# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:15:08 2022
#   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  34  16  .  2022-09-22  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_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  -0.295  4.3207  14.9972  35.6235
 TSQ  CB   C   CH2    0  -0.486  5.8665  11.8023  36.9707
 TSQ  CA   C   CH1    0  -0.212  5.7198  10.7531  35.8631
 TSQ  C    C   C      0   0.415  6.7507   9.6034  36.0174
 TSQ  C1   C   CH3    0  -0.970  0.9445  16.1952  34.4828
 TSQ  C2   C   CH3    0  -0.979  0.7764  16.7165  37.5142
 TSQ  C3   C   CH3    0  -0.976  2.9315  18.1295  35.8156
 TSQ  CZ   C   CR6    0  -0.183  3.1332  15.1153  36.3542
 TSQ  CE1  C   CR16   0  -0.289  2.8716  14.1270  37.3044
 TSQ  CD1  C   CR16   0  -0.296  3.7478  13.0689  37.5131
 TSQ  CG   C   CR6    0   0.114  4.9279  12.9591  36.7829
 TSQ  CD2  C   CR16   0  -0.288  5.1986  13.9448  35.8330
 TSQ  N    N   NH2    0  -0.807  4.3614  10.2368  35.8419
 TSQ  O    O   O      0  -0.599  6.3580   8.4541  35.7343
 TSQ  OXT  O   OC    -1  -0.603  7.8993   9.9335  36.3690
 TSQ  SI1  SI  SI     0   1.008  1.9418  16.5424  36.0454
 TSQ  H1   H   HCR6   0   0.239  4.5755  15.7431  34.8778
 TSQ  H2   H   HCH2   0   0.222  5.6787  11.3283  37.9380
 TSQ  H3   H   HCH2   0   0.231  6.8961  12.1615  36.9791
 TSQ  H4   H   HCH1   0   0.199  5.9875  11.2523  34.9142
 TSQ  H5   H   HCH3   0   0.241  0.3384  15.2940  34.5914
 TSQ  H6   H   HCH3   0   0.237  0.2696  17.0223  34.2540
 TSQ  H7   H   HCH3   0   0.240  1.5971  16.0528  33.6195
 TSQ  H8   H   HCH3   0   0.245  1.3221  16.9010  38.4410
 TSQ  H9   H   HCH3   0   0.245  0.0922  17.5533  37.3617
 TSQ  H10  H   HCH3   0   0.243  0.1683  15.8219  37.6596
 TSQ  H11  H   HCH3   0   0.243  3.5170  18.3657  36.7058
 TSQ  H12  H   HCH3   0   0.243  3.6233  18.0560  34.9747
 TSQ  H13  H   HCH3   0   0.241  2.2694  18.9752  35.6203
 TSQ  H14  H   HCR6   0   0.241  1.9680  14.1743  37.9021
 TSQ  H15  H   HCR6   0   0.235  3.5154  12.3188  38.2603
 TSQ  H16  H   HCR6   0   0.237  6.1129  13.8879  35.2521
 TSQ  H17  H   HNH2   0   0.331  3.7519  10.8772  35.3503
 TSQ  H18  H   HNH2   0   0.333  4.3640   9.3694  35.3218

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    1.886  0.020  1.886
 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    1.885  0.020  1.885
 TSQ  SI1  C2   single    1.883  0.020  1.883
 TSQ  CZ   CE1  aromatic  1.396  0.020  1.396
 TSQ  O    C    deloc     1.231  0.020  1.231
 TSQ  C    OXT  deloc     1.246  0.020  1.246
 TSQ  CG   CB   single    1.502  0.020  1.502
 TSQ  CG   CD1  aromatic  1.392  0.020  1.392
 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

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  118.49  3.000
 TSQ  H1   CE2  CZ   120.01  3.000
 TSQ  CD2  CE2  CZ   121.50  3.000
 TSQ  H3   CB   H2   107.35  3.000
 TSQ  H3   CB   CG   109.72  3.000
 TSQ  H2   CB   CG   109.71  3.000
 TSQ  H3   CB   CA   108.75  3.000
 TSQ  H2   CB   CA   109.03  3.000
 TSQ  CG   CB   CA   112.16  3.000
 TSQ  H4   CA   N    111.99  3.000
 TSQ  H4   CA   C    105.02  3.000
 TSQ  N    CA   C    111.00  2.800
 TSQ  H4   CA   CB   106.74  3.000
 TSQ  C    CA   CB   110.10  1.900
 TSQ  N    CA   CB   110.50  1.700
 TSQ  OXT  C    O    126.76  3.000
 TSQ  OXT  C    CA   116.38  3.000
 TSQ  O    C    CA   120.80  1.700
 TSQ  H7   C1   H6   107.62  3.000
 TSQ  H7   C1   H5   107.64  3.000
 TSQ  H6   C1   H5   107.64  3.000
 TSQ  H7   C1   SI1  111.30  3.000
 TSQ  H6   C1   SI1  111.16  3.000
 TSQ  H5   C1   SI1  111.30  3.000
 TSQ  H10  C2   H9   107.33  3.000
 TSQ  H10  C2   H8   107.70  3.000
 TSQ  H9   C2   H8   107.60  3.000
 TSQ  H10  C2   SI1  111.90  3.000
 TSQ  H9   C2   SI1  110.47  3.000
 TSQ  H8   C2   SI1  111.63  3.000
 TSQ  H13  C3   H12  107.38  3.000
 TSQ  H13  C3   H11  107.68  3.000
 TSQ  H12  C3   H11  107.64  3.000
 TSQ  H13  C3   SI1  110.84  3.000
 TSQ  H12  C3   SI1  111.72  3.000
 TSQ  H11  C3   SI1  111.38  3.000
 TSQ  SI1  CZ   CE1  121.96  3.000
 TSQ  CE1  CZ   CE2  117.05  3.000
 TSQ  SI1  CZ   CE2  120.99  3.000
 TSQ  H14  CE1  CD1  118.42  3.000
 TSQ  H14  CE1  CZ   120.04  3.000
 TSQ  CD1  CE1  CZ   121.55  3.000
 TSQ  H15  CD1  CG   119.26  3.000
 TSQ  H15  CD1  CE1  119.68  3.000
 TSQ  CG   CD1  CE1  121.05  3.000
 TSQ  CD2  CG   CD1  117.76  3.000
 TSQ  CD1  CG   CB   121.67  3.000
 TSQ  CD2  CG   CB   120.54  3.000
 TSQ  H16  CD2  CG   119.41  3.000
 TSQ  H16  CD2  CE2  119.51  3.000
 TSQ  CG   CD2  CE2  121.08  3.000
 TSQ  H18  N    H17  107.14  3.000
 TSQ  H18  N    CA   108.04  3.000
 TSQ  H17  N    CA   110.20  3.000
 TSQ  CZ   SI1  C3   109.01  3.000
 TSQ  CZ   SI1  C2   109.48  3.000
 TSQ  C3   SI1  C2   110.02  3.000
 TSQ  C2   SI1  C1   109.64  3.000
 TSQ  CZ   SI1  C1   109.31  3.000
 TSQ  C3   SI1  C1   109.38  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  Var_01    C1   SI1  CZ   CE2   77.89  30.0  2
 TSQ  Var_02    CD2  CG   CB   CA   -76.85  30.0  2
 TSQ  Var_03    H5   C1   SI1  CZ    62.16  30.0  3
 TSQ  Var_04    H11  C3   SI1  CZ   -60.94  30.0  3
 TSQ  Var_05    H8   C2   SI1  CZ    59.09  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

