# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:31:01 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-hexyl-2-(4-nitrophenoxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCc1ccc(Oc2ccc(cc2)[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
 JA1  JA1  5-hexyl-2-(4-nitrophenoxy)phenol  ligand  44  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JA1
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
 JA1  C     C  CR6    0   0.326  -0.4828  -2.0248   0.0209
 JA1  N     N  N      1   0.328   5.6833   1.6419  -1.1003
 JA1  O     O  OH1    0  -0.621  -0.1484  -2.8446  -0.9913
 JA1  C1    C  CR6    0   0.177   0.4618  -1.4858   0.8937
 JA1  O1    O  O2     0  -0.507   1.7801  -1.8580   0.7279
 JA1  C2    C  CR6    0   0.395   2.6790  -0.9588   0.2690
 JA1  O2    O  O      0  -0.385   6.8339   1.2739  -1.0299
 JA1  C3    C  CR16   0  -0.325   4.0180  -1.3396   0.3508
 JA1  O3    O  O     -1  -0.386   5.3494   2.7194  -1.5383
 JA1  C4    C  CR16   0  -0.257   5.0049  -0.4907  -0.1010
 JA1  C5    C  CR6    0   0.237   4.6500   0.7441  -0.6330
 JA1  C6    C  CR16   0  -0.255   3.3197   1.1280  -0.7225
 JA1  C7    C  CR16   0  -0.330   2.3291   0.2756  -0.2720
 JA1  C8    C  CR16   0  -0.278   0.0765  -0.6499   1.9253
 JA1  C9    C  CR16   0  -0.351  -1.2623  -0.3313   2.0903
 JA1  C10   C  CR6    0   0.152  -2.2274  -0.8567   1.2334
 JA1  C11   C  CH2    0  -0.502  -3.6816  -0.5184   1.4173
 JA1  C12   C  CH2    0  -0.415  -4.2975   0.2152   0.2265
 JA1  C13   C  CH2    0  -0.415  -5.7385   0.6351   0.4909
 JA1  C14   C  CH2    0  -0.407  -6.3987   1.3080  -0.7050
 JA1  C15   C  CH2    0  -0.418  -7.8229   1.7712  -0.4208
 JA1  C16   C  CH3    0  -0.663  -8.4819   2.4334  -1.6227
 JA1  C17   C  CR16   0  -0.401  -1.8234  -1.7066   0.2085
 JA1  HO    H  HOH1   0   0.476   0.7831  -3.0905  -0.9412
 JA1  H3    H  HCR6   0   0.292   4.2806  -2.3012   0.7709
 JA1  H4    H  HCR6   0   0.302   6.0391  -0.7938  -0.0293
 JA1  H6    H  HCR6   0   0.303   3.0391   2.0828  -1.1421
 JA1  H7    H  HCR6   0   0.300   1.2958   0.5834  -0.3503
 JA1  H8    H  HCR6   0   0.282   0.8233  -0.2495   2.6001
 JA1  H9    H  HCR6   0   0.254  -1.5574   0.3226   2.9011
 JA1  H11   H  HCH2   0   0.241  -4.2486  -1.4362   1.6021
 JA1  H11A  H  HCH2   0   0.239  -3.7911   0.0953   2.3153
 JA1  H12   H  HCH2   0   0.221  -3.6967   1.0988  -0.0103
 JA1  H12A  H  HCH2   0   0.218  -4.2626  -0.4273  -0.6589
 JA1  H13   H  HCH2   0   0.211  -6.3247  -0.2436   0.7825
 JA1  H13A  H  HCH2   0   0.211  -5.7621   1.3148   1.3496
 JA1  H14   H  HCH2   0   0.207  -5.7961   2.1674  -1.0200
 JA1  H14A  H  HCH2   0   0.208  -6.4069   0.6153  -1.5537
 JA1  H15   H  HCH2   0   0.210  -8.4232   0.9154  -0.0962
 JA1  H15A  H  HCH2   0   0.210  -7.8134   2.4702   0.4210
 JA1  H16   H  HCH3   0   0.216  -7.9201   3.3126  -1.9439
 JA1  H16A  H  HCH3   0   0.216  -8.5363   1.7497  -2.4720
 JA1  H16B  H  HCH3   0   0.226  -9.4980   2.7579  -1.3950
 JA1  H17   H  HCR6   0   0.261  -2.5539  -2.1406  -0.4648

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
 JA1  C1   C     aromatic  1.394  0.020  1.394
 JA1  C17  C     aromatic  1.390  0.020  1.390
 JA1  C    O     single    1.345  0.020  1.345
 JA1  C5   N     single    1.446  0.020  1.446
 JA1  N    O2    double    1.210  0.020  1.210
 JA1  N    O3    single    1.210  0.020  1.210
 JA1  O    HO    single    0.850  0.020  0.980
 JA1  C8   C1    aromatic  1.382  0.020  1.382
 JA1  C1   O1    single    1.380  0.020  1.380
 JA1  O1   C2    single    1.352  0.020  1.352
 JA1  C2   C7    aromatic  1.393  0.020  1.393
 JA1  C2   C3    aromatic  1.394  0.020  1.394
 JA1  C3   C4    aromatic  1.378  0.020  1.378
 JA1  C3   H3    single    0.930  0.020  1.080
 JA1  C4   C5    aromatic  1.391  0.020  1.391
 JA1  C4   H4    single    0.930  0.020  1.080
 JA1  C6   C5    aromatic  1.387  0.020  1.387
 JA1  C7   C6    aromatic  1.382  0.020  1.382
 JA1  C6   H6    single    0.930  0.020  1.080
 JA1  C7   H7    single    0.930  0.020  1.080
 JA1  C9   C8    aromatic  1.386  0.020  1.386
 JA1  C8   H8    single    0.930  0.020  1.080
 JA1  C9   C10   aromatic  1.393  0.020  1.393
 JA1  C9   H9    single    0.930  0.020  1.080
 JA1  C11  C10   single    1.504  0.020  1.504
 JA1  C10  C17   aromatic  1.391  0.020  1.391
 JA1  C11  C12   single    1.528  0.020  1.528
 JA1  C11  H11   single    0.970  0.020  1.090
 JA1  C11  H11A  single    0.970  0.020  1.090
 JA1  C13  C12   single    1.524  0.020  1.524
 JA1  C12  H12   single    0.970  0.020  1.090
 JA1  C12  H12A  single    0.970  0.020  1.090
 JA1  C13  C14   single    1.523  0.020  1.523
 JA1  C13  H13   single    0.970  0.020  1.090
 JA1  C13  H13A  single    0.970  0.020  1.090
 JA1  C14  C15   single    1.524  0.020  1.524
 JA1  C14  H14   single    0.970  0.020  1.090
 JA1  C14  H14A  single    0.970  0.020  1.090
 JA1  C15  C16   single    1.522  0.020  1.522
 JA1  C15  H15   single    0.970  0.020  1.090
 JA1  C15  H15A  single    0.970  0.020  1.090
 JA1  C16  H16   single    0.970  0.020  1.090
 JA1  C16  H16A  single    0.970  0.020  1.090
 JA1  C16  H16B  single    0.970  0.020  1.090
 JA1  C17  H17   single    0.930  0.020  1.080

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
 JA1  C17   C    C1    118.70  3.000
 JA1  C17   C    O     118.74  3.000
 JA1  C1    C    O     122.57  3.000
 JA1  C5    N    O3    118.20  3.000
 JA1  O3    N    O2    123.66  3.000
 JA1  C5    N    O2    118.15  3.000
 JA1  HO    O    C     110.88  3.000
 JA1  C8    C1   O1    121.26  3.000
 JA1  O1    C1   C     117.89  3.000
 JA1  C8    C1   C     120.80  3.000
 JA1  C2    O1   C1    119.78  3.000
 JA1  C7    C2   C3    120.41  3.000
 JA1  C3    C2   O1    115.91  3.000
 JA1  C7    C2   O1    123.68  3.000
 JA1  H3    C3   C4    120.07  3.000
 JA1  H3    C3   C2    119.91  3.000
 JA1  C4    C3   C2    120.02  3.000
 JA1  H4    C4   C5    121.27  3.000
 JA1  H4    C4   C3    119.41  3.000
 JA1  C5    C4   C3    119.32  3.000
 JA1  C6    C5   C4    121.00  3.000
 JA1  C6    C5   N     119.50  3.000
 JA1  C4    C5   N     119.50  3.000
 JA1  H6    C6   C7    119.05  3.000
 JA1  H6    C6   C5    121.25  3.000
 JA1  C7    C6   C5    119.70  3.000
 JA1  H7    C7   C6    119.07  3.000
 JA1  H7    C7   C2    121.38  3.000
 JA1  C6    C7   C2    119.55  3.000
 JA1  H8    C8   C9    120.45  3.000
 JA1  H8    C8   C1    119.75  3.000
 JA1  C9    C8   C1    119.80  3.000
 JA1  H9    C9   C10   119.97  3.000
 JA1  H9    C9   C8    119.42  3.000
 JA1  C10   C9   C8    120.61  3.000
 JA1  C17   C10  C11   120.54  3.000
 JA1  C17   C10  C9    118.83  3.000
 JA1  C11   C10  C9    120.63  3.000
 JA1  H11A  C11  H11   106.27  3.000
 JA1  H11A  C11  C12   109.28  3.000
 JA1  H11   C11  C12   108.98  3.000
 JA1  H11A  C11  C10   108.88  3.000
 JA1  H11   C11  C10   109.44  3.000
 JA1  C12   C11  C10   113.72  3.000
 JA1  H12A  C12  H12   106.34  3.000
 JA1  H12A  C12  C13   109.40  3.000
 JA1  H12   C12  C13   109.52  3.000
 JA1  H12A  C12  C11   109.62  3.000
 JA1  H12   C12  C11   109.57  3.000
 JA1  C13   C12  C11   112.22  3.000
 JA1  H13A  C13  H13   106.10  3.000
 JA1  H13A  C13  C14   109.40  3.000
 JA1  H13   C13  C14   109.36  3.000
 JA1  H13A  C13  C12   109.10  3.000
 JA1  H13   C13  C12   109.33  3.000
 JA1  C14   C13  C12   113.29  3.000
 JA1  H14A  C14  H14   106.10  3.000
 JA1  H14A  C14  C15   109.24  3.000
 JA1  H14   C14  C15   109.21  3.000
 JA1  H14A  C14  C13   109.40  3.000
 JA1  H14   C14  C13   109.51  3.000
 JA1  C15   C14  C13   113.14  3.000
 JA1  H15A  C15  H15   106.03  3.000
 JA1  H15A  C15  C16   109.47  3.000
 JA1  H15   C15  C16   109.68  3.000
 JA1  H15A  C15  C14   109.23  3.000
 JA1  H15   C15  C14   109.27  3.000
 JA1  C16   C15  C14   112.92  3.000
 JA1  H16B  C16  H16A  107.60  3.000
 JA1  H16B  C16  H16   107.53  3.000
 JA1  H16A  C16  H16   107.52  3.000
 JA1  H16B  C16  C15   111.59  3.000
 JA1  H16A  C16  C15   111.31  3.000
 JA1  H16   C16  C15   111.09  3.000
 JA1  H17   C17  C10   120.42  3.000
 JA1  H17   C17  C     118.31  3.000
 JA1  C10   C17  C     121.27  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
 JA1  CONST_01  C9   C8   C1   C       0.00   0.0  0
 JA1  CONST_02  C9   C10  C17  C       0.00   0.0  0
 JA1  CONST_03  C10  C17  C    C1      0.00   0.0  0
 JA1  CONST_04  C10  C9   C8   C1      0.00   0.0  0
 JA1  CONST_05  C5   C6   C7   C2      0.00   0.0  0
 JA1  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 JA1  CONST_07  C6   C7   C2   C3      0.00   0.0  0
 JA1  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 JA1  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 JA1  CONST_10  C7   C6   C5   C4      0.00   0.0  0
 JA1  CONST_11  C17  C    C1   C8      0.00   0.0  0
 JA1  CONST_12  C17  C10  C9   C8      0.00   0.0  0
 JA1  CONST_13  C11  C10  C17  C     180.00   0.0  0
 JA1  CONST_14  C3   C4   C5   N     180.00   0.0  0
 JA1  CONST_15  C7   C6   C5   N     180.00   0.0  0
 JA1  CONST_16  C8   C1   C    O     180.00   0.0  0
 JA1  CONST_17  C10  C17  C    O     180.00   0.0  0
 JA1  CONST_18  C17  C    C1   O1    180.00   0.0  0
 JA1  CONST_19  C9   C8   C1   O1    180.00   0.0  0
 JA1  CONST_20  C6   C7   C2   O1    180.00   0.0  0
 JA1  CONST_21  C4   C3   C2   O1    180.00   0.0  0
 JA1  CONST_22  C11  C10  C9   C8    180.00   0.0  0
 JA1  CONST_23  H8   C8   C1   C     180.00   0.0  0
 JA1  CONST_24  H17  C17  C    C1    180.00   0.0  0
 JA1  CONST_25  H9   C9   C8   C1    180.00   0.0  0
 JA1  CONST_26  H6   C6   C7   C2    180.00   0.0  0
 JA1  CONST_27  H4   C4   C3   C2    180.00   0.0  0
 JA1  CONST_28  H7   C7   C2   C3    180.00   0.0  0
 JA1  CONST_29  H3   C3   C4   C5    180.00   0.0  0
 JA1  CONST_30  C4   C5   N    O2      0.00   0.0  0
 JA1  CONST_31  C6   C5   N    O2    180.00   0.0  0
 JA1  CONST_32  C4   C5   N    O3    180.00   0.0  0
 JA1  CONST_33  C6   C5   N    O3      0.00   0.0  0
 JA1  Var_01    C7   C2   O1   C1    -11.42  30.0  2
 JA1  Var_02    C8   C1   O1   C2    -72.64  30.0  1
 JA1  Var_03    C12  C11  C10  C9    118.21  30.0  2
 JA1  Var_04    C13  C12  C11  C10  -175.63  30.0  3
 JA1  Var_05    C14  C13  C12  C11  -177.17  30.0  1
 JA1  Var_06    C15  C14  C13  C12  -177.94  30.0  3
 JA1  Var_07    C16  C15  C14  C13  -179.55  30.0  3
 JA1  Var_08    H16  C16  C15  C14   -59.89  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
 JA1  plan-1  C    0.020
 JA1  plan-1  O    0.020
 JA1  plan-1  C1   0.020
 JA1  plan-1  O1   0.020
 JA1  plan-1  C8   0.020
 JA1  plan-1  C9   0.020
 JA1  plan-1  C10  0.020
 JA1  plan-1  C11  0.020
 JA1  plan-1  C17  0.020
 JA1  plan-1  H8   0.020
 JA1  plan-1  H9   0.020
 JA1  plan-1  H17  0.020
 JA1  plan-2  N    0.020
 JA1  plan-2  O1   0.020
 JA1  plan-2  C2   0.020
 JA1  plan-2  C3   0.020
 JA1  plan-2  C4   0.020
 JA1  plan-2  C5   0.020
 JA1  plan-2  C6   0.020
 JA1  plan-2  C7   0.020
 JA1  plan-2  H3   0.020
 JA1  plan-2  H4   0.020
 JA1  plan-2  H6   0.020
 JA1  plan-2  H7   0.020
 JA1  plan-3  N    0.020
 JA1  plan-3  O2   0.020
 JA1  plan-3  O3   0.020
 JA1  plan-3  C5   0.020

