# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:53:26 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(cc1)C(=O)Nc2cc(ccc2N)c3sccc3
#
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
 20Y  20Y  4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide  ligand  42  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_20Y
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
 20Y  C14  C  CR6   0   0.312  -1.4596   1.3069  -0.2060
 20Y  C5   C  CR6   0   0.381   4.7354  -0.5558  -0.0196
 20Y  C6   C  CR16  0  -0.337   4.1243  -1.0139  -1.1926
 20Y  C11  C  C     0   0.525   0.5408   0.0235  -0.7671
 20Y  C7   C  CR16  0  -0.256   2.7767  -0.8223  -1.4103
 20Y  C8   C  CR6   0  -0.058   1.9903  -0.1510  -0.4749
 20Y  C9   C  CR16  0  -0.282   2.5995   0.2921   0.6955
 20Y  C10  C  CR16  0  -0.302   3.9510   0.0979   0.9332
 20Y  C1   C  CH3   0  -0.784   8.3832  -0.8477   0.8725
 20Y  C2   C  C     0   0.515   6.9517  -0.4435   1.1122
 20Y  O3   O  O     0  -0.464   6.6083   0.1708   2.1049
 20Y  O12  O  O     0  -0.464  -0.0385  -0.6857  -1.5724
 20Y  N13  N  NH1   0  -0.771  -0.0826   1.0244  -0.0947
 20Y  C15  C  CR16  0  -0.353  -2.4076   0.3501   0.1168
 20Y  C16  C  CR6   0   0.124  -3.7723   0.6193   0.0343
 20Y  C17  C  CR16  0  -0.322  -4.1572   1.9019  -0.3669
 20Y  C18  C  CR16  0  -0.312  -3.2206   2.8665  -0.6772
 20Y  C19  C  CR6   0   0.249  -1.8494   2.5911  -0.6199
 20Y  N20  N  NH2   0  -0.848  -0.9110   3.5546  -0.9016
 20Y  C21  C  CR5   0  -0.210  -4.7765  -0.3859   0.3719
 20Y  C22  C  CR15  0  -0.254  -6.0475  -0.1962   0.8433
 20Y  C23  C  CR15  0  -0.173  -6.7529  -1.4093   1.0580
 20Y  C24  C  CR15  0  -0.474  -6.0132  -2.5094   0.7499
 20Y  S25  S  S2    0   0.201  -4.4554  -2.0746   0.1824
 20Y  H1   H  HCR6  0   0.277   4.7150  -1.5294  -1.9408
 20Y  H2   H  HCR6  0   0.265   2.3328  -1.1929  -2.3242
 20Y  H3   H  HCR6  0   0.262   2.0263   0.7826   1.4724
 20Y  H4   H  HCR6  0   0.289   4.3755   0.4524   1.8566
 20Y  H5   H  HCH3  0   0.279   8.9346   0.0108   0.4847
 20Y  H6   H  HCH3  0   0.271   8.8441  -1.1378   1.8144
 20Y  H7   H  HCH3  0   0.258   8.4901  -1.6654   0.1624
 20Y  H8   H  HNH1  0   0.419   6.5111  -1.3024  -0.6605
 20Y  H9   H  HNH1  0   0.411   0.4718   1.6551   0.4646
 20Y  H10  H  HCR6  0   0.256  -2.0630  -0.6142   0.4700
 20Y  H11  H  HCR6  0   0.254  -5.2078   2.1468  -0.4592
 20Y  H12  H  HCR6  0   0.265  -3.5497   3.8466  -1.0006
 20Y  H13  H  HNH2  0   0.387  -1.2531   4.3561  -1.4073
 20Y  H14  H  HNH2  0   0.380  -0.0341   3.2259  -1.2753
 20Y  H15  H  HCR5  0   0.260  -6.4616   0.7807   1.0513
 20Y  H16  H  HCR5  0   0.266  -7.7645  -1.4590   1.4351
 20Y  H17  H  HCR5  0   0.294  -6.2966  -3.5478   0.8242
 20Y  N4   N  NH1   0  -0.735   6.0985  -0.8018   0.1118

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
 20Y  O3   C2   double    1.217  0.020  1.217
 20Y  C1   C2   single    1.507  0.020  1.507
 20Y  C2   N4   single    1.363  0.020  1.363
 20Y  N20  C19  single    1.374  0.020  1.374
 20Y  C10  C9   aromatic  1.386  0.020  1.386
 20Y  C10  C5   aromatic  1.397  0.020  1.397
 20Y  N4   C5   single    1.391  0.020  1.391
 20Y  C9   C8   aromatic  1.392  0.020  1.392
 20Y  C5   C6   aromatic  1.400  0.020  1.400
 20Y  O12  C11  double    1.220  0.020  1.220
 20Y  C8   C11  single    1.489  0.020  1.489
 20Y  C8   C7   aromatic  1.394  0.020  1.394
 20Y  C6   C7   aromatic  1.378  0.020  1.378
 20Y  C11  N13  single    1.357  0.020  1.357
 20Y  C19  C18  aromatic  1.400  0.020  1.400
 20Y  C19  C14  aromatic  1.404  0.020  1.404
 20Y  C18  C17  aromatic  1.380  0.020  1.380
 20Y  N13  C14  single    1.410  0.020  1.410
 20Y  C14  C15  aromatic  1.385  0.020  1.385
 20Y  C17  C16  aromatic  1.398  0.020  1.398
 20Y  C15  C16  aromatic  1.393  0.020  1.393
 20Y  C16  C21  single    1.460  0.020  1.460
 20Y  C21  C22  aromatic  1.369  0.020  1.369
 20Y  C21  S25  aromatic  1.729  0.020  1.729
 20Y  C22  C23  aromatic  1.420  0.020  1.420
 20Y  S25  C24  aromatic  1.714  0.020  1.714
 20Y  C23  C24  aromatic  1.361  0.020  1.361
 20Y  C6   H1   single    0.930  0.020  1.080
 20Y  C7   H2   single    0.930  0.020  1.080
 20Y  C9   H3   single    0.930  0.020  1.080
 20Y  C10  H4   single    0.930  0.020  1.080
 20Y  C1   H5   single    0.970  0.020  1.090
 20Y  C1   H6   single    0.970  0.020  1.090
 20Y  C1   H7   single    0.970  0.020  1.090
 20Y  N4   H8   single    0.860  0.020  1.020
 20Y  N13  H9   single    0.860  0.020  1.020
 20Y  C15  H10  single    0.930  0.020  1.080
 20Y  C17  H11  single    0.930  0.020  1.080
 20Y  C18  H12  single    0.930  0.020  1.080
 20Y  N20  H13  single    0.890  0.020  1.040
 20Y  N20  H14  single    0.890  0.020  1.040
 20Y  C22  H15  single    0.930  0.020  1.080
 20Y  C23  H16  single    0.930  0.020  1.080
 20Y  C24  H17  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
 20Y  C19  C14  C15  120.69  3.000
 20Y  C15  C14  N13  120.77  3.000
 20Y  C19  C14  N13  118.52  3.000
 20Y  N4   C5   C10  124.66  3.000
 20Y  N4   C5   C6   116.68  3.000
 20Y  C10  C5   C6   118.66  3.000
 20Y  H1   C6   C7   119.34  3.000
 20Y  H1   C6   C5   119.75  3.000
 20Y  C7   C6   C5   120.91  3.000
 20Y  N13  C11  O12  122.53  3.000
 20Y  N13  C11  C8   115.87  3.000
 20Y  O12  C11  C8   121.60  3.000
 20Y  H2   C7   C8   120.03  3.000
 20Y  H2   C7   C6   119.15  3.000
 20Y  C8   C7   C6   120.82  3.000
 20Y  C9   C8   C7   118.06  3.000
 20Y  C7   C8   C11  118.29  3.000
 20Y  C9   C8   C11  123.63  3.000
 20Y  H3   C9   C10  117.17  3.000
 20Y  H3   C9   C8   121.05  3.000
 20Y  C10  C9   C8   121.77  3.000
 20Y  H4   C10  C9   119.05  3.000
 20Y  H4   C10  C5   121.19  3.000
 20Y  C9   C10  C5   119.76  3.000
 20Y  H7   C1   H6   108.84  3.000
 20Y  H7   C1   H5   108.03  3.000
 20Y  H6   C1   H5   107.66  3.000
 20Y  H7   C1   C2   113.50  3.000
 20Y  H6   C1   C2   109.66  3.000
 20Y  H5   C1   C2   109.00  3.000
 20Y  N4   C2   O3   123.71  3.000
 20Y  N4   C2   C1   114.05  3.000
 20Y  O3   C2   C1   122.23  3.000
 20Y  H9   N13  C11  118.89  3.000
 20Y  H9   N13  C14  117.07  3.000
 20Y  C11  N13  C14  123.86  3.000
 20Y  H10  C15  C16  120.19  3.000
 20Y  H10  C15  C14  118.24  3.000
 20Y  C16  C15  C14  121.54  3.000
 20Y  C21  C16  C17  120.57  3.000
 20Y  C21  C16  C15  121.79  3.000
 20Y  C17  C16  C15  117.64  3.000
 20Y  H11  C17  C18  118.77  3.000
 20Y  H11  C17  C16  119.95  3.000
 20Y  C18  C17  C16  121.27  3.000
 20Y  H12  C18  C19  119.19  3.000
 20Y  H12  C18  C17  119.57  3.000
 20Y  C19  C18  C17  121.21  3.000
 20Y  N20  C19  C18  121.51  3.000
 20Y  C18  C19  C14  117.64  3.000
 20Y  N20  C19  C14  120.80  3.000
 20Y  H14  N20  H13  111.63  3.000
 20Y  H14  N20  C19  116.19  3.000
 20Y  H13  N20  C19  115.39  3.000
 20Y  S25  C21  C22  110.21  3.000
 20Y  S25  C21  C16  121.27  3.000
 20Y  C22  C21  C16  128.51  3.000
 20Y  H15  C22  C23  123.55  3.000
 20Y  H15  C22  C21  123.17  3.000
 20Y  C23  C22  C21  113.27  3.000
 20Y  H16  C23  C24  123.41  3.000
 20Y  H16  C23  C22  123.86  3.000
 20Y  C24  C23  C22  112.73  3.000
 20Y  H17  C24  S25  120.38  3.000
 20Y  H17  C24  C23  128.29  3.000
 20Y  S25  C24  C23  111.34  3.000
 20Y  C24  S25  C21   92.45  3.000
 20Y  H8   N4   C2   115.88  3.000
 20Y  H8   N4   C5   114.60  3.000
 20Y  C2   N4   C5   129.51  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
 20Y  CONST_01  C17  C18  C19  C14    0.00   0.0  0
 20Y  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 20Y  CONST_03  C21  C16  C15  C14  180.00   0.0  0
 20Y  CONST_04  C8   C9   C10  C5     0.00   0.0  0
 20Y  CONST_05  C8   C7   C6   C5     0.00   0.0  0
 20Y  CONST_06  C9   C10  C5   C6     0.00   0.0  0
 20Y  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 20Y  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 20Y  CONST_09  C10  C5   C6   C7     0.00   0.0  0
 20Y  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 20Y  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 20Y  CONST_14  C19  C18  C17  C16    0.00   0.0  0
 20Y  CONST_15  C19  C14  C15  C16    0.00   0.0  0
 20Y  CONST_16  C23  C22  C21  C16  180.00   0.0  0
 20Y  CONST_17  C24  S25  C21  C16  180.00   0.0  0
 20Y  CONST_20  C21  C16  C17  C18  180.00   0.0  0
 20Y  CONST_21  C24  C23  C22  C21    0.00   0.0  0
 20Y  CONST_22  C23  C24  S25  C21    0.00   0.0  0
 20Y  CONST_23  C24  S25  C21  C22    0.00   0.0  0
 20Y  CONST_24  S25  C24  C23  C22    0.00   0.0  0
 20Y  CONST_25  S25  C21  C22  C23    0.00   0.0  0
 20Y  CONST_26  C11  C8   C7   C6   180.00   0.0  0
 20Y  CONST_27  C10  C9   C8   C11  180.00   0.0  0
 20Y  CONST_28  N4   C5   C6   C7   180.00   0.0  0
 20Y  CONST_29  N4   C5   C10  C9   180.00   0.0  0
 20Y  CONST_30  C18  C19  C14  N13  180.00   0.0  0
 20Y  CONST_31  C16  C15  C14  N13  180.00   0.0  0
 20Y  CONST_32  N20  C19  C14  C15  180.00   0.0  0
 20Y  CONST_33  N20  C19  C18  C17  180.00   0.0  0
 20Y  CONST_34  H12  C18  C19  C14  180.00   0.0  0
 20Y  CONST_35  H3   C9   C10  C5   180.00   0.0  0
 20Y  CONST_36  H2   C7   C6   C5   180.00   0.0  0
 20Y  CONST_37  H4   C10  C5   C6   180.00   0.0  0
 20Y  CONST_38  H1   C6   C7   C8   180.00   0.0  0
 20Y  CONST_39  H11  C17  C16  C15  180.00   0.0  0
 20Y  CONST_40  H15  C22  C21  C16    0.00   0.0  0
 20Y  CONST_41  H10  C15  C16  C17  180.00   0.0  0
 20Y  CONST_42  H16  C23  C22  C21  180.00   0.0  0
 20Y  CONST_43  H17  C24  S25  C21  180.00   0.0  0
 20Y  CONST_44  C8   C11  N13  C14  180.00   0.0  0
 20Y  CONST_45  C2   N4   C5   C6   180.00   0.0  0
 20Y  CONST_48  C2   N4   C5   C10    0.00   0.0  0
 20Y  CONST_49  H13  N20  C19  C14  180.00   0.0  0
 20Y  CONST_51  H8   N4   C5   C6     0.00   0.0  0
 20Y  CONST_53  O12  C11  N13  C14    0.00   0.0  0
 20Y  CONST_54  O3   C2   N4   C5     0.00   0.0  0
 20Y  CONST_55  C1   C2   N4   C5   180.00   0.0  0
 20Y  Var_01    O12  C11  C8   C7    20.32  30.0  2
 20Y  Var_02    H5   C1   C2   O3   -80.05  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
 20Y  plan-1  C16  0.020
 20Y  plan-1  C21  0.020
 20Y  plan-1  C22  0.020
 20Y  plan-1  C23  0.020
 20Y  plan-1  C24  0.020
 20Y  plan-1  S25  0.020
 20Y  plan-1  H15  0.020
 20Y  plan-1  H16  0.020
 20Y  plan-1  H17  0.020
 20Y  plan-2  C5   0.020
 20Y  plan-2  C6   0.020
 20Y  plan-2  C11  0.020
 20Y  plan-2  C7   0.020
 20Y  plan-2  C8   0.020
 20Y  plan-2  C9   0.020
 20Y  plan-2  C10  0.020
 20Y  plan-2  H1   0.020
 20Y  plan-2  H2   0.020
 20Y  plan-2  H3   0.020
 20Y  plan-2  H4   0.020
 20Y  plan-2  N4   0.020
 20Y  plan-3  C14  0.020
 20Y  plan-3  N13  0.020
 20Y  plan-3  C15  0.020
 20Y  plan-3  C16  0.020
 20Y  plan-3  C17  0.020
 20Y  plan-3  C18  0.020
 20Y  plan-3  C19  0.020
 20Y  plan-3  N20  0.020
 20Y  plan-3  C21  0.020
 20Y  plan-3  H10  0.020
 20Y  plan-3  H11  0.020
 20Y  plan-3  H12  0.020
 20Y  plan-4  C14  0.020
 20Y  plan-4  C11  0.020
 20Y  plan-4  C8   0.020
 20Y  plan-4  O12  0.020
 20Y  plan-4  N13  0.020
 20Y  plan-4  H9   0.020
 20Y  plan-5  C5   0.020
 20Y  plan-5  C1   0.020
 20Y  plan-5  C2   0.020
 20Y  plan-5  O3   0.020
 20Y  plan-5  H8   0.020
 20Y  plan-5  N4   0.020
 20Y  plan-6  C19  0.020
 20Y  plan-6  N20  0.020
 20Y  plan-6  H13  0.020
 20Y  plan-6  H14  0.020

