# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 04:28:49 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-tert-butyl-N~3~-(3-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(Nc2cccc(Cl)c2)c3c(N)ncnc13
#
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
 9XP  9XP  1-tert-butyl-N~3~-(3-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,4-diamine  ligand  39  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9XP
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
 9XP  C4   C   CT    0   0.062  -1.7302   2.5866  -0.3100
 9XP  C5   C   CH3   0  -0.649  -0.3918   3.2651  -0.5800
 9XP  C6   C   CH3   0  -0.646  -2.2830   3.0712   1.0310
 9XP  N1   N   N     0  -0.307  -0.3045   0.5807  -0.4059
 9XP  C7   C   CH3   0  -0.649  -2.7006   2.9072  -1.4482
 9XP  C8   C   CR56  0   0.613  -2.4543   0.1704  -0.0392
 9XP  N2   N   NR5   0  -0.376  -1.5313   1.1252  -0.2454
 9XP  C9   C   CR16  0   0.054  -4.3965  -0.8168   0.3301
 9XP  C10  C   CR6   0   0.473  -2.5707  -2.1994   0.2262
 9XP  C11  C   CR56  0  -0.302  -1.7850  -1.0593  -0.0375
 9XP  C12  C   CR16  0  -0.359   2.8535  -2.3913  -0.6305
 9XP  N3   N   N     0  -0.466  -3.7723   0.3259   0.1409
 9XP  C13  C   CR16  0  -0.248   4.2195  -2.2167  -0.5257
 9XP  C14  C   CR16  0  -0.255   4.7613  -1.0055  -0.1111
 9XP  N4   N   N     0  -0.480  -3.8859  -2.0462   0.3895
 9XP  C    C   CR6   0  -0.025   3.8808   0.0181   0.1902
 9XP  C2   C   CR6   0   0.380   1.9754  -1.3446  -0.3194
 9XP  C1   C   CR16  0  -0.291   2.5052  -0.1177   0.0900
 9XP  C3   C   CR5   0   0.506  -0.4281  -0.7147  -0.2853
 9XP  N5   N   NH2   0  -0.822  -2.0703  -3.4394   0.3032
 9XP  H1   H   HCH3  0   0.239   0.0493   2.9455  -1.5233
 9XP  H2   H   HCH3  0   0.238  -0.5629   4.3403  -0.6352
 9XP  H3   H   HCH3  0   0.239   0.3293   3.0814   0.2158
 9XP  H4   H   HCH3  0   0.235  -1.5790   2.8604   1.8375
 9XP  H5   H   HCH3  0   0.234  -2.4421   4.1493   0.9969
 9XP  H6   H   HCH3  0   0.245  -3.2349   2.5988   1.2683
 9XP  H7   H   HCH3  0   0.246  -3.6890   2.4866  -1.2689
 9XP  H8   H   HCH3  0   0.234  -2.8068   3.9883  -1.5431
 9XP  H9   H   HCH3  0   0.235  -2.3265   2.5218  -2.3976
 9XP  H10  H   HCR6  0   0.254  -5.4714  -0.7562   0.4661
 9XP  H11  H   HCR6  0   0.270   2.4571  -3.3466  -0.9528
 9XP  H12  H   HCR6  0   0.268   4.8791  -3.0383  -0.7718
 9XP  H13  H   HCR6  0   0.274   5.8302  -0.8684  -0.0315
 9XP  H14  H   HCR6  0   0.301   1.8597   0.7172   0.3139
 9XP  H15  H   HNH1  0   0.407   0.3815  -2.4996  -0.7886
 9XP  H16  H   HNH2  0   0.405  -2.6824  -4.1764   0.6133
 9XP  H17  H   HNH2  0   0.402  -1.0884  -3.5956   0.4474
 9XP  N    N   NH1   0  -0.804   0.6199  -1.5995  -0.4058
 9XP  CL   CL  CL    0  -0.133   4.5137   1.5505   0.7083

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
 9XP  C6   C4   single    1.529  0.020  1.529
 9XP  C7   C4   single    1.530  0.020  1.530
 9XP  C4   N2   single    1.476  0.020  1.476
 9XP  C4   C5   single    1.525  0.020  1.525
 9XP  N2   N1   aromatic  1.352  0.020  1.352
 9XP  N2   C8   aromatic  1.344  0.020  1.344
 9XP  N1   C3   aromatic  1.307  0.020  1.307
 9XP  C8   N3   aromatic  1.339  0.020  1.339
 9XP  C8   C11  aromatic  1.400  0.020  1.400
 9XP  N3   C9   aromatic  1.316  0.020  1.316
 9XP  C3   C11  aromatic  1.422  0.020  1.422
 9XP  C3   N    single    1.377  0.020  1.377
 9XP  C11  C10  aromatic  1.410  0.020  1.410
 9XP  C9   N4   aromatic  1.333  0.020  1.333
 9XP  N    C2   single    1.382  0.020  1.382
 9XP  C10  N4   aromatic  1.334  0.020  1.334
 9XP  C10  N5   single    1.339  0.020  1.339
 9XP  C1   C2   aromatic  1.398  0.020  1.398
 9XP  C1   C    aromatic  1.386  0.020  1.386
 9XP  C2   C12  aromatic  1.401  0.020  1.401
 9XP  C    CL   single    1.737  0.020  1.737
 9XP  C    C14  aromatic  1.383  0.020  1.383
 9XP  C12  C13  aromatic  1.381  0.020  1.381
 9XP  C14  C13  aromatic  1.390  0.020  1.390
 9XP  C5   H1   single    0.970  0.020  1.090
 9XP  C5   H2   single    0.970  0.020  1.090
 9XP  C5   H3   single    0.970  0.020  1.090
 9XP  C6   H4   single    0.970  0.020  1.090
 9XP  C6   H5   single    0.970  0.020  1.090
 9XP  C6   H6   single    0.970  0.020  1.090
 9XP  C7   H7   single    0.970  0.020  1.090
 9XP  C7   H8   single    0.970  0.020  1.090
 9XP  C7   H9   single    0.970  0.020  1.090
 9XP  C9   H10  single    0.930  0.020  1.080
 9XP  C12  H11  single    0.930  0.020  1.080
 9XP  C13  H12  single    0.930  0.020  1.080
 9XP  C14  H13  single    0.930  0.020  1.080
 9XP  C1   H14  single    0.930  0.020  1.080
 9XP  N    H15  single    0.860  0.020  1.020
 9XP  N5   H16  single    0.890  0.020  1.040
 9XP  N5   H17  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
 9XP  N2   C4   C7   108.99  3.000
 9XP  N2   C4   C6   108.91  3.000
 9XP  C7   C4   C6   110.90  3.000
 9XP  N2   C4   C5   109.27  3.000
 9XP  C7   C4   C5   109.38  3.000
 9XP  C6   C4   C5   109.37  3.000
 9XP  H3   C5   H2   107.89  3.000
 9XP  H3   C5   H1   108.37  3.000
 9XP  H2   C5   H1   108.00  3.000
 9XP  H3   C5   C4   112.12  3.000
 9XP  H2   C5   C4   108.07  3.000
 9XP  H1   C5   C4   112.23  3.000
 9XP  H6   C6   H5   107.96  3.000
 9XP  H6   C6   H4   108.61  3.000
 9XP  H5   C6   H4   107.95  3.000
 9XP  H6   C6   C4   111.70  3.000
 9XP  H5   C6   C4   109.79  3.000
 9XP  H4   C6   C4   110.71  3.000
 9XP  C3   N1   N2   107.61  3.000
 9XP  H9   C7   H8   107.94  3.000
 9XP  H9   C7   H7   108.55  3.000
 9XP  H8   C7   H7   107.98  3.000
 9XP  H9   C7   C4   110.86  3.000
 9XP  H8   C7   C4   109.53  3.000
 9XP  H7   C7   C4   111.86  3.000
 9XP  N3   C8   C11  124.91  3.000
 9XP  C11  C8   N2   107.21  3.000
 9XP  N3   C8   N2   127.88  3.000
 9XP  C8   N2   N1   110.81  3.000
 9XP  C8   N2   C4   128.13  3.000
 9XP  N1   N2   C4   121.05  3.000
 9XP  H10  C9   N4   115.18  3.000
 9XP  H10  C9   N3   116.07  3.000
 9XP  N4   C9   N3   128.75  3.000
 9XP  N5   C10  N4   117.88  3.000
 9XP  N5   C10  C11  123.46  3.000
 9XP  N4   C10  C11  118.65  3.000
 9XP  C3   C11  C10  139.52  3.000
 9XP  C10  C11  C8   116.37  3.000
 9XP  C3   C11  C8   104.07  3.000
 9XP  H11  C12  C2   119.69  3.000
 9XP  H11  C12  C13  119.74  3.000
 9XP  C2   C12  C13  120.57  3.000
 9XP  C9   N3   C8   112.67  3.000
 9XP  H12  C13  C14  119.46  3.000
 9XP  H12  C13  C12  119.32  3.000
 9XP  C14  C13  C12  121.22  3.000
 9XP  H13  C14  C    121.31  3.000
 9XP  H13  C14  C13  121.20  3.000
 9XP  C    C14  C13  117.49  3.000
 9XP  C10  N4   C9   118.57  3.000
 9XP  C1   C    CL   118.01  3.000
 9XP  CL   C    C14  119.07  3.000
 9XP  C1   C    C14  122.92  3.000
 9XP  N    C2   C1   123.50  3.000
 9XP  C1   C2   C12  118.89  3.000
 9XP  N    C2   C12  117.58  3.000
 9XP  H14  C1   C2   120.89  3.000
 9XP  H14  C1   C    120.20  3.000
 9XP  C2   C1   C    118.91  3.000
 9XP  N    C3   C11  125.87  3.000
 9XP  N    C3   N1   123.84  3.000
 9XP  C11  C3   N1   110.28  3.000
 9XP  H17  N5   H16  115.85  3.000
 9XP  H17  N5   C10  121.15  3.000
 9XP  H16  N5   C10  117.92  3.000
 9XP  H15  N    C3   115.32  3.000
 9XP  H15  N    C2   114.89  3.000
 9XP  C3   N    C2   128.51  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
 9XP  CONST_01  N3   C8   N2   N1    180.00   0.0  0
 9XP  CONST_02  C11  C8   N2   N1      0.00   0.0  0
 9XP  CONST_03  C8   C11  C3   N1      0.00   0.0  0
 9XP  CONST_04  C10  C11  C3   N1    180.00   0.0  0
 9XP  CONST_05  C3   N1   N2   C8      0.00   0.0  0
 9XP  CONST_06  N4   C9   N3   C8      0.00   0.0  0
 9XP  CONST_07  N4   C10  C11  C8      0.00   0.0  0
 9XP  CONST_08  C11  C3   N1   N2      0.00   0.0  0
 9XP  CONST_09  C9   N3   C8   N2    180.00   0.0  0
 9XP  CONST_10  C3   C11  C8   N2      0.00   0.0  0
 9XP  CONST_11  C10  C11  C8   N2    180.00   0.0  0
 9XP  CONST_12  C11  C8   N3   C9      0.00   0.0  0
 9XP  CONST_13  C11  C10  N4   C9      0.00   0.0  0
 9XP  CONST_14  N3   C8   C11  C10     0.00   0.0  0
 9XP  CONST_15  N3   C9   N4   C10     0.00   0.0  0
 9XP  CONST_16  C    C1   C2   C12     0.00   0.0  0
 9XP  CONST_17  C    C14  C13  C12     0.00   0.0  0
 9XP  CONST_18  C3   C11  C8   N3    180.00   0.0  0
 9XP  CONST_19  C1   C2   C12  C13     0.00   0.0  0
 9XP  CONST_20  C1   C    C14  C13     0.00   0.0  0
 9XP  CONST_21  C2   C1   C    C14     0.00   0.0  0
 9XP  CONST_22  C2   C12  C13  C14     0.00   0.0  0
 9XP  CONST_23  C3   C11  C10  N4    180.00   0.0  0
 9XP  CONST_24  C3   N1   N2   C4    180.00   0.0  0
 9XP  CONST_25  N3   C8   N2   C4      0.00   0.0  0
 9XP  CONST_26  C11  C8   N2   C4    180.00   0.0  0
 9XP  CONST_27  N    C3   C11  C8    180.00   0.0  0
 9XP  CONST_28  N5   C10  C11  C8    180.00   0.0  0
 9XP  CONST_29  N    C3   N1   N2    180.00   0.0  0
 9XP  CONST_30  N5   C10  N4   C9    180.00   0.0  0
 9XP  CONST_31  N    C3   C11  C10     0.00   0.0  0
 9XP  CONST_32  N    C2   C12  C13   180.00   0.0  0
 9XP  CONST_33  CL   C    C14  C13   180.00   0.0  0
 9XP  CONST_34  C2   C1   C    CL    180.00   0.0  0
 9XP  CONST_35  N    C2   C1   C     180.00   0.0  0
 9XP  CONST_36  N5   C10  C11  C3      0.00   0.0  0
 9XP  CONST_37  H10  C9   N3   C8    180.00   0.0  0
 9XP  CONST_38  H14  C1   C2   C12   180.00   0.0  0
 9XP  CONST_39  H13  C14  C13  C12   180.00   0.0  0
 9XP  CONST_40  H11  C12  C13  C14   180.00   0.0  0
 9XP  CONST_41  H12  C13  C14  C     180.00   0.0  0
 9XP  CONST_42  H16  N5   C10  C11   180.00   0.0  0
 9XP  Var_01    C2   N    C3   N1     18.45  30.0  2
 9XP  Var_02    C3   N    C2   C12  -172.84  30.0  3
 9XP  Var_03    N1   N2   C4   C5      0.43  30.0  2
 9XP  Var_04    H4   C6   C4   N2     61.29  30.0  3
 9XP  Var_05    H7   C7   C4   N2     63.73  30.0  3
 9XP  Var_06    H1   C5   C4   N2     60.38  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
 9XP  plan-1  C12  0.020
 9XP  plan-1  C13  0.020
 9XP  plan-1  C14  0.020
 9XP  plan-1  C    0.020
 9XP  plan-1  C2   0.020
 9XP  plan-1  C1   0.020
 9XP  plan-1  H11  0.020
 9XP  plan-1  H12  0.020
 9XP  plan-1  H13  0.020
 9XP  plan-1  H14  0.020
 9XP  plan-1  N    0.020
 9XP  plan-1  CL   0.020
 9XP  plan-2  C4   0.020
 9XP  plan-2  N1   0.020
 9XP  plan-2  C8   0.020
 9XP  plan-2  N2   0.020
 9XP  plan-2  C9   0.020
 9XP  plan-2  C10  0.020
 9XP  plan-2  C11  0.020
 9XP  plan-2  N3   0.020
 9XP  plan-2  N4   0.020
 9XP  plan-2  C3   0.020
 9XP  plan-2  N5   0.020
 9XP  plan-2  H10  0.020
 9XP  plan-2  N    0.020
 9XP  plan-3  C10  0.020
 9XP  plan-3  N5   0.020
 9XP  plan-3  H16  0.020
 9XP  plan-3  H17  0.020

