# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:39:50 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2E,4R)-4-hydroxynon-2-enal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@@H](O)/C=C/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
 HNE  HNE  (2E,4R)-4-hydroxynon-2-enal  ligand  27  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HNE
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
 HNE  C1    C  C1    0   0.142  1.5000   2.2573  -0.2470
 HNE  C2    C  C1    0  -0.334  2.0758   0.9366  -0.0093
 HNE  C3    C  C1    0  -0.207  1.2789  -0.1325   0.0509
 HNE  C4    C  CH1   0   0.015  1.7389  -1.5353   0.3009
 HNE  C5    C  CH2   0  -0.460  1.2304  -2.0360   1.6490
 HNE  C6    C  CH2   0  -0.426  1.8376  -1.2986   2.8348
 HNE  C7    C  CH2   0  -0.404  1.3345  -1.8272   4.1717
 HNE  C8    C  CH2   0  -0.420  1.9465  -1.1091   5.3677
 HNE  C9    C  CH3   0  -0.662  1.4278  -1.6322   6.6998
 HNE  O10   O  OH1   0  -0.667  1.2296  -2.3962  -0.6970
 HNE  O11   O  O     0  -0.404  2.1424   3.2805  -0.3307
 HNE  H2    H  H     0   0.271  3.1514   0.8541   0.1077
 HNE  H3    H  H     0   0.278  0.2056  -0.0024  -0.0795
 HNE  H4    H  HCH1  0   0.225  2.8382  -1.5557   0.3117
 HNE  H5C1  H  HCH2  0   0.240  1.4702  -3.1012   1.7238
 HNE  H5C2  H  HCH2  0   0.227  0.1386  -1.9563   1.6783
 HNE  H10   H  HOH1  0   0.454  1.6115  -2.1406  -1.5430
 HNE  H6C1  H  HCH2  0   0.215  2.9290  -1.3843   2.7940
 HNE  H6C2  H  HCH2  0   0.221  1.6172  -0.2291   2.7642
 HNE  H7C1  H  HCH2  0   0.210  0.2437  -1.7322   4.2116
 HNE  H7C2  H  HCH2  0   0.210  1.5466  -2.8995   4.2448
 HNE  H8C1  H  HCH2  0   0.212  1.7412  -0.0370   5.2892
 HNE  H8C2  H  HCH2  0   0.212  3.0354  -1.2115   5.3315
 HNE  H9C1  H  HCH3  0   0.216  0.3459  -1.5086   6.7779
 HNE  H9C2  H  HCH3  0   0.216  1.6445  -2.6956   6.8175
 HNE  H9C3  H  HCH3  0   0.226  1.8815  -1.1076   7.5414
 HNE  H1    H  H     0   0.195  0.3995   2.2662  -0.3518

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
 HNE  C1   C2    single  1.460  0.020  1.460
 HNE  C1   O11   double  1.211  0.020  1.211
 HNE  C1   H1    single  0.930  0.020  1.080
 HNE  C2   C3    double  1.335  0.020  1.335
 HNE  C2   H2    single  0.930  0.020  1.080
 HNE  C3   C4    single  1.497  0.020  1.497
 HNE  C3   H3    single  0.930  0.020  1.080
 HNE  C4   C5    single  1.525  0.020  1.525
 HNE  C4   O10   single  1.413  0.020  1.413
 HNE  C4   H4    single  0.970  0.020  1.090
 HNE  C5   C6    single  1.523  0.020  1.523
 HNE  C5   H5C1  single  0.970  0.020  1.090
 HNE  C5   H5C2  single  0.970  0.020  1.090
 HNE  C6   C7    single  1.523  0.020  1.523
 HNE  C6   H6C1  single  0.970  0.020  1.090
 HNE  C6   H6C2  single  0.970  0.020  1.090
 HNE  C7   C8    single  1.523  0.020  1.523
 HNE  C7   H7C1  single  0.970  0.020  1.090
 HNE  C7   H7C2  single  0.970  0.020  1.090
 HNE  C8   C9    single  1.522  0.020  1.522
 HNE  C8   H8C1  single  0.970  0.020  1.090
 HNE  C8   H8C2  single  0.970  0.020  1.090
 HNE  C9   H9C1  single  0.970  0.020  1.090
 HNE  C9   H9C2  single  0.970  0.020  1.090
 HNE  C9   H9C3  single  0.970  0.020  1.090
 HNE  O10  H10   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
 HNE  H1    C1   O11   120.98  3.000
 HNE  H1    C1   C2    114.54  3.000
 HNE  O11   C1   C2    124.49  3.000
 HNE  H2    C2   C3    121.74  3.000
 HNE  H2    C2   C1    118.50  3.000
 HNE  C3    C2   C1    119.76  3.000
 HNE  H3    C3   C4    115.76  3.000
 HNE  H3    C3   C2    119.17  3.000
 HNE  C4    C3   C2    125.07  3.000
 HNE  H4    C4   O10   110.85  3.000
 HNE  H4    C4   C5    108.57  3.000
 HNE  O10   C4   C5    107.70  3.000
 HNE  H4    C4   C3    109.04  3.000
 HNE  O10   C4   C3    110.01  3.000
 HNE  C5    C4   C3    110.65  3.000
 HNE  H5C2  C5   H5C1  106.71  3.000
 HNE  H5C2  C5   C6    109.96  3.000
 HNE  H5C1  C5   C6    109.32  3.000
 HNE  H5C2  C5   C4    109.39  3.000
 HNE  H5C1  C5   C4    107.87  3.000
 HNE  C6    C5   C4    113.35  3.000
 HNE  H6C2  C6   H6C1  105.94  3.000
 HNE  H6C2  C6   C7    109.23  3.000
 HNE  H6C1  C6   C7    109.55  3.000
 HNE  H6C2  C6   C5    110.05  3.000
 HNE  H6C1  C6   C5    109.29  3.000
 HNE  C7    C6   C5    112.57  3.000
 HNE  H7C2  C7   H7C1  105.97  3.000
 HNE  H7C2  C7   C8    109.34  3.000
 HNE  H7C1  C7   C8    109.30  3.000
 HNE  H7C2  C7   C6    109.53  3.000
 HNE  H7C1  C7   C6    109.31  3.000
 HNE  C8    C7   C6    113.14  3.000
 HNE  H8C2  C8   H8C1  106.01  3.000
 HNE  H8C2  C8   C9    109.62  3.000
 HNE  H8C1  C8   C9    109.60  3.000
 HNE  H8C2  C8   C7    109.25  3.000
 HNE  H8C1  C8   C7    109.28  3.000
 HNE  C9    C8   C7    112.85  3.000
 HNE  H9C3  C9   H9C2  107.63  3.000
 HNE  H9C3  C9   H9C1  107.62  3.000
 HNE  H9C2  C9   H9C1  107.41  3.000
 HNE  H9C3  C9   C8    111.61  3.000
 HNE  H9C2  C9   C8    111.19  3.000
 HNE  H9C1  C9   C8    111.18  3.000
 HNE  H10   O10  C4    108.42  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
 HNE  Var_01  C4    C3  C2  C1  -179.39   0.0  2
 HNE  Var_02  O11   C1  C2  C3  -179.24  30.0  2
 HNE  Var_03  C7    C6  C5  C4  -179.10  30.0  3
 HNE  Var_04  C8    C7  C6  C5   179.32  30.0  3
 HNE  Var_05  C9    C8  C7  C6   179.37  30.0  3
 HNE  Var_06  H9C1  C9  C8  C7   -60.06  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
 HNE  chir_01  C4  C3  C5  O10  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
 HNE  plan-1  C1   0.020
 HNE  plan-1  C2   0.020
 HNE  plan-1  O11  0.020
 HNE  plan-1  H1   0.020
 HNE  plan-2  C1   0.020
 HNE  plan-2  C2   0.020
 HNE  plan-2  C3   0.020
 HNE  plan-2  C4   0.020
 HNE  plan-2  H2   0.020
 HNE  plan-2  H3   0.020

