# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:06:03 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (4-amino-1,2,5-oxadiazol-3-yl)(phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1C(=O)c2ccccc2
#
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
 1VK  1VK  (4-amino-1,2,5-oxadiazol-3-yl)(phenyl)methanone  ligand  21  14  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1VK
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
 1VK  C2   C  CR5   0   0.389  -2.6335   0.2858  -0.0154
 1VK  C6   C  CR5   0   0.033  -1.2457  -0.0174  -0.2378
 1VK  C7   C  C     0   0.371  -0.0815   0.8466   0.0418
 1VK  C10  C  CR16  0  -0.264   2.3393   1.1390  -0.3174
 1VK  C11  C  CR16  0  -0.242   3.6415   0.6707  -0.3217
 1VK  C12  C  CR16  0  -0.242   3.9084  -0.6453   0.0388
 1VK  C13  C  CR16  0  -0.240   2.8692  -1.4918   0.3989
 1VK  C14  C  CR16  0  -0.265   1.5604  -1.0338   0.3838
 1VK  N1   N  NH2   0  -0.838  -3.1592   1.3620   0.5987
 1VK  N3   N  N     0  -0.190  -3.3281  -0.7223  -0.4627
 1VK  O4   O  O     0  -0.203  -2.4179  -1.6118  -0.9448
 1VK  N5   N  N     0  -0.092  -1.1824  -1.1786  -0.8102
 1VK  O8   O  O     0  -0.377  -0.2896   2.0238   0.2585
 1VK  C9   C  CR6   0   0.001   1.2865   0.2859   0.0225
 1VK  H18  H  HCR6  0   0.268   4.4508   1.3315  -0.6026
 1VK  H19  H  HCR6  0   0.270   4.9279  -1.0083   0.0431
 1VK  H20  H  HCR6  0   0.269   3.0766  -2.5115   0.6941
 1VK  H21  H  HCR6  0   0.269   0.7661  -1.7037   0.6805
 1VK  H15  H  HNH2  0   0.405  -4.1522   1.5036   0.5069
 1VK  H16  H  HNH2  0   0.409  -2.6085   2.2040   0.5982
 1VK  H17  H  HCR6  0   0.271   2.1363   2.1650  -0.5942

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
 1VK  O8   C7   double    1.215  0.020  1.215
 1VK  C10  C11  aromatic  1.384  0.020  1.384
 1VK  C10  C9   aromatic  1.397  0.020  1.397
 1VK  C11  C12  aromatic  1.390  0.020  1.390
 1VK  C7   C9   single    1.479  0.020  1.479
 1VK  C7   C6   single    1.476  0.020  1.476
 1VK  C9   C14  aromatic  1.395  0.020  1.395
 1VK  C6   C2   aromatic  1.438  0.020  1.438
 1VK  C6   N5   aromatic  1.296  0.020  1.296
 1VK  N1   C2   single    1.346  0.020  1.346
 1VK  C12  C13  aromatic  1.388  0.020  1.388
 1VK  C2   N3   aromatic  1.303  0.020  1.303
 1VK  N5   O4   aromatic  1.316  0.020  1.316
 1VK  C14  C13  aromatic  1.387  0.020  1.387
 1VK  N3   O4   aromatic  1.361  0.020  1.361
 1VK  C10  H17  single    0.930  0.020  1.080
 1VK  C11  H18  single    0.930  0.020  1.080
 1VK  C12  H19  single    0.930  0.020  1.080
 1VK  C13  H20  single    0.930  0.020  1.080
 1VK  C14  H21  single    0.930  0.020  1.080
 1VK  N1   H15  single    0.890  0.020  1.040
 1VK  N1   H16  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
 1VK  N3   C2   N1   124.53  3.000
 1VK  N3   C2   C6   107.35  3.000
 1VK  N1   C2   C6   128.03  3.000
 1VK  N5   C6   C7   124.70  3.000
 1VK  N5   C6   C2   107.72  3.000
 1VK  C7   C6   C2   127.47  3.000
 1VK  C9   C7   O8   121.89  3.000
 1VK  C9   C7   C6   120.34  3.000
 1VK  O8   C7   C6   117.76  3.000
 1VK  H17  C10  C9   119.99  3.000
 1VK  H17  C10  C11  119.78  3.000
 1VK  C9   C10  C11  120.22  3.000
 1VK  H18  C11  C12  120.12  3.000
 1VK  H18  C11  C10  119.87  3.000
 1VK  C12  C11  C10  120.01  3.000
 1VK  H19  C12  C13  119.99  3.000
 1VK  H19  C12  C11  119.96  3.000
 1VK  C13  C12  C11  120.06  3.000
 1VK  H20  C13  C14  119.69  3.000
 1VK  H20  C13  C12  120.15  3.000
 1VK  C14  C13  C12  120.16  3.000
 1VK  H21  C14  C9   120.87  3.000
 1VK  H21  C14  C13  119.08  3.000
 1VK  C9   C14  C13  120.03  3.000
 1VK  H16  N1   H15  114.96  3.000
 1VK  H16  N1   C2   117.07  3.000
 1VK  H15  N1   C2   117.12  3.000
 1VK  O4   N3   C2   105.71  3.000
 1VK  N5   O4   N3   112.11  3.000
 1VK  O4   N5   C6   107.11  3.000
 1VK  C14  C9   C10  119.51  3.000
 1VK  C14  C9   C7   122.47  3.000
 1VK  C10  C9   C7   117.96  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
 1VK  CONST_01  O4   N5   C6   C2     0.00   0.0  0
 1VK  CONST_02  N5   O4   N3   C2     0.00   0.0  0
 1VK  CONST_03  O4   N3   C2   C6     0.00   0.0  0
 1VK  CONST_04  N3   O4   N5   C6     0.00   0.0  0
 1VK  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 1VK  CONST_06  C13  C14  C9   C10    0.00   0.0  0
 1VK  CONST_07  C14  C9   C10  C11    0.00   0.0  0
 1VK  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 1VK  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 1VK  CONST_10  C9   C14  C13  C12    0.00   0.0  0
 1VK  CONST_11  N5   C6   C2   N3     0.00   0.0  0
 1VK  CONST_12  C11  C10  C9   C7   180.00   0.0  0
 1VK  CONST_13  C13  C14  C9   C7   180.00   0.0  0
 1VK  CONST_14  N3   C2   C6   C7   180.00   0.0  0
 1VK  CONST_15  O4   N5   C6   C7   180.00   0.0  0
 1VK  CONST_16  N5   C6   C2   N1   180.00   0.0  0
 1VK  CONST_17  O4   N3   C2   N1   180.00   0.0  0
 1VK  CONST_18  H19  C12  C11  C10  180.00   0.0  0
 1VK  CONST_19  H21  C14  C9   C10  180.00   0.0  0
 1VK  CONST_20  H20  C13  C12  C11  180.00   0.0  0
 1VK  CONST_21  H17  C10  C11  C12  180.00   0.0  0
 1VK  CONST_22  H18  C11  C12  C13  180.00   0.0  0
 1VK  CONST_23  H15  N1   C2   C6   180.00   0.0  0
 1VK  Var_01    C9   C7   C6   C2   167.10  30.0  2
 1VK  Var_02    C10  C9   C7   C6   151.30  30.0  2

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
 1VK  plan-1  C2   0.020
 1VK  plan-1  C6   0.020
 1VK  plan-1  C7   0.020
 1VK  plan-1  N1   0.020
 1VK  plan-1  N3   0.020
 1VK  plan-1  O4   0.020
 1VK  plan-1  N5   0.020
 1VK  plan-2  C7   0.020
 1VK  plan-2  C10  0.020
 1VK  plan-2  C11  0.020
 1VK  plan-2  C12  0.020
 1VK  plan-2  C13  0.020
 1VK  plan-2  C14  0.020
 1VK  plan-2  C9   0.020
 1VK  plan-2  H18  0.020
 1VK  plan-2  H19  0.020
 1VK  plan-2  H20  0.020
 1VK  plan-2  H21  0.020
 1VK  plan-2  H17  0.020
 1VK  plan-3  C2   0.020
 1VK  plan-3  N1   0.020
 1VK  plan-3  H15  0.020
 1VK  plan-3  H16  0.020
 1VK  plan-4  C6   0.020
 1VK  plan-4  C7   0.020
 1VK  plan-4  O8   0.020
 1VK  plan-4  C9   0.020

