# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:48:40 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S)-2-aminohexanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N)C=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
 LYW  LYW  '(2S)-2-aminohexanal      '  ligand  21  8  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LYW
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
 LYW  C1   C  CH1   0  -0.209  -1.1426  -0.1733   0.4293
 LYW  N    N  NH2   0  -0.786  -1.4141  -1.4900  -0.0994
 LYW  C    C  C1    0   0.184  -2.3251   0.7364   0.2509
 LYW  O    O  O     0  -0.377  -3.3291   0.4616  -0.3559
 LYW  C2   C  CH2   0  -0.438   0.1001   0.5462  -0.1289
 LYW  C3   C  CH2   0  -0.412   1.4043  -0.1593   0.2189
 LYW  C4   C  CH2   0  -0.418   2.6281   0.5517  -0.3452
 LYW  C5   C  CH3   0  -0.662   3.9331  -0.1429   0.0176
 LYW  H1   H  HCH1  0   0.261  -1.0046  -0.2570   1.5166
 LYW  HN1  H  HNH2  0   0.343  -1.4983  -1.4501  -1.1082
 LYW  HN2  H  HNH2  0   0.355  -0.6355  -2.1049   0.0956
 LYW  H    H  H     0   0.190  -2.1986   1.7290   0.7216
 LYW  H21  H  HCH2  0   0.225   0.1361   1.5688   0.2609
 LYW  H22  H  HCH2  0   0.230  -0.0005   0.6331  -1.2164
 LYW  H31  H  HCH2  0   0.209   1.3854  -1.1879  -0.1549
 LYW  H32  H  HCH2  0   0.216   1.4943  -0.2305   1.3084
 LYW  H41  H  HCH2  0   0.214   2.6483   1.5831   0.0197
 LYW  H42  H  HCH2  0   0.214   2.5381   0.6174  -1.4336
 LYW  H51  H  HCH3  0   0.217   4.0655  -0.1948   1.0999
 LYW  H52  H  HCH3  0   0.217   3.9570  -1.1647  -0.3655
 LYW  H53  H  HCH3  0   0.227   4.7940   0.3844  -0.3948

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
 LYW  C1  N    single  1.445  0.020  1.445
 LYW  C1  C    single  1.503  0.020  1.503
 LYW  C1  C2   single  1.541  0.020  1.541
 LYW  C1  H1   single  0.970  0.020  1.090
 LYW  N   HN1  single  0.890  0.020  1.040
 LYW  N   HN2  single  0.890  0.020  1.040
 LYW  C   O    double  1.205  0.020  1.205
 LYW  C   H    single  0.930  0.020  1.080
 LYW  C2  C3   single  1.523  0.020  1.523
 LYW  C2  H21  single  0.970  0.020  1.090
 LYW  C2  H22  single  0.970  0.020  1.090
 LYW  C3  C4   single  1.524  0.020  1.524
 LYW  C3  H31  single  0.970  0.020  1.090
 LYW  C3  H32  single  0.970  0.020  1.090
 LYW  C4  C5   single  1.522  0.020  1.522
 LYW  C4  H41  single  0.970  0.020  1.090
 LYW  C4  H42  single  0.970  0.020  1.090
 LYW  C5  H51  single  0.970  0.020  1.090
 LYW  C5  H52  single  0.970  0.020  1.090
 LYW  C5  H53  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
 LYW  H1   C1  C2   107.02  3.000
 LYW  H1   C1  C    105.21  3.000
 LYW  C2   C1  C    108.00  3.000
 LYW  H1   C1  N    108.43  3.000
 LYW  C2   C1  N    116.40  3.000
 LYW  C    C1  N    111.13  3.000
 LYW  HN2  N   HN1  106.26  3.000
 LYW  HN2  N   C1   109.82  3.000
 LYW  HN1  N   C1   110.13  3.000
 LYW  H    C   O    120.96  3.000
 LYW  H    C   C1   113.76  3.000
 LYW  O    C   C1   125.28  3.000
 LYW  H22  C2  H21  106.40  3.000
 LYW  H22  C2  C3   110.00  3.000
 LYW  H21  C2  C3   108.85  3.000
 LYW  H22  C2  C1   108.82  3.000
 LYW  H21  C2  C1   109.49  3.000
 LYW  C3   C2  C1   113.05  3.000
 LYW  H32  C3  H31  106.25  3.000
 LYW  H32  C3  C4   109.42  3.000
 LYW  H31  C3  C4   109.02  3.000
 LYW  H32  C3  C2   109.12  3.000
 LYW  H31  C3  C2   110.03  3.000
 LYW  C4   C3  C2   112.78  3.000
 LYW  H42  C4  H41  106.06  3.000
 LYW  H42  C4  C5   109.57  3.000
 LYW  H41  C4  C5   109.57  3.000
 LYW  H42  C4  C3   109.28  3.000
 LYW  H41  C4  C3   109.34  3.000
 LYW  C5   C4  C3   112.80  3.000
 LYW  H53  C5  H52  107.61  3.000
 LYW  H53  C5  H51  107.58  3.000
 LYW  H52  C5  H51  107.51  3.000
 LYW  H53  C5  C4   111.47  3.000
 LYW  H52  C5  C4   111.25  3.000
 LYW  H51  C5  C4   111.22  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
 LYW  Var_01  C4   C3  C2  C1  179.56  30.0  3
 LYW  Var_02  C5   C4  C3  C2  179.25  30.0  3
 LYW  Var_03  H51  C5  C4  C3  -59.82  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
 LYW  chir_01  C1  N  C  C2  positiv

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
 LYW  plan-1  C1  0.020
 LYW  plan-1  C   0.020
 LYW  plan-1  O   0.020
 LYW  plan-1  H   0.020

