# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:00:04 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 4-(piperidin-1-yl)-1,2,5-oxadiazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1N2CCCCC2
#
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
 RUY  RUY  4-(piperidin-1-yl)-1,2,5-oxadiazol-3-amine  ligand  24  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RUY
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
 RUY  N1   N  NT    0  -0.494   0.5460   0.0983   0.0544
 RUY  N3   N  N     0  -0.172  -1.4416   1.3428  -0.2801
 RUY  C4   C  CH2   0  -0.300   1.3255   1.3280   0.1262
 RUY  C5   C  CH2   0  -0.441   2.7240   1.0234   0.6407
 RUY  C6   C  CR5   0   0.395  -0.8116   0.2379  -0.0356
 RUY  C7   C  CR5   0   0.343  -1.8020  -0.7841   0.2085
 RUY  C1   C  CH2   0  -0.445   3.4128  -0.0384  -0.2079
 RUY  C2   C  CH2   0  -0.437   2.5355  -1.2797  -0.3160
 RUY  C3   C  CH2   0  -0.321   1.1497  -0.9142  -0.8169
 RUY  N2   N  N     0  -0.177  -2.9717  -0.2438   0.0949
 RUY  N4   N  NH2   0  -0.837  -1.5670  -2.0983   0.4804
 RUY  O1   O  O     0  -0.251  -2.7587   1.0644  -0.2005
 RUY  H1   H  HCH2  0   0.219   1.3827   1.8121  -0.8594
 RUY  H2   H  HCH2  0   0.254   0.8213   2.0234   0.7978
 RUY  H3   H  HCH2  0   0.239   3.3054   1.9474   0.6516
 RUY  H4   H  HCH2  0   0.223   2.6520   0.6780   1.6759
 RUY  H5   H  HCH2  0   0.217   3.6042   0.3600  -1.2098
 RUY  H6   H  HCH2  0   0.238   4.3853  -0.2929   0.2180
 RUY  H7   H  HCH2  0   0.240   2.9773  -2.0099  -0.9967
 RUY  H8   H  HCH2  0   0.224   2.4493  -1.7613   0.6627
 RUY  H9   H  HCH2  0   0.260   0.5106  -1.7960  -0.8531
 RUY  H10  H  HCH2  0   0.228   1.2168  -0.5267  -1.8434
 RUY  H11  H  HNH2  0   0.397  -0.7539  -2.2669   1.0538
 RUY  H12  H  HNH2  0   0.399  -2.3691  -2.6131   0.8120

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
 RUY  C2  C1   single    1.524  0.020  1.524
 RUY  C2  C3   single    1.518  0.020  1.518
 RUY  C1  C5   single    1.524  0.020  1.524
 RUY  C3  N1   single    1.466  0.020  1.466
 RUY  C5  C4   single    1.521  0.020  1.521
 RUY  C4  N1   single    1.458  0.020  1.458
 RUY  N1  C6   single    1.368  0.020  1.368
 RUY  N4  C7   single    1.362  0.020  1.362
 RUY  C6  C7   aromatic  1.444  0.020  1.444
 RUY  C6  N3   aromatic  1.295  0.020  1.295
 RUY  C7  N2   aromatic  1.293  0.020  1.293
 RUY  N3  O1   aromatic  1.349  0.020  1.349
 RUY  N2  O1   aromatic  1.358  0.020  1.358
 RUY  C4  H1   single    0.970  0.020  1.090
 RUY  C4  H2   single    0.970  0.020  1.090
 RUY  C5  H3   single    0.970  0.020  1.090
 RUY  C5  H4   single    0.970  0.020  1.090
 RUY  C1  H5   single    0.970  0.020  1.090
 RUY  C1  H6   single    0.970  0.020  1.090
 RUY  C2  H7   single    0.970  0.020  1.090
 RUY  C2  H8   single    0.970  0.020  1.090
 RUY  C3  H9   single    0.970  0.020  1.090
 RUY  C3  H10  single    0.970  0.020  1.090
 RUY  N4  H11  single    0.890  0.020  1.040
 RUY  N4  H12  single    0.890  0.020  1.040

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
 RUY  C3   N1  C6   116.12  3.000
 RUY  C6   N1  C4   116.61  3.000
 RUY  C3   N1  C4   113.06  3.000
 RUY  O1   N3  C6   106.73  3.000
 RUY  H2   C4  H1   107.18  3.000
 RUY  H2   C4  C5   110.15  3.000
 RUY  H1   C4  C5   110.09  3.000
 RUY  H2   C4  N1   108.73  3.000
 RUY  H1   C4  N1   110.80  3.000
 RUY  C5   C4  N1   109.84  3.000
 RUY  H4   C5  H3   107.03  3.000
 RUY  H4   C5  C1   109.68  3.000
 RUY  H3   C5  C1   110.76  3.000
 RUY  H4   C5  C4   108.85  3.000
 RUY  H3   C5  C4   108.88  3.000
 RUY  C1   C5  C4   111.52  3.000
 RUY  C7   C6  N3   107.58  3.000
 RUY  N3   C6  N1   125.62  3.000
 RUY  C7   C6  N1   126.69  3.000
 RUY  N4   C7  N2   125.20  3.000
 RUY  N2   C7  C6   108.05  3.000
 RUY  N4   C7  C6   126.74  3.000
 RUY  H6   C1  H5   106.63  3.000
 RUY  H6   C1  C2   110.53  3.000
 RUY  H5   C1  C2   109.40  3.000
 RUY  H6   C1  C5   110.35  3.000
 RUY  H5   C1  C5   109.57  3.000
 RUY  C2   C1  C5   110.29  3.000
 RUY  H8   C2  H7   107.17  3.000
 RUY  H8   C2  C3   109.22  3.000
 RUY  H7   C2  C3   108.95  3.000
 RUY  H8   C2  C1   109.90  3.000
 RUY  H7   C2  C1   110.86  3.000
 RUY  C3   C2  C1   110.66  3.000
 RUY  H10  C3  H9   106.86  3.000
 RUY  H10  C3  C2   109.71  3.000
 RUY  H9   C3  C2   110.58  3.000
 RUY  H10  C3  N1   109.68  3.000
 RUY  H9   C3  N1   109.70  3.000
 RUY  C2   C3  N1   110.25  3.000
 RUY  O1   N2  C7   106.25  3.000
 RUY  H12  N4  H11  111.62  3.000
 RUY  H12  N4  C7   114.87  3.000
 RUY  H11  N4  C7   114.43  3.000
 RUY  N2   O1  N3   111.40  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
 RUY  CONST_01  N2   C7  C6  N3     0.00   0.0  0
 RUY  CONST_02  C7   N2  O1  N3     0.00   0.0  0
 RUY  CONST_03  O1   N2  C7  C6     0.00   0.0  0
 RUY  CONST_04  N2   O1  N3  C6     0.00   0.0  0
 RUY  CONST_05  O1   N3  C6  C7     0.00   0.0  0
 RUY  CONST_06  N2   C7  C6  N1   180.00   0.0  0
 RUY  CONST_07  O1   N3  C6  N1   180.00   0.0  0
 RUY  CONST_08  N4   C7  C6  N1     0.00   0.0  0
 RUY  CONST_09  N4   C7  C6  N3   180.00   0.0  0
 RUY  CONST_10  O1   N2  C7  N4   180.00   0.0  0
 RUY  CONST_12  H12  N4  C7  C6   180.00   0.0  0
 RUY  Var_01    C1   C2  C3  N1   -56.09  30.0  1
 RUY  Var_02    C1   C5  C4  N1    55.31  30.0  1
 RUY  Var_03    C3   N1  C6  N3  -125.22  30.0  3
 RUY  Var_04    C2   C1  C5  C4   -53.63  30.0  1
 RUY  Var_05    C2   C3  N1  C4    59.60  30.0  1
 RUY  Var_06    C3   C2  C1  C5    53.75  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
 RUY  plan-1  N1   0.020
 RUY  plan-1  N3   0.020
 RUY  plan-1  C6   0.020
 RUY  plan-1  C7   0.020
 RUY  plan-1  N2   0.020
 RUY  plan-1  N4   0.020
 RUY  plan-1  O1   0.020
 RUY  plan-2  C7   0.020
 RUY  plan-2  N4   0.020
 RUY  plan-2  H11  0.020
 RUY  plan-2  H12  0.020

