# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:40:28 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  25  10  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.442  -2.8591  -0.4974  -0.7252
 0JY  C    C  C     0   0.553  -2.1088   0.2052  -0.0968
 0JY  CA   C  CH1   0  -0.225  -0.7650  -0.2416   0.4493
 0JY  N    N  NH2   0  -0.784  -0.8011  -1.6777   0.6365
 0JY  CB   C  CH2   0  -0.417   0.3218   0.3203  -0.4909
 0JY  CAI  C  CT    0  -0.090   1.7986   0.1530  -0.0798
 0JY  CAB  C  CH3   0  -0.640   2.2985  -1.2861  -0.2375
 0JY  CAC  C  CH3   0  -0.638   2.6200   1.0364  -1.0258
 0JY  CAA  C  CH3   0  -0.651   2.0232   0.6253   1.3558
 0JY  H2   H  HCH1  0   0.269  -0.6455   0.2175   1.4347
 0JY  H3   H  HNH2  0   0.345  -0.6324  -2.1547  -0.2402
 0JY  H4   H  HNH2  0   0.357  -0.0568  -1.9587   1.2586
 0JY  H6   H  HCH2  0   0.232   0.1806  -0.1188  -1.4859
 0JY  H7   H  HCH2  0   0.236   0.1396   1.3934  -0.6077
 0JY  H8   H  HCH3  0   0.223   2.0879  -1.6718  -1.2374
 0JY  H9   H  HCH3  0   0.225   3.3796  -1.3288  -0.0884
 0JY  H10  H  HCH3  0   0.212   1.8547  -1.9723   0.4823
 0JY  H11  H  HCH3  0   0.223   2.3516   2.0898  -0.9214
 0JY  H12  H  HCH3  0   0.225   3.6879   0.9426  -0.8177
 0JY  H13  H  HCH3  0   0.224   2.4595   0.7544  -2.0688
 0JY  H14  H  HCH3  0   0.223   1.5090  -0.0048   2.0843
 0JY  H15  H  HCH3  0   0.231   3.0862   0.6032   1.6056
 0JY  H16  H  HCH3  0   0.225   1.6726   1.6502   1.4981
 0JY  O1   O  OH1   0  -0.595  -2.3567   1.4851   0.1626
 0JY  H1   H  HOH1  0   0.479  -3.1927   1.7519  -0.2487

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    double  1.205  0.020  1.205
 0JY  C    CA   single  1.518  0.020  1.518
 0JY  CA   N    single  1.449  0.020  1.449
 0JY  CA   CB   single  1.543  0.020  1.543
 0JY  CAC  CAI  single  1.533  0.020  1.533
 0JY  CB   CAI  single  1.542  0.020  1.542
 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   single  1.329  0.020  1.329
 0JY  O1   H1   single  0.850  0.020  0.980

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   112.23  3.000
 0JY  O1   C    O    123.17  3.000
 0JY  CA   C    O    124.57  3.000
 0JY  H2   CA   CB   108.62  3.000
 0JY  H2   CA   N    107.60  3.000
 0JY  CB   CA   N    117.21  3.000
 0JY  H2   CA   C    107.30  3.000
 0JY  CB   CA   C    107.29  3.000
 0JY  N    CA   C    108.43  3.000
 0JY  H4   N    H3   106.23  3.000
 0JY  H4   N    CA   109.69  3.000
 0JY  H3   N    CA   110.55  3.000
 0JY  H7   CB   H6   105.91  3.000
 0JY  H7   CB   CAI  107.10  3.000
 0JY  H6   CB   CAI  108.77  3.000
 0JY  H7   CB   CA   107.74  3.000
 0JY  H6   CB   CA   108.45  3.000
 0JY  CAI  CB   CA   118.20  3.000
 0JY  CAA  CAI  CAC  108.84  3.000
 0JY  CAA  CAI  CAB  109.82  3.000
 0JY  CAC  CAI  CAB  107.65  3.000
 0JY  CAA  CAI  CB   110.96  3.000
 0JY  CAB  CAI  CB   112.77  3.000
 0JY  CAC  CAI  CB   106.63  3.000
 0JY  H10  CAB  H9   106.77  3.000
 0JY  H10  CAB  H8   107.70  3.000
 0JY  H9   CAB  H8   107.57  3.000
 0JY  H10  CAB  CAI  113.02  3.000
 0JY  H9   CAB  CAI  110.23  3.000
 0JY  H8   CAB  CAI  111.29  3.000
 0JY  H13  CAC  H12  107.66  3.000
 0JY  H13  CAC  H11  107.71  3.000
 0JY  H12  CAC  H11  107.76  3.000
 0JY  H13  CAC  CAI  111.21  3.000
 0JY  H12  CAC  CAI  110.91  3.000
 0JY  H11  CAC  CAI  111.42  3.000
 0JY  H16  CAA  H15  107.55  3.000
 0JY  H16  CAA  H14  107.66  3.000
 0JY  H15  CAA  H14  107.11  3.000
 0JY  H16  CAA  CAI  111.41  3.000
 0JY  H15  CAA  CAI  110.59  3.000
 0JY  H14  CAA  CAI  112.29  3.000
 0JY  H1   O1   C    110.07  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  CONST_01  H1   O1   C    O      0.00   0.0  0
 0JY  Var_01    CAC  CAI  CB   CA  -168.69  30.0  3
 0JY  Var_02    H11  CAC  CAI  CB    61.98  30.0  3
 0JY  Var_03    H8   CAB  CAI  CB    51.83  30.0  3
 0JY  Var_04    H14  CAA  CAI  CB    66.37  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
 0JY  plan-1  H1  0.020

