# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 04:13:08 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-cyclopentyl-6-[[(2~{R})-1-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-1-oxidanylidene-propan-2-yl]amino]-5~{H}-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC1=Nc2n(ncc2C(=O)N1)C3CCCC3)C(=O)N4CC5(COC5)C4
#
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
 EZU  EZU  1-cyclopentyl-6-[[(2~{R})-1-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-1-oxidanylidene-propan-2-yl]amino]-5~{H}-pyrazolo[3,4-d]pyrimidin-4-one  ligand  51  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EZU
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
 EZU  N1   N  NR16  0  -0.756  -0.8308  -22.9391  -24.5086
 EZU  C2   C  CR6   0   0.783  -0.2038  -23.5122  -25.5821
 EZU  N3   N  N     0  -0.523  -0.3577  -24.7636  -25.9221
 EZU  C4   C  CR56  0   0.619  -1.2081  -25.4402  -25.1316
 EZU  C5   C  CR56  0  -0.362  -1.8894  -24.9586  -24.0175
 EZU  C6   C  CR6   0   0.512  -1.7090  -23.5945  -23.6379
 EZU  N7   N  NR5   0  -0.382  -1.5695  -26.7224  -25.2803
 EZU  N8   N  N     0  -0.268  -2.4556  -27.0992  -24.3354
 EZU  C9   C  CR15  0  -0.073  -2.6528  -26.0548  -23.5690
 EZU  O10  O  O     0  -0.452  -2.2156  -22.9990  -22.7049
 EZU  C11  C  CR15  0  -0.086  -1.2057  -27.6166  -26.3607
 EZU  N12  N  NH1   0  -0.689   0.5904  -22.7267  -26.3250
 EZU  C13  C  CH1   0  -0.169   1.3886  -23.2673  -27.4021
 EZU  C14  C  C     0   0.518   0.5666  -23.9438  -28.4966
 EZU  C15  C  CH3   0  -0.699   2.2403  -22.1581  -28.0085
 EZU  N16  N  N     0  -0.450  -0.5857  -23.3811  -28.8611
 EZU  O17  O  O     0  -0.495   1.0014  -24.9379  -29.0645
 EZU  C18  C  C     0  -0.230  -1.4748  -23.7997  -29.9294
 EZU  C19  C  C     0  -0.222  -2.3265  -22.5495  -29.6565
 EZU  C20  C  C     0  -0.237  -1.3637  -22.1970  -28.5131
 EZU  C21  C  C     0  -0.118  -2.6706  -21.5622  -30.7682
 EZU  O22  O  O     0  -0.506  -4.0754  -21.7388  -30.5545
 EZU  C23  C  C     0  -0.120  -3.8368  -22.6291  -29.4585
 EZU  C24  C  CH2   0  -0.457  -2.4139  -28.0049  -27.2478
 EZU  C25  C  CH2   0  -0.440  -2.6062  -29.5066  -27.0372
 EZU  C26  C  CH2   0  -0.449  -1.1857  -30.0066  -26.7883
 EZU  C27  C  CH2   0  -0.455  -0.6086  -28.9445  -25.8556
 EZU  H1   H  HNR6  0   0.424  -0.6596  -21.9616  -24.3064
 EZU  H2   H  HCR5  0   0.269  -3.3264  -26.1102  -22.7272
 EZU  H3   H  HCR5  0   0.273  -0.4709  -27.0676  -26.9489
 EZU  H4   H  HNH1  0   0.417   0.7619  -21.7764  -26.0361
 EZU  H5   H  HCH1  0   0.277   2.0503  -24.0459  -27.0121
 EZU  H6   H  HCH3  0   0.259   2.9107  -21.7394  -27.2577
 EZU  H7   H  HCH3  0   0.260   2.8513  -22.5579  -28.8154
 EZU  H8   H  HCH3  0   0.247   1.6275  -21.3505  -28.4103
 EZU  H9   H  H     0   0.248  -1.9763  -24.7521  -29.7381
 EZU  H10  H  H     0   0.249  -1.0046  -23.8371  -30.9150
 EZU  H11  H  H     0   0.256  -0.8296  -21.2511  -28.6277
 EZU  H12  H  H     0   0.254  -1.8168  -22.2304  -27.5205
 EZU  H13  H  H     0   0.222  -2.3556  -21.8604  -31.7728
 EZU  H14  H  H     0   0.219  -2.3427  -20.5335  -30.5855
 EZU  H15  H  H     0   0.220  -4.1948  -22.2285  -28.5045
 EZU  H16  H  H     0   0.222  -4.2772  -23.6188  -29.6143
 EZU  H17  H  HCH2  0   0.240  -2.1658  -27.8043  -28.2917
 EZU  H18  H  HCH2  0   0.246  -3.3012  -27.4176  -27.0113
 EZU  H19  H  HCH2  0   0.234  -3.0952  -29.9921  -27.8824
 EZU  H20  H  HCH2  0   0.222  -3.2216  -29.6891  -26.1522
 EZU  H21  H  HCH2  0   0.236  -1.1466  -31.0080  -26.3583
 EZU  H22  H  HCH2  0   0.223  -0.6285  -30.0316  -27.7289
 EZU  H23  H  HCH2  0   0.240  -0.9469  -29.1314  -24.8348
 EZU  H24  H  HCH2  0   0.245   0.4812  -28.9221  -25.8404

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
 EZU  O22  C21  single    1.432  0.020  1.432
 EZU  O22  C23  single    1.432  0.020  1.432
 EZU  C21  C19  single    1.526  0.020  1.526
 EZU  C23  C19  single    1.525  0.020  1.525
 EZU  C19  C20  single    1.536  0.020  1.536
 EZU  C19  C18  single    1.537  0.020  1.537
 EZU  C20  N16  single    1.459  0.020  1.459
 EZU  N16  C18  single    1.452  0.020  1.452
 EZU  N16  C14  single    1.333  0.020  1.333
 EZU  O17  C14  double    1.225  0.020  1.225
 EZU  C14  C13  single    1.527  0.020  1.527
 EZU  C26  C25  single    1.526  0.020  1.526
 EZU  C26  C27  single    1.527  0.020  1.527
 EZU  C25  C24  single    1.529  0.020  1.529
 EZU  C24  C11  single    1.548  0.020  1.548
 EZU  C15  C13  single    1.524  0.020  1.524
 EZU  C13  N12  single    1.446  0.020  1.446
 EZU  C27  C11  single    1.541  0.020  1.541
 EZU  C11  N7   single    1.449  0.020  1.449
 EZU  N3   C2   double    1.306  0.020  1.306
 EZU  N3   C4   single    1.344  0.020  1.344
 EZU  N12  C2   single    1.341  0.020  1.341
 EZU  N7   C4   aromatic  1.340  0.020  1.340
 EZU  N7   N8   aromatic  1.349  0.020  1.349
 EZU  C2   N1   single    1.369  0.020  1.369
 EZU  C4   C5   aromatic  1.392  0.020  1.392
 EZU  N8   C9   aromatic  1.310  0.020  1.310
 EZU  N1   C6   single    1.400  0.020  1.400
 EZU  C5   C9   aromatic  1.409  0.020  1.409
 EZU  C5   C6   single    1.427  0.020  1.427
 EZU  C6   O10  double    1.217  0.020  1.217
 EZU  N1   H1   single    0.860  0.020  1.020
 EZU  C9   H2   single    0.930  0.020  1.080
 EZU  C11  H3   single    0.970  0.020  1.090
 EZU  N12  H4   single    0.860  0.020  1.020
 EZU  C13  H5   single    0.970  0.020  1.090
 EZU  C15  H6   single    0.970  0.020  1.090
 EZU  C15  H7   single    0.970  0.020  1.090
 EZU  C15  H8   single    0.970  0.020  1.090
 EZU  C18  H9   single    0.970  0.020  1.090
 EZU  C18  H10  single    0.970  0.020  1.090
 EZU  C20  H11  single    0.970  0.020  1.090
 EZU  C20  H12  single    0.970  0.020  1.090
 EZU  C21  H13  single    0.970  0.020  1.090
 EZU  C21  H14  single    0.970  0.020  1.090
 EZU  C23  H15  single    0.970  0.020  1.090
 EZU  C23  H16  single    0.970  0.020  1.090
 EZU  C24  H17  single    0.970  0.020  1.090
 EZU  C24  H18  single    0.970  0.020  1.090
 EZU  C25  H19  single    0.970  0.020  1.090
 EZU  C25  H20  single    0.970  0.020  1.090
 EZU  C26  H21  single    0.970  0.020  1.090
 EZU  C26  H22  single    0.970  0.020  1.090
 EZU  C27  H23  single    0.970  0.020  1.090
 EZU  C27  H24  single    0.970  0.020  1.090

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
 EZU  H1   N1   C6   115.71  3.000
 EZU  H1   N1   C2   118.89  3.000
 EZU  C6   N1   C2   125.39  3.000
 EZU  N12  C2   N3   119.12  3.000
 EZU  N12  C2   N1   117.41  3.000
 EZU  N3   C2   N1   123.46  3.000
 EZU  C4   N3   C2   113.82  3.000
 EZU  N7   C4   C5   106.72  3.000
 EZU  C5   C4   N3   127.33  3.000
 EZU  N7   C4   N3   125.94  3.000
 EZU  C9   C5   C6   136.66  3.000
 EZU  C6   C5   C4   118.79  3.000
 EZU  C9   C5   C4   104.53  3.000
 EZU  O10  C6   C5   128.23  3.000
 EZU  O10  C6   N1   120.59  3.000
 EZU  C5   C6   N1   111.19  3.000
 EZU  C11  N7   N8   120.99  3.000
 EZU  N8   N7   C4   111.50  3.000
 EZU  C11  N7   C4   127.25  3.000
 EZU  C9   N8   N7   106.61  3.000
 EZU  H2   C9   N8   120.60  3.000
 EZU  H2   C9   C5   128.77  3.000
 EZU  N8   C9   C5   110.63  3.000
 EZU  H3   C11  C27  110.47  3.000
 EZU  H3   C11  C24  110.07  3.000
 EZU  C27  C11  C24  105.90  3.000
 EZU  H3   C11  N7   105.13  3.000
 EZU  C27  C11  N7   112.62  3.000
 EZU  C24  C11  N7   112.71  3.000
 EZU  H4   N12  C13  118.18  3.000
 EZU  H4   N12  C2   119.60  3.000
 EZU  C13  N12  C2   121.37  3.000
 EZU  H5   C13  C15  108.77  3.000
 EZU  H5   C13  C14  105.43  3.000
 EZU  C15  C13  C14  109.76  3.000
 EZU  H5   C13  N12  109.55  3.000
 EZU  C15  C13  N12  109.44  3.000
 EZU  C14  C13  N12  113.74  3.000
 EZU  O17  C14  N16  121.51  3.000
 EZU  O17  C14  C13  120.06  3.000
 EZU  N16  C14  C13  118.32  3.000
 EZU  H8   C15  H7   108.32  3.000
 EZU  H8   C15  H6   108.35  3.000
 EZU  H7   C15  H6   107.85  3.000
 EZU  H8   C15  C13  111.81  3.000
 EZU  H7   C15  C13  109.96  3.000
 EZU  H6   C15  C13  110.43  3.000
 EZU  C20  N16  C18   94.76  3.000
 EZU  C18  N16  C14  127.51  3.000
 EZU  C20  N16  C14  137.58  3.000
 EZU  H10  C18  H9   108.99  3.000
 EZU  H10  C18  C19  115.24  3.000
 EZU  H9   C18  C19  115.04  3.000
 EZU  H10  C18  N16  114.21  3.000
 EZU  H9   C18  N16  113.79  3.000
 EZU  C19  C18  N16   88.52  3.000
 EZU  C23  C19  C21   84.55  3.000
 EZU  C23  C19  C20  122.42  3.000
 EZU  C21  C19  C20  122.35  3.000
 EZU  C20  C19  C18   88.37  3.000
 EZU  C23  C19  C18  121.96  3.000
 EZU  C21  C19  C18  121.45  3.000
 EZU  H12  C20  H11  108.95  3.000
 EZU  H12  C20  C19  114.19  3.000
 EZU  H11  C20  C19  115.29  3.000
 EZU  H12  C20  N16  114.42  3.000
 EZU  H11  C20  N16  114.65  3.000
 EZU  C19  C20  N16   88.30  3.000
 EZU  H14  C21  H13  108.84  3.000
 EZU  H14  C21  O22  112.63  3.000
 EZU  H13  C21  O22  112.69  3.000
 EZU  H14  C21  C19  114.76  3.000
 EZU  H13  C21  C19  115.31  3.000
 EZU  O22  C21  C19   91.88  3.000
 EZU  C23  O22  C21   91.57  3.000
 EZU  H16  C23  H15  108.86  3.000
 EZU  H16  C23  O22  112.72  3.000
 EZU  H15  C23  O22  112.64  3.000
 EZU  H16  C23  C19  115.29  3.000
 EZU  H15  C23  C19  114.70  3.000
 EZU  O22  C23  C19   91.90  3.000
 EZU  H18  C24  H17  107.07  3.000
 EZU  H18  C24  C25  113.39  3.000
 EZU  H17  C24  C25  109.94  3.000
 EZU  H18  C24  C11  112.07  3.000
 EZU  H17  C24  C11  108.93  3.000
 EZU  C25  C24  C11  105.40  3.000
 EZU  H20  C25  H19  107.50  3.000
 EZU  H20  C25  C26  109.70  3.000
 EZU  H19  C25  C26  113.44  3.000
 EZU  H20  C25  C24  110.27  3.000
 EZU  H19  C25  C24  112.77  3.000
 EZU  C26  C25  C24  103.13  3.000
 EZU  H22  C26  H21  107.45  3.000
 EZU  H22  C26  C27  110.41  3.000
 EZU  H21  C26  C27  112.60  3.000
 EZU  H22  C26  C25  109.96  3.000
 EZU  H21  C26  C25  113.49  3.000
 EZU  C27  C26  C25  102.91  3.000
 EZU  H24  C27  H23  107.48  3.000
 EZU  H24  C27  C26  113.62  3.000
 EZU  H23  C27  C26  109.57  3.000
 EZU  H24  C27  C11  111.98  3.000
 EZU  H23  C27  C11  109.51  3.000
 EZU  C26  C27  C11  104.64  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
 EZU  CONST_01  C9   N8   N7   C4      0.00   0.0  0
 EZU  CONST_02  N8   C9   C5   C4      0.00   0.0  0
 EZU  CONST_03  N8   N7   C4   C5      0.00   0.0  0
 EZU  CONST_04  N7   N8   C9   C5      0.00   0.0  0
 EZU  CONST_05  C9   C5   C4   N7      0.00   0.0  0
 EZU  CONST_06  C11  N7   C4   N3      0.00   0.0  0
 EZU  CONST_07  C11  N7   C4   C5    180.00   0.0  0
 EZU  CONST_08  C11  N7   N8   C9    180.00   0.0  0
 EZU  CONST_09  C4   N3   C2   N1      0.00   0.0  0
 EZU  CONST_10  C5   C6   N1   C2      0.00   0.0  0
 EZU  CONST_11  C6   N1   C2   N3      0.00   0.0  0
 EZU  CONST_12  O10  C6   N1   C2    180.00   0.0  0
 EZU  CONST_13  N12  C2   N3   C4    180.00   0.0  0
 EZU  CONST_14  N12  C2   N1   C6    180.00   0.0  0
 EZU  CONST_15  H2   C9   C5   C4    180.00   0.0  0
 EZU  CONST_16  H1   N1   C2   N3    180.00   0.0  0
 EZU  CONST_17  C20  N16  C14  C13     0.00   0.0  0
 EZU  CONST_18  C18  N16  C14  C13   180.00   0.0  0
 EZU  CONST_19  C20  N16  C14  O17   180.00   0.0  0
 EZU  CONST_20  C18  N16  C14  O17     0.00   0.0  0
 EZU  CONST_21  C13  N12  C2   N1    180.00   0.0  0
 EZU  CONST_22  C13  N12  C2   N3      0.00   0.0  0
 EZU  CONST_23  H4   N12  C2   N1      0.00   0.0  0
 EZU  Var_01    C26  C25  C24  C11   -31.82  30.0  1
 EZU  Var_02    C25  C26  C27  C11   -37.04  30.0  1
 EZU  Var_03    C21  C19  C20  N16  -125.26  30.0  3
 EZU  Var_04    O22  C21  C19  C18   122.07  30.0  1
 EZU  Var_05    O22  C23  C19  C18  -121.61  30.0  1
 EZU  Var_06    C27  C26  C25  C24    42.70  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
 EZU  chir_01  C11  C24  C27  N7   positiv
 EZU  chir_02  C13  N12  C14  C15  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
 EZU  plan-1  C13  0.020
 EZU  plan-1  C14  0.020
 EZU  plan-1  N16  0.020
 EZU  plan-1  O17  0.020
 EZU  plan-1  C18  0.020
 EZU  plan-1  C20  0.020
 EZU  plan-2  N1   0.020
 EZU  plan-2  C2   0.020
 EZU  plan-2  N3   0.020
 EZU  plan-2  C4   0.020
 EZU  plan-2  C5   0.020
 EZU  plan-2  C6   0.020
 EZU  plan-2  N7   0.020
 EZU  plan-2  N8   0.020
 EZU  plan-2  C9   0.020
 EZU  plan-2  O10  0.020
 EZU  plan-2  C11  0.020
 EZU  plan-2  N12  0.020
 EZU  plan-2  C13  0.020
 EZU  plan-2  H1   0.020
 EZU  plan-2  H2   0.020
 EZU  plan-2  H4   0.020

