# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 21:49:54 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-(2-aminoethyl)-N-{5-[(1-cycloheptyl-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino]pyridin-2-yl}methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N(CCN)c1ccc(Nc2ncc3cnn(C4CCCCCC4)c3n2)cn1
#
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
 D36  D36  N-(2-aminoethyl)-N-{5-[(1-cycloheptyl-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino]pyridin-2-yl}methanesulfonamide  ligand  59  31  .  2022-07-24  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_D36
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
 D36  S     S  S     0   1.345   5.9360   1.4975   0.3082
 D36  C1    C  CH3   0  -0.782   5.7022   2.4751  -1.1543
 D36  N1    N  N     0  -0.708   5.1284   0.0595   0.0307
 D36  O1    O  OS    0  -0.654   7.3489   1.1524   0.3808
 D36  C2    C  CH2   0  -0.327   5.8983  -1.1510  -0.2554
 D36  N2    N  NH2   0  -0.801   7.0323  -3.1176   0.5895
 D36  O2    O  OS    0  -0.652   5.3279   2.1719   1.4415
 D36  C3    C  CH2   0  -0.291   6.4184  -1.8634   0.9877
 D36  N3    N  NH1   0  -0.766  -0.3955   0.1571   0.2930
 D36  C4    C  CR6   0   0.549   3.7309   0.0136   0.1408
 D36  N4    N  N     0  -0.499  -2.6125  -0.2794   0.0843
 D36  C5    C  CR16  0  -0.359   3.0641  -1.1698   0.4551
 D36  N5    N  NR5   0  -0.393  -4.8700  -1.0295  -0.2239
 D36  C6    C  CR16  0  -0.174   1.6832  -1.1708   0.5015
 D36  N6    N  N     0  -0.243  -5.4895  -2.1820  -0.5560
 D36  C7    C  CR6   0   0.257   0.9867   0.0095   0.2423
 D36  N7    N  N     0  -0.474  -0.9991  -2.0030  -0.3027
 D36  C8    C  CR6   0   0.602  -1.3732  -0.7486   0.0156
 D36  N8    N  N     0  -0.448   3.0739   1.1357  -0.0914
 D36  C9    C  CR56  0   0.620  -3.5365  -1.1864  -0.2003
 D36  C10   C  CH1   0  -0.081  -5.6404   0.1681   0.0737
 D36  C11   C  CH2   0  -0.425  -6.4614  -0.0647   1.3451
 D36  C12   C  CH2   0  -0.439  -7.0588   1.1869   1.9769
 D36  C13   C  CH2   0  -0.436  -7.9051   2.0737   1.0661
 D36  C14   C  CH2   0  -0.450  -7.0751   2.8169   0.0189
 D36  C15   C  CH2   0  -0.431  -6.7930   2.0450  -1.2718
 D36  C16   C  CH2   0  -0.448  -6.5120   0.5484  -1.1282
 D36  C17   C  CR15  0  -0.098  -4.5678  -3.0846  -0.7524
 D36  C18   C  CR56  0  -0.220  -3.2813  -2.5252  -0.5442
 D36  C19   C  CR16  0  -0.023  -1.9391  -2.8818  -0.5798
 D36  C20   C  CR16  0  -0.133   1.7535   1.1386  -0.0359
 D36  H1    H  HCH3  0   0.299   4.6463   2.6916  -1.2782
 D36  H1A   H  HCH3  0   0.301   6.2704   3.3949  -1.0209
 D36  H1B   H  HCH3  0   0.290   6.0860   1.9235  -2.0093
 D36  H2    H  HCH2  0   0.264   5.2432  -1.8125  -0.8254
 D36  H2A   H  HCH2  0   0.279   6.7281  -0.9097  -0.9190
 D36  HN2   H  HNH2  0   0.355   7.5474  -3.5065   1.3677
 D36  HN2A  H  HNH2  0   0.344   6.3141  -3.7954   0.3668
 D36  H3    H  HCH2  0   0.237   7.1760  -1.2392   1.4610
 D36  H3A   H  HCH2  0   0.205   5.6058  -1.9739   1.7191
 D36  HN3   H  HNH1  0   0.409  -0.7342   1.0994   0.4185
 D36  H5    H  HCR6  0   0.284   3.5966  -2.0820   0.6824
 D36  H6    H  HCR6  0   0.288   1.1631  -2.0813   0.7525
 D36  H10   H  HCH1  0   0.258  -4.8901   0.9442   0.2493
 D36  H11   H  HCH2  0   0.226  -7.2602  -0.7738   1.1074
 D36  H11A  H  HCH2  0   0.238  -5.8263  -0.5527   2.0894
 D36  H12   H  HCH2  0   0.233  -7.6612   0.8651   2.8304
 D36  H12A  H  HCH2  0   0.216  -6.2510   1.7975   2.3937
 D36  H13   H  HCH2  0   0.217  -8.6993   1.4898   0.5888
 D36  H13A  H  HCH2  0   0.232  -8.4141   2.8073   1.6959
 D36  H14   H  HCH2  0   0.234  -7.5721   3.7517  -0.2510
 D36  H14A  H  HCH2  0   0.216  -6.1298   3.1140   0.4839
 D36  H15   H  HCH2  0   0.227  -7.6431   2.1538  -1.9498
 D36  H15A  H  HCH2  0   0.226  -5.9471   2.5197  -1.7759
 D36  H16   H  HCH2  0   0.246  -6.0291   0.2088  -2.0471
 D36  H16A  H  HCH2  0   0.230  -7.4493  -0.0101  -1.0628
 D36  H17   H  HCR5  0   0.275  -4.8321  -4.0925  -1.0334
 D36  H19   H  HCR6  0   0.279  -1.6160  -3.8850  -0.8363
 D36  H20   H  HCR6  0   0.277   1.2657   2.0892  -0.2295

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
 D36  C1   S     single    1.775  0.020  1.775
 D36  O2   S     double    1.452  0.020  1.452
 D36  S    N1    single    1.672  0.020  1.672
 D36  S    O1    double    1.456  0.020  1.456
 D36  C1   H1    single    0.970  0.020  1.090
 D36  C1   H1A   single    0.970  0.020  1.090
 D36  C1   H1B   single    0.970  0.020  1.090
 D36  C2   N1    single    1.463  0.020  1.463
 D36  N1   C4    single    1.403  0.020  1.403
 D36  C3   C2    single    1.524  0.020  1.524
 D36  C2   H2    single    0.970  0.020  1.090
 D36  C2   H2A   single    0.970  0.020  1.090
 D36  N2   C3    single    1.452  0.020  1.452
 D36  N2   HN2   single    0.890  0.020  1.040
 D36  N2   HN2A  single    0.890  0.020  1.040
 D36  C3   H3    single    0.970  0.020  1.090
 D36  C3   H3A   single    0.970  0.020  1.090
 D36  C7   N3    single    1.391  0.020  1.391
 D36  N3   C8    single    1.361  0.020  1.361
 D36  N3   HN3   single    0.860  0.020  1.020
 D36  C4   C5    aromatic  1.394  0.020  1.394
 D36  C4   N8    aromatic  1.321  0.020  1.321
 D36  N4   C8    aromatic  1.327  0.020  1.327
 D36  N4   C9    aromatic  1.326  0.020  1.326
 D36  C5   C6    aromatic  1.382  0.020  1.382
 D36  C5   H5    single    0.930  0.020  1.080
 D36  C10  N5    single    1.455  0.020  1.455
 D36  N5   C9    aromatic  1.343  0.020  1.343
 D36  N5   N6    aromatic  1.350  0.020  1.350
 D36  C6   C7    aromatic  1.395  0.020  1.395
 D36  C6   H6    single    0.930  0.020  1.080
 D36  N6   C17   aromatic  1.305  0.020  1.305
 D36  C20  C7    aromatic  1.393  0.020  1.393
 D36  C8   N7    aromatic  1.347  0.020  1.347
 D36  N7   C19   aromatic  1.316  0.020  1.316
 D36  N8   C20   aromatic  1.322  0.020  1.322
 D36  C9   C18   aromatic  1.406  0.020  1.406
 D36  C16  C10   single    1.533  0.020  1.533
 D36  C11  C10   single    1.531  0.020  1.531
 D36  C10  H10   single    0.970  0.020  1.090
 D36  C12  C11   single    1.524  0.020  1.524
 D36  C11  H11   single    0.970  0.020  1.090
 D36  C11  H11A  single    0.970  0.020  1.090
 D36  C13  C12   single    1.527  0.020  1.527
 D36  C12  H12   single    0.970  0.020  1.090
 D36  C12  H12A  single    0.970  0.020  1.090
 D36  C14  C13   single    1.529  0.020  1.529
 D36  C13  H13   single    0.970  0.020  1.090
 D36  C13  H13A  single    0.970  0.020  1.090
 D36  C14  C15   single    1.530  0.020  1.530
 D36  C14  H14   single    0.970  0.020  1.090
 D36  C14  H14A  single    0.970  0.020  1.090
 D36  C15  C16   single    1.529  0.020  1.529
 D36  C15  H15   single    0.970  0.020  1.090
 D36  C15  H15A  single    0.970  0.020  1.090
 D36  C16  H16   single    0.970  0.020  1.090
 D36  C16  H16A  single    0.970  0.020  1.090
 D36  C18  C17   aromatic  1.418  0.020  1.418
 D36  C17  H17   single    0.930  0.020  1.080
 D36  C18  C19   aromatic  1.389  0.020  1.389
 D36  C19  H19   single    0.930  0.020  1.080
 D36  C20  H20   single    0.930  0.020  1.080

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
 D36  O2    S    O1   118.52  3.000
 D36  O1    S    N1   105.84  3.000
 D36  O2    S    N1   109.06  3.000
 D36  O1    S    C1   107.42  3.000
 D36  N1    S    C1   105.86  3.000
 D36  O2    S    C1   109.40  3.000
 D36  H1B   C1   H1A  109.91  3.000
 D36  H1B   C1   H1   110.79  3.000
 D36  H1A   C1   H1   110.68  3.000
 D36  H1B   C1   S    108.79  3.000
 D36  H1A   C1   S    107.19  3.000
 D36  H1    C1   S    109.40  3.000
 D36  C4    N1   C2   120.84  3.000
 D36  C4    N1   S    119.75  3.000
 D36  C2    N1   S    119.33  3.000
 D36  H2A   C2   H2   105.85  3.000
 D36  H2A   C2   C3   109.90  3.000
 D36  H2    C2   C3   110.33  3.000
 D36  H2A   C2   N1   109.68  3.000
 D36  H2    C2   N1   106.72  3.000
 D36  C3    C2   N1   114.01  3.000
 D36  HN2A  N2   HN2  105.86  3.000
 D36  HN2A  N2   C3   109.80  3.000
 D36  HN2   N2   C3   109.67  3.000
 D36  H3A   C3   H3   106.42  3.000
 D36  H3A   C3   N2   114.10  3.000
 D36  H3    C3   N2   108.66  3.000
 D36  H3A   C3   C2   109.72  3.000
 D36  H3    C3   C2   108.88  3.000
 D36  N2    C3   C2   108.92  3.000
 D36  HN3   N3   C8   113.92  3.000
 D36  HN3   N3   C7   115.92  3.000
 D36  C8    N3   C7   129.47  3.000
 D36  N8    C4   C5   121.52  3.000
 D36  N8    C4   N1   117.00  3.000
 D36  C5    C4   N1   121.47  3.000
 D36  C9    N4   C8   113.45  3.000
 D36  H5    C5   C6   119.01  3.000
 D36  H5    C5   C4   121.89  3.000
 D36  C6    C5   C4   119.09  3.000
 D36  C10   N5   C9   128.20  3.000
 D36  C9    N5   N6   111.12  3.000
 D36  C10   N5   N6   120.68  3.000
 D36  H6    C6   C7   121.13  3.000
 D36  H6    C6   C5   119.38  3.000
 D36  C7    C6   C5   119.48  3.000
 D36  C17   N6   N5   107.66  3.000
 D36  C20   C7   C6   116.63  3.000
 D36  C20   C7   N3   117.93  3.000
 D36  C6    C7   N3   125.39  3.000
 D36  C19   N7   C8   118.24  3.000
 D36  N7    C8   N4   126.93  3.000
 D36  N7    C8   N3   117.92  3.000
 D36  N4    C8   N3   115.15  3.000
 D36  C20   N8   C4   119.43  3.000
 D36  C18   C9   N5   106.69  3.000
 D36  C18   C9   N4   125.28  3.000
 D36  N5    C9   N4   128.03  3.000
 D36  H10   C10  C16  109.88  3.000
 D36  H10   C10  C11  110.02  3.000
 D36  C16   C10  C11  112.58  3.000
 D36  H10   C10  N5   104.70  3.000
 D36  C11   C10  N5   109.18  3.000
 D36  C16   C10  N5   110.18  3.000
 D36  H11A  C11  H11  106.41  3.000
 D36  H11A  C11  C12  108.18  3.000
 D36  H11   C11  C12  109.63  3.000
 D36  H11A  C11  C10  108.76  3.000
 D36  H11   C11  C10  108.04  3.000
 D36  C12   C11  C10  115.44  3.000
 D36  H12A  C12  H12  105.87  3.000
 D36  H12A  C12  C13  108.18  3.000
 D36  H12   C12  C13  109.35  3.000
 D36  H12A  C12  C11  109.06  3.000
 D36  H12   C12  C11  107.34  3.000
 D36  C13   C12  C11  116.55  3.000
 D36  H13A  C13  H13  105.74  3.000
 D36  H13A  C13  C14  108.74  3.000
 D36  H13   C13  C14  110.75  3.000
 D36  H13A  C13  C12  107.72  3.000
 D36  H13   C13  C12  110.62  3.000
 D36  C14   C13  C12  112.95  3.000
 D36  H14A  C14  H14  105.40  3.000
 D36  H14A  C14  C15  109.64  3.000
 D36  H14   C14  C15  107.89  3.000
 D36  H14A  C14  C13  108.05  3.000
 D36  H14   C14  C13  109.76  3.000
 D36  C15   C14  C13  115.64  3.000
 D36  H15A  C15  H15  105.82  3.000
 D36  H15A  C15  C16  109.03  3.000
 D36  H15   C15  C16  107.37  3.000
 D36  H15A  C15  C14  108.21  3.000
 D36  H15   C15  C14  109.25  3.000
 D36  C16   C15  C14  116.63  3.000
 D36  H16A  C16  H16  105.70  3.000
 D36  H16A  C16  C15  110.37  3.000
 D36  H16   C16  C15  107.84  3.000
 D36  H16A  C16  C10  108.30  3.000
 D36  H16   C16  C10  109.34  3.000
 D36  C15   C16  C10  114.89  3.000
 D36  H17   C17  C18  128.96  3.000
 D36  H17   C17  N6   120.81  3.000
 D36  C18   C17  N6   110.23  3.000
 D36  C19   C18  C17  140.48  3.000
 D36  C19   C18  C9   115.23  3.000
 D36  C17   C18  C9   104.30  3.000
 D36  H19   C19  C18  122.09  3.000
 D36  H19   C19  N7   117.04  3.000
 D36  C18   C19  N7   120.87  3.000
 D36  H20   C20  N8   116.31  3.000
 D36  H20   C20  C7   119.87  3.000
 D36  N8    C20  C7   123.82  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
 D36  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 D36  CONST_02  C7   C20  N8   C4      0.00   0.0  0
 D36  CONST_03  C19  N7   C8   N4      0.00   0.0  0
 D36  CONST_04  N6   N5   C9   N4    180.00   0.0  0
 D36  CONST_05  C17  C18  C9   N4    180.00   0.0  0
 D36  CONST_06  C19  C18  C9   N4      0.00   0.0  0
 D36  CONST_07  C20  N8   C4   C5      0.00   0.0  0
 D36  CONST_08  C20  C7   C6   C5      0.00   0.0  0
 D36  CONST_09  C8   N4   C9   N5    180.00   0.0  0
 D36  CONST_10  C17  C18  C9   N5      0.00   0.0  0
 D36  CONST_11  C19  C18  C9   N5    180.00   0.0  0
 D36  CONST_12  C18  C17  N6   N5      0.00   0.0  0
 D36  CONST_13  N8   C4   C5   C6      0.00   0.0  0
 D36  CONST_14  N8   C20  C7   C6      0.00   0.0  0
 D36  CONST_15  C18  C9   N5   N6      0.00   0.0  0
 D36  CONST_16  C9   C18  C17  N6      0.00   0.0  0
 D36  CONST_17  C19  C18  C17  N6    180.00   0.0  0
 D36  CONST_18  C9   N4   C8   N7      0.00   0.0  0
 D36  CONST_19  C9   C18  C19  N7      0.00   0.0  0
 D36  CONST_20  C17  C18  C19  N7    180.00   0.0  0
 D36  CONST_21  C18  C9   N4   C8      0.00   0.0  0
 D36  CONST_22  C18  C19  N7   C8      0.00   0.0  0
 D36  CONST_23  C17  N6   N5   C9      0.00   0.0  0
 D36  CONST_24  C10  N5   C9   N4      0.00   0.0  0
 D36  CONST_25  C18  C9   N5   C10   180.00   0.0  0
 D36  CONST_26  C17  N6   N5   C10   180.00   0.0  0
 D36  CONST_27  C6   C5   C4   N1    180.00   0.0  0
 D36  CONST_28  C20  N8   C4   N1    180.00   0.0  0
 D36  CONST_29  C5   C6   C7   N3    180.00   0.0  0
 D36  CONST_30  N8   C20  C7   N3    180.00   0.0  0
 D36  CONST_31  C9   N4   C8   N3    180.00   0.0  0
 D36  CONST_32  C19  N7   C8   N3    180.00   0.0  0
 D36  CONST_33  H6   C6   C5   C4    180.00   0.0  0
 D36  CONST_34  H20  C20  N8   C4    180.00   0.0  0
 D36  CONST_35  H17  C17  N6   N5    180.00   0.0  0
 D36  CONST_36  H5   C5   C6   C7    180.00   0.0  0
 D36  CONST_37  H19  C19  N7   C8    180.00   0.0  0
 D36  Var_01    C7   N3   C8   N4   -176.30  30.0  1
 D36  Var_02    C8   N3   C7   C6    -31.83  30.0  2
 D36  Var_03    C4   N1   S    C1    -77.26  30.0  3
 D36  Var_04    N2   C3   C2   N1    173.72  30.0  2
 D36  Var_05    H1   C1   S    N1     63.27  30.0  3
 D36  Var_06    HN2  N2   C3   C2    168.29  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
 D36  chir_01  C10  N5  C16  C11  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
 D36  plan-1  N1   0.020
 D36  plan-1  N3   0.020
 D36  plan-1  C4   0.020
 D36  plan-1  C5   0.020
 D36  plan-1  C6   0.020
 D36  plan-1  C7   0.020
 D36  plan-1  N8   0.020
 D36  plan-1  C20  0.020
 D36  plan-1  H5   0.020
 D36  plan-1  H6   0.020
 D36  plan-1  H20  0.020
 D36  plan-2  N3   0.020
 D36  plan-2  N4   0.020
 D36  plan-2  N5   0.020
 D36  plan-2  N6   0.020
 D36  plan-2  N7   0.020
 D36  plan-2  C8   0.020
 D36  plan-2  C9   0.020
 D36  plan-2  C10  0.020
 D36  plan-2  C17  0.020
 D36  plan-2  C18  0.020
 D36  plan-2  C19  0.020
 D36  plan-2  H17  0.020
 D36  plan-2  H19  0.020
 D36  plan-3  S    0.020
 D36  plan-3  N1   0.020
 D36  plan-3  C2   0.020
 D36  plan-3  C4   0.020

