# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:25:12 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-amino-1-tert-butyl-3-(4-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-2-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1[nH+]c(c2ccc(Cl)cc2)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
 PP2  PP2  4-amino-1-tert-butyl-3-(4-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-2-ium  ligand  38  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PP2
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
 PP2  C1   C   CR56  0   0.656   2.2806  -0.6138  -0.0003
 PP2  N2   N   N     0  -0.464   3.3545  -1.3981   0.0303
 PP2  C3   C   CR16  0   0.083   3.0410  -2.6768   0.1118
 PP2  N4   N   N     0  -0.468   1.8383  -3.2380   0.1939
 PP2  C5   C   CR6   0   0.486   0.7562  -2.4614   0.1850
 PP2  C6   C   CR56  0  -0.328   0.9464  -1.0554   0.0429
 PP2  C8   C   CR5   0   0.550   0.1517   0.0921  -0.0118
 PP2  N9   N   NR15  1  -0.454   0.9896   1.1152  -0.0651
 PP2  N10  N   NR5   0  -0.314   2.2756   0.7283  -0.0650
 PP2  C11  C   CR6   0   0.003  -1.2956   0.2822  -0.0233
 PP2  C12  C   CR16  0  -0.271  -1.8966   1.1836   0.8522
 PP2  C13  C   CR16  0  -0.195  -3.2685   1.3662   0.8280
 PP2  C14  C   CR6   0  -0.033  -4.0321   0.6443  -0.0777
 PP2  C15  C   CR16  0  -0.189  -3.4485  -0.2526  -0.9608
 PP2  C16  C   CR16  0  -0.311  -2.0763  -0.4303  -0.9314
 PP2  C22  C   CT    0   0.039   3.4189   1.6876  -0.1064
 PP2  C23  C   CH3   0  -0.731   2.8776   3.1108  -0.1734
 PP2  C24  C   CH3   0  -0.643   4.2451   1.3892  -1.3542
 PP2  C25  C   CH3   0  -0.642   4.2388   1.5011   1.1673
 PP2  N25  N   NH2   0  -0.800  -0.4316  -3.0276   0.3116
 PP2  CL   CL  CL    0  -0.101  -5.7431   0.8676  -0.1068
 PP2  H11  H   HCR6  0   0.276   3.8755  -3.3685   0.1230
 PP2  H1   H   HNR5  0   0.477   0.7499   2.0918  -0.1822
 PP2  H12  H   HCR6  0   0.289  -1.3016   1.7302   1.5721
 PP2  H13  H   HCR6  0   0.297  -3.7361   2.0588   1.5138
 PP2  H15  H   HCR6  0   0.298  -4.0522  -0.8006  -1.6706
 PP2  H16  H   HCR6  0   0.301  -1.6154  -1.1079  -1.6392
 PP2  H31  H   HCH3  0   0.265   2.3007   3.3012  -1.0807
 PP2  H32  H   HCH3  0   0.266   2.2839   3.3807   0.7021
 PP2  H33  H   HCH3  0   0.286   3.7309   3.7861  -0.1960
 PP2  H41  H   HCH3  0   0.252   5.0602   2.1099  -1.4160
 PP2  H42  H   HCH3  0   0.258   4.6802   0.3922  -1.3226
 PP2  H43  H   HCH3  0   0.250   3.6412   1.4801  -2.2571
 PP2  H51  H   HCH3  0   0.250   3.6299   1.6688   2.0558
 PP2  H52  H   HCH3  0   0.257   4.6740   0.5050   1.2234
 PP2  H53  H   HCH3  0   0.252   5.0541   2.2244   1.1719
 PP2  H2   H   HNH2  0   0.429  -1.2829  -2.4982   0.3952
 PP2  H3   H   HNH2  0   0.422  -0.4917  -4.0263   0.4316

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
 PP2  C1   N2   aromatic  1.330  0.020  1.330
 PP2  C1   C6   aromatic  1.406  0.020  1.406
 PP2  C1   N10  aromatic  1.344  0.020  1.344
 PP2  N2   C3   aromatic  1.319  0.020  1.319
 PP2  C3   N4   aromatic  1.330  0.020  1.330
 PP2  C3   H11  single    0.930  0.020  1.080
 PP2  N4   C5   aromatic  1.332  0.020  1.332
 PP2  C5   C6   aromatic  1.426  0.020  1.426
 PP2  C5   N25  single    1.322  0.020  1.322
 PP2  C6   C8   aromatic  1.397  0.020  1.397
 PP2  C8   N9   aromatic  1.324  0.020  1.324
 PP2  C8   C11  single    1.460  0.020  1.460
 PP2  N9   N10  aromatic  1.343  0.020  1.343
 PP2  N9   H1   single    0.860  0.020  1.020
 PP2  N10  C22  single    1.493  0.020  1.493
 PP2  C11  C12  aromatic  1.393  0.020  1.393
 PP2  C11  C16  aromatic  1.394  0.020  1.394
 PP2  C12  C13  aromatic  1.384  0.020  1.384
 PP2  C12  H12  single    0.930  0.020  1.080
 PP2  C13  C14  aromatic  1.387  0.020  1.387
 PP2  C13  H13  single    0.930  0.020  1.080
 PP2  C14  C15  aromatic  1.387  0.020  1.387
 PP2  C14  CL   single    1.726  0.020  1.726
 PP2  C15  C16  aromatic  1.384  0.020  1.384
 PP2  C15  H15  single    0.930  0.020  1.080
 PP2  C16  H16  single    0.930  0.020  1.080
 PP2  C22  C23  single    1.524  0.020  1.524
 PP2  C22  C24  single    1.526  0.020  1.526
 PP2  C22  C25  single    1.526  0.020  1.526
 PP2  C23  H31  single    0.970  0.020  1.090
 PP2  C23  H32  single    0.970  0.020  1.090
 PP2  C23  H33  single    0.970  0.020  1.090
 PP2  C24  H41  single    0.970  0.020  1.090
 PP2  C24  H42  single    0.970  0.020  1.090
 PP2  C24  H43  single    0.970  0.020  1.090
 PP2  C25  H51  single    0.970  0.020  1.090
 PP2  C25  H52  single    0.970  0.020  1.090
 PP2  C25  H53  single    0.970  0.020  1.090
 PP2  N25  H2   single    0.860  0.020  1.020
 PP2  N25  H3   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
 PP2  N10  C1   C6   108.16  3.000
 PP2  N10  C1   N2   126.37  3.000
 PP2  C6   C1   N2   125.47  3.000
 PP2  C3   N2   C1   112.40  3.000
 PP2  H11  C3   N4   115.24  3.000
 PP2  H11  C3   N2   115.87  3.000
 PP2  N4   C3   N2   128.89  3.000
 PP2  C5   N4   C3   119.23  3.000
 PP2  N25  C5   C6   123.49  3.000
 PP2  N25  C5   N4   118.66  3.000
 PP2  C6   C5   N4   117.85  3.000
 PP2  C8   C6   C5   137.56  3.000
 PP2  C8   C6   C1   106.30  3.000
 PP2  C5   C6   C1   116.06  3.000
 PP2  C11  C8   N9   121.78  3.000
 PP2  C11  C8   C6   132.18  3.000
 PP2  N9   C8   C6   106.04  3.000
 PP2  H1   N9   N10  120.31  3.000
 PP2  H1   N9   C8   126.90  3.000
 PP2  N10  N9   C8   112.55  3.000
 PP2  C22  N10  N9   123.25  3.000
 PP2  C22  N10  C1   129.81  3.000
 PP2  N9   N10  C1   106.94  3.000
 PP2  C16  C11  C12  119.92  3.000
 PP2  C16  C11  C8   119.60  3.000
 PP2  C12  C11  C8   120.48  3.000
 PP2  H12  C12  C13  119.34  3.000
 PP2  H12  C12  C11  120.51  3.000
 PP2  C13  C12  C11  120.13  3.000
 PP2  H13  C13  C14  120.63  3.000
 PP2  H13  C13  C12  120.14  3.000
 PP2  C14  C13  C12  119.23  3.000
 PP2  CL   C14  C15  119.34  3.000
 PP2  CL   C14  C13  119.30  3.000
 PP2  C15  C14  C13  121.36  3.000
 PP2  H15  C15  C16  120.17  3.000
 PP2  H15  C15  C14  120.72  3.000
 PP2  C16  C15  C14  119.11  3.000
 PP2  H16  C16  C15  119.24  3.000
 PP2  H16  C16  C11  120.50  3.000
 PP2  C15  C16  C11  120.24  3.000
 PP2  C25  C22  C24  111.57  3.000
 PP2  C25  C22  C23  109.97  3.000
 PP2  C24  C22  C23  109.81  3.000
 PP2  C25  C22  N10  108.04  3.000
 PP2  C24  C22  N10  108.16  3.000
 PP2  C23  C22  N10  109.22  3.000
 PP2  H33  C23  H32  106.83  3.000
 PP2  H33  C23  H31  106.79  3.000
 PP2  H32  C23  H31  109.63  3.000
 PP2  H33  C23  C22  107.57  3.000
 PP2  H32  C23  C22  112.87  3.000
 PP2  H31  C23  C22  112.77  3.000
 PP2  H43  C24  H42  108.77  3.000
 PP2  H43  C24  H41  108.20  3.000
 PP2  H42  C24  H41  107.97  3.000
 PP2  H43  C24  C22  111.17  3.000
 PP2  H42  C24  C22  111.83  3.000
 PP2  H41  C24  C22  108.78  3.000
 PP2  H53  C25  H52  107.93  3.000
 PP2  H53  C25  H51  108.20  3.000
 PP2  H52  C25  H51  108.79  3.000
 PP2  H53  C25  C22  108.93  3.000
 PP2  H52  C25  C22  111.69  3.000
 PP2  H51  C25  C22  111.19  3.000
 PP2  H3   N25  H2   117.46  3.000
 PP2  H3   N25  C5   119.31  3.000
 PP2  H2   N25  C5   122.89  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
 PP2  CONST_01  N4   C3   N2   C1      0.00   0.0  0
 PP2  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 PP2  CONST_03  N9   C8   C6   C1      0.00   0.0  0
 PP2  CONST_04  C11  C8   C6   C1    180.00   0.0  0
 PP2  CONST_05  C8   N9   N10  C1      0.00   0.0  0
 PP2  CONST_06  C5   C6   C1   N2      0.00   0.0  0
 PP2  CONST_07  C8   C6   C1   N2    180.00   0.0  0
 PP2  CONST_08  N9   N10  C1   N2    180.00   0.0  0
 PP2  CONST_09  C5   N4   C3   N2      0.00   0.0  0
 PP2  CONST_10  C6   C1   N2   C3      0.00   0.0  0
 PP2  CONST_11  N10  C1   N2   C3    180.00   0.0  0
 PP2  CONST_12  C6   C5   N4   C3      0.00   0.0  0
 PP2  CONST_13  C8   C6   C5   N4    180.00   0.0  0
 PP2  CONST_14  N10  C1   C6   C5    180.00   0.0  0
 PP2  CONST_15  N9   C8   C6   C5    180.00   0.0  0
 PP2  CONST_16  C11  C8   C6   C5      0.00   0.0  0
 PP2  CONST_17  N9   N10  C1   C6      0.00   0.0  0
 PP2  CONST_18  N10  N9   C8   C6      0.00   0.0  0
 PP2  CONST_21  N10  C1   C6   C8      0.00   0.0  0
 PP2  CONST_22  C13  C12  C11  C8    180.00   0.0  0
 PP2  CONST_23  C15  C16  C11  C8    180.00   0.0  0
 PP2  CONST_26  C11  C8   N9   N10   180.00   0.0  0
 PP2  CONST_27  C14  C13  C12  C11     0.00   0.0  0
 PP2  CONST_28  C14  C15  C16  C11     0.00   0.0  0
 PP2  CONST_29  C15  C16  C11  C12     0.00   0.0  0
 PP2  CONST_30  C15  C14  C13  C12     0.00   0.0  0
 PP2  CONST_31  C16  C11  C12  C13     0.00   0.0  0
 PP2  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 PP2  CONST_33  N25  C5   C6   C1    180.00   0.0  0
 PP2  CONST_34  C22  N10  C1   N2      0.00   0.0  0
 PP2  CONST_35  N25  C5   N4   C3    180.00   0.0  0
 PP2  CONST_36  C22  N10  C1   C6    180.00   0.0  0
 PP2  CONST_37  N25  C5   C6   C8      0.00   0.0  0
 PP2  CONST_38  C22  N10  N9   C8    180.00   0.0  0
 PP2  CONST_39  CL   C14  C13  C12   180.00   0.0  0
 PP2  CONST_40  CL   C14  C15  C16   180.00   0.0  0
 PP2  CONST_41  H11  C3   N2   C1    180.00   0.0  0
 PP2  CONST_42  H1   N9   N10  C1    180.00   0.0  0
 PP2  CONST_43  H12  C12  C11  C8      0.00   0.0  0
 PP2  CONST_44  H16  C16  C11  C8      0.00   0.0  0
 PP2  CONST_45  H13  C13  C12  C11   180.00   0.0  0
 PP2  CONST_46  H15  C15  C16  C11   180.00   0.0  0
 PP2  CONST_47  H2   N25  C5   N4    180.00   0.0  0
 PP2  CONST_48  H3   N25  C5   N4      0.00   0.0  0
 PP2  Var_01    C23  C22  N10  C1   -179.85  30.0  2
 PP2  Var_02    H31  C23  C22  N10   -62.88  30.0  3
 PP2  Var_03    H41  C24  C22  N10   177.75  30.0  3
 PP2  Var_04    H51  C25  C22  N10   -58.49  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
 PP2  plan-1  C8   0.020
 PP2  plan-1  C11  0.020
 PP2  plan-1  C12  0.020
 PP2  plan-1  C13  0.020
 PP2  plan-1  C14  0.020
 PP2  plan-1  C15  0.020
 PP2  plan-1  C16  0.020
 PP2  plan-1  CL   0.020
 PP2  plan-1  H12  0.020
 PP2  plan-1  H13  0.020
 PP2  plan-1  H15  0.020
 PP2  plan-1  H16  0.020
 PP2  plan-2  C1   0.020
 PP2  plan-2  N2   0.020
 PP2  plan-2  C3   0.020
 PP2  plan-2  N4   0.020
 PP2  plan-2  C5   0.020
 PP2  plan-2  C6   0.020
 PP2  plan-2  C8   0.020
 PP2  plan-2  N9   0.020
 PP2  plan-2  N10  0.020
 PP2  plan-2  C11  0.020
 PP2  plan-2  C22  0.020
 PP2  plan-2  N25  0.020
 PP2  plan-2  H11  0.020
 PP2  plan-2  H1   0.020
 PP2  plan-3  C5   0.020
 PP2  plan-3  N25  0.020
 PP2  plan-3  H2   0.020
 PP2  plan-3  H3   0.020

