# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:33:34 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-thiophen-2-yl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1sccc1)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
 TIH  TIH  3-thiophen-2-yl-L-alanine  L-peptide  19  11  .  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_TIH
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
 TIH  N    N  NH2    0  -0.795  16.8774  17.3327  16.9833
 TIH  CA   C  CH1    0  -0.200  16.2854  18.2466  16.0275
 TIH  C    C  C      0   0.412  15.8292  17.5126  14.7434
 TIH  O    O  O      0  -0.596  16.2800  16.3683  14.5476
 TIH  OXT  O  OC    -1  -0.611  15.0685  18.1604  13.9963
 TIH  CB   C  CH2    0  -0.521  17.1872  19.4392  15.6273
 TIH  CG   C  CR5    0  -0.133  18.3928  19.0600  14.8347
 TIH  CD   C  CR15   0  -0.234  18.5782  19.1511  13.4860
 TIH  CE1  C  CR15   0  -0.184  19.8402  18.6580  13.0531
 TIH  CE2  C  CR15   0  -0.477  20.6027  18.1965  14.0815
 TIH  SD   S  S2     0   0.178  19.7824  18.3581  15.5795
 TIH  H    H  HNH2   0   0.331  17.4114  17.8356  17.6815
 TIH  H2   H  HNH2   0   0.330  17.5119  16.7078  16.5036
 TIH  HA   H  HCH1   0   0.215  15.3977  18.6949  16.4889
 TIH  HB2  H  HCH2   0   0.245  16.5991  20.1416  15.0349
 TIH  HB3  H  HCH2   0   0.245  17.4833  19.9742  16.5348
 TIH  HD   H  HCR5   0   0.251  17.8284  19.5585  12.8216
 TIH  HE1  H  HCR5   0   0.258  20.1647  18.6516  12.0220
 TIH  HE2  H  HCR5   0   0.286  21.5943  17.7730  14.0402

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
 TIH  N    CA   single    1.458  0.019  1.458
 TIH  N    H    single    0.860  0.020  0.860
 TIH  N    H2   single    0.890  0.020  1.040
 TIH  CA   C    single    1.525  0.021  1.525
 TIH  CA   CB   single    1.521  0.033  1.521
 TIH  CA   HA   single    0.970  0.020  0.970
 TIH  C    O    deloc     1.231  0.020  1.231
 TIH  C    OXT  deloc     1.248  0.020  1.248
 TIH  CB   CG   single    1.492  0.020  1.492
 TIH  CB   HB2  single    0.970  0.020  1.090
 TIH  CB   HB3  single    0.970  0.020  1.090
 TIH  CG   CD   aromatic  1.364  0.020  1.364
 TIH  CG   SD   aromatic  1.726  0.020  1.726
 TIH  CD   CE1  aromatic  1.422  0.020  1.422
 TIH  CD   HD   single    0.930  0.020  1.080
 TIH  CE1  CE2  aromatic  1.361  0.020  1.361
 TIH  CE1  HE1  single    0.930  0.020  1.080
 TIH  CE2  SD   aromatic  1.716  0.020  1.716
 TIH  CE2  HE2  single    0.930  0.020  1.080

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
 TIH  H2   N    H    107.63  3.000
 TIH  H2   N    CA   109.46  3.000
 TIH  H    N    CA   114.00  3.000
 TIH  HA   CA   CB   109.00  3.000
 TIH  HA   CA   C    109.00  3.000
 TIH  CB   CA   C    110.50  1.500
 TIH  HA   CA   N    110.00  3.000
 TIH  CB   CA   N    110.40  1.500
 TIH  C    CA   N    111.00  2.800
 TIH  OXT  C    O    127.13  3.000
 TIH  OXT  C    CA   115.49  3.000
 TIH  O    C    CA   120.80  1.700
 TIH  HB3  CB   HB2  106.34  3.000
 TIH  HB3  CB   CG   110.26  3.000
 TIH  HB2  CB   CG   108.11  3.000
 TIH  HB3  CB   CA   108.66  3.000
 TIH  HB2  CB   CA   108.80  3.000
 TIH  CG   CB   CA   114.35  3.000
 TIH  SD   CG   CD   110.14  3.000
 TIH  SD   CG   CB   121.65  3.000
 TIH  CD   CG   CB   128.17  3.000
 TIH  HD   CD   CE1  123.97  3.000
 TIH  HD   CD   CG   122.56  3.000
 TIH  CE1  CD   CG   113.47  3.000
 TIH  HE1  CE1  CE2  123.41  3.000
 TIH  HE1  CE1  CD   123.96  3.000
 TIH  CE2  CE1  CD   112.62  3.000
 TIH  HE2  CE2  SD   120.65  3.000
 TIH  HE2  CE2  CE1  128.25  3.000
 TIH  SD   CE2  CE1  111.10  3.000
 TIH  CE2  SD   CG    92.66  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
 TIH  CONST_01  CE2  CE1  CD   CG     0.00   0.0  0
 TIH  CONST_02  CE1  CE2  SD   CG     0.00   0.0  0
 TIH  CONST_03  CE2  SD   CG   CD     0.00   0.0  0
 TIH  CONST_04  SD   CE2  CE1  CD     0.00   0.0  0
 TIH  CONST_05  SD   CG   CD   CE1    0.00   0.0  0
 TIH  CONST_06  CE1  CD   CG   CB   180.00   0.0  0
 TIH  CONST_07  CE2  SD   CG   CB   180.00   0.0  0
 TIH  CONST_08  HE1  CE1  CD   CG   180.00   0.0  0
 TIH  CONST_09  HE2  CE2  SD   CG   180.00   0.0  0
 TIH  CONST_10  HD   CD   CE1  CE2  180.00   0.0  0
 TIH  Var_01    CD   CG   CB   CA   100.57  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
 TIH  chir_01  CA  N  C  CB  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
 TIH  plan-1  CB   0.020
 TIH  plan-1  CG   0.020
 TIH  plan-1  CD   0.020
 TIH  plan-1  CE1  0.020
 TIH  plan-1  CE2  0.020
 TIH  plan-1  SD   0.020
 TIH  plan-1  HD   0.020
 TIH  plan-1  HE1  0.020
 TIH  plan-1  HE2  0.020
 TIH  plan-2  CA   0.020
 TIH  plan-2  C    0.020
 TIH  plan-2  O    0.020
 TIH  plan-2  OXT  0.020

