# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 02:24:08 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: 1-[4-(1-benzofuran-5-yl)pyridin-2-yl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)c2cc(ccn2)c3ccc4occc4c3
#
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
 RJ2  RJ2  1-[4-(1-benzofuran-5-yl)pyridin-2-yl]piperazine  ligand  38  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJ2
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
 RJ2  C1   C  CH2   0  -0.328  40.2603  2.1427   7.7848
 RJ2  N1   N  NT    0  -0.505  41.1733  3.3265   9.7352
 RJ2  O1   O  O     0  -0.430  44.0743  5.9837  17.5179
 RJ2  C2   C  CH2   0  -0.299  40.3803  3.4681   8.5209
 RJ2  N2   N  NH1   0  -0.573  39.7794  1.0543   8.6151
 RJ2  C3   C  CH2   0  -0.305  40.7652  2.2286  10.5931
 RJ2  N3   N  N     0  -0.473  41.9743  5.4732   9.4566
 RJ2  C4   C  CH2   0  -0.319  40.6117  0.9371   9.7954
 RJ2  C5   C  CR6   0   0.555  41.7400  4.4516  10.2836
 RJ2  C6   C  CR16  0  -0.483  42.0720  4.5382  11.6495
 RJ2  C7   C  CR6   0   0.195  42.6848  5.6817  12.1380
 RJ2  C8   C  CR16  0  -0.422  42.9417  6.7294  11.2498
 RJ2  C9   C  CR16  0  -0.054  42.5567  6.5630   9.9346
 RJ2  C10  C  CR6   0   0.067  43.0429  5.7902  13.5672
 RJ2  C11  C  CR16  0  -0.312  42.8532  7.0100  14.2437
 RJ2  C12  C  CR16  0  -0.323  43.1683  7.1650  15.5817
 RJ2  C13  C  CR56  0   0.357  43.6905  6.0574  16.2264
 RJ2  C14  C  CR15  0   0.022  44.5278  4.7176  17.7168
 RJ2  C15  C  CR15  0  -0.385  44.4510  3.9697  16.5990
 RJ2  C16  C  CR56  0   0.076  43.8967  4.8314  15.5910
 RJ2  C17  C  CR16  0  -0.393  43.5669  4.6954  14.2448
 RJ2  H1   H  HCH2  0   0.241  39.5918  2.2730   6.9320
 RJ2  H2   H  HCH2  0   0.224  41.2395  1.8607   7.3849
 RJ2  H3   H  HCH2  0   0.258  40.8459  4.2068   7.8746
 RJ2  H4   H  HCH2  0   0.212  39.3743  3.8390   8.7681
 RJ2  H5   H  HNH1  0   0.341  38.8237  1.2463   8.8964
 RJ2  H7   H  HCH2  0   0.250  41.5221  2.0536  11.3567
 RJ2  H8   H  HCH2  0   0.219  39.8234  2.4640  11.1102
 RJ2  H9   H  HCH2  0   0.243  40.2066  0.1668  10.4539
 RJ2  H10  H  HCH2  0   0.225  41.6033  0.5988   9.4792
 RJ2  H11  H  HCR6  0   0.267  41.8234  3.7445  12.3381
 RJ2  H12  H  HCR6  0   0.255  43.4334  7.6390  11.5661
 RJ2  H13  H  HCR6  0   0.253  42.7324  7.3584   9.2173
 RJ2  H14  H  HCR6  0   0.260  42.4282  7.8501  13.7098
 RJ2  H15  H  HCR6  0   0.273  43.0082  8.1051  16.0925
 RJ2  H16  H  HCR5  0   0.288  44.8754  4.4918  18.7126
 RJ2  H17  H  HCR5  0   0.267  44.7462  2.9379  16.4987
 RJ2  H18  H  HCR6  0   0.260  43.7372  3.7574  13.7312

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
 RJ2  C1   C2   single    1.521  0.020  1.521
 RJ2  C1   N2   single    1.451  0.020  1.451
 RJ2  C2   N1   single    1.457  0.020  1.457
 RJ2  N2   C4   single    1.449  0.020  1.449
 RJ2  N3   C9   aromatic  1.325  0.020  1.325
 RJ2  N3   C5   aromatic  1.335  0.020  1.335
 RJ2  N1   C5   single    1.374  0.020  1.374
 RJ2  N1   C3   single    1.452  0.020  1.452
 RJ2  C4   C3   single    1.526  0.020  1.526
 RJ2  C9   C8   aromatic  1.381  0.020  1.381
 RJ2  C5   C6   aromatic  1.408  0.020  1.408
 RJ2  C8   C7   aromatic  1.397  0.020  1.397
 RJ2  C6   C7   aromatic  1.386  0.020  1.386
 RJ2  C7   C10  single    1.477  0.020  1.477
 RJ2  C10  C17  aromatic  1.390  0.020  1.390
 RJ2  C10  C11  aromatic  1.408  0.020  1.408
 RJ2  C17  C16  aromatic  1.393  0.020  1.393
 RJ2  C11  C12  aromatic  1.383  0.020  1.383
 RJ2  C16  C13  aromatic  1.396  0.020  1.396
 RJ2  C16  C15  aromatic  1.437  0.020  1.437
 RJ2  C12  C13  aromatic  1.384  0.020  1.384
 RJ2  C13  O1   aromatic  1.349  0.020  1.349
 RJ2  C15  C14  aromatic  1.347  0.020  1.347
 RJ2  O1   C14  aromatic  1.359  0.020  1.359
 RJ2  C1   H1   single    0.970  0.020  1.090
 RJ2  C1   H2   single    0.970  0.020  1.090
 RJ2  C2   H3   single    0.970  0.020  1.090
 RJ2  C2   H4   single    0.970  0.020  1.090
 RJ2  N2   H5   single    0.890  0.020  1.040
 RJ2  C3   H7   single    0.970  0.020  1.090
 RJ2  C3   H8   single    0.970  0.020  1.090
 RJ2  C4   H9   single    0.970  0.020  1.090
 RJ2  C4   H10  single    0.970  0.020  1.090
 RJ2  C6   H11  single    0.930  0.020  1.080
 RJ2  C8   H12  single    0.930  0.020  1.080
 RJ2  C9   H13  single    0.930  0.020  1.080
 RJ2  C11  H14  single    0.930  0.020  1.080
 RJ2  C12  H15  single    0.930  0.020  1.080
 RJ2  C14  H16  single    0.930  0.020  1.080
 RJ2  C15  H17  single    0.930  0.020  1.080
 RJ2  C17  H18  single    0.930  0.020  1.080

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
 RJ2  H2   C1   H1   107.05  3.000
 RJ2  H2   C1   N2   108.20  3.000
 RJ2  H1   C1   N2   109.49  3.000
 RJ2  H2   C1   C2   109.32  3.000
 RJ2  H1   C1   C2   108.82  3.000
 RJ2  N2   C1   C2   113.76  3.000
 RJ2  C5   N1   C3   119.95  3.000
 RJ2  C3   N1   C2   114.39  3.000
 RJ2  C5   N1   C2   118.52  3.000
 RJ2  C14  O1   C13  106.61  3.000
 RJ2  H4   C2   H3   107.23  3.000
 RJ2  H4   C2   N1   110.07  3.000
 RJ2  H3   C2   N1   109.19  3.000
 RJ2  H4   C2   C1   109.29  3.000
 RJ2  H3   C2   C1   109.78  3.000
 RJ2  N1   C2   C1   111.20  3.000
 RJ2  H5   N2   C4   109.30  3.000
 RJ2  H5   N2   C1   109.21  3.000
 RJ2  C4   N2   C1   109.66  3.000
 RJ2  H8   C3   H7   107.44  3.000
 RJ2  H8   C3   C4   109.93  3.000
 RJ2  H7   C3   C4   107.49  3.000
 RJ2  H8   C3   N1   110.89  3.000
 RJ2  H7   C3   N1   109.90  3.000
 RJ2  C4   C3   N1   111.06  3.000
 RJ2  C9   N3   C5   118.89  3.000
 RJ2  H10  C4   H9   107.01  3.000
 RJ2  H10  C4   C3   108.75  3.000
 RJ2  H9   C4   C3   108.62  3.000
 RJ2  H10  C4   N2   108.07  3.000
 RJ2  H9   C4   N2   109.60  3.000
 RJ2  C3   C4   N2   114.53  3.000
 RJ2  C6   C5   N3   120.82  3.000
 RJ2  C6   C5   N1   122.33  3.000
 RJ2  N3   C5   N1   116.85  3.000
 RJ2  H11  C6   C7   118.90  3.000
 RJ2  H11  C6   C5   121.27  3.000
 RJ2  C7   C6   C5   119.78  3.000
 RJ2  C10  C7   C8   121.01  3.000
 RJ2  C10  C7   C6   120.57  3.000
 RJ2  C8   C7   C6   118.41  3.000
 RJ2  H12  C8   C9   120.46  3.000
 RJ2  H12  C8   C7   121.90  3.000
 RJ2  C9   C8   C7   117.64  3.000
 RJ2  H13  C9   C8   119.74  3.000
 RJ2  H13  C9   N3   115.82  3.000
 RJ2  C8   C9   N3   124.44  3.000
 RJ2  C17  C10  C11  119.94  3.000
 RJ2  C11  C10  C7   119.73  3.000
 RJ2  C17  C10  C7   120.33  3.000
 RJ2  H14  C11  C12  118.66  3.000
 RJ2  H14  C11  C10  119.24  3.000
 RJ2  C12  C11  C10  122.08  3.000
 RJ2  H15  C12  C13  122.10  3.000
 RJ2  H15  C12  C11  121.35  3.000
 RJ2  C13  C12  C11  116.55  3.000
 RJ2  C16  C13  C12  123.13  3.000
 RJ2  C12  C13  O1   126.65  3.000
 RJ2  C16  C13  O1   110.22  3.000
 RJ2  H16  C14  C15  131.93  3.000
 RJ2  H16  C14  O1   115.95  3.000
 RJ2  C15  C14  O1   112.12  3.000
 RJ2  H17  C15  C16  127.90  3.000
 RJ2  H17  C15  C14  126.37  3.000
 RJ2  C16  C15  C14  105.73  3.000
 RJ2  C17  C16  C15  135.29  3.000
 RJ2  C15  C16  C13  105.32  3.000
 RJ2  C17  C16  C13  119.39  3.000
 RJ2  H18  C17  C16  120.38  3.000
 RJ2  H18  C17  C10  120.69  3.000
 RJ2  C16  C17  C10  118.91  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
 RJ2  CONST_01  C17  C16  C13  O1   180.00   0.0  0
 RJ2  CONST_02  C15  C16  C13  O1     0.00   0.0  0
 RJ2  CONST_03  C11  C12  C13  O1   180.00   0.0  0
 RJ2  CONST_04  C16  C15  C14  O1     0.00   0.0  0
 RJ2  CONST_05  C7   C8   C9   N3     0.00   0.0  0
 RJ2  CONST_06  C7   C6   C5   N3     0.00   0.0  0
 RJ2  CONST_07  C8   C9   N3   C5     0.00   0.0  0
 RJ2  CONST_08  C8   C7   C6   C5     0.00   0.0  0
 RJ2  CONST_09  C10  C7   C6   C5   180.00   0.0  0
 RJ2  CONST_10  C9   N3   C5   C6     0.00   0.0  0
 RJ2  CONST_11  C9   C8   C7   C6     0.00   0.0  0
 RJ2  CONST_14  C16  C17  C10  C7   180.00   0.0  0
 RJ2  CONST_15  C12  C11  C10  C7   180.00   0.0  0
 RJ2  CONST_18  C10  C7   C8   C9   180.00   0.0  0
 RJ2  CONST_19  C13  C16  C17  C10    0.00   0.0  0
 RJ2  CONST_20  C15  C16  C17  C10  180.00   0.0  0
 RJ2  CONST_21  C13  C12  C11  C10    0.00   0.0  0
 RJ2  CONST_22  C16  C17  C10  C11    0.00   0.0  0
 RJ2  CONST_23  C16  C13  C12  C11    0.00   0.0  0
 RJ2  CONST_24  C17  C10  C11  C12    0.00   0.0  0
 RJ2  CONST_25  C17  C16  C13  C12    0.00   0.0  0
 RJ2  CONST_26  C15  C16  C13  C12  180.00   0.0  0
 RJ2  CONST_27  C14  O1   C13  C12  180.00   0.0  0
 RJ2  CONST_28  C14  C15  C16  C13    0.00   0.0  0
 RJ2  CONST_29  C15  C14  O1   C13    0.00   0.0  0
 RJ2  CONST_30  C17  C16  C15  C14  180.00   0.0  0
 RJ2  CONST_31  C16  C13  O1   C14    0.00   0.0  0
 RJ2  CONST_32  C9   N3   C5   N1   180.00   0.0  0
 RJ2  CONST_33  C7   C6   C5   N1   180.00   0.0  0
 RJ2  CONST_34  H11  C6   C5   N1     0.00   0.0  0
 RJ2  CONST_35  H15  C12  C13  O1     0.00   0.0  0
 RJ2  CONST_36  H17  C15  C14  O1   180.00   0.0  0
 RJ2  CONST_37  H12  C8   C9   N3   180.00   0.0  0
 RJ2  CONST_38  H13  C9   N3   C5   180.00   0.0  0
 RJ2  CONST_39  H18  C17  C10  C7     0.00   0.0  0
 RJ2  CONST_40  H14  C11  C10  C7     0.00   0.0  0
 RJ2  CONST_41  H16  C14  O1   C13  180.00   0.0  0
 RJ2  Var_01    C5   N1   C2   C1   159.38  30.0  1
 RJ2  Var_02    C3   C4   N2   C1    53.57  30.0  1
 RJ2  Var_03    N2   C1   C2   N1    52.88  30.0  1
 RJ2  Var_04    N2   C4   C3   N1   -51.34  30.0  1
 RJ2  Var_05    C4   N2   C1   C2   -54.16  30.0  1
 RJ2  Var_06    N3   C5   N1   C2   -24.95  30.0  2
 RJ2  Var_07    C4   C3   N1   C2    49.09  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
 RJ2  plan-1  N1   0.020
 RJ2  plan-1  N3   0.020
 RJ2  plan-1  C5   0.020
 RJ2  plan-1  C6   0.020
 RJ2  plan-1  C7   0.020
 RJ2  plan-1  C8   0.020
 RJ2  plan-1  C9   0.020
 RJ2  plan-1  C10  0.020
 RJ2  plan-1  H11  0.020
 RJ2  plan-1  H12  0.020
 RJ2  plan-1  H13  0.020
 RJ2  plan-2  O1   0.020
 RJ2  plan-2  C7   0.020
 RJ2  plan-2  C10  0.020
 RJ2  plan-2  C11  0.020
 RJ2  plan-2  C12  0.020
 RJ2  plan-2  C13  0.020
 RJ2  plan-2  C14  0.020
 RJ2  plan-2  C15  0.020
 RJ2  plan-2  C16  0.020
 RJ2  plan-2  C17  0.020
 RJ2  plan-2  H14  0.020
 RJ2  plan-2  H15  0.020
 RJ2  plan-2  H16  0.020
 RJ2  plan-2  H17  0.020
 RJ2  plan-2  H18  0.020

