# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 20:00:06 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2CCCN(C2)Cc3cccc(Oc4ccccc4)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
 952  952  5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione  ligand  54  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_952
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
 952  O2   O  O     0  -0.459  -7.7469   1.4522  -0.8310
 952  C22  C  CR6   0   0.555  -6.6150   1.1448  -0.5002
 952  C1   C  CR6   0  -0.180  -5.5252   2.0732  -0.2917
 952  C    C  CH3   0  -0.708  -5.7662   3.5330  -0.4940
 952  N2   N  NR16  0  -0.731  -6.2765  -0.1784  -0.2910
 952  C21  C  CR6   0   0.738  -5.0601  -0.6987   0.0754
 952  O1   O  O     0  -0.485  -4.8998  -1.8956   0.2100
 952  N    N  NR6   0  -0.549  -4.0724   0.2370   0.2679
 952  C2   C  CR16  0   0.054  -4.3335   1.5687   0.0758
 952  C3   C  CH1   0  -0.092  -2.7159  -0.1623   0.6772
 952  C7   C  CH2   0  -0.268  -1.9974  -0.9759  -0.3959
 952  N1   N  NT    0  -0.420  -0.6112  -1.1543  -0.0036
 952  C6   C  CH2   0  -0.281  -0.5064  -1.8843   1.2492
 952  C5   C  CH2   0  -0.447  -1.1941  -1.1297   2.3745
 952  C4   C  CH2   0  -0.442  -2.6542  -0.8440   2.0385
 952  C8   C  CH2   0  -0.315   0.1596  -1.7750  -1.0590
 952  C9   C  CR6   0   0.089   1.6474  -1.6341  -0.8623
 952  C14  C  CR16  0  -0.331   2.5042  -2.6766  -1.2053
 952  C13  C  CR16  0  -0.233   3.8755  -2.5166  -1.0809
 952  C12  C  CR16  0  -0.358   4.4179  -1.3285  -0.6094
 952  C11  C  CR6   0   0.387   3.5574  -0.2933  -0.2589
 952  C10  C  CR16  0  -0.369   2.1811  -0.4440  -0.3851
 952  O    O  O2    0  -0.517   3.9834   0.9107   0.2193
 952  C15  C  CR6   0   0.301   5.3318   1.1391   0.3430
 952  C20  C  CR16  0  -0.303   6.0260   1.7107  -0.7130
 952  C19  C  CR16  0  -0.254   7.3814   1.9762  -0.5697
 952  C18  C  CR16  0  -0.257   8.0354   1.6672   0.6160
 952  C17  C  CR16  0  -0.254   7.3274   1.0960   1.6656
 952  C16  C  CR16  0  -0.303   5.9718   0.8267   1.5332
 952  H2   H  HCH3  0   0.247  -6.5591   3.8997   0.1592
 952  H1   H  HCH3  0   0.247  -4.8665   4.1087  -0.2834
 952  H3   H  HCH3  0   0.247  -6.0691   3.7478  -1.5196
 952  H24  H  HNR6  0   0.423  -7.0085  -0.8635  -0.4331
 952  H4   H  HCR6  0   0.313  -3.4891   2.2236   0.2427
 952  H    H  HCH1  0   0.262  -2.1674   0.7779   0.7605
 952  H12  H  HCH2  0   0.214  -2.5031  -1.9379  -0.5592
 952  H11  H  HCH2  0   0.246  -2.0252  -0.4251  -1.3395
 952  H9   H  HCH2  0   0.195  -0.9422  -2.8950   1.1556
 952  H10  H  HCH2  0   0.244   0.5494  -2.0197   1.4908
 952  H8   H  HCH2  0   0.241  -1.1333  -1.7126   3.2952
 952  H7   H  HCH2  0   0.225  -0.6625  -0.1908   2.5529
 952  H6   H  HCH2  0   0.246  -3.1058  -0.2008   2.7969
 952  H5   H  HCH2  0   0.240  -3.2184  -1.7771   2.0244
 952  H14  H  HCH2  0   0.217  -0.0900  -2.8415  -1.1878
 952  H13  H  HCH2  0   0.256  -0.1098  -1.2895  -2.0024
 952  H18  H  HCR6  0   0.248   2.0982  -3.6124  -1.5691
 952  H17  H  HCR6  0   0.259   4.5399  -3.3283  -1.3480
 952  H16  H  HCR6  0   0.275   5.4908  -1.2266  -0.5170
 952  H15  H  HCR6  0   0.255   1.5216   0.3670  -0.1007
 952  H23  H  HCR6  0   0.272   5.5117   1.9533  -1.6346
 952  H22  H  HCR6  0   0.264   7.9257   2.4252  -1.3900
 952  H21  H  HCR6  0   0.260   9.0916   1.8751   0.7239
 952  H20  H  HCR6  0   0.264   7.8302   0.8551   2.5931
 952  H19  H  HCR6  0   0.273   5.4161   0.3823   2.3494

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
 952  C18  C19  aromatic  1.389  0.020  1.389
 952  C18  C17  aromatic  1.389  0.020  1.389
 952  C19  C20  aromatic  1.389  0.020  1.389
 952  C17  C16  aromatic  1.388  0.020  1.388
 952  C20  C15  aromatic  1.387  0.020  1.387
 952  O2   C22  double    1.219  0.020  1.219
 952  C16  C15  aromatic  1.387  0.020  1.387
 952  C15  O    single    1.373  0.020  1.373
 952  N2   C22  single    1.382  0.020  1.382
 952  N2   C21  single    1.373  0.020  1.373
 952  C22  C1   single    1.447  0.020  1.447
 952  C12  C13  aromatic  1.389  0.020  1.389
 952  C12  C11  aromatic  1.391  0.020  1.391
 952  O1   C21  double    1.215  0.020  1.215
 952  O    C11  single    1.364  0.020  1.364
 952  C21  N    single    1.374  0.020  1.374
 952  C13  C14  aromatic  1.386  0.020  1.386
 952  C11  C10  aromatic  1.390  0.020  1.390
 952  C1   C    single    1.493  0.020  1.493
 952  C1   C2   double    1.345  0.020  1.345
 952  N    C2   single    1.371  0.020  1.371
 952  N    C3   single    1.472  0.020  1.472
 952  C14  C9   aromatic  1.392  0.020  1.392
 952  C10  C9   aromatic  1.389  0.020  1.389
 952  C9   C8   single    1.507  0.020  1.507
 952  C3   C7   single    1.526  0.020  1.526
 952  C3   C4   single    1.524  0.020  1.524
 952  C7   N1   single    1.452  0.020  1.452
 952  N1   C8   single    1.447  0.020  1.447
 952  N1   C6   single    1.454  0.020  1.454
 952  C4   C5   single    1.525  0.020  1.525
 952  C6   C5   single    1.519  0.020  1.519
 952  C    H2   single    0.970  0.020  1.090
 952  C    H1   single    0.970  0.020  1.090
 952  C    H3   single    0.970  0.020  1.090
 952  N2   H24  single    0.860  0.020  1.020
 952  C2   H4   single    0.930  0.020  1.080
 952  C3   H    single    0.970  0.020  1.090
 952  C7   H12  single    0.970  0.020  1.090
 952  C7   H11  single    0.970  0.020  1.090
 952  C6   H9   single    0.970  0.020  1.090
 952  C6   H10  single    0.970  0.020  1.090
 952  C5   H8   single    0.970  0.020  1.090
 952  C5   H7   single    0.970  0.020  1.090
 952  C4   H6   single    0.970  0.020  1.090
 952  C4   H5   single    0.970  0.020  1.090
 952  C8   H14  single    0.970  0.020  1.090
 952  C8   H13  single    0.970  0.020  1.090
 952  C14  H18  single    0.930  0.020  1.080
 952  C13  H17  single    0.930  0.020  1.080
 952  C12  H16  single    0.930  0.020  1.080
 952  C10  H15  single    0.930  0.020  1.080
 952  C20  H23  single    0.930  0.020  1.080
 952  C19  H22  single    0.930  0.020  1.080
 952  C18  H21  single    0.930  0.020  1.080
 952  C17  H20  single    0.930  0.020  1.080
 952  C16  H19  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
 952  N2   C22  C1   114.09  3.000
 952  C1   C22  O2   125.24  3.000
 952  N2   C22  O2   120.68  3.000
 952  C2   C1   C    123.13  3.000
 952  C2   C1   C22  117.78  3.000
 952  C    C1   C22  119.09  3.000
 952  H3   C    H1   107.89  3.000
 952  H3   C    H2   107.16  3.000
 952  H1   C    H2   107.88  3.000
 952  H3   C    C1   111.39  3.000
 952  H1   C    C1   110.94  3.000
 952  H2   C    C1   111.40  3.000
 952  H24  N2   C21  114.93  3.000
 952  H24  N2   C22  116.71  3.000
 952  C21  N2   C22  128.35  3.000
 952  N    C21  O1   124.08  3.000
 952  N    C21  N2   114.60  3.000
 952  O1   C21  N2   121.32  3.000
 952  C3   N    C2   118.56  3.000
 952  C3   N    C21  121.11  3.000
 952  C2   N    C21  120.33  3.000
 952  H4   C2   N    114.70  3.000
 952  H4   C2   C1   120.45  3.000
 952  N    C2   C1   124.85  3.000
 952  H    C3   C4   107.27  3.000
 952  H    C3   C7   106.03  3.000
 952  C4   C3   C7   111.75  3.000
 952  H    C3   N    104.51  3.000
 952  C4   C3   N    114.02  3.000
 952  C7   C3   N    112.51  3.000
 952  H11  C7   H12  107.52  3.000
 952  H11  C7   N1   108.64  3.000
 952  H12  C7   N1   111.84  3.000
 952  H11  C7   C3   109.05  3.000
 952  H12  C7   C3   110.76  3.000
 952  N1   C7   C3   108.97  3.000
 952  C8   N1   C6   112.01  3.000
 952  C6   N1   C7   111.31  3.000
 952  C8   N1   C7   111.36  3.000
 952  H10  C6   H9   106.67  3.000
 952  H10  C6   C5   109.60  3.000
 952  H9   C6   C5   109.79  3.000
 952  H10  C6   N1   108.83  3.000
 952  H9   C6   N1   110.98  3.000
 952  C5   C6   N1   110.87  3.000
 952  H7   C5   H8   107.09  3.000
 952  H7   C5   C4   109.91  3.000
 952  H8   C5   C4   109.83  3.000
 952  H7   C5   C6   109.10  3.000
 952  H8   C5   C6   109.53  3.000
 952  C4   C5   C6   111.29  3.000
 952  H5   C4   H6   107.40  3.000
 952  H5   C4   C5   109.74  3.000
 952  H6   C4   C5   110.68  3.000
 952  H5   C4   C3   110.51  3.000
 952  H6   C4   C3   109.89  3.000
 952  C5   C4   C3   108.63  3.000
 952  H13  C8   H14  105.81  3.000
 952  H13  C8   C9   108.30  3.000
 952  H14  C8   C9   109.21  3.000
 952  H13  C8   N1   107.90  3.000
 952  H14  C8   N1   112.30  3.000
 952  C9   C8   N1   112.99  3.000
 952  C10  C9   C14  119.33  3.000
 952  C10  C9   C8   120.28  3.000
 952  C14  C9   C8   120.35  3.000
 952  H18  C14  C13  120.05  3.000
 952  H18  C14  C9   119.94  3.000
 952  C13  C14  C9   120.01  3.000
 952  H17  C13  C12  119.06  3.000
 952  H17  C13  C14  119.90  3.000
 952  C12  C13  C14  121.04  3.000
 952  H16  C12  C11  121.46  3.000
 952  H16  C12  C13  119.80  3.000
 952  C11  C12  C13  118.73  3.000
 952  O    C11  C10  115.90  3.000
 952  C10  C11  C12  120.59  3.000
 952  O    C11  C12  123.51  3.000
 952  H15  C10  C11  119.84  3.000
 952  H15  C10  C9   119.86  3.000
 952  C11  C10  C9   120.30  3.000
 952  C15  O    C11  119.03  3.000
 952  C16  C15  C20  121.01  3.000
 952  C16  C15  O    119.53  3.000
 952  C20  C15  O    119.44  3.000
 952  H23  C20  C19  120.57  3.000
 952  H23  C20  C15  120.17  3.000
 952  C19  C20  C15  119.26  3.000
 952  H22  C19  C18  120.18  3.000
 952  H22  C19  C20  119.48  3.000
 952  C18  C19  C20  120.34  3.000
 952  H21  C18  C17  120.08  3.000
 952  H21  C18  C19  120.14  3.000
 952  C17  C18  C19  119.77  3.000
 952  H20  C17  C16  119.48  3.000
 952  H20  C17  C18  120.16  3.000
 952  C16  C17  C18  120.36  3.000
 952  H19  C16  C17  120.58  3.000
 952  H19  C16  C15  120.17  3.000
 952  C17  C16  C15  119.25  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
 952  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 952  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 952  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 952  CONST_04  C11  C10  C9   C14    0.00   0.0  0
 952  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 952  CONST_06  C10  C9   C14  C13    0.00   0.0  0
 952  CONST_07  C18  C19  C20  C15    0.00   0.0  0
 952  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 952  CONST_09  C17  C18  C19  C20    0.00   0.0  0
 952  CONST_10  C17  C16  C15  C20    0.00   0.0  0
 952  CONST_11  C16  C17  C18  C19    0.00   0.0  0
 952  CONST_12  C16  C15  C20  C19    0.00   0.0  0
 952  CONST_13  N    C21  N2   C22    0.00   0.0  0
 952  CONST_14  C21  N2   C22  C1     0.00   0.0  0
 952  CONST_15  C2   N    C21  N2     0.00   0.0  0
 952  CONST_16  C3   N    C21  N2   180.00   0.0  0
 952  CONST_17  C13  C14  C9   C8   180.00   0.0  0
 952  CONST_18  C11  C10  C9   C8   180.00   0.0  0
 952  CONST_19  O    C11  C10  C9   180.00   0.0  0
 952  CONST_20  O    C11  C12  C13  180.00   0.0  0
 952  CONST_21  C19  C20  C15  O    180.00   0.0  0
 952  CONST_22  C17  C16  C15  O    180.00   0.0  0
 952  CONST_23  C21  N2   C22  O2   180.00   0.0  0
 952  CONST_24  O1   C21  N2   C22  180.00   0.0  0
 952  CONST_25  C2   N    C21  O1   180.00   0.0  0
 952  CONST_26  C3   N    C21  O1     0.00   0.0  0
 952  CONST_27  H17  C13  C14  C9   180.00   0.0  0
 952  CONST_28  H16  C12  C13  C14  180.00   0.0  0
 952  CONST_29  H15  C10  C9   C14  180.00   0.0  0
 952  CONST_30  H18  C14  C13  C12  180.00   0.0  0
 952  CONST_31  H22  C19  C20  C15  180.00   0.0  0
 952  CONST_32  H20  C17  C16  C15  180.00   0.0  0
 952  CONST_33  H21  C18  C19  C20  180.00   0.0  0
 952  CONST_34  H19  C16  C15  C20  180.00   0.0  0
 952  CONST_35  H23  C20  C19  C18  180.00   0.0  0
 952  CONST_36  H24  N2   C22  C1   180.00   0.0  0
 952  Var_01    C6   N1   C7   C3    61.35  30.0  1
 952  Var_02    C6   C5   C4   C3   -52.53  30.0  1
 952  Var_03    C5   C6   N1   C7   -60.96  30.0  1
 952  Var_04    C4   C5   C6   N1    56.36  30.0  1
 952  Var_05    C9   C8   N1   C7   163.98  30.0  3
 952  Var_06    C14  C9   C8   N1   142.63  30.0  3
 952  Var_07    C20  C15  O    C11   91.11  30.0  2
 952  Var_08    H2   C    C1   C22   58.68  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
 952  chir_01  C3  N  C7  C4  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
 952  plan-1  O2   0.020
 952  plan-1  C22  0.020
 952  plan-1  C1   0.020
 952  plan-1  C    0.020
 952  plan-1  N2   0.020
 952  plan-1  C21  0.020
 952  plan-1  O1   0.020
 952  plan-1  N    0.020
 952  plan-1  C2   0.020
 952  plan-1  C3   0.020
 952  plan-1  H24  0.020
 952  plan-1  H4   0.020
 952  plan-2  C8   0.020
 952  plan-2  C9   0.020
 952  plan-2  C14  0.020
 952  plan-2  C13  0.020
 952  plan-2  C12  0.020
 952  plan-2  C11  0.020
 952  plan-2  C10  0.020
 952  plan-2  O    0.020
 952  plan-2  H18  0.020
 952  plan-2  H17  0.020
 952  plan-2  H16  0.020
 952  plan-2  H15  0.020
 952  plan-3  O    0.020
 952  plan-3  C15  0.020
 952  plan-3  C20  0.020
 952  plan-3  C19  0.020
 952  plan-3  C18  0.020
 952  plan-3  C17  0.020
 952  plan-3  C16  0.020
 952  plan-3  H23  0.020
 952  plan-3  H22  0.020
 952  plan-3  H21  0.020
 952  plan-3  H20  0.020
 952  plan-3  H19  0.020

