# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 00:34:02 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 1-cyclopentyl-6-{(1R)-1-[3-(pyrimidin-2-yl)azetidin-1-yl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N1C[C@@H](C1)c2ncccn2)C3=Nc4n(ncc4C(=O)N3)C5CCCC5
#
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
 0WL  0WL  1-cyclopentyl-6-{(1R)-1-[3-(pyrimidin-2-yl)azetidin-1-yl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  50  27  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0WL
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
 0WL  C1   C  CR16  0  -0.347   6.6920  -0.7195  -1.4768
 0WL  C2   C  CR16  0  -0.027   6.2485  -1.8003  -0.7366
 0WL  C3   C  CR16  0  -0.024   5.8802   0.4027  -1.4610
 0WL  C4   C  CR15  0  -0.069  -4.2377   1.0628  -1.3132
 0WL  C5   C  CR56  0  -0.347  -3.0035   1.5887  -0.8864
 0WL  C6   C  CR56  0   0.597  -2.3777   0.5285  -0.2406
 0WL  C7   C  CR6   0   0.401   4.4053  -0.6456  -0.0954
 0WL  C8   C  CR6   0   0.514  -2.3209   2.8406  -0.9786
 0WL  C9   C  CR6   0   0.537  -0.5440   1.6671   0.2531
 0WL  C10  C  CH2   0  -0.457  -3.1325  -4.2061  -0.0132
 0WL  C11  C  CH2   0  -0.449  -4.1271  -3.8319   1.1003
 0WL  C12  C  CH2   0  -0.441  -3.0269  -2.9444  -0.8606
 0WL  C13  C  CH2   0  -0.449  -4.0489  -2.2965   1.2401
 0WL  C14  C  C     0  -0.254   2.8366   0.6073   1.5702
 0WL  C15  C  C     0  -0.247   1.8353  -0.2079  -0.0696
 0WL  C16  C  C     0  -0.392   3.1263  -0.6094   0.6718
 0WL  C17  C  CH1   0  -0.089  -3.0023  -1.8529   0.2060
 0WL  C18  C  CH3   0  -0.661   0.6712   2.6150   2.1995
 0WL  C19  C  CH1   0  -0.187   0.8152   1.8631   0.8763
 0WL  N20  N  N     0  -0.418   5.1136  -1.7697  -0.0476
 0WL  N21  N  N     0  -0.410   4.7458   0.4434  -0.7778
 0WL  N22  N  N     0  -0.259  -4.3456  -0.1955  -0.9584
 0WL  N23  N  N     0  -0.443  -1.1597   0.5352   0.3442
 0WL  N24  N  NR5   0  -0.387  -3.2160  -0.5164  -0.3077
 0WL  N25  N  NR16  0  -0.717  -1.0664   2.7600  -0.3691
 0WL  N26  N  N     0  -0.412   1.4491   0.5942   1.0940
 0WL  H1   H  HCR6  0   0.285   7.6158  -0.7491  -2.0353
 0WL  H2   H  HCR6  0   0.278   6.8211  -2.7203  -0.6947
 0WL  H3   H  HCR6  0   0.278   6.1508   1.2943  -2.0157
 0WL  H4   H  HCR5  0   0.277  -5.0322   1.5515  -1.8557
 0WL  H6   H  HCH2  0   0.240  -3.4508  -5.0771  -0.5861
 0WL  H7   H  HCH2  0   0.233  -5.1372  -4.1280   0.8153
 0WL  H8   H  HCH2  0   0.236  -3.8971  -4.3439   2.0345
 0WL  H9   H  HCH2  0   0.245  -2.1480  -2.9192  -1.5062
 0WL  H10  H  HCH2  0   0.234  -3.9135  -2.8293  -1.4895
 0WL  H11  H  HCH2  0   0.243  -5.0112  -1.8390   1.0077
 0WL  H12  H  HCH2  0   0.246  -3.7713  -1.9755   2.2438
 0WL  H13  H  H     0   0.242   2.9670   0.4768   2.6458
 0WL  H14  H  H     0   0.219   3.3998   1.4916   1.2454
 0WL  H15  H  H     0   0.218   2.0501   0.3956  -0.9611
 0WL  H16  H  H     0   0.240   1.1426  -1.0070  -0.3344
 0WL  H17  H  H     0   0.272   3.0024  -1.5483   1.2102
 0WL  H18  H  HCH1  0   0.272  -2.0132  -1.8310   0.6670
 0WL  H19  H  HCH3  0   0.242   0.0826   2.0326   2.9079
 0WL  H20  H  HCH3  0   0.256   1.6536   2.7989   2.6341
 0WL  H21  H  HCH3  0   0.245   0.1931   3.5838   2.0592
 0WL  H22  H  HCH1  0   0.240   1.4045   2.4942   0.1849
 0WL  H23  H  HNR6  0   0.428  -0.5001   3.5988  -0.4069
 0WL  O27  O  O     0  -0.458  -2.7026   3.8725  -1.5002
 0WL  H5   H  HCH2  0   0.228  -2.1553  -4.4428   0.4151

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
 0WL  C3   N21  aromatic  1.325  0.020  1.325
 0WL  C3   C1   aromatic  1.385  0.020  1.385
 0WL  N21  C7   aromatic  1.329  0.020  1.329
 0WL  C1   C2   aromatic  1.383  0.020  1.383
 0WL  C7   C16  single    1.492  0.020  1.492
 0WL  C7   N20  aromatic  1.330  0.020  1.330
 0WL  C2   N20  aromatic  1.328  0.020  1.328
 0WL  C16  C14  single    1.540  0.020  1.540
 0WL  C16  C15  single    1.542  0.020  1.542
 0WL  C10  C11  single    1.539  0.020  1.539
 0WL  C10  C12  single    1.523  0.020  1.523
 0WL  C14  N26  single    1.467  0.020  1.467
 0WL  C11  C13  single    1.544  0.020  1.544
 0WL  C15  N26  single    1.465  0.020  1.465
 0WL  C12  C17  single    1.526  0.020  1.526
 0WL  N26  C19  single    1.435  0.020  1.435
 0WL  C13  C17  single    1.537  0.020  1.537
 0WL  C17  N24  single    1.448  0.020  1.448
 0WL  C19  C18  single    1.529  0.020  1.529
 0WL  C19  C9   single    1.508  0.020  1.508
 0WL  N23  C9   double    1.292  0.020  1.292
 0WL  N23  C6   single    1.351  0.020  1.351
 0WL  N24  C6   aromatic  1.341  0.020  1.341
 0WL  N24  N22  aromatic  1.342  0.020  1.342
 0WL  C9   N25  single    1.362  0.020  1.362
 0WL  C6   C5   aromatic  1.390  0.020  1.390
 0WL  N22  C4   aromatic  1.312  0.020  1.312
 0WL  N25  C8   single    1.397  0.020  1.397
 0WL  C5   C4   aromatic  1.408  0.020  1.408
 0WL  C5   C8   single    1.429  0.020  1.429
 0WL  C8   O27  double    1.218  0.020  1.218
 0WL  C1   H1   single    0.930  0.020  1.080
 0WL  C2   H2   single    0.930  0.020  1.080
 0WL  C3   H3   single    0.930  0.020  1.080
 0WL  C4   H4   single    0.930  0.020  1.080
 0WL  C10  H5   single    0.970  0.020  1.090
 0WL  C10  H6   single    0.970  0.020  1.090
 0WL  C11  H7   single    0.970  0.020  1.090
 0WL  C11  H8   single    0.970  0.020  1.090
 0WL  C12  H9   single    0.970  0.020  1.090
 0WL  C12  H10  single    0.970  0.020  1.090
 0WL  C13  H11  single    0.970  0.020  1.090
 0WL  C13  H12  single    0.970  0.020  1.090
 0WL  C14  H13  single    0.970  0.020  1.090
 0WL  C14  H14  single    0.970  0.020  1.090
 0WL  C15  H15  single    0.970  0.020  1.090
 0WL  C15  H16  single    0.970  0.020  1.090
 0WL  C16  H17  single    0.970  0.020  1.090
 0WL  C17  H18  single    0.970  0.020  1.090
 0WL  C18  H19  single    0.970  0.020  1.090
 0WL  C18  H20  single    0.970  0.020  1.090
 0WL  C18  H21  single    0.970  0.020  1.090
 0WL  C19  H22  single    0.970  0.020  1.090
 0WL  N25  H23  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
 0WL  H1   C1   C3   121.97  3.000
 0WL  H1   C1   C2   121.98  3.000
 0WL  C3   C1   C2   116.05  3.000
 0WL  H2   C2   N20  116.79  3.000
 0WL  H2   C2   C1   120.95  3.000
 0WL  N20  C2   C1   122.26  3.000
 0WL  H3   C3   N21  116.88  3.000
 0WL  H3   C3   C1   120.94  3.000
 0WL  N21  C3   C1   122.18  3.000
 0WL  H4   C4   N22  120.65  3.000
 0WL  H4   C4   C5   128.96  3.000
 0WL  N22  C4   C5   110.39  3.000
 0WL  C8   C5   C6   118.89  3.000
 0WL  C8   C5   C4   136.60  3.000
 0WL  C6   C5   C4   104.51  3.000
 0WL  N24  C6   N23  126.08  3.000
 0WL  N24  C6   C5   106.83  3.000
 0WL  N23  C6   C5   127.09  3.000
 0WL  N21  C7   N20  125.07  3.000
 0WL  N20  C7   C16  117.31  3.000
 0WL  N21  C7   C16  117.62  3.000
 0WL  O27  C8   N25  121.15  3.000
 0WL  O27  C8   C5   128.34  3.000
 0WL  N25  C8   C5   110.51  3.000
 0WL  N25  C9   N23  123.55  3.000
 0WL  N25  C9   C19  115.48  3.000
 0WL  N23  C9   C19  120.95  3.000
 0WL  H6   C10  H5   107.09  3.000
 0WL  H6   C10  C12  112.94  3.000
 0WL  H5   C10  C12  109.59  3.000
 0WL  H6   C10  C11  112.69  3.000
 0WL  H5   C10  C11  110.29  3.000
 0WL  C12  C10  C11  104.23  3.000
 0WL  H8   C11  H7   106.97  3.000
 0WL  H8   C11  C13  112.27  3.000
 0WL  H7   C11  C13  109.92  3.000
 0WL  H8   C11  C10  111.69  3.000
 0WL  H7   C11  C10  110.09  3.000
 0WL  C13  C11  C10  105.94  3.000
 0WL  H10  C12  H9   108.10  3.000
 0WL  H10  C12  C17  109.87  3.000
 0WL  H9   C12  C17  112.59  3.000
 0WL  H10  C12  C10  110.54  3.000
 0WL  H9   C12  C10  113.84  3.000
 0WL  C17  C12  C10  101.81  3.000
 0WL  H12  C13  H11  107.31  3.000
 0WL  H12  C13  C17  111.18  3.000
 0WL  H11  C13  C17  109.66  3.000
 0WL  H12  C13  C11  112.91  3.000
 0WL  H11  C13  C11  110.69  3.000
 0WL  C17  C13  C11  105.11  3.000
 0WL  H14  C14  H13  109.07  3.000
 0WL  H14  C14  N26  113.35  3.000
 0WL  H13  C14  N26  115.59  3.000
 0WL  H14  C14  C16  111.55  3.000
 0WL  H13  C14  C16  117.26  3.000
 0WL  N26  C14  C16   88.94  3.000
 0WL  H16  C15  H15  109.27  3.000
 0WL  H16  C15  N26  115.26  3.000
 0WL  H15  C15  N26  113.30  3.000
 0WL  H16  C15  C16  117.25  3.000
 0WL  H15  C15  C16  111.71  3.000
 0WL  N26  C15  C16   88.94  3.000
 0WL  H17  C16  C15  111.52  3.000
 0WL  H17  C16  C14  111.79  3.000
 0WL  C15  C16  C14   85.25  3.000
 0WL  H17  C16  C7   109.31  3.000
 0WL  C15  C16  C7   118.48  3.000
 0WL  C14  C16  C7   118.71  3.000
 0WL  H18  C17  N24  105.38  3.000
 0WL  H18  C17  C13  109.80  3.000
 0WL  N24  C17  C13  113.88  3.000
 0WL  H18  C17  C12  108.91  3.000
 0WL  N24  C17  C12  114.19  3.000
 0WL  C13  C17  C12  104.65  3.000
 0WL  H21  C18  H20  107.27  3.000
 0WL  H21  C18  H19  108.79  3.000
 0WL  H20  C18  H19  108.53  3.000
 0WL  H21  C18  C19  111.55  3.000
 0WL  H20  C18  C19  110.07  3.000
 0WL  H19  C18  C19  110.53  3.000
 0WL  H22  C19  N26  111.35  3.000
 0WL  H22  C19  C18  108.09  3.000
 0WL  N26  C19  C18  110.20  3.000
 0WL  H22  C19  C9   107.22  3.000
 0WL  C18  C19  C9   109.67  3.000
 0WL  N26  C19  C9   110.24  3.000
 0WL  C7   N20  C2   117.14  3.000
 0WL  C7   N21  C3   117.31  3.000
 0WL  N24  N22  C4   106.93  3.000
 0WL  C9   N23  C6   113.79  3.000
 0WL  N22  N24  C17  121.12  3.000
 0WL  N22  N24  C6   111.34  3.000
 0WL  C17  N24  C6   127.53  3.000
 0WL  H23  N25  C9   117.85  3.000
 0WL  H23  N25  C8   115.98  3.000
 0WL  C9   N25  C8   126.16  3.000
 0WL  C19  N26  C15  118.69  3.000
 0WL  C19  N26  C14  117.33  3.000
 0WL  C15  N26  C14   90.76  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
 0WL  CONST_01  C7   N21  C3   C1     0.00   0.0  0
 0WL  CONST_02  C7   N20  C2   C1     0.00   0.0  0
 0WL  CONST_03  N21  C3   C1   C2     0.00   0.0  0
 0WL  CONST_04  N21  C7   N20  C2     0.00   0.0  0
 0WL  CONST_05  N20  C7   N21  C3     0.00   0.0  0
 0WL  CONST_06  N20  C2   C1   C3     0.00   0.0  0
 0WL  CONST_07  C6   N24  N22  C4     0.00   0.0  0
 0WL  CONST_08  N24  C6   C5   C4     0.00   0.0  0
 0WL  CONST_09  N22  N24  C6   C5     0.00   0.0  0
 0WL  CONST_10  N24  N22  C4   C5     0.00   0.0  0
 0WL  CONST_11  N22  C4   C5   C6     0.00   0.0  0
 0WL  CONST_12  C16  C7   N20  C2   180.00   0.0  0
 0WL  CONST_13  C16  C7   N21  C3   180.00   0.0  0
 0WL  CONST_14  C17  N24  N22  C4   180.00   0.0  0
 0WL  CONST_15  C17  N24  C6   C5   180.00   0.0  0
 0WL  CONST_16  N23  C6   N24  C17    0.00   0.0  0
 0WL  CONST_17  C9   N25  C8   C5     0.00   0.0  0
 0WL  CONST_18  N25  C9   N23  C6     0.00   0.0  0
 0WL  CONST_19  N23  C9   N25  C8     0.00   0.0  0
 0WL  CONST_20  C19  C9   N23  C6   180.00   0.0  0
 0WL  CONST_21  C19  C9   N25  C8   180.00   0.0  0
 0WL  CONST_22  O27  C8   N25  C9   180.00   0.0  0
 0WL  CONST_23  H3   C3   C1   C2   180.00   0.0  0
 0WL  CONST_24  H2   C2   C1   C3   180.00   0.0  0
 0WL  CONST_25  H4   C4   C5   C6   180.00   0.0  0
 0WL  CONST_26  H1   C1   C2   N20  180.00   0.0  0
 0WL  CONST_27  H23  N25  C8   C5   180.00   0.0  0
 0WL  Var_01    C17  C13  C11  C10   -0.42  30.0  1
 0WL  Var_02    C17  C12  C10  C11   40.70  30.0  1
 0WL  Var_03    C13  C11  C10  C12  -25.06  30.0  1
 0WL  Var_04    C16  C15  N26  C14   18.98  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
 0WL  chir_01  C16  C7   C14  C15  negativ
 0WL  chir_02  C17  C12  C13  N24  positiv
 0WL  chir_03  C19  N26  C18  C9   positiv

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
 0WL  plan-1  C1   0.020
 0WL  plan-1  C2   0.020
 0WL  plan-1  C3   0.020
 0WL  plan-1  C7   0.020
 0WL  plan-1  C16  0.020
 0WL  plan-1  N20  0.020
 0WL  plan-1  N21  0.020
 0WL  plan-1  H1   0.020
 0WL  plan-1  H2   0.020
 0WL  plan-1  H3   0.020
 0WL  plan-2  C4   0.020
 0WL  plan-2  C5   0.020
 0WL  plan-2  C6   0.020
 0WL  plan-2  C8   0.020
 0WL  plan-2  C9   0.020
 0WL  plan-2  C17  0.020
 0WL  plan-2  C19  0.020
 0WL  plan-2  N22  0.020
 0WL  plan-2  N23  0.020
 0WL  plan-2  N24  0.020
 0WL  plan-2  N25  0.020
 0WL  plan-2  H4   0.020
 0WL  plan-2  H23  0.020
 0WL  plan-2  O27  0.020

