# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:11:39 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 2,5-dihydroxy-N-methyl-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](Cc1cc(O)c(O)cc1O)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
 TYJ  TYJ  2,5-dihydroxy-N-methyl-L-tyrosine  L-peptide  28  16  .  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_TYJ
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
 TYJ  N     N  NH1    0  -0.577   -8.4937  17.8305  31.9016
 TYJ  CA    C  CH1    0  -0.237   -9.7513  17.8513  32.6279
 TYJ  C     C  C      0   0.413   -9.8227  16.7463  33.7240
 TYJ  O     O  O      0  -0.603  -10.9663  16.4241  34.1054
 TYJ  CN    C  CH3    0  -0.532   -8.2724  16.6681  31.0664
 TYJ  CB7   C  CH2    0  -0.508  -11.0103  17.8659  31.7323
 TYJ  CG5   C  CR6    0   0.031  -11.0170  18.9979  30.7422
 TYJ  CD12  C  CR6    0   0.312  -11.3354  20.3035  31.1223
 TYJ  CD21  C  CR16   0  -0.428  -10.6813  18.7858  29.4062
 TYJ  CE11  C  CR16   0  -0.469  -11.3085  21.3428  30.1962
 TYJ  CE21  C  CR6    0   0.245  -10.6493  19.8076  28.4719
 TYJ  CZ1   C  CR6    0   0.288  -10.9655  21.1061  28.8732
 TYJ  OZ    O  OH1    0  -0.655  -10.3341  19.6379  27.1587
 TYJ  OH1   O  OH1    0  -0.635  -10.9537  22.1428  28.0066
 TYJ  HA    H  HCH1   0   0.230   -9.7537  18.7978  33.1850
 TYJ  HCN1  H  HCH3   0   0.219   -7.3104  16.7665  30.5610
 TYJ  HCN2  H  HCH3   0   0.221   -8.2255  15.7705  31.6818
 TYJ  HCN3  H  HCH3   0   0.188   -9.0270  16.4940  30.2879
 TYJ  HB14  H  HCH2   0   0.227  -11.0894  16.9205  31.1886
 TYJ  HB26  H  HCH2   0   0.231  -11.8897  17.9192  32.3723
 TYJ  HD23  H  HCR6   0   0.260  -10.4434  17.7766  29.0847
 TYJ  HE12  H  HCR6   0   0.267  -11.5561  22.3550  30.4998
 TYJ  HOZ   H  HOH1   0   0.475  -10.0296  18.7388  26.9966
 TYJ  HO1   H  HOH1   0   0.468  -10.6619  21.8432  27.1376
 TYJ  H2    H  HNH1   0   0.335   -8.4365  18.6621  31.3270
 TYJ  OXT   O  OC    -1  -0.598   -8.7457  16.3109  34.1711
 TYJ  OG1   O  OH1    0  -0.638  -11.6711  20.5217  32.4176
 TYJ  HG1   H  HOH1   0   0.468  -11.8922  21.4492  32.5540

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
 TYJ  N     CA    single    1.458  0.019  1.458
 TYJ  N     CN    single    1.448  0.020  1.448
 TYJ  CA    C     single    1.525  0.021  1.525
 TYJ  CA    CB7   single    1.545  0.020  1.545
 TYJ  CA    HA    single    0.970  0.020  0.970
 TYJ  C     O     deloc     1.231  0.020  1.231
 TYJ  CN    HCN1  single    0.970  0.020  1.090
 TYJ  CN    HCN2  single    0.970  0.020  1.090
 TYJ  CN    HCN3  single    0.970  0.020  1.090
 TYJ  CB7   CG5   single    1.504  0.020  1.504
 TYJ  CB7   HB14  single    0.970  0.020  1.090
 TYJ  CB7   HB26  single    0.970  0.020  1.090
 TYJ  CG5   CD12  aromatic  1.397  0.020  1.397
 TYJ  CG5   CD21  aromatic  1.394  0.020  1.394
 TYJ  CD12  CE11  aromatic  1.392  0.020  1.392
 TYJ  CD21  CE21  aromatic  1.385  0.020  1.385
 TYJ  CD21  HD23  single    0.930  0.020  1.080
 TYJ  CE11  CZ1   aromatic  1.387  0.020  1.387
 TYJ  CE11  HE12  single    0.930  0.020  1.080
 TYJ  CE21  CZ1   aromatic  1.395  0.020  1.395
 TYJ  CE21  OZ    single    1.361  0.020  1.361
 TYJ  CZ1   OH1   single    1.351  0.020  1.351
 TYJ  OZ    HOZ   single    0.850  0.020  0.980
 TYJ  OH1   HO1   single    0.850  0.020  0.980
 TYJ  N     H2    single    0.890  0.020  1.040
 TYJ  C     OXT   deloc     1.245  0.020  1.245
 TYJ  CD12  OG1   single    1.356  0.020  1.356
 TYJ  OG1   HG1   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
 TYJ  H2    N     CN    108.86  3.000
 TYJ  H2    N     CA    108.72  3.000
 TYJ  CN    N     CA    115.61  3.000
 TYJ  HA    CA    CB7   106.51  3.000
 TYJ  HA    CA    C     109.00  3.000
 TYJ  CB7   CA    C     112.16  3.000
 TYJ  HA    CA    N     110.00  3.000
 TYJ  CB7   CA    N     114.57  3.000
 TYJ  C     CA    N     111.00  2.800
 TYJ  OXT   C     O     126.36  3.000
 TYJ  OXT   C     CA    117.46  3.000
 TYJ  O     C     CA    120.80  1.700
 TYJ  HCN3  CN    HCN2  107.43  3.000
 TYJ  HCN3  CN    HCN1  106.96  3.000
 TYJ  HCN2  CN    HCN1  107.33  3.000
 TYJ  HCN3  CN    N     115.54  3.000
 TYJ  HCN2  CN    N     110.00  3.000
 TYJ  HCN1  CN    N     109.23  3.000
 TYJ  HB26  CB7   HB14  106.02  3.000
 TYJ  HB26  CB7   CG5   110.28  3.000
 TYJ  HB14  CB7   CG5   108.86  3.000
 TYJ  HB26  CB7   CA    108.53  3.000
 TYJ  HB14  CB7   CA    109.82  3.000
 TYJ  CG5   CB7   CA    113.10  3.000
 TYJ  CD21  CG5   CD12  117.26  3.000
 TYJ  CD21  CG5   CB7   121.03  3.000
 TYJ  CD12  CG5   CB7   121.70  3.000
 TYJ  OG1   CD12  CE11  121.34  3.000
 TYJ  OG1   CD12  CG5   117.83  3.000
 TYJ  CE11  CD12  CG5   120.82  3.000
 TYJ  HD23  CD21  CE21  118.76  3.000
 TYJ  HD23  CD21  CG5   118.56  3.000
 TYJ  CE21  CD21  CG5   122.68  3.000
 TYJ  HE12  CE11  CZ1   118.84  3.000
 TYJ  HE12  CE11  CD12  120.37  3.000
 TYJ  CZ1   CE11  CD12  120.79  3.000
 TYJ  OZ    CE21  CZ1   116.48  3.000
 TYJ  OZ    CE21  CD21  124.35  3.000
 TYJ  CZ1   CE21  CD21  119.17  3.000
 TYJ  OH1   CZ1   CE21  121.84  3.000
 TYJ  OH1   CZ1   CE11  118.88  3.000
 TYJ  CE21  CZ1   CE11  119.28  3.000
 TYJ  HOZ   OZ    CE21  110.61  3.000
 TYJ  HO1   OH1   CZ1   110.01  3.000
 TYJ  HG1   OG1   CD12  110.31  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
 TYJ  CONST_01  CZ1   CE11  CD12  CG5     0.00   0.0  0
 TYJ  CONST_02  CZ1   CE21  CD21  CG5     0.00   0.0  0
 TYJ  CONST_03  CE21  CD21  CG5   CD12    0.00   0.0  0
 TYJ  CONST_04  CE21  CZ1   CE11  CD12    0.00   0.0  0
 TYJ  CONST_05  CE11  CD12  CG5   CD21    0.00   0.0  0
 TYJ  CONST_06  CE11  CZ1   CE21  CD21    0.00   0.0  0
 TYJ  CONST_07  CE11  CD12  CG5   CB7   180.00   0.0  0
 TYJ  CONST_08  CE21  CD21  CG5   CB7   180.00   0.0  0
 TYJ  CONST_09  OZ    CE21  CD21  CG5   180.00   0.0  0
 TYJ  CONST_10  OH1   CZ1   CE11  CD12  180.00   0.0  0
 TYJ  CONST_11  OG1   CD12  CG5   CD21  180.00   0.0  0
 TYJ  CONST_12  OH1   CZ1   CE21  CD21  180.00   0.0  0
 TYJ  CONST_13  OZ    CE21  CZ1   CE11  180.00   0.0  0
 TYJ  CONST_14  OG1   CD12  CE11  CZ1   180.00   0.0  0
 TYJ  CONST_15  HE12  CE11  CD12  CG5   180.00   0.0  0
 TYJ  CONST_16  HD23  CD21  CG5   CD12  180.00   0.0  0
 TYJ  Var_01    CD12  CG5   CB7   CA    -77.50  30.0  2
 TYJ  Var_02    HCN1  CN    N     CA    179.16  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
 TYJ  chir_01  CA  N  C  CB7  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
 TYJ  plan-1  CB7   0.020
 TYJ  plan-1  CG5   0.020
 TYJ  plan-1  CD12  0.020
 TYJ  plan-1  CD21  0.020
 TYJ  plan-1  CE11  0.020
 TYJ  plan-1  CE21  0.020
 TYJ  plan-1  CZ1   0.020
 TYJ  plan-1  OZ    0.020
 TYJ  plan-1  OH1   0.020
 TYJ  plan-1  HD23  0.020
 TYJ  plan-1  HE12  0.020
 TYJ  plan-1  OG1   0.020
 TYJ  plan-2  CA    0.020
 TYJ  plan-2  C     0.020
 TYJ  plan-2  O     0.020
 TYJ  plan-2  OXT   0.020

