# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:36:51 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  42  17  .  2022-03-18  2022-07-25
;
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  -0.702   0.7996   0.3817   1.3051
 GKL  C1   C  CH1    0   0.072   1.0855  -0.4861   0.2306
 GKL  C2   C  CH2    0  -0.310  -0.1323  -0.5546  -0.6842
 GKL  C3   C  CH1    0  -0.118   2.3501  -0.0272  -0.4921
 GKL  N1   N  NH2    0  -0.797   2.1435   1.2982  -1.0609
 GKL  C4   C  CH2    0  -0.398   3.5748  -0.1452   0.4242
 GKL  C5   C  CH1    0  -0.244   4.9197   0.1797  -0.2296
 GKL  C6   C  CH3    0  -0.647   6.0306   0.1439   0.8158
 GKL  C7   C  CH3    0  -0.657   5.2429  -0.7629  -1.3851
 GKL  N2   N  NH1    0  -0.640  -1.2822  -0.9274   0.1205
 GKL  C8   C  CH1    0  -0.092  -2.5635  -0.4306  -0.3440
 GKL  C    C  C      0   0.395  -2.6065   1.1082  -0.1693
 GKL  O    O  O      0  -0.603  -2.2861   1.5513   0.9520
 GKL  C10  C  CH1    0  -0.259  -3.7092  -1.0777   0.4498
 GKL  C11  C  CH3    0  -0.660  -5.0603  -0.4980   0.0380
 GKL  C12  C  CH3    0  -0.669  -3.7491  -2.5970   0.2827
 GKL  OXT  O  OC    -1  -0.614  -2.9751   1.7808  -1.1533
 GKL  H1   H  HCH2   0   0.231  -0.2951   0.4355  -1.1146
 GKL  H2   H  HCH2   0   0.208   0.0527  -1.2380  -1.5239
 GKL  H3   H  HCH1   0   0.218   2.4747  -0.7228  -1.3302
 GKL  H4   H  HNH2   0   0.333   2.0488   1.9710  -0.3089
 GKL  H5   H  HNH2   0   0.345   2.9611   1.5802  -1.5869
 GKL  H6   H  HCH2   0   0.217   3.4356   0.5191   1.2840
 GKL  H7   H  HCH2   0   0.201   3.6228  -1.1651   0.8258
 GKL  H8   H  HCH1   0   0.204   4.8747   1.2021  -0.6240
 GKL  H9   H  HCH3   0   0.211   6.1359  -0.8577   1.2404
 GKL  H10  H  HCH3   0   0.223   6.9938   0.4229   0.3853
 GKL  H11  H  HCH3   0   0.222   5.8225   0.8304   1.6384
 GKL  H12  H  HCH3   0   0.225   6.2204  -0.5362  -1.8148
 GKL  H13  H  HCH3   0   0.212   5.2650  -1.8007  -1.0426
 GKL  H14  H  HCH3   0   0.226   4.5122  -0.6977  -2.1925
 GKL  H15  H  HNH1   0   0.344  -1.2983  -1.9328   0.2213
 GKL  H16  H  HCH1   0   0.162  -2.7311  -0.6614  -1.4106
 GKL  H17  H  HCH1   0   0.212  -3.5379  -0.8480   1.5070
 GKL  H18  H  HCH3   0   0.212  -5.2315  -0.6337  -1.0324
 GKL  H19  H  HCH3   0   0.222  -5.8710  -1.0019   0.5667
 GKL  H20  H  HCH3   0   0.231  -5.1434   0.5667   0.2546
 GKL  H21  H  HCH3   0   0.215  -3.9017  -2.8706  -0.7645
 GKL  H22  H  HCH3   0   0.222  -2.8434  -3.0989   0.6276
 GKL  H23  H  HCH3   0   0.231  -4.5754  -3.0211   0.8559
 GKL  H25  H  HOH1   0   0.437  -0.1662   0.3353   1.4101
 GKL  H26  H  HCH1   0   0.178   1.2814  -1.5057   0.6061

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  1.410  0.020  1.410
 GKL  C1   C2   single  1.525  0.020  1.525
 GKL  C1   C3   single  1.527  0.020  1.527
 GKL  C2   H1   single  0.970  0.020  1.090
 GKL  C2   H2   single  0.970  0.020  1.090
 GKL  C2   N2   single  1.452  0.020  1.452
 GKL  C3   N1   single  1.457  0.020  1.457
 GKL  C3   C4   single  1.534  0.020  1.534
 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  1.451  0.020  1.451
 GKL  N2   H15  single  0.890  0.020  1.040
 GKL  C8   C    single  1.549  0.020  1.549
 GKL  C8   C10  single  1.537  0.020  1.537
 GKL  C8   H16  single  0.970  0.020  1.090
 GKL  C    O    deloc   1.231  0.020  1.231
 GKL  C    OXT  deloc   1.248  0.020  1.248
 GKL  C10  C11  single  1.527  0.020  1.527
 GKL  C10  C12  single  1.529  0.020  1.529
 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  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   104.73  3.000
 GKL  H26  C1   C3   106.95  3.000
 GKL  H26  C1   C2   107.72  3.000
 GKL  C3   C1   C2   113.01  3.000
 GKL  H26  C1   O1   110.19  3.000
 GKL  C3   C1   O1   110.09  3.000
 GKL  C2   C1   O1   108.83  3.000
 GKL  H2   C2   H1   106.74  3.000
 GKL  H2   C2   N2   113.41  3.000
 GKL  H1   C2   N2   109.46  3.000
 GKL  N2   C2   C1   108.15  3.000
 GKL  H2   C2   C1   110.62  3.000
 GKL  H1   C2   C1   108.36  3.000
 GKL  H3   C3   C4   108.49  3.000
 GKL  H3   C3   N1   107.15  3.000
 GKL  C4   C3   N1   114.61  3.000
 GKL  H3   C3   C1   105.38  3.000
 GKL  C4   C3   C1   110.81  3.000
 GKL  N1   C3   C1   109.92  3.000
 GKL  H5   N1   H4   106.03  3.000
 GKL  H5   N1   C3   109.98  3.000
 GKL  H4   N1   C3   109.11  3.000
 GKL  H7   C4   H6   106.38  3.000
 GKL  H7   C4   C5   108.38  3.000
 GKL  H6   C4   C5   108.56  3.000
 GKL  H7   C4   C3   108.97  3.000
 GKL  H6   C4   C3   108.71  3.000
 GKL  C5   C4   C3   115.47  3.000
 GKL  H8   C5   C7   108.20  3.000
 GKL  H8   C5   C6   107.34  3.000
 GKL  C7   C5   C6   110.49  3.000
 GKL  H8   C5   C4   108.39  3.000
 GKL  C7   C5   C4   112.25  3.000
 GKL  C6   C5   C4   110.01  3.000
 GKL  H11  C6   H10  107.74  3.000
 GKL  H11  C6   H9   107.58  3.000
 GKL  H10  C6   H9   107.61  3.000
 GKL  H11  C6   C5   111.27  3.000
 GKL  H10  C6   C5   111.49  3.000
 GKL  H9   C6   C5   110.96  3.000
 GKL  H14  C7   H13  107.59  3.000
 GKL  H14  C7   H12  107.22  3.000
 GKL  H13  C7   H12  107.60  3.000
 GKL  H14  C7   C5   112.44  3.000
 GKL  H13  C7   C5   110.70  3.000
 GKL  H12  C7   C5   111.07  3.000
 GKL  H15  N2   C8   111.01  3.000
 GKL  H15  N2   C2   108.86  3.000
 GKL  C8   N2   C2   115.72  3.000
 GKL  H16  C8   C10  107.33  3.000
 GKL  H16  C8   C    108.20  3.000
 GKL  C10  C8   C    109.83  3.000
 GKL  H16  C8   N2   111.83  3.000
 GKL  C10  C8   N2   110.42  3.000
 GKL  C    C8   N2   109.18  3.000
 GKL  OXT  C    O    126.40  3.000
 GKL  OXT  C    C8   117.04  3.000
 GKL  O    C    C8   116.55  3.000
 GKL  H17  C10  C12  108.54  3.000
 GKL  H17  C10  C11  108.61  3.000
 GKL  C12  C10  C11  108.94  3.000
 GKL  H17  C10  C8   107.09  3.000
 GKL  C12  C10  C8   112.42  3.000
 GKL  C11  C10  C8   111.13  3.000
 GKL  H20  C11  H19  107.36  3.000
 GKL  H20  C11  H18  107.70  3.000
 GKL  H19  C11  H18  107.51  3.000
 GKL  H20  C11  C10  112.63  3.000
 GKL  H19  C11  C10  110.58  3.000
 GKL  H18  C11  C10  110.84  3.000
 GKL  H23  C12  H22  106.48  3.000
 GKL  H23  C12  H21  107.47  3.000
 GKL  H22  C12  H21  107.67  3.000
 GKL  H23  C12  C10  110.40  3.000
 GKL  H22  C12  C10  113.63  3.000
 GKL  H21  C12  C10  110.92  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  Var_01  C8   N2   C2   C1   150.77  30.0  3
 GKL  Var_02  C6   C5   C4   C3   175.01  30.0  3
 GKL  Var_03  H9   C6   C5   C4    63.01  30.0  3
 GKL  Var_04  H12  C7   C5   C4  -178.04  30.0  3
 GKL  Var_05  H18  C11  C10  C8    57.73  30.0  3
 GKL  Var_06  H21  C12  C10  C8   -60.77  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

