# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 06:21:17 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (6~{R})-5-(5-fluoranyl-2-methoxy-pyrimidin-4-yl)-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(F)c(n1)N2Cc3cn(nc3[C@H]2C(C)C)c4cccc(c4)[S](C)(=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
 6Y8  6Y8  (6~{R})-5-(5-fluoranyl-2-methoxy-pyrimidin-4-yl)-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazole  ligand  52  30  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6Y8
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
 6Y8  C10  C  CR16  0  -0.236   4.7637  -1.4057   2.7348
 6Y8  C12  C  CR15  0  -0.023   0.4641  -1.2129   2.1473
 6Y8  C13  C  CR55  0  -0.128  -0.7250  -1.0065   1.5145
 6Y8  C15  C  CR6   0   0.442  -3.7695   0.2954   0.3018
 6Y8  C19  C  CH3   0  -0.414  -6.0577   3.5923  -2.0307
 6Y8  C16  C  CR6   0   0.344  -4.8808   0.1652   1.1658
 6Y8  C17  C  CR16  0  -0.157  -5.9590   0.9768   0.9747
 6Y8  N3   N  N     0  -0.479  -6.0157   1.8783  -0.0099
 6Y8  C18  C  CR6   0   0.587  -4.9567   1.9110  -0.7925
 6Y8  O2   O  O2    0  -0.453  -4.9287   2.7563  -1.8171
 6Y8  N4   N  N     0  -0.494  -3.8596   1.1812  -0.6848
 6Y8  N2   N  NR5   0  -0.541  -2.6436  -0.4395   0.4130
 6Y8  C3   C  CR15  0  -0.105  -1.5899  -0.3767  -0.6232
 6Y8  C1   C  CH1   0  -0.217  -1.7400  -1.4722  -1.6995
 6Y8  C2   C  CH3   0  -0.659  -3.1131  -1.4733  -2.3619
 6Y8  C    C  CH3   0  -0.670  -0.6468  -1.3181  -2.7522
 6Y8  C14  C  CH2   0  -0.350  -2.1987  -1.0379   1.6905
 6Y8  C4   C  CR55  0   0.297  -0.3839  -0.5953   0.2274
 6Y8  N1   N  NR5   0  -0.429   1.4265  -0.9158   1.2232
 6Y8  N    N  N     0  -0.303   0.9093  -0.5358   0.0420
 6Y8  C5   C  CR6   0   0.422   2.8195  -0.9478   1.3905
 6Y8  C11  C  CR16  0  -0.305   3.3869  -1.3911   2.5822
 6Y8  C9   C  CR16  0  -0.247   5.5986  -0.9836   1.7123
 6Y8  C7   C  CR6   0  -0.191   5.0131  -0.5537   0.5311
 6Y8  C6   C  CR16  0  -0.297   3.6410  -0.5246   0.3506
 6Y8  S    S  S     0   1.219   6.0553  -0.0181  -0.8074
 6Y8  O    O  OS    0  -0.665   5.2655   0.8413  -1.6863
 6Y8  O1   O  OS    0  -0.665   7.2941   0.5062  -0.2384
 6Y8  C8   C  CH3   0  -0.792   6.4263  -1.5238  -1.6750
 6Y8  H1   H  HCR6  0   0.283   5.1869  -1.7502   3.6680
 6Y8  H2   H  HCR5  0   0.309   0.7008  -1.5295   3.1485
 6Y8  H3   H  HCH3  0   0.231  -6.9646   3.0129  -2.2054
 6Y8  H4   H  HCH3  0   0.231  -6.2274   4.2653  -1.1896
 6Y8  H5   H  HCH3  0   0.248  -5.8288   4.1772  -2.9178
 6Y8  H6   H  HCR6  0   0.290  -6.8223   0.8899   1.6257
 6Y8  H7   H  HCR5  0   0.281  -1.6013   0.6074  -1.0968
 6Y8  H8   H  HCH1  0   0.225  -1.6065  -2.4388  -1.1995
 6Y8  H9   H  HCH3  0   0.223  -3.3106  -0.5306  -2.8737
 6Y8  H10  H  HCH3  0   0.233  -3.1643  -2.2729  -3.1026
 6Y8  H11  H  HCH3  0   0.230  -3.9167  -1.6441  -1.6455
 6Y8  H12  H  HCH3  0   0.241   0.3537  -1.3426  -2.3211
 6Y8  H13  H  HCH3  0   0.234  -0.7109  -2.1250  -3.4826
 6Y8  H14  H  HCH3  0   0.219  -0.7551  -0.3746  -3.2926
 6Y8  H15  H  HCH2  0   0.268  -2.5814  -2.0520   1.8254
 6Y8  H16  H  HCH2  0   0.273  -2.5232  -0.4338   2.5373
 6Y8  H17  H  HCR6  0   0.294   2.7729  -1.7293   3.4048
 6Y8  H18  H  HCR6  0   0.288   6.6719  -0.9924   1.8421
 6Y8  H19  H  HCR6  0   0.305   3.2078  -0.1745  -0.5748
 6Y8  H20  H  HCH3  0   0.297   6.9444  -2.2079  -1.0070
 6Y8  H21  H  HCH3  0   0.298   5.5028  -1.9711  -2.0349
 6Y8  H22  H  HCH3  0   0.314   7.0687  -1.2632  -2.5157
 6Y8  F    F  F     0  -0.306  -4.9163  -0.7707   2.1311

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
 6Y8  O    S    double    1.461  0.020  1.461
 6Y8  S    C8   single    1.777  0.020  1.777
 6Y8  S    O1   double    1.461  0.020  1.461
 6Y8  S    C7   single    1.779  0.020  1.779
 6Y8  C9   C7   aromatic  1.387  0.020  1.387
 6Y8  C9   C10  aromatic  1.386  0.020  1.386
 6Y8  C7   C6   aromatic  1.384  0.020  1.384
 6Y8  C10  C11  aromatic  1.385  0.020  1.385
 6Y8  C6   C5   aromatic  1.391  0.020  1.391
 6Y8  C11  C5   aromatic  1.392  0.020  1.392
 6Y8  C5   N1   single    1.403  0.020  1.403
 6Y8  N1   C12  aromatic  1.367  0.020  1.367
 6Y8  N1   N    aromatic  1.344  0.020  1.344
 6Y8  C12  C13  aromatic  1.363  0.020  1.363
 6Y8  N    C4   aromatic  1.308  0.020  1.308
 6Y8  C13  C4   aromatic  1.394  0.020  1.394
 6Y8  C13  C14  single    1.485  0.020  1.485
 6Y8  C4   C3   single    1.492  0.020  1.492
 6Y8  C    C1   single    1.525  0.020  1.525
 6Y8  C14  N2   single    1.479  0.020  1.479
 6Y8  C2   C1   single    1.524  0.020  1.524
 6Y8  C3   C1   single    1.543  0.020  1.543
 6Y8  C3   N2   single    1.479  0.020  1.479
 6Y8  N2   C15  single    1.349  0.020  1.349
 6Y8  F    C16  single    1.345  0.020  1.345
 6Y8  C15  C16  aromatic  1.414  0.020  1.414
 6Y8  C15  N4   aromatic  1.329  0.020  1.329
 6Y8  C16  C17  aromatic  1.363  0.020  1.363
 6Y8  N4   C18  aromatic  1.322  0.020  1.322
 6Y8  C17  N3   aromatic  1.336  0.020  1.336
 6Y8  C18  N3   aromatic  1.317  0.020  1.317
 6Y8  C18  O2   single    1.329  0.020  1.329
 6Y8  O2   C19  single    1.421  0.020  1.421
 6Y8  C10  H1   single    0.930  0.020  1.080
 6Y8  C12  H2   single    0.930  0.020  1.080
 6Y8  C19  H3   single    0.970  0.020  1.090
 6Y8  C19  H4   single    0.970  0.020  1.090
 6Y8  C19  H5   single    0.970  0.020  1.090
 6Y8  C17  H6   single    0.930  0.020  1.080
 6Y8  C3   H7   single    0.970  0.020  1.090
 6Y8  C1   H8   single    0.970  0.020  1.090
 6Y8  C2   H9   single    0.970  0.020  1.090
 6Y8  C2   H10  single    0.970  0.020  1.090
 6Y8  C2   H11  single    0.970  0.020  1.090
 6Y8  C    H12  single    0.970  0.020  1.090
 6Y8  C    H13  single    0.970  0.020  1.090
 6Y8  C    H14  single    0.970  0.020  1.090
 6Y8  C14  H15  single    0.970  0.020  1.090
 6Y8  C14  H16  single    0.970  0.020  1.090
 6Y8  C11  H17  single    0.930  0.020  1.080
 6Y8  C9   H18  single    0.930  0.020  1.080
 6Y8  C6   H19  single    0.930  0.020  1.080
 6Y8  C8   H20  single    0.970  0.020  1.090
 6Y8  C8   H21  single    0.970  0.020  1.090
 6Y8  C8   H22  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
 6Y8  H1   C10  C9   119.88  3.000
 6Y8  H1   C10  C11  119.18  3.000
 6Y8  C9   C10  C11  120.94  3.000
 6Y8  H2   C12  N1   122.55  3.000
 6Y8  H2   C12  C13  131.94  3.000
 6Y8  N1   C12  C13  105.52  3.000
 6Y8  C4   C13  C14  111.02  3.000
 6Y8  C14  C13  C12  143.90  3.000
 6Y8  C4   C13  C12  105.07  3.000
 6Y8  N2   C15  N4   118.74  3.000
 6Y8  N4   C15  C16  117.51  3.000
 6Y8  N2   C15  C16  123.74  3.000
 6Y8  H5   C19  H4   109.27  3.000
 6Y8  H5   C19  H3   109.30  3.000
 6Y8  H4   C19  H3   108.79  3.000
 6Y8  H5   C19  O2   105.78  3.000
 6Y8  H4   C19  O2   111.76  3.000
 6Y8  H3   C19  O2   111.86  3.000
 6Y8  C17  C16  F    119.61  3.000
 6Y8  C17  C16  C15  118.77  3.000
 6Y8  F    C16  C15  121.57  3.000
 6Y8  H6   C17  N3   117.55  3.000
 6Y8  H6   C17  C16  119.85  3.000
 6Y8  N3   C17  C16  122.59  3.000
 6Y8  C18  N3   C17  114.86  3.000
 6Y8  N4   C18  O2   113.36  3.000
 6Y8  O2   C18  N3   119.40  3.000
 6Y8  N4   C18  N3   127.24  3.000
 6Y8  C18  O2   C19  118.26  3.000
 6Y8  C18  N4   C15  118.99  3.000
 6Y8  C14  N2   C3   114.07  3.000
 6Y8  C3   N2   C15  120.90  3.000
 6Y8  C14  N2   C15  122.86  3.000
 6Y8  H7   C3   C4   112.81  3.000
 6Y8  H7   C3   C1   109.64  3.000
 6Y8  C4   C3   C1   111.86  3.000
 6Y8  H7   C3   N2   109.55  3.000
 6Y8  C1   C3   N2   112.90  3.000
 6Y8  C4   C3   N2    99.80  3.000
 6Y8  H8   C1   C    108.45  3.000
 6Y8  H8   C1   C2   107.89  3.000
 6Y8  C    C1   C2   110.23  3.000
 6Y8  H8   C1   C3   107.21  3.000
 6Y8  C2   C1   C3   113.03  3.000
 6Y8  C    C1   C3   109.87  3.000
 6Y8  H11  C2   H10  107.26  3.000
 6Y8  H11  C2   H9   108.08  3.000
 6Y8  H10  C2   H9   107.84  3.000
 6Y8  H11  C2   C1   112.25  3.000
 6Y8  H10  C2   C1   109.73  3.000
 6Y8  H9   C2   C1   111.49  3.000
 6Y8  H14  C    H13  107.57  3.000
 6Y8  H14  C    H12  107.83  3.000
 6Y8  H13  C    H12  107.60  3.000
 6Y8  H14  C    C1   110.94  3.000
 6Y8  H13  C    C1   110.21  3.000
 6Y8  H12  C    C1   112.50  3.000
 6Y8  H16  C14  H15  108.33  3.000
 6Y8  H16  C14  N2   110.94  3.000
 6Y8  H15  C14  N2   112.14  3.000
 6Y8  H16  C14  C13  112.08  3.000
 6Y8  H15  C14  C13  112.46  3.000
 6Y8  N2   C14  C13  100.82  3.000
 6Y8  N    C4   C3   135.39  3.000
 6Y8  C3   C4   C13  111.83  3.000
 6Y8  N    C4   C13  112.73  3.000
 6Y8  C5   N1   N    119.54  3.000
 6Y8  N    N1   C12  112.62  3.000
 6Y8  C5   N1   C12  127.83  3.000
 6Y8  N1   N    C4   104.06  3.000
 6Y8  C6   C5   C11  119.73  3.000
 6Y8  C11  C5   N1   120.92  3.000
 6Y8  C6   C5   N1   119.35  3.000
 6Y8  H17  C11  C5   121.31  3.000
 6Y8  H17  C11  C10  118.52  3.000
 6Y8  C5   C11  C10  120.18  3.000
 6Y8  H18  C9   C7   121.60  3.000
 6Y8  H18  C9   C10  120.46  3.000
 6Y8  C7   C9   C10  117.94  3.000
 6Y8  S    C7   C6   118.44  3.000
 6Y8  C6   C7   C9   122.42  3.000
 6Y8  S    C7   C9   119.14  3.000
 6Y8  H19  C6   C7   121.07  3.000
 6Y8  H19  C6   C5   120.15  3.000
 6Y8  C7   C6   C5   118.78  3.000
 6Y8  C8   S    O1   108.51  3.000
 6Y8  O1   S    O    118.79  3.000
 6Y8  C8   S    O    108.52  3.000
 6Y8  O1   S    C7   108.17  3.000
 6Y8  C8   S    C7   103.57  3.000
 6Y8  O    S    C7   108.24  3.000
 6Y8  H22  C8   H21  110.10  3.000
 6Y8  H22  C8   H20  110.09  3.000
 6Y8  H21  C8   H20  110.44  3.000
 6Y8  H22  C8   S    107.28  3.000
 6Y8  H21  C8   S    109.44  3.000
 6Y8  H20  C8   S    109.42  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
 6Y8  CONST_01  C6   C7   C9   C10     0.00   0.0  0
 6Y8  CONST_02  C6   C5   C11  C10     0.00   0.0  0
 6Y8  CONST_03  N1   C5   C11  C10   180.00   0.0  0
 6Y8  CONST_04  C6   C5   N1   C12   180.00   0.0  0
 6Y8  CONST_05  C11  C5   N1   C12     0.00   0.0  0
 6Y8  CONST_06  C4   N    N1   C12     0.00   0.0  0
 6Y8  CONST_07  N    C4   C13  C12     0.00   0.0  0
 6Y8  CONST_08  C5   N1   C12  C13   180.00   0.0  0
 6Y8  CONST_09  N    N1   C12  C13     0.00   0.0  0
 6Y8  CONST_10  N1   N    C4   C13     0.00   0.0  0
 6Y8  CONST_11  N3   C17  C16  C15     0.00   0.0  0
 6Y8  CONST_12  N3   C18  N4   C15     0.00   0.0  0
 6Y8  CONST_13  C18  N4   C15  C16     0.00   0.0  0
 6Y8  CONST_14  C18  N3   C17  C16     0.00   0.0  0
 6Y8  CONST_15  N4   C15  C16  C17     0.00   0.0  0
 6Y8  CONST_16  N4   C18  N3   C17     0.00   0.0  0
 6Y8  CONST_17  C5   N1   N    C4    180.00   0.0  0
 6Y8  CONST_18  N1   C12  C13  C4      0.00   0.0  0
 6Y8  CONST_19  C7   C6   C5   N1    180.00   0.0  0
 6Y8  CONST_20  C6   C5   N1   N       0.00   0.0  0
 6Y8  CONST_21  C11  C5   N1   N     180.00   0.0  0
 6Y8  CONST_22  C9   C7   C6   C5      0.00   0.0  0
 6Y8  CONST_23  C9   C10  C11  C5      0.00   0.0  0
 6Y8  CONST_24  C7   C9   C10  C11     0.00   0.0  0
 6Y8  CONST_25  C7   C6   C5   C11     0.00   0.0  0
 6Y8  CONST_26  N2   C15  C16  C17   180.00   0.0  0
 6Y8  CONST_27  N2   C15  N4   C18   180.00   0.0  0
 6Y8  CONST_28  S    C7   C9   C10   180.00   0.0  0
 6Y8  CONST_29  O2   C18  N4   C15   180.00   0.0  0
 6Y8  CONST_30  N2   C15  C16  F       0.00   0.0  0
 6Y8  CONST_31  N4   C15  C16  F     180.00   0.0  0
 6Y8  CONST_32  N3   C17  C16  F     180.00   0.0  0
 6Y8  CONST_33  O2   C18  N3   C17   180.00   0.0  0
 6Y8  CONST_34  S    C7   C6   C5    180.00   0.0  0
 6Y8  CONST_35  H6   C17  C16  C15   180.00   0.0  0
 6Y8  CONST_36  H2   C12  C13  C14     0.00   0.0  0
 6Y8  CONST_37  H19  C6   C5   N1      0.00   0.0  0
 6Y8  CONST_38  H17  C11  C5   N1      0.00   0.0  0
 6Y8  CONST_39  H1   C10  C11  C5    180.00   0.0  0
 6Y8  CONST_40  H18  C9   C10  C11   180.00   0.0  0
 6Y8  Var_01    N2   C14  C13  C12   172.05  30.0  1
 6Y8  Var_02    C3   N2   C14  C13    14.65  30.0  1
 6Y8  Var_03    C14  N2   C15  C16   -25.58  30.0  3
 6Y8  Var_04    N4   C18  O2   C19   179.95  30.0  1
 6Y8  Var_05    O    S    C7   C9   -158.26  30.0  1
 6Y8  Var_06    H3   C19  O2   C18   -60.02  30.0  3
 6Y8  Var_07    H12  C    C1   C3     56.51  30.0  3
 6Y8  Var_08    H9   C2   C1   C3     61.25  30.0  3
 6Y8  Var_09    H20  C8   S    C7    -60.57  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
 6Y8  chir_01  C3  C4  C1  N2  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
 6Y8  plan-1  C15  0.020
 6Y8  plan-1  C16  0.020
 6Y8  plan-1  C17  0.020
 6Y8  plan-1  N3   0.020
 6Y8  plan-1  C18  0.020
 6Y8  plan-1  O2   0.020
 6Y8  plan-1  N4   0.020
 6Y8  plan-1  N2   0.020
 6Y8  plan-1  H6   0.020
 6Y8  plan-1  F    0.020
 6Y8  plan-2  C10  0.020
 6Y8  plan-2  N1   0.020
 6Y8  plan-2  C5   0.020
 6Y8  plan-2  C11  0.020
 6Y8  plan-2  C9   0.020
 6Y8  plan-2  C7   0.020
 6Y8  plan-2  C6   0.020
 6Y8  plan-2  S    0.020
 6Y8  plan-2  H1   0.020
 6Y8  plan-2  H17  0.020
 6Y8  plan-2  H18  0.020
 6Y8  plan-2  H19  0.020
 6Y8  plan-3  C12  0.020
 6Y8  plan-3  C13  0.020
 6Y8  plan-3  C3   0.020
 6Y8  plan-3  C14  0.020
 6Y8  plan-3  C4   0.020
 6Y8  plan-3  N1   0.020
 6Y8  plan-3  N    0.020
 6Y8  plan-3  C5   0.020
 6Y8  plan-3  H2   0.020

