# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 23:04:15 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-{[(2S)-2-cyano-3-{3-[(4-methylbenzene-1-carbonyl)amino]phenyl}propanoyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C(=O)Nc2cccc(C[C@@H](C#N)C(=O)Nc3ccccc3C(O)=O)c2
#
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
 XAY  XAY  "2-{[(2S)-2-cyano-3-{3-[(4-methylbenzene-1-carbonyl)amino]phenyl}propanoyl]amino}benzoic acid"  ligand  52  32  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XAY
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
 XAY  O4   O  OC    -1  -0.544  24.7938  33.8196  18.0507
 XAY  C25  C  C      0   0.474  23.5895  33.6384  17.8478
 XAY  O3   O  O      0  -0.603  23.1006  32.9738  16.8903
 XAY  C24  C  C      0  -0.222  22.6078  34.2747  18.8303
 XAY  C23  C  C1     0  -0.286  23.1177  35.0823  19.8423
 XAY  C22  C  C1     0  -0.257  22.2978  35.6968  20.7746
 XAY  C21  C  C1     0  -0.252  20.9266  35.5039  20.6974
 XAY  C20  C  C1     0  -0.315  20.3800  34.7084  19.7029
 XAY  C19  C  C      0   0.353  21.2098  34.0876  18.7654
 XAY  N3   N  NH1    0  -0.775  20.7348  33.2716  17.7394
 XAY  C18  C  C      0   0.568  19.5032  32.7821  17.5411
 XAY  O2   O  O      0  -0.451  18.4966  33.0417  18.1754
 XAY  C17  C  CSP    0   0.154  18.0789  31.5191  16.0215
 XAY  N2   N  NS     0  -0.258  16.9994  31.2957  15.6952
 XAY  C13  C  C      0   0.136  19.6771  29.8460  18.0454
 XAY  C14  C  C1     0  -0.393  18.5757  28.9987  18.0328
 XAY  C12  C  C1     0  -0.316  20.2889  30.1391  19.2610
 XAY  C11  C  C1     0  -0.236  19.7812  29.6063  20.4362
 XAY  C10  C  C1     0  -0.307  18.6703  28.7768  20.4274
 XAY  C9   C  C      0   0.395  18.0636  28.4616  19.2124
 XAY  N1   N  NH1    0  -0.761  16.9231  27.6520  19.1199
 XAY  C8   C  C      0   0.518  16.6324  26.5735  19.8978
 XAY  O1   O  O      0  -0.453  17.3677  26.1691  20.7807
 XAY  C5   C  CR6    0  -0.066  15.3399  25.8959  19.5889
 XAY  C4   C  CR16   0  -0.277  14.2493  26.5585  19.0297
 XAY  C3   C  CR16   0  -0.282  13.0617  25.8834  18.7931
 XAY  C2   C  CR6    0   0.099  12.9287  24.5316  19.0989
 XAY  C1   C  CH3    0  -0.720  11.6568  23.7931  18.8092
 XAY  C7   C  CR16   0  -0.282  14.0211  23.8777  19.6685
 XAY  C6   C  CR16   0  -0.250  15.2050  24.5484  19.9190
 XAY  C15  C  CH2    0  -0.524  20.1856  30.4493  16.7674
 XAY  C16  C  CH1    0  -0.503  19.4649  31.7690  16.3909
 XAY  H18  H  H      0   0.249  24.1883  35.2260  19.8930
 XAY  H17  H  H      0   0.247  22.7234  36.3192  21.5508
 XAY  H16  H  H      0   0.253  20.2676  35.9769  21.4146
 XAY  H15  H  H      0   0.274  19.3115  34.5751  19.6579
 XAY  H14  H  HNH1   0   0.447  21.5413  32.9779  17.1365
 XAY  H12  H  H      0   0.264  18.1089  28.7417  17.0879
 XAY  H11  H  H      0   0.257  21.1621  30.7797  19.2905
 XAY  H10  H  H      0   0.258  20.2539  29.8421  21.3808
 XAY  H9   H  H      0   0.269  18.2836  28.3933  21.3589
 XAY  H8   H  HNH1   0   0.417  16.3701  27.7787  18.2857
 XAY  H5   H  HCR6   0   0.260  14.2979  27.6155  18.7983
 XAY  H4   H  HCR6   0   0.255  12.2222  26.4221  18.3704
 XAY  H1   H  HCH3   0   0.253  11.7135  23.2931  17.8401
 XAY  H3   H  HCH3   0   0.247  11.4629  23.0249  19.5572
 XAY  H2   H  HCH3   0   0.247  10.8003  24.4652  18.7787
 XAY  H7   H  HCR6   0   0.253  13.9409  22.8279  19.9245
 XAY  H6   H  HCR6   0   0.258  16.0340  24.0176  20.3684
 XAY  H13  H  HCH2   0   0.289  20.0717  29.7532  15.9354
 XAY  H21  H  HCH2   0   0.288  21.2506  30.6688  16.8485
 XAY  H19  H  HCH1   0   0.353  19.9649  32.1854  15.5102

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
 XAY  N2   C17  triple    1.150  0.020  1.150
 XAY  C17  C16  single    1.456  0.020  1.456
 XAY  C16  C15  single    1.550  0.020  1.550
 XAY  C16  C18  single    1.533  0.020  1.533
 XAY  C15  C13  single    1.502  0.020  1.502
 XAY  O2   C18  double    1.218  0.020  1.218
 XAY  C18  N3   single    1.340  0.020  1.340
 XAY  C13  C14  aromatic  1.390  0.020  1.390
 XAY  C13  C12  aromatic  1.392  0.020  1.392
 XAY  C14  C9   aromatic  1.394  0.020  1.394
 XAY  C12  C11  aromatic  1.387  0.020  1.387
 XAY  N3   C19  single    1.394  0.020  1.394
 XAY  C9   N1   single    1.402  0.020  1.402
 XAY  C9   C10  aromatic  1.394  0.020  1.394
 XAY  C11  C10  aromatic  1.386  0.020  1.386
 XAY  C20  C19  aromatic  1.397  0.020  1.397
 XAY  C20  C21  aromatic  1.386  0.020  1.386
 XAY  N1   C8   single    1.361  0.020  1.361
 XAY  C19  C24  aromatic  1.412  0.020  1.412
 XAY  C4   C3   aromatic  1.386  0.020  1.386
 XAY  C4   C5   aromatic  1.393  0.020  1.393
 XAY  C3   C2   aromatic  1.392  0.020  1.392
 XAY  C8   C5   single    1.492  0.020  1.492
 XAY  C8   O1   double    1.218  0.020  1.218
 XAY  O3   C25  deloc     1.264  0.020  1.264
 XAY  C21  C22  aromatic  1.387  0.020  1.387
 XAY  C5   C6   aromatic  1.394  0.020  1.394
 XAY  C2   C1   single    1.499  0.020  1.499
 XAY  C2   C7   aromatic  1.395  0.020  1.395
 XAY  C24  C25  single    1.528  0.020  1.528
 XAY  C24  C23  aromatic  1.391  0.020  1.391
 XAY  C6   C7   aromatic  1.384  0.020  1.384
 XAY  C25  O4   deloc     1.235  0.020  1.235
 XAY  C22  C23  aromatic  1.385  0.020  1.385
 XAY  C23  H18  single    0.930  0.020  1.080
 XAY  C22  H17  single    0.930  0.020  1.080
 XAY  C21  H16  single    0.930  0.020  1.080
 XAY  C20  H15  single    0.930  0.020  1.080
 XAY  N3   H14  single    0.860  0.020  1.020
 XAY  C14  H12  single    0.930  0.020  1.080
 XAY  C12  H11  single    0.930  0.020  1.080
 XAY  C11  H10  single    0.930  0.020  1.080
 XAY  C10  H9   single    0.930  0.020  1.080
 XAY  N1   H8   single    0.860  0.020  1.020
 XAY  C4   H5   single    0.930  0.020  1.080
 XAY  C3   H4   single    0.930  0.020  1.080
 XAY  C1   H1   single    0.970  0.020  1.090
 XAY  C1   H3   single    0.970  0.020  1.090
 XAY  C1   H2   single    0.970  0.020  1.090
 XAY  C7   H7   single    0.930  0.020  1.080
 XAY  C6   H6   single    0.930  0.020  1.080
 XAY  C15  H13  single    0.970  0.020  1.090
 XAY  C15  H21  single    0.970  0.020  1.090
 XAY  C16  H19  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
 XAY  C24  C25  O3   117.24  3.000
 XAY  C24  C25  O4   117.39  3.000
 XAY  O3   C25  O4   125.37  3.000
 XAY  C19  C24  C23  118.24  3.000
 XAY  C23  C24  C25  118.29  3.000
 XAY  C19  C24  C25  123.47  3.000
 XAY  H18  C23  C22  119.70  3.000
 XAY  H18  C23  C24  118.29  3.000
 XAY  C22  C23  C24  122.01  3.000
 XAY  H17  C22  C21  120.59  3.000
 XAY  H17  C22  C23  120.34  3.000
 XAY  C21  C22  C23  119.07  3.000
 XAY  H16  C21  C20  119.09  3.000
 XAY  H16  C21  C22  120.26  3.000
 XAY  C20  C21  C22  120.65  3.000
 XAY  H15  C20  C19  120.38  3.000
 XAY  H15  C20  C21  119.47  3.000
 XAY  C19  C20  C21  120.15  3.000
 XAY  N3   C19  C20  123.46  3.000
 XAY  C20  C19  C24  119.88  3.000
 XAY  N3   C19  C24  116.66  3.000
 XAY  H14  N3   C18  121.29  3.000
 XAY  H14  N3   C19  108.96  3.000
 XAY  C18  N3   C19  129.47  3.000
 XAY  C16  C18  O2   120.73  3.000
 XAY  O2   C18  N3   127.21  3.000
 XAY  C16  C18  N3   112.04  3.000
 XAY  C16  C17  N2   180.00  3.000
 XAY  C15  C13  C12  120.64  3.000
 XAY  C12  C13  C14  118.99  3.000
 XAY  C15  C13  C14  120.37  3.000
 XAY  H12  C14  C9   119.20  3.000
 XAY  H12  C14  C13  119.56  3.000
 XAY  C9   C14  C13  121.23  3.000
 XAY  H11  C12  C11  119.95  3.000
 XAY  H11  C12  C13  120.17  3.000
 XAY  C11  C12  C13  119.88  3.000
 XAY  H10  C11  C10  119.07  3.000
 XAY  H10  C11  C12  119.74  3.000
 XAY  C10  C11  C12  121.19  3.000
 XAY  H9   C10  C9   121.06  3.000
 XAY  H9   C10  C11  119.63  3.000
 XAY  C9   C10  C11  119.31  3.000
 XAY  N1   C9   C10  122.83  3.000
 XAY  C10  C9   C14  119.38  3.000
 XAY  N1   C9   C14  117.75  3.000
 XAY  H8   N1   C8   117.07  3.000
 XAY  H8   N1   C9   115.35  3.000
 XAY  C8   N1   C9   126.42  3.000
 XAY  C5   C8   O1   121.49  3.000
 XAY  O1   C8   N1   123.26  3.000
 XAY  C5   C8   N1   115.25  3.000
 XAY  C6   C5   C4   118.62  3.000
 XAY  C6   C5   C8   118.29  3.000
 XAY  C4   C5   C8   123.05  3.000
 XAY  H5   C4   C3   118.50  3.000
 XAY  H5   C4   C5   120.98  3.000
 XAY  C3   C4   C5   120.49  3.000
 XAY  H4   C3   C2   119.63  3.000
 XAY  H4   C3   C4   119.23  3.000
 XAY  C2   C3   C4   121.14  3.000
 XAY  C7   C2   C1   120.83  3.000
 XAY  C7   C2   C3   118.04  3.000
 XAY  C1   C2   C3   121.13  3.000
 XAY  H2   C1   H3   108.32  3.000
 XAY  H2   C1   H1   107.37  3.000
 XAY  H3   C1   H1   107.20  3.000
 XAY  H2   C1   C2   111.63  3.000
 XAY  H3   C1   C2   111.45  3.000
 XAY  H1   C1   C2   110.67  3.000
 XAY  H7   C7   C6   119.36  3.000
 XAY  H7   C7   C2   119.52  3.000
 XAY  C6   C7   C2   121.12  3.000
 XAY  H6   C6   C7   119.53  3.000
 XAY  H6   C6   C5   119.90  3.000
 XAY  C7   C6   C5   120.57  3.000
 XAY  H21  C15  H13  106.69  3.000
 XAY  H21  C15  C16  107.51  3.000
 XAY  H13  C15  C16  108.03  3.000
 XAY  H21  C15  C13  110.38  3.000
 XAY  H13  C15  C13  110.94  3.000
 XAY  C16  C15  C13  113.03  3.000
 XAY  H19  C16  C15  107.87  3.000
 XAY  H19  C16  C17  107.21  3.000
 XAY  C15  C16  C17  110.98  3.000
 XAY  H19  C16  C18  109.92  3.000
 XAY  C15  C16  C18  111.64  3.000
 XAY  C17  C16  C18  109.12  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
 XAY  CONST_01  C21  C20  C19  C24     0.00   0.0  0
 XAY  CONST_02  C21  C22  C23  C24     0.00   0.0  0
 XAY  CONST_03  C20  C19  C24  C23     0.00   0.0  0
 XAY  CONST_04  C20  C21  C22  C23     0.00   0.0  0
 XAY  CONST_05  C19  C20  C21  C22     0.00   0.0  0
 XAY  CONST_06  C19  C24  C23  C22     0.00   0.0  0
 XAY  CONST_07  C10  C9   C14  C13     0.00   0.0  0
 XAY  CONST_08  C10  C11  C12  C13     0.00   0.0  0
 XAY  CONST_09  C11  C12  C13  C14     0.00   0.0  0
 XAY  CONST_10  C11  C10  C9   C14     0.00   0.0  0
 XAY  CONST_11  C9   C14  C13  C12     0.00   0.0  0
 XAY  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 XAY  CONST_13  C2   C3   C4   C5      0.00   0.0  0
 XAY  CONST_14  C2   C7   C6   C5      0.00   0.0  0
 XAY  CONST_15  C7   C2   C3   C4      0.00   0.0  0
 XAY  CONST_16  C7   C6   C5   C4      0.00   0.0  0
 XAY  CONST_17  C6   C5   C4   C3      0.00   0.0  0
 XAY  CONST_18  C6   C7   C2   C3      0.00   0.0  0
 XAY  CONST_19  C20  C19  C24  C25   180.00   0.0  0
 XAY  CONST_20  C22  C23  C24  C25   180.00   0.0  0
 XAY  CONST_21  N3   C19  C24  C23   180.00   0.0  0
 XAY  CONST_22  N3   C19  C20  C21   180.00   0.0  0
 XAY  CONST_23  N1   C9   C14  C13   180.00   0.0  0
 XAY  CONST_24  C15  C13  C12  C11   180.00   0.0  0
 XAY  CONST_25  N1   C9   C10  C11   180.00   0.0  0
 XAY  CONST_26  C15  C13  C14  C9    180.00   0.0  0
 XAY  CONST_27  C3   C4   C5   C8    180.00   0.0  0
 XAY  CONST_28  C7   C6   C5   C8    180.00   0.0  0
 XAY  CONST_29  C1   C2   C3   C4    180.00   0.0  0
 XAY  CONST_30  C6   C7   C2   C1    180.00   0.0  0
 XAY  CONST_31  H15  C20  C19  C24   180.00   0.0  0
 XAY  CONST_32  H17  C22  C23  C24   180.00   0.0  0
 XAY  CONST_33  H16  C21  C22  C23   180.00   0.0  0
 XAY  CONST_34  H15  C20  C21  C22   180.00   0.0  0
 XAY  CONST_35  H18  C23  C22  C21   180.00   0.0  0
 XAY  CONST_36  H17  C22  C21  C20   180.00   0.0  0
 XAY  CONST_37  H16  C21  C20  C19   180.00   0.0  0
 XAY  CONST_38  H18  C23  C24  C19   180.00   0.0  0
 XAY  CONST_39  H10  C11  C12  C13   180.00   0.0  0
 XAY  CONST_40  H11  C12  C13  C14   180.00   0.0  0
 XAY  CONST_41  H9   C10  C9   C14   180.00   0.0  0
 XAY  CONST_42  H12  C14  C13  C12   180.00   0.0  0
 XAY  CONST_43  H9   C10  C11  C12   180.00   0.0  0
 XAY  CONST_44  H12  C14  C9   C10   180.00   0.0  0
 XAY  CONST_45  H11  C12  C11  C10   180.00   0.0  0
 XAY  CONST_46  H10  C11  C10  C9    180.00   0.0  0
 XAY  CONST_47  H4   C3   C4   C5    180.00   0.0  0
 XAY  CONST_48  H7   C7   C6   C5    180.00   0.0  0
 XAY  CONST_49  H6   C6   C5   C4    180.00   0.0  0
 XAY  CONST_50  H7   C7   C2   C3    180.00   0.0  0
 XAY  CONST_51  H5   C4   C3   C2    180.00   0.0  0
 XAY  CONST_52  H6   C6   C7   C2    180.00   0.0  0
 XAY  CONST_53  H4   C3   C2   C7    180.00   0.0  0
 XAY  CONST_54  H5   C4   C5   C6    180.00   0.0  0
 XAY  CONST_55  C5   C8   N1   C9    180.00   0.0  0
 XAY  CONST_56  C18  N3   C19  C24   180.00   0.0  0
 XAY  CONST_57  C18  N3   C19  C20     0.00   0.0  0
 XAY  CONST_60  H14  N3   C19  C24     0.00   0.0  0
 XAY  CONST_61  H14  N3   C19  C20   180.00   0.0  0
 XAY  CONST_64  C16  C18  N3   C19   180.00   0.0  0
 XAY  CONST_65  O2   C18  N3   C19     0.00   0.0  0
 XAY  CONST_66  O1   C8   N1   C9      0.00   0.0  0
 XAY  CONST_67  H8   N1   C8   C5      0.00   0.0  0
 XAY  CONST_68  H14  N3   C18  O2    180.00   0.0  0
 XAY  CONST_69  H8   N1   C8   O1    180.00   0.0  0
 XAY  CONST_70  H14  N3   C18  C16     0.00   0.0  0
 XAY  Var_01    C19  C24  C25  O4   -176.26  30.0  2
 XAY  Var_02    C23  C24  C25  O4      3.80  30.0  2
 XAY  Var_03    C19  C24  C25  O3      4.03  30.0  2
 XAY  Var_04    C23  C24  C25  O3   -175.92  30.0  2
 XAY  Var_05    C16  C15  C13  C14    86.43  30.0  2
 XAY  Var_06    C16  C15  C13  C12   -92.74  30.0  2
 XAY  Var_07    C4   C5   C8   N1    -27.64  30.0  2
 XAY  Var_08    C6   C5   C8   N1    154.66  30.0  2
 XAY  Var_09    C4   C5   C8   O1    152.93  30.0  2
 XAY  Var_10    C6   C5   C8   O1    -24.77  30.0  2
 XAY  Var_11    H13  C15  C13  C14   -35.09  30.0  2
 XAY  Var_12    H21  C15  C13  C14  -153.13  30.0  2
 XAY  Var_13    H13  C15  C13  C12   145.75  30.0  2
 XAY  Var_14    H21  C15  C13  C12    27.71  30.0  2
 XAY  Var_15    H1   C1   C2   C3     94.45  30.0  2
 XAY  Var_16    H3   C1   C2   C3   -146.35  30.0  2
 XAY  Var_17    H2   C1   C2   C3    -25.08  30.0  2
 XAY  Var_18    H1   C1   C2   C7    -84.73  30.0  2
 XAY  Var_19    H3   C1   C2   C7     34.47  30.0  2
 XAY  Var_20    H2   C1   C2   C7    155.74  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XAY  chir_01  C16  C17  C15  C18  positiv

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
 XAY  plan-1  C25  0.020
 XAY  plan-1  C24  0.020
 XAY  plan-1  C23  0.020
 XAY  plan-1  C22  0.020
 XAY  plan-1  C21  0.020
 XAY  plan-1  C20  0.020
 XAY  plan-1  C19  0.020
 XAY  plan-1  N3   0.020
 XAY  plan-1  H18  0.020
 XAY  plan-1  H17  0.020
 XAY  plan-1  H16  0.020
 XAY  plan-1  H15  0.020
 XAY  plan-2  O4   0.020
 XAY  plan-2  C25  0.020
 XAY  plan-2  O3   0.020
 XAY  plan-2  C24  0.020
 XAY  plan-3  C13  0.020
 XAY  plan-3  C14  0.020
 XAY  plan-3  C12  0.020
 XAY  plan-3  C11  0.020
 XAY  plan-3  C10  0.020
 XAY  plan-3  C9   0.020
 XAY  plan-3  N1   0.020
 XAY  plan-3  C15  0.020
 XAY  plan-3  H12  0.020
 XAY  plan-3  H11  0.020
 XAY  plan-3  H10  0.020
 XAY  plan-3  H9   0.020
 XAY  plan-4  C8   0.020
 XAY  plan-4  C5   0.020
 XAY  plan-4  C4   0.020
 XAY  plan-4  C3   0.020
 XAY  plan-4  C2   0.020
 XAY  plan-4  C1   0.020
 XAY  plan-4  C7   0.020
 XAY  plan-4  C6   0.020
 XAY  plan-4  H5   0.020
 XAY  plan-4  H4   0.020
 XAY  plan-4  H7   0.020
 XAY  plan-4  H6   0.020
 XAY  plan-5  C19  0.020
 XAY  plan-5  N3   0.020
 XAY  plan-5  C18  0.020
 XAY  plan-5  O2   0.020
 XAY  plan-5  C16  0.020
 XAY  plan-5  H14  0.020
 XAY  plan-6  C9   0.020
 XAY  plan-6  N1   0.020
 XAY  plan-6  C8   0.020
 XAY  plan-6  O1   0.020
 XAY  plan-6  C5   0.020
 XAY  plan-6  H8   0.020

