# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:32:02 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: O-tert-butyl-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)Oc1ccc(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
 TY1  TY1  'O-tert-butyl-L-tyrosine  '  L-peptide  35  17  .  2016-04-26  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_TY1
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
 TY1  N     N  NH2    0  -0.797  18.5862  -18.3645  2.5995
 TY1  CG    C  CR6    0   0.130  15.7126  -17.5526  3.2897
 TY1  CL    C  CR6    0   0.335  14.8078  -16.0797  5.5168
 TY1  CZ    C  CH2    0  -0.488  16.1828  -18.3375  2.0974
 TY1  CAA   C  CH3    0  -0.663  14.4962  -13.0574  6.0672
 TY1  CAB   C  CH3    0  -0.672  16.4238  -14.2681  7.1075
 TY1  CAC   C  CH3    0  -0.654  14.3115  -13.9278  8.4005
 TY1  CBL   C  CT     0   0.181  14.9051  -14.1749  7.0215
 TY1  C     C  C      0   0.411  17.7032  -16.4812  1.2357
 TY1  CA    C  CH1    0  -0.208  17.5958  -17.9796  1.6094
 TY1  CD1   C  CR16   0  -0.302  14.8359  -16.4799  3.1416
 TY1  CD2   C  CR16   0  -0.298  16.1205  -17.8757  4.5838
 TY1  CE1   C  CR16   0  -0.317  14.3790  -15.7543  4.2344
 TY1  CE2   C  CR16   0  -0.311  15.6822  -17.1503  5.6817
 TY1  O     O  O      0  -0.609  16.8381  -16.0579  0.4428
 TY1  H     H  HNH2   0   0.329  18.7887  -19.3522  2.5187
 TY1  H2    H  HNH2   0   0.333  19.4450  -17.8648  2.4153
 TY1  HZ    H  HCH2   0   0.226  16.1637  -19.4060  2.3345
 TY1  HZA   H  HCH2   0   0.227  15.4870  -18.1936  1.2700
 TY1  HAA   H  HCH3   0   0.234  14.8367  -12.0973  6.4576
 TY1  HAAA  H  HCH3   0   0.234  14.9372  -13.1796  5.0772
 TY1  HAAB  H  HCH3   0   0.231  13.4113  -13.0088  5.9595
 TY1  HAB   H  HCH3   0   0.238  16.8253  -13.3284  7.4885
 TY1  HABA  H  HCH3   0   0.234  16.7380  -15.0650  7.7835
 TY1  HABB  H  HCH3   0   0.234  16.8784  -14.4473  6.1321
 TY1  HAC   H  HCH3   0   0.225  14.6672  -12.9780  8.8000
 TY1  HACA  H  HCH3   0   0.232  13.2220  -13.8846  8.3579
 TY1  HACB  H  HCH3   0   0.231  14.5980  -14.7147  9.0999
 TY1  OXT   O  OC    -1  -0.598  18.6514  -15.8352  1.7224
 TY1  HA    H  HCH1   0   0.199  17.7305  -18.5288  0.6621
 TY1  HD1   H  HCR6   0   0.237  14.4925  -16.2100  2.1507
 TY1  HD2   H  HCR6   0   0.233  16.7915  -18.7108  4.7363
 TY1  HE1   H  HCR6   0   0.253  13.6698  -14.9498  4.0868
 TY1  HE2   H  HCR6   0   0.247  16.0060  -17.4248  6.6785
 TY1  OH    O  O2     0  -0.514  14.3243  -15.4360  6.6149

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
 TY1  N    H     single    0.860  0.020  0.860
 TY1  N    H2    single    0.890  0.020  1.040
 TY1  CG   CD2   aromatic  1.395  0.020  1.395
 TY1  OH   CBL   single    1.447  0.020  1.447
 TY1  CL   OH    single    1.362  0.020  1.362
 TY1  CL   CE2   aromatic  1.392  0.020  1.392
 TY1  CZ   CG    single    1.503  0.020  1.503
 TY1  CZ   HZ    single    0.970  0.020  1.090
 TY1  CZ   HZA   single    0.970  0.020  1.090
 TY1  CAA  CBL   single    1.525  0.020  1.525
 TY1  CAA  HAA   single    0.970  0.020  1.090
 TY1  CAA  HAAA  single    0.970  0.020  1.090
 TY1  CAA  HAAB  single    0.970  0.020  1.090
 TY1  CAB  HAB   single    0.970  0.020  1.090
 TY1  CAB  HABA  single    0.970  0.020  1.090
 TY1  CAB  HABB  single    0.970  0.020  1.090
 TY1  CAC  HAC   single    0.970  0.020  1.090
 TY1  CAC  HACA  single    0.970  0.020  1.090
 TY1  CAC  HACB  single    0.970  0.020  1.090
 TY1  CBL  CAB   single    1.524  0.020  1.524
 TY1  CBL  CAC   single    1.522  0.020  1.522
 TY1  C    CA    single    1.525  0.021  1.525
 TY1  C    OXT   deloc     1.246  0.020  1.246
 TY1  CA   N     single    1.458  0.019  1.458
 TY1  CA   CZ    single    1.537  0.020  1.537
 TY1  CA   HA    single    0.970  0.020  0.970
 TY1  CD1  CG    aromatic  1.393  0.020  1.393
 TY1  CD1  CE1   aromatic  1.389  0.020  1.389
 TY1  CD1  HD1   single    0.930  0.020  1.080
 TY1  CD2  CE2   aromatic  1.387  0.020  1.387
 TY1  CD2  HD2   single    0.930  0.020  1.080
 TY1  CE1  CL    aromatic  1.391  0.020  1.391
 TY1  CE1  HE1   single    0.930  0.020  1.080
 TY1  CE2  HE2   single    0.930  0.020  1.080
 TY1  O    C     deloc     1.231  0.020  1.231

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
 TY1  H2    N    H     107.34  3.000
 TY1  H2    N    CA    108.91  3.000
 TY1  H     N    CA    114.00  3.000
 TY1  CD2   CG   CD1   117.45  3.000
 TY1  CD1   CG   CZ    120.97  3.000
 TY1  CD2   CG   CZ    121.58  3.000
 TY1  CE2   CL   CE1   118.87  3.000
 TY1  CE1   CL   OH    121.57  3.000
 TY1  CE2   CL   OH    119.42  3.000
 TY1  HZA   CZ   HZ    106.38  3.000
 TY1  HZA   CZ   CA    108.35  3.000
 TY1  HZ    CZ   CA    108.18  3.000
 TY1  CA    CZ   CG    114.70  3.000
 TY1  HZA   CZ   CG    109.47  3.000
 TY1  HZ    CZ   CG    109.42  3.000
 TY1  HAAB  CAA  HAAA  108.50  3.000
 TY1  HAAB  CAA  HAA   107.85  3.000
 TY1  HAAA  CAA  HAA   107.29  3.000
 TY1  HAAB  CAA  CBL   111.16  3.000
 TY1  HAAA  CAA  CBL   112.17  3.000
 TY1  HAA   CAA  CBL   109.70  3.000
 TY1  HABB  CAB  HABA  108.30  3.000
 TY1  HABB  CAB  HAB   107.49  3.000
 TY1  HABA  CAB  HAB   107.87  3.000
 TY1  HABB  CAB  CBL   112.01  3.000
 TY1  HABA  CAB  CBL   111.50  3.000
 TY1  HAB   CAB  CBL   109.50  3.000
 TY1  HACB  CAC  HACA  108.41  3.000
 TY1  HACB  CAC  HAC   107.92  3.000
 TY1  HACA  CAC  HAC   107.80  3.000
 TY1  HACB  CAC  CBL   111.18  3.000
 TY1  HACA  CAC  CBL   111.14  3.000
 TY1  HAC   CAC  CBL   110.27  3.000
 TY1  CAC   CBL  CAB   110.34  3.000
 TY1  CAC   CBL  CAA   110.08  3.000
 TY1  CAB   CBL  CAA   110.32  3.000
 TY1  CAC   CBL  OH    103.87  3.000
 TY1  CAB   CBL  OH    111.26  3.000
 TY1  CAA   CBL  OH    110.80  3.000
 TY1  OXT   C    O     126.86  3.000
 TY1  O     C    CA    120.80  1.700
 TY1  OXT   C    CA    117.40  3.000
 TY1  HA    CA   C     109.00  3.000
 TY1  HA    CA   CZ    105.60  3.000
 TY1  C     CA   CZ    111.45  3.000
 TY1  HA    CA   N     110.00  3.000
 TY1  CZ    CA   N     110.41  3.000
 TY1  C     CA   N     111.00  2.800
 TY1  HD1   CD1  CE1   119.03  3.000
 TY1  HD1   CD1  CG    119.26  3.000
 TY1  CE1   CD1  CG    121.70  3.000
 TY1  HD2   CD2  CE2   119.20  3.000
 TY1  HD2   CD2  CG    119.40  3.000
 TY1  CE2   CD2  CG    121.40  3.000
 TY1  HE1   CE1  CD1   119.77  3.000
 TY1  HE1   CE1  CL    120.10  3.000
 TY1  CD1   CE1  CL    120.12  3.000
 TY1  HE2   CE2  CD2   120.10  3.000
 TY1  HE2   CE2  CL    119.44  3.000
 TY1  CD2   CE2  CL    120.46  3.000
 TY1  CBL   OH   CL    119.74  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
 TY1  CONST_01  CL   CE2  CD2  CG      0.00   0.0  0
 TY1  CONST_02  CL   CE1  CD1  CG      0.00   0.0  0
 TY1  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 TY1  CONST_04  CE2  CL   CE1  CD1     0.00   0.0  0
 TY1  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 TY1  CONST_06  CE1  CL   CE2  CD2     0.00   0.0  0
 TY1  CONST_07  CD2  CE2  CL   OH    180.00   0.0  0
 TY1  CONST_08  CD1  CE1  CL   OH    180.00   0.0  0
 TY1  CONST_09  CE2  CD2  CG   CZ    180.00   0.0  0
 TY1  CONST_10  CE1  CD1  CG   CZ    180.00   0.0  0
 TY1  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 TY1  CONST_12  HE1  CE1  CD1  CG    180.00   0.0  0
 TY1  CONST_13  HD2  CD2  CE2  CL    180.00   0.0  0
 TY1  CONST_14  HD1  CD1  CE1  CL    180.00   0.0  0
 TY1  Var_01    CE2  CL   OH   CBL   100.76  30.0  2
 TY1  Var_02    CD2  CG   CZ   CA    -79.65  30.0  2
 TY1  Var_03    CAA  CBL  OH   CL     72.86  30.0  3
 TY1  Var_04    HAA  CAA  CBL  OH    172.88  30.0  3
 TY1  Var_05    HAB  CAB  CBL  OH   -175.71  30.0  3
 TY1  Var_06    HAC  CAC  CBL  OH   -178.67  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
 TY1  chir_01  CA  C  N  CZ  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
 TY1  plan-1  CG   0.020
 TY1  plan-1  CL   0.020
 TY1  plan-1  CZ   0.020
 TY1  plan-1  CD1  0.020
 TY1  plan-1  CD2  0.020
 TY1  plan-1  CE1  0.020
 TY1  plan-1  CE2  0.020
 TY1  plan-1  HD1  0.020
 TY1  plan-1  HD2  0.020
 TY1  plan-1  HE1  0.020
 TY1  plan-1  HE2  0.020
 TY1  plan-1  OH   0.020
 TY1  plan-2  C    0.020
 TY1  plan-2  CA   0.020
 TY1  plan-2  O    0.020
 TY1  plan-2  OXT  0.020

