# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:13:52 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{R},4~{S},5~{S})-5-azanyl-6-methyl-4-oxidanyl-2-(phenylmethyl)heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)[C@@H](O)C[C@@H](Cc1ccccc1)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
 1QI  1QI  '(2~{R},4~{S},5~{S})-5-azanyl-6-methyl-4-oxidanyl-2-(phenylmethyl)heptanoic acid'  peptide  41  19  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_1QI
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
 1QI  C1   C  CH2    0  -0.499  133.6025  -24.2034  86.3708
 1QI  C2   C  CH1    0  -0.306  134.3657  -23.6403  85.1611
 1QI  C3   C  CH2    0  -0.469  134.9650  -22.2583  85.4844
 1QI  C4   C  CH1    0   0.060  136.4041  -22.2819  85.9839
 1QI  C5   C  CH1    0  -0.091  136.9226  -20.8897  86.4048
 1QI  O1   O  OH1    0  -0.670  136.4907  -23.1781  87.0799
 1QI  C8   C  CR6    0   0.131  133.0684  -25.5896  86.1471
 1QI  C9   C  CR16   0  -0.318  133.8675  -26.7044  86.3982
 1QI  C10  C  CR16   0  -0.238  133.3924  -27.9914  86.1840
 1QI  C11  C  CR16   0  -0.275  132.1009  -28.1873  85.7106
 1QI  C12  C  CR16   0  -0.240  131.2948  -27.0861  85.4530
 1QI  C13  C  CR16   0  -0.303  131.7762  -25.8014  85.6698
 1QI  C14  C  C      0   0.411  133.4194  -23.5445  83.9441
 1QI  C34  C  CH1    0  -0.242  136.8121  -19.8207  85.3036
 1QI  C35  C  CH3    0  -0.638  137.1405  -18.4333  85.8465
 1QI  C36  C  CH3    0  -0.670  137.6647  -20.1283  84.0738
 1QI  N1   N  NH2    0  -0.801  138.2836  -20.9263  86.9315
 1QI  H1   H  HCH2   0   0.240  134.2607  -24.2097  87.2399
 1QI  H3   H  HCH1   0   0.198  135.1794  -24.3318  84.9152
 1QI  H4   H  HCH2   0   0.238  134.9503  -21.6411  84.5839
 1QI  H5   H  HCH2   0   0.211  134.3293  -21.7363  86.2090
 1QI  H6   H  HCH1   0   0.187  137.0369  -22.6555  85.1633
 1QI  H7   H  HCH1   0   0.214  136.2799  -20.5572  87.2303
 1QI  H8   H  HOH1   0   0.439  137.4159  -23.4002  87.2168
 1QI  H9   H  HCR6   0   0.238  134.8748  -26.5606  86.7735
 1QI  H10  H  HCR6   0   0.246  134.0288  -28.8425  86.3919
 1QI  H11  H  HCR6   0   0.247  131.7257  -29.1894  85.5466
 1QI  H12  H  HCR6   0   0.246  130.2860  -27.2270  85.0854
 1QI  H13  H  HCR6   0   0.235  131.1420  -24.9480  85.4630
 1QI  H15  H  HCH1   0   0.225  135.7668  -19.7932  84.9824
 1QI  H16  H  HCH3   0   0.216  136.5277  -18.1910  86.7173
 1QI  H17  H  HCH3   0   0.214  138.1858  -18.3571  86.1452
 1QI  H18  H  HCH3   0   0.217  136.9525  -17.6700  85.0892
 1QI  H19  H  HCH3   0   0.227  137.3967  -21.0776  83.6079
 1QI  H20  H  HCH3   0   0.227  137.5368  -19.3511  83.3187
 1QI  H21  H  HCH3   0   0.215  138.7286  -20.1653  84.3181
 1QI  H2   H  HNH2   0   0.342  138.3130  -21.4291  87.8084
 1QI  H    H  HNH2   0   0.337  138.9007  -21.4202  86.2970
 1QI  OXY  O  OC    -1  -0.606  133.7082  -24.2140  82.9321
 1QI  H14  H  HCH2   0   0.223  132.7791  -23.5240  86.6050
 1QI  O    O  O      0  -0.615  132.4328  -22.7872  84.0760

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
 1QI  C14  O    deloc     1.251  0.020  1.251
 1QI  C14  C2   single    1.545  0.020  1.545
 1QI  C36  C34  single    1.528  0.020  1.528
 1QI  C2   C3   single    1.541  0.020  1.541
 1QI  C2   C1   single    1.537  0.020  1.537
 1QI  C12  C13  aromatic  1.389  0.020  1.389
 1QI  C12  C11  aromatic  1.389  0.020  1.389
 1QI  C34  C35  single    1.526  0.020  1.526
 1QI  C34  C5   single    1.539  0.020  1.539
 1QI  C13  C8   aromatic  1.394  0.020  1.394
 1QI  C3   C4   single    1.523  0.020  1.523
 1QI  C11  C10  aromatic  1.389  0.020  1.389
 1QI  C8   C1   single    1.502  0.020  1.502
 1QI  C8   C9   aromatic  1.394  0.020  1.394
 1QI  C4   C5   single    1.544  0.020  1.544
 1QI  C4   O1   single    1.419  0.020  1.419
 1QI  C10  C9   aromatic  1.388  0.020  1.388
 1QI  C5   N1   single    1.460  0.020  1.460
 1QI  C1   H1   single    0.970  0.020  1.090
 1QI  C2   H3   single    0.970  0.020  1.090
 1QI  C3   H4   single    0.970  0.020  1.090
 1QI  C3   H5   single    0.970  0.020  1.090
 1QI  C4   H6   single    0.970  0.020  1.090
 1QI  C5   H7   single    0.970  0.020  1.090
 1QI  O1   H8   single    0.850  0.020  0.980
 1QI  C9   H9   single    0.930  0.020  1.080
 1QI  C10  H10  single    0.930  0.020  1.080
 1QI  C11  H11  single    0.930  0.020  1.080
 1QI  C12  H12  single    0.930  0.020  1.080
 1QI  C13  H13  single    0.930  0.020  1.080
 1QI  C34  H15  single    0.970  0.020  1.090
 1QI  C35  H16  single    0.970  0.020  1.090
 1QI  C35  H17  single    0.970  0.020  1.090
 1QI  C35  H18  single    0.970  0.020  1.090
 1QI  C36  H19  single    0.970  0.020  1.090
 1QI  C36  H20  single    0.970  0.020  1.090
 1QI  C36  H21  single    0.970  0.020  1.090
 1QI  N1   H2   single    0.890  0.020  1.040
 1QI  N1   H    single    0.890  0.020  1.040
 1QI  C14  OXY  deloc     1.247  0.020  1.247
 1QI  C1   H14  single    0.970  0.020  1.090

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
 1QI  H14  C1   H1   106.71  3.000
 1QI  H14  C1   C8   109.74  3.000
 1QI  H1   C1   C8   109.15  3.000
 1QI  H14  C1   C2   108.36  3.000
 1QI  H1   C1   C2   109.25  3.000
 1QI  C8   C1   C2   113.41  3.000
 1QI  H3   C2   C14  108.49  3.000
 1QI  H3   C2   C3   108.92  3.000
 1QI  C14  C2   C3   110.36  3.000
 1QI  H3   C2   C1   108.31  3.000
 1QI  C3   C2   C1   110.89  3.000
 1QI  C14  C2   C1   109.79  3.000
 1QI  H5   C3   H4   105.56  3.000
 1QI  H5   C3   C4   109.78  3.000
 1QI  H4   C3   C4   106.97  3.000
 1QI  H5   C3   C2   109.89  3.000
 1QI  H4   C3   C2   109.20  3.000
 1QI  C4   C3   C2   114.98  3.000
 1QI  H6   C4   O1   109.04  3.000
 1QI  H6   C4   C5   108.42  3.000
 1QI  O1   C4   C5   109.79  3.000
 1QI  H6   C4   C3   107.67  3.000
 1QI  O1   C4   C3   108.71  3.000
 1QI  C5   C4   C3   113.12  3.000
 1QI  H7   C5   N1   106.38  3.000
 1QI  H7   C5   C34  106.60  3.000
 1QI  N1   C5   C34  110.03  3.000
 1QI  H7   C5   C4   106.35  3.000
 1QI  N1   C5   C4   112.88  3.000
 1QI  C34  C5   C4   114.03  3.000
 1QI  H8   O1   C4   108.34  3.000
 1QI  C13  C8   C9   118.13  3.000
 1QI  C9   C8   C1   120.48  3.000
 1QI  C13  C8   C1   121.39  3.000
 1QI  H9   C9   C10  119.61  3.000
 1QI  H9   C9   C8   119.24  3.000
 1QI  C10  C9   C8   121.15  3.000
 1QI  H10  C10  C11  120.06  3.000
 1QI  H10  C10  C9   119.85  3.000
 1QI  C11  C10  C9   120.09  3.000
 1QI  H11  C11  C12  120.31  3.000
 1QI  H11  C11  C10  120.28  3.000
 1QI  C12  C11  C10  119.40  3.000
 1QI  H12  C12  C13  119.75  3.000
 1QI  H12  C12  C11  120.03  3.000
 1QI  C13  C12  C11  120.22  3.000
 1QI  H13  C13  C12  119.74  3.000
 1QI  H13  C13  C8   119.24  3.000
 1QI  C12  C13  C8   121.02  3.000
 1QI  OXY  C14  O    126.39  3.000
 1QI  OXY  C14  C2   117.65  3.000
 1QI  O    C14  C2   115.96  3.000
 1QI  H15  C34  C36  107.57  3.000
 1QI  H15  C34  C35  106.70  3.000
 1QI  C36  C34  C35  110.45  3.000
 1QI  H15  C34  C5   107.23  3.000
 1QI  C35  C34  C5   111.20  3.000
 1QI  C36  C34  C5   113.34  3.000
 1QI  H18  C35  H17  107.84  3.000
 1QI  H18  C35  H16  107.55  3.000
 1QI  H17  C35  H16  107.71  3.000
 1QI  H18  C35  C34  110.61  3.000
 1QI  H17  C35  C34  111.57  3.000
 1QI  H16  C35  C34  111.39  3.000
 1QI  H21  C36  H20  107.04  3.000
 1QI  H21  C36  H19  107.79  3.000
 1QI  H20  C36  H19  107.18  3.000
 1QI  H21  C36  C34  111.74  3.000
 1QI  H20  C36  C34  110.38  3.000
 1QI  H19  C36  C34  112.45  3.000
 1QI  H    N1   H2   106.43  3.000
 1QI  H    N1   C5   110.73  3.000
 1QI  H2   N1   C5   110.64  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
 1QI  CONST_01  C11  C12  C13  C8     0.00   0.0  0
 1QI  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 1QI  CONST_03  C12  C13  C8   C9     0.00   0.0  0
 1QI  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 1QI  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 1QI  CONST_06  C13  C8   C9   C10    0.00   0.0  0
 1QI  CONST_07  C12  C13  C8   C1   180.00   0.0  0
 1QI  CONST_08  C10  C9   C8   C1   180.00   0.0  0
 1QI  CONST_09  H12  C12  C13  C8   180.00   0.0  0
 1QI  CONST_10  H10  C10  C9   C8   180.00   0.0  0
 1QI  CONST_11  H13  C13  C8   C9   180.00   0.0  0
 1QI  CONST_12  H11  C11  C10  C9   180.00   0.0  0
 1QI  CONST_13  H9   C9   C10  C11  180.00   0.0  0
 1QI  Var_01    C13  C8   C1   C2   -92.90  30.0  2
 1QI  Var_02    H19  C36  C34  C5    59.36  30.0  3
 1QI  Var_03    H16  C35  C34  C5   -54.17  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
 1QI  chir_01  C2  C14  C3  C1   negativ
 1QI  chir_02  C4  O1   C5  C3   positiv
 1QI  chir_03  C5  N1   C4  C34  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
 1QI  plan-1  C1   0.020
 1QI  plan-1  C8   0.020
 1QI  plan-1  C9   0.020
 1QI  plan-1  C10  0.020
 1QI  plan-1  C11  0.020
 1QI  plan-1  C12  0.020
 1QI  plan-1  C13  0.020
 1QI  plan-1  H9   0.020
 1QI  plan-1  H10  0.020
 1QI  plan-1  H11  0.020
 1QI  plan-1  H12  0.020
 1QI  plan-1  H13  0.020
 1QI  plan-2  C2   0.020
 1QI  plan-2  C14  0.020
 1QI  plan-2  OXY  0.020
 1QI  plan-2  O    0.020

