# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 02:23:45 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: cyclopropyl[(3S)-3-{[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]amino}pyrrolidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c2ncnc(N[C@H]3CCN(C3)C(=O)C4CC4)c2nc1c5cnc(C)nc5
#
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
 Y5Y  Y5Y  cyclopropyl[(3S)-3-{[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]amino}pyrrolidin-1-yl]methanone  ligand  53  29  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y5Y
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
 Y5Y  C1   C  CH3   0  -0.667  32.8778  16.1084  32.4695
 Y5Y  C2   C  CH2   0  -0.342  33.9542  15.4723  31.6087
 Y5Y  C4   C  CR5   0   0.463  35.1512  13.4115  32.5409
 Y5Y  C5   C  CR6   0  -0.143  34.3092  12.3796  31.9438
 Y5Y  C6   C  CR16  0  -0.020  34.8915  11.2496  31.3792
 Y5Y  C8   C  CR6   0   0.359  32.8551  10.3887  30.8777
 Y5Y  N10  N  N     0  -0.399  32.2012  11.4199  31.4082
 Y5Y  C11  C  CR16  0  -0.030  32.9179  12.3961  31.9353
 Y5Y  C16  C  CH1   0  -0.133  39.8368  14.1685  35.7085
 Y5Y  C18  C  CH2   0  -0.515  40.3912  12.9164  36.3786
 Y5Y  C19  C  CH2   0  -0.268  41.1663  12.2223  35.2629
 Y5Y  C23  C  CH1   0  -0.429  42.8742  14.3167  32.6097
 Y5Y  C24  C  CH2   0  -0.459  44.2049  14.2432  31.9089
 Y5Y  C30  C  CR56  0   0.485  35.9666  15.3678  33.0735
 Y5Y  N3   N  NR5   0  -0.533  34.9541  14.7621  32.3908
 Y5Y  N7   N  N     0  -0.401  34.1796  10.2675  30.8532
 Y5Y  C9   C  CH3   0  -0.728  32.0349   9.2997  30.2696
 Y5Y  N12  N  N     0  -0.456  36.2087  13.1276  33.2577
 Y5Y  C13  C  CR56  0   0.012  36.7300  14.3396  33.6006
 Y5Y  C14  C  CR6   0   0.490  37.8558  14.7208  34.3579
 Y5Y  N15  N  NH1   0  -0.655  38.6644  13.8231  34.9314
 Y5Y  N20  N  NT    0  -0.480  41.6078  13.3306  34.4237
 Y5Y  O22  O  O     0  -0.511  42.8039  11.9920  33.0787
 Y5Y  C25  C  CH2   0  -0.462  42.9565  14.1855  31.1087
 Y5Y  C26  C  CH2   0  -0.271  41.0076  14.5980  34.8234
 Y5Y  N27  N  N     0  -0.488  38.1032  16.0258  34.4974
 Y5Y  C28  C  CR16  0   0.036  37.2825  16.9065  33.9254
 Y5Y  N29  N  N     0  -0.458  36.2020  16.6730  33.2038
 Y5Y  H1   H  HCH3  0   0.246  32.1517  16.6109  31.8313
 Y5Y  H2   H  HCH3  0   0.239  32.3464  15.3688  33.0681
 Y5Y  H3   H  HCH3  0   0.244  33.3033  16.8493  33.1447
 Y5Y  H4   H  HCH2  0   0.277  34.4742  16.2357  31.0297
 Y5Y  H5   H  HCH2  0   0.274  33.5265  14.7758  30.8896
 Y5Y  H6   H  HCR6  0   0.277  35.9709  11.1463  31.3516
 Y5Y  H7   H  HCR6  0   0.283  32.3624  13.2103  32.3886
 Y5Y  H8   H  HCH1  0   0.279  39.5845  14.9488  36.4269
 Y5Y  H9   H  HCH2  0   0.271  39.6177  12.2845  36.8152
 Y5Y  H10  H  HCH2  0   0.269  41.0655  13.2165  37.1816
 Y5Y  H11  H  HCH2  0   0.241  40.5333  11.5328  34.6967
 Y5Y  H12  H  HCH2  0   0.253  42.0119  11.6487  35.6429
 Y5Y  H13  H  HCH1  0   0.285  42.5960  15.2916  32.9859
 Y5Y  H14  H  HCH2  0   0.254  44.7814  13.3350  32.0238
 Y5Y  H15  H  HCH2  0   0.259  44.7915  15.1520  31.8869
 Y5Y  H16  H  HCH3  0   0.253  32.6610   8.4784  29.9315
 Y5Y  H17  H  HCH3  0   0.260  31.3077   8.9204  30.9877
 Y5Y  H18  H  HCH3  0   0.262  31.4714   9.6821  29.4170
 Y5Y  H19  H  HNH1  0   0.409  38.4304  12.8495  34.8113
 Y5Y  H20  H  HCH2  0   0.255  42.6706  13.2343  30.6795
 Y5Y  H21  H  HCH2  0   0.259  42.6703  15.0506  30.5257
 Y5Y  H22  H  HCH2  0   0.250  41.7059  15.2097  35.4024
 Y5Y  H23  H  HCH2  0   0.266  40.6744  15.1817  33.9673
 Y5Y  H24  H  HCR6  0   0.249  37.5416  17.9491  34.0764
 Y5Y  C21  C  C     0   0.590  42.4303  13.1219  33.3805

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
 Y5Y  C9   C8   single    1.493  0.020  1.493
 Y5Y  N7   C8   aromatic  1.330  0.020  1.330
 Y5Y  N7   C6   aromatic  1.322  0.020  1.322
 Y5Y  C8   N10  aromatic  1.331  0.020  1.331
 Y5Y  C6   C5   aromatic  1.391  0.020  1.391
 Y5Y  N10  C11  aromatic  1.321  0.020  1.321
 Y5Y  C25  C23  single    1.509  0.020  1.509
 Y5Y  C25  C24  single    1.484  0.020  1.484
 Y5Y  C2   N3   single    1.455  0.020  1.455
 Y5Y  C2   C1   single    1.518  0.020  1.518
 Y5Y  C5   C11  aromatic  1.391  0.020  1.391
 Y5Y  C5   C4   single    1.460  0.020  1.460
 Y5Y  C23  C24  single    1.506  0.020  1.506
 Y5Y  C23  C21  single    1.490  0.020  1.490
 Y5Y  N3   C4   aromatic  1.373  0.020  1.373
 Y5Y  N3   C30  aromatic  1.363  0.020  1.363
 Y5Y  C4   N12  aromatic  1.309  0.020  1.309
 Y5Y  O22  C21  double    1.228  0.020  1.228
 Y5Y  C30  N29  aromatic  1.333  0.020  1.333
 Y5Y  C30  C13  aromatic  1.385  0.020  1.385
 Y5Y  N12  C13  aromatic  1.363  0.020  1.363
 Y5Y  C21  N20  single    1.345  0.020  1.345
 Y5Y  N29  C28  aromatic  1.320  0.020  1.320
 Y5Y  C13  C14  aromatic  1.409  0.020  1.409
 Y5Y  C28  N27  aromatic  1.333  0.020  1.333
 Y5Y  N20  C26  single    1.458  0.020  1.458
 Y5Y  N20  C19  single    1.459  0.020  1.459
 Y5Y  C14  N27  aromatic  1.336  0.020  1.336
 Y5Y  C14  N15  single    1.337  0.020  1.337
 Y5Y  C26  C16  single    1.529  0.020  1.529
 Y5Y  N15  C16  single    1.448  0.020  1.448
 Y5Y  C19  C18  single    1.526  0.020  1.526
 Y5Y  C16  C18  single    1.524  0.020  1.524
 Y5Y  C1   H1   single    0.970  0.020  1.090
 Y5Y  C1   H2   single    0.970  0.020  1.090
 Y5Y  C1   H3   single    0.970  0.020  1.090
 Y5Y  C2   H4   single    0.970  0.020  1.090
 Y5Y  C2   H5   single    0.970  0.020  1.090
 Y5Y  C6   H6   single    0.930  0.020  1.080
 Y5Y  C11  H7   single    0.930  0.020  1.080
 Y5Y  C16  H8   single    0.970  0.020  1.090
 Y5Y  C18  H9   single    0.970  0.020  1.090
 Y5Y  C18  H10  single    0.970  0.020  1.090
 Y5Y  C19  H11  single    0.970  0.020  1.090
 Y5Y  C19  H12  single    0.970  0.020  1.090
 Y5Y  C23  H13  single    0.970  0.020  1.090
 Y5Y  C24  H14  single    0.970  0.020  1.090
 Y5Y  C24  H15  single    0.970  0.020  1.090
 Y5Y  C9   H16  single    0.970  0.020  1.090
 Y5Y  C9   H17  single    0.970  0.020  1.090
 Y5Y  C9   H18  single    0.970  0.020  1.090
 Y5Y  N15  H19  single    0.860  0.020  1.020
 Y5Y  C25  H20  single    0.970  0.020  1.090
 Y5Y  C25  H21  single    0.970  0.020  1.090
 Y5Y  C26  H22  single    0.970  0.020  1.090
 Y5Y  C26  H23  single    0.970  0.020  1.090
 Y5Y  C28  H24  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
 Y5Y  H3   C1   H2   108.16  3.000
 Y5Y  H3   C1   H1   108.05  3.000
 Y5Y  H2   C1   H1   108.05  3.000
 Y5Y  H3   C1   C2   111.08  3.000
 Y5Y  H2   C1   C2   111.89  3.000
 Y5Y  H1   C1   C2   109.49  3.000
 Y5Y  H5   C2   H4   106.53  3.000
 Y5Y  H5   C2   N3   108.23  3.000
 Y5Y  H4   C2   N3   107.43  3.000
 Y5Y  H5   C2   C1   111.35  3.000
 Y5Y  H4   C2   C1   110.24  3.000
 Y5Y  N3   C2   C1   112.78  3.000
 Y5Y  N12  C4   N3   112.91  3.000
 Y5Y  N12  C4   C5   122.47  3.000
 Y5Y  N3   C4   C5   124.60  3.000
 Y5Y  C11  C5   C6   115.20  3.000
 Y5Y  C11  C5   C4   124.82  3.000
 Y5Y  C6   C5   C4   119.93  3.000
 Y5Y  H6   C6   N7   117.06  3.000
 Y5Y  H6   C6   C5   120.28  3.000
 Y5Y  N7   C6   C5   122.65  3.000
 Y5Y  C9   C8   N7   118.23  3.000
 Y5Y  N7   C8   N10  124.54  3.000
 Y5Y  C9   C8   N10  117.23  3.000
 Y5Y  C11  N10  C8   117.71  3.000
 Y5Y  H7   C11  N10  116.33  3.000
 Y5Y  H7   C11  C5   121.22  3.000
 Y5Y  N10  C11  C5   122.43  3.000
 Y5Y  H8   C16  C26  110.95  3.000
 Y5Y  H8   C16  N15  109.68  3.000
 Y5Y  C26  C16  N15  112.10  3.000
 Y5Y  H8   C16  C18  112.47  3.000
 Y5Y  N15  C16  C18  109.53  3.000
 Y5Y  C26  C16  C18  101.93  3.000
 Y5Y  H10  C18  H9   107.66  3.000
 Y5Y  H10  C18  C19  110.45  3.000
 Y5Y  H9   C18  C19  112.93  3.000
 Y5Y  H10  C18  C16  108.81  3.000
 Y5Y  H9   C18  C16  113.21  3.000
 Y5Y  C19  C18  C16  103.70  3.000
 Y5Y  H12  C19  H11  107.32  3.000
 Y5Y  H12  C19  N20  111.44  3.000
 Y5Y  H11  C19  N20  110.87  3.000
 Y5Y  H12  C19  C18  112.24  3.000
 Y5Y  H11  C19  C18  111.79  3.000
 Y5Y  N20  C19  C18  103.23  3.000
 Y5Y  H13  C23  C25  116.01  3.000
 Y5Y  H13  C23  C24  115.68  3.000
 Y5Y  C25  C23  C24   58.97  3.000
 Y5Y  H13  C23  C21  117.80  3.000
 Y5Y  C24  C23  C21  117.71  3.000
 Y5Y  C25  C23  C21  117.47  3.000
 Y5Y  H15  C24  H14  114.73  3.000
 Y5Y  H15  C24  C25  118.54  3.000
 Y5Y  H14  C24  C25  118.23  3.000
 Y5Y  H15  C24  C23  116.59  3.000
 Y5Y  H14  C24  C23  117.55  3.000
 Y5Y  C25  C24  C23   60.62  3.000
 Y5Y  N29  C30  C13  126.34  3.000
 Y5Y  C13  C30  N3   105.67  3.000
 Y5Y  N29  C30  N3   127.98  3.000
 Y5Y  C30  N3   C4   106.01  3.000
 Y5Y  C30  N3   C2   124.25  3.000
 Y5Y  C4   N3   C2   129.62  3.000
 Y5Y  C8   N7   C6   117.46  3.000
 Y5Y  H18  C9   H17  106.98  3.000
 Y5Y  H18  C9   H16  108.62  3.000
 Y5Y  H17  C9   H16  109.05  3.000
 Y5Y  H18  C9   C8   110.26  3.000
 Y5Y  H17  C9   C8   110.61  3.000
 Y5Y  H16  C9   C8   111.20  3.000
 Y5Y  C13  N12  C4   104.71  3.000
 Y5Y  C14  C13  N12  132.93  3.000
 Y5Y  C14  C13  C30  116.36  3.000
 Y5Y  N12  C13  C30  110.71  3.000
 Y5Y  N27  C14  N15  119.94  3.000
 Y5Y  N15  C14  C13  122.13  3.000
 Y5Y  N27  C14  C13  117.93  3.000
 Y5Y  H19  N15  C14  117.17  3.000
 Y5Y  H19  N15  C16  118.81  3.000
 Y5Y  C14  N15  C16  124.02  3.000
 Y5Y  C26  N20  C21  126.82  3.000
 Y5Y  C26  N20  C19  112.22  3.000
 Y5Y  C21  N20  C19  120.90  3.000
 Y5Y  H21  C25  H20  114.79  3.000
 Y5Y  H21  C25  C24  118.82  3.000
 Y5Y  H20  C25  C24  118.06  3.000
 Y5Y  H21  C25  C23  116.88  3.000
 Y5Y  H20  C25  C23  117.17  3.000
 Y5Y  C24  C25  C23   60.41  3.000
 Y5Y  H23  C26  H22  108.17  3.000
 Y5Y  H23  C26  N20  112.12  3.000
 Y5Y  H22  C26  N20  111.61  3.000
 Y5Y  H23  C26  C16  111.81  3.000
 Y5Y  H22  C26  C16  109.84  3.000
 Y5Y  N20  C26  C16  103.27  3.000
 Y5Y  C28  N27  C14  119.13  3.000
 Y5Y  H24  C28  N29  116.21  3.000
 Y5Y  H24  C28  N27  115.35  3.000
 Y5Y  N29  C28  N27  128.44  3.000
 Y5Y  C28  N29  C30  111.79  3.000
 Y5Y  O22  C21  N20  121.31  3.000
 Y5Y  N20  C21  C23  117.33  3.000
 Y5Y  O22  C21  C23  121.36  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
 Y5Y  CONST_01  N7   C6   C5   C4    180.00   0.0  0
 Y5Y  CONST_02  N10  C11  C5   C4    180.00   0.0  0
 Y5Y  CONST_03  N29  C30  N3   C4    180.00   0.0  0
 Y5Y  CONST_04  C13  C30  N3   C4      0.00   0.0  0
 Y5Y  CONST_05  C30  C13  N12  C4      0.00   0.0  0
 Y5Y  CONST_06  C14  C13  N12  C4    180.00   0.0  0
 Y5Y  CONST_07  C8   N7   C6   C5      0.00   0.0  0
 Y5Y  CONST_08  C8   N10  C11  C5      0.00   0.0  0
 Y5Y  CONST_09  C30  N3   C4   C5    180.00   0.0  0
 Y5Y  CONST_10  C13  N12  C4   C5    180.00   0.0  0
 Y5Y  CONST_11  N10  C8   N7   C6      0.00   0.0  0
 Y5Y  CONST_12  N10  C11  C5   C6      0.00   0.0  0
 Y5Y  CONST_15  N7   C8   N10  C11     0.00   0.0  0
 Y5Y  CONST_16  N7   C6   C5   C11     0.00   0.0  0
 Y5Y  CONST_19  N12  C4   N3   C30     0.00   0.0  0
 Y5Y  CONST_20  N27  C28  N29  C30     0.00   0.0  0
 Y5Y  CONST_21  N27  C14  C13  C30     0.00   0.0  0
 Y5Y  CONST_22  C13  N12  C4   N3      0.00   0.0  0
 Y5Y  CONST_23  C28  N29  C30  N3    180.00   0.0  0
 Y5Y  CONST_24  N12  C13  C30  N3      0.00   0.0  0
 Y5Y  CONST_25  C14  C13  C30  N3    180.00   0.0  0
 Y5Y  CONST_26  N29  C30  C13  N12   180.00   0.0  0
 Y5Y  CONST_27  N27  C14  C13  N12   180.00   0.0  0
 Y5Y  CONST_28  C28  N29  C30  C13     0.00   0.0  0
 Y5Y  CONST_29  C28  N27  C14  C13     0.00   0.0  0
 Y5Y  CONST_30  N29  C30  C13  C14     0.00   0.0  0
 Y5Y  CONST_31  N29  C28  N27  C14     0.00   0.0  0
 Y5Y  CONST_32  C5   C4   N3   C2      0.00   0.0  0
 Y5Y  CONST_33  N12  C4   N3   C2    180.00   0.0  0
 Y5Y  CONST_34  N29  C30  N3   C2      0.00   0.0  0
 Y5Y  CONST_35  C13  C30  N3   C2    180.00   0.0  0
 Y5Y  CONST_36  C9   C8   N7   C6    180.00   0.0  0
 Y5Y  CONST_37  C9   C8   N10  C11   180.00   0.0  0
 Y5Y  CONST_38  N15  C14  C13  C30   180.00   0.0  0
 Y5Y  CONST_39  N15  C14  C13  N12     0.00   0.0  0
 Y5Y  CONST_40  C28  N27  C14  N15   180.00   0.0  0
 Y5Y  CONST_41  C23  C21  N20  C19   180.00   0.0  0
 Y5Y  CONST_42  C26  N20  C21  C23     0.00   0.0  0
 Y5Y  CONST_43  C13  C14  N15  C16   180.00   0.0  0
 Y5Y  CONST_44  N27  C14  N15  C16     0.00   0.0  0
 Y5Y  CONST_45  H6   C6   C5   C4      0.00   0.0  0
 Y5Y  CONST_46  H7   C11  C5   C4      0.00   0.0  0
 Y5Y  CONST_47  H24  C28  N29  C30   180.00   0.0  0
 Y5Y  CONST_48  O22  C21  N20  C19     0.00   0.0  0
 Y5Y  CONST_49  C26  N20  C21  O22   180.00   0.0  0
 Y5Y  CONST_50  H19  N15  C14  C13     0.00   0.0  0
 Y5Y  Var_01    C19  N20  C26  C16   -16.26  30.0  1
 Y5Y  Var_02    N20  C19  C18  C16    29.74  30.0  1
 Y5Y  Var_03    C26  N20  C19  C18    -8.37  30.0  1
 Y5Y  Var_04    C24  C25  C23  C21  -107.39  30.0  1
 Y5Y  Var_05    N20  C21  C23  C24   152.19  30.0  3
 Y5Y  Var_06    H14  C24  C25  C23   107.47  30.0  1
 Y5Y  Var_07    C4   N3   C2   C1    106.79  30.0  2
 Y5Y  Var_08    H16  C9   C8   N10  -175.95  30.0  2
 Y5Y  Var_09    H1   C1   C2   N3   -179.13  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
 Y5Y  chir_01  C16  C26  N15  C18  negativ
 Y5Y  chir_02  C23  C25  C24  C21  both

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
 Y5Y  plan-1  C16  0.020
 Y5Y  plan-1  C14  0.020
 Y5Y  plan-1  N15  0.020
 Y5Y  plan-1  H19  0.020
 Y5Y  plan-2  C4   0.020
 Y5Y  plan-2  C5   0.020
 Y5Y  plan-2  C6   0.020
 Y5Y  plan-2  C8   0.020
 Y5Y  plan-2  N10  0.020
 Y5Y  plan-2  C11  0.020
 Y5Y  plan-2  N7   0.020
 Y5Y  plan-2  C9   0.020
 Y5Y  plan-2  H6   0.020
 Y5Y  plan-2  H7   0.020
 Y5Y  plan-3  C2   0.020
 Y5Y  plan-3  C4   0.020
 Y5Y  plan-3  C5   0.020
 Y5Y  plan-3  C30  0.020
 Y5Y  plan-3  N3   0.020
 Y5Y  plan-3  N12  0.020
 Y5Y  plan-3  C13  0.020
 Y5Y  plan-3  C14  0.020
 Y5Y  plan-3  N15  0.020
 Y5Y  plan-3  N27  0.020
 Y5Y  plan-3  C28  0.020
 Y5Y  plan-3  N29  0.020
 Y5Y  plan-3  H24  0.020
 Y5Y  plan-4  C19  0.020
 Y5Y  plan-4  C23  0.020
 Y5Y  plan-4  N20  0.020
 Y5Y  plan-4  O22  0.020
 Y5Y  plan-4  C26  0.020
 Y5Y  plan-4  C21  0.020

