# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:03:24 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 1-cyclohexyl-3-(2-pyridin-4-ylethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCc1ccncc1)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
 AWP  AWP  1-cyclohexyl-3-(2-pyridin-4-ylethyl)urea  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 GRAND
;

data_comp_AWP
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
 AWP  N1   N  N     0  -0.412  -6.4400   0.3687  -0.5397
 AWP  N3   N  NH1   0  -0.686   2.1273  -0.6106   0.1968
 AWP  C4   C  CR16  0  -0.374  -4.6960  -1.1979  -0.0623
 AWP  C5   C  CR6   0   0.204  -3.8978  -0.2049   0.4956
 AWP  C6   C  CH2   0  -0.537  -2.5179  -0.5018   1.0013
 AWP  C7   C  CH2   0  -0.242  -1.4832  -0.2799  -0.1019
 AWP  C8   C  C     0   0.732   0.9536  -0.0779  -0.2304
 AWP  C10  C  CH2   0  -0.441   4.4558  -1.2207  -0.1599
 AWP  C13  C  CH2   0  -0.439   5.2322   1.6083   0.0913
 AWP  C1   C  CR16  0  -0.370  -4.4160   1.0861   0.5159
 AWP  C2   C  CR16  0  -0.060  -5.6783   1.3184  -0.0075
 AWP  C3   C  CR16  0  -0.059  -5.9459  -0.8639  -0.5610
 AWP  N2   N  NH1   0  -0.690  -0.1577  -0.5792   0.3864
 AWP  O1   O  O     0  -0.548   0.8913   0.7882  -1.0975
 AWP  C9   C  CH1   0  -0.046   3.4146  -0.1079  -0.2369
 AWP  C11  C  CH2   0  -0.437   5.8249  -0.7315  -0.6221
 AWP  C12  C  CH2   0  -0.430   6.2775   0.4999   0.1562
 AWP  C14  C  CH2   0  -0.426   3.8681   1.1142   0.5627
 AWP  H1   H  HNH1  0   0.383   2.1214  -1.1892   1.0229
 AWP  H2   H  HCR6  0   0.264  -4.3545  -2.2247  -0.1080
 AWP  H3   H  HCH2  0   0.259  -2.2783   0.1394   1.8520
 AWP  H4   H  HCH2  0   0.257  -2.4686  -1.5371   1.3481
 AWP  H5   H  HCH2  0   0.230  -1.7452  -0.8898  -0.9748
 AWP  H6   H  HCH2  0   0.247  -1.5130   0.7606  -0.4223
 AWP  H8   H  HCH2  0   0.236   4.1306  -2.0689  -0.7678
 AWP  H9   H  HCH2  0   0.230   5.5477   2.4641   0.6930
 AWP  H10  H  HCH2  0   0.212   5.1506   1.9708  -0.9396
 AWP  H11  H  HCR6  0   0.265  -3.8491   1.9064   0.9384
 AWP  H12  H  HCR6  0   0.262  -6.0922   2.3208   0.0064
 AWP  H13  H  HCR6  0   0.262  -6.5769  -1.6317  -0.9958
 AWP  H14  H  HNH1  0   0.387  -0.0610  -1.4551   0.8775
 AWP  H15  H  HCH1  0   0.229   3.3109   0.1848  -1.2854
 AWP  H16  H  HCH2  0   0.232   6.5574  -1.5353  -0.5197
 AWP  H17  H  HCH2  0   0.213   5.7797  -0.4878  -1.6889
 AWP  H18  H  HCH2  0   0.228   7.2342   0.8577  -0.2317
 AWP  H19  H  HCH2  0   0.210   6.4496   0.2243   1.2022
 AWP  H20  H  HCH2  0   0.208   3.9215   0.8428   1.6232
 AWP  H21  H  HCH2  0   0.233   3.1215   1.9074   0.4759
 AWP  H7   H  HCH2  0   0.214   4.5266  -1.5817   0.8735

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
 AWP  C2   C1   aromatic  1.386  0.020  1.386
 AWP  C2   N1   aromatic  1.329  0.020  1.329
 AWP  C1   C5   aromatic  1.391  0.020  1.391
 AWP  N1   C3   aromatic  1.328  0.020  1.328
 AWP  O1   C8   double    1.227  0.020  1.227
 AWP  C5   C6   single    1.499  0.020  1.499
 AWP  C5   C4   aromatic  1.391  0.020  1.391
 AWP  C6   C7   single    1.529  0.020  1.529
 AWP  C3   C4   aromatic  1.387  0.020  1.387
 AWP  C8   N3   single    1.358  0.020  1.358
 AWP  C8   N2   single    1.366  0.020  1.366
 AWP  C10  C11  single    1.526  0.020  1.526
 AWP  C10  C9   single    1.526  0.020  1.526
 AWP  N3   C9   single    1.448  0.020  1.448
 AWP  C11  C12  single    1.525  0.020  1.525
 AWP  C7   N2   single    1.444  0.020  1.444
 AWP  C9   C14  single    1.529  0.020  1.529
 AWP  C12  C13  single    1.525  0.020  1.525
 AWP  C14  C13  single    1.525  0.020  1.525
 AWP  N3   H1   single    0.860  0.020  1.020
 AWP  C4   H2   single    0.930  0.020  1.080
 AWP  C6   H3   single    0.970  0.020  1.090
 AWP  C6   H4   single    0.970  0.020  1.090
 AWP  C7   H5   single    0.970  0.020  1.090
 AWP  C7   H6   single    0.970  0.020  1.090
 AWP  C10  H7   single    0.970  0.020  1.090
 AWP  C10  H8   single    0.970  0.020  1.090
 AWP  C13  H9   single    0.970  0.020  1.090
 AWP  C13  H10  single    0.970  0.020  1.090
 AWP  C1   H11  single    0.930  0.020  1.080
 AWP  C2   H12  single    0.930  0.020  1.080
 AWP  C3   H13  single    0.930  0.020  1.080
 AWP  N2   H14  single    0.890  0.020  1.040
 AWP  C9   H15  single    0.970  0.020  1.090
 AWP  C11  H16  single    0.970  0.020  1.090
 AWP  C11  H17  single    0.970  0.020  1.090
 AWP  C12  H18  single    0.970  0.020  1.090
 AWP  C12  H19  single    0.970  0.020  1.090
 AWP  C14  H20  single    0.970  0.020  1.090
 AWP  C14  H21  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
 AWP  C3   N1   C2   117.16  3.000
 AWP  H1   N3   C9   116.72  3.000
 AWP  H1   N3   C8   118.54  3.000
 AWP  C9   N3   C8   122.53  3.000
 AWP  H2   C4   C3   119.83  3.000
 AWP  H2   C4   C5   120.85  3.000
 AWP  C3   C4   C5   119.32  3.000
 AWP  C1   C5   C6   121.44  3.000
 AWP  C6   C5   C4   121.47  3.000
 AWP  C1   C5   C4   117.04  3.000
 AWP  H4   C6   H3   107.40  3.000
 AWP  H4   C6   C7   109.63  3.000
 AWP  H3   C6   C7   109.18  3.000
 AWP  H4   C6   C5   109.64  3.000
 AWP  H3   C6   C5   110.39  3.000
 AWP  C7   C6   C5   110.54  3.000
 AWP  H6   C7   H5   106.90  3.000
 AWP  H6   C7   N2   108.82  3.000
 AWP  H5   C7   N2   111.91  3.000
 AWP  H6   C7   C6   109.42  3.000
 AWP  H5   C7   C6   109.39  3.000
 AWP  N2   C7   C6   110.32  3.000
 AWP  O1   C8   N2   122.46  3.000
 AWP  N2   C8   N3   114.65  3.000
 AWP  O1   C8   N3   122.90  3.000
 AWP  H8   C10  H7   106.72  3.000
 AWP  H8   C10  C11  110.32  3.000
 AWP  H7   C10  C11  109.45  3.000
 AWP  H8   C10  C9   109.57  3.000
 AWP  H7   C10  C9   109.36  3.000
 AWP  C11  C10  C9   111.30  3.000
 AWP  H10  C13  H9   106.28  3.000
 AWP  H10  C13  C14  109.35  3.000
 AWP  H9   C13  C14  109.98  3.000
 AWP  H10  C13  C12  109.36  3.000
 AWP  H9   C13  C12  110.36  3.000
 AWP  C14  C13  C12  111.37  3.000
 AWP  H11  C1   C2   119.81  3.000
 AWP  H11  C1   C5   120.91  3.000
 AWP  C2   C1   C5   119.29  3.000
 AWP  H12  C2   C1   119.84  3.000
 AWP  H12  C2   N1   116.55  3.000
 AWP  C1   C2   N1   123.61  3.000
 AWP  H13  C3   C4   119.87  3.000
 AWP  H13  C3   N1   116.55  3.000
 AWP  C4   C3   N1   123.59  3.000
 AWP  H14  N2   C8   117.42  3.000
 AWP  H14  N2   C7   115.63  3.000
 AWP  C8   N2   C7   121.20  3.000
 AWP  H15  C9   C14  108.40  3.000
 AWP  H15  C9   C10  107.95  3.000
 AWP  C14  C9   C10  110.74  3.000
 AWP  H15  C9   N3   107.20  3.000
 AWP  C14  C9   N3   112.61  3.000
 AWP  C10  C9   N3   109.77  3.000
 AWP  H17  C11  H16  106.43  3.000
 AWP  H17  C11  C12  109.25  3.000
 AWP  H16  C11  C12  110.32  3.000
 AWP  H17  C11  C10  109.23  3.000
 AWP  H16  C11  C10  109.72  3.000
 AWP  C12  C11  C10  111.75  3.000
 AWP  H19  C12  H18  106.50  3.000
 AWP  H19  C12  C11  109.31  3.000
 AWP  H18  C12  C11  110.05  3.000
 AWP  H19  C12  C13  109.34  3.000
 AWP  H18  C12  C13  110.31  3.000
 AWP  C11  C12  C13  111.20  3.000
 AWP  H21  C14  H20  106.86  3.000
 AWP  H21  C14  C9   109.63  3.000
 AWP  H20  C14  C9   108.81  3.000
 AWP  H21  C14  C13  110.57  3.000
 AWP  H20  C14  C13  109.61  3.000
 AWP  C9   C14  C13  111.25  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
 AWP  CONST_01  C5   C1   C2   N1      0.00   0.0  0
 AWP  CONST_02  C5   C4   C3   N1      0.00   0.0  0
 AWP  CONST_03  C2   C1   C5   C4      0.00   0.0  0
 AWP  CONST_04  C2   N1   C3   C4      0.00   0.0  0
 AWP  CONST_05  C3   N1   C2   C1      0.00   0.0  0
 AWP  CONST_06  C3   C4   C5   C1      0.00   0.0  0
 AWP  CONST_07  C2   C1   C5   C6    180.00   0.0  0
 AWP  CONST_08  C3   C4   C5   C6    180.00   0.0  0
 AWP  CONST_09  H11  C1   C2   N1    180.00   0.0  0
 AWP  CONST_10  H2   C4   C3   N1    180.00   0.0  0
 AWP  CONST_11  H12  C2   C1   C5    180.00   0.0  0
 AWP  CONST_12  H13  C3   C4   C5    180.00   0.0  0
 AWP  CONST_13  C9   N3   C8   O1      0.00   0.0  0
 AWP  CONST_14  C9   N3   C8   N2    180.00   0.0  0
 AWP  CONST_15  O1   C8   N2   C7      0.00   0.0  0
 AWP  CONST_16  C7   N2   C8   N3    180.00   0.0  0
 AWP  CONST_17  H1   N3   C8   O1    180.00   0.0  0
 AWP  Var_01    C13  C12  C11  C10   -54.47  30.0  1
 AWP  Var_02    C12  C11  C10  C9     55.10  30.0  1
 AWP  Var_03    C12  C13  C14  C9    -55.84  30.0  1
 AWP  Var_04    C14  C13  C12  C11    54.77  30.0  1
 AWP  Var_05    C7   C6   C5   C4     91.40  30.0  2
 AWP  Var_06    N2   C7   C6   C5   -179.46  30.0  3
 AWP  Var_07    C8   N2   C7   C6   -159.16  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
 AWP  chir_01  C9  C10  N3  C14  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
 AWP  plan-1  N1   0.020
 AWP  plan-1  C4   0.020
 AWP  plan-1  C5   0.020
 AWP  plan-1  C6   0.020
 AWP  plan-1  C1   0.020
 AWP  plan-1  C2   0.020
 AWP  plan-1  C3   0.020
 AWP  plan-1  H2   0.020
 AWP  plan-1  H11  0.020
 AWP  plan-1  H12  0.020
 AWP  plan-1  H13  0.020
 AWP  plan-2  N3   0.020
 AWP  plan-2  C7   0.020
 AWP  plan-2  C8   0.020
 AWP  plan-2  N2   0.020
 AWP  plan-2  O1   0.020
 AWP  plan-2  C9   0.020
 AWP  plan-2  H1   0.020
 AWP  plan-2  H14  0.020

