# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:40:36 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-(1,1-dioxidothiomorpholin-4-yl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Nc2nc(nc3n(C)ncc23)N4CC[S](=O)(=O)CC4)c1
#
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
 NZS  NZS  6-(1,1-dioxidothiomorpholin-4-yl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  47  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_NZS
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
 NZS  C1    C  CR56  0  -0.291  -0.2472  -2.6633  -0.1057
 NZS  N1    N  N     0  -0.523   1.9823  -1.8323   0.3999
 NZS  O1    O  O2    0  -0.473  -6.1703   0.9638  -0.8909
 NZS  S1    S  S     0   1.205   3.7597   2.2928  -0.8127
 NZS  C2    C  CR56  0   0.608   1.1325  -2.7972   0.0531
 NZS  N2    N  N     0  -0.547   0.0721  -0.3993   0.4777
 NZS  O2    O  OS    0  -0.677   4.0038   2.5428  -2.2323
 NZS  C3    C  CR6   0   0.656   1.3852  -0.6691   0.6051
 NZS  N3    N  N     0  -0.259   0.3216  -4.7823  -0.5405
 NZS  O3    O  OS    0  -0.688   4.4170   3.1612   0.1677
 NZS  C4    C  CR6   0   0.548  -0.7553  -1.3652   0.1273
 NZS  N4    N  NR5   0  -0.374   1.4268  -4.0800  -0.2197
 NZS  C5    C  CR15  0  -0.114  -0.6891  -3.9531  -0.4792
 NZS  N5    N  NH1   0  -0.774  -2.0789  -1.1389  -0.0229
 NZS  C6    C  CH3   0  -0.522   2.7193  -4.7139  -0.1926
 NZS  N6    N  NT    0  -0.486   2.1740   0.3748   1.0106
 NZS  C7    C  CR6   0   0.394  -2.8355   0.0250   0.1290
 NZS  C8    C  CR16  0  -0.464  -4.1097   0.0040  -0.4324
 NZS  C9    C  CR6   0   0.401  -4.9626   1.0980  -0.3126
 NZS  C10   C  CR16  0  -0.398  -4.5384   2.2362   0.3697
 NZS  C11   C  CR16  0  -0.236  -3.2666   2.2404   0.9269
 NZS  C12   C  CR16  0  -0.334  -2.4078   1.1592   0.8243
 NZS  C13   C  CH3   0  -0.437  -7.0805   2.0431  -0.8137
 NZS  C14   C  CH2   0  -0.360   1.7090   1.7404   0.9003
 NZS  C15   C  CH2   0  -0.612   1.9998   2.3241  -0.4826
 NZS  C16   C  CH2   0  -0.613   4.1717   0.5985  -0.4110
 NZS  C17   C  CH2   0  -0.350   3.6143   0.2365   0.9655
 NZS  H5    H  HCR5  0   0.270  -1.6891  -4.2959  -0.6990
 NZS  HN5   H  HNH1  0   0.424  -2.6027  -1.9315  -0.3611
 NZS  H6    H  HCH3  0   0.257   2.7583  -5.4791   0.5809
 NZS  H6A   H  HCH3  0   0.259   2.9382  -5.1676  -1.1573
 NZS  H6B   H  HCH3  0   0.261   3.4699  -3.9578   0.0201
 NZS  H8    H  HCR6  0   0.273  -4.4532  -0.8710  -0.9734
 NZS  H10   H  HCR6  0   0.278  -5.1719   3.1054   0.4775
 NZS  H11   H  HCR6  0   0.260  -2.9358   3.1188   1.4660
 NZS  H12   H  HCR6  0   0.286  -1.4334   1.1940   1.2800
 NZS  H13   H  HCH3  0   0.260  -7.9835   1.7220  -1.3268
 NZS  H13A  H  HCH3  0   0.229  -7.3333   2.2928   0.2197
 NZS  H13B  H  HCH3  0   0.229  -6.6961   2.9387  -1.3084
 NZS  H14   H  HCH2  0   0.310   0.6405   1.7927   1.0811
 NZS  H14A  H  HCH2  0   0.280   2.1963   2.3404   1.6701
 NZS  H15   H  HCH2  0   0.327   1.6927   3.3695  -0.5543
 NZS  H15A  H  HCH2  0   0.304   1.5035   1.7545  -1.2696
 NZS  H16   H  HCH2  0   0.305   3.7554  -0.0407  -1.1912
 NZS  H16A  H  HCH2  0   0.326   5.2609   0.5305  -0.4402
 NZS  H17   H  HCH2  0   0.281   4.0504   0.8806   1.7305
 NZS  H17A  H  HCH2  0   0.301   3.8989  -0.7847   1.1998

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
 NZS  C4   C1    aromatic  1.413  0.020  1.413
 NZS  C1   C5    aromatic  1.414  0.020  1.414
 NZS  C1   C2    aromatic  1.395  0.020  1.395
 NZS  C3   N1    aromatic  1.324  0.020  1.324
 NZS  N1   C2    aromatic  1.332  0.020  1.332
 NZS  C13  O1    single    1.414  0.020  1.414
 NZS  C9   O1    single    1.346  0.020  1.346
 NZS  O3   S1    double    1.465  0.020  1.465
 NZS  O2   S1    double    1.462  0.020  1.462
 NZS  S1   C16   single    1.789  0.020  1.789
 NZS  S1   C15   single    1.791  0.020  1.791
 NZS  C2   N4    aromatic  1.344  0.020  1.344
 NZS  N2   C4    aromatic  1.319  0.020  1.319
 NZS  N2   C3    aromatic  1.347  0.020  1.347
 NZS  N6   C3    single    1.370  0.020  1.370
 NZS  C5   N3    aromatic  1.309  0.020  1.309
 NZS  N4   N3    aromatic  1.348  0.020  1.348
 NZS  N5   C4    single    1.351  0.020  1.351
 NZS  N4   C6    single    1.440  0.020  1.440
 NZS  C5   H5    single    0.930  0.020  1.080
 NZS  C7   N5    single    1.396  0.020  1.396
 NZS  N5   HN5   single    0.860  0.020  1.020
 NZS  C6   H6    single    0.970  0.020  1.090
 NZS  C6   H6A   single    0.970  0.020  1.090
 NZS  C6   H6B   single    0.970  0.020  1.090
 NZS  C17  N6    single    1.448  0.020  1.448
 NZS  C14  N6    single    1.447  0.020  1.447
 NZS  C12  C7    aromatic  1.398  0.020  1.398
 NZS  C7   C8    aromatic  1.393  0.020  1.393
 NZS  C9   C8    aromatic  1.392  0.020  1.392
 NZS  C8   H8    single    0.930  0.020  1.080
 NZS  C10  C9    aromatic  1.393  0.020  1.393
 NZS  C11  C10   aromatic  1.389  0.020  1.389
 NZS  C10  H10   single    0.930  0.020  1.080
 NZS  C11  C12   aromatic  1.385  0.020  1.385
 NZS  C11  H11   single    0.930  0.020  1.080
 NZS  C12  H12   single    0.930  0.020  1.080
 NZS  C13  H13   single    0.970  0.020  1.090
 NZS  C13  H13A  single    0.970  0.020  1.090
 NZS  C13  H13B  single    0.970  0.020  1.090
 NZS  C15  C14   single    1.529  0.020  1.529
 NZS  C14  H14   single    0.970  0.020  1.090
 NZS  C14  H14A  single    0.970  0.020  1.090
 NZS  C15  H15   single    0.970  0.020  1.090
 NZS  C15  H15A  single    0.970  0.020  1.090
 NZS  C16  C17   single    1.528  0.020  1.528
 NZS  C16  H16   single    0.970  0.020  1.090
 NZS  C16  H16A  single    0.970  0.020  1.090
 NZS  C17  H17   single    0.970  0.020  1.090
 NZS  C17  H17A  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
 NZS  C5    C1   C4    140.28  3.000
 NZS  C5    C1   C2    104.58  3.000
 NZS  C4    C1   C2    115.14  3.000
 NZS  C3    N1   C2    112.91  3.000
 NZS  C13   O1   C9    118.56  3.000
 NZS  C16   S1   C15   101.62  3.000
 NZS  C15   S1   O3    107.89  3.000
 NZS  C16   S1   O3    107.92  3.000
 NZS  C15   S1   O2    109.88  3.000
 NZS  C16   S1   O2    109.97  3.000
 NZS  O3    S1   O2    118.26  3.000
 NZS  N4    C2   N1    127.20  3.000
 NZS  N4    C2   C1    106.56  3.000
 NZS  N1    C2   C1    126.24  3.000
 NZS  C4    N2   C3    119.34  3.000
 NZS  N6    C3   N2    115.90  3.000
 NZS  N6    C3   N1    117.12  3.000
 NZS  N2    C3   N1    126.97  3.000
 NZS  C5    N3   N4    106.97  3.000
 NZS  N5    C4   N2    121.42  3.000
 NZS  N5    C4   C1    119.19  3.000
 NZS  N2    C4   C1    119.39  3.000
 NZS  C6    N4   N3    120.73  3.000
 NZS  C6    N4   C2    127.80  3.000
 NZS  N3    N4   C2    111.46  3.000
 NZS  H5    C5   N3    120.30  3.000
 NZS  H5    C5   C1    129.27  3.000
 NZS  N3    C5   C1    110.43  3.000
 NZS  HN5   N5   C7    114.21  3.000
 NZS  HN5   N5   C4    114.48  3.000
 NZS  C7    N5   C4    131.17  3.000
 NZS  H6B   C6   H6A   108.95  3.000
 NZS  H6B   C6   H6    108.99  3.000
 NZS  H6A   C6   H6    109.24  3.000
 NZS  H6B   C6   N4    108.51  3.000
 NZS  H6A   C6   N4    110.33  3.000
 NZS  H6    C6   N4    110.79  3.000
 NZS  C17   N6   C14   114.05  3.000
 NZS  C14   N6   C3    120.78  3.000
 NZS  C17   N6   C3    119.40  3.000
 NZS  C12   C7   C8    119.53  3.000
 NZS  C8    C7   N5    116.06  3.000
 NZS  C12   C7   N5    124.38  3.000
 NZS  H8    C8   C9    118.87  3.000
 NZS  H8    C8   C7    120.20  3.000
 NZS  C9    C8   C7    120.93  3.000
 NZS  C10   C9   C8    119.84  3.000
 NZS  C10   C9   O1    124.42  3.000
 NZS  C8    C9   O1    115.75  3.000
 NZS  H10   C10  C11   119.63  3.000
 NZS  H10   C10  C9    121.83  3.000
 NZS  C11   C10  C9    118.55  3.000
 NZS  H11   C11  C12   118.76  3.000
 NZS  H11   C11  C10   118.83  3.000
 NZS  C12   C11  C10   122.42  3.000
 NZS  H12   C12  C11   120.33  3.000
 NZS  H12   C12  C7    120.93  3.000
 NZS  C11   C12  C7    118.74  3.000
 NZS  H13B  C13  H13A  108.79  3.000
 NZS  H13B  C13  H13   108.70  3.000
 NZS  H13A  C13  H13   108.77  3.000
 NZS  H13B  C13  O1    111.98  3.000
 NZS  H13A  C13  O1    112.02  3.000
 NZS  H13   C13  O1    106.47  3.000
 NZS  H14A  C14  H14   107.21  3.000
 NZS  H14A  C14  C15   110.08  3.000
 NZS  H14   C14  C15   108.63  3.000
 NZS  H14A  C14  N6    108.77  3.000
 NZS  H14   C14  N6    110.45  3.000
 NZS  C15   C14  N6    111.61  3.000
 NZS  H15A  C15  H15   108.94  3.000
 NZS  H15A  C15  C14   111.51  3.000
 NZS  H15   C15  C14   111.80  3.000
 NZS  H15A  C15  S1    107.76  3.000
 NZS  H15   C15  S1    106.32  3.000
 NZS  C14   C15  S1    110.30  3.000
 NZS  H16A  C16  H16   108.97  3.000
 NZS  H16A  C16  C17   111.91  3.000
 NZS  H16   C16  C17   111.47  3.000
 NZS  H16A  C16  S1    106.42  3.000
 NZS  H16   C16  S1    107.84  3.000
 NZS  C17   C16  S1    110.03  3.000
 NZS  H17A  C17  H17   107.41  3.000
 NZS  H17A  C17  C16   108.75  3.000
 NZS  H17   C17  C16   110.24  3.000
 NZS  H17A  C17  N6    110.12  3.000
 NZS  H17   C17  N6    108.63  3.000
 NZS  C16   C17  N6    111.61  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
 NZS  CONST_01  C3   N2   C4   C1      0.00   0.0  0
 NZS  CONST_02  N4   N3   C5   C1      0.00   0.0  0
 NZS  CONST_03  C3   N1   C2   C1      0.00   0.0  0
 NZS  CONST_04  N3   N4   C2   C1      0.00   0.0  0
 NZS  CONST_05  C4   N2   C3   N1      0.00   0.0  0
 NZS  CONST_06  C4   C1   C2   N1      0.00   0.0  0
 NZS  CONST_07  C5   C1   C2   N1    180.00   0.0  0
 NZS  CONST_08  N3   N4   C2   N1    180.00   0.0  0
 NZS  CONST_09  N2   C4   C1   C2      0.00   0.0  0
 NZS  CONST_10  N3   C5   C1   C2      0.00   0.0  0
 NZS  CONST_11  N2   C3   N1   C2      0.00   0.0  0
 NZS  CONST_12  C5   N3   N4   C2      0.00   0.0  0
 NZS  CONST_13  C5   C1   C4   N2    180.00   0.0  0
 NZS  CONST_14  N4   C2   N1   C3    180.00   0.0  0
 NZS  CONST_15  C4   C1   C5   N3    180.00   0.0  0
 NZS  CONST_16  N4   C2   C1   C4    180.00   0.0  0
 NZS  CONST_17  C5   C1   C2   N4      0.00   0.0  0
 NZS  CONST_18  C10  C11  C12  C7      0.00   0.0  0
 NZS  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 NZS  CONST_20  C11  C12  C7   C8      0.00   0.0  0
 NZS  CONST_21  C11  C10  C9   C8      0.00   0.0  0
 NZS  CONST_22  C12  C7   C8   C9      0.00   0.0  0
 NZS  CONST_23  C12  C11  C10  C9      0.00   0.0  0
 NZS  CONST_24  N6   C3   N1   C2    180.00   0.0  0
 NZS  CONST_25  N6   C3   N2   C4    180.00   0.0  0
 NZS  CONST_26  C6   N4   C2   C1    180.00   0.0  0
 NZS  CONST_27  C6   N4   C2   N1      0.00   0.0  0
 NZS  CONST_28  C7   C8   C9   O1    180.00   0.0  0
 NZS  CONST_29  C11  C10  C9   O1    180.00   0.0  0
 NZS  CONST_30  N5   C4   C1   C2    180.00   0.0  0
 NZS  CONST_31  N5   C4   N2   C3    180.00   0.0  0
 NZS  CONST_32  N5   C4   C1   C5      0.00   0.0  0
 NZS  CONST_33  C6   N4   N3   C5    180.00   0.0  0
 NZS  CONST_34  C11  C12  C7   N5    180.00   0.0  0
 NZS  CONST_35  C9   C8   C7   N5    180.00   0.0  0
 NZS  CONST_36  H5   C5   C1   C2    180.00   0.0  0
 NZS  CONST_37  H11  C11  C12  C7    180.00   0.0  0
 NZS  CONST_38  H12  C12  C7   C8    180.00   0.0  0
 NZS  CONST_39  H10  C10  C9   C8    180.00   0.0  0
 NZS  CONST_40  H8   C8   C9   C10   180.00   0.0  0
 NZS  Var_01    C17  N6   C3   N1     10.89  30.0  1
 NZS  Var_02    N6   C17  C16  S1     59.85  30.0  1
 NZS  Var_03    N6   C14  C15  S1    -59.24  30.0  1
 NZS  Var_04    C16  C17  N6   C3     85.97  30.0  1
 NZS  Var_05    C15  C14  N6   C3    -86.00  30.0  1
 NZS  Var_06    C16  S1   C15  C14    49.99  30.0  1
 NZS  Var_07    C17  C16  S1   C15   -50.19  30.0  1
 NZS  Var_08    C7   N5   C4   C1   -179.45  30.0  1
 NZS  Var_09    C12  C7   N5   C4    -17.98  30.0  3
 NZS  Var_10    H6   C6   N4   C2    115.40  30.0  2
 NZS  Var_11    H13  C13  O1   C9   -179.28  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
 NZS  plan-1  O1   0.020
 NZS  plan-1  N5   0.020
 NZS  plan-1  C7   0.020
 NZS  plan-1  C8   0.020
 NZS  plan-1  C9   0.020
 NZS  plan-1  C10  0.020
 NZS  plan-1  C11  0.020
 NZS  plan-1  C12  0.020
 NZS  plan-1  H8   0.020
 NZS  plan-1  H10  0.020
 NZS  plan-1  H11  0.020
 NZS  plan-1  H12  0.020
 NZS  plan-2  C1   0.020
 NZS  plan-2  N1   0.020
 NZS  plan-2  C2   0.020
 NZS  plan-2  N2   0.020
 NZS  plan-2  C3   0.020
 NZS  plan-2  N3   0.020
 NZS  plan-2  C4   0.020
 NZS  plan-2  N4   0.020
 NZS  plan-2  C5   0.020
 NZS  plan-2  N5   0.020
 NZS  plan-2  C6   0.020
 NZS  plan-2  N6   0.020
 NZS  plan-2  H5   0.020

