# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:04:17 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2~{S},4~{R})-5-(4-aminophenyl)-4-azanyl-2-methyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C[C@@H](N)Cc1ccc(N)cc1)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
 6YJ  6YJ  '(2~{S},4~{R})-5-(4-aminophenyl)-4-azanyl-2-methyl-pentanoic acid'  peptide  33  16  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6YJ
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
 6YJ  N3   N  NH2    0  -0.787  -0.5911  -0.9281   1.3415
 6YJ  C20  C  CR6    0   0.278   4.2095   0.4389   0.2804
 6YJ  C21  C  CR16   0  -0.310   3.3649   1.2313  -0.5055
 6YJ  C18  C  CR16   0  -0.317   2.5332  -1.3049   0.1917
 6YJ  C16  C  CH2    0  -0.507   0.3204  -0.9964  -0.9974
 6YJ  C19  C  CR16   0  -0.313   3.7697  -0.8440   0.6192
 6YJ  C26  C  C      0   0.408  -3.4803   1.0232   0.2739
 6YJ  C15  C  CH1    0  -0.089  -0.7931  -0.5216  -0.0413
 6YJ  C17  C  CR6    0   0.106   1.6847  -0.5215  -0.5875
 6YJ  C22  C  CR16   0  -0.301   2.1334   0.7551  -0.9237
 6YJ  C23  C  CH2    0  -0.388  -2.1510  -1.0049  -0.5403
 6YJ  C24  C  CH1    0  -0.329  -3.3496  -0.5119   0.2609
 6YJ  C25  C  CH3    0  -0.661  -4.6411  -1.1070  -0.3048
 6YJ  H10  H  HNH2   0   0.328  -0.5477  -1.9409   1.3910
 6YJ  H20  H  HCR6   0   0.250   3.6786   2.2286  -0.7917
 6YJ  H23  H  HCR6   0   0.241   2.2278  -2.3076   0.4693
 6YJ  H24  H  HCH2   0   0.225   0.3012  -2.0909  -1.0379
 6YJ  H25  H  HCH2   0   0.227   0.0921  -0.6430  -2.0074
 6YJ  H26  H  HCR6   0   0.250   4.4006  -1.4850   1.2244
 6YJ  H35  H  HCH1   0   0.218  -0.7932   0.5736  -0.0604
 6YJ  H36  H  HCR6   0   0.239   1.5065   1.3958  -1.5342
 6YJ  H37  H  HNH2   0   0.374   6.1036   0.2273   0.9726
 6YJ  H38  H  HNH2   0   0.374   5.8202   1.6679   0.1958
 6YJ  H39  H  HCH2   0   0.204  -2.2682  -0.7004  -1.5839
 6YJ  H40  H  HCH2   0   0.197  -2.1490  -2.1033  -0.5430
 6YJ  H41  H  HCH1   0   0.195  -3.2411  -0.8518   1.2938
 6YJ  H42  H  HCH3   0   0.220  -5.5128  -0.7918   0.2720
 6YJ  H43  H  HCH3   0   0.210  -4.7944  -0.7937  -1.3398
 6YJ  H44  H  HCH3   0   0.216  -4.6140  -2.1990  -0.2910
 6YJ  H2   H  HNH2   0   0.344   0.3108  -0.5994   1.6663
 6YJ  N4   N  NH2    0  -0.860   5.4157   0.9291   0.7492
 6YJ  O3   O  O      0  -0.619  -3.2200   1.6260  -0.7891
 6YJ  O4   O  OC    -1  -0.625  -3.8865   1.5471   1.3325

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
 6YJ  C25  C24  single    1.530  0.020  1.530
 6YJ  C23  C24  single    1.524  0.020  1.524
 6YJ  C23  C15  single    1.525  0.020  1.525
 6YJ  C24  C26  single    1.541  0.020  1.541
 6YJ  C16  C15  single    1.543  0.020  1.543
 6YJ  C16  C17  single    1.502  0.020  1.502
 6YJ  C15  N3   single    1.455  0.020  1.455
 6YJ  C22  C17  aromatic  1.394  0.020  1.394
 6YJ  C22  C21  aromatic  1.385  0.020  1.385
 6YJ  C26  O3   deloc     1.249  0.020  1.249
 6YJ  C26  O4   deloc     1.249  0.020  1.249
 6YJ  C17  C18  aromatic  1.393  0.020  1.393
 6YJ  C21  C20  aromatic  1.400  0.020  1.400
 6YJ  C18  C19  aromatic  1.387  0.020  1.387
 6YJ  C20  C19  aromatic  1.398  0.020  1.398
 6YJ  C20  N4   single    1.384  0.020  1.384
 6YJ  N3   H10  single    0.890  0.020  1.040
 6YJ  C21  H20  single    0.930  0.020  1.080
 6YJ  C18  H23  single    0.930  0.020  1.080
 6YJ  C16  H24  single    0.970  0.020  1.090
 6YJ  C16  H25  single    0.970  0.020  1.090
 6YJ  C19  H26  single    0.930  0.020  1.080
 6YJ  C15  H35  single    0.970  0.020  1.090
 6YJ  C22  H36  single    0.930  0.020  1.080
 6YJ  N4   H37  single    0.890  0.020  1.040
 6YJ  N4   H38  single    0.890  0.020  1.040
 6YJ  C23  H39  single    0.970  0.020  1.090
 6YJ  C23  H40  single    0.970  0.020  1.090
 6YJ  C24  H41  single    0.970  0.020  1.090
 6YJ  C25  H42  single    0.970  0.020  1.090
 6YJ  C25  H43  single    0.970  0.020  1.090
 6YJ  C25  H44  single    0.970  0.020  1.090
 6YJ  N3   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
 6YJ  H2   N3   H10  105.66  3.000
 6YJ  H2   N3   C15  109.72  3.000
 6YJ  H10  N3   C15  109.33  3.000
 6YJ  N4   C20  C19  121.15  3.000
 6YJ  N4   C20  C21  121.04  3.000
 6YJ  C19  C20  C21  117.76  3.000
 6YJ  H20  C21  C22  119.60  3.000
 6YJ  H20  C21  C20  119.64  3.000
 6YJ  C22  C21  C20  120.76  3.000
 6YJ  H23  C18  C17  119.45  3.000
 6YJ  H23  C18  C19  118.65  3.000
 6YJ  C17  C18  C19  121.90  3.000
 6YJ  H25  C16  H24  106.55  3.000
 6YJ  H25  C16  C17  109.84  3.000
 6YJ  H24  C16  C17  110.00  3.000
 6YJ  H25  C16  C15  108.79  3.000
 6YJ  H24  C16  C15  108.53  3.000
 6YJ  C17  C16  C15  112.91  3.000
 6YJ  H26  C19  C18  119.63  3.000
 6YJ  H26  C19  C20  119.66  3.000
 6YJ  C18  C19  C20  120.71  3.000
 6YJ  O4   C26  O3   125.91  3.000
 6YJ  O4   C26  C24  116.91  3.000
 6YJ  O3   C26  C24  117.12  3.000
 6YJ  H35  C15  C23  108.12  3.000
 6YJ  H35  C15  C16  107.28  3.000
 6YJ  C23  C15  C16  110.02  3.000
 6YJ  H35  C15  N3   107.20  3.000
 6YJ  C16  C15  N3   113.75  3.000
 6YJ  C23  C15  N3   110.24  3.000
 6YJ  C22  C17  C16  121.08  3.000
 6YJ  C22  C17  C18  116.98  3.000
 6YJ  C16  C17  C18  121.88  3.000
 6YJ  H36  C22  C17  119.38  3.000
 6YJ  H36  C22  C21  118.74  3.000
 6YJ  C17  C22  C21  121.88  3.000
 6YJ  H40  C23  H39  106.04  3.000
 6YJ  H40  C23  C24  109.04  3.000
 6YJ  H39  C23  C24  109.11  3.000
 6YJ  H40  C23  C15  108.43  3.000
 6YJ  H39  C23  C15  108.63  3.000
 6YJ  C24  C23  C15  115.20  3.000
 6YJ  H41  C24  C25  108.20  3.000
 6YJ  H41  C24  C23  108.55  3.000
 6YJ  C25  C24  C23  110.10  3.000
 6YJ  H41  C24  C26  108.08  3.000
 6YJ  C23  C24  C26  113.18  3.000
 6YJ  C25  C24  C26  108.60  3.000
 6YJ  H44  C25  H43  107.60  3.000
 6YJ  H44  C25  H42  107.56  3.000
 6YJ  H43  C25  H42  107.80  3.000
 6YJ  H44  C25  C24  111.29  3.000
 6YJ  H43  C25  C24  110.93  3.000
 6YJ  H42  C25  C24  111.48  3.000
 6YJ  H38  N4   H37  110.99  3.000
 6YJ  H38  N4   C20  115.06  3.000
 6YJ  H37  N4   C20  115.05  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
 6YJ  CONST_01  C17  C22  C21  C20    0.00   0.0  0
 6YJ  CONST_02  C17  C18  C19  C20    0.00   0.0  0
 6YJ  CONST_03  C18  C17  C22  C21    0.00   0.0  0
 6YJ  CONST_04  C18  C19  C20  C21    0.00   0.0  0
 6YJ  CONST_05  C22  C17  C18  C19    0.00   0.0  0
 6YJ  CONST_06  C22  C21  C20  C19    0.00   0.0  0
 6YJ  CONST_07  C16  C17  C22  C21  180.00   0.0  0
 6YJ  CONST_08  N4   C20  C19  C18  180.00   0.0  0
 6YJ  CONST_09  C19  C18  C17  C16  180.00   0.0  0
 6YJ  CONST_10  N4   C20  C21  C22  180.00   0.0  0
 6YJ  CONST_11  H36  C22  C21  C20  180.00   0.0  0
 6YJ  CONST_12  H23  C18  C19  C20  180.00   0.0  0
 6YJ  CONST_13  H26  C19  C20  C21  180.00   0.0  0
 6YJ  CONST_14  H20  C21  C20  C19  180.00   0.0  0
 6YJ  Var_01    C15  C16  C17  C18   94.43  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
 6YJ  chir_01  C15  C23  C16  N3   positiv
 6YJ  chir_02  C24  C25  C23  C26  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
 6YJ  plan-1  C20  0.020
 6YJ  plan-1  C21  0.020
 6YJ  plan-1  C18  0.020
 6YJ  plan-1  C16  0.020
 6YJ  plan-1  C19  0.020
 6YJ  plan-1  C17  0.020
 6YJ  plan-1  C22  0.020
 6YJ  plan-1  H20  0.020
 6YJ  plan-1  H23  0.020
 6YJ  plan-1  H26  0.020
 6YJ  plan-1  H36  0.020
 6YJ  plan-1  N4   0.020
 6YJ  plan-2  C20  0.020
 6YJ  plan-2  H37  0.020
 6YJ  plan-2  H38  0.020
 6YJ  plan-2  N4   0.020
 6YJ  plan-3  C26  0.020
 6YJ  plan-3  C24  0.020
 6YJ  plan-3  O3   0.020
 6YJ  plan-3  O4   0.020

