# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:38:40 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-[1-(2-methylpropanoyl)piperidin-4-yl]-3-[4-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=O)N1CCC(CC1)NC(=O)Nc2ccc(cc2)C(F)(F)F
#
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
 2RU  2RU  1-[1-(2-methylpropanoyl)piperidin-4-yl]-3-[4-(trifluoromethyl)phenyl]urea  ligand  47  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 PERFECT
;

data_comp_2RU
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
 2RU  F23  F  F     0  -0.318  -7.4998   0.7544   0.1270
 2RU  C20  C  CT    0   1.050  -6.8077  -0.1992  -0.5215
 2RU  F21  F  F     0  -0.310  -7.1391  -1.3624   0.0543
 2RU  F22  F  F     0  -0.310  -7.2888  -0.2291  -1.7713
 2RU  C19  C  CR6   0  -0.224  -5.3390   0.0536  -0.4856
 2RU  C18  C  CR16  0  -0.263  -4.7300   0.8228  -1.4721
 2RU  C17  C  CR16  0  -0.346  -3.3787   1.0921  -1.4077
 2RU  C24  C  CR16  0  -0.264  -4.5650  -0.4262   0.5627
 2RU  C25  C  CR16  0  -0.309  -3.2075  -0.1611   0.6366
 2RU  C1   C  CR6   0   0.391  -2.5910   0.6072  -0.3558
 2RU  N2   N  NH1   0  -0.794  -1.2464   0.9374  -0.3874
 2RU  C3   C  C     0   0.751  -0.2376   0.5324   0.4597
 2RU  O16  O  O     0  -0.514  -0.4209  -0.1899   1.4273
 2RU  N4   N  NH1   0  -0.689   0.9738   1.0365   0.1245
 2RU  C5   C  CH1   0  -0.069   2.1975   0.6102   0.7701
 2RU  C15  C  CH2   0  -0.441   3.2303   1.7314   0.7181
 2RU  C14  C  CH2   0  -0.326   4.5534   1.2745   1.3215
 2RU  N8   N  NT    0  -0.449   5.0335   0.0732   0.6597
 2RU  C7   C  CH2   0  -0.339   4.1004  -1.0336   0.7773
 2RU  C6   C  CH2   0  -0.421   2.7604  -0.6682   0.1484
 2RU  C9   C  C     0   0.578   6.1062   0.1251  -0.1650
 2RU  O13  O  O     0  -0.505   6.7599   1.1525  -0.3030
 2RU  C10  C  CH1   0  -0.401   6.5264  -1.1541  -0.8781
 2RU  C12  C  CH3   0  -0.638   7.3830  -0.8441  -2.0986
 2RU  C11  C  CH3   0  -0.653   7.2881  -2.0565   0.0983
 2RU  H1   H  HCR6  0   0.273  -5.2959   1.2194  -2.3044
 2RU  H2   H  HCR6  0   0.278  -2.9217   1.6856  -2.1905
 2RU  H3   H  HCR6  0   0.271  -5.0086  -1.0222   1.3496
 2RU  H4   H  HCR6  0   0.288  -2.6437  -0.5550   1.4647
 2RU  H5   H  HNH1  0   0.413  -0.9813   1.5274  -1.1617
 2RU  H6   H  HNH1  0   0.395   1.0779   1.5100  -0.7603
 2RU  H7   H  HCH1  0   0.249   1.9654   0.4115   1.8194
 2RU  H8   H  HCH2  0   0.233   3.3982   2.0404  -0.3190
 2RU  H9   H  HCH2  0   0.252   2.8640   2.6044   1.2626
 2RU  H10  H  HCH2  0   0.269   5.3012   2.0577   1.2454
 2RU  H11  H  HCH2  0   0.244   4.4200   1.0535   2.3854
 2RU  H12  H  HCH2  0   0.273   4.4978  -1.9370   0.3255
 2RU  H13  H  HCH2  0   0.250   3.9634  -1.2555   1.8404
 2RU  H14  H  HCH2  0   0.249   2.0566  -1.4923   0.2836
 2RU  H15  H  HCH2  0   0.229   2.8945  -0.5234  -0.9284
 2RU  H16  H  HCH1  0   0.255   5.6409  -1.6897  -1.2288
 2RU  H17  H  HCH3  0   0.223   8.3092  -0.3407  -1.8233
 2RU  H18  H  HCH3  0   0.227   7.6469  -1.7748  -2.6027
 2RU  H19  H  HCH3  0   0.231   6.8567  -0.2157  -2.8172
 2RU  H20  H  HCH3  0   0.239   6.6961  -2.3319   0.9717
 2RU  H21  H  HCH3  0   0.240   7.5881  -2.9777  -0.4017
 2RU  H22  H  HCH3  0   0.231   8.1926  -1.5584   0.4508

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
 2RU  F21  C20  single    1.340  0.020  1.340
 2RU  F22  C20  single    1.340  0.020  1.340
 2RU  C20  F23  single    1.345  0.020  1.345
 2RU  C20  C19  single    1.491  0.020  1.491
 2RU  C18  C19  aromatic  1.391  0.020  1.391
 2RU  C18  C17  aromatic  1.379  0.020  1.379
 2RU  C19  C24  aromatic  1.389  0.020  1.389
 2RU  C17  C1   aromatic  1.401  0.020  1.401
 2RU  C24  C25  aromatic  1.385  0.020  1.385
 2RU  C25  C1   aromatic  1.398  0.020  1.398
 2RU  C1   N2   single    1.385  0.020  1.385
 2RU  N2   C3   single    1.378  0.020  1.378
 2RU  C3   O16  double    1.221  0.020  1.221
 2RU  C3   N4   single    1.354  0.020  1.354
 2RU  N4   C5   single    1.448  0.020  1.448
 2RU  C5   C15  single    1.525  0.020  1.525
 2RU  C5   C6   single    1.529  0.020  1.529
 2RU  C15  C14  single    1.524  0.020  1.524
 2RU  C6   C7   single    1.525  0.020  1.525
 2RU  C12  C10  single    1.523  0.020  1.523
 2RU  C14  N8   single    1.453  0.020  1.453
 2RU  C7   N8   single    1.452  0.020  1.452
 2RU  N8   C9   single    1.354  0.020  1.354
 2RU  C10  C9   single    1.524  0.020  1.524
 2RU  C10  C11  single    1.532  0.020  1.532
 2RU  C9   O13  double    1.226  0.020  1.226
 2RU  C18  H1   single    0.930  0.020  1.080
 2RU  C17  H2   single    0.930  0.020  1.080
 2RU  C24  H3   single    0.930  0.020  1.080
 2RU  C25  H4   single    0.930  0.020  1.080
 2RU  N2   H5   single    0.860  0.020  1.020
 2RU  N4   H6   single    0.860  0.020  1.020
 2RU  C5   H7   single    0.970  0.020  1.090
 2RU  C15  H8   single    0.970  0.020  1.090
 2RU  C15  H9   single    0.970  0.020  1.090
 2RU  C14  H10  single    0.970  0.020  1.090
 2RU  C14  H11  single    0.970  0.020  1.090
 2RU  C7   H12  single    0.970  0.020  1.090
 2RU  C7   H13  single    0.970  0.020  1.090
 2RU  C6   H14  single    0.970  0.020  1.090
 2RU  C6   H15  single    0.970  0.020  1.090
 2RU  C10  H16  single    0.970  0.020  1.090
 2RU  C12  H17  single    0.970  0.020  1.090
 2RU  C12  H18  single    0.970  0.020  1.090
 2RU  C12  H19  single    0.970  0.020  1.090
 2RU  C11  H20  single    0.970  0.020  1.090
 2RU  C11  H21  single    0.970  0.020  1.090
 2RU  C11  H22  single    0.970  0.020  1.090

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
 2RU  C19  C20  F22  112.34  3.000
 2RU  C19  C20  F21  112.37  3.000
 2RU  F22  C20  F21  107.02  3.000
 2RU  C19  C20  F23  112.03  3.000
 2RU  F22  C20  F23  106.31  3.000
 2RU  F21  C20  F23  106.33  3.000
 2RU  C24  C19  C18  118.84  3.000
 2RU  C24  C19  C20  120.58  3.000
 2RU  C18  C19  C20  120.52  3.000
 2RU  H1   C18  C17  118.48  3.000
 2RU  H1   C18  C19  121.28  3.000
 2RU  C17  C18  C19  120.24  3.000
 2RU  H2   C17  C1   119.67  3.000
 2RU  H2   C17  C18  119.11  3.000
 2RU  C1   C17  C18  121.22  3.000
 2RU  H3   C24  C25  117.93  3.000
 2RU  H3   C24  C19  120.71  3.000
 2RU  C25  C24  C19  121.36  3.000
 2RU  H4   C25  C1   121.08  3.000
 2RU  H4   C25  C24  118.97  3.000
 2RU  C1   C25  C24  119.96  3.000
 2RU  N2   C1   C25  125.12  3.000
 2RU  N2   C1   C17  116.51  3.000
 2RU  C25  C1   C17  118.38  3.000
 2RU  H5   N2   C3   116.82  3.000
 2RU  H5   N2   C1   114.33  3.000
 2RU  C3   N2   C1   128.80  3.000
 2RU  N4   C3   O16  123.41  3.000
 2RU  N4   C3   N2   113.15  3.000
 2RU  O16  C3   N2   123.43  3.000
 2RU  H6   N4   C5   116.24  3.000
 2RU  H6   N4   C3   118.95  3.000
 2RU  C5   N4   C3   122.41  3.000
 2RU  H7   C5   C6   108.46  3.000
 2RU  H7   C5   C15  108.07  3.000
 2RU  C6   C5   C15  110.58  3.000
 2RU  H7   C5   N4   107.59  3.000
 2RU  C6   C5   N4   112.09  3.000
 2RU  C15  C5   N4   109.92  3.000
 2RU  H9   C15  H8   107.34  3.000
 2RU  H9   C15  C14  109.48  3.000
 2RU  H8   C15  C14  109.05  3.000
 2RU  H9   C15  C5   110.09  3.000
 2RU  H8   C15  C5   110.09  3.000
 2RU  C14  C15  C5   110.73  3.000
 2RU  H11  C14  H10  107.32  3.000
 2RU  H11  C14  N8   108.42  3.000
 2RU  H10  C14  N8   109.69  3.000
 2RU  H11  C14  C15  109.84  3.000
 2RU  H10  C14  C15  110.72  3.000
 2RU  N8   C14  C15  110.75  3.000
 2RU  C9   N8   C7   125.98  3.000
 2RU  C9   N8   C14  120.49  3.000
 2RU  C7   N8   C14  112.39  3.000
 2RU  H13  C7   H12  106.34  3.000
 2RU  H13  C7   C6   109.83  3.000
 2RU  H12  C7   C6   110.46  3.000
 2RU  H13  C7   N8   108.27  3.000
 2RU  H12  C7   N8   111.43  3.000
 2RU  C6   C7   N8   110.40  3.000
 2RU  H15  C6   H14  107.49  3.000
 2RU  H15  C6   C7   109.25  3.000
 2RU  H14  C6   C7   109.54  3.000
 2RU  H15  C6   C5   109.54  3.000
 2RU  H14  C6   C5   110.08  3.000
 2RU  C7   C6   C5   110.87  3.000
 2RU  C10  C9   O13  120.27  3.000
 2RU  O13  C9   N8   121.55  3.000
 2RU  C10  C9   N8   118.12  3.000
 2RU  H16  C10  C11  108.58  3.000
 2RU  H16  C10  C12  107.35  3.000
 2RU  C11  C10  C12  110.54  3.000
 2RU  H16  C10  C9   109.77  3.000
 2RU  C11  C10  C9   109.47  3.000
 2RU  C12  C10  C9   111.06  3.000
 2RU  H19  C12  H18  107.70  3.000
 2RU  H19  C12  H17  108.10  3.000
 2RU  H18  C12  H17  107.77  3.000
 2RU  H19  C12  C10  111.97  3.000
 2RU  H18  C12  C10  109.44  3.000
 2RU  H17  C12  C10  111.69  3.000
 2RU  H22  C11  H21  107.81  3.000
 2RU  H22  C11  H20  107.85  3.000
 2RU  H21  C11  H20  107.65  3.000
 2RU  H22  C11  C10  110.44  3.000
 2RU  H21  C11  C10  110.01  3.000
 2RU  H20  C11  C10  112.90  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
 2RU  CONST_01  C1   C17  C18  C19    0.00   0.0  0
 2RU  CONST_02  C1   C25  C24  C19    0.00   0.0  0
 2RU  CONST_03  C25  C24  C19  C18    0.00   0.0  0
 2RU  CONST_04  C25  C1   C17  C18    0.00   0.0  0
 2RU  CONST_05  C24  C19  C18  C17    0.00   0.0  0
 2RU  CONST_06  C24  C25  C1   C17    0.00   0.0  0
 2RU  CONST_07  C17  C18  C19  C20  180.00   0.0  0
 2RU  CONST_08  C25  C24  C19  C20  180.00   0.0  0
 2RU  CONST_09  N2   C1   C17  C18  180.00   0.0  0
 2RU  CONST_10  N2   C1   C25  C24  180.00   0.0  0
 2RU  CONST_11  H2   C17  C18  C19  180.00   0.0  0
 2RU  CONST_12  H4   C25  C24  C19  180.00   0.0  0
 2RU  CONST_13  H3   C24  C19  C18  180.00   0.0  0
 2RU  CONST_14  H1   C18  C19  C24  180.00   0.0  0
 2RU  CONST_15  C10  C9   N8   C14  180.00   0.0  0
 2RU  CONST_16  O13  C9   N8   C14    0.00   0.0  0
 2RU  CONST_17  C10  C9   N8   C7     0.00   0.0  0
 2RU  CONST_18  O13  C9   N8   C7   180.00   0.0  0
 2RU  CONST_19  C3   N2   C1   C17  180.00   0.0  0
 2RU  CONST_20  C3   N2   C1   C25    0.00   0.0  0
 2RU  CONST_21  H5   N2   C1   C17    0.00   0.0  0
 2RU  CONST_22  O16  C3   N2   C1     0.00   0.0  0
 2RU  CONST_23  C5   N4   C3   O16    0.00   0.0  0
 2RU  CONST_24  N4   C3   N2   C1   180.00   0.0  0
 2RU  CONST_25  C5   N4   C3   N2   180.00   0.0  0
 2RU  CONST_26  H6   N4   C3   O16  180.00   0.0  0
 2RU  Var_01    N8   C14  C15  C5    55.62  30.0  1
 2RU  Var_02    N8   C7   C6   C5   -55.83  30.0  1
 2RU  Var_03    C7   N8   C14  C15  -60.02  30.0  1
 2RU  Var_04    C6   C7   N8   C14   59.99  30.0  1
 2RU  Var_05    C18  C19  C20  F23  -88.89  30.0  2
 2RU  Var_06    C12  C10  C9   N8   159.74  30.0  2
 2RU  Var_07    H17  C12  C10  C9    62.19  30.0  3
 2RU  Var_08    H20  C11  C10  C9    59.39  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
 2RU  chir_01  C5  N4  C15  C6  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
 2RU  plan-1  C20  0.020
 2RU  plan-1  C19  0.020
 2RU  plan-1  C18  0.020
 2RU  plan-1  C17  0.020
 2RU  plan-1  C24  0.020
 2RU  plan-1  C25  0.020
 2RU  plan-1  C1   0.020
 2RU  plan-1  N2   0.020
 2RU  plan-1  H1   0.020
 2RU  plan-1  H2   0.020
 2RU  plan-1  H3   0.020
 2RU  plan-1  H4   0.020
 2RU  plan-2  C1   0.020
 2RU  plan-2  N2   0.020
 2RU  plan-2  C3   0.020
 2RU  plan-2  O16  0.020
 2RU  plan-2  N4   0.020
 2RU  plan-2  C5   0.020
 2RU  plan-2  H5   0.020
 2RU  plan-2  H6   0.020
 2RU  plan-3  C14  0.020
 2RU  plan-3  N8   0.020
 2RU  plan-3  C7   0.020
 2RU  plan-3  C9   0.020
 2RU  plan-3  O13  0.020
 2RU  plan-3  C10  0.020

