCS  CB   SG   single    1.818  0.020  1.818
 BCS  CB   HB2  single    0.970  0.020  1.090
 BCS  CB   HB3  single    0.970  0.020  1.090
 BCS  SG   CD   single    1.824  0.020  1.824
 BCS  CD   CE   single    1.497  0.020  1.497
 BCS  CD   HD2  single    0.970  0.020  1.090
 BCS  CD   HD3  single    0.970  0.020  1.090
 BCS  CE   CZ1  aromatic  1.392  0.020  1.392
 BCS  CE   CZ2  aromatic  1.395  0.020  1.395
 BCS  CZ1  CT1  aromatic  1.390  0.020  1.390
 BCS  CZ1  HZ1  single    0.930  0.020  1.080
 BCS  CZ2  CT2  aromatic  1.386  0.020  1.386
 BCS  CZ2  HZ2  single    0.930  0.020  1.080
 BCS  CT1  CH   aromatic  1.387  0.020  1.387
 BCS  CT1  HT1  single    0.930  0.020  1.080
 BCS  CT2  CH   aromatic  1.391  0.020  1.391
 BCS  CT2  HT2  single    0.930  0.020  1.080
 BCS  CH   HH   single    0.930  0.020  1.080
 BCS  C    O    deloc     1.231  0.020  1.231
 BCS  C    OXT  deloc     1.248  0.020  1.248

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
 BCS  H2   N    H    106.95  3.000
 BCS  H2   N    CA   109.39  3.000
 BCS  H    N    CA   114.00  3.000
 BCS  HA   CA   C    109.00  3.000
 BCS  HA   CA   CB   109.00  3.000
 BCS  C    CA   CB   110.10  1.900
 BCS  HA   CA   N    110.00  3.000
 BCS  C    CA   N    111.00  2.800
 BCS  CB   CA   N    110.50  1.700
 BCS  HB3  CB   HB2  107.69  3.000
 BCS  HB3  CB   SG   108.61  3.000
 BCS  HB2  CB   SG   105.12  3.000
 BCS  HB3  CB   CA   111.05  3.000
 BCS  HB2  CB   CA   109.89  3.000
 BCS  SG   CB   CA   114.14  3.000
 BCS  CD   SG   CB   100.80  3.000
 BCS  HD3  CD   HD2  107.22  3.000
 BCS  HD3  CD   CE   111.10  3.000
 BCS  HD2  CD   CE   111.32  3.000
 BCS  HD3  CD   SG   104.80  3.000
 BCS  HD2  CD   SG   109.33  3.000
 BCS  CE   CD   SG   112.73  3.000
 BCS  CZ2  CE   CZ1  118.68  3.000
 BCS  CZ2  CE   CD   120.54  3.000
 BCS  CZ1  CE   CD   120.77  3.000
 BCS  HZ1  CZ1  CT1  119.66  3.000
 BCS  HZ1  CZ1  CE   119.60  3.000
 BCS  CT1  CZ1  CE   120.74  3.000
 BCS  HZ2  CZ2  CT2  119.78  3.000
 BCS  HZ2  CZ2  CE   119.50  3.000
 BCS  CT2  CZ2  CE   120.72  3.000
 BCS  HT1  CT1  CH   120.15  3.000
 BCS  HT1  CT1  CZ1  119.73  3.000
 BCS  CH   CT1  CZ1  120.12  3.000
 BCS  HT2  CT2  CH   120.02  3.000
 BCS  HT2  CT2  CZ2  119.80  3.000
 BCS  CH   CT2  CZ2  120.17  3.000
 BCS  HH   CH   CT2  120.18  3.000
 BCS  HH   CH   CT1  120.25  3.000
 BCS  CT2  CH   CT1  119.57  3.000
 BCS  OXT  C    O    127.10  3.000
 BCS  OXT  C    CA   115.40  3.000
 BCS  O    C    CA   120.80  1.700

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
 BCS  CONST_01  CH   CT1  CZ1  CE     0.00   0.0  0
 BCS  CONST_02  CH   CT2  CZ2  CE     0.00   0.0  0
 BCS  CONST_03  CT2  CZ2  CE   CZ1    0.00   0.0  0
 BCS  CONST_04  CT2  CH   CT1  CZ1    0.00   0.0  0
 BCS  CONST_05  CT1  CZ1  CE   CZ2    0.00   0.0  0
 BCS  CONST_06  CT1  CH   CT2  CZ2    0.00   0.0  0
 BCS  CONST_07  CT1  CZ1  CE   CD   180.00   0.0  0
 BCS  CONST_08  CT2  CZ2  CE   CD   180.00   0.0  0
 BCS  CONST_09  HT1  CT1  CZ1  CE   180.00   0.0  0
 BCS  CONST_10  HT2  CT2  CZ2  CE   180.00   0.0  0
 BCS  CONST_11  HZ2  CZ2  CE   CZ1  180.00   0.0  0
 BCS  CONST_12  HH   CH   CT1  CZ1  180.00   0.0  0
 BCS  CONST_13  HZ1  CZ1  CE   CZ2  180.00   0.0  0
 BCS  Var_01    CZ1  CE   CD   SG    99.84  30.0  2
 BCS  Var_02    CE   CD   SG   CB   -66.67  30.0  3
 BCS  Var_03    HB2  CB   SG   CD   166.26  30.0  2

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
 BCS  chir_01  CA  N  CB  C  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
 BCS  plan-1  CD   0.020
 BCS  plan-1  CE   0.020
 BCS  plan-1  CZ1  0.020
 BCS  plan-1  CZ2  0.020
 BCS  plan-1  CT1  0.020
 BCS  plan-1  CT2  0.020
 BCS  plan-1  CH   0.020
 BCS  plan-1  HZ1  0.020
 BCS  plan-1  HZ2  0.020
 BCS  plan-1  HT1  0.020
 BCS  plan-1  HT2  0.020
 BCS  plan-1  HH   0.020
 BCS  plan-2  CA   0.020
 BCS  plan-2  C    0.020
 BCS  plan-2  O    0.020
 BCS  plan-2  OXT  0.020

