# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:58:48 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-(9H-purin-6-yl)-2,9-diazaspiro[5.5]undecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CC2(C1)CCNCC2)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
 QNI  QNI  2-(9H-purin-6-yl)-2,9-diazaspiro[5.5]undecane  ligand  40  20  .  2022-07-22  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_QNI
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
 QNI  C12   C  CR15  0   0.115   3.9631  -1.7666   0.0294
 QNI  N3    N  N     0  -0.459   2.8017  -1.5591   0.5764
 QNI  N4    N  NR15  0  -0.646   4.3351  -0.7713  -0.8170
 QNI  C13   C  CR56  0   0.454   3.3353   0.1492  -0.8144
 QNI  N5    N  N     0  -0.452   3.2812   1.2890  -1.5016
 QNI  C     C  CR16  0   0.038   2.1592   1.9401  -1.2557
 QNI  C11   C  CR56  0  -0.009   2.3766  -0.3547   0.0642
 QNI  C1    C  CR6   0   0.527   1.2144   0.4423   0.2412
 QNI  N     N  N     0  -0.494   1.1642   1.5897  -0.4543
 QNI  N1    N  NT    0  -0.475   0.1853   0.1495   1.0510
 QNI  C10   C  CH2   0  -0.287  -1.0156   0.9643   1.1085
 QNI  C5    C  CT    0  -0.099  -2.2263   0.2429   0.5022
 QNI  C4    C  CH2   0  -0.431  -2.3863  -1.1039   1.2279
 QNI  C3    C  CH2   0  -0.435  -1.0960  -1.9162   1.2698
 QNI  C2    C  CH2   0  -0.337   0.0593  -1.0837   1.8088
 QNI  C9    C  CH2   0  -0.424  -2.0367   0.0611  -1.0114
 QNI  C8    C  CH2   0  -0.320  -3.3122  -0.4246  -1.6999
 QNI  N2    N  NH1   0  -0.575  -4.4824   0.3986  -1.4364
 QNI  C7    C  CH2   0  -0.322  -4.6931   0.5916  -0.0099
 QNI  C6    C  CH2   0  -0.421  -3.4637   1.1209   0.7261
 QNI  H12   H  HCR5  0   0.289   4.5922  -2.6255   0.2054
 QNI  H4    H  HNR5  0   0.425   5.1922  -0.7252  -1.3468
 QNI  H     H  HCR6  0   0.246   2.0295   2.8847  -1.7746
 QNI  H101  H  HCH2  0   0.239  -1.2196   1.1810   2.1644
 QNI  H102  H  HCH2  0   0.268  -0.8400   1.9112   0.6048
 QNI  H21C  H  HCH2  0   0.288   0.9884  -1.6432   1.7866
 QNI  H22C  H  HCH2  0   0.235  -0.1379  -0.8150   2.8528
 QNI  H41C  H  HCH2  0   0.223  -2.7055  -0.9025   2.2575
 QNI  H42C  H  HCH2  0   0.238  -3.1816  -1.7032   0.7799
 QNI  H91C  H  HCH2  0   0.222  -1.7447   1.0221  -1.4499
 QNI  H92C  H  HCH2  0   0.228  -1.2215  -0.6339  -1.2302
 QNI  H61C  H  HCH2  0   0.223  -3.6768   1.2021   1.7971
 QNI  H62C  H  HCH2  0   0.221  -3.2518   2.1373   0.3714
 QNI  H31C  H  HCH2  0   0.240  -1.2283  -2.7921   1.9087
 QNI  H32C  H  HCH2  0   0.226  -0.8385  -2.2916   0.2758
 QNI  H81C  H  HCH2  0   0.235  -3.1527  -0.4642  -2.7796
 QNI  H82C  H  HCH2  0   0.216  -3.5381  -1.4503  -1.3902
 QNI  H2    H  HNH1  0   0.335  -4.3400   1.3065  -1.8652
 QNI  H71C  H  HCH2  0   0.235  -5.5313   1.2778   0.1286
 QNI  H72C  H  HCH2  0   0.219  -5.0046  -0.3637   0.4248

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
 QNI  C12  N3    aromatic  1.300  0.020  1.300
 QNI  C12  N4    aromatic  1.358  0.020  1.358
 QNI  N3   C11   aromatic  1.376  0.020  1.376
 QNI  N4   C13   aromatic  1.359  0.020  1.359
 QNI  C13  N5    aromatic  1.332  0.020  1.332
 QNI  C13  C11   aromatic  1.395  0.020  1.395
 QNI  N5   C     aromatic  1.320  0.020  1.320
 QNI  C    N     aromatic  1.325  0.020  1.325
 QNI  C11  C1    aromatic  1.420  0.020  1.420
 QNI  C1   N     aromatic  1.343  0.020  1.343
 QNI  C1   N1    single    1.342  0.020  1.342
 QNI  N1   C10   single    1.452  0.020  1.452
 QNI  N1   C2    single    1.453  0.020  1.453
 QNI  C10  C5    single    1.534  0.020  1.534
 QNI  C5   C4    single    1.538  0.020  1.538
 QNI  C5   C9    single    1.536  0.020  1.536
 QNI  C5   C6    single    1.534  0.020  1.534
 QNI  C4   C3    single    1.525  0.020  1.525
 QNI  C3   C2    single    1.523  0.020  1.523
 QNI  C9   C8    single    1.529  0.020  1.529
 QNI  C8   N2    single    1.455  0.020  1.455
 QNI  N2   C7    single    1.455  0.020  1.455
 QNI  C7   C6    single    1.528  0.020  1.528
 QNI  C12  H12   single    0.930  0.020  1.080
 QNI  N4   H4    single    0.860  0.020  1.020
 QNI  C    H     single    0.930  0.020  1.080
 QNI  C10  H101  single    0.970  0.020  1.090
 QNI  C10  H102  single    0.970  0.020  1.090
 QNI  C2   H21C  single    0.970  0.020  1.090
 QNI  C2   H22C  single    0.970  0.020  1.090
 QNI  C4   H41C  single    0.970  0.020  1.090
 QNI  C4   H42C  single    0.970  0.020  1.090
 QNI  C9   H91C  single    0.970  0.020  1.090
 QNI  C9   H92C  single    0.970  0.020  1.090
 QNI  C6   H61C  single    0.970  0.020  1.090
 QNI  C6   H62C  single    0.970  0.020  1.090
 QNI  C3   H31C  single    0.970  0.020  1.090
 QNI  C3   H32C  single    0.970  0.020  1.090
 QNI  C8   H81C  single    0.970  0.020  1.090
 QNI  C8   H82C  single    0.970  0.020  1.090
 QNI  N2   H2    single    0.890  0.020  1.040
 QNI  C7   H71C  single    0.970  0.020  1.090
 QNI  C7   H72C  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
 QNI  H12   C12  N4    121.68  3.000
 QNI  H12   C12  N3    125.38  3.000
 QNI  N4    C12  N3    112.94  3.000
 QNI  C11   N3   C12   105.00  3.000
 QNI  H4    N4   C13   126.52  3.000
 QNI  H4    N4   C12   126.40  3.000
 QNI  C13   N4   C12   107.07  3.000
 QNI  C11   C13  N5    127.31  3.000
 QNI  C11   C13  N4    105.20  3.000
 QNI  N5    C13  N4    127.48  3.000
 QNI  C     N5   C13   111.13  3.000
 QNI  H     C    N     115.44  3.000
 QNI  H     C    N5    116.21  3.000
 QNI  N     C    N5    128.35  3.000
 QNI  C1    C11  C13   115.99  3.000
 QNI  C1    C11  N3    134.23  3.000
 QNI  C13   C11  N3    109.78  3.000
 QNI  N1    C1   N     118.06  3.000
 QNI  N1    C1   C11   125.47  3.000
 QNI  N     C1   C11   116.46  3.000
 QNI  C1    N    C     120.75  3.000
 QNI  C2    N1   C10   112.57  3.000
 QNI  C2    N1   C1    124.51  3.000
 QNI  C10   N1   C1    122.39  3.000
 QNI  H102  C10  H101  107.70  3.000
 QNI  H102  C10  C5    110.73  3.000
 QNI  H101  C10  C5    109.06  3.000
 QNI  H102  C10  N1    109.68  3.000
 QNI  H101  C10  N1    107.62  3.000
 QNI  C5    C10  N1    111.91  3.000
 QNI  C6    C5   C9    108.13  3.000
 QNI  C6    C5   C4    110.39  3.000
 QNI  C9    C5   C4    111.97  3.000
 QNI  C6    C5   C10   108.05  3.000
 QNI  C9    C5   C10   110.34  3.000
 QNI  C4    C5   C10   107.90  3.000
 QNI  H42C  C4   H41C  105.90  3.000
 QNI  H42C  C4   C3    109.58  3.000
 QNI  H41C  C4   C3    108.56  3.000
 QNI  H42C  C4   C5    111.27  3.000
 QNI  H41C  C4   C5    108.20  3.000
 QNI  C3    C4   C5    113.03  3.000
 QNI  H32C  C3   H31C  106.55  3.000
 QNI  H32C  C3   C2    109.32  3.000
 QNI  H31C  C3   C2    108.86  3.000
 QNI  H32C  C3   C4    110.93  3.000
 QNI  H31C  C3   C4    109.92  3.000
 QNI  C2    C3   C4    111.13  3.000
 QNI  H22C  C2   H21C  107.47  3.000
 QNI  H22C  C2   C3    109.56  3.000
 QNI  H21C  C2   C3    111.14  3.000
 QNI  H22C  C2   N1    107.72  3.000
 QNI  H21C  C2   N1    110.66  3.000
 QNI  C3    C2   N1    110.19  3.000
 QNI  H92C  C9   H91C  106.18  3.000
 QNI  H92C  C9   C8    109.27  3.000
 QNI  H91C  C9   C8    108.71  3.000
 QNI  H92C  C9   C5    111.37  3.000
 QNI  H91C  C9   C5    108.86  3.000
 QNI  C8    C9   C5    112.23  3.000
 QNI  H82C  C8   H81C  106.01  3.000
 QNI  H82C  C8   N2    108.23  3.000
 QNI  H81C  C8   N2    108.49  3.000
 QNI  H82C  C8   C9    110.02  3.000
 QNI  H81C  C8   C9    109.56  3.000
 QNI  N2    C8   C9    114.19  3.000
 QNI  H2    N2   C7    108.43  3.000
 QNI  H2    N2   C8    108.48  3.000
 QNI  C7    N2   C8    111.66  3.000
 QNI  H72C  C7   H71C  106.23  3.000
 QNI  H72C  C7   C6    109.88  3.000
 QNI  H71C  C7   C6    109.80  3.000
 QNI  H72C  C7   N2    108.35  3.000
 QNI  H71C  C7   N2    108.59  3.000
 QNI  C6    C7   N2    113.70  3.000
 QNI  H62C  C6   H61C  106.56  3.000
 QNI  H62C  C6   C7    108.70  3.000
 QNI  H61C  C6   C7    109.90  3.000
 QNI  H62C  C6   C5    109.11  3.000
 QNI  H61C  C6   C5    110.01  3.000
 QNI  C7    C6   C5    112.37  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
 QNI  CONST_01  C13  C11  N3   C12     0.00   0.0  0
 QNI  CONST_02  C1   C11  N3   C12   180.00   0.0  0
 QNI  CONST_03  N5   C13  N4   C12   180.00   0.0  0
 QNI  CONST_04  C11  C13  N4   C12     0.00   0.0  0
 QNI  CONST_05  C13  N4   C12  N3      0.00   0.0  0
 QNI  CONST_06  N4   C13  C11  N3      0.00   0.0  0
 QNI  CONST_07  N5   C13  C11  N3    180.00   0.0  0
 QNI  CONST_08  N    C1   C11  N3    180.00   0.0  0
 QNI  CONST_09  C11  N3   C12  N4      0.00   0.0  0
 QNI  CONST_10  C    N5   C13  N4    180.00   0.0  0
 QNI  CONST_11  C1   C11  C13  N4    180.00   0.0  0
 QNI  CONST_12  N    C    N5   C13     0.00   0.0  0
 QNI  CONST_13  N    C1   C11  C13     0.00   0.0  0
 QNI  CONST_14  C1   C11  C13  N5      0.00   0.0  0
 QNI  CONST_15  C1   N    C    N5      0.00   0.0  0
 QNI  CONST_16  C11  C13  N5   C       0.00   0.0  0
 QNI  CONST_17  C11  C1   N    C       0.00   0.0  0
 QNI  CONST_18  N1   C1   C11  N3      0.00   0.0  0
 QNI  CONST_19  N1   C1   C11  C13   180.00   0.0  0
 QNI  CONST_20  N1   C1   N    C     180.00   0.0  0
 QNI  CONST_21  H4   N4   C12  N3    180.00   0.0  0
 QNI  CONST_22  H12  C12  N4   C13   180.00   0.0  0
 QNI  CONST_23  H    C    N5   C13   180.00   0.0  0
 QNI  Var_01    C10  N1   C1   C11  -175.41  30.0  2
 QNI  Var_02    C5   C10  N1   C1    110.12  30.0  1
 QNI  Var_03    C3   C2   N1   C1   -112.19  30.0  1
 QNI  Var_04    C4   C5   C10  N1     55.42  30.0  3
 QNI  Var_05    C4   C3   C2   N1    -53.77  30.0  1
 QNI  Var_06    C3   C4   C5   C10   -51.24  30.0  3
 QNI  Var_07    C8   C9   C5   C10  -169.84  30.0  1
 QNI  Var_08    C7   C6   C5   C10   171.95  30.0  1
 QNI  Var_09    C2   C3   C4   C5     51.74  30.0  1
 QNI  Var_10    N2   C8   C9   C5     53.71  30.0  1
 QNI  Var_11    N2   C7   C6   C5    -54.74  30.0  1
 QNI  Var_12    C7   N2   C8   C9    -52.66  30.0  1
 QNI  Var_13    C6   C7   N2   C8     52.99  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
 QNI  plan-1  C12  0.020
 QNI  plan-1  N3   0.020
 QNI  plan-1  N4   0.020
 QNI  plan-1  C13  0.020
 QNI  plan-1  N5   0.020
 QNI  plan-1  C    0.020
 QNI  plan-1  C11  0.020
 QNI  plan-1  C1   0.020
 QNI  plan-1  N    0.020
 QNI  plan-1  N1   0.020
 QNI  plan-1  H12  0.020
 QNI  plan-1  H4   0.020
 QNI  plan-1  H    0.020

