# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 09:25:03 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: (5S)-5-[(4-{[(2R)-6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-1-benzopyran-2-yl]methoxy}phenyl)methyl]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(C)c2O[C@](C)(CCc2c(C)c1O)COc3ccc(C[C@@H]4SC(=O)NC4=O)cc3
#
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
 GD4  GD4  (5S)-5-[(4-{[(2R)-6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-1-benzopyran-2-yl]methoxy}phenyl)methyl]-1,3-thiazolidine-2,4-dione  ligand  58  31  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GD4
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
 GD4  CAM  C  C     0  -0.449   3.0701   2.3862   0.4236
 GD4  CAL  C  C     0  -0.513   4.5531   2.4239   0.0869
 GD4  CBB  C  CR66  0  -0.025   5.1672   1.0486   0.0842
 GD4  CAZ  C  CR6   0  -0.078   6.5576   0.8879   0.0645
 GD4  CAC  C  CH3   0  -0.766   7.4570   2.0934   0.0057
 GD4  CBA  C  CR6   0   0.272   7.0912  -0.3986   0.1227
 GD4  OAG  O  OH1   0  -0.642   8.4349  -0.6190   0.1359
 GD4  CAX  C  CR6   0  -0.041   6.2705  -1.5309   0.1480
 GD4  CAA  C  CH3   0  -0.731   6.8791  -2.9043   0.2198
 GD4  CAY  C  CR6   0  -0.068   4.8859  -1.3704   0.0941
 GD4  CAB  C  CH3   0  -0.739   3.9760  -2.5673   0.0646
 GD4  CBC  C  CR66  0   0.336   4.3504  -0.0783   0.0891
 GD4  OAR  O  O     0  -0.497   2.9929   0.0071   0.1141
 GD4  CBE  C  CR6   0   0.146   2.3823   1.2282  -0.2911
 GD4  CAD  C  CH3   0  -0.672   2.4474   1.3769  -1.8080
 GD4  CAN  C  CH2   0  -0.170   0.9461   1.1427   0.2009
 GD4  OAQ  O  O2    0  -0.470   0.3079   0.0458  -0.4158
 GD4  CAW  C  CR6   0   0.381  -0.9609  -0.2439  -0.0728
 GD4  CAK  C  CR16  0  -0.369  -1.7196   0.4883   0.8352
 GD4  CAI  C  CR16  0  -0.286  -3.0230   0.0934   1.1196
 GD4  CAJ  C  CR16  0  -0.335  -1.5247  -1.3666  -0.6848
 GD4  CAH  C  CR16  0  -0.279  -2.8198  -1.7428  -0.3881
 GD4  CAV  C  CR6   0   0.087  -3.5943  -1.0210   0.5219
 GD4  CAO  C  CH2   0  -0.498  -5.0140  -1.4204   0.8077
 GD4  CBD  C  CH1   0  -0.550  -5.9572  -0.9875  -0.3171
 GD4  SAS  S  S2    0   0.085  -5.9653   0.8152  -0.5507
 GD4  CAT  C  C     0   0.404  -7.7106   0.9257  -0.3196
 GD4  OAE  O  O     0  -0.401  -8.3387   1.9472  -0.3687
 GD4  NAP  N  NH1   0  -0.658  -8.2343  -0.3212  -0.0758
 GD4  CAU  C  C     0   0.622  -7.3918  -1.3966  -0.0430
 GD4  OAF  O  O     0  -0.411  -7.7364  -2.5287   0.1837
 GD4  H1   H  H     0   0.246   2.9397   2.2637   1.5028
 GD4  H2   H  H     0   0.250   2.5982   3.3313   0.1501
 GD4  H3   H  H     0   0.252   4.7066   2.8988  -0.8873
 GD4  H4   H  H     0   0.263   5.0634   3.0639   0.8096
 GD4  H5   H  HCH3  0   0.256   7.6944   2.4773   1.0013
 GD4  H6   H  HCH3  0   0.242   8.4030   1.8891  -0.4978
 GD4  H7   H  HCH3  0   0.263   6.9965   2.9094  -0.5482
 GD4  H8   H  HOH1  0   0.472   8.9079   0.1827   0.3778
 GD4  H9   H  HCH3  0   0.243   6.9855  -3.3512  -0.7725
 GD4  H10  H  HCH3  0   0.250   7.8688  -2.8862   0.6701
 GD4  H11  H  HCH3  0   0.243   6.2636  -3.5823   0.8094
 GD4  H12  H  HCH3  0   0.242   3.8253  -2.9853   1.0637
 GD4  H13  H  HCH3  0   0.254   2.9945  -2.3184  -0.3311
 GD4  H14  H  HCH3  0   0.241   4.3885  -3.3643  -0.5534
 GD4  H15  H  HCH3  0   0.243   3.4775   1.4255  -2.1621
 GD4  H16  H  HCH3  0   0.248   1.9635   0.5413  -2.3117
 GD4  H17  H  HCH3  0   0.235   1.9507   2.2973  -2.1179
 GD4  H18  H  HCH2  0   0.237   0.9377   1.0293   1.2918
 GD4  H19  H  HCH2  0   0.230   0.4319   2.0800  -0.0418
 GD4  H20  H  HCR6  0   0.280  -1.3227   1.3631   1.3323
 GD4  H21  H  HCR6  0   0.256  -3.5984   0.6747   1.8299
 GD4  H22  H  HCR6  0   0.262  -0.9346  -1.9407  -1.3883
 GD4  H23  H  HCR6  0   0.255  -3.2342  -2.6210  -0.8701
 GD4  H24  H  HCH2  0   0.282  -5.0911  -2.5055   0.9052
 GD4  H25  H  HCH2  0   0.278  -5.3504  -0.9845   1.7501
 GD4  H26  H  HCH1  0   0.354  -5.6523  -1.4551  -1.2569
 GD4  H27  H  HNH1  0   0.440  -9.2281  -0.4274   0.0916

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
 GD4  CAA  CAX  single    1.504  0.020  1.504
 GD4  CAB  CAY  single    1.504  0.020  1.504
 GD4  CAX  CAY  aromatic  1.395  0.020  1.395
 GD4  CAX  CBA  aromatic  1.399  0.020  1.399
 GD4  CAY  CBC  aromatic  1.399  0.020  1.399
 GD4  OAG  CBA  single    1.362  0.020  1.362
 GD4  CBA  CAZ  aromatic  1.394  0.020  1.394
 GD4  CBC  OAR  single    1.360  0.020  1.360
 GD4  CBC  CBB  aromatic  1.392  0.020  1.392
 GD4  OAR  CBE  single    1.424  0.020  1.424
 GD4  CAZ  CBB  aromatic  1.400  0.020  1.400
 GD4  CAZ  CAC  single    1.505  0.020  1.505
 GD4  CAD  CBE  single    1.526  0.020  1.526
 GD4  CBB  CAL  single    1.506  0.020  1.506
 GD4  CAM  CBE  single    1.525  0.020  1.525
 GD4  CAM  CAL  single    1.521  0.020  1.521
 GD4  CBE  CAN  single    1.520  0.020  1.520
 GD4  CAN  OAQ  single    1.411  0.020  1.411
 GD4  OAQ  CAW  single    1.346  0.020  1.346
 GD4  CAW  CAJ  aromatic  1.397  0.020  1.397
 GD4  CAW  CAK  aromatic  1.392  0.020  1.392
 GD4  CAJ  CAH  aromatic  1.381  0.020  1.381
 GD4  CAK  CAI  aromatic  1.391  0.020  1.391
 GD4  CAH  CAV  aromatic  1.396  0.020  1.396
 GD4  CAI  CAV  aromatic  1.388  0.020  1.388
 GD4  CAV  CAO  single    1.502  0.020  1.502
 GD4  CAO  CBD  single    1.530  0.020  1.530
 GD4  CBD  SAS  single    1.818  0.020  1.818
 GD4  CBD  CAU  single    1.517  0.020  1.517
 GD4  SAS  CAT  single    1.764  0.020  1.764
 GD4  OAF  CAU  double    1.205  0.020  1.205
 GD4  CAU  NAP  single    1.367  0.020  1.367
 GD4  CAT  NAP  single    1.374  0.020  1.374
 GD4  CAT  OAE  double    1.200  0.020  1.200
 GD4  CAM  H1   single    0.970  0.020  1.090
 GD4  CAM  H2   single    0.970  0.020  1.090
 GD4  CAL  H3   single    0.970  0.020  1.090
 GD4  CAL  H4   single    0.970  0.020  1.090
 GD4  CAC  H5   single    0.970  0.020  1.090
 GD4  CAC  H6   single    0.970  0.020  1.090
 GD4  CAC  H7   single    0.970  0.020  1.090
 GD4  OAG  H8   single    0.850  0.020  0.980
 GD4  CAA  H9   single    0.970  0.020  1.090
 GD4  CAA  H10  single    0.970  0.020  1.090
 GD4  CAA  H11  single    0.970  0.020  1.090
 GD4  CAB  H12  single    0.970  0.020  1.090
 GD4  CAB  H13  single    0.970  0.020  1.090
 GD4  CAB  H14  single    0.970  0.020  1.090
 GD4  CAD  H15  single    0.970  0.020  1.090
 GD4  CAD  H16  single    0.970  0.020  1.090
 GD4  CAD  H17  single    0.970  0.020  1.090
 GD4  CAN  H18  single    0.970  0.020  1.090
 GD4  CAN  H19  single    0.970  0.020  1.090
 GD4  CAK  H20  single    0.930  0.020  1.080
 GD4  CAI  H21  single    0.930  0.020  1.080
 GD4  CAJ  H22  single    0.930  0.020  1.080
 GD4  CAH  H23  single    0.930  0.020  1.080
 GD4  CAO  H24  single    0.970  0.020  1.090
 GD4  CAO  H25  single    0.970  0.020  1.090
 GD4  CBD  H26  single    0.970  0.020  1.090
 GD4  NAP  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
 GD4  H2   CAM  H1   107.02  3.000
 GD4  H2   CAM  CBE  110.20  3.000
 GD4  H1   CAM  CBE  108.88  3.000
 GD4  H2   CAM  CAL  110.16  3.000
 GD4  H1   CAM  CAL  109.72  3.000
 GD4  CBE  CAM  CAL  110.78  3.000
 GD4  H4   CAL  H3   105.62  3.000
 GD4  H4   CAL  CBB  110.23  3.000
 GD4  H3   CAL  CBB  109.72  3.000
 GD4  H4   CAL  CAM  108.88  3.000
 GD4  H3   CAL  CAM  110.15  3.000
 GD4  CBB  CAL  CAM  112.04  3.000
 GD4  CBC  CBB  CAZ  119.34  3.000
 GD4  CAZ  CBB  CAL  120.66  3.000
 GD4  CBC  CBB  CAL  120.00  3.000
 GD4  CBA  CAZ  CAC  120.80  3.000
 GD4  CAC  CAZ  CBB  120.14  3.000
 GD4  CBA  CAZ  CBB  119.05  3.000
 GD4  H7   CAC  H6   105.81  3.000
 GD4  H7   CAC  H5   106.99  3.000
 GD4  H6   CAC  H5   107.32  3.000
 GD4  H7   CAC  CAZ  111.56  3.000
 GD4  H6   CAC  CAZ  112.72  3.000
 GD4  H5   CAC  CAZ  112.05  3.000
 GD4  CAX  CBA  OAG  116.60  3.000
 GD4  OAG  CBA  CAZ  121.84  3.000
 GD4  CAX  CBA  CAZ  121.55  3.000
 GD4  H8   OAG  CBA  110.66  3.000
 GD4  CAY  CAX  CAA  120.57  3.000
 GD4  CAY  CAX  CBA  119.24  3.000
 GD4  CAA  CAX  CBA  120.18  3.000
 GD4  H11  CAA  H10  107.49  3.000
 GD4  H11  CAA  H9   106.97  3.000
 GD4  H10  CAA  H9   107.09  3.000
 GD4  H11  CAA  CAX  111.45  3.000
 GD4  H10  CAA  CAX  111.89  3.000
 GD4  H9   CAA  CAX  111.67  3.000
 GD4  CBC  CAY  CAB  120.24  3.000
 GD4  CBC  CAY  CAX  119.11  3.000
 GD4  CAB  CAY  CAX  120.65  3.000
 GD4  H14  CAB  H13  107.63  3.000
 GD4  H14  CAB  H12  106.90  3.000
 GD4  H13  CAB  H12  107.20  3.000
 GD4  H14  CAB  CAY  111.36  3.000
 GD4  H13  CAB  CAY  111.79  3.000
 GD4  H12  CAB  CAY  111.70  3.000
 GD4  OAR  CBC  CAY  116.10  3.000
 GD4  OAR  CBC  CBB  122.34  3.000
 GD4  CAY  CBC  CBB  121.55  3.000
 GD4  CBE  OAR  CBC  118.45  3.000
 GD4  CAN  CBE  CAD  111.56  3.000
 GD4  CAN  CBE  OAR  105.35  3.000
 GD4  CAD  CBE  OAR  110.38  3.000
 GD4  CAN  CBE  CAM  108.49  3.000
 GD4  CAD  CBE  CAM  111.89  3.000
 GD4  OAR  CBE  CAM  108.93  3.000
 GD4  H17  CAD  H16  108.28  3.000
 GD4  H17  CAD  H15  107.48  3.000
 GD4  H16  CAD  H15  107.68  3.000
 GD4  H17  CAD  CBE  110.20  3.000
 GD4  H16  CAD  CBE  111.48  3.000
 GD4  H15  CAD  CBE  111.56  3.000
 GD4  H19  CAN  H18  107.76  3.000
 GD4  H19  CAN  OAQ  110.84  3.000
 GD4  H18  CAN  OAQ  110.54  3.000
 GD4  H19  CAN  CBE  108.87  3.000
 GD4  H18  CAN  CBE  109.57  3.000
 GD4  OAQ  CAN  CBE  109.24  3.000
 GD4  CAW  OAQ  CAN  118.84  3.000
 GD4  CAJ  CAW  CAK  119.25  3.000
 GD4  CAK  CAW  OAQ  124.54  3.000
 GD4  CAJ  CAW  OAQ  116.21  3.000
 GD4  H20  CAK  CAI  118.65  3.000
 GD4  H20  CAK  CAW  121.70  3.000
 GD4  CAI  CAK  CAW  119.66  3.000
 GD4  H21  CAI  CAV  119.65  3.000
 GD4  H21  CAI  CAK  118.64  3.000
 GD4  CAV  CAI  CAK  121.71  3.000
 GD4  H22  CAJ  CAH  120.42  3.000
 GD4  H22  CAJ  CAW  119.37  3.000
 GD4  CAH  CAJ  CAW  120.21  3.000
 GD4  H23  CAH  CAV  119.77  3.000
 GD4  H23  CAH  CAJ  118.92  3.000
 GD4  CAV  CAH  CAJ  121.30  3.000
 GD4  CAO  CAV  CAH  120.72  3.000
 GD4  CAO  CAV  CAI  121.38  3.000
 GD4  CAH  CAV  CAI  117.88  3.000
 GD4  H25  CAO  H24  107.33  3.000
 GD4  H25  CAO  CBD  109.37  3.000
 GD4  H24  CAO  CBD  107.64  3.000
 GD4  H25  CAO  CAV  110.45  3.000
 GD4  H24  CAO  CAV  110.36  3.000
 GD4  CBD  CAO  CAV  111.56  3.000
 GD4  H26  CBD  CAU  107.69  3.000
 GD4  H26  CBD  SAS  108.36  3.000
 GD4  CAU  CBD  SAS  106.65  3.000
 GD4  H26  CBD  CAO  109.82  3.000
 GD4  CAU  CBD  CAO  111.95  3.000
 GD4  SAS  CBD  CAO  112.19  3.000
 GD4  CAT  SAS  CBD   92.85  3.000
 GD4  NAP  CAT  OAE  125.46  3.000
 GD4  OAE  CAT  SAS  124.46  3.000
 GD4  NAP  CAT  SAS  110.09  3.000
 GD4  H27  NAP  CAU  121.21  3.000
 GD4  H27  NAP  CAT  119.88  3.000
 GD4  CAU  NAP  CAT  118.91  3.000
 GD4  OAF  CAU  NAP  124.58  3.000
 GD4  NAP  CAU  CBD  111.50  3.000
 GD4  OAF  CAU  CBD  123.91  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
 GD4  CONST_01  CAX  CAY  CBC  CBB     0.00   0.0  0
 GD4  CONST_02  CAX  CBA  CAZ  CBB     0.00   0.0  0
 GD4  CONST_03  CAY  CAX  CBA  CAZ     0.00   0.0  0
 GD4  CONST_04  CAY  CBC  CBB  CAZ     0.00   0.0  0
 GD4  CONST_05  CBC  CAY  CAX  CBA     0.00   0.0  0
 GD4  CONST_06  CBC  CBB  CAZ  CBA     0.00   0.0  0
 GD4  CONST_07  CAV  CAH  CAJ  CAW     0.00   0.0  0
 GD4  CONST_08  CAV  CAI  CAK  CAW     0.00   0.0  0
 GD4  CONST_09  CAH  CAJ  CAW  CAK     0.00   0.0  0
 GD4  CONST_10  CAH  CAV  CAI  CAK     0.00   0.0  0
 GD4  CONST_11  CAJ  CAW  CAK  CAI     0.00   0.0  0
 GD4  CONST_12  CAJ  CAH  CAV  CAI     0.00   0.0  0
 GD4  CONST_13  CAT  NAP  CAU  CBD     0.00   0.0  0
 GD4  CONST_14  CAC  CAZ  CBB  CAL     0.00   0.0  0
 GD4  CONST_15  CAB  CAY  CBC  CBB   180.00   0.0  0
 GD4  CONST_16  OAG  CBA  CAZ  CBB   180.00   0.0  0
 GD4  CONST_17  CAA  CAX  CBA  CAZ   180.00   0.0  0
 GD4  CONST_18  CAX  CBA  CAZ  CAC   180.00   0.0  0
 GD4  CONST_19  CBC  CBB  CAZ  CAC   180.00   0.0  0
 GD4  CONST_20  CAB  CAY  CAX  CBA   180.00   0.0  0
 GD4  CONST_21  CAY  CAX  CBA  OAG   180.00   0.0  0
 GD4  CONST_22  CBC  CAY  CAX  CAA   180.00   0.0  0
 GD4  CONST_23  OAR  CBC  CAY  CAB     0.00   0.0  0
 GD4  CONST_24  CAH  CAJ  CAW  OAQ   180.00   0.0  0
 GD4  CONST_25  CAI  CAK  CAW  OAQ   180.00   0.0  0
 GD4  CONST_26  CAO  CAV  CAI  CAK   180.00   0.0  0
 GD4  CONST_27  CAO  CAV  CAH  CAJ   180.00   0.0  0
 GD4  CONST_28  OAF  CAU  NAP  CAT   180.00   0.0  0
 GD4  CONST_29  H23  CAH  CAJ  CAW   180.00   0.0  0
 GD4  CONST_30  H21  CAI  CAK  CAW   180.00   0.0  0
 GD4  CONST_31  H22  CAJ  CAW  CAK   180.00   0.0  0
 GD4  CONST_32  H20  CAK  CAW  CAJ   180.00   0.0  0
 GD4  CONST_33  H27  NAP  CAU  CBD   180.00   0.0  0
 GD4  Var_01    CBC  CBB  CAL  CAM    13.49  30.0  1
 GD4  Var_02    CBE  CAM  CAL  CBB   -42.05  30.0  1
 GD4  Var_03    NAP  CAT  SAS  CBD     0.34  30.0  1
 GD4  Var_04    CAU  NAP  CAT  SAS     0.24  30.0  1
 GD4  Var_05    CBD  CAO  CAV  CAI   101.03  30.0  2
 GD4  Var_06    CAJ  CAW  OAQ  CAN  -178.00  30.0  2
 GD4  Var_07    H5   CAC  CAZ  CBB    88.14  30.0  2
 GD4  Var_08    H9   CAA  CAX  CBA   -95.12  30.0  2
 GD4  Var_09    H12  CAB  CAY  CAX    80.57  30.0  2
 GD4  Var_10    H18  CAN  OAQ  CAW    56.54  30.0  1

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
 GD4  chir_01  CBE  OAR  CAM  CAN  positiv
 GD4  chir_02  CBD  CAO  SAS  CAU  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
 GD4  plan-1  OAQ  0.020
 GD4  plan-1  CAW  0.020
 GD4  plan-1  CAK  0.020
 GD4  plan-1  CAI  0.020
 GD4  plan-1  CAJ  0.020
 GD4  plan-1  CAH  0.020
 GD4  plan-1  CAV  0.020
 GD4  plan-1  CAO  0.020
 GD4  plan-1  H20  0.020
 GD4  plan-1  H21  0.020
 GD4  plan-1  H22  0.020
 GD4  plan-1  H23  0.020
 GD4  plan-2  CAL  0.020
 GD4  plan-2  CBB  0.020
 GD4  plan-2  CAZ  0.020
 GD4  plan-2  CAC  0.020
 GD4  plan-2  CBA  0.020
 GD4  plan-2  OAG  0.020
 GD4  plan-2  CAX  0.020
 GD4  plan-2  CAA  0.020
 GD4  plan-2  CAY  0.020
 GD4  plan-2  CAB  0.020
 GD4  plan-2  CBC  0.020
 GD4  plan-2  OAR  0.020
 GD4  plan-3  CBD  0.020
 GD4  plan-3  CAT  0.020
 GD4  plan-3  NAP  0.020
 GD4  plan-3  CAU  0.020
 GD4  plan-3  OAF  0.020
 GD4  plan-3  H27  0.020
 GD4  plan-4  SAS  0.020
 GD4  plan-4  CAT  0.020
 GD4  plan-4  OAE  0.020
 GD4  plan-4  NAP  0.020

