# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:34:37 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2R,4S,5S)-5-amino-2-benzyl-4-hydroxy-6-phenylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)C[C@@H](Cc2ccccc2)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
 PJJ  PJJ  '(2R,4S,5S)-5-amino-2-benzyl-4-hydroxy-6-phenylhexanoic acid'  peptide  45  23  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PJJ
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
 PJJ  N    N  NH2    0  -0.802  -2.3995   1.7134   0.5349
 PJJ  C1   C  CH1    0  -0.093  -2.1450   0.3724   0.0285
 PJJ  C2   C  CH1    0   0.047  -0.7346   0.3027  -0.5762
 PJJ  O1   O  OH1    0  -0.675  -0.5638   1.2904  -1.5755
 PJJ  C3   C  CH2    0  -0.534  -3.1986  -0.1252  -0.9773
 PJJ  C4   C  CR6    0   0.147  -4.5788  -0.1581  -0.3883
 PJJ  C5   C  CR16   0  -0.327  -5.4827   0.8800  -0.6027
 PJJ  C6   C  CR16   0  -0.307  -4.9717  -1.2173   0.4300
 PJJ  C7   C  CR16   0  -0.240  -6.7446   0.8614  -0.0211
 PJJ  C8   C  CR16   0  -0.240  -6.2301  -1.2411   1.0144
 PJJ  C9   C  CR16   0  -0.275  -7.1224  -0.1991   0.7910
 PJJ  C10  C  CH2    0  -0.453   0.3417   0.3773   0.4991
 PJJ  CA   C  CH1    0  -0.316   1.7736   0.2424  -0.0188
 PJJ  C    C  C      0   0.423   1.9839  -1.1169  -0.7137
 PJJ  O    O  O      0  -0.622   1.7726  -2.1310  -0.0125
 PJJ  C13  C  CH2    0  -0.492   2.7503   0.4031   1.1559
 PJJ  C14  C  C      0   0.140   4.1926   0.3348   0.7419
 PJJ  C15  C  C1     0  -0.321   4.8563   1.4742   0.2897
 PJJ  C16  C  C1     0  -0.302   4.8947  -0.8685   0.7716
 PJJ  C17  C  C1     0  -0.242   6.1812   1.4167  -0.1221
 PJJ  C18  C  C1     0  -0.244   6.2201  -0.9327   0.3620
 PJJ  C19  C  C1     0  -0.277   6.8692   0.2103  -0.0872
 PJJ  OXT  O  OC    -1  -0.614   2.3403  -1.1126  -1.9077
 PJJ  H1   H  HNH2   0   0.338  -2.7192   2.3132  -0.2170
 PJJ  H3   H  HCH1   0   0.231  -2.1575  -0.3076   0.8869
 PJJ  H4   H  HCH1   0   0.221  -0.6468  -0.6585  -1.0944
 PJJ  H5   H  HOH1   0   0.438  -0.5112   2.1438  -1.1307
 PJJ  H6   H  HCH2   0   0.241  -3.1841   0.5227  -1.8590
 PJJ  H7   H  HCH2   0   0.241  -2.9171  -1.1267  -1.3146
 PJJ  H8   H  HCR6   0   0.243  -5.2012   1.7094  -1.2416
 PJJ  H9   H  HCR6   0   0.244  -4.2828  -2.0358   0.6074
 PJJ  H10  H  HCR6   0   0.252  -7.4349   1.6748  -0.2059
 PJJ  H11  H  HCR6   0   0.251  -6.5164  -2.0753   1.6425
 PJJ  H12  H  HCR6   0   0.252  -8.1056  -0.2159   1.2434
 PJJ  H13  H  HCH2   0   0.217   0.2328   1.3193   1.0496
 PJJ  H14  H  HCH2   0   0.214   0.1575  -0.4196   1.2252
 PJJ  H15  H  HCH1   0   0.200   1.9705   1.0447  -0.7367
 PJJ  H16  H  HCH2   0   0.229   2.5575   1.3650   1.6401
 PJJ  H17  H  HCH2   0   0.228   2.5410  -0.3708   1.8979
 PJJ  H18  H  H      0   0.239   4.3281   2.4210   0.2653
 PJJ  H19  H  H      0   0.239   4.3931  -1.7657   1.1130
 PJJ  H20  H  H      0   0.249   6.6779   2.3156  -0.4653
 PJJ  H21  H  H      0   0.248   6.7483  -1.8775   0.3944
 PJJ  H22  H  H      0   0.249   7.9036   0.1615  -0.4031
 PJJ  H2   H  HNH2   0   0.353  -3.1550   1.6941   1.2066

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
 PJJ  N    C1   single    1.456  0.020  1.456
 PJJ  C1   C2   single    1.536  0.020  1.536
 PJJ  C1   C3   single    1.539  0.020  1.539
 PJJ  C2   O1   single    1.415  0.020  1.415
 PJJ  C2   C10  single    1.523  0.020  1.523
 PJJ  C3   C4   single    1.501  0.020  1.501
 PJJ  C4   C5   aromatic  1.393  0.020  1.393
 PJJ  C4   C6   aromatic  1.395  0.020  1.395
 PJJ  C5   C7   aromatic  1.390  0.020  1.390
 PJJ  C6   C8   aromatic  1.388  0.020  1.388
 PJJ  C7   C9   aromatic  1.388  0.020  1.388
 PJJ  C8   C9   aromatic  1.390  0.020  1.390
 PJJ  C10  CA   single    1.529  0.020  1.529
 PJJ  CA   C    single    1.525  0.021  1.525
 PJJ  CA   C13  single    1.536  0.020  1.536
 PJJ  C    O    deloc     1.231  0.020  1.231
 PJJ  C    OXT  deloc     1.246  0.020  1.246
 PJJ  C13  C14  single    1.502  0.020  1.502
 PJJ  C14  C15  aromatic  1.394  0.020  1.394
 PJJ  C14  C16  aromatic  1.393  0.020  1.393
 PJJ  C15  C17  aromatic  1.389  0.020  1.389
 PJJ  C16  C18  aromatic  1.389  0.020  1.389
 PJJ  C17  C19  aromatic  1.389  0.020  1.389
 PJJ  C18  C19  aromatic  1.389  0.020  1.389
 PJJ  N    H1   single    0.890  0.020  1.040
 PJJ  N    H2   single    0.890  0.020  1.040
 PJJ  C1   H3   single    0.970  0.020  1.090
 PJJ  C2   H4   single    0.970  0.020  1.090
 PJJ  O1   H5   single    0.850  0.020  0.980
 PJJ  C3   H6   single    0.970  0.020  1.090
 PJJ  C3   H7   single    0.970  0.020  1.090
 PJJ  C5   H8   single    0.930  0.020  1.080
 PJJ  C6   H9   single    0.930  0.020  1.080
 PJJ  C7   H10  single    0.930  0.020  1.080
 PJJ  C8   H11  single    0.930  0.020  1.080
 PJJ  C9   H12  single    0.930  0.020  1.080
 PJJ  C10  H13  single    0.970  0.020  1.090
 PJJ  C10  H14  single    0.970  0.020  1.090
 PJJ  CA   H15  single    0.970  0.020  1.090
 PJJ  C13  H16  single    0.970  0.020  1.090
 PJJ  C13  H17  single    0.970  0.020  1.090
 PJJ  C15  H18  single    0.930  0.020  1.080
 PJJ  C16  H19  single    0.930  0.020  1.080
 PJJ  C17  H20  single    0.930  0.020  1.080
 PJJ  C18  H21  single    0.930  0.020  1.080
 PJJ  C19  H22  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
 PJJ  H2   N    H1   105.57  3.000
 PJJ  H2   N    C1   110.13  3.000
 PJJ  H1   N    C1   110.01  3.000
 PJJ  H3   C1   C3   107.67  3.000
 PJJ  H3   C1   C2   106.91  3.000
 PJJ  C3   C1   C2   110.89  3.000
 PJJ  H3   C1   N    107.29  3.000
 PJJ  C3   C1   N    113.91  3.000
 PJJ  C2   C1   N    109.83  3.000
 PJJ  H4   C2   C10  108.68  3.000
 PJJ  H4   C2   O1   105.58  3.000
 PJJ  C10  C2   O1   112.27  3.000
 PJJ  H4   C2   C1   107.43  3.000
 PJJ  C10  C2   C1   111.63  3.000
 PJJ  O1   C2   C1   110.92  3.000
 PJJ  H5   O1   C2   107.38  3.000
 PJJ  H7   C3   H6   106.87  3.000
 PJJ  H7   C3   C4   109.73  3.000
 PJJ  H6   C3   C4   109.96  3.000
 PJJ  H7   C3   C1   108.74  3.000
 PJJ  H6   C3   C1   109.03  3.000
 PJJ  C4   C3   C1   112.34  3.000
 PJJ  C6   C4   C5   118.26  3.000
 PJJ  C6   C4   C3   120.39  3.000
 PJJ  C5   C4   C3   121.32  3.000
 PJJ  H8   C5   C7   119.52  3.000
 PJJ  H8   C5   C4   119.49  3.000
 PJJ  C7   C5   C4   120.98  3.000
 PJJ  H9   C6   C8   119.62  3.000
 PJJ  H9   C6   C4   119.35  3.000
 PJJ  C8   C6   C4   121.03  3.000
 PJJ  H10  C7   C9   120.02  3.000
 PJJ  H10  C7   C5   119.83  3.000
 PJJ  C9   C7   C5   120.15  3.000
 PJJ  H11  C8   C9   120.08  3.000
 PJJ  H11  C8   C6   119.82  3.000
 PJJ  C9   C8   C6   120.11  3.000
 PJJ  H12  C9   C8   120.29  3.000
 PJJ  H12  C9   C7   120.24  3.000
 PJJ  C8   C9   C7   119.48  3.000
 PJJ  H14  C10  H13  106.02  3.000
 PJJ  H14  C10  CA   108.57  3.000
 PJJ  H13  C10  CA   109.82  3.000
 PJJ  H14  C10  C2   108.29  3.000
 PJJ  H13  C10  C2   109.04  3.000
 PJJ  CA   C10  C2   114.73  3.000
 PJJ  H15  CA   C13  108.09  3.000
 PJJ  H15  CA   C    109.05  3.000
 PJJ  C13  CA   C    110.51  3.000
 PJJ  H15  CA   C10  109.02  3.000
 PJJ  C13  CA   C10  109.10  3.000
 PJJ  C    CA   C10  111.01  3.000
 PJJ  OXT  C    O    126.03  3.000
 PJJ  OXT  C    CA   120.80  1.700
 PJJ  O    C    CA   120.80  1.700
 PJJ  H17  C13  H16  106.77  3.000
 PJJ  H17  C13  C14  109.81  3.000
 PJJ  H16  C13  C14  109.34  3.000
 PJJ  H17  C13  CA   108.88  3.000
 PJJ  H16  C13  CA   108.57  3.000
 PJJ  C14  C13  CA   113.26  3.000
 PJJ  C16  C14  C15  118.22  3.000
 PJJ  C16  C14  C13  121.14  3.000
 PJJ  C15  C14  C13  120.63  3.000
 PJJ  H18  C15  C17  119.62  3.000
 PJJ  H18  C15  C14  119.27  3.000
 PJJ  C17  C15  C14  121.11  3.000
 PJJ  H19  C16  C18  119.79  3.000
 PJJ  H19  C16  C14  119.25  3.000
 PJJ  C18  C16  C14  120.96  3.000
 PJJ  H20  C17  C19  120.11  3.000
 PJJ  H20  C17  C15  119.82  3.000
 PJJ  C19  C17  C15  120.07  3.000
 PJJ  H21  C18  C19  119.98  3.000
 PJJ  H21  C18  C16  119.80  3.000
 PJJ  C19  C18  C16  120.22  3.000
 PJJ  H22  C19  C18  120.25  3.000
 PJJ  H22  C19  C17  120.33  3.000
 PJJ  C18  C19  C17  119.42  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
 PJJ  CONST_01  C9   C7   C5   C4     0.00   0.0  0
 PJJ  CONST_02  C9   C8   C6   C4     0.00   0.0  0
 PJJ  CONST_03  C8   C6   C4   C5     0.00   0.0  0
 PJJ  CONST_04  C8   C9   C7   C5     0.00   0.0  0
 PJJ  CONST_05  C7   C5   C4   C6     0.00   0.0  0
 PJJ  CONST_06  C7   C9   C8   C6     0.00   0.0  0
 PJJ  CONST_07  C19  C17  C15  C14    0.00   0.0  0
 PJJ  CONST_08  C19  C18  C16  C14    0.00   0.0  0
 PJJ  CONST_09  C18  C16  C14  C15    0.00   0.0  0
 PJJ  CONST_10  C18  C19  C17  C15    0.00   0.0  0
 PJJ  CONST_11  C17  C15  C14  C16    0.00   0.0  0
 PJJ  CONST_12  C17  C19  C18  C16    0.00   0.0  0
 PJJ  CONST_13  C7   C5   C4   C3   180.00   0.0  0
 PJJ  CONST_14  C8   C6   C4   C3   180.00   0.0  0
 PJJ  CONST_15  C17  C15  C14  C13  180.00   0.0  0
 PJJ  CONST_16  C18  C16  C14  C13  180.00   0.0  0
 PJJ  CONST_17  H10  C7   C5   C4   180.00   0.0  0
 PJJ  CONST_18  H11  C8   C6   C4   180.00   0.0  0
 PJJ  CONST_19  H9   C6   C4   C5   180.00   0.0  0
 PJJ  CONST_20  H12  C9   C7   C5   180.00   0.0  0
 PJJ  CONST_21  H8   C5   C4   C6   180.00   0.0  0
 PJJ  CONST_22  H20  C17  C15  C14  180.00   0.0  0
 PJJ  CONST_23  H21  C18  C16  C14  180.00   0.0  0
 PJJ  CONST_24  H19  C16  C14  C15  180.00   0.0  0
 PJJ  CONST_25  H22  C19  C17  C15  180.00   0.0  0
 PJJ  CONST_26  H18  C15  C14  C16  180.00   0.0  0
 PJJ  Var_01    C5   C4   C3   C1    97.73  30.0  2
 PJJ  Var_02    C15  C14  C13  CA    85.57  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
 PJJ  chir_01  C1  N    C2  C3   positiv
 PJJ  chir_02  C2  O1   C1  C10  positiv
 PJJ  chir_03  CA  C13  C   C10  negativ

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
 PJJ  plan-1  C3   0.020
 PJJ  plan-1  C4   0.020
 PJJ  plan-1  C5   0.020
 PJJ  plan-1  C6   0.020
 PJJ  plan-1  C7   0.020
 PJJ  plan-1  C8   0.020
 PJJ  plan-1  C9   0.020
 PJJ  plan-1  H8   0.020
 PJJ  plan-1  H9   0.020
 PJJ  plan-1  H10  0.020
 PJJ  plan-1  H11  0.020
 PJJ  plan-1  H12  0.020
 PJJ  plan-2  C13  0.020
 PJJ  plan-2  C14  0.020
 PJJ  plan-2  C15  0.020
 PJJ  plan-2  C16  0.020
 PJJ  plan-2  C17  0.020
 PJJ  plan-2  C18  0.020
 PJJ  plan-2  C19  0.020
 PJJ  plan-2  H18  0.020
 PJJ  plan-2  H19  0.020
 PJJ  plan-2  H20  0.020
 PJJ  plan-2  H21  0.020
 PJJ  plan-2  H22  0.020
 PJJ  plan-3  CA   0.020
 PJJ  plan-3  C    0.020
 PJJ  plan-3  O    0.020
 PJJ  plan-3  OXT  0.020

