# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:35:07 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 9-(9H-purin-6-yl)-1,9-diazaspiro[5.5]undecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC2(CCN(CC2)c3ncnc4[nH]cnc34)NC1
#
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
 SIJ  SIJ  9-(9H-purin-6-yl)-1,9-diazaspiro[5.5]undecane  ligand  40  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SIJ
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
 SIJ  C12   C  CR15  0   0.114   3.8329  -2.0353   0.5091
 SIJ  N3    N  N     0  -0.458   2.6548  -1.5776   0.8151
 SIJ  N4    N  NR15  0  -0.646   4.5051  -1.2325  -0.3562
 SIJ  C13   C  CR56  0   0.455   3.6973  -0.1739  -0.6275
 SIJ  N5    N  N     0  -0.450   3.9575   0.8624  -1.4231
 SIJ  C     C  CR16  0   0.040   2.9468   1.7111  -1.4458
 SIJ  C11   C  CR56  0  -0.009   2.5365  -0.4010   0.1115
 SIJ  C1    C  CR6   0   0.516   1.5234   0.5876  -0.0008
 SIJ  N     N  N     0  -0.496   1.7897   1.6293  -0.8045
 SIJ  N1    N  NT    0  -0.465   0.3477   0.5756   0.6490
 SIJ  C10   C  CH2   0  -0.310  -0.6893   1.5555   0.3623
 SIJ  C9    C  CH2   0  -0.428  -1.7633   0.9479  -0.5303
 SIJ  C4    C  CT    0   0.064  -2.3827  -0.3171   0.0871
 SIJ  C3    C  CH2   0  -0.431  -1.2434  -1.2657   0.4757
 SIJ  C2    C  CH2   0  -0.335  -0.1806  -0.5918   1.3362
 SIJ  N2    N  NH1   0  -0.588  -3.1016   0.0418   1.3130
 SIJ  C8    C  CH2   0  -0.320  -4.3562   0.7485   1.1009
 SIJ  C7    C  CH2   0  -0.436  -5.3009   0.0529   0.1258
 SIJ  C6    C  CH2   0  -0.445  -4.5845  -0.2371  -1.1884
 SIJ  C5    C  CH2   0  -0.407  -3.2998  -1.0178  -0.9276
 SIJ  H12   H  HCR5  0   0.290   4.2635  -2.9512   0.8831
 SIJ  H4    H  HNR5  0   0.424   5.4313  -1.3911  -0.7219
 SIJ  H     H  HCR6  0   0.247   3.0722   2.5902  -2.0697
 SIJ  H101  H  HCH2  0   0.242  -1.1291   1.8592   1.3145
 SIJ  H102  H  HCH2  0   0.265  -0.2494   2.4328  -0.1009
 SIJ  H21C  H  HCH2  0   0.283   0.6184  -1.2862   1.5734
 SIJ  H22C  H  HCH2  0   0.243  -0.6212  -0.2567   2.2781
 SIJ  H91C  H  HCH2  0   0.240  -2.5242   1.7061  -0.7276
 SIJ  H92C  H  HCH2  0   0.231  -1.3243   0.6914  -1.4995
 SIJ  H31C  H  HCH2  0   0.236  -1.6470  -2.1304   1.0135
 SIJ  H32C  H  HCH2  0   0.232  -0.7756  -1.6550  -0.4345
 SIJ  H2    H  HNH1  0   0.336  -3.2986  -0.8099   1.8271
 SIJ  H51C  H  HCH2  0   0.221  -2.7551  -1.1906  -1.8609
 SIJ  H52C  H  HCH2  0   0.214  -3.5596  -2.0074  -0.5323
 SIJ  H81C  H  HCH2  0   0.234  -4.8370   0.8747   2.0735
 SIJ  H82C  H  HCH2  0   0.216  -4.1416   1.7588   0.7389
 SIJ  H71C  H  HCH2  0   0.210  -5.6456  -0.8882   0.5682
 SIJ  H72C  H  HCH2  0   0.223  -6.1889   0.6683  -0.0407
 SIJ  H61C  H  HCH2  0   0.231  -5.2329  -0.8010  -1.8632
 SIJ  H62C  H  HCH2  0   0.216  -4.3553   0.7049  -1.6974

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
 SIJ  C12  N3    aromatic  1.300  0.020  1.300
 SIJ  C12  N4    aromatic  1.358  0.020  1.358
 SIJ  N3   C11   aromatic  1.376  0.020  1.376
 SIJ  N4   C13   aromatic  1.359  0.020  1.359
 SIJ  C13  N5    aromatic  1.332  0.020  1.332
 SIJ  C13  C11   aromatic  1.395  0.020  1.395
 SIJ  N5   C     aromatic  1.320  0.020  1.320
 SIJ  C    N     aromatic  1.326  0.020  1.326
 SIJ  C11  C1    aromatic  1.420  0.020  1.420
 SIJ  C1   N     aromatic  1.342  0.020  1.342
 SIJ  C1   N1    single    1.343  0.020  1.343
 SIJ  N1   C10   single    1.455  0.020  1.455
 SIJ  N1   C2    single    1.454  0.020  1.454
 SIJ  C10  C9    single    1.523  0.020  1.523
 SIJ  C9   C4    single    1.538  0.020  1.538
 SIJ  C4   C3    single    1.533  0.020  1.533
 SIJ  C4   N2    single    1.466  0.020  1.466
 SIJ  C4   C5    single    1.537  0.020  1.537
 SIJ  C3   C2    single    1.525  0.020  1.525
 SIJ  N2   C8    single    1.455  0.020  1.455
 SIJ  C8   C7    single    1.526  0.020  1.526
 SIJ  C7   C6    single    1.525  0.020  1.525
 SIJ  C6   C5    single    1.526  0.020  1.526
 SIJ  C12  H12   single    0.930  0.020  1.080
 SIJ  N4   H4    single    0.860  0.020  1.020
 SIJ  C    H     single    0.930  0.020  1.080
 SIJ  C10  H101  single    0.970  0.020  1.090
 SIJ  C10  H102  single    0.970  0.020  1.090
 SIJ  C2   H21C  single    0.970  0.020  1.090
 SIJ  C2   H22C  single    0.970  0.020  1.090
 SIJ  C9   H91C  single    0.970  0.020  1.090
 SIJ  C9   H92C  single    0.970  0.020  1.090
 SIJ  C3   H31C  single    0.970  0.020  1.090
 SIJ  C3   H32C  single    0.970  0.020  1.090
 SIJ  N2   H2    single    0.890  0.020  1.040
 SIJ  C5   H51C  single    0.970  0.020  1.090
 SIJ  C5   H52C  single    0.970  0.020  1.090
 SIJ  C8   H81C  single    0.970  0.020  1.090
 SIJ  C8   H82C  single    0.970  0.020  1.090
 SIJ  C7   H71C  single    0.970  0.020  1.090
 SIJ  C7   H72C  single    0.970  0.020  1.090
 SIJ  C6   H61C  single    0.970  0.020  1.090
 SIJ  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
 SIJ  H12   C12  N4    121.67  3.000
 SIJ  H12   C12  N3    125.36  3.000
 SIJ  N4    C12  N3    112.97  3.000
 SIJ  C11   N3   C12   104.98  3.000
 SIJ  H4    N4   C13   126.59  3.000
 SIJ  H4    N4   C12   126.34  3.000
 SIJ  C13   N4   C12   107.06  3.000
 SIJ  C11   C13  N5    127.28  3.000
 SIJ  C11   C13  N4    105.20  3.000
 SIJ  N5    C13  N4    127.52  3.000
 SIJ  C     N5   C13   111.16  3.000
 SIJ  H     C    N     115.40  3.000
 SIJ  H     C    N5    116.25  3.000
 SIJ  N     C    N5    128.35  3.000
 SIJ  C1    C11  C13   116.01  3.000
 SIJ  C1    C11  N3    134.20  3.000
 SIJ  C13   C11  N3    109.79  3.000
 SIJ  N1    C1   N     118.04  3.000
 SIJ  N1    C1   C11   125.45  3.000
 SIJ  N     C1   C11   116.50  3.000
 SIJ  C1    N    C     120.71  3.000
 SIJ  C2    N1   C10   112.01  3.000
 SIJ  C2    N1   C1    123.62  3.000
 SIJ  C10   N1   C1    121.49  3.000
 SIJ  H102  C10  H101  108.09  3.000
 SIJ  H102  C10  C9    111.00  3.000
 SIJ  H101  C10  C9    109.76  3.000
 SIJ  H102  C10  N1    109.85  3.000
 SIJ  H101  C10  N1    107.60  3.000
 SIJ  C9    C10  N1    110.45  3.000
 SIJ  H92C  C9   H91C  106.39  3.000
 SIJ  H92C  C9   C4    108.92  3.000
 SIJ  H91C  C9   C4    111.28  3.000
 SIJ  H92C  C9   C10   109.25  3.000
 SIJ  H91C  C9   C10   108.67  3.000
 SIJ  C4    C9   C10   112.15  3.000
 SIJ  C5    C4   N2    111.79  3.000
 SIJ  C5    C4   C3    109.20  3.000
 SIJ  N2    C4   C3    107.70  3.000
 SIJ  C5    C4   C9    110.51  3.000
 SIJ  N2    C4   C9    109.38  3.000
 SIJ  C3    C4   C9    108.15  3.000
 SIJ  H32C  C3   H31C  106.55  3.000
 SIJ  H32C  C3   C2    109.18  3.000
 SIJ  H31C  C3   C2    109.19  3.000
 SIJ  H32C  C3   C4    109.08  3.000
 SIJ  H31C  C3   C4    109.83  3.000
 SIJ  C2    C3   C4    112.82  3.000
 SIJ  H22C  C2   H21C  107.75  3.000
 SIJ  H22C  C2   C3    109.94  3.000
 SIJ  H21C  C2   C3    110.73  3.000
 SIJ  H22C  C2   N1    107.92  3.000
 SIJ  H21C  C2   N1    110.47  3.000
 SIJ  C3    C2   N1    109.97  3.000
 SIJ  H2    N2   C8    108.31  3.000
 SIJ  H2    N2   C4    108.28  3.000
 SIJ  C8    N2   C4    114.82  3.000
 SIJ  H82C  C8   H81C  105.91  3.000
 SIJ  H82C  C8   C7    109.32  3.000
 SIJ  H81C  C8   C7    110.44  3.000
 SIJ  H82C  C8   N2    109.11  3.000
 SIJ  H81C  C8   N2    107.81  3.000
 SIJ  C7    C8   N2    113.93  3.000
 SIJ  H72C  C7   H71C  106.83  3.000
 SIJ  H72C  C7   C6    110.95  3.000
 SIJ  H71C  C7   C6    109.42  3.000
 SIJ  H72C  C7   C8    110.11  3.000
 SIJ  H71C  C7   C8    109.17  3.000
 SIJ  C6    C7   C8    110.29  3.000
 SIJ  H62C  C6   H61C  106.33  3.000
 SIJ  H62C  C6   C5    110.09  3.000
 SIJ  H61C  C6   C5    109.95  3.000
 SIJ  H62C  C6   C7    109.59  3.000
 SIJ  H61C  C6   C7    110.59  3.000
 SIJ  C5    C6   C7    110.22  3.000
 SIJ  H52C  C5   H51C  106.43  3.000
 SIJ  H52C  C5   C6    108.90  3.000
 SIJ  H51C  C5   C6    110.74  3.000
 SIJ  H52C  C5   C4    108.35  3.000
 SIJ  H51C  C5   C4    109.75  3.000
 SIJ  C6    C5   C4    112.46  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
 SIJ  CONST_01  C13  C11  N3   C12     0.00   0.0  0
 SIJ  CONST_02  C1   C11  N3   C12   180.00   0.0  0
 SIJ  CONST_03  N5   C13  N4   C12   180.00   0.0  0
 SIJ  CONST_04  C11  C13  N4   C12     0.00   0.0  0
 SIJ  CONST_05  C13  N4   C12  N3      0.00   0.0  0
 SIJ  CONST_06  N4   C13  C11  N3      0.00   0.0  0
 SIJ  CONST_07  N5   C13  C11  N3    180.00   0.0  0
 SIJ  CONST_08  N    C1   C11  N3    180.00   0.0  0
 SIJ  CONST_09  C11  N3   C12  N4      0.00   0.0  0
 SIJ  CONST_10  C    N5   C13  N4    180.00   0.0  0
 SIJ  CONST_11  C1   C11  C13  N4    180.00   0.0  0
 SIJ  CONST_12  N    C    N5   C13     0.00   0.0  0
 SIJ  CONST_13  N    C1   C11  C13     0.00   0.0  0
 SIJ  CONST_14  C1   C11  C13  N5      0.00   0.0  0
 SIJ  CONST_15  C1   N    C    N5      0.00   0.0  0
 SIJ  CONST_16  C11  C13  N5   C       0.00   0.0  0
 SIJ  CONST_17  C11  C1   N    C       0.00   0.0  0
 SIJ  CONST_18  N1   C1   C11  N3      0.00   0.0  0
 SIJ  CONST_19  N1   C1   C11  C13   180.00   0.0  0
 SIJ  CONST_20  N1   C1   N    C     180.00   0.0  0
 SIJ  CONST_21  H4   N4   C12  N3    180.00   0.0  0
 SIJ  CONST_22  H12  C12  N4   C13   180.00   0.0  0
 SIJ  CONST_23  H    C    N5   C13   180.00   0.0  0
 SIJ  Var_01    C10  N1   C1   C11  -173.24  30.0  2
 SIJ  Var_02    C9   C10  N1   C1    101.17  30.0  1
 SIJ  Var_03    C3   C2   N1   C1   -101.20  30.0  1
 SIJ  Var_04    C4   C9   C10  N1     56.61  30.0  1
 SIJ  Var_05    C4   C3   C2   N1    -56.42  30.0  1
 SIJ  Var_06    C3   C4   C9   C10   -51.88  30.0  3
 SIJ  Var_07    C2   C3   C4   C9     52.05  30.0  3
 SIJ  Var_08    C8   N2   C4   C9     73.03  30.0  1
 SIJ  Var_09    C6   C5   C4   C9    -70.83  30.0  1
 SIJ  Var_10    C7   C8   N2   C4     51.82  30.0  1
 SIJ  Var_11    C7   C6   C5   C4    -54.18  30.0  1
 SIJ  Var_12    C6   C7   C8   N2    -53.29  30.0  1
 SIJ  Var_13    C5   C6   C7   C8     54.01  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
 SIJ  plan-1  C12  0.020
 SIJ  plan-1  N3   0.020
 SIJ  plan-1  N4   0.020
 SIJ  plan-1  C13  0.020
 SIJ  plan-1  N5   0.020
 SIJ  plan-1  C    0.020
 SIJ  plan-1  C11  0.020
 SIJ  plan-1  C1   0.020
 SIJ  plan-1  N    0.020
 SIJ  plan-1  N1   0.020
 SIJ  plan-1  H12  0.020
 SIJ  plan-1  H4   0.020
 SIJ  plan-1  H    0.020

