# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:48:37 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-chloro-N,1-dimethyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(Cl)nc2n(C)ncc12
#
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
 D07  D07  6-chloro-N,1-dimethyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  21  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D07
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
 D07  C2  C   CH3   0  -0.522   3.1414   1.8183  -0.0436
 D07  C3  C   CR15  0  -0.106   2.0764  -1.5210  -0.0889
 D07  C5  C   CR6   0   0.527  -0.5682  -1.3029   0.0037
 D07  C4  C   CR6   0   0.291  -1.0795   0.9170   0.0738
 D07  N2  N   N     0  -0.441   0.1255   1.4138   0.0447
 D07  C1  C   CR56  0   0.591   1.0505   0.4432  -0.0090
 D07  N3  N   N     0  -0.473  -1.4928  -0.3369   0.0590
 D07  C6  C   CH3   0  -0.518  -2.3572  -2.9672   0.0315
 D07  C   C   CR56  0  -0.214   0.7962  -0.9275  -0.0333
 D07  N1  N   N     0  -0.250   3.0058  -0.5978  -0.0968
 D07  N   N   NR5   0  -0.365   2.3838   0.5921  -0.0483
 D07  H1  H   HCH3  0   0.263   3.7557   1.8850  -0.9394
 D07  H2  H   HCH3  0   0.263   2.4499   2.6554  -0.0250
 D07  H3  H   HCH3  0   0.263   3.7797   1.8660   0.8365
 D07  H4  H   HCR5  0   0.275   2.3436  -2.5662  -0.1227
 D07  H5  H   HNH1  0   0.416  -0.2692  -3.2876  -0.0488
 D07  H6  H   HCH3  0   0.245  -2.8365  -2.6485   0.9573
 D07  H7  H   HCH3  0   0.246  -2.9194  -2.5556  -0.8064
 D07  H8  H   HCH3  0   0.258  -2.3970  -4.0508  -0.0232
 D07  N4  N   NH1   0  -0.638  -0.9700  -2.5669  -0.0144
 D07  CL  CL  CL    0  -0.111  -2.3604   2.0896   0.1447

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
 D07  C2  N   single    1.441  0.020  1.441
 D07  N   N1  aromatic  1.343  0.020  1.343
 D07  N   C1  aromatic  1.342  0.020  1.342
 D07  N1  C3  aromatic  1.310  0.020  1.310
 D07  C1  N2  aromatic  1.342  0.020  1.342
 D07  C1  C   aromatic  1.394  0.020  1.394
 D07  N2  C4  aromatic  1.304  0.020  1.304
 D07  C3  C   aromatic  1.412  0.020  1.412
 D07  C   C5  aromatic  1.416  0.020  1.416
 D07  C4  CL  single    1.738  0.020  1.738
 D07  C4  N3  aromatic  1.320  0.020  1.320
 D07  C5  N3  aromatic  1.338  0.020  1.338
 D07  C5  N4  single    1.326  0.020  1.326
 D07  N4  C6  single    1.445  0.020  1.445
 D07  C2  H1  single    0.970  0.020  1.090
 D07  C2  H2  single    0.970  0.020  1.090
 D07  C2  H3  single    0.970  0.020  1.090
 D07  C3  H4  single    0.930  0.020  1.080
 D07  N4  H5  single    0.860  0.020  1.020
 D07  C6  H6  single    0.970  0.020  1.090
 D07  C6  H7  single    0.970  0.020  1.090
 D07  C6  H8  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
 D07  H3  C2  H2  109.02  3.000
 D07  H3  C2  H1  109.39  3.000
 D07  H2  C2  H1  109.05  3.000
 D07  H3  C2  N   110.38  3.000
 D07  H2  C2  N   108.73  3.000
 D07  H1  C2  N   110.25  3.000
 D07  H4  C3  N1  120.44  3.000
 D07  H4  C3  C   129.24  3.000
 D07  N1  C3  C   110.32  3.000
 D07  C   C5  N3  118.40  3.000
 D07  N3  C5  N4  118.62  3.000
 D07  C   C5  N4  122.98  3.000
 D07  N3  C4  N2  130.62  3.000
 D07  N3  C4  CL  114.24  3.000
 D07  N2  C4  CL  115.15  3.000
 D07  C1  N2  C4  111.24  3.000
 D07  N   C1  C   106.84  3.000
 D07  C   C1  N2  125.88  3.000
 D07  N   C1  N2  127.28  3.000
 D07  C4  N3  C5  118.01  3.000
 D07  H8  C6  H7  108.62  3.000
 D07  H8  C6  H6  108.56  3.000
 D07  H7  C6  H6  108.41  3.000
 D07  H8  C6  N4  108.07  3.000
 D07  H7  C6  N4  111.49  3.000
 D07  H6  C6  N4  111.60  3.000
 D07  C1  C   C5  115.85  3.000
 D07  C5  C   C3  139.76  3.000
 D07  C1  C   C3  104.39  3.000
 D07  N   N1  C3  107.19  3.000
 D07  N1  N   C1  111.27  3.000
 D07  C1  N   C2  128.06  3.000
 D07  N1  N   C2  120.68  3.000
 D07  H5  N4  C6  118.14  3.000
 D07  H5  N4  C5  118.18  3.000
 D07  C6  N4  C5  123.68  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
 D07  CONST_01  C1  N   N1  C3     0.00   0.0  0
 D07  CONST_02  N   C1  C   C3     0.00   0.0  0
 D07  CONST_03  N2  C1  C   C3   180.00   0.0  0
 D07  CONST_04  N3  C5  C   C3   180.00   0.0  0
 D07  CONST_05  N   C1  C   C5   180.00   0.0  0
 D07  CONST_06  N2  C1  C   C5     0.00   0.0  0
 D07  CONST_07  N1  C3  C   C5   180.00   0.0  0
 D07  CONST_08  N2  C4  N3  C5     0.00   0.0  0
 D07  CONST_09  N   C1  N2  C4   180.00   0.0  0
 D07  CONST_10  C   C1  N2  C4     0.00   0.0  0
 D07  CONST_11  C   C5  N3  C4     0.00   0.0  0
 D07  CONST_12  N1  N   C1  N2   180.00   0.0  0
 D07  CONST_13  N3  C4  N2  C1     0.00   0.0  0
 D07  CONST_14  N1  C3  C   C1     0.00   0.0  0
 D07  CONST_15  N3  C5  C   C1     0.00   0.0  0
 D07  CONST_16  N1  N   C1  C      0.00   0.0  0
 D07  CONST_17  N   N1  C3  C      0.00   0.0  0
 D07  CONST_18  C3  N1  N   C2   180.00   0.0  0
 D07  CONST_19  N2  C1  N   C2     0.00   0.0  0
 D07  CONST_20  C   C1  N   C2   180.00   0.0  0
 D07  CONST_21  N4  C5  C   C3     0.00   0.0  0
 D07  CONST_22  C1  C   C5  N4   180.00   0.0  0
 D07  CONST_23  C4  N3  C5  N4   180.00   0.0  0
 D07  CONST_24  CL  C4  N3  C5   180.00   0.0  0
 D07  CONST_25  C1  N2  C4  CL   180.00   0.0  0
 D07  CONST_26  H4  C3  C   C5     0.00   0.0  0
 D07  CONST_27  C6  N4  C5  N3     0.00   0.0  0
 D07  CONST_28  C   C5  N4  C6   180.00   0.0  0
 D07  CONST_29  H5  N4  C5  N3   180.00   0.0  0
 D07  Var_01    H1  C2  N   C1  -120.80  30.0  2
 D07  Var_02    H6  C6  N4  C5   -62.18  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
 D07  plan-1  C2  0.020
 D07  plan-1  C3  0.020
 D07  plan-1  C5  0.020
 D07  plan-1  C4  0.020
 D07  plan-1  N2  0.020
 D07  plan-1  C1  0.020
 D07  plan-1  N3  0.020
 D07  plan-1  C   0.020
 D07  plan-1  N1  0.020
 D07  plan-1  N   0.020
 D07  plan-1  H4  0.020
 D07  plan-1  N4  0.020
 D07  plan-1  CL  0.020
 D07  plan-2  C5  0.020
 D07  plan-2  C6  0.020
 D07  plan-2  H5  0.020
 D07  plan-2  N4  0.020

