# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 16:22:18 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: ~{N}-[(2~{R})-2-(4-nitrophenyl)-2-oxidanyl-ethyl]-1,3-benzodioxole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CNC(=O)c1ccc2OCOc2c1)c3ccc(cc3)[N+]([O-])=O
#
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
 8YW  8YW  ~{N}-[(2~{R})-2-(4-nitrophenyl)-2-oxidanyl-ethyl]-1,3-benzodioxole-5-carboxamide  ligand  38  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8YW
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
 8YW  O24  O  O      0  -0.380  -7.3023  -1.2980  -1.0594
 8YW  O25  O  O     -1  -0.380  -7.7439   0.0584   0.5262
 8YW  N23  N  N      1   0.330  -6.9732  -0.4750  -0.2371
 8YW  C3   C  CR6    0   0.238  -5.5707  -0.1037  -0.1644
 8YW  C4   C  CR16   0  -0.251  -4.6672  -0.6865  -1.0424
 8YW  C5   C  CR16   0  -0.284  -3.3365  -0.3250  -0.9613
 8YW  C2   C  CR16   0  -0.246  -5.1628   0.8271   0.7780
 8YW  C1   C  CR16   0  -0.319  -3.8241   1.1786   0.8412
 8YW  C6   C  CR6    0   0.102  -2.8960   0.6053  -0.0202
 8YW  C7   C  CH1    0  -0.020  -1.4228   0.9468   0.0398
 8YW  O22  O  OH1    0  -0.651  -1.1483   2.0947   0.7957
 8YW  C9   C  CH2    0  -0.328  -0.6345  -0.2661   0.5510
 8YW  N10  N  NH1    0  -0.641   0.7850  -0.0264   0.5334
 8YW  C11  C  C      0   0.526   1.6453  -0.6534  -0.2898
 8YW  O12  O  O      0  -0.488   1.3171  -1.5658  -1.0363
 8YW  C13  C  CR6    0  -0.053   3.0626  -0.1893  -0.2207
 8YW  C18  C  CR16   0  -0.365   4.0644  -1.1341  -0.5053
 8YW  C17  C  CR56   0   0.319   5.3612  -0.6990  -0.4601
 8YW  O19  O  O      0  -0.485   6.4939  -1.4033  -0.6836
 8YW  C20  C  CH2    0   0.072   7.5826  -0.5143  -0.4670
 8YW  O21  O  O      0  -0.479   7.0261   0.7729  -0.2212
 8YW  C16  C  CR56   0   0.308   5.6875   0.6209  -0.1791
 8YW  C15  C  CR16   0  -0.330   4.7244   1.5644   0.0787
 8YW  C14  C  CR16   0  -0.302   3.3948   1.1306   0.0601
 8YW  H1   H  HCR6   0   0.298  -4.9856  -1.4071  -1.7814
 8YW  H2   H  HCR6   0   0.272  -2.6336  -0.7744  -1.6522
 8YW  H3   H  HCR6   0   0.298  -5.8654   1.2820   1.4608
 8YW  H4   H  HCR6   0   0.266  -3.5238   1.9149   1.5739
 8YW  H5   H  HCH1   0   0.270  -1.0852   1.1669  -0.9781
 8YW  H6   H  HOH1   0   0.456  -1.2577   1.8942   1.7330
 8YW  H7   H  HCH2   0   0.268  -0.9567  -0.5040   1.5689
 8YW  H8   H  HCH2   0   0.269  -0.8469  -1.1399  -0.0623
 8YW  H9   H  HNH1   0   0.406   1.1393   0.6699   1.1677
 8YW  H10  H  HCR6   0   0.277   3.8193  -2.1608  -0.7401
 8YW  H11  H  HCH2   0   0.241   8.1619  -0.8370   0.4023
 8YW  H12  H  HCR6   0   0.281   4.9740   2.5971   0.2791
 8YW  H13  H  HCR6   0   0.261   2.6205   1.8652   0.2386
 8YW  H15  H  HCH2   0   0.246   8.2159  -0.4804  -1.3548

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
 8YW  O19  C20  single    1.422  0.020  1.422
 8YW  O19  C17  single    1.352  0.020  1.352
 8YW  C20  O21  single    1.424  0.020  1.424
 8YW  C17  C18  aromatic  1.369  0.020  1.369
 8YW  C17  C16  aromatic  1.388  0.020  1.388
 8YW  C18  C13  aromatic  1.406  0.020  1.406
 8YW  O21  C16  single    1.348  0.020  1.348
 8YW  O12  C11  double    1.224  0.020  1.224
 8YW  C16  C15  aromatic  1.373  0.020  1.373
 8YW  C13  C11  single    1.493  0.020  1.493
 8YW  C13  C14  aromatic  1.390  0.020  1.390
 8YW  C11  N10  single    1.346  0.020  1.346
 8YW  C15  C14  aromatic  1.399  0.020  1.399
 8YW  O25  N23  single    1.209  0.020  1.209
 8YW  C9   N10  single    1.440  0.020  1.440
 8YW  C9   C7   single    1.534  0.020  1.534
 8YW  C5   C4   aromatic  1.381  0.020  1.381
 8YW  C5   C6   aromatic  1.395  0.020  1.395
 8YW  C4   C3   aromatic  1.388  0.020  1.388
 8YW  N23  C3   single    1.453  0.020  1.453
 8YW  N23  O24  double    1.209  0.020  1.209
 8YW  C6   C7   single    1.513  0.020  1.513
 8YW  C6   C1   aromatic  1.390  0.020  1.390
 8YW  C3   C2   aromatic  1.386  0.020  1.386
 8YW  C7   O22  single    1.402  0.020  1.402
 8YW  C1   C2   aromatic  1.386  0.020  1.386
 8YW  C4   H1   single    0.930  0.020  1.080
 8YW  C5   H2   single    0.930  0.020  1.080
 8YW  C2   H3   single    0.930  0.020  1.080
 8YW  C1   H4   single    0.930  0.020  1.080
 8YW  C7   H5   single    0.970  0.020  1.090
 8YW  O22  H6   single    0.850  0.020  0.980
 8YW  C9   H7   single    0.970  0.020  1.090
 8YW  C9   H8   single    0.970  0.020  1.090
 8YW  N10  H9   single    0.860  0.020  1.020
 8YW  C18  H10  single    0.930  0.020  1.080
 8YW  C20  H11  single    0.970  0.020  1.090
 8YW  C15  H12  single    0.930  0.020  1.080
 8YW  C14  H13  single    0.930  0.020  1.080
 8YW  C20  H15  single    0.970  0.020  1.090

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
 8YW  C3   N23  O25  118.11  3.000
 8YW  C3   N23  O24  118.09  3.000
 8YW  O25  N23  O24  123.80  3.000
 8YW  C2   C3   C4   121.37  3.000
 8YW  C2   C3   N23  119.33  3.000
 8YW  C4   C3   N23  119.30  3.000
 8YW  H1   C4   C5   119.92  3.000
 8YW  H1   C4   C3   121.40  3.000
 8YW  C5   C4   C3   118.68  3.000
 8YW  H2   C5   C6   120.14  3.000
 8YW  H2   C5   C4   118.62  3.000
 8YW  C6   C5   C4   121.23  3.000
 8YW  H3   C2   C1   119.53  3.000
 8YW  H3   C2   C3   121.41  3.000
 8YW  C1   C2   C3   119.06  3.000
 8YW  H4   C1   C6   121.03  3.000
 8YW  H4   C1   C2   118.16  3.000
 8YW  C6   C1   C2   120.81  3.000
 8YW  C7   C6   C1   122.16  3.000
 8YW  C1   C6   C5   118.84  3.000
 8YW  C7   C6   C5   118.99  3.000
 8YW  H5   C7   C9   108.08  3.000
 8YW  H5   C7   O22  106.04  3.000
 8YW  C9   C7   O22  111.54  3.000
 8YW  H5   C7   C6   107.98  3.000
 8YW  O22  C7   C6   113.38  3.000
 8YW  C9   C7   C6   109.57  3.000
 8YW  H6   O22  C7   109.36  3.000
 8YW  H8   C9   H7   106.99  3.000
 8YW  H8   C9   N10  108.62  3.000
 8YW  H7   C9   N10  109.76  3.000
 8YW  H8   C9   C7   110.28  3.000
 8YW  H7   C9   C7   109.31  3.000
 8YW  N10  C9   C7   111.77  3.000
 8YW  H9   N10  C11  118.88  3.000
 8YW  H9   N10  C9   117.04  3.000
 8YW  C11  N10  C9   124.07  3.000
 8YW  C13  C11  O12  120.97  3.000
 8YW  C13  C11  N10  115.70  3.000
 8YW  O12  C11  N10  123.31  3.000
 8YW  C14  C13  C18  120.58  3.000
 8YW  C14  C13  C11  122.11  3.000
 8YW  C18  C13  C11  117.27  3.000
 8YW  H10  C18  C17  121.59  3.000
 8YW  H10  C18  C13  121.35  3.000
 8YW  C17  C18  C13  117.05  3.000
 8YW  C16  C17  O19  109.37  3.000
 8YW  C16  C17  C18  122.12  3.000
 8YW  O19  C17  C18  128.51  3.000
 8YW  C20  O19  C17  106.89  3.000
 8YW  H15  C20  H11  110.40  3.000
 8YW  H15  C20  O21  109.83  3.000
 8YW  H11  C20  O21  109.68  3.000
 8YW  H15  C20  O19  109.87  3.000
 8YW  H11  C20  O19  110.01  3.000
 8YW  O21  C20  O19  106.99  3.000
 8YW  C16  O21  C20  106.96  3.000
 8YW  C15  C16  O21  128.70  3.000
 8YW  C15  C16  C17  121.77  3.000
 8YW  O21  C16  C17  109.53  3.000
 8YW  H12  C15  C14  121.21  3.000
 8YW  H12  C15  C16  121.97  3.000
 8YW  C14  C15  C16  116.83  3.000
 8YW  H13  C14  C15  117.86  3.000
 8YW  H13  C14  C13  120.47  3.000
 8YW  C15  C14  C13  121.63  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
 8YW  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 8YW  CONST_02  C6   C1   C2   C3      0.00   0.0  0
 8YW  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 8YW  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 8YW  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 8YW  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 8YW  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 8YW  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 8YW  CONST_09  C15  C16  C17  C18     0.00   0.0  0
 8YW  CONST_10  C15  C14  C13  C18     0.00   0.0  0
 8YW  CONST_11  C14  C13  C18  C17     0.00   0.0  0
 8YW  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 8YW  CONST_13  C5   C4   C3   N23   180.00   0.0  0
 8YW  CONST_14  C1   C2   C3   N23   180.00   0.0  0
 8YW  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 8YW  CONST_16  C7   C6   C1   C2    180.00   0.0  0
 8YW  CONST_17  C17  C18  C13  C11   180.00   0.0  0
 8YW  CONST_18  C15  C14  C13  C11   180.00   0.0  0
 8YW  CONST_19  H2   C5   C4   C3    180.00   0.0  0
 8YW  CONST_20  H4   C1   C2   C3    180.00   0.0  0
 8YW  CONST_21  H3   C2   C3   C4    180.00   0.0  0
 8YW  CONST_22  H1   C4   C3   C2    180.00   0.0  0
 8YW  CONST_23  H12  C15  C14  C13   180.00   0.0  0
 8YW  CONST_24  H13  C14  C13  C18   180.00   0.0  0
 8YW  CONST_25  H10  C18  C17  O19     0.00   0.0  0
 8YW  CONST_26  C4   C3   N23  O24     0.00   0.0  0
 8YW  CONST_27  C2   C3   N23  O24   180.00   0.0  0
 8YW  CONST_28  C4   C3   N23  O25   180.00   0.0  0
 8YW  CONST_29  C2   C3   N23  O25     0.00   0.0  0
 8YW  CONST_30  C13  C11  N10  C9    180.00   0.0  0
 8YW  CONST_31  H9   N10  C11  C13     0.00   0.0  0
 8YW  CONST_32  O12  C11  N10  C9      0.00   0.0  0
 8YW  Var_01    O21  C20  O19  C17    -5.01  30.0  1
 8YW  Var_02    C16  C17  O19  C20     3.13  30.0  1
 8YW  Var_03    C15  C16  O21  C20   177.39  30.0  1
 8YW  Var_04    C18  C13  C11  N10   150.00  30.0  2
 8YW  Var_05    C11  N10  C9   C7   -111.76  30.0  3

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
 8YW  chir_01  C7  C9  C6  O22  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
 8YW  plan-1  N23  0.020
 8YW  plan-1  C3   0.020
 8YW  plan-1  C4   0.020
 8YW  plan-1  C5   0.020
 8YW  plan-1  C2   0.020
 8YW  plan-1  C1   0.020
 8YW  plan-1  C6   0.020
 8YW  plan-1  C7   0.020
 8YW  plan-1  H1   0.020
 8YW  plan-1  H2   0.020
 8YW  plan-1  H3   0.020
 8YW  plan-1  H4   0.020
 8YW  plan-2  C11  0.020
 8YW  plan-2  C13  0.020
 8YW  plan-2  C18  0.020
 8YW  plan-2  C17  0.020
 8YW  plan-2  O19  0.020
 8YW  plan-2  O21  0.020
 8YW  plan-2  C16  0.020
 8YW  plan-2  C15  0.020
 8YW  plan-2  C14  0.020
 8YW  plan-2  H10  0.020
 8YW  plan-2  H12  0.020
 8YW  plan-2  H13  0.020
 8YW  plan-3  C9   0.020
 8YW  plan-3  N10  0.020
 8YW  plan-3  C11  0.020
 8YW  plan-3  O12  0.020
 8YW  plan-3  C13  0.020
 8YW  plan-3  H9   0.020
 8YW  plan-4  O24  0.020
 8YW  plan-4  O25  0.020
 8YW  plan-4  N23  0.020
 8YW  plan-4  C3   0.020

