# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 07:13:41 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H](CC#N)CC(C)=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
 2K6  2K6  (3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile  ligand  31  16  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2K6
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
 2K6  C1   C  CH3   0  -0.437   4.9855  -0.9601   0.8043
 2K6  O1   O  O2    0  -0.471   4.2792  -0.4853  -0.3247
 2K6  C2   C  CR6   0   0.368   2.9432  -0.3400  -0.2333
 2K6  C3   C  CR16  0  -0.327   2.2890   0.1345  -1.3706
 2K6  C4   C  CR16  0  -0.304   0.9170   0.3128  -1.3611
 2K6  C5   C  CR16  0  -0.367   2.1961  -0.6288   0.9068
 2K6  C6   C  CR16  0  -0.290   0.8197  -0.4432   0.8946
 2K6  C7   C  CR6   0   0.145   0.1544   0.0267  -0.2314
 2K6  C8   C  CH1   0  -0.345  -1.3424   0.2256  -0.2377
 2K6  C9   C  CH2   0  -0.554  -2.0720  -1.0954  -0.0034
 2K6  C10  C  C     0   0.400  -3.5581  -1.0820  -0.2715
 2K6  C11  C  CH3   0  -0.769  -4.2989  -2.3094   0.1768
 2K6  C12  C  CH2   0  -0.529  -1.7662   1.2625   0.8195
 2K6  C13  C  CSP   0   0.127  -1.1050   2.5408   0.6149
 2K6  N1   N  NS    0  -0.274  -0.5867   3.5535   0.4414
 2K6  H1   H  HCH3  0   0.228   4.6656  -1.9638   1.0961
 2K6  H2   H  HCH3  0   0.260   6.0341  -0.9971   0.5201
 2K6  H3   H  HCH3  0   0.228   4.8776  -0.2930   1.6637
 2K6  H4   H  HCR6  0   0.262   2.8627   0.3660  -2.2598
 2K6  H5   H  HCR6  0   0.254   0.4309   0.6853  -2.2551
 2K6  H6   H  HCR6  0   0.278   2.6620  -0.9974   1.8101
 2K6  H7   H  HCR6  0   0.253   0.2679  -0.6773   1.7983
 2K6  H8   H  HCH1  0   0.278  -1.6298   0.6112  -1.2189
 2K6  H9   H  HCH2  0   0.303  -1.6489  -1.8651  -0.6591
 2K6  H10  H  HCH2  0   0.270  -1.8978  -1.4693   1.0106
 2K6  H13  H  HCH3  0   0.270  -4.2757  -2.3661   1.2673
 2K6  H14  H  HCH3  0   0.261  -5.3346  -2.2977  -0.1556
 2K6  H15  H  HCH3  0   0.264  -3.8074  -3.2110  -0.1924
 2K6  H16  H  HCH2  0   0.319  -2.8425   1.4361   0.7905
 2K6  H17  H  HCH2  0   0.302  -1.5231   0.9118   1.8256
 2K6  O2   O  O     0  -0.403  -4.1081  -0.1538  -0.8210

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
 2K6  C9   C10  single    1.510  0.020  1.510
 2K6  C9   C8   single    1.527  0.020  1.527
 2K6  C10  C11  single    1.502  0.020  1.502
 2K6  N1   C13  triple    1.151  0.020  1.151
 2K6  C13  C12  single    1.454  0.020  1.454
 2K6  C12  C8   single    1.540  0.020  1.540
 2K6  C8   C7   single    1.510  0.020  1.510
 2K6  C7   C4   aromatic  1.393  0.020  1.393
 2K6  C7   C6   aromatic  1.390  0.020  1.390
 2K6  C4   C3   aromatic  1.384  0.020  1.384
 2K6  C6   C5   aromatic  1.389  0.020  1.389
 2K6  C3   C2   aromatic  1.395  0.020  1.395
 2K6  C5   C2   aromatic  1.393  0.020  1.393
 2K6  C2   O1   single    1.347  0.020  1.347
 2K6  O1   C1   single    1.414  0.020  1.414
 2K6  C1   H1   single    0.970  0.020  1.090
 2K6  C1   H2   single    0.970  0.020  1.090
 2K6  C1   H3   single    0.970  0.020  1.090
 2K6  C3   H4   single    0.930  0.020  1.080
 2K6  C4   H5   single    0.930  0.020  1.080
 2K6  C5   H6   single    0.930  0.020  1.080
 2K6  C6   H7   single    0.930  0.020  1.080
 2K6  C8   H8   single    0.970  0.020  1.090
 2K6  C9   H9   single    0.970  0.020  1.090
 2K6  C9   H10  single    0.970  0.020  1.090
 2K6  C11  H13  single    0.970  0.020  1.090
 2K6  C11  H14  single    0.970  0.020  1.090
 2K6  C11  H15  single    0.970  0.020  1.090
 2K6  C12  H16  single    0.970  0.020  1.090
 2K6  C12  H17  single    0.970  0.020  1.090
 2K6  C10  O2   double    1.211  0.020  1.211

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
 2K6  H3   C1   H2   108.75  3.000
 2K6  H3   C1   H1   108.75  3.000
 2K6  H2   C1   H1   108.71  3.000
 2K6  H3   C1   O1   111.93  3.000
 2K6  H2   C1   O1   106.53  3.000
 2K6  H1   C1   O1   112.05  3.000
 2K6  C2   O1   C1   118.52  3.000
 2K6  C5   C2   C3   119.09  3.000
 2K6  C5   C2   O1   124.40  3.000
 2K6  C3   C2   O1   116.51  3.000
 2K6  H4   C3   C4   120.22  3.000
 2K6  H4   C3   C2   119.58  3.000
 2K6  C4   C3   C2   120.21  3.000
 2K6  H5   C4   C7   119.62  3.000
 2K6  H5   C4   C3   118.91  3.000
 2K6  C7   C4   C3   121.47  3.000
 2K6  H6   C5   C6   118.68  3.000
 2K6  H6   C5   C2   121.56  3.000
 2K6  C6   C5   C2   119.76  3.000
 2K6  H7   C6   C7   120.30  3.000
 2K6  H7   C6   C5   117.91  3.000
 2K6  C7   C6   C5   121.79  3.000
 2K6  C8   C7   C6   121.50  3.000
 2K6  C6   C7   C4   117.68  3.000
 2K6  C8   C7   C4   120.82  3.000
 2K6  H8   C8   C12  107.84  3.000
 2K6  H8   C8   C9   108.50  3.000
 2K6  C12  C8   C9   110.21  3.000
 2K6  H8   C8   C7   108.12  3.000
 2K6  C12  C8   C7   111.01  3.000
 2K6  C9   C8   C7   111.04  3.000
 2K6  H10  C9   H9   104.65  3.000
 2K6  H10  C9   C10  108.91  3.000
 2K6  H9   C9   C10  106.25  3.000
 2K6  H10  C9   C8   111.20  3.000
 2K6  H9   C9   C8   109.35  3.000
 2K6  C10  C9   C8   115.80  3.000
 2K6  O2   C10  C11  122.54  3.000
 2K6  O2   C10  C9   122.30  3.000
 2K6  C11  C10  C9   115.16  3.000
 2K6  H15  C11  H14  109.53  3.000
 2K6  H15  C11  H13  106.58  3.000
 2K6  H14  C11  H13  109.02  3.000
 2K6  H15  C11  C10  110.61  3.000
 2K6  H14  C11  C10  111.69  3.000
 2K6  H13  C11  C10  109.26  3.000
 2K6  H17  C12  H16  107.17  3.000
 2K6  H17  C12  C13  108.10  3.000
 2K6  H16  C12  C13  107.77  3.000
 2K6  H17  C12  C8   110.77  3.000
 2K6  H16  C12  C8   111.13  3.000
 2K6  C13  C12  C8   111.73  3.000
 2K6  N1   C13  C12  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
 2K6  CONST_01  C7   C4   C3   C2     0.00   0.0  0
 2K6  CONST_02  C7   C6   C5   C2     0.00   0.0  0
 2K6  CONST_03  C6   C7   C4   C3     0.00   0.0  0
 2K6  CONST_04  C6   C5   C2   C3     0.00   0.0  0
 2K6  CONST_05  C5   C6   C7   C4     0.00   0.0  0
 2K6  CONST_06  C5   C2   C3   C4     0.00   0.0  0
 2K6  CONST_07  C4   C3   C2   O1   180.00   0.0  0
 2K6  CONST_08  C6   C5   C2   O1   180.00   0.0  0
 2K6  CONST_09  C8   C7   C4   C3   180.00   0.0  0
 2K6  CONST_10  C8   C7   C6   C5   180.00   0.0  0
 2K6  CONST_11  H5   C4   C3   C2   180.00   0.0  0
 2K6  CONST_12  H7   C6   C5   C2   180.00   0.0  0
 2K6  CONST_13  H6   C5   C2   C3   180.00   0.0  0
 2K6  CONST_14  H4   C3   C2   C5   180.00   0.0  0
 2K6  Var_01    C3   C2   O1   C1   179.84  30.0  3
 2K6  Var_02    H1   C1   O1   C2    61.51  30.0  3
 2K6  Var_03    C11  C10  C9   C8  -170.27  30.0  3
 2K6  Var_04    H13  C11  C10  C9    66.64  30.0  3
 2K6  Var_05    H16  C12  C13  N1   -63.19  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
 2K6  chir_01  C8  C9  C12  C7  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
 2K6  plan-1  O1   0.020
 2K6  plan-1  C2   0.020
 2K6  plan-1  C3   0.020
 2K6  plan-1  C4   0.020
 2K6  plan-1  C5   0.020
 2K6  plan-1  C6   0.020
 2K6  plan-1  C7   0.020
 2K6  plan-1  C8   0.020
 2K6  plan-1  H4   0.020
 2K6  plan-1  H5   0.020
 2K6  plan-1  H6   0.020
 2K6  plan-1  H7   0.020
 2K6  plan-2  C9   0.020
 2K6  plan-2  C10  0.020
 2K6  plan-2  C11  0.020
 2K6  plan-2  O2   0.020

