# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:44:20 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-({2-[(3R)-3-aminopiperidin-1-yl]-5-methyl-6,9-dioxo-5,6,7,9-tetrahydro-1H-imidazo[1,2-a]purin-1-yl}methyl)-4-fluorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)CN2C(=O)c3n(Cc4cc(F)ccc4C#N)c(nc3N=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
 6AJ  6AJ  2-({2-[(3R)-3-aminopiperidin-1-yl]-5-methyl-6,9-dioxo-5,6,7,9-tetrahydro-1H-imidazo[1,2-a]purin-1-yl}methyl)-4-fluorobenzonitrile  ligand  53  32  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6AJ
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
 6AJ  C1   C  CR6   0   0.196   0.8137   2.1169  -0.3948
 6AJ  C2   C  CR16  0  -0.455   0.4540   3.2724  -1.0672
 6AJ  C3   C  CR6   0   0.571   0.1100   4.4021  -0.3509
 6AJ  C4   C  CR16  0  -0.420   0.0926   4.4310   1.0304
 6AJ  C5   C  CR16  0  -0.216   0.4533   3.2820   1.7069
 6AJ  C6   C  CR6   0  -0.011   0.8205   2.1324   1.0053
 6AJ  C7   C  CR6   0   0.568  -1.8773   0.2416  -0.7780
 6AJ  C8   C  CR56  0   0.077  -0.7164  -0.5109  -0.4564
 6AJ  C9   C  CR56  0   0.317  -0.7760  -1.7373   0.1838
 6AJ  C11  C  CR5   0   0.704   1.2612  -1.4341  -0.3146
 6AJ  C15  C  CH2   0  -0.423   1.2340   0.9127  -1.1969
 6AJ  C17  C  CH2   0  -0.293   3.2583  -2.5048   0.4707
 6AJ  C18  C  CH1   0  -0.115   4.7459  -2.1842   0.5587
 6AJ  C19  C  CH2   0  -0.454   5.3722  -2.2402  -0.8399
 6AJ  C20  C  CH2   0  -0.447   4.6252  -1.3424  -1.8188
 6AJ  C21  C  CH2   0  -0.333   3.1428  -1.6676  -1.8139
 6AJ  C30  C  CSP   0   0.021   1.2205   0.9926   1.7647
 6AJ  C26  C  CR5   0   0.516  -5.1430  -0.9991   0.3348
 6AJ  C23  C  CR56  0   0.822  -2.9613  -1.6009   0.3958
 6AJ  C25  C  CH2   0  -0.404  -4.3520   0.0772  -0.3753
 6AJ  N31  N  NS    0  -0.244   1.5486   0.1028   2.4197
 6AJ  N10  N  N     0  -0.494   0.4481  -2.3022   0.2545
 6AJ  N13  N  N     0  -0.491  -1.9187  -2.3121   0.6424
 6AJ  N12  N  NR5   0  -0.533   0.6177  -0.3184  -0.7528
 6AJ  N16  N  NT    0  -0.534   2.6127  -1.5743  -0.4480
 6AJ  N24  N  N     0  -0.616  -2.9968  -0.4058  -0.2531
 6AJ  N27  N  NR5   0  -0.573  -4.2429  -1.9471   0.7427
 6AJ  N22  N  NH2   0  -0.790   4.9247  -0.9172   1.2544
 6AJ  O28  O  O     0  -0.425  -6.3353  -1.0283   0.5095
 6AJ  F32  F  F     0  -0.300  -0.2287   5.5044  -1.0235
 6AJ  H1   H  HCR6  0   0.291   0.4327   3.2936  -2.1489
 6AJ  H2   H  HCR6  0   0.298  -0.1925   5.3267   1.5649
 6AJ  H3   H  HCR6  0   0.295   0.4569   3.2751   2.7880
 6AJ  H4   H  HCH2  0   0.304   1.0174   1.0833  -2.2515
 6AJ  H5   H  HCH2  0   0.305   2.3141   0.7867  -1.1026
 6AJ  H6   H  HCH2  0   0.227   3.1227  -3.5427   0.1405
 6AJ  H7   H  HCH2  0   0.258   2.8024  -2.4040   1.4544
 6AJ  H8   H  HCH1  0   0.237   5.2031  -2.9692   1.1696
 6AJ  H9   H  HCH2  0   0.238   6.4259  -1.9550  -0.7835
 6AJ  H10  H  HCH2  0   0.219   5.3478  -3.2734  -1.2025
 6AJ  H11  H  HCH2  0   0.224   4.7677  -0.2900  -1.5566
 6AJ  H12  H  HCH2  0   0.246   5.0132  -1.4698  -2.8308
 6AJ  H13  H  HCH2  0   0.271   2.5999  -0.9903  -2.4730
 6AJ  H14  H  HCH2  0   0.240   2.9793  -2.6834  -2.2002
 6AJ  H15  H  HCH2  0   0.320  -4.6637   0.1610  -1.4180
 6AJ  H16  H  HCH2  0   0.320  -4.4877   1.0454   0.1090
 6AJ  H17  H  HCH3  0   0.267  -4.2443  -3.0814   2.5037
 6AJ  H18  H  HCH3  0   0.271  -5.6391  -3.3032   1.4346
 6AJ  H19  H  HCH3  0   0.267  -4.0748  -4.0082   1.0009
 6AJ  H20  H  HNH2  0   0.342   5.8833  -0.6053   1.1556
 6AJ  H21  H  HNH2  0   0.340   4.3508  -0.2044   0.8212
 6AJ  O14  O  O     0  -0.466  -1.9888   1.2817  -1.4044
 6AJ  C29  C  CH3   0  -0.533  -4.5641  -3.1562   1.4659

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
 6AJ  N22  C18  single    1.456  0.020  1.456
 6AJ  C19  C20  single    1.524  0.020  1.524
 6AJ  C19  C18  single    1.533  0.020  1.533
 6AJ  F32  C3   single    1.335  0.020  1.335
 6AJ  C20  C21  single    1.518  0.020  1.518
 6AJ  C3   C4   aromatic  1.382  0.020  1.382
 6AJ  C3   C2   aromatic  1.381  0.020  1.381
 6AJ  C18  C17  single    1.524  0.020  1.524
 6AJ  C4   C5   aromatic  1.381  0.020  1.381
 6AJ  C2   C1   aromatic  1.384  0.020  1.384
 6AJ  C5   C6   aromatic  1.396  0.020  1.396
 6AJ  C1   C6   aromatic  1.400  0.020  1.400
 6AJ  C1   C15  single    1.507  0.020  1.507
 6AJ  C21  N16  single    1.468  0.020  1.468
 6AJ  C6   C30  single    1.427  0.020  1.427
 6AJ  C15  N12  single    1.447  0.020  1.447
 6AJ  N16  C17  single    1.458  0.020  1.458
 6AJ  N16  C11  single    1.365  0.020  1.365
 6AJ  C30  N31  triple    1.153  0.020  1.153
 6AJ  N12  C11  aromatic  1.360  0.020  1.360
 6AJ  N12  C8   aromatic  1.380  0.020  1.380
 6AJ  C11  N10  aromatic  1.319  0.020  1.319
 6AJ  C8   C7   single    1.420  0.020  1.420
 6AJ  C8   C9   aromatic  1.385  0.020  1.385
 6AJ  O14  C7   double    1.219  0.020  1.219
 6AJ  N10  C9   aromatic  1.350  0.020  1.350
 6AJ  C7   N24  single    1.396  0.020  1.396
 6AJ  C9   N13  single    1.359  0.020  1.359
 6AJ  N24  C23  single    1.360  0.020  1.360
 6AJ  N24  C25  single    1.444  0.020  1.444
 6AJ  N13  C23  double    1.286  0.020  1.286
 6AJ  C23  N27  single    1.372  0.020  1.372
 6AJ  C25  C26  single    1.513  0.020  1.513
 6AJ  N27  C26  single    1.369  0.020  1.369
 6AJ  N27  C29  single    1.445  0.020  1.445
 6AJ  C26  O28  double    1.205  0.020  1.205
 6AJ  C2   H1   single    0.930  0.020  1.080
 6AJ  C4   H2   single    0.930  0.020  1.080
 6AJ  C5   H3   single    0.930  0.020  1.080
 6AJ  C15  H4   single    0.970  0.020  1.090
 6AJ  C15  H5   single    0.970  0.020  1.090
 6AJ  C17  H6   single    0.970  0.020  1.090
 6AJ  C17  H7   single    0.970  0.020  1.090
 6AJ  C18  H8   single    0.970  0.020  1.090
 6AJ  C19  H9   single    0.970  0.020  1.090
 6AJ  C19  H10  single    0.970  0.020  1.090
 6AJ  C20  H11  single    0.970  0.020  1.090
 6AJ  C20  H12  single    0.970  0.020  1.090
 6AJ  C21  H13  single    0.970  0.020  1.090
 6AJ  C21  H14  single    0.970  0.020  1.090
 6AJ  C25  H15  single    0.970  0.020  1.090
 6AJ  C25  H16  single    0.970  0.020  1.090
 6AJ  C29  H17  single    0.970  0.020  1.090
 6AJ  C29  H18  single    0.970  0.020  1.090
 6AJ  C29  H19  single    0.970  0.020  1.090
 6AJ  N22  H20  single    0.890  0.020  1.040
 6AJ  N22  H21  single    0.890  0.020  1.040

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
 6AJ  C15  C1   C6   122.67  3.000
 6AJ  C15  C1   C2   118.75  3.000
 6AJ  C6   C1   C2   118.54  3.000
 6AJ  H1   C2   C3   119.83  3.000
 6AJ  H1   C2   C1   120.46  3.000
 6AJ  C3   C2   C1   119.70  3.000
 6AJ  F32  C3   C4   118.89  3.000
 6AJ  C4   C3   C2   122.60  3.000
 6AJ  F32  C3   C2   118.51  3.000
 6AJ  H2   C4   C5   121.05  3.000
 6AJ  H2   C4   C3   120.99  3.000
 6AJ  C5   C4   C3   117.96  3.000
 6AJ  H3   C5   C6   119.77  3.000
 6AJ  H3   C5   C4   119.73  3.000
 6AJ  C6   C5   C4   120.50  3.000
 6AJ  C30  C6   C5   117.65  3.000
 6AJ  C30  C6   C1   121.65  3.000
 6AJ  C5   C6   C1   120.69  3.000
 6AJ  O14  C7   N24  121.04  3.000
 6AJ  N24  C7   C8   108.95  3.000
 6AJ  O14  C7   C8   130.01  3.000
 6AJ  N12  C8   C9   105.33  3.000
 6AJ  C9   C8   C7   122.60  3.000
 6AJ  N12  C8   C7   131.88  3.000
 6AJ  N13  C9   N10  124.60  3.000
 6AJ  N13  C9   C8   124.53  3.000
 6AJ  N10  C9   C8   110.84  3.000
 6AJ  N16  C11  N12  121.39  3.000
 6AJ  N12  C11  N10  112.79  3.000
 6AJ  N16  C11  N10  125.80  3.000
 6AJ  H5   C15  H4   107.35  3.000
 6AJ  H5   C15  N12  107.27  3.000
 6AJ  H4   C15  N12  110.21  3.000
 6AJ  H5   C15  C1   108.80  3.000
 6AJ  H4   C15  C1   109.54  3.000
 6AJ  N12  C15  C1   113.45  3.000
 6AJ  H7   C17  H6   107.92  3.000
 6AJ  H7   C17  N16  108.95  3.000
 6AJ  H6   C17  N16  111.05  3.000
 6AJ  H7   C17  C18  109.70  3.000
 6AJ  H6   C17  C18  109.68  3.000
 6AJ  N16  C17  C18  109.52  3.000
 6AJ  H8   C18  N22  107.82  3.000
 6AJ  H8   C18  C19  108.19  3.000
 6AJ  N22  C18  C19  114.67  3.000
 6AJ  H8   C18  C17  106.79  3.000
 6AJ  C19  C18  C17  109.77  3.000
 6AJ  N22  C18  C17  109.29  3.000
 6AJ  H10  C19  H9   106.54  3.000
 6AJ  H10  C19  C20  109.40  3.000
 6AJ  H9   C19  C20  110.61  3.000
 6AJ  H10  C19  C18  109.11  3.000
 6AJ  H9   C19  C18  109.70  3.000
 6AJ  C20  C19  C18  111.35  3.000
 6AJ  H12  C20  H11  106.75  3.000
 6AJ  H12  C20  C21  108.98  3.000
 6AJ  H11  C20  C21  109.43  3.000
 6AJ  H12  C20  C19  110.64  3.000
 6AJ  H11  C20  C19  110.43  3.000
 6AJ  C21  C20  C19  110.52  3.000
 6AJ  H14  C21  H13  106.72  3.000
 6AJ  H14  C21  N16  109.39  3.000
 6AJ  H13  C21  N16  110.08  3.000
 6AJ  H14  C21  C20  110.02  3.000
 6AJ  H13  C21  C20  110.57  3.000
 6AJ  N16  C21  C20  110.00  3.000
 6AJ  N31  C30  C6   180.00  3.000
 6AJ  O28  C26  N27  126.17  3.000
 6AJ  O28  C26  C25  127.05  3.000
 6AJ  N27  C26  C25  106.78  3.000
 6AJ  N27  C23  N24  108.53  3.000
 6AJ  N27  C23  N13  124.70  3.000
 6AJ  N24  C23  N13  126.77  3.000
 6AJ  H16  C25  H15  108.69  3.000
 6AJ  H16  C25  N24  112.09  3.000
 6AJ  H15  C25  N24  112.00  3.000
 6AJ  H16  C25  C26  110.97  3.000
 6AJ  H15  C25  C26  110.71  3.000
 6AJ  N24  C25  C26  102.30  3.000
 6AJ  C11  N10  C9   105.14  3.000
 6AJ  C23  N13  C9   112.53  3.000
 6AJ  C15  N12  C11  126.53  3.000
 6AJ  C11  N12  C8   105.88  3.000
 6AJ  C15  N12  C8   126.61  3.000
 6AJ  C21  N16  C17  112.69  3.000
 6AJ  C17  N16  C11  116.24  3.000
 6AJ  C21  N16  C11  117.06  3.000
 6AJ  C25  N24  C23  111.03  3.000
 6AJ  C25  N24  C7   124.46  3.000
 6AJ  C23  N24  C7   124.47  3.000
 6AJ  C29  N27  C23  123.04  3.000
 6AJ  C29  N27  C26  125.61  3.000
 6AJ  C23  N27  C26  111.34  3.000
 6AJ  H21  N22  H20  106.14  3.000
 6AJ  H21  N22  C18  109.79  3.000
 6AJ  H20  N22  C18  109.72  3.000
 6AJ  H19  C29  H18  109.11  3.000
 6AJ  H19  C29  H17  109.24  3.000
 6AJ  H18  C29  H17  109.14  3.000
 6AJ  H19  C29  N27  109.97  3.000
 6AJ  H18  C29  N27  108.60  3.000
 6AJ  H17  C29  N27  110.76  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
 6AJ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 6AJ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 6AJ  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 6AJ  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 6AJ  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 6AJ  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 6AJ  CONST_07  N10  C11  N12  C8      0.00   0.0  0
 6AJ  CONST_08  C11  N10  C9   C8      0.00   0.0  0
 6AJ  CONST_09  C11  N12  C8   C9      0.00   0.0  0
 6AJ  CONST_10  N12  C11  N10  C9      0.00   0.0  0
 6AJ  CONST_11  N12  C8   C9   N10     0.00   0.0  0
 6AJ  CONST_12  N16  C11  N12  C8    180.00   0.0  0
 6AJ  CONST_13  N16  C11  N10  C9    180.00   0.0  0
 6AJ  CONST_14  N13  C23  N24  C7      0.00   0.0  0
 6AJ  CONST_15  N27  C23  N24  C7    180.00   0.0  0
 6AJ  CONST_16  C26  C25  N24  C7    180.00   0.0  0
 6AJ  CONST_17  C23  N24  C7   C8      0.00   0.0  0
 6AJ  CONST_18  C25  N24  C7   C8    180.00   0.0  0
 6AJ  CONST_19  N24  C23  N13  C9      0.00   0.0  0
 6AJ  CONST_20  N27  C23  N13  C9    180.00   0.0  0
 6AJ  CONST_21  C23  N24  C25  C26     0.00   0.0  0
 6AJ  CONST_22  N24  C23  N27  C26     0.00   0.0  0
 6AJ  CONST_23  N13  C23  N27  C26   180.00   0.0  0
 6AJ  CONST_24  C25  C26  N27  C23     0.00   0.0  0
 6AJ  CONST_25  N13  C23  N24  C25   180.00   0.0  0
 6AJ  CONST_26  N27  C23  N24  C25     0.00   0.0  0
 6AJ  CONST_27  N27  C26  C25  N24     0.00   0.0  0
 6AJ  CONST_28  F32  C3   C2   C1    180.00   0.0  0
 6AJ  CONST_29  C30  C6   C1   C2    180.00   0.0  0
 6AJ  CONST_30  C15  C1   C2   C3    180.00   0.0  0
 6AJ  CONST_31  C30  C6   C5   C4    180.00   0.0  0
 6AJ  CONST_32  F32  C3   C4   C5    180.00   0.0  0
 6AJ  CONST_33  C15  C1   C6   C5    180.00   0.0  0
 6AJ  CONST_35  C15  N12  C8   C9    180.00   0.0  0
 6AJ  CONST_36  N16  C11  N12  C15     0.00   0.0  0
 6AJ  CONST_37  N10  C11  N12  C15   180.00   0.0  0
 6AJ  CONST_38  O14  C7   N24  C23   180.00   0.0  0
 6AJ  CONST_39  O28  C26  N27  C23   180.00   0.0  0
 6AJ  CONST_40  O14  C7   N24  C25     0.00   0.0  0
 6AJ  CONST_41  C29  N27  C26  C25   180.00   0.0  0
 6AJ  CONST_42  N24  C23  N27  C29   180.00   0.0  0
 6AJ  CONST_43  N13  C23  N27  C29     0.00   0.0  0
 6AJ  CONST_44  H3   C5   C6   C1    180.00   0.0  0
 6AJ  CONST_45  H2   C4   C3   C2    180.00   0.0  0
 6AJ  CONST_46  H1   C2   C3   C4    180.00   0.0  0
 6AJ  CONST_47  O28  C26  N27  C29     0.00   0.0  0
 6AJ  Var_01    C20  C21  N16  C11   160.66  30.0  1
 6AJ  Var_02    C18  C17  N16  C11  -159.36  30.0  1
 6AJ  Var_03    N12  C11  N16  C17   157.09  30.0  2
 6AJ  Var_04    C21  C20  C19  C18   -53.27  30.0  1
 6AJ  Var_05    N16  C21  C20  C19    55.14  30.0  1
 6AJ  Var_06    C11  N12  C15  C1   -120.94  30.0  2
 6AJ  Var_07    N12  C15  C1   C2   -133.86  30.0  2
 6AJ  Var_08    H15  C25  N24  C7     60.39  30.0  1
 6AJ  Var_09    H17  C29  N27  C26  -107.07  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
 6AJ  chir_01  C18  N22  C19  C17  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
 6AJ  plan-1  C1   0.020
 6AJ  plan-1  C2   0.020
 6AJ  plan-1  C3   0.020
 6AJ  plan-1  C4   0.020
 6AJ  plan-1  C5   0.020
 6AJ  plan-1  C6   0.020
 6AJ  plan-1  C15  0.020
 6AJ  plan-1  C30  0.020
 6AJ  plan-1  N31  0.020
 6AJ  plan-1  F32  0.020
 6AJ  plan-1  H1   0.020
 6AJ  plan-1  H2   0.020
 6AJ  plan-1  H3   0.020
 6AJ  plan-2  C7   0.020
 6AJ  plan-2  C8   0.020
 6AJ  plan-2  C9   0.020
 6AJ  plan-2  C11  0.020
 6AJ  plan-2  C15  0.020
 6AJ  plan-2  C26  0.020
 6AJ  plan-2  C23  0.020
 6AJ  plan-2  C25  0.020
 6AJ  plan-2  N10  0.020
 6AJ  plan-2  N13  0.020
 6AJ  plan-2  N12  0.020
 6AJ  plan-2  N16  0.020
 6AJ  plan-2  N24  0.020
 6AJ  plan-2  N27  0.020
 6AJ  plan-2  O28  0.020
 6AJ  plan-2  O14  0.020
 6AJ  plan-2  C29  0.020

