# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:51:33 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (2Z)-3,7-dimethylocta-2,6-dienenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(C)=C/C#N
#
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
 CTV  CTV  (2Z)-3,7-dimethylocta-2,6-dienenitrile  ligand  26  11  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CTV
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
 CTV  C1   C  CH3   0  -0.724   2.3504   1.2309   0.5934
 CTV  N1   N  NS    0  -0.280  -1.4808   2.6574   0.7902
 CTV  C2   C  CH3   0  -0.706   4.0090  -0.3243  -0.5082
 CTV  C3   C  C     0   0.095   2.6296  -0.1400   0.0532
 CTV  C4   C  C1    0  -0.269   1.7431  -1.1387   0.0470
 CTV  C5   C  CH2   0  -0.501   0.3343  -1.0805   0.5570
 CTV  C6   C  CH2   0  -0.515  -0.6481  -0.6453  -0.5471
 CTV  C7   C  C     0   0.183  -2.0646  -0.6758  -0.0594
 CTV  C8   C  C1    0  -0.377  -2.6605   0.3870   0.5046
 CTV  C9   C  CH3   0  -0.717  -2.7901  -1.9728  -0.1839
 CTV  C10  C  CSP   0   0.069  -2.0025   1.6364   0.6543
 CTV  H1   H  HCH3  0   0.237   3.0564   1.4863   1.3878
 CTV  H1A  H  HCH3  0   0.238   2.4842   1.9801  -0.1908
 CTV  H2   H  HCH3  0   0.232   4.7688  -0.1391   0.2556
 CTV  H2A  H  HCH3  0   0.237   4.1609  -1.3305  -0.8979
 CTV  H2B  H  HCH3  0   0.232   4.2028   0.3865  -1.3156
 CTV  H4   H  H     0   0.227   2.0461  -2.0846  -0.3942
 CTV  H5   H  HCH2  0   0.249   0.0439  -2.0647   0.9328
 CTV  H5A  H  HCH2  0   0.247   0.2470  -0.3908   1.3993
 CTV  H6   H  HCH2  0   0.259  -0.3694   0.3533  -0.8898
 CTV  H6A  H  HCH2  0   0.264  -0.5488  -1.3169  -1.4033
 CTV  H8   H  H     0   0.305  -3.6733   0.3359   0.8849
 CTV  H9   H  HCH3  0   0.256  -2.2203  -2.7783   0.2845
 CTV  H9A  H  HCH3  0   0.255  -3.7799  -1.9414   0.2668
 CTV  H9B  H  HCH3  0   0.262  -2.8949  -2.2392  -1.2377
 CTV  H15  H  HCH3  0   0.240   1.3431   1.3480   0.9891

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
 CTV  C1  C3   single  1.500  0.020  1.500
 CTV  C1  H1   single  0.970  0.020  1.090
 CTV  C1  H1A  single  0.970  0.020  1.090
 CTV  N1  C10  triple  1.155  0.020  1.155
 CTV  C2  C3   single  1.501  0.020  1.501
 CTV  C2  H2   single  0.970  0.020  1.090
 CTV  C2  H2A  single  0.970  0.020  1.090
 CTV  C2  H2B  single  0.970  0.020  1.090
 CTV  C3  C4   double  1.335  0.020  1.335
 CTV  C4  C5   single  1.499  0.020  1.499
 CTV  C4  H4   single  0.930  0.020  1.080
 CTV  C5  C6   single  1.541  0.020  1.541
 CTV  C5  H5   single  0.970  0.020  1.090
 CTV  C5  H5A  single  0.970  0.020  1.090
 CTV  C6  C7   single  1.498  0.020  1.498
 CTV  C6  H6   single  0.970  0.020  1.090
 CTV  C6  H6A  single  0.970  0.020  1.090
 CTV  C7  C8   double  1.343  0.020  1.343
 CTV  C7  C9   single  1.491  0.020  1.491
 CTV  C8  C10  single  1.420  0.020  1.420
 CTV  C8  H8   single  0.930  0.020  1.080
 CTV  C9  H9   single  0.970  0.020  1.090
 CTV  C9  H9A  single  0.970  0.020  1.090
 CTV  C9  H9B  single  0.970  0.020  1.090
 CTV  C1  H15  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
 CTV  H15  C1   H1A  107.48  3.000
 CTV  H15  C1   H1   107.96  3.000
 CTV  H1A  C1   H1   106.39  3.000
 CTV  H15  C1   C3   113.68  3.000
 CTV  H1A  C1   C3   110.20  3.000
 CTV  H1   C1   C3   110.80  3.000
 CTV  H2B  C2   H2A  108.15  3.000
 CTV  H2B  C2   H2   106.43  3.000
 CTV  H2A  C2   H2   108.03  3.000
 CTV  H2B  C2   C3   111.06  3.000
 CTV  H2A  C2   C3   112.05  3.000
 CTV  H2   C2   C3   110.90  3.000
 CTV  C4   C3   C2   121.10  3.000
 CTV  C4   C3   C1   124.17  3.000
 CTV  C2   C3   C1   114.72  3.000
 CTV  H4   C4   C5   115.71  3.000
 CTV  H4   C4   C3   117.89  3.000
 CTV  C5   C4   C3   126.38  3.000
 CTV  H5A  C5   H5   106.40  3.000
 CTV  H5A  C5   C6   108.86  3.000
 CTV  H5   C5   C6   109.36  3.000
 CTV  H5A  C5   C4   111.22  3.000
 CTV  H5   C5   C4   109.37  3.000
 CTV  C6   C5   C4   111.49  3.000
 CTV  H6A  C6   H6   107.04  3.000
 CTV  H6A  C6   C7   109.17  3.000
 CTV  H6   C6   C7   111.23  3.000
 CTV  H6A  C6   C5   109.26  3.000
 CTV  H6   C6   C5   108.70  3.000
 CTV  C7   C6   C5   111.33  3.000
 CTV  C9   C7   C8   120.50  3.000
 CTV  C9   C7   C6   116.77  3.000
 CTV  C8   C7   C6   122.69  3.000
 CTV  H8   C8   C10  115.96  3.000
 CTV  H8   C8   C7   121.68  3.000
 CTV  C10  C8   C7   122.35  3.000
 CTV  H9B  C9   H9A  108.63  3.000
 CTV  H9B  C9   H9   106.50  3.000
 CTV  H9A  C9   H9   108.56  3.000
 CTV  H9B  C9   C7   109.84  3.000
 CTV  H9A  C9   C7   112.52  3.000
 CTV  H9   C9   C7   110.60  3.000
 CTV  C8   C10  N1   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
 CTV  Var_01  C5   C4  C3   C1     0.40   0.0  2
 CTV  Var_02  C10  C8  C7   C6     1.54   0.0  2
 CTV  Var_03  C7   C8  C10  N1  -160.99  30.0  1
 CTV  Var_04  C6   C5  C4   C3    89.85  30.0  3
 CTV  Var_05  C7   C6  C5   C4   176.24  30.0  3
 CTV  Var_06  C8   C7  C6   C5    90.66  30.0  3
 CTV  Var_07  H2   C2  C3   C1    59.84  30.0  3
 CTV  Var_08  H1   C1  C3   C2   -58.65  30.0  3
 CTV  Var_09  H9   C9  C7   C6    53.50  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
 CTV  plan-1  C1   0.020
 CTV  plan-1  C2   0.020
 CTV  plan-1  C3   0.020
 CTV  plan-1  C4   0.020
 CTV  plan-1  C5   0.020
 CTV  plan-1  H4   0.020
 CTV  plan-2  C6   0.020
 CTV  plan-2  C7   0.020
 CTV  plan-2  C8   0.020
 CTV  plan-2  C9   0.020
 CTV  plan-2  C10  0.020
 CTV  plan-2  H8   0.020

