# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:01:08 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N-[(2S)-2-amino-3-phenylpropyl]-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CN[C@@H](Cc1ccccc1)C(O)=O)Cc2ccccc2
#
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
 PUK  PUK  N-[(2S)-2-amino-3-phenylpropyl]-L-phenylalanine  peptide  43  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PUK
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
 PUK  N    N  NH2    0  -0.780   1.3179   1.1740   0.1070
 PUK  C1   C  CH1    0  -0.114   1.4078  -0.2763   0.1704
 PUK  C2   C  CH2    0  -0.255   0.1484  -0.9734   0.6895
 PUK  C3   C  CH2    0  -0.515   2.6056  -0.6800   1.0376
 PUK  C4   C  CR6    0   0.170   3.9154  -0.1705   0.5110
 PUK  C5   C  CR16   0  -0.311   4.4698   1.0182   0.9792
 PUK  C6   C  CR16   0  -0.315   4.5969  -0.8700  -0.4831
 PUK  C7   C  CR16   0  -0.245   5.6722   1.4945   0.4733
 PUK  C8   C  CR16   0  -0.242   5.7977  -0.3972  -0.9968
 PUK  C9   C  CR16   0  -0.277   6.3404   0.7889  -0.5193
 PUK  N2   N  NH1    0  -0.601  -1.0015  -0.6919  -0.1431
 PUK  C10  C  CH1    0  -0.155  -2.2380  -1.2465   0.3677
 PUK  C    C  C      0   0.396  -2.2929  -2.7918   0.3036
 PUK  O    O  O      0  -0.598  -1.5544  -3.3730  -0.5110
 PUK  C12  C  CH2    0  -0.518  -3.4241  -0.7030  -0.4488
 PUK  C13  C  C      0   0.105  -3.5214   0.7968  -0.4159
 PUK  C14  C  C1     0  -0.311  -3.0178   1.5726  -1.4587
 PUK  C15  C  C1     0  -0.304  -4.0808   1.4500   0.6822
 PUK  C16  C  C1     0  -0.240  -3.0684   2.9604  -1.4084
 PUK  C17  C  C1     0  -0.241  -4.1350   2.8354   0.7368
 PUK  C18  C  C1     0  -0.273  -3.6272   3.5972  -0.3091
 PUK  OXT  O  OC    -1  -0.620  -3.1281  -3.3218   1.0658
 PUK  H    H  HNH2   0   0.342   0.6384   1.4655  -0.5832
 PUK  H1   H  HCH1   0   0.227   1.5894  -0.6299  -0.8505
 PUK  H3   H  HCH2   0   0.218   0.3185  -2.0517   0.6949
 PUK  H4   H  HCH2   0   0.172  -0.0085  -0.6744   1.7430
 PUK  H5   H  HCH2   0   0.237   2.4440  -0.3142   2.0568
 PUK  H6   H  HCH2   0   0.242   2.6347  -1.7709   1.1013
 PUK  H7   H  HCR6   0   0.238   3.9571   1.5763   1.7535
 PUK  H8   H  HCR6   0   0.242   4.1851  -1.8007  -0.8579
 PUK  H9   H  HCR6   0   0.249   6.0876   2.4189   0.8546
 PUK  H10  H  HCR6   0   0.250   6.3126  -0.9591  -1.7658
 PUK  H11  H  HCR6   0   0.250   7.2786   1.1572  -0.9142
 PUK  H12  H  HNH1   0   0.323  -1.1136   0.3148  -0.1829
 PUK  H13  H  HCH1   0   0.182  -2.4014  -0.9553   1.4205
 PUK  H14  H  HCH2   0   0.238  -3.3228  -1.0428  -1.4832
 PUK  H15  H  HCH2   0   0.246  -4.3401  -1.1431  -0.0506
 PUK  H16  H  H      0   0.250  -2.5816   1.0830  -2.3219
 PUK  H17  H  H      0   0.245  -4.4848   0.8672   1.5023
 PUK  H18  H  H      0   0.252  -2.6718   3.5421  -2.2309
 PUK  H19  H  H      0   0.252  -4.5775   3.3224   1.5965
 PUK  H20  H  H      0   0.252  -3.6707   4.6780  -0.2678
 PUK  H2   H  HNH2   0   0.336   1.0109   1.5482   0.9981

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
 PUK  N    C1   single    1.454  0.020  1.454
 PUK  N    H    single    0.860  0.020  0.860
 PUK  C1   C2   single    1.530  0.020  1.530
 PUK  C1   C3   single    1.533  0.020  1.533
 PUK  C1   H1   single    0.970  0.020  1.090
 PUK  C2   H3   single    0.970  0.020  1.090
 PUK  C2   H4   single    0.970  0.020  1.090
 PUK  C2   N2   single    1.447  0.020  1.447
 PUK  C3   C4   single    1.501  0.020  1.501
 PUK  C3   H5   single    0.970  0.020  1.090
 PUK  C3   H6   single    0.970  0.020  1.090
 PUK  C4   C5   aromatic  1.393  0.020  1.393
 PUK  C4   C6   aromatic  1.394  0.020  1.394
 PUK  C5   C7   aromatic  1.389  0.020  1.389
 PUK  C5   H7   single    0.930  0.020  1.080
 PUK  C6   C8   aromatic  1.389  0.020  1.389
 PUK  C6   H8   single    0.930  0.020  1.080
 PUK  C7   C9   aromatic  1.389  0.020  1.389
 PUK  C7   H9   single    0.930  0.020  1.080
 PUK  C8   C9   aromatic  1.389  0.020  1.389
 PUK  C8   H10  single    0.930  0.020  1.080
 PUK  C9   H11  single    0.930  0.020  1.080
 PUK  N2   C10  single    1.448  0.020  1.448
 PUK  N2   H12  single    0.890  0.020  1.040
 PUK  C10  C    single    1.548  0.020  1.548
 PUK  C10  C12  single    1.539  0.020  1.539
 PUK  C10  H13  single    0.970  0.020  1.090
 PUK  C    O    deloc     1.231  0.020  1.231
 PUK  C    OXT  deloc     1.249  0.020  1.249
 PUK  C12  C13  single    1.503  0.020  1.503
 PUK  C12  H14  single    0.970  0.020  1.090
 PUK  C12  H15  single    0.970  0.020  1.090
 PUK  C13  C14  aromatic  1.394  0.020  1.394
 PUK  C13  C15  aromatic  1.395  0.020  1.395
 PUK  C14  C16  aromatic  1.390  0.020  1.390
 PUK  C14  H16  single    0.930  0.020  1.080
 PUK  C15  C17  aromatic  1.388  0.020  1.388
 PUK  C15  H17  single    0.930  0.020  1.080
 PUK  C16  C18  aromatic  1.388  0.020  1.388
 PUK  C16  H18  single    0.930  0.020  1.080
 PUK  C17  C18  aromatic  1.390  0.020  1.390
 PUK  C17  H19  single    0.930  0.020  1.080
 PUK  C18  H20  single    0.930  0.020  1.080
 PUK  N    H2   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
 PUK  H2   N    H    106.85  3.000
 PUK  H2   N    C1   110.39  3.000
 PUK  H    N    C1   111.01  3.000
 PUK  H1   C1   C3   108.22  3.000
 PUK  H1   C1   C2   107.79  3.000
 PUK  C3   C1   C2   109.34  3.000
 PUK  H1   C1   N    106.95  3.000
 PUK  C3   C1   N    109.60  3.000
 PUK  C2   C1   N    114.72  3.000
 PUK  H4   C2   H3   106.52  3.000
 PUK  H4   C2   N2   112.50  3.000
 PUK  H3   C2   N2   108.59  3.000
 PUK  N2   C2   C1   111.72  3.000
 PUK  H4   C2   C1   108.46  3.000
 PUK  H3   C2   C1   108.87  3.000
 PUK  H6   C3   H5   106.45  3.000
 PUK  H6   C3   C4   109.64  3.000
 PUK  H5   C3   C4   110.00  3.000
 PUK  H6   C3   C1   108.45  3.000
 PUK  H5   C3   C1   108.86  3.000
 PUK  C4   C3   C1   113.21  3.000
 PUK  C6   C4   C5   118.27  3.000
 PUK  C6   C4   C3   120.44  3.000
 PUK  C5   C4   C3   121.28  3.000
 PUK  H7   C5   C7   119.56  3.000
 PUK  H7   C5   C4   119.44  3.000
 PUK  C7   C5   C4   120.99  3.000
 PUK  H8   C6   C8   119.51  3.000
 PUK  H8   C6   C4   119.44  3.000
 PUK  C8   C6   C4   121.04  3.000
 PUK  H9   C7   C9   120.05  3.000
 PUK  H9   C7   C5   119.78  3.000
 PUK  C9   C7   C5   120.17  3.000
 PUK  H10  C8   C9   120.10  3.000
 PUK  H10  C8   C6   119.81  3.000
 PUK  C9   C8   C6   120.09  3.000
 PUK  H11  C9   C8   120.25  3.000
 PUK  H11  C9   C7   120.31  3.000
 PUK  C8   C9   C7   119.43  3.000
 PUK  H12  N2   C10  107.44  3.000
 PUK  H12  N2   C2   107.67  3.000
 PUK  C10  N2   C2   113.64  3.000
 PUK  H13  C10  C12  107.37  3.000
 PUK  H13  C10  C    107.31  3.000
 PUK  C12  C10  C    107.66  3.000
 PUK  H13  C10  N2   111.19  3.000
 PUK  C12  C10  N2   109.61  3.000
 PUK  C    C10  N2   113.46  3.000
 PUK  OXT  C    O    126.77  3.000
 PUK  OXT  C    C10  114.98  3.000
 PUK  O    C    C10  118.21  3.000
 PUK  H15  C12  H14  107.31  3.000
 PUK  H15  C12  C13  109.87  3.000
 PUK  H14  C12  C13  109.67  3.000
 PUK  H15  C12  C10  108.11  3.000
 PUK  H14  C12  C10  108.71  3.000
 PUK  C13  C12  C10  112.99  3.000
 PUK  C15  C13  C14  118.24  3.000
 PUK  C15  C13  C12  120.69  3.000
 PUK  C14  C13  C12  121.03  3.000
 PUK  H16  C14  C16  119.64  3.000
 PUK  H16  C14  C13  119.32  3.000
 PUK  C16  C14  C13  121.04  3.000
 PUK  H17  C15  C17  119.50  3.000
 PUK  H17  C15  C13  119.55  3.000
 PUK  C17  C15  C13  120.95  3.000
 PUK  H18  C16  C18  120.18  3.000
 PUK  H18  C16  C14  119.72  3.000
 PUK  C18  C16  C14  120.10  3.000
 PUK  H19  C17  C18  120.02  3.000
 PUK  H19  C17  C15  119.76  3.000
 PUK  C18  C17  C15  120.22  3.000
 PUK  H20  C18  C17  120.25  3.000
 PUK  H20  C18  C16  120.30  3.000
 PUK  C17  C18  C16  119.45  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
 PUK  CONST_01  C9   C7   C5   C4      0.00   0.0  0
 PUK  CONST_02  C9   C8   C6   C4      0.00   0.0  0
 PUK  CONST_03  C8   C6   C4   C5      0.00   0.0  0
 PUK  CONST_04  C8   C9   C7   C5      0.00   0.0  0
 PUK  CONST_05  C7   C5   C4   C6      0.00   0.0  0
 PUK  CONST_06  C7   C9   C8   C6      0.00   0.0  0
 PUK  CONST_07  C18  C16  C14  C13     0.00   0.0  0
 PUK  CONST_08  C18  C17  C15  C13     0.00   0.0  0
 PUK  CONST_09  C17  C15  C13  C14     0.00   0.0  0
 PUK  CONST_10  C17  C18  C16  C14     0.00   0.0  0
 PUK  CONST_11  C16  C14  C13  C15     0.00   0.0  0
 PUK  CONST_12  C16  C18  C17  C15     0.00   0.0  0
 PUK  CONST_13  C7   C5   C4   C3    180.00   0.0  0
 PUK  CONST_14  C8   C6   C4   C3    180.00   0.0  0
 PUK  CONST_15  C16  C14  C13  C12   180.00   0.0  0
 PUK  CONST_16  C17  C15  C13  C12   180.00   0.0  0
 PUK  CONST_17  H9   C7   C5   C4    180.00   0.0  0
 PUK  CONST_18  H10  C8   C6   C4    180.00   0.0  0
 PUK  CONST_19  H8   C6   C4   C5    180.00   0.0  0
 PUK  CONST_20  H11  C9   C7   C5    180.00   0.0  0
 PUK  CONST_21  H7   C5   C4   C6    180.00   0.0  0
 PUK  CONST_22  H18  C16  C14  C13   180.00   0.0  0
 PUK  CONST_23  H19  C17  C15  C13   180.00   0.0  0
 PUK  CONST_24  H17  C15  C13  C14   180.00   0.0  0
 PUK  CONST_25  H20  C18  C16  C14   180.00   0.0  0
 PUK  CONST_26  H16  C14  C13  C15   180.00   0.0  0
 PUK  Var_01    C5   C4   C3   C1     95.25  30.0  2
 PUK  Var_02    C14  C13  C12  C10    98.28  30.0  2
 PUK  Var_03    C10  N2   C2   C1   -175.49  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
 PUK  chir_01  C1   N   C2   C3  positiv
 PUK  chir_02  C10  N2  C12  C   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
 PUK  plan-1  C3   0.020
 PUK  plan-1  C4   0.020
 PUK  plan-1  C5   0.020
 PUK  plan-1  C6   0.020
 PUK  plan-1  C7   0.020
 PUK  plan-1  C8   0.020
 PUK  plan-1  C9   0.020
 PUK  plan-1  H7   0.020
 PUK  plan-1  H8   0.020
 PUK  plan-1  H9   0.020
 PUK  plan-1  H10  0.020
 PUK  plan-1  H11  0.020
 PUK  plan-2  C12  0.020
 PUK  plan-2  C13  0.020
 PUK  plan-2  C14  0.020
 PUK  plan-2  C15  0.020
 PUK  plan-2  C16  0.020
 PUK  plan-2  C17  0.020
 PUK  plan-2  C18  0.020
 PUK  plan-2  H16  0.020
 PUK  plan-2  H17  0.020
 PUK  plan-2  H18  0.020
 PUK  plan-2  H19  0.020
 PUK  plan-2  H20  0.020
 PUK  plan-3  C10  0.020
 PUK  plan-3  C    0.020
 PUK  plan-3  O    0.020
 PUK  plan-3  OXT  0.020

