# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:51:01 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3-[3-[2-aminocarbonyl-5-(phenylmethyl)phenyl]phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Cc2ccccc2)cc1c3cccc(CCC(O)=O)c3
#
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
 X28  X28  '3-[3-[2-aminocarbonyl-5-(phenylmethyl)phenyl]phenyl]propanoic acid'  ligand  47  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X28
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
 X28  C1    C  CR16   0  -0.257   3.3755  -4.0389   1.2452
 X28  C2    C  CR16   0  -0.229   2.3144  -3.9438   0.3551
 X28  C3    C  CR16   0  -0.306   2.2820  -2.9220  -0.5855
 X28  C4    C  CR6    0   0.167   3.3052  -1.9802  -0.6492
 X28  C5    C  CR16   0  -0.280   4.3659  -2.0851   0.2476
 X28  C6    C  CR16   0  -0.221   4.4038  -3.1061   1.1870
 X28  C7    C  CH2    0  -0.614   3.2467  -0.8388  -1.6348
 X28  C8    C  CR6    0   0.219   2.6509   0.3901  -0.9967
 X28  C9    C  CR16   0  -0.283   3.4569   1.4065  -0.5006
 X28  C10   C  CR16   0  -0.195   2.8882   2.5074   0.1225
 X28  C11   C  CR6    0  -0.160   1.5095   2.6118   0.2721
 X28  C12   C  CR6    0   0.044   0.6801   1.6042  -0.2368
 X28  C13   C  CR16   0  -0.411   1.2715   0.5131  -0.8664
 X28  C14   C  C      0   0.107  -0.7960   1.6827  -0.1903
 X28  C15   C  C1     0  -0.406  -1.4682   2.8254  -0.6231
 X28  C16   C  C1     0  -0.254  -2.8530   2.8554  -0.6266
 X28  C17   C  C1     0  -0.311  -3.5814   1.7490  -0.2071
 X28  C18   C  C      0   0.179  -2.9338   0.5950   0.2246
 X28  C19   C  C1     0  -0.356  -1.5405   0.5832   0.2274
 X28  C20   C  CH2    0  -0.506  -3.7044  -0.6320   0.6254
 X28  C21   C  CH2    0  -0.553  -3.7112  -1.6751  -0.4900
 X28  C22   C  C      0   0.460  -4.4888  -2.9673  -0.1825
 X28  O23   O  O      0  -0.561  -5.3053  -2.9425   0.7594
 X28  O24   O  OC    -1  -0.573  -4.2499  -3.9392  -0.9292
 X28  C25   C  C      0   0.463   0.9570   3.7441   1.0835
 X28  O26   O  O      0  -0.397   0.2396   3.5434   2.0511
 X28  N27   N  NH2    0  -0.788   1.3456   4.9646   0.6865
 X28  H1    H  HCR6   0   0.248   3.4037  -4.8361   1.9766
 X28  H2    H  HCR6   0   0.257   1.5098  -4.6670   0.3896
 X28  H6    H  HCR6   0   0.241   5.2383  -3.1749   1.8730
 X28  H3    H  HCR6   0   0.231   1.4522  -2.8628  -1.2802
 X28  H5    H  HCR6   0   0.223   5.1720  -1.3612   0.2108
 X28  H71C  H  HCH2   0   0.269   4.2494  -0.6117  -2.0014
 X28  H72C  H  HCH2   0   0.263   2.6496  -1.1306  -2.5011
 X28  H9    H  HCR6   0   0.241   4.5340   1.3417  -0.5978
 X28  H13   H  HCR6   0   0.247   0.6339  -0.2542  -1.2918
 X28  H10   H  HCR6   0   0.253   3.5334   3.2810   0.5204
 X28  H15   H  H      0   0.224  -0.9122   3.6860  -0.9750
 X28  H19   H  H      0   0.234  -1.0220  -0.3035   0.5775
 X28  H16   H  H      0   0.229  -3.3689   3.7438  -0.9679
 X28  H17   H  H      0   0.247  -4.6646   1.7841  -0.2188
 X28  H201  H  HCH2   0   0.229  -3.2633  -1.0653   1.5272
 X28  H202  H  HCH2   0   0.247  -4.7291  -0.3590   0.8813
 X28  H211  H  HCH2   0   0.199  -4.1437  -1.2297  -1.3945
 X28  H212  H  HCH2   0   0.181  -2.6834  -1.9344  -0.7617
 X28  H271  H  HNH2   0   0.380   1.8850   5.1033  -0.1505
 X28  H272  H  HNH2   0   0.379   1.0702   5.7832   1.2052

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
 X28  C1   C2    aromatic  1.388  0.020  1.388
 X28  C1   C6    aromatic  1.390  0.020  1.390
 X28  C2   C3    aromatic  1.389  0.020  1.389
 X28  C3   C4    aromatic  1.392  0.020  1.392
 X28  C4   C5    aromatic  1.393  0.020  1.393
 X28  C4   C7    single    1.509  0.020  1.509
 X28  C5   C6    aromatic  1.388  0.020  1.388
 X28  C7   C8    single    1.507  0.020  1.507
 X28  C8   C9    aromatic  1.389  0.020  1.389
 X28  C8   C13   aromatic  1.391  0.020  1.391
 X28  C9   C10   aromatic  1.387  0.020  1.387
 X28  C10  C11   aromatic  1.391  0.020  1.391
 X28  C11  C12   aromatic  1.401  0.020  1.401
 X28  C11  C25   single    1.499  0.020  1.499
 X28  C12  C13   aromatic  1.392  0.020  1.392
 X28  C12  C14   single    1.479  0.020  1.479
 X28  C14  C15   aromatic  1.395  0.020  1.395
 X28  C14  C19   aromatic  1.392  0.020  1.392
 X28  C15  C16   aromatic  1.385  0.020  1.385
 X28  C16  C17   aromatic  1.390  0.020  1.390
 X28  C17  C18   aromatic  1.392  0.020  1.392
 X28  C18  C19   aromatic  1.393  0.020  1.393
 X28  C18  C20   single    1.503  0.020  1.503
 X28  C20  C21   single    1.527  0.020  1.527
 X28  C21  C22   single    1.539  0.020  1.539
 X28  C22  O23   deloc     1.247  0.020  1.247
 X28  C22  O24   deloc     1.249  0.020  1.249
 X28  C25  O26   double    1.221  0.020  1.221
 X28  C25  N27   single    1.341  0.020  1.341
 X28  C1   H1    single    0.930  0.020  1.080
 X28  C2   H2    single    0.930  0.020  1.080
 X28  C6   H6    single    0.930  0.020  1.080
 X28  C3   H3    single    0.930  0.020  1.080
 X28  C5   H5    single    0.930  0.020  1.080
 X28  C7   H71C  single    0.970  0.020  1.090
 X28  C7   H72C  single    0.970  0.020  1.090
 X28  C9   H9    single    0.930  0.020  1.080
 X28  C13  H13   single    0.930  0.020  1.080
 X28  C10  H10   single    0.930  0.020  1.080
 X28  C15  H15   single    0.930  0.020  1.080
 X28  C19  H19   single    0.930  0.020  1.080
 X28  C16  H16   single    0.930  0.020  1.080
 X28  C17  H17   single    0.930  0.020  1.080
 X28  C20  H201  single    0.970  0.020  1.090
 X28  C20  H202  single    0.970  0.020  1.090
 X28  C21  H211  single    0.970  0.020  1.090
 X28  C21  H212  single    0.970  0.020  1.090
 X28  N27  H271  single    0.860  0.020  1.020
 X28  N27  H272  single    0.860  0.020  1.020

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
 X28  H1    C1   C6    120.23  3.000
 X28  H1    C1   C2    120.24  3.000
 X28  C6    C1   C2    119.52  3.000
 X28  H2    C2   C3    119.71  3.000
 X28  H2    C2   C1    120.13  3.000
 X28  C3    C2   C1    120.16  3.000
 X28  H3    C3   C4    119.76  3.000
 X28  H3    C3   C2    119.47  3.000
 X28  C4    C3   C2    120.76  3.000
 X28  C7    C4   C5    120.46  3.000
 X28  C7    C4   C3    120.87  3.000
 X28  C5    C4   C3    118.64  3.000
 X28  H5    C5   C6    119.60  3.000
 X28  H5    C5   C4    119.61  3.000
 X28  C6    C5   C4    120.79  3.000
 X28  H6    C6   C5    119.78  3.000
 X28  H6    C6   C1    120.09  3.000
 X28  C5    C6   C1    120.14  3.000
 X28  H72C  C7   H71C  106.94  3.000
 X28  H72C  C7   C8    109.74  3.000
 X28  H71C  C7   C8    109.61  3.000
 X28  H72C  C7   C4    109.71  3.000
 X28  H71C  C7   C4    109.94  3.000
 X28  C8    C7   C4    110.82  3.000
 X28  C13   C8   C9    118.51  3.000
 X28  C13   C8   C7    120.24  3.000
 X28  C9    C8   C7    121.23  3.000
 X28  H9    C9   C10   119.70  3.000
 X28  H9    C9   C8    120.08  3.000
 X28  C10   C9   C8    120.22  3.000
 X28  H10   C10  C11   119.83  3.000
 X28  H10   C10  C9    119.19  3.000
 X28  C11   C10  C9    120.96  3.000
 X28  C25   C11  C12   121.46  3.000
 X28  C25   C11  C10   118.71  3.000
 X28  C12   C11  C10   119.60  3.000
 X28  C14   C12  C13   118.69  3.000
 X28  C14   C12  C11   122.78  3.000
 X28  C13   C12  C11   118.47  3.000
 X28  H13   C13  C12   118.83  3.000
 X28  H13   C13  C8    118.93  3.000
 X28  C12   C13  C8    122.22  3.000
 X28  C19   C14  C15   118.85  3.000
 X28  C19   C14  C12   120.09  3.000
 X28  C15   C14  C12   120.98  3.000
 X28  H15   C15  C16   119.68  3.000
 X28  H15   C15  C14   120.29  3.000
 X28  C16   C15  C14   120.03  3.000
 X28  H16   C16  C17   119.92  3.000
 X28  H16   C16  C15   119.67  3.000
 X28  C17   C16  C15   120.41  3.000
 X28  H17   C17  C18   119.68  3.000
 X28  H17   C17  C16   119.66  3.000
 X28  C18   C17  C16   120.66  3.000
 X28  C20   C18  C19   120.34  3.000
 X28  C20   C18  C17   121.39  3.000
 X28  C19   C18  C17   118.22  3.000
 X28  H19   C19  C18   119.04  3.000
 X28  H19   C19  C14   119.13  3.000
 X28  C18   C19  C14   121.83  3.000
 X28  H202  C20  H201  106.53  3.000
 X28  H202  C20  C21   109.76  3.000
 X28  H201  C20  C21   109.48  3.000
 X28  H202  C20  C18   109.87  3.000
 X28  H201  C20  C18   109.67  3.000
 X28  C21   C20  C18   111.41  3.000
 X28  H212  C21  H211  105.17  3.000
 X28  H212  C21  C22   108.98  3.000
 X28  H211  C21  C22   107.84  3.000
 X28  H212  C21  C20   109.81  3.000
 X28  H211  C21  C20   109.06  3.000
 X28  C22   C21  C20   115.46  3.000
 X28  O24   C22  O23   126.34  3.000
 X28  O24   C22  C21   115.93  3.000
 X28  O23   C22  C21   117.71  3.000
 X28  N27   C25  O26   123.67  3.000
 X28  N27   C25  C11   114.87  3.000
 X28  O26   C25  C11   121.43  3.000
 X28  H272  N27  H271  117.59  3.000
 X28  H272  N27  C25   120.52  3.000
 X28  H271  N27  C25   121.84  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
 X28  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 X28  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 X28  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 X28  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 X28  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 X28  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 X28  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 X28  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 X28  CONST_09  C14   C12  C13  C8    180.00   0.0  0
 X28  CONST_10  C12   C13  C8   C9      0.00   0.0  0
 X28  CONST_11  C12   C11  C10  C9      0.00   0.0  0
 X28  CONST_12  C13   C8   C9   C10     0.00   0.0  0
 X28  CONST_13  C13   C12  C11  C10     0.00   0.0  0
 X28  CONST_14  C14   C12  C11  C10   180.00   0.0  0
 X28  CONST_17  C16   C15  C14  C12   180.00   0.0  0
 X28  CONST_18  C18   C19  C14  C12   180.00   0.0  0
 X28  CONST_21  C17   C16  C15  C14     0.00   0.0  0
 X28  CONST_22  C17   C18  C19  C14     0.00   0.0  0
 X28  CONST_23  C18   C19  C14  C15     0.00   0.0  0
 X28  CONST_24  C18   C17  C16  C15     0.00   0.0  0
 X28  CONST_25  C19   C14  C15  C16     0.00   0.0  0
 X28  CONST_26  C19   C18  C17  C16     0.00   0.0  0
 X28  CONST_27  C7    C4   C3   C2    180.00   0.0  0
 X28  CONST_28  C7    C4   C5   C6    180.00   0.0  0
 X28  CONST_29  C10   C9   C8   C7    180.00   0.0  0
 X28  CONST_30  C12   C13  C8   C7    180.00   0.0  0
 X28  CONST_31  C25   C11  C10  C9    180.00   0.0  0
 X28  CONST_32  C25   C11  C12  C13   180.00   0.0  0
 X28  CONST_33  C25   C11  C12  C14     0.00   0.0  0
 X28  CONST_34  C20   C18  C19  C14   180.00   0.0  0
 X28  CONST_35  C20   C18  C17  C16   180.00   0.0  0
 X28  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 X28  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 X28  CONST_38  H6    C6   C1   C2    180.00   0.0  0
 X28  CONST_39  H1    C1   C2   C3    180.00   0.0  0
 X28  CONST_40  H2    C2   C3   C4    180.00   0.0  0
 X28  CONST_41  H10   C10  C9   C8    180.00   0.0  0
 X28  CONST_42  H13   C13  C8   C9    180.00   0.0  0
 X28  CONST_43  H9    C9   C10  C11   180.00   0.0  0
 X28  CONST_44  H15   C15  C14  C12     0.00   0.0  0
 X28  CONST_45  H19   C19  C14  C12     0.00   0.0  0
 X28  CONST_46  H16   C16  C15  C14   180.00   0.0  0
 X28  CONST_47  H17   C17  C16  C15   180.00   0.0  0
 X28  CONST_48  H271  N27  C25  C11     0.00   0.0  0
 X28  CONST_49  H272  N27  C25  C11   180.00   0.0  0
 X28  Var_01    C8    C7   C4   C3     94.24  30.0  2
 X28  Var_02    C9    C8   C7   C4     98.16  30.0  2
 X28  Var_03    O26   C25  C11  C10  -122.75  30.0  2
 X28  Var_04    C21   C20  C18  C17   100.70  30.0  2
 X28  Var_05    C22   C21  C20  C18  -179.41  30.0  3
 X28  Var_06    O23   C22  C21  C20    17.50  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
 X28  plan-1  C1    0.020
 X28  plan-1  C2    0.020
 X28  plan-1  C3    0.020
 X28  plan-1  C4    0.020
 X28  plan-1  C5    0.020
 X28  plan-1  C6    0.020
 X28  plan-1  C7    0.020
 X28  plan-1  H1    0.020
 X28  plan-1  H2    0.020
 X28  plan-1  H6    0.020
 X28  plan-1  H3    0.020
 X28  plan-1  H5    0.020
 X28  plan-2  C7    0.020
 X28  plan-2  C8    0.020
 X28  plan-2  C9    0.020
 X28  plan-2  C10   0.020
 X28  plan-2  C11   0.020
 X28  plan-2  C12   0.020
 X28  plan-2  C13   0.020
 X28  plan-2  C14   0.020
 X28  plan-2  C25   0.020
 X28  plan-2  H9    0.020
 X28  plan-2  H13   0.020
 X28  plan-2  H10   0.020
 X28  plan-3  C12   0.020
 X28  plan-3  C14   0.020
 X28  plan-3  C15   0.020
 X28  plan-3  C16   0.020
 X28  plan-3  C17   0.020
 X28  plan-3  C18   0.020
 X28  plan-3  C19   0.020
 X28  plan-3  C20   0.020
 X28  plan-3  H15   0.020
 X28  plan-3  H19   0.020
 X28  plan-3  H16   0.020
 X28  plan-3  H17   0.020
 X28  plan-4  C11   0.020
 X28  plan-4  C25   0.020
 X28  plan-4  O26   0.020
 X28  plan-4  N27   0.020
 X28  plan-4  H271  0.020
 X28  plan-4  H272  0.020
 X28  plan-5  C21   0.020
 X28  plan-5  C22   0.020
 X28  plan-5  O23   0.020
 X28  plan-5  O24   0.020

