# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 08:53:02 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-[(3S)-3-amino-4-phenylbutyl]-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCN[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
 Q00  Q00  N-[(3S)-3-amino-4-phenylbutyl]-L-phenylalanine  peptide  47  23  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q00
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
 Q00  N    N  NH2   0  -0.781  -2.5987   1.7219   0.2695
 Q00  C1   C  CH1   0  -0.090  -2.1611   0.3889  -0.1109
 Q00  C2   C  CH2   0  -0.451  -0.7787   0.3284  -0.7688
 Q00  C3   C  CH2   0  -0.514  -3.2052  -0.2478  -1.0367
 Q00  C4   C  CR6   0   0.170  -4.5439  -0.4224  -0.3813
 Q00  C5   C  CR16  0  -0.311  -5.5573   0.5202  -0.5359
 Q00  C6   C  CR16  0  -0.315  -4.7916  -1.5314   0.4258
 Q00  C7   C  CR16  0  -0.245  -6.7855   0.3582   0.0919
 Q00  C8   C  CR16  0  -0.241  -6.0154  -1.6969   1.0610
 Q00  C9   C  CR16  0  -0.276  -7.0186  -0.7506   0.8957
 Q00  C10  C  CH2   0  -0.268   0.3323   0.8886   0.1049
 Q00  N2   N  NH1   0  -0.603   1.6256   0.6972  -0.5284
 Q00  C11  C  CH1   0  -0.166   2.7352   1.1814   0.2502
 Q00  C    C  C     0   0.536   2.8155   2.6959   0.1626
 Q00  O    O  O     0  -0.432   2.3539   3.3642  -0.7254
 Q00  C13  C  CH2   0  -0.527   4.0639   0.6072  -0.2822
 Q00  C14  C  CR6   0   0.100   4.1136  -0.8922  -0.1698
 Q00  C15  C  CR16  0  -0.309   3.9620  -1.7031  -1.2917
 Q00  C16  C  CR16  0  -0.295   4.2919  -1.4991   1.0732
 Q00  C17  C  CR16  0  -0.242   3.9881  -3.0882  -1.1771
 Q00  C18  C  CR16  0  -0.240   4.3185  -2.8806   1.1914
 Q00  C19  C  CR16  0  -0.268   4.1661  -3.6806   0.0647
 Q00  OXT  O  OH1   0  -0.594   3.5023   3.2031   1.1807
 Q00  H    H  HNH2  0   0.349  -1.9888   2.1045   0.9806
 Q00  H25  H  HCH1  0   0.226  -2.1247  -0.2096   0.8069
 Q00  H3   H  HCH2  0   0.218  -0.5491  -0.7153  -1.0118
 Q00  H4   H  HCH2  0   0.220  -0.8005   0.8742  -1.7185
 Q00  H5   H  HCH2  0   0.237  -3.3020   0.3687  -1.9364
 Q00  H6   H  HCH2  0   0.243  -2.8290  -1.2197  -1.3671
 Q00  H7   H  HCR6  0   0.238  -5.3858   1.3876  -1.1617
 Q00  H8   H  HCR6  0   0.242  -4.0166  -2.2785   0.5573
 Q00  H9   H  HCR6  0   0.250  -7.5628   1.0991  -0.0470
 Q00  H10  H  HCR6  0   0.250  -6.1869  -2.5675   1.6815
 Q00  H11  H  HCR6  0   0.250  -7.9755  -0.8780   1.3857
 Q00  H12  H  HCH2  0   0.218   0.1731   1.9592   0.2553
 Q00  H13  H  HCH2  0   0.196   0.2873   0.4237   1.1034
 Q00  H14  H  HNH1  0   0.353   1.7554  -0.2935  -0.6959
 Q00  H15  H  HCH1  0   0.246   2.6544   0.9132   1.3165
 Q00  H16  H  HCH2  0   0.264   4.1878   0.9086  -1.3249
 Q00  H17  H  HCH2  0   0.273   4.8897   1.0454   0.2807
 Q00  H18  H  HCR6  0   0.255   3.8264  -1.2493  -2.2667
 Q00  H19  H  HCR6  0   0.251   4.4157  -0.8834   1.9571
 Q00  H20  H  HCR6  0   0.257   3.8701  -3.7032  -2.0600
 Q00  H21  H  HCR6  0   0.256   4.4630  -3.3345   2.1635
 Q00  H22  H  HCR6  0   0.256   4.1876  -4.7588   0.1558
 Q00  HXT  H  HOH1  0   0.482   3.5926   4.1622   1.0757
 Q00  H2   H  HNH2  0   0.334  -2.5284   2.3447  -0.5275

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
 Q00  N    C1   single    1.454  0.020  1.454
 Q00  N    H    single    0.860  0.020  0.860
 Q00  C1   C2   single    1.532  0.020  1.532
 Q00  C1   C3   single    1.534  0.020  1.534
 Q00  C1   H25  single    0.970  0.020  1.090
 Q00  C2   C10  single    1.520  0.020  1.520
 Q00  C2   H3   single    0.970  0.020  1.090
 Q00  C2   H4   single    0.970  0.020  1.090
 Q00  C3   C4   single    1.501  0.020  1.501
 Q00  C3   H5   single    0.970  0.020  1.090
 Q00  C3   H6   single    0.970  0.020  1.090
 Q00  C4   C5   aromatic  1.393  0.020  1.393
 Q00  C4   C6   aromatic  1.394  0.020  1.394
 Q00  C5   C7   aromatic  1.389  0.020  1.389
 Q00  C5   H7   single    0.930  0.020  1.080
 Q00  C6   C8   aromatic  1.389  0.020  1.389
 Q00  C6   H8   single    0.930  0.020  1.080
 Q00  C7   C9   aromatic  1.389  0.020  1.389
 Q00  C7   H9   single    0.930  0.020  1.080
 Q00  C8   C9   aromatic  1.389  0.020  1.389
 Q00  C8   H10  single    0.930  0.020  1.080
 Q00  C9   H11  single    0.930  0.020  1.080
 Q00  C10  H12  single    0.970  0.020  1.090
 Q00  C10  H13  single    0.970  0.020  1.090
 Q00  C10  N2   single    1.453  0.020  1.453
 Q00  N2   C11  single    1.439  0.020  1.439
 Q00  N2   H14  single    0.890  0.020  1.040
 Q00  C11  C    single    1.519  0.020  1.519
 Q00  C11  C13  single    1.542  0.020  1.542
 Q00  C11  H15  single    0.970  0.020  1.090
 Q00  C    O    double    1.231  0.020  1.231
 Q00  C    OXT  single    1.329  0.020  1.329
 Q00  C13  C14  single    1.504  0.020  1.504
 Q00  C13  H16  single    0.970  0.020  1.090
 Q00  C13  H17  single    0.970  0.020  1.090
 Q00  C14  C15  aromatic  1.393  0.020  1.393
 Q00  C14  C16  aromatic  1.395  0.020  1.395
 Q00  C15  C17  aromatic  1.390  0.020  1.390
 Q00  C15  H18  single    0.930  0.020  1.080
 Q00  C16  C18  aromatic  1.387  0.020  1.387
 Q00  C16  H19  single    0.930  0.020  1.080
 Q00  C17  C19  aromatic  1.387  0.020  1.387
 Q00  C17  H20  single    0.930  0.020  1.080
 Q00  C18  C19  aromatic  1.390  0.020  1.390
 Q00  C18  H21  single    0.930  0.020  1.080
 Q00  C19  H22  single    0.930  0.020  1.080
 Q00  OXT  HXT  single    0.850  0.020  0.980
 Q00  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
 Q00  H2   N    H    106.16  3.000
 Q00  H2   N    C1   109.67  3.000
 Q00  H    N    C1   110.44  3.000
 Q00  H25  C1   C3   107.53  3.000
 Q00  H25  C1   C2   107.94  3.000
 Q00  C3   C1   C2   109.79  3.000
 Q00  H25  C1   N    106.95  3.000
 Q00  C3   C1   N    109.49  3.000
 Q00  C2   C1   N    114.85  3.000
 Q00  H4   C2   H3   106.64  3.000
 Q00  H4   C2   C10  109.22  3.000
 Q00  H3   C2   C10  108.98  3.000
 Q00  H4   C2   C1   109.55  3.000
 Q00  H3   C2   C1   108.78  3.000
 Q00  C10  C2   C1   113.45  3.000
 Q00  H6   C3   H5   106.42  3.000
 Q00  H6   C3   C4   109.60  3.000
 Q00  H5   C3   C4   110.21  3.000
 Q00  H6   C3   C1   108.50  3.000
 Q00  H5   C3   C1   108.81  3.000
 Q00  C4   C3   C1   113.07  3.000
 Q00  C6   C4   C5   118.26  3.000
 Q00  C6   C4   C3   120.26  3.000
 Q00  C5   C4   C3   121.46  3.000
 Q00  H7   C5   C7   119.63  3.000
 Q00  H7   C5   C4   119.40  3.000
 Q00  C7   C5   C4   120.96  3.000
 Q00  H8   C6   C8   119.49  3.000
 Q00  H8   C6   C4   119.43  3.000
 Q00  C8   C6   C4   121.08  3.000
 Q00  H9   C7   C9   120.00  3.000
 Q00  H9   C7   C5   119.81  3.000
 Q00  C9   C7   C5   120.20  3.000
 Q00  H10  C8   C9   120.10  3.000
 Q00  H10  C8   C6   119.84  3.000
 Q00  C9   C8   C6   120.06  3.000
 Q00  H11  C9   C8   120.30  3.000
 Q00  H11  C9   C7   120.27  3.000
 Q00  C8   C9   C7   119.43  3.000
 Q00  H13  C10  H12  106.42  3.000
 Q00  H13  C10  N2   112.06  3.000
 Q00  H12  C10  N2   108.59  3.000
 Q00  N2   C10  C2   110.58  3.000
 Q00  H13  C10  C2   109.59  3.000
 Q00  H12  C10  C2   109.48  3.000
 Q00  H14  N2   C11  108.64  3.000
 Q00  H14  N2   C10  108.36  3.000
 Q00  C11  N2   C10  113.96  3.000
 Q00  H15  C11  C13  107.85  3.000
 Q00  H15  C11  C    107.59  3.000
 Q00  C13  C11  C    107.80  3.000
 Q00  H15  C11  N2   112.63  3.000
 Q00  C13  C11  N2   110.62  3.000
 Q00  C    C11  N2   110.17  3.000
 Q00  OXT  C    O    123.48  3.000
 Q00  OXT  C    C11  111.33  3.000
 Q00  O    C    C11  125.16  3.000
 Q00  H17  C13  H16  107.20  3.000
 Q00  H17  C13  C14  109.68  3.000
 Q00  H16  C13  C14  110.04  3.000
 Q00  H17  C13  C11  108.92  3.000
 Q00  H16  C13  C11  108.94  3.000
 Q00  C14  C13  C11  111.95  3.000
 Q00  C16  C14  C15  118.59  3.000
 Q00  C16  C14  C13  120.30  3.000
 Q00  C15  C14  C13  121.10  3.000
 Q00  H18  C15  C17  119.58  3.000
 Q00  H18  C15  C14  119.64  3.000
 Q00  C17  C15  C14  120.78  3.000
 Q00  H19  C16  C18  119.60  3.000
 Q00  H19  C16  C14  119.61  3.000
 Q00  C18  C16  C14  120.79  3.000
 Q00  H20  C17  C19  120.10  3.000
 Q00  H20  C17  C15  119.79  3.000
 Q00  C19  C17  C15  120.11  3.000
 Q00  H21  C18  C19  120.08  3.000
 Q00  H21  C18  C16  119.79  3.000
 Q00  C19  C18  C16  120.14  3.000
 Q00  H22  C19  C18  120.19  3.000
 Q00  H22  C19  C17  120.22  3.000
 Q00  C18  C19  C17  119.59  3.000
 Q00  HXT  OXT  C    110.06  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
 Q00  CONST_01  C9   C7   C5   C4      0.00   0.0  0
 Q00  CONST_02  C9   C8   C6   C4      0.00   0.0  0
 Q00  CONST_03  C8   C6   C4   C5      0.00   0.0  0
 Q00  CONST_04  C8   C9   C7   C5      0.00   0.0  0
 Q00  CONST_05  C7   C5   C4   C6      0.00   0.0  0
 Q00  CONST_06  C7   C9   C8   C6      0.00   0.0  0
 Q00  CONST_07  C19  C17  C15  C14     0.00   0.0  0
 Q00  CONST_08  C19  C18  C16  C14     0.00   0.0  0
 Q00  CONST_09  C18  C16  C14  C15     0.00   0.0  0
 Q00  CONST_10  C18  C19  C17  C15     0.00   0.0  0
 Q00  CONST_11  C17  C15  C14  C16     0.00   0.0  0
 Q00  CONST_12  C17  C19  C18  C16     0.00   0.0  0
 Q00  CONST_13  C7   C5   C4   C3    180.00   0.0  0
 Q00  CONST_14  C8   C6   C4   C3    180.00   0.0  0
 Q00  CONST_15  C17  C15  C14  C13   180.00   0.0  0
 Q00  CONST_16  C18  C16  C14  C13   180.00   0.0  0
 Q00  CONST_17  H9   C7   C5   C4    180.00   0.0  0
 Q00  CONST_18  H10  C8   C6   C4    180.00   0.0  0
 Q00  CONST_19  H8   C6   C4   C5    180.00   0.0  0
 Q00  CONST_20  H11  C9   C7   C5    180.00   0.0  0
 Q00  CONST_21  H7   C5   C4   C6    180.00   0.0  0
 Q00  CONST_22  H20  C17  C15  C14   180.00   0.0  0
 Q00  CONST_23  H21  C18  C16  C14   180.00   0.0  0
 Q00  CONST_24  H19  C16  C14  C15   180.00   0.0  0
 Q00  CONST_25  H22  C19  C17  C15   180.00   0.0  0
 Q00  CONST_26  H18  C15  C14  C16   180.00   0.0  0
 Q00  CONST_27  HXT  OXT  C    C11   180.00   0.0  0
 Q00  Var_01    C5   C4   C3   C1     95.62  30.0  2
 Q00  Var_02    C15  C14  C13  C11   105.19  30.0  2
 Q00  Var_03    N2   C10  C2   C1    175.14  30.0  3
 Q00  Var_04    C11  N2   C10  C2   -178.95  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
 Q00  chir_01  C1   N   C2  C3   positiv
 Q00  chir_02  C11  N2  C   C13  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
 Q00  plan-1  C3   0.020
 Q00  plan-1  C4   0.020
 Q00  plan-1  C5   0.020
 Q00  plan-1  C6   0.020
 Q00  plan-1  C7   0.020
 Q00  plan-1  C8   0.020
 Q00  plan-1  C9   0.020
 Q00  plan-1  H7   0.020
 Q00  plan-1  H8   0.020
 Q00  plan-1  H9   0.020
 Q00  plan-1  H10  0.020
 Q00  plan-1  H11  0.020
 Q00  plan-2  C13  0.020
 Q00  plan-2  C14  0.020
 Q00  plan-2  C15  0.020
 Q00  plan-2  C16  0.020
 Q00  plan-2  C17  0.020
 Q00  plan-2  C18  0.020
 Q00  plan-2  C19  0.020
 Q00  plan-2  H18  0.020
 Q00  plan-2  H19  0.020
 Q00  plan-2  H20  0.020
 Q00  plan-2  H21  0.020
 Q00  plan-2  H22  0.020
 Q00  plan-3  C11  0.020
 Q00  plan-3  C    0.020
 Q00  plan-3  O    0.020
 Q00  plan-3  OXT  0.020
 Q00  plan-3  HXT  0.020

