# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:04:30 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=S)c2ncn(C3CCCCC3)c2N1
#
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
 UO8  UO8  "2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione"
  ligand  32  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UO8
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
 UO8  C01  C  CH2   0  -0.455  51.6267  67.3534  286.6300
 UO8  C02  C  CH2   0  -0.433  50.7267  66.4582  285.7632
 UO8  C03  C  CH2   0  -0.462  51.0461  64.9656  285.9349
 UO8  C04  C  CH1   0  -0.108  52.5389  64.7944  286.1928
 UO8  C05  C  CH2   0  -0.437  52.9555  65.4139  287.5369
 UO8  C06  C  CH2   0  -0.450  52.0732  66.6189  287.8881
 UO8  C08  C  CR15  0   0.093  53.9016  62.9443  285.1680
 UO8  C10  C  CR56  0   0.043  53.3086  61.2434  286.2755
 UO8  C11  C  CR56  0   0.626  52.6070  62.3167  286.7780
 UO8  C13  C  CR6   0   0.683  51.5738  60.9291  288.3167
 UO8  C15  C  CR6   0   0.071  53.0969  59.9488  286.8375
 UO8  N07  N  NR5   0  -0.502  52.9778  63.4070  286.0742
 UO8  N09  N  N     0  -0.431  54.1210  61.6699  285.2593
 UO8  N12  N  NR16  0  -0.726  51.7255  62.1829  287.8008
 UO8  N14  N  N     0  -0.489  52.2150  59.8750  287.8622
 UO8  N17  N  NH2   0  -0.826  50.7297  60.7886  289.3385
 UO8  S16  S  S1    0  -0.449  53.8817  58.5791  286.2756
 UO8  H1   H  HCH2  0   0.225  52.5104  67.6619  286.0634
 UO8  H2   H  HCH2  0   0.240  51.0990  68.2724  286.8900
 UO8  H3   H  HCH2  0   0.235  50.8334  66.7375  284.7131
 UO8  H4   H  HCH2  0   0.235  49.6792  66.6212  286.0215
 UO8  H5   H  HCH2  0   0.233  50.4661  64.5611  286.7688
 UO8  H6   H  HCH2  0   0.260  50.7488  64.4071  285.0460
 UO8  H7   H  HCH1  0   0.283  53.0706  65.3102  285.3899
 UO8  H8   H  HCH2  0   0.239  52.8956  64.6754  288.3395
 UO8  H9   H  HCH2  0   0.249  54.0038  65.7112  287.4724
 UO8  H10  H  HCH2  0   0.242  52.6172  67.2871  288.5572
 UO8  H11  H  HCH2  0   0.228  51.1911  66.2837  288.4406
 UO8  H12  H  HCR5  0   0.295  54.3697  63.6213  284.4685
 UO8  H13  H  HNR6  0   0.448  51.1987  62.9614  288.1723
 UO8  H14  H  HNH2  0   0.418  50.5840  59.8704  289.7212
 UO8  H15  H  HNH2  0   0.421  50.1966  61.5517  289.7191

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
 UO8  C08  N09  aromatic  1.296  0.020  1.296
 UO8  C08  N07  aromatic  1.374  0.020  1.374
 UO8  N09  C10  aromatic  1.369  0.020  1.369
 UO8  C02  C03  single    1.536  0.020  1.536
 UO8  C02  C01  single    1.537  0.020  1.537
 UO8  C03  C04  single    1.525  0.020  1.525
 UO8  N07  C04  single    1.460  0.020  1.460
 UO8  N07  C11  aromatic  1.350  0.020  1.350
 UO8  C04  C05  single    1.537  0.020  1.537
 UO8  C10  C11  aromatic  1.377  0.020  1.377
 UO8  C10  C15  single    1.427  0.020  1.427
 UO8  S16  C15  double    1.676  0.020  1.676
 UO8  C01  C06  single    1.524  0.020  1.524
 UO8  C11  N12  single    1.357  0.020  1.357
 UO8  C15  N14  single    1.354  0.020  1.354
 UO8  C05  C06  single    1.534  0.020  1.534
 UO8  N12  C13  single    1.364  0.020  1.364
 UO8  N14  C13  double    1.315  0.020  1.315
 UO8  C13  N17  single    1.333  0.020  1.333
 UO8  C01  H1   single    0.970  0.020  1.090
 UO8  C01  H2   single    0.970  0.020  1.090
 UO8  C02  H3   single    0.970  0.020  1.090
 UO8  C02  H4   single    0.970  0.020  1.090
 UO8  C03  H5   single    0.970  0.020  1.090
 UO8  C03  H6   single    0.970  0.020  1.090
 UO8  C04  H7   single    0.970  0.020  1.090
 UO8  C05  H8   single    0.970  0.020  1.090
 UO8  C05  H9   single    0.970  0.020  1.090
 UO8  C06  H10  single    0.970  0.020  1.090
 UO8  C06  H11  single    0.970  0.020  1.090
 UO8  C08  H12  single    0.930  0.020  1.080
 UO8  N12  H13  single    0.860  0.020  1.020
 UO8  N17  H14  single    0.860  0.020  1.020
 UO8  N17  H15  single    0.860  0.020  1.020

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
 UO8  H2   C01  H1   106.05  3.000
 UO8  H2   C01  C06  110.55  3.000
 UO8  H1   C01  C06  109.07  3.000
 UO8  H2   C01  C02  109.98  3.000
 UO8  H1   C01  C02  110.18  3.000
 UO8  C06  C01  C02  110.88  3.000
 UO8  H4   C02  H3   106.46  3.000
 UO8  H4   C02  C03  108.56  3.000
 UO8  H3   C02  C03  109.62  3.000
 UO8  H4   C02  C01  109.97  3.000
 UO8  H3   C02  C01  109.65  3.000
 UO8  C03  C02  C01  112.40  3.000
 UO8  H6   C03  H5   106.71  3.000
 UO8  H6   C03  C04  110.31  3.000
 UO8  H5   C03  C04  110.42  3.000
 UO8  H6   C03  C02  110.47  3.000
 UO8  H5   C03  C02  109.54  3.000
 UO8  C04  C03  C02  109.37  3.000
 UO8  H7   C04  N07  104.05  3.000
 UO8  H7   C04  C05  108.68  3.000
 UO8  N07  C04  C05  111.87  3.000
 UO8  H7   C04  C03  107.41  3.000
 UO8  C05  C04  C03  111.59  3.000
 UO8  N07  C04  C03  112.79  3.000
 UO8  H9   C05  H8   106.27  3.000
 UO8  H9   C05  C06  110.61  3.000
 UO8  H8   C05  C06  109.35  3.000
 UO8  H9   C05  C04  108.56  3.000
 UO8  H8   C05  C04  110.79  3.000
 UO8  C06  C05  C04  111.15  3.000
 UO8  H11  C06  H10  106.27  3.000
 UO8  H11  C06  C05  109.81  3.000
 UO8  H10  C06  C05  109.56  3.000
 UO8  H11  C06  C01  109.18  3.000
 UO8  H10  C06  C01  110.93  3.000
 UO8  C05  C06  C01  110.98  3.000
 UO8  H12  C08  N09  126.05  3.000
 UO8  H12  C08  N07  120.48  3.000
 UO8  N09  C08  N07  113.47  3.000
 UO8  N09  C10  C15  131.52  3.000
 UO8  C15  C10  C11  119.19  3.000
 UO8  N09  C10  C11  109.29  3.000
 UO8  N12  C11  N07  130.63  3.000
 UO8  N12  C11  C10  121.95  3.000
 UO8  N07  C11  C10  107.42  3.000
 UO8  N17  C13  N14  119.29  3.000
 UO8  N17  C13  N12  117.21  3.000
 UO8  N14  C13  N12  123.49  3.000
 UO8  S16  C15  N14  120.95  3.000
 UO8  N14  C15  C10  116.36  3.000
 UO8  S16  C15  C10  122.69  3.000
 UO8  C11  N07  C08  104.86  3.000
 UO8  C11  N07  C04  129.99  3.000
 UO8  C08  N07  C04  125.14  3.000
 UO8  C10  N09  C08  104.95  3.000
 UO8  H13  N12  C13  120.73  3.000
 UO8  H13  N12  C11  122.66  3.000
 UO8  C13  N12  C11  116.61  3.000
 UO8  C15  N14  C13  122.38  3.000
 UO8  H15  N17  H14  118.17  3.000
 UO8  H15  N17  C13  123.08  3.000
 UO8  H14  N17  C13  118.69  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
 UO8  CONST_01  C11  C10  N09  C08     0.00   0.0  0
 UO8  CONST_02  C10  C11  N07  C08     0.00   0.0  0
 UO8  CONST_03  N07  C08  N09  C10     0.00   0.0  0
 UO8  CONST_04  N09  C08  N07  C11     0.00   0.0  0
 UO8  CONST_05  N09  C10  C11  N07     0.00   0.0  0
 UO8  CONST_06  N09  C08  N07  C04   180.00   0.0  0
 UO8  CONST_07  C10  C11  N07  C04   180.00   0.0  0
 UO8  CONST_08  N12  C11  N07  C04     0.00   0.0  0
 UO8  CONST_09  N14  C13  N12  C11     0.00   0.0  0
 UO8  CONST_10  N12  C13  N14  C15     0.00   0.0  0
 UO8  CONST_11  N17  C13  N12  C11   180.00   0.0  0
 UO8  CONST_12  N17  C13  N14  C15   180.00   0.0  0
 UO8  CONST_13  H12  C08  N07  C04     0.00   0.0  0
 UO8  CONST_14  H12  C08  N09  C10   180.00   0.0  0
 UO8  CONST_15  H12  C08  N07  C11   180.00   0.0  0
 UO8  CONST_16  H13  N12  C13  N14   180.00   0.0  0
 UO8  CONST_17  H14  N17  C13  N12   180.00   0.0  0
 UO8  CONST_18  H15  N17  C13  N12     0.00   0.0  0
 UO8  CONST_19  H14  N17  C13  N14     0.00   0.0  0
 UO8  CONST_20  H15  N17  C13  N14   180.00   0.0  0
 UO8  CONST_21  H13  N12  C13  N17     0.00   0.0  0
 UO8  Var_01    C04  C03  C02  C01   -33.22  30.0  1
 UO8  Var_02    C04  C05  C06  C01   -32.29  30.0  1
 UO8  Var_03    C05  C06  C01  C02    64.36  30.0  1
 UO8  Var_04    C06  C01  C02  C03   -28.71  30.0  1
 UO8  Var_05    H5   C03  C02  C01    87.92  30.0  1
 UO8  Var_06    H6   C03  C02  C01  -154.82  30.0  1
 UO8  Var_07    H8   C05  C06  C01  -154.92  30.0  1
 UO8  Var_08    H9   C05  C06  C01    88.38  30.0  1
 UO8  Var_09    H10  C06  C01  C02  -173.60  30.0  1
 UO8  Var_10    H11  C06  C01  C02   -56.81  30.0  1
 UO8  Var_11    H1   C01  C02  C03    92.14  30.0  1
 UO8  Var_12    H2   C01  C02  C03  -151.29  30.0  1
 UO8  Var_13    H3   C02  C03  C04    88.99  30.0  1
 UO8  Var_14    H4   C02  C03  C04  -155.10  30.0  1
 UO8  Var_15    H10  C06  C05  C04  -155.12  30.0  1
 UO8  Var_16    H11  C06  C05  C04    88.52  30.0  1
 UO8  Var_17    H1   C01  C06  C05   -57.15  30.0  1
 UO8  Var_18    H2   C01  C06  C05  -173.39  30.0  1
 UO8  Var_19    H3   C02  C01  C06  -150.91  30.0  1
 UO8  Var_20    H4   C02  C01  C06    92.36  30.0  1

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
 UO8  chir_01  C04  C03  N07  C05  positiv

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
 UO8  plan-1  C04  0.020
 UO8  plan-1  C08  0.020
 UO8  plan-1  C10  0.020
 UO8  plan-1  C11  0.020
 UO8  plan-1  C13  0.020
 UO8  plan-1  C15  0.020
 UO8  plan-1  N07  0.020
 UO8  plan-1  N09  0.020
 UO8  plan-1  N12  0.020
 UO8  plan-1  N14  0.020
 UO8  plan-1  N17  0.020
 UO8  plan-1  S16  0.020
 UO8  plan-1  H12  0.020
 UO8  plan-1  H13  0.020
 UO8  plan-1  H14  0.020
 UO8  plan-1  H15  0.020

