# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:21:33 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[7-(methanesulfonyl)-1H-indol-3-yl]-N-[(3S)-piperidin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc2c1[nH]cc2c3nc(N[C@H]4CCCNC4)ncc3C(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
 3I3  3I3  "4-[7-(methanesulfonyl)-1H-indol-3-yl]-N-[(3S)-piperidin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine"  ligand  50  30  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3I3
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
 3I3  C1   C  CH3   0  -0.787  38.6267  31.1903  -41.8211
 3I3  C5   C  CR6   0  -0.257  38.3793  28.5322  -42.6515
 3I3  C6   C  CR16  0  -0.273  38.8430  27.5646  -41.7793
 3I3  C7   C  CR16  0  -0.249  39.6073  26.4950  -42.2510
 3I3  C8   C  CR16  0  -0.357  39.9277  26.3807  -43.5899
 3I3  C11  C  CR15  0  -0.050  38.9046  28.6749  -46.2091
 3I3  C15  C  CR6   0   0.305  40.3814  26.6763  -46.8038
 3I3  C17  C  CR6   0   0.607  42.2646  25.3751  -46.9644
 3I3  C19  C  CR16  0  -0.018  41.0052  25.5832  -48.8171
 3I3  C30  C  CH2   0  -0.289  45.6893  25.4323  -42.9218
 3I3  C32  C  CH2   0  -0.281  44.4601  26.3330  -44.7798
 3I3  S2   S  S     0   1.216  37.4336  29.8863  -42.0188
 3I3  O3   O  OS    0  -0.667  36.4763  30.2980  -43.0463
 3I3  O4   O  OS    0  -0.656  36.9292  29.5199  -40.6997
 3I3  C9   C  CR56  0   0.064  39.4761  27.3485  -44.4895
 3I3  C10  C  CR5   0  -0.057  39.5943  27.5263  -45.9142
 3I3  N12  N  NR15  0  -0.688  38.3706  29.2006  -45.0799
 3I3  C14  C  CR56  0   0.431  38.6875  28.4171  -44.0110
 3I3  N16  N  N     0  -0.498  41.4650  26.1588  -46.2403
 3I3  N18  N  N     0  -0.457  42.0894  25.0897  -48.2656
 3I3  C20  C  CR6   0  -0.430  40.0741  26.3730  -48.1438
 3I3  F22  F  F     0  -0.306  38.6192  26.0766  -49.9565
 3I3  F23  F  F     0  -0.310  37.7430  26.7296  -48.1108
 3I3  F24  F  F     0  -0.322  38.9242  28.0901  -49.2882
 3I3  N25  N  NH1   0  -0.664  43.3261  24.8237  -46.3648
 3I3  C26  C  CH1   0  -0.064  43.6967  25.0238  -44.9802
 3I3  C28  C  CH2   0  -0.455  44.5431  23.8511  -44.4964
 3I3  C29  C  CH2   0  -0.435  44.9989  24.0835  -43.0591
 3I3  N31  N  NH1   0  -0.597  44.7962  26.4833  -43.3776
 3I3  H1   H  HCH3  0   0.297  39.3881  30.8773  -41.1106
 3I3  H2   H  HCH3  0   0.295  39.0781  31.4182  -42.7847
 3I3  H3   H  HCH3  0   0.309  38.0946  32.0634  -41.4435
 3I3  H4   H  HCR6  0   0.281  38.6152  27.6333  -40.7244
 3I3  H5   H  HCR6  0   0.264  39.9546  25.7485  -41.5499
 3I3  H6   H  HCR6  0   0.267  40.5292  25.5521  -43.9342
 3I3  H7   H  HCR5  0   0.298  38.7774  29.1958  -47.1427
 3I3  H8   H  HCR6  0   0.282  40.8583  25.3305  -49.8611
 3I3  H9   H  HCH2  0   0.187  46.6339  25.4083  -43.4903
 3I3  H10  H  HCH2  0   0.232  45.9497  25.6182  -41.8780
 3I3  H11  H  HCH2  0   0.187  45.3471  26.3181  -45.4360
 3I3  H12  H  HCH2  0   0.236  43.8376  27.1740  -45.0911
 3I3  H13  H  HNR5  0   0.421  37.8044  30.0343  -45.0508
 3I3  H14  H  HNH1  0   0.396  43.9416  24.2852  -46.9552
 3I3  H15  H  HCH1  0   0.252  42.7833  25.0665  -44.3821
 3I3  H16  H  HCH2  0   0.245  43.9788  22.9194  -44.5778
 3I3  H17  H  HCH2  0   0.221  45.4218  23.7541  -45.1447
 3I3  H18  H  HCH2  0   0.220  44.1335  24.0536  -42.3911
 3I3  H19  H  HCH2  0   0.234  45.6745  23.2853  -42.7465
 3I3  H20  H  HNH1  0   0.353  45.2253  27.3869  -43.2289
 3I3  C21  C  CT    0   1.071  38.8479  26.8144  -48.8620

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
 3I3  F22  C21  single    1.340  0.020  1.340
 3I3  F24  C21  single    1.347  0.020  1.347
 3I3  C21  F23  single    1.339  0.020  1.339
 3I3  C21  C20  single    1.488  0.020  1.488
 3I3  C19  N18  aromatic  1.313  0.020  1.313
 3I3  C19  C20  aromatic  1.394  0.020  1.394
 3I3  N18  C17  aromatic  1.344  0.020  1.344
 3I3  C20  C15  aromatic  1.408  0.020  1.408
 3I3  C17  N25  single    1.338  0.020  1.338
 3I3  C17  N16  aromatic  1.333  0.020  1.333
 3I3  C15  N16  aromatic  1.326  0.020  1.326
 3I3  C15  C10  single    1.461  0.020  1.461
 3I3  N25  C26  single    1.447  0.020  1.447
 3I3  C11  C10  aromatic  1.372  0.020  1.372
 3I3  C11  N12  aromatic  1.355  0.020  1.355
 3I3  C10  C9   aromatic  1.441  0.020  1.441
 3I3  N12  C14  aromatic  1.363  0.020  1.363
 3I3  C26  C32  single    1.529  0.020  1.529
 3I3  C26  C28  single    1.525  0.020  1.525
 3I3  C32  N31  single    1.450  0.020  1.450
 3I3  C28  C29  single    1.526  0.020  1.526
 3I3  C9   C14  aromatic  1.412  0.020  1.412
 3I3  C9   C8   aromatic  1.396  0.020  1.396
 3I3  C14  C5   aromatic  1.399  0.020  1.399
 3I3  C8   C7   aromatic  1.381  0.020  1.381
 3I3  N31  C30  single    1.453  0.020  1.453
 3I3  C29  C30  single    1.521  0.020  1.521
 3I3  O3   S2   double    1.463  0.020  1.463
 3I3  C5   S2   single    1.769  0.020  1.769
 3I3  C5   C6   aromatic  1.383  0.020  1.383
 3I3  C7   C6   aromatic  1.397  0.020  1.397
 3I3  S2   C1   single    1.778  0.020  1.778
 3I3  S2   O4   double    1.459  0.020  1.459
 3I3  C1   H1   single    0.970  0.020  1.090
 3I3  C1   H2   single    0.970  0.020  1.090
 3I3  C1   H3   single    0.970  0.020  1.090
 3I3  C6   H4   single    0.930  0.020  1.080
 3I3  C7   H5   single    0.930  0.020  1.080
 3I3  C8   H6   single    0.930  0.020  1.080
 3I3  C11  H7   single    0.930  0.020  1.080
 3I3  C19  H8   single    0.930  0.020  1.080
 3I3  C30  H9   single    0.970  0.020  1.090
 3I3  C30  H10  single    0.970  0.020  1.090
 3I3  C32  H11  single    0.970  0.020  1.090
 3I3  C32  H12  single    0.970  0.020  1.090
 3I3  N12  H13  single    0.860  0.020  1.020
 3I3  N25  H14  single    0.860  0.020  1.020
 3I3  C26  H15  single    0.970  0.020  1.090
 3I3  C28  H16  single    0.970  0.020  1.090
 3I3  C28  H17  single    0.970  0.020  1.090
 3I3  C29  H18  single    0.970  0.020  1.090
 3I3  C29  H19  single    0.970  0.020  1.090
 3I3  N31  H20  single    0.890  0.020  1.040

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
 3I3  H3   C1   H2   109.97  3.000
 3I3  H3   C1   H1   110.24  3.000
 3I3  H2   C1   H1   110.39  3.000
 3I3  H3   C1   S2   107.36  3.000
 3I3  H2   C1   S2   109.48  3.000
 3I3  H1   C1   S2   109.35  3.000
 3I3  C14  C5   S2   121.90  3.000
 3I3  S2   C5   C6   119.30  3.000
 3I3  C14  C5   C6   118.79  3.000
 3I3  H4   C6   C7   119.56  3.000
 3I3  H4   C6   C5   120.02  3.000
 3I3  C7   C6   C5   120.42  3.000
 3I3  H5   C7   C8   119.78  3.000
 3I3  H5   C7   C6   119.04  3.000
 3I3  C8   C7   C6   121.18  3.000
 3I3  H6   C8   C9   120.42  3.000
 3I3  H6   C8   C7   120.11  3.000
 3I3  C9   C8   C7   119.47  3.000
 3I3  H7   C11  N12  119.23  3.000
 3I3  H7   C11  C10  130.61  3.000
 3I3  N12  C11  C10  110.11  3.000
 3I3  C20  C15  N16  119.91  3.000
 3I3  N16  C15  C10  114.12  3.000
 3I3  C20  C15  C10  125.97  3.000
 3I3  N25  C17  N18  116.73  3.000
 3I3  N25  C17  N16  118.34  3.000
 3I3  N18  C17  N16  124.93  3.000
 3I3  H8   C19  C20  120.43  3.000
 3I3  H8   C19  N18  115.40  3.000
 3I3  C20  C19  N18  124.17  3.000
 3I3  H10  C30  H9   106.99  3.000
 3I3  H10  C30  N31  108.87  3.000
 3I3  H9   C30  N31  112.38  3.000
 3I3  H10  C30  C29  110.21  3.000
 3I3  H9   C30  C29  108.83  3.000
 3I3  N31  C30  C29  109.52  3.000
 3I3  H12  C32  H11  107.41  3.000
 3I3  H12  C32  N31  109.16  3.000
 3I3  H11  C32  N31  112.97  3.000
 3I3  H12  C32  C26  109.73  3.000
 3I3  H11  C32  C26  108.17  3.000
 3I3  N31  C32  C26  109.35  3.000
 3I3  O4   S2   O3   118.63  3.000
 3I3  O4   S2   C5   108.42  3.000
 3I3  O3   S2   C5   108.30  3.000
 3I3  O4   S2   C1   108.39  3.000
 3I3  C5   S2   C1   104.03  3.000
 3I3  O3   S2   C1   108.10  3.000
 3I3  C14  C9   C10  106.72  3.000
 3I3  C14  C9   C8   119.14  3.000
 3I3  C10  C9   C8   134.12  3.000
 3I3  C9   C10  C15  125.08  3.000
 3I3  C9   C10  C11  105.94  3.000
 3I3  C15  C10  C11  128.85  3.000
 3I3  H13  N12  C14  125.69  3.000
 3I3  H13  N12  C11  124.48  3.000
 3I3  C14  N12  C11  109.81  3.000
 3I3  N12  C14  C9   107.41  3.000
 3I3  C9   C14  C5   120.99  3.000
 3I3  N12  C14  C5   131.60  3.000
 3I3  C17  N16  C15  119.25  3.000
 3I3  C19  N18  C17  115.77  3.000
 3I3  C21  C20  C19  119.03  3.000
 3I3  C19  C20  C15  115.84  3.000
 3I3  C21  C20  C15  125.13  3.000
 3I3  H14  N25  C26  118.53  3.000
 3I3  H14  N25  C17  116.22  3.000
 3I3  C26  N25  C17  125.09  3.000
 3I3  H15  C26  C28  108.68  3.000
 3I3  H15  C26  N25  108.36  3.000
 3I3  C28  C26  N25  109.83  3.000
 3I3  H15  C26  C32  108.20  3.000
 3I3  C28  C26  C32  109.87  3.000
 3I3  N25  C26  C32  111.82  3.000
 3I3  H17  C28  H16  107.14  3.000
 3I3  H17  C28  C29  109.34  3.000
 3I3  H16  C28  C29  110.76  3.000
 3I3  H17  C28  C26  108.98  3.000
 3I3  H16  C28  C26  110.21  3.000
 3I3  C29  C28  C26  110.33  3.000
 3I3  H19  C29  H18  107.16  3.000
 3I3  H19  C29  C28  110.08  3.000
 3I3  H18  C29  C28  109.57  3.000
 3I3  H19  C29  C30  109.97  3.000
 3I3  H18  C29  C30  109.16  3.000
 3I3  C28  C29  C30  110.83  3.000
 3I3  H20  N31  C32  109.46  3.000
 3I3  H20  N31  C30  109.85  3.000
 3I3  C32  N31  C30  111.78  3.000
 3I3  F24  C21  F23  106.51  3.000
 3I3  F23  C21  F22  106.42  3.000
 3I3  F24  C21  F22  105.83  3.000
 3I3  F23  C21  C20  112.98  3.000
 3I3  F24  C21  C20  112.76  3.000
 3I3  F22  C21  C20  111.82  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
 3I3  CONST_01  C11  N12  C14  C5    180.00   0.0  0
 3I3  CONST_02  C10  C9   C14  C5    180.00   0.0  0
 3I3  CONST_03  C8   C9   C14  C5      0.00   0.0  0
 3I3  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 3I3  CONST_05  N12  C14  C5   C6    180.00   0.0  0
 3I3  CONST_06  C9   C14  C5   C6      0.00   0.0  0
 3I3  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 3I3  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 3I3  CONST_09  C14  C9   C8   C7      0.00   0.0  0
 3I3  CONST_10  C14  C5   C6   C7      0.00   0.0  0
 3I3  CONST_11  C15  C10  C9   C8      0.00   0.0  0
 3I3  CONST_12  C11  C10  C9   C8    180.00   0.0  0
 3I3  CONST_13  N12  C14  C9   C8    180.00   0.0  0
 3I3  CONST_16  C14  C9   C10  C11     0.00   0.0  0
 3I3  CONST_17  C9   C14  N12  C11     0.00   0.0  0
 3I3  CONST_18  N18  C19  C20  C15     0.00   0.0  0
 3I3  CONST_19  N18  C17  N16  C15     0.00   0.0  0
 3I3  CONST_20  N12  C11  C10  C15   180.00   0.0  0
 3I3  CONST_21  C14  C9   C10  C15   180.00   0.0  0
 3I3  CONST_22  C20  C19  N18  C17     0.00   0.0  0
 3I3  CONST_23  C20  C15  N16  C17     0.00   0.0  0
 3I3  CONST_24  C10  C15  N16  C17   180.00   0.0  0
 3I3  CONST_25  N16  C17  N18  C19     0.00   0.0  0
 3I3  CONST_26  N16  C15  C20  C19     0.00   0.0  0
 3I3  CONST_27  C10  C15  C20  C19   180.00   0.0  0
 3I3  CONST_30  N12  C11  C10  C9      0.00   0.0  0
 3I3  CONST_31  C14  N12  C11  C10     0.00   0.0  0
 3I3  CONST_32  N12  C14  C9   C10     0.00   0.0  0
 3I3  CONST_33  S2   C5   C6   C7    180.00   0.0  0
 3I3  CONST_34  N25  C17  N16  C15   180.00   0.0  0
 3I3  CONST_35  N25  C17  N18  C19   180.00   0.0  0
 3I3  CONST_36  N18  C19  C20  C21   180.00   0.0  0
 3I3  CONST_37  N16  C15  C20  C21   180.00   0.0  0
 3I3  CONST_38  C10  C15  C20  C21     0.00   0.0  0
 3I3  CONST_39  N12  C14  C5   S2      0.00   0.0  0
 3I3  CONST_40  C9   C14  C5   S2    180.00   0.0  0
 3I3  CONST_41  C26  N25  C17  N16     0.00   0.0  0
 3I3  CONST_42  C26  N25  C17  N18   180.00   0.0  0
 3I3  CONST_43  H13  N12  C14  C5      0.00   0.0  0
 3I3  CONST_44  H5   C7   C6   C5    180.00   0.0  0
 3I3  CONST_45  H6   C8   C7   C6    180.00   0.0  0
 3I3  CONST_46  H4   C6   C7   C8    180.00   0.0  0
 3I3  CONST_47  H8   C19  C20  C15   180.00   0.0  0
 3I3  CONST_48  H7   C11  C10  C15     0.00   0.0  0
 3I3  CONST_49  H8   C19  N18  C17   180.00   0.0  0
 3I3  CONST_50  H7   C11  C10  C9    180.00   0.0  0
 3I3  CONST_51  H13  N12  C14  C9    180.00   0.0  0
 3I3  CONST_52  H5   C7   C8   C9    180.00   0.0  0
 3I3  CONST_53  H13  N12  C11  C10   180.00   0.0  0
 3I3  CONST_54  H6   C8   C9   C10     0.00   0.0  0
 3I3  CONST_55  H7   C11  N12  C14   180.00   0.0  0
 3I3  CONST_56  H6   C8   C9   C14   180.00   0.0  0
 3I3  CONST_57  H4   C6   C5   C14   180.00   0.0  0
 3I3  CONST_58  H14  N25  C17  N16   180.00   0.0  0
 3I3  CONST_59  H14  N25  C17  N18     0.00   0.0  0
 3I3  Var_01    C26  C32  N31  C30    63.24  30.0  1
 3I3  Var_02    C26  C28  C29  C30   -53.21  30.0  1
 3I3  Var_03    C29  C30  N31  C32   -62.18  30.0  1
 3I3  Var_04    N31  C30  C29  C28    56.37  30.0  1
 3I3  Var_05    H11  C32  N31  C30   -57.28  30.0  1
 3I3  Var_06    H12  C32  N31  C30  -176.70  30.0  1
 3I3  Var_07    H16  C28  C29  C30  -175.53  30.0  1
 3I3  Var_08    H17  C28  C29  C30    66.63  30.0  1
 3I3  Var_09    H9   C30  N31  C32    58.90  30.0  1
 3I3  Var_10    H10  C30  N31  C32   177.25  30.0  1
 3I3  Var_11    H20  N31  C32  C26  -174.82  30.0  1
 3I3  Var_12    H18  C29  C28  C26    67.31  30.0  1
 3I3  Var_13    H19  C29  C28  C26  -175.09  30.0  1
 3I3  Var_14    H9   C30  C29  C28   -66.84  30.0  1
 3I3  Var_15    H10  C30  C29  C28   176.12  30.0  1
 3I3  Var_16    H20  N31  C30  C29   176.10  30.0  1
 3I3  Var_17    H18  C29  C30  N31   -64.40  30.0  1
 3I3  Var_18    H19  C29  C30  N31   178.31  30.0  1
 3I3  Var_19    C14  C5   S2   C1    -82.50  30.0  3
 3I3  Var_20    C6   C5   S2   C1     96.74  30.0  3
 3I3  Var_21    O3   S2   C5   C6   -148.43  30.0  2
 3I3  Var_22    O4   S2   C5   C6    -18.48  30.0  2
 3I3  Var_23    F22  C21  C20  C15  -161.42  30.0  3
 3I3  Var_24    F24  C21  C20  C15    79.47  30.0  3
 3I3  Var_25    F23  C21  C20  C15   -41.38  30.0  3
 3I3  Var_26    F22  C21  C20  C19    17.81  30.0  3
 3I3  Var_27    F24  C21  C20  C19  -101.30  30.0  3
 3I3  Var_28    F23  C21  C20  C19   137.85  30.0  3
 3I3  Var_29    C14  C5   S2   O3     32.33  30.0  3
 3I3  Var_30    C14  C5   S2   O4    162.29  30.0  3
 3I3  Var_31    H1   C1   S2   C5    -61.18  30.0  3
 3I3  Var_32    H2   C1   S2   C5     59.88  30.0  3
 3I3  Var_33    H3   C1   S2   C5    179.22  30.0  3
 3I3  Var_34    H1   C1   S2   O3   -176.15  30.0  3
 3I3  Var_35    H2   C1   S2   O3    -55.10  30.0  3
 3I3  Var_36    H3   C1   S2   O3     64.25  30.0  3
 3I3  Var_37    H1   C1   S2   O4     54.06  30.0  3
 3I3  Var_38    H2   C1   S2   O4    175.11  30.0  3
 3I3  Var_39    H3   C1   S2   O4    -65.54  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
 3I3  chir_01  C26  N25  C32  C28  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
 3I3  plan-1  C15  0.020
 3I3  plan-1  C17  0.020
 3I3  plan-1  C19  0.020
 3I3  plan-1  C10  0.020
 3I3  plan-1  N16  0.020
 3I3  plan-1  N18  0.020
 3I3  plan-1  C20  0.020
 3I3  plan-1  N25  0.020
 3I3  plan-1  H8   0.020
 3I3  plan-1  C21  0.020
 3I3  plan-2  C5   0.020
 3I3  plan-2  C6   0.020
 3I3  plan-2  C7   0.020
 3I3  plan-2  C8   0.020
 3I3  plan-2  C11  0.020
 3I3  plan-2  C15  0.020
 3I3  plan-2  S2   0.020
 3I3  plan-2  C9   0.020
 3I3  plan-2  C10  0.020
 3I3  plan-2  N12  0.020
 3I3  plan-2  C14  0.020
 3I3  plan-2  H4   0.020
 3I3  plan-2  H5   0.020
 3I3  plan-2  H6   0.020
 3I3  plan-2  H7   0.020
 3I3  plan-2  H13  0.020
 3I3  plan-3  C17  0.020
 3I3  plan-3  N25  0.020
 3I3  plan-3  C26  0.020
 3I3  plan-3  H14  0.020

