# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:17:49 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 6-[(2R)-oxiran-2-yl]-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC[C@@H]1CO1)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
 EXY  EXY  6-[(2R)-oxiran-2-yl]-L-norleucine  L-peptide  26  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_EXY
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
 EXY  N    N  NH2    0  -0.806  25.8340  -42.8080  3.9637
 EXY  CA   C  CH1    0  -0.193  25.9838  -42.6782  5.4057
 EXY  C    C  C      0   0.398  24.7914  -43.3213  6.1537
 EXY  O    O  O      0  -0.612  24.9701  -43.5485  7.3670
 EXY  OXT  O  OC    -1  -0.603  23.7482  -43.5289  5.5010
 EXY  CB   C  CH2    0  -0.439  26.1752  -41.2305  5.8878
 EXY  CG   C  CH2    0  -0.419  24.9967  -40.3014  5.6231
 EXY  CD   C  CH2    0  -0.415  25.3037  -38.8561  5.9945
 EXY  CE   C  CH2    0  -0.459  24.1292  -37.9168  5.7409
 EXY  CF   C  CH1    0   0.011  24.4187  -36.5026  6.1526
 EXY  CH   C  CH2    0  -0.248  23.9115  -35.3552  5.4089
 EXY  OF   O  O2     0  -0.487  25.2710  -35.7460  5.3023
 EXY  H    H  HNH2   0   0.328  24.8606  -42.6622  3.7289
 EXY  H2   H  HNH2   0   0.327  26.3643  -42.0876  3.4887
 EXY  HA   H  HCH1   0   0.202  26.8858  -43.2259  5.7071
 EXY  HB2  H  HCH2   0   0.207  26.3983  -41.2393  6.9585
 EXY  HB3  H  HCH2   0   0.206  27.0667  -40.8187  5.3997
 EXY  HG2  H  HCH2   0   0.202  24.7186  -40.3484  4.5651
 EXY  HG3  H  HCH2   0   0.213  24.1200  -40.6359  6.1867
 EXY  HD2  H  HCH2   0   0.213  25.5885  -38.8043  7.0511
 EXY  HD3  H  HCH2   0   0.215  26.1739  -38.5129  5.4261
 EXY  HE2  H  HCH2   0   0.227  23.8481  -37.9457  4.6834
 EXY  HE3  H  HCH2   0   0.226  23.2561  -38.2618  6.3035
 EXY  HF   H  HCH1   0   0.243  24.6200  -36.3644  7.2156
 EXY  HH1  H  HCH2   0   0.232  23.2989  -35.5217  4.5260
 EXY  HH2  H  HCH2   0   0.232  23.7234  -34.4147  5.9206

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
 EXY  N   CA   single  1.458  0.019  1.458
 EXY  CA  C    single  1.525  0.021  1.525
 EXY  CA  CB   single  1.530  0.020  1.530
 EXY  C   O    deloc   1.231  0.020  1.231
 EXY  C   OXT  deloc   1.248  0.020  1.248
 EXY  CB  CG   single  1.524  0.020  1.524
 EXY  CG  CD   single  1.523  0.020  1.523
 EXY  CD  CE   single  1.525  0.020  1.525
 EXY  CE  CF   single  1.501  0.020  1.501
 EXY  CF  CH   single  1.458  0.020  1.458
 EXY  CF  OF   single  1.422  0.020  1.422
 EXY  CH  OF   single  1.419  0.020  1.419
 EXY  N   H    single  0.860  0.020  0.860
 EXY  N   H2   single  0.890  0.020  1.040
 EXY  CA  HA   single  0.970  0.020  0.970
 EXY  CB  HB2  single  0.970  0.020  1.090
 EXY  CB  HB3  single  0.970  0.020  1.090
 EXY  CG  HG2  single  0.970  0.020  1.090
 EXY  CG  HG3  single  0.970  0.020  1.090
 EXY  CD  HD2  single  0.970  0.020  1.090
 EXY  CD  HD3  single  0.970  0.020  1.090
 EXY  CE  HE2  single  0.970  0.020  1.090
 EXY  CE  HE3  single  0.970  0.020  1.090
 EXY  CF  HF   single  0.970  0.020  1.090
 EXY  CH  HH1  single  0.970  0.020  1.090
 EXY  CH  HH2  single  0.970  0.020  1.090

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
 EXY  H2   N   H    107.00  3.000
 EXY  H2   N   CA   110.32  3.000
 EXY  H    N   CA   114.00  3.000
 EXY  HA   CA  CB   109.00  3.000
 EXY  HA   CA  C    109.00  3.000
 EXY  CB   CA  C    110.10  1.900
 EXY  HA   CA  N    110.00  3.000
 EXY  CB   CA  N    110.50  1.700
 EXY  C    CA  N    111.00  2.800
 EXY  OXT  C   O    126.74  3.000
 EXY  OXT  C   CA   117.42  3.000
 EXY  O    C   CA   120.80  1.700
 EXY  HB3  CB  HB2  105.84  3.000
 EXY  HB3  CB  CG   108.81  3.000
 EXY  HB2  CB  CG   109.43  3.000
 EXY  HB3  CB  CA   108.37  3.000
 EXY  HB2  CB  CA   108.95  3.000
 EXY  CG   CB  CA   115.04  3.000
 EXY  HG3  CG  HG2  106.32  3.000
 EXY  HG3  CG  CD   109.01  3.000
 EXY  HG2  CG  CD   109.12  3.000
 EXY  HG3  CG  CB   110.10  3.000
 EXY  HG2  CG  CB   109.76  3.000
 EXY  CD   CG  CB   112.34  3.000
 EXY  HD3  CD  HD2  106.22  3.000
 EXY  HD3  CD  CE   109.44  3.000
 EXY  HD2  CD  CE   109.36  3.000
 EXY  HD3  CD  CG   109.33  3.000
 EXY  HD2  CD  CG   109.42  3.000
 EXY  CE   CD  CG   112.86  3.000
 EXY  HE3  CE  HE2  106.46  3.000
 EXY  HE3  CE  CF   108.05  3.000
 EXY  HE2  CE  CF   109.84  3.000
 EXY  HE3  CE  CD   109.56  3.000
 EXY  HE2  CE  CD   110.01  3.000
 EXY  CF   CE  CD   112.71  3.000
 EXY  HF   CF  OF   113.88  3.000
 EXY  HF   CF  CH   117.48  3.000
 EXY  OF   CF  CH    58.99  3.000
 EXY  HF   CF  CE   114.98  3.000
 EXY  OF   CF  CE   116.93  3.000
 EXY  CH   CF  CE   122.30  3.000
 EXY  HH2  CH  HH1  114.65  3.000
 EXY  HH2  CH  OF   116.08  3.000
 EXY  HH1  CH  OF   115.89  3.000
 EXY  HH2  CH  CF   120.05  3.000
 EXY  HH1  CH  CF   119.30  3.000
 EXY  OF   CH  CF    59.22  3.000
 EXY  CH   OF  CF    61.79  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
 EXY  Var_01  OF   CH  CF  CE  -104.19  30.0  1
 EXY  Var_02  HH1  CH  OF  CF  -110.13  30.0  1
 EXY  Var_03  CH   CF  CE  CD   144.01  30.0  3
 EXY  Var_04  CF   CE  CD  CG   178.00  30.0  3
 EXY  Var_05  CD   CG  CB  CA  -174.18  30.0  3
 EXY  Var_06  CE   CD  CG  CB  -179.71  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
 EXY  chir_01  CA  N   C   CB  positiv
 EXY  chir_02  CF  CE  CH  OF  both

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
 EXY  plan-1  CA   0.020
 EXY  plan-1  C    0.020
 EXY  plan-1  O    0.020
 EXY  plan-1  OXT  0.020

