# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:38:36 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: (~{E})-4-methylnon-4-enedial
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(CCC=O)=C/CCCC=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
 S1N  S1N  (~{E})-4-methylnon-4-enedial  ligand  28  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S1N
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
 S1N  C12  C  C1    0   0.190  184.3120   99.9970  150.6993
 S1N  C1   C  CH3   0  -0.728  183.5801  100.7130  156.8255
 S1N  C2   C  C     0   0.095  182.4575  101.4503  156.1574
 S1N  C3   C  CH2   0  -0.511  181.1991  101.5858  156.9760
 S1N  C4   C  CH2   0  -0.556  181.3948  102.4690  158.2158
 S1N  C5   C  C1    0   0.189  181.8464  103.8391  157.8186
 S1N  C8   C  C1    0  -0.259  182.5196  101.9774  154.9315
 S1N  C9   C  CH2   0  -0.487  183.6664  101.9447  153.9703
 S1N  C10  C  CH2   0  -0.434  183.4033  100.9833  152.8095
 S1N  C11  C  CH2   0  -0.548  184.5151  101.0304  151.7608
 S1N  O6   O  O     0  -0.382  182.7719  104.4396  158.3070
 S1N  O13  O  O     0  -0.383  184.3135  100.2047  149.5106
 S1N  H1   H  H     0   0.181  184.1554   98.9740  151.0900
 S1N  H2   H  HCH3  0   0.239  183.2533   99.7123  157.1190
 S1N  H3   H  HCH3  0   0.245  184.4586  100.6045  156.1932
 S1N  H4   H  HCH3  0   0.239  183.8962  101.2156  157.7426
 S1N  H5   H  HCH2  0   0.249  180.3968  102.0047  156.3640
 S1N  H6   H  HCH2  0   0.255  180.8577  100.6016  157.3087
 S1N  H7   H  HCH2  0   0.281  180.4302  102.5795  158.7240
 S1N  H8   H  HCH2  0   0.254  182.0916  102.0321  158.9315
 S1N  H9   H  H     0   0.182  181.2422  104.2958  157.0127
 S1N  H10  H  H     0   0.228  181.6274  102.4705  154.5514
 S1N  H11  H  HCH2  0   0.237  184.6025  101.6690  154.4593
 S1N  H12  H  HCH2  0   0.236  183.8180  102.9508  153.5664
 S1N  H13  H  HCH2  0   0.239  182.4458  101.2274  152.3416
 S1N  H14  H  HCH2  0   0.234  183.3068   99.9670  153.2023
 S1N  H15  H  HCH2  0   0.263  185.4718  100.8015  152.2458
 S1N  H16  H  HCH2  0   0.252  184.5994  102.0214  151.3113

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
 S1N  O13  C12  double  1.207  0.020  1.207
 S1N  C12  C11  single  1.495  0.020  1.495
 S1N  C11  C10  single  1.529  0.020  1.529
 S1N  C10  C9   single  1.530  0.020  1.530
 S1N  C9   C8   single  1.497  0.020  1.497
 S1N  C8   C2   double  1.336  0.020  1.336
 S1N  C2   C1   single  1.500  0.020  1.500
 S1N  C2   C3   single  1.507  0.020  1.507
 S1N  C3   C4   single  1.535  0.020  1.535
 S1N  C4   C5   single  1.496  0.020  1.496
 S1N  C5   O6   double  1.207  0.020  1.207
 S1N  C12  H1   single  0.930  0.020  1.080
 S1N  C1   H2   single  0.970  0.020  1.090
 S1N  C1   H3   single  0.970  0.020  1.090
 S1N  C1   H4   single  0.970  0.020  1.090
 S1N  C3   H5   single  0.970  0.020  1.090
 S1N  C3   H6   single  0.970  0.020  1.090
 S1N  C4   H7   single  0.970  0.020  1.090
 S1N  C4   H8   single  0.970  0.020  1.090
 S1N  C5   H9   single  0.930  0.020  1.080
 S1N  C8   H10  single  0.930  0.020  1.080
 S1N  C9   H11  single  0.970  0.020  1.090
 S1N  C9   H12  single  0.970  0.020  1.090
 S1N  C10  H13  single  0.970  0.020  1.090
 S1N  C10  H14  single  0.970  0.020  1.090
 S1N  C11  H15  single  0.970  0.020  1.090
 S1N  C11  H16  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
 S1N  H1   C12  O13  120.48  3.000
 S1N  H1   C12  C11  114.06  3.000
 S1N  O13  C12  C11  125.47  3.000
 S1N  H4   C1   H3   107.46  3.000
 S1N  H4   C1   H2   106.40  3.000
 S1N  H3   C1   H2   107.84  3.000
 S1N  H4   C1   C2   111.36  3.000
 S1N  H3   C1   C2   113.23  3.000
 S1N  H2   C1   C2   110.24  3.000
 S1N  C8   C2   C3   120.12  3.000
 S1N  C3   C2   C1   115.28  3.000
 S1N  C8   C2   C1   124.60  3.000
 S1N  H6   C3   H5   106.63  3.000
 S1N  H6   C3   C4   108.18  3.000
 S1N  H5   C3   C4   108.99  3.000
 S1N  H6   C3   C2   110.18  3.000
 S1N  H5   C3   C2   110.08  3.000
 S1N  C4   C3   C2   112.58  3.000
 S1N  H8   C4   H7   107.37  3.000
 S1N  H8   C4   C5   110.38  3.000
 S1N  H7   C4   C5   107.25  3.000
 S1N  H8   C4   C3   112.40  3.000
 S1N  H7   C4   C3   108.69  3.000
 S1N  C5   C4   C3   110.55  3.000
 S1N  H9   C5   O6   120.56  3.000
 S1N  H9   C5   C4   113.99  3.000
 S1N  O6   C5   C4   125.44  3.000
 S1N  H10  C8   C9   114.45  3.000
 S1N  H10  C8   C2   117.46  3.000
 S1N  C9   C8   C2   128.05  3.000
 S1N  H12  C9   H11  106.18  3.000
 S1N  H12  C9   C10  108.75  3.000
 S1N  H11  C9   C10  109.18  3.000
 S1N  H12  C9   C8   108.84  3.000
 S1N  H11  C9   C8   112.02  3.000
 S1N  C10  C9   C8   111.67  3.000
 S1N  H14  C10  H13  106.49  3.000
 S1N  H14  C10  C11  109.82  3.000
 S1N  H13  C10  C11  109.65  3.000
 S1N  H14  C10  C9   109.06  3.000
 S1N  H13  C10  C9   109.57  3.000
 S1N  C11  C10  C9   112.09  3.000
 S1N  H16  C11  H15  107.71  3.000
 S1N  H16  C11  C10  111.50  3.000
 S1N  H15  C11  C10  108.93  3.000
 S1N  H16  C11  C12  110.22  3.000
 S1N  H15  C11  C12  106.75  3.000
 S1N  C10  C11  C12  111.52  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
 S1N  Var_01  C9   C8   C2   C1      0.78   0.0  2
 S1N  Var_02  C9   C10  C11  C12   174.65  30.0  3
 S1N  Var_03  C4   C3   C2   C1     66.25  30.0  3
 S1N  Var_04  C10  C9   C8   C2    106.89  30.0  1
 S1N  Var_05  C5   C4   C3   C2     58.74  30.0  3
 S1N  Var_06  O6   C5   C4   C3   -131.72  30.0  3
 S1N  Var_07  C11  C10  C9   C8    175.15  30.0  1
 S1N  Var_08  O13  C12  C11  C10   128.24  30.0  2
 S1N  Var_09  H2   C1   C2   C3     57.09  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
 S1N  plan-1  C12  0.020
 S1N  plan-1  C11  0.020
 S1N  plan-1  O13  0.020
 S1N  plan-1  H1   0.020
 S1N  plan-2  C1   0.020
 S1N  plan-2  C2   0.020
 S1N  plan-2  C3   0.020
 S1N  plan-2  C8   0.020
 S1N  plan-2  C9   0.020
 S1N  plan-2  H10  0.020
 S1N  plan-3  C4   0.020
 S1N  plan-3  C5   0.020
 S1N  plan-3  O6   0.020
 S1N  plan-3  H9   0.020

