# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:59:14 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: ~{N}-cyclohexyl-4-methyl-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)C(=O)NC2CCCCC2
#
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
 UAE  UAE  "~{N}-cyclohexyl-4-methyl-piperidine-1-carboxamide"
  ligand  40  16  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UAE
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
 UAE  C4   C  CH2   0  -0.318  -15.7464  -28.5978   0.3794
 UAE  C5   C  C     0   0.732  -13.6331  -28.3726   1.5423
 UAE  C6   C  CH1   0  -0.045  -11.5324  -28.2016   2.8086
 UAE  C11  C  CH2   0  -0.427  -10.9067  -26.8829   2.3526
 UAE  C7   C  CH2   0  -0.441  -11.1172  -28.5272   4.2412
 UAE  C8   C  CH2   0  -0.435   -9.5989  -28.5494   4.3867
 UAE  C9   C  CH2   0  -0.428   -8.9723  -27.2390   3.9223
 UAE  C10  C  CH2   0  -0.437   -9.3880  -26.9117   2.4924
 UAE  C12  C  CH2   0  -0.345  -15.8081  -28.2530   2.7561
 UAE  C13  C  CH2   0  -0.406  -16.2888  -29.6773   3.0073
 UAE  N1   N  NT    0  -0.486  -14.9938  -28.1794   1.5522
 UAE  N2   N  NH1   0  -0.689  -12.9801  -28.1913   2.7218
 UAE  C3   C  CH2   0  -0.416  -16.2284  -30.0371   0.5248
 UAE  C1   C  CH3   0  -0.650  -17.4446  -31.6815   2.0016
 UAE  C2   C  CH1   0  -0.236  -17.0496  -30.2260   1.8001
 UAE  O1   O  O     0  -0.542  -13.0323  -28.6845   0.5173
 UAE  H1   H  HCH2  0   0.254  -15.1398  -28.4726  -0.5132
 UAE  H2   H  HCH2  0   0.232  -16.6059  -27.9276   0.2820
 UAE  H3   H  HCH1  0   0.229  -11.1662  -29.0028   2.1610
 UAE  H4   H  HCH2  0   0.207  -11.3158  -26.0693   2.9627
 UAE  H5   H  HCH2  0   0.231  -11.1917  -26.6794   1.3183
 UAE  H6   H  HCH2  0   0.213  -11.5338  -27.7716   4.9184
 UAE  H7   H  HCH2  0   0.235  -11.5453  -29.4879   4.5377
 UAE  H8   H  HCH2  0   0.213   -9.1918  -29.3751   3.7932
 UAE  H9   H  HCH2  0   0.230   -9.3308  -28.7537   5.4256
 UAE  H10  H  HCH2  0   0.227   -7.8838  -27.2935   3.9991
 UAE  H11  H  HCH2  0   0.209   -9.2918  -26.4285   4.5861
 UAE  H12  H  HCH2  0   0.211   -8.9762  -27.6666   1.8137
 UAE  H13  H  HCH2  0   0.228   -8.9650  -25.9537   2.1818
 UAE  H14  H  HCH2  0   0.252  -15.2863  -27.8604   3.6263
 UAE  H15  H  HCH2  0   0.244  -16.6695  -27.5939   2.6119
 UAE  H16  H  HCH2  0   0.232  -16.9286  -29.6930   3.8939
 UAE  H17  H  HCH2  0   0.217  -15.4262  -30.3159   3.2291
 UAE  H18  H  HNH1  0   0.386  -13.4491  -27.7185   3.4762
 UAE  H19  H  HCH2  0   0.229  -16.8234  -30.3152  -0.3495
 UAE  H20  H  HCH2  0   0.215  -15.3598  -30.7050   0.5422
 UAE  H21  H  HCH3  0   0.224  -18.0495  -31.8084   2.9012
 UAE  H22  H  HCH3  0   0.224  -18.0233  -32.0561   1.1555
 UAE  H23  H  HCH3  0   0.214  -16.5595  -32.3134   2.1033
 UAE  H24  H  HCH1  0   0.213  -17.9671  -29.6320   1.6940

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
 UAE  O1   C5   double  1.228  0.020  1.228
 UAE  C3   C4   single  1.525  0.020  1.525
 UAE  C3   C2   single  1.529  0.020  1.529
 UAE  C4   N1   single  1.455  0.020  1.455
 UAE  C5   N1   single  1.374  0.020  1.374
 UAE  C5   N2   single  1.360  0.020  1.360
 UAE  N1   C12  single  1.455  0.020  1.455
 UAE  C1   C2   single  1.522  0.020  1.522
 UAE  C2   C13  single  1.529  0.020  1.529
 UAE  C11  C10  single  1.525  0.020  1.525
 UAE  C11  C6   single  1.529  0.020  1.529
 UAE  N2   C6   single  1.450  0.020  1.450
 UAE  C10  C9   single  1.525  0.020  1.525
 UAE  C6   C7   single  1.527  0.020  1.527
 UAE  C12  C13  single  1.524  0.020  1.524
 UAE  C9   C8   single  1.525  0.020  1.525
 UAE  C7   C8   single  1.525  0.020  1.525
 UAE  C4   H1   single  0.970  0.020  1.090
 UAE  C4   H2   single  0.970  0.020  1.090
 UAE  C6   H3   single  0.970  0.020  1.090
 UAE  C11  H4   single  0.970  0.020  1.090
 UAE  C11  H5   single  0.970  0.020  1.090
 UAE  C7   H6   single  0.970  0.020  1.090
 UAE  C7   H7   single  0.970  0.020  1.090
 UAE  C8   H8   single  0.970  0.020  1.090
 UAE  C8   H9   single  0.970  0.020  1.090
 UAE  C9   H10  single  0.970  0.020  1.090
 UAE  C9   H11  single  0.970  0.020  1.090
 UAE  C10  H12  single  0.970  0.020  1.090
 UAE  C10  H13  single  0.970  0.020  1.090
 UAE  C12  H14  single  0.970  0.020  1.090
 UAE  C12  H15  single  0.970  0.020  1.090
 UAE  C13  H16  single  0.970  0.020  1.090
 UAE  C13  H17  single  0.970  0.020  1.090
 UAE  N2   H18  single  0.890  0.020  1.040
 UAE  C3   H19  single  0.970  0.020  1.090
 UAE  C3   H20  single  0.970  0.020  1.090
 UAE  C1   H21  single  0.970  0.020  1.090
 UAE  C1   H22  single  0.970  0.020  1.090
 UAE  C1   H23  single  0.970  0.020  1.090
 UAE  C2   H24  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
 UAE  H2   C4   H1   107.15  3.000
 UAE  H2   C4   C3   109.78  3.000
 UAE  H1   C4   C3   111.32  3.000
 UAE  H2   C4   N1   107.58  3.000
 UAE  H1   C4   N1   109.89  3.000
 UAE  C3   C4   N1   110.98  3.000
 UAE  O1   C5   N2   121.50  3.000
 UAE  N2   C5   N1   116.77  3.000
 UAE  O1   C5   N1   121.73  3.000
 UAE  H3   C6   N2   107.70  3.000
 UAE  H3   C6   C7   107.97  3.000
 UAE  N2   C6   C7   109.22  3.000
 UAE  H3   C6   C11  108.56  3.000
 UAE  C7   C6   C11  110.64  3.000
 UAE  N2   C6   C11  112.60  3.000
 UAE  H5   C11  H4   106.95  3.000
 UAE  H5   C11  C10  110.49  3.000
 UAE  H4   C11  C10  109.54  3.000
 UAE  H5   C11  C6   109.66  3.000
 UAE  H4   C11  C6   108.75  3.000
 UAE  C10  C11  C6   111.33  3.000
 UAE  H7   C7   H6   106.82  3.000
 UAE  H7   C7   C8   110.56  3.000
 UAE  H6   C7   C8   109.22  3.000
 UAE  H7   C7   C6   109.61  3.000
 UAE  H6   C7   C6   109.22  3.000
 UAE  C8   C7   C6   111.30  3.000
 UAE  H9   C8   H8   106.45  3.000
 UAE  H9   C8   C9   110.46  3.000
 UAE  H8   C8   C9   109.27  3.000
 UAE  H9   C8   C7   109.74  3.000
 UAE  H8   C8   C7   109.22  3.000
 UAE  C9   C8   C7   111.56  3.000
 UAE  H11  C9   H10  106.55  3.000
 UAE  H11  C9   C10  109.27  3.000
 UAE  H10  C9   C10  110.39  3.000
 UAE  H11  C9   C8   109.36  3.000
 UAE  H10  C9   C8   110.19  3.000
 UAE  C10  C9   C8   110.98  3.000
 UAE  H13  C10  H12  106.42  3.000
 UAE  H13  C10  C9   110.45  3.000
 UAE  H12  C10  C9   109.30  3.000
 UAE  H13  C10  C11  110.06  3.000
 UAE  H12  C10  C11  109.30  3.000
 UAE  C9   C10  C11  111.19  3.000
 UAE  H15  C12  H14  105.41  3.000
 UAE  H15  C12  N1   107.52  3.000
 UAE  H14  C12  N1   112.03  3.000
 UAE  H15  C12  C13  109.65  3.000
 UAE  H14  C12  C13  110.89  3.000
 UAE  N1   C12  C13  111.10  3.000
 UAE  H17  C13  H16  106.74  3.000
 UAE  H17  C13  C2   110.02  3.000
 UAE  H16  C13  C2   110.11  3.000
 UAE  H17  C13  C12  109.25  3.000
 UAE  H16  C13  C12  109.37  3.000
 UAE  C2   C13  C12  111.24  3.000
 UAE  C12  N1   C5   123.56  3.000
 UAE  C12  N1   C4   111.27  3.000
 UAE  C5   N1   C4   117.77  3.000
 UAE  H18  N2   C6   115.07  3.000
 UAE  H18  N2   C5   119.27  3.000
 UAE  C6   N2   C5   122.02  3.000
 UAE  H20  C3   H19  106.80  3.000
 UAE  H20  C3   C2   109.71  3.000
 UAE  H19  C3   C2   110.08  3.000
 UAE  H20  C3   C4   109.05  3.000
 UAE  H19  C3   C4   109.62  3.000
 UAE  C2   C3   C4   111.47  3.000
 UAE  H23  C1   H22  107.65  3.000
 UAE  H23  C1   H21  107.76  3.000
 UAE  H22  C1   H21  107.77  3.000
 UAE  H23  C1   C2   110.82  3.000
 UAE  H22  C1   C2   111.30  3.000
 UAE  H21  C1   C2   111.36  3.000
 UAE  H24  C2   C1   108.26  3.000
 UAE  H24  C2   C3   107.55  3.000
 UAE  C1   C2   C3   111.60  3.000
 UAE  H24  C2   C13  107.33  3.000
 UAE  C1   C2   C13  111.59  3.000
 UAE  C3   C2   C13  110.31  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
 UAE  CONST_01  O1   C5   N1   C4      0.00   0.0  0
 UAE  CONST_03  N2   C5   N1   C4    180.00   0.0  0
 UAE  CONST_04  N1   C5   N2   C6    180.00   0.0  0
 UAE  CONST_06  O1   C5   N2   C6      0.00   0.0  0
 UAE  CONST_07  H18  N2   C5   N1      0.00   0.0  0
 UAE  Var_01    C13  C12  N1   C4     60.38  30.0  1
 UAE  Var_02    C9   C10  C11  C6    -56.07  30.0  1
 UAE  Var_03    C9   C8   C7   C6     55.50  30.0  1
 UAE  Var_04    C8   C9   C10  C11    55.39  30.0  1
 UAE  Var_05    C10  C9   C8   C7    -55.21  30.0  1
 UAE  Var_06    C3   C4   N1   C12   -60.13  30.0  1
 UAE  Var_07    C2   C3   C4   N1     55.67  30.0  1
 UAE  Var_08    C2   C13  C12  N1    -55.94  30.0  1
 UAE  Var_09    C3   C4   N1   C5     90.98  30.0  1
 UAE  Var_10    C13  C12  N1   C5    -88.75  30.0  1
 UAE  Var_11    H14  C12  N1   C4   -174.97  30.0  1
 UAE  Var_12    H15  C12  N1   C4    -59.61  30.0  1
 UAE  Var_13    H12  C10  C11  C6     64.68  30.0  1
 UAE  Var_14    H13  C10  C11  C6   -178.79  30.0  1
 UAE  Var_15    H8   C8   C7   C6    -65.40  30.0  1
 UAE  Var_16    H9   C8   C7   C6    178.26  30.0  1
 UAE  Var_17    H10  C9   C10  C11   177.86  30.0  1
 UAE  Var_18    H11  C9   C10  C11   -65.28  30.0  1
 UAE  Var_19    H10  C9   C8   C7   -177.79  30.0  1
 UAE  Var_20    H11  C9   C8   C7     65.42  30.0  1
 UAE  Var_21    H12  C10  C9   C8    -65.36  30.0  1
 UAE  Var_22    H13  C10  C9   C8    177.89  30.0  1
 UAE  Var_23    H4   C11  C10  C9     64.25  30.0  1
 UAE  Var_24    H5   C11  C10  C9   -178.18  30.0  1
 UAE  Var_25    H6   C7   C8   C9    -65.17  30.0  1
 UAE  Var_26    H7   C7   C8   C9    177.58  30.0  1
 UAE  Var_27    H8   C8   C9   C10    65.66  30.0  1
 UAE  Var_28    H9   C8   C9   C10  -177.55  30.0  1
 UAE  Var_29    H1   C4   N1   C12   176.31  30.0  1
 UAE  Var_30    H2   C4   N1   C12    59.98  30.0  1
 UAE  Var_31    H19  C3   C4   N1    177.79  30.0  1
 UAE  Var_32    H20  C3   C4   N1    -65.62  30.0  1
 UAE  Var_33    H16  C13  C12  N1   -177.79  30.0  1
 UAE  Var_34    H17  C13  C12  N1     65.71  30.0  1
 UAE  Var_35    H1   C4   C3   C2    178.40  30.0  1
 UAE  Var_36    H2   C4   C3   C2    -63.12  30.0  1
 UAE  Var_37    H14  C12  C13  C2    178.77  30.0  1
 UAE  Var_38    H15  C12  C13  C2     62.78  30.0  1
 UAE  Var_39    H1   C4   N1   C5    -32.58  30.0  1
 UAE  Var_40    H2   C4   N1   C5   -148.92  30.0  1
 UAE  Var_41    H14  C12  N1   C5     35.90  30.0  1
 UAE  Var_42    H15  C12  N1   C5    151.26  30.0  1

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
 UAE  chir_01  C6  C11  N2  C7   positiv
 UAE  chir_02  C2  C3   C1  C13  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
 UAE  plan-1  C4   0.020
 UAE  plan-1  C5   0.020
 UAE  plan-1  C6   0.020
 UAE  plan-1  C12  0.020
 UAE  plan-1  N1   0.020
 UAE  plan-1  N2   0.020
 UAE  plan-1  O1   0.020
 UAE  plan-1  H18  0.020

