# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 14:01:29 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(1,3-benzodioxol-4-ylcarbonyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1cccc2OCOc12
#
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
 ONZ  ONZ  N-(1,3-benzodioxol-4-ylcarbonyl)glycine  ligand  25  16  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ONZ
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
 ONZ  C10  C  CR16  0  -0.263  -1.6906  -2.4666   0.1091
 ONZ  C9   C  CR16  0  -0.306  -0.5553  -1.6914   0.2400
 ONZ  C11  C  CR16  0  -0.341  -2.9622  -1.8858   0.0156
 ONZ  C8   C  CR6   0  -0.155  -0.6229  -0.2861   0.2949
 ONZ  C12  C  CR56  0   0.311  -3.0201  -0.5174   0.0730
 ONZ  C16  C  CR56  0   0.302  -1.8847   0.2683   0.2219
 ONZ  C6   C  C     0   0.557   0.5753   0.5792   0.4660
 ONZ  C2   C  C     0   0.524   4.1196  -0.1192  -0.2051
 ONZ  C14  C  CH2   0   0.069  -3.6357   1.6161  -0.0293
 ONZ  C4   C  CH2   0  -0.375   2.9576   0.8073   0.0481
 ONZ  N5   N  NH1   0  -0.655   1.7161   0.0945  -0.0550
 ONZ  O3   O  O     0  -0.434   4.0161  -1.2818  -0.5008
 ONZ  O7   O  O     0  -0.480   0.5159   1.6527   1.0471
 ONZ  O1   O  OH1   0  -0.586   5.2701   0.5180  -0.0697
 ONZ  O13  O  O     0  -0.483  -4.1124   0.2792   0.0147
 ONZ  O15  O  O     0  -0.468  -2.2423   1.5674   0.2555
 ONZ  H1   H  HCR6  0   0.267  -1.5994  -3.5435   0.0805
 ONZ  H2   H  HCR6  0   0.261   0.4036  -2.1847   0.3310
 ONZ  H3   H  HCR6  0   0.281  -3.8524  -2.4900  -0.0935
 ONZ  H4   H  HCH2  0   0.239  -3.7946   2.0373  -1.0268
 ONZ  H5   H  HCH2  0   0.248  -4.1432   2.2169   0.7256
 ONZ  H6   H  HCH2  0   0.296   3.0624   1.2428   1.0438
 ONZ  H7   H  HCH2  0   0.291   3.0158   1.6398  -0.6623
 ONZ  H8   H  HNH1  0   0.409   1.6890  -0.7155  -0.6542
 ONZ  H9   H  HOH1  0   0.489   6.0102  -0.0834  -0.2426

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
 ONZ  O3   C2   double    1.204  0.020  1.204
 ONZ  O1   C2   single    1.322  0.020  1.322
 ONZ  C2   C4   single    1.508  0.020  1.508
 ONZ  C4   N5   single    1.435  0.020  1.435
 ONZ  N5   C6   single    1.345  0.020  1.345
 ONZ  O15  C14  single    1.423  0.020  1.423
 ONZ  O15  C16  single    1.348  0.020  1.348
 ONZ  C14  O13  single    1.420  0.020  1.420
 ONZ  C6   O7   double    1.222  0.020  1.222
 ONZ  C6   C8   single    1.488  0.020  1.488
 ONZ  O13  C12  single    1.353  0.020  1.353
 ONZ  C16  C8   aromatic  1.380  0.020  1.380
 ONZ  C16  C12  aromatic  1.389  0.020  1.389
 ONZ  C8   C9   aromatic  1.408  0.020  1.408
 ONZ  C12  C11  aromatic  1.371  0.020  1.371
 ONZ  C9   C10  aromatic  1.381  0.020  1.381
 ONZ  C11  C10  aromatic  1.401  0.020  1.401
 ONZ  C10  H1   single    0.930  0.020  1.080
 ONZ  C9   H2   single    0.930  0.020  1.080
 ONZ  C11  H3   single    0.930  0.020  1.080
 ONZ  C14  H4   single    0.970  0.020  1.090
 ONZ  C14  H5   single    0.970  0.020  1.090
 ONZ  C4   H6   single    0.970  0.020  1.090
 ONZ  C4   H7   single    0.970  0.020  1.090
 ONZ  N5   H8   single    0.860  0.020  1.020
 ONZ  O1   H9   single    0.850  0.020  0.980

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
 ONZ  H1   C10  C11  119.19  3.000
 ONZ  H1   C10  C9   119.50  3.000
 ONZ  C11  C10  C9   121.31  3.000
 ONZ  H2   C9   C8   119.62  3.000
 ONZ  H2   C9   C10  118.72  3.000
 ONZ  C8   C9   C10  121.64  3.000
 ONZ  H3   C11  C12  121.82  3.000
 ONZ  H3   C11  C10  121.48  3.000
 ONZ  C12  C11  C10  116.70  3.000
 ONZ  C6   C8   C16  120.58  3.000
 ONZ  C16  C8   C9   116.28  3.000
 ONZ  C6   C8   C9   123.12  3.000
 ONZ  O13  C12  C16  109.36  3.000
 ONZ  C16  C12  C11  122.32  3.000
 ONZ  O13  C12  C11  128.31  3.000
 ONZ  O15  C16  C12  109.33  3.000
 ONZ  C12  C16  C8   121.73  3.000
 ONZ  O15  C16  C8   128.93  3.000
 ONZ  O7   C6   N5   122.83  3.000
 ONZ  O7   C6   C8   121.76  3.000
 ONZ  N5   C6   C8   115.41  3.000
 ONZ  O1   C2   O3   124.43  3.000
 ONZ  O1   C2   C4   110.93  3.000
 ONZ  O3   C2   C4   124.64  3.000
 ONZ  H5   C14  H4   110.57  3.000
 ONZ  H5   C14  O15  109.65  3.000
 ONZ  H4   C14  O15  109.74  3.000
 ONZ  H5   C14  O13  109.94  3.000
 ONZ  H4   C14  O13  109.99  3.000
 ONZ  O15  C14  O13  106.88  3.000
 ONZ  H7   C4   H6   106.44  3.000
 ONZ  H7   C4   N5   112.13  3.000
 ONZ  H6   C4   N5   110.28  3.000
 ONZ  H7   C4   C2   108.49  3.000
 ONZ  H6   C4   C2   108.92  3.000
 ONZ  N5   C4   C2   110.45  3.000
 ONZ  H8   N5   C4   117.71  3.000
 ONZ  H8   N5   C6   119.82  3.000
 ONZ  C4   N5   C6   121.81  3.000
 ONZ  H9   O1   C2   110.31  3.000
 ONZ  C14  O13  C12  106.53  3.000
 ONZ  C14  O15  C16  106.72  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
 ONZ  CONST_01  C16  C8   C9   C10    0.00   0.0  0
 ONZ  CONST_02  C16  C12  C11  C10    0.00   0.0  0
 ONZ  CONST_03  C12  C16  C8   C9     0.00   0.0  0
 ONZ  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 ONZ  CONST_05  C8   C16  C12  C11    0.00   0.0  0
 ONZ  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 ONZ  CONST_07  C6   C8   C9   C10  180.00   0.0  0
 ONZ  CONST_08  C6   C8   C16  C12  180.00   0.0  0
 ONZ  CONST_09  O15  C16  C8   C6     0.00   0.0  0
 ONZ  CONST_10  H3   C11  C10  C9   180.00   0.0  0
 ONZ  CONST_11  H2   C9   C10  C11  180.00   0.0  0
 ONZ  CONST_12  H1   C10  C9   C8   180.00   0.0  0
 ONZ  CONST_13  C4   N5   C6   C8   180.00   0.0  0
 ONZ  CONST_14  H8   N5   C6   C8     0.00   0.0  0
 ONZ  CONST_15  O7   C6   N5   C4     0.00   0.0  0
 ONZ  CONST_16  H9   O1   C2   C4   180.00   0.0  0
 ONZ  Var_01    O15  C14  O13  C12  -10.58  30.0  1
 ONZ  Var_02    O13  C14  O15  C16   10.49  30.0  1
 ONZ  Var_03    N5   C6   C8   C9    30.77  30.0  2
 ONZ  Var_04    C2   C4   N5   C6   161.80  30.0  1
 ONZ  Var_05    O3   C2   C4   N5     2.55  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
 ONZ  plan-1  C8   0.020
 ONZ  plan-1  C6   0.020
 ONZ  plan-1  C4   0.020
 ONZ  plan-1  N5   0.020
 ONZ  plan-1  O7   0.020
 ONZ  plan-1  H8   0.020
 ONZ  plan-2  C10  0.020
 ONZ  plan-2  C9   0.020
 ONZ  plan-2  C11  0.020
 ONZ  plan-2  C8   0.020
 ONZ  plan-2  C12  0.020
 ONZ  plan-2  C16  0.020
 ONZ  plan-2  C6   0.020
 ONZ  plan-2  O13  0.020
 ONZ  plan-2  O15  0.020
 ONZ  plan-2  H1   0.020
 ONZ  plan-2  H2   0.020
 ONZ  plan-2  H3   0.020
 ONZ  plan-3  C2   0.020
 ONZ  plan-3  C4   0.020
 ONZ  plan-3  O3   0.020
 ONZ  plan-3  O1   0.020
 ONZ  plan-3  H9   0.020

