# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:09:31 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)c2cccc(c2)C(=O)Nc3ccccc3CC(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
 J7B  J7B  '2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid'  ligand  47  27  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J7B
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
 J7B  C1   C  CR6   0  -0.022  -0.0603  -0.1466   0.8559
 J7B  C2   C  CR16  0  -0.341  -1.3152  -0.6113   0.4751
 J7B  C3   C  CR6   0   0.110  -2.4753   0.0848   0.8056
 J7B  C11  C  CR16  0  -0.302   5.6423  -0.8676  -1.0403
 J7B  C12  C  CR16  0  -0.247   6.0744  -1.9614  -0.3071
 J7B  C13  C  CR16  0  -0.271   5.2392  -2.5131   0.6542
 J7B  C14  C  CR16  0  -0.270   3.9881  -1.9639   0.8825
 J7B  C15  C  CH2   0  -0.684   3.9416   0.8358  -1.7069
 J7B  C16  C  C     0   0.574   3.9628   2.1695  -1.0016
 J7B  C19  C  CR6   0   0.114  -3.8025  -0.4196   0.3962
 J7B  C21  C  CR16  0  -0.358  -4.8172   0.4660   0.0326
 J7B  C22  C  CR6   0   0.104  -6.0760   0.0122  -0.3459
 J7B  C23  C  CR16  0  -0.318  -6.3128  -1.3594  -0.3702
 J7B  C24  C  CR16  0  -0.226  -5.3147  -2.2534  -0.0089
 J7B  C25  C  CR16  0  -0.329  -4.0656  -1.7899   0.3731
 J7B  C26  C  CH2   0  -0.335  -7.1809   0.9773  -0.6996
 J7B  C4   C  CR16  0  -0.307  -2.3534   1.2630   1.5449
 J7B  C5   C  CR16  0  -0.224  -1.1087   1.7257   1.9401
 J7B  C6   C  CR16  0  -0.315   0.0397   1.0277   1.5988
 J7B  C7   C  C     0   0.529   1.1305  -0.9654   0.4744
 J7B  N8   N  NH1   0  -0.774   2.2995  -0.2856   0.3986
 J7B  C9   C  CR6   0   0.294   3.5558  -0.8668   0.1425
 J7B  C10  C  CR6   0   0.098   4.3816  -0.3126  -0.8399
 J7B  O17  O  O     0  -0.447   3.6747   2.3269   0.1622
 J7B  O18  O  OH1   0  -0.577   4.2989   3.1607  -1.8071
 J7B  O20  O  O     0  -0.462   1.0355  -2.1577   0.2397
 J7B  N27  N  NH2   0  -0.794  -6.6790   2.1943  -1.3101
 J7B  H1   H  HCR6  0   0.260  -1.3834  -1.5207  -0.1085
 J7B  H2   H  HCR6  0   0.259   6.2894  -0.4397  -1.7964
 J7B  H3   H  HCR6  0   0.260   7.0566  -2.3784  -0.4855
 J7B  H4   H  HCR6  0   0.262   5.5636  -3.3659   1.2360
 J7B  H5   H  HCR6  0   0.267   3.3536  -2.3788   1.6533
 J7B  H6   H  HCH2  0   0.315   2.9139   0.6817  -2.0562
 J7B  H7   H  HCH2  0   0.302   4.5628   0.8822  -2.6009
 J7B  H8   H  HCR6  0   0.247  -4.6246   1.5316   0.0197
 J7B  H9   H  HCR6  0   0.249  -7.2828  -1.7320  -0.6784
 J7B  H10  H  HCR6  0   0.256  -5.5111  -3.3177  -0.0252
 J7B  H11  H  HCR6  0   0.253  -3.3009  -2.4973   0.6689
 J7B  H12  H  HCH2  0   0.216  -7.9243   0.4452  -1.3076
 J7B  H13  H  HCH2  0   0.243  -7.6986   1.2578   0.2229
 J7B  H14  H  HCR6  0   0.263  -3.2397   1.8119   1.8370
 J7B  H15  H  HCR6  0   0.268  -1.0330   2.6281   2.5317
 J7B  H16  H  HCR6  0   0.261   0.9961   1.3957   1.9479
 J7B  H17  H  HNH1  0   0.414   2.2917   0.7199   0.4849
 J7B  H18  H  HOH1  0   0.485   4.2546   4.0068  -1.3351
 J7B  H19  H  HNH2  0   0.344  -6.3526   1.9964  -2.2476
 J7B  H20  H  HNH2  0   0.355  -7.4376   2.8558  -1.4101

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
 J7B  C6   C5   aromatic  1.387  0.020  1.387
 J7B  C6   C1   aromatic  1.393  0.020  1.393
 J7B  O20  C7   double    1.219  0.020  1.219
 J7B  C5   C4   aromatic  1.385  0.020  1.385
 J7B  C7   C1   single    1.495  0.020  1.495
 J7B  C7   N8   single    1.354  0.020  1.354
 J7B  C1   C2   aromatic  1.391  0.020  1.391
 J7B  C4   C3   aromatic  1.396  0.020  1.396
 J7B  C14  C13  aromatic  1.385  0.020  1.385
 J7B  C14  C9   aromatic  1.392  0.020  1.392
 J7B  C13  C12  aromatic  1.388  0.020  1.388
 J7B  N8   C9   single    1.408  0.020  1.408
 J7B  C2   C3   aromatic  1.393  0.020  1.393
 J7B  C9   C10  aromatic  1.398  0.020  1.398
 J7B  C3   C19  single    1.478  0.020  1.478
 J7B  C12  C11  aromatic  1.386  0.020  1.386
 J7B  C10  C11  aromatic  1.392  0.020  1.392
 J7B  C10  C15  single    1.505  0.020  1.505
 J7B  C19  C21  aromatic  1.395  0.020  1.395
 J7B  C19  C25  aromatic  1.395  0.020  1.395
 J7B  C21  C22  aromatic  1.391  0.020  1.391
 J7B  C15  C16  single    1.509  0.020  1.509
 J7B  O17  C16  double    1.209  0.020  1.209
 J7B  C25  C24  aromatic  1.386  0.020  1.386
 J7B  C26  C22  single    1.509  0.020  1.509
 J7B  C26  N27  single    1.451  0.020  1.451
 J7B  C16  O18  single    1.321  0.020  1.321
 J7B  C22  C23  aromatic  1.392  0.020  1.392
 J7B  C24  C23  aromatic  1.388  0.020  1.388
 J7B  C2   H1   single    0.930  0.020  1.080
 J7B  C11  H2   single    0.930  0.020  1.080
 J7B  C12  H3   single    0.930  0.020  1.080
 J7B  C13  H4   single    0.930  0.020  1.080
 J7B  C14  H5   single    0.930  0.020  1.080
 J7B  C15  H6   single    0.970  0.020  1.090
 J7B  C15  H7   single    0.970  0.020  1.090
 J7B  C21  H8   single    0.930  0.020  1.080
 J7B  C23  H9   single    0.930  0.020  1.080
 J7B  C24  H10  single    0.930  0.020  1.080
 J7B  C25  H11  single    0.930  0.020  1.080
 J7B  C26  H12  single    0.970  0.020  1.090
 J7B  C26  H13  single    0.970  0.020  1.090
 J7B  C4   H14  single    0.930  0.020  1.080
 J7B  C5   H15  single    0.930  0.020  1.080
 J7B  C6   H16  single    0.930  0.020  1.080
 J7B  N8   H17  single    0.860  0.020  1.020
 J7B  O18  H18  single    0.850  0.020  0.980
 J7B  N27  H19  single    0.890  0.020  1.040
 J7B  N27  H20  single    0.890  0.020  1.040

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
 J7B  C7   C1   C6   122.73  3.000
 J7B  C7   C1   C2   117.76  3.000
 J7B  C6   C1   C2   119.49  3.000
 J7B  H1   C2   C3   119.69  3.000
 J7B  H1   C2   C1   119.01  3.000
 J7B  C3   C2   C1   121.29  3.000
 J7B  C4   C3   C19  120.88  3.000
 J7B  C19  C3   C2   120.78  3.000
 J7B  C4   C3   C2   118.34  3.000
 J7B  H2   C11  C10  118.95  3.000
 J7B  H2   C11  C12  119.66  3.000
 J7B  C10  C11  C12  121.39  3.000
 J7B  H3   C12  C13  120.49  3.000
 J7B  H3   C12  C11  120.00  3.000
 J7B  C13  C12  C11  119.51  3.000
 J7B  H4   C13  C14  119.64  3.000
 J7B  H4   C13  C12  120.35  3.000
 J7B  C14  C13  C12  120.00  3.000
 J7B  H5   C14  C9   119.94  3.000
 J7B  H5   C14  C13  119.70  3.000
 J7B  C9   C14  C13  120.35  3.000
 J7B  H7   C15  H6   106.20  3.000
 J7B  H7   C15  C10  109.79  3.000
 J7B  H6   C15  C10  110.51  3.000
 J7B  H7   C15  C16  109.75  3.000
 J7B  H6   C15  C16  106.64  3.000
 J7B  C10  C15  C16  113.65  3.000
 J7B  O18  C16  O17  123.36  3.000
 J7B  O18  C16  C15  112.45  3.000
 J7B  O17  C16  C15  124.17  3.000
 J7B  C25  C19  C21  118.81  3.000
 J7B  C25  C19  C3   120.61  3.000
 J7B  C21  C19  C3   120.58  3.000
 J7B  H8   C21  C22  118.61  3.000
 J7B  H8   C21  C19  119.89  3.000
 J7B  C22  C21  C19  121.48  3.000
 J7B  C26  C22  C23  120.10  3.000
 J7B  C23  C22  C21  118.70  3.000
 J7B  C26  C22  C21  121.19  3.000
 J7B  H9   C23  C24  119.75  3.000
 J7B  H9   C23  C22  119.73  3.000
 J7B  C24  C23  C22  120.52  3.000
 J7B  H10  C24  C25  119.77  3.000
 J7B  H10  C24  C23  119.93  3.000
 J7B  C25  C24  C23  120.30  3.000
 J7B  H11  C25  C24  119.55  3.000
 J7B  H11  C25  C19  120.25  3.000
 J7B  C24  C25  C19  120.19  3.000
 J7B  H13  C26  H12  105.71  3.000
 J7B  H13  C26  N27  107.66  3.000
 J7B  H12  C26  N27  114.05  3.000
 J7B  H13  C26  C22  108.23  3.000
 J7B  H12  C26  C22  108.39  3.000
 J7B  N27  C26  C22  112.44  3.000
 J7B  H14  C4   C5   119.29  3.000
 J7B  H14  C4   C3   119.94  3.000
 J7B  C5   C4   C3   120.75  3.000
 J7B  H15  C5   C6   119.78  3.000
 J7B  H15  C5   C4   119.83  3.000
 J7B  C6   C5   C4   120.38  3.000
 J7B  H16  C6   C5   118.76  3.000
 J7B  H16  C6   C1   121.46  3.000
 J7B  C5   C6   C1   119.75  3.000
 J7B  O20  C7   N8   123.19  3.000
 J7B  N8   C7   C1   115.28  3.000
 J7B  O20  C7   C1   121.53  3.000
 J7B  H17  N8   C9   115.70  3.000
 J7B  H17  N8   C7   119.25  3.000
 J7B  C9   N8   C7   124.98  3.000
 J7B  C10  C9   N8   119.43  3.000
 J7B  C10  C9   C14  120.17  3.000
 J7B  N8   C9   C14  120.38  3.000
 J7B  C9   C10  C15  122.33  3.000
 J7B  C15  C10  C11  119.09  3.000
 J7B  C9   C10  C11  118.56  3.000
 J7B  H18  O18  C16  110.26  3.000
 J7B  H20  N27  H19  106.15  3.000
 J7B  H20  N27  C26  109.31  3.000
 J7B  H19  N27  C26  109.71  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
 J7B  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 J7B  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 J7B  CONST_03  C19  C3   C2   C1    180.00   0.0  0
 J7B  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 J7B  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 J7B  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 J7B  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 J7B  CONST_10  C22  C21  C19  C3    180.00   0.0  0
 J7B  CONST_11  C24  C25  C19  C3    180.00   0.0  0
 J7B  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 J7B  CONST_13  C14  C9   C10  C11     0.00   0.0  0
 J7B  CONST_14  C9   C14  C13  C12     0.00   0.0  0
 J7B  CONST_15  C9   C10  C11  C12     0.00   0.0  0
 J7B  CONST_16  C10  C9   C14  C13     0.00   0.0  0
 J7B  CONST_17  C10  C11  C12  C13     0.00   0.0  0
 J7B  CONST_18  C5   C4   C3   C19   180.00   0.0  0
 J7B  CONST_19  C23  C22  C21  C19     0.00   0.0  0
 J7B  CONST_20  C23  C24  C25  C19     0.00   0.0  0
 J7B  CONST_22  C24  C25  C19  C21     0.00   0.0  0
 J7B  CONST_23  C24  C23  C22  C21     0.00   0.0  0
 J7B  CONST_24  C25  C19  C21  C22     0.00   0.0  0
 J7B  CONST_25  C25  C24  C23  C22     0.00   0.0  0
 J7B  CONST_27  C7   C1   C2   C3    180.00   0.0  0
 J7B  CONST_28  N8   C9   C10  C11   180.00   0.0  0
 J7B  CONST_29  C15  C10  C11  C12   180.00   0.0  0
 J7B  CONST_30  N8   C9   C14  C13   180.00   0.0  0
 J7B  CONST_31  C15  C10  C9   C14   180.00   0.0  0
 J7B  CONST_32  C26  C22  C21  C19   180.00   0.0  0
 J7B  CONST_33  C26  C22  C23  C24   180.00   0.0  0
 J7B  CONST_34  C7   C1   C6   C5    180.00   0.0  0
 J7B  CONST_35  H15  C5   C6   C1    180.00   0.0  0
 J7B  CONST_36  H16  C6   C1   C2    180.00   0.0  0
 J7B  CONST_37  H14  C4   C3   C2    180.00   0.0  0
 J7B  CONST_38  H8   C21  C19  C3      0.00   0.0  0
 J7B  CONST_39  H11  C25  C19  C3      0.00   0.0  0
 J7B  CONST_40  H4   C13  C12  C11   180.00   0.0  0
 J7B  CONST_41  H5   C14  C13  C12   180.00   0.0  0
 J7B  CONST_42  H2   C11  C12  C13   180.00   0.0  0
 J7B  CONST_43  H3   C12  C13  C14   180.00   0.0  0
 J7B  CONST_44  H1   C2   C3   C19     0.00   0.0  0
 J7B  CONST_45  H10  C24  C25  C19   180.00   0.0  0
 J7B  CONST_46  H9   C23  C22  C21   180.00   0.0  0
 J7B  CONST_47  C9   N8   C7   C1    180.00   0.0  0
 J7B  CONST_51  O20  C7   N8   C9      0.00   0.0  0
 J7B  CONST_52  H18  O18  C16  C15   180.00   0.0  0
 J7B  Var_01    O20  C7   C1   C2    -23.20  30.0  2
 J7B  Var_02    C16  C15  C10  C11  -105.36  30.0  2
 J7B  Var_03    N27  C26  C22  C21    32.09  30.0  1
 J7B  Var_04    O17  C16  C15  C10   -36.30  30.0  3
 J7B  Var_05    H19  N27  C26  C22    71.72  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
 J7B  plan-1  C11  0.020
 J7B  plan-1  C12  0.020
 J7B  plan-1  C13  0.020
 J7B  plan-1  C14  0.020
 J7B  plan-1  C15  0.020
 J7B  plan-1  N8   0.020
 J7B  plan-1  C9   0.020
 J7B  plan-1  C10  0.020
 J7B  plan-1  H2   0.020
 J7B  plan-1  H3   0.020
 J7B  plan-1  H4   0.020
 J7B  plan-1  H5   0.020
 J7B  plan-2  C3   0.020
 J7B  plan-2  C19  0.020
 J7B  plan-2  C21  0.020
 J7B  plan-2  C22  0.020
 J7B  plan-2  C23  0.020
 J7B  plan-2  C24  0.020
 J7B  plan-2  C25  0.020
 J7B  plan-2  C26  0.020
 J7B  plan-2  H8   0.020
 J7B  plan-2  H9   0.020
 J7B  plan-2  H10  0.020
 J7B  plan-2  H11  0.020
 J7B  plan-3  C1   0.020
 J7B  plan-3  C2   0.020
 J7B  plan-3  C3   0.020
 J7B  plan-3  C19  0.020
 J7B  plan-3  C4   0.020
 J7B  plan-3  C5   0.020
 J7B  plan-3  C6   0.020
 J7B  plan-3  C7   0.020
 J7B  plan-3  H1   0.020
 J7B  plan-3  H14  0.020
 J7B  plan-3  H15  0.020
 J7B  plan-3  H16  0.020
 J7B  plan-4  C1   0.020
 J7B  plan-4  C7   0.020
 J7B  plan-4  N8   0.020
 J7B  plan-4  C9   0.020
 J7B  plan-4  O20  0.020
 J7B  plan-4  H17  0.020
 J7B  plan-5  C15  0.020
 J7B  plan-5  C16  0.020
 J7B  plan-5  O17  0.020
 J7B  plan-5  O18  0.020
 J7B  plan-5  H18  0.020

