# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 04:54:57 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCc2cc(ccc12)N3CCN(CC3)C(=O)c4ccc5OCOc5c4
#
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
 6SR  6SR  5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one  ligand  47  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6SR
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
 6SR  C1   C  C     0   0.521   2.2991   1.6464  -0.1892
 6SR  C2   C  CR6   0  -0.091   3.4592   0.7562   0.1175
 6SR  C3   C  CR16  0  -0.361   4.1939   0.2380  -0.9621
 6SR  C4   C  CR56  0   0.312   5.3083  -0.4978  -0.6574
 6SR  C5   C  CR56  0   0.305   5.7240  -0.6987   0.6512
 6SR  C6   C  CR16  0  -0.332   5.0341  -0.1792   1.7180
 6SR  C7   C  CR16  0  -0.272   3.8797   0.5541   1.4255
 6SR  O8   O  O     0  -0.485   6.1564  -1.1330  -1.4997
 6SR  C9   C  CH2   0   0.070   7.2302  -1.6157  -0.7027
 6SR  O10  O  O     0  -0.481   6.8408  -1.4579   0.6570
 6SR  O11  O  O     0  -0.486   2.4324   2.5513  -1.0025
 6SR  N12  N  NT    0  -0.458   1.1499   1.4395   0.4925
 6SR  C13  C  CH2   0  -0.320   0.7583   0.2012   1.1350
 6SR  C14  C  CH2   0  -0.299  -0.4101  -0.4514   0.4073
 6SR  N15  N  NT    0  -0.529  -1.5192   0.4684   0.2448
 6SR  C16  C  CH2   0  -0.305  -1.1221   1.7248  -0.3735
 6SR  C17  C  CH2   0  -0.321   0.0368   2.3593   0.3729
 6SR  C18  C  CR6   0   0.427  -2.8024  -0.0034   0.1020
 6SR  C19  C  CR16  0  -0.373  -3.0756  -1.3960   0.0968
 6SR  C20  C  CR16  0  -0.259  -4.3626  -1.8764   0.0068
 6SR  C21  C  CR56  0  -0.063  -5.4232  -0.9807  -0.0937
 6SR  C22  C  CR56  0   0.109  -5.1754   0.3876  -0.1090
 6SR  C23  C  CR16  0  -0.419  -3.8921   0.8827  -0.0172
 6SR  C24  C  CH2   0  -0.500  -6.4547   1.1713  -0.2250
 6SR  C25  C  CH2   0  -0.588  -7.5572   0.1042  -0.2667
 6SR  C26  C  CR5   0   0.332  -6.8523  -1.2416  -0.1925
 6SR  O27  O  O     0  -0.425  -7.3984  -2.3275  -0.2106
 6SR  H1   H  HCR6  0   0.278   3.8834   0.4000  -1.9856
 6SR  H2   H  HCR6  0   0.279   5.3623  -0.3254   2.7377
 6SR  H3   H  HCR6  0   0.274   3.3194   0.9835   2.2462
 6SR  H4   H  HCH2  0   0.247   7.4049  -2.6701  -0.9159
 6SR  H5   H  HCH2  0   0.283   1.5806  -0.5077   1.1488
 6SR  H6   H  HCH2  0   0.254   0.4755   0.4059   2.1711
 6SR  H7   H  HCH2  0   0.235  -0.0720  -0.8422  -0.5622
 6SR  H8   H  HCH2  0   0.270  -0.7131  -1.3005   1.0161
 6SR  H9   H  HCH2  0   0.241  -0.8395   1.5581  -1.4213
 6SR  H10  H  HCH2  0   0.273  -1.9424   2.4356  -0.3693
 6SR  H11  H  HCH2  0   0.257  -0.2877   2.6399   1.3789
 6SR  H12  H  HCH2  0   0.274   0.3503   3.2620  -0.1437
 6SR  H13  H  HCR6  0   0.273  -2.2711  -2.1144   0.1412
 6SR  H14  H  HCR6  0   0.259  -4.5344  -2.9458   0.0019
 6SR  H15  H  HCR6  0   0.264  -3.7484   1.9542  -0.0117
 6SR  H16  H  HCH2  0   0.266  -6.5730   1.8523   0.6196
 6SR  H17  H  HCH2  0   0.279  -8.2549   0.1925   0.5685
 6SR  H19  H  HCH2  0   0.238   8.1333  -1.0297  -0.9001
 6SR  H18  H  HCH2  0   0.267  -6.4497   1.7895  -1.1244
 6SR  H20  H  HCH2  0   0.279  -8.1556   0.1532  -1.1787

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
 6SR  O11  C1   double    1.224  0.020  1.224
 6SR  C9   O8   single    1.422  0.020  1.422
 6SR  C9   O10  single    1.423  0.020  1.423
 6SR  O8   C4   single    1.354  0.020  1.354
 6SR  O10  C5   single    1.350  0.020  1.350
 6SR  C4   C5   aromatic  1.388  0.020  1.388
 6SR  C4   C3   aromatic  1.370  0.020  1.370
 6SR  C5   C6   aromatic  1.373  0.020  1.373
 6SR  C3   C2   aromatic  1.405  0.020  1.405
 6SR  C6   C7   aromatic  1.399  0.020  1.399
 6SR  C7   C2   aromatic  1.389  0.020  1.389
 6SR  C2   C1   single    1.494  0.020  1.494
 6SR  C1   N12  single    1.352  0.020  1.352
 6SR  C13  N12  single    1.449  0.020  1.449
 6SR  C13  C14  single    1.523  0.020  1.523
 6SR  N12  C17  single    1.449  0.020  1.449
 6SR  C14  N15  single    1.450  0.020  1.450
 6SR  C17  C16  single    1.517  0.020  1.517
 6SR  C16  N15  single    1.456  0.020  1.456
 6SR  N15  C18  single    1.375  0.020  1.375
 6SR  C18  C19  aromatic  1.419  0.020  1.419
 6SR  C18  C23  aromatic  1.410  0.020  1.410
 6SR  C19  C20  aromatic  1.377  0.020  1.377
 6SR  C23  C22  aromatic  1.378  0.020  1.378
 6SR  C20  C21  aromatic  1.392  0.020  1.392
 6SR  C22  C21  aromatic  1.391  0.020  1.391
 6SR  C22  C24  single    1.505  0.020  1.505
 6SR  C21  C26  single    1.456  0.020  1.456
 6SR  C24  C25  single    1.535  0.020  1.535
 6SR  C26  O27  double    1.216  0.020  1.216
 6SR  C26  C25  single    1.521  0.020  1.521
 6SR  C3   H1   single    0.930  0.020  1.080
 6SR  C6   H2   single    0.930  0.020  1.080
 6SR  C7   H3   single    0.930  0.020  1.080
 6SR  C9   H4   single    0.970  0.020  1.090
 6SR  C13  H5   single    0.970  0.020  1.090
 6SR  C13  H6   single    0.970  0.020  1.090
 6SR  C14  H7   single    0.970  0.020  1.090
 6SR  C14  H8   single    0.970  0.020  1.090
 6SR  C16  H9   single    0.970  0.020  1.090
 6SR  C16  H10  single    0.970  0.020  1.090
 6SR  C17  H11  single    0.970  0.020  1.090
 6SR  C17  H12  single    0.970  0.020  1.090
 6SR  C19  H13  single    0.930  0.020  1.080
 6SR  C20  H14  single    0.930  0.020  1.080
 6SR  C23  H15  single    0.930  0.020  1.080
 6SR  C24  H16  single    0.970  0.020  1.090
 6SR  C25  H17  single    0.970  0.020  1.090
 6SR  C9   H19  single    0.970  0.020  1.090
 6SR  C24  H18  single    0.970  0.020  1.090
 6SR  C25  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
 6SR  N12  C1   O11  122.73  3.000
 6SR  N12  C1   C2   117.73  3.000
 6SR  O11  C1   C2   119.50  3.000
 6SR  C7   C2   C3   120.78  3.000
 6SR  C7   C2   C1   121.01  3.000
 6SR  C3   C2   C1   117.91  3.000
 6SR  H1   C3   C4   121.63  3.000
 6SR  H1   C3   C2   121.44  3.000
 6SR  C4   C3   C2   116.91  3.000
 6SR  O8   C4   C5   109.34  3.000
 6SR  C5   C4   C3   122.09  3.000
 6SR  O8   C4   C3   128.57  3.000
 6SR  O10  C5   C6   128.69  3.000
 6SR  C6   C5   C4   121.84  3.000
 6SR  O10  C5   C4   109.46  3.000
 6SR  H2   C6   C7   121.25  3.000
 6SR  H2   C6   C5   121.96  3.000
 6SR  C7   C6   C5   116.79  3.000
 6SR  H3   C7   C6   118.46  3.000
 6SR  H3   C7   C2   119.98  3.000
 6SR  C6   C7   C2   121.55  3.000
 6SR  C9   O8   C4   106.48  3.000
 6SR  H19  C9   H4   110.51  3.000
 6SR  H19  C9   O10  109.80  3.000
 6SR  H4   C9   O10  109.76  3.000
 6SR  H19  C9   O8   109.90  3.000
 6SR  H4   C9   O8   109.87  3.000
 6SR  O10  C9   O8   106.94  3.000
 6SR  C9   O10  C5   106.53  3.000
 6SR  C17  N12  C13  111.81  3.000
 6SR  C17  N12  C1   120.95  3.000
 6SR  C13  N12  C1   125.73  3.000
 6SR  H6   C13  H5   107.82  3.000
 6SR  H6   C13  C14  109.54  3.000
 6SR  H5   C13  C14  107.89  3.000
 6SR  H6   C13  N12  109.27  3.000
 6SR  H5   C13  N12  111.03  3.000
 6SR  C14  C13  N12  111.20  3.000
 6SR  H8   C14  H7   107.58  3.000
 6SR  H8   C14  N15  110.17  3.000
 6SR  H7   C14  N15  111.23  3.000
 6SR  H8   C14  C13  106.30  3.000
 6SR  H7   C14  C13  109.74  3.000
 6SR  N15  C14  C13  111.62  3.000
 6SR  C18  N15  C16  120.45  3.000
 6SR  C18  N15  C14  120.52  3.000
 6SR  C16  N15  C14  112.74  3.000
 6SR  H10  C16  H9   107.32  3.000
 6SR  H10  C16  C17  107.54  3.000
 6SR  H9   C16  C17  109.65  3.000
 6SR  H10  C16  N15  110.95  3.000
 6SR  H9   C16  N15  110.15  3.000
 6SR  C17  C16  N15  111.12  3.000
 6SR  H12  C17  H11  108.05  3.000
 6SR  H12  C17  C16  109.51  3.000
 6SR  H11  C17  C16  109.46  3.000
 6SR  H12  C17  N12  110.18  3.000
 6SR  H11  C17  N12  108.35  3.000
 6SR  C16  C17  N12  111.22  3.000
 6SR  C23  C18  C19  117.89  3.000
 6SR  C23  C18  N15  120.98  3.000
 6SR  C19  C18  N15  121.12  3.000
 6SR  H13  C19  C20  117.85  3.000
 6SR  H13  C19  C18  120.62  3.000
 6SR  C20  C19  C18  121.51  3.000
 6SR  H14  C20  C21  120.94  3.000
 6SR  H14  C20  C19  119.55  3.000
 6SR  C21  C20  C19  119.51  3.000
 6SR  C26  C21  C22  110.52  3.000
 6SR  C26  C21  C20  129.61  3.000
 6SR  C22  C21  C20  119.88  3.000
 6SR  C24  C22  C23  127.55  3.000
 6SR  C24  C22  C21  111.21  3.000
 6SR  C23  C22  C21  121.23  3.000
 6SR  H15  C23  C22  118.69  3.000
 6SR  H15  C23  C18  121.32  3.000
 6SR  C22  C23  C18  119.97  3.000
 6SR  H18  C24  H16  106.55  3.000
 6SR  H18  C24  C25  112.00  3.000
 6SR  H16  C24  C25  112.15  3.000
 6SR  H18  C24  C22  110.77  3.000
 6SR  H16  C24  C22  110.94  3.000
 6SR  C25  C24  C22  104.51  3.000
 6SR  H20  C25  H17  106.57  3.000
 6SR  H20  C25  C26  109.54  3.000
 6SR  H17  C25  C26  109.29  3.000
 6SR  H20  C25  C24  112.65  3.000
 6SR  H17  C25  C24  112.45  3.000
 6SR  C26  C25  C24  106.31  3.000
 6SR  O27  C26  C25  125.55  3.000
 6SR  C25  C26  C21  107.44  3.000
 6SR  O27  C26  C21  127.01  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
 6SR  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 6SR  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 6SR  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 6SR  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 6SR  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 6SR  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 6SR  CONST_07  C21  C20  C19  C18    0.00   0.0  0
 6SR  CONST_08  C21  C22  C23  C18    0.00   0.0  0
 6SR  CONST_09  C22  C23  C18  C19    0.00   0.0  0
 6SR  CONST_10  C22  C21  C20  C19    0.00   0.0  0
 6SR  CONST_11  C23  C18  C19  C20    0.00   0.0  0
 6SR  CONST_12  C23  C22  C21  C20    0.00   0.0  0
 6SR  CONST_13  C20  C19  C18  N15  180.00   0.0  0
 6SR  CONST_14  C22  C23  C18  N15  180.00   0.0  0
 6SR  CONST_15  C4   C3   C2   C1   180.00   0.0  0
 6SR  CONST_16  C6   C7   C2   C1   180.00   0.0  0
 6SR  CONST_18  C17  N12  C1   C2   180.00   0.0  0
 6SR  CONST_19  H2   C6   C7   C2   180.00   0.0  0
 6SR  CONST_20  H3   C7   C2   C3   180.00   0.0  0
 6SR  CONST_21  H1   C3   C4   C5   180.00   0.0  0
 6SR  CONST_22  H13  C19  C18  N15    0.00   0.0  0
 6SR  CONST_23  H15  C23  C18  N15    0.00   0.0  0
 6SR  CONST_24  H14  C20  C19  C18  180.00   0.0  0
 6SR  CONST_26  C17  N12  C1   O11    0.00   0.0  0
 6SR  Var_01    O10  C9   O8   C4    10.94  30.0  1
 6SR  Var_02    O8   C9   O10  C5   -10.82  30.0  1
 6SR  Var_03    N15  C14  C13  N12  -53.27  30.0  1
 6SR  Var_04    N15  C16  C17  N12   54.59  30.0  1
 6SR  Var_05    C16  C17  N12  C13  -56.31  30.0  1
 6SR  Var_06    C16  N15  C14  C13   52.78  30.0  1
 6SR  Var_07    C17  N12  C13  C14   55.43  30.0  1
 6SR  Var_08    C17  C16  N15  C14  -53.37  30.0  1
 6SR  Var_09    C19  C18  N15  C14   -0.60  30.0  2
 6SR  Var_10    C25  C26  C21  C20  179.56  30.0  1
 6SR  Var_11    C25  C24  C22  C21    0.58  30.0  1
 6SR  Var_12    C24  C25  C26  C21    0.76  30.0  1
 6SR  Var_13    C26  C25  C24  C22   -0.80  30.0  1
 6SR  Var_14    N12  C1   C2   C3   135.48  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
 6SR  plan-1  C1   0.020
 6SR  plan-1  C2   0.020
 6SR  plan-1  C3   0.020
 6SR  plan-1  C4   0.020
 6SR  plan-1  C5   0.020
 6SR  plan-1  C6   0.020
 6SR  plan-1  C7   0.020
 6SR  plan-1  O8   0.020
 6SR  plan-1  O10  0.020
 6SR  plan-1  H1   0.020
 6SR  plan-1  H2   0.020
 6SR  plan-1  H3   0.020
 6SR  plan-2  N15  0.020
 6SR  plan-2  C18  0.020
 6SR  plan-2  C19  0.020
 6SR  plan-2  C20  0.020
 6SR  plan-2  C21  0.020
 6SR  plan-2  C22  0.020
 6SR  plan-2  C23  0.020
 6SR  plan-2  C24  0.020
 6SR  plan-2  C26  0.020
 6SR  plan-2  H13  0.020
 6SR  plan-2  H14  0.020
 6SR  plan-2  H15  0.020
 6SR  plan-3  C1   0.020
 6SR  plan-3  C2   0.020
 6SR  plan-3  O11  0.020
 6SR  plan-3  N12  0.020
 6SR  plan-3  C13  0.020
 6SR  plan-3  C17  0.020
 6SR  plan-4  C21  0.020
 6SR  plan-4  C25  0.020
 6SR  plan-4  C26  0.020
 6SR  plan-4  O27  0.020

