# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:41:35 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-hexyl-2-(2-nitrophenoxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCc1ccc(Oc2ccccc2[N+]([O-])=O)c(O)c1
#
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
 1TN  1TN  5-hexyl-2-(2-nitrophenoxy)phenol  ligand  44  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1TN
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
 1TN  C10  C  CH2    0  -0.407   -6.7146   0.6516  -0.0637
 1TN  C15  C  CR6    0   0.407    3.0761  -0.2712  -0.3171
 1TN  C17  C  CR16   0  -0.268    5.3877  -0.5205   0.3943
 1TN  C20  C  CR16   0  -0.344    2.9324  -1.6533  -0.2312
 1TN  C01  C  CR16   0  -0.341   -1.2699  -0.6270  -1.5990
 1TN  C02  C  CR16   0  -0.291    0.0469  -0.2000  -1.7067
 1TN  C03  C  CR6    0   0.210    0.7763   0.0827  -0.5685
 1TN  C04  C  CR6    0   0.341    0.2031  -0.0530   0.6963
 1TN  C05  C  CR16   0  -0.443   -1.1128  -0.4877   0.7893
 1TN  C06  C  CR6    0   0.150   -1.8600  -0.7821  -0.3482
 1TN  C07  C  CH2    0  -0.507   -3.2906  -1.2204  -0.2130
 1TN  C08  C  CH2    0  -0.409   -4.2728  -0.0490  -0.2456
 1TN  C09  C  CH2    0  -0.416   -5.7115  -0.4932  -0.0151
 1TN  C11  C  CH2    0  -0.419   -8.1425   0.2080   0.2304
 1TN  O14  O  O2     0  -0.483    2.0684   0.5483  -0.6721
 1TN  C16  C  CR6    0   0.160    4.3236   0.2809  -0.0023
 1TN  C18  C  CR16   0  -0.272    5.2330  -1.8907   0.4584
 1TN  C19  C  CR16   0  -0.225    4.0003  -2.4493   0.1439
 1TN  N21  N  N      1   0.334    4.5498   1.7098  -0.0722
 1TN  O22  O  O     -1  -0.383    5.3136   2.1929   0.7330
 1TN  O23  O  O      0  -0.372    3.9862   2.3405  -0.9334
 1TN  H1   H  HCH2   0   0.206   -6.4216   1.4242   0.6561
 1TN  H2   H  HCH2   0   0.207   -6.6781   1.1290  -1.0492
 1TN  H3   H  HCR6   0   0.298    6.3394  -0.0695   0.6376
 1TN  H4   H  HCR6   0   0.297    1.9814  -2.1135  -0.4642
 1TN  H5   H  HCR6   0   0.251   -1.8320  -0.8518  -2.4967
 1TN  H6   H  HCR6   0   0.273    0.5115  -0.0860  -2.6781
 1TN  H7   H  HCR6   0   0.269   -1.5628  -0.6071   1.7699
 1TN  H8   H  HCH2   0   0.240   -3.5369  -1.9220  -1.0144
 1TN  H9   H  HCH2   0   0.238   -3.4161  -1.7660   0.7264
 1TN  H10  H  HCH2   0   0.220   -3.9913   0.6829   0.5182
 1TN  H11  H  HCH2   0   0.210   -5.7788  -0.9938   0.9573
 1TN  H12  H  HCH2   0   0.210   -8.4347  -0.5674  -0.4847
 1TN  H13  H  HCH2   0   0.210   -8.1754  -0.2650   1.2169
 1TN  H15  H  HOH1   0   0.481    0.4798   0.0952   2.5767
 1TN  H16  H  HCR6   0   0.275    6.0657  -2.5154   0.7486
 1TN  H17  H  HCR6   0   0.281    3.8635  -3.5214   0.1908
 1TN  C12  C  CH3    0  -0.661   -9.1452   1.3522   0.1798
 1TN  H18  H  HCH2   0   0.220   -4.1932   0.4675  -1.2077
 1TN  H19  H  HCH2   0   0.211   -5.9829  -1.2483  -0.7610
 1TN  H14  H  HCH3   0   0.215   -8.9039   2.1228   0.9142
 1TN  H20  H  HCH3   0   0.215   -9.1529   1.8275  -0.8031
 1TN  H21  H  HCH3   0   0.225  -10.1587   1.0058   0.3857
 1TN  O13  O  OH1    0  -0.617    0.9720   0.2358   1.7595

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
 1TN  O23  N21  double    1.207  0.020  1.207
 1TN  O13  C04  single    1.344  0.020  1.344
 1TN  C05  C04  aromatic  1.389  0.020  1.389
 1TN  C05  C06  aromatic  1.392  0.020  1.392
 1TN  C04  C03  aromatic  1.395  0.020  1.395
 1TN  C06  C07  single    1.502  0.020  1.502
 1TN  C06  C01  aromatic  1.392  0.020  1.392
 1TN  C03  O14  single    1.377  0.020  1.377
 1TN  C03  C02  aromatic  1.381  0.020  1.381
 1TN  O14  C15  single    1.346  0.020  1.346
 1TN  C07  C08  single    1.529  0.020  1.529
 1TN  C01  C02  aromatic  1.388  0.020  1.388
 1TN  N21  O22  single    1.211  0.020  1.211
 1TN  N21  C16  single    1.448  0.020  1.448
 1TN  C15  C16  aromatic  1.400  0.020  1.400
 1TN  C15  C20  aromatic  1.392  0.020  1.392
 1TN  C16  C17  aromatic  1.390  0.020  1.390
 1TN  C08  C09  single    1.523  0.020  1.523
 1TN  C09  C10  single    1.523  0.020  1.523
 1TN  C20  C19  aromatic  1.384  0.020  1.384
 1TN  C17  C18  aromatic  1.380  0.020  1.380
 1TN  C19  C18  aromatic  1.389  0.020  1.389
 1TN  C10  C11  single    1.524  0.020  1.524
 1TN  C10  H1   single    0.970  0.020  1.090
 1TN  C10  H2   single    0.970  0.020  1.090
 1TN  C17  H3   single    0.930  0.020  1.080
 1TN  C20  H4   single    0.930  0.020  1.080
 1TN  C01  H5   single    0.930  0.020  1.080
 1TN  C02  H6   single    0.930  0.020  1.080
 1TN  C05  H7   single    0.930  0.020  1.080
 1TN  C07  H8   single    0.970  0.020  1.090
 1TN  C07  H9   single    0.970  0.020  1.090
 1TN  C08  H10  single    0.970  0.020  1.090
 1TN  C09  H11  single    0.970  0.020  1.090
 1TN  C11  H12  single    0.970  0.020  1.090
 1TN  C11  H13  single    0.970  0.020  1.090
 1TN  O13  H15  single    0.850  0.020  0.980
 1TN  C18  H16  single    0.930  0.020  1.080
 1TN  C19  H17  single    0.930  0.020  1.080
 1TN  C11  C12  single    1.522  0.020  1.522
 1TN  C08  H18  single    0.970  0.020  1.090
 1TN  C09  H19  single    0.970  0.020  1.090
 1TN  C12  H14  single    0.970  0.020  1.090
 1TN  C12  H20  single    0.970  0.020  1.090
 1TN  C12  H21  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
 1TN  H2   C10  H1   105.95  3.000
 1TN  H2   C10  C11  109.37  3.000
 1TN  H1   C10  C11  109.20  3.000
 1TN  H2   C10  C09  109.54  3.000
 1TN  H1   C10  C09  109.45  3.000
 1TN  C11  C10  C09  113.09  3.000
 1TN  C16  C15  O14  119.08  3.000
 1TN  C16  C15  C20  118.01  3.000
 1TN  O14  C15  C20  122.90  3.000
 1TN  H3   C17  C18  120.16  3.000
 1TN  H3   C17  C16  119.85  3.000
 1TN  C18  C17  C16  119.98  3.000
 1TN  H4   C20  C19  119.48  3.000
 1TN  H4   C20  C15  119.98  3.000
 1TN  C19  C20  C15  120.54  3.000
 1TN  H5   C01  C06  120.13  3.000
 1TN  H5   C01  C02  119.46  3.000
 1TN  C06  C01  C02  120.41  3.000
 1TN  H6   C02  C03  119.41  3.000
 1TN  H6   C02  C01  120.60  3.000
 1TN  C03  C02  C01  119.99  3.000
 1TN  O14  C03  C04  119.10  3.000
 1TN  O14  C03  C02  120.18  3.000
 1TN  C04  C03  C02  120.68  3.000
 1TN  O13  C04  C05  123.81  3.000
 1TN  C05  C04  C03  118.71  3.000
 1TN  O13  C04  C03  117.48  3.000
 1TN  H7   C05  C06  119.49  3.000
 1TN  H7   C05  C04  119.19  3.000
 1TN  C06  C05  C04  121.32  3.000
 1TN  C07  C06  C05  119.94  3.000
 1TN  C07  C06  C01  121.14  3.000
 1TN  C05  C06  C01  118.89  3.000
 1TN  H9   C07  H8   106.49  3.000
 1TN  H9   C07  C08  109.08  3.000
 1TN  H8   C07  C08  109.35  3.000
 1TN  H9   C07  C06  109.40  3.000
 1TN  H8   C07  C06  109.62  3.000
 1TN  C08  C07  C06  112.72  3.000
 1TN  H18  C08  H10  106.20  3.000
 1TN  H18  C08  C09  109.83  3.000
 1TN  H10  C08  C09  109.41  3.000
 1TN  H18  C08  C07  109.48  3.000
 1TN  H10  C08  C07  109.40  3.000
 1TN  C09  C08  C07  112.33  3.000
 1TN  H19  C09  H11  105.91  3.000
 1TN  H19  C09  C08  109.39  3.000
 1TN  H11  C09  C08  109.00  3.000
 1TN  H19  C09  C10  109.46  3.000
 1TN  H11  C09  C10  109.35  3.000
 1TN  C08  C09  C10  113.45  3.000
 1TN  C12  C11  H13  109.58  3.000
 1TN  C12  C11  H12  109.57  3.000
 1TN  H13  C11  H12  105.94  3.000
 1TN  C12  C11  C10  113.08  3.000
 1TN  H13  C11  C10  109.14  3.000
 1TN  H12  C11  C10  109.28  3.000
 1TN  C03  O14  C15  118.46  3.000
 1TN  N21  C16  C17  117.58  3.000
 1TN  C17  C16  C15  121.26  3.000
 1TN  N21  C16  C15  121.16  3.000
 1TN  H16  C18  C19  120.80  3.000
 1TN  H16  C18  C17  120.00  3.000
 1TN  C19  C18  C17  119.21  3.000
 1TN  H17  C19  C18  120.05  3.000
 1TN  H17  C19  C20  118.96  3.000
 1TN  C18  C19  C20  120.99  3.000
 1TN  O23  N21  O22  124.10  3.000
 1TN  O22  N21  C16  117.40  3.000
 1TN  O23  N21  C16  118.49  3.000
 1TN  H21  C12  H20  107.56  3.000
 1TN  H21  C12  H14  107.61  3.000
 1TN  H20  C12  H14  107.45  3.000
 1TN  H21  C12  C11  111.54  3.000
 1TN  H20  C12  C11  111.21  3.000
 1TN  H14  C12  C11  111.26  3.000
 1TN  H15  O13  C04  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
 1TN  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 1TN  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 1TN  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 1TN  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 1TN  CONST_05  C04  C05  C06  C01     0.00   0.0  0
 1TN  CONST_06  C04  C03  C02  C01     0.00   0.0  0
 1TN  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 1TN  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 1TN  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 1TN  CONST_10  C06  C01  C02  C03     0.00   0.0  0
 1TN  CONST_11  C19  C20  C15  C16     0.00   0.0  0
 1TN  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 1TN  CONST_13  O14  C15  C16  C17   180.00   0.0  0
 1TN  CONST_14  N21  C16  C15  C20   180.00   0.0  0
 1TN  CONST_15  O14  C03  C02  C01   180.00   0.0  0
 1TN  CONST_16  O13  C04  C03  C02   180.00   0.0  0
 1TN  CONST_17  C07  C06  C01  C02   180.00   0.0  0
 1TN  CONST_18  C07  C06  C05  C04   180.00   0.0  0
 1TN  CONST_19  O14  C03  C04  C05   180.00   0.0  0
 1TN  CONST_20  O13  C04  C05  C06   180.00   0.0  0
 1TN  CONST_21  C19  C20  C15  O14   180.00   0.0  0
 1TN  CONST_22  N21  C16  C17  C18   180.00   0.0  0
 1TN  CONST_23  H3   C17  C16  C15   180.00   0.0  0
 1TN  CONST_24  H17  C19  C20  C15   180.00   0.0  0
 1TN  CONST_25  H16  C18  C19  C20   180.00   0.0  0
 1TN  CONST_26  H7   C05  C06  C01   180.00   0.0  0
 1TN  CONST_27  H5   C01  C02  C03   180.00   0.0  0
 1TN  CONST_28  H6   C02  C03  C04   180.00   0.0  0
 1TN  CONST_29  H4   C20  C15  C16   180.00   0.0  0
 1TN  Var_01    C04  C03  O14  C15    73.17  30.0  2
 1TN  Var_02    C16  C15  O14  C03  -159.72  30.0  2
 1TN  Var_03    C08  C07  C06  C01   -87.68  30.0  2
 1TN  Var_04    C09  C08  C07  C06  -176.19  30.0  3
 1TN  Var_05    C07  C08  C09  C10  -179.11  30.0  2
 1TN  Var_06    C11  C10  C09  C08  -177.39  30.0  3
 1TN  Var_07    C12  C11  C10  C09  -179.92  30.0  3
 1TN  Var_08    H14  C12  C11  C10   -60.29  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
 1TN  plan-1  C15  0.020
 1TN  plan-1  C17  0.020
 1TN  plan-1  C20  0.020
 1TN  plan-1  O14  0.020
 1TN  plan-1  C16  0.020
 1TN  plan-1  C18  0.020
 1TN  plan-1  C19  0.020
 1TN  plan-1  N21  0.020
 1TN  plan-1  H3   0.020
 1TN  plan-1  H4   0.020
 1TN  plan-1  H16  0.020
 1TN  plan-1  H17  0.020
 1TN  plan-2  C01  0.020
 1TN  plan-2  C02  0.020
 1TN  plan-2  C03  0.020
 1TN  plan-2  C04  0.020
 1TN  plan-2  C05  0.020
 1TN  plan-2  C06  0.020
 1TN  plan-2  C07  0.020
 1TN  plan-2  O14  0.020
 1TN  plan-2  H5   0.020
 1TN  plan-2  H6   0.020
 1TN  plan-2  H7   0.020
 1TN  plan-2  O13  0.020
 1TN  plan-3  C16  0.020
 1TN  plan-3  N21  0.020
 1TN  plan-3  O22  0.020
 1TN  plan-3  O23  0.020

