# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 05:10:52 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(C2CCN(CC2)Cc3cccc(Oc4ccccc4)n3)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
 95W  95W  5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione  ligand  53  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_95W
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
 95W  O2   O  O     0  -0.461  -6.2032  -2.8098  -0.5250
 95W  C21  C  CR6   0   0.553  -5.3338  -2.0035  -0.2423
 95W  C1   C  CR6   0  -0.181  -5.5571  -0.6044   0.0493
 95W  C    C  CH3   0  -0.707  -6.9522  -0.0720   0.0272
 95W  N3   N  NR16  0  -0.732  -4.0082  -2.3880  -0.1816
 95W  C20  C  CR6   0   0.734  -2.9085  -1.6136   0.0972
 95W  O1   O  O     0  -0.478  -1.7905  -2.0885   0.1220
 95W  N    N  NR6   0  -0.548  -3.1890  -0.2909   0.3418
 95W  C2   C  CR16  0   0.054  -4.4823   0.1590   0.3197
 95W  C3   C  CH1   0  -0.088  -2.1126   0.6625   0.6599
 95W  C19  C  CH2   0  -0.430  -1.4481   0.4026   2.0057
 95W  C18  C  CH2   0  -0.288  -0.4492   1.5175   2.2911
 95W  N1   N  NT    0  -0.402   0.5342   1.6177   1.2296
 95W  C5   C  CH2   0  -0.287  -0.1002   1.9194  -0.0400
 95W  C4   C  CH2   0  -0.436  -1.0604   0.8054  -0.4315
 95W  C6   C  CH2   0  -0.312   1.5909   2.5465   1.5701
 95W  C7   C  CR6   0   0.219   2.6934   2.5316   0.5455
 95W  N2   N  N     0  -0.428   3.1999   1.3360   0.2387
 95W  C11  C  CR6   0   0.486   4.1135   1.2589  -0.6938
 95W  C10  C  CR16  0  -0.392   4.6434   2.3609  -1.3665
 95W  C9   C  CR16  0  -0.144   4.1436   3.5987  -1.0205
 95W  C8   C  CR16  0  -0.360   3.1404   3.6938  -0.0584
 95W  O    O  O2    0  -0.519   4.5977   0.0413  -1.0350
 95W  C12  C  CR6   0   0.357   3.9271  -1.0855  -0.6185
 95W  C17  C  CR16  0  -0.286   2.6282  -1.3397  -1.0403
 95W  C16  C  CR16  0  -0.252   2.0067  -2.5151  -0.6492
 95W  C15  C  CR16  0  -0.264   2.6769  -3.4345   0.1506
 95W  C14  C  CR16  0  -0.255   3.9767  -3.1711   0.5579
 95W  C13  C  CR16  0  -0.326   4.6053  -1.9899   0.1809
 95W  H1   H  HCH3  0   0.245  -7.4170  -0.2181  -0.9488
 95W  H2   H  HCH3  0   0.246  -7.5829  -0.5737   0.7627
 95W  H3   H  HCH3  0   0.246  -6.9662   0.9941   0.2477
 95W  H    H  HNR6  0   0.422  -3.8076  -3.3624  -0.3709
 95W  H4   H  HCR6  0   0.311  -4.5983   1.2123   0.5374
 95W  H5   H  HCH1  0   0.253  -2.6223   1.6273   0.7304
 95W  H22  H  HCH2  0   0.244  -2.1957   0.3698   2.8012
 95W  H23  H  HCH2  0   0.243  -0.9261  -0.5545   1.9930
 95W  H21  H  HCH2  0   0.192  -0.9934   2.4692   2.4305
 95W  H20  H  HCH2  0   0.243   0.0641   1.3085   3.2323
 95W  H9   H  HCH2  0   0.192  -0.6363   2.8856  -0.0060
 95W  H8   H  HCH2  0   0.249   0.6603   2.0096  -0.8170
 95W  H7   H  HCH2  0   0.255  -0.4923  -0.1168  -0.5432
 95W  H6   H  HCH2  0   0.242  -1.5288   1.0410  -1.3895
 95W  H11  H  HCH2  0   0.211   1.2298   3.5802   1.6988
 95W  H10  H  HCH2  0   0.254   2.0061   2.2402   2.5361
 95W  H14  H  HCR6  0   0.277   5.4038   2.2425  -2.1260
 95W  H13  H  HCR6  0   0.276   4.5137   4.4883  -1.5129
 95W  H12  H  HCR6  0   0.265   2.7094   4.6502   0.2040
 95W  H19  H  HCR6  0   0.263   2.1023  -0.6263  -1.6614
 95W  H18  H  HCR6  0   0.259   0.9921  -2.7124  -0.9695
 95W  H17  H  HCR6  0   0.257   2.1888  -4.3525   0.4500
 95W  H16  H  HCR6  0   0.261   4.5073  -3.8814   1.1782
 95W  H15  H  HCR6  0   0.267   5.6172  -1.7762   0.5010

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
 95W  C9   C10  aromatic  1.379  0.020  1.379
 95W  C9   C8   aromatic  1.393  0.020  1.393
 95W  C10  C11  aromatic  1.396  0.020  1.396
 95W  C8   C7   aromatic  1.384  0.020  1.384
 95W  C11  O    single    1.354  0.020  1.354
 95W  C11  N2   aromatic  1.308  0.020  1.308
 95W  C7   N2   aromatic  1.334  0.020  1.334
 95W  C7   C6   single    1.505  0.020  1.505
 95W  O    C12  single    1.376  0.020  1.376
 95W  C6   N1   single    1.447  0.020  1.447
 95W  C13  C12  aromatic  1.385  0.020  1.385
 95W  C13  C14  aromatic  1.390  0.020  1.390
 95W  C12  C17  aromatic  1.389  0.020  1.389
 95W  N1   C18  single    1.450  0.020  1.450
 95W  N1   C5   single    1.451  0.020  1.451
 95W  C18  C19  single    1.524  0.020  1.524
 95W  C14  C15  aromatic  1.387  0.020  1.387
 95W  C17  C16  aromatic  1.386  0.020  1.386
 95W  C5   C4   single    1.522  0.020  1.522
 95W  C19  C3   single    1.523  0.020  1.523
 95W  C15  C16  aromatic  1.391  0.020  1.391
 95W  C4   C3   single    1.523  0.020  1.523
 95W  C3   N    single    1.473  0.020  1.473
 95W  N    C2   single    1.369  0.020  1.369
 95W  N    C20  single    1.374  0.020  1.374
 95W  O1   C20  double    1.215  0.020  1.215
 95W  C2   C1   double    1.346  0.020  1.346
 95W  C20  N3   single    1.374  0.020  1.374
 95W  C1   C    single    1.493  0.020  1.493
 95W  C1   C21  single    1.447  0.020  1.447
 95W  N3   C21  single    1.382  0.020  1.382
 95W  C21  O2   double    1.219  0.020  1.219
 95W  C    H1   single    0.970  0.020  1.090
 95W  C    H2   single    0.970  0.020  1.090
 95W  C    H3   single    0.970  0.020  1.090
 95W  N3   H    single    0.860  0.020  1.020
 95W  C2   H4   single    0.930  0.020  1.080
 95W  C3   H5   single    0.970  0.020  1.090
 95W  C19  H22  single    0.970  0.020  1.090
 95W  C19  H23  single    0.970  0.020  1.090
 95W  C18  H21  single    0.970  0.020  1.090
 95W  C18  H20  single    0.970  0.020  1.090
 95W  C5   H9   single    0.970  0.020  1.090
 95W  C5   H8   single    0.970  0.020  1.090
 95W  C4   H7   single    0.970  0.020  1.090
 95W  C4   H6   single    0.970  0.020  1.090
 95W  C6   H11  single    0.970  0.020  1.090
 95W  C6   H10  single    0.970  0.020  1.090
 95W  C10  H14  single    0.930  0.020  1.080
 95W  C9   H13  single    0.930  0.020  1.080
 95W  C8   H12  single    0.930  0.020  1.080
 95W  C17  H19  single    0.930  0.020  1.080
 95W  C16  H18  single    0.930  0.020  1.080
 95W  C15  H17  single    0.930  0.020  1.080
 95W  C14  H16  single    0.930  0.020  1.080
 95W  C13  H15  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
 95W  N3   C21  C1   114.11  3.000
 95W  N3   C21  O2   120.70  3.000
 95W  C1   C21  O2   125.20  3.000
 95W  C2   C1   C    123.15  3.000
 95W  C    C1   C21  119.08  3.000
 95W  C2   C1   C21  117.77  3.000
 95W  H3   C    H2   107.84  3.000
 95W  H3   C    H1   107.87  3.000
 95W  H2   C    H1   107.17  3.000
 95W  H3   C    C1   110.98  3.000
 95W  H2   C    C1   111.48  3.000
 95W  H1   C    C1   111.32  3.000
 95W  H    N3   C20  114.94  3.000
 95W  H    N3   C21  116.72  3.000
 95W  C20  N3   C21  128.33  3.000
 95W  N    C20  O1   124.09  3.000
 95W  O1   C20  N3   121.37  3.000
 95W  N    C20  N3   114.54  3.000
 95W  C3   N    C2   118.75  3.000
 95W  C2   N    C20  120.41  3.000
 95W  C3   N    C20  120.82  3.000
 95W  H4   C2   N    114.70  3.000
 95W  H4   C2   C1   120.47  3.000
 95W  N    C2   C1   124.83  3.000
 95W  H5   C3   C4   106.59  3.000
 95W  H5   C3   C19  107.27  3.000
 95W  C4   C3   C19  110.35  3.000
 95W  H5   C3   N    104.15  3.000
 95W  C4   C3   N    114.27  3.000
 95W  C19  C3   N    113.54  3.000
 95W  H23  C19  H22  108.05  3.000
 95W  H23  C19  C18  109.31  3.000
 95W  H22  C19  C18  109.53  3.000
 95W  H23  C19  C3   110.39  3.000
 95W  H22  C19  C3   110.49  3.000
 95W  C18  C19  C3   109.07  3.000
 95W  H20  C18  H21  106.71  3.000
 95W  H20  C18  N1   108.98  3.000
 95W  H21  C18  N1   111.51  3.000
 95W  H20  C18  C19  109.23  3.000
 95W  H21  C18  C19  109.32  3.000
 95W  N1   C18  C19  110.97  3.000
 95W  C6   N1   C5   113.05  3.000
 95W  C5   N1   C18  110.99  3.000
 95W  C6   N1   C18  111.54  3.000
 95W  H8   C5   H9   106.72  3.000
 95W  H8   C5   C4   108.49  3.000
 95W  H9   C5   C4   109.98  3.000
 95W  H8   C5   N1   109.60  3.000
 95W  H9   C5   N1   111.52  3.000
 95W  C4   C5   N1   110.41  3.000
 95W  H6   C4   H7   108.45  3.000
 95W  H6   C4   C5   109.77  3.000
 95W  H7   C4   C5   108.49  3.000
 95W  H6   C4   C3   110.65  3.000
 95W  H7   C4   C3   110.77  3.000
 95W  C5   C4   C3   108.68  3.000
 95W  H10  C6   H11  106.46  3.000
 95W  H10  C6   C7   108.66  3.000
 95W  H11  C6   C7   109.19  3.000
 95W  H10  C6   N1   107.75  3.000
 95W  H11  C6   N1   112.95  3.000
 95W  C7   C6   N1   111.61  3.000
 95W  C8   C7   N2   121.97  3.000
 95W  N2   C7   C6   116.33  3.000
 95W  C8   C7   C6   121.69  3.000
 95W  C11  N2   C7   118.82  3.000
 95W  O    C11  C10  116.92  3.000
 95W  O    C11  N2   118.85  3.000
 95W  C10  C11  N2   124.23  3.000
 95W  H14  C10  C9   121.97  3.000
 95W  H14  C10  C11  121.27  3.000
 95W  C9   C10  C11  116.75  3.000
 95W  H13  C9   C8   120.30  3.000
 95W  H13  C9   C10  119.99  3.000
 95W  C8   C9   C10  119.70  3.000
 95W  H12  C8   C9   120.99  3.000
 95W  H12  C8   C7   120.53  3.000
 95W  C9   C8   C7   118.47  3.000
 95W  C12  O    C11  119.07  3.000
 95W  C13  C12  C17  120.92  3.000
 95W  C17  C12  O    120.91  3.000
 95W  C13  C12  O    118.10  3.000
 95W  H19  C17  C16  120.20  3.000
 95W  H19  C17  C12  120.54  3.000
 95W  C16  C17  C12  119.26  3.000
 95W  H18  C16  C15  120.11  3.000
 95W  H18  C16  C17  119.45  3.000
 95W  C15  C16  C17  120.45  3.000
 95W  H17  C15  C14  120.16  3.000
 95W  H17  C15  C16  120.17  3.000
 95W  C14  C15  C16  119.66  3.000
 95W  H16  C14  C13  119.44  3.000
 95W  H16  C14  C15  120.21  3.000
 95W  C13  C14  C15  120.35  3.000
 95W  H15  C13  C14  120.68  3.000
 95W  H15  C13  C12  119.97  3.000
 95W  C14  C13  C12  119.35  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
 95W  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 95W  CONST_02  C10  C11  N2   C7      0.00   0.0  0
 95W  CONST_03  C9   C10  C11  N2      0.00   0.0  0
 95W  CONST_04  C9   C8   C7   N2      0.00   0.0  0
 95W  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 95W  CONST_06  C8   C7   N2   C11     0.00   0.0  0
 95W  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 95W  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 95W  CONST_09  C14  C13  C12  C17     0.00   0.0  0
 95W  CONST_10  C14  C15  C16  C17     0.00   0.0  0
 95W  CONST_11  C13  C12  C17  C16     0.00   0.0  0
 95W  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 95W  CONST_13  N    C20  N3   C21     0.00   0.0  0
 95W  CONST_14  C20  N3   C21  C1      0.00   0.0  0
 95W  CONST_15  C3   N    C20  N3    180.00   0.0  0
 95W  CONST_16  C2   N    C20  N3      0.00   0.0  0
 95W  CONST_17  C9   C8   C7   C6    180.00   0.0  0
 95W  CONST_18  C11  N2   C7   C6    180.00   0.0  0
 95W  CONST_19  O    C11  N2   C7    180.00   0.0  0
 95W  CONST_20  O    C11  C10  C9    180.00   0.0  0
 95W  CONST_21  C14  C13  C12  O     180.00   0.0  0
 95W  CONST_22  C16  C17  C12  O     180.00   0.0  0
 95W  CONST_23  C20  N3   C21  O2    180.00   0.0  0
 95W  CONST_24  O1   C20  N3   C21   180.00   0.0  0
 95W  CONST_25  C3   N    C20  O1      0.00   0.0  0
 95W  CONST_26  C2   N    C20  O1    180.00   0.0  0
 95W  CONST_27  H13  C9   C8   C7    180.00   0.0  0
 95W  CONST_28  H14  C10  C11  N2    180.00   0.0  0
 95W  CONST_29  H12  C8   C7   N2    180.00   0.0  0
 95W  CONST_30  H16  C14  C13  C12   180.00   0.0  0
 95W  CONST_31  H18  C16  C17  C12   180.00   0.0  0
 95W  CONST_32  H15  C13  C12  C17   180.00   0.0  0
 95W  CONST_33  H17  C15  C16  C17   180.00   0.0  0
 95W  CONST_34  H19  C17  C16  C15   180.00   0.0  0
 95W  CONST_35  H    N3   C21  C1    180.00   0.0  0
 95W  Var_01    N1   C18  C19  C3    -57.10  30.0  1
 95W  Var_02    N1   C5   C4   C3     59.08  30.0  1
 95W  Var_03    C5   N1   C18  C19    60.71  30.0  1
 95W  Var_04    C4   C5   N1   C18   -61.69  30.0  1
 95W  Var_05    C7   C6   N1   C18   173.30  30.0  1
 95W  Var_06    C8   C7   C6   N1    127.22  30.0  1
 95W  Var_07    C13  C12  O    C11  -120.23  30.0  2
 95W  Var_08    H1   C    C1   C21   -58.88  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
 95W  chir_01  C3  C19  C4  N  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
 95W  plan-1  O2   0.020
 95W  plan-1  C21  0.020
 95W  plan-1  C1   0.020
 95W  plan-1  C    0.020
 95W  plan-1  N3   0.020
 95W  plan-1  C20  0.020
 95W  plan-1  O1   0.020
 95W  plan-1  N    0.020
 95W  plan-1  C2   0.020
 95W  plan-1  C3   0.020
 95W  plan-1  H    0.020
 95W  plan-1  H4   0.020
 95W  plan-2  C6   0.020
 95W  plan-2  C7   0.020
 95W  plan-2  N2   0.020
 95W  plan-2  C11  0.020
 95W  plan-2  C10  0.020
 95W  plan-2  C9   0.020
 95W  plan-2  C8   0.020
 95W  plan-2  O    0.020
 95W  plan-2  H14  0.020
 95W  plan-2  H13  0.020
 95W  plan-2  H12  0.020
 95W  plan-3  O    0.020
 95W  plan-3  C12  0.020
 95W  plan-3  C17  0.020
 95W  plan-3  C16  0.020
 95W  plan-3  C15  0.020
 95W  plan-3  C14  0.020
 95W  plan-3  C13  0.020
 95W  plan-3  H19  0.020
 95W  plan-3  H18  0.020
 95W  plan-3  H17  0.020
 95W  plan-3  H16  0.020
 95W  plan-3  H15  0.020

