# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:48:30 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 6-(2H-indazol-4-yl)-1-methyl-N-[3-(methylsulfonyl)propyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc2c(NCCC[S](C)(=O)=O)nc(nc12)c3cccc4n[nH]cc34
#
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
 NZU  NZU  6-(2H-indazol-4-yl)-1-methyl-N-[3-(methylsulfonyl)propyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  46  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NZU
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
 NZU  C1    C  CH3   0  -0.495   4.5544   3.9229   0.0235
 NZU  N2    N  NR5   0  -0.382   3.1545   3.5898  -0.0015
 NZU  C3    C  CR56  0   0.614   2.5983   2.3635  -0.0115
 NZU  C4    C  CR56  0  -0.253   1.2160   2.5540  -0.0095
 NZU  C5    C  CR15  0  -0.091   1.0522   3.9570   0.0062
 NZU  N6    N  N     0  -0.241   2.2185   4.5519   0.0122
 NZU  C7    C  CR6   0   0.558   0.4490   1.3694  -0.0214
 NZU  N8    N  N     0  -0.533   1.0672   0.1954  -0.0298
 NZU  C9    C  CR6   0   0.395   2.4094   0.1544  -0.0263
 NZU  N10   N  N     0  -0.482   3.2277   1.1918  -0.0198
 NZU  C11   C  CR6   0  -0.022   3.0271  -1.1856  -0.0206
 NZU  C12   C  CR16  0  -0.326   4.3953  -1.3192   0.0202
 NZU  C13   C  CR16  0  -0.234   5.0356  -2.5816   0.0410
 NZU  C14   C  CR16  0  -0.280   4.3246  -3.7478   0.0270
 NZU  C15   C  CR56  0   0.249   2.9174  -3.6541  -0.0154
 NZU  C16   C  CR56  0  -0.095   2.2628  -2.3850  -0.0454
 NZU  C17   C  CR15  0   0.002   0.9125  -2.7177  -0.1018
 NZU  N18   N  NR15  0  -0.389   0.8715  -4.0522  -0.0965
 NZU  N19   N  N     0  -0.295   2.0408  -4.6607  -0.0437
 NZU  N21   N  NH1   0  -0.673  -0.8902   1.3976  -0.0224
 NZU  C22   C  CH2   0  -0.222  -1.7291   0.2234  -0.0266
 NZU  C23   C  CH2   0  -0.489  -3.1879   0.6525   0.0125
 NZU  C24   C  CH2   0  -0.591  -4.1223  -0.5460   0.0127
 NZU  S25   S  S     0   1.194  -5.8275   0.0348   0.0265
 NZU  O26   O  OS    0  -0.634  -6.0526   0.7256   1.2874
 NZU  O27   O  OS    0  -0.634  -6.0727   0.7211  -1.2331
 NZU  C28   C  CH3   0  -0.767  -6.7849  -1.4730   0.0363
 NZU  H1    H  HCH3  0   0.246   4.8299   4.3701   0.9770
 NZU  H1A   H  HCH3  0   0.254   5.1290   3.0127  -0.1178
 NZU  H1B   H  HCH3  0   0.248   4.7893   4.6179  -0.7793
 NZU  H5    H  HCR5  0   0.234   0.1487   4.5470   0.0107
 NZU  H12   H  HCR6  0   0.246   5.0082  -0.4292   0.0398
 NZU  H13   H  HCR6  0   0.238   6.1165  -2.6115   0.0694
 NZU  H14   H  HCR6  0   0.242   4.8150  -4.7120   0.0453
 NZU  H17   H  HCR5  0   0.272   0.0216  -2.1245  -0.1622
 NZU  HN21  H  HNH1  0   0.379  -1.3385   2.2973  -0.0155
 NZU  H22   H  HCH2  0   0.230  -1.5372  -0.3753  -0.9222
 NZU  H22A  H  HCH2  0   0.229  -1.4979  -0.4072   0.8367
 NZU  H23   H  HCH2  0   0.266  -3.3689   1.2525   0.9073
 NZU  H23A  H  HCH2  0   0.264  -3.4062   1.2806  -0.8545
 NZU  H24   H  HCH2  0   0.269  -3.9914  -1.1628  -0.8784
 NZU  H24A  H  HCH2  0   0.268  -3.9785  -1.1725   0.8951
 NZU  H28   H  HCH3  0   0.266  -6.5706  -2.0486   0.9336
 NZU  H28A  H  HCH3  0   0.299  -7.8323  -1.1741   0.0400
 NZU  H28B  H  HCH3  0   0.264  -6.5773  -2.0562  -0.8578
 NZU  HN18  H  HNR5  0   0.400   0.0313  -4.6037  -0.1440

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
 NZU  N2   C1    single    1.439  0.020  1.439
 NZU  C1   H1    single    0.970  0.020  1.090
 NZU  C1   H1A   single    0.970  0.020  1.090
 NZU  C1   H1B   single    0.970  0.020  1.090
 NZU  C3   N2    aromatic  1.347  0.020  1.347
 NZU  N2   N6    aromatic  1.342  0.020  1.342
 NZU  N10  C3    aromatic  1.330  0.020  1.330
 NZU  C4   C3    aromatic  1.395  0.020  1.395
 NZU  C7   C4    aromatic  1.411  0.020  1.411
 NZU  C4   C5    aromatic  1.413  0.020  1.413
 NZU  C5   N6    aromatic  1.309  0.020  1.309
 NZU  C5   H5    single    0.930  0.020  1.080
 NZU  N8   C7    aromatic  1.327  0.020  1.327
 NZU  N21  C7    single    1.340  0.020  1.340
 NZU  N8   C9    aromatic  1.343  0.020  1.343
 NZU  C11  C9    single    1.476  0.020  1.476
 NZU  C9   N10   aromatic  1.321  0.020  1.321
 NZU  C12  C11   aromatic  1.375  0.020  1.375
 NZU  C11  C16   aromatic  1.422  0.020  1.422
 NZU  C13  C12   aromatic  1.416  0.020  1.416
 NZU  C12  H12   single    0.930  0.020  1.080
 NZU  C13  C14   aromatic  1.366  0.020  1.366
 NZU  C13  H13   single    0.930  0.020  1.080
 NZU  C14  C15   aromatic  1.411  0.020  1.411
 NZU  C14  H14   single    0.930  0.020  1.080
 NZU  C15  N19   aromatic  1.335  0.020  1.335
 NZU  C15  C16   aromatic  1.428  0.020  1.428
 NZU  C16  C17   aromatic  1.392  0.020  1.392
 NZU  N18  C17   aromatic  1.335  0.020  1.335
 NZU  C17  H17   single    0.930  0.020  1.080
 NZU  N19  N18   aromatic  1.319  0.020  1.319
 NZU  C22  N21   single    1.443  0.020  1.443
 NZU  N21  HN21  single    0.860  0.020  1.020
 NZU  C22  C23   single    1.521  0.020  1.521
 NZU  C22  H22   single    0.970  0.020  1.090
 NZU  C22  H22A  single    0.970  0.020  1.090
 NZU  C23  C24   single    1.520  0.020  1.520
 NZU  C23  H23   single    0.970  0.020  1.090
 NZU  C23  H23A  single    0.970  0.020  1.090
 NZU  C24  S25   single    1.801  0.020  1.801
 NZU  C24  H24   single    0.970  0.020  1.090
 NZU  C24  H24A  single    0.970  0.020  1.090
 NZU  C28  S25   single    1.786  0.020  1.786
 NZU  O27  S25   double    1.455  0.020  1.455
 NZU  S25  O26   double    1.455  0.020  1.455
 NZU  C28  H28   single    0.970  0.020  1.090
 NZU  C28  H28A  single    0.970  0.020  1.090
 NZU  C28  H28B  single    0.970  0.020  1.090
 NZU  N18  HN18  single    0.860  0.020  1.020

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
 NZU  H1B   C1   H1A   108.99  3.000
 NZU  H1B   C1   H1    109.23  3.000
 NZU  H1A   C1   H1    108.93  3.000
 NZU  H1B   C1   N2    110.19  3.000
 NZU  H1A   C1   N2    108.57  3.000
 NZU  H1    C1   N2    110.89  3.000
 NZU  N6    N2   C3    111.39  3.000
 NZU  N6    N2   C1    120.81  3.000
 NZU  C3    N2   C1    127.79  3.000
 NZU  N10   C3   C4    126.09  3.000
 NZU  C4    C3   N2    106.55  3.000
 NZU  N10   C3   N2    127.36  3.000
 NZU  C7    C4   C5    140.42  3.000
 NZU  C5    C4   C3    104.50  3.000
 NZU  C7    C4   C3    115.08  3.000
 NZU  H5    C5   N6    119.83  3.000
 NZU  H5    C5   C4    129.80  3.000
 NZU  N6    C5   C4    110.37  3.000
 NZU  C5    N6   N2    107.18  3.000
 NZU  N21   C7   N8    118.98  3.000
 NZU  N21   C7   C4    121.71  3.000
 NZU  N8    C7   C4    119.31  3.000
 NZU  C9    N8   C7    119.52  3.000
 NZU  C11   C9   N10   116.98  3.000
 NZU  N10   C9   N8    126.52  3.000
 NZU  C11   C9   N8    116.50  3.000
 NZU  C9    N10  C3    113.49  3.000
 NZU  C16   C11  C12   116.95  3.000
 NZU  C16   C11  C9    122.73  3.000
 NZU  C12   C11  C9    120.32  3.000
 NZU  H12   C12  C13   118.53  3.000
 NZU  H12   C12  C11   118.99  3.000
 NZU  C13   C12  C11   122.48  3.000
 NZU  H13   C13  C14   119.79  3.000
 NZU  H13   C13  C12   118.49  3.000
 NZU  C14   C13  C12   121.72  3.000
 NZU  H14   C14  C15   120.78  3.000
 NZU  H14   C14  C13   121.65  3.000
 NZU  C15   C14  C13   117.56  3.000
 NZU  N19   C15  C16   111.63  3.000
 NZU  C16   C15  C14   121.11  3.000
 NZU  N19   C15  C14   127.25  3.000
 NZU  C17   C16  C15   103.48  3.000
 NZU  C17   C16  C11   136.35  3.000
 NZU  C15   C16  C11   120.17  3.000
 NZU  H17   C17  N18   121.86  3.000
 NZU  H17   C17  C16   132.55  3.000
 NZU  N18   C17  C16   105.57  3.000
 NZU  HN18  N18  N19   119.29  3.000
 NZU  HN18  N18  C17   124.98  3.000
 NZU  N19   N18  C17   115.72  3.000
 NZU  N18   N19  C15   103.59  3.000
 NZU  HN21  N21  C22   117.97  3.000
 NZU  HN21  N21  C7    117.69  3.000
 NZU  C22   N21  C7    124.34  3.000
 NZU  H22A  C22  H22   107.06  3.000
 NZU  H22A  C22  C23   110.19  3.000
 NZU  H22   C22  C23   110.10  3.000
 NZU  H22A  C22  N21   110.11  3.000
 NZU  H22   C22  N21   110.22  3.000
 NZU  C23   C22  N21   109.14  3.000
 NZU  H23A  C23  H23   107.52  3.000
 NZU  H23A  C23  C24   109.30  3.000
 NZU  H23   C23  C24   109.34  3.000
 NZU  H23A  C23  C22   109.47  3.000
 NZU  H23   C23  C22   109.57  3.000
 NZU  C24   C23  C22   111.54  3.000
 NZU  H24A  C24  H24   108.65  3.000
 NZU  H24A  C24  S25   107.67  3.000
 NZU  H24   C24  S25   107.57  3.000
 NZU  H24A  C24  C23   111.82  3.000
 NZU  H24   C24  C23   111.82  3.000
 NZU  S25   C24  C23   109.13  3.000
 NZU  C28   S25  O27   108.21  3.000
 NZU  O27   S25  O26   120.00  3.000
 NZU  C28   S25  O26   108.25  3.000
 NZU  O26   S25  C24   107.82  3.000
 NZU  O27   S25  C24   107.76  3.000
 NZU  C28   S25  C24   103.61  3.000
 NZU  H28B  C28  H28A  109.49  3.000
 NZU  H28B  C28  H28   110.91  3.000
 NZU  H28A  C28  H28   109.39  3.000
 NZU  H28B  C28  S25   110.24  3.000
 NZU  H28A  C28  S25   106.49  3.000
 NZU  H28   C28  S25   110.22  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
 NZU  CONST_01  C9    N10  C3   N2    180.00   0.0  0
 NZU  CONST_02  C7    C4   C3   N2    180.00   0.0  0
 NZU  CONST_03  C5    C4   C3   N2      0.00   0.0  0
 NZU  CONST_04  C4    C5   N6   N2      0.00   0.0  0
 NZU  CONST_05  C5    N6   N2   C3      0.00   0.0  0
 NZU  CONST_06  N8    C9   N10  C3      0.00   0.0  0
 NZU  CONST_07  C11   C9   N10  C3    180.00   0.0  0
 NZU  CONST_08  N8    C7   C4   C3      0.00   0.0  0
 NZU  CONST_09  N6    C5   C4   C3      0.00   0.0  0
 NZU  CONST_10  N6    N2   C3   C4      0.00   0.0  0
 NZU  CONST_11  C9    N10  C3   C4      0.00   0.0  0
 NZU  CONST_12  C9    N8   C7   C4      0.00   0.0  0
 NZU  CONST_13  N10   C3   C4   C5    180.00   0.0  0
 NZU  CONST_14  N8    C7   C4   C5    180.00   0.0  0
 NZU  CONST_15  N10   C3   N2   N6    180.00   0.0  0
 NZU  CONST_16  C7    C4   C5   N6    180.00   0.0  0
 NZU  CONST_17  N10   C3   C4   C7      0.00   0.0  0
 NZU  CONST_18  C11   C9   N8   C7    180.00   0.0  0
 NZU  CONST_19  N10   C9   N8   C7      0.00   0.0  0
 NZU  CONST_20  C12   C11  C9   N8    180.00   0.0  0
 NZU  CONST_21  C16   C11  C9   N8      0.00   0.0  0
 NZU  CONST_22  C13   C12  C11  C9    180.00   0.0  0
 NZU  CONST_23  C15   C16  C11  C9    180.00   0.0  0
 NZU  CONST_24  C17   C16  C11  C9      0.00   0.0  0
 NZU  CONST_25  C12   C11  C9   N10     0.00   0.0  0
 NZU  CONST_26  C16   C11  C9   N10   180.00   0.0  0
 NZU  CONST_27  C14   C13  C12  C11     0.00   0.0  0
 NZU  CONST_28  C14   C15  C16  C11     0.00   0.0  0
 NZU  CONST_29  N19   C15  C16  C11   180.00   0.0  0
 NZU  CONST_30  N18   C17  C16  C11   180.00   0.0  0
 NZU  CONST_31  C15   C16  C11  C12     0.00   0.0  0
 NZU  CONST_32  C17   C16  C11  C12   180.00   0.0  0
 NZU  CONST_33  C15   C14  C13  C12     0.00   0.0  0
 NZU  CONST_34  C16   C11  C12  C13     0.00   0.0  0
 NZU  CONST_35  N19   C15  C14  C13   180.00   0.0  0
 NZU  CONST_36  C16   C15  C14  C13     0.00   0.0  0
 NZU  CONST_37  N18   N19  C15  C14   180.00   0.0  0
 NZU  CONST_38  C17   C16  C15  C14   180.00   0.0  0
 NZU  CONST_39  C17   N18  N19  C15     0.00   0.0  0
 NZU  CONST_40  N18   C17  C16  C15     0.00   0.0  0
 NZU  CONST_41  N18   N19  C15  C16     0.00   0.0  0
 NZU  CONST_42  N19   N18  C17  C16     0.00   0.0  0
 NZU  CONST_43  N19   C15  C16  C17     0.00   0.0  0
 NZU  CONST_44  N10   C3   N2   C1      0.00   0.0  0
 NZU  CONST_45  C4    C3   N2   C1    180.00   0.0  0
 NZU  CONST_46  C5    N6   N2   C1    180.00   0.0  0
 NZU  CONST_47  N21   C7   C4   C3    180.00   0.0  0
 NZU  CONST_48  N21   C7   C4   C5      0.00   0.0  0
 NZU  CONST_49  N21   C7   N8   C9    180.00   0.0  0
 NZU  CONST_50  H5    C5   N6   N2    180.00   0.0  0
 NZU  CONST_51  H12   C12  C11  C9      0.00   0.0  0
 NZU  CONST_52  H13   C13  C12  C11   180.00   0.0  0
 NZU  CONST_53  H17   C17  C16  C11     0.00   0.0  0
 NZU  CONST_54  H14   C14  C13  C12   180.00   0.0  0
 NZU  CONST_55  HN18  N18  N19  C15   180.00   0.0  0
 NZU  CONST_56  C22   N21  C7   C4    180.00   0.0  0
 NZU  CONST_57  C22   N21  C7   N8      0.00   0.0  0
 NZU  CONST_58  HN21  N21  C7   C4      0.00   0.0  0
 NZU  Var_01    H1    C1   N2   C3   -111.17  30.0  2
 NZU  Var_02    C23   C22  N21  C7    178.45  30.0  1
 NZU  Var_03    C24   C23  C22  N21  -179.88  30.0  3
 NZU  Var_04    S25   C24  C23  C22  -178.88  30.0  3
 NZU  Var_05    C28   S25  C24  C23  -179.64  30.0  3
 NZU  Var_06    H28   C28  S25  C24    61.71  30.0  3

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
 NZU  plan-1  C1    0.020
 NZU  plan-1  N2    0.020
 NZU  plan-1  C3    0.020
 NZU  plan-1  C4    0.020
 NZU  plan-1  C5    0.020
 NZU  plan-1  N6    0.020
 NZU  plan-1  C7    0.020
 NZU  plan-1  N8    0.020
 NZU  plan-1  C9    0.020
 NZU  plan-1  N10   0.020
 NZU  plan-1  C11   0.020
 NZU  plan-1  N21   0.020
 NZU  plan-1  H5    0.020
 NZU  plan-2  C9    0.020
 NZU  plan-2  C11   0.020
 NZU  plan-2  C12   0.020
 NZU  plan-2  C13   0.020
 NZU  plan-2  C14   0.020
 NZU  plan-2  C15   0.020
 NZU  plan-2  C16   0.020
 NZU  plan-2  C17   0.020
 NZU  plan-2  N18   0.020
 NZU  plan-2  N19   0.020
 NZU  plan-2  H12   0.020
 NZU  plan-2  H13   0.020
 NZU  plan-2  H14   0.020
 NZU  plan-2  H17   0.020
 NZU  plan-2  HN18  0.020
 NZU  plan-3  C7    0.020
 NZU  plan-3  N21   0.020
 NZU  plan-3  C22   0.020
 NZU  plan-3  HN21  0.020

