# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:58:46 2021
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-(trimethylsilyl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Si](C)(C)c1ccc(C[C@H](N)C(O)=O)cc1
#
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
 TSQ  TSQ  4-(trimethylsilyl)-L-phenylalanine  L-peptide  35  16  .  2022-09-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TSQ
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
 TSQ  CE2  C   CR16  0  -0.301   4.2229  14.8928  35.4405
 TSQ  CB   C   CH2   0  -0.509   5.9503  11.8555  36.9152
 TSQ  CA   C   CH1   0  -0.193   5.6683  10.6974  35.9377
 TSQ  C    C   C     0   0.538   6.6733   9.5859  36.1643
 TSQ  C1   C   CH3   0  -0.976   1.2012  16.3333  34.2878
 TSQ  C2   C   CH3   0  -0.985   0.5893  16.4923  37.3133
 TSQ  C3   C   CH3   0  -0.975   2.8975  18.1478  36.1064
 TSQ  CZ   C   CR6   0  -0.174   3.1446  15.1008  36.3080
 TSQ  CE1  C   CR16  0  -0.293   3.0138  14.2249  37.3851
 TSQ  CD1  C   CR16  0  -0.284   3.9156  13.1866  37.5889
 TSQ  CG   C   CR6   0   0.086   4.9847  12.9908  36.7212
 TSQ  CD2  C   CR16  0  -0.281   5.1261  13.8613  35.6407
 TSQ  N    N   NH2   0  -0.794   4.3318  10.1885  36.1465
 TSQ  O    O   O     0  -0.433   6.4060   8.4823  36.5651
 TSQ  OXT  O   OH1   0  -0.595   7.9055   9.9737  35.8563
 TSQ  SI1  SI  SI    0   1.015   1.9447  16.5252  36.0084
 TSQ  H1   H   HCR6  0   0.245   4.3675  15.5508  34.5897
 TSQ  H2   H   HCH2  0   0.258   5.8844  11.4774  37.9381
 TSQ  H3   H   HCH2  0   0.265   6.9693  12.2143  36.7626
 TSQ  H4   H   HCH1  0   0.256   5.8459  11.0757  34.9187
 TSQ  H5   H   HCH3  0   0.244   0.6508  15.3950  34.2000
 TSQ  H6   H   HCH3  0   0.241   0.5085  17.1472  34.0647
 TSQ  H7   H   HCH3  0   0.242   1.9742  16.3382  33.5169
 TSQ  H8   H   HCH3  0   0.246   0.9974  16.5769  38.3220
 TSQ  H9   H   HCH3  0   0.249  -0.0982  17.3276  37.1679
 TSQ  H10  H   HCH3  0   0.246   0.0029  15.5730  37.2661
 TSQ  H11  H   HCH3  0   0.244   3.3354  18.2891  37.0960
 TSQ  H12  H   HCH3  0   0.242   3.7097  18.1784  35.3776
 TSQ  H13  H   HCH3  0   0.241   2.2439  18.9996  35.9074
 TSQ  H14  H   HCR6  0   0.249   2.1964  14.3445  38.0868
 TSQ  H15  H   HCR6  0   0.246   3.7896  12.5223  38.4359
 TSQ  H16  H   HCR6  0   0.246   5.9541  13.7337  34.9519
 TSQ  H17  H   HNH2  0   0.358   3.6668  10.9202  35.9292
 TSQ  H18  H   HNH2  0   0.353   4.1374   9.4385  35.4953
 TSQ  HXT  H   HOH1  0   0.483   8.5343   9.2562  36.0259

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
 TSQ  C1   SI1  single    1.884  0.020  1.884
 TSQ  CE2  CD2  aromatic  1.386  0.020  1.386
 TSQ  CE2  CZ   aromatic  1.399  0.020  1.399
 TSQ  CD2  CG   aromatic  1.395  0.020  1.395
 TSQ  N    CA   single    1.458  0.019  1.458
 TSQ  CA   C    single    1.525  0.021  1.525
 TSQ  CA   CB   single    1.530  0.020  1.530
 TSQ  C3   SI1  single    1.884  0.020  1.884
 TSQ  SI1  CZ   single    1.886  0.020  1.886
 TSQ  SI1  C2   single    1.882  0.020  1.882
 TSQ  CZ   CE1  aromatic  1.395  0.020  1.395
 TSQ  O    C    double    1.231  0.020  1.231
 TSQ  C    OXT  single    1.328  0.020  1.328
 TSQ  CG   CB   single    1.503  0.020  1.503
 TSQ  CG   CD1  aromatic  1.391  0.020  1.391
 TSQ  CE1  CD1  aromatic  1.390  0.020  1.390
 TSQ  CE2  H1   single    0.930  0.020  1.080
 TSQ  CB   H2   single    0.970  0.020  1.090
 TSQ  CB   H3   single    0.970  0.020  1.090
 TSQ  CA   H4   single    0.970  0.020  1.090
 TSQ  C1   H5   single    0.970  0.020  1.090
 TSQ  C1   H6   single    0.970  0.020  1.090
 TSQ  C1   H7   single    0.970  0.020  1.090
 TSQ  C2   H8   single    0.970  0.020  1.090
 TSQ  C2   H9   single    0.970  0.020  1.090
 TSQ  C2   H10  single    0.970  0.020  1.090
 TSQ  C3   H11  single    0.970  0.020  1.090
 TSQ  C3   H12  single    0.970  0.020  1.090
 TSQ  C3   H13  single    0.970  0.020  1.090
 TSQ  CE1  H14  single    0.930  0.020  1.080
 TSQ  CD1  H15  single    0.930  0.020  1.080
 TSQ  CD2  H16  single    0.930  0.020  1.080
 TSQ  N    H17  single    0.890  0.020  1.040
 TSQ  N    H18  single    0.890  0.020  1.040
 TSQ  OXT  HXT  single    0.850  0.020  0.980

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
 TSQ  H1   CE2  CD2  118.54  3.000
 TSQ  H1   CE2  CZ   119.90  3.000
 TSQ  CD2  CE2  CZ   121.56  3.000
 TSQ  H3   CB   H2   107.53  3.000
 TSQ  H3   CB   CG   109.48  3.000
 TSQ  H2   CB   CG   110.09  3.000
 TSQ  H3   CB   CA   109.22  3.000
 TSQ  H2   CB   CA   108.83  3.000
 TSQ  CG   CB   CA   111.60  3.000
 TSQ  H4   CA   N    113.80  3.000
 TSQ  H4   CA   C    106.46  3.000
 TSQ  N    CA   C    111.00  2.800
 TSQ  H4   CA   CB   107.41  3.000
 TSQ  C    CA   CB   110.10  1.900
 TSQ  N    CA   CB   110.50  1.700
 TSQ  OXT  C    O    123.42  3.000
 TSQ  OXT  C    CA   111.50  3.000
 TSQ  O    C    CA   120.80  1.700
 TSQ  H7   C1   H6   107.56  3.000
 TSQ  H7   C1   H5   107.70  3.000
 TSQ  H6   C1   H5   107.73  3.000
 TSQ  H7   C1   SI1  111.41  3.000
 TSQ  H6   C1   SI1  111.16  3.000
 TSQ  H5   C1   SI1  111.10  3.000
 TSQ  H10  C2   H9   107.49  3.000
 TSQ  H10  C2   H8   107.82  3.000
 TSQ  H9   C2   H8   107.42  3.000
 TSQ  H10  C2   SI1  111.82  3.000
 TSQ  H9   C2   SI1  110.36  3.000
 TSQ  H8   C2   SI1  111.73  3.000
 TSQ  H13  C3   H12  107.57  3.000
 TSQ  H13  C3   H11  107.72  3.000
 TSQ  H12  C3   H11  107.65  3.000
 TSQ  H13  C3   SI1  111.07  3.000
 TSQ  H12  C3   SI1  111.45  3.000
 TSQ  H11  C3   SI1  111.19  3.000
 TSQ  SI1  CZ   CE1  122.50  3.000
 TSQ  CE1  CZ   CE2  117.24  3.000
 TSQ  SI1  CZ   CE2  120.26  3.000
 TSQ  H14  CE1  CD1  118.47  3.000
 TSQ  H14  CE1  CZ   120.10  3.000
 TSQ  CD1  CE1  CZ   121.43  3.000
 TSQ  H15  CD1  CG   119.38  3.000
 TSQ  H15  CD1  CE1  119.79  3.000
 TSQ  CG   CD1  CE1  120.82  3.000
 TSQ  CD2  CG   CD1  118.25  3.000
 TSQ  CD1  CG   CB   121.31  3.000
 TSQ  CD2  CG   CB   120.42  3.000
 TSQ  H16  CD2  CG   119.74  3.000
 TSQ  H16  CD2  CE2  119.57  3.000
 TSQ  CG   CD2  CE2  120.69  3.000
 TSQ  H18  N    H17  105.75  3.000
 TSQ  H18  N    CA   110.22  3.000
 TSQ  H17  N    CA   108.78  3.000
 TSQ  HXT  OXT  C    110.20  3.000
 TSQ  CZ   SI1  C3   108.68  3.000
 TSQ  CZ   SI1  C2   109.57  3.000
 TSQ  C3   SI1  C2   110.07  3.000
 TSQ  C2   SI1  C1   110.32  3.000
 TSQ  CZ   SI1  C1   108.61  3.000
 TSQ  C3   SI1  C1   109.55  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
 TSQ  CONST_01  CD1  CG   CD2  CE2    0.00   0.0  0
 TSQ  CONST_02  CD1  CE1  CZ   CE2    0.00   0.0  0
 TSQ  CONST_03  CG   CD2  CE2  CZ     0.00   0.0  0
 TSQ  CONST_04  CG   CD1  CE1  CZ     0.00   0.0  0
 TSQ  CONST_05  CD2  CE2  CZ   CE1    0.00   0.0  0
 TSQ  CONST_06  CD2  CG   CD1  CE1    0.00   0.0  0
 TSQ  CONST_07  CB   CG   CD2  CE2  180.00   0.0  0
 TSQ  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 TSQ  CONST_09  SI1  CZ   CE1  CD1  180.00   0.0  0
 TSQ  CONST_10  SI1  CZ   CE2  CD2  180.00   0.0  0
 TSQ  CONST_11  H14  CE1  CZ   CE2  180.00   0.0  0
 TSQ  CONST_12  H16  CD2  CE2  CZ   180.00   0.0  0
 TSQ  CONST_13  H15  CD1  CE1  CZ   180.00   0.0  0
 TSQ  CONST_14  H1   CE2  CZ   CE1  180.00   0.0  0
 TSQ  CONST_15  HXT  OXT  C    CA   180.00   0.0  0
 TSQ  Var_01    C1   SI1  CZ   CE2   57.65  30.0  2
 TSQ  Var_02    CD2  CG   CB   CA   -76.28  30.0  3
 TSQ  Var_03    H5   C1   SI1  CZ    60.86  30.0  3
 TSQ  Var_04    H11  C3   SI1  CZ   -61.81  30.0  3
 TSQ  Var_05    H8   C2   SI1  CZ    59.05  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
 TSQ  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
 TSQ  plan-1  CE2  0.020
 TSQ  plan-1  CB   0.020
 TSQ  plan-1  CZ   0.020
 TSQ  plan-1  CE1  0.020
 TSQ  plan-1  CD1  0.020
 TSQ  plan-1  CG   0.020
 TSQ  plan-1  CD2  0.020
 TSQ  plan-1  SI1  0.020
 TSQ  plan-1  H1   0.020
 TSQ  plan-1  H14  0.020
 TSQ  plan-1  H15  0.020
 TSQ  plan-1  H16  0.020
 TSQ  plan-2  CA   0.020
 TSQ  plan-2  C    0.020
 TSQ  plan-2  O    0.020
 TSQ  plan-2  OXT  0.020
 TSQ  plan-2  HXT  0.020

