# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 08:51:31 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: (11alpha,16beta)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@]4(C)[C@@]3(F)[C@@H](O)C[C@]2(C)[C@@]1(O)C(=O)CO[P](O)(O)=O
#
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
 3T5  3T5  '(11alpha,16beta)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate'  ligand  62  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3T5
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
 3T5  F     F  F     0  -0.382  38.0020  -11.3928  16.0892
 3T5  P     P  P     0   1.443  43.0258  -17.6991  13.0961
 3T5  C1    C  CH3   0  -0.682  38.0536  -15.9924  16.3169
 3T5  O1    O  OH1   0  -0.657  39.0068  -14.0341  18.2967
 3T5  C2    C  CT    0  -0.087  38.3385  -14.8101  15.3791
 3T5  C3    C  CH2   0  -0.435  39.4495  -13.9187  15.9300
 3T5  O3    O  OH1   0  -0.671  39.0943  -14.3004  13.1560
 3T5  C4    C  CH1   0  -0.030  39.0404  -13.1542  17.1962
 3T5  C5    C  CT    0   0.434  37.6991  -12.4014  17.0229
 3T5  O5    O  O2    0  -0.576  41.7366  -17.3388  13.9599
 3T5  O6    O  O     0  -0.706  42.8495  -17.8478  11.6378
 3T5  C7    C  CT    0  -0.292  37.2104  -11.6106  18.2850
 3T5  O7    O  OH1   0  -0.740  44.0437  -16.5448  13.5324
 3T5  C8    C  CH3   0  -0.651  36.7399  -12.4963  19.4640
 3T5  O8    O  OH1   0  -0.727  43.4441  -19.0057  13.9051
 3T5  C9    C  C1    0  -0.118  38.3244  -10.7567  18.8065
 3T5  C10   C  C1    0  -0.379  38.2875   -9.4281  18.8870
 3T5  C11   C  C     0   0.398  37.1213   -8.6684  18.4264
 3T5  C12   C  C1    0  -0.470  36.0034   -9.4528  17.9115
 3T5  C13   C  C     0   0.260  36.0282  -10.7889  17.8305
 3T5  C14   C  CH2   0  -0.510  34.8849  -11.5619  17.2616
 3T5  C15   C  CH2   0  -0.419  35.3502  -12.4105  16.0804
 3T5  C16   C  CH1   0  -0.305  36.5806  -13.2553  16.4049
 3T5  C17   C  CH1   0  -0.191  37.1011  -13.9341  15.1435
 3T5  C18   C  CH2   0  -0.439  36.1565  -14.8356  14.3542
 3T5  C19   C  CH1   0  -0.232  37.0942  -15.7192  13.4928
 3T5  C20   C  CH3   0  -0.719  36.8433  -15.5873  11.9962
 3T5  C21   C  CT    0   0.136  38.5425  -15.3464  13.9226
 3T5  C22   C  C     0   0.353  39.5030  -16.5307  13.8651
 3T5  C23   C  CH2   0  -0.258  40.9680  -16.1879  13.6590
 3T5  H1    H  HCH3  0   0.254  37.5837  -15.6727  17.2419
 3T5  H1A   H  HCH3  0   0.241  37.3984  -16.7378  15.8705
 3T5  H1B   H  HCH3  0   0.233  38.9795  -16.4978  16.5967
 3T5  HO1   H  HOH1  0   0.460  39.4456  -13.6217  19.0452
 3T5  H3    H  HCH2  0   0.241  40.3480  -14.4885  16.1853
 3T5  H3A   H  HCH2  0   0.253  39.7425  -13.1859  15.1775
 3T5  HO3   H  HOH1  0   0.464  38.9276  -14.4586  12.2204
 3T5  H4    H  HCH1  0   0.256  39.8117  -12.3904  17.3497
 3T5  HO7   H  HOH1  0   0.500  44.7133  -16.3381  12.8672
 3T5  H8    H  HCH3  0   0.251  36.1454  -11.8895  20.1471
 3T5  H8A   H  HCH3  0   0.252  36.1304  -13.3388  19.1455
 3T5  H8B   H  HCH3  0   0.248  37.5743  -12.8946  20.0333
 3T5  HO8   H  HOH1  0   0.505  43.9778  -19.6284  13.3942
 3T5  H9    H  H     0   0.277  39.1980  -11.2743  19.1871
 3T5  H10   H  H     0   0.267  39.1202   -8.8738  19.3031
 3T5  H12   H  H     0   0.254  35.1287   -8.9046  17.5777
 3T5  H14   H  HCH2  0   0.258  34.4564  -12.2114  18.0312
 3T5  H14A  H  HCH2  0   0.264  34.0901  -10.8834  16.9496
 3T5  H15   H  HCH2  0   0.255  34.5357  -13.0658  15.7673
 3T5  H15A  H  HCH2  0   0.234  35.5658  -11.7550  15.2322
 3T5  H16   H  HCH1  0   0.250  36.2915  -14.0158  17.1366
 3T5  H17   H  HCH1  0   0.244  37.4054  -13.1296  14.4664
 3T5  H18   H  HCH2  0   0.234  35.5453  -15.4521  15.0177
 3T5  H18A  H  HCH2  0   0.243  35.4667  -14.2621  13.7326
 3T5  H19   H  HCH1  0   0.255  36.9361  -16.7655  13.7540
 3T5  H20   H  HCH3  0   0.238  37.5551  -16.1662  11.4023
 3T5  H20A  H  HCH3  0   0.256  35.8498  -15.9651  11.7550
 3T5  H20B  H  HCH3  0   0.229  36.8723  -14.5489  11.6585
 3T5  H23   H  HCH2  0   0.283  41.2756  -15.3564  14.2966
 3T5  H23A  H  HCH2  0   0.275  41.1052  -15.8592  12.6234
 3T5  O2    O  O     0  -0.449  37.0897   -7.4467  18.4781
 3T5  O4    O  O     0  -0.370  39.1547  -17.6790  13.9689

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
 3T5  F    C5    single  1.407  0.020  1.407
 3T5  O6   P     double  1.476  0.020  1.476
 3T5  P    O7    single  1.600  0.020  1.600
 3T5  P    O8    single  1.593  0.020  1.593
 3T5  P    O5    single  1.593  0.020  1.593
 3T5  C2   C1    single  1.536  0.020  1.536
 3T5  C1   H1    single  0.970  0.020  1.090
 3T5  C1   H1A   single  0.970  0.020  1.090
 3T5  C1   H1B   single  0.970  0.020  1.090
 3T5  C4   O1    single  1.409  0.020  1.409
 3T5  O1   HO1   single  0.850  0.020  0.980
 3T5  C21  C2    single  1.565  0.020  1.565
 3T5  C17  C2    single  1.534  0.020  1.534
 3T5  C2   C3    single  1.527  0.020  1.527
 3T5  C11  O2    double  1.223  0.020  1.223
 3T5  C3   C4    single  1.535  0.020  1.535
 3T5  C3   H3    single  0.970  0.020  1.090
 3T5  C3   H3A   single  0.970  0.020  1.090
 3T5  O3   C21   single  1.409  0.020  1.409
 3T5  O3   HO3   single  0.850  0.020  0.980
 3T5  C5   C4    single  1.548  0.020  1.548
 3T5  C4   H4    single  0.970  0.020  1.090
 3T5  C22  O4    double  1.204  0.020  1.204
 3T5  C16  C5    single  1.537  0.020  1.537
 3T5  C5   C7    single  1.568  0.020  1.568
 3T5  C23  O5    single  1.416  0.020  1.416
 3T5  C13  C7    single  1.510  0.020  1.510
 3T5  C7   C9    single  1.497  0.020  1.497
 3T5  C7   C8    single  1.548  0.020  1.548
 3T5  O7   HO7   single  0.850  0.020  0.980
 3T5  C8   H8    single  0.970  0.020  1.090
 3T5  C8   H8A   single  0.970  0.020  1.090
 3T5  C8   H8B   single  0.970  0.020  1.090
 3T5  O8   HO8   single  0.850  0.020  0.980
 3T5  C9   C10   double  1.332  0.020  1.332
 3T5  C9   H9    single  0.930  0.020  1.080
 3T5  C11  C10   single  1.466  0.020  1.466
 3T5  C10  H10   single  0.930  0.020  1.080
 3T5  C12  C11   single  1.459  0.020  1.459
 3T5  C13  C12   double  1.339  0.020  1.339
 3T5  C12  H12   single  0.930  0.020  1.080
 3T5  C14  C13   single  1.493  0.020  1.493
 3T5  C15  C14   single  1.527  0.020  1.527
 3T5  C14  H14   single  0.970  0.020  1.090
 3T5  C14  H14A  single  0.970  0.020  1.090
 3T5  C15  C16   single  1.527  0.020  1.527
 3T5  C15  H15   single  0.970  0.020  1.090
 3T5  C15  H15A  single  0.970  0.020  1.090
 3T5  C17  C16   single  1.524  0.020  1.524
 3T5  C16  H16   single  0.970  0.020  1.090
 3T5  C18  C17   single  1.526  0.020  1.526
 3T5  C17  H17   single  0.970  0.020  1.090
 3T5  C19  C18   single  1.550  0.020  1.550
 3T5  C18  H18   single  0.970  0.020  1.090
 3T5  C18  H18A  single  0.970  0.020  1.090
 3T5  C20  C19   single  1.523  0.020  1.523
 3T5  C19  C21   single  1.556  0.020  1.556
 3T5  C19  H19   single  0.970  0.020  1.090
 3T5  C20  H20   single  0.970  0.020  1.090
 3T5  C20  H20A  single  0.970  0.020  1.090
 3T5  C20  H20B  single  0.970  0.020  1.090
 3T5  C22  C21   single  1.526  0.020  1.526
 3T5  C23  C22   single  1.519  0.020  1.519
 3T5  C23  H23   single  0.970  0.020  1.090
 3T5  C23  H23A  single  0.970  0.020  1.090

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
 3T5  O8    P    O7    106.64  3.000
 3T5  O8    P    O6    116.77  3.000
 3T5  O7    P    O6    114.72  3.000
 3T5  O8    P    O5     97.05  3.000
 3T5  O7    P    O5    101.76  3.000
 3T5  O6    P    O5    117.49  3.000
 3T5  H1B   C1   H1A   107.38  3.000
 3T5  H1B   C1   H1    106.57  3.000
 3T5  H1A   C1   H1    106.90  3.000
 3T5  H1B   C1   C2    110.83  3.000
 3T5  H1A   C1   C2    112.86  3.000
 3T5  H1    C1   C2    111.96  3.000
 3T5  HO1   O1   C4    109.24  3.000
 3T5  C21   C2   C17    99.08  3.000
 3T5  C17   C2   C3    107.99  3.000
 3T5  C21   C2   C3    116.15  3.000
 3T5  C3    C2   C1    111.35  3.000
 3T5  C17   C2   C1    112.57  3.000
 3T5  C21   C2   C1    109.18  3.000
 3T5  H3A   C3   H3    106.88  3.000
 3T5  H3A   C3   C4    107.83  3.000
 3T5  H3    C3   C4    106.61  3.000
 3T5  H3A   C3   C2    109.80  3.000
 3T5  H3    C3   C2    112.19  3.000
 3T5  C4    C3   C2    113.23  3.000
 3T5  HO3   O3   C21   109.80  3.000
 3T5  H4    C4   C5    106.65  3.000
 3T5  H4    C4   C3    105.97  3.000
 3T5  C5    C4   C3    112.39  3.000
 3T5  H4    C4   O1    110.02  3.000
 3T5  C5    C4   O1    111.74  3.000
 3T5  C3    C4   O1    109.85  3.000
 3T5  C16   C5   C7    112.15  3.000
 3T5  C7    C5   C4    115.17  3.000
 3T5  C16   C5   C4    113.92  3.000
 3T5  C7    C5   F     103.87  3.000
 3T5  C16   C5   F     106.74  3.000
 3T5  C4    C5   F     103.67  3.000
 3T5  C23   O5   P     120.52  3.000
 3T5  C13   C7   C9    112.15  3.000
 3T5  C9    C7   C8    106.69  3.000
 3T5  C13   C7   C8    107.62  3.000
 3T5  C8    C7   C5    114.80  3.000
 3T5  C9    C7   C5    109.64  3.000
 3T5  C13   C7   C5    106.04  3.000
 3T5  HO7   O7   P     114.05  3.000
 3T5  H8B   C8   H8A   107.46  3.000
 3T5  H8B   C8   H8    107.14  3.000
 3T5  H8A   C8   H8    108.01  3.000
 3T5  H8B   C8   C7    112.06  3.000
 3T5  H8A   C8   C7    112.99  3.000
 3T5  H8    C8   C7    108.94  3.000
 3T5  HO8   O8   P     113.90  3.000
 3T5  H9    C9   C10   118.51  3.000
 3T5  H9    C9   C7    116.71  3.000
 3T5  C10   C9   C7    124.71  3.000
 3T5  H10   C10  C11   117.83  3.000
 3T5  H10   C10  C9    120.83  3.000
 3T5  C11   C10  C9    121.34  3.000
 3T5  C12   C11  C10   116.21  3.000
 3T5  C12   C11  O2    122.13  3.000
 3T5  C10   C11  O2    121.66  3.000
 3T5  H12   C12  C13   120.04  3.000
 3T5  H12   C12  C11   117.03  3.000
 3T5  C13   C12  C11   122.93  3.000
 3T5  C14   C13  C12   121.72  3.000
 3T5  C14   C13  C7    115.63  3.000
 3T5  C12   C13  C7    122.65  3.000
 3T5  H14A  C14  H14   106.55  3.000
 3T5  H14A  C14  C15   110.27  3.000
 3T5  H14   C14  C15   109.48  3.000
 3T5  H14A  C14  C13   110.18  3.000
 3T5  H14   C14  C13   109.83  3.000
 3T5  C15   C14  C13   110.44  3.000
 3T5  H15A  C15  H15   106.53  3.000
 3T5  H15A  C15  C16   109.73  3.000
 3T5  H15   C15  C16   109.28  3.000
 3T5  H15A  C15  C14   109.08  3.000
 3T5  H15   C15  C14   109.16  3.000
 3T5  C16   C15  C14   112.86  3.000
 3T5  H16   C16  C17   109.52  3.000
 3T5  H16   C16  C15   108.28  3.000
 3T5  C17   C16  C15   110.22  3.000
 3T5  H16   C16  C5    108.03  3.000
 3T5  C17   C16  C5    109.37  3.000
 3T5  C15   C16  C5    111.37  3.000
 3T5  H17   C17  C18   106.64  3.000
 3T5  H17   C17  C16   106.24  3.000
 3T5  C18   C17  C16   118.68  3.000
 3T5  H17   C17  C2    106.88  3.000
 3T5  C18   C17  C2    103.96  3.000
 3T5  C16   C17  C2    113.74  3.000
 3T5  H18A  C18  H18   106.78  3.000
 3T5  H18A  C18  C19   111.43  3.000
 3T5  H18   C18  C19   110.75  3.000
 3T5  H18A  C18  C17   112.05  3.000
 3T5  H18   C18  C17   111.44  3.000
 3T5  C19   C18  C17   104.47  3.000
 3T5  H19   C19  C21   107.38  3.000
 3T5  H19   C19  C20   107.14  3.000
 3T5  C21   C19  C20   113.83  3.000
 3T5  H19   C19  C18   109.04  3.000
 3T5  C21   C19  C18   105.85  3.000
 3T5  C20   C19  C18   113.40  3.000
 3T5  H20B  C20  H20A  106.58  3.000
 3T5  H20B  C20  H20   108.55  3.000
 3T5  H20A  C20  H20   106.84  3.000
 3T5  H20B  C20  C19   112.44  3.000
 3T5  H20A  C20  C19   109.73  3.000
 3T5  H20   C20  C19   112.39  3.000
 3T5  C22   C21  C19   112.93  3.000
 3T5  C22   C21  O3    108.01  3.000
 3T5  C19   C21  O3    113.07  3.000
 3T5  C22   C21  C2    112.52  3.000
 3T5  C19   C21  C2    102.58  3.000
 3T5  O3    C21  C2    107.63  3.000
 3T5  C23   C22  C21   115.92  3.000
 3T5  C23   C22  O4    120.39  3.000
 3T5  C21   C22  O4    123.69  3.000
 3T5  H23A  C23  H23   106.76  3.000
 3T5  H23A  C23  C22   108.48  3.000
 3T5  H23   C23  C22   111.37  3.000
 3T5  H23A  C23  O5    112.13  3.000
 3T5  H23   C23  O5    109.99  3.000
 3T5  C22   C23  O5    108.13  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
 3T5  Var_01  C11  C12  C13  C7     0.95   0.0  0
 3T5  Var_02  C15  C14  C13  C7   -57.07  30.0  1
 3T5  Var_03  C11  C10  C9   C7    -1.43  30.0  1
 3T5  Var_04  C12  C11  C10  C9     1.48  30.0  1
 3T5  Var_05  C13  C12  C11  C10   -1.26  30.0  1
 3T5  Var_06  C16  C15  C14  C13   50.67  30.0  1
 3T5  Var_07  C21  C22  C23  O5   165.70  30.0  3
 3T5  Var_08  C22  C23  O5   P    142.00  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
 3T5  chir_01  C2   C21  C17  C3   positiv
 3T5  chir_02  C4   O1   C5   C3   positiv
 3T5  chir_03  C5   C4   C16  C7   negativ
 3T5  chir_04  C7   C13  C9   C5   positiv
 3T5  chir_05  C16  C17  C15  C5   positiv
 3T5  chir_06  C17  C2   C16  C18  positiv
 3T5  chir_07  C19  C18  C20  C21  negativ
 3T5  chir_08  C21  C22  C19  C2   negativ

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
 3T5  plan-1  C10  0.020
 3T5  plan-1  C11  0.020
 3T5  plan-1  C12  0.020
 3T5  plan-1  O2   0.020
 3T5  plan-2  C21  0.020
 3T5  plan-2  C22  0.020
 3T5  plan-2  C23  0.020
 3T5  plan-2  O4   0.020
 3T5  plan-3  C7   0.020
 3T5  plan-3  C11  0.020
 3T5  plan-3  C12  0.020
 3T5  plan-3  C13  0.020
 3T5  plan-3  C14  0.020
 3T5  plan-3  H12  0.020

