# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:39:19 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-(7-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2ccc(cc2c1)c3nn(CC4CCNCC4)c5ncnc(N)c35
#
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
 UWB  UWB  3-(7-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  56  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UWB
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
 UWB  N5   N  NH2   0  -0.814   0.7148  -3.0776  -0.5842
 UWB  C    C  CR6   0   0.427  -0.5857  -2.7786  -0.5231
 UWB  C3   C  CR56  0  -0.253  -1.0939  -1.6136   0.0995
 UWB  C4   C  CR5   0   0.259  -0.6407  -0.4714   0.8168
 UWB  N2   N  N     0  -0.272  -1.6719   0.2163   1.2530
 UWB  N3   N  NR5   0  -0.370  -2.7829  -0.4154   0.8503
 UWB  C5   C  CH2   0  -0.286  -4.1002   0.1173   1.1236
 UWB  C6   C  CH1   0  -0.273  -4.7551   0.7588  -0.0942
 UWB  C10  C  CH2   0  -0.416  -6.1741   1.2057   0.2534
 UWB  C9   C  CH2   0  -0.293  -6.8334   1.8679  -0.9469
 UWB  N4   N  NH1   0  -0.595  -6.0328   2.9943  -1.3923
 UWB  C8   C  CH2   0  -0.291  -4.7058   2.5801  -1.8123
 UWB  C7   C  CH2   0  -0.413  -3.9634   1.9414  -0.6470
 UWB  C2   C  CR56  0   0.582  -2.4874  -1.5198   0.1418
 UWB  N1   N  N     0  -0.465  -3.3571  -2.3760  -0.4026
 UWB  C1   C  CR16  0   0.051  -2.7524  -3.3782  -1.0052
 UWB  N    N  N     0  -0.476  -1.4464  -3.6276  -1.0889
 UWB  C11  C  CR6   0   0.044   0.7265  -0.0228   1.0977
 UWB  C16  C  CR16  0  -0.425   1.6923  -0.0640   0.1225
 UWB  C15  C  CR66  0   0.172   3.0189   0.3549   0.3852
 UWB  C17  C  CR16  0  -0.446   4.0193   0.3029  -0.6042
 UWB  C18  C  CR6   0   0.408   5.3065   0.7050  -0.3262
 UWB  O    O  O2    0  -0.473   6.2013   0.6209  -1.3262
 UWB  C21  C  CH2   0  -0.191   7.5552   0.9886  -1.0900
 UWB  C22  C  CH3   0  -0.681   8.3277   0.7647  -2.3679
 UWB  C19  C  CR16  0  -0.379   5.6284   1.1797   0.9682
 UWB  C20  C  CR16  0  -0.291   4.6628   1.2417   1.9370
 UWB  C14  C  CR66  0   0.088   3.3372   0.8370   1.6807
 UWB  C13  C  CR16  0  -0.296   2.3210   0.8930   2.6637
 UWB  C12  C  CR16  0  -0.295   1.0510   0.4779   2.3850
 UWB  H1   H  HNH2  0   0.414   1.3853  -2.5970  -0.0094
 UWB  H2   H  HNH2  0   0.404   0.9829  -3.9807  -0.9390
 UWB  H3   H  HCH2  0   0.265  -4.7244  -0.6970   1.4971
 UWB  H4   H  HCH2  0   0.264  -3.9861   0.8427   1.9295
 UWB  H5   H  HCH1  0   0.232  -4.8306  -0.0035  -0.8800
 UWB  H6   H  HCH2  0   0.232  -6.7732   0.3510   0.5791
 UWB  H7   H  HCH2  0   0.216  -6.1433   1.9150   1.0874
 UWB  H8   H  HCH2  0   0.186  -6.9677   1.1076  -1.7354
 UWB  H9   H  HCH2  0   0.232  -7.8292   2.2260  -0.6783
 UWB  H10  H  HNH1  0   0.350  -6.5009   3.4570  -2.1605
 UWB  H12  H  HCH2  0   0.185  -4.7332   1.8614  -2.6489
 UWB  H13  H  HCH2  0   0.231  -4.1583   3.4562  -2.1662
 UWB  H14  H  HCH2  0   0.214  -3.8224   2.6886   0.1416
 UWB  H15  H  HCH2  0   0.233  -2.9705   1.6276  -0.9777
 UWB  H16  H  HCR6  0   0.255  -3.3953  -4.1066  -1.4882
 UWB  H17  H  HCR6  0   0.269   1.4435  -0.3944  -0.8797
 UWB  H18  H  HCR6  0   0.259   3.7717  -0.0610  -1.5947
 UWB  H19  H  HCH2  0   0.226   7.6168   2.0393  -0.7881
 UWB  H20  H  HCH2  0   0.226   7.9766   0.3849  -0.2799
 UWB  H21  H  HCH3  0   0.235   7.9346   1.3715  -3.1838
 UWB  H22  H  HCH3  0   0.238   9.3689   1.0459  -2.2136
 UWB  H23  H  HCH3  0   0.235   8.3043  -0.2823  -2.6701
 UWB  H24  H  HCR6  0   0.285   6.6326   1.4973   1.2122
 UWB  H25  H  HCR6  0   0.264   4.9230   1.6071   2.9228
 UWB  H26  H  HCR6  0   0.258   2.5672   1.2634   3.6517
 UWB  H27  H  HCR6  0   0.254   0.2862   0.5112   3.1492

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
 UWB  C20  C19  aromatic  1.369  0.020  1.369
 UWB  C20  C14  aromatic  1.410  0.020  1.410
 UWB  C13  C14  aromatic  1.415  0.020  1.415
 UWB  C13  C12  aromatic  1.365  0.020  1.365
 UWB  C19  C18  aromatic  1.416  0.020  1.416
 UWB  C14  C15  aromatic  1.418  0.020  1.418
 UWB  C12  C11  aromatic  1.419  0.020  1.419
 UWB  C18  O    single    1.345  0.020  1.345
 UWB  C18  C17  aromatic  1.377  0.020  1.377
 UWB  C15  C17  aromatic  1.408  0.020  1.408
 UWB  C15  C16  aromatic  1.416  0.020  1.416
 UWB  O    C21  single    1.423  0.020  1.423
 UWB  C11  C16  aromatic  1.373  0.020  1.373
 UWB  C11  C4   single    1.466  0.020  1.466
 UWB  C22  C21  single    1.510  0.020  1.510
 UWB  N5   C    single    1.336  0.020  1.336
 UWB  C4   C3   aromatic  1.423  0.020  1.423
 UWB  C4   N2   aromatic  1.314  0.020  1.314
 UWB  C    C3   aromatic  1.415  0.020  1.415
 UWB  C    N    aromatic  1.335  0.020  1.335
 UWB  C3   C2   aromatic  1.397  0.020  1.397
 UWB  N2   N3   aromatic  1.340  0.020  1.340
 UWB  N    C1   aromatic  1.332  0.020  1.332
 UWB  C5   N3   single    1.447  0.020  1.447
 UWB  C5   C6   single    1.524  0.020  1.524
 UWB  C2   N3   aromatic  1.345  0.020  1.345
 UWB  C2   N1   aromatic  1.336  0.020  1.336
 UWB  C1   N1   aromatic  1.316  0.020  1.316
 UWB  C6   C10  single    1.528  0.020  1.528
 UWB  C6   C7   single    1.527  0.020  1.527
 UWB  C10  C9   single    1.521  0.020  1.521
 UWB  C7   C8   single    1.522  0.020  1.522
 UWB  C9   N4   single    1.452  0.020  1.452
 UWB  N4   C8   single    1.452  0.020  1.452
 UWB  N5   H1   single    0.890  0.020  1.040
 UWB  N5   H2   single    0.890  0.020  1.040
 UWB  C5   H3   single    0.970  0.020  1.090
 UWB  C5   H4   single    0.970  0.020  1.090
 UWB  C6   H5   single    0.970  0.020  1.090
 UWB  C10  H6   single    0.970  0.020  1.090
 UWB  C10  H7   single    0.970  0.020  1.090
 UWB  C9   H8   single    0.970  0.020  1.090
 UWB  C9   H9   single    0.970  0.020  1.090
 UWB  N4   H10  single    0.890  0.020  1.040
 UWB  C8   H12  single    0.970  0.020  1.090
 UWB  C8   H13  single    0.970  0.020  1.090
 UWB  C7   H14  single    0.970  0.020  1.090
 UWB  C7   H15  single    0.970  0.020  1.090
 UWB  C1   H16  single    0.930  0.020  1.080
 UWB  C16  H17  single    0.930  0.020  1.080
 UWB  C17  H18  single    0.930  0.020  1.080
 UWB  C21  H19  single    0.970  0.020  1.090
 UWB  C21  H20  single    0.970  0.020  1.090
 UWB  C22  H21  single    0.970  0.020  1.090
 UWB  C22  H22  single    0.970  0.020  1.090
 UWB  C22  H23  single    0.970  0.020  1.090
 UWB  C19  H24  single    0.930  0.020  1.080
 UWB  C20  H25  single    0.930  0.020  1.080
 UWB  C13  H26  single    0.930  0.020  1.080
 UWB  C12  H27  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
 UWB  H2   N5   H1   116.91  3.000
 UWB  H2   N5   C    118.44  3.000
 UWB  H1   N5   C    121.07  3.000
 UWB  N    C    C3   118.59  3.000
 UWB  N    C    N5   117.77  3.000
 UWB  C3   C    N5   123.64  3.000
 UWB  C2   C3   C4   104.39  3.000
 UWB  C2   C3   C    115.26  3.000
 UWB  C4   C3   C    140.19  3.000
 UWB  C11  C4   N2   120.54  3.000
 UWB  N2   C4   C3   109.72  3.000
 UWB  C11  C4   C3   129.74  3.000
 UWB  N3   N2   C4   107.71  3.000
 UWB  C2   N3   C5   127.00  3.000
 UWB  C2   N3   N2   111.30  3.000
 UWB  C5   N3   N2   121.63  3.000
 UWB  H4   C5   H3   107.65  3.000
 UWB  H4   C5   C6   110.83  3.000
 UWB  H3   C5   C6   109.97  3.000
 UWB  H4   C5   N3   106.81  3.000
 UWB  H3   C5   N3   108.09  3.000
 UWB  C6   C5   N3   113.28  3.000
 UWB  H5   C6   C7   108.33  3.000
 UWB  H5   C6   C10  107.59  3.000
 UWB  C7   C6   C10  109.72  3.000
 UWB  H5   C6   C5   108.02  3.000
 UWB  C7   C6   C5   113.11  3.000
 UWB  C10  C6   C5   109.90  3.000
 UWB  H7   C10  H6   107.14  3.000
 UWB  H7   C10  C9   109.34  3.000
 UWB  H6   C10  C9   109.75  3.000
 UWB  H7   C10  C6   109.66  3.000
 UWB  H6   C10  C6   110.36  3.000
 UWB  C9   C10  C6   110.51  3.000
 UWB  H9   C9   H8   106.90  3.000
 UWB  H9   C9   N4   108.90  3.000
 UWB  H8   C9   N4   112.49  3.000
 UWB  H9   C9   C10  110.12  3.000
 UWB  H8   C9   C10  108.46  3.000
 UWB  N4   C9   C10  109.92  3.000
 UWB  H10  N4   C8   109.49  3.000
 UWB  H10  N4   C9   109.43  3.000
 UWB  C8   N4   C9   111.79  3.000
 UWB  H13  C8   H12  106.81  3.000
 UWB  H13  C8   C7   109.89  3.000
 UWB  H12  C8   C7   108.62  3.000
 UWB  H13  C8   N4   108.85  3.000
 UWB  H12  C8   N4   112.49  3.000
 UWB  C7   C8   N4   110.11  3.000
 UWB  H15  C7   H14  107.27  3.000
 UWB  H15  C7   C8   109.39  3.000
 UWB  H14  C7   C8   109.12  3.000
 UWB  H15  C7   C6   111.00  3.000
 UWB  H14  C7   C6   109.54  3.000
 UWB  C8   C7   C6   110.45  3.000
 UWB  N1   C2   N3   126.71  3.000
 UWB  N1   C2   C3   126.42  3.000
 UWB  N3   C2   C3   106.87  3.000
 UWB  C1   N1   C2   112.04  3.000
 UWB  H16  C1   N    115.29  3.000
 UWB  H16  C1   N1   116.27  3.000
 UWB  N    C1   N1   128.43  3.000
 UWB  C1   N    C    119.10  3.000
 UWB  C12  C11  C16  119.60  3.000
 UWB  C16  C11  C4   120.71  3.000
 UWB  C12  C11  C4   119.68  3.000
 UWB  H17  C16  C15  118.47  3.000
 UWB  H17  C16  C11  120.28  3.000
 UWB  C15  C16  C11  121.23  3.000
 UWB  C14  C15  C17  119.67  3.000
 UWB  C17  C15  C16  121.63  3.000
 UWB  C14  C15  C16  118.70  3.000
 UWB  H18  C17  C18  119.74  3.000
 UWB  H18  C17  C15  119.49  3.000
 UWB  C18  C17  C15  120.76  3.000
 UWB  C19  C18  O    123.34  3.000
 UWB  O    C18  C17  116.98  3.000
 UWB  C19  C18  C17  119.68  3.000
 UWB  C21  O    C18  119.59  3.000
 UWB  H20  C21  H19  107.67  3.000
 UWB  H20  C21  C22  110.34  3.000
 UWB  H19  C21  C22  110.30  3.000
 UWB  H20  C21  O    110.28  3.000
 UWB  H19  C21  O    110.33  3.000
 UWB  C22  C21  O    107.94  3.000
 UWB  H23  C22  H22  107.92  3.000
 UWB  H23  C22  H21  108.63  3.000
 UWB  H22  C22  H21  107.87  3.000
 UWB  H23  C22  C21  111.48  3.000
 UWB  H22  C22  C21  109.32  3.000
 UWB  H21  C22  C21  111.50  3.000
 UWB  H24  C19  C20  118.82  3.000
 UWB  H24  C19  C18  121.07  3.000
 UWB  C20  C19  C18  120.11  3.000
 UWB  H25  C20  C14  119.22  3.000
 UWB  H25  C20  C19  119.33  3.000
 UWB  C14  C20  C19  121.44  3.000
 UWB  C13  C14  C20  122.54  3.000
 UWB  C13  C14  C15  119.13  3.000
 UWB  C20  C14  C15  118.34  3.000
 UWB  H26  C13  C12  120.11  3.000
 UWB  H26  C13  C14  118.94  3.000
 UWB  C12  C13  C14  120.96  3.000
 UWB  H27  C12  C13  120.29  3.000
 UWB  H27  C12  C11  119.34  3.000
 UWB  C13  C12  C11  120.36  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
 UWB  CONST_01  C11  C4   C3   C      0.00   0.0  0
 UWB  CONST_02  N2   C4   C3   C    180.00   0.0  0
 UWB  CONST_03  N3   C2   C3   C    180.00   0.0  0
 UWB  CONST_04  N1   C2   C3   C      0.00   0.0  0
 UWB  CONST_05  N1   C1   N    C      0.00   0.0  0
 UWB  CONST_08  N3   N2   C4   C3     0.00   0.0  0
 UWB  CONST_09  C1   N    C    C3     0.00   0.0  0
 UWB  CONST_10  N2   N3   C2   C3     0.00   0.0  0
 UWB  CONST_11  C1   N1   C2   C3     0.00   0.0  0
 UWB  CONST_12  C13  C12  C11  C4   180.00   0.0  0
 UWB  CONST_13  C15  C16  C11  C4   180.00   0.0  0
 UWB  CONST_14  N    C    C3   C4   180.00   0.0  0
 UWB  CONST_15  N3   C2   C3   C4     0.00   0.0  0
 UWB  CONST_16  N1   C2   C3   C4   180.00   0.0  0
 UWB  CONST_17  C2   N3   N2   C4     0.00   0.0  0
 UWB  CONST_20  C2   C3   C4   N2     0.00   0.0  0
 UWB  CONST_21  N1   C2   N3   N2   180.00   0.0  0
 UWB  CONST_22  C11  C4   N2   N3   180.00   0.0  0
 UWB  CONST_23  C1   N1   C2   N3   180.00   0.0  0
 UWB  CONST_24  C11  C4   C3   C2   180.00   0.0  0
 UWB  CONST_25  N    C    C3   C2     0.00   0.0  0
 UWB  CONST_26  N    C1   N1   C2     0.00   0.0  0
 UWB  CONST_27  C14  C13  C12  C11    0.00   0.0  0
 UWB  CONST_28  C14  C15  C16  C11    0.00   0.0  0
 UWB  CONST_29  C17  C15  C16  C11  180.00   0.0  0
 UWB  CONST_30  C20  C14  C15  C16  180.00   0.0  0
 UWB  CONST_31  C13  C14  C15  C16    0.00   0.0  0
 UWB  CONST_32  C18  C17  C15  C16  180.00   0.0  0
 UWB  CONST_33  C13  C12  C11  C16    0.00   0.0  0
 UWB  CONST_34  C19  C20  C14  C15    0.00   0.0  0
 UWB  CONST_35  C12  C13  C14  C15    0.00   0.0  0
 UWB  CONST_36  C19  C18  C17  C15    0.00   0.0  0
 UWB  CONST_37  C12  C11  C16  C15    0.00   0.0  0
 UWB  CONST_38  C20  C19  C18  C17    0.00   0.0  0
 UWB  CONST_39  C20  C14  C15  C17    0.00   0.0  0
 UWB  CONST_40  C13  C14  C15  C17  180.00   0.0  0
 UWB  CONST_41  C14  C20  C19  C18    0.00   0.0  0
 UWB  CONST_42  C14  C15  C17  C18    0.00   0.0  0
 UWB  CONST_43  C13  C14  C20  C19  180.00   0.0  0
 UWB  CONST_44  C12  C13  C14  C20  180.00   0.0  0
 UWB  CONST_45  C4   C3   C    N5     0.00   0.0  0
 UWB  CONST_46  C2   C3   C    N5   180.00   0.0  0
 UWB  CONST_47  C1   N    C    N5   180.00   0.0  0
 UWB  CONST_48  C5   N3   C2   C3   180.00   0.0  0
 UWB  CONST_49  C5   N3   N2   C4   180.00   0.0  0
 UWB  CONST_50  N1   C2   N3   C5     0.00   0.0  0
 UWB  CONST_51  O    C18  C17  C15  180.00   0.0  0
 UWB  CONST_52  C20  C19  C18  O    180.00   0.0  0
 UWB  CONST_53  H16  C1   N    C    180.00   0.0  0
 UWB  CONST_54  H27  C12  C11  C4     0.00   0.0  0
 UWB  CONST_55  H17  C16  C11  C4     0.00   0.0  0
 UWB  CONST_56  H26  C13  C12  C11  180.00   0.0  0
 UWB  CONST_57  H18  C17  C15  C16    0.00   0.0  0
 UWB  CONST_58  H25  C20  C14  C15  180.00   0.0  0
 UWB  CONST_59  H24  C19  C18  C17  180.00   0.0  0
 UWB  CONST_60  H1   N5   C    C3     0.00   0.0  0
 UWB  CONST_61  H2   N5   C    C3   180.00   0.0  0
 UWB  Var_01    N4   C9   C10  C6   -57.41  30.0  1
 UWB  Var_02    N4   C8   C7   C6    57.11  30.0  1
 UWB  Var_03    C8   N4   C9   C10   61.36  30.0  1
 UWB  Var_04    C7   C8   N4   C9   -61.27  30.0  1
 UWB  Var_05    C6   C5   N3   N2   104.12  30.0  3
 UWB  Var_06    C19  C18  O    C21    1.68  30.0  2
 UWB  Var_07    C22  C21  O    C18  178.72  30.0  3
 UWB  Var_08    H21  C22  C21  O     60.47  30.0  3

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
 UWB  chir_01  C6  C5  C10  C7  negativ

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
 UWB  plan-1  N5   0.020
 UWB  plan-1  C    0.020
 UWB  plan-1  C3   0.020
 UWB  plan-1  C4   0.020
 UWB  plan-1  N2   0.020
 UWB  plan-1  N3   0.020
 UWB  plan-1  C5   0.020
 UWB  plan-1  C2   0.020
 UWB  plan-1  N1   0.020
 UWB  plan-1  C1   0.020
 UWB  plan-1  N    0.020
 UWB  plan-1  C11  0.020
 UWB  plan-1  H16  0.020
 UWB  plan-2  C4   0.020
 UWB  plan-2  C11  0.020
 UWB  plan-2  C16  0.020
 UWB  plan-2  C15  0.020
 UWB  plan-2  C17  0.020
 UWB  plan-2  C18  0.020
 UWB  plan-2  O    0.020
 UWB  plan-2  C19  0.020
 UWB  plan-2  C20  0.020
 UWB  plan-2  C14  0.020
 UWB  plan-2  C13  0.020
 UWB  plan-2  C12  0.020
 UWB  plan-2  H17  0.020
 UWB  plan-2  H18  0.020
 UWB  plan-2  H24  0.020
 UWB  plan-2  H25  0.020
 UWB  plan-2  H26  0.020
 UWB  plan-2  H27  0.020
 UWB  plan-3  N5   0.020
 UWB  plan-3  C    0.020
 UWB  plan-3  H1   0.020
 UWB  plan-3  H2   0.020

