# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 05:44:25 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-cyclohexyl-3-decylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCNC(=O)NC1CCCCC1
#
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
 CDU  CDU  '1-cyclohexyl-3-decylurea '  ligand  54  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CDU
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
 CDU  C1    C  CH2   0  -0.439   1.0323   1.1881  -7.1332
 CDU  C2    C  CH2   0  -0.431  -0.1269   0.9123  -8.0853
 CDU  C3    C  CH2   0  -0.436  -0.7729  -0.4352  -7.7787
 CDU  C4    C  CH2   0  -0.439  -1.2209  -0.5232  -6.3226
 CDU  C5    C  CH1   0  -0.052  -0.0621  -0.2475  -5.3676
 CDU  C6    C  CH2   0  -0.426   0.5802   1.1059  -5.6781
 CDU  N1    N  NH1   0  -0.686  -0.5287  -0.3379  -3.9990
 CDU  C8    C  C     0   0.729   0.3048  -0.6206  -2.9598
 CDU  O     O  O     0  -0.551   1.4579  -1.0113  -3.1173
 CDU  N2    N  NH1   0  -0.688  -0.2455  -0.4377  -1.7279
 CDU  C11   C  CH2   0  -0.239   0.4088  -0.8798  -0.5160
 CDU  C12   C  CH2   0  -0.455  -0.1797  -0.1683   0.6923
 CDU  C13   C  CH2   0  -0.419   0.4214  -0.6476   2.0068
 CDU  C14   C  CH2   0  -0.412  -0.1758   0.0627   3.2148
 CDU  C15   C  CH2   0  -0.413   0.3888  -0.4166   4.5458
 CDU  C16   C  CH2   0  -0.412  -0.2301   0.2949   5.7423
 CDU  C17   C  CH2   0  -0.412   0.3101  -0.1838   7.0837
 CDU  C18   C  CH2   0  -0.406  -0.3246   0.5279   8.2717
 CDU  C19   C  CH2   0  -0.419   0.2027   0.0498   9.6187
 CDU  C20   C  CH3   0  -0.663  -0.4432   0.7668  10.7961
 CDU  HC11  H  HCH2  0   0.212   1.8273   0.4551  -7.3093
 CDU  HC12  H  HCH2  0   0.230   1.4662   2.1703  -7.3341
 CDU  HC21  H  HCH2  0   0.228   0.2173   0.9393  -9.1219
 CDU  HC22  H  HCH2  0   0.210  -0.8750   1.7055  -7.9825
 CDU  HC31  H  HCH2  0   0.213  -0.0509  -1.2336  -7.9822
 CDU  HC32  H  HCH2  0   0.231  -1.6245  -0.6105  -8.4398
 CDU  HC41  H  HCH2  0   0.236  -1.6444  -1.5083  -6.1121
 CDU  HC42  H  HCH2  0   0.213  -2.0161   0.2108  -6.1433
 CDU  HC51  H  HCH1  0   0.230   0.6891  -1.0291  -5.5090
 CDU  HC61  H  HCH2  0   0.208  -0.1542   1.8954  -5.4790
 CDU  HC62  H  HCH2  0   0.232   1.4222   1.2758  -5.0034
 CDU  HN1   H  HNH1  0   0.380  -1.3873   0.1497  -3.7920
 CDU  HN2   H  HNH1  0   0.384  -1.2465  -0.3292  -1.6703
 CDU  H111  H  HCH2  0   0.233   1.4744  -0.6620  -0.5900
 CDU  H112  H  HCH2  0   0.214   0.3153  -1.9652  -0.3845
 CDU  H121  H  HCH2  0   0.219  -1.2638  -0.3270   0.7156
 CDU  H122  H  HCH2  0   0.224  -0.0272   0.9099   0.5861
 CDU  H131  H  HCH2  0   0.213   1.5060  -0.4954   1.9925
 CDU  H132  H  HCH2  0   0.213   0.2671  -1.7274   2.1058
 CDU  H141  H  HCH2  0   0.208  -1.2626  -0.0770   3.2129
 CDU  H142  H  HCH2  0   0.209  -0.0113   1.1416   3.1189
 CDU  H151  H  HCH2  0   0.208   1.4747  -0.2713   4.5566
 CDU  H152  H  HCH2  0   0.207   0.2275  -1.4961   4.6409
 CDU  H161  H  HCH2  0   0.206  -1.3170   0.1566   5.7204
 CDU  H162  H  HCH2  0   0.207  -0.0631   1.3738   5.6487
 CDU  H171  H  HCH2  0   0.206   1.3961  -0.0406   7.1121
 CDU  H172  H  HCH2  0   0.206   0.1460  -1.2632   7.1767
 CDU  H181  H  HCH2  0   0.205  -1.4112   0.3888   8.2382
 CDU  H182  H  HCH2  0   0.206  -0.1576   1.6071   8.1801
 CDU  H191  H  HCH2  0   0.210   1.2874   0.1916   9.6538
 CDU  H192  H  HCH2  0   0.210   0.0366  -1.0282   9.7093
 CDU  H201  H  HCH3  0   0.226  -0.0506   0.4097  11.7487
 CDU  H202  H  HCH3  0   0.215  -0.2650   1.8428  10.7479
 CDU  H203  H  HCH3  0   0.216  -1.5242   0.6148  10.8058

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
 CDU  C1   C2    single  1.525  0.020  1.525
 CDU  C1   C6    single  1.526  0.020  1.526
 CDU  C1   HC11  single  0.970  0.020  1.090
 CDU  C1   HC12  single  0.970  0.020  1.090
 CDU  C2   C3    single  1.526  0.020  1.526
 CDU  C2   HC21  single  0.970  0.020  1.090
 CDU  C2   HC22  single  0.970  0.020  1.090
 CDU  C3   C4    single  1.526  0.020  1.526
 CDU  C3   HC31  single  0.970  0.020  1.090
 CDU  C3   HC32  single  0.970  0.020  1.090
 CDU  C4   C5    single  1.527  0.020  1.527
 CDU  C4   HC41  single  0.970  0.020  1.090
 CDU  C4   HC42  single  0.970  0.020  1.090
 CDU  C5   C6    single  1.530  0.020  1.530
 CDU  C5   N1    single  1.449  0.020  1.449
 CDU  C5   HC51  single  0.970  0.020  1.090
 CDU  C6   HC61  single  0.970  0.020  1.090
 CDU  C6   HC62  single  0.970  0.020  1.090
 CDU  N1   C8    single  1.362  0.020  1.362
 CDU  N1   HN1   single  0.890  0.020  1.040
 CDU  C8   O     double  1.228  0.020  1.228
 CDU  C8   N2    single  1.362  0.020  1.362
 CDU  N2   C11   single  1.446  0.020  1.446
 CDU  N2   HN2   single  0.890  0.020  1.040
 CDU  C11  C12   single  1.521  0.020  1.521
 CDU  C11  H111  single  0.970  0.020  1.090
 CDU  C11  H112  single  0.970  0.020  1.090
 CDU  C12  C13   single  1.523  0.020  1.523
 CDU  C12  H121  single  0.970  0.020  1.090
 CDU  C12  H122  single  0.970  0.020  1.090
 CDU  C13  C14   single  1.523  0.020  1.523
 CDU  C13  H131  single  0.970  0.020  1.090
 CDU  C13  H132  single  0.970  0.020  1.090
 CDU  C14  C15   single  1.523  0.020  1.523
 CDU  C14  H141  single  0.970  0.020  1.090
 CDU  C14  H142  single  0.970  0.020  1.090
 CDU  C15  C16   single  1.523  0.020  1.523
 CDU  C15  H151  single  0.970  0.020  1.090
 CDU  C15  H152  single  0.970  0.020  1.090
 CDU  C16  C17   single  1.523  0.020  1.523
 CDU  C16  H161  single  0.970  0.020  1.090
 CDU  C16  H162  single  0.970  0.020  1.090
 CDU  C17  C18   single  1.523  0.020  1.523
 CDU  C17  H171  single  0.970  0.020  1.090
 CDU  C17  H172  single  0.970  0.020  1.090
 CDU  C18  C19   single  1.524  0.020  1.524
 CDU  C18  H181  single  0.970  0.020  1.090
 CDU  C18  H182  single  0.970  0.020  1.090
 CDU  C19  C20   single  1.522  0.020  1.522
 CDU  C19  H191  single  0.970  0.020  1.090
 CDU  C19  H192  single  0.970  0.020  1.090
 CDU  C20  H201  single  0.970  0.020  1.090
 CDU  C20  H202  single  0.970  0.020  1.090
 CDU  C20  H203  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
 CDU  HC12  C1   HC11  106.48  3.000
 CDU  HC12  C1   C6    109.97  3.000
 CDU  HC11  C1   C6    109.41  3.000
 CDU  HC12  C1   C2    110.47  3.000
 CDU  HC11  C1   C2    109.28  3.000
 CDU  C6    C1   C2    111.12  3.000
 CDU  HC22  C2   HC21  106.64  3.000
 CDU  HC22  C2   C3    109.37  3.000
 CDU  HC21  C2   C3    110.24  3.000
 CDU  HC22  C2   C1    109.25  3.000
 CDU  HC21  C2   C1    110.39  3.000
 CDU  C3    C2   C1    110.86  3.000
 CDU  HC32  C3   HC31  106.52  3.000
 CDU  HC32  C3   C4    109.84  3.000
 CDU  HC31  C3   C4    109.19  3.000
 CDU  HC32  C3   C2    110.51  3.000
 CDU  HC31  C3   C2    109.11  3.000
 CDU  C4    C3   C2    111.54  3.000
 CDU  HC42  C4   HC41  106.91  3.000
 CDU  HC42  C4   C5    109.10  3.000
 CDU  HC41  C4   C5    109.66  3.000
 CDU  HC42  C4   C3    109.28  3.000
 CDU  HC41  C4   C3    110.46  3.000
 CDU  C5    C4   C3    111.32  3.000
 CDU  HC51  C5   N1    107.39  3.000
 CDU  HC51  C5   C6    108.53  3.000
 CDU  N1    C5   C6    112.46  3.000
 CDU  HC51  C5   C4    108.15  3.000
 CDU  N1    C5   C4    109.58  3.000
 CDU  C6    C5   C4    110.58  3.000
 CDU  HC62  C6   HC61  106.99  3.000
 CDU  HC62  C6   C5    109.62  3.000
 CDU  HC61  C6   C5    108.60  3.000
 CDU  HC62  C6   C1    110.63  3.000
 CDU  HC61  C6   C1    109.44  3.000
 CDU  C5    C6   C1    111.44  3.000
 CDU  HN1   N1   C8    117.69  3.000
 CDU  HN1   N1   C5    115.96  3.000
 CDU  C8    N1   C5    122.46  3.000
 CDU  N2    C8   O     122.58  3.000
 CDU  N2    C8   N1    114.53  3.000
 CDU  O     C8   N1    122.89  3.000
 CDU  HN2   N2   C11   115.72  3.000
 CDU  HN2   N2   C8    117.86  3.000
 CDU  C11   N2   C8    122.29  3.000
 CDU  H112  C11  H111  106.80  3.000
 CDU  H112  C11  C12   109.55  3.000
 CDU  H111  C11  C12   109.80  3.000
 CDU  H112  C11  N2    111.36  3.000
 CDU  H111  C11  N2    108.92  3.000
 CDU  C12   C11  N2    110.35  3.000
 CDU  H122  C12  H121  106.42  3.000
 CDU  H122  C12  C13   109.81  3.000
 CDU  H121  C12  C13   109.07  3.000
 CDU  H122  C12  C11   109.27  3.000
 CDU  H121  C12  C11   109.38  3.000
 CDU  C13   C12  C11   112.70  3.000
 CDU  H132  C13  H131  106.12  3.000
 CDU  H132  C13  C14   109.43  3.000
 CDU  H131  C13  C14   109.50  3.000
 CDU  H132  C13  C12   109.43  3.000
 CDU  H131  C13  C12   109.63  3.000
 CDU  C14   C13  C12   112.52  3.000
 CDU  H142  C14  H141  105.92  3.000
 CDU  H142  C14  C15   109.31  3.000
 CDU  H141  C14  C15   109.21  3.000
 CDU  H142  C14  C13   109.32  3.000
 CDU  H141  C14  C13   109.15  3.000
 CDU  C15   C14  C13   113.64  3.000
 CDU  H152  C15  H151  106.00  3.000
 CDU  H152  C15  C16   109.40  3.000
 CDU  H151  C15  C16   109.45  3.000
 CDU  H152  C15  C14   109.35  3.000
 CDU  H151  C15  C14   109.53  3.000
 CDU  C16   C15  C14   112.88  3.000
 CDU  H162  C16  H161  105.88  3.000
 CDU  H162  C16  C17   109.31  3.000
 CDU  H161  C16  C17   109.25  3.000
 CDU  H162  C16  C15   109.32  3.000
 CDU  H161  C16  C15   109.17  3.000
 CDU  C17   C16  C15   113.63  3.000
 CDU  H172  C17  H171  105.96  3.000
 CDU  H172  C17  C18   109.36  3.000
 CDU  H171  C17  C18   109.37  3.000
 CDU  H172  C17  C16   109.34  3.000
 CDU  H171  C17  C16   109.47  3.000
 CDU  C18   C17  C16   113.09  3.000
 CDU  H182  C18  H181  105.88  3.000
 CDU  H182  C18  C19   109.28  3.000
 CDU  H181  C18  C19   109.29  3.000
 CDU  H182  C18  C17   109.35  3.000
 CDU  H181  C18  C17   109.27  3.000
 CDU  C19   C18  C17   113.50  3.000
 CDU  H192  C19  H191  105.98  3.000
 CDU  H192  C19  C20   109.61  3.000
 CDU  H191  C19  C20   109.55  3.000
 CDU  H192  C19  C18   109.25  3.000
 CDU  H191  C19  C18   109.31  3.000
 CDU  C20   C19  C18   112.90  3.000
 CDU  H203  C20  H202  107.41  3.000
 CDU  H203  C20  H201  107.64  3.000
 CDU  H202  C20  H201  107.61  3.000
 CDU  H203  C20  C19   111.19  3.000
 CDU  H202  C20  C19   111.16  3.000
 CDU  H201  C20  C19   111.63  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
 CDU  CONST_01  O     C8   N1   C5      0.00   0.0  0
 CDU  CONST_02  N2    C8   N1   C5    180.00   0.0  0
 CDU  CONST_03  C11   N2   C8   O       0.00   0.0  0
 CDU  CONST_04  C11   N2   C8   N1    180.00   0.0  0
 CDU  CONST_05  HN1   N1   C8   O     180.00   0.0  0
 CDU  CONST_06  HN2   N2   C8   O     180.00   0.0  0
 CDU  Var_01    C4    C3   C2   C1     55.46  30.0  1
 CDU  Var_02    C5    C6   C1   C2     56.12  30.0  1
 CDU  Var_03    C5    C4   C3   C2    -55.67  30.0  1
 CDU  Var_04    C6    C1   C2   C3    -55.55  30.0  1
 CDU  Var_05    C12   C11  N2   C8    161.68  30.0  3
 CDU  Var_06    C13   C12  C11  N2    177.01  30.0  3
 CDU  Var_07    C14   C13  C12  C11  -179.71  30.0  3
 CDU  Var_08    C15   C14  C13  C12   178.89  30.0  3
 CDU  Var_09    C16   C15  C14  C13  -179.42  30.0  3
 CDU  Var_10    C17   C16  C15  C14   179.29  30.0  3
 CDU  Var_11    C18   C17  C16  C15  -179.55  30.0  3
 CDU  Var_12    C19   C18  C17  C16   179.63  30.0  3
 CDU  Var_13    C20   C19  C18  C17  -179.84  30.0  3
 CDU  Var_14    H201  C20  C19  C18  -179.96  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
 CDU  chir_01  C5  C4  C6  N1  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
 CDU  plan-1  C5   0.020
 CDU  plan-1  N1   0.020
 CDU  plan-1  C8   0.020
 CDU  plan-1  O    0.020
 CDU  plan-1  N2   0.020
 CDU  plan-1  C11  0.020
 CDU  plan-1  HN1  0.020
 CDU  plan-1  HN2  0.020

