# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:13:55 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2S)-2,6-diaminohexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)CO
#
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
 LYJ  LYJ  (2S)-2,6-diaminohexan-1-ol  ligand  25  9  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LYJ
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
 LYJ  C     C  CH2   0  -0.126  -2.8604  -0.7620   0.1995
 LYJ  N     N  NH2   0  -0.786  -1.9329   1.4843   0.3715
 LYJ  O     O  OH1   0  -0.670  -4.0622  -0.2549  -0.3314
 LYJ  CA    C  CH1   0  -0.133  -1.7011   0.1503  -0.1668
 LYJ  CB    C  CH2   0  -0.421  -0.3817  -0.4936   0.2733
 LYJ  CD    C  CH2   0  -0.422   2.1554  -0.4241   0.2033
 LYJ  CE    C  CH2   0  -0.272   3.3879   0.2628  -0.3636
 LYJ  CG    C  CH2   0  -0.424   0.8551   0.2330  -0.2404
 LYJ  NZ    N  NH2   0  -0.801   4.6068  -0.4011   0.0776
 LYJ  H     H  HCH2  0   0.181  -2.9096  -0.8504   1.2956
 LYJ  HA    H  HCH2  0   0.194  -2.6462  -1.7674  -0.1855
 LYJ  HN    H  HNH2  0   0.332  -1.8803   1.4481   1.3843
 LYJ  HNA   H  HNH2  0   0.345  -1.1874   2.1056   0.0834
 LYJ  HO    H  HOH1  0   0.451  -4.7639  -0.8765  -0.1195
 LYJ  HAA   H  HCH1  0   0.216  -1.6813   0.2398  -1.2600
 LYJ  HB    H  HCH2  0   0.210  -0.3530  -0.5424   1.3684
 LYJ  HBA   H  HCH2  0   0.211  -0.3474  -1.5305  -0.0783
 LYJ  HD    H  HCH2  0   0.212   2.1627  -1.4757  -0.0998
 LYJ  HDA   H  HCH2  0   0.211   2.2089  -0.4195   1.2980
 LYJ  HE    H  HCH2  0   0.210   3.3508   0.2148  -1.4559
 LYJ  HEA   H  HCH2  0   0.186   3.3516   1.3313  -0.1041
 LYJ  HG    H  HCH2  0   0.212   0.8191   0.2659  -1.3351
 LYJ  HGA   H  HCH2  0   0.206   0.8466   1.2755   0.0945
 LYJ  HNZ   H  HNH2  0   0.345   5.4082   0.0429  -0.3518
 LYJ  HNZA  H  HNH2  0   0.336   4.7201  -0.2605   1.0742

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
 LYJ  CA  C     single  1.520  0.020  1.520
 LYJ  C   O     single  1.408  0.020  1.408
 LYJ  C   H     single  0.970  0.020  1.090
 LYJ  C   HA    single  0.970  0.020  1.090
 LYJ  N   CA    single  1.457  0.020  1.457
 LYJ  N   HN    single  0.890  0.020  1.040
 LYJ  N   HNA   single  0.890  0.020  1.040
 LYJ  O   HO    single  0.850  0.020  0.980
 LYJ  CA  CB    single  1.533  0.020  1.533
 LYJ  CA  HAA   single  0.970  0.020  1.090
 LYJ  CG  CB    single  1.524  0.020  1.524
 LYJ  CB  HB    single  0.970  0.020  1.090
 LYJ  CB  HBA   single  0.970  0.020  1.090
 LYJ  CE  CD    single  1.521  0.020  1.521
 LYJ  CG  CD    single  1.523  0.020  1.523
 LYJ  CD  HD    single  0.970  0.020  1.090
 LYJ  CD  HDA   single  0.970  0.020  1.090
 LYJ  CE  NZ    single  1.456  0.020  1.456
 LYJ  CE  HE    single  0.970  0.020  1.090
 LYJ  CE  HEA   single  0.970  0.020  1.090
 LYJ  CG  HG    single  0.970  0.020  1.090
 LYJ  CG  HGA   single  0.970  0.020  1.090
 LYJ  NZ  HNZ   single  0.890  0.020  1.040
 LYJ  NZ  HNZA  single  0.890  0.020  1.040

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
 LYJ  HA    C   H    106.52  3.000
 LYJ  HA    C   CA   108.45  3.000
 LYJ  H     C   CA   108.80  3.000
 LYJ  HA    C   O    111.35  3.000
 LYJ  H     C   O    111.48  3.000
 LYJ  CA    C   O    110.12  3.000
 LYJ  HNA   N   HN   105.53  3.000
 LYJ  HNA   N   CA   109.85  3.000
 LYJ  HN    N   CA   109.14  3.000
 LYJ  HO    O   C    107.88  3.000
 LYJ  HAA   CA  CB   107.75  3.000
 LYJ  HAA   CA  N    107.24  3.000
 LYJ  CB    CA  N    114.55  3.000
 LYJ  HAA   CA  C    107.63  3.000
 LYJ  CB    CA  C    109.59  3.000
 LYJ  N     CA  C    109.82  3.000
 LYJ  HBA   CB  HB   106.12  3.000
 LYJ  HBA   CB  CG   108.53  3.000
 LYJ  HB    CB  CG   109.67  3.000
 LYJ  HBA   CB  CA   109.42  3.000
 LYJ  HB    CB  CA   109.14  3.000
 LYJ  CG    CB  CA   113.68  3.000
 LYJ  HDA   CD  HD   106.28  3.000
 LYJ  HDA   CD  CG   109.32  3.000
 LYJ  HD    CD  CG   109.85  3.000
 LYJ  HDA   CD  CE   109.32  3.000
 LYJ  HD    CD  CE   108.99  3.000
 LYJ  CG    CD  CE   112.86  3.000
 LYJ  HEA   CE  HE   106.08  3.000
 LYJ  HEA   CE  NZ   113.51  3.000
 LYJ  HE    CE  NZ   108.11  3.000
 LYJ  HEA   CE  CD   108.91  3.000
 LYJ  HE    CE  CD   108.96  3.000
 LYJ  NZ    CE  CD   111.07  3.000
 LYJ  HGA   CG  HG   106.07  3.000
 LYJ  HGA   CG  CD   109.16  3.000
 LYJ  HG    CG  CD   109.39  3.000
 LYJ  HGA   CG  CB   110.16  3.000
 LYJ  HG    CG  CB   108.93  3.000
 LYJ  CD    CG  CB   112.89  3.000
 LYJ  HNZA  NZ  HNZ  105.55  3.000
 LYJ  HNZA  NZ  CE   109.17  3.000
 LYJ  HNZ   NZ  CE   109.53  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
 LYJ  Var_01  CD   CG  CB  CA  -179.81  30.0  1
 LYJ  Var_02  CE   CD  CG  CB   177.29  30.0  3
 LYJ  Var_03  NZ   CE  CD  CG  -179.63  30.0  1
 LYJ  Var_04  HNZ  NZ  CE  CD   176.97  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
 LYJ  chir_01  CA  C  N  CB  negativ

