# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 14:17:13 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (5R)-1-methyl-7-[5-(propan-2-yloxy)pyridin-3-yl]-1,7-diazaspiro[4.4]nonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1cncc(c1)N2CC[C@]3(CCCN3C)C2
#
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
 TII  TII  (5R)-1-methyl-7-[5-(propan-2-yloxy)pyridin-3-yl]-1,7-diazaspiro[4.4]nonane  ligand  45  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_TII
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
 TII  C17   C  CH3   0  -0.534  -4.0396   0.6882   1.8896
 TII  N16   N  NT    0  -0.447  -3.5863   0.9930   0.5583
 TII  C18   C  CH2   0  -0.268  -4.6173   1.4281  -0.3598
 TII  C19   C  CH2   0  -0.452  -3.8637   1.5220  -1.6741
 TII  C20   C  CH2   0  -0.476  -2.9791   0.2781  -1.6200
 TII  C15   C  CT    0   0.138  -2.7245   0.0289  -0.1126
 TII  C1    C  CH2   0  -0.261  -1.2520   0.2441   0.2533
 TII  C14   C  CH2   0  -0.488  -2.9032  -1.4612   0.2256
 TII  C13   C  CH2   0  -0.282  -1.6116  -2.0749  -0.2933
 TII  N2    N  NT    0  -0.527  -0.6343  -1.0189  -0.0819
 TII  C3    C  CR6   0   0.363   0.7012  -1.2005  -0.2175
 TII  C12   C  CR16  0  -0.432   1.6151  -0.1824   0.1050
 TII  C7    C  CR6   0   0.352   2.9725  -0.4114  -0.0576
 TII  O8    O  O2    0  -0.483   3.9476   0.4662   0.2301
 TII  C9    C  CH1   0  -0.002   3.6389   1.8075   0.6239
 TII  C11   C  CH3   0  -0.665   4.8955   2.3546   1.2710
 TII  C10   C  CH3   0  -0.680   3.2078   2.6429  -0.5699
 TII  C6    C  CR16  0  -0.208   3.3920  -1.6581  -0.5355
 TII  N5    N  N     0  -0.367   2.5343  -2.6180  -0.8305
 TII  C4    C  CR16  0  -0.205   1.2351  -2.4158  -0.6861
 TII  H173  H  HCH3  0   0.198  -4.7544  -0.1461   1.9415
 TII  H171  H  HCH3  0   0.231  -3.1989   0.4472   2.5427
 TII  H172  H  HCH3  0   0.237  -4.5302   1.5654   2.3149
 TII  H181  H  HCH2  0   0.189  -5.4513   0.7099  -0.4403
 TII  H182  H  HCH2  0   0.229  -5.0429   2.3814  -0.0356
 TII  H191  H  HCH2  0   0.236  -4.5200   1.5343  -2.5439
 TII  H192  H  HCH2  0   0.228  -3.2624   2.4332  -1.6937
 TII  H201  H  HCH2  0   0.237  -3.5133  -0.5721  -2.0504
 TII  H202  H  HCH2  0   0.248  -2.0523   0.3866  -2.1850
 TII  H11   H  HCH2  0   0.237  -0.8238   1.0738  -0.3172
 TII  H12   H  HCH2  0   0.231  -1.1416   0.4847   1.3188
 TII  H141  H  HCH2  0   0.246  -2.9693  -1.6093   1.3058
 TII  H142  H  HCH2  0   0.252  -3.7889  -1.9051  -0.2297
 TII  H131  H  HCH2  0   0.246  -1.3382  -2.9838   0.2488
 TII  H132  H  HCH2  0   0.230  -1.6916  -2.3412  -1.3547
 TII  H120  H  HCR6  0   0.292   1.2513   0.7586   0.4917
 TII  H9    H  HCH1  0   0.230   2.8410   1.7933   1.3745
 TII  H113  H  HCH3  0   0.230   5.7244   2.3836   0.5619
 TII  H111  H  HCH3  0   0.235   4.7172   3.3710   1.6211
 TII  H112  H  HCH3  0   0.241   5.1942   1.7546   2.1309
 TII  H102  H  HCH3  0   0.233   4.0031   2.6927  -1.3154
 TII  H103  H  HCH3  0   0.241   2.3114   2.2551  -1.0549
 TII  H101  H  HCH3  0   0.239   2.9869   3.6596  -0.2444
 TII  H6    H  HCR6  0   0.248   4.4492  -1.8619  -0.6696
 TII  H4    H  HCR6  0   0.257   0.5850  -3.2398  -0.9559

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
 TII  C10  C9    single    1.520  0.020  1.520
 TII  O8   C9    single    1.432  0.020  1.432
 TII  O8   C7    single    1.343  0.020  1.343
 TII  C6   C7    aromatic  1.400  0.020  1.400
 TII  C6   N5    aromatic  1.321  0.020  1.321
 TII  C9   C11   single    1.516  0.020  1.516
 TII  C7   C12   aromatic  1.386  0.020  1.386
 TII  N5   C4    aromatic  1.323  0.020  1.323
 TII  C12  C3    aromatic  1.406  0.020  1.406
 TII  C4   C3    aromatic  1.408  0.020  1.408
 TII  C3   N2    single    1.355  0.020  1.355
 TII  N2   C1    single    1.445  0.020  1.445
 TII  N2   C13   single    1.454  0.020  1.454
 TII  C1   C15   single    1.533  0.020  1.533
 TII  C13  C14   single    1.521  0.020  1.521
 TII  C14  C15   single    1.538  0.020  1.538
 TII  C15  C20   single    1.549  0.020  1.549
 TII  C15  N16   single    1.457  0.020  1.457
 TII  C20  C19   single    1.527  0.020  1.527
 TII  N16  C18   single    1.447  0.020  1.447
 TII  N16  C17   single    1.439  0.020  1.439
 TII  C19  C18   single    1.518  0.020  1.518
 TII  C17  H173  single    0.970  0.020  1.090
 TII  C17  H171  single    0.970  0.020  1.090
 TII  C17  H172  single    0.970  0.020  1.090
 TII  C18  H181  single    0.970  0.020  1.090
 TII  C18  H182  single    0.970  0.020  1.090
 TII  C19  H191  single    0.970  0.020  1.090
 TII  C19  H192  single    0.970  0.020  1.090
 TII  C20  H201  single    0.970  0.020  1.090
 TII  C20  H202  single    0.970  0.020  1.090
 TII  C1   H11   single    0.970  0.020  1.090
 TII  C1   H12   single    0.970  0.020  1.090
 TII  C14  H141  single    0.970  0.020  1.090
 TII  C14  H142  single    0.970  0.020  1.090
 TII  C13  H131  single    0.970  0.020  1.090
 TII  C13  H132  single    0.970  0.020  1.090
 TII  C12  H120  single    0.930  0.020  1.080
 TII  C9   H9    single    0.970  0.020  1.090
 TII  C11  H113  single    0.970  0.020  1.090
 TII  C11  H111  single    0.970  0.020  1.090
 TII  C11  H112  single    0.970  0.020  1.090
 TII  C10  H102  single    0.970  0.020  1.090
 TII  C10  H103  single    0.970  0.020  1.090
 TII  C10  H101  single    0.970  0.020  1.090
 TII  C6   H6    single    0.930  0.020  1.080
 TII  C4   H4    single    0.930  0.020  1.080

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
 TII  H172  C17  H171  106.89  3.000
 TII  H172  C17  H173  107.41  3.000
 TII  H171  C17  H173  107.75  3.000
 TII  H172  C17  N16   109.38  3.000
 TII  H171  C17  N16   110.96  3.000
 TII  H173  C17  N16   114.15  3.000
 TII  C15   N16  C18   109.16  3.000
 TII  C18   N16  C17   115.22  3.000
 TII  C15   N16  C17   118.18  3.000
 TII  H182  C18  H181  107.15  3.000
 TII  H182  C18  C19   113.34  3.000
 TII  H181  C18  C19   110.63  3.000
 TII  H182  C18  N16   110.57  3.000
 TII  H181  C18  N16   112.88  3.000
 TII  C19   C18  N16   102.37  3.000
 TII  H192  C19  H191  107.94  3.000
 TII  H192  C19  C20   111.18  3.000
 TII  H191  C19  C20   112.72  3.000
 TII  H192  C19  C18   109.91  3.000
 TII  H191  C19  C18   113.13  3.000
 TII  C20   C19  C18   101.92  3.000
 TII  H202  C20  H201  106.78  3.000
 TII  H202  C20  C15   112.36  3.000
 TII  H201  C20  C15   109.79  3.000
 TII  H202  C20  C19   113.12  3.000
 TII  H201  C20  C19   109.67  3.000
 TII  C15   C20  C19   105.11  3.000
 TII  C14   C15  C1    101.26  3.000
 TII  C14   C15  C20   110.53  3.000
 TII  C1    C15  C20   111.57  3.000
 TII  C20   C15  N16   104.15  3.000
 TII  C14   C15  N16   118.10  3.000
 TII  C1    C15  N16   111.44  3.000
 TII  H12   C1   H11   107.49  3.000
 TII  H12   C1   N2    111.94  3.000
 TII  H11   C1   N2    111.99  3.000
 TII  H12   C1   C15   111.04  3.000
 TII  H11   C1   C15   110.98  3.000
 TII  N2    C1   C15   103.45  3.000
 TII  H142  C14  H141  107.98  3.000
 TII  H142  C14  C13   112.52  3.000
 TII  H141  C14  C13   109.51  3.000
 TII  H142  C14  C15   113.39  3.000
 TII  H141  C14  C15   110.84  3.000
 TII  C13   C14  C15   102.54  3.000
 TII  H132  C13  H131  107.23  3.000
 TII  H132  C13  N2    111.46  3.000
 TII  H131  C13  N2    111.32  3.000
 TII  H132  C13  C14   111.47  3.000
 TII  H131  C13  C14   112.25  3.000
 TII  N2    C13  C14   103.18  3.000
 TII  C3    N2   C13   123.41  3.000
 TII  C13   N2   C1    112.40  3.000
 TII  C3    N2   C1    124.17  3.000
 TII  C4    C3   C12   117.07  3.000
 TII  C4    C3   N2    121.53  3.000
 TII  C12   C3   N2    121.39  3.000
 TII  H120  C12  C7    121.04  3.000
 TII  H120  C12  C3    119.60  3.000
 TII  C7    C12  C3    119.35  3.000
 TII  C6    C7   O8    115.95  3.000
 TII  C6    C7   C12   118.73  3.000
 TII  O8    C7   C12   125.30  3.000
 TII  C9    O8   C7    120.97  3.000
 TII  H9    C9   C10   109.80  3.000
 TII  H9    C9   C11   108.42  3.000
 TII  C10   C9   C11   111.85  3.000
 TII  H9    C9   O8    109.48  3.000
 TII  C11   C9   O8    106.08  3.000
 TII  C10   C9   O8    111.11  3.000
 TII  H112  C11  H111  107.75  3.000
 TII  H112  C11  H113  108.60  3.000
 TII  H111  C11  H113  107.96  3.000
 TII  H112  C11  C9    111.42  3.000
 TII  H111  C11  C9    109.77  3.000
 TII  H113  C11  C9    111.22  3.000
 TII  H101  C10  H103  107.33  3.000
 TII  H101  C10  H102  108.01  3.000
 TII  H103  C10  H102  108.15  3.000
 TII  H101  C10  C9    109.61  3.000
 TII  H103  C10  C9    112.77  3.000
 TII  H102  C10  C9    110.80  3.000
 TII  H6    C6   N5    117.95  3.000
 TII  H6    C6   C7    120.11  3.000
 TII  N5    C6   C7    121.94  3.000
 TII  C4    N5   C6    120.16  3.000
 TII  H4    C4   N5    116.47  3.000
 TII  H4    C4   C3    120.79  3.000
 TII  N5    C4   C3    122.74  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
 TII  CONST_01  C6    C7   C12  C3     0.00   0.0  0
 TII  CONST_02  C6    N5   C4   C3     0.00   0.0  0
 TII  CONST_03  N5    C6   C7   C12    0.00   0.0  0
 TII  CONST_04  N5    C4   C3   C12    0.00   0.0  0
 TII  CONST_05  C4    N5   C6   C7     0.00   0.0  0
 TII  CONST_06  C4    C3   C12  C7     0.00   0.0  0
 TII  CONST_07  C7    C12  C3   N2   180.00   0.0  0
 TII  CONST_08  N5    C4   C3   N2   180.00   0.0  0
 TII  CONST_09  O8    C7   C12  C3   180.00   0.0  0
 TII  CONST_10  N5    C6   C7   O8   180.00   0.0  0
 TII  CONST_11  H120  C12  C3   N2     0.00   0.0  0
 TII  CONST_12  H4    C4   C3   N2     0.00   0.0  0
 TII  CONST_13  H6    C6   C7   C12  180.00   0.0  0
 TII  Var_01    C20   C19  C18  N16   40.75  30.0  1
 TII  Var_02    C15   C20  C19  C18  -29.17  30.0  1
 TII  Var_03    C15   N16  C18  C19  -38.53  30.0  1
 TII  Var_04    C3    N2   C1   C15  164.13  30.0  1
 TII  Var_05    N2    C13  C14  C15   32.79  30.0  1
 TII  Var_06    C12   C3   N2   C1     7.04  30.0  3
 TII  Var_07    C14   C13  N2   C1   -11.74  30.0  1
 TII  Var_08    C6    C7   O8   C9   174.96  30.0  2
 TII  Var_09    H173  C17  N16  C18   62.65  30.0  3
 TII  Var_10    C10   C9   O8   C7   -75.49  30.0  3
 TII  Var_11    H102  C10  C9   O8   -60.44  30.0  3
 TII  Var_12    H113  C11  C9   O8    62.19  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
 TII  chir_01  C15  C14  C20  N16  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
 TII  plan-1  N2    0.020
 TII  plan-1  C3    0.020
 TII  plan-1  C12   0.020
 TII  plan-1  C7    0.020
 TII  plan-1  O8    0.020
 TII  plan-1  C6    0.020
 TII  plan-1  N5    0.020
 TII  plan-1  C4    0.020
 TII  plan-1  H120  0.020
 TII  plan-1  H6    0.020
 TII  plan-1  H4    0.020

