# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 06:11:26 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  65  34  .  2021-08-24  2021-08-24  
;
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   0.521    4.4173   2.7120   0.1970
 TJE  O2   O  O     0  -0.491    3.5681   2.6294   1.0697
 TJE  C10  C  CH3   0  -0.782    5.4600   3.8055   0.1761
 TJE  N1   N  NH1   0  -0.624    4.5244   1.8391  -0.8251
 TJE  C8   C  CH1   0  -0.192    3.6632   0.7167  -1.0676
 TJE  C11  C  C     0   0.564    2.2721   1.1610  -1.5304
 TJE  O3   O  O     0  -0.461    1.8818   2.3114  -1.4702
 TJE  C7   C  CH2   0  -0.548    3.5588  -0.2700   0.1183
 TJE  C4   C  CR6   0   0.131    4.9087  -0.7051   0.6118
 TJE  C3   C  CR16  0  -0.299    5.4744  -0.1637   1.7630
 TJE  C5   C  CR16  0  -0.291    5.6450  -1.6611  -0.0819
 TJE  C2   C  CR16  0  -0.325    6.7265  -0.5563   2.2105
 TJE  C6   C  CR16  0  -0.370    6.9002  -2.0646   0.3479
 TJE  C1   C  CR6   0   0.338    7.4498  -1.5116   1.5017
 TJE  O1   O  OH1   0  -0.635    8.6644  -1.8650   1.9724
 TJE  N2   N  NH1   0  -0.633    1.5209   0.1524  -2.0225
 TJE  C12  C  CH1   0  -0.343    0.1076   0.2657  -2.3025
 TJE  C13  C  CH3   0  -0.681   -0.2839  -0.5844  -3.5021
 TJE  P1   P  P     0   1.259   -0.7696  -0.2692  -0.7756
 TJE  O4   O  OH1   0  -0.746   -0.2647   0.7373   0.3841
 TJE  C14  C  CH2   0  -0.733   -2.5403   0.0523  -0.9919
 TJE  C15  C  CH1   0  -0.365   -3.3576  -0.3924   0.2250
 TJE  C16  C  CH2   0  -0.410   -4.8222   0.0367   0.0569
 TJE  C17  C  CH2   0  -0.524   -5.7072  -0.3125   1.2551
 TJE  C18  C  CR6   0   0.139   -7.1065   0.2045   1.0705
 TJE  C19  C  CR16  0  -0.308   -8.0326  -0.5134   0.3157
 TJE  C20  C  CR16  0  -0.239   -9.3148  -0.0247   0.1073
 TJE  C21  C  CR16  0  -0.273   -9.6940   1.1948   0.6546
 TJE  C22  C  CR16  0  -0.240   -8.7806   1.9190   1.4090
 TJE  C23  C  CR16  0  -0.315   -7.4979   1.4261   1.6129
 TJE  C24  C  C     0   0.553   -3.2982  -1.8986   0.3788
 TJE  O5   O  OH1   0  -0.588   -2.9729  -2.2790   1.6057
 TJE  O6   O  O     0  -0.444   -3.5774  -2.6688  -0.5061
 TJE  O7   O  O     0  -0.706   -0.4589  -1.6745  -0.3855
 TJE  H10  H  HCH3  0   0.259    5.3700   4.4306   1.0604
 TJE  H11  H  HCH3  0   0.260    6.4665   3.3866   0.1438
 TJE  H12  H  HCH3  0   0.265    5.3419   4.4335  -0.7081
 TJE  H9   H  HNH1  0   0.405    5.2578   1.9922  -1.4966
 TJE  H8   H  HCH1  0   0.297    4.1203   0.1722  -1.8984
 TJE  H6   H  HCH2  0   0.274    2.9793   0.1781   0.9231
 TJE  H7   H  HCH2  0   0.253    2.9990  -1.1471  -0.2143
 TJE  H3   H  HCR6  0   0.247    4.9266   0.5811   2.3269
 TJE  H4   H  HCR6  0   0.250    5.2335  -2.1119  -0.9785
 TJE  H2   H  HCR6  0   0.259    7.1445  -0.1242   3.1116
 TJE  H5   H  HCR6  0   0.268    7.4484  -2.8122  -0.2145
 TJE  H1   H  HOH1  0   0.473    9.0569  -2.5429   1.4114
 TJE  H13  H  HNH1  0   0.406    1.9070  -0.7789  -2.0431
 TJE  H14  H  HCH1  0   0.301   -0.1268   1.3127  -2.5041
 TJE  H15  H  HCH3  0   0.266    0.2576  -0.2476  -4.3852
 TJE  H16  H  HCH3  0   0.244   -0.0552  -1.6380  -3.3396
 TJE  H17  H  HCH3  0   0.253   -1.3493  -0.5001  -3.7127
 TJE  H18  H  HOH1  0   0.484   -0.2564   1.6753   0.1533
 TJE  H19  H  HCH2  0   0.300   -2.6867   1.1210  -1.1678
 TJE  H20  H  HCH2  0   0.291   -2.8889  -0.4658  -1.8884
 TJE  H21  H  HCH1  0   0.279   -2.9632   0.0826   1.1270
 TJE  H22  H  HCH2  0   0.255   -4.8390   1.1185  -0.0968
 TJE  H23  H  HCH2  0   0.242   -5.2305  -0.4130  -0.8526
 TJE  H24  H  HCH2  0   0.251   -5.7405  -1.3955   1.3986
 TJE  H25  H  HCH2  0   0.250   -5.2684   0.1097   2.1626
 TJE  H26  H  HCR6  0   0.245   -7.7486  -1.4689  -0.1111
 TJE  H27  H  HCR6  0   0.253  -10.0199  -0.5976  -0.4813
 TJE  H28  H  HCR6  0   0.253  -10.6950   1.5751   0.4969
 TJE  H29  H  HCR6  0   0.253   -9.0666   2.8688   1.8425
 TJE  H30  H  HCR6  0   0.247   -6.7938   1.9963   2.2079
 TJE  H31  H  HOH1  0   0.478   -2.9872  -3.2465   1.6682

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  1.393  0.020  1.393
 TJE  C2   C3   aromatic  1.386  0.020  1.386
 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    1.502  0.020  1.502
 TJE  O6   C24  double    1.206  0.020  1.206
 TJE  O5   C24  single    1.325  0.020  1.325
 TJE  C24  C15  single    1.515  0.020  1.515
 TJE  C22  C23  aromatic  1.389  0.020  1.389
 TJE  C22  C21  aromatic  1.388  0.020  1.388
 TJE  C7   C8   single    1.546  0.020  1.546
 TJE  C23  C18  aromatic  1.393  0.020  1.393
 TJE  C21  C20  aromatic  1.389  0.020  1.389
 TJE  C16  C15  single    1.535  0.020  1.535
 TJE  C16  C17  single    1.530  0.020  1.530
 TJE  C15  C14  single    1.532  0.020  1.532
 TJE  C18  C17  single    1.503  0.020  1.503
 TJE  C18  C19  aromatic  1.394  0.020  1.394
 TJE  C8   N1   single    1.435  0.020  1.435
 TJE  C8   C11  single    1.532  0.020  1.532
 TJE  O7   P1   double    1.491  0.020  1.491
 TJE  N1   C9   single    1.348  0.020  1.348
 TJE  C20  C19  aromatic  1.388  0.020  1.388
 TJE  C9   O2   double    1.220  0.020  1.220
 TJE  C9   C10  single    1.511  0.020  1.511
 TJE  C14  P1   single    1.813  0.020  1.813
 TJE  C11  O3   double    1.216  0.020  1.216
 TJE  C11  N2   single    1.350  0.020  1.350
 TJE  P1   O4   single    1.616  0.020  1.616
 TJE  P1   C12  single    1.840  0.020  1.840
 TJE  N2   C12  single    1.445  0.020  1.445
 TJE  C12  C13  single    1.521  0.020  1.521
 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    0.860  0.020  1.020
 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  O4   H18  single    0.850  0.020  0.980
 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
 TJE  O5   H31  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
 TJE  N1   C9   C10  113.78  3.000
 TJE  C10  C9   O2   122.61  3.000
 TJE  N1   C9   O2   123.61  3.000
 TJE  H12  C10  H11  107.28  3.000
 TJE  H12  C10  H10  108.63  3.000
 TJE  H11  C10  H10  108.76  3.000
 TJE  H12  C10  C9   110.67  3.000
 TJE  H11  C10  C9   111.05  3.000
 TJE  H10  C10  C9   110.36  3.000
 TJE  H9   N1   C8   116.34  3.000
 TJE  H9   N1   C9   117.73  3.000
 TJE  C8   N1   C9   125.91  3.000
 TJE  H8   C8   C7   107.05  3.000
 TJE  H8   C8   C11  107.13  3.000
 TJE  C7   C8   C11  110.82  3.000
 TJE  H8   C8   N1   105.48  3.000
 TJE  C11  C8   N1   111.66  3.000
 TJE  C7   C8   N1   114.21  3.000
 TJE  N2   C11  O3   123.09  3.000
 TJE  N2   C11  C8   113.49  3.000
 TJE  O3   C11  C8   123.42  3.000
 TJE  H7   C7   H6   106.43  3.000
 TJE  H7   C7   C4   109.15  3.000
 TJE  H6   C7   C4   110.79  3.000
 TJE  H7   C7   C8   108.27  3.000
 TJE  H6   C7   C8   109.90  3.000
 TJE  C4   C7   C8   112.10  3.000
 TJE  C5   C4   C3   117.66  3.000
 TJE  C5   C4   C7   120.71  3.000
 TJE  C3   C4   C7   121.62  3.000
 TJE  H3   C3   C2   118.91  3.000
 TJE  H3   C3   C4   119.50  3.000
 TJE  C2   C3   C4   121.58  3.000
 TJE  H4   C5   C6   118.60  3.000
 TJE  H4   C5   C4   119.79  3.000
 TJE  C6   C5   C4   121.61  3.000
 TJE  H2   C2   C1   119.78  3.000
 TJE  H2   C2   C3   120.27  3.000
 TJE  C1   C2   C3   119.94  3.000
 TJE  H5   C6   C1   120.27  3.000
 TJE  H5   C6   C5   119.83  3.000
 TJE  C1   C6   C5   119.90  3.000
 TJE  O1   C1   C6   122.69  3.000
 TJE  C6   C1   C2   119.29  3.000
 TJE  O1   C1   C2   118.01  3.000
 TJE  H1   O1   C1   110.35  3.000
 TJE  H13  N2   C12  116.29  3.000
 TJE  H13  N2   C11  118.96  3.000
 TJE  C12  N2   C11  123.78  3.000
 TJE  H14  C12  P1   109.24  3.000
 TJE  H14  C12  C13  109.58  3.000
 TJE  P1   C12  C13  111.66  3.000
 TJE  H14  C12  N2   108.72  3.000
 TJE  C13  C12  N2   111.14  3.000
 TJE  P1   C12  N2   106.41  3.000
 TJE  H17  C13  H16  107.99  3.000
 TJE  H17  C13  H15  107.79  3.000
 TJE  H16  C13  H15  108.38  3.000
 TJE  H17  C13  C12  111.15  3.000
 TJE  H16  C13  C12  111.62  3.000
 TJE  H15  C13  C12  109.78  3.000
 TJE  O7   P1   C14  113.70  3.000
 TJE  C14  P1   O4   106.28  3.000
 TJE  O7   P1   O4   109.51  3.000
 TJE  O4   P1   C12  105.39  3.000
 TJE  C14  P1   C12  108.36  3.000
 TJE  O7   P1   C12  113.06  3.000
 TJE  H18  O4   P1   115.84  3.000
 TJE  H20  C14  H19  106.79  3.000
 TJE  H20  C14  C15  110.11  3.000
 TJE  H19  C14  C15  109.90  3.000
 TJE  H20  C14  P1   109.00  3.000
 TJE  H19  C14  P1   108.88  3.000
 TJE  C15  C14  P1   112.02  3.000
 TJE  H21  C15  C24  109.52  3.000
 TJE  H21  C15  C16  108.25  3.000
 TJE  C24  C15  C16  109.05  3.000
 TJE  H21  C15  C14  109.68  3.000
 TJE  C16  C15  C14  109.93  3.000
 TJE  C24  C15  C14  110.38  3.000
 TJE  H23  C16  H22  106.51  3.000
 TJE  H23  C16  C17  109.97  3.000
 TJE  H22  C16  C17  109.10  3.000
 TJE  H23  C16  C15  109.41  3.000
 TJE  H22  C16  C15  107.87  3.000
 TJE  C17  C16  C15  113.72  3.000
 TJE  H25  C17  H24  106.62  3.000
 TJE  H25  C17  C18  110.05  3.000
 TJE  H24  C17  C18  109.18  3.000
 TJE  H25  C17  C16  109.26  3.000
 TJE  H24  C17  C16  110.28  3.000
 TJE  C18  C17  C16  111.34  3.000
 TJE  C23  C18  C19  118.43  3.000
 TJE  C19  C18  C17  120.52  3.000
 TJE  C23  C18  C17  121.03  3.000
 TJE  H26  C19  C20  119.55  3.000
 TJE  H26  C19  C18  119.54  3.000
 TJE  C20  C19  C18  120.91  3.000
 TJE  H27  C20  C21  120.07  3.000
 TJE  H27  C20  C19  119.80  3.000
 TJE  C21  C20  C19  120.13  3.000
 TJE  H28  C21  C22  120.28  3.000
 TJE  H28  C21  C20  120.22  3.000
 TJE  C22  C21  C20  119.49  3.000
 TJE  H29  C22  C23  119.77  3.000
 TJE  H29  C22  C21  120.09  3.000
 TJE  C23  C22  C21  120.14  3.000
 TJE  H30  C23  C22  119.59  3.000
 TJE  H30  C23  C18  119.51  3.000
 TJE  C22  C23  C18  120.90  3.000
 TJE  O6   C24  O5   123.56  3.000
 TJE  O5   C24  C15  112.89  3.000
 TJE  O6   C24  C15  123.46  3.000
 TJE  H31  O5   C24  110.03  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_30  C12  N2   C11  C8   180.00   0.0  0
 TJE  CONST_31  C12  N2   C11  O3     0.00   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  CONST_34  H31  O5   C24  C15  180.00   0.0  0
 TJE  Var_01    C3   C4   C7   C8   101.80  30.0  3
 TJE  Var_02    C23  C18  C17  C16  -95.74  30.0  2
 TJE  Var_03    C18  C17  C16  C15  176.53  30.0  3
 TJE  Var_04    C15  C14  P1   C12  178.75  30.0  1
 TJE  Var_05    H10  C10  C9   O2     3.68  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
 TJE  chir_05  P1   C14  O4   C12  both

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
 TJE  plan-5  H31  0.020

