# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 13:37:45 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 4-methyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C[C@H](N)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
 0JY  0JY  '4-methyl-L-leucine       '  ligand  24  10  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0JY
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
 0JY  O    O  O      0  -0.611  -2.7557  -0.5678  -0.8673
 0JY  C    C  C      0   0.408  -2.1213   0.2900  -0.2220
 0JY  CA   C  CH1    0  -0.214  -0.7994  -0.1607   0.4404
 0JY  N    N  NH2    0  -0.798  -0.8608  -1.5802   0.7555
 0JY  CB   C  CH2    0  -0.398   0.3405   0.3107  -0.4831
 0JY  CAI  C  CT     0  -0.086   1.8083   0.1406  -0.0387
 0JY  CAB  C  CH3    0  -0.640   2.3102  -1.2958  -0.2148
 0JY  CAC  C  CH3    0  -0.639   2.6623   1.0367  -0.9428
 0JY  CAA  C  CH3    0  -0.648   2.0009   0.5842   1.4111
 0JY  H2   H  HCH1   0   0.204  -0.7078   0.3792   1.3887
 0JY  H3   H  HNH2   0   0.324  -0.9795  -2.1081  -0.1000
 0JY  H4   H  HNH2   0   0.335   0.0066  -1.8922   1.1700
 0JY  H6   H  HCH2   0   0.205   0.2176  -0.1672  -1.4637
 0JY  H7   H  HCH2   0   0.210   0.1753   1.3805  -0.6501
 0JY  H8   H  HCH3   0   0.219   2.1542  -1.6428  -1.2389
 0JY  H9   H  HCH3   0   0.218   3.3808  -1.3569  -0.0048
 0JY  H10  H  HCH3   0   0.213   1.8178  -2.0068   0.4469
 0JY  H11  H  HCH3   0   0.219   2.4008   2.0900  -0.8200
 0JY  H12  H  HCH3   0   0.219   3.7254   0.9284  -0.7153
 0JY  H13  H  HCH3   0   0.220   2.5220   0.7818  -1.9961
 0JY  H14  H  HCH3   0   0.222   1.4586  -0.0511   2.1139
 0JY  H15  H  HCH3   0   0.222   3.0569   0.5485   1.6898
 0JY  H16  H  HCH3   0   0.220   1.6546   1.6095   1.5616
 0JY  O1   O  OC    -1  -0.625  -2.4240   1.4951  -0.0964

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
 0JY  O    C    deloc   1.247  0.020  1.247
 0JY  C    CA   single  1.546  0.020  1.546
 0JY  CA   N    single  1.455  0.020  1.455
 0JY  CA   CB   single  1.541  0.020  1.541
 0JY  CAC  CAI  single  1.533  0.020  1.533
 0JY  CB   CAI  single  1.543  0.020  1.543
 0JY  CAI  CAB  single  1.532  0.020  1.532
 0JY  CAI  CAA  single  1.528  0.020  1.528
 0JY  CA   H2   single  0.970  0.020  1.090
 0JY  N    H3   single  0.890  0.020  1.040
 0JY  N    H4   single  0.890  0.020  1.040
 0JY  CB   H6   single  0.970  0.020  1.090
 0JY  CB   H7   single  0.970  0.020  1.090
 0JY  CAB  H8   single  0.970  0.020  1.090
 0JY  CAB  H9   single  0.970  0.020  1.090
 0JY  CAB  H10  single  0.970  0.020  1.090
 0JY  CAC  H11  single  0.970  0.020  1.090
 0JY  CAC  H12  single  0.970  0.020  1.090
 0JY  CAC  H13  single  0.970  0.020  1.090
 0JY  CAA  H14  single  0.970  0.020  1.090
 0JY  CAA  H15  single  0.970  0.020  1.090
 0JY  CAA  H16  single  0.970  0.020  1.090
 0JY  C    O1   deloc   1.249  0.020  1.249

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
 0JY  O1   C    CA   116.46  3.000
 0JY  O1   C    O    126.34  3.000
 0JY  CA   C    O    117.15  3.000
 0JY  H2   CA   CB   107.84  3.000
 0JY  H2   CA   N    107.28  3.000
 0JY  CB   CA   N    117.35  3.000
 0JY  H2   CA   C    107.39  3.000
 0JY  CB   CA   C    106.65  3.000
 0JY  N    CA   C    109.94  3.000
 0JY  H4   N    H3   106.63  3.000
 0JY  H4   N    CA   110.71  3.000
 0JY  H3   N    CA   109.31  3.000
 0JY  H7   CB   H6   105.79  3.000
 0JY  H7   CB   CAI  107.16  3.000
 0JY  H6   CB   CAI  108.40  3.000
 0JY  H7   CB   CA   106.18  3.000
 0JY  H6   CB   CA   108.63  3.000
 0JY  CAI  CB   CA   119.82  3.000
 0JY  CAA  CAI  CAC  108.64  3.000
 0JY  CAA  CAI  CAB  109.87  3.000
 0JY  CAC  CAI  CAB  107.33  3.000
 0JY  CAA  CAI  CB   111.16  3.000
 0JY  CAB  CAI  CB   112.46  3.000
 0JY  CAC  CAI  CB   107.20  3.000
 0JY  H10  CAB  H9   106.84  3.000
 0JY  H10  CAB  H8   107.32  3.000
 0JY  H9   CAB  H8   107.59  3.000
 0JY  H10  CAB  CAI  113.22  3.000
 0JY  H9   CAB  CAI  110.57  3.000
 0JY  H8   CAB  CAI  111.03  3.000
 0JY  H13  CAC  H12  107.61  3.000
 0JY  H13  CAC  H11  107.61  3.000
 0JY  H12  CAC  H11  107.76  3.000
 0JY  H13  CAC  CAI  111.14  3.000
 0JY  H12  CAC  CAI  111.18  3.000
 0JY  H11  CAC  CAI  111.35  3.000
 0JY  H16  CAA  H15  107.57  3.000
 0JY  H16  CAA  H14  107.46  3.000
 0JY  H15  CAA  H14  107.27  3.000
 0JY  H16  CAA  CAI  111.29  3.000
 0JY  H15  CAA  CAI  110.74  3.000
 0JY  H14  CAA  CAI  112.28  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
 0JY  Var_01  CAC  CAI  CB   CA  -164.19  30.0  3
 0JY  Var_02  H11  CAC  CAI  CB    62.61  30.0  3
 0JY  Var_03  H8   CAB  CAI  CB    53.94  30.0  3
 0JY  Var_04  H14  CAA  CAI  CB    65.35  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
 0JY  chir_01  CA  C  N  CB  negativ

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
 0JY  plan-1  O   0.020
 0JY  plan-1  C   0.020
 0JY  plan-1  CA  0.020
 0JY  plan-1  O1  0.020

