# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:26:46 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (6~{R})-3-methyl-6-prop-1-en-2-yl-cyclohex-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)[C@H]1CCC(=CC1=O)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
 IT9  IT9  (6~{R})-3-methyl-6-prop-1-en-2-yl-cyclohex-2-en-1-one  ligand  25  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 GRAND
;

data_comp_IT9
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
 IT9  C4   C  CH1   0  -0.477  -0.6694   0.3564  -0.3877
 IT9  C5   C  CH2   0  -0.445   0.1079   1.3649   0.4610
 IT9  C6   C  CH2   0  -0.501   1.5681   1.4086   0.0428
 IT9  C7   C  C     0   0.221  -2.1444   0.3251  -0.0865
 IT9  C8   C  C2    0  -0.600  -3.0399   0.5046  -1.0539
 IT9  C9   C  CH3   0  -0.731  -2.5491   0.1124   1.3419
 IT9  C1   C  C     0   0.145   2.1849   0.0475  -0.0425
 IT9  C2   C  C1    0  -0.399   1.4293  -1.0569  -0.1585
 IT9  C3   C  C     0   0.423  -0.0287  -1.0183  -0.2756
 IT9  H    H  HCH1  0   0.286  -0.5383   0.6430  -1.4411
 IT9  H6   H  HCH2  0   0.254  -0.3400   2.3549   0.3614
 IT9  H5   H  HCH2  0   0.241   0.0447   1.0910   1.5176
 IT9  H7   H  HCH2  0   0.263   1.6702   1.8905  -0.9374
 IT9  H8   H  HCH2  0   0.262   2.1460   2.0260   0.7354
 IT9  H9   H  H     0   0.233  -2.7412   0.6711  -2.0818
 IT9  H10  H  H     0   0.231  -4.1043   0.4914  -0.8531
 IT9  H12  H  HCH3  0   0.240  -2.0894  -0.7849   1.7606
 IT9  H13  H  HCH3  0   0.242  -2.2348   0.9480   1.9709
 IT9  H11  H  HCH3  0   0.244  -3.6298   0.0153   1.4382
 IT9  H1   H  HCH3  0   0.256   4.0431   0.3406   0.9618
 IT9  H2   H  HCH3  0   0.251   4.0530  -1.0206  -0.1717
 IT9  H3   H  HCH3  0   0.254   4.0999   0.6492  -0.7594
 IT9  H4   H  H     0   0.251   1.8931  -2.0369  -0.2044
 IT9  C    C  CH3   0  -0.720   3.6740  -0.0142  -0.0032
 IT9  O    O  O     0  -0.425  -0.6860  -2.0410  -0.3383

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
 IT9  C   C1   single  1.491  0.020  1.491
 IT9  C9  C7   single  1.500  0.020  1.500
 IT9  C6  C1   single  1.497  0.020  1.497
 IT9  C6  C5   single  1.519  0.020  1.519
 IT9  C1  C2   double  1.343  0.020  1.343
 IT9  C7  C8   double  1.330  0.020  1.330
 IT9  C7  C4   single  1.506  0.020  1.506
 IT9  C2  C3   single  1.463  0.020  1.463
 IT9  C5  C4   single  1.530  0.020  1.530
 IT9  C4  C3   single  1.521  0.020  1.521
 IT9  C3  O    double  1.217  0.020  1.217
 IT9  C4  H    single  0.970  0.020  1.090
 IT9  C5  H6   single  0.970  0.020  1.090
 IT9  C5  H5   single  0.970  0.020  1.090
 IT9  C6  H7   single  0.970  0.020  1.090
 IT9  C6  H8   single  0.970  0.020  1.090
 IT9  C8  H9   single  0.930  0.020  1.080
 IT9  C8  H10  single  0.930  0.020  1.080
 IT9  C9  H12  single  0.970  0.020  1.090
 IT9  C9  H13  single  0.970  0.020  1.090
 IT9  C9  H11  single  0.970  0.020  1.090
 IT9  C   H1   single  0.970  0.020  1.090
 IT9  C   H2   single  0.970  0.020  1.090
 IT9  C   H3   single  0.970  0.020  1.090
 IT9  C2  H4   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
 IT9  H    C4  C3   104.83  3.000
 IT9  H    C4  C7   108.29  3.000
 IT9  C3   C4  C7   112.28  3.000
 IT9  H    C4  C5   107.39  3.000
 IT9  C3   C4  C5   109.93  3.000
 IT9  C7   C4  C5   113.60  3.000
 IT9  H5   C5  H6   106.96  3.000
 IT9  H5   C5  C6   109.19  3.000
 IT9  H6   C5  C6   110.08  3.000
 IT9  H5   C5  C4   109.97  3.000
 IT9  H6   C5  C4   109.80  3.000
 IT9  C6   C5  C4   110.76  3.000
 IT9  H8   C6  H7   105.59  3.000
 IT9  H8   C6  C1   109.39  3.000
 IT9  H7   C6  C1   108.07  3.000
 IT9  H8   C6  C5   110.48  3.000
 IT9  H7   C6  C5   110.36  3.000
 IT9  C1   C6  C5   112.68  3.000
 IT9  C9   C7  C8   122.01  3.000
 IT9  C8   C7  C4   120.73  3.000
 IT9  C9   C7  C4   117.24  3.000
 IT9  H10  C8  H9   116.66  3.000
 IT9  H10  C8  C7   121.66  3.000
 IT9  H9   C8  C7   121.68  3.000
 IT9  H11  C9  H13  107.62  3.000
 IT9  H11  C9  H12  108.10  3.000
 IT9  H13  C9  H12  106.67  3.000
 IT9  H11  C9  C7   111.38  3.000
 IT9  H13  C9  C7   111.24  3.000
 IT9  H12  C9  C7   111.61  3.000
 IT9  C2   C1  C    122.01  3.000
 IT9  C2   C1  C6   121.39  3.000
 IT9  C    C1  C6   116.60  3.000
 IT9  H4   C2  C3   116.51  3.000
 IT9  H4   C2  C1   120.38  3.000
 IT9  C3   C2  C1   123.08  3.000
 IT9  C2   C3  O    121.34  3.000
 IT9  O    C3  C4   121.88  3.000
 IT9  C2   C3  C4   116.71  3.000
 IT9  H3   C   H2   108.58  3.000
 IT9  H3   C   H1   106.41  3.000
 IT9  H2   C   H1   108.63  3.000
 IT9  H3   C   C1   110.24  3.000
 IT9  H2   C   C1   112.45  3.000
 IT9  H1   C   C1   110.32  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
 IT9  Var_01  C1   C6  C5  C4  -49.68  30.0  1
 IT9  Var_02  C1   C2  C3  C4    5.36  30.0  1
 IT9  Var_03  C2   C1  C6  C5   19.77  30.0  1
 IT9  Var_04  C3   C2  C1  C6    3.07  30.0  1
 IT9  Var_05  H1   C   C1  C6   64.42  30.0  3
 IT9  Var_06  H9   C8  C7  C4    0.40   0.0  2
 IT9  Var_07  H12  C9  C7  C4  -53.87  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
 IT9  chir_01  C4  C7  C5  C3  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
 IT9  plan-1  C4   0.020
 IT9  plan-1  C2   0.020
 IT9  plan-1  C3   0.020
 IT9  plan-1  O    0.020
 IT9  plan-2  C4   0.020
 IT9  plan-2  C7   0.020
 IT9  plan-2  C8   0.020
 IT9  plan-2  C9   0.020
 IT9  plan-2  H9   0.020
 IT9  plan-2  H10  0.020

