# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:09:38 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-({8-[(3R)-3-aminopiperidin-1-yl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl}methyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N3CCC[C@@H](N)C3)n(Cc4ccccc4C#N)c2C1=O
#
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
 XIH  XIH  2-({8-[(3R)-3-aminopiperidin-1-yl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl}methyl)benzonitrile  ligand  52  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XIH
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
 XIH  C5    C  CR56  0   0.128   1.0778   0.6306   0.3238
 XIH  C6    C  CR56  0   0.463   0.7884   1.8344  -0.2518
 XIH  C8    C  CR5   0   0.713  -1.0634   1.0671   0.4086
 XIH  C10   C  CH2   0  -0.337  -2.8381   0.7746   2.0369
 XIH  C13   C  CH1   0  -0.098  -4.6783   0.9727  -0.2098
 XIH  C15   C  CH2   0  -0.284  -3.3114   1.6504  -0.1894
 XIH  C20   C  CR16  0  -0.219  -0.1710  -2.8093  -2.3460
 XIH  C21   C  CR16  0  -0.259   0.6431  -3.9139  -2.1284
 XIH  C22   C  CR16  0  -0.239   1.1326  -4.1632  -0.8598
 XIH  C24   C  CSP   0   0.032   1.3342  -3.5942   1.4860
 XIH  C28   C  CR6   0   0.717   3.0671   2.2311  -0.7544
 XIH  N     N  NR6   0  -0.603   3.3333   1.0059  -0.1521
 XIH  C3    C  CR6   0   0.577   2.4005   0.1423   0.4407
 XIH  O     O  OC    0  -0.468   2.7554  -0.8951   0.9757
 XIH  N7    N  N     0  -0.499  -0.5238   2.1179  -0.1948
 XIH  N9    N  NT    0  -0.529  -2.3938   0.8893   0.6451
 XIH  C11   C  CH2   0  -0.444  -4.1738   0.0572   2.0887
 XIH  C12   C  CH2   0  -0.450  -5.1953   0.7758   1.2148
 XIH  N16   N  NR5   0  -0.536  -0.1426   0.1293   0.7429
 XIH  C18   C  CR6   0   0.147  -0.0034  -2.1844  -0.0181
 XIH  C19   C  CR16  0  -0.282  -0.4899  -1.9584  -1.2994
 XIH  C23   C  CR6   0  -0.004   0.8122  -3.2996   0.1896
 XIH  N25   N  NS    0  -0.251   1.7493  -3.8712   2.5245
 XIH  N26   N  NR6   0  -0.594   1.7526   2.6353  -0.7845
 XIH  C27   C  CH3   0  -0.536   1.3694   3.9076  -1.3745
 XIH  O29   O  OC    0  -0.491   3.9540   2.9164  -1.2289
 XIH  H101  H  HCH2  0   0.271  -2.0901   0.2453   2.6256
 XIH  H102  H  HCH2  0   0.243  -2.9358   1.7772   2.4761
 XIH  H13   H  HCH1  0   0.227  -4.5435  -0.0122  -0.6700
 XIH  H151  H  HCH2  0   0.215  -3.4173   2.6824   0.1773
 XIH  H152  H  HCH2  0   0.257  -2.9166   1.7023  -1.2031
 XIH  H171  H  HCH2  0   0.296   0.1221  -1.4891   2.0302
 XIH  H172  H  HCH2  0   0.311  -1.4596  -1.3618   1.2903
 XIH  H20   H  HCR6  0   0.275  -0.5629  -2.6110  -3.3347
 XIH  H21   H  HCR6  0   0.275   0.8932  -4.5793  -2.9433
 XIH  H22   H  HCR6  0   0.282   1.7666  -5.0195  -0.6750
 XIH  H1    H  HCH3  0   0.269   5.3529   1.2791  -0.5967
 XIH  H2    H  HCH3  0   0.253   5.0477   0.4728   0.9436
 XIH  H3    H  HCH3  0   0.253   4.8293  -0.4071  -0.5761
 XIH  H111  H  HCH2  0   0.229  -4.0429  -0.9742   1.7483
 XIH  H112  H  HCH2  0   0.243  -4.5168   0.0127   3.1239
 XIH  H121  H  HCH2  0   0.238  -6.1393   0.2253   1.1929
 XIH  H122  H  HCH2  0   0.213  -5.4122   1.7602   1.6470
 XIH  H141  H  HNH2  0   0.349  -6.4360   1.2466  -1.1828
 XIH  H142  H  HNH2  0   0.337  -5.8015   2.6144  -0.6120
 XIH  H19   H  HCR6  0   0.267  -1.1367  -1.1094  -1.4859
 XIH  H271  H  HCH3  0   0.272   2.2481   4.4004  -1.7714
 XIH  H272  H  HCH3  0   0.258   0.6574   3.7462  -2.1812
 XIH  H273  H  HCH3  0   0.258   0.9116   4.5479  -0.6224
 XIH  C17   C  CH2   0  -0.423  -0.3927  -1.2511   1.1008
 XIH  C     C  CH3   0  -0.529   4.7213   0.5607  -0.0910
 XIH  N14   N  NH2   0  -0.792  -5.5605   1.7433  -1.0724

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
 XIH  C5   C6    aromatic  1.365  0.020  1.365
 XIH  C5   C3    aromatic  1.415  0.020  1.415
 XIH  C5   N16   aromatic  1.384  0.020  1.384
 XIH  C6   N7    aromatic  1.344  0.020  1.344
 XIH  C6   N26   aromatic  1.362  0.020  1.362
 XIH  C8   N7    aromatic  1.326  0.020  1.326
 XIH  C8   N9    single    1.363  0.020  1.363
 XIH  C8   N16   aromatic  1.356  0.020  1.356
 XIH  C10  N9    single    1.465  0.020  1.465
 XIH  C10  C11   single    1.517  0.020  1.517
 XIH  C10  H101  single    0.970  0.020  1.090
 XIH  C10  H102  single    0.970  0.020  1.090
 XIH  C13  C15   single    1.526  0.020  1.526
 XIH  C13  C12   single    1.528  0.020  1.528
 XIH  C13  N14   single    1.455  0.020  1.455
 XIH  C13  H13   single    0.970  0.020  1.090
 XIH  C15  N9    single    1.455  0.020  1.455
 XIH  C15  H151  single    0.970  0.020  1.090
 XIH  C15  H152  single    0.970  0.020  1.090
 XIH  C17  N16   single    1.448  0.020  1.448
 XIH  C17  C18   single    1.508  0.020  1.508
 XIH  C17  H171  single    0.970  0.020  1.090
 XIH  C17  H172  single    0.970  0.020  1.090
 XIH  C20  C21   aromatic  1.389  0.020  1.389
 XIH  C20  C19   aromatic  1.386  0.020  1.386
 XIH  C20  H20   single    0.930  0.020  1.080
 XIH  C21  C22   aromatic  1.383  0.020  1.383
 XIH  C21  H21   single    0.930  0.020  1.080
 XIH  C22  C23   aromatic  1.396  0.020  1.396
 XIH  C22  H22   single    0.930  0.020  1.080
 XIH  C24  C23   single    1.428  0.020  1.428
 XIH  C24  N25   triple    1.152  0.020  1.152
 XIH  C28  N     aromatic  1.391  0.020  1.391
 XIH  C28  N26   aromatic  1.376  0.020  1.376
 XIH  C28  O29   double    1.217  0.020  1.217
 XIH  C    N     single    1.459  0.020  1.459
 XIH  C    H1    single    0.970  0.020  1.090
 XIH  C    H2    single    0.970  0.020  1.090
 XIH  C    H3    single    0.970  0.020  1.090
 XIH  N    C3    aromatic  1.403  0.020  1.403
 XIH  C3   O     double    1.220  0.020  1.220
 XIH  C11  C12   single    1.524  0.020  1.524
 XIH  C11  H111  single    0.970  0.020  1.090
 XIH  C11  H112  single    0.970  0.020  1.090
 XIH  C12  H121  single    0.970  0.020  1.090
 XIH  C12  H122  single    0.970  0.020  1.090
 XIH  N14  H141  single    0.890  0.020  1.040
 XIH  N14  H142  single    0.890  0.020  1.040
 XIH  C18  C19   aromatic  1.389  0.020  1.389
 XIH  C18  C23   aromatic  1.397  0.020  1.397
 XIH  C19  H19   single    0.930  0.020  1.080
 XIH  N26  C27   single    1.454  0.020  1.454
 XIH  C27  H271  single    0.970  0.020  1.090
 XIH  C27  H272  single    0.970  0.020  1.090
 XIH  C27  H273  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
 XIH  N16   C5   C3    132.40  3.000
 XIH  N16   C5   C6    105.07  3.000
 XIH  C3    C5   C6    122.50  3.000
 XIH  N26   C6   N7    125.72  3.000
 XIH  N26   C6   C5    122.23  3.000
 XIH  N7    C6   C5    112.03  3.000
 XIH  N16   C8   N9    121.99  3.000
 XIH  N16   C8   N7    112.57  3.000
 XIH  N9    C8   N7    125.41  3.000
 XIH  H102  C10  H101  106.76  3.000
 XIH  H102  C10  C11   109.85  3.000
 XIH  H101  C10  C11   110.88  3.000
 XIH  H102  C10  N9    109.58  3.000
 XIH  H101  C10  N9    110.07  3.000
 XIH  C11   C10  N9    109.66  3.000
 XIH  H13   C13  N14   107.57  3.000
 XIH  H13   C13  C12   108.51  3.000
 XIH  N14   C13  C12   114.57  3.000
 XIH  H13   C13  C15   107.14  3.000
 XIH  N14   C13  C15   108.42  3.000
 XIH  C12   C13  C15   110.36  3.000
 XIH  H152  C15  H151  107.48  3.000
 XIH  H152  C15  N9    109.28  3.000
 XIH  H151  C15  N9    111.11  3.000
 XIH  H152  C15  C13   109.48  3.000
 XIH  H151  C15  C13   109.55  3.000
 XIH  N9    C15  C13   109.89  3.000
 XIH  H20   C20  C19   119.62  3.000
 XIH  H20   C20  C21   120.07  3.000
 XIH  C19   C20  C21   120.31  3.000
 XIH  H21   C21  C22   119.91  3.000
 XIH  H21   C21  C20   120.45  3.000
 XIH  C22   C21  C20   119.64  3.000
 XIH  H22   C22  C23   119.73  3.000
 XIH  H22   C22  C21   120.48  3.000
 XIH  C23   C22  C21   119.79  3.000
 XIH  N25   C24  C23   180.00  3.000
 XIH  O29   C28  N26   121.49  3.000
 XIH  O29   C28  N     121.69  3.000
 XIH  N26   C28  N     116.81  3.000
 XIH  C3    N    C     115.29  3.000
 XIH  C3    N    C28   126.73  3.000
 XIH  C     N    C28   117.96  3.000
 XIH  O     C3   N     121.03  3.000
 XIH  O     C3   C5    126.99  3.000
 XIH  N     C3   C5    111.98  3.000
 XIH  C8    N7   C6    104.44  3.000
 XIH  C15   N9   C10   113.23  3.000
 XIH  C15   N9   C8    116.60  3.000
 XIH  C10   N9   C8    118.10  3.000
 XIH  H112  C11  H111  107.11  3.000
 XIH  H112  C11  C12   110.64  3.000
 XIH  H111  C11  C12   110.26  3.000
 XIH  H112  C11  C10   109.17  3.000
 XIH  H111  C11  C10   109.26  3.000
 XIH  C12   C11  C10   110.33  3.000
 XIH  H122  C12  H121  106.81  3.000
 XIH  H122  C12  C11   109.25  3.000
 XIH  H121  C12  C11   110.65  3.000
 XIH  H122  C12  C13   108.58  3.000
 XIH  H121  C12  C13   109.78  3.000
 XIH  C11   C12  C13   111.62  3.000
 XIH  C17   N16  C8    127.08  3.000
 XIH  C17   N16  C5    124.91  3.000
 XIH  C8    N16  C5    105.88  3.000
 XIH  C23   C18  C19   118.13  3.000
 XIH  C23   C18  C17   122.30  3.000
 XIH  C19   C18  C17   119.56  3.000
 XIH  H19   C19  C18   119.69  3.000
 XIH  H19   C19  C20   119.24  3.000
 XIH  C18   C19  C20   121.07  3.000
 XIH  C18   C23  C24   120.86  3.000
 XIH  C18   C23  C22   121.06  3.000
 XIH  C24   C23  C22   118.08  3.000
 XIH  C27   N26  C28   121.19  3.000
 XIH  C27   N26  C6    119.13  3.000
 XIH  C28   N26  C6    119.68  3.000
 XIH  H273  C27  H272  108.92  3.000
 XIH  H273  C27  H271  109.08  3.000
 XIH  H272  C27  H271  109.08  3.000
 XIH  H273  C27  N26   110.19  3.000
 XIH  H272  C27  N26   110.09  3.000
 XIH  H271  C27  N26   109.46  3.000
 XIH  H172  C17  H171  107.00  3.000
 XIH  H172  C17  C18   108.60  3.000
 XIH  H171  C17  C18   112.09  3.000
 XIH  H172  C17  N16   108.01  3.000
 XIH  H171  C17  N16   109.74  3.000
 XIH  C18   C17  N16   111.22  3.000
 XIH  H3    C    H2    108.80  3.000
 XIH  H3    C    H1    108.92  3.000
 XIH  H2    C    H1    108.83  3.000
 XIH  H3    C    N     110.32  3.000
 XIH  H2    C    N     110.47  3.000
 XIH  H1    C    N     109.46  3.000
 XIH  H142  N14  H141  105.39  3.000
 XIH  H142  N14  C13   109.26  3.000
 XIH  H141  N14  C13   109.22  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
 XIH  CONST_01  C8    N7   C6   C5      0.00   0.0  0
 XIH  CONST_02  C28   N26  C6   C5      0.00   0.0  0
 XIH  CONST_03  C28   N    C3   C5      0.00   0.0  0
 XIH  CONST_04  N7    C8   N16  C5      0.00   0.0  0
 XIH  CONST_05  N     C3   C5   C6      0.00   0.0  0
 XIH  CONST_06  C8    N16  C5   C6      0.00   0.0  0
 XIH  CONST_07  N16   C8   N7   C6      0.00   0.0  0
 XIH  CONST_08  N     C28  N26  C6      0.00   0.0  0
 XIH  CONST_09  N26   C6   N7   C8    180.00   0.0  0
 XIH  CONST_10  C3    C5   N16  C8    180.00   0.0  0
 XIH  CONST_11  C23   C22  C21  C20     0.00   0.0  0
 XIH  CONST_12  C23   C18  C19  C20     0.00   0.0  0
 XIH  CONST_13  C18   C19  C20  C21     0.00   0.0  0
 XIH  CONST_14  C18   C23  C22  C21     0.00   0.0  0
 XIH  CONST_15  C19   C20  C21  C22     0.00   0.0  0
 XIH  CONST_16  C19   C18  C23  C22     0.00   0.0  0
 XIH  CONST_17  N7    C6   N26  C28   180.00   0.0  0
 XIH  CONST_18  N16   C5   C3   N     180.00   0.0  0
 XIH  CONST_19  N7    C6   C5   C3    180.00   0.0  0
 XIH  CONST_20  N26   C6   C5   C3      0.00   0.0  0
 XIH  CONST_21  N26   C28  N    C3      0.00   0.0  0
 XIH  CONST_22  N16   C5   C6   N7      0.00   0.0  0
 XIH  CONST_23  N26   C6   C5   N16   180.00   0.0  0
 XIH  CONST_24  N9    C8   N16  C5    180.00   0.0  0
 XIH  CONST_25  N9    C8   N7   C6    180.00   0.0  0
 XIH  CONST_26  C27   N26  C6   C5    180.00   0.0  0
 XIH  CONST_27  C     N    C3   C5    180.00   0.0  0
 XIH  CONST_28  O     C3   C5   C6    180.00   0.0  0
 XIH  CONST_30  O29   C28  N26  C6    180.00   0.0  0
 XIH  CONST_33  N9    C8   N16  C17     0.00   0.0  0
 XIH  CONST_34  C20   C19  C18  C17   180.00   0.0  0
 XIH  CONST_35  C22   C23  C18  C17   180.00   0.0  0
 XIH  CONST_36  C24   C23  C22  C21   180.00   0.0  0
 XIH  CONST_37  C19   C18  C23  C24   180.00   0.0  0
 XIH  CONST_38  O     C3   N    C28   180.00   0.0  0
 XIH  CONST_39  N26   C28  N    C     180.00   0.0  0
 XIH  CONST_40  C27   N26  C28  N     180.00   0.0  0
 XIH  CONST_41  O29   C28  N    C3    180.00   0.0  0
 XIH  CONST_42  N16   C5   C3   O       0.00   0.0  0
 XIH  CONST_43  C27   N26  C6   N7      0.00   0.0  0
 XIH  CONST_44  H22   C22  C21  C20   180.00   0.0  0
 XIH  CONST_45  H19   C19  C20  C21   180.00   0.0  0
 XIH  CONST_46  H20   C20  C21  C22   180.00   0.0  0
 XIH  CONST_47  H21   C21  C20  C19   180.00   0.0  0
 XIH  CONST_48  O29   C28  N    C       0.00   0.0  0
 XIH  CONST_49  O     C3   N    C       0.00   0.0  0
 XIH  CONST_50  O29   C28  N26  C27     0.00   0.0  0
 XIH  Var_01    C11   C10  N9   C8   -157.71  30.0  1
 XIH  Var_02    C13   C15  N9   C8    157.67  30.0  1
 XIH  Var_03    N7    C8   N9   C10  -118.63  30.0  2
 XIH  Var_04    C13   C12  C11  C10    53.49  30.0  1
 XIH  Var_05    C12   C11  C10  N9    -55.90  30.0  1
 XIH  Var_06    C18   C17  N16  C5    -55.29  30.0  3
 XIH  Var_07    C19   C18  C17  N16   -51.82  30.0  2
 XIH  Var_08    H271  C27  N26  C6   -178.46  30.0  2
 XIH  Var_09    H1    C    N    C28    -2.79  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
 XIH  chir_01  C13  C15  C12  N14  negativ

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
 XIH  plan-1  C20  0.020
 XIH  plan-1  C21  0.020
 XIH  plan-1  C22  0.020
 XIH  plan-1  C24  0.020
 XIH  plan-1  C18  0.020
 XIH  plan-1  C19  0.020
 XIH  plan-1  C23  0.020
 XIH  plan-1  N25  0.020
 XIH  plan-1  H20  0.020
 XIH  plan-1  H21  0.020
 XIH  plan-1  H22  0.020
 XIH  plan-1  H19  0.020
 XIH  plan-1  C17  0.020
 XIH  plan-2  C5   0.020
 XIH  plan-2  C6   0.020
 XIH  plan-2  C8   0.020
 XIH  plan-2  C28  0.020
 XIH  plan-2  N    0.020
 XIH  plan-2  C3   0.020
 XIH  plan-2  O    0.020
 XIH  plan-2  N7   0.020
 XIH  plan-2  N9   0.020
 XIH  plan-2  N16  0.020
 XIH  plan-2  N26  0.020
 XIH  plan-2  C27  0.020
 XIH  plan-2  O29  0.020
 XIH  plan-2  C17  0.020
 XIH  plan-2  C    0.020

