# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:15:15 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N-[(2,4-dichlorophenyl)methyl]-4-pyrimidin-2-yloxy-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CNC(=O)N2CCC(CC2)Oc3ncccn3)c(Cl)c1
#
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
 24D  24D  N-[(2,4-dichlorophenyl)methyl]-4-pyrimidin-2-yloxy-piperidine-1-carboxamide  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_24D
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
 24D  CL1   CL  CL    0  -0.115   4.8961  -3.4890   0.4259
 24D  C2    C   CR6   0  -0.064   4.2501  -1.9013   0.1923
 24D  C3    C   CR16  0  -0.186   4.8374  -1.0497  -0.7271
 24D  C4    C   CR16  0  -0.329   4.2978   0.2157  -0.9008
 24D  C5    C   CR6   0   0.196   3.1935   0.6541  -0.1791
 24D  C6    C   CH2   0  -0.355   2.6268   2.0280  -0.4170
 24D  N7    N   NH1   0  -0.671   1.3194   1.9535  -1.0177
 24D  C8    C   C     0   0.746   0.2487   2.6415  -0.5425
 24D  O9    O   O     0  -0.538   0.3544   3.4520   0.3712
 24D  N10   N   NT    0  -0.487  -0.9491   2.4061  -1.1723
 24D  C11   C   CH2   0  -0.331  -2.1298   3.0809  -0.6627
 24D  C12   C   CH2   0  -0.457  -2.8677   2.2197   0.3581
 24D  C13   C   CH1   0   0.047  -3.2283   0.8828  -0.2680
 24D  C14   C   CH2   0  -0.459  -1.9976   0.2037  -0.8524
 24D  C15   C   CH2   0  -0.350  -1.2845   1.1472  -1.8183
 24D  O16   O   O2    0  -0.467  -3.8171   0.0824   0.7648
 24D  C17   C   CR6   0   0.592  -4.5934  -0.9454   0.4488
 24D  N18   N   N     0  -0.434  -5.0425  -1.6160   1.5031
 24D  C19   C   CR16  0  -0.023  -5.8305  -2.6474   1.2462
 24D  C20   C   CR16  0  -0.374  -6.1803  -3.0198  -0.0435
 24D  C21   C   CR16  0  -0.000  -5.6504  -2.2444  -1.0570
 24D  N22   N   N     0  -0.459  -4.8552  -1.2075  -0.8201
 24D  C23   C   CR6   0  -0.106   2.6381  -0.2345   0.7389
 24D  CL24  CL  CL    0  -0.104   1.2777   0.2497   1.6942
 24D  C25   C   CR16  0  -0.153   3.1492  -1.5068   0.9365
 24D  H3    H   HCR6  0   0.286   5.6973  -1.3632  -1.3022
 24D  H4    H   HCR6  0   0.276   4.7498   0.8840  -1.6231
 24D  H6    H   HCH2  0   0.273   2.5467   2.5787   0.5190
 24D  H6A   H   HCH2  0   0.264   3.3163   2.5877  -1.0542
 24D  HN7   H   HNH1  0   0.398   1.2590   1.4545  -1.8879
 24D  H11   H   HCH2  0   0.268  -1.8529   4.0366  -0.2277
 24D  H11A  H   HCH2  0   0.245  -2.7848   3.2945  -1.5130
 24D  H12   H   HCH2  0   0.237  -2.2282   2.0679   1.2322
 24D  H12A  H   HCH2  0   0.251  -3.7694   2.7377   0.6924
 24D  H13   H   HCH1  0   0.238  -3.9641   1.0441  -1.0620
 24D  H14   H   HCH2  0   0.230  -1.3142  -0.0754  -0.0448
 24D  H14A  H   HCH2  0   0.256  -2.2768  -0.7092  -1.3814
 24D  H15   H   HCH2  0   0.253  -1.9300   1.3661  -2.6733
 24D  H15A  H   HCH2  0   0.263  -0.4083   0.6519  -2.2276
 24D  H19   H   HCR6  0   0.282  -6.1966  -3.2014   2.1034
 24D  H20   H   HCR6  0   0.281  -6.8220  -3.8646  -0.2419
 24D  H21   H   HCR6  0   0.280  -5.8660  -2.4596  -2.0972
 24D  H25   H   HCR6  0   0.301   2.6992  -2.1749   1.6576

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
 24D  CL1  C2    single    1.730  0.020  1.730
 24D  C2   C3    aromatic  1.384  0.020  1.384
 24D  C2   C25   aromatic  1.386  0.020  1.386
 24D  C3   C4    aromatic  1.387  0.020  1.387
 24D  C4   C5    aromatic  1.390  0.020  1.390
 24D  C5   C6    single    1.505  0.020  1.505
 24D  C5   C23   aromatic  1.393  0.020  1.393
 24D  C6   N7    single    1.441  0.020  1.441
 24D  N7   C8    single    1.359  0.020  1.359
 24D  C8   O9    double    1.226  0.020  1.226
 24D  C8   N10   single    1.374  0.020  1.374
 24D  N10  C11   single    1.452  0.020  1.452
 24D  N10  C15   single    1.454  0.020  1.454
 24D  C11  C12   single    1.526  0.020  1.526
 24D  C12  C13   single    1.520  0.020  1.520
 24D  C13  C14   single    1.522  0.020  1.522
 24D  C13  O16   single    1.433  0.020  1.433
 24D  C14  C15   single    1.527  0.020  1.527
 24D  O16  C17   single    1.326  0.020  1.326
 24D  C17  N18   aromatic  1.328  0.020  1.328
 24D  C17  N22   aromatic  1.322  0.020  1.322
 24D  N18  C19   aromatic  1.323  0.020  1.323
 24D  C19  C20   aromatic  1.387  0.020  1.387
 24D  C20  C21   aromatic  1.382  0.020  1.382
 24D  C21  N22   aromatic  1.328  0.020  1.328
 24D  C23  CL24  single    1.731  0.020  1.731
 24D  C23  C25   aromatic  1.385  0.020  1.385
 24D  C3   H3    single    0.930  0.020  1.080
 24D  C4   H4    single    0.930  0.020  1.080
 24D  C6   H6    single    0.970  0.020  1.090
 24D  C6   H6A   single    0.970  0.020  1.090
 24D  N7   HN7   single    0.860  0.020  1.020
 24D  C11  H11   single    0.970  0.020  1.090
 24D  C11  H11A  single    0.970  0.020  1.090
 24D  C12  H12   single    0.970  0.020  1.090
 24D  C12  H12A  single    0.970  0.020  1.090
 24D  C13  H13   single    0.970  0.020  1.090
 24D  C14  H14   single    0.970  0.020  1.090
 24D  C14  H14A  single    0.970  0.020  1.090
 24D  C15  H15   single    0.970  0.020  1.090
 24D  C15  H15A  single    0.970  0.020  1.090
 24D  C19  H19   single    0.930  0.020  1.080
 24D  C20  H20   single    0.930  0.020  1.080
 24D  C21  H21   single    0.930  0.020  1.080
 24D  C25  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
 24D  C25   C2   C3    121.24  3.000
 24D  C25   C2   CL1   119.03  3.000
 24D  C3    C2   CL1   119.73  3.000
 24D  H3    C3   C4    120.50  3.000
 24D  H3    C3   C2    120.84  3.000
 24D  C4    C3   C2    118.66  3.000
 24D  H4    C4   C5    118.90  3.000
 24D  H4    C4   C3    118.97  3.000
 24D  C5    C4   C3    122.13  3.000
 24D  C23   C5   C6    122.43  3.000
 24D  C23   C5   C4    117.24  3.000
 24D  C6    C5   C4    120.32  3.000
 24D  H6A   C6   H6    106.77  3.000
 24D  H6A   C6   N7    110.85  3.000
 24D  H6    C6   N7    108.53  3.000
 24D  H6A   C6   C5    108.79  3.000
 24D  H6    C6   C5    110.70  3.000
 24D  N7    C6   C5    111.12  3.000
 24D  HN7   N7   C8    120.46  3.000
 24D  HN7   N7   C6    116.19  3.000
 24D  C8    N7   C6    122.90  3.000
 24D  N10   C8   O9    122.02  3.000
 24D  N10   C8   N7    116.11  3.000
 24D  O9    C8   N7    121.84  3.000
 24D  C15   N10  C11   111.75  3.000
 24D  C15   N10  C8    123.58  3.000
 24D  C11   N10  C8    117.94  3.000
 24D  H11A  C11  H11   106.99  3.000
 24D  H11A  C11  C12   109.90  3.000
 24D  H11   C11  C12   110.61  3.000
 24D  H11A  C11  N10   107.74  3.000
 24D  H11   C11  N10   110.01  3.000
 24D  C12   C11  N10   111.45  3.000
 24D  H12A  C12  H12   107.69  3.000
 24D  H12A  C12  C13   110.33  3.000
 24D  H12   C12  C13   110.24  3.000
 24D  H12A  C12  C11   109.65  3.000
 24D  H12   C12  C11   109.28  3.000
 24D  C13   C12  C11   109.61  3.000
 24D  H13   C13  O16   109.20  3.000
 24D  H13   C13  C14   109.31  3.000
 24D  O16   C13  C14   111.08  3.000
 24D  H13   C13  C12   109.19  3.000
 24D  O16   C13  C12   106.98  3.000
 24D  C14   C13  C12   111.03  3.000
 24D  H14A  C14  H14   107.70  3.000
 24D  H14A  C14  C15   109.24  3.000
 24D  H14   C14  C15   109.44  3.000
 24D  H14A  C14  C13   110.64  3.000
 24D  H14   C14  C13   109.60  3.000
 24D  C15   C14  C13   110.17  3.000
 24D  H15A  C15  H15   105.83  3.000
 24D  H15A  C15  C14   109.47  3.000
 24D  H15   C15  C14   110.04  3.000
 24D  H15A  C15  N10   112.08  3.000
 24D  H15   C15  N10   108.07  3.000
 24D  C14   C15  N10   111.20  3.000
 24D  C17   O16  C13   120.11  3.000
 24D  N22   C17  N18   126.52  3.000
 24D  N22   C17  O16   119.89  3.000
 24D  N18   C17  O16   113.59  3.000
 24D  C19   N18  C17   116.16  3.000
 24D  H19   C19  C20   120.84  3.000
 24D  H19   C19  N18   116.48  3.000
 24D  C20   C19  N18   122.68  3.000
 24D  H20   C20  C21   122.18  3.000
 24D  H20   C20  C19   122.07  3.000
 24D  C21   C20  C19   115.76  3.000
 24D  H21   C21  N22   116.45  3.000
 24D  H21   C21  C20   121.07  3.000
 24D  N22   C21  C20   122.48  3.000
 24D  C21   N22  C17   116.40  3.000
 24D  C25   C23  CL24  117.90  3.000
 24D  C25   C23  C5    122.19  3.000
 24D  CL24  C23  C5    119.90  3.000
 24D  H25   C25  C23   120.61  3.000
 24D  H25   C25  C2    120.85  3.000
 24D  C23   C25  C2    118.54  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
 24D  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 24D  CONST_02  C5    C23  C25  C2     0.00   0.0  0
 24D  CONST_03  C23   C25  C2   C3     0.00   0.0  0
 24D  CONST_04  C23   C5   C4   C3     0.00   0.0  0
 24D  CONST_05  C25   C2   C3   C4     0.00   0.0  0
 24D  CONST_06  C25   C23  C5   C4     0.00   0.0  0
 24D  CONST_07  C20   C19  N18  C17    0.00   0.0  0
 24D  CONST_08  C20   C21  N22  C17    0.00   0.0  0
 24D  CONST_09  C21   N22  C17  N18    0.00   0.0  0
 24D  CONST_10  C21   C20  C19  N18    0.00   0.0  0
 24D  CONST_11  N22   C17  N18  C19    0.00   0.0  0
 24D  CONST_12  N22   C21  C20  C19    0.00   0.0  0
 24D  CONST_13  C4    C3   C2   CL1  180.00   0.0  0
 24D  CONST_14  C23   C25  C2   CL1  180.00   0.0  0
 24D  CONST_15  CL24  C23  C25  C2   180.00   0.0  0
 24D  CONST_16  C6    C5   C4   C3   180.00   0.0  0
 24D  CONST_17  CL24  C23  C5   C4   180.00   0.0  0
 24D  CONST_18  C25   C23  C5   C6   180.00   0.0  0
 24D  CONST_19  C19   N18  C17  O16  180.00   0.0  0
 24D  CONST_20  C21   N22  C17  O16  180.00   0.0  0
 24D  CONST_21  H4    C4   C3   C2   180.00   0.0  0
 24D  CONST_22  H25   C25  C2   C3   180.00   0.0  0
 24D  CONST_23  H3    C3   C4   C5   180.00   0.0  0
 24D  CONST_24  H19   C19  N18  C17  180.00   0.0  0
 24D  CONST_25  H21   C21  N22  C17  180.00   0.0  0
 24D  CONST_26  H20   C20  C19  N18  180.00   0.0  0
 24D  CONST_27  C11   N10  C8   O9     0.00   0.0  0
 24D  CONST_29  C11   N10  C8   N7   180.00   0.0  0
 24D  CONST_31  N10   C8   N7   C6   180.00   0.0  0
 24D  CONST_32  HN7   N7   C8   N10    0.00   0.0  0
 24D  CONST_33  O9    C8   N7   C6     0.00   0.0  0
 24D  Var_01    C13   C12  C11  N10  -56.56  30.0  1
 24D  Var_02    C13   C14  C15  N10   55.56  30.0  1
 24D  Var_03    C14   C15  N10  C11  -58.80  30.0  1
 24D  Var_04    C15   N10  C11  C12   59.52  30.0  1
 24D  Var_05    N18   C17  O16  C13  178.42  30.0  2
 24D  Var_06    N7    C6   C5   C4   112.35  30.0  2
 24D  Var_07    C8    N7   C6   C5   130.44  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
 24D  chir_01  C13  C12  C14  O16  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
 24D  plan-1  CL1   0.020
 24D  plan-1  C2    0.020
 24D  plan-1  C3    0.020
 24D  plan-1  C4    0.020
 24D  plan-1  C5    0.020
 24D  plan-1  C6    0.020
 24D  plan-1  C23   0.020
 24D  plan-1  CL24  0.020
 24D  plan-1  C25   0.020
 24D  plan-1  H3    0.020
 24D  plan-1  H4    0.020
 24D  plan-1  H25   0.020
 24D  plan-2  O16   0.020
 24D  plan-2  C17   0.020
 24D  plan-2  N18   0.020
 24D  plan-2  C19   0.020
 24D  plan-2  C20   0.020
 24D  plan-2  C21   0.020
 24D  plan-2  N22   0.020
 24D  plan-2  H19   0.020
 24D  plan-2  H20   0.020
 24D  plan-2  H21   0.020
 24D  plan-3  C6    0.020
 24D  plan-3  N7    0.020
 24D  plan-3  C8    0.020
 24D  plan-3  O9    0.020
 24D  plan-3  N10   0.020
 24D  plan-3  C11   0.020
 24D  plan-3  C15   0.020
 24D  plan-3  HN7   0.020

