# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:02:39 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-(5-bromothiophen-2-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1sc(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
 33W  33W  3-(5-bromothiophen-2-yl)-L-alanine  L-peptide  19  12  .  2016-04-22  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_33W
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
 33W  C4   C   CR15   0  -0.149   6.6404  48.4652  30.4421
 33W  C5   C   CR15   0  -0.233   7.0477  47.1564  30.0627
 33W  N    N   NH2    0  -0.789   8.5538  44.5054  32.0345
 33W  CA   C   CH1    0  -0.237   9.6530  44.9246  31.1751
 33W  CB   C   CH2    0  -0.477   9.1111  45.6454  29.9402
 33W  C1   C   CR5    0  -0.155   8.3769  46.9106  30.2421
 33W  C3   C   CR5    0  -0.350   7.6916  49.1872  30.9076
 33W  S2   S   S2     0   0.258   9.1676  48.3026  30.9034
 33W  BR   BR  BR     0  -0.009   7.6590  50.9454  31.5252
 33W  C    C   C      0   0.408  10.7775  45.7223  31.8870
 33W  O    O   O      0  -0.602  11.4520  46.4947  31.1716
 33W  OXT  O   OC    -1  -0.593  10.9405  45.4943  33.1000
 33W  H4   H   HCR5   0   0.277   5.6277  48.8348  30.3695
 33W  H5   H   HCR5   0   0.262   6.3707  46.4152  29.6600
 33W  HA   H   HCH1   0   0.232  10.1333  44.0093  30.8015
 33W  HB3  H   HCH2   0   0.245   8.4126  44.9854  29.4208
 33W  HB2  H   HCH2   0   0.249   9.9314  45.8403  29.2496
 33W  H    H   HNH2   0   0.333   8.9600  44.1512  32.8923
 33W  H2   H   HNH2   0   0.330   8.0345  45.3284  32.3233

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
 33W  CB  C1   single    1.494  0.020  1.494
 33W  CB  CA   single    1.521  0.033  1.521
 33W  C1  S2   aromatic  1.732  0.020  1.732
 33W  C1  C5   aromatic  1.364  0.020  1.364
 33W  S2  C3   aromatic  1.721  0.020  1.721
 33W  C5  C4   aromatic  1.422  0.020  1.422
 33W  C3  C4   aromatic  1.358  0.020  1.358
 33W  C3  BR   single    1.864  0.020  1.864
 33W  CA  N    single    1.458  0.019  1.458
 33W  CA  C    single    1.525  0.021  1.525
 33W  O   C    deloc     1.231  0.020  1.231
 33W  C   OXT  deloc     1.245  0.020  1.245
 33W  C4  H4   single    0.930  0.020  1.080
 33W  C5  H5   single    0.930  0.020  1.080
 33W  N   H    single    0.860  0.020  0.860
 33W  N   H2   single    0.890  0.020  1.040
 33W  CA  HA   single    0.970  0.020  0.970
 33W  CB  HB3  single    0.970  0.020  1.090
 33W  CB  HB2  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
 33W  H4   C4  C3   124.54  3.000
 33W  H4   C4  C5   124.42  3.000
 33W  C3   C4  C5   111.05  3.000
 33W  H5   C5  C1   122.39  3.000
 33W  H5   C5  C4   123.41  3.000
 33W  C1   C5  C4   114.20  3.000
 33W  H2   N   H    104.34  3.000
 33W  H2   N   CA   108.70  3.000
 33W  H    N   CA   114.00  3.000
 33W  HA   CA  C    109.00  3.000
 33W  HA   CA  CB   109.00  3.000
 33W  C    CA  CB   110.50  1.500
 33W  HA   CA  N    110.00  3.000
 33W  C    CA  N    111.00  2.800
 33W  CB   CA  N    110.40  1.500
 33W  HB2  CB  HB3  106.74  3.000
 33W  HB2  CB  C1   110.28  3.000
 33W  HB3  CB  C1   107.07  3.000
 33W  HB2  CB  CA   109.23  3.000
 33W  HB3  CB  CA   109.01  3.000
 33W  C1   CB  CA   114.22  3.000
 33W  S2   C1  CB   122.25  3.000
 33W  S2   C1  C5   110.51  3.000
 33W  CB   C1  C5   127.25  3.000
 33W  BR   C3  S2   120.05  3.000
 33W  BR   C3  C4   127.00  3.000
 33W  S2   C3  C4   112.95  3.000
 33W  C3   S2  C1    91.29  3.000
 33W  OXT  C   O    126.88  3.000
 33W  OXT  C   CA   116.60  3.000
 33W  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
 33W  CONST_01  S2  C1  C5  C4     0.00   0.0  0
 33W  CONST_02  C1  S2  C3  C4     0.00   0.0  0
 33W  CONST_03  C3  S2  C1  C5     0.00   0.0  0
 33W  CONST_04  S2  C3  C4  C5     0.00   0.0  0
 33W  CONST_05  C3  C4  C5  C1     0.00   0.0  0
 33W  CONST_06  CB  C1  C5  C4   180.00   0.0  0
 33W  CONST_07  BR  C3  C4  C5   180.00   0.0  0
 33W  CONST_08  C3  S2  C1  CB   180.00   0.0  0
 33W  CONST_09  BR  C3  S2  C1   180.00   0.0  0
 33W  CONST_10  H4  C4  C5  C1   180.00   0.0  0
 33W  CONST_11  H5  C5  C4  C3   180.00   0.0  0
 33W  Var_01    CA  CB  C1  C5  -113.40  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
 33W  chir_01  CA  CB  N  C  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
 33W  plan-1  C4   0.020
 33W  plan-1  C5   0.020
 33W  plan-1  CB   0.020
 33W  plan-1  C1   0.020
 33W  plan-1  C3   0.020
 33W  plan-1  S2   0.020
 33W  plan-1  BR   0.020
 33W  plan-1  H4   0.020
 33W  plan-1  H5   0.020
 33W  plan-2  CA   0.020
 33W  plan-2  C    0.020
 33W  plan-2  O    0.020
 33W  plan-2  OXT  0.020

