# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:30:01 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(C2CCN(CC2)Cc3cc(Oc4cccc(Cl)c4)c5ccccc5n3)C(=O)NC1=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
 YUI  YUI  1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione  ligand  59  34  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YUI
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
 YUI  O2   O   O     0  -0.462  -6.5191  -3.6344   1.5895
 YUI  C25  C   CR6   0   0.553  -5.8160  -2.8185   1.0186
 YUI  C1   C   CR6   0  -0.181  -6.2979  -1.6584   0.3017
 YUI  C    C   CH3   0  -0.706  -7.7677  -1.4025   0.2348
 YUI  N3   N   NR16  0  -0.732  -4.4410  -2.9522   1.0164
 YUI  C24  C   CR6   0   0.731  -3.5050  -2.1347   0.4296
 YUI  O1   O   O     0  -0.469  -2.3172  -2.3737   0.5081
 YUI  N    N   NR6   0  -0.547  -4.0313  -1.0527  -0.2360
 YUI  C2   C   CR16  0   0.053  -5.3856  -0.8548  -0.2756
 YUI  C3   C   CH1   0  -0.090  -3.1538  -0.0880  -0.9197
 YUI  C23  C   CH2   0  -0.432  -2.3670  -0.6928  -2.0768
 YUI  C22  C   CH2   0  -0.284  -1.5810   0.4077  -2.7776
 YUI  N1   N   NT    0  -0.425  -0.7026   1.0718  -1.8361
 YUI  C5   C   CH2   0  -0.293  -1.4500   1.7083  -0.7685
 YUI  C4   C   CH2   0  -0.434  -2.2384   0.6789   0.0266
 YUI  C6   C   CH2   0  -0.328   0.2545   1.9620  -2.4460
 YUI  C7   C   CR6   0   0.185   1.4334   2.2188  -1.5374
 YUI  N2   N   N     0  -0.472   2.0401   3.3714  -1.6354
 YUI  C21  C   CR66  0   0.189   3.1177   3.5995  -0.8437
 YUI  C20  C   CR16  0  -0.303   3.7779   4.8436  -0.9504
 YUI  C19  C   CR16  0  -0.253   4.8606   5.1298  -0.1621
 YUI  C18  C   CR16  0  -0.253   5.3350   4.1868   0.7697
 YUI  C17  C   CR16  0  -0.298   4.7164   2.9712   0.8995
 YUI  C16  C   CR66  0  -0.005   3.5998   2.6559   0.0966
 YUI  C9   C   CR6   0   0.445   2.8990   1.4230   0.1746
 YUI  C8   C   CR16  0  -0.404   1.8328   1.1978  -0.6485
 YUI  O    O   O2    0  -0.501   3.3549   0.5339   1.0815
 YUI  C10  C   CR6   0   0.309   2.6220  -0.6071   1.3096
 YUI  C15  C   CR16  0  -0.267   3.1215  -1.8090   0.8392
 YUI  C14  C   CR6   0  -0.037   2.3922  -2.9625   1.0893
 YUI  CL   CL  CL    0  -0.120   3.0034  -4.4782   0.5161
 YUI  C13  C   CR16  0  -0.212   1.1872  -2.9280   1.7709
 YUI  C12  C   CR16  0  -0.236   0.7130  -1.7064   2.2289
 YUI  C11  C   CR16  0  -0.290   1.4271  -0.5392   2.0104
 YUI  H2   H   HCH3  0   0.245  -8.1942  -1.2614   1.2291
 YUI  H1   H   HCH3  0   0.246  -7.9799  -0.5078  -0.3486
 YUI  H3   H   HCH3  0   0.245  -8.2974  -2.2368  -0.2271
 YUI  H    H   HNR6  0   0.421  -4.0610  -3.7541   1.5036
 YUI  H4   H   HCR6  0   0.311  -5.6982   0.0268  -0.8190
 YUI  H5   H   HCH1  0   0.256  -3.8435   0.6396  -1.3555
 YUI  H24  H   HCH2  0   0.246  -1.6733  -1.4509  -1.7160
 YUI  H23  H   HCH2  0   0.243  -3.0482  -1.1670  -2.7869
 YUI  H21  H   HCH2  0   0.245  -0.9784  -0.0329  -3.5742
 YUI  H22  H   HCH2  0   0.196  -2.2804   1.1135  -3.2587
 YUI  H9   H   HCH2  0   0.248  -0.7588   2.2194  -0.0953
 YUI  H8   H   HCH2  0   0.205  -2.1301   2.4819  -1.1666
 YUI  H7   H   HCH2  0   0.241  -2.8298   1.1840   0.7936
 YUI  H6   H   HCH2  0   0.256  -1.5433   0.0018   0.5232
 YUI  H11  H   HCH2  0   0.265   0.6328   1.4910  -3.3595
 YUI  H10  H   HCH2  0   0.225  -0.1739   2.9291  -2.7506
 YUI  H20  H   HCR6  0   0.260   3.4032   5.5627  -1.6674
 YUI  H19  H   HCR6  0   0.264   5.3555   6.0879  -0.2519
 YUI  H18  H   HCR6  0   0.263   6.1920   4.4247   1.3855
 YUI  H17  H   HCR6  0   0.263   5.0894   2.2542   1.6182
 YUI  H12  H   HCR6  0   0.289   1.2557   0.2842  -0.6245
 YUI  H16  H   HCR6  0   0.296   4.0552  -1.8416   0.2933
 YUI  H15  H   HCR6  0   0.282   0.6264  -3.8358   1.9433
 YUI  H14  H   HCR6  0   0.272  -0.2294  -1.6676   2.7570
 YUI  H13  H   HCR6  0   0.286   1.0528   0.4115   2.3672

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
 YUI  O2   C25  double    1.219  0.020  1.219
 YUI  C25  N3   single    1.381  0.020  1.381
 YUI  C25  C1   single    1.446  0.020  1.446
 YUI  N3   C24  single    1.374  0.020  1.374
 YUI  C    C1   single    1.493  0.020  1.493
 YUI  C1   C2   double    1.346  0.020  1.346
 YUI  C24  O1   double    1.214  0.020  1.214
 YUI  C24  N    single    1.375  0.020  1.375
 YUI  C2   N    single    1.369  0.020  1.369
 YUI  N    C3   single    1.472  0.020  1.472
 YUI  C4   C3   single    1.524  0.020  1.524
 YUI  C4   C5   single    1.521  0.020  1.521
 YUI  C3   C23  single    1.524  0.020  1.524
 YUI  C5   N1   single    1.450  0.020  1.450
 YUI  C23  C22  single    1.523  0.020  1.523
 YUI  N1   C22  single    1.449  0.020  1.449
 YUI  N1   C6   single    1.442  0.020  1.442
 YUI  C6   C7   single    1.510  0.020  1.510
 YUI  C7   N2   aromatic  1.306  0.020  1.306
 YUI  C7   C8   aromatic  1.411  0.020  1.411
 YUI  N2   C21  aromatic  1.357  0.020  1.357
 YUI  C8   C9   aromatic  1.366  0.020  1.366
 YUI  C21  C20  aromatic  1.412  0.020  1.412
 YUI  C21  C16  aromatic  1.417  0.020  1.417
 YUI  C20  C19  aromatic  1.369  0.020  1.369
 YUI  C9   C16  aromatic  1.420  0.020  1.420
 YUI  C9   O    single    1.349  0.020  1.349
 YUI  C11  C12  aromatic  1.386  0.020  1.386
 YUI  C11  C10  aromatic  1.387  0.020  1.387
 YUI  C12  C13  aromatic  1.388  0.020  1.388
 YUI  C16  C17  aromatic  1.411  0.020  1.411
 YUI  O    C10  single    1.375  0.020  1.375
 YUI  C10  C15  aromatic  1.384  0.020  1.384
 YUI  C19  C18  aromatic  1.408  0.020  1.408
 YUI  C13  C14  aromatic  1.385  0.020  1.385
 YUI  C17  C18  aromatic  1.370  0.020  1.370
 YUI  C15  C14  aromatic  1.387  0.020  1.387
 YUI  C14  CL   single    1.732  0.020  1.732
 YUI  C    H2   single    0.970  0.020  1.090
 YUI  C    H1   single    0.970  0.020  1.090
 YUI  C    H3   single    0.970  0.020  1.090
 YUI  N3   H    single    0.860  0.020  1.020
 YUI  C2   H4   single    0.930  0.020  1.080
 YUI  C3   H5   single    0.970  0.020  1.090
 YUI  C23  H24  single    0.970  0.020  1.090
 YUI  C23  H23  single    0.970  0.020  1.090
 YUI  C22  H21  single    0.970  0.020  1.090
 YUI  C22  H22  single    0.970  0.020  1.090
 YUI  C5   H9   single    0.970  0.020  1.090
 YUI  C5   H8   single    0.970  0.020  1.090
 YUI  C4   H7   single    0.970  0.020  1.090
 YUI  C4   H6   single    0.970  0.020  1.090
 YUI  C6   H11  single    0.970  0.020  1.090
 YUI  C6   H10  single    0.970  0.020  1.090
 YUI  C20  H20  single    0.930  0.020  1.080
 YUI  C19  H19  single    0.930  0.020  1.080
 YUI  C18  H18  single    0.930  0.020  1.080
 YUI  C17  H17  single    0.930  0.020  1.080
 YUI  C8   H12  single    0.930  0.020  1.080
 YUI  C15  H16  single    0.930  0.020  1.080
 YUI  C13  H15  single    0.930  0.020  1.080
 YUI  C12  H14  single    0.930  0.020  1.080
 YUI  C11  H13  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
 YUI  N3   C25  C1   114.10  3.000
 YUI  C1   C25  O2   125.23  3.000
 YUI  N3   C25  O2   120.67  3.000
 YUI  C2   C1   C    123.07  3.000
 YUI  C2   C1   C25  117.75  3.000
 YUI  C    C1   C25  119.18  3.000
 YUI  H3   C    H1   107.88  3.000
 YUI  H3   C    H2   107.15  3.000
 YUI  H1   C    H2   107.81  3.000
 YUI  H3   C    C1   111.46  3.000
 YUI  H1   C    C1   110.89  3.000
 YUI  H2   C    C1   111.47  3.000
 YUI  H    N3   C24  114.89  3.000
 YUI  H    N3   C25  116.71  3.000
 YUI  C24  N3   C25  128.39  3.000
 YUI  N    C24  O1   124.10  3.000
 YUI  N    C24  N3   114.46  3.000
 YUI  O1   C24  N3   121.44  3.000
 YUI  C3   N    C2   118.78  3.000
 YUI  C3   N    C24  120.81  3.000
 YUI  C2   N    C24  120.42  3.000
 YUI  H4   C2   N    114.72  3.000
 YUI  H4   C2   C1   120.41  3.000
 YUI  N    C2   C1   124.88  3.000
 YUI  H5   C3   C4   106.96  3.000
 YUI  H5   C3   C23  106.68  3.000
 YUI  C4   C3   C23  111.17  3.000
 YUI  H5   C3   N    104.19  3.000
 YUI  C23  C3   N    113.58  3.000
 YUI  C4   C3   N    113.55  3.000
 YUI  H23  C23  H24  108.08  3.000
 YUI  H23  C23  C22  109.66  3.000
 YUI  H24  C23  C22  109.06  3.000
 YUI  H23  C23  C3   110.11  3.000
 YUI  H24  C23  C3   110.70  3.000
 YUI  C22  C23  C3   109.20  3.000
 YUI  H22  C22  H21  106.84  3.000
 YUI  H22  C22  N1   111.98  3.000
 YUI  H21  C22  N1   108.94  3.000
 YUI  H22  C22  C23  109.60  3.000
 YUI  H21  C22  C23  109.21  3.000
 YUI  N1   C22  C23  110.19  3.000
 YUI  C6   N1   C5   112.48  3.000
 YUI  C6   N1   C22  114.23  3.000
 YUI  C5   N1   C22  111.53  3.000
 YUI  H8   C5   H9   106.51  3.000
 YUI  H8   C5   C4   110.08  3.000
 YUI  H9   C5   C4   108.82  3.000
 YUI  H8   C5   N1   111.07  3.000
 YUI  H9   C5   N1   109.45  3.000
 YUI  C4   C5   N1   110.79  3.000
 YUI  H6   C4   H7   108.22  3.000
 YUI  H6   C4   C5   109.15  3.000
 YUI  H7   C4   C5   109.56  3.000
 YUI  H6   C4   C3   110.69  3.000
 YUI  H7   C4   C3   110.09  3.000
 YUI  C5   C4   C3   109.11  3.000
 YUI  H10  C6   H11  106.35  3.000
 YUI  H10  C6   C7   108.71  3.000
 YUI  H11  C6   C7   107.78  3.000
 YUI  H10  C6   N1   113.63  3.000
 YUI  H11  C6   N1   108.45  3.000
 YUI  C7   C6   N1   111.62  3.000
 YUI  C8   C7   N2   123.65  3.000
 YUI  C8   C7   C6   118.47  3.000
 YUI  N2   C7   C6   117.87  3.000
 YUI  C21  N2   C7   118.26  3.000
 YUI  C16  C21  C20  118.54  3.000
 YUI  C16  C21  N2   123.08  3.000
 YUI  C20  C21  N2   118.38  3.000
 YUI  H20  C20  C19  121.07  3.000
 YUI  H20  C20  C21  118.25  3.000
 YUI  C19  C20  C21  120.67  3.000
 YUI  H19  C19  C18  119.59  3.000
 YUI  H19  C19  C20  119.93  3.000
 YUI  C18  C19  C20  120.49  3.000
 YUI  H18  C18  C17  119.92  3.000
 YUI  H18  C18  C19  119.76  3.000
 YUI  C17  C18  C19  120.32  3.000
 YUI  H17  C17  C16  120.19  3.000
 YUI  H17  C17  C18  119.70  3.000
 YUI  C16  C17  C18  120.11  3.000
 YUI  C9   C16  C17  123.59  3.000
 YUI  C17  C16  C21  119.88  3.000
 YUI  C9   C16  C21  116.53  3.000
 YUI  O    C9   C8   124.07  3.000
 YUI  O    C9   C16  116.24  3.000
 YUI  C8   C9   C16  119.69  3.000
 YUI  H12  C8   C9   122.88  3.000
 YUI  H12  C8   C7   118.31  3.000
 YUI  C9   C8   C7   118.76  3.000
 YUI  C10  O    C9   118.56  3.000
 YUI  C11  C10  C15  121.68  3.000
 YUI  C15  C10  O    118.15  3.000
 YUI  C11  C10  O    120.16  3.000
 YUI  H16  C15  C14  121.30  3.000
 YUI  H16  C15  C10  120.60  3.000
 YUI  C14  C15  C10  118.10  3.000
 YUI  C13  C14  CL   119.46  3.000
 YUI  CL   C14  C15  118.84  3.000
 YUI  C13  C14  C15  121.70  3.000
 YUI  H15  C13  C12  120.61  3.000
 YUI  H15  C13  C14  120.61  3.000
 YUI  C12  C13  C14  118.78  3.000
 YUI  H14  C12  C11  119.74  3.000
 YUI  H14  C12  C13  119.38  3.000
 YUI  C11  C12  C13  120.88  3.000
 YUI  H13  C11  C12  120.65  3.000
 YUI  H13  C11  C10  120.50  3.000
 YUI  C12  C11  C10  118.84  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
 YUI  CONST_01  C20  C21  N2   C7    180.00   0.0  0
 YUI  CONST_02  C16  C21  N2   C7      0.00   0.0  0
 YUI  CONST_03  C16  C9   C8   C7      0.00   0.0  0
 YUI  CONST_04  C9   C8   C7   N2      0.00   0.0  0
 YUI  CONST_05  C19  C20  C21  N2    180.00   0.0  0
 YUI  CONST_06  C9   C16  C21  N2      0.00   0.0  0
 YUI  CONST_07  C17  C16  C21  N2    180.00   0.0  0
 YUI  CONST_08  C8   C7   N2   C21     0.00   0.0  0
 YUI  CONST_09  C18  C19  C20  C21     0.00   0.0  0
 YUI  CONST_10  C8   C9   C16  C21     0.00   0.0  0
 YUI  CONST_11  C18  C17  C16  C21     0.00   0.0  0
 YUI  CONST_12  C9   C16  C21  C20   180.00   0.0  0
 YUI  CONST_13  C17  C16  C21  C20     0.00   0.0  0
 YUI  CONST_14  C17  C18  C19  C20     0.00   0.0  0
 YUI  CONST_15  C16  C21  C20  C19     0.00   0.0  0
 YUI  CONST_16  C16  C17  C18  C19     0.00   0.0  0
 YUI  CONST_17  C9   C16  C17  C18   180.00   0.0  0
 YUI  CONST_18  C8   C9   C16  C17   180.00   0.0  0
 YUI  CONST_19  C13  C12  C11  C10     0.00   0.0  0
 YUI  CONST_20  C13  C14  C15  C10     0.00   0.0  0
 YUI  CONST_21  C12  C11  C10  C15     0.00   0.0  0
 YUI  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 YUI  CONST_23  C11  C12  C13  C14     0.00   0.0  0
 YUI  CONST_24  C11  C10  C15  C14     0.00   0.0  0
 YUI  CONST_25  N    C24  N3   C25     0.00   0.0  0
 YUI  CONST_26  C24  N3   C25  C1      0.00   0.0  0
 YUI  CONST_27  C2   N    C24  N3      0.00   0.0  0
 YUI  CONST_28  C3   N    C24  N3    180.00   0.0  0
 YUI  CONST_29  C21  N2   C7   C6    180.00   0.0  0
 YUI  CONST_30  C9   C8   C7   C6    180.00   0.0  0
 YUI  CONST_31  O    C9   C8   C7    180.00   0.0  0
 YUI  CONST_32  O    C9   C16  C21   180.00   0.0  0
 YUI  CONST_33  O    C9   C16  C17     0.00   0.0  0
 YUI  CONST_34  C12  C11  C10  O     180.00   0.0  0
 YUI  CONST_35  C14  C15  C10  O     180.00   0.0  0
 YUI  CONST_36  CL   C14  C15  C10   180.00   0.0  0
 YUI  CONST_37  C12  C13  C14  CL    180.00   0.0  0
 YUI  CONST_38  C24  N3   C25  O2    180.00   0.0  0
 YUI  CONST_39  O1   C24  N3   C25   180.00   0.0  0
 YUI  CONST_40  C2   N    C24  O1    180.00   0.0  0
 YUI  CONST_41  C3   N    C24  O1      0.00   0.0  0
 YUI  CONST_42  H12  C8   C7   N2    180.00   0.0  0
 YUI  CONST_43  H20  C20  C21  N2      0.00   0.0  0
 YUI  CONST_44  H19  C19  C20  C21   180.00   0.0  0
 YUI  CONST_45  H17  C17  C16  C21   180.00   0.0  0
 YUI  CONST_46  H18  C18  C19  C20   180.00   0.0  0
 YUI  CONST_47  H14  C12  C11  C10   180.00   0.0  0
 YUI  CONST_48  H13  C11  C10  C15   180.00   0.0  0
 YUI  CONST_49  H15  C13  C14  C15   180.00   0.0  0
 YUI  CONST_50  H16  C15  C14  C13   180.00   0.0  0
 YUI  CONST_51  H    N3   C25  C1    180.00   0.0  0
 YUI  Var_01    N1   C5   C4   C3    -56.73  30.0  1
 YUI  Var_02    N1   C22  C23  C3     57.54  30.0  1
 YUI  Var_03    C5   N1   C22  C23   -61.67  30.0  1
 YUI  Var_04    C4   C5   N1   C22    61.49  30.0  1
 YUI  Var_05    C7   C6   N1   C22  -158.89  30.0  3
 YUI  Var_06    N2   C7   C6   N1   -150.07  30.0  2
 YUI  Var_07    C11  C10  O    C9    -72.85  30.0  2
 YUI  Var_08    H2   C    C1   C25    60.81  30.0  3

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
 YUI  chir_01  C3  N  C4  C23  negativ

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
 YUI  plan-1  O2   0.020
 YUI  plan-1  C25  0.020
 YUI  plan-1  C1   0.020
 YUI  plan-1  C    0.020
 YUI  plan-1  N3   0.020
 YUI  plan-1  C24  0.020
 YUI  plan-1  O1   0.020
 YUI  plan-1  N    0.020
 YUI  plan-1  C2   0.020
 YUI  plan-1  C3   0.020
 YUI  plan-1  H    0.020
 YUI  plan-1  H4   0.020
 YUI  plan-2  O    0.020
 YUI  plan-2  C10  0.020
 YUI  plan-2  C15  0.020
 YUI  plan-2  C14  0.020
 YUI  plan-2  CL   0.020
 YUI  plan-2  C13  0.020
 YUI  plan-2  C12  0.020
 YUI  plan-2  C11  0.020
 YUI  plan-2  H16  0.020
 YUI  plan-2  H15  0.020
 YUI  plan-2  H14  0.020
 YUI  plan-2  H13  0.020
 YUI  plan-3  C6   0.020
 YUI  plan-3  C7   0.020
 YUI  plan-3  N2   0.020
 YUI  plan-3  C21  0.020
 YUI  plan-3  C20  0.020
 YUI  plan-3  C19  0.020
 YUI  plan-3  C18  0.020
 YUI  plan-3  C17  0.020
 YUI  plan-3  C16  0.020
 YUI  plan-3  C9   0.020
 YUI  plan-3  C8   0.020
 YUI  plan-3  O    0.020
 YUI  plan-3  H20  0.020
 YUI  plan-3  H19  0.020
 YUI  plan-3  H18  0.020
 YUI  plan-3  H17  0.020
 YUI  plan-3  H12  0.020

