# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 00:25:39 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 4-({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(Cc4ccc(cc4)C#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
 75M  75M  4-({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_75M
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
 75M  C4   C  CR56  0   0.457   0.7794  -1.6000  -0.1942
 75M  C2   C  CR6   0   0.570  -0.7038  -0.2876   1.2932
 75M  N1   N  NR6   0  -0.607  -1.6451  -1.2849   1.0468
 75M  C6   C  CR5   0   0.710   2.5500  -0.4711  -0.2428
 75M  C3   C  CR56  0   0.114   0.5340  -0.5275   0.6171
 75M  N5   N  N     0  -0.486   2.0035  -1.5786  -0.7307
 75M  N7   N  NR5   0  -0.534   1.7108   0.1936   0.5896
 75M  N8   N  N     0  -0.591  -0.2060  -2.5269  -0.3881
 75M  C9   C  CR56  0   0.760  -1.4135  -2.3623   0.2232
 75M  N10  N  N     0  -0.499  -2.2436  -3.3210  -0.0765
 75M  C11  C  CR15  0  -0.189  -1.5417  -4.1472  -0.9189
 75M  C12  C  CR15  0  -0.124  -0.2820  -3.6855  -1.1338
 75M  O13  O  O     0  -0.467  -0.9532   0.6617   2.0186
 75M  C14  C  CH2   0  -0.498   2.0325   1.3439   1.4138
 75M  C15  C  CSP   0   0.109   1.4920   2.5905   0.8843
 75M  C16  C  CSP   0   0.018   1.0596   3.6242   0.4482
 75M  C17  C  CH3   0  -0.818   0.5303   4.8721  -0.0766
 75M  N18  N  NT    0  -0.533   3.8219  -0.0440  -0.4899
 75M  C19  C  CH2   0  -0.292   4.7640  -1.0617  -0.9436
 75M  C20  C  CH1   0  -0.120   6.1859  -0.5997  -0.6505
 75M  C21  C  CH2   0  -0.449   6.4409   0.7415  -1.3482
 75M  C22  C  CH2   0  -0.449   5.3861   1.7753  -0.9694
 75M  C23  C  CH2   0  -0.325   3.9887   1.2288  -1.2023
 75M  N24  N  NH2   0  -0.792   6.4045  -0.5948   0.7893
 75M  C25  C  CH2   0  -0.434  -2.9708  -1.1528   1.6480
 75M  C26  C  CR6   0   0.151  -3.8604  -0.2420   0.8423
 75M  C27  C  CR16  0  -0.287  -4.4549  -0.7038  -0.3311
 75M  C28  C  CR16  0  -0.225  -5.2572   0.1282  -1.0904
 75M  C29  C  CR6   0  -0.006  -5.4753   1.4405  -0.6708
 75M  C30  C  CR16  0  -0.227  -4.8935   1.9117   0.5049
 75M  C31  C  CR16  0  -0.284  -4.0887   1.0686   1.2515
 75M  C32  C  CSP   0   0.057  -6.3041   2.3047  -1.4475
 75M  N33  N  NS    0  -0.252  -6.9730   3.0026  -2.0748
 75M  H1   H  HCR5  0   0.266  -1.9900  -5.0372  -1.3303
 75M  H2   H  HCR5  0   0.303   0.5444  -4.0460  -1.7204
 75M  H3   H  HCH2  0   0.313   1.6561   1.1631   2.4200
 75M  H4   H  HCH2  0   0.302   3.1201   1.3957   1.4910
 75M  H5   H  HCH3  0   0.271   0.5296   5.6457   0.6910
 75M  H6   H  HCH3  0   0.269   1.1284   5.2314  -0.9140
 75M  H7   H  HCH3  0   0.270  -0.4950   4.7460  -0.4250
 75M  H8   H  HCH2  0   0.258   4.5616  -1.9956  -0.4210
 75M  H9   H  HCH2  0   0.228   4.6480  -1.2484  -2.0190
 75M  H10  H  HCH1  0   0.243   6.8573  -1.3484  -1.0815
 75M  H11  H  HCH2  0   0.239   7.4422   1.1057  -1.1035
 75M  H12  H  HCH2  0   0.220   6.4198   0.5886  -2.4323
 75M  H13  H  HCH2  0   0.224   5.4911   2.0702   0.0787
 75M  H14  H  HCH2  0   0.248   5.5130   2.6827  -1.5626
 75M  H15  H  HCH2  0   0.239   3.8238   1.0688  -2.2769
 75M  H16  H  HCH2  0   0.265   3.2390   1.9461  -0.8703
 75M  H17  H  HNH2  0   0.345   7.3348  -0.2472   0.9878
 75M  H18  H  HNH2  0   0.339   5.7670   0.0562   1.2318
 75M  H20  H  HCH2  0   0.300  -3.4021  -2.1496   1.7133
 75M  H21  H  HCH2  0   0.297  -2.8539  -0.7803   2.6631
 75M  H22  H  HCR6  0   0.273  -4.2920  -1.7250  -0.6504
 75M  H23  H  HCR6  0   0.281  -5.7167  -0.2360  -1.9990
 75M  H24  H  HCR6  0   0.282  -5.0678   2.9288   0.8284
 75M  H25  H  HCR6  0   0.269  -3.6328   1.4353   2.1608

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
 75M  N24  C20  single    1.456  0.020  1.456
 75M  C21  C20  single    1.533  0.020  1.533
 75M  C21  C22  single    1.525  0.020  1.525
 75M  C19  C20  single    1.523  0.020  1.523
 75M  C19  N18  single    1.459  0.020  1.459
 75M  C17  C16  single    1.454  0.020  1.454
 75M  C23  C22  single    1.518  0.020  1.518
 75M  C23  N18  single    1.468  0.020  1.468
 75M  C16  C15  triple    1.202  0.020  1.202
 75M  N18  C6   single    1.364  0.020  1.364
 75M  C15  C14  single    1.458  0.020  1.458
 75M  C14  N7   single    1.451  0.020  1.451
 75M  C6   N7   aromatic  1.356  0.020  1.356
 75M  C6   N5   aromatic  1.328  0.020  1.328
 75M  N7   C3   aromatic  1.380  0.020  1.380
 75M  N5   C4   aromatic  1.337  0.020  1.337
 75M  C3   C4   aromatic  1.367  0.020  1.367
 75M  C3   C2   single    1.431  0.020  1.431
 75M  C4   N8   aromatic  1.367  0.020  1.367
 75M  O13  C2   double    1.221  0.020  1.221
 75M  C2   N1   single    1.393  0.020  1.393
 75M  N8   C12  aromatic  1.380  0.020  1.380
 75M  N8   C9   aromatic  1.363  0.020  1.363
 75M  N1   C9   single    1.376  0.020  1.376
 75M  N1   C25  single    1.462  0.020  1.462
 75M  C12  C11  aromatic  1.359  0.020  1.359
 75M  C9   N10  aromatic  1.303  0.020  1.303
 75M  C31  C30  aromatic  1.384  0.020  1.384
 75M  C31  C26  aromatic  1.392  0.020  1.392
 75M  C25  C26  single    1.507  0.020  1.507
 75M  C11  N10  aromatic  1.373  0.020  1.373
 75M  C30  C29  aromatic  1.394  0.020  1.394
 75M  C26  C27  aromatic  1.394  0.020  1.394
 75M  C29  C28  aromatic  1.395  0.020  1.395
 75M  C29  C32  single    1.427  0.020  1.427
 75M  C27  C28  aromatic  1.383  0.020  1.383
 75M  C32  N33  triple    1.152  0.020  1.152
 75M  C11  H1   single    0.930  0.020  1.080
 75M  C12  H2   single    0.930  0.020  1.080
 75M  C14  H3   single    0.970  0.020  1.090
 75M  C14  H4   single    0.970  0.020  1.090
 75M  C17  H5   single    0.970  0.020  1.090
 75M  C17  H6   single    0.970  0.020  1.090
 75M  C17  H7   single    0.970  0.020  1.090
 75M  C19  H8   single    0.970  0.020  1.090
 75M  C19  H9   single    0.970  0.020  1.090
 75M  C20  H10  single    0.970  0.020  1.090
 75M  C21  H11  single    0.970  0.020  1.090
 75M  C21  H12  single    0.970  0.020  1.090
 75M  C22  H13  single    0.970  0.020  1.090
 75M  C22  H14  single    0.970  0.020  1.090
 75M  C23  H15  single    0.970  0.020  1.090
 75M  C23  H16  single    0.970  0.020  1.090
 75M  N24  H17  single    0.890  0.020  1.040
 75M  N24  H18  single    0.890  0.020  1.040
 75M  C25  H20  single    0.970  0.020  1.090
 75M  C25  H21  single    0.970  0.020  1.090
 75M  C27  H22  single    0.930  0.020  1.080
 75M  C28  H23  single    0.930  0.020  1.080
 75M  C30  H24  single    0.930  0.020  1.080
 75M  C31  H25  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
 75M  N8   C4   N5   127.90  3.000
 75M  N8   C4   C3   119.14  3.000
 75M  N5   C4   C3   112.95  3.000
 75M  O13  C2   C3   126.02  3.000
 75M  O13  C2   N1   121.59  3.000
 75M  C3   C2   N1   112.39  3.000
 75M  C25  N1   C9   118.01  3.000
 75M  C25  N1   C2   118.38  3.000
 75M  C9   N1   C2   123.55  3.000
 75M  N18  C6   N7   122.32  3.000
 75M  N7   C6   N5   112.31  3.000
 75M  N18  C6   N5   125.33  3.000
 75M  N7   C3   C2   131.26  3.000
 75M  C2   C3   C4   124.56  3.000
 75M  N7   C3   C4   104.18  3.000
 75M  C6   N5   C4   104.05  3.000
 75M  C14  N7   C3   126.28  3.000
 75M  C3   N7   C6   106.49  3.000
 75M  C14  N7   C6   126.86  3.000
 75M  C12  N8   C9   107.15  3.000
 75M  C9   N8   C4   119.54  3.000
 75M  C12  N8   C4   133.30  3.000
 75M  N10  C9   N8   111.86  3.000
 75M  N10  C9   N1   127.34  3.000
 75M  N8   C9   N1   120.80  3.000
 75M  C11  N10  C9   104.96  3.000
 75M  H1   C11  C12  127.28  3.000
 75M  H1   C11  N10  121.21  3.000
 75M  C12  C11  N10  111.50  3.000
 75M  H2   C12  C11  133.21  3.000
 75M  H2   C12  N8   122.26  3.000
 75M  C11  C12  N8   104.53  3.000
 75M  H4   C14  H3   106.66  3.000
 75M  H4   C14  C15  110.76  3.000
 75M  H3   C14  C15  110.44  3.000
 75M  H4   C14  N7   107.38  3.000
 75M  H3   C14  N7   108.44  3.000
 75M  C15  C14  N7   112.91  3.000
 75M  C16  C15  C14  180.00  3.000
 75M  C17  C16  C15  180.00  3.000
 75M  H7   C17  H6   107.98  3.000
 75M  H7   C17  H5   107.85  3.000
 75M  H6   C17  H5   107.91  3.000
 75M  H7   C17  C16  111.01  3.000
 75M  H6   C17  C16  111.13  3.000
 75M  H5   C17  C16  110.81  3.000
 75M  C23  N18  C19  112.36  3.000
 75M  C23  N18  C6   117.73  3.000
 75M  C19  N18  C6   116.10  3.000
 75M  H9   C19  H8   107.74  3.000
 75M  H9   C19  C20  109.80  3.000
 75M  H8   C19  C20  109.95  3.000
 75M  H9   C19  N18  110.79  3.000
 75M  H8   C19  N18  109.20  3.000
 75M  C20  C19  N18  109.35  3.000
 75M  H10  C20  N24  107.43  3.000
 75M  H10  C20  C21  108.50  3.000
 75M  N24  C20  C21  114.96  3.000
 75M  H10  C20  C19  106.83  3.000
 75M  C21  C20  C19  109.45  3.000
 75M  N24  C20  C19  109.35  3.000
 75M  H12  C21  H11  106.61  3.000
 75M  H12  C21  C22  109.10  3.000
 75M  H11  C21  C22  110.61  3.000
 75M  H12  C21  C20  108.98  3.000
 75M  H11  C21  C20  110.00  3.000
 75M  C22  C21  C20  111.41  3.000
 75M  H14  C22  H13  106.59  3.000
 75M  H14  C22  C23  108.84  3.000
 75M  H13  C22  C23  109.42  3.000
 75M  H14  C22  C21  110.37  3.000
 75M  H13  C22  C21  110.76  3.000
 75M  C23  C22  C21  110.76  3.000
 75M  H16  C23  H15  106.90  3.000
 75M  H16  C23  C22  110.46  3.000
 75M  H15  C23  C22  109.91  3.000
 75M  H16  C23  N18  110.16  3.000
 75M  H15  C23  N18  109.35  3.000
 75M  C22  C23  N18  110.01  3.000
 75M  H18  N24  H17  105.78  3.000
 75M  H18  N24  C20  109.85  3.000
 75M  H17  N24  C20  109.44  3.000
 75M  H21  C25  H20  107.48  3.000
 75M  H21  C25  C26  110.82  3.000
 75M  H20  C25  C26  110.60  3.000
 75M  H21  C25  N1   108.50  3.000
 75M  H20  C25  N1   107.55  3.000
 75M  C26  C25  N1   111.73  3.000
 75M  C31  C26  C27  119.30  3.000
 75M  C27  C26  C25  120.11  3.000
 75M  C31  C26  C25  120.59  3.000
 75M  H22  C27  C28  119.54  3.000
 75M  H22  C27  C26  119.78  3.000
 75M  C28  C27  C26  120.68  3.000
 75M  H23  C28  C29  120.21  3.000
 75M  H23  C28  C27  120.35  3.000
 75M  C29  C28  C27  119.44  3.000
 75M  C32  C29  C30  119.78  3.000
 75M  C32  C29  C28  119.78  3.000
 75M  C30  C29  C28  120.43  3.000
 75M  H24  C30  C31  120.35  3.000
 75M  H24  C30  C29  120.20  3.000
 75M  C31  C30  C29  119.46  3.000
 75M  H25  C31  C30  119.48  3.000
 75M  H25  C31  C26  119.83  3.000
 75M  C30  C31  C26  120.69  3.000
 75M  N33  C32  C29  180.00  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
 75M  CONST_01  N7   C6   N5   C4      0.00   0.0  0
 75M  CONST_02  C6   N7   C3   C4      0.00   0.0  0
 75M  CONST_03  C11  C12  N8   C4    180.00   0.0  0
 75M  CONST_04  N10  C9   N8   C4    180.00   0.0  0
 75M  CONST_05  C3   C4   N5   C6      0.00   0.0  0
 75M  CONST_06  N8   C4   N5   C6    180.00   0.0  0
 75M  CONST_07  N5   C6   N7   C3      0.00   0.0  0
 75M  CONST_08  C12  N8   C4   C3    180.00   0.0  0
 75M  CONST_09  C9   N8   C4   C3      0.00   0.0  0
 75M  CONST_10  N7   C3   C4   N5      0.00   0.0  0
 75M  CONST_11  C12  N8   C4   N5      0.00   0.0  0
 75M  CONST_12  C9   N8   C4   N5    180.00   0.0  0
 75M  CONST_13  N8   C4   C3   N7    180.00   0.0  0
 75M  CONST_14  N10  C11  C12  N8      0.00   0.0  0
 75M  CONST_15  C11  N10  C9   N8      0.00   0.0  0
 75M  CONST_16  C11  C12  N8   C9      0.00   0.0  0
 75M  CONST_17  C12  C11  N10  C9      0.00   0.0  0
 75M  CONST_18  C12  N8   C9   N10     0.00   0.0  0
 75M  CONST_19  C29  C30  C31  C26     0.00   0.0  0
 75M  CONST_20  C29  C28  C27  C26     0.00   0.0  0
 75M  CONST_21  C30  C31  C26  C27     0.00   0.0  0
 75M  CONST_22  C30  C29  C28  C27     0.00   0.0  0
 75M  CONST_23  C31  C30  C29  C28     0.00   0.0  0
 75M  CONST_24  C31  C26  C27  C28     0.00   0.0  0
 75M  CONST_25  N18  C6   N5   C4    180.00   0.0  0
 75M  CONST_26  N18  C6   N7   C3    180.00   0.0  0
 75M  CONST_27  C9   N1   C2   C3      0.00   0.0  0
 75M  CONST_28  C14  N7   C3   C4    180.00   0.0  0
 75M  CONST_29  C14  N7   C3   C2      0.00   0.0  0
 75M  CONST_30  C14  N7   C6   N5    180.00   0.0  0
 75M  CONST_31  N18  C6   N7   C14     0.00   0.0  0
 75M  CONST_32  C30  C31  C26  C25   180.00   0.0  0
 75M  CONST_33  C28  C27  C26  C25   180.00   0.0  0
 75M  CONST_34  C32  C29  C28  C27   180.00   0.0  0
 75M  CONST_35  C32  C29  C30  C31   180.00   0.0  0
 75M  CONST_36  C25  N1   C2   C3    180.00   0.0  0
 75M  CONST_37  O13  C2   N1   C9    180.00   0.0  0
 75M  CONST_38  H2   C12  N8   C4      0.00   0.0  0
 75M  CONST_39  H1   C11  C12  N8    180.00   0.0  0
 75M  CONST_40  H24  C30  C31  C26   180.00   0.0  0
 75M  CONST_41  H23  C28  C27  C26   180.00   0.0  0
 75M  CONST_42  H25  C31  C26  C27   180.00   0.0  0
 75M  CONST_43  H22  C27  C28  C29   180.00   0.0  0
 75M  CONST_44  C25  N1   C2   O13     0.00   0.0  0
 75M  Var_01    C20  C19  N18  C6   -157.79  30.0  1
 75M  Var_02    C22  C23  N18  C6    160.42  30.0  1
 75M  Var_03    C19  N18  C6   N5    -20.87  30.0  2
 75M  Var_04    C21  C22  C23  N18    54.53  30.0  1
 75M  Var_05    C23  C22  C21  C20   -52.70  30.0  1
 75M  Var_06    C26  C25  N1   C2     81.90  30.0  3
 75M  Var_07    C31  C26  C25  N1   -102.01  30.0  2
 75M  Var_08    C15  C14  N7   C6    105.10  30.0  2
 75M  Var_09    H5   C17  C16  C15    86.26  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
 75M  chir_01  C20  N24  C21  C19  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
 75M  plan-1  C25  0.020
 75M  plan-1  C26  0.020
 75M  plan-1  C27  0.020
 75M  plan-1  C28  0.020
 75M  plan-1  C29  0.020
 75M  plan-1  C30  0.020
 75M  plan-1  C31  0.020
 75M  plan-1  C32  0.020
 75M  plan-1  N33  0.020
 75M  plan-1  H22  0.020
 75M  plan-1  H23  0.020
 75M  plan-1  H24  0.020
 75M  plan-1  H25  0.020
 75M  plan-2  C4   0.020
 75M  plan-2  C2   0.020
 75M  plan-2  N1   0.020
 75M  plan-2  C6   0.020
 75M  plan-2  C3   0.020
 75M  plan-2  N5   0.020
 75M  plan-2  N7   0.020
 75M  plan-2  N8   0.020
 75M  plan-2  C9   0.020
 75M  plan-2  N10  0.020
 75M  plan-2  C11  0.020
 75M  plan-2  C12  0.020
 75M  plan-2  O13  0.020
 75M  plan-2  C14  0.020
 75M  plan-2  N18  0.020
 75M  plan-2  C25  0.020
 75M  plan-2  H1   0.020
 75M  plan-2  H2   0.020

