# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:07:10 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 1-{4-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]phenyl}ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3ccc4OCOc4c3
#
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
 41N  41N  1-{4-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]phenyl}ethanone  ligand  46  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_41N
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
 41N  C3   C  CR16  0  -0.286  -3.8142  -0.5627  -1.5754
 41N  C4   C  CR6   0  -0.089  -3.2943  -0.7461  -0.3015
 41N  O8   O  O     0  -0.484  -5.6678   1.4377   1.4497
 41N  C11  C  C     0   0.520  -2.1783  -1.7238  -0.1247
 41N  C14  C  CH2   0  -0.321  -0.0559  -2.2712   0.9353
 41N  C15  C  CH2   0  -0.308   1.2006  -1.9653   0.1358
 41N  C2   C  CR16  0  -0.335  -4.8925   0.2959  -1.8092
 41N  C5   C  CR16  0  -0.350  -3.8634  -0.0971   0.8083
 41N  C6   C  CR56  0   0.314  -4.9304   0.7268   0.5643
 41N  C7   C  CR56  0   0.305  -5.4305   0.9264  -0.7147
 41N  C9   C  CH2   0   0.069  -6.5364   2.2570   0.6782
 41N  O10  O  O     0  -0.480  -6.4823   1.7720  -0.6586
 41N  O12  O  O     0  -0.483  -2.2621  -2.8379  -0.6241
 41N  N13  N  NT    0  -0.456  -1.1229  -1.3391   0.6301
 41N  N16  N  NT    0  -0.524   1.6042  -0.5864   0.3385
 41N  C17  C  CH2   0  -0.293   0.5334   0.3625   0.0741
 41N  C18  C  CH2   0  -0.329  -0.7188   0.0336   0.8703
 41N  C20  C  CR6   0   0.401   2.9119  -0.2175   0.1149
 41N  C21  C  CR16  0  -0.330   3.3543   1.0924   0.3938
 41N  C22  C  CR16  0  -0.250   4.6690   1.4545   0.2134
 41N  C23  C  CR6   0  -0.063   5.6240   0.5456  -0.2560
 41N  C24  C  CR16  0  -0.269   5.1895  -0.7486  -0.5384
 41N  C25  C  CR16  0  -0.349   3.8710  -1.1259  -0.3662
 41N  C26  C  C     0   0.356   7.0259   0.9728  -0.4311
 41N  C27  C  CH3   0  -0.801   8.0230  -0.0410  -0.9293
 41N  O28  O  O     0  -0.416   7.3696   2.1138  -0.1786
 41N  H1   H  HCR6  0   0.266  -3.3703  -1.0826  -2.4138
 41N  H3   H  HCH2  0   0.257   0.1685  -2.1929   2.0028
 41N  H4   H  HCH2  0   0.267   1.9819  -2.6351   0.4915
 41N  H5   H  HCH2  0   0.235   1.0310  -2.1827  -0.9278
 41N  H6   H  HCR6  0   0.279  -5.2850   0.4463  -2.8053
 41N  H7   H  HCR6  0   0.286  -3.4874  -0.2486   1.8120
 41N  H8   H  HCH2  0   0.248  -7.5547   2.1774   1.0581
 41N  H9   H  HCH2  0   0.237  -6.1938   3.2962   0.7092
 41N  H10  H  HCH2  0   0.272   0.8374   1.3708   0.3402
 41N  H11  H  HCH2  0   0.236   0.2882   0.3678  -0.9969
 41N  H12  H  HCH2  0   0.284  -1.5006   0.7297   0.5800
 41N  H13  H  HCH2  0   0.257  -0.5283   0.1700   1.9381
 41N  H14  H  HCR6  0   0.269   2.6710   1.8332   0.7843
 41N  H15  H  HCR6  0   0.259   4.9648   2.4669   0.4556
 41N  H16  H  HCR6  0   0.259   5.8796  -1.4914  -0.9178
 41N  H17  H  HCR6  0   0.274   3.5958  -2.1357  -0.6328
 41N  H18  H  HCH3  0   0.264   8.0789  -0.8988  -0.2576
 41N  H19  H  HCH3  0   0.264   7.7348  -0.4218  -1.9104
 41N  H20  H  HCH3  0   0.266   9.0107   0.4075  -1.0068
 41N  H2   H  HCH2  0   0.274  -0.3786  -3.2888   0.7339

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
 41N  O10  C9   single    1.423  0.020  1.423
 41N  O10  C7   single    1.351  0.020  1.351
 41N  C9   O8   single    1.422  0.020  1.422
 41N  C7   C2   aromatic  1.373  0.020  1.373
 41N  C7   C6   aromatic  1.388  0.020  1.388
 41N  O8   C6   single    1.354  0.020  1.354
 41N  C2   C3   aromatic  1.398  0.020  1.398
 41N  C6   C5   aromatic  1.370  0.020  1.370
 41N  C3   C4   aromatic  1.388  0.020  1.388
 41N  C5   C4   aromatic  1.406  0.020  1.406
 41N  C4   C11  single    1.494  0.020  1.494
 41N  C11  O12  double    1.224  0.020  1.224
 41N  C11  N13  single    1.353  0.020  1.353
 41N  C18  N13  single    1.451  0.020  1.451
 41N  C18  C17  single    1.520  0.020  1.520
 41N  N13  C14  single    1.449  0.020  1.449
 41N  C17  N16  single    1.455  0.020  1.455
 41N  C14  C15  single    1.520  0.020  1.520
 41N  N16  C15  single    1.451  0.020  1.451
 41N  N16  C20  single    1.377  0.020  1.377
 41N  C25  C20  aromatic  1.406  0.020  1.406
 41N  C25  C24  aromatic  1.382  0.020  1.382
 41N  C20  C21  aromatic  1.410  0.020  1.410
 41N  C24  C23  aromatic  1.394  0.020  1.394
 41N  C21  C22  aromatic  1.375  0.020  1.375
 41N  C23  C22  aromatic  1.400  0.020  1.400
 41N  C23  C26  single    1.476  0.020  1.476
 41N  C27  C26  single    1.507  0.020  1.507
 41N  C26  O28  double    1.218  0.020  1.218
 41N  C3   H1   single    0.930  0.020  1.080
 41N  C14  H2   single    0.970  0.020  1.090
 41N  C14  H3   single    0.970  0.020  1.090
 41N  C15  H4   single    0.970  0.020  1.090
 41N  C15  H5   single    0.970  0.020  1.090
 41N  C2   H6   single    0.930  0.020  1.080
 41N  C5   H7   single    0.930  0.020  1.080
 41N  C9   H8   single    0.970  0.020  1.090
 41N  C9   H9   single    0.970  0.020  1.090
 41N  C17  H10  single    0.970  0.020  1.090
 41N  C17  H11  single    0.970  0.020  1.090
 41N  C18  H12  single    0.970  0.020  1.090
 41N  C18  H13  single    0.970  0.020  1.090
 41N  C21  H14  single    0.930  0.020  1.080
 41N  C22  H15  single    0.930  0.020  1.080
 41N  C24  H16  single    0.930  0.020  1.080
 41N  C25  H17  single    0.930  0.020  1.080
 41N  C27  H18  single    0.970  0.020  1.090
 41N  C27  H19  single    0.970  0.020  1.090
 41N  C27  H20  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
 41N  H1   C3   C2   118.82  3.000
 41N  H1   C3   C4   119.61  3.000
 41N  C2   C3   C4   121.57  3.000
 41N  C5   C4   C11  120.73  3.000
 41N  C11  C4   C3   118.35  3.000
 41N  C5   C4   C3   120.78  3.000
 41N  C9   O8   C6   106.29  3.000
 41N  N13  C11  O12  122.67  3.000
 41N  N13  C11  C4   117.54  3.000
 41N  O12  C11  C4   119.75  3.000
 41N  H3   C14  H2   108.00  3.000
 41N  H3   C14  N13  108.10  3.000
 41N  H2   C14  N13  110.17  3.000
 41N  H3   C14  C15  109.22  3.000
 41N  H2   C14  C15  109.66  3.000
 41N  N13  C14  C15  111.61  3.000
 41N  H5   C15  H4   107.78  3.000
 41N  H5   C15  N16  111.49  3.000
 41N  H4   C15  N16  109.84  3.000
 41N  H5   C15  C14  109.97  3.000
 41N  H4   C15  C14  107.30  3.000
 41N  N16  C15  C14  110.34  3.000
 41N  H6   C2   C7   121.89  3.000
 41N  H6   C2   C3   121.30  3.000
 41N  C7   C2   C3   116.81  3.000
 41N  H7   C5   C6   121.32  3.000
 41N  H7   C5   C4   121.78  3.000
 41N  C6   C5   C4   116.90  3.000
 41N  C7   C6   C5   122.09  3.000
 41N  C5   C6   O8   128.58  3.000
 41N  C7   C6   O8   109.32  3.000
 41N  O10  C7   C6   109.41  3.000
 41N  C6   C7   C2   121.83  3.000
 41N  O10  C7   C2   128.74  3.000
 41N  H9   C9   H8   110.60  3.000
 41N  H9   C9   O10  109.77  3.000
 41N  H8   C9   O10  109.76  3.000
 41N  H9   C9   O8   109.91  3.000
 41N  H8   C9   O8   109.86  3.000
 41N  O10  C9   O8   106.87  3.000
 41N  C9   O10  C7   106.38  3.000
 41N  C18  N13  C14  111.63  3.000
 41N  C14  N13  C11  120.58  3.000
 41N  C18  N13  C11  125.34  3.000
 41N  C20  N16  C17  119.65  3.000
 41N  C20  N16  C15  119.74  3.000
 41N  C17  N16  C15  112.93  3.000
 41N  H11  C17  H10  107.26  3.000
 41N  H11  C17  C18  109.13  3.000
 41N  H10  C17  C18  107.64  3.000
 41N  H11  C17  N16  110.16  3.000
 41N  H10  C17  N16  110.78  3.000
 41N  C18  C17  N16  111.72  3.000
 41N  H13  C18  H12  107.84  3.000
 41N  H13  C18  C17  109.95  3.000
 41N  H12  C18  C17  108.32  3.000
 41N  H13  C18  N13  109.16  3.000
 41N  H12  C18  N13  111.20  3.000
 41N  C17  C18  N13  110.33  3.000
 41N  C25  C20  C21  116.99  3.000
 41N  C21  C20  N16  120.97  3.000
 41N  C25  C20  N16  122.03  3.000
 41N  H14  C21  C22  118.11  3.000
 41N  H14  C21  C20  120.64  3.000
 41N  C22  C21  C20  121.22  3.000
 41N  H15  C22  C23  119.74  3.000
 41N  H15  C22  C21  118.57  3.000
 41N  C23  C22  C21  121.69  3.000
 41N  C26  C23  C24  122.73  3.000
 41N  C26  C23  C22  120.00  3.000
 41N  C24  C23  C22  117.27  3.000
 41N  H16  C24  C25  117.67  3.000
 41N  H16  C24  C23  120.62  3.000
 41N  C25  C24  C23  121.70  3.000
 41N  H17  C25  C24  117.87  3.000
 41N  H17  C25  C20  120.98  3.000
 41N  C24  C25  C20  121.13  3.000
 41N  O28  C26  C27  120.80  3.000
 41N  O28  C26  C23  120.97  3.000
 41N  C27  C26  C23  118.23  3.000
 41N  H20  C27  H19  108.64  3.000
 41N  H20  C27  H18  108.76  3.000
 41N  H19  C27  H18  107.02  3.000
 41N  H20  C27  C26  110.31  3.000
 41N  H19  C27  C26  110.94  3.000
 41N  H18  C27  C26  111.07  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
 41N  CONST_01  C6   C7   C2   C3     0.00   0.0  0
 41N  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 41N  CONST_03  C7   C2   C3   C4     0.00   0.0  0
 41N  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 41N  CONST_05  C5   C6   C7   C2     0.00   0.0  0
 41N  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 41N  CONST_07  C23  C24  C25  C20    0.00   0.0  0
 41N  CONST_08  C23  C22  C21  C20    0.00   0.0  0
 41N  CONST_09  C24  C25  C20  C21    0.00   0.0  0
 41N  CONST_10  C24  C23  C22  C21    0.00   0.0  0
 41N  CONST_11  C25  C20  C21  C22    0.00   0.0  0
 41N  CONST_12  C25  C24  C23  C22    0.00   0.0  0
 41N  CONST_13  C24  C25  C20  N16  180.00   0.0  0
 41N  CONST_14  C22  C21  C20  N16  180.00   0.0  0
 41N  CONST_15  C2   C3   C4   C11  180.00   0.0  0
 41N  CONST_16  C6   C5   C4   C11  180.00   0.0  0
 41N  CONST_17  C26  C23  C22  C21  180.00   0.0  0
 41N  CONST_18  C26  C23  C24  C25  180.00   0.0  0
 41N  CONST_20  C14  N13  C11  C4   180.00   0.0  0
 41N  CONST_21  H7   C5   C4   C3   180.00   0.0  0
 41N  CONST_22  H6   C2   C3   C4   180.00   0.0  0
 41N  CONST_23  H1   C3   C4   C5   180.00   0.0  0
 41N  CONST_24  H17  C25  C20  N16    0.00   0.0  0
 41N  CONST_25  H14  C21  C20  N16    0.00   0.0  0
 41N  CONST_26  H16  C24  C25  C20  180.00   0.0  0
 41N  CONST_27  H15  C22  C21  C20  180.00   0.0  0
 41N  CONST_28  O12  C11  N13  C14    0.00   0.0  0
 41N  Var_01    C17  C18  N13  C14   56.19  30.0  1
 41N  Var_02    C17  N16  C15  C14  -53.23  30.0  1
 41N  Var_03    C18  N13  C14  C15  -57.12  30.0  1
 41N  Var_04    C18  C17  N16  C15   53.76  30.0  1
 41N  Var_05    C25  C20  N16  C15    2.93  30.0  2
 41N  Var_06    O10  C9   O8   C6    12.91  30.0  1
 41N  Var_07    N16  C17  C18  N13  -54.13  30.0  1
 41N  Var_08    N16  C15  C14  N13   54.60  30.0  1
 41N  Var_09    N13  C11  C4   C3   134.48  30.0  2
 41N  Var_10    C27  C26  C23  C22  179.56  30.0  2
 41N  Var_11    H18  C27  C26  C23  -59.11  30.0  3

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
 41N  plan-1  N16  0.020
 41N  plan-1  C20  0.020
 41N  plan-1  C21  0.020
 41N  plan-1  C22  0.020
 41N  plan-1  C23  0.020
 41N  plan-1  C24  0.020
 41N  plan-1  C25  0.020
 41N  plan-1  C26  0.020
 41N  plan-1  H14  0.020
 41N  plan-1  H15  0.020
 41N  plan-1  H16  0.020
 41N  plan-1  H17  0.020
 41N  plan-2  C3   0.020
 41N  plan-2  C4   0.020
 41N  plan-2  O8   0.020
 41N  plan-2  C11  0.020
 41N  plan-2  C2   0.020
 41N  plan-2  C5   0.020
 41N  plan-2  C6   0.020
 41N  plan-2  C7   0.020
 41N  plan-2  O10  0.020
 41N  plan-2  H1   0.020
 41N  plan-2  H6   0.020
 41N  plan-2  H7   0.020
 41N  plan-3  C4   0.020
 41N  plan-3  C11  0.020
 41N  plan-3  C14  0.020
 41N  plan-3  O12  0.020
 41N  plan-3  N13  0.020
 41N  plan-3  C18  0.020
 41N  plan-4  C23  0.020
 41N  plan-4  C26  0.020
 41N  plan-4  C27  0.020
 41N  plan-4  O28  0.020

