# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:08:00 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 5-(2-phenylethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2c(CCc3ccccc3)c[nH]c2n1
#
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
 H0V  H0V  5-(2-phenylethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  34  19  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H0V
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
 H0V  CAF   C  CR16  0  -0.317  -3.3976  -1.3278   0.1898
 H0V  CAD   C  CR16  0  -0.239  -4.7209  -1.6834  -0.0387
 H0V  CAC   C  CR16  0  -0.274  -5.7110  -0.7100  -0.0521
 H0V  CAE   C  CR16  0  -0.241  -5.3672   0.6190   0.1639
 H0V  CAG   C  CR16  0  -0.307  -4.0434   0.9684   0.3927
 H0V  CAN   C  CR6   0   0.137  -3.0406   0.0003   0.4110
 H0V  CAI   C  CH2   0  -0.514  -1.6038   0.3866   0.6176
 H0V  CAJ   C  CH2   0  -0.562  -0.9480   0.8892  -0.6805
 H0V  CAQ   C  CR5   0   0.016   0.4998   1.2035  -0.4945
 H0V  C5    C  CR56  0  -0.147   1.5855   0.2853  -0.2809
 H0V  C6    C  CR6   0   0.403   1.7840  -1.1083  -0.2448
 H0V  NAB   N  NH2   0  -0.830   0.7799  -1.9924  -0.4388
 H0V  N1    N  N     0  -0.519   2.9877  -1.6042   0.0206
 H0V  C2    C  CR6   0   0.515   4.0064  -0.7561   0.2326
 H0V  NAA   N  NH2   0  -0.826   5.2184  -1.3340   0.4577
 H0V  N3    N  N     0  -0.511   3.9628   0.5690   0.1987
 H0V  C4    C  CR56  0   0.497   2.7432   1.0427  -0.0589
 H0V  NAM   N  NR15  0  -0.673   2.4003   2.3462  -0.1441
 H0V  CAH   C  CR15  0  -0.090   1.0483   2.4471  -0.4020
 H0V  HAF   H  HCR6  0   0.241  -2.6317  -2.0953   0.2018
 H0V  HAD   H  HCR6  0   0.253  -4.9782  -2.7221  -0.2027
 H0V  HAC   H  HCR6  0   0.253  -6.7432  -0.9847  -0.2267
 H0V  HAE   H  HCR6  0   0.253  -6.1324   1.3845   0.1579
 H0V  HAG   H  HCR6  0   0.246  -3.7856   2.0073   0.5649
 H0V  HAI1  H  HCH2  0   0.250  -1.5263   1.1741   1.3709
 H0V  HAI2  H  HCH2  0   0.246  -1.0425  -0.4678   1.0032
 H0V  HAJ1  H  HCH2  0   0.239  -1.0886   0.1442  -1.4709
 H0V  HAJ2  H  HCH2  0   0.259  -1.4750   1.7838  -1.0211
 H0V  HAH   H  HCR5  0   0.280   0.5780   3.4128  -0.4954
 H0V  HAB1  H  HNH2  0   0.399  -0.0435  -1.6986  -0.9352
 H0V  HAB2  H  HNH2  0   0.392   1.0375  -2.9564  -0.5741
 H0V  HAA1  H  HNH2  0   0.383   5.2151  -2.2930   0.7605
 H0V  HAA2  H  HNH2  0   0.383   5.9252  -0.7561   0.8797
 H0V  HAM   H  HNR5  0   0.405   3.0308   3.1212  -0.0216

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
 H0V  CAF  CAD   aromatic  1.389  0.020  1.389
 H0V  CAF  CAN   aromatic  1.393  0.020  1.393
 H0V  CAD  CAC   aromatic  1.389  0.020  1.389
 H0V  CAC  CAE   aromatic  1.390  0.020  1.390
 H0V  CAE  CAG   aromatic  1.388  0.020  1.388
 H0V  CAG  CAN   aromatic  1.394  0.020  1.394
 H0V  CAN  CAI   single    1.502  0.020  1.502
 H0V  CAI  CAJ   single    1.539  0.020  1.539
 H0V  CAJ  CAQ   single    1.493  0.020  1.493
 H0V  CAQ  C5    aromatic  1.438  0.020  1.438
 H0V  CAQ  CAH   aromatic  1.362  0.020  1.362
 H0V  C5   C6    aromatic  1.408  0.020  1.408
 H0V  C5   C4    aromatic  1.401  0.020  1.401
 H0V  C6   NAB   single    1.352  0.020  1.352
 H0V  C6   N1    aromatic  1.329  0.020  1.329
 H0V  N1   C2    aromatic  1.342  0.020  1.342
 H0V  C2   NAA   single    1.361  0.020  1.361
 H0V  C2   N3    aromatic  1.326  0.020  1.326
 H0V  N3   C4    aromatic  1.333  0.020  1.333
 H0V  C4   NAM   aromatic  1.351  0.020  1.351
 H0V  NAM  CAH   aromatic  1.380  0.020  1.380
 H0V  CAF  HAF   single    0.930  0.020  1.080
 H0V  CAD  HAD   single    0.930  0.020  1.080
 H0V  CAC  HAC   single    0.930  0.020  1.080
 H0V  CAE  HAE   single    0.930  0.020  1.080
 H0V  CAG  HAG   single    0.930  0.020  1.080
 H0V  CAI  HAI1  single    0.970  0.020  1.090
 H0V  CAI  HAI2  single    0.970  0.020  1.090
 H0V  CAJ  HAJ1  single    0.970  0.020  1.090
 H0V  CAJ  HAJ2  single    0.970  0.020  1.090
 H0V  CAH  HAH   single    0.930  0.020  1.080
 H0V  NAB  HAB1  single    0.890  0.020  1.040
 H0V  NAB  HAB2  single    0.890  0.020  1.040
 H0V  NAA  HAA1  single    0.890  0.020  1.040
 H0V  NAA  HAA2  single    0.890  0.020  1.040
 H0V  NAM  HAM   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
 H0V  HAF   CAF  CAN   119.48  3.000
 H0V  HAF   CAF  CAD   119.56  3.000
 H0V  CAN   CAF  CAD   120.96  3.000
 H0V  HAD   CAD  CAC   120.11  3.000
 H0V  HAD   CAD  CAF   119.80  3.000
 H0V  CAC   CAD  CAF   120.09  3.000
 H0V  HAC   CAC  CAE   120.24  3.000
 H0V  HAC   CAC  CAD   120.25  3.000
 H0V  CAE   CAC  CAD   119.51  3.000
 H0V  HAE   CAE  CAG   119.80  3.000
 H0V  HAE   CAE  CAC   120.04  3.000
 H0V  CAG   CAE  CAC   120.15  3.000
 H0V  HAG   CAG  CAN   119.50  3.000
 H0V  HAG   CAG  CAE   119.62  3.000
 H0V  CAN   CAG  CAE   120.89  3.000
 H0V  CAI   CAN  CAG   120.75  3.000
 H0V  CAI   CAN  CAF   120.81  3.000
 H0V  CAG   CAN  CAF   118.40  3.000
 H0V  HAI2  CAI  HAI1  106.49  3.000
 H0V  HAI2  CAI  CAJ   109.52  3.000
 H0V  HAI1  CAI  CAJ   108.42  3.000
 H0V  HAI2  CAI  CAN   109.80  3.000
 H0V  HAI1  CAI  CAN   110.37  3.000
 H0V  CAJ   CAI  CAN   112.06  3.000
 H0V  HAJ2  CAJ  HAJ1  105.67  3.000
 H0V  HAJ2  CAJ  CAQ   109.52  3.000
 H0V  HAJ1  CAJ  CAQ   110.95  3.000
 H0V  HAJ2  CAJ  CAI   108.96  3.000
 H0V  HAJ1  CAJ  CAI   109.38  3.000
 H0V  CAQ   CAJ  CAI   112.14  3.000
 H0V  CAH   CAQ  C5    105.59  3.000
 H0V  CAH   CAQ  CAJ   126.23  3.000
 H0V  C5    CAQ  CAJ   128.04  3.000
 H0V  C4    C5   C6    114.48  3.000
 H0V  C4    C5   CAQ   107.60  3.000
 H0V  C6    C5   CAQ   137.92  3.000
 H0V  N1    C6   NAB   117.23  3.000
 H0V  N1    C6   C5    120.15  3.000
 H0V  NAB   C6   C5    122.60  3.000
 H0V  HAB2  NAB  HAB1  115.02  3.000
 H0V  HAB2  NAB  C6    117.09  3.000
 H0V  HAB1  NAB  C6    119.22  3.000
 H0V  C2    N1   C6    118.90  3.000
 H0V  N3    C2   NAA   117.23  3.000
 H0V  N3    C2   N1    127.03  3.000
 H0V  NAA   C2   N1    115.69  3.000
 H0V  HAA2  NAA  HAA1  115.07  3.000
 H0V  HAA2  NAA  C2    116.81  3.000
 H0V  HAA1  NAA  C2    116.85  3.000
 H0V  C4    N3   C2    112.95  3.000
 H0V  NAM   C4   N3    125.96  3.000
 H0V  NAM   C4   C5    107.57  3.000
 H0V  N3    C4   C5    126.46  3.000
 H0V  HAM   NAM  CAH   125.45  3.000
 H0V  HAM   NAM  C4    125.20  3.000
 H0V  CAH   NAM  C4    109.33  3.000
 H0V  HAH   CAH  NAM   120.59  3.000
 H0V  HAH   CAH  CAQ   129.50  3.000
 H0V  NAM   CAH  CAQ   109.90  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
 H0V  CONST_01  CAE   CAC  CAD  CAF     0.00   0.0  0
 H0V  CONST_02  CAE   CAG  CAN  CAF     0.00   0.0  0
 H0V  CONST_03  CAG   CAN  CAF  CAD     0.00   0.0  0
 H0V  CONST_04  CAG   CAE  CAC  CAD     0.00   0.0  0
 H0V  CONST_05  CAN   CAF  CAD  CAC     0.00   0.0  0
 H0V  CONST_06  CAN   CAG  CAE  CAC     0.00   0.0  0
 H0V  CONST_07  N1    C6   C5   CAQ   180.00   0.0  0
 H0V  CONST_08  N3    C4   C5   CAQ   180.00   0.0  0
 H0V  CONST_09  NAM   C4   C5   CAQ     0.00   0.0  0
 H0V  CONST_10  C4    NAM  CAH  CAQ     0.00   0.0  0
 H0V  CONST_11  NAM   CAH  CAQ  C5      0.00   0.0  0
 H0V  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 H0V  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 H0V  CONST_14  CAH   NAM  C4   C5      0.00   0.0  0
 H0V  CONST_15  CAH   CAQ  C5   C6    180.00   0.0  0
 H0V  CONST_16  N3    C4   C5   C6      0.00   0.0  0
 H0V  CONST_17  NAM   C4   C5   C6    180.00   0.0  0
 H0V  CONST_18  N3    C2   N1   C6      0.00   0.0  0
 H0V  CONST_19  C4    C5   C6   N1      0.00   0.0  0
 H0V  CONST_20  C4    N3   C2   N1      0.00   0.0  0
 H0V  CONST_21  NAM   C4   N3   C2    180.00   0.0  0
 H0V  CONST_22  CAH   NAM  C4   N3    180.00   0.0  0
 H0V  CONST_23  CAH   CAQ  C5   C4      0.00   0.0  0
 H0V  CONST_24  CAI   CAN  CAF  CAD   180.00   0.0  0
 H0V  CONST_25  CAI   CAN  CAG  CAE   180.00   0.0  0
 H0V  CONST_26  C6    C5   CAQ  CAJ     0.00   0.0  0
 H0V  CONST_27  C4    C5   CAQ  CAJ   180.00   0.0  0
 H0V  CONST_28  NAM   CAH  CAQ  CAJ   180.00   0.0  0
 H0V  CONST_29  NAB   C6   C5   CAQ     0.00   0.0  0
 H0V  CONST_30  NAA   C2   N1   C6    180.00   0.0  0
 H0V  CONST_31  C4    C5   C6   NAB   180.00   0.0  0
 H0V  CONST_32  C2    N1   C6   NAB   180.00   0.0  0
 H0V  CONST_33  C4    N3   C2   NAA   180.00   0.0  0
 H0V  CONST_34  HAC   CAC  CAD  CAF   180.00   0.0  0
 H0V  CONST_35  HAG   CAG  CAN  CAF   180.00   0.0  0
 H0V  CONST_36  HAE   CAE  CAC  CAD   180.00   0.0  0
 H0V  CONST_37  HAF   CAF  CAD  CAC   180.00   0.0  0
 H0V  CONST_38  HAD   CAD  CAC  CAE   180.00   0.0  0
 H0V  CONST_39  HAM   NAM  CAH  CAQ   180.00   0.0  0
 H0V  CONST_40  HAH   CAH  CAQ  C5    180.00   0.0  0
 H0V  CONST_42  HAB2  NAB  C6   C5    180.00   0.0  0
 H0V  Var_01    CAJ   CAI  CAN  CAF    96.80  30.0  2
 H0V  Var_02    CAQ   CAJ  CAI  CAN  -176.90  30.0  3
 H0V  Var_03    C5    CAQ  CAJ  CAI    70.43  30.0  2

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
 H0V  plan-1  CAF   0.020
 H0V  plan-1  CAD   0.020
 H0V  plan-1  CAC   0.020
 H0V  plan-1  CAE   0.020
 H0V  plan-1  CAG   0.020
 H0V  plan-1  CAN   0.020
 H0V  plan-1  CAI   0.020
 H0V  plan-1  HAF   0.020
 H0V  plan-1  HAD   0.020
 H0V  plan-1  HAC   0.020
 H0V  plan-1  HAE   0.020
 H0V  plan-1  HAG   0.020
 H0V  plan-2  CAJ   0.020
 H0V  plan-2  CAQ   0.020
 H0V  plan-2  C5    0.020
 H0V  plan-2  C6    0.020
 H0V  plan-2  NAB   0.020
 H0V  plan-2  N1    0.020
 H0V  plan-2  C2    0.020
 H0V  plan-2  NAA   0.020
 H0V  plan-2  N3    0.020
 H0V  plan-2  C4    0.020
 H0V  plan-2  NAM   0.020
 H0V  plan-2  CAH   0.020
 H0V  plan-2  HAH   0.020
 H0V  plan-2  HAM   0.020
 H0V  plan-3  C6    0.020
 H0V  plan-3  NAB   0.020
 H0V  plan-3  HAB1  0.020
 H0V  plan-3  HAB2  0.020
 H0V  plan-4  C2    0.020
 H0V  plan-4  NAA   0.020
 H0V  plan-4  HAA1  0.020
 H0V  plan-4  HAA2  0.020

