# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 22:49:00 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (1~{R},3~{R})-2-[(~{S})-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl)ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc([C@@H](O)C2[C@H](O)CCC[C@H]2O)c(Cl)c1OCCC3OCCO3
#
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
 9P5  9P5  "(1R,3R)-2-[(S)-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl)ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol"
  ligand  56  29  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9P5
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
 9P5  C22  C   CH2   0  -0.240  -6.6627  -2.1721  84.0206
 9P5  C10  C   CR6   0  -0.224   0.2976  -3.1260  82.5168
 9P5  C11  C   CH1   0  -0.018   2.6972  -3.2912  81.6285
 9P5  C21  C   CH2   0  -0.195  -7.1663  -3.4961  83.4324
 9P5  C12  C   CH1   0  -0.348   3.8176  -4.0754  82.3262
 9P5  C13  C   CH1   0   0.077   5.0451  -4.2508  81.3841
 9P5  C14  C   CH2   0  -0.478   5.9102  -5.4414  81.8000
 9P5  C15  C   CH2   0  -0.459   5.8662  -5.6557  83.3044
 9P5  C16  C   CH2   0  -0.464   4.4483  -6.0383  83.7442
 9P5  C17  C   CH1   0   0.092   3.3666  -5.4425  82.8305
 9P5  C1   C   CR15  0   0.330  -4.9202  -3.2270  83.1230
 9P5  C2   C   CH2   0  -0.528  -3.9404  -3.2225  81.9703
 9P5  C3   C   CH2   0  -0.197  -2.7175  -2.3629  82.1927
 9P5  C5   C   CR6   0   0.530  -0.6623  -2.5488  83.3517
 9P5  C6   C   CR6   0  -0.351  -0.2404  -1.6322  84.3108
 9P5  C7   C   CR16  0  -0.222   1.0966  -1.2739  84.4074
 9P5  C8   C   CR16  0  -0.320   2.0119  -1.8162  83.5280
 9P5  C9   C   CR6   0   0.238   1.6399  -2.7672  82.5814
 9P5  O4   O   O2    0  -0.483  -1.9544  -2.9189  83.2790
 9P5  O18  O   OH1   0  -0.663   2.1362  -5.3221  83.5090
 9P5  O19  O   OH1   0  -0.659   3.3057  -2.1846  80.9835
 9P5  O20  O   O     0  -0.505  -6.0169  -4.0566  82.8192
 9P5  O23  O   O     0  -0.490  -5.4551  -1.9519  83.3233
 9P5  O25  O   OH1   0  -0.671   4.6860  -4.4537  80.0339
 9P5  S24  S   S     0   1.225  -1.3950  -0.9111  85.4608
 9P5  H1   H   HCH2  0   0.252  -7.3367  -1.3345  83.8451
 9P5  H2   H   HCH2  0   0.224  -6.4865  -2.2590  85.0992
 9P5  H3   H   HCH1  0   0.236   2.2260  -3.9478  80.8905
 9P5  H4   H   HCH2  0   0.229  -7.9401  -3.3458  82.6760
 9P5  H5   H   HCH2  0   0.223  -7.5650  -4.1567  84.2065
 9P5  H6   H   HCH1  0   0.251   4.1618  -3.4894  83.1883
 9P5  H7   H   HCH1  0   0.212   5.6520  -3.3428  81.4805
 9P5  H8   H   HCH2  0   0.225   5.5473  -6.3434  81.2965
 9P5  H9   H   HCH2  0   0.240   6.9338  -5.2851  81.4537
 9P5  H10  H   HCH2  0   0.239   6.5773  -6.4278  83.6015
 9P5  H11  H   HCH2  0   0.225   6.1848  -4.7402  83.8105
 9P5  H12  H   HCH2  0   0.227   4.2669  -5.6847  84.7622
 9P5  H13  H   HCH2  0   0.228   4.3397  -7.1262  83.7629
 9P5  H14  H   HCH1  0   0.200   3.2387  -6.0941  81.9534
 9P5  H15  H   HCR5  0   0.198  -4.4390  -3.5836  84.0504
 9P5  H16  H   HCH2  0   0.251  -4.4512  -2.8536  81.0769
 9P5  H17  H   HCH2  0   0.254  -3.6280  -4.2481  81.7608
 9P5  H18  H   HCH2  0   0.247  -2.1202  -2.3465  81.2789
 9P5  H19  H   HCH2  0   0.249  -2.9830  -1.3333  82.4364
 9P5  H20  H   HCR6  0   0.288   1.4222  -0.5673  85.1572
 9P5  H21  H   HCR6  0   0.271   3.0469  -1.5084  83.5944
 9P5  H22  H   HCH3  0   0.296  -1.1267  -2.7823  86.8875
 9P5  H23  H   HCH3  0   0.309  -2.6361  -1.8810  87.1905
 9P5  H24  H   HCH3  0   0.301  -2.5261  -2.9817  85.7920
 9P5  H25  H   HOH1  0   0.447   1.8062  -6.2078  83.6902
 9P5  H26  H   HOH1  0   0.459   2.6359  -1.7172  80.4722
 9P5  H27  H   HOH1  0   0.446   4.3391  -3.6168  79.7048
 9P5  CL   CL  CL    0  -0.089  -0.2451  -4.3558  81.4311
 9P5  C29  C   CH3   0  -0.797  -1.9775  -2.2886  86.4235
 9P5  O26  O   OS    0  -0.661  -0.6179  -0.0431  86.3432
 9P5  O27  O   OS    0  -0.656  -2.5189  -0.3190  84.7424

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
 9P5  O25  C13  single    1.412  0.020  1.412
 9P5  O19  C11  single    1.418  0.020  1.418
 9P5  CL   C10  single    1.728  0.020  1.728
 9P5  C13  C14  single    1.529  0.020  1.529
 9P5  C13  C12  single    1.557  0.020  1.557
 9P5  C2   C3   single    1.511  0.020  1.511
 9P5  C2   C1   single    1.513  0.020  1.513
 9P5  C11  C12  single    1.535  0.020  1.535
 9P5  C11  C9   single    1.517  0.020  1.517
 9P5  C14  C15  single    1.520  0.020  1.520
 9P5  C3   O4   single    1.439  0.020  1.439
 9P5  C12  C17  single    1.525  0.020  1.525
 9P5  O20  C1   single    1.408  0.020  1.408
 9P5  O20  C21  single    1.418  0.020  1.418
 9P5  C10  C9   aromatic  1.391  0.020  1.391
 9P5  C10  C5   aromatic  1.397  0.020  1.397
 9P5  C9   C8   aromatic  1.392  0.020  1.392
 9P5  C1   O23  single    1.397  0.020  1.397
 9P5  C17  C16  single    1.536  0.020  1.536
 9P5  C17  O18  single    1.410  0.020  1.410
 9P5  C15  C16  single    1.533  0.020  1.533
 9P5  O4   C5   single    1.346  0.020  1.346
 9P5  C5   C6   aromatic  1.392  0.020  1.392
 9P5  C21  C22  single    1.534  0.020  1.534
 9P5  C8   C7   aromatic  1.380  0.020  1.380
 9P5  O23  C22  single    1.412  0.020  1.412
 9P5  O27  S24  double    1.459  0.020  1.459
 9P5  C6   C7   aromatic  1.388  0.020  1.388
 9P5  C6   S24  single    1.782  0.020  1.782
 9P5  S24  O26  double    1.461  0.020  1.461
 9P5  S24  C29  single    1.779  0.020  1.779
 9P5  C22  H1   single    0.970  0.020  1.090
 9P5  C22  H2   single    0.970  0.020  1.090
 9P5  C11  H3   single    0.970  0.020  1.090
 9P5  C21  H4   single    0.970  0.020  1.090
 9P5  C21  H5   single    0.970  0.020  1.090
 9P5  C12  H6   single    0.970  0.020  1.090
 9P5  C13  H7   single    0.970  0.020  1.090
 9P5  C14  H8   single    0.970  0.020  1.090
 9P5  C14  H9   single    0.970  0.020  1.090
 9P5  C15  H10  single    0.970  0.020  1.090
 9P5  C15  H11  single    0.970  0.020  1.090
 9P5  C16  H12  single    0.970  0.020  1.090
 9P5  C16  H13  single    0.970  0.020  1.090
 9P5  C17  H14  single    0.970  0.020  1.090
 9P5  C1   H15  single    0.970  0.020  1.090
 9P5  C2   H16  single    0.970  0.020  1.090
 9P5  C2   H17  single    0.970  0.020  1.090
 9P5  C3   H18  single    0.970  0.020  1.090
 9P5  C3   H19  single    0.970  0.020  1.090
 9P5  C7   H20  single    0.930  0.020  1.080
 9P5  C8   H21  single    0.930  0.020  1.080
 9P5  C29  H22  single    0.970  0.020  1.090
 9P5  C29  H23  single    0.970  0.020  1.090
 9P5  C29  H24  single    0.970  0.020  1.090
 9P5  O18  H25  single    0.850  0.020  0.980
 9P5  O19  H26  single    0.850  0.020  0.980
 9P5  O25  H27  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
 9P5  H2   C22  H1   108.59  3.000
 9P5  H2   C22  O23  111.15  3.000
 9P5  H1   C22  O23  109.25  3.000
 9P5  H2   C22  C21  111.20  3.000
 9P5  H1   C22  C21  113.51  3.000
 9P5  O23  C22  C21  103.07  3.000
 9P5  CL   C10  C9   121.06  3.000
 9P5  C9   C10  C5   121.92  3.000
 9P5  CL   C10  C5   116.99  3.000
 9P5  H3   C11  O19  110.25  3.000
 9P5  H3   C11  C9   109.32  3.000
 9P5  O19  C11  C9   108.38  3.000
 9P5  H3   C11  C12  108.31  3.000
 9P5  C9   C11  C12  113.56  3.000
 9P5  O19  C11  C12  106.98  3.000
 9P5  H5   C21  H4   108.37  3.000
 9P5  H5   C21  O20  111.29  3.000
 9P5  H4   C21  O20  109.20  3.000
 9P5  H5   C21  C22  111.71  3.000
 9P5  H4   C21  C22  112.30  3.000
 9P5  O20  C21  C22  103.94  3.000
 9P5  H6   C12  C17  108.15  3.000
 9P5  H6   C12  C13  106.74  3.000
 9P5  C17  C12  C13  109.40  3.000
 9P5  H6   C12  C11  108.24  3.000
 9P5  C17  C12  C11  113.09  3.000
 9P5  C13  C12  C11  110.97  3.000
 9P5  H7   C13  O25  110.11  3.000
 9P5  H7   C13  C14  107.92  3.000
 9P5  O25  C13  C14  106.98  3.000
 9P5  H7   C13  C12  106.85  3.000
 9P5  C14  C13  C12  111.66  3.000
 9P5  O25  C13  C12  113.22  3.000
 9P5  H9   C14  H8   106.42  3.000
 9P5  H9   C14  C15  111.17  3.000
 9P5  H8   C14  C15  109.23  3.000
 9P5  H9   C14  C13  109.43  3.000
 9P5  H8   C14  C13  109.20  3.000
 9P5  C15  C14  C13  111.25  3.000
 9P5  H11  C15  H10  106.06  3.000
 9P5  H11  C15  C16  110.22  3.000
 9P5  H10  C15  C16  110.37  3.000
 9P5  H11  C15  C14  109.36  3.000
 9P5  H10  C15  C14  110.52  3.000
 9P5  C16  C15  C14  110.23  3.000
 9P5  H13  C16  H12  106.83  3.000
 9P5  H13  C16  C17  109.03  3.000
 9P5  H12  C16  C17  108.16  3.000
 9P5  H13  C16  C15  110.19  3.000
 9P5  H12  C16  C15  109.88  3.000
 9P5  C17  C16  C15  112.57  3.000
 9P5  H14  C17  O18  109.44  3.000
 9P5  H14  C17  C16  109.05  3.000
 9P5  O18  C17  C16  111.18  3.000
 9P5  H14  C17  C12  107.56  3.000
 9P5  O18  C17  C12  109.91  3.000
 9P5  C16  C17  C12  109.63  3.000
 9P5  H15  C1   O23  109.96  3.000
 9P5  H15  C1   O20  109.29  3.000
 9P5  O23  C1   O20  105.69  3.000
 9P5  H15  C1   C2   111.02  3.000
 9P5  O23  C1   C2   110.76  3.000
 9P5  O20  C1   C2   109.98  3.000
 9P5  H17  C2   H16  107.08  3.000
 9P5  H17  C2   C3   109.32  3.000
 9P5  H16  C2   C3   107.84  3.000
 9P5  H17  C2   C1   109.18  3.000
 9P5  H16  C2   C1   108.73  3.000
 9P5  C3   C2   C1   114.43  3.000
 9P5  H19  C3   H18  107.81  3.000
 9P5  H19  C3   O4   108.97  3.000
 9P5  H18  C3   O4   110.32  3.000
 9P5  H19  C3   C2   111.89  3.000
 9P5  H18  C3   C2   109.16  3.000
 9P5  O4   C3   C2   108.68  3.000
 9P5  O4   C5   C6   120.61  3.000
 9P5  C6   C5   C10  118.39  3.000
 9P5  O4   C5   C10  120.91  3.000
 9P5  S24  C6   C7   118.35  3.000
 9P5  S24  C6   C5   120.98  3.000
 9P5  C7   C6   C5   120.67  3.000
 9P5  H20  C7   C8   119.95  3.000
 9P5  H20  C7   C6   120.50  3.000
 9P5  C8   C7   C6   119.55  3.000
 9P5  H21  C8   C9   119.45  3.000
 9P5  H21  C8   C7   118.91  3.000
 9P5  C9   C8   C7   121.62  3.000
 9P5  C8   C9   C11  118.48  3.000
 9P5  C8   C9   C10  117.75  3.000
 9P5  C11  C9   C10  123.67  3.000
 9P5  C5   O4   C3   116.33  3.000
 9P5  H25  O18  C17  108.14  3.000
 9P5  H26  O19  C11  108.76  3.000
 9P5  C1   O20  C21  107.76  3.000
 9P5  C1   O23  C22  104.83  3.000
 9P5  H27  O25  C13  107.05  3.000
 9P5  O27  S24  O26  117.75  3.000
 9P5  O26  S24  C29  107.90  3.000
 9P5  O27  S24  C29  109.17  3.000
 9P5  C29  S24  C6   104.37  3.000
 9P5  O26  S24  C6   106.59  3.000
 9P5  O27  S24  C6   110.21  3.000
 9P5  H24  C29  H23  110.03  3.000
 9P5  H24  C29  H22  110.70  3.000
 9P5  H23  C29  H22  110.02  3.000
 9P5  H24  C29  S24  110.17  3.000
 9P5  H23  C29  S24  106.80  3.000
 9P5  H22  C29  S24  109.04  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
 9P5  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 9P5  CONST_02  C7   C6   C5   C10     0.00   0.0  0
 9P5  CONST_03  C8   C9   C10  C5      0.00   0.0  0
 9P5  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 9P5  CONST_05  C9   C10  C5   C6      0.00   0.0  0
 9P5  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 9P5  CONST_07  S24  C6   C5   C10   180.00   0.0  0
 9P5  CONST_08  C5   C10  C9   C11   180.00   0.0  0
 9P5  CONST_09  C7   C8   C9   C11   180.00   0.0  0
 9P5  CONST_10  CL   C10  C5   C6    180.00   0.0  0
 9P5  CONST_11  O4   C5   C6   C7    180.00   0.0  0
 9P5  CONST_12  CL   C10  C9   C8    180.00   0.0  0
 9P5  CONST_13  S24  C6   C7   C8    180.00   0.0  0
 9P5  CONST_14  O4   C5   C10  C9    180.00   0.0  0
 9P5  CONST_15  H21  C8   C9   C10   180.00   0.0  0
 9P5  CONST_16  H20  C7   C6   C5    180.00   0.0  0
 9P5  CONST_17  H21  C8   C7   C6    180.00   0.0  0
 9P5  CONST_18  H20  C7   C8   C9    180.00   0.0  0
 9P5  Var_01    C1   O20  C21  C22     5.27  30.0  1
 9P5  Var_02    C1   O23  C22  C21   -34.62  30.0  1
 9P5  Var_03    C16  C15  C14  C13    64.52  30.0  1
 9P5  Var_04    C17  C16  C15  C14   -29.29  30.0  1
 9P5  Var_05    O23  C22  C21  O20    17.90  30.0  1
 9P5  Var_06    H10  C15  C14  C13  -173.21  30.0  1
 9P5  Var_07    H11  C15  C14  C13   -56.81  30.0  1
 9P5  Var_08    H12  C16  C15  C14  -149.90  30.0  1
 9P5  Var_09    H13  C16  C15  C14    92.65  30.0  1
 9P5  Var_10    H8   C14  C15  C16   -56.10  30.0  1
 9P5  Var_11    H9   C14  C15  C16  -173.25  30.0  1
 9P5  Var_12    H10  C15  C16  C17  -151.65  30.0  1
 9P5  Var_13    H11  C15  C16  C17    91.52  30.0  1
 9P5  Var_14    H4   C21  O20  C1    125.29  30.0  1
 9P5  Var_15    H5   C21  O20  C1   -115.12  30.0  1
 9P5  Var_16    H1   C22  O23  C1   -155.60  30.0  1
 9P5  Var_17    H2   C22  O23  C1     84.58  30.0  1
 9P5  Var_18    H1   C22  C21  O20   135.94  30.0  1
 9P5  Var_19    H2   C22  C21  O20  -101.26  30.0  1
 9P5  Var_20    H4   C21  C22  O23  -100.01  30.0  1
 9P5  Var_21    H5   C21  C22  O23   138.00  30.0  1
 9P5  Var_22    C3   O4   C5   C10   -78.38  30.0  2
 9P5  Var_23    C6   C5   O4   C3    105.06  30.0  2
 9P5  Var_24    O27  S24  C6   C5    -53.09  30.0  2
 9P5  Var_25    O26  S24  C6   C5    178.05  30.0  2
 9P5  Var_26    C29  S24  C6   C5     64.01  30.0  2
 9P5  Var_27    O27  S24  C6   C7    127.91  30.0  2
 9P5  Var_28    O26  S24  C6   C7     -0.95  30.0  2
 9P5  Var_29    C29  S24  C6   C7   -114.99  30.0  2
 9P5  Var_30    O4   C3   C2   C1     64.94  30.0  3
 9P5  Var_31    C5   O4   C3   C2    160.24  30.0  3
 9P5  Var_32    H18  C3   C2   C1   -174.69  30.0  3
 9P5  Var_33    H19  C3   C2   C1    -55.44  30.0  3
 9P5  Var_34    H18  C3   O4   C5     40.60  30.0  1
 9P5  Var_35    H19  C3   O4   C5    -77.59  30.0  1
 9P5  Var_36    H22  C29  S24  C6     57.19  30.0  3
 9P5  Var_37    H23  C29  S24  C6    176.04  30.0  3
 9P5  Var_38    H24  C29  S24  C6    -64.48  30.0  3
 9P5  Var_39    H16  C2   C3   O4   -173.95  30.0  1
 9P5  Var_40    H17  C2   C3   O4    -57.86  30.0  1
 9P5  Var_41    H22  C29  S24  O26   -55.91  30.0  3
 9P5  Var_42    H23  C29  S24  O26    62.94  30.0  3
 9P5  Var_43    H24  C29  S24  O26  -177.59  30.0  3
 9P5  Var_44    H22  C29  S24  O27   175.01  30.0  3
 9P5  Var_45    H23  C29  S24  O27   -66.14  30.0  3
 9P5  Var_46    H24  C29  S24  O27    53.33  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
 9P5  chir_01  C11  O19  C12  C9   negativ
 9P5  chir_02  C12  C13  C11  C17  negativ
 9P5  chir_03  C13  O25  C12  C14  negativ
 9P5  chir_04  C17  O18  C12  C16  negativ
 9P5  chir_05  C1   C2   O20  O23  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
 9P5  plan-1  C10  0.020
 9P5  plan-1  C11  0.020
 9P5  plan-1  C5   0.020
 9P5  plan-1  C6   0.020
 9P5  plan-1  C7   0.020
 9P5  plan-1  C8   0.020
 9P5  plan-1  C9   0.020
 9P5  plan-1  O4   0.020
 9P5  plan-1  S24  0.020
 9P5  plan-1  H20  0.020
 9P5  plan-1  H21  0.020
 9P5  plan-1  CL   0.020

