# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:01:30 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-phenyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2c([nH]cc2c3ccccc3)n1
#
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
 KP2  KP2  5-phenyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  28  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KP2
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
 KP2  C1   C  CR16  0  -0.314  -2.8445  -0.9126  -0.7816
 KP2  C2   C  CR16  0  -0.239  -4.1508  -0.4447  -0.7839
 KP2  C3   C  CR16  0  -0.270  -4.5157   0.6188   0.0317
 KP2  C4   C  CR16  0  -0.235  -3.5644   1.2029   0.8578
 KP2  C5   C  CR16  0  -0.347  -2.2608   0.7272   0.8694
 KP2  C6   C  CR6   0   0.029  -1.8780  -0.3344   0.0447
 KP2  C7   C  CR5   0  -0.009  -0.5075  -0.8549   0.0692
 KP2  C8   C  CR56  0  -0.150   0.7405  -0.1378   0.0460
 KP2  C9   C  CR6   0   0.401   1.1898   1.1885  -0.1355
 KP2  N1   N  NH2   0  -0.827   0.3534   2.2247  -0.3203
 KP2  N2   N  N     0  -0.518   2.4924   1.4553  -0.1174
 KP2  C10  C  CR6   0   0.516   3.3628   0.4477   0.0397
 KP2  N3   N  NH2   0  -0.826   4.6742   0.8034   0.1177
 KP2  N4   N  N     0  -0.512   3.0770  -0.8432   0.1502
 KP2  C11  C  CR56  0   0.499   1.7668  -1.0854   0.1442
 KP2  N5   N  NR15  0  -0.669   1.1919  -2.3082   0.2146
 KP2  C12  C  CR15  0  -0.070  -0.1742  -2.1762   0.1690
 KP2  H1   H  HCR6  0   0.248  -2.5664  -1.7278  -1.4382
 KP2  H2   H  HCR6  0   0.257  -4.8823  -0.9054  -1.4352
 KP2  H3   H  HCR6  0   0.256  -5.5325   0.9889   0.0232
 KP2  H4   H  HCR6  0   0.257  -3.8381   2.0269   1.5042
 KP2  H5   H  HCR6  0   0.261  -1.5392   1.1712   1.5443
 KP2  H6   H  HNH2  0   0.407  -0.6133   2.0677  -0.5450
 KP2  H7   H  HNH2  0   0.393   0.7444   3.1099  -0.5949
 KP2  H8   H  HNH2  0   0.383   4.9216   1.7074  -0.2474
 KP2  H9   H  HNH2  0   0.383   5.3506   0.0778  -0.0503
 KP2  H10  H  HNR5  0   0.409   1.6892  -3.1786   0.3104
 KP2  H11  H  HCR5  0   0.286  -0.8154  -3.0394   0.2452

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
 KP2  N1   C9   single    1.344  0.020  1.344
 KP2  N2   C9   aromatic  1.330  0.020  1.330
 KP2  N2   C10  aromatic  1.341  0.020  1.341
 KP2  C9   C8   aromatic  1.412  0.020  1.412
 KP2  C1   C2   aromatic  1.388  0.020  1.388
 KP2  C1   C6   aromatic  1.397  0.020  1.397
 KP2  N3   C10  single    1.361  0.020  1.361
 KP2  C10  N4   aromatic  1.327  0.020  1.327
 KP2  C2   C3   aromatic  1.389  0.020  1.389
 KP2  C8   C7   aromatic  1.440  0.020  1.440
 KP2  C8   C11  aromatic  1.400  0.020  1.400
 KP2  C6   C7   single    1.466  0.020  1.466
 KP2  C6   C5   aromatic  1.398  0.020  1.398
 KP2  C7   C12  aromatic  1.366  0.020  1.366
 KP2  C3   C4   aromatic  1.389  0.020  1.389
 KP2  N4   C11  aromatic  1.332  0.020  1.332
 KP2  C11  N5   aromatic  1.353  0.020  1.353
 KP2  C5   C4   aromatic  1.388  0.020  1.388
 KP2  C12  N5   aromatic  1.373  0.020  1.373
 KP2  C1   H1   single    0.930  0.020  1.080
 KP2  C2   H2   single    0.930  0.020  1.080
 KP2  C3   H3   single    0.930  0.020  1.080
 KP2  C4   H4   single    0.930  0.020  1.080
 KP2  C5   H5   single    0.930  0.020  1.080
 KP2  N1   H6   single    0.890  0.020  1.040
 KP2  N1   H7   single    0.890  0.020  1.040
 KP2  N3   H8   single    0.890  0.020  1.040
 KP2  N3   H9   single    0.890  0.020  1.040
 KP2  N5   H10  single    0.860  0.020  1.020
 KP2  C12  H11  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
 KP2  H1   C1   C6   119.50  3.000
 KP2  H1   C1   C2   119.64  3.000
 KP2  C6   C1   C2   120.85  3.000
 KP2  H2   C2   C3   120.11  3.000
 KP2  H2   C2   C1   119.58  3.000
 KP2  C3   C2   C1   120.30  3.000
 KP2  H3   C3   C4   120.30  3.000
 KP2  H3   C3   C2   120.27  3.000
 KP2  C4   C3   C2   119.43  3.000
 KP2  H4   C4   C5   119.57  3.000
 KP2  H4   C4   C3   120.14  3.000
 KP2  C5   C4   C3   120.28  3.000
 KP2  H5   C5   C6   119.77  3.000
 KP2  H5   C5   C4   119.37  3.000
 KP2  C6   C5   C4   120.85  3.000
 KP2  C7   C6   C5   121.05  3.000
 KP2  C5   C6   C1   118.29  3.000
 KP2  C7   C6   C1   120.64  3.000
 KP2  C12  C7   C8   105.75  3.000
 KP2  C12  C7   C6   124.93  3.000
 KP2  C8   C7   C6   129.29  3.000
 KP2  C11  C8   C9   114.29  3.000
 KP2  C11  C8   C7   107.29  3.000
 KP2  C9   C8   C7   138.23  3.000
 KP2  N2   C9   N1   117.17  3.000
 KP2  N2   C9   C8   119.90  3.000
 KP2  N1   C9   C8   122.94  3.000
 KP2  H7   N1   H6   116.77  3.000
 KP2  H7   N1   C9   118.30  3.000
 KP2  H6   N1   C9   120.58  3.000
 KP2  C10  N2   C9   119.12  3.000
 KP2  N4   C10  N3   117.20  3.000
 KP2  N4   C10  N2   126.95  3.000
 KP2  N3   C10  N2   115.83  3.000
 KP2  H9   N3   H8   114.97  3.000
 KP2  H9   N3   C10  116.73  3.000
 KP2  H8   N3   C10  116.82  3.000
 KP2  C11  N4   C10  112.85  3.000
 KP2  N5   C11  N4   125.58  3.000
 KP2  N5   C11  C8   107.68  3.000
 KP2  N4   C11  C8   126.73  3.000
 KP2  H10  N5   C12  125.27  3.000
 KP2  H10  N5   C11  125.19  3.000
 KP2  C12  N5   C11  109.52  3.000
 KP2  H11  C12  N5   120.83  3.000
 KP2  H11  C12  C7   129.38  3.000
 KP2  N5   C12  C7   109.76  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
 KP2  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 KP2  CONST_04  C4   C5   C6   C1     0.00  0.0  0
 KP2  CONST_05  C7   C6   C1   C2   180.00  0.0  0
 KP2  CONST_06  C5   C6   C1   C2     0.00  0.0  0
 KP2  CONST_07  C5   C4   C3   C2     0.00  0.0  0
 KP2  CONST_08  C6   C1   C2   C3     0.00  0.0  0
 KP2  CONST_09  C6   C5   C4   C3     0.00  0.0  0
 KP2  CONST_10  C7   C6   C5   C4   180.00  0.0  0
 KP2  CONST_13  C9   C8   C7   C6     0.00  0.0  0
 KP2  CONST_14  C11  C8   C7   C6   180.00  0.0  0
 KP2  CONST_15  N5   C12  C7   C6   180.00  0.0  0
 KP2  CONST_16  N2   C9   C8   C7   180.00  0.0  0
 KP2  CONST_17  N4   C11  C8   C7   180.00  0.0  0
 KP2  CONST_18  N5   C11  C8   C7     0.00  0.0  0
 KP2  CONST_19  C11  N5   C12  C7     0.00  0.0  0
 KP2  CONST_20  C10  N2   C9   C8     0.00  0.0  0
 KP2  CONST_21  N5   C12  C7   C8     0.00  0.0  0
 KP2  CONST_22  C10  N4   C11  C8     0.00  0.0  0
 KP2  CONST_23  C12  N5   C11  C8     0.00  0.0  0
 KP2  CONST_24  N4   C10  N2   C9     0.00  0.0  0
 KP2  CONST_25  C12  C7   C8   C9   180.00  0.0  0
 KP2  CONST_26  N4   C11  C8   C9     0.00  0.0  0
 KP2  CONST_27  N5   C11  C8   C9   180.00  0.0  0
 KP2  CONST_28  C11  C8   C9   N2     0.00  0.0  0
 KP2  CONST_29  C11  N4   C10  N2     0.00  0.0  0
 KP2  CONST_30  N5   C11  N4   C10  180.00  0.0  0
 KP2  CONST_31  C12  N5   C11  N4   180.00  0.0  0
 KP2  CONST_32  C12  C7   C8   C11    0.00  0.0  0
 KP2  CONST_33  N1   C9   C8   C7     0.00  0.0  0
 KP2  CONST_34  N3   C10  N2   C9   180.00  0.0  0
 KP2  CONST_35  C10  N2   C9   N1   180.00  0.0  0
 KP2  CONST_36  C11  C8   C9   N1   180.00  0.0  0
 KP2  CONST_37  C11  N4   C10  N3   180.00  0.0  0
 KP2  CONST_38  H3   C3   C2   C1   180.00  0.0  0
 KP2  CONST_39  H5   C5   C6   C1   180.00  0.0  0
 KP2  CONST_40  H4   C4   C3   C2   180.00  0.0  0
 KP2  CONST_41  H1   C1   C2   C3   180.00  0.0  0
 KP2  CONST_42  H2   C2   C3   C4   180.00  0.0  0
 KP2  CONST_43  H11  C12  C7   C6     0.00  0.0  0
 KP2  CONST_44  H10  N5   C12  C7   180.00  0.0  0
 KP2  CONST_45  H6   N1   C9   C8     0.00  0.0  0
 KP2  CONST_46  H7   N1   C9   C8   180.00  0.0  0

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
 KP2  plan-1  C1   0.020
 KP2  plan-1  C2   0.020
 KP2  plan-1  C3   0.020
 KP2  plan-1  C4   0.020
 KP2  plan-1  C5   0.020
 KP2  plan-1  C6   0.020
 KP2  plan-1  C7   0.020
 KP2  plan-1  H1   0.020
 KP2  plan-1  H2   0.020
 KP2  plan-1  H3   0.020
 KP2  plan-1  H4   0.020
 KP2  plan-1  H5   0.020
 KP2  plan-2  C6   0.020
 KP2  plan-2  C7   0.020
 KP2  plan-2  C8   0.020
 KP2  plan-2  C9   0.020
 KP2  plan-2  N1   0.020
 KP2  plan-2  N2   0.020
 KP2  plan-2  C10  0.020
 KP2  plan-2  N3   0.020
 KP2  plan-2  N4   0.020
 KP2  plan-2  C11  0.020
 KP2  plan-2  N5   0.020
 KP2  plan-2  C12  0.020
 KP2  plan-2  H10  0.020
 KP2  plan-2  H11  0.020
 KP2  plan-3  C9   0.020
 KP2  plan-3  N1   0.020
 KP2  plan-3  H6   0.020
 KP2  plan-3  H7   0.020
 KP2  plan-4  C10  0.020
 KP2  plan-4  N3   0.020
 KP2  plan-4  H8   0.020
 KP2  plan-4  H9   0.020

