# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:01:14 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  34  14  .  2022-03-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   4.7764   0.6838  -0.8279
 1OL  C2   C  CH3    0  -0.661   3.6750   1.1502   1.3713
 1OL  C3   C  CH1    0  -0.221   3.7187   0.2147   0.1671
 1OL  C4   C  CH2    0  -0.394   2.3604   0.1035  -0.5277
 1OL  N    N  NH2    0  -0.797   1.6043  -1.8868   0.6606
 1OL  C5   C  CH1    0  -0.114   1.2428  -0.5210   0.3050
 1OL  C6   C  CH1    0   0.042  -0.1206  -0.3615  -0.3963
 1OL  O1   O  OH1    0  -0.674  -0.1260  -0.9392  -1.6927
 1OL  C7   C  CH2    0  -0.439  -1.2714  -0.8872   0.4538
 1OL  CA   C  CH1    0  -0.341  -2.6596  -0.5242  -0.0589
 1OL  C9   C  CH3    0  -0.661  -3.7325  -1.2491   0.7574
 1OL  C    C  C      0   0.413  -2.9544   0.9900  -0.0230
 1OL  O    O  O      0  -0.613  -2.3889   1.6669   0.8607
 1OL  H1   H  HCH3   0   0.221   5.7585   0.7628  -0.3576
 1OL  H20  H  HCH3   0   0.221   4.8662  -0.0054  -1.6697
 1OL  H3   H  HCH3   0   0.209   4.5259   1.6681  -1.2327
 1OL  H4   H  HCH3   0   0.222   4.6629   1.2504   1.8254
 1OL  H5   H  HCH3   0   0.209   3.3453   2.1498   1.0755
 1OL  H6   H  HCH3   0   0.226   2.9980   0.7948   2.1490
 1OL  H7   H  HCH1   0   0.211   3.9998  -0.7826   0.5191
 1OL  H8   H  HCH2   0   0.206   2.0440   1.1039  -0.8469
 1OL  H9   H  HCH2   0   0.212   2.4782  -0.4796  -1.4477
 1OL  H10  H  HNH2   0   0.350   0.8938  -2.3055   1.2474
 1OL  H11  H  HCH1   0   0.215   1.1542   0.0404   1.2424
 1OL  H12  H  HCH1   0   0.211  -0.2679   0.7122  -0.5532
 1OL  H13  H  HOH1   0   0.433  -0.1865  -1.8948  -1.5929
 1OL  H14  H  HCH2   0   0.200  -1.1919  -1.9801   0.5243
 1OL  H15  H  HCH2   0   0.212  -1.1559  -0.5103   1.4733
 1OL  H16  H  HCH1   0   0.199  -2.7526  -0.8623  -1.0962
 1OL  H17  H  HCH3   0   0.224  -4.7350  -1.0052   0.4031
 1OL  H18  H  HCH3   0   0.218  -3.6123  -2.3328   0.6936
 1OL  H19  H  HCH3   0   0.211  -3.6740  -0.9738   1.8130
 1OL  OXT  O  OC    -1  -0.625  -3.7793   1.4157  -0.8585
 1OL  H2   H  HNH2   0   0.329   1.6703  -2.4624  -0.1707

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  1.457  0.020  1.457
 1OL  N   H10  single  0.890  0.020  1.040
 1OL  C5  C6   single  1.541  0.020  1.541
 1OL  C5  H11  single  0.970  0.020  1.090
 1OL  C6  O1   single  1.419  0.020  1.419
 1OL  C6  H12  single  0.970  0.020  1.090
 1OL  C6  C7   single  1.524  0.020  1.524
 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  1.531  0.020  1.531
 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    deloc   1.231  0.020  1.231
 1OL  C   OXT  deloc   1.249  0.020  1.249
 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  107.56  3.000
 1OL  H3   C1  H1   107.49  3.000
 1OL  H20  C1  H1   107.69  3.000
 1OL  H3   C1  C3   111.06  3.000
 1OL  H20  C1  C3   111.45  3.000
 1OL  H1   C1  C3   111.40  3.000
 1OL  H6   C2  H5   107.68  3.000
 1OL  H6   C2  H4   107.15  3.000
 1OL  H5   C2  H4   107.55  3.000
 1OL  H6   C2  C3   112.38  3.000
 1OL  H5   C2  C3   110.84  3.000
 1OL  H4   C2  C3   111.02  3.000
 1OL  H7   C3  C4   107.94  3.000
 1OL  H7   C3  C2   108.20  3.000
 1OL  C4   C3  C2   112.19  3.000
 1OL  H7   C3  C1   108.17  3.000
 1OL  C4   C3  C1   109.98  3.000
 1OL  C2   C3  C1   110.24  3.000
 1OL  H9   C4  H8   105.79  3.000
 1OL  H9   C4  C5   108.60  3.000
 1OL  H8   C4  C5   108.70  3.000
 1OL  H9   C4  C3   108.94  3.000
 1OL  H8   C4  C3   108.79  3.000
 1OL  C5   C4  C3   115.59  3.000
 1OL  H2   N   H10  106.64  3.000
 1OL  H2   N   C5   110.39  3.000
 1OL  H10  N   C5   110.80  3.000
 1OL  H11  C5  C6   105.34  3.000
 1OL  H11  C5  N    106.94  3.000
 1OL  C6   C5  N    115.31  3.000
 1OL  H11  C5  C4   108.42  3.000
 1OL  C6   C5  C4   110.91  3.000
 1OL  N    C5  C4   109.56  3.000
 1OL  H12  C6  C7   108.45  3.000
 1OL  C7   C6  O1   111.48  3.000
 1OL  H12  C6  O1   105.52  3.000
 1OL  C7   C6  C5   112.23  3.000
 1OL  H12  C6  C5   106.59  3.000
 1OL  O1   C6  C5   112.14  3.000
 1OL  H13  O1  C6   108.04  3.000
 1OL  H15  C7  H14  106.00  3.000
 1OL  H15  C7  CA   109.15  3.000
 1OL  H14  C7  CA   108.94  3.000
 1OL  H15  C7  C6   108.75  3.000
 1OL  H14  C7  C6   108.93  3.000
 1OL  CA   C7  C6   114.71  3.000
 1OL  H16  CA  C    107.98  3.000
 1OL  H16  CA  C9   107.43  3.000
 1OL  C    CA  C9   108.57  3.000
 1OL  H16  CA  C7   108.82  3.000
 1OL  C    CA  C7   113.57  3.000
 1OL  C9   CA  C7   110.26  3.000
 1OL  H19  C9  H18  107.49  3.000
 1OL  H19  C9  H17  107.86  3.000
 1OL  H18  C9  H17  107.70  3.000
 1OL  H19  C9  CA   111.00  3.000
 1OL  H18  C9  CA   111.20  3.000
 1OL  H17  C9  CA   111.41  3.000
 1OL  OXT  C   O    126.00  3.000
 1OL  OXT  C   CA   120.80  1.700
 1OL  O    C   CA   120.80  1.700

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  Var_01  C5  C4  C3  C1  172.73  30.0  3
 1OL  Var_02  H4  C2  C3  C1  -54.53  30.0  3
 1OL  Var_03  H1  C1  C3  C2   56.29  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

