# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:45:40 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: S-(4-bromobenzyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCc1ccc(Br)cc1)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
 PBB  PBB  S-(4-bromobenzyl)-L-cysteine  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_PBB
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
 PBB  CA   C   CH1    0  -0.195  24.6806   -5.1395  6.6676
 PBB  C    C   C      0   0.388  25.5282   -4.3655  5.6182
 PBB  O    O   O      0  -0.594  24.9719   -3.4245  5.0217
 PBB  OXT  O   OC    -1  -0.606  26.6947   -4.7803  5.4506
 PBB  N    N   NH2    0  -0.783  23.5228   -4.4376  7.1907
 PBB  CB   C   CH2    0  -0.574  24.2443   -6.4619  6.0365
 PBB  SG   S   S2     0  -0.020  23.6014   -7.6910  7.2061
 PBB  BR   BR  BR     0  -0.054  28.9220  -11.2830  4.2524
 PBB  C1   C   C      0   0.155  26.0712   -8.9533  7.1310
 PBB  C2   C   C1     0  -0.293  27.1110   -8.2992  6.4763
 PBB  C3   C   C1     0  -0.219  27.9610   -8.9820  5.6157
 PBB  C4   C   C      0  -0.122  27.7679  -10.3391  5.4151
 PBB  C5   C   C1     0  -0.217  26.7395  -11.0176  6.0555
 PBB  C6   C   C1     0  -0.285  25.8981  -10.3171  6.9051
 PBB  C7   C   CH2    0  -0.671  25.1430   -8.2039  8.0347
 PBB  HA   H   HCH1   0   0.223  25.3459   -5.3627  7.5076
 PBB  H    H   HNH2   0   0.336  23.8414   -3.6654  7.7632
 PBB  H2   H   HNH2   0   0.324  23.0505   -3.9971  6.4085
 PBB  HB2  H   HCH2   0   0.270  23.4320   -6.2871  5.3257
 PBB  HB3  H   HCH2   0   0.272  25.0609   -6.9161  5.4748
 PBB  HC2  H   H      0   0.264  27.2543   -7.2343  6.6178
 PBB  H3   H   H      0   0.277  28.7599   -8.4505  5.1160
 PBB  H5   H   H      0   0.277  26.5899  -12.0778  5.9014
 PBB  H6   H   H      0   0.262  25.0944  -10.8469  7.4026
 PBB  H71  H   HCH2   0   0.288  25.6326   -7.3261  8.4586
 PBB  H72  H   HCH2   0   0.297  24.8201   -8.8287  8.8686

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
 PBB  CA  C    single    1.525  0.021  1.525
 PBB  CA  N    single    1.458  0.019  1.458
 PBB  CA  CB   single    1.530  0.020  1.530
 PBB  CA  HA   single    0.970  0.020  0.970
 PBB  C   O    deloc     1.231  0.020  1.231
 PBB  C   OXT  deloc     1.249  0.020  1.249
 PBB  N   H    single    0.860  0.020  0.860
 PBB  N   H2   single    0.890  0.020  1.040
 PBB  CB  SG   single    1.814  0.020  1.814
 PBB  CB  HB2  single    0.970  0.020  1.090
 PBB  CB  HB3  single    0.970  0.020  1.090
 PBB  SG  C7   single    1.824  0.020  1.824
 PBB  BR  C4   single    1.891  0.020  1.891
 PBB  C1  C2   aromatic  1.392  0.020  1.392
 PBB  C1  C6   aromatic  1.393  0.020  1.393
 PBB  C1  C7   single    1.497  0.020  1.497
 PBB  C2  C3   aromatic  1.389  0.020  1.389
 PBB  C2  HC2  single    0.930  0.020  1.080
 PBB  C3  C4   aromatic  1.385  0.020  1.385
 PBB  C3  H3   single    0.930  0.020  1.080
 PBB  C4  C5   aromatic  1.389  0.020  1.389
 PBB  C5  C6   aromatic  1.386  0.020  1.386
 PBB  C5  H5   single    0.930  0.020  1.080
 PBB  C6  H6   single    0.930  0.020  1.080
 PBB  C7  H71  single    0.970  0.020  1.090
 PBB  C7  H72  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
 PBB  HA   CA  CB   109.00  3.000
 PBB  HA   CA  N    110.00  3.000
 PBB  CB   CA  N    110.50  1.700
 PBB  HA   CA  C    109.00  3.000
 PBB  CB   CA  C    110.10  1.900
 PBB  N    CA  C    111.00  2.800
 PBB  OXT  C   O    127.13  3.000
 PBB  OXT  C   CA   115.74  3.000
 PBB  O    C   CA   120.80  1.700
 PBB  H2   N   H    104.56  3.000
 PBB  H2   N   CA   107.67  3.000
 PBB  H    N   CA   114.00  3.000
 PBB  HB3  CB  HB2  106.74  3.000
 PBB  HB3  CB  SG   108.38  3.000
 PBB  HB2  CB  SG   105.32  3.000
 PBB  HB3  CB  CA   111.06  3.000
 PBB  HB2  CB  CA   110.00  3.000
 PBB  SG   CB  CA   114.89  3.000
 PBB  C7   SG  CB   100.60  3.000
 PBB  C7   C1  C6   120.73  3.000
 PBB  C7   C1  C2   120.79  3.000
 PBB  C6   C1  C2   118.46  3.000
 PBB  HC2  C2  C3   118.88  3.000
 PBB  HC2  C2  C1   119.94  3.000
 PBB  C3   C2  C1   121.17  3.000
 PBB  H3   C3  C4   121.15  3.000
 PBB  H3   C3  C2   119.77  3.000
 PBB  C4   C3  C2   119.08  3.000
 PBB  C5   C4  C3   121.01  3.000
 PBB  C5   C4  BR   119.45  3.000
 PBB  C3   C4  BR   119.54  3.000
 PBB  H5   C5  C6   119.92  3.000
 PBB  H5   C5  C4   121.04  3.000
 PBB  C6   C5  C4   119.04  3.000
 PBB  H6   C6  C5   118.99  3.000
 PBB  H6   C6  C1   119.76  3.000
 PBB  C5   C6  C1   121.25  3.000
 PBB  H72  C7  H71  107.26  3.000
 PBB  H72  C7  C1   111.00  3.000
 PBB  H71  C7  C1   111.05  3.000
 PBB  H72  C7  SG   104.96  3.000
 PBB  H71  C7  SG   109.25  3.000
 PBB  C1   C7  SG   113.00  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
 PBB  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 PBB  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 PBB  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 PBB  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 PBB  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 PBB  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 PBB  CONST_07  C2   C3  C4  BR  180.00   0.0  0
 PBB  CONST_08  C6   C5  C4  BR  180.00   0.0  0
 PBB  CONST_09  C7   C1  C2  C3  180.00   0.0  0
 PBB  CONST_10  C7   C1  C6  C5  180.00   0.0  0
 PBB  CONST_11  H3   C3  C2  C1  180.00   0.0  0
 PBB  CONST_12  H5   C5  C6  C1  180.00   0.0  0
 PBB  CONST_13  H6   C6  C1  C2  180.00   0.0  0
 PBB  CONST_14  HC2  C2  C3  C4  180.00   0.0  0
 PBB  Var_01    C2   C1  C7  SG   96.21  30.0  2
 PBB  Var_02    C1   C7  SG  CB  -67.82  30.0  3
 PBB  Var_03    HB2  CB  SG  C7  165.95  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
 PBB  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
 PBB  plan-1  BR   0.020
 PBB  plan-1  C1   0.020
 PBB  plan-1  C2   0.020
 PBB  plan-1  C3   0.020
 PBB  plan-1  C4   0.020
 PBB  plan-1  C5   0.020
 PBB  plan-1  C6   0.020
 PBB  plan-1  C7   0.020
 PBB  plan-1  HC2  0.020
 PBB  plan-1  H3   0.020
 PBB  plan-1  H5   0.020
 PBB  plan-1  H6   0.020
 PBB  plan-2  CA   0.020
 PBB  plan-2  C    0.020
 PBB  plan-2  O    0.020
 PBB  plan-2  OXT  0.020

