# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 07:40:58 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: [(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](n1c2[C@@H](CCCc2c3cc(F)cc(c13)[S](C)(=O)=O)CC(O)=O)c4ccc(cc4)C(F)(F)F
#
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
 DY1  DY1  '[(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid'  ligand  57  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DY1
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
 DY1  C2   C  CR16  0  -0.434  32.7238  -6.7856  11.6836
 DY1  C3   C  CR6   0  -0.195  31.8002  -6.3260  12.6128
 DY1  C5   C  CR56  0   0.056  30.6876  -5.1421  10.8101
 DY1  C7   C  CR5   0   0.351  29.0220  -4.1108  11.8777
 DY1  C9   C  CH3   0  -0.695  28.5998  -4.7756  15.0454
 DY1  C10  C  CR6   0   0.101  30.1030  -2.8380  14.3034
 DY1  C11  C  CR16  0  -0.250  30.9838  -2.2587  13.3930
 DY1  C12  C  CR16  0  -0.270  31.2922  -0.9096  13.4549
 DY1  C13  C  CR6   0  -0.208  30.7229  -0.1135  14.4399
 DY1  C15  C  CR16  0  -0.295  29.5483  -2.0303  15.2922
 DY1  C20  C  CH2   0  -0.442  27.6276  -2.3136  10.9827
 DY1  C21  C  CH2   0  -0.459  27.6995  -2.9840   9.6138
 DY1  C22  C  CH2   0  -0.512  29.0464  -3.6734   9.3862
 DY1  C1   C  CR6   0   0.561  32.6155  -6.4239  10.3485
 DY1  S    S  S     0   1.198  31.8891  -6.9982  14.2620
 DY1  O2   O  OS    0  -0.664  32.6260  -6.0750  15.1256
 DY1  O3   O  OS    0  -0.656  30.5324  -7.3768  14.6532
 DY1  C23  C  CH3   0  -0.809  32.8364  -8.4977  14.1345
 DY1  C4   C  CR56  0   0.353  30.7878  -5.4474  12.1918
 DY1  N    N  NR5   0  -0.583  29.7655  -4.7830  12.8422
 DY1  C8   C  CH1   0  -0.196  29.8097  -4.3291  14.2376
 DY1  C14  C  CR16  0  -0.252  29.8537  -0.6807  15.3632
 DY1  C16  C  CT    0   1.052  31.0500   1.3410  14.5517
 DY1  F2   F  F     0  -0.303  31.7088   1.8067  13.4866
 DY1  F1   F  F     0  -0.313  29.9474   2.0912  14.6897
 DY1  F    F  F     0  -0.315  31.8155   1.5939  15.6251
 DY1  C17  C  CH1   0  -0.374  27.7837  -3.3162  12.1355
 DY1  O1   O  O     0  -0.439  24.2518  -3.6964  11.9575
 DY1  O    O  OH1   0  -0.589  25.3929  -2.7811  13.6400
 DY1  C6   C  CR5   0   0.002  29.5499  -4.3042  10.6413
 DY1  C    C  CR16  0  -0.526  31.5983  -5.6339   9.8786
 DY1  H1   H  HCR6  0   0.300  33.5274  -7.4506  11.9651
 DY1  H2   H  HCH3  0   0.257  28.8040  -4.6782  16.1107
 DY1  H3   H  HCH3  0   0.232  27.7058  -4.1937  14.8273
 DY1  H4   H  HCH3  0   0.269  28.3921  -5.8235  14.8450
 DY1  H5   H  HCR6  0   0.269  31.4449  -2.8560  12.6170
 DY1  H6   H  HCR6  0   0.272  31.9770  -0.4957  12.7276
 DY1  H7   H  HCR6  0   0.271  28.8637  -2.4417  16.0213
 DY1  H8   H  HCH2  0   0.281  26.4399  -4.8175  11.3170
 DY1  H9   H  HCH2  0   0.298  26.7481  -5.0097  13.0245
 DY1  H10  H  HCH2  0   0.245  28.4212  -1.5654  11.0679
 DY1  H11  H  HCH2  0   0.247  26.6861  -1.7682  11.0845
 DY1  H12  H  HCH2  0   0.247  27.5343  -2.2404   8.8326
 DY1  H13  H  HCH2  0   0.233  26.8894  -3.7110   9.5133
 DY1  H14  H  HCH2  0   0.245  28.9603  -4.4125   8.5853
 DY1  H15  H  HCH2  0   0.242  29.7824  -2.9399   9.0402
 DY1  H16  H  HCH3  0   0.328  32.7892  -8.9348  15.1319
 DY1  H17  H  HCH3  0   0.307  32.3810  -9.1737  13.4157
 DY1  H18  H  HCH3  0   0.302  33.8732  -8.2926  13.8840
 DY1  H19  H  HCH1  0   0.286  30.6781  -4.7996  14.6892
 DY1  H20  H  HCR6  0   0.275  29.3994  -0.0820  16.1421
 DY1  H21  H  HCH1  0   0.281  27.8779  -2.7496  13.0645
 DY1  H22  H  HOH1  0   0.483  24.5466  -2.3462  13.8244
 DY1  H23  H  HCR6  0   0.279  31.5112  -5.3981   8.8254
 DY1  C18  C  CH2   0  -0.556  26.5726  -4.2636  12.2451
 DY1  F3   F  F     0  -0.317  33.5323  -6.9013   9.4911
 DY1  C19  C  C     0   0.532  25.2818  -3.5628  12.5706

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
 DY1  C22  C21  single    1.530  0.020  1.530
 DY1  C22  C6   single    1.492  0.020  1.492
 DY1  C21  C20  single    1.526  0.020  1.526
 DY1  F3   C1   single    1.343  0.020  1.343
 DY1  C    C1   aromatic  1.371  0.020  1.371
 DY1  C    C5   aromatic  1.392  0.020  1.392
 DY1  C1   C2   aromatic  1.388  0.020  1.388
 DY1  C6   C5   aromatic  1.423  0.020  1.423
 DY1  C6   C7   aromatic  1.358  0.020  1.358
 DY1  C5   C4   aromatic  1.419  0.020  1.419
 DY1  C20  C17  single    1.536  0.020  1.536
 DY1  O1   C19  double    1.206  0.020  1.206
 DY1  C2   C3   aromatic  1.388  0.020  1.388
 DY1  C7   C17  single    1.494  0.020  1.494
 DY1  C7   N    aromatic  1.391  0.020  1.391
 DY1  C17  C18  single    1.542  0.020  1.542
 DY1  C18  C19  single    1.504  0.020  1.504
 DY1  C4   C3   aromatic  1.405  0.020  1.405
 DY1  C4   N    aromatic  1.382  0.020  1.382
 DY1  C19  O    single    1.329  0.020  1.329
 DY1  C3   S    single    1.783  0.020  1.783
 DY1  N    C8   single    1.468  0.020  1.468
 DY1  C11  C12  aromatic  1.385  0.020  1.385
 DY1  C11  C10  aromatic  1.393  0.020  1.393
 DY1  C12  C13  aromatic  1.389  0.020  1.389
 DY1  F2   C16  single    1.336  0.020  1.336
 DY1  C8   C10  single    1.521  0.020  1.521
 DY1  C8   C9   single    1.522  0.020  1.522
 DY1  S    C23  single    1.778  0.020  1.778
 DY1  S    O2   double    1.463  0.020  1.463
 DY1  S    O3   double    1.462  0.020  1.462
 DY1  C10  C15  aromatic  1.392  0.020  1.392
 DY1  C13  C16  single    1.495  0.020  1.495
 DY1  C13  C14  aromatic  1.389  0.020  1.389
 DY1  C16  F1   single    1.341  0.020  1.341
 DY1  C16  F    single    1.343  0.020  1.343
 DY1  C15  C14  aromatic  1.386  0.020  1.386
 DY1  C2   H1   single    0.930  0.020  1.080
 DY1  C9   H2   single    0.970  0.020  1.090
 DY1  C9   H3   single    0.970  0.020  1.090
 DY1  C9   H4   single    0.970  0.020  1.090
 DY1  C11  H5   single    0.930  0.020  1.080
 DY1  C12  H6   single    0.930  0.020  1.080
 DY1  C15  H7   single    0.930  0.020  1.080
 DY1  C18  H8   single    0.970  0.020  1.090
 DY1  C18  H9   single    0.970  0.020  1.090
 DY1  C20  H10  single    0.970  0.020  1.090
 DY1  C20  H11  single    0.970  0.020  1.090
 DY1  C21  H12  single    0.970  0.020  1.090
 DY1  C21  H13  single    0.970  0.020  1.090
 DY1  C22  H14  single    0.970  0.020  1.090
 DY1  C22  H15  single    0.970  0.020  1.090
 DY1  C23  H16  single    0.970  0.020  1.090
 DY1  C23  H17  single    0.970  0.020  1.090
 DY1  C23  H18  single    0.970  0.020  1.090
 DY1  C8   H19  single    0.970  0.020  1.090
 DY1  C14  H20  single    0.930  0.020  1.080
 DY1  C17  H21  single    0.970  0.020  1.090
 DY1  O    H22  single    0.850  0.020  0.980
 DY1  C    H23  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
 DY1  H1   C2   C1   117.98  3.000
 DY1  H1   C2   C3   121.62  3.000
 DY1  C1   C2   C3   120.38  3.000
 DY1  C4   C3   S    123.28  3.000
 DY1  S    C3   C2   117.45  3.000
 DY1  C4   C3   C2   119.06  3.000
 DY1  C    C5   C6   130.65  3.000
 DY1  C6   C5   C4   107.38  3.000
 DY1  C    C5   C4   121.96  3.000
 DY1  C6   C7   C17  123.71  3.000
 DY1  C17  C7   N    125.49  3.000
 DY1  C6   C7   N    110.77  3.000
 DY1  H4   C9   H3   108.75  3.000
 DY1  H4   C9   H2   107.60  3.000
 DY1  H3   C9   H2   107.58  3.000
 DY1  H4   C9   C8   109.69  3.000
 DY1  H3   C9   C8   112.94  3.000
 DY1  H2   C9   C8   110.12  3.000
 DY1  C8   C10  C15  121.51  3.000
 DY1  C15  C10  C11  118.35  3.000
 DY1  C8   C10  C11  120.09  3.000
 DY1  H5   C11  C12  118.34  3.000
 DY1  H5   C11  C10  120.56  3.000
 DY1  C12  C11  C10  121.11  3.000
 DY1  H6   C12  C13  121.15  3.000
 DY1  H6   C12  C11  118.93  3.000
 DY1  C13  C12  C11  119.92  3.000
 DY1  C16  C13  C14  118.98  3.000
 DY1  C14  C13  C12  119.60  3.000
 DY1  C16  C13  C12  121.41  3.000
 DY1  H7   C15  C14  118.40  3.000
 DY1  H7   C15  C10  120.69  3.000
 DY1  C14  C15  C10  120.91  3.000
 DY1  H11  C20  H10  106.04  3.000
 DY1  H11  C20  C17  110.08  3.000
 DY1  H10  C20  C17  108.32  3.000
 DY1  H11  C20  C21  110.09  3.000
 DY1  H10  C20  C21  109.65  3.000
 DY1  C17  C20  C21  112.45  3.000
 DY1  H13  C21  H12  105.98  3.000
 DY1  H13  C21  C22  109.82  3.000
 DY1  H12  C21  C22  109.51  3.000
 DY1  H13  C21  C20  109.86  3.000
 DY1  H12  C21  C20  109.62  3.000
 DY1  C22  C21  C20  111.89  3.000
 DY1  H15  C22  H14  105.92  3.000
 DY1  H15  C22  C6   108.79  3.000
 DY1  H14  C22  C6   110.92  3.000
 DY1  H15  C22  C21  109.68  3.000
 DY1  H14  C22  C21  110.13  3.000
 DY1  C6   C22  C21  111.24  3.000
 DY1  C    C1   F3   119.51  3.000
 DY1  C    C1   C2   122.54  3.000
 DY1  F3   C1   C2   117.93  3.000
 DY1  C23  S    O3   107.17  3.000
 DY1  O3   S    O2   118.22  3.000
 DY1  C23  S    O2   107.82  3.000
 DY1  O3   S    C3   107.39  3.000
 DY1  O2   S    C3   109.46  3.000
 DY1  C23  S    C3   106.15  3.000
 DY1  H18  C23  H17  111.40  3.000
 DY1  H18  C23  H16  109.15  3.000
 DY1  H17  C23  H16  109.74  3.000
 DY1  H18  C23  S    111.46  3.000
 DY1  H17  C23  S    110.41  3.000
 DY1  H16  C23  S    104.44  3.000
 DY1  N    C4   C5   107.62  3.000
 DY1  N    C4   C3   133.84  3.000
 DY1  C5   C4   C3   118.51  3.000
 DY1  C8   N    C4   125.02  3.000
 DY1  C8   N    C7   121.72  3.000
 DY1  C4   N    C7   107.54  3.000
 DY1  H19  C8   N    106.58  3.000
 DY1  H19  C8   C10  104.62  3.000
 DY1  N    C8   C10  110.49  3.000
 DY1  H19  C8   C9   106.73  3.000
 DY1  C10  C8   C9   114.71  3.000
 DY1  N    C8   C9   112.95  3.000
 DY1  H20  C14  C15  118.89  3.000
 DY1  H20  C14  C13  121.00  3.000
 DY1  C15  C14  C13  120.11  3.000
 DY1  F    C16  F1   106.33  3.000
 DY1  F    C16  F2   106.88  3.000
 DY1  F1   C16  F2   107.01  3.000
 DY1  F    C16  C13  111.58  3.000
 DY1  F1   C16  C13  111.85  3.000
 DY1  F2   C16  C13  112.79  3.000
 DY1  H21  C17  C20  107.98  3.000
 DY1  H21  C17  C18  109.03  3.000
 DY1  C20  C17  C18  112.01  3.000
 DY1  H21  C17  C7   110.56  3.000
 DY1  C18  C17  C7   109.67  3.000
 DY1  C20  C17  C7   107.58  3.000
 DY1  H22  O    C19  110.12  3.000
 DY1  C22  C6   C7   125.05  3.000
 DY1  C7   C6   C5   106.65  3.000
 DY1  C22  C6   C5   128.20  3.000
 DY1  H23  C    C1   121.23  3.000
 DY1  H23  C    C5   121.41  3.000
 DY1  C1   C    C5   117.35  3.000
 DY1  H9   C18  H8   106.26  3.000
 DY1  H9   C18  C19  107.54  3.000
 DY1  H8   C18  C19  108.47  3.000
 DY1  H9   C18  C17  110.12  3.000
 DY1  H8   C18  C17  110.35  3.000
 DY1  C19  C18  C17  113.78  3.000
 DY1  O    C19  O1   123.06  3.000
 DY1  O    C19  C18  112.10  3.000
 DY1  O1   C19  C18  124.83  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
 DY1  CONST_01  C5   C    C1   C2      0.00   0.0  0
 DY1  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 DY1  CONST_03  N    C4   C3   C2    180.00   0.0  0
 DY1  CONST_04  C    C1   C2   C3      0.00   0.0  0
 DY1  CONST_05  C    C5   C4   C3      0.00   0.0  0
 DY1  CONST_06  C6   C5   C4   C3    180.00   0.0  0
 DY1  CONST_07  C7   N    C4   C3    180.00   0.0  0
 DY1  CONST_08  N    C7   C6   C5      0.00   0.0  0
 DY1  CONST_09  C7   N    C4   C5      0.00   0.0  0
 DY1  CONST_10  C    C5   C6   C7    180.00   0.0  0
 DY1  CONST_11  C4   C5   C6   C7      0.00   0.0  0
 DY1  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 DY1  CONST_13  C13  C14  C15  C10     0.00   0.0  0
 DY1  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 DY1  CONST_15  C14  C15  C10  C11     0.00   0.0  0
 DY1  CONST_16  C15  C10  C11  C12     0.00   0.0  0
 DY1  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 DY1  CONST_18  C6   C5   C    C1    180.00   0.0  0
 DY1  CONST_19  C4   C5   C    C1      0.00   0.0  0
 DY1  CONST_20  C4   C3   C2   C1      0.00   0.0  0
 DY1  CONST_21  C6   C7   N    C4      0.00   0.0  0
 DY1  CONST_22  C    C5   C4   N     180.00   0.0  0
 DY1  CONST_23  C6   C5   C4   N       0.00   0.0  0
 DY1  CONST_24  F3   C1   C2   C3    180.00   0.0  0
 DY1  CONST_26  F3   C1   C    C5    180.00   0.0  0
 DY1  CONST_27  S    C3   C4   C5    180.00   0.0  0
 DY1  CONST_29  C16  C13  C12  C11   180.00   0.0  0
 DY1  CONST_30  C8   C10  C11  C12   180.00   0.0  0
 DY1  CONST_31  C16  C13  C14  C15   180.00   0.0  0
 DY1  CONST_32  S    C3   C2   C1    180.00   0.0  0
 DY1  CONST_33  N    C4   C3   S       0.00   0.0  0
 DY1  CONST_36  C14  C15  C10  C8    180.00   0.0  0
 DY1  CONST_37  H23  C    C1   C2    180.00   0.0  0
 DY1  CONST_38  H6   C12  C11  C10   180.00   0.0  0
 DY1  CONST_39  H20  C14  C15  C10   180.00   0.0  0
 DY1  CONST_40  H7   C15  C10  C11   180.00   0.0  0
 DY1  CONST_41  H5   C11  C12  C13   180.00   0.0  0
 DY1  CONST_42  H1   C2   C3   C4    180.00   0.0  0
 DY1  CONST_43  H22  O    C19  C18   180.00   0.0  0
 DY1  Var_01    C21  C22  C6   C5    173.25  30.0  1
 DY1  Var_02    C6   C22  C21  C20    37.29  30.0  1
 DY1  Var_03    C17  C20  C21  C22   -61.11  30.0  1
 DY1  Var_04    C23  S    C3   C2    -18.20  30.0  2
 DY1  Var_05    F2   C16  C13  C12    11.99  30.0  2
 DY1  Var_06    O1   C19  C18  C17   128.99  30.0  3
 DY1  Var_07    H16  C23  S    C3   -174.53  30.0  3

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
 DY1  chir_01  C8   N    C10  C9   negativ
 DY1  chir_02  C17  C20  C7   C18  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
 DY1  plan-1  C10  0.020
 DY1  plan-1  C11  0.020
 DY1  plan-1  C12  0.020
 DY1  plan-1  C13  0.020
 DY1  plan-1  C15  0.020
 DY1  plan-1  C8   0.020
 DY1  plan-1  C14  0.020
 DY1  plan-1  C16  0.020
 DY1  plan-1  H5   0.020
 DY1  plan-1  H6   0.020
 DY1  plan-1  H7   0.020
 DY1  plan-1  H20  0.020
 DY1  plan-2  C2   0.020
 DY1  plan-2  C3   0.020
 DY1  plan-2  C5   0.020
 DY1  plan-2  C7   0.020
 DY1  plan-2  C22  0.020
 DY1  plan-2  C1   0.020
 DY1  plan-2  S    0.020
 DY1  plan-2  C4   0.020
 DY1  plan-2  N    0.020
 DY1  plan-2  C8   0.020
 DY1  plan-2  C17  0.020
 DY1  plan-2  C6   0.020
 DY1  plan-2  C    0.020
 DY1  plan-2  H1   0.020
 DY1  plan-2  H23  0.020
 DY1  plan-2  F3   0.020
 DY1  plan-3  O1   0.020
 DY1  plan-3  O    0.020
 DY1  plan-3  H22  0.020
 DY1  plan-3  C18  0.020
 DY1  plan-3  C19  0.020

