# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:35:01 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 5-methyl-1-[(3S)-1-{3-[3-(trifluoromethyl)phenoxy]benzyl}piperidin-3-yl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2CCCN(C2)Cc3cccc(Oc4cccc(c4)C(F)(F)F)c3)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
 14D  14D  5-methyl-1-[(3S)-1-{3-[3-(trifluoromethyl)phenoxy]benzyl}piperidin-3-yl]pyrimidine-2,4(1H,3H)-dione  ligand  57  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_14D
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
 14D  C1   C  CH3   0  -0.706   6.5211   3.1005   2.3349
 14D  C2   C  CR6   0  -0.181   6.4480   1.9493   1.3863
 14D  C3   C  CR16  0   0.055   5.3007   1.5391   0.8162
 14D  N1   N  NR6   0  -0.549   5.1926   0.4898  -0.0587
 14D  C4   C  CR6   0   0.737   6.3033  -0.2377  -0.4120
 14D  O1   O  O     0  -0.484   6.2828  -1.1798  -1.1789
 14D  N2   N  NR16  0  -0.732   7.4711   0.1813   0.1757
 14D  C5   C  CR6   0   0.554   7.6592   1.2300   1.0564
 14D  O2   O  O     0  -0.459   8.7684   1.4855   1.4910
 14D  C6   C  CH1   0  -0.089   3.8689   0.1759  -0.6195
 14D  C7   C  CH2   0  -0.441   3.7788   0.3628  -2.1289
 14D  C8   C  CH2   0  -0.446   2.3406   0.1002  -2.5640
 14D  C9   C  CH2   0  -0.282   1.8523  -1.2450  -2.0536
 14D  N3   N  NT    0  -0.421   1.9675  -1.3168  -0.6064
 14D  C10  C  CH2   0  -0.270   3.3513  -1.1946  -0.1863
 14D  C11  C  CH2   0  -0.312   1.3340  -2.4995  -0.0666
 14D  C12  C  CR6   0   0.084  -0.1700  -2.4372  -0.1632
 14D  C13  C  CR16  0  -0.325  -0.9109  -3.5764  -0.4594
 14D  C14  C  CR16  0  -0.234  -2.2963  -3.5121  -0.5148
 14D  C15  C  CR16  0  -0.344  -2.9641  -2.3177  -0.2868
 14D  C16  C  CR6   0   0.371  -2.2172  -1.1832   0.0110
 14D  C17  C  CR16  0  -0.367  -0.8331  -1.2391   0.0778
 14D  O3   O  O2    0  -0.511  -2.7827   0.0490   0.1959
 14D  C18  C  CR6   0   0.349  -4.0710   0.1503   0.6322
 14D  C19  C  CR16  0  -0.298  -4.4855  -0.4451   1.8193
 14D  C20  C  CR16  0  -0.234  -5.7886  -0.2638   2.2478
 14D  C21  C  CR16  0  -0.294  -6.6799   0.5074   1.5116
 14D  C22  C  CR6   0  -0.183  -6.2502   1.0993   0.3339
 14D  C23  C  CR16  0  -0.351  -4.9453   0.9187  -0.1156
 14D  C24  C  CT    0   1.054  -7.1640   1.9561  -0.4865
 14D  F1   F  F     0  -0.313  -7.2061   1.5522  -1.7640
 14D  F2   F  F     0  -0.301  -8.4193   1.9552  -0.0331
 14D  F3   F  F     0  -0.314  -6.7537   3.2330  -0.5051
 14D  H1   H  HCH3  0   0.246   6.9040   2.7910   3.3083
 14D  H2   H  HCH3  0   0.246   7.1832   3.8831   1.9616
 14D  H3   H  HCH3  0   0.247   5.5372   3.5416   2.4864
 14D  H4   H  HCR6  0   0.311   4.3688   2.0425   1.0341
 14D  H5   H  HNR6  0   0.423   8.2926  -0.3550  -0.0757
 14D  H6   H  HCH1  0   0.261   3.1978   0.9066  -0.1636
 14D  H7   H  HCH2  0   0.246   4.0860   1.3761  -2.3970
 14D  H8   H  HCH2  0   0.240   4.4478  -0.3301  -2.6403
 14D  H9   H  HCH2  0   0.225   1.6848   0.8858  -2.1782
 14D  H10  H  HCH2  0   0.241   2.2684   0.1273  -3.6528
 14D  H11  H  HCH2  0   0.245   0.8069  -1.3855  -2.3352
 14D  H12  H  HCH2  0   0.196   2.4249  -2.0571  -2.5358
 14D  H14  H  HCH2  0   0.215   3.9761  -1.9979  -0.6014
 14D  H15  H  HCH2  0   0.247   3.3986  -1.2681   0.9033
 14D  H16  H  HCH2  0   0.218   1.6916  -3.4252  -0.5470
 14D  H17  H  HCH2  0   0.256   1.6105  -2.5811   0.9895
 14D  H18  H  HCR6  0   0.249  -0.4047  -4.5128  -0.6601
 14D  H19  H  HCR6  0   0.261  -2.8681  -4.3985  -0.7569
 14D  H20  H  HCR6  0   0.278  -4.0434  -2.2794  -0.3567
 14D  H21  H  HCR6  0   0.258  -0.2638  -0.3430   0.2928
 14D  H22  H  HCR6  0   0.290  -3.7970  -1.0403   2.4054
 14D  H23  H  HCR6  0   0.277  -6.1150  -0.7230   3.1707
 14D  H24  H  HCR6  0   0.275  -7.6915   0.6354   1.8694
 14D  H25  H  HCR6  0   0.287  -4.5970   1.3705  -1.0363

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
 14D  O2   C5   double    1.218  0.020  1.218
 14D  N2   C5   single    1.382  0.020  1.382
 14D  N2   C4   single    1.373  0.020  1.373
 14D  C5   C2   single    1.447  0.020  1.447
 14D  F1   C24  single    1.340  0.020  1.340
 14D  O1   C4   double    1.215  0.020  1.215
 14D  C4   N1   single    1.374  0.020  1.374
 14D  C2   C1   single    1.493  0.020  1.493
 14D  C2   C3   double    1.345  0.020  1.345
 14D  F3   C24  single    1.341  0.020  1.341
 14D  C24  F2   single    1.335  0.020  1.335
 14D  C24  C22  single    1.497  0.020  1.497
 14D  N1   C3   single    1.370  0.020  1.370
 14D  N1   C6   single    1.471  0.020  1.471
 14D  C22  C21  aromatic  1.386  0.020  1.386
 14D  C22  C23  aromatic  1.392  0.020  1.392
 14D  C21  C20  aromatic  1.390  0.020  1.390
 14D  C6   C10  single    1.528  0.020  1.528
 14D  C6   C7   single    1.524  0.020  1.524
 14D  C23  C18  aromatic  1.384  0.020  1.384
 14D  C20  C19  aromatic  1.384  0.020  1.384
 14D  C10  N3   single    1.451  0.020  1.451
 14D  C7   C8   single    1.525  0.020  1.525
 14D  C18  C19  aromatic  1.391  0.020  1.391
 14D  C18  O3   single    1.364  0.020  1.364
 14D  N3   C11  single    1.446  0.020  1.446
 14D  N3   C9   single    1.454  0.020  1.454
 14D  O3   C16  single    1.368  0.020  1.368
 14D  C8   C9   single    1.519  0.020  1.519
 14D  C17  C16  aromatic  1.387  0.020  1.387
 14D  C17  C12  aromatic  1.390  0.020  1.390
 14D  C11  C12  single    1.508  0.020  1.508
 14D  C16  C15  aromatic  1.391  0.020  1.391
 14D  C12  C13  aromatic  1.391  0.020  1.391
 14D  C15  C14  aromatic  1.387  0.020  1.387
 14D  C13  C14  aromatic  1.388  0.020  1.388
 14D  C1   H1   single    0.970  0.020  1.090
 14D  C1   H2   single    0.970  0.020  1.090
 14D  C1   H3   single    0.970  0.020  1.090
 14D  C3   H4   single    0.930  0.020  1.080
 14D  N2   H5   single    0.860  0.020  1.020
 14D  C6   H6   single    0.970  0.020  1.090
 14D  C7   H7   single    0.970  0.020  1.090
 14D  C7   H8   single    0.970  0.020  1.090
 14D  C8   H9   single    0.970  0.020  1.090
 14D  C8   H10  single    0.970  0.020  1.090
 14D  C9   H11  single    0.970  0.020  1.090
 14D  C9   H12  single    0.970  0.020  1.090
 14D  C10  H14  single    0.970  0.020  1.090
 14D  C10  H15  single    0.970  0.020  1.090
 14D  C11  H16  single    0.970  0.020  1.090
 14D  C11  H17  single    0.970  0.020  1.090
 14D  C13  H18  single    0.930  0.020  1.080
 14D  C14  H19  single    0.930  0.020  1.080
 14D  C15  H20  single    0.930  0.020  1.080
 14D  C17  H21  single    0.930  0.020  1.080
 14D  C19  H22  single    0.930  0.020  1.080
 14D  C20  H23  single    0.930  0.020  1.080
 14D  C21  H24  single    0.930  0.020  1.080
 14D  C23  H25  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
 14D  H3   C1   H2   107.78  3.000
 14D  H3   C1   H1   107.94  3.000
 14D  H2   C1   H1   107.21  3.000
 14D  H3   C1   C2   110.88  3.000
 14D  H2   C1   C2   111.43  3.000
 14D  H1   C1   C2   111.43  3.000
 14D  C5   C2   C3   117.76  3.000
 14D  C3   C2   C1   123.09  3.000
 14D  C5   C2   C1   119.15  3.000
 14D  H4   C3   N1   114.65  3.000
 14D  H4   C3   C2   120.51  3.000
 14D  N1   C3   C2   124.84  3.000
 14D  C6   N1   C4   121.08  3.000
 14D  C6   N1   C3   118.53  3.000
 14D  C4   N1   C3   120.38  3.000
 14D  N2   C4   O1   121.41  3.000
 14D  O1   C4   N1   124.00  3.000
 14D  N2   C4   N1   114.58  3.000
 14D  H5   N2   C5   116.72  3.000
 14D  H5   N2   C4   114.97  3.000
 14D  C5   N2   C4   128.32  3.000
 14D  O2   C5   N2   120.68  3.000
 14D  N2   C5   C2   114.11  3.000
 14D  O2   C5   C2   125.21  3.000
 14D  H6   C6   C10  105.89  3.000
 14D  H6   C6   C7   107.17  3.000
 14D  C10  C6   C7   111.77  3.000
 14D  H6   C6   N1   104.54  3.000
 14D  C7   C6   N1   113.86  3.000
 14D  C10  C6   N1   112.84  3.000
 14D  H8   C7   H7   107.57  3.000
 14D  H8   C7   C8   109.59  3.000
 14D  H7   C7   C8   110.79  3.000
 14D  H8   C7   C6   110.51  3.000
 14D  H7   C7   C6   109.90  3.000
 14D  C8   C7   C6   108.49  3.000
 14D  H10  C8   H9   107.13  3.000
 14D  H10  C8   C9   109.62  3.000
 14D  H9   C8   C9   108.95  3.000
 14D  H10  C8   C7   110.03  3.000
 14D  H9   C8   C7   109.94  3.000
 14D  C9   C8   C7   111.08  3.000
 14D  H12  C9   H11  106.81  3.000
 14D  H12  C9   N3   110.92  3.000
 14D  H11  C9   N3   109.05  3.000
 14D  H12  C9   C8   109.74  3.000
 14D  H11  C9   C8   109.58  3.000
 14D  N3   C9   C8   110.66  3.000
 14D  C11  N3   C10  112.24  3.000
 14D  C11  N3   C9   112.17  3.000
 14D  C10  N3   C9   111.08  3.000
 14D  H15  C10  H14  107.62  3.000
 14D  H15  C10  N3   108.92  3.000
 14D  H14  C10  N3   111.79  3.000
 14D  H15  C10  C6   109.16  3.000
 14D  H14  C10  C6   110.85  3.000
 14D  N3   C10  C6   108.45  3.000
 14D  H17  C11  H16  106.01  3.000
 14D  H17  C11  C12  108.46  3.000
 14D  H16  C11  C12  109.28  3.000
 14D  H17  C11  N3   108.09  3.000
 14D  H16  C11  N3   112.46  3.000
 14D  C12  C11  N3   112.28  3.000
 14D  C17  C12  C13  119.25  3.000
 14D  C13  C12  C11  120.73  3.000
 14D  C17  C12  C11  120.00  3.000
 14D  H18  C13  C14  119.94  3.000
 14D  H18  C13  C12  119.90  3.000
 14D  C14  C13  C12  120.15  3.000
 14D  H19  C14  C15  119.18  3.000
 14D  H19  C14  C13  119.89  3.000
 14D  C15  C14  C13  120.92  3.000
 14D  H20  C15  C16  121.37  3.000
 14D  H20  C15  C14  120.00  3.000
 14D  C16  C15  C14  118.63  3.000
 14D  O3   C16  C17  116.25  3.000
 14D  C17  C16  C15  120.90  3.000
 14D  O3   C16  C15  122.80  3.000
 14D  H21  C17  C16  120.05  3.000
 14D  H21  C17  C12  119.77  3.000
 14D  C16  C17  C12  120.16  3.000
 14D  C18  O3   C16  120.03  3.000
 14D  C23  C18  C19  120.70  3.000
 14D  C19  C18  O3   121.51  3.000
 14D  C23  C18  O3   117.73  3.000
 14D  H22  C19  C20  120.22  3.000
 14D  H22  C19  C18  120.51  3.000
 14D  C20  C19  C18  119.26  3.000
 14D  H23  C20  C21  119.62  3.000
 14D  H23  C20  C19  119.54  3.000
 14D  C21  C20  C19  120.84  3.000
 14D  H24  C21  C22  121.39  3.000
 14D  H24  C21  C20  119.39  3.000
 14D  C22  C21  C20  119.23  3.000
 14D  C24  C22  C23  118.00  3.000
 14D  C23  C22  C21  120.63  3.000
 14D  C24  C22  C21  121.38  3.000
 14D  H25  C23  C22  121.46  3.000
 14D  H25  C23  C18  119.20  3.000
 14D  C22  C23  C18  119.34  3.000
 14D  F3   C24  F2   107.04  3.000
 14D  F2   C24  F1   107.10  3.000
 14D  F3   C24  F1   106.45  3.000
 14D  F2   C24  C22  112.79  3.000
 14D  F3   C24  C22  111.45  3.000
 14D  F1   C24  C22  111.65  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
 14D  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 14D  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 14D  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 14D  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 14D  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 14D  CONST_06  C17  C12  C13  C14     0.00   0.0  0
 14D  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 14D  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 14D  CONST_09  C22  C21  C20  C19     0.00   0.0  0
 14D  CONST_10  C22  C23  C18  C19     0.00   0.0  0
 14D  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 14D  CONST_12  C23  C18  C19  C20     0.00   0.0  0
 14D  CONST_13  C4   N2   C5   C2      0.00   0.0  0
 14D  CONST_14  N2   C4   N1   C3      0.00   0.0  0
 14D  CONST_15  C5   N2   C4   N1      0.00   0.0  0
 14D  CONST_16  C6   N1   C4   N2    180.00   0.0  0
 14D  CONST_17  C16  C17  C12  C11   180.00   0.0  0
 14D  CONST_18  C14  C13  C12  C11   180.00   0.0  0
 14D  CONST_19  O3   C16  C17  C12   180.00   0.0  0
 14D  CONST_20  O3   C16  C15  C14   180.00   0.0  0
 14D  CONST_21  C22  C23  C18  O3    180.00   0.0  0
 14D  CONST_22  C20  C19  C18  O3    180.00   0.0  0
 14D  CONST_23  C24  C22  C23  C18   180.00   0.0  0
 14D  CONST_24  C24  C22  C21  C20   180.00   0.0  0
 14D  CONST_25  O1   C4   N1   C3    180.00   0.0  0
 14D  CONST_26  O2   C5   N2   C4    180.00   0.0  0
 14D  CONST_27  C5   N2   C4   O1    180.00   0.0  0
 14D  CONST_28  C6   N1   C4   O1      0.00   0.0  0
 14D  CONST_29  H19  C14  C13  C12   180.00   0.0  0
 14D  CONST_30  H21  C17  C12  C13   180.00   0.0  0
 14D  CONST_31  H20  C15  C14  C13   180.00   0.0  0
 14D  CONST_32  H18  C13  C14  C15   180.00   0.0  0
 14D  CONST_33  H23  C20  C19  C18   180.00   0.0  0
 14D  CONST_34  H24  C21  C20  C19   180.00   0.0  0
 14D  CONST_35  H25  C23  C18  C19   180.00   0.0  0
 14D  CONST_36  H22  C19  C20  C21   180.00   0.0  0
 14D  CONST_37  H5   N2   C5   C2    180.00   0.0  0
 14D  Var_01    C9   N3   C10  C6     62.14  30.0  1
 14D  Var_02    C9   C8   C7   C6    -52.68  30.0  1
 14D  Var_03    N3   C9   C8   C7     56.88  30.0  1
 14D  Var_04    C10  N3   C9   C8    -61.95  30.0  1
 14D  Var_05    C12  C11  N3   C9    -70.37  30.0  3
 14D  Var_06    C17  C12  C11  N3    -39.24  30.0  2
 14D  Var_07    C23  C18  O3   C16  -126.46  30.0  2
 14D  Var_08    F1   C24  C22  C21  -127.14  30.0  3
 14D  Var_09    H1   C1   C2   C3    120.14  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
 14D  chir_01  C6  N1  C10  C7  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
 14D  plan-1  C1   0.020
 14D  plan-1  C2   0.020
 14D  plan-1  C3   0.020
 14D  plan-1  N1   0.020
 14D  plan-1  C4   0.020
 14D  plan-1  O1   0.020
 14D  plan-1  N2   0.020
 14D  plan-1  C5   0.020
 14D  plan-1  O2   0.020
 14D  plan-1  C6   0.020
 14D  plan-1  H4   0.020
 14D  plan-1  H5   0.020
 14D  plan-2  C11  0.020
 14D  plan-2  C12  0.020
 14D  plan-2  C13  0.020
 14D  plan-2  C14  0.020
 14D  plan-2  C15  0.020
 14D  plan-2  C16  0.020
 14D  plan-2  C17  0.020
 14D  plan-2  O3   0.020
 14D  plan-2  H18  0.020
 14D  plan-2  H19  0.020
 14D  plan-2  H20  0.020
 14D  plan-2  H21  0.020
 14D  plan-3  O3   0.020
 14D  plan-3  C18  0.020
 14D  plan-3  C19  0.020
 14D  plan-3  C20  0.020
 14D  plan-3  C21  0.020
 14D  plan-3  C22  0.020
 14D  plan-3  C23  0.020
 14D  plan-3  C24  0.020
 14D  plan-3  H22  0.020
 14D  plan-3  H23  0.020
 14D  plan-3  H24  0.020
 14D  plan-3  H25  0.020

