# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:29:53 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(Cc2cccc(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
 9XV  9XV  1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  40  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_9XV
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
 9XV  C4   C   CR6   0   0.431  -1.2976   2.1385   0.4087
 9XV  C5   C   CR56  0  -0.250  -1.2349   0.8271  -0.1140
 9XV  C6   C   CR56  0   0.595  -2.2720  -0.0327   0.2612
 9XV  N1   N   N     0  -0.467  -3.3004   0.2939   1.0545
 9XV  N3   N   N     0  -0.480  -2.3248   2.4676   1.1953
 9XV  CAJ  C   CH3   0  -0.647  -2.1617  -3.5512  -1.0696
 9XV  CAK  C   CH3   0  -0.649  -4.2313  -2.2045  -0.7286
 9XV  CAL  C   CH3   0  -0.646  -2.8355  -2.9108   1.2451
 9XV  NAH  N   NR5   0  -0.380  -2.0268  -1.2222  -0.3266
 9XV  NAG  N   N     0  -0.271  -0.8952  -1.1686  -1.0489
 9XV  C2   C   CR16  0   0.052  -3.2460   1.5433   1.4633
 9XV  NAR  N   NH2   0  -0.821  -0.3888   3.0810   0.1441
 9XV  CAF  C   CR5   0   0.295  -0.4004   0.0391  -0.9493
 9XV  CAE  C   CH2   0  -0.601   0.8616   0.4064  -1.6546
 9XV  CAD  C   CR6   0   0.062   1.9659   0.8452  -0.7227
 9XV  CAC  C   CR16  0  -0.231   2.1918   0.1641   0.4707
 9XV  CAB  C   CR6   0  -0.022   3.2182   0.5698   1.3061
 9XV  CL   CL  CL    0  -0.127   3.4892  -0.2894   2.7883
 9XV  CAV  C   CR16  0  -0.227   4.0329   1.6469   0.9893
 9XV  CAU  C   CR16  0  -0.246   3.8044   2.3212  -0.2000
 9XV  CAT  C   CR16  0  -0.311   2.7805   1.9251  -1.0505
 9XV  H1   H   HCH3  0   0.238  -1.1584  -3.7959  -0.7234
 9XV  H2   H   HCH3  0   0.237  -2.7730  -4.4512  -1.0011
 9XV  H3   H   HCH3  0   0.238  -2.1035  -3.2667  -2.1194
 9XV  H4   H   HCH3  0   0.234  -4.8137  -3.1248  -0.6779
 9XV  H5   H   HCH3  0   0.246  -4.7412  -1.4506  -0.1312
 9XV  H6   H   HCH3  0   0.235  -4.2155  -1.8730  -1.7677
 9XV  H7   H   HCH3  0   0.235  -1.8240  -3.0974   1.6092
 9XV  H8   H   HCH3  0   0.245  -3.3013  -2.1633   1.8855
 9XV  H9   H   HCH3  0   0.234  -3.4050  -3.8357   1.3419
 9XV  H10  H   HCR6  0   0.252  -4.0557   1.8703   2.1078
 9XV  H11  H   HNH2  0   0.404  -0.4470   3.9616   0.6280
 9XV  H12  H   HNH2  0   0.415   0.4822   2.8662  -0.3094
 9XV  H13  H   HCH2  0   0.291   1.1950  -0.4621  -2.2278
 9XV  H14  H   HCH2  0   0.275   0.6715   1.1981  -2.3840
 9XV  H15  H   HCR6  0   0.276   1.5695  -0.6787   0.7455
 9XV  H16  H   HCR6  0   0.281   4.8250   1.9570   1.6568
 9XV  H17  H   HCR6  0   0.272   4.4280   3.1655  -0.4620
 9XV  H18  H   HCR6  0   0.271   2.6128   2.4616  -1.9768
 9XV  CAI  C   CT    0   0.061  -2.8142  -2.4676  -0.2184

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
 9XV  CAJ  CAI  single    1.525  0.020  1.525
 9XV  CAK  CAI  single    1.529  0.020  1.529
 9XV  CAI  NAH  single    1.477  0.020  1.477
 9XV  CAI  CAL  single    1.529  0.020  1.529
 9XV  NAH  NAG  aromatic  1.344  0.020  1.344
 9XV  NAH  C6   aromatic  1.349  0.020  1.349
 9XV  NAG  CAF  aromatic  1.309  0.020  1.309
 9XV  C6   N1   aromatic  1.339  0.020  1.339
 9XV  C6   C5   aromatic  1.398  0.020  1.398
 9XV  N1   C2   aromatic  1.316  0.020  1.316
 9XV  CAE  CAF  single    1.492  0.020  1.492
 9XV  CAE  CAD  single    1.510  0.020  1.510
 9XV  C5   CAF  aromatic  1.420  0.020  1.420
 9XV  C5   C4   aromatic  1.413  0.020  1.413
 9XV  C2   N3   aromatic  1.332  0.020  1.332
 9XV  C4   N3   aromatic  1.335  0.020  1.335
 9XV  C4   NAR  single    1.336  0.020  1.336
 9XV  CAD  CAC  aromatic  1.393  0.020  1.393
 9XV  CAD  CAT  aromatic  1.392  0.020  1.392
 9XV  CAC  CAB  aromatic  1.384  0.020  1.384
 9XV  CAT  CAU  aromatic  1.389  0.020  1.389
 9XV  CAB  CL   single    1.734  0.020  1.734
 9XV  CAB  CAV  aromatic  1.387  0.020  1.387
 9XV  CAU  CAV  aromatic  1.386  0.020  1.386
 9XV  CAJ  H1   single    0.970  0.020  1.090
 9XV  CAJ  H2   single    0.970  0.020  1.090
 9XV  CAJ  H3   single    0.970  0.020  1.090
 9XV  CAK  H4   single    0.970  0.020  1.090
 9XV  CAK  H5   single    0.970  0.020  1.090
 9XV  CAK  H6   single    0.970  0.020  1.090
 9XV  CAL  H7   single    0.970  0.020  1.090
 9XV  CAL  H8   single    0.970  0.020  1.090
 9XV  CAL  H9   single    0.970  0.020  1.090
 9XV  C2   H10  single    0.930  0.020  1.080
 9XV  NAR  H11  single    0.860  0.020  1.020
 9XV  NAR  H12  single    0.860  0.020  1.020
 9XV  CAE  H13  single    0.970  0.020  1.090
 9XV  CAE  H14  single    0.970  0.020  1.090
 9XV  CAC  H15  single    0.930  0.020  1.080
 9XV  CAV  H16  single    0.930  0.020  1.080
 9XV  CAU  H17  single    0.930  0.020  1.080
 9XV  CAT  H18  single    0.930  0.020  1.080

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
 9XV  NAR  C4   N3   117.79  3.000
 9XV  NAR  C4   C5   123.46  3.000
 9XV  N3   C4   C5   118.74  3.000
 9XV  CAF  C5   C6   104.63  3.000
 9XV  CAF  C5   C4   139.37  3.000
 9XV  C6   C5   C4   116.00  3.000
 9XV  NAH  C6   N1   127.77  3.000
 9XV  N1   C6   C5   125.35  3.000
 9XV  NAH  C6   C5   106.88  3.000
 9XV  C2   N1   C6   112.57  3.000
 9XV  C2   N3   C4   118.66  3.000
 9XV  H3   CAJ  H2   107.83  3.000
 9XV  H3   CAJ  H1   108.41  3.000
 9XV  H2   CAJ  H1   108.12  3.000
 9XV  H3   CAJ  CAI  112.05  3.000
 9XV  H2   CAJ  CAI  108.16  3.000
 9XV  H1   CAJ  CAI  112.12  3.000
 9XV  H6   CAK  H5   108.60  3.000
 9XV  H6   CAK  H4   107.98  3.000
 9XV  H5   CAK  H4   107.99  3.000
 9XV  H6   CAK  CAI  110.90  3.000
 9XV  H5   CAK  CAI  111.72  3.000
 9XV  H4   CAK  CAI  109.54  3.000
 9XV  H9   CAL  H8   107.86  3.000
 9XV  H9   CAL  H7   108.03  3.000
 9XV  H8   CAL  H7   108.53  3.000
 9XV  H9   CAL  CAI  109.76  3.000
 9XV  H8   CAL  CAI  111.70  3.000
 9XV  H7   CAL  CAI  110.85  3.000
 9XV  NAG  NAH  CAI  121.46  3.000
 9XV  NAG  NAH  C6   110.61  3.000
 9XV  CAI  NAH  C6   127.91  3.000
 9XV  CAF  NAG  NAH  108.32  3.000
 9XV  H10  C2   N3   115.23  3.000
 9XV  H10  C2   N1   116.09  3.000
 9XV  N3   C2   N1   128.68  3.000
 9XV  H12  NAR  H11  117.00  3.000
 9XV  H12  NAR  C4   121.88  3.000
 9XV  H11  NAR  C4   118.87  3.000
 9XV  CAE  CAF  NAG  120.73  3.000
 9XV  CAE  CAF  C5   129.71  3.000
 9XV  NAG  CAF  C5   109.55  3.000
 9XV  H14  CAE  H13  106.18  3.000
 9XV  H14  CAE  CAD  109.17  3.000
 9XV  H13  CAE  CAD  109.37  3.000
 9XV  H14  CAE  CAF  110.28  3.000
 9XV  H13  CAE  CAF  108.09  3.000
 9XV  CAD  CAE  CAF  113.48  3.000
 9XV  CAT  CAD  CAC  119.10  3.000
 9XV  CAT  CAD  CAE  120.54  3.000
 9XV  CAC  CAD  CAE  120.35  3.000
 9XV  H15  CAC  CAB  120.06  3.000
 9XV  H15  CAC  CAD  120.32  3.000
 9XV  CAB  CAC  CAD  119.62  3.000
 9XV  CAV  CAB  CL   119.22  3.000
 9XV  CAV  CAB  CAC  121.68  3.000
 9XV  CL   CAB  CAC  119.10  3.000
 9XV  H16  CAV  CAU  120.73  3.000
 9XV  H16  CAV  CAB  120.79  3.000
 9XV  CAU  CAV  CAB  118.48  3.000
 9XV  H17  CAU  CAT  119.95  3.000
 9XV  H17  CAU  CAV  119.50  3.000
 9XV  CAT  CAU  CAV  120.55  3.000
 9XV  H18  CAT  CAU  119.77  3.000
 9XV  H18  CAT  CAD  119.67  3.000
 9XV  CAU  CAT  CAD  120.57  3.000
 9XV  NAH  CAI  CAL  108.77  3.000
 9XV  CAL  CAI  CAK  110.87  3.000
 9XV  NAH  CAI  CAK  108.94  3.000
 9XV  CAL  CAI  CAJ  109.53  3.000
 9XV  NAH  CAI  CAJ  109.28  3.000
 9XV  CAK  CAI  CAJ  109.43  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
 9XV  CONST_01  NAH  C6   C5   C4   180.00   0.0  0
 9XV  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 9XV  CONST_03  NAG  CAF  C5   C4   180.00   0.0  0
 9XV  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 9XV  CONST_05  NAG  NAH  C6   C5     0.00   0.0  0
 9XV  CONST_06  C2   N1   C6   C5     0.00   0.0  0
 9XV  CONST_07  NAH  NAG  CAF  C5     0.00   0.0  0
 9XV  CONST_08  C2   N3   C4   C5     0.00   0.0  0
 9XV  CONST_09  CAF  NAG  NAH  C6     0.00   0.0  0
 9XV  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 9XV  CONST_11  NAG  CAF  C5   C6     0.00   0.0  0
 9XV  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 9XV  CONST_13  NAG  NAH  C6   N1   180.00   0.0  0
 9XV  CONST_14  CAF  C5   C6   N1   180.00   0.0  0
 9XV  CONST_15  CAF  C5   C4   N3   180.00   0.0  0
 9XV  CONST_16  C2   N1   C6   NAH  180.00   0.0  0
 9XV  CONST_17  CAF  C5   C6   NAH    0.00   0.0  0
 9XV  CONST_18  CAV  CAB  CAC  CAD    0.00   0.0  0
 9XV  CONST_19  CAV  CAU  CAT  CAD    0.00   0.0  0
 9XV  CONST_20  CAU  CAT  CAD  CAC    0.00   0.0  0
 9XV  CONST_21  CAU  CAV  CAB  CAC    0.00   0.0  0
 9XV  CONST_22  CAT  CAD  CAC  CAB    0.00   0.0  0
 9XV  CONST_23  CAT  CAU  CAV  CAB    0.00   0.0  0
 9XV  CONST_24  CAE  CAF  C5   C4     0.00   0.0  0
 9XV  CONST_25  CAI  NAH  C6   C5   180.00   0.0  0
 9XV  CONST_26  CAE  CAF  C5   C6   180.00   0.0  0
 9XV  CONST_27  NAR  C4   C5   C6   180.00   0.0  0
 9XV  CONST_28  CAI  NAH  C6   N1     0.00   0.0  0
 9XV  CONST_29  CAF  NAG  NAH  CAI  180.00   0.0  0
 9XV  CONST_30  CAE  CAF  NAG  NAH  180.00   0.0  0
 9XV  CONST_31  NAR  C4   N3   C2   180.00   0.0  0
 9XV  CONST_32  CAF  C5   C4   NAR    0.00   0.0  0
 9XV  CONST_33  CAB  CAC  CAD  CAE  180.00   0.0  0
 9XV  CONST_34  CAU  CAT  CAD  CAE  180.00   0.0  0
 9XV  CONST_35  CL   CAB  CAC  CAD  180.00   0.0  0
 9XV  CONST_36  CAU  CAV  CAB  CL   180.00   0.0  0
 9XV  CONST_37  H10  C2   N3   C4   180.00   0.0  0
 9XV  CONST_38  H17  CAU  CAT  CAD  180.00   0.0  0
 9XV  CONST_39  H18  CAT  CAD  CAC  180.00   0.0  0
 9XV  CONST_40  H16  CAV  CAB  CAC  180.00   0.0  0
 9XV  CONST_41  H15  CAC  CAB  CAV  180.00   0.0  0
 9XV  CONST_42  H11  NAR  C4   C5   180.00   0.0  0
 9XV  CONST_43  H12  NAR  C4   C5     0.00   0.0  0
 9XV  Var_01    CAD  CAE  CAF  C5    60.34  30.0  2
 9XV  Var_02    CAC  CAD  CAE  CAF   41.83  30.0  2
 9XV  Var_03    CAJ  CAI  NAH  C6   179.42  30.0  2
 9XV  Var_04    H1   CAJ  CAI  NAH   62.59  30.0  3
 9XV  Var_05    H4   CAK  CAI  NAH  178.51  30.0  3
 9XV  Var_06    H7   CAL  CAI  NAH  -60.17  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
 9XV  plan-1  CAE  0.020
 9XV  plan-1  CAD  0.020
 9XV  plan-1  CAC  0.020
 9XV  plan-1  CAB  0.020
 9XV  plan-1  CL   0.020
 9XV  plan-1  CAV  0.020
 9XV  plan-1  CAU  0.020
 9XV  plan-1  CAT  0.020
 9XV  plan-1  H15  0.020
 9XV  plan-1  H16  0.020
 9XV  plan-1  H17  0.020
 9XV  plan-1  H18  0.020
 9XV  plan-2  C4   0.020
 9XV  plan-2  C5   0.020
 9XV  plan-2  C6   0.020
 9XV  plan-2  N1   0.020
 9XV  plan-2  N3   0.020
 9XV  plan-2  NAH  0.020
 9XV  plan-2  NAG  0.020
 9XV  plan-2  C2   0.020
 9XV  plan-2  NAR  0.020
 9XV  plan-2  CAF  0.020
 9XV  plan-2  CAE  0.020
 9XV  plan-2  H10  0.020
 9XV  plan-2  CAI  0.020
 9XV  plan-3  C4   0.020
 9XV  plan-3  NAR  0.020
 9XV  plan-3  H11  0.020
 9XV  plan-3  H12  0.020

