# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:00:49 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccncc1NC(=O)CCCc2ccccc2
#
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
 YC8  YC8  '3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid'  ligand  36  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YC8
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
 YC8  C1    C  C      0   0.471  -3.9024   1.7228   0.0060
 YC8  N1    N  N      0  -0.392  -4.1917  -2.5810  -0.3018
 YC8  O1    O  O      0  -0.595  -2.7796   2.2524   0.2064
 YC8  C2    C  CR6    0  -0.127  -3.9495   0.1965  -0.0929
 YC8  O2    O  OC    -1  -0.553  -4.9758   2.3216  -0.1210
 YC8  C3    C  CR16   0  -0.343  -5.1713  -0.4171  -0.3304
 YC8  O3    O  O      0  -0.478  -0.1466  -1.7979   0.4479
 YC8  C4    C  CR16   0  -0.087  -5.2524  -1.7945  -0.4279
 YC8  C5    C  CR16   0  -0.136  -3.0118  -2.0231  -0.0751
 YC8  C6    C  CR6    0   0.271  -2.8223  -0.6385   0.0402
 YC8  C7    C  C      0   0.549  -0.3747  -0.5989   0.4743
 YC8  C8    C  CH2    0  -0.594   0.7060   0.4201   0.7729
 YC8  C9    C  CH2    0  -0.410   2.0950  -0.0250   0.3405
 YC8  C10   C  CH2    0  -0.507   3.1499   1.0340   0.6663
 YC8  C11   C  C      0   0.135   4.5232   0.6055   0.2314
 YC8  C12   C  C1     0  -0.313   5.3479  -0.1244   1.0851
 YC8  C13   C  C1     0  -0.240   6.5980  -0.5624   0.6679
 YC8  C14   C  C1     0  -0.275   7.0450  -0.2767  -0.6158
 YC8  C15   C  C1     0  -0.239   6.2328   0.4511  -1.4761
 YC8  C16   C  C1     0  -0.313   4.9837   0.8872  -1.0532
 YC8  HN2   H  HNH1   0   0.428  -1.6974   0.9866   0.3075
 YC8  H3    H  HCR6   0   0.262  -6.0605   0.1873  -0.4410
 YC8  H4    H  HCR6   0   0.256  -6.2038  -2.2794  -0.6155
 YC8  H5    H  HCR6   0   0.276  -2.1737  -2.6960   0.0193
 YC8  H8    H  HCH2   0   0.254   0.4569   1.3786   0.3106
 YC8  H8A   H  HCH2   0   0.274   0.6943   0.5988   1.8543
 YC8  H9    H  HCH2   0   0.235   2.3609  -0.9626   0.8326
 YC8  H9A   H  HCH2   0   0.234   2.1042  -0.2229  -0.7348
 YC8  H10   H  HCH2   0   0.240   2.8820   1.9745   0.1772
 YC8  H10A  H  HCH2   0   0.240   3.1440   1.2289   1.7421
 YC8  H12   H  H      0   0.245   5.0095  -0.3503   2.0901
 YC8  H13   H  H      0   0.252   7.2243  -1.1264   1.3475
 YC8  H14   H  H      0   0.252   8.0194  -0.6171  -0.9412
 YC8  H15   H  H      0   0.252   6.5722   0.6827  -2.4777
 YC8  H16   H  H      0   0.245   4.3593   1.4594  -1.7300
 YC8  N2    N  NH1    0  -0.771  -1.5908  -0.0406   0.2716

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
 YC8  O1   C1    deloc     1.257  0.020  1.257
 YC8  O2   C1    deloc     1.236  0.020  1.236
 YC8  C1   C2    single    1.530  0.020  1.530
 YC8  C5   N1    aromatic  1.325  0.020  1.325
 YC8  N1   C4    aromatic  1.326  0.020  1.326
 YC8  C6   C2    aromatic  1.409  0.020  1.409
 YC8  C2   C3    aromatic  1.388  0.020  1.388
 YC8  C7   N2    single    1.353  0.020  1.353
 YC8  N2   C6    single    1.388  0.020  1.388
 YC8  N2   HN2   single    0.860  0.020  1.020
 YC8  C3   C4    aromatic  1.383  0.020  1.383
 YC8  C3   H3    single    0.930  0.020  1.080
 YC8  C7   O3    double    1.221  0.020  1.221
 YC8  C4   H4    single    0.930  0.020  1.080
 YC8  C6   C5    aromatic  1.402  0.020  1.402
 YC8  C5   H5    single    0.930  0.020  1.080
 YC8  C8   C7    single    1.515  0.020  1.515
 YC8  C9   C8    single    1.521  0.020  1.521
 YC8  C8   H8    single    0.970  0.020  1.090
 YC8  C8   H8A   single    0.970  0.020  1.090
 YC8  C10  C9    single    1.530  0.020  1.530
 YC8  C9   H9    single    0.970  0.020  1.090
 YC8  C9   H9A   single    0.970  0.020  1.090
 YC8  C11  C10   single    1.503  0.020  1.503
 YC8  C10  H10   single    0.970  0.020  1.090
 YC8  C10  H10A  single    0.970  0.020  1.090
 YC8  C12  C11   aromatic  1.393  0.020  1.393
 YC8  C11  C16   aromatic  1.393  0.020  1.393
 YC8  C13  C12   aromatic  1.389  0.020  1.389
 YC8  C12  H12   single    0.930  0.020  1.080
 YC8  C13  C14   aromatic  1.389  0.020  1.389
 YC8  C13  H13   single    0.930  0.020  1.080
 YC8  C14  C15   aromatic  1.389  0.020  1.389
 YC8  C14  H14   single    0.930  0.020  1.080
 YC8  C15  C16   aromatic  1.389  0.020  1.389
 YC8  C15  H15   single    0.930  0.020  1.080
 YC8  C16  H16   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
 YC8  O2    C1   C2   116.74  3.000
 YC8  C2    C1   O1   117.25  3.000
 YC8  O2    C1   O1   126.01  3.000
 YC8  C5    N1   C4   118.60  3.000
 YC8  C6    C2   C3   117.29  3.000
 YC8  C3    C2   C1   118.63  3.000
 YC8  C6    C2   C1   124.08  3.000
 YC8  H3    C3   C4   120.09  3.000
 YC8  H3    C3   C2   119.64  3.000
 YC8  C4    C3   C2   120.26  3.000
 YC8  H4    C4   C3   120.60  3.000
 YC8  H4    C4   N1   116.93  3.000
 YC8  C3    C4   N1   122.47  3.000
 YC8  H5    C5   C6   120.24  3.000
 YC8  H5    C5   N1   116.37  3.000
 YC8  C6    C5   N1   123.39  3.000
 YC8  C5    C6   N2   123.97  3.000
 YC8  C5    C6   C2   117.98  3.000
 YC8  N2    C6   C2   118.05  3.000
 YC8  C8    C7   O3   122.11  3.000
 YC8  C8    C7   N2   113.14  3.000
 YC8  O3    C7   N2   124.74  3.000
 YC8  H8A   C8   H8   105.78  3.000
 YC8  H8A   C8   C9   109.75  3.000
 YC8  H8    C8   C9   110.14  3.000
 YC8  H8A   C8   C7   107.25  3.000
 YC8  H8    C8   C7   110.11  3.000
 YC8  C9    C8   C7   113.48  3.000
 YC8  H9A   C9   H9   106.61  3.000
 YC8  H9A   C9   C10  109.20  3.000
 YC8  H9    C9   C10  109.30  3.000
 YC8  H9A   C9   C8   109.89  3.000
 YC8  H9    C9   C8   110.21  3.000
 YC8  C10   C9   C8   111.50  3.000
 YC8  H10A  C10  H10  106.59  3.000
 YC8  H10A  C10  C11  109.90  3.000
 YC8  H10   C10  C11  109.86  3.000
 YC8  H10A  C10  C9   109.23  3.000
 YC8  H10   C10  C9   109.34  3.000
 YC8  C11   C10  C9   111.78  3.000
 YC8  C16   C11  C12  118.36  3.000
 YC8  C16   C11  C10  120.74  3.000
 YC8  C12   C11  C10  120.85  3.000
 YC8  H12   C12  C13  119.58  3.000
 YC8  H12   C12  C11  119.49  3.000
 YC8  C13   C12  C11  120.93  3.000
 YC8  H13   C13  C14  120.07  3.000
 YC8  H13   C13  C12  119.77  3.000
 YC8  C14   C13  C12  120.16  3.000
 YC8  H14   C14  C15  120.33  3.000
 YC8  H14   C14  C13  120.19  3.000
 YC8  C15   C14  C13  119.48  3.000
 YC8  H15   C15  C16  119.76  3.000
 YC8  H15   C15  C14  120.12  3.000
 YC8  C16   C15  C14  120.12  3.000
 YC8  H16   C16  C15  119.58  3.000
 YC8  H16   C16  C11  119.46  3.000
 YC8  C15   C16  C11  120.96  3.000
 YC8  HN2   N2   C7   119.84  3.000
 YC8  HN2   N2   C6   110.02  3.000
 YC8  C7    N2   C6   130.12  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
 YC8  CONST_01  C2   C6   C5   N1      0.00   0.0  0
 YC8  CONST_02  C2   C3   C4   N1      0.00   0.0  0
 YC8  CONST_03  C5   C6   C2   C3      0.00   0.0  0
 YC8  CONST_04  C5   N1   C4   C3      0.00   0.0  0
 YC8  CONST_05  C6   C5   N1   C4      0.00   0.0  0
 YC8  CONST_06  C6   C2   C3   C4      0.00   0.0  0
 YC8  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 YC8  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 YC8  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 YC8  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 YC8  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 YC8  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 YC8  CONST_13  C5   C6   C2   C1    180.00   0.0  0
 YC8  CONST_14  C4   C3   C2   C1    180.00   0.0  0
 YC8  CONST_15  N2   C6   C5   N1    180.00   0.0  0
 YC8  CONST_16  C3   C2   C6   N2    180.00   0.0  0
 YC8  CONST_17  C13  C12  C11  C10   180.00   0.0  0
 YC8  CONST_18  C15  C16  C11  C10   180.00   0.0  0
 YC8  CONST_19  H3   C3   C4   N1    180.00   0.0  0
 YC8  CONST_20  H5   C5   C6   C2    180.00   0.0  0
 YC8  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 YC8  CONST_22  H13  C13  C12  C11   180.00   0.0  0
 YC8  CONST_23  H15  C15  C16  C11   180.00   0.0  0
 YC8  CONST_24  H16  C16  C11  C12   180.00   0.0  0
 YC8  CONST_25  H14  C14  C13  C12   180.00   0.0  0
 YC8  CONST_26  H12  C12  C13  C14   180.00   0.0  0
 YC8  CONST_27  C7   N2   C6   C2    180.00   0.0  0
 YC8  CONST_28  C7   N2   C6   C5      0.00   0.0  0
 YC8  CONST_29  HN2  N2   C6   C2      0.00   0.0  0
 YC8  CONST_30  C6   N2   C7   O3      0.00   0.0  0
 YC8  CONST_31  C8   C7   N2   C6    180.00   0.0  0
 YC8  Var_01    C6   C2   C1   O1      0.68  30.0  2
 YC8  Var_02    C12  C11  C10  C9    -88.97  30.0  2
 YC8  Var_03    C11  C10  C9   C8   -179.53  30.0  2
 YC8  Var_04    C9   C8   C7   N2   -151.60  30.0  2
 YC8  Var_05    C10  C9   C8   C7   -179.84  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
 YC8  plan-1  C1   0.020
 YC8  plan-1  N1   0.020
 YC8  plan-1  C2   0.020
 YC8  plan-1  C3   0.020
 YC8  plan-1  C4   0.020
 YC8  plan-1  C5   0.020
 YC8  plan-1  C6   0.020
 YC8  plan-1  H3   0.020
 YC8  plan-1  H4   0.020
 YC8  plan-1  H5   0.020
 YC8  plan-1  N2   0.020
 YC8  plan-2  C10  0.020
 YC8  plan-2  C11  0.020
 YC8  plan-2  C12  0.020
 YC8  plan-2  C13  0.020
 YC8  plan-2  C14  0.020
 YC8  plan-2  C15  0.020
 YC8  plan-2  C16  0.020
 YC8  plan-2  H12  0.020
 YC8  plan-2  H13  0.020
 YC8  plan-2  H14  0.020
 YC8  plan-2  H15  0.020
 YC8  plan-2  H16  0.020
 YC8  plan-3  O3   0.020
 YC8  plan-3  C6   0.020
 YC8  plan-3  C7   0.020
 YC8  plan-3  C8   0.020
 YC8  plan-3  HN2  0.020
 YC8  plan-3  N2   0.020
 YC8  plan-4  C1   0.020
 YC8  plan-4  O1   0.020
 YC8  plan-4  C2   0.020
 YC8  plan-4  O2   0.020

