# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:21:13 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: (5S)-7-(pyrazin-2-yl)-2-oxa-7-azaspiro[4.4]nonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@]2(CCN(C2)c3cnccn3)CO1
#
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
 U0S  U0S  (5S)-7-(pyrazin-2-yl)-2-oxa-7-azaspiro[4.4]nonane  ligand  30  15  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_U0S
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
 U0S  C10   C  CH2   0  -0.153  7.3971  -18.7313  -2.5996
 U0S  C13   C  CH2   0  -0.226  5.0098  -20.9323  -0.6757
 U0S  C01   C  CR16  0  -0.160  2.3150  -24.8252   0.8503
 U0S  C02   C  CR16  0  -0.100  2.1789  -23.4510   0.8667
 U0S  C04   C  CR6   0   0.485  4.1979  -23.1891  -0.1439
 U0S  C06   C  CH2   0  -0.286  6.4334  -22.8361  -1.1364
 U0S  C07   C  CH2   0  -0.458  7.2411  -21.5492  -1.2443
 U0S  C08   C  CR5   0  -0.184  6.1820  -20.4822  -1.5403
 U0S  C09   C  CH2   0  -0.495  6.6500  -19.0499  -1.3089
 U0S  C12   C  CH2   0  -0.117  5.8621  -20.4176  -3.0342
 U0S  C14   C  CR16  0  -0.170  4.3311  -24.6014  -0.1703
 U0S  N03   N  N     0  -0.434  3.1039  -22.6339   0.3798
 U0S  N05   N  NT    0  -0.507  5.1480  -22.3768  -0.6391
 U0S  N15   N  N     0  -0.345  3.4041  -25.3885   0.3218
 U0S  O11   O  O     0  -0.502  6.8587  -19.5898  -3.6009
 U0S  H102  H  HCH2  0   0.221  7.2801  -17.6858  -2.8977
 U0S  H101  H  HCH2  0   0.212  8.4690  -18.9290  -2.4975
 U0S  H131  H  HCH2  0   0.240  5.0759  -20.5035   0.3306
 U0S  H132  H  HCH2  0   0.245  4.0450  -20.6328  -1.0914
 U0S  H021  H  HCR6  0   0.263  1.2929  -22.9902   1.2892
 U0S  H061  H  HCH2  0   0.253  6.8969  -23.5519  -0.4536
 U0S  H062  H  HCH2  0   0.239  6.3286  -23.3329  -2.1078
 U0S  H072  H  HCH2  0   0.250  7.7257  -21.3310  -0.2897
 U0S  H071  H  HCH2  0   0.259  8.0205  -21.6139  -2.0042
 U0S  H091  H  HCH2  0   0.255  7.2791  -18.9469  -0.4238
 U0S  H092  H  HCH2  0   0.250  5.7875  -18.3896  -1.1859
 U0S  H122  H  HCH2  0   0.205  4.8604  -19.9933  -3.1892
 U0S  H121  H  HCH2  0   0.229  5.8877  -21.3911  -3.5326
 U0S  H141  H  HCR6  0   0.270  5.2032  -25.0736  -0.6074
 U0S  H011  H  HCR6  0   0.260  1.5506  -25.4754   1.2560

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
 U0S  C02  C01   aromatic  1.381  0.020  1.381
 U0S  N03  C02   aromatic  1.327  0.020  1.327
 U0S  C04  N03   aromatic  1.334  0.020  1.334
 U0S  C06  N05   single    1.453  0.020  1.453
 U0S  C07  C06   single    1.523  0.020  1.523
 U0S  C08  C07   single    1.532  0.020  1.532
 U0S  C10  C09   single    1.525  0.020  1.525
 U0S  O11  C10   single    1.425  0.020  1.425
 U0S  C12  O11   single    1.414  0.020  1.414
 U0S  C09  C08   single    1.524  0.020  1.524
 U0S  C13  C08   single    1.525  0.020  1.525
 U0S  N05  C04   single    1.344  0.020  1.344
 U0S  C14  C04   aromatic  1.419  0.020  1.419
 U0S  N15  C14   aromatic  1.312  0.020  1.312
 U0S  C01  N15   aromatic  1.335  0.020  1.335
 U0S  N05  C13   single    1.452  0.020  1.452
 U0S  C08  C12   single    1.529  0.020  1.529
 U0S  C10  H102  single    0.970  0.020  1.090
 U0S  C10  H101  single    0.970  0.020  1.090
 U0S  C13  H131  single    0.970  0.020  1.090
 U0S  C13  H132  single    0.970  0.020  1.090
 U0S  C01  H011  single    0.930  0.020  1.080
 U0S  C02  H021  single    0.930  0.020  1.080
 U0S  C06  H061  single    0.970  0.020  1.090
 U0S  C06  H062  single    0.970  0.020  1.090
 U0S  C07  H072  single    0.970  0.020  1.090
 U0S  C07  H071  single    0.970  0.020  1.090
 U0S  C09  H091  single    0.970  0.020  1.090
 U0S  C09  H092  single    0.970  0.020  1.090
 U0S  C12  H122  single    0.970  0.020  1.090
 U0S  C12  H121  single    0.970  0.020  1.090
 U0S  C14  H141  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
 U0S  H101  C10  H102  107.63  3.000
 U0S  H101  C10  O11   109.08  3.000
 U0S  H102  C10  O11   110.13  3.000
 U0S  H101  C10  C09   111.28  3.000
 U0S  H102  C10  C09   112.22  3.000
 U0S  O11   C10  C09   106.49  3.000
 U0S  H132  C13  H131  107.18  3.000
 U0S  H132  C13  N05   111.50  3.000
 U0S  H131  C13  N05   111.13  3.000
 U0S  H132  C13  C08   112.48  3.000
 U0S  H131  C13  C08   111.03  3.000
 U0S  N05   C13  C08   103.59  3.000
 U0S  H011  C01  N15   118.09  3.000
 U0S  H011  C01  C02   121.58  3.000
 U0S  N15   C01  C02   120.33  3.000
 U0S  H021  C02  N03   116.80  3.000
 U0S  H021  C02  C01   120.53  3.000
 U0S  N03   C02  C01   122.66  3.000
 U0S  N05   C04  N03   118.21  3.000
 U0S  N05   C04  C14   121.89  3.000
 U0S  N03   C04  C14   119.90  3.000
 U0S  H062  C06  H061  107.31  3.000
 U0S  H062  C06  N05   111.23  3.000
 U0S  H061  C06  N05   111.63  3.000
 U0S  H062  C06  C07   111.77  3.000
 U0S  H061  C06  C07   111.89  3.000
 U0S  N05   C06  C07   103.08  3.000
 U0S  H071  C07  H072  107.67  3.000
 U0S  H071  C07  C08   113.63  3.000
 U0S  H072  C07  C08   109.66  3.000
 U0S  H071  C07  C06   112.22  3.000
 U0S  H072  C07  C06   110.00  3.000
 U0S  C08   C07  C06   103.62  3.000
 U0S  C12   C08  C09    99.95  3.000
 U0S  C12   C08  C07   111.27  3.000
 U0S  C09   C08  C07   114.37  3.000
 U0S  C12   C08  C13   113.94  3.000
 U0S  C09   C08  C13   115.30  3.000
 U0S  C07   C08  C13   102.49  3.000
 U0S  H092  C09  H091  107.86  3.000
 U0S  H092  C09  C08   110.02  3.000
 U0S  H091  C09  C08   112.89  3.000
 U0S  H092  C09  C10   110.83  3.000
 U0S  H091  C09  C10   112.61  3.000
 U0S  C08   C09  C10   102.60  3.000
 U0S  H121  C12  H122  107.50  3.000
 U0S  H121  C12  O11   108.78  3.000
 U0S  H122  C12  O11   111.09  3.000
 U0S  H121  C12  C08   113.74  3.000
 U0S  H122  C12  C08   110.17  3.000
 U0S  O11   C12  C08   105.59  3.000
 U0S  H141  C14  N15   117.29  3.000
 U0S  H141  C14  C04   121.11  3.000
 U0S  N15   C14  C04   121.60  3.000
 U0S  C04   N03  C02   117.36  3.000
 U0S  C06   N05  C04   124.08  3.000
 U0S  C04   N05  C13   122.91  3.000
 U0S  C06   N05  C13   112.97  3.000
 U0S  C14   N15  C01   118.15  3.000
 U0S  C12   O11  C10   109.72  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
 U0S  CONST_01  C04   N03  C02  C01     0.00   0.0  0
 U0S  CONST_02  C04   C14  N15  C01     0.00   0.0  0
 U0S  CONST_03  C14   N15  C01  C02     0.00   0.0  0
 U0S  CONST_04  C14   C04  N03  C02     0.00   0.0  0
 U0S  CONST_05  N15   C01  C02  N03     0.00   0.0  0
 U0S  CONST_06  N15   C14  C04  N03     0.00   0.0  0
 U0S  CONST_07  N05   C04  N03  C02   180.00   0.0  0
 U0S  CONST_08  N15   C14  C04  N05   180.00   0.0  0
 U0S  CONST_09  H141  C14  N15  C01   180.00   0.0  0
 U0S  CONST_10  H021  C02  N03  C04   180.00   0.0  0
 U0S  CONST_11  H011  C01  N15  C14   180.00   0.0  0
 U0S  Var_01    C08   C12  O11  C10   -23.58  30.0  1
 U0S  Var_02    C07   C06  N05  C13    10.99  30.0  1
 U0S  Var_03    N03   C04  N05  C13    -2.52  30.0  2
 U0S  Var_04    C08   C13  N05  C04  -169.71  30.0  1
 U0S  Var_05    N05   C06  C07  C08   -30.12  30.0  1
 U0S  Var_06    O11   C10  C09  C08    24.60  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
 U0S  chir_01  C08  C09  C13  C12  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
 U0S  plan-1  C01   0.020
 U0S  plan-1  C02   0.020
 U0S  plan-1  C04   0.020
 U0S  plan-1  C14   0.020
 U0S  plan-1  N03   0.020
 U0S  plan-1  N05   0.020
 U0S  plan-1  N15   0.020
 U0S  plan-1  H021  0.020
 U0S  plan-1  H141  0.020
 U0S  plan-1  H011  0.020

