# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:35:42 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-hexyl-1-methyl-5-(2-methylphenoxy)pyridin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC1=CC(=O)C(=CN1C)Oc2ccccc2C
#
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
 VT4  VT4  2-hexyl-1-methyl-5-(2-methylphenoxy)pyridin-4(1H)-one  ligand  47  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VT4
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
 VT4  C1    C  CR16  0  -0.534  -0.4242  -0.7394  -1.3257
 VT4  C2    C  CR6   0   0.426  -1.2112  -1.2073  -0.3136
 VT4  C4    C  CR16  0  -0.056   0.6808  -1.3813   1.0700
 VT4  C5    C  CR6   0   0.098   1.4994  -0.9308   0.0909
 VT4  C6    C  CR6   0   0.406   0.9970  -0.5670  -1.2170
 VT4  C8    C  CR6   0   0.343   3.4761   0.3182   0.3227
 VT4  C9    C  CR6   0   0.012   4.8617   0.2772   0.1452
 VT4  C10   C  CR16  0  -0.296   5.5539   1.4821   0.1804
 VT4  C11   C  CR16  0  -0.263   4.9038   2.6940   0.3808
 VT4  C12   C  CR16  0  -0.268   3.5295   2.7059   0.5588
 VT4  C13   C  CR16  0  -0.333   2.8107   1.5175   0.5335
 VT4  C14   C  CH2   0  -0.545  -2.6940  -1.3329  -0.4962
 VT4  C15   C  CH2   0  -0.418  -3.4496  -0.0751  -0.0567
 VT4  C16   C  CH2   0  -0.417  -4.9497  -0.2063  -0.2843
 VT4  C17   C  CH2   0  -0.409  -5.7221   1.0474   0.1039
 VT4  C18   C  CH2   0  -0.419  -7.2206   0.9285  -0.1466
 VT4  C19   C  CH3   0  -0.662  -7.9849   2.1868   0.2403
 VT4  O17   O  O     0  -0.502   1.7303  -0.1597  -2.1244
 VT4  C80   C  CH3   0  -0.714   5.5679  -1.0262  -0.0807
 VT4  O7    O  O2    0  -0.498   2.8426  -0.8913   0.3244
 VT4  N     N  NR6   0  -0.497  -0.6570  -1.5278   0.8886
 VT4  H1    H  HCR6  0   0.264  -0.8984  -0.4999  -2.2693
 VT4  H141  H  HCH2  0   0.273  -2.8845  -1.5062  -1.5566
 VT4  H142  H  HCH2  0   0.268  -3.0857  -2.2068   0.0289
 VT4  H4    H  HCR6  0   0.318   1.0696  -1.6586   2.0399
 VT4  H13   H  HCR6  0   0.269   1.7388   1.5377   0.6847
 VT4  H10   H  HCR6  0   0.249   6.6288   1.4678   0.0432
 VT4  H801  H  HCH3  0   0.244   5.2003  -1.5325  -0.9749
 VT4  H802  H  HCH3  0   0.243   6.6379  -0.8662  -0.2050
 VT4  H803  H  HCH3  0   0.244   5.4312  -1.7145   0.7549
 VT4  H11   H  HCR6  0   0.250   5.4690   3.6164   0.3989
 VT4  H12   H  HCR6  0   0.256   3.0058   3.6387   0.7229
 VT4  H151  H  HCH2  0   0.227  -3.2580   0.1388   0.9993
 VT4  H152  H  HCH2  0   0.235  -3.0639   0.7826  -0.6156
 VT4  H161  H  HCH2  0   0.216  -5.1337  -0.4367  -1.3393
 VT4  H162  H  HCH2  0   0.216  -5.3314  -1.0615   0.2840
 VT4  H171  H  HCH2  0   0.210  -5.5488   1.2713   1.1623
 VT4  H172  H  HCH2  0   0.209  -5.3283   1.9042  -0.4543
 VT4  H181  H  HCH2  0   0.211  -7.3914   0.7041  -1.2039
 VT4  H182  H  HCH2  0   0.211  -7.6140   0.0730   0.4112
 VT4  H191  H  HCH3  0   0.216  -7.8679   2.4079   1.3030
 VT4  H192  H  HCH3  0   0.216  -7.6231   3.0535  -0.3165
 VT4  H193  H  HCH3  0   0.226  -9.0521   2.0872   0.0394
 VT4  H211  H  HCH3  0   0.273  -1.8379  -3.0646   1.7202
 VT4  H212  H  HCH3  0   0.278  -0.8298  -2.1720   2.8599
 VT4  H213  H  HCH3  0   0.268  -2.2877  -1.4240   2.2236
 VT4  C21   C  CH3   0  -0.542  -1.4558  -2.0790   1.9782

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
 VT4  C1   C2    double    1.365  0.020  1.365
 VT4  C1   C6    single    1.436  0.020  1.436
 VT4  C2   C14   single    1.499  0.020  1.499
 VT4  C2   N     single    1.362  0.020  1.362
 VT4  C4   C5    double    1.353  0.020  1.353
 VT4  C4   N     single    1.358  0.020  1.358
 VT4  C5   C6    single    1.448  0.020  1.448
 VT4  C5   O7    single    1.364  0.020  1.364
 VT4  C6   O17   double    1.236  0.020  1.236
 VT4  C8   C9    aromatic  1.398  0.020  1.398
 VT4  C8   C13   aromatic  1.388  0.020  1.388
 VT4  C8   O7    single    1.365  0.020  1.365
 VT4  C9   C10   aromatic  1.390  0.020  1.390
 VT4  C9   C80   single    1.500  0.020  1.500
 VT4  C10  C11   aromatic  1.390  0.020  1.390
 VT4  C11  C12   aromatic  1.386  0.020  1.386
 VT4  C12  C13   aromatic  1.389  0.020  1.389
 VT4  C14  C15   single    1.532  0.020  1.532
 VT4  C15  C16   single    1.523  0.020  1.523
 VT4  C16  C17   single    1.523  0.020  1.523
 VT4  C17  C18   single    1.524  0.020  1.524
 VT4  C18  C19   single    1.522  0.020  1.522
 VT4  C21  N     single    1.459  0.020  1.459
 VT4  C1   H1    single    0.930  0.020  1.080
 VT4  C14  H141  single    0.970  0.020  1.090
 VT4  C14  H142  single    0.970  0.020  1.090
 VT4  C4   H4    single    0.930  0.020  1.080
 VT4  C13  H13   single    0.930  0.020  1.080
 VT4  C10  H10   single    0.930  0.020  1.080
 VT4  C80  H801  single    0.970  0.020  1.090
 VT4  C80  H802  single    0.970  0.020  1.090
 VT4  C80  H803  single    0.970  0.020  1.090
 VT4  C11  H11   single    0.930  0.020  1.080
 VT4  C12  H12   single    0.930  0.020  1.080
 VT4  C15  H151  single    0.970  0.020  1.090
 VT4  C15  H152  single    0.970  0.020  1.090
 VT4  C16  H161  single    0.970  0.020  1.090
 VT4  C16  H162  single    0.970  0.020  1.090
 VT4  C17  H171  single    0.970  0.020  1.090
 VT4  C17  H172  single    0.970  0.020  1.090
 VT4  C18  H181  single    0.970  0.020  1.090
 VT4  C18  H182  single    0.970  0.020  1.090
 VT4  C19  H191  single    0.970  0.020  1.090
 VT4  C19  H192  single    0.970  0.020  1.090
 VT4  C19  H193  single    0.970  0.020  1.090
 VT4  C21  H211  single    0.970  0.020  1.090
 VT4  C21  H212  single    0.970  0.020  1.090
 VT4  C21  H213  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
 VT4  H1    C1   C6    118.22  3.000
 VT4  H1    C1   C2    118.00  3.000
 VT4  C6    C1   C2    123.77  3.000
 VT4  N     C2   C14   119.35  3.000
 VT4  N     C2   C1    120.04  3.000
 VT4  C14   C2   C1    120.58  3.000
 VT4  H4    C4   N     116.52  3.000
 VT4  H4    C4   C5    121.12  3.000
 VT4  N     C4   C5    122.36  3.000
 VT4  O7    C5   C6    119.29  3.000
 VT4  O7    C5   C4    118.79  3.000
 VT4  C6    C5   C4    121.82  3.000
 VT4  O17   C6   C5    122.71  3.000
 VT4  O17   C6   C1    124.85  3.000
 VT4  C5    C6   C1    112.45  3.000
 VT4  O7    C8   C13   122.89  3.000
 VT4  O7    C8   C9    115.73  3.000
 VT4  C13   C8   C9    121.34  3.000
 VT4  C80   C9   C10   121.52  3.000
 VT4  C80   C9   C8    120.77  3.000
 VT4  C10   C9   C8    117.71  3.000
 VT4  H10   C10  C11   119.59  3.000
 VT4  H10   C10  C9    118.64  3.000
 VT4  C11   C10  C9    121.77  3.000
 VT4  H11   C11  C12   120.57  3.000
 VT4  H11   C11  C10   120.10  3.000
 VT4  C12   C11  C10   119.33  3.000
 VT4  H12   C12  C13   119.33  3.000
 VT4  H12   C12  C11   120.44  3.000
 VT4  C13   C12  C11   120.23  3.000
 VT4  H13   C13  C12   119.59  3.000
 VT4  H13   C13  C8    120.80  3.000
 VT4  C12   C13  C8    119.61  3.000
 VT4  H142  C14  H141  106.11  3.000
 VT4  H142  C14  C15   110.01  3.000
 VT4  H141  C14  C15   108.85  3.000
 VT4  H142  C14  C2    111.30  3.000
 VT4  H141  C14  C2    107.72  3.000
 VT4  C15   C14  C2    112.59  3.000
 VT4  H152  C15  H151  106.15  3.000
 VT4  H152  C15  C16   109.78  3.000
 VT4  H151  C15  C16   109.48  3.000
 VT4  H152  C15  C14   108.86  3.000
 VT4  H151  C15  C14   110.55  3.000
 VT4  C16   C15  C14   111.86  3.000
 VT4  H162  C16  H161  106.07  3.000
 VT4  H162  C16  C17   109.49  3.000
 VT4  H161  C16  C17   109.48  3.000
 VT4  H162  C16  C15   109.44  3.000
 VT4  H161  C16  C15   109.12  3.000
 VT4  C17   C16  C15   112.99  3.000
 VT4  H172  C17  H171  105.98  3.000
 VT4  H172  C17  C18   109.31  3.000
 VT4  H171  C17  C18   109.29  3.000
 VT4  H172  C17  C16   109.36  3.000
 VT4  H171  C17  C16   109.53  3.000
 VT4  C18   C17  C16   113.12  3.000
 VT4  H182  C18  H181  106.02  3.000
 VT4  H182  C18  C19   109.64  3.000
 VT4  H181  C18  C19   109.68  3.000
 VT4  H182  C18  C17   109.31  3.000
 VT4  H181  C18  C17   109.17  3.000
 VT4  C19   C18  C17   112.80  3.000
 VT4  H193  C19  H192  107.63  3.000
 VT4  H193  C19  H191  107.62  3.000
 VT4  H192  C19  H191  107.47  3.000
 VT4  H193  C19  C18   111.66  3.000
 VT4  H192  C19  C18   111.11  3.000
 VT4  H191  C19  C18   111.16  3.000
 VT4  H803  C80  H802  107.65  3.000
 VT4  H803  C80  H801  107.01  3.000
 VT4  H802  C80  H801  107.80  3.000
 VT4  H803  C80  C9    111.96  3.000
 VT4  H802  C80  C9    110.62  3.000
 VT4  H801  C80  C9    111.59  3.000
 VT4  C8    O7   C5    118.84  3.000
 VT4  C21   N    C4    118.71  3.000
 VT4  C21   N    C2    121.68  3.000
 VT4  C4    N    C2    119.56  3.000
 VT4  H213  C21  H212  108.04  3.000
 VT4  H213  C21  H211  109.30  3.000
 VT4  H212  C21  H211  108.52  3.000
 VT4  H213  C21  N     111.10  3.000
 VT4  H212  C21  N     108.86  3.000
 VT4  H211  C21  N     110.94  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
 VT4  CONST_01  C11   C10  C9   C8      0.00   0.0  0
 VT4  CONST_02  C11   C12  C13  C8      0.00   0.0  0
 VT4  CONST_03  C12   C13  C8   C9      0.00   0.0  0
 VT4  CONST_04  C12   C11  C10  C9      0.00   0.0  0
 VT4  CONST_05  C13   C8   C9   C10     0.00   0.0  0
 VT4  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 VT4  CONST_07  O7    C8   C9   C10   180.00   0.0  0
 VT4  CONST_08  C80   C9   C10  C11   180.00   0.0  0
 VT4  CONST_09  O7    C8   C13  C12   180.00   0.0  0
 VT4  CONST_10  C80   C9   C8   C13   180.00   0.0  0
 VT4  CONST_11  H10   C10  C9   C8    180.00   0.0  0
 VT4  CONST_12  H12   C12  C13  C8    180.00   0.0  0
 VT4  CONST_13  H13   C13  C8   C9    180.00   0.0  0
 VT4  CONST_14  H11   C11  C10  C9    180.00   0.0  0
 VT4  Var_01    C9    C8   O7   C5   -160.62  30.0  2
 VT4  Var_02    C15   C14  C2   C1    -91.46  30.0  3
 VT4  Var_03    H211  C21  N    C2     65.72  30.0  3
 VT4  Var_04    H801  C80  C9   C8     59.58  30.0  2
 VT4  Var_05    C16   C15  C14  C2    178.45  30.0  3
 VT4  Var_06    C17   C16  C15  C14  -178.22  30.0  3
 VT4  Var_07    C18   C17  C16  C15   178.95  30.0  3
 VT4  Var_08    C19   C18  C17  C16  -179.84  30.0  3
 VT4  Var_09    H191  C19  C18  C17   -60.68  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
 VT4  plan-1  C1   0.020
 VT4  plan-1  C2   0.020
 VT4  plan-1  C4   0.020
 VT4  plan-1  C5   0.020
 VT4  plan-1  C6   0.020
 VT4  plan-1  C14  0.020
 VT4  plan-1  O17  0.020
 VT4  plan-1  O7   0.020
 VT4  plan-1  N    0.020
 VT4  plan-1  H1   0.020
 VT4  plan-1  H4   0.020
 VT4  plan-1  C21  0.020
 VT4  plan-2  C8   0.020
 VT4  plan-2  C9   0.020
 VT4  plan-2  C10  0.020
 VT4  plan-2  C11  0.020
 VT4  plan-2  C12  0.020
 VT4  plan-2  C13  0.020
 VT4  plan-2  C80  0.020
 VT4  plan-2  O7   0.020
 VT4  plan-2  H13  0.020
 VT4  plan-2  H10  0.020
 VT4  plan-2  H11  0.020
 VT4  plan-2  H12  0.020

