# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:48:34 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-cyclopentyl-3-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(nc(c3cnc4[nH]ccc4c3)c12)C5CCCC5
#
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
 9HE  9HE  1-cyclopentyl-3-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)pyrazolo[3,4-d]pyrimidin-4-amine  ligand  41  24  .  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_9HE
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
 9HE  CAI  C  CH2   0  -0.449  -3.6352  -1.4946   1.3701
 9HE  CAG  C  CH2   0  -0.449  -4.5770  -2.6536   0.9791
 9HE  CAH  C  CH2   0  -0.457  -4.9432  -2.4166  -0.4954
 9HE  CAJ  C  CH2   0  -0.440  -3.7551  -1.6417  -1.0512
 9HE  CAW  C  CH1   0  -0.085  -3.4551  -0.6675   0.0852
 9HE  NAX  N  NR5   0  -0.386  -2.1668  -0.0172  -0.0153
 9HE  NAN  N  N     0  -0.278  -1.0346  -0.7326  -0.0504
 9HE  C4   C  CR56  0   0.579  -1.9117   1.3032  -0.0430
 9HE  N3   N  N     0  -0.466  -2.8042   2.2979  -0.0122
 9HE  C2   C  CR16  0   0.056  -2.2308   3.4811  -0.0773
 9HE  N1   N  N     0  -0.478  -0.9360   3.7710  -0.1982
 9HE  C6   C  CR6   0   0.432  -0.0520   2.7715  -0.2464
 9HE  NAA  N  NH2   0  -0.816   1.2360   3.0847  -0.4060
 9HE  C5   C  CR56  0  -0.271  -0.5232   1.4440  -0.1213
 9HE  CAR  C  CR5   0   0.268  -0.0294   0.1103  -0.1115
 9HE  CAP  C  CR6   0  -0.075   1.3516  -0.3766  -0.1482
 9HE  CAF  C  CR16  0  -0.298   2.3374   0.1860   0.6540
 9HE  CAS  C  CR56  0   0.027   3.6202  -0.3453   0.5833
 9HE  CAD  C  CR15  0  -0.446   4.8780  -0.0867   1.2054
 9HE  CAB  C  CR15  0   0.004   5.7538  -0.9991   0.6926
 9HE  NAO  N  NR15  0  -0.661   5.1171  -1.8091  -0.2079
 9HE  CAT  C  CR56  0   0.469   3.8141  -1.4368  -0.2968
 9HE  NAM  N  N     0  -0.419   2.8906  -1.9955  -1.0628
 9HE  CAE  C  CR16  0  -0.100   1.6849  -1.4622  -0.9797
 9HE  H1   H  HCH2  0   0.244  -4.0366  -0.8820   2.1775
 9HE  H2   H  HCH2  0   0.243  -2.6696  -1.8751   1.7046
 9HE  H3   H  HCH2  0   0.232  -4.0612  -3.6085   1.0873
 9HE  H4   H  HCH2  0   0.236  -5.4605  -2.6993   1.6156
 9HE  H5   H  HCH2  0   0.239  -5.1378  -3.3433  -1.0359
 9HE  H6   H  HCH2  0   0.226  -5.8467  -1.8054  -0.5677
 9HE  H7   H  HCH2  0   0.233  -2.9028  -2.3093  -1.2031
 9HE  H8   H  HCH2  0   0.245  -3.9614  -1.1345  -1.9944
 9HE  H9   H  HCH1  0   0.270  -4.1893   0.1399   0.0615
 9HE  H10  H  HCR6  0   0.254  -2.8955   4.3378  -0.0383
 9HE  H11  H  HNH2  0   0.405   1.4849   4.0434  -0.5842
 9HE  H12  H  HNH2  0   0.414   1.9232   2.3837  -0.6226
 9HE  H13  H  HCR6  0   0.277   2.1098   0.9986   1.3341
 9HE  H14  H  HCR5  0   0.256   5.1052   0.6749   1.9335
 9HE  H15  H  HCR5  0   0.292   6.8023  -1.1364   0.9011
 9HE  H16  H  HNR5  0   0.414   5.5472  -2.5614  -0.7215
 9HE  H17  H  HCR6  0   0.257   0.9186  -1.9016  -1.6085

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
 9HE  NAO  CAB  aromatic  1.368  0.020  1.368
 9HE  NAO  CAT  aromatic  1.358  0.020  1.358
 9HE  CAB  CAD  aromatic  1.365  0.020  1.365
 9HE  CAT  NAM  aromatic  1.324  0.020  1.324
 9HE  CAT  CAS  aromatic  1.416  0.020  1.416
 9HE  NAM  CAE  aromatic  1.321  0.020  1.321
 9HE  CAD  CAS  aromatic  1.427  0.020  1.427
 9HE  CAS  CAF  aromatic  1.390  0.020  1.390
 9HE  CAH  CAJ  single    1.524  0.020  1.524
 9HE  CAH  CAG  single    1.538  0.020  1.538
 9HE  CAE  CAP  aromatic  1.407  0.020  1.407
 9HE  CAJ  CAW  single    1.527  0.020  1.527
 9HE  CAF  CAP  aromatic  1.390  0.020  1.390
 9HE  CAP  CAR  single    1.465  0.020  1.465
 9HE  NAN  CAR  aromatic  1.313  0.020  1.313
 9HE  NAN  NAX  aromatic  1.340  0.020  1.340
 9HE  CAG  CAI  single    1.544  0.020  1.544
 9HE  CAR  C5   aromatic  1.422  0.020  1.422
 9HE  CAW  NAX  single    1.447  0.020  1.447
 9HE  CAW  CAI  single    1.539  0.020  1.539
 9HE  NAX  C4   aromatic  1.345  0.020  1.345
 9HE  C5   C4   aromatic  1.398  0.020  1.398
 9HE  C5   C6   aromatic  1.414  0.020  1.414
 9HE  C4   N3   aromatic  1.337  0.020  1.337
 9HE  NAA  C6   single    1.335  0.020  1.335
 9HE  C6   N1   aromatic  1.335  0.020  1.335
 9HE  N3   C2   aromatic  1.316  0.020  1.316
 9HE  N1   C2   aromatic  1.332  0.020  1.332
 9HE  CAI  H1   single    0.970  0.020  1.090
 9HE  CAI  H2   single    0.970  0.020  1.090
 9HE  CAG  H3   single    0.970  0.020  1.090
 9HE  CAG  H4   single    0.970  0.020  1.090
 9HE  CAH  H5   single    0.970  0.020  1.090
 9HE  CAH  H6   single    0.970  0.020  1.090
 9HE  CAJ  H7   single    0.970  0.020  1.090
 9HE  CAJ  H8   single    0.970  0.020  1.090
 9HE  CAW  H9   single    0.970  0.020  1.090
 9HE  C2   H10  single    0.930  0.020  1.080
 9HE  NAA  H11  single    0.860  0.020  1.020
 9HE  NAA  H12  single    0.860  0.020  1.020
 9HE  CAF  H13  single    0.930  0.020  1.080
 9HE  CAD  H14  single    0.930  0.020  1.080
 9HE  CAB  H15  single    0.930  0.020  1.080
 9HE  NAO  H16  single    0.860  0.020  1.020
 9HE  CAE  H17  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
 9HE  H2   CAI  H1   107.16  3.000
 9HE  H2   CAI  CAW  109.88  3.000
 9HE  H1   CAI  CAW  111.07  3.000
 9HE  H2   CAI  CAG  110.86  3.000
 9HE  H1   CAI  CAG  112.64  3.000
 9HE  CAW  CAI  CAG  105.27  3.000
 9HE  H4   CAG  H3   106.78  3.000
 9HE  H4   CAG  CAH  111.93  3.000
 9HE  H3   CAG  CAH  110.04  3.000
 9HE  H4   CAG  CAI  112.22  3.000
 9HE  H3   CAG  CAI  110.10  3.000
 9HE  CAH  CAG  CAI  105.81  3.000
 9HE  H6   CAH  H5   107.16  3.000
 9HE  H6   CAH  CAJ  109.64  3.000
 9HE  H5   CAH  CAJ  112.99  3.000
 9HE  H6   CAH  CAG  110.27  3.000
 9HE  H5   CAH  CAG  112.76  3.000
 9HE  CAJ  CAH  CAG  104.03  3.000
 9HE  H8   CAJ  H7   108.14  3.000
 9HE  H8   CAJ  CAW  112.59  3.000
 9HE  H7   CAJ  CAW  109.87  3.000
 9HE  H8   CAJ  CAH  113.86  3.000
 9HE  H7   CAJ  CAH  110.37  3.000
 9HE  CAW  CAJ  CAH  101.90  3.000
 9HE  H9   CAW  NAX  105.37  3.000
 9HE  H9   CAW  CAJ  108.89  3.000
 9HE  NAX  CAW  CAJ  114.22  3.000
 9HE  H9   CAW  CAI  109.69  3.000
 9HE  NAX  CAW  CAI  113.82  3.000
 9HE  CAJ  CAW  CAI  104.81  3.000
 9HE  C4   NAX  NAN  111.31  3.000
 9HE  C4   NAX  CAW  127.71  3.000
 9HE  NAN  NAX  CAW  120.96  3.000
 9HE  CAR  NAN  NAX  107.77  3.000
 9HE  C5   C4   N3   126.13  3.000
 9HE  N3   C4   NAX  127.11  3.000
 9HE  C5   C4   NAX  106.76  3.000
 9HE  C2   N3   C4   112.14  3.000
 9HE  H10  C2   N1   115.26  3.000
 9HE  H10  C2   N3   116.17  3.000
 9HE  N1   C2   N3   128.56  3.000
 9HE  C6   N1   C2   118.93  3.000
 9HE  C5   C6   NAA  123.52  3.000
 9HE  NAA  C6   N1   117.86  3.000
 9HE  C5   C6   N1   118.61  3.000
 9HE  H12  NAA  H11  117.20  3.000
 9HE  H12  NAA  C6   121.44  3.000
 9HE  H11  NAA  C6   118.90  3.000
 9HE  CAR  C5   C6   139.92  3.000
 9HE  C6   C5   C4   115.50  3.000
 9HE  CAR  C5   C4   104.48  3.000
 9HE  CAP  CAR  C5   129.71  3.000
 9HE  C5   CAR  NAN  109.67  3.000
 9HE  CAP  CAR  NAN  120.62  3.000
 9HE  CAE  CAP  CAF  119.03  3.000
 9HE  CAF  CAP  CAR  121.31  3.000
 9HE  CAE  CAP  CAR  119.64  3.000
 9HE  H13  CAF  CAS  120.80  3.000
 9HE  H13  CAF  CAP  121.11  3.000
 9HE  CAS  CAF  CAP  118.06  3.000
 9HE  CAT  CAS  CAD  106.86  3.000
 9HE  CAD  CAS  CAF  136.22  3.000
 9HE  CAT  CAS  CAF  116.91  3.000
 9HE  H14  CAD  CAB  126.22  3.000
 9HE  H14  CAD  CAS  127.47  3.000
 9HE  CAB  CAD  CAS  106.31  3.000
 9HE  H15  CAB  NAO  120.29  3.000
 9HE  H15  CAB  CAD  129.56  3.000
 9HE  NAO  CAB  CAD  110.15  3.000
 9HE  H16  NAO  CAT  125.52  3.000
 9HE  H16  NAO  CAB  125.38  3.000
 9HE  CAT  NAO  CAB  109.10  3.000
 9HE  NAM  CAT  NAO  126.27  3.000
 9HE  NAM  CAT  CAS  126.14  3.000
 9HE  NAO  CAT  CAS  107.58  3.000
 9HE  CAE  NAM  CAT  115.47  3.000
 9HE  H17  CAE  NAM  116.42  3.000
 9HE  H17  CAE  CAP  119.20  3.000
 9HE  NAM  CAE  CAP  124.38  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
 9HE  CONST_01  CAP  CAR  NAN  NAX  180.00   0.0  0
 9HE  CONST_02  C5   CAR  NAN  NAX    0.00   0.0  0
 9HE  CONST_03  CAR  C5   C4   NAX    0.00   0.0  0
 9HE  CONST_04  C6   C5   C4   NAX  180.00   0.0  0
 9HE  CONST_05  C2   N3   C4   NAX  180.00   0.0  0
 9HE  CONST_08  C4   C5   CAR  NAN    0.00   0.0  0
 9HE  CONST_09  C6   C5   CAR  NAN  180.00   0.0  0
 9HE  CONST_10  C5   C4   NAX  NAN    0.00   0.0  0
 9HE  CONST_11  N3   C4   NAX  NAN  180.00   0.0  0
 9HE  CONST_12  CAR  NAN  NAX  C4     0.00   0.0  0
 9HE  CONST_13  CAP  CAR  C5   C4   180.00   0.0  0
 9HE  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 9HE  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 9HE  CONST_16  CAR  C5   C4   N3   180.00   0.0  0
 9HE  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 9HE  CONST_18  C6   N1   C2   N3     0.00   0.0  0
 9HE  CONST_19  C5   C4   N3   C2     0.00   0.0  0
 9HE  CONST_20  C5   C6   N1   C2     0.00   0.0  0
 9HE  CONST_21  CAR  C5   C6   N1   180.00   0.0  0
 9HE  CONST_22  CAP  CAR  C5   C6     0.00   0.0  0
 9HE  CONST_25  NAM  CAE  CAP  CAR  180.00   0.0  0
 9HE  CONST_26  CAS  CAF  CAP  CAR  180.00   0.0  0
 9HE  CONST_27  CAT  NAM  CAE  CAP    0.00   0.0  0
 9HE  CONST_28  CAT  CAS  CAF  CAP    0.00   0.0  0
 9HE  CONST_29  CAD  CAS  CAF  CAP  180.00   0.0  0
 9HE  CONST_30  NAO  CAT  CAS  CAF  180.00   0.0  0
 9HE  CONST_31  NAM  CAT  CAS  CAF    0.00   0.0  0
 9HE  CONST_32  CAB  CAD  CAS  CAF  180.00   0.0  0
 9HE  CONST_33  NAM  CAE  CAP  CAF    0.00   0.0  0
 9HE  CONST_34  CAB  NAO  CAT  CAS    0.00   0.0  0
 9HE  CONST_35  CAE  NAM  CAT  CAS    0.00   0.0  0
 9HE  CONST_36  NAO  CAB  CAD  CAS    0.00   0.0  0
 9HE  CONST_37  CAE  CAP  CAF  CAS    0.00   0.0  0
 9HE  CONST_38  CAT  NAO  CAB  CAD    0.00   0.0  0
 9HE  CONST_39  NAO  CAT  CAS  CAD    0.00   0.0  0
 9HE  CONST_40  NAM  CAT  CAS  CAD  180.00   0.0  0
 9HE  CONST_41  NAM  CAT  NAO  CAB  180.00   0.0  0
 9HE  CONST_42  CAT  CAS  CAD  CAB    0.00   0.0  0
 9HE  CONST_43  CAE  NAM  CAT  NAO  180.00   0.0  0
 9HE  CONST_44  CAR  NAN  NAX  CAW  180.00   0.0  0
 9HE  CONST_45  C5   C4   NAX  CAW  180.00   0.0  0
 9HE  CONST_46  N3   C4   NAX  CAW    0.00   0.0  0
 9HE  CONST_47  NAA  C6   C5   C4   180.00   0.0  0
 9HE  CONST_48  NAA  C6   N1   C2   180.00   0.0  0
 9HE  CONST_49  CAR  C5   C6   NAA    0.00   0.0  0
 9HE  CONST_50  H10  C2   N3   C4   180.00   0.0  0
 9HE  CONST_51  H17  CAE  CAP  CAR    0.00   0.0  0
 9HE  CONST_52  H13  CAF  CAP  CAR    0.00   0.0  0
 9HE  CONST_53  H14  CAD  CAS  CAF    0.00   0.0  0
 9HE  CONST_54  H16  NAO  CAT  CAS  180.00   0.0  0
 9HE  CONST_55  H15  CAB  CAD  CAS  180.00   0.0  0
 9HE  CONST_56  H11  NAA  C6   N1     0.00   0.0  0
 9HE  CONST_57  H12  NAA  C6   N1   180.00   0.0  0
 9HE  Var_01    CAJ  CAH  CAG  CAI   27.05  30.0  1
 9HE  Var_02    CAW  CAJ  CAH  CAG  -41.38  30.0  1
 9HE  Var_03    CAW  CAI  CAG  CAH   -2.14  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 9HE  chir_01  CAW  CAJ  NAX  CAI  positiv

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
 9HE  plan-1  CAW  0.020
 9HE  plan-1  NAX  0.020
 9HE  plan-1  NAN  0.020
 9HE  plan-1  C4   0.020
 9HE  plan-1  N3   0.020
 9HE  plan-1  C2   0.020
 9HE  plan-1  N1   0.020
 9HE  plan-1  C6   0.020
 9HE  plan-1  NAA  0.020
 9HE  plan-1  C5   0.020
 9HE  plan-1  CAR  0.020
 9HE  plan-1  CAP  0.020
 9HE  plan-1  H10  0.020
 9HE  plan-2  CAR  0.020
 9HE  plan-2  CAP  0.020
 9HE  plan-2  CAF  0.020
 9HE  plan-2  CAS  0.020
 9HE  plan-2  CAD  0.020
 9HE  plan-2  CAB  0.020
 9HE  plan-2  NAO  0.020
 9HE  plan-2  CAT  0.020
 9HE  plan-2  NAM  0.020
 9HE  plan-2  CAE  0.020
 9HE  plan-2  H13  0.020
 9HE  plan-2  H14  0.020
 9HE  plan-2  H15  0.020
 9HE  plan-2  H16  0.020
 9HE  plan-2  H17  0.020
 9HE  plan-3  C6   0.020
 9HE  plan-3  NAA  0.020
 9HE  plan-3  H11  0.020
 9HE  plan-3  H12  0.020

