# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:09:43 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-(1-benzylpiperidin-4-yl)-N'-methylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)NC1CCN(CC1)Cc2ccccc2
#
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
 8U7  8U7  N-(1-benzylpiperidin-4-yl)-N'-methylurea  ligand  39  18  .  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_8U7
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
 8U7  N1   N  NH1   0  -0.674  -5.2532   0.7148  -0.8432
 8U7  N3   N  NT    0  -0.414   0.9465  -0.7710   0.1955
 8U7  C4   C  CH2   0  -0.442  -0.6803   1.0676   0.1813
 8U7  C5   C  CH2   0  -0.281   0.5712   0.4856   0.8178
 8U7  C6   C  CH2   0  -0.285  -0.1138  -1.7543   0.3175
 8U7  C7   C  CH2   0  -0.434  -1.3919  -1.2601  -0.3423
 8U7  C8   C  CH2   0  -0.317   2.2084  -1.2681   0.6990
 8U7  C10  C  CR16  0  -0.315   4.3981  -0.1084   1.1598
 8U7  C13  C  CR16  0  -0.242   4.5788   0.7689  -1.4597
 8U7  C1   C  CH3   0  -0.504  -6.6362   0.3723  -0.6271
 8U7  C2   C  C     0   0.729  -4.2694   0.2398  -0.0415
 8U7  N2   N  NH1   0  -0.685  -3.0076   0.6225  -0.3847
 8U7  C3   C  CH1   0  -0.061  -1.8325   0.0741   0.2553
 8U7  C9   C  CR6   0   0.087   3.3800  -0.4239   0.2664
 8U7  C11  C  CR16  0  -0.242   5.5013   0.6325   0.7515
 8U7  C12  C  CR16  0  -0.272   5.5954   1.0732  -0.5608
 8U7  C14  C  CR16  0  -0.284   3.4814   0.0267  -1.0488
 8U7  O1   O  O     0  -0.553  -4.5115  -0.4542   0.9430
 8U7  H1   H  HNH1  0   0.393  -5.0193   1.2358  -1.6708
 8U7  H3   H  HCH2  0   0.240  -0.9505   1.9966   0.6883
 8U7  H4   H  HCH2  0   0.221  -0.4686   1.3152  -0.8642
 8U7  H5   H  HCH2  0   0.190   0.4011   0.3572   1.9023
 8U7  H6   H  HCH2  0   0.244   1.3941   1.1952   0.7144
 8U7  H7   H  HCH2  0   0.238   0.2099  -2.6818  -0.1606
 8U7  H8   H  HCH2  0   0.188  -0.3209  -1.9992   1.3747
 8U7  H9   H  HCH2  0   0.216  -1.2200  -1.1366  -1.4163
 8U7  H10  H  HCH2  0   0.237  -2.1798  -2.0068  -0.2205
 8U7  H11  H  HCH2  0   0.210   2.2141  -1.3621   1.7983
 8U7  H12  H  HCH2  0   0.250   2.3500  -2.2819   0.3109
 8U7  H14  H  HCR6  0   0.251   4.6424   1.1125  -2.4845
 8U7  H15  H  HCH3  0   0.226  -6.8245  -0.6976  -0.7362
 8U7  H16  H  HCH3  0   0.230  -6.9820   0.6790   0.3604
 8U7  H17  H  HCH3  0   0.244  -7.2350   0.8953  -1.3681
 8U7  H18  H  HNH1  0   0.381  -2.8670   1.0456  -1.2893
 8U7  H19  H  HCH1  0   0.232  -2.0768  -0.0836   1.3091
 8U7  H20  H  HCR6  0   0.252   6.2818   0.8710   1.4629
 8U7  H21  H  HCR6  0   0.252   6.4515   1.6528  -0.8815
 8U7  H22  H  HCR6  0   0.243   2.6860  -0.1980  -1.7488
 8U7  H13  H  HCR6  0   0.247   4.3270  -0.4412   2.1891

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
 8U7  C12  C13  aromatic  1.391  0.020  1.391
 8U7  C12  C11  aromatic  1.387  0.020  1.387
 8U7  C13  C14  aromatic  1.387  0.020  1.387
 8U7  C11  C10  aromatic  1.390  0.020  1.390
 8U7  C14  C9   aromatic  1.394  0.020  1.394
 8U7  C10  C9   aromatic  1.391  0.020  1.391
 8U7  C9   C8   single    1.507  0.020  1.507
 8U7  C8   N3   single    1.447  0.020  1.447
 8U7  N3   C6   single    1.451  0.020  1.451
 8U7  N3   C5   single    1.452  0.020  1.452
 8U7  C6   C7   single    1.521  0.020  1.521
 8U7  C5   C4   single    1.520  0.020  1.520
 8U7  C7   C3   single    1.527  0.020  1.527
 8U7  C4   C3   single    1.523  0.020  1.523
 8U7  C3   N2   single    1.446  0.020  1.446
 8U7  N2   C2   single    1.363  0.020  1.363
 8U7  O1   C2   double    1.229  0.020  1.229
 8U7  C2   N1   single    1.355  0.020  1.355
 8U7  N1   C1   single    1.441  0.020  1.441
 8U7  N1   H1   single    0.860  0.020  1.020
 8U7  C4   H3   single    0.970  0.020  1.090
 8U7  C4   H4   single    0.970  0.020  1.090
 8U7  C5   H5   single    0.970  0.020  1.090
 8U7  C5   H6   single    0.970  0.020  1.090
 8U7  C6   H7   single    0.970  0.020  1.090
 8U7  C6   H8   single    0.970  0.020  1.090
 8U7  C7   H9   single    0.970  0.020  1.090
 8U7  C7   H10  single    0.970  0.020  1.090
 8U7  C8   H11  single    0.970  0.020  1.090
 8U7  C8   H12  single    0.970  0.020  1.090
 8U7  C10  H13  single    0.930  0.020  1.080
 8U7  C13  H14  single    0.930  0.020  1.080
 8U7  C1   H15  single    0.970  0.020  1.090
 8U7  C1   H16  single    0.970  0.020  1.090
 8U7  C1   H17  single    0.970  0.020  1.090
 8U7  N2   H18  single    0.890  0.020  1.040
 8U7  C3   H19  single    0.970  0.020  1.090
 8U7  C11  H20  single    0.930  0.020  1.080
 8U7  C12  H21  single    0.930  0.020  1.080
 8U7  C14  H22  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
 8U7  H1   N1   C2   119.98  3.000
 8U7  H1   N1   C1   118.01  3.000
 8U7  C2   N1   C1   121.65  3.000
 8U7  C8   N3   C6   112.04  3.000
 8U7  C6   N3   C5   111.20  3.000
 8U7  C8   N3   C5   111.95  3.000
 8U7  H4   C4   H3   107.39  3.000
 8U7  H4   C4   C3   109.88  3.000
 8U7  H3   C4   C3   110.18  3.000
 8U7  H4   C4   C5   109.10  3.000
 8U7  H3   C4   C5   109.57  3.000
 8U7  C3   C4   C5   110.66  3.000
 8U7  H6   C5   H5   106.54  3.000
 8U7  H6   C5   C4   109.40  3.000
 8U7  H5   C5   C4   109.19  3.000
 8U7  H6   C5   N3   109.10  3.000
 8U7  H5   C5   N3   111.09  3.000
 8U7  C4   C5   N3   111.40  3.000
 8U7  H8   C6   H7   106.63  3.000
 8U7  H8   C6   C7   109.25  3.000
 8U7  H7   C6   C7   109.57  3.000
 8U7  H8   C6   N3   111.57  3.000
 8U7  H7   C6   N3   108.78  3.000
 8U7  C7   C6   N3   110.94  3.000
 8U7  H10  C7   H9   107.45  3.000
 8U7  H10  C7   C3   110.22  3.000
 8U7  H9   C7   C3   109.31  3.000
 8U7  H10  C7   C6   109.62  3.000
 8U7  H9   C7   C6   109.29  3.000
 8U7  C3   C7   C6   110.89  3.000
 8U7  H12  C8   H11  105.88  3.000
 8U7  H12  C8   C9   108.44  3.000
 8U7  H11  C8   C9   109.24  3.000
 8U7  H12  C8   N3   107.92  3.000
 8U7  H11  C8   N3   112.37  3.000
 8U7  C9   C8   N3   112.68  3.000
 8U7  H13  C10  C11  119.63  3.000
 8U7  H13  C10  C9   119.49  3.000
 8U7  C11  C10  C9   120.87  3.000
 8U7  H14  C13  C14  119.78  3.000
 8U7  H14  C13  C12  119.96  3.000
 8U7  C14  C13  C12  120.26  3.000
 8U7  H17  C1   H16  107.91  3.000
 8U7  H17  C1   H15  107.97  3.000
 8U7  H16  C1   H15  108.15  3.000
 8U7  H17  C1   N1   108.19  3.000
 8U7  H16  C1   N1   111.92  3.000
 8U7  H15  C1   N1   112.54  3.000
 8U7  O1   C2   N2   122.89  3.000
 8U7  O1   C2   N1   121.94  3.000
 8U7  N2   C2   N1   115.14  3.000
 8U7  H18  N2   C3   116.28  3.000
 8U7  H18  N2   C2   118.22  3.000
 8U7  C3   N2   C2   122.31  3.000
 8U7  H19  C3   N2   107.44  3.000
 8U7  H19  C3   C7   108.40  3.000
 8U7  N2   C3   C7   113.11  3.000
 8U7  H19  C3   C4   108.06  3.000
 8U7  N2   C3   C4   110.23  3.000
 8U7  C7   C3   C4   109.43  3.000
 8U7  C14  C9   C10  118.66  3.000
 8U7  C10  C9   C8   120.77  3.000
 8U7  C14  C9   C8   120.55  3.000
 8U7  H20  C11  C12  120.17  3.000
 8U7  H20  C11  C10  119.77  3.000
 8U7  C12  C11  C10  120.06  3.000
 8U7  H21  C12  C11  120.26  3.000
 8U7  H21  C12  C13  120.25  3.000
 8U7  C11  C12  C13  119.49  3.000
 8U7  H22  C14  C9   119.30  3.000
 8U7  H22  C14  C13  120.04  3.000
 8U7  C9   C14  C13  120.66  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
 8U7  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 8U7  CONST_02  C13  C14  C9   C10    0.00   0.0  0
 8U7  CONST_03  C12  C13  C14  C9     0.00   0.0  0
 8U7  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 8U7  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 8U7  CONST_06  C14  C9   C10  C11    0.00   0.0  0
 8U7  CONST_07  C13  C14  C9   C8   180.00   0.0  0
 8U7  CONST_08  C11  C10  C9   C8   180.00   0.0  0
 8U7  CONST_09  H21  C12  C11  C10  180.00   0.0  0
 8U7  CONST_10  H22  C14  C9   C10  180.00   0.0  0
 8U7  CONST_11  H20  C11  C12  C13  180.00   0.0  0
 8U7  CONST_12  H14  C13  C14  C9   180.00   0.0  0
 8U7  CONST_13  H13  C10  C11  C12  180.00   0.0  0
 8U7  CONST_14  O1   C2   N2   C3     0.00   0.0  0
 8U7  CONST_15  C3   N2   C2   N1   180.00   0.0  0
 8U7  CONST_16  O1   C2   N1   C1     0.00   0.0  0
 8U7  CONST_17  N2   C2   N1   C1   180.00   0.0  0
 8U7  CONST_18  H18  N2   C2   O1   180.00   0.0  0
 8U7  CONST_19  H1   N1   C2   O1   180.00   0.0  0
 8U7  Var_01    C3   C7   C6   N3   -56.96  30.0  1
 8U7  Var_02    C3   C4   C5   N3    56.81  30.0  1
 8U7  Var_03    C6   N3   C5   C4   -59.63  30.0  1
 8U7  Var_04    C7   C6   N3   C5    59.51  30.0  1
 8U7  Var_05    C14  C9   C8   N3   -43.95  30.0  3
 8U7  Var_06    C9   C8   N3   C5   -69.12  30.0  2
 8U7  Var_07    H15  C1   N1   C2   -62.71  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
 8U7  chir_01  C3  C7  C4  N2  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
 8U7  plan-1  C8   0.020
 8U7  plan-1  C10  0.020
 8U7  plan-1  C13  0.020
 8U7  plan-1  C9   0.020
 8U7  plan-1  C11  0.020
 8U7  plan-1  C12  0.020
 8U7  plan-1  C14  0.020
 8U7  plan-1  H14  0.020
 8U7  plan-1  H20  0.020
 8U7  plan-1  H21  0.020
 8U7  plan-1  H22  0.020
 8U7  plan-1  H13  0.020
 8U7  plan-2  N1   0.020
 8U7  plan-2  C1   0.020
 8U7  plan-2  C2   0.020
 8U7  plan-2  N2   0.020
 8U7  plan-2  C3   0.020
 8U7  plan-2  O1   0.020
 8U7  plan-2  H1   0.020
 8U7  plan-2  H18  0.020

