# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 09:19:08 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 9-(9H-purin-6-yl)-2,9-diazaspiro[5.5]undecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCC2(C1)CCN(CC2)c3ncnc4[nH]cnc34
#
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
 15I  15I  9-(9H-purin-6-yl)-2,9-diazaspiro[5.5]undecane  ligand  40  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_15I
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
 15I  C12   C  CR15  0   0.115   3.8895  -2.0139   0.4567
 15I  N3    N  N     0  -0.459   2.6978  -1.5836   0.7498
 15I  N4    N  NR15  0  -0.646   4.5627  -1.1813  -0.3790
 15I  C13   C  CR56  0   0.455   3.7406  -0.1324  -0.6447
 15I  N5    N  N     0  -0.450   3.9963   0.9246  -1.4141
 15I  C     C  CR16  0   0.041   2.9713   1.7557  -1.4387
 15I  C11   C  CR56  0  -0.011   2.5713  -0.3949   0.0685
 15I  C1    C  CR6   0   0.520   1.5443   0.5799  -0.0396
 15I  N     N  N     0  -0.497   1.8055   1.6416  -0.8184
 15I  N1    N  NT    0  -0.463   0.3594   0.5347   0.5892
 15I  C10   C  CH2   0  -0.329  -0.6799   1.5227   0.3473
 15I  C9    C  CH2   0  -0.410  -1.8072   0.9296  -0.4901
 15I  C4    C  CT    0  -0.104  -2.3971  -0.3530   0.1142
 15I  C3    C  CH2   0  -0.412  -1.2477  -1.3001   0.4781
 15I  C2    C  CH2   0  -0.352  -0.1461  -0.6317   1.2933
 15I  C8    C  CH2   0  -0.267  -3.2436  -0.0431   1.3576
 15I  N2    N  NH1   0  -0.593  -4.3990   0.7625   1.0120
 15I  C7    C  CH2   0  -0.290  -5.3043   0.0531   0.1265
 15I  C6    C  CH2   0  -0.437  -4.5921  -0.2702  -1.1782
 15I  C5    C  CH2   0  -0.416  -3.3106  -1.0511  -0.9035
 15I  H12   H  HCR5  0   0.290   4.3293  -2.9300   0.8193
 15I  H4    H  HNR5  0   0.425   5.4968  -1.3174  -0.7336
 15I  H     H  HCR6  0   0.247   3.0920   2.6486  -2.0436
 15I  H101  H  HCH2  0   0.241  -1.0561   1.8519   1.3202
 15I  H102  H  HCH2  0   0.272  -0.2539   2.3907  -0.1457
 15I  H21C  H  HCH2  0   0.290   0.6573  -1.3329   1.4939
 15I  H22C  H  HCH2  0   0.242  -0.5292  -0.2981   2.2628
 15I  H91C  H  HCH2  0   0.239  -2.5849   1.6853  -0.6108
 15I  H92C  H  HCH2  0   0.225  -1.4182   0.7101  -1.4905
 15I  H31C  H  HCH2  0   0.233  -1.6288  -2.1622   1.0347
 15I  H32C  H  HCH2  0   0.230  -0.8054  -1.6960  -0.4431
 15I  H81C  H  HCH2  0   0.193  -3.5301  -1.0049   1.8193
 15I  H82C  H  HCH2  0   0.229  -2.6639   0.4996   2.1079
 15I  H51C  H  HCH2  0   0.226  -2.7582  -1.2264  -1.8321
 15I  H52C  H  HCH2  0   0.216  -3.5754  -2.0401  -0.5099
 15I  H2    H  HNH1  0   0.351  -4.8857   1.0287   1.8575
 15I  H71C  H  HCH2  0   0.181  -5.6705  -0.8880   0.5717
 15I  H72C  H  HCH2  0   0.228  -6.1804   0.6776  -0.0613
 15I  H61C  H  HCH2  0   0.229  -5.2536  -0.8506  -1.8253
 15I  H62C  H  HCH2  0   0.218  -4.3644   0.6585  -1.7085

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
 15I  C12  N3    aromatic  1.300  0.020  1.300
 15I  C12  N4    aromatic  1.358  0.020  1.358
 15I  N3   C11   aromatic  1.376  0.020  1.376
 15I  N4   C13   aromatic  1.359  0.020  1.359
 15I  C13  N5    aromatic  1.332  0.020  1.332
 15I  C13  C11   aromatic  1.395  0.020  1.395
 15I  N5   C     aromatic  1.320  0.020  1.320
 15I  C    N     aromatic  1.326  0.020  1.326
 15I  C11  C1    aromatic  1.420  0.020  1.420
 15I  C1   N     aromatic  1.342  0.020  1.342
 15I  C1   N1    single    1.342  0.020  1.342
 15I  N1   C10   single    1.454  0.020  1.454
 15I  N1   C2    single    1.453  0.020  1.453
 15I  C10  C9    single    1.524  0.020  1.524
 15I  C9   C4    single    1.536  0.020  1.536
 15I  C4   C3    single    1.533  0.020  1.533
 15I  C4   C8    single    1.536  0.020  1.536
 15I  C4   C5    single    1.535  0.020  1.535
 15I  C3   C2    single    1.525  0.020  1.525
 15I  C8   N2    single    1.450  0.020  1.450
 15I  N2   C7    single    1.452  0.020  1.452
 15I  C7   C6    single    1.521  0.020  1.521
 15I  C6   C5    single    1.526  0.020  1.526
 15I  C12  H12   single    0.930  0.020  1.080
 15I  N4   H4    single    0.860  0.020  1.020
 15I  C    H     single    0.930  0.020  1.080
 15I  C10  H101  single    0.970  0.020  1.090
 15I  C10  H102  single    0.970  0.020  1.090
 15I  C2   H21C  single    0.970  0.020  1.090
 15I  C2   H22C  single    0.970  0.020  1.090
 15I  C9   H91C  single    0.970  0.020  1.090
 15I  C9   H92C  single    0.970  0.020  1.090
 15I  C3   H31C  single    0.970  0.020  1.090
 15I  C3   H32C  single    0.970  0.020  1.090
 15I  C8   H81C  single    0.970  0.020  1.090
 15I  C8   H82C  single    0.970  0.020  1.090
 15I  C5   H51C  single    0.970  0.020  1.090
 15I  C5   H52C  single    0.970  0.020  1.090
 15I  N2   H2    single    0.890  0.020  1.040
 15I  C7   H71C  single    0.970  0.020  1.090
 15I  C7   H72C  single    0.970  0.020  1.090
 15I  C6   H61C  single    0.970  0.020  1.090
 15I  C6   H62C  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
 15I  H12   C12  N4    121.68  3.000
 15I  H12   C12  N3    125.36  3.000
 15I  N4    C12  N3    112.96  3.000
 15I  C11   N3   C12   104.98  3.000
 15I  H4    N4   C13   126.57  3.000
 15I  H4    N4   C12   126.36  3.000
 15I  C13   N4   C12   107.08  3.000
 15I  C11   C13  N5    127.28  3.000
 15I  C11   C13  N4    105.18  3.000
 15I  N5    C13  N4    127.54  3.000
 15I  C     N5   C13   111.18  3.000
 15I  H     C    N     115.43  3.000
 15I  H     C    N5    116.24  3.000
 15I  N     C    N5    128.32  3.000
 15I  C1    C11  C13   115.99  3.000
 15I  C1    C11  N3    134.20  3.000
 15I  C13   C11  N3    109.81  3.000
 15I  N1    C1   N     118.05  3.000
 15I  N1    C1   C11   125.43  3.000
 15I  N     C1   C11   116.51  3.000
 15I  C1    N    C     120.72  3.000
 15I  C2    N1   C10   112.17  3.000
 15I  C2    N1   C1    124.13  3.000
 15I  C10   N1   C1    122.01  3.000
 15I  H102  C10  H101  107.36  3.000
 15I  H102  C10  C9    110.60  3.000
 15I  H101  C10  C9    110.57  3.000
 15I  H102  C10  N1    109.78  3.000
 15I  H101  C10  N1    107.60  3.000
 15I  C9    C10  N1    110.82  3.000
 15I  H92C  C9   H91C  106.90  3.000
 15I  H92C  C9   C4    109.17  3.000
 15I  H91C  C9   C4    110.38  3.000
 15I  H92C  C9   C10   108.49  3.000
 15I  H91C  C9   C10   108.56  3.000
 15I  C4    C9   C10   113.13  3.000
 15I  C5    C4   C8    107.48  3.000
 15I  C5    C4   C3    108.82  3.000
 15I  C8    C4   C3    110.23  3.000
 15I  C5    C4   C9    110.33  3.000
 15I  C8    C4   C9    111.21  3.000
 15I  C3    C4   C9    108.75  3.000
 15I  H32C  C3   H31C  106.46  3.000
 15I  H32C  C3   C2    108.43  3.000
 15I  H31C  C3   C2    108.97  3.000
 15I  H32C  C3   C4    109.04  3.000
 15I  H31C  C3   C4    110.25  3.000
 15I  C2    C3   C4    113.44  3.000
 15I  H22C  C2   H21C  107.00  3.000
 15I  H22C  C2   C3    110.75  3.000
 15I  H21C  C2   C3    110.51  3.000
 15I  H22C  C2   N1    107.84  3.000
 15I  H21C  C2   N1    110.54  3.000
 15I  C3    C2   N1    110.13  3.000
 15I  H82C  C8   H81C  106.44  3.000
 15I  H82C  C8   N2    108.09  3.000
 15I  H81C  C8   N2    112.13  3.000
 15I  H82C  C8   C4    111.33  3.000
 15I  H81C  C8   C4    107.79  3.000
 15I  N2    C8   C4    111.00  3.000
 15I  H2    N2   C7    109.78  3.000
 15I  H2    N2   C8    109.30  3.000
 15I  C7    N2   C8    111.76  3.000
 15I  H72C  C7   H71C  106.90  3.000
 15I  H72C  C7   C6    110.47  3.000
 15I  H71C  C7   C6    108.67  3.000
 15I  H72C  C7   N2    109.02  3.000
 15I  H71C  C7   N2    112.18  3.000
 15I  C6    C7   N2    109.58  3.000
 15I  H62C  C6   H61C  106.86  3.000
 15I  H62C  C6   C5    110.32  3.000
 15I  H61C  C6   C5    110.08  3.000
 15I  H62C  C6   C7    109.44  3.000
 15I  H61C  C6   C7    109.73  3.000
 15I  C5    C6   C7    110.35  3.000
 15I  H52C  C5   H51C  106.37  3.000
 15I  H52C  C5   C6    108.87  3.000
 15I  H51C  C5   C6    110.68  3.000
 15I  H52C  C5   C4    108.40  3.000
 15I  H51C  C5   C4    109.56  3.000
 15I  C6    C5   C4    112.73  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
 15I  CONST_01  C13  C11  N3   C12     0.00   0.0  0
 15I  CONST_02  C1   C11  N3   C12   180.00   0.0  0
 15I  CONST_03  N5   C13  N4   C12   180.00   0.0  0
 15I  CONST_04  C11  C13  N4   C12     0.00   0.0  0
 15I  CONST_05  C13  N4   C12  N3      0.00   0.0  0
 15I  CONST_06  N4   C13  C11  N3      0.00   0.0  0
 15I  CONST_07  N5   C13  C11  N3    180.00   0.0  0
 15I  CONST_08  N    C1   C11  N3    180.00   0.0  0
 15I  CONST_09  C11  N3   C12  N4      0.00   0.0  0
 15I  CONST_10  C    N5   C13  N4    180.00   0.0  0
 15I  CONST_11  C1   C11  C13  N4    180.00   0.0  0
 15I  CONST_12  N    C    N5   C13     0.00   0.0  0
 15I  CONST_13  N    C1   C11  C13     0.00   0.0  0
 15I  CONST_14  C1   C11  C13  N5      0.00   0.0  0
 15I  CONST_15  C1   N    C    N5      0.00   0.0  0
 15I  CONST_16  C11  C13  N5   C       0.00   0.0  0
 15I  CONST_17  C11  C1   N    C       0.00   0.0  0
 15I  CONST_18  N1   C1   C11  N3      0.00   0.0  0
 15I  CONST_19  N1   C1   C11  C13   180.00   0.0  0
 15I  CONST_20  N1   C1   N    C     180.00   0.0  0
 15I  CONST_21  H4   N4   C12  N3    180.00   0.0  0
 15I  CONST_22  H12  C12  N4   C13   180.00   0.0  0
 15I  CONST_23  H    C    N5   C13   180.00   0.0  0
 15I  Var_01    C10  N1   C1   C11  -175.27  30.0  2
 15I  Var_02    C9   C10  N1   C1    106.12  30.0  1
 15I  Var_03    C3   C2   N1   C1   -105.60  30.0  1
 15I  Var_04    C4   C9   C10  N1     54.59  30.0  1
 15I  Var_05    C4   C3   C2   N1    -55.58  30.0  1
 15I  Var_06    C3   C4   C9   C10   -49.06  30.0  3
 15I  Var_07    C2   C3   C4   C9     49.77  30.0  3
 15I  Var_08    N2   C8   C4   C9     64.02  30.0  1
 15I  Var_09    C6   C5   C4   C9    -69.00  30.0  1
 15I  Var_10    C7   N2   C8   C4     63.89  30.0  1
 15I  Var_11    C7   C6   C5   C4    -52.96  30.0  1
 15I  Var_12    C6   C7   N2   C8    -61.99  30.0  1
 15I  Var_13    C5   C6   C7   N2     55.52  30.0  1

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
 15I  plan-1  C12  0.020
 15I  plan-1  N3   0.020
 15I  plan-1  N4   0.020
 15I  plan-1  C13  0.020
 15I  plan-1  N5   0.020
 15I  plan-1  C    0.020
 15I  plan-1  C11  0.020
 15I  plan-1  C1   0.020
 15I  plan-1  N    0.020
 15I  plan-1  N1   0.020
 15I  plan-1  H12  0.020
 15I  plan-1  H4   0.020
 15I  plan-1  H    0.020

