# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:46:44 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-(hex-5-yn-1-yl)hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)NCCCCC#C
#
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
 AKS  AKS  N-(hex-5-yn-1-yl)hexanamide  ligand  35  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AKS
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
 AKS  C1   C  CH2   0  -0.419   5.9613  -0.2649  -0.1267
 AKS  C2   C  CH2   0  -0.409   4.6598   0.5007   0.0799
 AKS  C3   C  CH2   0  -0.413   3.4325  -0.4021   0.0908
 AKS  C4   C  CH2   0  -0.578   2.1485   0.3798   0.3272
 AKS  C5   C  C     0   0.559   0.9095  -0.4907   0.3770
 AKS  C6   C  CH3   0  -0.662   7.1804   0.6468  -0.1414
 AKS  H1   H  HCH2  0   0.211   6.0696  -1.0108   0.6670
 AKS  H2   H  HCH2  0   0.211   5.9102  -0.8252  -1.0652
 AKS  H3   H  HCH2  0   0.209   4.7129   1.0530   1.0254
 AKS  H4   H  HCH2  0   0.210   4.5530   1.2563  -0.7058
 AKS  H5   H  HCH2  0   0.220   3.3723  -0.9412  -0.8601
 AKS  H6   H  HCH2  0   0.221   3.5493  -1.1597   0.8691
 AKS  H7   H  HCH2  0   0.265   2.2115   0.9022   1.2890
 AKS  H8   H  HCH2  0   0.247   2.0339   1.1622  -0.4281
 AKS  H12  H  HCH3  0   0.226   8.1042   0.0832  -0.2731
 AKS  O1   O  O     0  -0.508   0.9273  -1.6338   0.8164
 AKS  N1   N  NH1   0  -0.645  -0.2156   0.1004  -0.0557
 AKS  C7   C  CH2   0  -0.241  -1.5189  -0.5285  -0.0286
 AKS  C8   C  CH2   0  -0.469  -2.6226   0.5185  -0.0261
 AKS  C9   C  CH2   0  -0.426  -4.0033  -0.1219  -0.0112
 AKS  C10  C  CH2   0  -0.575  -5.1145   0.9306  -0.0177
 AKS  C11  C  CSP   0   0.285  -6.4472   0.3404  -0.0232
 AKS  C12  C  CSP1  0  -0.567  -7.5400  -0.1629  -0.0325
 AKS  H9   H  HCH3  0   0.216   7.1162   1.3735  -0.9526
 AKS  H10  H  HCH3  0   0.216   7.2640   1.2033   0.7941
 AKS  H11  H  HNH1  0   0.397  -0.1481   1.0149  -0.4737
 AKS  H13  H  HCH2  0   0.229  -1.6438  -1.1978  -0.8866
 AKS  H14  H  HCH2  0   0.236  -1.5956  -1.1457   0.8680
 AKS  H15  H  HCH2  0   0.235  -2.5031   1.1680   0.8462
 AKS  H16  H  HCH2  0   0.232  -2.5259   1.1582  -0.9101
 AKS  H17  H  HCH2  0   0.236  -4.1191  -0.7760  -0.8794
 AKS  H18  H  HCH2  0   0.236  -4.1099  -0.7552   0.8734
 AKS  H19  H  HCH2  0   0.268  -5.0155   1.5786   0.8570
 AKS  H20  H  HCH2  0   0.268  -5.0076   1.5760  -0.8934
 AKS  H22  H  H     0   0.277  -8.5086  -0.6074  -0.0312

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
 AKS  C1   C2   single  1.524  0.020  1.524
 AKS  C5   C4   single  1.515  0.020  1.515
 AKS  C3   C4   single  1.522  0.020  1.522
 AKS  C3   C2   single  1.524  0.020  1.524
 AKS  C1   C6   single  1.522  0.020  1.522
 AKS  C1   H1   single  0.939  0.020  1.096
 AKS  C1   H2   single  0.939  0.020  1.096
 AKS  C2   H3   single  0.939  0.020  1.096
 AKS  C2   H4   single  0.939  0.020  1.096
 AKS  C3   H5   single  0.939  0.020  1.096
 AKS  C3   H6   single  0.939  0.020  1.096
 AKS  C4   H7   single  0.939  0.020  1.096
 AKS  C4   H8   single  0.939  0.020  1.096
 AKS  C6   H12  single  0.939  0.020  1.096
 AKS  C5   O1   double  1.225  0.020  1.225
 AKS  C5   N1   single  1.343  0.020  1.343
 AKS  N1   C7   single  1.447  0.020  1.447
 AKS  C7   C8   single  1.521  0.020  1.521
 AKS  C8   C9   single  1.522  0.020  1.522
 AKS  C9   C10  single  1.531  0.020  1.531
 AKS  C10  C11  single  1.458  0.020  1.458
 AKS  C11  C12  triple  1.203  0.020  1.203
 AKS  C6   H9   single  0.939  0.020  1.096
 AKS  C6   H10  single  0.939  0.020  1.096
 AKS  N1   H11  single  0.868  0.020  1.013
 AKS  C7   H13  single  0.939  0.020  1.096
 AKS  C7   H14  single  0.939  0.020  1.096
 AKS  C8   H15  single  0.939  0.020  1.096
 AKS  C8   H16  single  0.939  0.020  1.096
 AKS  C9   H17  single  0.939  0.020  1.096
 AKS  C9   H18  single  0.939  0.020  1.096
 AKS  C10  H19  single  0.939  0.020  1.096
 AKS  C10  H20  single  0.939  0.020  1.096
 AKS  C12  H22  single  0.913  0.020  1.066

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
 AKS  H2   C1   H1   106.12  3.000
 AKS  H2   C1   C6   109.62  3.000
 AKS  H1   C1   C6   109.63  3.000
 AKS  H2   C1   C2   109.49  3.000
 AKS  H1   C1   C2   109.18  3.000
 AKS  C6   C1   C2   112.60  3.000
 AKS  H4   C2   H3   106.01  3.000
 AKS  H4   C2   C3   109.59  3.000
 AKS  H3   C2   C3   109.36  3.000
 AKS  H4   C2   C1   109.43  3.000
 AKS  H3   C2   C1   109.18  3.000
 AKS  C3   C2   C1   113.03  3.000
 AKS  H6   C3   H5   106.45  3.000
 AKS  H6   C3   C4   109.62  3.000
 AKS  H5   C3   C4   109.97  3.000
 AKS  H6   C3   C2   109.26  3.000
 AKS  H5   C3   C2   109.26  3.000
 AKS  C4   C3   C2   112.10  3.000
 AKS  H8   C4   H7   105.73  3.000
 AKS  H8   C4   C5   110.37  3.000
 AKS  H7   C4   C5   106.97  3.000
 AKS  H8   C4   C3   110.41  3.000
 AKS  H7   C4   C3   109.43  3.000
 AKS  C5   C4   C3   113.57  3.000
 AKS  N1   C5   O1   122.60  3.000
 AKS  N1   C5   C4   114.95  3.000
 AKS  O1   C5   C4   122.42  3.000
 AKS  H10  C6   H9   107.58  3.000
 AKS  H10  C6   H12  107.59  3.000
 AKS  H9   C6   H12  107.72  3.000
 AKS  H10  C6   C1   110.99  3.000
 AKS  H9   C6   C1   111.04  3.000
 AKS  H12  C6   C1   111.73  3.000
 AKS  H11  N1   C7   117.54  3.000
 AKS  H11  N1   C5   118.49  3.000
 AKS  C7   N1   C5   123.87  3.000
 AKS  H14  C7   H13  106.85  3.000
 AKS  H14  C7   C8   109.69  3.000
 AKS  H13  C7   C8   109.82  3.000
 AKS  H14  C7   N1   108.94  3.000
 AKS  H13  C7   N1   110.70  3.000
 AKS  C8   C7   N1   110.75  3.000
 AKS  H16  C8   H15  106.68  3.000
 AKS  H16  C8   C9   109.49  3.000
 AKS  H15  C8   C9   109.94  3.000
 AKS  H16  C8   C7   109.66  3.000
 AKS  H15  C8   C7   109.31  3.000
 AKS  C9   C8   C7   111.63  3.000
 AKS  H18  C9   H17  106.61  3.000
 AKS  H18  C9   C10  109.33  3.000
 AKS  H17  C9   C10  109.34  3.000
 AKS  H18  C9   C8   109.88  3.000
 AKS  H17  C9   C8   109.88  3.000
 AKS  C10  C9   C8   111.67  3.000
 AKS  H20  C10  H19  106.39  3.000
 AKS  H20  C10  C11  109.00  3.000
 AKS  H19  C10  C11  109.02  3.000
 AKS  H20  C10  C9   109.78  3.000
 AKS  H19  C10  C9   109.79  3.000
 AKS  C11  C10  C9   112.67  3.000
 AKS  C12  C11  C10  180.00  3.000
 AKS  H22  C12  C11  180.00  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
 AKS  CONST_01  C7   N1   C5  C4   180.00   0.0  0
 AKS  CONST_02  C7   N1   C5  O1     0.00   0.0  0
 AKS  CONST_03  H11  N1   C5  C4     0.00   0.0  0
 AKS  Var_01    C4   C3   C2  C1   178.81  30.0  2
 AKS  Var_02    C5   C4   C3  C2  -178.63  30.0  3
 AKS  Var_03    O1   C5   C4  C3    32.78  30.0  1
 AKS  Var_04    C6   C1   C2  C3   179.77  30.0  1
 AKS  Var_05    C8   C7   N1  C5   156.68  30.0  3
 AKS  Var_06    C9   C8   C7  N1   179.45  30.0  3
 AKS  Var_07    C10  C9   C8  C7  -179.64  30.0  3
 AKS  Var_08    C11  C10  C9  C8   179.17  30.0  3
 AKS  Var_09    H12  C6   C1  C2   179.04  30.0  3

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
 AKS  plan-1  C4   0.020
 AKS  plan-1  C5   0.020
 AKS  plan-1  O1   0.020
 AKS  plan-1  N1   0.020
 AKS  plan-1  C7   0.020
 AKS  plan-1  H11  0.020

