# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:58:09 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: tridec-12-en-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CCCCCCCCCC=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
 2TD  2TD  'tridec-12-en-2-one       '  ligand  38  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2TD
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
 2TD  O1    O  O     0  -0.409  -5.8885  -1.4392   0.0190
 2TD  C2    C  C     0   0.392  -5.8382  -0.2300  -0.0308
 2TD  C1    C  CH3   0  -0.767  -7.0783   0.6193  -0.1091
 2TD  C3    C  CH2   0  -0.557  -4.5328   0.5237  -0.0208
 2TD  C4    C  CH2   0  -0.415  -3.2810  -0.3375   0.0054
 2TD  C5    C  CH2   0  -0.414  -2.0108   0.5048   0.0166
 2TD  C6    C  CH2   0  -0.413  -0.7395  -0.3343   0.0397
 2TD  C7    C  CH2   0  -0.412   0.5316   0.5056   0.0553
 2TD  C8    C  CH2   0  -0.413   1.8054  -0.3301   0.0832
 2TD  C9    C  CH2   0  -0.414   3.0744   0.5130   0.1038
 2TD  C10   C  CH2   0  -0.417   4.3477  -0.3222   0.1444
 2TD  C11   C  CH2   0  -0.483   5.6162   0.5321   0.1645
 2TD  C12   C  C1    0  -0.150   6.8570  -0.2941   0.2807
 2TD  C13   C  C2    0  -0.543   7.8400  -0.3364  -0.6116
 2TD  H1    H  HCH3  0   0.257  -7.9822   0.0151  -0.0698
 2TD  H1A   H  HCH3  0   0.261  -7.0938   1.3433   0.7074
 2TD  H1B   H  HCH3  0   0.263  -7.0747   1.1954  -1.0366
 2TD  H3    H  HCH2  0   0.261  -4.5255   1.1898  -0.8916
 2TD  H3A   H  HCH2  0   0.263  -4.5527   1.1997   0.8427
 2TD  H4    H  HCH2  0   0.221  -3.2940  -0.9855   0.8863
 2TD  H4A   H  HCH2  0   0.220  -3.2686  -1.0008  -0.8642
 2TD  H5    H  HCH2  0   0.210  -1.9978   1.1584  -0.8628
 2TD  H5A   H  HCH2  0   0.210  -2.0218   1.1698   0.8875
 2TD  H6    H  HCH2  0   0.208  -0.7526  -0.9886   0.9188
 2TD  H6A   H  HCH2  0   0.208  -0.7258  -0.9983  -0.8319
 2TD  H7    H  HCH2  0   0.207   0.5457   1.1598  -0.8239
 2TD  H7A   H  HCH2  0   0.207   0.5157   1.1704   0.9264
 2TD  H8    H  HCH2  0   0.208   1.7905  -0.9843   0.9623
 2TD  H8A   H  HCH2  0   0.208   1.8242  -0.9942  -0.7882
 2TD  H9    H  HCH2  0   0.210   3.0937   1.1629  -0.7784
 2TD  H9A   H  HCH2  0   0.209   3.0517   1.1811   0.9720
 2TD  H10   H  HCH2  0   0.214   4.3311  -0.9682   1.0290
 2TD  H10A  H  HCH2  0   0.217   4.3771  -0.9911  -0.7218
 2TD  H11   H  HCH2  0   0.227   5.6606   1.1530  -0.7349
 2TD  H11A  H  HCH2  0   0.229   5.5605   1.2188   1.0167
 2TD  H12   H  H     0   0.236   6.9299  -0.9126   1.1725
 2TD  H13   H  H     0   0.233   8.7102  -0.9640  -0.4683
 2TD  H13A  H  H     0   0.229   7.8145   0.2585  -1.5176

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
 2TD  O1   C2    double  1.211  0.020  1.211
 2TD  C1   C2    single  1.505  0.020  1.505
 2TD  C2   C3    single  1.507  0.020  1.507
 2TD  C1   H1    single  0.970  0.020  1.090
 2TD  C1   H1A   single  0.970  0.020  1.090
 2TD  C1   H1B   single  0.970  0.020  1.090
 2TD  C3   C4    single  1.520  0.020  1.520
 2TD  C3   H3    single  0.970  0.020  1.090
 2TD  C3   H3A   single  0.970  0.020  1.090
 2TD  C4   C5    single  1.524  0.020  1.524
 2TD  C4   H4    single  0.970  0.020  1.090
 2TD  C4   H4A   single  0.970  0.020  1.090
 2TD  C5   C6    single  1.523  0.020  1.523
 2TD  C5   H5    single  0.970  0.020  1.090
 2TD  C5   H5A   single  0.970  0.020  1.090
 2TD  C6   C7    single  1.524  0.020  1.524
 2TD  C6   H6    single  0.970  0.020  1.090
 2TD  C6   H6A   single  0.970  0.020  1.090
 2TD  C7   C8    single  1.524  0.020  1.524
 2TD  C7   H7    single  0.970  0.020  1.090
 2TD  C7   H7A   single  0.970  0.020  1.090
 2TD  C8   C9    single  1.524  0.020  1.524
 2TD  C8   H8    single  0.970  0.020  1.090
 2TD  C8   H8A   single  0.970  0.020  1.090
 2TD  C9   C10   single  1.523  0.020  1.523
 2TD  C9   H9    single  0.970  0.020  1.090
 2TD  C9   H9A   single  0.970  0.020  1.090
 2TD  C10  C11   single  1.529  0.020  1.529
 2TD  C10  H10   single  0.970  0.020  1.090
 2TD  C10  H10A  single  0.970  0.020  1.090
 2TD  C11  C12   single  1.495  0.020  1.495
 2TD  C11  H11   single  0.970  0.020  1.090
 2TD  C11  H11A  single  0.970  0.020  1.090
 2TD  C12  C13   double  1.328  0.020  1.328
 2TD  C12  H12   single  0.930  0.020  1.080
 2TD  C13  H13   single  0.930  0.020  1.080
 2TD  C13  H13A  single  0.930  0.020  1.080

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
 2TD  C3    C2   C1   115.58  3.000
 2TD  C3    C2   O1   122.33  3.000
 2TD  C1    C2   O1   122.09  3.000
 2TD  H1B   C1   H1A  106.59  3.000
 2TD  H1B   C1   H1   109.06  3.000
 2TD  H1A   C1   H1   109.24  3.000
 2TD  H1B   C1   C2   109.83  3.000
 2TD  H1A   C1   C2   110.31  3.000
 2TD  H1    C1   C2   111.67  3.000
 2TD  H3A   C3   H3   104.53  3.000
 2TD  H3A   C3   C4   110.53  3.000
 2TD  H3    C3   C4   110.64  3.000
 2TD  H3A   C3   C2   107.32  3.000
 2TD  H3    C3   C2   107.71  3.000
 2TD  C4    C3   C2   115.47  3.000
 2TD  H4A   C4   H4   106.33  3.000
 2TD  H4A   C4   C5   109.36  3.000
 2TD  H4    C4   C5   109.36  3.000
 2TD  H4A   C4   C3   109.83  3.000
 2TD  H4    C4   C3   109.87  3.000
 2TD  C5    C4   C3   111.93  3.000
 2TD  H5A   C5   H5   106.02  3.000
 2TD  H5A   C5   C6   109.30  3.000
 2TD  H5    C5   C6   109.32  3.000
 2TD  H5A   C5   C4   109.44  3.000
 2TD  H5    C5   C4   109.49  3.000
 2TD  C6    C5   C4   113.03  3.000
 2TD  H6A   C6   H6   106.05  3.000
 2TD  H6A   C6   C7   109.38  3.000
 2TD  H6    C6   C7   109.33  3.000
 2TD  H6A   C6   C5   109.39  3.000
 2TD  H6    C6   C5   109.33  3.000
 2TD  C7    C6   C5   113.12  3.000
 2TD  H7A   C7   H7   106.01  3.000
 2TD  H7A   C7   C8   109.29  3.000
 2TD  H7    C7   C8   109.35  3.000
 2TD  H7A   C7   C6   109.29  3.000
 2TD  H7    C7   C6   109.37  3.000
 2TD  C8    C7   C6   113.28  3.000
 2TD  H8A   C8   H8   106.04  3.000
 2TD  H8A   C8   C9   109.38  3.000
 2TD  H8    C8   C9   109.32  3.000
 2TD  H8A   C8   C7   109.40  3.000
 2TD  H8    C8   C7   109.31  3.000
 2TD  C9    C8   C7   113.14  3.000
 2TD  H9A   C9   H9   106.06  3.000
 2TD  H9A   C9   C10  109.30  3.000
 2TD  H9    C9   C10  109.38  3.000
 2TD  H9A   C9   C8   109.32  3.000
 2TD  H9    C9   C8   109.39  3.000
 2TD  C10   C9   C8   113.15  3.000
 2TD  H10A  C10  H10  106.20  3.000
 2TD  H10A  C10  C11  109.24  3.000
 2TD  H10   C10  C11  109.35  3.000
 2TD  H10A  C10  C9   109.65  3.000
 2TD  H10   C10  C9   109.40  3.000
 2TD  C11   C10  C9   112.79  3.000
 2TD  H11A  C11  H11  106.60  3.000
 2TD  H11A  C11  C12  109.15  3.000
 2TD  H11   C11  C12  110.12  3.000
 2TD  H11A  C11  C10  108.55  3.000
 2TD  H11   C11  C10  109.87  3.000
 2TD  C12   C11  C10  112.37  3.000
 2TD  H12   C12  C13  118.89  3.000
 2TD  H12   C12  C11  115.69  3.000
 2TD  C13   C12  C11  125.42  3.000
 2TD  H13A  C13  H13  116.60  3.000
 2TD  H13A  C13  C12  121.77  3.000
 2TD  H13   C13  C12  121.63  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
 2TD  Var_01  C4   C3   C2   O1      2.12  30.0  3
 2TD  Var_02  C5   C4   C3   C2   -179.90  30.0  3
 2TD  Var_03  C6   C5   C4   C3   -179.87  30.0  3
 2TD  Var_04  C7   C6   C5   C4   -179.82  30.0  3
 2TD  Var_05  C8   C7   C6   C5    179.81  30.0  3
 2TD  Var_06  C9   C8   C7   C6   -179.79  30.0  3
 2TD  Var_07  C10  C9   C8   C7    179.48  30.0  3
 2TD  Var_08  C11  C10  C9   C8    179.99  30.0  3
 2TD  Var_09  C12  C11  C10  C9    176.83  30.0  3
 2TD  Var_10  C13  C12  C11  C10   119.11  30.0  3
 2TD  Var_11  H13  C13  C12  C11  -179.54   0.0  2
 2TD  Var_12  H1   C1   C2   O1      2.51  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
 2TD  plan-1  O1    0.020
 2TD  plan-1  C2    0.020
 2TD  plan-1  C1    0.020
 2TD  plan-1  C3    0.020
 2TD  plan-2  C11   0.020
 2TD  plan-2  C12   0.020
 2TD  plan-2  C13   0.020
 2TD  plan-2  H12   0.020
 2TD  plan-2  H13   0.020
 2TD  plan-2  H13A  0.020

