# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 19:11:11 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (2S)-2-{[(S)-{(1R)-1-[(N-acetyl-L-tyrosyl)amino]ethyl}(hydroxy)phosphoryl]methyl}-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](Cc1ccc(O)cc1)NC(C)=O)[P](O)(=O)C[C@@H](CCc2ccccc2)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
 TJE  TJE  '(2S)-2-{[(S)-{(1R)-1-[(N-acetyl-L-tyrosyl)amino]ethyl}(hydroxy)phosphoryl]methyl}-4-phenylbutanoic acid'  ligand  63  34  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJE
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
 TJE  C9   C  C      0   0.520    4.5417   2.8297   0.0283
 TJE  O2   O  O      0  -0.495    3.6686   2.8630   0.8816
 TJE  C10  C  CH3    0  -0.779    5.6765   3.8287  -0.0031
 TJE  N1   N  NH1    0  -0.624    4.6145   1.8898  -0.9341
 TJE  C8   C  CH1    0  -0.199    3.6673   0.8320  -1.1594
 TJE  C11  C  C      0   0.556    2.3454   1.3618  -1.7310
 TJE  O3   O  O      0  -0.477    2.0643   2.5467  -1.7466
 TJE  C7   C  CH2    0  -0.548    3.4140  -0.0634   0.0740
 TJE  C4   C  CR6    0   0.135    4.6900  -0.6148   0.6415
 TJE  C3   C  CR16   0  -0.301    5.2966  -0.0578   1.7643
 TJE  C5   C  CR16   0  -0.293    5.3177  -1.7041   0.0440
 TJE  C2   C  CR16   0  -0.325    6.4827  -0.5628   2.2756
 TJE  C6   C  CR16   0  -0.370    6.5060  -2.2216   0.5378
 TJE  C1   C  CR6    0   0.336    7.0969  -1.6511   1.6620
 TJE  O1   O  OH1    0  -0.636    8.2498  -2.1121   2.1929
 TJE  N2   N  NH1    0  -0.623    1.5622   0.3922  -2.2408
 TJE  C12  C  CH1    0  -0.326    0.1188   0.5050  -2.3817
 TJE  C13  C  CH3    0  -0.671   -0.3535  -0.2220  -3.6300
 TJE  P1   P  P      0   1.198   -0.5600  -0.1922  -0.7873
 TJE  O4   O  OP    -1  -0.806   -0.1384   0.7440   0.3272
 TJE  C14  C  CH2    0  -0.703   -2.3781  -0.0805  -1.0096
 TJE  C15  C  CH1    0  -0.319   -3.1585  -0.3838   0.2698
 TJE  C16  C  CH2    0  -0.394   -4.6356  -0.0319   0.0822
 TJE  C17  C  CH2    0  -0.513   -5.4813  -0.2498   1.3395
 TJE  C18  C  C      0   0.143   -6.9052   0.1832   1.1355
 TJE  C19  C  C1     0  -0.316   -7.8526  -0.7010   0.6223
 TJE  C20  C  C1     0  -0.240   -9.1599  -0.2942   0.3902
 TJE  C21  C  C1     0  -0.276   -9.5433   1.0119   0.6680
 TJE  C22  C  C1     0  -0.240   -8.6089   1.9041   1.1785
 TJE  C23  C  C1     0  -0.315   -7.3029   1.4911   1.4083
 TJE  C24  C  C      0   0.418   -3.0155  -1.8622   0.6818
 TJE  O5   O  OC    -1  -0.626   -2.5532  -2.1059   1.8146
 TJE  O6   O  O      0  -0.625   -3.4158  -2.7081  -0.1458
 TJE  O7   O  O      0  -0.818   -0.1046  -1.6399  -0.7411
 TJE  H10  H  HCH3   0   0.257    5.4713   4.6512   0.6771
 TJE  H11  H  HCH3   0   0.264    6.6073   3.3499   0.3061
 TJE  H12  H  HCH3   0   0.256    5.8330   4.2305  -1.0044
 TJE  H9   H  HNH1   0   0.401    5.3653   1.9653  -1.5994
 TJE  H8   H  HCH1   0   0.285    4.1225   0.1985  -1.9265
 TJE  H6   H  HCH2   0   0.272    2.8547   0.4930   0.8220
 TJE  H7   H  HCH2   0   0.249    2.7654  -0.8882  -0.2303
 TJE  H3   H  HCR6   0   0.245    4.8346   0.7904   2.2546
 TJE  H4   H  HCR6   0   0.248    4.8696  -2.1706  -0.8267
 TJE  H2   H  HCR6   0   0.257    6.9342  -0.1155   3.1529
 TJE  H5   H  HCR6   0   0.266    6.9677  -3.0723   0.0488
 TJE  H1   H  HOH1   0   0.472    8.5758  -2.8623   1.6835
 TJE  H13  H  HNH1   0   0.383    1.8807  -0.5582  -2.1190
 TJE  H14  H  HCH1   0   0.244   -0.1320   1.5638  -2.4578
 TJE  H15  H  HCH3   0   0.231    0.1317   0.1726  -4.5242
 TJE  H16  H  HCH3   0   0.221   -0.1377  -1.2899  -3.5682
 TJE  H17  H  HCH3   0   0.233   -1.4302  -0.1117  -3.7593
 TJE  H19  H  HCH2   0   0.221   -2.6089   0.9362  -1.3497
 TJE  H20  H  HCH2   0   0.225   -2.7037  -0.7566  -1.8037
 TJE  H21  H  HCH1   0   0.194   -2.7607   0.2446   1.0733
 TJE  H22  H  HCH2   0   0.213   -4.7193   1.0170  -0.2220
 TJE  H23  H  HCH2   0   0.210   -5.0500  -0.6243  -0.7393
 TJE  H24  H  HCH2   0   0.239   -5.4579  -1.3058   1.6191
 TJE  H25  H  HCH2   0   0.230   -5.0392   0.3056   2.1715
 TJE  H26  H  H      0   0.243   -7.5614  -1.7221   0.4023
 TJE  H27  H  H      0   0.250   -9.8814  -0.9989  -0.0042
 TJE  H28  H  H      0   0.250  -10.5626   1.3302   0.4905
 TJE  H29  H  H      0   0.250   -8.8973   2.9235   1.4022
 TJE  H30  H  H      0   0.243   -6.5812   2.1943   1.8087

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
 TJE  O1   C1   single    1.350  0.020  1.350
 TJE  C1   C2   aromatic  1.392  0.020  1.392
 TJE  C1   C6   aromatic  1.392  0.020  1.392
 TJE  C2   C3   aromatic  1.387  0.020  1.387
 TJE  C6   C5   aromatic  1.387  0.020  1.387
 TJE  C3   C4   aromatic  1.392  0.020  1.392
 TJE  C5   C4   aromatic  1.392  0.020  1.392
 TJE  C4   C7   single    1.501  0.020  1.501
 TJE  O6   C24  deloc     1.249  0.020  1.249
 TJE  O5   C24  deloc     1.248  0.020  1.248
 TJE  C24  C15  single    1.541  0.020  1.541
 TJE  C22  C23  aromatic  1.389  0.020  1.389
 TJE  C22  C21  aromatic  1.389  0.020  1.389
 TJE  C7   C8   single    1.545  0.020  1.545
 TJE  C23  C18  aromatic  1.394  0.020  1.394
 TJE  C21  C20  aromatic  1.389  0.020  1.389
 TJE  C16  C15  single    1.530  0.020  1.530
 TJE  C16  C17  single    1.531  0.020  1.531
 TJE  C15  C14  single    1.529  0.020  1.529
 TJE  C18  C17  single    1.502  0.020  1.502
 TJE  C18  C19  aromatic  1.394  0.020  1.394
 TJE  C8   N1   single    1.438  0.020  1.438
 TJE  C8   C11  single    1.535  0.020  1.535
 TJE  O7   P1   deloc     1.518  0.020  1.518
 TJE  N1   C9   single    1.347  0.020  1.347
 TJE  C20  C19  aromatic  1.389  0.020  1.389
 TJE  C9   O2   double    1.221  0.020  1.221
 TJE  C9   C10  single    1.512  0.020  1.512
 TJE  C14  P1   single    1.835  0.020  1.835
 TJE  C11  O3   double    1.218  0.020  1.218
 TJE  C11  N2   single    1.347  0.020  1.347
 TJE  P1   O4   deloc     1.515  0.020  1.515
 TJE  P1   C12  single    1.868  0.020  1.868
 TJE  N2   C12  single    1.455  0.020  1.455
 TJE  C12  C13  single    1.520  0.020  1.520
 TJE  O1   H1   single    0.850  0.020  0.980
 TJE  C2   H2   single    0.930  0.020  1.080
 TJE  C3   H3   single    0.930  0.020  1.080
 TJE  C5   H4   single    0.930  0.020  1.080
 TJE  C6   H5   single    0.930  0.020  1.080
 TJE  C7   H6   single    0.970  0.020  1.090
 TJE  C7   H7   single    0.970  0.020  1.090
 TJE  C8   H8   single    0.970  0.020  1.090
 TJE  N1   H9   single    0.860  0.020  1.020
 TJE  C10  H10  single    0.970  0.020  1.090
 TJE  C10  H11  single    0.970  0.020  1.090
 TJE  C10  H12  single    0.970  0.020  1.090
 TJE  N2   H13  single    0.890  0.020  1.040
 TJE  C12  H14  single    0.970  0.020  1.090
 TJE  C13  H15  single    0.970  0.020  1.090
 TJE  C13  H16  single    0.970  0.020  1.090
 TJE  C13  H17  single    0.970  0.020  1.090
 TJE  C14  H19  single    0.970  0.020  1.090
 TJE  C14  H20  single    0.970  0.020  1.090
 TJE  C15  H21  single    0.970  0.020  1.090
 TJE  C16  H22  single    0.970  0.020  1.090
 TJE  C16  H23  single    0.970  0.020  1.090
 TJE  C17  H24  single    0.970  0.020  1.090
 TJE  C17  H25  single    0.970  0.020  1.090
 TJE  C19  H26  single    0.930  0.020  1.080
 TJE  C20  H27  single    0.930  0.020  1.080
 TJE  C21  H28  single    0.930  0.020  1.080
 TJE  C22  H29  single    0.930  0.020  1.080
 TJE  C23  H30  single    0.930  0.020  1.080

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
 TJE  N1   C9   C10  113.93  3.000
 TJE  C10  C9   O2   122.20  3.000
 TJE  N1   C9   O2   123.83  3.000
 TJE  H12  C10  H11  107.43  3.000
 TJE  H12  C10  H10  108.85  3.000
 TJE  H11  C10  H10  108.40  3.000
 TJE  H12  C10  C9   111.73  3.000
 TJE  H11  C10  C9   110.13  3.000
 TJE  H10  C10  C9   110.20  3.000
 TJE  H9   N1   C8   116.32  3.000
 TJE  H9   N1   C9   117.41  3.000
 TJE  C8   N1   C9   126.14  3.000
 TJE  H8   C8   C7   107.00  3.000
 TJE  H8   C8   C11  107.29  3.000
 TJE  C7   C8   C11  110.86  3.000
 TJE  H8   C8   N1   105.18  3.000
 TJE  C11  C8   N1   111.83  3.000
 TJE  C7   C8   N1   114.17  3.000
 TJE  N2   C11  O3   124.15  3.000
 TJE  N2   C11  C8   113.17  3.000
 TJE  O3   C11  C8   122.65  3.000
 TJE  H7   C7   H6   105.82  3.000
 TJE  H7   C7   C4   109.43  3.000
 TJE  H6   C7   C4   111.42  3.000
 TJE  H7   C7   C8   108.21  3.000
 TJE  H6   C7   C8   109.69  3.000
 TJE  C4   C7   C8   112.03  3.000
 TJE  C5   C4   C3   117.56  3.000
 TJE  C5   C4   C7   120.56  3.000
 TJE  C3   C4   C7   121.88  3.000
 TJE  H3   C3   C2   118.88  3.000
 TJE  H3   C3   C4   119.50  3.000
 TJE  C2   C3   C4   121.62  3.000
 TJE  H4   C5   C6   118.64  3.000
 TJE  H4   C5   C4   119.66  3.000
 TJE  C6   C5   C4   121.70  3.000
 TJE  H2   C2   C1   119.73  3.000
 TJE  H2   C2   C3   120.31  3.000
 TJE  C1   C2   C3   119.96  3.000
 TJE  H5   C6   C1   120.32  3.000
 TJE  H5   C6   C5   119.80  3.000
 TJE  C1   C6   C5   119.88  3.000
 TJE  O1   C1   C6   122.68  3.000
 TJE  C6   C1   C2   119.27  3.000
 TJE  O1   C1   C2   118.05  3.000
 TJE  H1   O1   C1   110.29  3.000
 TJE  H13  N2   C12  113.44  3.000
 TJE  H13  N2   C11  116.65  3.000
 TJE  C12  N2   C11  123.92  3.000
 TJE  H14  C12  P1   109.78  3.000
 TJE  H14  C12  C13  109.61  3.000
 TJE  P1   C12  C13  114.18  3.000
 TJE  H14  C12  N2   108.07  3.000
 TJE  C13  C12  N2   110.54  3.000
 TJE  P1   C12  N2   104.41  3.000
 TJE  H17  C13  H16  107.52  3.000
 TJE  H17  C13  H15  107.78  3.000
 TJE  H16  C13  H15  108.20  3.000
 TJE  H17  C13  C12  110.85  3.000
 TJE  H16  C13  C12  111.11  3.000
 TJE  H15  C13  C12  111.22  3.000
 TJE  O7   P1   C14  111.03  3.000
 TJE  C14  P1   O4   109.10  3.000
 TJE  O7   P1   O4   118.89  3.000
 TJE  O4   P1   C12  107.22  3.000
 TJE  C14  P1   C12  103.53  3.000
 TJE  O7   P1   C12  105.84  3.000
 TJE  H20  C14  H19  106.60  3.000
 TJE  H20  C14  C15  109.47  3.000
 TJE  H19  C14  C15  109.63  3.000
 TJE  H20  C14  P1   110.22  3.000
 TJE  H19  C14  P1   107.61  3.000
 TJE  C15  C14  P1   113.09  3.000
 TJE  H21  C15  C24  108.70  3.000
 TJE  H21  C15  C16  107.98  3.000
 TJE  C24  C15  C16  110.06  3.000
 TJE  H21  C15  C14  108.35  3.000
 TJE  C16  C15  C14  110.15  3.000
 TJE  C24  C15  C14  111.50  3.000
 TJE  H23  C16  H22  106.32  3.000
 TJE  H23  C16  C17  109.28  3.000
 TJE  H22  C16  C17  108.80  3.000
 TJE  H23  C16  C15  109.46  3.000
 TJE  H22  C16  C15  109.16  3.000
 TJE  C17  C16  C15  113.57  3.000
 TJE  H25  C17  H24  106.71  3.000
 TJE  H25  C17  C18  109.88  3.000
 TJE  H24  C17  C18  109.49  3.000
 TJE  H25  C17  C16  109.22  3.000
 TJE  H24  C17  C16  109.63  3.000
 TJE  C18  C17  C16  111.78  3.000
 TJE  C23  C18  C19  118.25  3.000
 TJE  C19  C18  C17  120.75  3.000
 TJE  C23  C18  C17  120.96  3.000
 TJE  H26  C19  C20  119.65  3.000
 TJE  H26  C19  C18  119.31  3.000
 TJE  C20  C19  C18  121.03  3.000
 TJE  H27  C20  C21  120.05  3.000
 TJE  H27  C20  C19  119.83  3.000
 TJE  C21  C20  C19  120.12  3.000
 TJE  H28  C21  C22  120.32  3.000
 TJE  H28  C21  C20  120.23  3.000
 TJE  C22  C21  C20  119.45  3.000
 TJE  H29  C22  C23  119.75  3.000
 TJE  H29  C22  C21  120.09  3.000
 TJE  C23  C22  C21  120.15  3.000
 TJE  H30  C23  C22  119.61  3.000
 TJE  H30  C23  C18  119.39  3.000
 TJE  C22  C23  C18  120.99  3.000
 TJE  O6   C24  O5   126.02  3.000
 TJE  O5   C24  C15  117.67  3.000
 TJE  O6   C24  C15  116.27  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
 TJE  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 TJE  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 TJE  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 TJE  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 TJE  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 TJE  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 TJE  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 TJE  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 TJE  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 TJE  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 TJE  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 TJE  CONST_12  C23  C18  C19  C20     0.00   0.0  0
 TJE  CONST_13  C2   C3   C4   C7    180.00   0.0  0
 TJE  CONST_14  C6   C5   C4   C7    180.00   0.0  0
 TJE  CONST_15  O1   C1   C2   C3    180.00   0.0  0
 TJE  CONST_16  O1   C1   C6   C5    180.00   0.0  0
 TJE  CONST_17  C22  C23  C18  C17   180.00   0.0  0
 TJE  CONST_18  C20  C19  C18  C17   180.00   0.0  0
 TJE  CONST_19  H2   C2   C3   C4    180.00   0.0  0
 TJE  CONST_20  H5   C6   C5   C4    180.00   0.0  0
 TJE  CONST_21  H4   C5   C4   C3    180.00   0.0  0
 TJE  CONST_22  H3   C3   C4   C5    180.00   0.0  0
 TJE  CONST_23  H29  C22  C23  C18   180.00   0.0  0
 TJE  CONST_24  H27  C20  C19  C18   180.00   0.0  0
 TJE  CONST_25  H30  C23  C18  C19   180.00   0.0  0
 TJE  CONST_26  H28  C21  C20  C19   180.00   0.0  0
 TJE  CONST_27  H26  C19  C20  C21   180.00   0.0  0
 TJE  CONST_28  C8   N1   C9   O2      0.00   0.0  0
 TJE  CONST_29  C8   N1   C9   C10   180.00   0.0  0
 TJE  CONST_32  H9   N1   C9   O2    180.00   0.0  0
 TJE  CONST_33  H13  N2   C11  C8      0.00   0.0  0
 TJE  Var_01    C3   C4   C7   C8    100.42  30.0  2
 TJE  Var_02    C23  C18  C17  C16   -89.56  30.0  3
 TJE  Var_03    C18  C17  C16  C15   176.65  30.0  3
 TJE  Var_04    C15  C14  P1   C12  -170.47  30.0  1
 TJE  Var_05    H10  C10  C9   O2    -11.95  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
 TJE  chir_01  C8   C7   N1   C11  positiv
 TJE  chir_02  C12  P1   N2   C13  negativ
 TJE  chir_04  C15  C24  C16  C14  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
 TJE  plan-1  C7   0.020
 TJE  plan-1  C4   0.020
 TJE  plan-1  C3   0.020
 TJE  plan-1  C5   0.020
 TJE  plan-1  C2   0.020
 TJE  plan-1  C6   0.020
 TJE  plan-1  C1   0.020
 TJE  plan-1  O1   0.020
 TJE  plan-1  H3   0.020
 TJE  plan-1  H4   0.020
 TJE  plan-1  H2   0.020
 TJE  plan-1  H5   0.020
 TJE  plan-2  C17  0.020
 TJE  plan-2  C18  0.020
 TJE  plan-2  C19  0.020
 TJE  plan-2  C20  0.020
 TJE  plan-2  C21  0.020
 TJE  plan-2  C22  0.020
 TJE  plan-2  C23  0.020
 TJE  plan-2  H26  0.020
 TJE  plan-2  H27  0.020
 TJE  plan-2  H28  0.020
 TJE  plan-2  H29  0.020
 TJE  plan-2  H30  0.020
 TJE  plan-3  C9   0.020
 TJE  plan-3  O2   0.020
 TJE  plan-3  C10  0.020
 TJE  plan-3  N1   0.020
 TJE  plan-3  C8   0.020
 TJE  plan-3  H9   0.020
 TJE  plan-4  C8   0.020
 TJE  plan-4  C11  0.020
 TJE  plan-4  O3   0.020
 TJE  plan-4  N2   0.020
 TJE  plan-4  C12  0.020
 TJE  plan-4  H13  0.020
 TJE  plan-5  C15  0.020
 TJE  plan-5  C24  0.020
 TJE  plan-5  O5   0.020
 TJE  plan-5  O6   0.020

