# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:40:08 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (betaR)-3-chloro-beta-hydroxy-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](O)c1ccc(O)c(Cl)c1)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
 OMY  OMY  (betaR)-3-chloro-beta-hydroxy-L-tyrosine  L-peptide  24  15  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OMY
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
 OMY  N    N   NH2    0  -0.823  12.6783  29.4975  45.0542
 OMY  CA   C   CH1    0  -0.261  11.3728  29.0794  44.5756
 OMY  OCZ  O   OH1    0  -0.614  13.8960  23.3113  43.6475
 OMY  CE2  C   CR16   0  -0.326  13.5899  25.0845  45.1582
 OMY  CE1  C   CR6    0  -0.148  12.0126  24.8051  43.3943
 OMY  CZ   C   CR6    0   0.396  13.1715  24.3720  44.0383
 OMY  CG   C   CR6    0   0.086  11.7253  26.6159  44.9616
 OMY  CD2  C   CR16   0  -0.305  12.8779  26.1833  45.6110
 OMY  CD1  C   CR16   0  -0.264  11.3028  25.9047  43.8448
 OMY  CB   C   CH1    0  -0.020  10.9538  27.8444  45.3989
 OMY  C    C   C      0   0.421  10.3326  30.2271  44.7172
 OMY  ODE  O   OH1    0  -0.677  11.1467  28.1362  46.7569
 OMY  OXT  O   OC    -1  -0.599   9.1421  29.9047  44.5510
 OMY  HN1  H   HNH2   0   0.350  13.4273  29.0794  44.5203
 OMY  HN2  H   HNH2   0   0.351  12.7438  30.5035  44.9676
 OMY  HA   H   HCH1   0   0.230  11.3790  28.8016  43.5119
 OMY  HCZ  H   HOH1   0   0.465  13.5122  22.8944  42.8655
 OMY  HE2  H   HCR6   0   0.267  14.4848  24.7620  45.6762
 OMY  HD2  H   HCR6   0   0.247  13.2308  26.6999  46.4934
 OMY  HD1  H   HCR6   0   0.269  10.4052  26.2062  43.3173
 OMY  HB   H   HCH1   0   0.235   9.8895  27.6612  45.2289
 OMY  HDE  H   HOH1   0   0.434  11.9301  28.7177  46.7504
 OMY  CL   CL  CL     0  -0.124  11.4517  23.9288  42.0012
 OMY  O    O   O      0  -0.592  10.7802  31.3682  44.9431

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
 OMY  N    CA   single    1.458  0.019  1.458
 OMY  OCZ  CZ   single    1.343  0.020  1.343
 OMY  CZ   CE2  aromatic  1.392  0.020  1.392
 OMY  CZ   CE1  aromatic  1.395  0.020  1.395
 OMY  CE2  CD2  aromatic  1.385  0.020  1.385
 OMY  CD2  CG   aromatic  1.392  0.020  1.392
 OMY  CG   CD1  aromatic  1.390  0.020  1.390
 OMY  CG   CB   single    1.515  0.020  1.515
 OMY  CD1  CE1  aromatic  1.384  0.020  1.384
 OMY  CE1  CL   single    1.739  0.020  1.739
 OMY  C    O    deloc     1.231  0.020  1.231
 OMY  C    CA   single    1.525  0.021  1.525
 OMY  C    OXT  deloc     1.244  0.020  1.244
 OMY  CA   CB   single    1.530  0.020  1.530
 OMY  CB   ODE  single    1.402  0.020  1.402
 OMY  N    HN1  single    0.890  0.020  1.040
 OMY  N    HN2  single    0.890  0.020  1.040
 OMY  CA   HA   single    0.970  0.020  0.970
 OMY  OCZ  HCZ  single    0.850  0.020  0.980
 OMY  CE2  HE2  single    0.930  0.020  1.080
 OMY  CD2  HD2  single    0.930  0.020  1.080
 OMY  CD1  HD1  single    0.930  0.020  1.080
 OMY  CB   HB   single    0.970  0.020  1.090
 OMY  ODE  HDE  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
 OMY  HN2  N    HN1  108.55  3.000
 OMY  HN2  N    CA   108.44  3.000
 OMY  HN1  N    CA   111.91  3.000
 OMY  HA   CA   C    109.00  3.000
 OMY  HA   CA   CB   109.00  3.000
 OMY  C    CA   CB   110.10  1.900
 OMY  HA   CA   N    110.00  3.000
 OMY  CB   CA   N    110.50  1.700
 OMY  C    CA   N    111.00  2.800
 OMY  HCZ  OCZ  CZ   111.24  3.000
 OMY  HE2  CE2  CD2  120.30  3.000
 OMY  HE2  CE2  CZ   118.73  3.000
 OMY  CD2  CE2  CZ   120.97  3.000
 OMY  CL   CE1  CD1  119.71  3.000
 OMY  CL   CE1  CZ   118.79  3.000
 OMY  CD1  CE1  CZ   121.50  3.000
 OMY  CE1  CZ   CE2  117.54  3.000
 OMY  CE1  CZ   OCZ  124.00  3.000
 OMY  CE2  CZ   OCZ  118.45  3.000
 OMY  CB   CG   CD1  119.47  3.000
 OMY  CB   CG   CD2  122.61  3.000
 OMY  CD1  CG   CD2  117.88  3.000
 OMY  HD2  CD2  CG   120.15  3.000
 OMY  HD2  CD2  CE2  118.54  3.000
 OMY  CG   CD2  CE2  121.30  3.000
 OMY  HD1  CD1  CG   120.04  3.000
 OMY  HD1  CD1  CE1  119.16  3.000
 OMY  CG   CD1  CE1  120.81  3.000
 OMY  HB   CB   ODE  108.62  3.000
 OMY  HB   CB   CG   108.36  3.000
 OMY  ODE  CB   CG   112.22  3.000
 OMY  HB   CB   CA   108.41  3.000
 OMY  ODE  CB   CA   108.23  3.000
 OMY  CG   CB   CA   110.91  3.000
 OMY  OXT  C    O    127.23  3.000
 OMY  OXT  C    CA   115.88  3.000
 OMY  O    C    CA   120.80  1.700
 OMY  HDE  ODE  CB   103.18  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
 OMY  CONST_01  CD1  CE1  CZ   CE2    0.00  0.0  0
 OMY  CONST_02  CD1  CG   CD2  CE2    0.00  0.0  0
 OMY  CONST_03  CD2  CE2  CZ   CE1    0.00  0.0  0
 OMY  CONST_04  CD2  CG   CD1  CE1    0.00  0.0  0
 OMY  CONST_05  CG   CD2  CE2  CZ     0.00  0.0  0
 OMY  CONST_06  CG   CD1  CE1  CZ     0.00  0.0  0
 OMY  CONST_07  CD2  CE2  CZ   OCZ  180.00  0.0  0
 OMY  CONST_08  CD1  CE1  CZ   OCZ  180.00  0.0  0
 OMY  CONST_09  CL   CE1  CZ   CE2  180.00  0.0  0
 OMY  CONST_10  CB   CG   CD2  CE2  180.00  0.0  0
 OMY  CONST_11  CB   CG   CD1  CE1  180.00  0.0  0
 OMY  CONST_12  CL   CE1  CD1  CG   180.00  0.0  0
 OMY  CONST_13  HE2  CE2  CZ   CE1  180.00  0.0  0
 OMY  CONST_14  HD2  CD2  CE2  CZ   180.00  0.0  0
 OMY  CONST_15  HD1  CD1  CE1  CZ   180.00  0.0  0

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
 OMY  chir_01  CA  N    C   CB  positiv
 OMY  chir_02  CB  ODE  CA  CG  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
 OMY  plan-1  OCZ  0.020
 OMY  plan-1  CE2  0.020
 OMY  plan-1  CE1  0.020
 OMY  plan-1  CZ   0.020
 OMY  plan-1  CG   0.020
 OMY  plan-1  CD2  0.020
 OMY  plan-1  CD1  0.020
 OMY  plan-1  CB   0.020
 OMY  plan-1  HE2  0.020
 OMY  plan-1  HD2  0.020
 OMY  plan-1  HD1  0.020
 OMY  plan-1  CL   0.020
 OMY  plan-2  CA   0.020
 OMY  plan-2  C    0.020
 OMY  plan-2  OXT  0.020
 OMY  plan-2  O    0.020

