# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:18:06 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2S)-2-amino-4-(2-amino-3-hydroxyphenyl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)c1cccc(O)c1N)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
 3DJ  3DJ  '(2S)-2-amino-4-(2-amino-3-hydroxyphenyl)-4-oxobutanoic acid'  ligand  28  16  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3DJ
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
 3DJ  C1   C  C     0   0.417  -0.1594  -0.4727   0.2507
 3DJ  C    C  C     0   0.545  -3.8987   0.4066   0.0651
 3DJ  OXT  O  OH1   0  -0.593  -4.0290   0.9938   1.2491
 3DJ  CA   C  CH1   0  -0.214  -2.6979  -0.5197   0.0245
 3DJ  N    N  NH2   0  -0.784  -2.8246  -1.4087  -1.1076
 3DJ  CB   C  CH2   0  -0.600  -1.4233   0.3414   0.0489
 3DJ  O2   O  O     0  -0.438  -0.2462  -1.6611   0.5235
 3DJ  CD2  C  CR6   0  -0.088   1.1392   0.2086   0.1198
 3DJ  CE2  C  CR16  0  -0.325   1.1804   1.5953  -0.1159
 3DJ  CZ   C  CR16  0  -0.266   2.3680   2.2647  -0.2817
 3DJ  CE1  C  CR16  0  -0.332   3.5689   1.5575  -0.1944
 3DJ  CD1  C  CR6   0   0.297   3.5680   0.2038   0.0428
 3DJ  O3   O  OH1   0  -0.651   4.7559  -0.4595   0.1015
 3DJ  CG   C  CR6   0   0.236   2.3553  -0.5135   0.1980
 3DJ  N1   N  NH2   0  -0.856   2.4386  -1.8487   0.4496
 3DJ  H1   H  HOH1  0   0.483  -4.7808   1.6051   1.2369
 3DJ  H2   H  HCH1  0   0.279  -2.7275  -1.1242   0.9353
 3DJ  H3   H  HNH2  0   0.344  -2.7205  -0.8959  -1.9745
 3DJ  H4   H  HNH2  0   0.358  -2.0777  -2.0886  -1.0801
 3DJ  H6   H  HCH2  0   0.292  -1.4686   1.0857   0.8500
 3DJ  H7   H  HCH2  0   0.281  -1.3564   0.9068  -0.8851
 3DJ  H8   H  HCR6  0   0.265   0.2604   2.1595  -0.1712
 3DJ  H9   H  HCR6  0   0.257   2.3779   3.3307  -0.4603
 3DJ  H10  H  HCR6  0   0.269   4.5170   2.0690  -0.3068
 3DJ  H11  H  HOH1  0   0.468   4.7762  -1.0413   0.8721
 3DJ  H12  H  HNH2  0   0.405   1.5741  -2.3639   0.4540
 3DJ  H13  H  HNH2  0   0.384   3.2289  -2.3451   0.0710
 3DJ  O    O  O     0  -0.435  -4.6397   0.6101  -0.8618

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
 3DJ  N    CA   single    1.445  0.020  1.445
 3DJ  CA   C    single    1.517  0.020  1.517
 3DJ  CA   CB   single    1.538  0.020  1.538
 3DJ  O    C    double    1.204  0.020  1.204
 3DJ  O2   C1   double    1.222  0.020  1.222
 3DJ  N1   CG   single    1.361  0.020  1.361
 3DJ  C    OXT  single    1.328  0.020  1.328
 3DJ  C1   CB   single    1.517  0.020  1.517
 3DJ  C1   CD2  single    1.472  0.020  1.472
 3DJ  CG   CD2  aromatic  1.417  0.020  1.417
 3DJ  CG   CD1  aromatic  1.418  0.020  1.418
 3DJ  O3   CD1  single    1.362  0.020  1.362
 3DJ  CD2  CE2  aromatic  1.407  0.020  1.407
 3DJ  CD1  CE1  aromatic  1.374  0.020  1.374
 3DJ  CE2  CZ   aromatic  1.373  0.020  1.373
 3DJ  CE1  CZ   aromatic  1.396  0.020  1.396
 3DJ  OXT  H1   single    0.850  0.020  0.980
 3DJ  CA   H2   single    0.970  0.020  1.090
 3DJ  N    H3   single    0.890  0.020  1.040
 3DJ  N    H4   single    0.890  0.020  1.040
 3DJ  CB   H6   single    0.970  0.020  1.090
 3DJ  CB   H7   single    0.970  0.020  1.090
 3DJ  CE2  H8   single    0.930  0.020  1.080
 3DJ  CZ   H9   single    0.930  0.020  1.080
 3DJ  CE1  H10  single    0.930  0.020  1.080
 3DJ  O3   H11  single    0.850  0.020  0.980
 3DJ  N1   H12  single    0.890  0.020  1.040
 3DJ  N1   H13  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
 3DJ  CD2  C1   O2   122.16  3.000
 3DJ  CD2  C1   CB   118.34  3.000
 3DJ  O2   C1   CB   119.49  3.000
 3DJ  CA   C    OXT  111.81  3.000
 3DJ  OXT  C    O    123.45  3.000
 3DJ  CA   C    O    124.73  3.000
 3DJ  H1   OXT  C    110.11  3.000
 3DJ  H2   CA   CB   108.58  3.000
 3DJ  H2   CA   N    108.07  3.000
 3DJ  CB   CA   N    115.43  3.000
 3DJ  H2   CA   C    107.09  3.000
 3DJ  CB   CA   C    108.27  3.000
 3DJ  N    CA   C    109.10  3.000
 3DJ  H4   N    H3   106.74  3.000
 3DJ  H4   N    CA   109.14  3.000
 3DJ  H3   N    CA   110.50  3.000
 3DJ  H7   CB   H6   106.02  3.000
 3DJ  H7   CB   CA   109.05  3.000
 3DJ  H6   CB   CA   110.98  3.000
 3DJ  H7   CB   C1   109.88  3.000
 3DJ  H6   CB   C1   107.58  3.000
 3DJ  CA   CB   C1   113.08  3.000
 3DJ  CG   CD2  CE2  119.11  3.000
 3DJ  CE2  CD2  C1   119.78  3.000
 3DJ  CG   CD2  C1   121.09  3.000
 3DJ  H8   CE2  CZ   118.39  3.000
 3DJ  H8   CE2  CD2  119.88  3.000
 3DJ  CZ   CE2  CD2  121.73  3.000
 3DJ  H9   CZ   CE1  120.12  3.000
 3DJ  H9   CZ   CE2  120.57  3.000
 3DJ  CE1  CZ   CE2  119.30  3.000
 3DJ  H10  CE1  CD1  118.92  3.000
 3DJ  H10  CE1  CZ   120.48  3.000
 3DJ  CD1  CE1  CZ   120.60  3.000
 3DJ  CG   CD1  O3   119.67  3.000
 3DJ  O3   CD1  CE1  119.12  3.000
 3DJ  CG   CD1  CE1  121.19  3.000
 3DJ  H11  O3   CD1  110.26  3.000
 3DJ  N1   CG   CD1  117.66  3.000
 3DJ  CD1  CG   CD2  118.06  3.000
 3DJ  N1   CG   CD2  124.25  3.000
 3DJ  H13  N1   H12  115.04  3.000
 3DJ  H13  N1   CG   117.52  3.000
 3DJ  H12  N1   CG   116.77  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
 3DJ  CONST_01  CE1  CD1  CG   CD2     0.00   0.0  0
 3DJ  CONST_02  CE1  CZ   CE2  CD2     0.00   0.0  0
 3DJ  CONST_03  CD1  CG   CD2  CE2     0.00   0.0  0
 3DJ  CONST_04  CD1  CE1  CZ   CE2     0.00   0.0  0
 3DJ  CONST_05  CG   CD2  CE2  CZ      0.00   0.0  0
 3DJ  CONST_06  CG   CD1  CE1  CZ      0.00   0.0  0
 3DJ  CONST_07  CD1  CG   CD2  C1    180.00   0.0  0
 3DJ  CONST_08  CZ   CE2  CD2  C1    180.00   0.0  0
 3DJ  CONST_09  O3   CD1  CG   CD2   180.00   0.0  0
 3DJ  CONST_10  N1   CG   CD2  CE2   180.00   0.0  0
 3DJ  CONST_11  O3   CD1  CE1  CZ    180.00   0.0  0
 3DJ  CONST_12  N1   CG   CD1  CE1   180.00   0.0  0
 3DJ  CONST_13  H9   CZ   CE2  CD2   180.00   0.0  0
 3DJ  CONST_14  H10  CE1  CZ   CE2   180.00   0.0  0
 3DJ  CONST_15  H8   CE2  CZ   CE1   180.00   0.0  0
 3DJ  CONST_16  H12  N1   CG   CD2     0.00   0.0  0
 3DJ  CONST_18  H1   OXT  C    O       0.00   0.0  0
 3DJ  Var_01    CG   CD2  C1   CB   -175.28  30.0  2
 3DJ  Var_02    CD2  C1   CB   CA    172.24  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
 3DJ  chir_01  CA  N  C  CB  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
 3DJ  plan-1  C1   0.020
 3DJ  plan-1  CD2  0.020
 3DJ  plan-1  CE2  0.020
 3DJ  plan-1  CZ   0.020
 3DJ  plan-1  CE1  0.020
 3DJ  plan-1  CD1  0.020
 3DJ  plan-1  O3   0.020
 3DJ  plan-1  CG   0.020
 3DJ  plan-1  N1   0.020
 3DJ  plan-1  H8   0.020
 3DJ  plan-1  H9   0.020
 3DJ  plan-1  H10  0.020
 3DJ  plan-2  CG   0.020
 3DJ  plan-2  N1   0.020
 3DJ  plan-2  H12  0.020
 3DJ  plan-2  H13  0.020
 3DJ  plan-3  C1   0.020
 3DJ  plan-3  CB   0.020
 3DJ  plan-3  O2   0.020
 3DJ  plan-3  CD2  0.020
 3DJ  plan-4  C    0.020
 3DJ  plan-4  OXT  0.020
 3DJ  plan-4  CA   0.020
 3DJ  plan-4  H1   0.020
 3DJ  plan-4  O    0.020

