# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:21:51 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin-3-yl]-1-(tetrahydro-2H-pyran-4-yl)-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]1CN(C[C@H]1C2=Nc3n(ncc3C(=O)N2)C4CCOCC4)Cc5ncccn5
#
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
 7RG  7RG  6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin-3-yl]-1-(tetrahydro-2H-pyran-4-yl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  54  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7RG
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
 7RG  N1    N  NR5   0  -0.384   3.3494  -0.0870   0.4654
 7RG  N2    N  N     0  -0.258   4.4850   0.4210   0.9712
 7RG  C3    C  CR15  0  -0.068   4.3235   1.7208   1.0392
 7RG  C4    C  CR56  0  -0.349   3.0490   2.0827   0.5626
 7RG  C5    C  CR6   0   0.515   2.3150   3.2945   0.3755
 7RG  O6    O  O     0  -0.457   2.6621   4.4340   0.6275
 7RG  N7    N  NR16  0  -0.714   1.0595   3.0267  -0.1753
 7RG  C8    C  CR6   0   0.554   0.5598   1.7985  -0.4908
 7RG  N9    N  N     0  -0.462   1.2233   0.7012  -0.3207
 7RG  C10   C  CR56  0   0.609   2.4566   0.8787   0.2007
 7RG  C11   C  CR15  0  -0.409  -0.8423   1.7905  -1.0163
 7RG  C12   C  CH2   0  -0.246  -1.8929   1.9244   0.1169
 7RG  N13   N  NR5   0  -0.417  -2.7569   0.7650  -0.0403
 7RG  C14   C  CH2   0  -0.256  -2.7217   0.4095  -1.4443
 7RG  C15   C  CR15  0  -0.239  -1.2414   0.5185  -1.7758
 7RG  C16   C  CH2   0  -0.343  -4.0687   0.9648   0.5114
 7RG  C17   C  CR6   0   0.348  -4.8997  -0.2907   0.5531
 7RG  N18   N  N     0  -0.393  -4.2895  -1.4432   0.7999
 7RG  C19   C  CR16  0  -0.030  -5.0518  -2.5268   0.8624
 7RG  C20   C  CR16  0  -0.343  -6.4246  -2.4783   0.6909
 7RG  C21   C  CR16  0  -0.029  -6.9613  -1.2264   0.4490
 7RG  N22   N  N     0  -0.414  -6.2072  -0.1371   0.3734
 7RG  C23   C  CH1   0  -0.104   3.2094  -1.5114   0.2285
 7RG  C24   C  CH2   0  -0.453   3.4149  -2.3211   1.5037
 7RG  C25   C  CH2   0  -0.188   3.3088  -3.8048   1.1802
 7RG  O26   O  O2    0  -0.481   4.2285  -4.1948   0.1847
 7RG  C27   C  CH2   0  -0.187   4.0183  -3.5016  -1.0256
 7RG  C28   C  CH2   0  -0.453   4.1675  -1.9967  -0.8545
 7RG  C29   C  CH3   0  -0.663  -0.9196   0.5691  -3.2577
 7RG  H3    H  HCR5  0   0.277   5.1102   2.3539   1.4198
 7RG  HN7   H  HNR6  0   0.430   0.4746   3.8331  -0.3570
 7RG  H11   H  HCR5  0   0.290  -0.9509   2.6473  -1.6892
 7RG  H12   H  HCH2  0   0.245  -1.4500   1.9406   1.1168
 7RG  H12A  H  HCH2  0   0.222  -2.4367   2.8716  -0.0062
 7RG  H14   H  HCH2  0   0.242  -3.1094  -0.5975  -1.6106
 7RG  H14A  H  HCH2  0   0.192  -3.3117   1.1028  -2.0703
 7RG  H15   H  HCR5  0   0.253  -0.7315  -0.3365  -1.3270
 7RG  H16   H  HCH2  0   0.270  -3.9630   1.3217   1.5425
 7RG  H16A  H  HCH2  0   0.221  -4.6413   1.7389  -0.0235
 7RG  H19   H  HCR6  0   0.276  -4.5490  -3.4670   1.0606
 7RG  H20   H  HCR6  0   0.283  -7.0402  -3.3640   0.7434
 7RG  H21   H  HCR6  0   0.278  -8.0280  -1.0938   0.3068
 7RG  H23   H  HCH1  0   0.269   2.1811  -1.6474  -0.1165
 7RG  H24   H  HCH2  0   0.242   4.3986  -2.1029   1.9259
 7RG  H24A  H  HCH2  0   0.251   2.6642  -2.0590   2.2525
 7RG  H25   H  HCH2  0   0.244   3.5219  -4.4023   2.0674
 7RG  H25A  H  HCH2  0   0.203   2.2818  -4.0379   0.8628
 7RG  H27   H  HCH2  0   0.244   4.7487  -3.8767  -1.7437
 7RG  H27A  H  HCH2  0   0.203   3.0178  -3.7258  -1.4247
 7RG  H28   H  HCH2  0   0.250   3.9541  -1.5027  -1.8050
 7RG  H28A  H  HCH2  0   0.241   5.1948  -1.7515  -0.5733
 7RG  H29   H  HCH3  0   0.221  -1.4085   1.4180  -3.7403
 7RG  H29A  H  HCH3  0   0.233   0.1544   0.6643  -3.4232
 7RG  H29B  H  HCH3  0   0.234  -1.2503  -0.3398  -3.7621

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
 7RG  C23  N1    single    1.451  0.020  1.451
 7RG  N1   C10   aromatic  1.342  0.020  1.342
 7RG  N1   N2    aromatic  1.343  0.020  1.343
 7RG  N2   C3    aromatic  1.312  0.020  1.312
 7RG  C4   C3    aromatic  1.408  0.020  1.408
 7RG  C3   H3    single    0.930  0.020  1.080
 7RG  C10  C4    aromatic  1.390  0.020  1.390
 7RG  C4   C5    single    1.429  0.020  1.429
 7RG  N7   C5    single    1.397  0.020  1.397
 7RG  C5   O6    double    1.218  0.020  1.218
 7RG  C8   N7    single    1.363  0.020  1.363
 7RG  N7   HN7   single    0.860  0.020  1.020
 7RG  C11  C8    single    1.497  0.020  1.497
 7RG  N9   C8    double    1.294  0.020  1.294
 7RG  N9   C10   single    1.351  0.020  1.351
 7RG  C12  C11   single    1.551  0.020  1.551
 7RG  C15  C11   single    1.534  0.020  1.534
 7RG  C11  H11   single    0.970  0.020  1.090
 7RG  N13  C12   single    1.454  0.020  1.454
 7RG  C12  H12   single    0.970  0.020  1.090
 7RG  C12  H12A  single    0.970  0.020  1.090
 7RG  C16  N13   single    1.437  0.020  1.437
 7RG  N13  C14   single    1.449  0.020  1.449
 7RG  C14  C15   single    1.521  0.020  1.521
 7RG  C14  H14   single    0.970  0.020  1.090
 7RG  C14  H14A  single    0.970  0.020  1.090
 7RG  C15  C29   single    1.517  0.020  1.517
 7RG  C15  H15   single    0.970  0.020  1.090
 7RG  C17  C16   single    1.506  0.020  1.506
 7RG  C16  H16   single    0.970  0.020  1.090
 7RG  C16  H16A  single    0.970  0.020  1.090
 7RG  N18  C17   aromatic  1.327  0.020  1.327
 7RG  N22  C17   aromatic  1.329  0.020  1.329
 7RG  C19  N18   aromatic  1.326  0.020  1.326
 7RG  C20  C19   aromatic  1.384  0.020  1.384
 7RG  C19  H19   single    0.930  0.020  1.080
 7RG  C20  C21   aromatic  1.383  0.020  1.383
 7RG  C20  H20   single    0.930  0.020  1.080
 7RG  C21  N22   aromatic  1.327  0.020  1.327
 7RG  C21  H21   single    0.930  0.020  1.080
 7RG  C24  C23   single    1.525  0.020  1.525
 7RG  C28  C23   single    1.525  0.020  1.525
 7RG  C23  H23   single    0.970  0.020  1.090
 7RG  C25  C24   single    1.522  0.020  1.522
 7RG  C24  H24   single    0.970  0.020  1.090
 7RG  C24  H24A  single    0.970  0.020  1.090
 7RG  C25  O26   single    1.410  0.020  1.410
 7RG  C25  H25   single    0.970  0.020  1.090
 7RG  C25  H25A  single    0.970  0.020  1.090
 7RG  O26  C27   single    1.410  0.020  1.410
 7RG  C27  C28   single    1.522  0.020  1.522
 7RG  C27  H27   single    0.970  0.020  1.090
 7RG  C27  H27A  single    0.970  0.020  1.090
 7RG  C28  H28   single    0.970  0.020  1.090
 7RG  C28  H28A  single    0.970  0.020  1.090
 7RG  C29  H29   single    0.970  0.020  1.090
 7RG  C29  H29A  single    0.970  0.020  1.090
 7RG  C29  H29B  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
 7RG  C23   N1   C10   127.61  3.000
 7RG  C10   N1   N2    111.39  3.000
 7RG  C23   N1   N2    120.97  3.000
 7RG  C3    N2   N1    106.88  3.000
 7RG  H3    C3   C4    128.94  3.000
 7RG  H3    C3   N2    120.66  3.000
 7RG  C4    C3   N2    110.40  3.000
 7RG  C10   C4   C5    118.79  3.000
 7RG  C5    C4   C3    136.65  3.000
 7RG  C10   C4   C3    104.56  3.000
 7RG  N7    C5   O6    121.15  3.000
 7RG  O6    C5   C4    128.32  3.000
 7RG  N7    C5   C4    110.53  3.000
 7RG  HN7   N7   C8    117.67  3.000
 7RG  HN7   N7   C5    115.92  3.000
 7RG  C8    N7   C5    126.41  3.000
 7RG  C11   C8   N9    121.46  3.000
 7RG  N9    C8   N7    123.09  3.000
 7RG  C11   C8   N7    115.42  3.000
 7RG  C10   N9   C8    114.05  3.000
 7RG  N9    C10  C4    127.13  3.000
 7RG  N9    C10  N1    126.10  3.000
 7RG  C4    C10  N1    106.77  3.000
 7RG  H11   C11  C15   108.59  3.000
 7RG  H11   C11  C12   108.32  3.000
 7RG  C15   C11  C12   104.90  3.000
 7RG  H11   C11  C8    107.72  3.000
 7RG  C15   C11  C8    114.94  3.000
 7RG  C12   C11  C8    112.17  3.000
 7RG  H12A  C12  H12   106.86  3.000
 7RG  H12A  C12  N13   112.39  3.000
 7RG  H12   C12  N13   110.56  3.000
 7RG  H12A  C12  C11   109.12  3.000
 7RG  H12   C12  C11   113.26  3.000
 7RG  N13   C12  C11   104.75  3.000
 7RG  C16   N13  C14   115.36  3.000
 7RG  C14   N13  C12   106.61  3.000
 7RG  C16   N13  C12   112.95  3.000
 7RG  H14A  C14  H14   107.62  3.000
 7RG  H14A  C14  C15   110.57  3.000
 7RG  H14   C14  C15   112.25  3.000
 7RG  H14A  C14  N13   112.47  3.000
 7RG  H14   C14  N13   111.43  3.000
 7RG  C15   C14  N13   102.55  3.000
 7RG  H15   C15  C29   109.18  3.000
 7RG  H15   C15  C14   107.98  3.000
 7RG  C29   C15  C14   114.94  3.000
 7RG  H15   C15  C11   108.92  3.000
 7RG  C29   C15  C11   113.62  3.000
 7RG  C14   C15  C11   101.81  3.000
 7RG  H16A  C16  H16   106.14  3.000
 7RG  H16A  C16  C17   108.21  3.000
 7RG  H16   C16  C17   107.37  3.000
 7RG  H16A  C16  N13   112.70  3.000
 7RG  H16   C16  N13   108.56  3.000
 7RG  C17   C16  N13   113.48  3.000
 7RG  N22   C17  N18   125.31  3.000
 7RG  N22   C17  C16   116.28  3.000
 7RG  N18   C17  C16   118.38  3.000
 7RG  C19   N18  C17   117.00  3.000
 7RG  H19   C19  C20   120.85  3.000
 7RG  H19   C19  N18   116.78  3.000
 7RG  C20   C19  N18   122.37  3.000
 7RG  H20   C20  C21   121.97  3.000
 7RG  H20   C20  C19   122.04  3.000
 7RG  C21   C20  C19   115.99  3.000
 7RG  H21   C21  N22   116.82  3.000
 7RG  H21   C21  C20   121.02  3.000
 7RG  N22   C21  C20   122.16  3.000
 7RG  C21   N22  C17   117.17  3.000
 7RG  H23   C23  C28   109.10  3.000
 7RG  H23   C23  C24   108.95  3.000
 7RG  C28   C23  C24   109.89  3.000
 7RG  H23   C23  N1    105.34  3.000
 7RG  C28   C23  N1    111.58  3.000
 7RG  C24   C23  N1    111.83  3.000
 7RG  H24A  C24  H24   107.82  3.000
 7RG  H24A  C24  C25   109.37  3.000
 7RG  H24   C24  C25   109.85  3.000
 7RG  H24A  C24  C23   110.69  3.000
 7RG  H24   C24  C23   109.79  3.000
 7RG  C25   C24  C23   109.30  3.000
 7RG  H25A  C25  H25   107.52  3.000
 7RG  H25A  C25  O26   110.28  3.000
 7RG  H25   C25  O26   107.18  3.000
 7RG  H25A  C25  C24   109.44  3.000
 7RG  H25   C25  C24   110.33  3.000
 7RG  O26   C25  C24   111.97  3.000
 7RG  C27   O26  C25   111.88  3.000
 7RG  H27A  C27  H27   107.46  3.000
 7RG  H27A  C27  C28   109.35  3.000
 7RG  H27   C27  C28   110.38  3.000
 7RG  H27A  C27  O26   110.29  3.000
 7RG  H27   C27  O26   107.22  3.000
 7RG  C28   C27  O26   112.02  3.000
 7RG  H28A  C28  H28   107.82  3.000
 7RG  H28A  C28  C27   110.05  3.000
 7RG  H28   C28  C27   109.28  3.000
 7RG  H28A  C28  C23   109.66  3.000
 7RG  H28   C28  C23   110.57  3.000
 7RG  C27   C28  C23   109.44  3.000
 7RG  H29B  C29  H29A  107.52  3.000
 7RG  H29B  C29  H29   107.92  3.000
 7RG  H29A  C29  H29   107.81  3.000
 7RG  H29B  C29  C15   111.07  3.000
 7RG  H29A  C29  C15   111.09  3.000
 7RG  H29   C29  C15   111.26  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
 7RG  CONST_01  C3   C4   C10  N1      0.00   0.0  0
 7RG  CONST_02  C4   C3   N2   N1      0.00   0.0  0
 7RG  CONST_03  C4   C10  N1   N2      0.00   0.0  0
 7RG  CONST_04  C10  C4   C3   N2      0.00   0.0  0
 7RG  CONST_05  C10  N1   N2   C3      0.00   0.0  0
 7RG  CONST_06  C20  C19  N18  C17     0.00   0.0  0
 7RG  CONST_07  C20  C21  N22  C17     0.00   0.0  0
 7RG  CONST_08  C21  N22  C17  N18     0.00   0.0  0
 7RG  CONST_09  C21  C20  C19  N18     0.00   0.0  0
 7RG  CONST_10  N22  C17  N18  C19     0.00   0.0  0
 7RG  CONST_11  N22  C21  C20  C19     0.00   0.0  0
 7RG  CONST_12  C23  N1   N2   C3    180.00   0.0  0
 7RG  CONST_13  C23  N1   C10  C4    180.00   0.0  0
 7RG  CONST_14  C23  N1   C10  N9      0.00   0.0  0
 7RG  CONST_15  C8   N7   C5   C4      0.00   0.0  0
 7RG  CONST_16  C11  C8   N7   C5    180.00   0.0  0
 7RG  CONST_17  N9   C8   N7   C5      0.00   0.0  0
 7RG  CONST_18  C10  N9   C8   N7      0.00   0.0  0
 7RG  CONST_19  C11  C8   N9   C10   180.00   0.0  0
 7RG  CONST_20  C19  N18  C17  C16   180.00   0.0  0
 7RG  CONST_21  C21  N22  C17  C16   180.00   0.0  0
 7RG  CONST_22  C8   N7   C5   O6    180.00   0.0  0
 7RG  CONST_23  H3   C3   N2   N1    180.00   0.0  0
 7RG  CONST_24  H19  C19  N18  C17   180.00   0.0  0
 7RG  CONST_25  H21  C21  N22  C17   180.00   0.0  0
 7RG  CONST_26  H20  C20  C19  N18   180.00   0.0  0
 7RG  CONST_27  HN7  N7   C5   C4    180.00   0.0  0
 7RG  Var_01    C14  N13  C12  C11   -27.96  30.0  1
 7RG  Var_02    C15  C14  N13  C12    43.90  30.0  1
 7RG  Var_03    O26  C25  C24  C23    56.79  30.0  1
 7RG  Var_04    O26  C27  C28  C23   -56.38  30.0  1
 7RG  Var_05    C28  C27  O26  C25    60.13  30.0  1
 7RG  Var_06    C17  C16  N13  C12  -170.85  30.0  2
 7RG  Var_07    N18  C17  C16  N13    35.32  30.0  2

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
 7RG  chir_01  C11  C8   C12  C15  positiv
 7RG  chir_02  C15  C11  C14  C29  negativ
 7RG  chir_03  C23  N1   C24  C28  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
 7RG  plan-1  C16  0.020
 7RG  plan-1  C17  0.020
 7RG  plan-1  N18  0.020
 7RG  plan-1  C19  0.020
 7RG  plan-1  C20  0.020
 7RG  plan-1  C21  0.020
 7RG  plan-1  N22  0.020
 7RG  plan-1  H19  0.020
 7RG  plan-1  H20  0.020
 7RG  plan-1  H21  0.020
 7RG  plan-2  N1   0.020
 7RG  plan-2  N2   0.020
 7RG  plan-2  C3   0.020
 7RG  plan-2  C4   0.020
 7RG  plan-2  C5   0.020
 7RG  plan-2  O6   0.020
 7RG  plan-2  N7   0.020
 7RG  plan-2  C8   0.020
 7RG  plan-2  N9   0.020
 7RG  plan-2  C10  0.020
 7RG  plan-2  C11  0.020
 7RG  plan-2  C23  0.020
 7RG  plan-2  H3   0.020
 7RG  plan-2  HN7  0.020

