# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:30:10 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2R,4S,5S)-5-amino-4-hydroxy-2,7-dimethyloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)C[C@@H](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
 1OL  1OL  '(2R,4S,5S)-5-amino-4-hydroxy-2,7-dimethyloctanoic acid'  peptide  35  14  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1OL
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
 1OL  C1   C  CH3   0  -0.654   4.7630   0.7345  -0.8541
 1OL  C2   C  CH3   0  -0.662   3.6899   1.1435   1.3709
 1OL  C3   C  CH1   0  -0.221   3.7194   0.2389   0.1430
 1OL  C4   C  CH2   0  -0.395   2.3529   0.1429  -0.5375
 1OL  N    N  NH2   0  -0.796   1.6092  -1.8591   0.6385
 1OL  C5   C  CH1   0  -0.117   1.2450  -0.4912   0.3010
 1OL  C6   C  CH1   0   0.038  -0.1248  -0.3232  -0.3868
 1OL  O1   O  OH1   0  -0.667  -0.1543  -0.8835  -1.6870
 1OL  C7   C  CH2   0  -0.458  -1.2625  -0.8646   0.4746
 1OL  CA   C  CH1   0  -0.368  -2.6596  -0.5389  -0.0398
 1OL  C9   C  CH3   0  -0.659  -3.7293  -1.3038   0.7514
 1OL  C    C  C     0   0.555  -2.9658   0.9368   0.0575
 1OL  O    O  O     0  -0.446  -2.4918   1.6921   0.8709
 1OL  H1   H  HCH3  0   0.222   5.7512   0.8025  -0.3954
 1OL  H20  H  HCH3  0   0.221   4.8420   0.0672  -1.7144
 1OL  H3   H  HCH3  0   0.210   4.5059   1.7284  -1.2300
 1OL  H4   H  HCH3  0   0.223   4.6842   1.2365   1.8122
 1OL  H5   H  HCH3  0   0.210   3.3514   2.1490   1.1068
 1OL  H6   H  HCH3  0   0.226   3.0270   0.7647   2.1497
 1OL  H7   H  HCH1  0   0.213   4.0064  -0.7661   0.4666
 1OL  H8   H  HCH2  0   0.208   2.0356   1.1490  -0.8372
 1OL  H9   H  HCH2  0   0.214   2.4585  -0.4265  -1.4674
 1OL  H10  H  HNH2  0   0.352   0.9194  -2.2841   1.2445
 1OL  H11  H  HCH1  0   0.222   1.1649   0.0609   1.2441
 1OL  H12  H  HCH1  0   0.220  -0.2682   0.7533  -0.5333
 1OL  H13  H  HOH1  0   0.437  -0.1588  -1.8428  -1.6037
 1OL  H14  H  HCH2  0   0.232  -1.1766  -1.9547   0.5379
 1OL  H15  H  HCH2  0   0.236  -1.1507  -0.4956   1.4975
 1OL  H16  H  HCH1  0   0.266  -2.7389  -0.8359  -1.0887
 1OL  H17  H  HCH3  0   0.245  -4.7369  -1.0719   0.4076
 1OL  H18  H  HCH3  0   0.246  -3.5768  -2.3762   0.6310
 1OL  H19  H  HCH3  0   0.232  -3.6690  -1.0746   1.8162
 1OL  OXT  O  OH1   0  -0.593  -3.8732   1.3194  -0.8356
 1OL  HXT  H  HOH1  0   0.477  -4.0921   2.2542  -0.7048
 1OL  H2   H  HNH2  0   0.332   1.6646  -2.4328  -0.1946

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
 1OL  C1   C3   single  1.526  0.020  1.526
 1OL  C1   H1   single  0.970  0.020  1.090
 1OL  C1   H20  single  0.970  0.020  1.090
 1OL  C1   H3   single  0.970  0.020  1.090
 1OL  C2   C3   single  1.525  0.020  1.525
 1OL  C2   H4   single  0.970  0.020  1.090
 1OL  C2   H5   single  0.970  0.020  1.090
 1OL  C2   H6   single  0.970  0.020  1.090
 1OL  C3   C4   single  1.530  0.020  1.530
 1OL  C3   H7   single  0.970  0.020  1.090
 1OL  C4   C5   single  1.527  0.020  1.527
 1OL  C4   H8   single  0.970  0.020  1.090
 1OL  C4   H9   single  0.970  0.020  1.090
 1OL  N    C5   single  1.455  0.020  1.455
 1OL  N    H10  single  0.890  0.020  1.040
 1OL  C5   C6   single  1.542  0.020  1.542
 1OL  C5   H11  single  0.970  0.020  1.090
 1OL  C6   O1   single  1.416  0.020  1.416
 1OL  C6   H12  single  0.970  0.020  1.090
 1OL  C6   C7   single  1.526  0.020  1.526
 1OL  O1   H13  single  0.850  0.020  0.980
 1OL  C7   CA   single  1.524  0.020  1.524
 1OL  C7   H14  single  0.970  0.020  1.090
 1OL  C7   H15  single  0.970  0.020  1.090
 1OL  CA   C9   single  1.535  0.020  1.535
 1OL  CA   C    single  1.525  0.021  1.525
 1OL  CA   H16  single  0.970  0.020  1.090
 1OL  C9   H17  single  0.970  0.020  1.090
 1OL  C9   H18  single  0.970  0.020  1.090
 1OL  C9   H19  single  0.970  0.020  1.090
 1OL  C    O    double  1.231  0.020  1.231
 1OL  C    OXT  single  1.329  0.020  1.329
 1OL  OXT  HXT  single  0.850  0.020  0.980
 1OL  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
 1OL  H3   C1   H20  107.57  3.000
 1OL  H3   C1   H1   107.50  3.000
 1OL  H20  C1   H1   107.68  3.000
 1OL  H3   C1   C3   111.04  3.000
 1OL  H20  C1   C3   111.46  3.000
 1OL  H1   C1   C3   111.39  3.000
 1OL  H6   C2   H5   107.68  3.000
 1OL  H6   C2   H4   107.13  3.000
 1OL  H5   C2   H4   107.54  3.000
 1OL  H6   C2   C3   112.37  3.000
 1OL  H5   C2   C3   110.91  3.000
 1OL  H4   C2   C3   110.99  3.000
 1OL  H7   C3   C4   107.96  3.000
 1OL  H7   C3   C2   108.16  3.000
 1OL  C4   C3   C2   112.21  3.000
 1OL  H7   C3   C1   108.19  3.000
 1OL  C4   C3   C1   109.92  3.000
 1OL  C2   C3   C1   110.28  3.000
 1OL  H9   C4   H8   105.82  3.000
 1OL  H9   C4   C5   108.67  3.000
 1OL  H8   C4   C5   108.73  3.000
 1OL  H9   C4   C3   108.91  3.000
 1OL  H8   C4   C3   108.81  3.000
 1OL  C5   C4   C3   115.46  3.000
 1OL  H2   N    H10  106.98  3.000
 1OL  H2   N    C5   110.81  3.000
 1OL  H10  N    C5   111.29  3.000
 1OL  H11  C5   C6   105.31  3.000
 1OL  H11  C5   N    106.99  3.000
 1OL  C6   C5   N    115.35  3.000
 1OL  H11  C5   C4   108.45  3.000
 1OL  C6   C5   C4   110.75  3.000
 1OL  N    C5   C4   109.64  3.000
 1OL  H12  C6   C7   109.05  3.000
 1OL  C7   C6   O1   111.24  3.000
 1OL  H12  C6   O1   105.26  3.000
 1OL  C7   C6   C5   111.83  3.000
 1OL  H12  C6   C5   106.43  3.000
 1OL  O1   C6   C5   112.64  3.000
 1OL  H13  O1   C6   108.35  3.000
 1OL  H15  C7   H14  105.89  3.000
 1OL  H15  C7   CA   109.72  3.000
 1OL  H14  C7   CA   107.70  3.000
 1OL  H15  C7   C6   109.40  3.000
 1OL  H14  C7   C6   109.10  3.000
 1OL  CA   C7   C6   114.65  3.000
 1OL  H16  CA   C    108.21  3.000
 1OL  H16  CA   C9   107.98  3.000
 1OL  C    CA   C9   108.21  3.000
 1OL  H16  CA   C7   109.41  3.000
 1OL  C    CA   C7   111.89  3.000
 1OL  C9   CA   C7   111.01  3.000
 1OL  H19  C9   H18  107.87  3.000
 1OL  H19  C9   H17  108.32  3.000
 1OL  H18  C9   H17  107.70  3.000
 1OL  H19  C9   CA   111.10  3.000
 1OL  H18  C9   CA   109.63  3.000
 1OL  H17  C9   CA   112.07  3.000
 1OL  OXT  C    O    122.73  3.000
 1OL  OXT  C    CA   120.80  1.700
 1OL  O    C    CA   120.80  1.700
 1OL  HXT  OXT  C    109.94  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
 1OL  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 1OL  Var_01    C5   C4   C3  C1  173.35  30.0  3
 1OL  Var_02    H4   C2   C3  C1  -54.34  30.0  3
 1OL  Var_03    H1   C1   C3  C2   56.34  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
 1OL  chir_01  C5  C4  N   C6  positiv
 1OL  chir_02  C6  O1  C5  C7  positiv
 1OL  chir_03  CA  C   C9  C7  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
 1OL  plan-1  CA   0.020
 1OL  plan-1  C    0.020
 1OL  plan-1  O    0.020
 1OL  plan-1  OXT  0.020
 1OL  plan-1  HXT  0.020

