# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:57:59 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [2-[(6~{R})-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazol-5-yl]-4-(trifluoromethyl)pyrimidin-5-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H]1N(Cc2cn(nc12)c3cccc(c3)[S](C)(=O)=O)c4ncc(CO)c(n4)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
 6Y4  6Y4  '[2-[(6~{R})-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazol-5-yl]-4-(trifluoromethyl)pyrimidin-5-yl]methanol'  ligand  55  33  .  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_6Y4
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
 6Y4  N4   N  NR5   0  -0.429  -2.2998   1.0411  -0.1653
 6Y4  C8   C  CR15  0  -0.027  -1.3167   1.9446  -0.4601
 6Y4  N3   N  NR5   0  -0.544   1.7012  -0.0768  -0.4702
 6Y4  C5   C  CR16  0  -0.013   4.3516  -1.7568   1.0700
 6Y4  C4   C  CR6   0   0.645   2.9196  -0.3356   0.0460
 6Y4  C3   C  CR6   0   0.003   5.0263   0.3851   0.4659
 6Y4  C6   C  CH2   0  -0.332   1.2960   1.3013  -0.7917
 6Y4  C7   C  CR55  0  -0.137  -0.1692   1.2165  -0.5604
 6Y4  C2   C  CR6   0  -0.078   5.3929  -0.8275   1.0365
 6Y4  C1   C  CH2   0  -0.204   6.7444  -1.1588   1.6129
 6Y4  N2   N  N     0  -0.444   3.1445  -1.5331   0.5944
 6Y4  N1   N  N     0  -0.482   3.8310   0.6375  -0.0249
 6Y4  C9   C  CR55  0   0.295  -0.5564  -0.1025  -0.3174
 6Y4  C14  C  CR6   0   0.422  -3.6628   1.2924   0.0509
 6Y4  O3   O  OS    0  -0.666  -8.3325  -0.4411   0.0316
 6Y4  C15  C  CR16  0  -0.296  -4.5490   0.2231   0.1294
 6Y4  C11  C  CH1   0  -0.219   0.4921  -1.8934  -1.7315
 6Y4  C10  C  CR15  0  -0.104   0.5938  -1.0488  -0.4436
 6Y4  C16  C  CR6   0  -0.192  -5.8905   0.4856   0.3467
 6Y4  C17  C  CH3   0  -0.791  -7.0825  -1.2139   2.2164
 6Y4  C21  C  CT    0   1.047   6.0074   1.5322   0.3414
 6Y4  C20  C  CR16  0  -0.305  -4.1361   2.5945   0.1874
 6Y4  C19  C  CR16  0  -0.236  -5.4864   2.8271   0.3933
 6Y4  C18  C  CR16  0  -0.246  -6.3847   1.7748   0.4761
 6Y4  F3   F  F     0  -0.311   6.6292   1.7697   1.5029
 6Y4  F1   F  F     0  -0.313   6.9535   1.2524  -0.5654
 6Y4  F2   F  F     0  -0.290   5.4203   2.6608  -0.0322
 6Y4  O1   O  OH1   0  -0.665   6.9057  -2.5557   1.5991
 6Y4  N5   N  N     0  -0.302  -1.8367  -0.2180  -0.0788
 6Y4  S    S  S     0   1.218  -7.0130  -0.8886   0.4704
 6Y4  O2   O  OS    0  -0.665  -6.4037  -2.0401  -0.1914
 6Y4  H1   H  HCR5  0   0.307  -1.5144   2.9970  -0.5735
 6Y4  H2   H  HCR6  0   0.279   4.5118  -2.7338   1.5094
 6Y4  H3   H  HCH2  0   0.270   1.7988   2.0095  -0.1334
 6Y4  H4   H  HCH2  0   0.262   1.5537   1.5700  -1.8200
 6Y4  H5   H  HCH2  0   0.216   7.5395  -0.6708   1.0398
 6Y4  H6   H  HCH2  0   0.234   6.8058  -0.7647   2.6345
 6Y4  H7   H  HCH3  0   0.231   1.6521  -3.2074  -2.9811
 6Y4  H8   H  HCH3  0   0.229   2.6285  -1.9857  -2.1831
 6Y4  H9   H  HCH3  0   0.221   2.0215  -3.3642  -1.2637
 6Y4  H10  H  HCR6  0   0.304  -4.1895  -0.7893   0.0165
 6Y4  H11  H  HCH3  0   0.218  -0.5324  -3.5579  -0.7908
 6Y4  H12  H  HCH3  0   0.241  -1.6309  -2.3610  -1.4782
 6Y4  H13  H  HCH3  0   0.233  -0.7574  -3.4627  -2.5352
 6Y4  H14  H  HCH1  0   0.224   0.2948  -1.1988  -2.5565
 6Y4  H15  H  HCR5  0   0.274   0.7026  -1.7109   0.4189
 6Y4  H16  H  HCH3  0   0.313  -7.7708  -2.0459   2.3635
 6Y4  H17  H  HCH3  0   0.298  -6.0912  -1.4810   2.5745
 6Y4  H18  H  HCH3  0   0.297  -7.4485  -0.3309   2.7353
 6Y4  H19  H  HCR6  0   0.294  -3.4634   3.4391   0.1423
 6Y4  H20  H  HCR6  0   0.282  -5.8376   3.8445   0.4955
 6Y4  H21  H  HCR6  0   0.288  -7.4370   1.9621   0.6385
 6Y4  H22  H  HOH1  0   0.465   7.6553  -2.7726   2.1604
 6Y4  C13  C  CH3   0  -0.655   1.7756  -2.6506  -2.0507
 6Y4  C12  C  CH3   0  -0.668  -0.6775  -2.8673  -1.6248

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
 6Y4  O1   C1   single    1.406  0.020  1.406
 6Y4  C1   C2   single    1.506  0.020  1.506
 6Y4  F1   C21  single    1.340  0.020  1.340
 6Y4  F3   C21  single    1.339  0.020  1.339
 6Y4  C2   C5   aromatic  1.396  0.020  1.396
 6Y4  C2   C3   aromatic  1.389  0.020  1.389
 6Y4  C21  C3   single    1.514  0.020  1.514
 6Y4  C21  F2   single    1.326  0.020  1.326
 6Y4  C5   N2   aromatic  1.317  0.020  1.317
 6Y4  C3   N1   aromatic  1.317  0.020  1.317
 6Y4  N2   C4   aromatic  1.336  0.020  1.336
 6Y4  N1   C4   aromatic  1.335  0.020  1.335
 6Y4  C4   N3   single    1.348  0.020  1.348
 6Y4  N3   C10  single    1.474  0.020  1.474
 6Y4  N3   C6   single    1.472  0.020  1.472
 6Y4  C10  C11  single    1.543  0.020  1.543
 6Y4  C10  C9   single    1.495  0.020  1.495
 6Y4  C11  C12  single    1.526  0.020  1.526
 6Y4  C11  C13  single    1.524  0.020  1.524
 6Y4  C6   C7   single    1.486  0.020  1.486
 6Y4  C9   C7   aromatic  1.396  0.020  1.396
 6Y4  C9   N5   aromatic  1.307  0.020  1.307
 6Y4  C7   C8   aromatic  1.363  0.020  1.363
 6Y4  N5   N4   aromatic  1.344  0.020  1.344
 6Y4  C8   N4   aromatic  1.367  0.020  1.367
 6Y4  N4   C14  single    1.403  0.020  1.403
 6Y4  C14  C20  aromatic  1.392  0.020  1.392
 6Y4  C14  C15  aromatic  1.391  0.020  1.391
 6Y4  C20  C19  aromatic  1.386  0.020  1.386
 6Y4  C15  C16  aromatic  1.384  0.020  1.384
 6Y4  C19  C18  aromatic  1.386  0.020  1.386
 6Y4  C16  C18  aromatic  1.387  0.020  1.387
 6Y4  C16  S    single    1.779  0.020  1.779
 6Y4  C17  S    single    1.777  0.020  1.777
 6Y4  O3   S    double    1.461  0.020  1.461
 6Y4  S    O2   double    1.461  0.020  1.461
 6Y4  C8   H1   single    0.930  0.020  1.080
 6Y4  C5   H2   single    0.930  0.020  1.080
 6Y4  C6   H3   single    0.970  0.020  1.090
 6Y4  C6   H4   single    0.970  0.020  1.090
 6Y4  C1   H5   single    0.970  0.020  1.090
 6Y4  C1   H6   single    0.970  0.020  1.090
 6Y4  C13  H7   single    0.970  0.020  1.090
 6Y4  C13  H8   single    0.970  0.020  1.090
 6Y4  C13  H9   single    0.970  0.020  1.090
 6Y4  C15  H10  single    0.930  0.020  1.080
 6Y4  C12  H11  single    0.970  0.020  1.090
 6Y4  C12  H12  single    0.970  0.020  1.090
 6Y4  C12  H13  single    0.970  0.020  1.090
 6Y4  C11  H14  single    0.970  0.020  1.090
 6Y4  C10  H15  single    0.970  0.020  1.090
 6Y4  C17  H16  single    0.970  0.020  1.090
 6Y4  C17  H17  single    0.970  0.020  1.090
 6Y4  C17  H18  single    0.970  0.020  1.090
 6Y4  C20  H19  single    0.930  0.020  1.080
 6Y4  C19  H20  single    0.930  0.020  1.080
 6Y4  C18  H21  single    0.930  0.020  1.080
 6Y4  O1   H22  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
 6Y4  N5   N4   C14  119.51  3.000
 6Y4  C14  N4   C8   127.84  3.000
 6Y4  N5   N4   C8   112.65  3.000
 6Y4  H1   C8   C7   131.99  3.000
 6Y4  H1   C8   N4   122.45  3.000
 6Y4  C7   C8   N4   105.56  3.000
 6Y4  C10  N3   C6   114.50  3.000
 6Y4  C6   N3   C4   120.80  3.000
 6Y4  C10  N3   C4   123.06  3.000
 6Y4  H2   C5   N2   115.81  3.000
 6Y4  H2   C5   C2   119.99  3.000
 6Y4  N2   C5   C2   124.19  3.000
 6Y4  N1   C4   N2   124.06  3.000
 6Y4  N1   C4   N3   117.17  3.000
 6Y4  N2   C4   N3   118.76  3.000
 6Y4  C21  C3   N1   114.35  3.000
 6Y4  N1   C3   C2   124.05  3.000
 6Y4  C21  C3   C2   121.59  3.000
 6Y4  H4   C6   H3   107.44  3.000
 6Y4  H4   C6   C7   113.13  3.000
 6Y4  H3   C6   C7   113.45  3.000
 6Y4  H4   C6   N3   111.75  3.000
 6Y4  H3   C6   N3   110.46  3.000
 6Y4  C7   C6   N3   100.60  3.000
 6Y4  C9   C7   C6   110.77  3.000
 6Y4  C9   C7   C8   104.98  3.000
 6Y4  C6   C7   C8   144.23  3.000
 6Y4  C1   C2   C3   125.87  3.000
 6Y4  C3   C2   C5   113.21  3.000
 6Y4  C1   C2   C5   120.90  3.000
 6Y4  H6   C1   H5   106.67  3.000
 6Y4  H6   C1   O1   111.08  3.000
 6Y4  H5   C1   O1   110.75  3.000
 6Y4  H6   C1   C2   109.13  3.000
 6Y4  H5   C1   C2   110.68  3.000
 6Y4  O1   C1   C2   108.52  3.000
 6Y4  C4   N2   C5   117.06  3.000
 6Y4  C3   N1   C4   117.40  3.000
 6Y4  N5   C9   C10  135.47  3.000
 6Y4  N5   C9   C7   112.76  3.000
 6Y4  C10  C9   C7   111.72  3.000
 6Y4  C20  C14  C15  119.79  3.000
 6Y4  C15  C14  N4   119.34  3.000
 6Y4  C20  C14  N4   120.87  3.000
 6Y4  H10  C15  C16  121.11  3.000
 6Y4  H10  C15  C14  120.17  3.000
 6Y4  C16  C15  C14  118.72  3.000
 6Y4  H14  C11  C10  107.04  3.000
 6Y4  H14  C11  C12  108.61  3.000
 6Y4  C10  C11  C12  109.97  3.000
 6Y4  H14  C11  C13  107.99  3.000
 6Y4  C12  C11  C13  110.06  3.000
 6Y4  C10  C11  C13  113.03  3.000
 6Y4  H15  C10  C11  109.49  3.000
 6Y4  H15  C10  C9   113.17  3.000
 6Y4  C11  C10  C9   111.48  3.000
 6Y4  H15  C10  N3   109.82  3.000
 6Y4  C9   C10  N3    99.33  3.000
 6Y4  C11  C10  N3   113.29  3.000
 6Y4  S    C16  C18  119.14  3.000
 6Y4  S    C16  C15  118.43  3.000
 6Y4  C18  C16  C15  122.43  3.000
 6Y4  H18  C17  H17  110.44  3.000
 6Y4  H18  C17  H16  110.05  3.000
 6Y4  H17  C17  H16  110.11  3.000
 6Y4  H18  C17  S    109.47  3.000
 6Y4  H17  C17  S    109.44  3.000
 6Y4  H16  C17  S    107.28  3.000
 6Y4  F2   C21  F1   107.43  3.000
 6Y4  F2   C21  F3   107.41  3.000
 6Y4  F1   C21  F3   107.23  3.000
 6Y4  F2   C21  C3   112.40  3.000
 6Y4  F3   C21  C3   111.34  3.000
 6Y4  F1   C21  C3   110.78  3.000
 6Y4  H19  C20  C19  118.79  3.000
 6Y4  H19  C20  C14  121.01  3.000
 6Y4  C19  C20  C14  120.19  3.000
 6Y4  H20  C19  C18  119.88  3.000
 6Y4  H20  C19  C20  119.25  3.000
 6Y4  C18  C19  C20  120.87  3.000
 6Y4  H21  C18  C19  120.55  3.000
 6Y4  H21  C18  C16  121.46  3.000
 6Y4  C19  C18  C16  117.99  3.000
 6Y4  H22  O1   C1   107.93  3.000
 6Y4  C9   N5   N4   104.05  3.000
 6Y4  O2   S    C17  108.49  3.000
 6Y4  O2   S    C16  108.31  3.000
 6Y4  C17  S    C16  103.56  3.000
 6Y4  O2   S    O3   118.82  3.000
 6Y4  C17  S    O3   108.41  3.000
 6Y4  C16  S    O3   108.21  3.000
 6Y4  H9   C13  H8   108.09  3.000
 6Y4  H9   C13  H7   107.88  3.000
 6Y4  H8   C13  H7   107.24  3.000
 6Y4  H9   C13  C11  111.34  3.000
 6Y4  H8   C13  C11  112.42  3.000
 6Y4  H7   C13  C11  109.68  3.000
 6Y4  H13  C12  H12  107.57  3.000
 6Y4  H13  C12  H11  107.57  3.000
 6Y4  H12  C12  H11  107.90  3.000
 6Y4  H13  C12  C11  110.26  3.000
 6Y4  H12  C12  C11  112.56  3.000
 6Y4  H11  C12  C11  110.80  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
 6Y4  CONST_01  C7   C9   N5   N4      0.00   0.0  0
 6Y4  CONST_02  C9   C7   C8   N4      0.00   0.0  0
 6Y4  CONST_03  C19  C20  C14  N4    180.00   0.0  0
 6Y4  CONST_04  C16  C15  C14  N4    180.00   0.0  0
 6Y4  CONST_05  N5   C9   C7   C8      0.00   0.0  0
 6Y4  CONST_06  C9   N5   N4   C8      0.00   0.0  0
 6Y4  CONST_07  C20  C14  N4   C8      0.00   0.0  0
 6Y4  CONST_08  C15  C14  N4   C8    180.00   0.0  0
 6Y4  CONST_09  N1   C3   C2   C5      0.00   0.0  0
 6Y4  CONST_10  N1   C4   N2   C5      0.00   0.0  0
 6Y4  CONST_11  C2   C5   N2   C4      0.00   0.0  0
 6Y4  CONST_12  C2   C3   N1   C4      0.00   0.0  0
 6Y4  CONST_13  N2   C5   C2   C3      0.00   0.0  0
 6Y4  CONST_14  N2   C4   N1   C3      0.00   0.0  0
 6Y4  CONST_15  N5   N4   C8   C7      0.00   0.0  0
 6Y4  CONST_16  C14  N4   C8   C7    180.00   0.0  0
 6Y4  CONST_17  C14  N4   N5   C9    180.00   0.0  0
 6Y4  CONST_18  C18  C19  C20  C14     0.00   0.0  0
 6Y4  CONST_19  C18  C16  C15  C14     0.00   0.0  0
 6Y4  CONST_20  N5   N4   C14  C15     0.00   0.0  0
 6Y4  CONST_21  C19  C20  C14  C15     0.00   0.0  0
 6Y4  CONST_22  C19  C18  C16  C15     0.00   0.0  0
 6Y4  CONST_23  C20  C14  C15  C16     0.00   0.0  0
 6Y4  CONST_24  C20  C19  C18  C16     0.00   0.0  0
 6Y4  CONST_25  N5   N4   C14  C20   180.00   0.0  0
 6Y4  CONST_26  C5   N2   C4   N3    180.00   0.0  0
 6Y4  CONST_27  C3   N1   C4   N3    180.00   0.0  0
 6Y4  CONST_28  C21  C3   C2   C5    180.00   0.0  0
 6Y4  CONST_29  C21  C3   N1   C4    180.00   0.0  0
 6Y4  CONST_30  N2   C5   C2   C1    180.00   0.0  0
 6Y4  CONST_31  N1   C3   C2   C1    180.00   0.0  0
 6Y4  CONST_32  S    C16  C15  C14   180.00   0.0  0
 6Y4  CONST_33  S    C16  C18  C19   180.00   0.0  0
 6Y4  CONST_34  H19  C20  C14  N4      0.00   0.0  0
 6Y4  CONST_35  H10  C15  C14  N4      0.00   0.0  0
 6Y4  CONST_36  H2   C5   N2   C4    180.00   0.0  0
 6Y4  CONST_37  H1   C8   C7   C6      0.00   0.0  0
 6Y4  CONST_38  H20  C19  C20  C14   180.00   0.0  0
 6Y4  CONST_39  H21  C18  C16  C15   180.00   0.0  0
 6Y4  Var_01    N3   C6   C7   C8    170.50  30.0  1
 6Y4  Var_02    C7   C6   N3   C4   -149.35  30.0  1
 6Y4  Var_03    N2   C4   N3   C6    165.40  30.0  1
 6Y4  Var_04    O1   C1   C2   C5     24.78  30.0  3
 6Y4  Var_05    F1   C21  C3   C2     69.69  30.0  3
 6Y4  Var_06    C15  C16  S    O3   -152.01  30.0  2
 6Y4  Var_07    H11  C12  C11  C10   -61.36  30.0  3
 6Y4  Var_08    H7   C13  C11  C10  -178.59  30.0  3
 6Y4  Var_09    H16  C17  S    C16   179.28  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
 6Y4  chir_01  C10  N3  C11  C9  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
 6Y4  plan-1  N3   0.020
 6Y4  plan-1  C5   0.020
 6Y4  plan-1  C4   0.020
 6Y4  plan-1  C3   0.020
 6Y4  plan-1  C2   0.020
 6Y4  plan-1  C1   0.020
 6Y4  plan-1  N2   0.020
 6Y4  plan-1  N1   0.020
 6Y4  plan-1  C21  0.020
 6Y4  plan-1  H2   0.020
 6Y4  plan-2  N4   0.020
 6Y4  plan-2  C14  0.020
 6Y4  plan-2  C15  0.020
 6Y4  plan-2  C16  0.020
 6Y4  plan-2  C20  0.020
 6Y4  plan-2  C19  0.020
 6Y4  plan-2  C18  0.020
 6Y4  plan-2  S    0.020
 6Y4  plan-2  H10  0.020
 6Y4  plan-2  H19  0.020
 6Y4  plan-2  H20  0.020
 6Y4  plan-2  H21  0.020
 6Y4  plan-3  N4   0.020
 6Y4  plan-3  C8   0.020
 6Y4  plan-3  C6   0.020
 6Y4  plan-3  C7   0.020
 6Y4  plan-3  C9   0.020
 6Y4  plan-3  C14  0.020
 6Y4  plan-3  C10  0.020
 6Y4  plan-3  N5   0.020
 6Y4  plan-3  H1   0.020

