# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:06:15 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2R)-2-hydroxyhexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](O)C(N)=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
 HYH  HYH  '(2R)-2-hydroxyhexanamide '  ligand  22  9  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HYH
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
 HYH  O1   O  O     0  -0.492  -2.7143   0.3990  -0.9539
 HYH  C5   C  C     0   0.475  -2.1093  -0.2480  -0.1089
 HYH  N    N  NH2   0  -0.794  -2.4898  -1.4553   0.3178
 HYH  C4   C  CH1   0  -0.063  -0.8087   0.2898   0.4848
 HYH  O    O  OH1   0  -0.662  -0.7957   1.6884   0.4119
 HYH  C3   C  CH2   0  -0.453   0.3757  -0.3541  -0.2436
 HYH  C2   C  CH2   0  -0.407   1.7280   0.1309   0.2609
 HYH  C1   C  CH2   0  -0.422   2.8910  -0.5620  -0.4388
 HYH  C    C  CH3   0  -0.662   4.2475  -0.0767   0.0524
 HYH  H1   H  HNH2  0   0.405  -3.2931  -1.9138  -0.0818
 HYH  H2   H  HNH2  0   0.411  -1.9813  -1.9527   1.0287
 HYH  H3   H  HCH1  0   0.249  -0.7529   0.0241   1.5458
 HYH  H4   H  HOH1  0   0.439  -1.1878   1.9359  -0.4351
 HYH  H5   H  HCH2  0   0.230   0.3148  -1.4400  -0.1239
 HYH  H6   H  HCH2  0   0.229   0.2887  -0.1590  -1.3185
 HYH  H7   H  HCH2  0   0.219   1.8114   1.2115   0.1183
 HYH  H8   H  HCH2  0   0.212   1.7989  -0.0437   1.3404
 HYH  H9   H  HCH2  0   0.212   2.8116  -1.6433  -0.2897
 HYH  H10  H  HCH2  0   0.213   2.8119  -0.3995  -1.5181
 HYH  H11  H  HCH3  0   0.217   4.3676   0.9949  -0.1172
 HYH  H12  H  HCH3  0   0.216   4.3656  -0.2542   1.1229
 HYH  H13  H  HCH3  0   0.227   5.0648  -0.5860  -0.4594

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
 HYH  N   C5   single  1.336  0.020  1.336
 HYH  C5  O1   double  1.224  0.020  1.224
 HYH  C5  C4   single  1.528  0.020  1.528
 HYH  C3  C4   single  1.532  0.020  1.532
 HYH  C3  C2   single  1.523  0.020  1.523
 HYH  C1  C2   single  1.524  0.020  1.524
 HYH  C1  C    single  1.522  0.020  1.522
 HYH  C4  O    single  1.401  0.020  1.401
 HYH  N   H1   single  0.860  0.020  1.020
 HYH  N   H2   single  0.860  0.020  1.020
 HYH  C4  H3   single  0.970  0.020  1.090
 HYH  O   H4   single  0.850  0.020  0.980
 HYH  C3  H5   single  0.970  0.020  1.090
 HYH  C3  H6   single  0.970  0.020  1.090
 HYH  C2  H7   single  0.970  0.020  1.090
 HYH  C2  H8   single  0.970  0.020  1.090
 HYH  C1  H9   single  0.970  0.020  1.090
 HYH  C1  H10  single  0.970  0.020  1.090
 HYH  C   H11  single  0.970  0.020  1.090
 HYH  C   H12  single  0.970  0.020  1.090
 HYH  C   H13  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
 HYH  C4   C5  N    115.89  3.000
 HYH  C4   C5  O1   120.19  3.000
 HYH  N    C5  O1   123.88  3.000
 HYH  H2   N   H1   117.28  3.000
 HYH  H2   N   C5   121.93  3.000
 HYH  H1   N   C5   120.78  3.000
 HYH  H3   C4  C3   108.62  3.000
 HYH  H3   C4  O    106.99  3.000
 HYH  C3   C4  O    112.82  3.000
 HYH  H3   C4  C5   109.54  3.000
 HYH  O    C4  C5   109.83  3.000
 HYH  C3   C4  C5   108.99  3.000
 HYH  H4   O   C4   107.33  3.000
 HYH  H6   C3  H5   106.23  3.000
 HYH  H6   C3  C2   109.80  3.000
 HYH  H5   C3  C2   109.23  3.000
 HYH  H6   C3  C4   109.27  3.000
 HYH  H5   C3  C4   108.79  3.000
 HYH  C2   C3  C4   113.27  3.000
 HYH  H8   C2  H7   106.32  3.000
 HYH  H8   C2  C1   109.30  3.000
 HYH  H7   C2  C1   109.35  3.000
 HYH  H8   C2  C3   109.46  3.000
 HYH  H7   C2  C3   109.84  3.000
 HYH  C1   C2  C3   112.38  3.000
 HYH  H10  C1  H9   106.01  3.000
 HYH  H10  C1  C    109.59  3.000
 HYH  H9   C1  C    109.62  3.000
 HYH  H10  C1  C2   109.28  3.000
 HYH  H9   C1  C2   109.35  3.000
 HYH  C    C1  C2   112.77  3.000
 HYH  H13  C   H12  107.65  3.000
 HYH  H13  C   H11  107.65  3.000
 HYH  H12  C   H11  107.47  3.000
 HYH  H13  C   C1   111.56  3.000
 HYH  H12  C   C1   111.16  3.000
 HYH  H11  C   C1   111.16  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
 HYH  CONST_01  H1   N   C5  O1    0.00   0.0  0
 HYH  CONST_02  H2   N   C5  O1  180.00   0.0  0
 HYH  Var_01    C1   C2  C3  C4  177.75  30.0  3
 HYH  Var_02    C    C1  C2  C3  179.61  30.0  1
 HYH  Var_03    H11  C   C1  C2  -59.94  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
 HYH  chir_01  C4  C5  C3  O  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
 HYH  plan-1  O1  0.020
 HYH  plan-1  C5  0.020
 HYH  plan-1  N   0.020
 HYH  plan-1  C4  0.020
 HYH  plan-1  H1  0.020
 HYH  plan-1  H2  0.020

