# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 01:48:38 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-[4-(4-hexyl-2-oxidanyl-phenoxy)phenoxy]pyridin-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCc1ccc(Oc2ccc(Oc3cccc(O)n3)cc2)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
 F9T  F9T  6-[4-(4-hexyl-2-oxidanyl-phenoxy)phenoxy]pyridin-2-ol  ligand  53  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F9T
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
 F9T  CAA  C  CH3   0  -0.657  36.0753  38.5575   4.1164
 F9T  CAN  C  CH2   0  -0.424  36.5008  39.6430   5.0958
 F9T  CAO  C  CH2   0  -0.413  36.5005  41.0303   4.4635
 F9T  CAP  C  CH2   0  -0.424  36.8064  42.1689   5.4316
 F9T  CAQ  C  CH2   0  -0.415  38.1937  42.1033   6.0588
 F9T  CAR  C  CH2   0  -0.502  38.4905  43.3184   6.9396
 F9T  CAV  C  CR6   0   0.146  39.8438  43.2336   7.5865
 F9T  CAM  C  CR16  0  -0.437  40.0139  42.4831   8.7483
 F9T  CAW  C  CR6   0   0.332  41.2607  42.3489   9.3447
 F9T  OAC  O  OH1   0  -0.617  41.4784  41.6406  10.4666
 F9T  CAF  C  CR16  0  -0.342  40.9510  43.8564   7.0221
 F9T  CAK  C  CR16  0  -0.298  42.2053  43.7225   7.6041
 F9T  CBA  C  CR6   0   0.221  42.3624  42.9768   8.7563
 F9T  OAU  O  O2    0  -0.502  43.5924  42.8918   9.3577
 F9T  CAY  C  CR6   0   0.376  44.2570  41.7042   9.3206
 F9T  CAJ  C  CR16  0  -0.339  43.9563  40.6846   8.4264
 F9T  CAH  C  CR16  0  -0.294  44.7026  39.5134   8.4424
 F9T  CAI  C  CR16  0  -0.331  45.3021  41.5521  10.2271
 F9T  CAG  C  CR16  0  -0.285  46.0411  40.3824  10.2418
 F9T  CAX  C  CR6   0   0.283  45.7360  39.3647   9.3492
 F9T  OAT  O  O2    0  -0.481  46.4321  38.1779   9.3943
 F9T  CAZ  C  CR6   0   0.497  47.6672  38.1215   8.8503
 F9T  CAE  C  CR16  0  -0.441  48.2189  39.1381   8.0819
 F9T  CAD  C  CR16  0  -0.137  49.4995  38.9200   7.5879
 F9T  CAL  C  CR16  0  -0.408  50.1727  37.7448   7.8572
 F9T  CBB  C  CR6   0   0.480  49.5037  36.8026   8.6385
 F9T  OAB  O  OH1   0  -0.610  50.1177  35.6535   8.9214
 F9T  NAS  N  N     0  -0.488  48.2891  36.9876   9.1186
 F9T  H1   H  HCH3  0   0.224  36.0778  37.5717   4.5830
 F9T  H2   H  HCH3  0   0.214  35.0687  38.7412   3.7364
 F9T  H3   H  HCH3  0   0.215  36.7475  38.5172   3.2572
 F9T  H4   H  HCH2  0   0.216  37.4956  39.4068   5.4824
 F9T  H5   H  HCH2  0   0.208  35.8312  39.6413   5.9620
 F9T  H6   H  HCH2  0   0.206  37.2205  41.0507   3.6375
 F9T  H7   H  HCH2  0   0.215  35.5202  41.2099   4.0103
 F9T  H8   H  HCH2  0   0.218  36.7029  43.1212   4.9017
 F9T  H9   H  HCH2  0   0.210  36.0530  42.1826   6.2270
 F9T  H10  H  HCH2  0   0.225  38.2936  41.1961   6.6614
 F9T  H11  H  HCH2  0   0.217  38.9514  42.0328   5.2714
 F9T  H12  H  HCH2  0   0.238  38.4275  44.2273   6.3357
 F9T  H13  H  HCH2  0   0.236  37.7171  43.4006   7.7087
 F9T  H14  H  HCR6  0   0.265  39.1547  41.9989   9.2031
 F9T  H15  H  HOH1  0   0.478  40.6575  41.2401  10.7760
 F9T  H16  H  HCR6  0   0.246  40.8391  44.4473   6.1216
 F9T  H17  H  HCR6  0   0.266  43.0704  44.2050   7.1661
 F9T  H18  H  HCR6  0   0.283  43.1499  40.7878   7.7122
 F9T  H19  H  HCR6  0   0.276  44.4703  38.7171   7.7467
 F9T  H20  H  HCR6  0   0.273  45.5296  42.3475  10.9253
 F9T  H21  H  HCR6  0   0.279  46.8483  40.2606  10.9534
 F9T  H22  H  HCR6  0   0.283  47.6902  40.0553   7.8681
 F9T  H24  H  HCR6  0   0.276  49.9717  39.6830   6.9831
 F9T  H25  H  HCR6  0   0.271  51.1692  37.5552   7.4843
 F9T  H23  H  HOH1  0   0.471  49.5347  35.1090   9.4677

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
 F9T  CAO  CAN  single    1.525  0.020  1.525
 F9T  CAO  CAP  single    1.526  0.020  1.526
 F9T  CAN  CAA  single    1.523  0.020  1.523
 F9T  CAP  CAQ  single    1.524  0.020  1.524
 F9T  CAQ  CAR  single    1.530  0.020  1.530
 F9T  CAL  CAD  aromatic  1.381  0.020  1.381
 F9T  CAL  CBB  aromatic  1.395  0.020  1.395
 F9T  CAD  CAE  aromatic  1.390  0.020  1.390
 F9T  CAR  CAV  single    1.502  0.020  1.502
 F9T  CAF  CAK  aromatic  1.389  0.020  1.389
 F9T  CAF  CAV  aromatic  1.390  0.020  1.390
 F9T  OAB  CBB  single    1.333  0.020  1.333
 F9T  CBB  NAS  aromatic  1.319  0.020  1.319
 F9T  CAK  CBA  aromatic  1.381  0.020  1.381
 F9T  CAV  CAM  aromatic  1.393  0.020  1.393
 F9T  CAE  CAZ  aromatic  1.389  0.020  1.389
 F9T  NAS  CAZ  aromatic  1.321  0.020  1.321
 F9T  CAZ  OAT  single    1.351  0.020  1.351
 F9T  CBA  OAU  single    1.372  0.020  1.372
 F9T  CBA  CAW  aromatic  1.398  0.020  1.398
 F9T  CAM  CAW  aromatic  1.389  0.020  1.389
 F9T  CAJ  CAH  aromatic  1.389  0.020  1.389
 F9T  CAJ  CAY  aromatic  1.389  0.020  1.389
 F9T  CAH  CAX  aromatic  1.383  0.020  1.383
 F9T  OAU  CAY  single    1.361  0.020  1.361
 F9T  CAW  OAC  single    1.345  0.020  1.345
 F9T  CAY  CAI  aromatic  1.392  0.020  1.392
 F9T  CAX  OAT  single    1.377  0.020  1.377
 F9T  CAX  CAG  aromatic  1.388  0.020  1.388
 F9T  CAI  CAG  aromatic  1.384  0.020  1.384
 F9T  CAA  H1   single    0.970  0.020  1.090
 F9T  CAA  H2   single    0.970  0.020  1.090
 F9T  CAA  H3   single    0.970  0.020  1.090
 F9T  CAN  H4   single    0.970  0.020  1.090
 F9T  CAN  H5   single    0.970  0.020  1.090
 F9T  CAO  H6   single    0.970  0.020  1.090
 F9T  CAO  H7   single    0.970  0.020  1.090
 F9T  CAP  H8   single    0.970  0.020  1.090
 F9T  CAP  H9   single    0.970  0.020  1.090
 F9T  CAQ  H10  single    0.970  0.020  1.090
 F9T  CAQ  H11  single    0.970  0.020  1.090
 F9T  CAR  H12  single    0.970  0.020  1.090
 F9T  CAR  H13  single    0.970  0.020  1.090
 F9T  CAM  H14  single    0.930  0.020  1.080
 F9T  OAC  H15  single    0.850  0.020  0.980
 F9T  CAF  H16  single    0.930  0.020  1.080
 F9T  CAK  H17  single    0.930  0.020  1.080
 F9T  CAJ  H18  single    0.930  0.020  1.080
 F9T  CAH  H19  single    0.930  0.020  1.080
 F9T  CAI  H20  single    0.930  0.020  1.080
 F9T  CAG  H21  single    0.930  0.020  1.080
 F9T  CAE  H22  single    0.930  0.020  1.080
 F9T  CAD  H24  single    0.930  0.020  1.080
 F9T  CAL  H25  single    0.930  0.020  1.080
 F9T  OAB  H23  single    0.850  0.020  0.980

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
 F9T  H3   CAA  H2   107.46  3.000
 F9T  H3   CAA  H1   107.57  3.000
 F9T  H2   CAA  H1   107.65  3.000
 F9T  H3   CAA  CAN  111.13  3.000
 F9T  H2   CAA  CAN  111.20  3.000
 F9T  H1   CAA  CAN  111.63  3.000
 F9T  H5   CAN  H4   106.05  3.000
 F9T  H5   CAN  CAO  109.23  3.000
 F9T  H4   CAN  CAO  110.09  3.000
 F9T  H5   CAN  CAA  109.68  3.000
 F9T  H4   CAN  CAA  109.13  3.000
 F9T  CAO  CAN  CAA  112.45  3.000
 F9T  H7   CAO  H6   105.86  3.000
 F9T  H7   CAO  CAP  108.65  3.000
 F9T  H6   CAO  CAP  109.43  3.000
 F9T  H7   CAO  CAN  108.73  3.000
 F9T  H6   CAO  CAN  109.23  3.000
 F9T  CAP  CAO  CAN  114.58  3.000
 F9T  H9   CAP  H8   106.00  3.000
 F9T  H9   CAP  CAQ  109.13  3.000
 F9T  H8   CAP  CAQ  108.83  3.000
 F9T  H9   CAP  CAO  109.40  3.000
 F9T  H8   CAP  CAO  108.85  3.000
 F9T  CAQ  CAP  CAO  114.30  3.000
 F9T  H11  CAQ  H10  106.24  3.000
 F9T  H11  CAQ  CAR  109.32  3.000
 F9T  H10  CAQ  CAR  108.90  3.000
 F9T  H11  CAQ  CAP  109.68  3.000
 F9T  H10  CAQ  CAP  110.22  3.000
 F9T  CAR  CAQ  CAP  112.29  3.000
 F9T  H13  CAR  H12  106.57  3.000
 F9T  H13  CAR  CAV  109.78  3.000
 F9T  H12  CAR  CAV  109.68  3.000
 F9T  H13  CAR  CAQ  109.11  3.000
 F9T  H12  CAR  CAQ  109.34  3.000
 F9T  CAV  CAR  CAQ  112.20  3.000
 F9T  CAF  CAV  CAM  118.85  3.000
 F9T  CAM  CAV  CAR  119.96  3.000
 F9T  CAF  CAV  CAR  121.15  3.000
 F9T  H14  CAM  CAW  119.16  3.000
 F9T  H14  CAM  CAV  119.52  3.000
 F9T  CAW  CAM  CAV  121.32  3.000
 F9T  CBA  CAW  OAC  117.40  3.000
 F9T  OAC  CAW  CAM  123.69  3.000
 F9T  CBA  CAW  CAM  118.91  3.000
 F9T  H15  OAC  CAW  110.40  3.000
 F9T  H16  CAF  CAK  119.63  3.000
 F9T  H16  CAF  CAV  119.99  3.000
 F9T  CAK  CAF  CAV  120.39  3.000
 F9T  H17  CAK  CBA  119.14  3.000
 F9T  H17  CAK  CAF  120.58  3.000
 F9T  CBA  CAK  CAF  120.27  3.000
 F9T  OAU  CBA  CAK  120.07  3.000
 F9T  OAU  CBA  CAW  119.62  3.000
 F9T  CAK  CBA  CAW  120.26  3.000
 F9T  CAY  OAU  CBA  118.68  3.000
 F9T  CAI  CAY  CAJ  120.11  3.000
 F9T  CAI  CAY  OAU  116.37  3.000
 F9T  CAJ  CAY  OAU  123.51  3.000
 F9T  H18  CAJ  CAH  119.24  3.000
 F9T  H18  CAJ  CAY  121.08  3.000
 F9T  CAH  CAJ  CAY  119.68  3.000
 F9T  H19  CAH  CAX  120.18  3.000
 F9T  H19  CAH  CAJ  119.84  3.000
 F9T  CAX  CAH  CAJ  119.98  3.000
 F9T  H20  CAI  CAG  120.14  3.000
 F9T  H20  CAI  CAY  119.84  3.000
 F9T  CAG  CAI  CAY  120.02  3.000
 F9T  H21  CAG  CAX  120.27  3.000
 F9T  H21  CAG  CAI  120.01  3.000
 F9T  CAX  CAG  CAI  119.72  3.000
 F9T  OAT  CAX  CAG  120.01  3.000
 F9T  CAG  CAX  CAH  120.48  3.000
 F9T  OAT  CAX  CAH  119.47  3.000
 F9T  CAZ  OAT  CAX  119.02  3.000
 F9T  NAS  CAZ  CAE  123.63  3.000
 F9T  NAS  CAZ  OAT  112.61  3.000
 F9T  CAE  CAZ  OAT  123.75  3.000
 F9T  H22  CAE  CAD  120.93  3.000
 F9T  H22  CAE  CAZ  122.47  3.000
 F9T  CAD  CAE  CAZ  116.61  3.000
 F9T  H24  CAD  CAL  119.75  3.000
 F9T  H24  CAD  CAE  119.35  3.000
 F9T  CAL  CAD  CAE  120.90  3.000
 F9T  H25  CAL  CBB  121.13  3.000
 F9T  H25  CAL  CAD  122.11  3.000
 F9T  CBB  CAL  CAD  116.76  3.000
 F9T  NAS  CBB  OAB  117.89  3.000
 F9T  NAS  CBB  CAL  123.42  3.000
 F9T  OAB  CBB  CAL  118.70  3.000
 F9T  H23  OAB  CBB  109.12  3.000
 F9T  CBB  NAS  CAZ  118.69  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
 F9T  CONST_01  CBA  CAK  CAF  CAV     0.00   0.0  0
 F9T  CONST_02  CBA  CAW  CAM  CAV     0.00   0.0  0
 F9T  CONST_03  CAK  CAF  CAV  CAM     0.00   0.0  0
 F9T  CONST_04  CAK  CBA  CAW  CAM     0.00   0.0  0
 F9T  CONST_05  CAF  CAK  CBA  CAW     0.00   0.0  0
 F9T  CONST_06  CAF  CAV  CAM  CAW     0.00   0.0  0
 F9T  CONST_07  CAX  CAH  CAJ  CAY     0.00   0.0  0
 F9T  CONST_08  CAX  CAG  CAI  CAY     0.00   0.0  0
 F9T  CONST_09  CAG  CAX  CAH  CAJ     0.00   0.0  0
 F9T  CONST_10  CAG  CAI  CAY  CAJ     0.00   0.0  0
 F9T  CONST_11  CAI  CAY  CAJ  CAH     0.00   0.0  0
 F9T  CONST_12  CAI  CAG  CAX  CAH     0.00   0.0  0
 F9T  CONST_13  CAL  CAD  CAE  CAZ     0.00   0.0  0
 F9T  CONST_14  CAL  CBB  NAS  CAZ     0.00   0.0  0
 F9T  CONST_15  CBB  CAL  CAD  CAE     0.00   0.0  0
 F9T  CONST_16  CBB  NAS  CAZ  CAE     0.00   0.0  0
 F9T  CONST_17  NAS  CBB  CAL  CAD     0.00   0.0  0
 F9T  CONST_18  NAS  CAZ  CAE  CAD     0.00   0.0  0
 F9T  CONST_19  CAK  CAF  CAV  CAR   180.00   0.0  0
 F9T  CONST_20  CAW  CAM  CAV  CAR   180.00   0.0  0
 F9T  CONST_21  OAC  CAW  CAM  CAV   180.00   0.0  0
 F9T  CONST_22  OAU  CBA  CAW  CAM   180.00   0.0  0
 F9T  CONST_23  CAK  CBA  CAW  OAC   180.00   0.0  0
 F9T  CONST_24  OAU  CBA  CAK  CAF   180.00   0.0  0
 F9T  CONST_25  CAH  CAJ  CAY  OAU   180.00   0.0  0
 F9T  CONST_26  CAG  CAI  CAY  OAU   180.00   0.0  0
 F9T  CONST_27  OAT  CAX  CAH  CAJ   180.00   0.0  0
 F9T  CONST_28  OAT  CAX  CAG  CAI   180.00   0.0  0
 F9T  CONST_29  CAD  CAE  CAZ  OAT   180.00   0.0  0
 F9T  CONST_30  CBB  NAS  CAZ  OAT   180.00   0.0  0
 F9T  CONST_31  OAB  CBB  NAS  CAZ   180.00   0.0  0
 F9T  CONST_32  OAB  CBB  CAL  CAD   180.00   0.0  0
 F9T  CONST_33  H17  CAK  CAF  CAV   180.00   0.0  0
 F9T  CONST_34  H16  CAF  CAV  CAM   180.00   0.0  0
 F9T  CONST_35  H14  CAM  CAV  CAF   180.00   0.0  0
 F9T  CONST_36  H19  CAH  CAJ  CAY   180.00   0.0  0
 F9T  CONST_37  H21  CAG  CAI  CAY   180.00   0.0  0
 F9T  CONST_38  H20  CAI  CAY  CAJ   180.00   0.0  0
 F9T  CONST_39  H18  CAJ  CAY  CAI   180.00   0.0  0
 F9T  CONST_40  H24  CAD  CAE  CAZ   180.00   0.0  0
 F9T  CONST_41  H25  CAL  CAD  CAE   180.00   0.0  0
 F9T  CONST_42  H22  CAE  CAD  CAL   180.00   0.0  0
 F9T  Var_01    CAJ  CAY  OAU  CBA    17.98  30.0  2
 F9T  Var_02    CAE  CAZ  OAT  CAX    -9.11  30.0  2
 F9T  Var_03    CAF  CAV  CAR  CAQ    95.87  30.0  2
 F9T  Var_04    CAV  CAR  CAQ  CAP   178.45  30.0  3
 F9T  Var_05    CAP  CAO  CAN  CAA   175.13  30.0  2
 F9T  Var_06    CAQ  CAP  CAO  CAN    62.61  30.0  3
 F9T  Var_07    CAR  CAQ  CAP  CAO   175.78  30.0  3
 F9T  Var_08    H1   CAA  CAN  CAO  -179.86  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
 F9T  plan-1  CAR  0.020
 F9T  plan-1  CAV  0.020
 F9T  plan-1  CAM  0.020
 F9T  plan-1  CAW  0.020
 F9T  plan-1  OAC  0.020
 F9T  plan-1  CAF  0.020
 F9T  plan-1  CAK  0.020
 F9T  plan-1  CBA  0.020
 F9T  plan-1  OAU  0.020
 F9T  plan-1  H14  0.020
 F9T  plan-1  H16  0.020
 F9T  plan-1  H17  0.020
 F9T  plan-2  OAU  0.020
 F9T  plan-2  CAY  0.020
 F9T  plan-2  CAJ  0.020
 F9T  plan-2  CAH  0.020
 F9T  plan-2  CAI  0.020
 F9T  plan-2  CAG  0.020
 F9T  plan-2  CAX  0.020
 F9T  plan-2  OAT  0.020
 F9T  plan-2  H18  0.020
 F9T  plan-2  H19  0.020
 F9T  plan-2  H20  0.020
 F9T  plan-2  H21  0.020
 F9T  plan-3  OAT  0.020
 F9T  plan-3  CAZ  0.020
 F9T  plan-3  CAE  0.020
 F9T  plan-3  CAD  0.020
 F9T  plan-3  CAL  0.020
 F9T  plan-3  CBB  0.020
 F9T  plan-3  OAB  0.020
 F9T  plan-3  NAS  0.020
 F9T  plan-3  H22  0.020
 F9T  plan-3  H24  0.020
 F9T  plan-3  H25  0.020

