# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:41:33 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]ccc2c(n1)N3CCCC3
#
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
 JR2  JR2  4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine  ligand  28  15  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JR2
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
 JR2  N1    N  N     0  -0.541  -0.1353  -1.5376   0.1027
 JR2  C2    C  CR6   0   0.503  -1.4363  -1.8490   0.1398
 JR2  N3    N  N     0  -0.514  -2.4618  -1.0111   0.0850
 JR2  C4    C  CR56  0   0.481  -2.0801   0.2648  -0.0016
 JR2  C5    C  CR56  0  -0.116  -0.7645   0.7503  -0.0456
 JR2  C6    C  CR6   0   0.505   0.2311  -0.2577   0.0056
 JR2  NAA   N  NH2   0  -0.827  -1.7237  -3.1753   0.2877
 JR2  CAB   C  CR15  0  -0.036  -2.1807   2.4885  -0.1195
 JR2  CAC   C  CR15  0  -0.435  -0.8552   2.1815  -0.1171
 JR2  CAD   C  CH2   0  -0.482   3.8517  -0.2911   0.2270
 JR2  CAE   C  CH2   0  -0.475   3.5991   0.9775  -0.5797
 JR2  CAF   C  CH2   0  -0.258   2.5465  -1.0627   0.0781
 JR2  CAG   C  CH2   0  -0.274   2.1402   1.2992  -0.2745
 JR2  NAJ   N  NR15  0  -0.665  -2.9156   1.3266  -0.0526
 JR2  NAO   N  NR5   0  -0.497   1.5470  -0.0081  -0.0362
 JR2  HNAA  H  HNH2  0   0.380  -0.9978  -3.8190   0.0213
 JR2  HNAB  H  HNH2  0   0.380  -2.6524  -3.4621   0.0271
 JR2  HAB   H  HCR5  0   0.277  -2.6702   3.4472  -0.1639
 JR2  HAC   H  HCR5  0   0.252  -0.0561   2.9016  -0.1554
 JR2  HADA  H  HCH2  0   0.238   4.0255  -0.0439   1.2766
 JR2  HAE   H  HCH2  0   0.252   4.2630   1.7995  -0.3150
 JR2  HAEA  H  HCH2  0   0.240   3.7239   0.7781  -1.6463
 JR2  HAF   H  HCH2  0   0.230   2.5528  -1.6913  -0.8180
 JR2  HAFA  H  HCH2  0   0.244   2.3395  -1.7123   0.9284
 JR2  HAG   H  HCH2  0   0.237   2.0558   1.9378   0.6107
 JR2  HAGA  H  HCH2  0   0.248   1.6531   1.8115  -1.1053
 JR2  HNAJ  H  HNR5  0   0.405  -3.9205   1.2717  -0.0339
 JR2  HAD   H  HCH2  0   0.250   4.7091  -0.8620  -0.1271

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
 JR2  N1   C2    aromatic  1.338  0.020  1.338
 JR2  N1   C6    aromatic  1.335  0.020  1.335
 JR2  C2   N3    aromatic  1.325  0.020  1.325
 JR2  C2   NAA   single    1.365  0.020  1.365
 JR2  N3   C4    aromatic  1.335  0.020  1.335
 JR2  C4   C5    aromatic  1.403  0.020  1.403
 JR2  C4   NAJ   aromatic  1.352  0.020  1.352
 JR2  C5   C6    aromatic  1.418  0.020  1.418
 JR2  C5   CAC   aromatic  1.436  0.020  1.436
 JR2  C6   NAO   single    1.340  0.020  1.340
 JR2  CAB  CAC   aromatic  1.361  0.020  1.361
 JR2  CAB  NAJ   aromatic  1.376  0.020  1.376
 JR2  CAD  CAE   single    1.524  0.020  1.524
 JR2  CAD  CAF   single    1.523  0.020  1.523
 JR2  CAE  CAG   single    1.525  0.020  1.525
 JR2  CAF  NAO   single    1.457  0.020  1.457
 JR2  CAG  NAO   single    1.455  0.020  1.455
 JR2  NAA  HNAA  single    0.890  0.020  1.040
 JR2  NAA  HNAB  single    0.890  0.020  1.040
 JR2  CAB  HAB   single    0.930  0.020  1.080
 JR2  CAC  HAC   single    0.930  0.020  1.080
 JR2  CAD  HAD   single    0.970  0.020  1.090
 JR2  CAD  HADA  single    0.970  0.020  1.090
 JR2  CAE  HAE   single    0.970  0.020  1.090
 JR2  CAE  HAEA  single    0.970  0.020  1.090
 JR2  CAF  HAF   single    0.970  0.020  1.090
 JR2  CAF  HAFA  single    0.970  0.020  1.090
 JR2  CAG  HAG   single    0.970  0.020  1.090
 JR2  CAG  HAGA  single    0.970  0.020  1.090
 JR2  NAJ  HNAJ  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
 JR2  C6    N1   C2    119.47  3.000
 JR2  NAA   C2   N3    117.12  3.000
 JR2  NAA   C2   N1    115.70  3.000
 JR2  N3    C2   N1    127.15  3.000
 JR2  C4    N3   C2    112.69  3.000
 JR2  NAJ   C4   C5    107.85  3.000
 JR2  NAJ   C4   N3    125.20  3.000
 JR2  C5    C4   N3    126.95  3.000
 JR2  CAC   C5   C6    139.02  3.000
 JR2  CAC   C5   C4    106.69  3.000
 JR2  C6    C5   C4    114.29  3.000
 JR2  NAO   C6   C5    123.78  3.000
 JR2  NAO   C6   N1    116.77  3.000
 JR2  C5    C6   N1    119.45  3.000
 JR2  HNAB  NAA  HNAA  114.51  3.000
 JR2  HNAB  NAA  C2    116.31  3.000
 JR2  HNAA  NAA  C2    116.17  3.000
 JR2  HAB   CAB  NAJ   120.71  3.000
 JR2  HAB   CAB  CAC   130.05  3.000
 JR2  NAJ   CAB  CAC   109.24  3.000
 JR2  HAC   CAC  CAB   124.91  3.000
 JR2  HAC   CAC  C5    128.44  3.000
 JR2  CAB   CAC  C5    106.65  3.000
 JR2  HADA  CAD  HAD   107.80  3.000
 JR2  HADA  CAD  CAF   110.17  3.000
 JR2  HAD   CAD  CAF   112.15  3.000
 JR2  HADA  CAD  CAE   110.28  3.000
 JR2  HAD   CAD  CAE   113.24  3.000
 JR2  CAF   CAD  CAE   103.17  3.000
 JR2  HAEA  CAE  HAE   107.78  3.000
 JR2  HAEA  CAE  CAG   110.08  3.000
 JR2  HAE   CAE  CAG   112.04  3.000
 JR2  HAEA  CAE  CAD   110.24  3.000
 JR2  HAE   CAE  CAD   113.48  3.000
 JR2  CAG   CAE  CAD   103.19  3.000
 JR2  HAFA  CAF  HAF   107.31  3.000
 JR2  HAFA  CAF  NAO   111.24  3.000
 JR2  HAF   CAF  NAO   110.81  3.000
 JR2  HAFA  CAF  CAD   112.85  3.000
 JR2  HAF   CAF  CAD   111.47  3.000
 JR2  NAO   CAF  CAD   103.22  3.000
 JR2  HAGA  CAG  HAG   107.91  3.000
 JR2  HAGA  CAG  NAO   111.38  3.000
 JR2  HAG   CAG  NAO   111.11  3.000
 JR2  HAGA  CAG  CAE   111.95  3.000
 JR2  HAG   CAG  CAE   111.02  3.000
 JR2  NAO   CAG  CAE   103.49  3.000
 JR2  HNAJ  NAJ  CAB   125.44  3.000
 JR2  HNAJ  NAJ  C4    124.99  3.000
 JR2  CAB   NAJ  C4    109.56  3.000
 JR2  CAG   NAO  CAF   112.54  3.000
 JR2  CAG   NAO  C6    124.94  3.000
 JR2  CAF   NAO  C6    122.42  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
 JR2  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 JR2  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 JR2  CONST_03  CAC   C5   C6   N1    180.00   0.0  0
 JR2  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 JR2  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 JR2  CONST_06  NAJ   C4   N3   C2    180.00   0.0  0
 JR2  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 JR2  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 JR2  CONST_09  CAC   C5   C4   N3    180.00   0.0  0
 JR2  CONST_10  CAB   NAJ  C4   N3    180.00   0.0  0
 JR2  CONST_11  CAB   CAC  C5   C4      0.00   0.0  0
 JR2  CONST_12  CAC   CAB  NAJ  C4      0.00   0.0  0
 JR2  CONST_13  CAB   NAJ  C4   C5      0.00   0.0  0
 JR2  CONST_14  NAJ   CAB  CAC  C5      0.00   0.0  0
 JR2  CONST_15  NAJ   C4   C5   C6    180.00   0.0  0
 JR2  CONST_16  CAB   CAC  C5   C6    180.00   0.0  0
 JR2  CONST_17  NAJ   C4   C5   CAC     0.00   0.0  0
 JR2  CONST_18  NAO   C6   N1   C2    180.00   0.0  0
 JR2  CONST_19  NAO   C6   C5   C4    180.00   0.0  0
 JR2  CONST_20  NAO   C6   C5   CAC     0.00   0.0  0
 JR2  CONST_21  NAA   C2   N3   C4    180.00   0.0  0
 JR2  CONST_22  NAA   C2   N1   C6    180.00   0.0  0
 JR2  CONST_23  HNAJ  NAJ  C4   N3      0.00   0.0  0
 JR2  CONST_24  HAC   CAC  C5   C4    180.00   0.0  0
 JR2  CONST_25  HAB   CAB  NAJ  C4    180.00   0.0  0
 JR2  Var_01    CAF   NAO  C6   N1     -2.70  30.0  2
 JR2  Var_02    CAD   CAF  NAO  C6   -170.29  30.0  1
 JR2  Var_03    CAE   CAG  NAO  C6   -165.84  30.0  1
 JR2  Var_04    NAO   CAG  CAE  CAD   -30.00  30.0  1
 JR2  Var_05    NAO   CAF  CAD  CAE   -31.37  30.0  1
 JR2  Var_06    CAG   CAE  CAD  CAF    38.18  30.0  1

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
 JR2  plan-1  N1    0.020
 JR2  plan-1  C2    0.020
 JR2  plan-1  N3    0.020
 JR2  plan-1  C4    0.020
 JR2  plan-1  C5    0.020
 JR2  plan-1  C6    0.020
 JR2  plan-1  NAA   0.020
 JR2  plan-1  CAB   0.020
 JR2  plan-1  CAC   0.020
 JR2  plan-1  NAJ   0.020
 JR2  plan-1  NAO   0.020
 JR2  plan-1  HAB   0.020
 JR2  plan-1  HAC   0.020
 JR2  plan-1  HNAJ  0.020
 JR2  plan-2  C2    0.020
 JR2  plan-2  NAA   0.020
 JR2  plan-2  HNAA  0.020
 JR2  plan-2  HNAB  0.020

