# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:37:39 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (betaR)-3-chloro-beta-hydroxy-D-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
 OMZ  OMZ  (betaR)-3-chloro-beta-hydroxy-D-tyrosine  D-peptide  24  15  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OMZ
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
 OMZ  N    N   NH2    0  -0.795  17.0952  25.7790  26.3059
 OMZ  CA   C   CH1    0  -0.221  16.1513  24.7483  25.9320
 OMZ  C    C   C      0   0.405  14.7976  24.9102  26.6662
 OMZ  O    O   O      0  -0.609  14.0137  23.9434  26.5664
 OMZ  OXT  O   OC    -1  -0.590  14.5952  25.9792  27.2687
 OMZ  CB   C   CH1    0  -0.007  15.8957  24.6293  24.4139
 OMZ  OC   O   OH1    0  -0.661  17.1337  24.3042  23.8166
 OMZ  CG   C   CR6    0   0.041  15.3067  25.8926  23.8320
 OMZ  CD1  C   CR16   0  -0.250  13.9285  26.0645  23.7979
 OMZ  CD2  C   CR16   0  -0.297  16.1066  26.9242  23.3454
 OMZ  CE1  C   CR6    0  -0.153  13.3742  27.2300  23.2981
 OMZ  CL   CL  CL     0  -0.123  11.6459  27.4133  23.2626
 OMZ  CE2  C   CR16   0  -0.328  15.5508  28.0883  22.8422
 OMZ  CZ   C   CR6    0   0.401  14.1706  28.2654  22.8092
 OMZ  OH   O   OH1    0  -0.612  13.6853  29.4110  22.3064
 OMZ  H    H   HNH2   0   0.334  17.8768  25.7977  25.6626
 OMZ  H2   H   HNH2   0   0.332  16.6433  26.6829  26.2610
 OMZ  HA   H   HCH1   0   0.220  16.5666  23.7777  26.2329
 OMZ  HB   H   HCH1   0   0.212  15.1747  23.8147  24.2714
 OMZ  HC   H   HOH1   0   0.448  17.0034  24.2266  22.8658
 OMZ  HD1  H   HCR6   0   0.266  13.2766  25.2837  24.1696
 OMZ  HD2  H   HCR6   0   0.254  17.1835  26.8214  23.3429
 OMZ  HE2  H   HCR6   0   0.268  16.1870  28.8786  22.4635
 OMZ  HH   H   HOH1   0   0.466  12.7201  29.4206  22.3261

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
 OMZ  N    CA   single    1.458  0.019  1.458
 OMZ  CA   C    single    1.525  0.021  1.525
 OMZ  CA   CB   single    1.521  0.033  1.521
 OMZ  C    O    deloc     1.231  0.020  1.231
 OMZ  C    OXT  deloc     1.244  0.020  1.244
 OMZ  CL   CE1  single    1.738  0.020  1.738
 OMZ  CB   OC   single    1.413  0.020  1.413
 OMZ  CB   CG   single    1.510  0.020  1.510
 OMZ  CG   CD1  aromatic  1.389  0.020  1.389
 OMZ  CG   CD2  aromatic  1.393  0.020  1.393
 OMZ  CD1  CE1  aromatic  1.384  0.020  1.384
 OMZ  CD2  CE2  aromatic  1.385  0.020  1.385
 OMZ  CE1  CZ   aromatic  1.395  0.020  1.395
 OMZ  CE2  CZ   aromatic  1.392  0.020  1.392
 OMZ  CZ   OH   single    1.342  0.020  1.342
 OMZ  N    H    single    0.860  0.020  0.860
 OMZ  N    H2   single    0.890  0.020  1.040
 OMZ  CA   HA   single    0.970  0.020  0.970
 OMZ  CB   HB   single    0.970  0.020  1.090
 OMZ  OC   HC   single    0.850  0.020  0.980
 OMZ  CD1  HD1  single    0.930  0.020  1.080
 OMZ  CD2  HD2  single    0.930  0.020  1.080
 OMZ  CE2  HE2  single    0.930  0.020  1.080
 OMZ  OH   HH   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
 OMZ  H2   N    H    107.47  3.000
 OMZ  H2   N    CA   109.49  3.000
 OMZ  H    N    CA   114.00  3.000
 OMZ  HA   CA   CB   109.00  3.000
 OMZ  HA   CA   C    110.00  3.000
 OMZ  CB   CA   C    110.50  1.500
 OMZ  HA   CA   N    110.00  3.000
 OMZ  CB   CA   N    110.40  1.500
 OMZ  C    CA   N    111.00  2.800
 OMZ  OXT  C    O    127.02  3.000
 OMZ  OXT  C    CA   120.80  1.700
 OMZ  O    C    CA   120.80  1.700
 OMZ  HB   CB   CG   108.34  3.000
 OMZ  HB   CB   OC   110.49  3.000
 OMZ  CG   CB   OC   111.80  3.000
 OMZ  HB   CB   CA   107.08  3.000
 OMZ  CG   CB   CA   112.26  3.000
 OMZ  OC   CB   CA   106.77  3.000
 OMZ  HC   OC   CB   108.51  3.000
 OMZ  CD2  CG   CD1  117.99  3.000
 OMZ  CD2  CG   CB   122.00  3.000
 OMZ  CD1  CG   CB   119.99  3.000
 OMZ  HD1  CD1  CE1  119.34  3.000
 OMZ  HD1  CD1  CG   119.97  3.000
 OMZ  CE1  CD1  CG   120.69  3.000
 OMZ  HD2  CD2  CE2  118.60  3.000
 OMZ  HD2  CD2  CG   120.13  3.000
 OMZ  CE2  CD2  CG   121.27  3.000
 OMZ  CZ   CE1  CL   118.83  3.000
 OMZ  CZ   CE1  CD1  121.54  3.000
 OMZ  CL   CE1  CD1  119.63  3.000
 OMZ  HE2  CE2  CZ   118.78  3.000
 OMZ  HE2  CE2  CD2  120.32  3.000
 OMZ  CZ   CE2  CD2  120.91  3.000
 OMZ  OH   CZ   CE2  118.43  3.000
 OMZ  OH   CZ   CE1  123.96  3.000
 OMZ  CE2  CZ   CE1  117.61  3.000
 OMZ  HH   OH   CZ   111.25  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
 OMZ  CONST_01  CZ   CE1  CD1  CG     0.00  0.0  0
 OMZ  CONST_02  CZ   CE2  CD2  CG     0.00  0.0  0
 OMZ  CONST_03  CE2  CD2  CG   CD1    0.00  0.0  0
 OMZ  CONST_04  CE2  CZ   CE1  CD1    0.00  0.0  0
 OMZ  CONST_05  CE1  CD1  CG   CD2    0.00  0.0  0
 OMZ  CONST_06  CE1  CZ   CE2  CD2    0.00  0.0  0
 OMZ  CONST_07  CE1  CD1  CG   CB   180.00  0.0  0
 OMZ  CONST_08  CE2  CD2  CG   CB   180.00  0.0  0
 OMZ  CONST_09  CL   CE1  CD1  CG   180.00  0.0  0
 OMZ  CONST_10  OH   CZ   CE1  CD1  180.00  0.0  0
 OMZ  CONST_11  OH   CZ   CE2  CD2  180.00  0.0  0
 OMZ  CONST_12  CE2  CZ   CE1  CL   180.00  0.0  0
 OMZ  CONST_13  HE2  CE2  CD2  CG   180.00  0.0  0
 OMZ  CONST_14  HD2  CD2  CG   CD1  180.00  0.0  0
 OMZ  CONST_15  HD1  CD1  CG   CD2  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
 OMZ  chir_01  CA  N   C   CB  negativ
 OMZ  chir_02  CB  OC  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
 OMZ  plan-1  CB   0.020
 OMZ  plan-1  CG   0.020
 OMZ  plan-1  CD1  0.020
 OMZ  plan-1  CD2  0.020
 OMZ  plan-1  CE1  0.020
 OMZ  plan-1  CL   0.020
 OMZ  plan-1  CE2  0.020
 OMZ  plan-1  CZ   0.020
 OMZ  plan-1  OH   0.020
 OMZ  plan-1  HD1  0.020
 OMZ  plan-1  HD2  0.020
 OMZ  plan-1  HE2  0.020
 OMZ  plan-2  CA   0.020
 OMZ  plan-2  C    0.020
 OMZ  plan-2  O    0.020
 OMZ  plan-2  OXT  0.020

