# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:38:44 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-[(1E)-1-bromo-1-(2-methoxyphenyl)-3-oxo-3-(piperidin-1-yl)prop-1-en-2-yl]-4-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1\C(Br)=C(\NC(=O)c2ccc(cc2)[N+]([O-])=O)C(=O)N3CCCCC3
#
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
 0YP  0YP  N-[(1E)-1-bromo-1-(2-methoxyphenyl)-3-oxo-3-(piperidin-1-yl)prop-1-en-2-yl]-4-nitrobenzamide  ligand  53  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0YP
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
 0YP  C1   C   C      0   0.557  -1.8523   0.7551  -0.1592
 0YP  N1   N   NH1    0  -0.717  -0.9630  -0.1408   0.3346
 0YP  O1   O   O      0  -0.440  -1.5106   1.7992  -0.6801
 0YP  C2   C   C      0   0.305   0.4114   0.0850   0.3368
 0YP  N2   N   NT     0  -0.428   1.5673   2.2038  -0.1727
 0YP  O2   O   O      0  -0.485   0.4598   1.9031   1.7837
 0YP  C3   C   C      0   0.510   0.8188   1.5029   0.6850
 0YP  C4   C   CH2    0  -0.305   1.9681   3.5582   0.1829
 0YP  C5   C   CH2    0  -0.436   3.4103   3.8201  -0.2218
 0YP  C6   C   CH2    0  -0.444   3.6199   3.5393  -1.7036
 0YP  C7   C   CH2    0  -0.439   3.1798   2.1178  -2.0258
 0YP  C8   C   CH2    0  -0.303   1.7469   1.8681  -1.5777
 0YP  C9   C   C      0  -0.210   1.3095  -0.9030   0.2918
 0YP  C10  C   CR6    0  -0.077   2.7531  -0.7306   0.4907
 0YP  C11  C   CR6    0   0.390   3.6535  -1.0557  -0.5372
 0YP  C12  C   CR16   0  -0.374   5.0206  -0.8930  -0.3334
 0YP  C13  C   CR16   0  -0.238   5.4844  -0.3981   0.8791
 0YP  C14  C   CR16   0  -0.272   4.6042  -0.0692   1.8977
 0YP  C15  C   CR16   0  -0.249   3.2430  -0.2474   1.6989
 0YP  C16  C   CR6    0  -0.027  -3.2918   0.3831  -0.0153
 0YP  C17  C   CR16   0  -0.259  -4.2225   1.4121   0.0977
 0YP  C18  C   CR16   0  -0.253  -5.5693   1.1282   0.2301
 0YP  C19  C   CR6    0   0.259  -5.9741  -0.1980   0.2277
 0YP  C20  C   CR16   0  -0.250  -5.0702  -1.2391   0.0924
 0YP  C21  C   CR16   0  -0.276  -3.7243  -0.9399  -0.0277
 0YP  N01  N   N      1   0.332  -7.3931  -0.5070   0.3668
 0YP  O01  O   O     -1  -0.371  -7.7182  -1.6694   0.3912
 0YP  C02  C   CH3    0  -0.440   3.9545  -1.8197  -2.7630
 0YP  O02  O   O      0  -0.370  -8.1670   0.4156   0.4511
 0YP  O03  O   O2     0  -0.457   3.1056  -1.4889  -1.6809
 0YP  BR1  BR  BR     0  -0.025   0.7237  -2.7007   0.0869
 0YP  H1   H   HNH1   0   0.424  -1.3055  -0.9587   0.8172
 0YP  H3   H   HCH2   0   0.234   1.3031   4.2689  -0.3232
 0YP  H4   H   HCH2   0   0.264   1.8382   3.6981   1.2523
 0YP  H5   H   HCH2   0   0.240   3.6593   4.8553   0.0196
 0YP  H6   H   HCH2   0   0.224   4.0698   3.1820   0.3736
 0YP  H7   H   HCH2   0   0.216   3.0343   4.2510  -2.2954
 0YP  H8   H   HCH2   0   0.239   4.6658   3.6866  -1.9796
 0YP  H9   H   HCH2   0   0.239   3.2467   1.9191  -3.0976
 0YP  H10  H   HCH2   0   0.233   3.8449   1.4106  -1.5250
 0YP  H11  H   HCH2   0   0.267   1.4659   0.8332  -1.7518
 0YP  H12  H   HCH2   0   0.240   1.0644   2.4888  -2.1696
 0YP  H14  H   HCR6   0   0.284   5.7331  -1.1339  -1.1106
 0YP  H15  H   HCR6   0   0.265   6.5499  -0.2714   1.0204
 0YP  H16  H   HCR6   0   0.258   4.9702   0.3135   2.8404
 0YP  H17  H   HCR6   0   0.263   2.5451  -0.0124   2.4923
 0YP  H18  H   HCR6   0   0.285  -3.8966   2.4429   0.0934
 0YP  H19  H   HCR6   0   0.307  -6.2803   1.9344   0.3318
 0YP  H20  H   HCR6   0   0.308  -5.3940  -2.2690   0.0752
 0YP  H21  H   HCR6   0   0.277  -3.0302  -1.7595  -0.1584
 0YP  H01  H   HCH3   0   0.234   4.6457  -2.6265  -2.5074
 0YP  H04  H   HCH3   0   0.262   3.3073  -2.1537  -3.5697
 0YP  H05  H   HCH3   0   0.230   4.5293  -0.9555  -3.1053

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
 0YP  C02  O03  single    1.415  0.020  1.415
 0YP  C6   C7   single    1.523  0.020  1.523
 0YP  C6   C5   single    1.523  0.020  1.523
 0YP  C7   C8   single    1.522  0.020  1.522
 0YP  O03  C11  single    1.340  0.020  1.340
 0YP  C5   C4   single    1.521  0.020  1.521
 0YP  C8   N2   single    1.456  0.020  1.456
 0YP  C12  C11  aromatic  1.392  0.020  1.392
 0YP  C12  C13  aromatic  1.389  0.020  1.389
 0YP  BR1  C9   single    1.902  0.020  1.902
 0YP  C11  C10  aromatic  1.405  0.020  1.405
 0YP  C4   N2   single    1.456  0.020  1.456
 0YP  N2   C3   single    1.337  0.020  1.337
 0YP  C13  C14  aromatic  1.386  0.020  1.386
 0YP  C10  C9   single    1.467  0.020  1.467
 0YP  C10  C15  aromatic  1.390  0.020  1.390
 0YP  C9   C2   double    1.336  0.020  1.336
 0YP  C3   C2   single    1.516  0.020  1.516
 0YP  C3   O2   double    1.223  0.020  1.223
 0YP  C2   N1   single    1.393  0.020  1.393
 0YP  C14  C15  aromatic  1.387  0.020  1.387
 0YP  O1   C1   double    1.216  0.020  1.216
 0YP  N1   C1   single    1.356  0.020  1.356
 0YP  C1   C16  single    1.494  0.020  1.494
 0YP  C16  C17  aromatic  1.392  0.020  1.392
 0YP  C16  C21  aromatic  1.392  0.020  1.392
 0YP  C17  C18  aromatic  1.383  0.020  1.383
 0YP  C21  C20  aromatic  1.384  0.020  1.384
 0YP  C18  C19  aromatic  1.387  0.020  1.387
 0YP  C20  C19  aromatic  1.385  0.020  1.385
 0YP  C19  N01  single    1.459  0.020  1.459
 0YP  N01  O02  double    1.207  0.020  1.207
 0YP  N01  O01  single    1.207  0.020  1.207
 0YP  N1   H1   single    0.860  0.020  1.020
 0YP  C4   H3   single    0.970  0.020  1.090
 0YP  C4   H4   single    0.970  0.020  1.090
 0YP  C5   H5   single    0.970  0.020  1.090
 0YP  C5   H6   single    0.970  0.020  1.090
 0YP  C6   H7   single    0.970  0.020  1.090
 0YP  C6   H8   single    0.970  0.020  1.090
 0YP  C7   H9   single    0.970  0.020  1.090
 0YP  C7   H10  single    0.970  0.020  1.090
 0YP  C8   H11  single    0.970  0.020  1.090
 0YP  C8   H12  single    0.970  0.020  1.090
 0YP  C12  H14  single    0.930  0.020  1.080
 0YP  C13  H15  single    0.930  0.020  1.080
 0YP  C14  H16  single    0.930  0.020  1.080
 0YP  C15  H17  single    0.930  0.020  1.080
 0YP  C17  H18  single    0.930  0.020  1.080
 0YP  C18  H19  single    0.930  0.020  1.080
 0YP  C20  H20  single    0.930  0.020  1.080
 0YP  C21  H21  single    0.930  0.020  1.080
 0YP  C02  H01  single    0.970  0.020  1.090
 0YP  C02  H04  single    0.970  0.020  1.090
 0YP  C02  H05  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
 0YP  C16  C1   O1   121.74  3.000
 0YP  C16  C1   N1   115.63  3.000
 0YP  O1   C1   N1   122.63  3.000
 0YP  H1   N1   C2   117.74  3.000
 0YP  H1   N1   C1   119.14  3.000
 0YP  C2   N1   C1   122.74  3.000
 0YP  C9   C2   C3   121.25  3.000
 0YP  C3   C2   N1   114.66  3.000
 0YP  C9   C2   N1   122.91  3.000
 0YP  C8   N2   C4   114.59  3.000
 0YP  C4   N2   C3   119.01  3.000
 0YP  C8   N2   C3   124.57  3.000
 0YP  O2   C3   N2   124.69  3.000
 0YP  O2   C3   C2   115.69  3.000
 0YP  N2   C3   C2   119.57  3.000
 0YP  H4   C4   H3   107.35  3.000
 0YP  H4   C4   C5   110.68  3.000
 0YP  H3   C4   C5   109.91  3.000
 0YP  H4   C4   N2   109.10  3.000
 0YP  H3   C4   N2   108.84  3.000
 0YP  C5   C4   N2   110.87  3.000
 0YP  H6   C5   H5   107.17  3.000
 0YP  H6   C5   C6   109.82  3.000
 0YP  H5   C5   C6   111.02  3.000
 0YP  H6   C5   C4   109.05  3.000
 0YP  H5   C5   C4   108.72  3.000
 0YP  C6   C5   C4   110.96  3.000
 0YP  H8   C6   H7   106.73  3.000
 0YP  H8   C6   C7   110.45  3.000
 0YP  H7   C6   C7   109.74  3.000
 0YP  H8   C6   C5   110.67  3.000
 0YP  H7   C6   C5   109.42  3.000
 0YP  C7   C6   C5   109.77  3.000
 0YP  H10  C7   H9   107.15  3.000
 0YP  H10  C7   C8   109.39  3.000
 0YP  H9   C7   C8   108.47  3.000
 0YP  H10  C7   C6   109.35  3.000
 0YP  H9   C7   C6   111.09  3.000
 0YP  C8   C7   C6   111.28  3.000
 0YP  H12  C8   H11  106.97  3.000
 0YP  H12  C8   C7   109.53  3.000
 0YP  H11  C8   C7   110.64  3.000
 0YP  H12  C8   N2   108.29  3.000
 0YP  H11  C8   N2   110.03  3.000
 0YP  C7   C8   N2   111.25  3.000
 0YP  BR1  C9   C10  115.38  3.000
 0YP  C10  C9   C2   124.75  3.000
 0YP  BR1  C9   C2   119.71  3.000
 0YP  C15  C10  C11  119.37  3.000
 0YP  C15  C10  C9   120.34  3.000
 0YP  C11  C10  C9   120.28  3.000
 0YP  O03  C11  C12  124.35  3.000
 0YP  C12  C11  C10  119.70  3.000
 0YP  O03  C11  C10  115.93  3.000
 0YP  H14  C12  C13  119.11  3.000
 0YP  H14  C12  C11  121.06  3.000
 0YP  C13  C12  C11  119.82  3.000
 0YP  H15  C13  C14  120.10  3.000
 0YP  H15  C13  C12  118.97  3.000
 0YP  C14  C13  C12  120.93  3.000
 0YP  H16  C14  C15  120.17  3.000
 0YP  H16  C14  C13  120.66  3.000
 0YP  C15  C14  C13  119.17  3.000
 0YP  H17  C15  C14  119.98  3.000
 0YP  H17  C15  C10  119.03  3.000
 0YP  C14  C15  C10  120.99  3.000
 0YP  C21  C16  C17  119.70  3.000
 0YP  C21  C16  C1   122.37  3.000
 0YP  C17  C16  C1   117.91  3.000
 0YP  H18  C17  C18  119.33  3.000
 0YP  H18  C17  C16  120.19  3.000
 0YP  C18  C17  C16  120.48  3.000
 0YP  H19  C18  C19  121.46  3.000
 0YP  H19  C18  C17  119.81  3.000
 0YP  C19  C18  C17  118.73  3.000
 0YP  N01  C19  C20  118.99  3.000
 0YP  N01  C19  C18  119.11  3.000
 0YP  C20  C19  C18  121.90  3.000
 0YP  H20  C20  C21  119.76  3.000
 0YP  H20  C20  C19  121.52  3.000
 0YP  C21  C20  C19  118.72  3.000
 0YP  H21  C21  C20  118.07  3.000
 0YP  H21  C21  C16  121.44  3.000
 0YP  C20  C21  C16  120.46  3.000
 0YP  O02  N01  O01  124.19  3.000
 0YP  O01  N01  C19  117.89  3.000
 0YP  O02  N01  C19  117.92  3.000
 0YP  H05  C02  H04  108.89  3.000
 0YP  H05  C02  H01  108.93  3.000
 0YP  H04  C02  H01  108.87  3.000
 0YP  H05  C02  O03  111.73  3.000
 0YP  H04  C02  O03  106.39  3.000
 0YP  H01  C02  O03  111.92  3.000
 0YP  C02  O03  C11  118.89  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
 0YP  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 0YP  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 0YP  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 0YP  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 0YP  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 0YP  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 0YP  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 0YP  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 0YP  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 0YP  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 0YP  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 0YP  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 0YP  CONST_13  C18  C17  C16  C1    180.00   0.0  0
 0YP  CONST_14  C20  C21  C16  C1    180.00   0.0  0
 0YP  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 0YP  CONST_16  C14  C15  C10  C9    180.00   0.0  0
 0YP  CONST_17  O03  C11  C12  C13   180.00   0.0  0
 0YP  CONST_18  O03  C11  C10  C15   180.00   0.0  0
 0YP  CONST_19  N01  C19  C18  C17   180.00   0.0  0
 0YP  CONST_20  N01  C19  C20  C21   180.00   0.0  0
 0YP  CONST_21  H14  C12  C11  C10   180.00   0.0  0
 0YP  CONST_22  H16  C14  C15  C10   180.00   0.0  0
 0YP  CONST_23  H15  C13  C12  C11   180.00   0.0  0
 0YP  CONST_24  H17  C15  C10  C11   180.00   0.0  0
 0YP  CONST_25  H19  C18  C17  C16   180.00   0.0  0
 0YP  CONST_26  H20  C20  C21  C16   180.00   0.0  0
 0YP  CONST_27  H21  C21  C16  C17   180.00   0.0  0
 0YP  CONST_28  H18  C17  C18  C19   180.00   0.0  0
 0YP  CONST_30  C4   N2   C3   C2    180.00   0.0  0
 0YP  CONST_31  C8   N2   C3   O2    180.00   0.0  0
 0YP  CONST_32  C4   N2   C3   O2      0.00   0.0  0
 0YP  CONST_33  O02  N01  C19  C18     0.00   0.0  0
 0YP  CONST_34  O01  N01  C19  C18   180.00   0.0  0
 0YP  CONST_35  O02  N01  C19  C20   180.00   0.0  0
 0YP  CONST_36  O01  N01  C19  C20     0.00   0.0  0
 0YP  CONST_38  C16  C1   N1   C2    180.00   0.0  0
 0YP  CONST_39  H1   N1   C1   C16     0.00   0.0  0
 0YP  CONST_40  C2   N1   C1   O1      0.00   0.0  0
 0YP  Var_01    C6   C7   C8   N2    -53.58  30.0  1
 0YP  Var_02    C6   C5   C4   N2     55.15  30.0  1
 0YP  Var_03    C7   C6   C5   C4    -55.34  30.0  1
 0YP  Var_04    C7   C8   N2   C4     54.63  30.0  1
 0YP  Var_05    C8   C7   C6   C5     54.54  30.0  1
 0YP  Var_06    C8   N2   C4   C5    -55.41  30.0  1
 0YP  Var_07    C17  C16  C1   N1    150.76  30.0  2
 0YP  Var_08    C11  C10  C9   C2   -118.57  30.0  2
 0YP  Var_09    C10  C9   C2   N1   -170.50   0.0  2
 0YP  Var_10    H01  C02  O03  C11    60.50  30.0  3
 0YP  Var_11    C9   C2   N1   C1   -152.05  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
 0YP  plan-1  C9   0.020
 0YP  plan-1  C10  0.020
 0YP  plan-1  C11  0.020
 0YP  plan-1  C12  0.020
 0YP  plan-1  C13  0.020
 0YP  plan-1  C14  0.020
 0YP  plan-1  C15  0.020
 0YP  plan-1  O03  0.020
 0YP  plan-1  H14  0.020
 0YP  plan-1  H15  0.020
 0YP  plan-1  H16  0.020
 0YP  plan-1  H17  0.020
 0YP  plan-2  C1   0.020
 0YP  plan-2  C16  0.020
 0YP  plan-2  C17  0.020
 0YP  plan-2  C18  0.020
 0YP  plan-2  C19  0.020
 0YP  plan-2  C20  0.020
 0YP  plan-2  C21  0.020
 0YP  plan-2  N01  0.020
 0YP  plan-2  H18  0.020
 0YP  plan-2  H19  0.020
 0YP  plan-2  H20  0.020
 0YP  plan-2  H21  0.020
 0YP  plan-3  N1   0.020
 0YP  plan-3  C2   0.020
 0YP  plan-3  N2   0.020
 0YP  plan-3  O2   0.020
 0YP  plan-3  C3   0.020
 0YP  plan-3  C4   0.020
 0YP  plan-3  C8   0.020
 0YP  plan-3  C9   0.020
 0YP  plan-3  C10  0.020
 0YP  plan-3  BR1  0.020
 0YP  plan-4  C19  0.020
 0YP  plan-4  N01  0.020
 0YP  plan-4  O01  0.020
 0YP  plan-4  O02  0.020
 0YP  plan-5  C1   0.020
 0YP  plan-5  N1   0.020
 0YP  plan-5  O1   0.020
 0YP  plan-5  C2   0.020
 0YP  plan-5  C16  0.020
 0YP  plan-5  H1   0.020

