# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:57:42 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-methyl-D-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@](C)(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
 2JN  2JN  '2-methyl-D-norleucine    '  D-peptide  25  10  .  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_2JN
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
 2JN  OAE  O  O     0  -0.445  -2.0490  -1.6521   0.1796
 2JN  CAG  C  C     0   0.578  -2.0115  -0.4678  -0.0506
 2JN  CAQ  C  CT    0  -0.062  -0.7510   0.3906   0.0692
 2JN  CAA  C  CH3   0  -0.662  -0.7908   0.9987   1.4791
 2JN  NAC  N  NH2   0  -0.786  -0.8223   1.4772  -0.8955
 2JN  CAO  C  CH2   0  -0.402   0.4809  -0.5171  -0.1045
 2JN  CAM  C  CH2   0  -0.422   1.8192   0.1981   0.0390
 2JN  CAK  C  CH2   0  -0.415   2.9992  -0.7262  -0.2362
 2JN  CAI  C  CH3   0  -0.662   4.3431  -0.0260  -0.0903
 2JN  O1   O  OH1   0  -0.582  -3.0896   0.2286  -0.3811
 2JN  H1   H  HCH3  0   0.239  -0.7102   0.2273   2.2449
 2JN  H2   H  HCH3  0   0.245   0.0420   1.6904   1.6133
 2JN  H3   H  HCH3  0   0.248  -1.7107   1.5595   1.6425
 2JN  H4   H  HNH2  0   0.350  -0.0671   2.1286  -0.7216
 2JN  H5   H  HNH2  0   0.347  -0.6709   1.1237  -1.8336
 2JN  H7   H  HCH2  0   0.223   0.4419  -1.3358   0.6179
 2JN  H8   H  HCH2  0   0.225   0.4348  -0.9819  -1.0962
 2JN  H9   H  HCH2  0   0.204   1.8690   1.0497  -0.6473
 2JN  H10  H  HCH2  0   0.219   1.9215   0.6086   1.0483
 2JN  H11  H  HCH2  0   0.212   2.9590  -1.5820   0.4456
 2JN  H12  H  HCH2  0   0.212   2.9089  -1.1403  -1.2454
 2JN  H13  H  HCH3  0   0.216   4.4339   0.8080  -0.7884
 2JN  H14  H  HCH3  0   0.216   4.4724   0.3734   0.9174
 2JN  H15  H  HCH3  0   0.226   5.1718  -0.7085  -0.2830
 2JN  H16  H  HOH1  0   0.476  -3.8602  -0.3587  -0.3789

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
 2JN  CAG  OAE  double  1.207  0.020  1.207
 2JN  CAG  CAQ  single  1.530  0.020  1.530
 2JN  CAA  CAQ  single  1.536  0.020  1.536
 2JN  CAQ  NAC  single  1.455  0.020  1.455
 2JN  CAQ  CAO  single  1.540  0.020  1.540
 2JN  CAO  CAM  single  1.524  0.020  1.524
 2JN  CAM  CAK  single  1.524  0.020  1.524
 2JN  CAK  CAI  single  1.522  0.020  1.522
 2JN  CAG  O1   single  1.325  0.020  1.325
 2JN  CAA  H1   single  0.970  0.020  1.090
 2JN  CAA  H2   single  0.970  0.020  1.090
 2JN  CAA  H3   single  0.970  0.020  1.090
 2JN  NAC  H4   single  0.890  0.020  1.040
 2JN  NAC  H5   single  0.890  0.020  1.040
 2JN  CAO  H7   single  0.970  0.020  1.090
 2JN  CAO  H8   single  0.970  0.020  1.090
 2JN  CAM  H9   single  0.970  0.020  1.090
 2JN  CAM  H10  single  0.970  0.020  1.090
 2JN  CAK  H11  single  0.970  0.020  1.090
 2JN  CAK  H12  single  0.970  0.020  1.090
 2JN  CAI  H13  single  0.970  0.020  1.090
 2JN  CAI  H14  single  0.970  0.020  1.090
 2JN  CAI  H15  single  0.970  0.020  1.090
 2JN  O1   H16  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
 2JN  O1   CAG  CAQ  113.27  3.000
 2JN  O1   CAG  OAE  122.53  3.000
 2JN  CAQ  CAG  OAE  124.14  3.000
 2JN  CAO  CAQ  NAC  113.87  3.000
 2JN  CAO  CAQ  CAA  110.95  3.000
 2JN  NAC  CAQ  CAA  108.16  3.000
 2JN  CAO  CAQ  CAG  108.64  3.000
 2JN  NAC  CAQ  CAG  109.08  3.000
 2JN  CAA  CAQ  CAG  105.83  3.000
 2JN  H3   CAA  H2   107.44  3.000
 2JN  H3   CAA  H1   108.74  3.000
 2JN  H2   CAA  H1   107.81  3.000
 2JN  H3   CAA  CAQ  111.30  3.000
 2JN  H2   CAA  CAQ  110.13  3.000
 2JN  H1   CAA  CAQ  111.27  3.000
 2JN  H5   NAC  H4   105.78  3.000
 2JN  H5   NAC  CAQ  110.23  3.000
 2JN  H4   NAC  CAQ  109.28  3.000
 2JN  H8   CAO  H7   106.20  3.000
 2JN  H8   CAO  CAM  108.73  3.000
 2JN  H7   CAO  CAM  108.71  3.000
 2JN  H8   CAO  CAQ  108.56  3.000
 2JN  H7   CAO  CAQ  109.79  3.000
 2JN  CAM  CAO  CAQ  114.53  3.000
 2JN  H10  CAM  H9   106.39  3.000
 2JN  H10  CAM  CAK  108.77  3.000
 2JN  H9   CAM  CAK  108.86  3.000
 2JN  H10  CAM  CAO  110.17  3.000
 2JN  H9   CAM  CAO  110.24  3.000
 2JN  CAK  CAM  CAO  112.22  3.000
 2JN  H12  CAK  H11  105.98  3.000
 2JN  H12  CAK  CAI  109.59  3.000
 2JN  H11  CAK  CAI  109.40  3.000
 2JN  H12  CAK  CAM  109.40  3.000
 2JN  H11  CAK  CAM  109.46  3.000
 2JN  CAI  CAK  CAM  112.79  3.000
 2JN  H15  CAI  H14  107.58  3.000
 2JN  H15  CAI  H13  107.58  3.000
 2JN  H14  CAI  H13  107.52  3.000
 2JN  H15  CAI  CAK  111.47  3.000
 2JN  H14  CAI  CAK  111.18  3.000
 2JN  H13  CAI  CAK  111.32  3.000
 2JN  H16  O1   CAG  109.14  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
 2JN  CONST_01  H16  O1   CAG  OAE     0.00   0.0  0
 2JN  Var_01    CAK  CAM  CAO  CAQ  -176.08  30.0  3
 2JN  Var_02    CAI  CAK  CAM  CAO  -179.74  30.0  3
 2JN  Var_03    H13  CAI  CAK  CAM   -60.39  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
 2JN  chir_01  CAQ  CAA  NAC  CAO  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
 2JN  plan-1  OAE  0.020
 2JN  plan-1  CAG  0.020
 2JN  plan-1  CAQ  0.020
 2JN  plan-1  O1   0.020
 2JN  plan-1  H16  0.020

