# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:39:03 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2Z)-4-({3-[3-(hexyloxy)phenyl]propyl}amino)-2-hydroxy-4-oxobut-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCOc1cccc(CCCNC(=O)\C=C(/O)C(O)=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
 TH9  TH9  '(2Z)-4-({3-[3-(hexyloxy)phenyl]propyl}amino)-2-hydroxy-4-oxobut-2-enoic acid'  ligand  51  25  .  2021-08-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TH9
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
 TH9  CAA  C  CH3    0  -0.663  10.7214   3.0563  -0.5512
 TH9  OAB  O  O      0  -0.554  -7.3064   2.1514   2.0207
 TH9  OAC  O  O      0  -0.514  -5.2064  -0.5358  -1.8265
 TH9  OAD  O  OC    -1  -0.608  -8.9114   2.1978   0.4564
 TH9  OAE  O  OH1    0  -0.599  -7.6193   0.8467  -1.2136
 TH9  CAF  C  C1     0  -0.558  -5.7333   0.6049   0.2042
 TH9  CAG  C  CR16   0  -0.227   2.3779  -2.9193   1.6925
 TH9  CAH  C  CR16   0  -0.332   1.1764  -2.9796   1.0092
 TH9  CAI  C  CR16   0  -0.401   3.4006  -2.0702   1.2808
 TH9  CAJ  C  CR16   0  -0.418   1.9908  -1.3303  -0.5296
 TH9  CAK  C  CH2    0  -0.419   9.7829   2.1640   0.2486
 TH9  CAL  C  CH2    0  -0.407   8.4701   1.8904  -0.4755
 TH9  CAM  C  CH2    0  -0.425   7.5377   0.9734   0.3048
 TH9  CAN  C  CH2    0  -0.456   6.2139   0.7252  -0.4097
 TH9  CAO  C  CH2    0  -0.467  -1.3878  -1.3260  -0.1254
 TH9  CAP  C  CH2    0  -0.231  -2.7194  -1.3362  -0.8585
 TH9  CAQ  C  CH2    0  -0.169   5.3540  -0.2595   0.3538
 TH9  NAS  N  NH1    0  -0.667  -3.6884  -0.5223  -0.1627
 TH9  OAT  O  O2     0  -0.480   4.1244  -0.4173  -0.3363
 TH9  CAU  C  C      0   0.399  -7.7909   1.8830   0.9181
 TH9  CAV  C  C      0   0.576  -4.8888  -0.1912  -0.6906
 TH9  CAW  C  C      0   0.209  -6.9680   1.0528  -0.0787
 TH9  CAX  C  CR6    0   0.152   0.9735  -2.1761  -0.1149
 TH9  CAY  C  CR6    0   0.405   3.2057  -1.2707   0.1579
 TH9  H1   H  HCH3   0   0.226  11.6517   3.2464  -0.0144
 TH9  H2   H  HCH3   0   0.216  10.9791   2.5972  -1.5073
 TH9  H3   H  HCH3   0   0.216  10.2592   4.0217  -0.7652
 TH9  H5   H  HOH1   0   0.451  -8.4725   1.3128  -1.0545
 TH9  H6   H  H      0   0.255  -5.3450   0.8609   1.1810
 TH9  H7   H  HCR6   0   0.255   2.5328  -3.5428   2.5639
 TH9  H8   H  HCR6   0   0.242   0.3934  -3.6487   1.3452
 TH9  H9   H  HCR6   0   0.275   4.3266  -2.0512   1.8390
 TH9  H10  H  HCR6   0   0.250   1.8499  -0.7003  -1.4012
 TH9  H11  H  HCH2   0   0.211  10.2782   1.2134   0.4699
 TH9  H12  H  HCH2   0   0.211   9.5709   2.6269   1.2173
 TH9  H13  H  HCH2   0   0.210   7.9637   2.8401  -0.6798
 TH9  H14  H  HCH2   0   0.209   8.6819   1.4440  -1.4533
 TH9  H15  H  HCH2   0   0.215   8.0422   0.0183   0.4870
 TH9  H16  H  HCH2   0   0.216   7.3427   1.4071   1.2912
 TH9  H17  H  HCH2   0   0.229   5.6770   1.6708  -0.5272
 TH9  H18  H  HCH2   0   0.227   6.4046   0.3381  -1.4152
 TH9  H19  H  HCH2   0   0.240  -1.0183  -0.2995  -0.0470
 TH9  H20  H  HCH2   0   0.236  -1.5264  -1.6911   0.8972
 TH9  H21  H  HCH2   0   0.229  -2.5823  -0.9539  -1.8731
 TH9  H22  H  HCH2   0   0.223  -3.0767  -2.3679  -0.9577
 TH9  H23  H  HCH2   0   0.218   5.8745  -1.2208   0.4356
 TH9  H24  H  HCH2   0   0.218   5.1711   0.1022   1.3730
 TH9  H25  H  HCH2   0   0.245  -0.7165  -3.2163  -0.9085
 TH9  H26  H  HCH2   0   0.244  -0.2124  -1.8303  -1.8584
 TH9  H27  H  HNH1   0   0.394  -3.4988  -0.2805   0.7961
 TH9  CAR  C  CH2    0  -0.509  -0.3457  -2.1903  -0.8351

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
 TH9  CAA  CAK  single    1.522  0.020  1.522
 TH9  OAB  CAU  deloc     1.234  0.020  1.234
 TH9  CAF  CAV  single    1.466  0.020  1.466
 TH9  CAF  CAW  double    1.344  0.020  1.344
 TH9  CAG  CAH  aromatic  1.383  0.020  1.383
 TH9  CAG  CAI  aromatic  1.392  0.020  1.392
 TH9  CAH  CAX  aromatic  1.397  0.020  1.397
 TH9  CAI  CAY  aromatic  1.392  0.020  1.392
 TH9  CAL  CAK  single    1.524  0.020  1.524
 TH9  CAL  CAM  single    1.523  0.020  1.523
 TH9  CAM  CAN  single    1.525  0.020  1.525
 TH9  CAP  CAO  single    1.520  0.020  1.520
 TH9  CAQ  CAN  single    1.514  0.020  1.514
 TH9  CAR  CAO  single    1.529  0.020  1.529
 TH9  NAS  CAP  single    1.444  0.020  1.444
 TH9  NAS  CAV  single    1.352  0.020  1.352
 TH9  OAT  CAQ  single    1.419  0.020  1.419
 TH9  CAU  OAD  deloc     1.252  0.020  1.252
 TH9  CAU  CAW  single    1.536  0.020  1.536
 TH9  CAV  OAC  double    1.229  0.020  1.229
 TH9  CAW  OAE  single    1.325  0.020  1.325
 TH9  CAX  CAJ  aromatic  1.386  0.020  1.386
 TH9  CAX  CAR  single    1.503  0.020  1.503
 TH9  CAY  CAJ  aromatic  1.397  0.020  1.397
 TH9  CAY  OAT  single    1.348  0.020  1.348
 TH9  CAA  H1   single    0.970  0.020  1.090
 TH9  CAA  H2   single    0.970  0.020  1.090
 TH9  CAA  H3   single    0.970  0.020  1.090
 TH9  OAE  H5   single    0.850  0.020  0.980
 TH9  CAF  H6   single    0.930  0.020  1.080
 TH9  CAG  H7   single    0.930  0.020  1.080
 TH9  CAH  H8   single    0.930  0.020  1.080
 TH9  CAI  H9   single    0.930  0.020  1.080
 TH9  CAJ  H10  single    0.930  0.020  1.080
 TH9  CAK  H11  single    0.970  0.020  1.090
 TH9  CAK  H12  single    0.970  0.020  1.090
 TH9  CAL  H13  single    0.970  0.020  1.090
 TH9  CAL  H14  single    0.970  0.020  1.090
 TH9  CAM  H15  single    0.970  0.020  1.090
 TH9  CAM  H16  single    0.970  0.020  1.090
 TH9  CAN  H17  single    0.970  0.020  1.090
 TH9  CAN  H18  single    0.970  0.020  1.090
 TH9  CAO  H19  single    0.970  0.020  1.090
 TH9  CAO  H20  single    0.970  0.020  1.090
 TH9  CAP  H21  single    0.970  0.020  1.090
 TH9  CAP  H22  single    0.970  0.020  1.090
 TH9  CAQ  H23  single    0.970  0.020  1.090
 TH9  CAQ  H24  single    0.970  0.020  1.090
 TH9  CAR  H25  single    0.970  0.020  1.090
 TH9  CAR  H26  single    0.970  0.020  1.090
 TH9  NAS  H27  single    0.860  0.020  1.020

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
 TH9  H3   CAA  H2   107.47  3.000
 TH9  H3   CAA  H1   107.67  3.000
 TH9  H2   CAA  H1   107.64  3.000
 TH9  H3   CAA  CAK  111.13  3.000
 TH9  H2   CAA  CAK  111.06  3.000
 TH9  H1   CAA  CAK  111.69  3.000
 TH9  H5   OAE  CAW  102.35  3.000
 TH9  H6   CAF  CAW  116.17  3.000
 TH9  H6   CAF  CAV  118.22  3.000
 TH9  CAW  CAF  CAV  125.60  3.000
 TH9  H7   CAG  CAI  118.97  3.000
 TH9  H7   CAG  CAH  119.78  3.000
 TH9  CAI  CAG  CAH  121.25  3.000
 TH9  H8   CAH  CAX  120.00  3.000
 TH9  H8   CAH  CAG  120.09  3.000
 TH9  CAX  CAH  CAG  119.91  3.000
 TH9  H9   CAI  CAY  121.74  3.000
 TH9  H9   CAI  CAG  119.17  3.000
 TH9  CAY  CAI  CAG  119.09  3.000
 TH9  H10  CAJ  CAY  118.91  3.000
 TH9  H10  CAJ  CAX  119.97  3.000
 TH9  CAY  CAJ  CAX  121.12  3.000
 TH9  H12  CAK  H11  106.02  3.000
 TH9  H12  CAK  CAL  109.25  3.000
 TH9  H11  CAK  CAL  109.27  3.000
 TH9  H12  CAK  CAA  109.67  3.000
 TH9  H11  CAK  CAA  109.65  3.000
 TH9  CAL  CAK  CAA  112.75  3.000
 TH9  H14  CAL  H13  106.03  3.000
 TH9  H14  CAL  CAM  109.29  3.000
 TH9  H13  CAL  CAM  109.54  3.000
 TH9  H14  CAL  CAK  109.31  3.000
 TH9  H13  CAL  CAK  109.34  3.000
 TH9  CAM  CAL  CAK  113.08  3.000
 TH9  H16  CAM  H15  106.11  3.000
 TH9  H16  CAM  CAN  109.39  3.000
 TH9  H15  CAM  CAN  109.63  3.000
 TH9  H16  CAM  CAL  109.39  3.000
 TH9  H15  CAM  CAL  109.16  3.000
 TH9  CAN  CAM  CAL  112.92  3.000
 TH9  H18  CAN  H17  107.02  3.000
 TH9  H18  CAN  CAQ  109.41  3.000
 TH9  H17  CAN  CAQ  109.73  3.000
 TH9  H18  CAN  CAM  109.69  3.000
 TH9  H17  CAN  CAM  109.63  3.000
 TH9  CAQ  CAN  CAM  111.27  3.000
 TH9  H20  CAO  H19  106.79  3.000
 TH9  H20  CAO  CAR  109.36  3.000
 TH9  H19  CAO  CAR  109.49  3.000
 TH9  H20  CAO  CAP  109.72  3.000
 TH9  H19  CAO  CAP  109.68  3.000
 TH9  CAR  CAO  CAP  111.68  3.000
 TH9  H22  CAP  H21  106.63  3.000
 TH9  H22  CAP  NAS  110.81  3.000
 TH9  H21  CAP  NAS  109.53  3.000
 TH9  H22  CAP  CAO  109.60  3.000
 TH9  H21  CAP  CAO  109.60  3.000
 TH9  NAS  CAP  CAO  110.59  3.000
 TH9  H24  CAQ  H23  107.39  3.000
 TH9  H24  CAQ  OAT  110.13  3.000
 TH9  H23  CAQ  OAT  110.51  3.000
 TH9  H24  CAQ  CAN  110.42  3.000
 TH9  H23  CAQ  CAN  109.77  3.000
 TH9  OAT  CAQ  CAN  108.62  3.000
 TH9  H27  NAS  CAV  118.69  3.000
 TH9  H27  NAS  CAP  117.89  3.000
 TH9  CAV  NAS  CAP  123.05  3.000
 TH9  CAY  OAT  CAQ  118.87  3.000
 TH9  CAW  CAU  OAD  112.08  3.000
 TH9  CAW  CAU  OAB  119.15  3.000
 TH9  OAD  CAU  OAB  128.77  3.000
 TH9  NAS  CAV  CAF  113.96  3.000
 TH9  NAS  CAV  OAC  121.44  3.000
 TH9  CAF  CAV  OAC  124.59  3.000
 TH9  CAU  CAW  CAF  122.39  3.000
 TH9  CAU  CAW  OAE  112.13  3.000
 TH9  CAF  CAW  OAE  125.48  3.000
 TH9  CAR  CAX  CAJ  120.42  3.000
 TH9  CAR  CAX  CAH  120.52  3.000
 TH9  CAJ  CAX  CAH  119.02  3.000
 TH9  OAT  CAY  CAJ  116.06  3.000
 TH9  OAT  CAY  CAI  124.33  3.000
 TH9  CAJ  CAY  CAI  119.61  3.000
 TH9  H26  CAR  H25  106.71  3.000
 TH9  H26  CAR  CAX  109.78  3.000
 TH9  H25  CAR  CAX  109.79  3.000
 TH9  H26  CAR  CAO  109.37  3.000
 TH9  H25  CAR  CAO  109.30  3.000
 TH9  CAX  CAR  CAO  111.75  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
 TH9  CONST_01  CAJ  CAX  CAH  CAG    0.00   0.0  0
 TH9  CONST_02  CAJ  CAY  CAI  CAG    0.00   0.0  0
 TH9  CONST_03  CAY  CAI  CAG  CAH    0.00   0.0  0
 TH9  CONST_04  CAY  CAJ  CAX  CAH    0.00   0.0  0
 TH9  CONST_05  CAX  CAH  CAG  CAI    0.00   0.0  0
 TH9  CONST_06  CAX  CAJ  CAY  CAI    0.00   0.0  0
 TH9  CONST_07  CAR  CAX  CAH  CAG  180.00   0.0  0
 TH9  CONST_08  OAT  CAY  CAI  CAG  180.00   0.0  0
 TH9  CONST_09  CAY  CAJ  CAX  CAR  180.00   0.0  0
 TH9  CONST_10  CAX  CAJ  CAY  OAT  180.00   0.0  0
 TH9  CONST_11  H9   CAI  CAG  CAH  180.00   0.0  0
 TH9  CONST_12  H10  CAJ  CAX  CAH  180.00   0.0  0
 TH9  CONST_13  H8   CAH  CAG  CAI  180.00   0.0  0
 TH9  CONST_14  H7   CAG  CAH  CAX  180.00   0.0  0
 TH9  CONST_15  CAP  NAS  CAV  OAC    0.00   0.0  0
 TH9  CONST_16  CAP  NAS  CAV  CAF  180.00   0.0  0
 TH9  CONST_17  H27  NAS  CAV  OAC  180.00   0.0  0
 TH9  Var_01    CAO  CAR  CAX  CAH   80.10  30.0  2
 TH9  Var_02    CAX  CAR  CAO  CAP  179.74  30.0  1
 TH9  Var_03    H23  CAQ  OAT  CAY   58.54  30.0  3
 TH9  Var_04    CAV  CAF  CAW  OAE   -0.05   0.0  2
 TH9  Var_05    CAM  CAL  CAK  CAA  178.74  30.0  1
 TH9  Var_06    CAF  CAW  CAU  OAB   -0.02  30.0  2
 TH9  Var_07    CAW  CAF  CAV  OAC    0.89  30.0  1
 TH9  Var_08    CAN  CAM  CAL  CAK  178.81  30.0  3
 TH9  Var_09    CAQ  CAN  CAM  CAL  176.33  30.0  3
 TH9  Var_10    OAT  CAQ  CAN  CAM  178.23  30.0  1
 TH9  Var_11    CAV  NAS  CAP  CAO  169.82  30.0  1
 TH9  Var_12    NAS  CAP  CAO  CAR  179.53  30.0  1
 TH9  Var_13    H1   CAA  CAK  CAL  179.60  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
 TH9  plan-1  CAG  0.020
 TH9  plan-1  CAH  0.020
 TH9  plan-1  CAI  0.020
 TH9  plan-1  CAJ  0.020
 TH9  plan-1  OAT  0.020
 TH9  plan-1  CAX  0.020
 TH9  plan-1  CAY  0.020
 TH9  plan-1  H7   0.020
 TH9  plan-1  H8   0.020
 TH9  plan-1  H9   0.020
 TH9  plan-1  H10  0.020
 TH9  plan-1  CAR  0.020
 TH9  plan-2  OAC  0.020
 TH9  plan-2  CAF  0.020
 TH9  plan-2  CAP  0.020
 TH9  plan-2  NAS  0.020
 TH9  plan-2  CAV  0.020
 TH9  plan-2  H27  0.020
 TH9  plan-3  OAB  0.020
 TH9  plan-3  OAD  0.020
 TH9  plan-3  CAU  0.020
 TH9  plan-3  CAW  0.020
 TH9  plan-4  OAE  0.020
 TH9  plan-4  CAF  0.020
 TH9  plan-4  CAU  0.020
 TH9  plan-4  CAV  0.020
 TH9  plan-4  CAW  0.020
 TH9  plan-4  H6   0.020

