# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:03:32 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S)-2-amino-3-oxopropyl hexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)OC[C@H](N)C=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
 2JG  2JG  '(2S)-2-amino-3-oxopropyl hexanoate'  L-peptide  30  13  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2JG
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
 2JG  C8   C  C     0   0.588   0.4379  -18.7960  -23.0539
 2JG  C10  C  CH2   0  -0.583   0.6706  -17.3708  -23.4851
 2JG  C11  C  CH2   0  -0.427  -0.2506  -16.3702  -22.8002
 2JG  C12  C  CH2   0  -0.410  -1.7056  -16.4848  -23.2375
 2JG  C13  C  CH2   0  -0.417  -2.6030  -15.4444  -22.5788
 2JG  C14  C  CH3   0  -0.659  -4.0528  -15.5410  -23.0318
 2JG  N    N  NH2   0  -0.808  -1.7415  -20.9172  -24.4949
 2JG  CA   C  CH1   0  -0.224  -0.4651  -21.5541  -24.7740
 2JG  CB   C  CH2   0  -0.166   0.6133  -21.0582  -23.8239
 2JG  OG   O  O2    0  -0.466   0.7800  -19.6526  -24.0168
 2JG  O9   O  O     0  -0.440   0.0322  -19.1266  -21.9693
 2JG  C    C  C1    0   0.173  -0.6314  -23.0512  -24.6663
 2JG  H1   H  HCH2  0   0.287   1.7147  -17.1386  -23.2476
 2JG  H2   H  HCH2  0   0.259   0.5849  -17.2935  -24.5707
 2JG  H3   H  HCH2  0   0.232   0.1124  -15.3650  -23.0300
 2JG  H4   H  HCH2  0   0.224  -0.1759  -16.4777  -21.7153
 2JG  H5   H  HCH2  0   0.214  -2.0900  -17.4853  -23.0116
 2JG  H6   H  HCH2  0   0.210  -1.7647  -16.3760  -24.3261
 2JG  H7   H  HCH2  0   0.211  -2.2163  -14.4443  -22.7979
 2JG  H8   H  HCH2  0   0.212  -2.5489  -15.5576  -21.4918
 2JG  H9   H  HCH3  0   0.225  -4.6758  -14.7902  -22.5446
 2JG  H10  H  HCH3  0   0.216  -4.1403  -15.3932  -24.1097
 2JG  H11  H  HCH3  0   0.215  -4.4741  -16.5208  -22.7996
 2JG  H13  H  HNH2  0   0.358  -2.4792  -21.3734  -25.0193
 2JG  H15  H  HCH1  0   0.265  -0.1211  -21.3891  -25.8114
 2JG  H16  H  HCH2  0   0.246   0.3482  -21.2846  -22.7916
 2JG  H17  H  HCH2  0   0.253   1.5719  -21.5226  -24.0523
 2JG  H18  H  H     0   0.212  -1.5843  -23.4333  -25.0792
 2JG  H12  H  HNH2  0   0.363  -1.7284  -19.9644  -24.8353
 2JG  O    O  O     0  -0.364   0.1902  -23.8020  -24.2098

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
 2JG  O    C    double  1.231  0.020  1.231
 2JG  C    CA   single  1.525  0.021  1.525
 2JG  CA   CB   single  1.530  0.020  1.530
 2JG  CA   N    single  1.458  0.019  1.458
 2JG  CB   OG   single  1.428  0.020  1.428
 2JG  OG   C8   single  1.333  0.020  1.333
 2JG  C14  C13  single  1.522  0.020  1.522
 2JG  C12  C13  single  1.524  0.020  1.524
 2JG  C12  C11  single  1.524  0.020  1.524
 2JG  C8   C10  single  1.507  0.020  1.507
 2JG  C8   O9   double  1.204  0.020  1.204
 2JG  C10  C11  single  1.523  0.020  1.523
 2JG  C10  H1   single  0.970  0.020  1.090
 2JG  C10  H2   single  0.970  0.020  1.090
 2JG  C11  H3   single  0.970  0.020  1.090
 2JG  C11  H4   single  0.970  0.020  1.090
 2JG  C12  H5   single  0.970  0.020  1.090
 2JG  C12  H6   single  0.970  0.020  1.090
 2JG  C13  H7   single  0.970  0.020  1.090
 2JG  C13  H8   single  0.970  0.020  1.090
 2JG  C14  H9   single  0.970  0.020  1.090
 2JG  C14  H10  single  0.970  0.020  1.090
 2JG  C14  H11  single  0.970  0.020  1.090
 2JG  N    H12  single  0.890  0.020  1.040
 2JG  N    H13  single  0.890  0.020  1.040
 2JG  CA   H15  single  0.970  0.020  1.090
 2JG  CB   H16  single  0.970  0.020  1.090
 2JG  CB   H17  single  0.970  0.020  1.090
 2JG  C    H18  single  0.930  0.020  1.080

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
 2JG  O9   C8   OG   124.09  3.000
 2JG  O9   C8   C10  124.70  3.000
 2JG  OG   C8   C10  111.18  3.000
 2JG  H2   C10  H1   105.98  3.000
 2JG  H2   C10  C11  110.69  3.000
 2JG  H1   C10  C11  109.86  3.000
 2JG  H2   C10  C8   109.83  3.000
 2JG  H1   C10  C8   106.59  3.000
 2JG  C11  C10  C8   113.53  3.000
 2JG  H4   C11  H3   106.05  3.000
 2JG  H4   C11  C12  110.05  3.000
 2JG  H3   C11  C12  109.02  3.000
 2JG  H4   C11  C10  109.91  3.000
 2JG  H3   C11  C10  107.98  3.000
 2JG  C12  C11  C10  113.53  3.000
 2JG  H6   C12  H5   106.06  3.000
 2JG  H6   C12  C13  109.27  3.000
 2JG  H5   C12  C13  109.14  3.000
 2JG  H6   C12  C11  109.22  3.000
 2JG  H5   C12  C11  110.16  3.000
 2JG  C13  C12  C11  112.77  3.000
 2JG  H8   C13  H7   106.02  3.000
 2JG  H8   C13  C14  109.64  3.000
 2JG  H7   C13  C14  109.57  3.000
 2JG  H8   C13  C12  109.25  3.000
 2JG  H7   C13  C12  109.23  3.000
 2JG  C14  C13  C12  112.90  3.000
 2JG  H11  C14  H10  107.50  3.000
 2JG  H11  C14  H9   107.61  3.000
 2JG  H10  C14  H9   107.59  3.000
 2JG  H11  C14  C13  111.18  3.000
 2JG  H10  C14  C13  111.20  3.000
 2JG  H9   C14  C13  111.57  3.000
 2JG  H13  N    H12  105.02  3.000
 2JG  H13  N    CA   110.04  3.000
 2JG  H12  N    CA   109.67  3.000
 2JG  H15  CA   C    104.43  3.000
 2JG  H15  CA   CB   108.48  3.000
 2JG  C    CA   CB   110.10  1.900
 2JG  H15  CA   N    112.84  3.000
 2JG  CB   CA   N    110.50  1.700
 2JG  C    CA   N    111.00  2.800
 2JG  H17  CB   H16  108.91  3.000
 2JG  H17  CB   OG   106.76  3.000
 2JG  H16  CB   OG   111.15  3.000
 2JG  H17  CB   CA   110.74  3.000
 2JG  H16  CB   CA   110.59  3.000
 2JG  OG   CB   CA   108.62  3.000
 2JG  CB   OG   C8   120.31  3.000
 2JG  H18  C    CA   114.24  3.000
 2JG  H18  C    O    120.95  3.000
 2JG  CA   C    O    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
 2JG  Var_01  CA   CB   OG   C8    112.85  30.0  1
 2JG  Var_02  C12  C11  C10  C8    -69.39  30.0  3
 2JG  Var_03  C13  C12  C11  C10  -177.98  30.0  1
 2JG  Var_04  C14  C13  C12  C11   179.01  30.0  3
 2JG  Var_05  OG   C8   C10  C11   152.44  30.0  2
 2JG  Var_06  H9   C14  C13  C12   179.76  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
 2JG  chir_01  CA  C  CB  N  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
 2JG  plan-1  CA   0.020
 2JG  plan-1  C    0.020
 2JG  plan-1  H18  0.020
 2JG  plan-1  O    0.020
 2JG  plan-2  C8   0.020
 2JG  plan-2  C10  0.020
 2JG  plan-2  OG   0.020
 2JG  plan-2  O9   0.020

