# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:16:31 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-[(2S,3S)-3-amino-2-hydroxy-5-methylhexyl]-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)CN[C@@H](C(C)C)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
 GKL  GKL  N-[(2S,3S)-3-amino-2-hydroxy-5-methylhexyl]-L-valine  peptide  43  17  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GKL
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
 GKL  O1   O  OH1   0  -0.669   0.9440   0.5994   1.6730
 GKL  C1   C  CH1   0   0.030   1.0484  -0.2233   0.5292
 GKL  C2   C  CH2   0  -0.292  -0.2168  -0.1715  -0.3188
 GKL  C3   C  CH1   0  -0.119   2.2918   0.1080  -0.3057
 GKL  N1   N  NH2   0  -0.804   2.1867   1.4705  -0.8199
 GKL  C4   C  CH2   0  -0.404   3.5761  -0.1608   0.4841
 GKL  C5   C  CH1   0  -0.238   4.8754   0.0294  -0.3011
 GKL  C6   C  CH3   0  -0.648   6.0758  -0.0957   0.6321
 GKL  C7   C  CH3   0  -0.658   4.9946  -0.9595  -1.4572
 GKL  N2   N  NH1   0  -0.606  -1.3746  -0.6303   0.4226
 GKL  C8   C  CH1   0  -0.120  -2.6284  -0.4075  -0.2604
 GKL  C    C  C     0   0.522  -2.9730   1.0693  -0.1439
 GKL  O    O  O     0  -0.433  -2.8536   1.7191   0.8631
 GKL  C10  C  CH1   0  -0.269  -3.7542  -1.2531   0.3734
 GKL  C11  C  CH3   0  -0.667  -5.1450  -0.8342  -0.0970
 GKL  C12  C  CH3   0  -0.663  -3.5415  -2.7356   0.0700
 GKL  OXT  O  OH1   0  -0.591  -3.4453   1.5678  -1.2816
 GKL  H1   H  HCH2  0   0.226  -0.3768   0.8636  -0.6370
 GKL  H2   H  HCH2  0   0.205  -0.0526  -0.7469  -1.2430
 GKL  H3   H  HCH1  0   0.225   2.2643  -0.5649  -1.1687
 GKL  H4   H  HNH2  0   0.338   2.4923   2.1272  -0.1104
 GKL  H5   H  HNH2  0   0.352   2.8196   1.5992  -1.5980
 GKL  H6   H  HCH2  0   0.216   3.5874   0.5005   1.3575
 GKL  H7   H  HCH2  0   0.205   3.5531  -1.1850   0.8766
 GKL  H8   H  HCH1  0   0.204   4.8833   1.0441  -0.7162
 GKL  H9   H  HCH3  0   0.211   6.1115  -1.0866   1.0922
 GKL  H10  H  HCH3  0   0.223   7.0147   0.0505   0.0950
 GKL  H11  H  HCH3  0   0.223   6.0344   0.6407   1.4366
 GKL  H12  H  HCH3  0   0.226   5.9346  -0.8260  -1.9952
 GKL  H13  H  HCH3  0   0.212   4.9679  -1.9883  -1.0886
 GKL  H14  H  HCH3  0   0.226   4.1882  -0.8487  -2.1832
 GKL  H15  H  HNH1  0   0.350  -1.2669  -1.6155   0.6242
 GKL  H16  H  HCH1  0   0.224  -2.5806  -0.6636  -1.3316
 GKL  H17  H  HCH1  0   0.237  -3.6937  -1.0995   1.4560
 GKL  H18  H  HCH3  0   0.225  -5.2318  -0.8844  -1.1842
 GKL  H19  H  HCH3  0   0.238  -5.8947  -1.5047   0.3236
 GKL  H20  H  HCH3  0   0.235  -5.4118   0.1751   0.2174
 GKL  H21  H  HCH3  0   0.225  -3.5862  -2.9182  -1.0058
 GKL  H22  H  HCH3  0   0.230  -2.5875  -3.1205   0.4325
 GKL  H23  H  HCH3  0   0.240  -4.3218  -3.3345   0.5410
 GKL  HXT  H  HOH1  0   0.478  -3.7043   2.4934  -1.1553
 GKL  H25  H  HOH1  0   0.439   0.6059   1.4561   1.3923
 GKL  H26  H  HCH1  0   0.219   1.1683  -1.2459   0.9079

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
 GKL  O1   C1   single  1.413  0.020  1.413
 GKL  C1   C2   single  1.524  0.020  1.524
 GKL  C1   C3   single  1.534  0.020  1.534
 GKL  C2   H1   single  0.970  0.020  1.090
 GKL  C2   H2   single  0.970  0.020  1.090
 GKL  C2   N2   single  1.449  0.020  1.449
 GKL  C3   N1   single  1.460  0.020  1.460
 GKL  C3   C4   single  1.531  0.020  1.531
 GKL  C3   H3   single  0.970  0.020  1.090
 GKL  N1   H4   single  0.890  0.020  1.040
 GKL  N1   H5   single  0.890  0.020  1.040
 GKL  C4   C5   single  1.530  0.020  1.530
 GKL  C4   H6   single  0.970  0.020  1.090
 GKL  C4   H7   single  0.970  0.020  1.090
 GKL  C5   C6   single  1.526  0.020  1.526
 GKL  C5   C7   single  1.526  0.020  1.526
 GKL  C5   H8   single  0.970  0.020  1.090
 GKL  C6   H9   single  0.970  0.020  1.090
 GKL  C6   H10  single  0.970  0.020  1.090
 GKL  C6   H11  single  0.970  0.020  1.090
 GKL  C7   H12  single  0.970  0.020  1.090
 GKL  C7   H13  single  0.970  0.020  1.090
 GKL  C7   H14  single  0.970  0.020  1.090
 GKL  N2   C8   single  1.445  0.020  1.445
 GKL  N2   H15  single  0.890  0.020  1.040
 GKL  C8   C    single  1.521  0.020  1.521
 GKL  C8   C10  single  1.544  0.020  1.544
 GKL  C8   H16  single  0.970  0.020  1.090
 GKL  C    O    double  1.231  0.020  1.231
 GKL  C    OXT  single  1.329  0.020  1.329
 GKL  C10  C11  single  1.527  0.020  1.527
 GKL  C10  C12  single  1.528  0.020  1.528
 GKL  C10  H17  single  0.970  0.020  1.090
 GKL  C11  H18  single  0.970  0.020  1.090
 GKL  C11  H19  single  0.970  0.020  1.090
 GKL  C11  H20  single  0.970  0.020  1.090
 GKL  C12  H21  single  0.970  0.020  1.090
 GKL  C12  H22  single  0.970  0.020  1.090
 GKL  C12  H23  single  0.970  0.020  1.090
 GKL  OXT  HXT  single  0.850  0.020  0.980
 GKL  O1   H25  single  0.850  0.020  0.980
 GKL  C1   H26  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
 GKL  H25  O1   C1   107.94  3.000
 GKL  H26  C1   C3   107.50  3.000
 GKL  H26  C1   C2   108.33  3.000
 GKL  C3   C1   C2   111.27  3.000
 GKL  H26  C1   O1   105.75  3.000
 GKL  C3   C1   O1   112.01  3.000
 GKL  C2   C1   O1   111.67  3.000
 GKL  H2   C2   H1   105.78  3.000
 GKL  H2   C2   N2   112.53  3.000
 GKL  H1   C2   N2   109.34  3.000
 GKL  N2   C2   C1   111.58  3.000
 GKL  H2   C2   C1   109.00  3.000
 GKL  H1   C2   C1   108.38  3.000
 GKL  H3   C3   C4   108.65  3.000
 GKL  H3   C3   N1   107.11  3.000
 GKL  C4   C3   N1   113.94  3.000
 GKL  H3   C3   C1   106.02  3.000
 GKL  C4   C3   C1   111.17  3.000
 GKL  N1   C3   C1   109.56  3.000
 GKL  H5   N1   H4   105.51  3.000
 GKL  H5   N1   C3   110.16  3.000
 GKL  H4   N1   C3   109.65  3.000
 GKL  H7   C4   H6   106.17  3.000
 GKL  H7   C4   C5   108.51  3.000
 GKL  H6   C4   C5   108.99  3.000
 GKL  H7   C4   C3   109.31  3.000
 GKL  H6   C4   C3   108.29  3.000
 GKL  C5   C4   C3   115.19  3.000
 GKL  H8   C5   C7   108.20  3.000
 GKL  H8   C5   C6   107.57  3.000
 GKL  C7   C5   C6   110.41  3.000
 GKL  H8   C5   C4   108.39  3.000
 GKL  C7   C5   C4   112.00  3.000
 GKL  C6   C5   C4   110.12  3.000
 GKL  H11  C6   H10  107.75  3.000
 GKL  H11  C6   H9   107.61  3.000
 GKL  H10  C6   H9   107.49  3.000
 GKL  H11  C6   C5   111.45  3.000
 GKL  H10  C6   C5   111.40  3.000
 GKL  H9   C6   C5   110.95  3.000
 GKL  H14  C7   H13  107.58  3.000
 GKL  H14  C7   H12  107.24  3.000
 GKL  H13  C7   H12  107.61  3.000
 GKL  H14  C7   C5   112.37  3.000
 GKL  H13  C7   C5   110.64  3.000
 GKL  H12  C7   C5   111.19  3.000
 GKL  H15  N2   C8   109.68  3.000
 GKL  H15  N2   C2   108.99  3.000
 GKL  C8   N2   C2   113.74  3.000
 GKL  H16  C8   C10  107.65  3.000
 GKL  H16  C8   C    108.05  3.000
 GKL  C10  C8   C    109.58  3.000
 GKL  H16  C8   N2   112.69  3.000
 GKL  C10  C8   N2   110.74  3.000
 GKL  C    C8   N2   108.07  3.000
 GKL  OXT  C    O    123.28  3.000
 GKL  OXT  C    C8   112.29  3.000
 GKL  O    C    C8   124.43  3.000
 GKL  H17  C10  C12  108.94  3.000
 GKL  H17  C10  C11  108.44  3.000
 GKL  C12  C10  C11  109.38  3.000
 GKL  H17  C10  C8   106.78  3.000
 GKL  C12  C10  C8   110.39  3.000
 GKL  C11  C10  C8   112.80  3.000
 GKL  H20  C11  H19  106.85  3.000
 GKL  H20  C11  H18  108.07  3.000
 GKL  H19  C11  H18  107.53  3.000
 GKL  H20  C11  C10  112.83  3.000
 GKL  H19  C11  C10  109.81  3.000
 GKL  H18  C11  C10  111.50  3.000
 GKL  H23  C12  H22  106.76  3.000
 GKL  H23  C12  H21  107.72  3.000
 GKL  H22  C12  H21  107.71  3.000
 GKL  H23  C12  C10  110.33  3.000
 GKL  H22  C12  C10  113.46  3.000
 GKL  H21  C12  C10  110.62  3.000
 GKL  HXT  OXT  C    109.97  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
 GKL  CONST_01  HXT  OXT  C    C8   180.00   0.0  0
 GKL  Var_01    C8   N2   C2   C1   170.89  30.0  3
 GKL  Var_02    C6   C5   C4   C3   172.96  30.0  3
 GKL  Var_03    H9   C6   C5   C4    61.08  30.0  3
 GKL  Var_04    H12  C7   C5   C4  -178.83  30.0  3
 GKL  Var_05    H18  C11  C10  C8    56.96  30.0  3
 GKL  Var_06    H21  C12  C10  C8   -62.47  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
 GKL  chir_01  C1  O1  C2  C3   negativ
 GKL  chir_02  C3  N1  C4  C1   negativ
 GKL  chir_03  C8  N2  C   C10  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
 GKL  plan-1  C8   0.020
 GKL  plan-1  C    0.020
 GKL  plan-1  O    0.020
 GKL  plan-1  OXT  0.020
 GKL  plan-1  HXT  0.020

