# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:29:41 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-chloro-D-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(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
 3MY  3MY  '3-chloro-D-tyrosine      '  D-peptide  23  14  .  2016-04-22  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_3MY
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
 3MY  OBD   O   OH1    0  -0.614  15.1863  21.4460  39.1504
 3MY  CZ    C   CR6    0   0.397  15.8276  21.7810  38.0191
 3MY  CE2   C   CR6    0  -0.150  17.1588  22.1940  37.9730
 3MY  CD2   C   CR16   0  -0.256  17.7770  22.5267  36.7798
 3MY  CL    CL  CL     0  -0.126  18.0530  22.2955  39.4615
 3MY  CE1   C   CR16   0  -0.329  15.1319  21.7138  36.8157
 3MY  CD1   C   CR16   0  -0.293  15.7486  22.0536  35.6233
 3MY  CG    C   CR6    0   0.083  17.0795  22.4641  35.5776
 3MY  CB    C   CH2    0  -0.486  17.7283  22.8705  34.2838
 3MY  CA    C   CH1    0  -0.218  17.7455  24.3933  34.0686
 3MY  C     C   C      0   0.392  18.6915  25.0798  35.0908
 3MY  O     O   O      0  -0.616  19.8791  24.6895  35.0725
 3MY  N     N   NH2    0  -0.784  16.3823  24.8982  34.0235
 3MY  OXT   O   OC    -1  -0.596  18.2046  25.9502  35.8366
 3MY  HBD   H   HOH1   0   0.465  15.7672  21.5324  39.9169
 3MY  HE1   H   HCR6   0   0.267  14.0975  21.3933  36.8264
 3MY  HD2   H   HCR6   0   0.264  18.8139  22.8369  36.7880
 3MY  HD1   H   HCR6   0   0.250  15.1796  21.9913  34.7038
 3MY  HB1C  H   HCH2   0   0.237  18.7535  22.5017  34.2434
 3MY  HB2C  H   HCH2   0   0.232  17.1889  22.4081  33.4543
 3MY  HA    H   HCH1   0   0.222  18.1820  24.5536  33.0756
 3MY  HN1   H   HNH2   0   0.327  16.0150  24.9040  34.9684
 3MY  HN2   H   HNH2   0   0.333  16.4105  25.8764  33.7629

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
 3MY  OBD  CZ    single    1.343  0.020  1.343
 3MY  CZ   CE2   aromatic  1.395  0.020  1.395
 3MY  CZ   CE1   aromatic  1.392  0.020  1.392
 3MY  CE2  CD2   aromatic  1.384  0.020  1.384
 3MY  CE2  CL    single    1.739  0.020  1.739
 3MY  CD2  CG    aromatic  1.391  0.020  1.391
 3MY  CE1  CD1   aromatic  1.385  0.020  1.385
 3MY  CD1  CG    aromatic  1.394  0.020  1.394
 3MY  CG   CB    single    1.503  0.020  1.503
 3MY  CB   CA    single    1.530  0.020  1.530
 3MY  CA   C     single    1.525  0.021  1.525
 3MY  CA   N     single    1.458  0.019  1.458
 3MY  C    O     deloc     1.231  0.020  1.231
 3MY  C    OXT   deloc     1.245  0.020  1.245
 3MY  OBD  HBD   single    0.850  0.020  0.980
 3MY  CE1  HE1   single    0.930  0.020  1.080
 3MY  CD2  HD2   single    0.930  0.020  1.080
 3MY  CD1  HD1   single    0.930  0.020  1.080
 3MY  CB   HB1C  single    0.970  0.020  1.090
 3MY  CB   HB2C  single    0.970  0.020  1.090
 3MY  CA   HA    single    0.970  0.020  0.970
 3MY  N    HN1   single    0.890  0.020  1.040
 3MY  N    HN2   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
 3MY  HBD   OBD  CZ    111.04  3.000
 3MY  CE1   CZ   CE2   117.58  3.000
 3MY  CE1   CZ   OBD   118.54  3.000
 3MY  CE2   CZ   OBD   123.89  3.000
 3MY  CL    CE2  CD2   119.60  3.000
 3MY  CL    CE2  CZ    118.67  3.000
 3MY  CD2   CE2  CZ    121.73  3.000
 3MY  HD2   CD2  CG    119.99  3.000
 3MY  HD2   CD2  CE2   119.35  3.000
 3MY  CG    CD2  CE2   120.67  3.000
 3MY  HE1   CE1  CD1   120.43  3.000
 3MY  HE1   CE1  CZ    118.90  3.000
 3MY  CD1   CE1  CZ    120.68  3.000
 3MY  HD1   CD1  CG    119.40  3.000
 3MY  HD1   CD1  CE1   118.88  3.000
 3MY  CG    CD1  CE1   121.72  3.000
 3MY  CB    CG   CD1   121.33  3.000
 3MY  CB    CG   CD2   121.01  3.000
 3MY  CD1   CG   CD2   117.63  3.000
 3MY  HB2C  CB   HB1C  107.04  3.000
 3MY  HB2C  CB   CA    108.57  3.000
 3MY  HB1C  CB   CA    108.61  3.000
 3MY  HB2C  CB   CG    109.03  3.000
 3MY  HB1C  CB   CG    110.26  3.000
 3MY  CA    CB   CG    113.13  3.000
 3MY  HA    CA   N     110.00  3.000
 3MY  HA    CA   C     109.00  3.000
 3MY  N     CA   C     111.00  2.800
 3MY  HA    CA   CB    109.00  3.000
 3MY  N     CA   CB    110.50  1.700
 3MY  C     CA   CB    110.10  1.900
 3MY  OXT   C    O     126.75  3.000
 3MY  OXT   C    CA    117.71  3.000
 3MY  O     C    CA    120.80  1.700
 3MY  HN2   N    HN1   104.15  3.000
 3MY  HN2   N    CA    108.49  3.000
 3MY  HN1   N    CA    108.22  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
 3MY  CONST_01  CG   CD2  CE2  CZ     0.00   0.0  0
 3MY  CONST_02  CG   CD1  CE1  CZ     0.00   0.0  0
 3MY  CONST_03  CD1  CE1  CZ   CE2    0.00   0.0  0
 3MY  CONST_04  CD1  CG   CD2  CE2    0.00   0.0  0
 3MY  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 3MY  CONST_06  CE1  CD1  CG   CD2    0.00   0.0  0
 3MY  CONST_07  CD2  CE2  CZ   OBD  180.00   0.0  0
 3MY  CONST_08  CD1  CE1  CZ   OBD  180.00   0.0  0
 3MY  CONST_09  CB   CG   CD2  CE2  180.00   0.0  0
 3MY  CONST_10  CE1  CZ   CE2  CL   180.00   0.0  0
 3MY  CONST_11  CG   CD2  CE2  CL   180.00   0.0  0
 3MY  CONST_12  CB   CG   CD1  CE1  180.00   0.0  0
 3MY  CONST_13  HD2  CD2  CE2  CZ   180.00   0.0  0
 3MY  CONST_14  HD1  CD1  CE1  CZ   180.00   0.0  0
 3MY  CONST_15  HE1  CE1  CZ   CE2  180.00   0.0  0
 3MY  Var_01    CA   CB   CG   CD2  -80.38  30.0  2

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
 3MY  chir_01  CA  CB  C  N  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
 3MY  plan-1  OBD  0.020
 3MY  plan-1  CZ   0.020
 3MY  plan-1  CE2  0.020
 3MY  plan-1  CD2  0.020
 3MY  plan-1  CL   0.020
 3MY  plan-1  CE1  0.020
 3MY  plan-1  CD1  0.020
 3MY  plan-1  CG   0.020
 3MY  plan-1  CB   0.020
 3MY  plan-1  HE1  0.020
 3MY  plan-1  HD2  0.020
 3MY  plan-1  HD1  0.020
 3MY  plan-2  CA   0.020
 3MY  plan-2  C    0.020
 3MY  plan-2  O    0.020
 3MY  plan-2  OXT  0.020

