# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:59:59 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-[(1S)-1-methylhexyl]-4,6-dinitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](C)c1cc(cc(c1O)[N+]([O-])=O)[N+]([O-])=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
 DNT  DNT  2-[(1S)-1-methylhexyl]-4,6-dinitrophenol  ligand  38  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DNT
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
 DNT  C13   C  CH3    0  -0.662   7.1234   0.0828   1.5110
 DNT  C12   C  CH2    0  -0.419   6.1726  -0.3023   0.3861
 DNT  C11   C  CH2    0  -0.406   4.7233   0.0578   0.6886
 DNT  C9    C  CH2    0  -0.424   3.7603  -0.3362  -0.4249
 DNT  C8    C  CH2    0  -0.399   2.3172   0.0314  -0.1021
 DNT  C7    C  CH1    0  -0.322   1.2964  -0.4831  -1.1265
 DNT  C10   C  CH3    0  -0.655   1.5096   0.0991  -2.5247
 DNT  C6    C  CR6    0   0.057  -0.1051  -0.1941  -0.6360
 DNT  C1    C  CR6    0   0.343  -0.9880  -1.2356  -0.2795
 DNT  O1    O  OH1    0  -0.578  -0.5538  -2.4716  -0.4013
 DNT  C2    C  CR6    0   0.198  -2.2794  -0.8969   0.1848
 DNT  C3    C  CR16   0  -0.355  -2.6926   0.4214   0.3015
 DNT  C4    C  CR6    0   0.286  -1.8091   1.4125  -0.0481
 DNT  C5    C  CR16   0  -0.315  -0.5297   1.1091  -0.5110
 DNT  N4    N  N      1   0.325  -2.2197   2.7968   0.0673
 DNT  O61   O  O     -1  -0.375  -1.4267   3.6494  -0.2566
 DNT  O41   O  O      0  -0.376  -3.3323   3.0287   0.4787
 DNT  N6    N  N      1   0.365  -3.2237  -1.9195   0.5629
 DNT  O62   O  O     -1  -0.349  -4.3127  -1.5943   0.9535
 DNT  O42   O  O      0  -0.418  -2.8750  -3.0874   0.4705
 DNT  H131  H  HCH3   0   0.216   7.1083   1.1596   1.6892
 DNT  H132  H  HCH3   0   0.216   6.8451  -0.4077   2.4459
 DNT  H133  H  HCH3   0   0.226   8.1515  -0.2002   1.2826
 DNT  H121  H  HCH2   0   0.211   6.4829   0.1899  -0.5408
 DNT  H122  H  HCH2   0   0.211   6.2459  -1.3779   0.1973
 DNT  H111  H  HCH2   0   0.208   4.4164  -0.4284   1.6212
 DNT  H112  H  HCH2   0   0.209   4.6479   1.1357   0.8702
 DNT  H91   H  HCH2   0   0.219   4.0746   0.1450  -1.3559
 DNT  H92   H  HCH2   0   0.212   3.8303  -1.4158  -0.5997
 DNT  H81   H  HCH2   0   0.231   2.0582  -0.3769   0.8799
 DNT  H82   H  HCH2   0   0.220   2.2293   1.1197  -0.0119
 DNT  H7    H  HCH1   0   0.259   1.4273  -1.5637  -1.2013
 DNT  H101  H  HCH3   0   0.243   2.4821  -0.1911  -2.9217
 DNT  H102  H  HCH3   0   0.241   0.7509  -0.2636  -3.2188
 DNT  H103  H  HCH3   0   0.224   1.4686   1.1903  -2.5233
 DNT  HO1   H  HOH1   0   0.493  -1.2572  -3.0923  -0.1250
 DNT  H3    H  HCR6   0   0.335  -3.6844   0.6542   0.6592
 DNT  H5    H  HCR6   0   0.304   0.1493   1.9089  -0.7747

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
 DNT  C13  C12   single    1.522  0.020  1.522
 DNT  C13  H131  single    0.970  0.020  1.090
 DNT  C13  H132  single    0.970  0.020  1.090
 DNT  C13  H133  single    0.970  0.020  1.090
 DNT  C12  C11   single    1.524  0.020  1.524
 DNT  C12  H121  single    0.970  0.020  1.090
 DNT  C12  H122  single    0.970  0.020  1.090
 DNT  C11  C9    single    1.524  0.020  1.524
 DNT  C11  H111  single    0.970  0.020  1.090
 DNT  C11  H112  single    0.970  0.020  1.090
 DNT  C9   C8    single    1.524  0.020  1.524
 DNT  C9   H91   single    0.970  0.020  1.090
 DNT  C9   H92   single    0.970  0.020  1.090
 DNT  C8   C7    single    1.535  0.020  1.535
 DNT  C8   H81   single    0.970  0.020  1.090
 DNT  C8   H82   single    0.970  0.020  1.090
 DNT  C7   C10   single    1.530  0.020  1.530
 DNT  C7   C6    single    1.513  0.020  1.513
 DNT  C7   H7    single    0.970  0.020  1.090
 DNT  C10  H101  single    0.970  0.020  1.090
 DNT  C10  H102  single    0.970  0.020  1.090
 DNT  C10  H103  single    0.970  0.020  1.090
 DNT  C6   C1    aromatic  1.411  0.020  1.411
 DNT  C6   C5    aromatic  1.376  0.020  1.376
 DNT  C1   O1    single    1.316  0.020  1.316
 DNT  C1   C2    aromatic  1.414  0.020  1.414
 DNT  O1   HO1   single    0.850  0.020  0.980
 DNT  C2   C3    aromatic  1.386  0.020  1.386
 DNT  C2   N6    single    1.442  0.020  1.442
 DNT  C3   C4    aromatic  1.373  0.020  1.373
 DNT  C3   H3    single    0.930  0.020  1.080
 DNT  C4   C5    aromatic  1.394  0.020  1.394
 DNT  C4   N4    single    1.449  0.020  1.449
 DNT  C5   H5    single    0.930  0.020  1.080
 DNT  N4   O61   single    1.209  0.020  1.209
 DNT  N4   O41   double    1.209  0.020  1.209
 DNT  N6   O62   single    1.202  0.020  1.202
 DNT  N6   O42   double    1.222  0.020  1.222

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
 DNT  H133  C13  H132  107.64  3.000
 DNT  H133  C13  H131  107.65  3.000
 DNT  H132  C13  H131  107.45  3.000
 DNT  H133  C13  C12   111.61  3.000
 DNT  H132  C13  C12   111.09  3.000
 DNT  H131  C13  C12   111.20  3.000
 DNT  H122  C12  H121  106.08  3.000
 DNT  H122  C12  C11   109.28  3.000
 DNT  H121  C12  C11   109.37  3.000
 DNT  H122  C12  C13   109.52  3.000
 DNT  H121  C12  C13   109.57  3.000
 DNT  C11   C12  C13   112.80  3.000
 DNT  H112  C11  H111  106.03  3.000
 DNT  H112  C11  C9    109.39  3.000
 DNT  H111  C11  C9    109.28  3.000
 DNT  H112  C11  C12   109.32  3.000
 DNT  H111  C11  C12   109.31  3.000
 DNT  C9    C11  C12   113.26  3.000
 DNT  H92   C9   H91   106.22  3.000
 DNT  H92   C9   C8    109.38  3.000
 DNT  H91   C9   C8    110.26  3.000
 DNT  H92   C9   C11   109.32  3.000
 DNT  H91   C9   C11   109.05  3.000
 DNT  C8    C9   C11   112.42  3.000
 DNT  H82   C8   H81   106.12  3.000
 DNT  H82   C8   C7    109.55  3.000
 DNT  H81   C8   C7    108.45  3.000
 DNT  H82   C8   C9    109.45  3.000
 DNT  H81   C8   C9    108.91  3.000
 DNT  C7    C8   C9    114.06  3.000
 DNT  H7    C7   C6    108.83  3.000
 DNT  H7    C7   C10   107.31  3.000
 DNT  C6    C7   C10   110.66  3.000
 DNT  H7    C7   C8    107.33  3.000
 DNT  C6    C7   C8    109.62  3.000
 DNT  C10   C7   C8    112.94  3.000
 DNT  H103  C10  H102  107.88  3.000
 DNT  H103  C10  H101  107.47  3.000
 DNT  H102  C10  H101  107.49  3.000
 DNT  H103  C10  C7    111.96  3.000
 DNT  H102  C10  C7    110.99  3.000
 DNT  H101  C10  C7    110.86  3.000
 DNT  C5    C6   C1    118.88  3.000
 DNT  C5    C6   C7    119.75  3.000
 DNT  C1    C6   C7    121.37  3.000
 DNT  C2    C1   O1    123.85  3.000
 DNT  C2    C1   C6    118.54  3.000
 DNT  O1    C1   C6    117.61  3.000
 DNT  HO1   O1   C1    109.44  3.000
 DNT  N6    C2   C3    117.19  3.000
 DNT  N6    C2   C1    120.95  3.000
 DNT  C3    C2   C1    121.85  3.000
 DNT  H3    C3   C4    121.32  3.000
 DNT  H3    C3   C2    120.44  3.000
 DNT  C4    C3   C2    118.24  3.000
 DNT  N4    C4   C5    119.64  3.000
 DNT  N4    C4   C3    119.15  3.000
 DNT  C5    C4   C3    121.20  3.000
 DNT  H5    C5   C4    119.75  3.000
 DNT  H5    C5   C6    118.97  3.000
 DNT  C4    C5   C6    121.29  3.000
 DNT  O41   N4   O61   124.05  3.000
 DNT  O41   N4   C4    118.13  3.000
 DNT  O61   N4   C4    117.83  3.000
 DNT  O42   N6   O62   122.79  3.000
 DNT  O42   N6   C2    118.09  3.000
 DNT  O62   N6   C2    119.11  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
 DNT  CONST_01  C3    C2   C1   C6      0.00   0.0  0
 DNT  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 DNT  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 DNT  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 DNT  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 DNT  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 DNT  CONST_07  C2    C1   C6   C7    180.00   0.0  0
 DNT  CONST_08  C4    C5   C6   C7    180.00   0.0  0
 DNT  CONST_09  N6    C2   C1   C6    180.00   0.0  0
 DNT  CONST_10  N4    C4   C5   C6    180.00   0.0  0
 DNT  CONST_11  C5    C6   C1   O1    180.00   0.0  0
 DNT  CONST_12  C3    C2   C1   O1    180.00   0.0  0
 DNT  CONST_13  N4    C4   C3   C2    180.00   0.0  0
 DNT  CONST_14  N6    C2   C3   C4    180.00   0.0  0
 DNT  CONST_15  H5    C5   C6   C1    180.00   0.0  0
 DNT  CONST_16  H3    C3   C2   C1    180.00   0.0  0
 DNT  CONST_17  O62   N6   C2   C1    180.00   0.0  0
 DNT  CONST_18  O42   N6   C2   C1      0.00   0.0  0
 DNT  CONST_19  O62   N6   C2   C3      0.00   0.0  0
 DNT  CONST_20  O42   N6   C2   C3    180.00   0.0  0
 DNT  CONST_21  O61   N4   C4   C3    180.00   0.0  0
 DNT  CONST_22  O41   N4   C4   C3      0.00   0.0  0
 DNT  CONST_23  O61   N4   C4   C5      0.00   0.0  0
 DNT  CONST_24  O41   N4   C4   C5    180.00   0.0  0
 DNT  Var_01    C9    C11  C12  C13  -179.41  30.0  3
 DNT  Var_02    C8    C9   C11  C12   179.95  30.0  3
 DNT  Var_03    C7    C8   C9   C11  -173.71  30.0  3
 DNT  Var_04    H131  C13  C12  C11   -60.84  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
 DNT  chir_01  C7  C8  C10  C6  positiv

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
 DNT  plan-1  C7   0.020
 DNT  plan-1  C6   0.020
 DNT  plan-1  C1   0.020
 DNT  plan-1  O1   0.020
 DNT  plan-1  C2   0.020
 DNT  plan-1  C3   0.020
 DNT  plan-1  C4   0.020
 DNT  plan-1  C5   0.020
 DNT  plan-1  N4   0.020
 DNT  plan-1  N6   0.020
 DNT  plan-1  H3   0.020
 DNT  plan-1  H5   0.020
 DNT  plan-2  C4   0.020
 DNT  plan-2  N4   0.020
 DNT  plan-2  O61  0.020
 DNT  plan-2  O41  0.020
 DNT  plan-3  C2   0.020
 DNT  plan-3  N6   0.020
 DNT  plan-3  O62  0.020
 DNT  plan-3  O42  0.020

