# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 23:29:01 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-methyl-2-[(2E)-non-2-en-1-yl]quinolin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC/C=C/CC1=C(C)C(=O)c2ccccc2N1
#
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
 F2D  F2D  "3-methyl-2-[(2E)-non-2-en-1-yl]quinolin-4(1H)-one"
  ligand  46  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F2D
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
 F2D  C1    C  CR66  0  -0.111  12.5315  27.3384  14.9440
 F2D  C2    C  CR16  0  -0.299  12.3383  28.5301  14.2299
 F2D  C3    C  CR16  0  -0.255  13.0071  28.7653  13.0514
 F2D  C4    C  CR16  0  -0.254  13.8955  27.8036  12.5516
 F2D  C5    C  CR16  0  -0.314  14.1054  26.6259  13.2284
 F2D  C6    C  CR66  0   0.367  13.4201  26.3887  14.4289
 F2D  C18   C  CR6   0   0.348  12.9830  24.9446  16.2811
 F2D  C19   C  CR6   0  -0.184  12.0987  25.8217  16.8477
 F2D  C20   C  CR6   0   0.422  11.8214  27.0885  16.2046
 F2D  C22   C  CH3   0  -0.745  11.4093  25.4901  18.1389
 F2D  C23   C  CH2   0  -0.605  13.2880  23.5934  16.8652
 F2D  C24   C  C1    0  -0.192  12.2633  22.5758  16.4492
 F2D  C25   C  C1    0  -0.213  11.6370  21.7559  17.2876
 F2D  C26   C  CH2   0  -0.490  10.6737  20.6898  16.8614
 F2D  C27   C  CH2   0  -0.408  11.3309  19.3121  16.7225
 F2D  C28   C  CH2   0  -0.421  11.9842  18.7920  17.9963
 F2D  C29   C  CH2   0  -0.413  12.5887  17.4035  17.8144
 F2D  C30   C  CH2   0  -0.425  13.3874  16.9062  19.0167
 F2D  C31   C  CH3   0  -0.664  12.5514  16.6988  20.2730
 F2D  N13   N  NR16  0  -0.744  13.6134  25.2268  15.1180
 F2D  O21   O  O     0  -0.474  11.0384  27.9227  16.6671
 F2D  H2    H  HCR6  0   0.257  11.6519  29.2677  14.6236
 F2D  H3    H  HCR6  0   0.257  12.8503  29.6885  12.5099
 F2D  H4    H  HCR6  0   0.265  14.4231  27.9868  11.6246
 F2D  H5    H  HCR6  0   0.274  14.7908  25.8796  12.8448
 F2D  H221  H  HCH3  0   0.253  10.6855  26.2609  18.3914
 F2D  H22   H  HCH3  0   0.242  10.8776  24.5388  18.0867
 F2D  H222  H  HCH3  0   0.240  12.1130  25.4176  18.9711
 F2D  H231  H  HCH2  0   0.278  14.2796  23.2728  16.5287
 F2D  H23   H  HCH2  0   0.280  13.3381  23.6568  17.9529
 F2D  H24   H  H     0   0.246  12.0562  22.5126  15.3832
 F2D  H25   H  H     0   0.239  11.8577  21.8296  18.3498
 F2D  H26   H  HCH2  0   0.236  10.2256  20.9625  15.9028
 F2D  H261  H  HCH2  0   0.228   9.8550  20.6258  17.5843
 F2D  H27   H  HCH2  0   0.218  10.5733  18.5969  16.3870
 F2D  H271  H  HCH2  0   0.212  12.0800  19.3628  15.9260
 F2D  H28   H  HCH2  0   0.210  12.7735  19.4806  18.3172
 F2D  H281  H  HCH2  0   0.213  11.2449  18.7804  18.8034
 F2D  H291  H  HCH2  0   0.206  11.7938  16.6859  17.5827
 F2D  H29   H  HCH2  0   0.214  13.2442  17.4201  16.9378
 F2D  H30   H  HCH2  0   0.219  13.8743  15.9636  18.7526
 F2D  H301  H  HCH2  0   0.209  14.1946  17.6145  19.2274
 F2D  H312  H  HCH3  0   0.225  13.1562  16.2966  21.0868
 F2D  H31   H  HCH3  0   0.220  12.1091  17.6305  20.6276
 F2D  H311  H  HCH3  0   0.214  11.7362  15.9956  20.0907
 F2D  H1    H  HNR6  0   0.420  14.2585  24.5487  14.7394

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
 F2D  C4   C3    aromatic  1.401  0.020  1.401
 F2D  C4   C5    aromatic  1.374  0.020  1.374
 F2D  C3   C2    aromatic  1.375  0.020  1.375
 F2D  C5   C6    aromatic  1.403  0.020  1.403
 F2D  C2   C1    aromatic  1.403  0.020  1.403
 F2D  C6   N13   single    1.365  0.020  1.365
 F2D  C6   C1    aromatic  1.399  0.020  1.399
 F2D  N13  C18   single    1.353  0.020  1.353
 F2D  C1   C20   single    1.468  0.020  1.468
 F2D  C18  C23   single    1.503  0.020  1.503
 F2D  C18  C19   double    1.368  0.020  1.368
 F2D  C24  C23   single    1.503  0.020  1.503
 F2D  C24  C25   double    1.329  0.020  1.329
 F2D  C20  O21   double    1.234  0.020  1.234
 F2D  C20  C19   single    1.447  0.020  1.447
 F2D  C27  C26   single    1.533  0.020  1.533
 F2D  C27  C28   single    1.523  0.020  1.523
 F2D  C26  C25   single    1.499  0.020  1.499
 F2D  C19  C22   single    1.501  0.020  1.501
 F2D  C28  C29   single    1.525  0.020  1.525
 F2D  C29  C30   single    1.527  0.020  1.527
 F2D  C30  C31   single    1.523  0.020  1.523
 F2D  C2   H2    single    0.930  0.020  1.080
 F2D  C3   H3    single    0.930  0.020  1.080
 F2D  C4   H4    single    0.930  0.020  1.080
 F2D  C5   H5    single    0.930  0.020  1.080
 F2D  C22  H221  single    0.970  0.020  1.090
 F2D  C22  H22   single    0.970  0.020  1.090
 F2D  C22  H222  single    0.970  0.020  1.090
 F2D  C23  H231  single    0.970  0.020  1.090
 F2D  C23  H23   single    0.970  0.020  1.090
 F2D  C24  H24   single    0.930  0.020  1.080
 F2D  C25  H25   single    0.930  0.020  1.080
 F2D  C26  H26   single    0.970  0.020  1.090
 F2D  C26  H261  single    0.970  0.020  1.090
 F2D  C27  H27   single    0.970  0.020  1.090
 F2D  C27  H271  single    0.970  0.020  1.090
 F2D  C28  H28   single    0.970  0.020  1.090
 F2D  C28  H281  single    0.970  0.020  1.090
 F2D  C29  H291  single    0.970  0.020  1.090
 F2D  C29  H29   single    0.970  0.020  1.090
 F2D  C30  H30   single    0.970  0.020  1.090
 F2D  C30  H301  single    0.970  0.020  1.090
 F2D  C31  H312  single    0.970  0.020  1.090
 F2D  C31  H31   single    0.970  0.020  1.090
 F2D  C31  H311  single    0.970  0.020  1.090
 F2D  N13  H1    single    0.860  0.020  1.020

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
 F2D  C20   C1   C6    120.51  3.000
 F2D  C20   C1   C2    121.00  3.000
 F2D  C6    C1   C2    118.48  3.000
 F2D  H2    C2   C3    120.25  3.000
 F2D  H2    C2   C1    118.78  3.000
 F2D  C3    C2   C1    120.97  3.000
 F2D  H3    C3   C4    119.93  3.000
 F2D  H3    C3   C2    120.30  3.000
 F2D  C4    C3   C2    119.77  3.000
 F2D  H4    C4   C5    119.49  3.000
 F2D  H4    C4   C3    119.89  3.000
 F2D  C5    C4   C3    120.61  3.000
 F2D  H5    C5   C6    119.72  3.000
 F2D  H5    C5   C4    120.83  3.000
 F2D  C6    C5   C4    119.45  3.000
 F2D  N13   C6   C5    120.46  3.000
 F2D  N13   C6   C1    118.82  3.000
 F2D  C5    C6   C1    120.71  3.000
 F2D  N13   C18  C23   115.28  3.000
 F2D  C23   C18  C19   123.12  3.000
 F2D  N13   C18  C19   121.57  3.000
 F2D  C22   C19  C20   119.18  3.000
 F2D  C22   C19  C18   120.77  3.000
 F2D  C20   C19  C18   120.05  3.000
 F2D  O21   C20  C19   123.14  3.000
 F2D  C19   C20  C1    115.96  3.000
 F2D  O21   C20  C1    120.90  3.000
 F2D  H222  C22  H22   107.01  3.000
 F2D  H222  C22  H221  107.40  3.000
 F2D  H22   C22  H221  107.75  3.000
 F2D  H222  C22  C19   111.97  3.000
 F2D  H22   C22  C19   112.04  3.000
 F2D  H221  C22  C19   110.43  3.000
 F2D  H23   C23  H231  106.37  3.000
 F2D  H23   C23  C24   110.29  3.000
 F2D  H231  C23  C24   109.52  3.000
 F2D  H23   C23  C18   110.16  3.000
 F2D  H231  C23  C18   109.11  3.000
 F2D  C24   C23  C18   111.27  3.000
 F2D  H24   C24  C25   119.51  3.000
 F2D  H24   C24  C23   116.13  3.000
 F2D  C25   C24  C23   124.35  3.000
 F2D  H25   C25  C26   117.16  3.000
 F2D  H25   C25  C24   118.59  3.000
 F2D  C26   C25  C24   124.21  3.000
 F2D  H261  C26  H26   106.70  3.000
 F2D  H261  C26  C27   109.16  3.000
 F2D  H26   C26  C27   108.70  3.000
 F2D  H261  C26  C25   109.55  3.000
 F2D  H26   C26  C25   109.60  3.000
 F2D  C27   C26  C25   112.93  3.000
 F2D  H271  C27  H27   106.31  3.000
 F2D  H271  C27  C28   109.32  3.000
 F2D  H27   C27  C28   109.27  3.000
 F2D  H271  C27  C26   108.53  3.000
 F2D  H27   C27  C26   108.56  3.000
 F2D  C28   C27  C26   114.52  3.000
 F2D  H281  C28  H28   106.10  3.000
 F2D  H281  C28  C29   110.25  3.000
 F2D  H28   C28  C29   108.77  3.000
 F2D  H281  C28  C27   109.30  3.000
 F2D  H28   C28  C27   109.83  3.000
 F2D  C29   C28  C27   112.40  3.000
 F2D  H29   C29  H291  105.97  3.000
 F2D  H29   C29  C30   108.80  3.000
 F2D  H291  C29  C30   109.43  3.000
 F2D  H29   C29  C28   108.61  3.000
 F2D  H291  C29  C28   109.51  3.000
 F2D  C30   C29  C28   114.20  3.000
 F2D  H301  C30  H30   106.02  3.000
 F2D  H301  C30  C31   109.52  3.000
 F2D  H30   C30  C31   109.04  3.000
 F2D  H301  C30  C29   109.07  3.000
 F2D  H30   C30  C29   108.88  3.000
 F2D  C31   C30  C29   114.00  3.000
 F2D  H311  C31  H31   107.56  3.000
 F2D  H311  C31  H312  107.52  3.000
 F2D  H31   C31  H312  107.30  3.000
 F2D  H311  C31  C30   111.08  3.000
 F2D  H31   C31  C30   111.99  3.000
 F2D  H312  C31  C30   111.18  3.000
 F2D  H1    N13  C18   118.69  3.000
 F2D  H1    N13  C6    118.23  3.000
 F2D  C18   N13  C6    123.08  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
 F2D  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 F2D  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 F2D  CONST_03  C5    C4   C3   C2      0.00   0.0  0
 F2D  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 F2D  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 F2D  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 F2D  CONST_07  H3    C3   C2   C1    180.00   0.0  0
 F2D  CONST_08  H5    C5   C6   C1    180.00   0.0  0
 F2D  CONST_09  H4    C4   C3   C2    180.00   0.0  0
 F2D  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 F2D  CONST_11  H2    C2   C3   C4    180.00   0.0  0
 F2D  CONST_12  H3    C3   C4   C5    180.00   0.0  0
 F2D  CONST_13  H4    C4   C5   C6    180.00   0.0  0
 F2D  CONST_14  H2    C2   C1   C6    180.00   0.0  0
 F2D  CONST_15  H2    C2   C1   C20     0.00   0.0  0
 F2D  CONST_16  H5    C5   C6   N13     0.00   0.0  0
 F2D  Var_01    C18   N13  C6   C1      0.11  30.0  1
 F2D  Var_02    C18   C19  C20  C1      0.36  30.0  1
 F2D  Var_03    C19   C20  C1   C2    179.79  30.0  1
 F2D  Var_04    C18   N13  C6   C5    179.87  30.0  1
 F2D  Var_05    C19   C18  N13  C6     -0.04  30.0  1
 F2D  Var_06    C19   C20  C1   C6     -0.29  30.0  1
 F2D  Var_07    N13   C18  C19  C20    -0.21  30.0  1
 F2D  Var_08    C22   C19  C20  C1   -179.85  30.0  1
 F2D  Var_09    O21   C20  C1   C2     -0.10  30.0  1
 F2D  Var_10    C23   C18  N13  C6    177.87  30.0  1
 F2D  Var_11    O21   C20  C1   C6    179.82  30.0  1
 F2D  Var_12    O21   C20  C19  C18  -179.76  30.0  1
 F2D  Var_13    C23   C18  C19  C20  -177.94  30.0  1
 F2D  Var_14    N13   C18  C19  C22  -180.00  30.0  1
 F2D  Var_15    H1    N13  C6   C1   -179.84  30.0  1
 F2D  Var_16    H1    N13  C6   C5     -0.08  30.0  1
 F2D  Var_17    H1    N13  C18  C19   179.91  30.0  1
 F2D  Var_18    C24   C23  C18  C19    83.37  30.0  3
 F2D  Var_19    C23   C18  C19  C22     2.27  30.0  1
 F2D  Var_20    O21   C20  C19  C22     0.03  30.0  1
 F2D  Var_21    N13   C18  C23  C24   -94.50  30.0  2
 F2D  Var_22    H221  C22  C19  C18  -175.21  30.0  3
 F2D  Var_23    H22   C22  C19  C18   -55.10  30.0  3
 F2D  Var_24    H222  C22  C19  C18    65.15  30.0  3
 F2D  Var_25    H231  C23  C18  C19  -155.68  30.0  3
 F2D  Var_26    H23   C23  C18  C19   -39.26  30.0  3
 F2D  Var_27    H221  C22  C19  C20     5.00  30.0  3
 F2D  Var_28    H22   C22  C19  C20   125.11  30.0  3
 F2D  Var_29    H222  C22  C19  C20  -114.64  30.0  3
 F2D  Var_30    H1    N13  C18  C23    -2.18  30.0  1
 F2D  Var_31    H231  C23  C18  N13    26.45  30.0  3
 F2D  Var_32    H23   C23  C18  N13   142.87  30.0  3
 F2D  Var_33    C25   C24  C23  C18  -130.44  30.0  1
 F2D  Var_34    H24   C24  C23  C18    50.96  30.0  1
 F2D  Var_35    C26   C25  C24  C23  -176.36   0.0  2
 F2D  Var_36    C27   C26  C25  C24    95.74  30.0  1
 F2D  Var_37    C28   C27  C26  C25    58.94  30.0  2
 F2D  Var_38    C29   C28  C27  C26   178.42  30.0  3
 F2D  Var_39    C30   C29  C28  C27   173.60  30.0  3
 F2D  Var_40    C31   C30  C29  C28    64.50  30.0  3
 F2D  Var_41    H25   C25  C24  C23     1.24   0.0  2
 F2D  Var_42    H24   C24  C25  C26     2.19   0.0  2
 F2D  Var_43    H26   C26  C25  C24   -25.61  30.0  1
 F2D  Var_44    H261  C26  C25  C24  -142.36  30.0  1
 F2D  Var_45    H231  C23  C24  C25   108.84  30.0  3
 F2D  Var_46    H23   C23  C24  C25    -7.89  30.0  3
 F2D  Var_47    H27   C27  C26  C25  -178.65  30.0  2
 F2D  Var_48    H271  C27  C26  C25   -63.50  30.0  2
 F2D  Var_49    H28   C28  C27  C26   -60.34  30.0  3
 F2D  Var_50    H281  C28  C27  C26    55.67  30.0  3
 F2D  Var_51    H25   C25  C26  C27   -81.90  30.0  3
 F2D  Var_52    H291  C29  C28  C27   -63.30  30.0  3
 F2D  Var_53    H29   C29  C28  C27    51.99  30.0  3
 F2D  Var_54    H26   C26  C27  C28  -179.21  30.0  3
 F2D  Var_55    H261  C26  C27  C28   -63.17  30.0  3
 F2D  Var_56    H30   C30  C29  C28  -173.51  30.0  3
 F2D  Var_57    H301  C30  C29  C28   -58.24  30.0  3
 F2D  Var_58    H27   C27  C28  C29    56.41  30.0  2
 F2D  Var_59    H271  C27  C28  C29   -59.56  30.0  2
 F2D  Var_60    H312  C31  C30  C29   177.14  30.0  3
 F2D  Var_61    H31   C31  C30  C29   -62.84  30.0  3
 F2D  Var_62    H311  C31  C30  C29    57.45  30.0  3
 F2D  Var_63    H28   C28  C29  C30    51.75  30.0  1
 F2D  Var_64    H281  C28  C29  C30   -64.19  30.0  1
 F2D  Var_65    H291  C29  C30  C31   -58.64  30.0  1
 F2D  Var_66    H29   C29  C30  C31  -174.00  30.0  1
 F2D  Var_67    H25   C25  C24  H24   179.79   0.0  2

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
 F2D  plan-1  C1   0.020
 F2D  plan-1  C19  0.020
 F2D  plan-1  C20  0.020
 F2D  plan-1  O21  0.020
 F2D  plan-2  C1   0.020
 F2D  plan-2  C2   0.020
 F2D  plan-2  C3   0.020
 F2D  plan-2  C4   0.020
 F2D  plan-2  C5   0.020
 F2D  plan-2  C6   0.020
 F2D  plan-2  C20  0.020
 F2D  plan-2  N13  0.020
 F2D  plan-2  H2   0.020
 F2D  plan-2  H3   0.020
 F2D  plan-2  H4   0.020
 F2D  plan-2  H5   0.020
 F2D  plan-3  C6   0.020
 F2D  plan-3  C18  0.020
 F2D  plan-3  N13  0.020
 F2D  plan-3  H1   0.020
 F2D  plan-4  C23  0.020
 F2D  plan-4  C24  0.020
 F2D  plan-4  C25  0.020
 F2D  plan-4  C26  0.020
 F2D  plan-4  H24  0.020
 F2D  plan-4  H25  0.020

