# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:58:08 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: ethyl {3-[(4-amino-1,2,5-oxadiazol-3-yl)carbonyl]phenoxy}acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)COc1cccc(c1)C(=O)c2nonc2N
#
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
 1VJ  1VJ  'ethyl {3-[(4-amino-1,2,5-oxadiazol-3-yl)carbonyl]phenoxy}acetate'  ligand  34  21  .  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_1VJ
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
 1VJ  C1   C  CH3   0  -0.689   8.0049  -0.2646  -0.1852
 1VJ  C2   C  CH2   0  -0.181   6.8435   0.6985  -0.1908
 1VJ  C6   C  CH2   0  -0.302   3.3481  -0.4290   0.0577
 1VJ  C8   C  CR6   0   0.413   0.9878  -0.3796   0.1627
 1VJ  C10  C  CR16  0  -0.227  -0.3603  -2.3496   0.4476
 1VJ  C11  C  CR16  0  -0.283  -1.5178  -1.5939   0.3993
 1VJ  C12  C  CR6   0   0.018  -1.4171  -0.2104   0.2409
 1VJ  C13  C  CR16  0  -0.372  -0.1693   0.3930   0.1395
 1VJ  C14  C  C     0   0.365  -2.6039   0.6776   0.2378
 1VJ  C16  C  CR5   0   0.038  -3.8714   0.2160  -0.3571
 1VJ  O3   O  O2    0  -0.456   5.6351  -0.0752  -0.0725
 1VJ  C4   C  C     0   0.563   4.4802   0.5632  -0.0746
 1VJ  O5   O  O     0  -0.434   4.3448   1.7531  -0.1676
 1VJ  O7   O  O2    0  -0.464   2.1475   0.2943   0.0296
 1VJ  C9   C  CR16  0  -0.367   0.8912  -1.7600   0.3211
 1VJ  O15  O  O     0  -0.374  -2.5607   1.8027   0.6917
 1VJ  N17  N  N     0  -0.092  -3.9957  -0.8437  -1.0941
 1VJ  O18  O  O     0  -0.201  -5.2513  -0.9028  -1.4789
 1VJ  N19  N  N     0  -0.193  -5.9867   0.1347  -0.9936
 1VJ  C20  C  CR5   0   0.394  -5.1558   0.8609  -0.2982
 1VJ  N21  N  NH2   0  -0.838  -5.4818   2.0168   0.3024
 1VJ  H22  H  HCH3  0   0.238   8.0401  -0.8436   0.7375
 1VJ  H24  H  HCH3  0   0.239   7.9597  -0.9516  -1.0297
 1VJ  H23  H  HCH3  0   0.242   8.9346   0.2984  -0.2610
 1VJ  H25  H  HCH2  0   0.241   6.9095   1.3980   0.6444
 1VJ  H26  H  HCH2  0   0.241   6.8172   1.2765  -1.1162
 1VJ  H28  H  HCH2  0   0.276   3.4105  -1.1531  -0.7633
 1VJ  H27  H  HCH2  0   0.276   3.4708  -0.9852   0.9947
 1VJ  H30  H  HCR6  0   0.274  -0.4242  -3.4206   0.5838
 1VJ  H31  H  HCR6  0   0.268  -2.4764  -2.0782   0.5130
 1VJ  H32  H  HCR6  0   0.278  -0.0848   1.4662   0.0231
 1VJ  H29  H  HCR6  0   0.295   1.7687  -2.3911   0.3520
 1VJ  H34  H  HNH2  0   0.410  -4.8584   2.3841   0.9995
 1VJ  H33  H  HNH2  0   0.406  -6.4586   2.2185   0.4375

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
 1VJ  C1   C2   single    1.509  0.020  1.509
 1VJ  C2   O3   single    1.440  0.020  1.440
 1VJ  O3   C4   single    1.320  0.020  1.320
 1VJ  C4   C6   single    1.511  0.020  1.511
 1VJ  C4   O5   double    1.201  0.020  1.201
 1VJ  C6   O7   single    1.402  0.020  1.402
 1VJ  O7   C8   single    1.348  0.020  1.348
 1VJ  O15  C14  double    1.214  0.020  1.214
 1VJ  C13  C8   aromatic  1.391  0.020  1.391
 1VJ  C13  C12  aromatic  1.390  0.020  1.390
 1VJ  C8   C9   aromatic  1.393  0.020  1.393
 1VJ  C14  C12  single    1.482  0.020  1.482
 1VJ  C14  C16  single    1.474  0.020  1.474
 1VJ  C12  C11  aromatic  1.396  0.020  1.396
 1VJ  N21  C20  single    1.343  0.020  1.343
 1VJ  C16  C20  aromatic  1.438  0.020  1.438
 1VJ  C16  N17  aromatic  1.297  0.020  1.297
 1VJ  C9   C10  aromatic  1.389  0.020  1.389
 1VJ  C20  N19  aromatic  1.304  0.020  1.304
 1VJ  N17  O18  aromatic  1.315  0.020  1.315
 1VJ  C11  C10  aromatic  1.383  0.020  1.383
 1VJ  N19  O18  aromatic  1.361  0.020  1.361
 1VJ  C1   H22  single    0.970  0.020  1.090
 1VJ  C1   H24  single    0.970  0.020  1.090
 1VJ  C1   H23  single    0.970  0.020  1.090
 1VJ  C2   H25  single    0.970  0.020  1.090
 1VJ  C2   H26  single    0.970  0.020  1.090
 1VJ  C6   H28  single    0.970  0.020  1.090
 1VJ  C6   H27  single    0.970  0.020  1.090
 1VJ  C10  H30  single    0.930  0.020  1.080
 1VJ  C11  H31  single    0.930  0.020  1.080
 1VJ  C13  H32  single    0.930  0.020  1.080
 1VJ  C9   H29  single    0.930  0.020  1.080
 1VJ  N21  H34  single    0.890  0.020  1.040
 1VJ  N21  H33  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
 1VJ  H23  C1   H24  107.89  3.000
 1VJ  H23  C1   H22  107.81  3.000
 1VJ  H24  C1   H22  108.82  3.000
 1VJ  H23  C1   C2   109.07  3.000
 1VJ  H24  C1   C2   111.57  3.000
 1VJ  H22  C1   C2   111.54  3.000
 1VJ  H26  C2   H25  108.11  3.000
 1VJ  H26  C2   O3   109.52  3.000
 1VJ  H25  C2   O3   109.41  3.000
 1VJ  H26  C2   C1   111.08  3.000
 1VJ  H25  C2   C1   111.08  3.000
 1VJ  O3   C2   C1   107.62  3.000
 1VJ  H27  C6   H28  107.36  3.000
 1VJ  H27  C6   O7   112.00  3.000
 1VJ  H28  C6   O7   111.99  3.000
 1VJ  H27  C6   C4   108.91  3.000
 1VJ  H28  C6   C4   108.99  3.000
 1VJ  O7   C6   C4   107.52  3.000
 1VJ  C9   C8   O7   124.50  3.000
 1VJ  C9   C8   C13  119.63  3.000
 1VJ  O7   C8   C13  115.87  3.000
 1VJ  H30  C10  C9   119.02  3.000
 1VJ  H30  C10  C11  119.73  3.000
 1VJ  C9   C10  C11  121.25  3.000
 1VJ  H31  C11  C12  121.35  3.000
 1VJ  H31  C11  C10  119.61  3.000
 1VJ  C12  C11  C10  119.01  3.000
 1VJ  C14  C12  C13  117.30  3.000
 1VJ  C14  C12  C11  122.43  3.000
 1VJ  C13  C12  C11  120.21  3.000
 1VJ  H32  C13  C12  120.54  3.000
 1VJ  H32  C13  C8   119.16  3.000
 1VJ  C12  C13  C8   120.29  3.000
 1VJ  O15  C14  C16  118.14  3.000
 1VJ  C16  C14  C12  120.11  3.000
 1VJ  O15  C14  C12  121.73  3.000
 1VJ  C20  C16  N17  107.70  3.000
 1VJ  N17  C16  C14  124.58  3.000
 1VJ  C20  C16  C14  127.65  3.000
 1VJ  C4   O3   C2   118.33  3.000
 1VJ  O5   C4   O3   125.31  3.000
 1VJ  O5   C4   C6   124.94  3.000
 1VJ  O3   C4   C6   109.75  3.000
 1VJ  C8   O7   C6   118.49  3.000
 1VJ  H29  C9   C10  118.73  3.000
 1VJ  H29  C9   C8   121.70  3.000
 1VJ  C10  C9   C8   119.57  3.000
 1VJ  O18  N17  C16  107.14  3.000
 1VJ  N19  O18  N17  112.18  3.000
 1VJ  C20  N19  O18  105.68  3.000
 1VJ  N21  C20  N19  124.27  3.000
 1VJ  N19  C20  C16  107.30  3.000
 1VJ  N21  C20  C16  128.39  3.000
 1VJ  H33  N21  H34  115.83  3.000
 1VJ  H33  N21  C20  117.92  3.000
 1VJ  H34  N21  C20  118.31  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
 1VJ  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 1VJ  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 1VJ  CONST_03  C13  C8   C9   C10     0.00   0.0  0
 1VJ  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 1VJ  CONST_05  C9   C8   C13  C12     0.00   0.0  0
 1VJ  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 1VJ  CONST_07  O18  N19  C20  C16     0.00   0.0  0
 1VJ  CONST_08  N19  O18  N17  C16     0.00   0.0  0
 1VJ  CONST_09  N19  C20  C16  N17     0.00   0.0  0
 1VJ  CONST_10  C20  N19  O18  N17     0.00   0.0  0
 1VJ  CONST_11  C20  C16  N17  O18     0.00   0.0  0
 1VJ  CONST_12  C14  C12  C13  C8    180.00   0.0  0
 1VJ  CONST_13  O7   C8   C9   C10   180.00   0.0  0
 1VJ  CONST_14  C14  C12  C11  C10   180.00   0.0  0
 1VJ  CONST_15  O7   C8   C13  C12   180.00   0.0  0
 1VJ  CONST_16  N19  C20  C16  C14   180.00   0.0  0
 1VJ  CONST_17  O18  N17  C16  C14   180.00   0.0  0
 1VJ  CONST_18  N21  C20  C16  N17   180.00   0.0  0
 1VJ  CONST_19  N21  C20  N19  O18   180.00   0.0  0
 1VJ  CONST_20  H30  C10  C9   C8    180.00   0.0  0
 1VJ  CONST_21  H32  C13  C12  C11   180.00   0.0  0
 1VJ  CONST_22  H29  C9   C10  C11   180.00   0.0  0
 1VJ  CONST_23  H31  C11  C12  C13   180.00   0.0  0
 1VJ  CONST_25  H33  N21  C20  C16   180.00   0.0  0
 1VJ  Var_01    C16  C14  C12  C11   -35.37  30.0  2
 1VJ  Var_02    C20  C16  C14  C12   171.28  30.0  2
 1VJ  Var_03    C13  C8   O7   C6    179.43  30.0  2
 1VJ  Var_04    C4   C6   O7   C8   -178.55  30.0  1
 1VJ  Var_05    C6   C4   O3   C2    179.97  30.0  3
 1VJ  Var_06    O7   C6   C4   O3   -179.11  30.0  3
 1VJ  Var_07    H22  C1   C2   O3    -60.31  30.0  3
 1VJ  Var_08    H25  C2   O3   C4     60.13  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
 1VJ  plan-1  C14  0.020
 1VJ  plan-1  C16  0.020
 1VJ  plan-1  N17  0.020
 1VJ  plan-1  O18  0.020
 1VJ  plan-1  N19  0.020
 1VJ  plan-1  C20  0.020
 1VJ  plan-1  N21  0.020
 1VJ  plan-2  C8   0.020
 1VJ  plan-2  C10  0.020
 1VJ  plan-2  C11  0.020
 1VJ  plan-2  C12  0.020
 1VJ  plan-2  C13  0.020
 1VJ  plan-2  C14  0.020
 1VJ  plan-2  O7   0.020
 1VJ  plan-2  C9   0.020
 1VJ  plan-2  H30  0.020
 1VJ  plan-2  H31  0.020
 1VJ  plan-2  H32  0.020
 1VJ  plan-2  H29  0.020
 1VJ  plan-3  C20  0.020
 1VJ  plan-3  N21  0.020
 1VJ  plan-3  H34  0.020
 1VJ  plan-3  H33  0.020
 1VJ  plan-4  C12  0.020
 1VJ  plan-4  C14  0.020
 1VJ  plan-4  C16  0.020
 1VJ  plan-4  O15  0.020
 1VJ  plan-5  C6   0.020
 1VJ  plan-5  O3   0.020
 1VJ  plan-5  C4   0.020
 1VJ  plan-5  O5   0.020

