# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 23:29:48 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 2-({2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-4-oxo-3,4-dihydro-5H-imidazo[2,1-b]purin-5-yl}methyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CCn1c(nc2n3ccnc3N(Cc4ccccc4C#N)C(=O)c12)N5CCC[C@@H](N)C5
#
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
 75J  75J  2-({2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-4-oxo-3,4-dihydro-5H-imidazo[2,1-b]purin-5-yl}methyl)benzonitrile  ligand  57  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_75J
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
 75J  C1   C  CR16  0  -0.261  -5.5934   1.7902  -1.8926
 75J  C2   C  CR16  0  -0.234  -6.1419   1.3641  -0.6958
 75J  C3   C  CR16  0  -0.219  -4.2663   1.5016  -2.1759
 75J  C4   C  CR16  0  -0.304  -3.4852   0.7921  -1.2721
 75J  C5   C  CR6   0   0.148  -4.0118   0.3553  -0.0666
 75J  C6   C  CR6   0  -0.006  -5.3541   0.6521   0.2074
 75J  C11  C  CR56  0   0.458   0.6503  -1.4582  -0.2856
 75J  C12  C  CR56  0   0.117   0.4425  -0.2789   0.3776
 75J  C13  C  CR6   0   0.557  -0.8315   0.1882   0.8289
 75J  N15  N  N     0  -0.484  -2.5765  -2.7430  -0.5147
 75J  C16  C  CR15  0  -0.196  -1.8890  -3.7328  -1.1736
 75J  C17  C  CR15  0  -0.118  -0.5568  -3.4677  -1.2222
 75J  C23  C  CH2   0  -0.293   4.7660  -1.5045  -0.3089
 75J  C24  C  CH1   0  -0.119   6.1523  -1.1368   0.2098
 75J  C26  C  CH2   0  -0.449   5.7256   1.2296  -0.5657
 75J  C27  C  CH2   0  -0.324   4.3485   0.7848  -1.0220
 75J  C7   C  CH2   0  -0.389  -3.2053  -0.4034   0.9569
 75J  N8   N  NR6   0  -0.627  -1.8568  -0.7102   0.5314
 75J  C9   C  CR56  0   0.743  -1.6649  -1.8848  -0.1612
 75J  N10  N  N     0  -0.591  -0.4187  -2.2650  -0.5602
 75J  N18  N  N     0  -0.482   1.9318  -1.6541  -0.6099
 75J  C19  C  CR5   0   0.705   2.5519  -0.5799  -0.1354
 75J  N20  N  NR5   0  -0.531   1.7012   0.2758   0.4825
 75J  N22  N  NT    0  -0.536   3.8930  -0.3413  -0.1986
 75J  C25  C  CH2   0  -0.451   6.6993   0.0567  -0.5836
 75J  N28  N  NH2   0  -0.793   6.0851  -0.9341   1.6507
 75J  C29  C  CSP   0   0.106   1.8213   2.6980   0.5303
 75J  C30  C  CSP   0   0.022   1.6381   3.7290  -0.0608
 75J  C31  C  CH3   0  -0.818   1.4139   4.9761  -0.7733
 75J  C32  C  CSP   0   0.029  -5.9367   0.2221   1.4376
 75J  N33  N  NS    0  -0.245  -6.4020  -0.1277   2.4323
 75J  H1   H  HCR6  0   0.276  -6.1974   2.3437  -2.5979
 75J  H2   H  HCR6  0   0.284  -7.1740   1.5792  -0.4553
 75J  H3   H  HCR6  0   0.276  -3.8295   1.8322  -3.1087
 75J  H4   H  HCR6  0   0.260  -2.4546   0.5828  -1.5251
 75J  H5   H  HCR5  0   0.266  -2.3992  -4.5896  -1.5837
 75J  H6   H  HCR5  0   0.303   0.2823  -3.9912  -1.6453
 75J  H7   H  HCH2  0   0.312   1.4974   1.4406   2.1828
 75J  H8   H  HCH2  0   0.302   3.1158   1.3583   1.5176
 75J  H9   H  HCH2  0   0.230   4.8353  -1.8499  -1.3482
 75J  H10  H  HCH2  0   0.258   4.3551  -2.3194   0.2865
 75J  H11  H  HCH1  0   0.243   6.8004  -1.9991   0.0279
 75J  H12  H  HCH2  0   0.248   6.0774   2.0303  -1.2188
 75J  H13  H  HCH2  0   0.224   5.6526   1.6561   0.4390
 75J  H14  H  HCH2  0   0.266   3.6368   1.6068  -0.9579
 75J  H15  H  HCH2  0   0.238   4.3840   0.4739  -2.0753
 75J  H16  H  HCH2  0   0.305  -3.1468   0.1735   1.8799
 75J  H17  H  HCH2  0   0.300  -3.7022  -1.3422   1.2034
 75J  H18  H  HCH2  0   0.239   7.6710   0.3555  -0.1827
 75J  H19  H  HCH2  0   0.220   6.8723  -0.2529  -1.6196
 75J  H20  H  HNH2  0   0.346   6.9876  -0.6279   1.9938
 75J  H21  H  HNH2  0   0.339   5.4394  -0.1823   1.8602
 75J  H23  H  HCH3  0   0.271   1.4679   5.8259  -0.0927
 75J  H24  H  HCH3  0   0.269   2.1613   5.1235  -1.5529
 75J  H25  H  HCH3  0   0.270   0.4303   4.9860  -1.2429
 75J  O14  O  O     0  -0.463  -1.0506   1.2355   1.4151
 75J  C21  C  CH2   0  -0.495   2.0614   1.4533   1.2509

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
 75J  N28  C24  single    1.457  0.020  1.457
 75J  C25  C24  single    1.534  0.020  1.534
 75J  C25  C26  single    1.525  0.020  1.525
 75J  C23  C24  single    1.525  0.020  1.525
 75J  C23  N22  single    1.459  0.020  1.459
 75J  C27  C26  single    1.517  0.020  1.517
 75J  C27  N22  single    1.468  0.020  1.468
 75J  C31  C30  single    1.454  0.020  1.454
 75J  N22  C19  single    1.364  0.020  1.364
 75J  C30  C29  triple    1.202  0.020  1.202
 75J  C29  C21  single    1.458  0.020  1.458
 75J  C21  N20  single    1.451  0.020  1.451
 75J  C19  N20  aromatic  1.356  0.020  1.356
 75J  C19  N18  aromatic  1.328  0.020  1.328
 75J  N20  C12  aromatic  1.380  0.020  1.380
 75J  N18  C11  aromatic  1.336  0.020  1.336
 75J  C12  C11  aromatic  1.369  0.020  1.369
 75J  C12  C13  single    1.430  0.020  1.430
 75J  C11  N10  aromatic  1.367  0.020  1.367
 75J  O14  C13  double    1.220  0.020  1.220
 75J  C13  N8   single    1.395  0.020  1.395
 75J  N10  C17  aromatic  1.380  0.020  1.380
 75J  N10  C9   aromatic  1.363  0.020  1.363
 75J  C17  C16  aromatic  1.359  0.020  1.359
 75J  N8   C9   single    1.377  0.020  1.377
 75J  N8   C7   single    1.447  0.020  1.447
 75J  C9   N15  aromatic  1.301  0.020  1.301
 75J  C4   C3   aromatic  1.389  0.020  1.389
 75J  C4   C5   aromatic  1.386  0.020  1.386
 75J  C7   C5   single    1.508  0.020  1.508
 75J  C16  N15  aromatic  1.374  0.020  1.374
 75J  C3   C1   aromatic  1.387  0.020  1.387
 75J  C5   C6   aromatic  1.402  0.020  1.402
 75J  C1   C2   aromatic  1.384  0.020  1.384
 75J  C6   C2   aromatic  1.394  0.020  1.394
 75J  C6   C32  single    1.427  0.020  1.427
 75J  C32  N33  triple    1.153  0.020  1.153
 75J  C1   H1   single    0.930  0.020  1.080
 75J  C2   H2   single    0.930  0.020  1.080
 75J  C3   H3   single    0.930  0.020  1.080
 75J  C4   H4   single    0.930  0.020  1.080
 75J  C16  H5   single    0.930  0.020  1.080
 75J  C17  H6   single    0.930  0.020  1.080
 75J  C21  H7   single    0.970  0.020  1.090
 75J  C21  H8   single    0.970  0.020  1.090
 75J  C23  H9   single    0.970  0.020  1.090
 75J  C23  H10  single    0.970  0.020  1.090
 75J  C24  H11  single    0.970  0.020  1.090
 75J  C26  H12  single    0.970  0.020  1.090
 75J  C26  H13  single    0.970  0.020  1.090
 75J  C27  H14  single    0.970  0.020  1.090
 75J  C27  H15  single    0.970  0.020  1.090
 75J  C7   H16  single    0.970  0.020  1.090
 75J  C7   H17  single    0.970  0.020  1.090
 75J  C25  H18  single    0.970  0.020  1.090
 75J  C25  H19  single    0.970  0.020  1.090
 75J  N28  H20  single    0.890  0.020  1.040
 75J  N28  H21  single    0.890  0.020  1.040
 75J  C31  H23  single    0.970  0.020  1.090
 75J  C31  H24  single    0.970  0.020  1.090
 75J  C31  H25  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
 75J  H1   C1   C3   120.51  3.000
 75J  H1   C1   C2   120.03  3.000
 75J  C3   C1   C2   119.45  3.000
 75J  H2   C2   C6   119.79  3.000
 75J  H2   C2   C1   120.62  3.000
 75J  C6   C2   C1   119.58  3.000
 75J  H3   C3   C4   119.34  3.000
 75J  H3   C3   C1   119.92  3.000
 75J  C4   C3   C1   120.74  3.000
 75J  H4   C4   C5   120.30  3.000
 75J  H4   C4   C3   118.84  3.000
 75J  C5   C4   C3   120.87  3.000
 75J  C7   C5   C6   119.08  3.000
 75J  C6   C5   C4   117.85  3.000
 75J  C7   C5   C4   123.07  3.000
 75J  C32  C6   C5   119.70  3.000
 75J  C32  C6   C2   118.79  3.000
 75J  C5   C6   C2   121.51  3.000
 75J  N18  C11  N10  127.92  3.000
 75J  N10  C11  C12  119.14  3.000
 75J  N18  C11  C12  112.92  3.000
 75J  N20  C12  C13  131.11  3.000
 75J  C13  C12  C11  124.72  3.000
 75J  N20  C12  C11  104.17  3.000
 75J  O14  C13  N8   121.55  3.000
 75J  N8   C13  C12  112.15  3.000
 75J  O14  C13  C12  126.30  3.000
 75J  C9   N15  C16  104.78  3.000
 75J  H5   C16  C17  127.24  3.000
 75J  H5   C16  N15  121.22  3.000
 75J  C17  C16  N15  111.54  3.000
 75J  H6   C17  N10  122.33  3.000
 75J  H6   C17  C16  133.13  3.000
 75J  N10  C17  C16  104.54  3.000
 75J  H10  C23  H9   107.82  3.000
 75J  H10  C23  N22  109.23  3.000
 75J  H9   C23  N22  111.13  3.000
 75J  H10  C23  C24  109.71  3.000
 75J  H9   C23  C24  109.91  3.000
 75J  N22  C23  C24  109.03  3.000
 75J  H11  C24  N28  107.55  3.000
 75J  H11  C24  C25  108.42  3.000
 75J  N28  C24  C25  114.82  3.000
 75J  H11  C24  C23  106.97  3.000
 75J  C25  C24  C23  109.62  3.000
 75J  N28  C24  C23  109.15  3.000
 75J  H13  C26  H12  106.56  3.000
 75J  H13  C26  C25  110.70  3.000
 75J  H12  C26  C25  110.58  3.000
 75J  H13  C26  C27  109.26  3.000
 75J  H12  C26  C27  109.12  3.000
 75J  C25  C26  C27  110.52  3.000
 75J  H15  C27  H14  106.92  3.000
 75J  H15  C27  N22  109.32  3.000
 75J  H14  C27  N22  110.08  3.000
 75J  H15  C27  C26  109.99  3.000
 75J  H14  C27  C26  110.74  3.000
 75J  N22  C27  C26  109.75  3.000
 75J  H17  C7   H16  106.79  3.000
 75J  H17  C7   N8   107.97  3.000
 75J  H16  C7   N8   108.13  3.000
 75J  H17  C7   C5   110.06  3.000
 75J  H16  C7   C5   109.71  3.000
 75J  N8   C7   C5   113.92  3.000
 75J  C9   N8   C7   117.30  3.000
 75J  C7   N8   C13  119.05  3.000
 75J  C9   N8   C13  123.65  3.000
 75J  N10  C9   N8   120.84  3.000
 75J  N8   C9   N15  127.00  3.000
 75J  N10  C9   N15  112.16  3.000
 75J  C9   N10  C17  106.99  3.000
 75J  C9   N10  C11  119.45  3.000
 75J  C17  N10  C11  133.55  3.000
 75J  C19  N18  C11  104.04  3.000
 75J  N22  C19  N20  121.86  3.000
 75J  N20  C19  N18  112.36  3.000
 75J  N22  C19  N18  125.75  3.000
 75J  C19  N20  C21  126.70  3.000
 75J  C19  N20  C12  106.50  3.000
 75J  C21  N20  C12  126.37  3.000
 75J  C19  N22  C27  117.74  3.000
 75J  C19  N22  C23  116.91  3.000
 75J  C27  N22  C23  112.57  3.000
 75J  H19  C25  H18  106.49  3.000
 75J  H19  C25  C26  109.24  3.000
 75J  H18  C25  C26  110.68  3.000
 75J  H19  C25  C24  109.01  3.000
 75J  H18  C25  C24  109.88  3.000
 75J  C26  C25  C24  111.39  3.000
 75J  H21  N28  H20  105.88  3.000
 75J  H21  N28  C24  109.71  3.000
 75J  H20  N28  C24  109.64  3.000
 75J  C30  C29  C21  180.00  3.000
 75J  C31  C30  C29  180.00  3.000
 75J  H25  C31  H24  108.02  3.000
 75J  H25  C31  H23  107.86  3.000
 75J  H24  C31  H23  107.89  3.000
 75J  H25  C31  C30  110.99  3.000
 75J  H24  C31  C30  111.14  3.000
 75J  H23  C31  C30  110.80  3.000
 75J  N33  C32  C6   180.00  3.000
 75J  H8   C21  H7   106.86  3.000
 75J  H8   C21  C29  110.74  3.000
 75J  H7   C21  C29  110.33  3.000
 75J  H8   C21  N20  107.36  3.000
 75J  H7   C21  N20  108.36  3.000
 75J  C29  C21  N20  112.96  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
 75J  CONST_01  C5   C4   C3   C1     0.00   0.0  0
 75J  CONST_02  C5   C6   C2   C1     0.00   0.0  0
 75J  CONST_03  C4   C3   C1   C2     0.00   0.0  0
 75J  CONST_04  C4   C5   C6   C2     0.00   0.0  0
 75J  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 75J  CONST_06  C6   C2   C1   C3     0.00   0.0  0
 75J  CONST_07  N20  C19  N18  C11    0.00   0.0  0
 75J  CONST_08  C19  N20  C12  C11    0.00   0.0  0
 75J  CONST_09  C16  C17  N10  C11  180.00   0.0  0
 75J  CONST_10  N15  C9   N10  C11  180.00   0.0  0
 75J  CONST_11  N18  C19  N20  C12    0.00   0.0  0
 75J  CONST_12  C19  N18  C11  C12    0.00   0.0  0
 75J  CONST_13  C17  N10  C11  C12  180.00   0.0  0
 75J  CONST_14  C9   N10  C11  C12    0.00   0.0  0
 75J  CONST_15  C17  N10  C9   N15    0.00   0.0  0
 75J  CONST_16  N10  C17  C16  N15    0.00   0.0  0
 75J  CONST_17  C9   N10  C17  C16    0.00   0.0  0
 75J  CONST_18  N10  C9   N15  C16    0.00   0.0  0
 75J  CONST_19  N18  C11  N10  C17    0.00   0.0  0
 75J  CONST_20  C9   N15  C16  C17    0.00   0.0  0
 75J  CONST_21  N18  C11  N10  C9   180.00   0.0  0
 75J  CONST_22  C19  N18  C11  N10  180.00   0.0  0
 75J  CONST_23  N20  C12  C11  N10  180.00   0.0  0
 75J  CONST_24  N20  C12  C11  N18    0.00   0.0  0
 75J  CONST_25  N22  C19  N18  C11  180.00   0.0  0
 75J  CONST_26  N22  C19  N20  C12  180.00   0.0  0
 75J  CONST_27  C9   N8   C13  C12    0.00   0.0  0
 75J  CONST_28  C32  C6   C2   C1   180.00   0.0  0
 75J  CONST_29  C7   C5   C6   C2   180.00   0.0  0
 75J  CONST_30  C7   C5   C4   C3   180.00   0.0  0
 75J  CONST_31  C32  C6   C5   C4   180.00   0.0  0
 75J  CONST_32  C21  N20  C12  C11  180.00   0.0  0
 75J  CONST_33  C21  N20  C12  C13    0.00   0.0  0
 75J  CONST_34  N22  C19  N20  C21    0.00   0.0  0
 75J  CONST_35  N18  C19  N20  C21  180.00   0.0  0
 75J  CONST_36  C7   N8   C13  C12  180.00   0.0  0
 75J  CONST_37  O14  C13  N8   C9   180.00   0.0  0
 75J  CONST_38  H4   C4   C3   C1   180.00   0.0  0
 75J  CONST_39  H3   C3   C1   C2   180.00   0.0  0
 75J  CONST_40  H2   C2   C1   C3   180.00   0.0  0
 75J  CONST_41  H1   C1   C3   C4   180.00   0.0  0
 75J  CONST_42  H6   C17  N10  C11    0.00   0.0  0
 75J  CONST_43  H5   C16  N15  C9   180.00   0.0  0
 75J  CONST_44  O14  C13  N8   C7     0.00   0.0  0
 75J  Var_01    C26  C27  N22  C23  -61.37  30.0  1
 75J  Var_02    N20  C19  N22  C23  152.96  30.0  2
 75J  Var_03    C27  C26  C25  C24  -53.06  30.0  1
 75J  Var_04    C27  N22  C23  C24   62.62  30.0  1
 75J  Var_05    C25  C26  C27  N22   55.12  30.0  1
 75J  Var_06    N8   C7   C5   C4    -3.79  30.0  3
 75J  Var_07    C13  N8   C7   C5    91.21  30.0  2
 75J  Var_08    C29  C21  N20  C12  -84.13  30.0  2
 75J  Var_09    H23  C31  C30  C29   58.44  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
 75J  chir_01  C24  N28  C25  C23  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
 75J  plan-1  C1   0.020
 75J  plan-1  C2   0.020
 75J  plan-1  C3   0.020
 75J  plan-1  C4   0.020
 75J  plan-1  C5   0.020
 75J  plan-1  C6   0.020
 75J  plan-1  C7   0.020
 75J  plan-1  C32  0.020
 75J  plan-1  N33  0.020
 75J  plan-1  H1   0.020
 75J  plan-1  H2   0.020
 75J  plan-1  H3   0.020
 75J  plan-1  H4   0.020
 75J  plan-2  C11  0.020
 75J  plan-2  C12  0.020
 75J  plan-2  C13  0.020
 75J  plan-2  N15  0.020
 75J  plan-2  C16  0.020
 75J  plan-2  C17  0.020
 75J  plan-2  C7   0.020
 75J  plan-2  N8   0.020
 75J  plan-2  C9   0.020
 75J  plan-2  N10  0.020
 75J  plan-2  N18  0.020
 75J  plan-2  C19  0.020
 75J  plan-2  N20  0.020
 75J  plan-2  N22  0.020
 75J  plan-2  H5   0.020
 75J  plan-2  H6   0.020
 75J  plan-2  O14  0.020
 75J  plan-2  C21  0.020

