# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 18:52:29 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(4-chlorophenyl)-N'-[(2R)-1-hydroxybutan-2-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](CO)NC(=O)Nc1ccc(Cl)cc1
#
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
 H0D  H0D  N-(4-chlorophenyl)-N'-[(2R)-1-hydroxybutan-2-yl]urea  ligand  31  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_H0D
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
 H0D  N1   N   NH1   0  -0.671   2.4212   0.1977   0.0602
 H0D  C4   C   CH2   0  -0.145   4.5434   0.3669  -1.1293
 H0D  C5   C   C     0   0.727   1.1773  -0.1406  -0.3435
 H0D  C6   C   CR6   0   0.383  -1.1784   0.5417   0.0180
 H0D  C7   C   CR16  0  -0.310  -1.7645   0.0297  -1.1418
 H0D  C8   C   CR16  0  -0.205  -3.1451  -0.0101  -1.2676
 H0D  C10  C   CR16  0  -0.202  -3.3902   0.9925   0.9018
 H0D  C1   C   CH3   0  -0.666   3.4494  -2.1377   1.6506
 H0D  C2   C   CH2   0  -0.416   4.3074  -1.1138   0.9223
 H0D  C3   C   CH1   0  -0.117   3.6210  -0.5241  -0.3119
 H0D  O1   O   OH1   0  -0.674   4.9338   1.4670  -0.3389
 H0D  O2   O   O     0  -0.519   0.9357  -1.0504  -1.1231
 H0D  N2   N   NH1   0  -0.786   0.1949   0.6514   0.2130
 H0D  C9   C   CR6   0  -0.061  -3.9535   0.4679  -0.2503
 H0D  C11  C   CR16  0  -0.350  -2.0135   1.0222   1.0302
 H0D  CL1  CL  CL    0  -0.140  -5.6795   0.4144  -0.4204
 H0D  H1   H   HNH1  0   0.392   2.5437   0.9886   0.6727
 H0D  H2   H   HCH2  0   0.200   5.4071  -0.2270  -1.4553
 H0D  H3   H   HCH2  0   0.209   4.0111   0.6885  -2.0331
 H0D  H4   H   HCR6  0   0.278  -1.1615  -0.3334  -1.9580
 H0D  H5   H   HCR6  0   0.279  -3.5820  -0.4096  -2.1727
 H0D  H6   H   HCR6  0   0.280  -4.0125   1.3702   1.7017
 H0D  H7   H   HCH3  0   0.232   3.9621  -2.5144   2.5359
 H0D  H8   H   HCH3  0   0.221   2.5029  -1.7066   1.9781
 H0D  H9   H   HCH3  0   0.219   3.2218  -2.9928   1.0116
 H0D  H10  H   HCH2  0   0.223   4.5866  -0.3090   1.6075
 H0D  H11  H   HCH2  0   0.225   5.2423  -1.5819   0.6019
 H0D  H12  H   HCH1  0   0.255   3.3159  -1.3440  -0.9641
 H0D  H13  H   HOH1  0   0.458   5.4618   2.0595  -0.8808
 H0D  H14  H   HNH1  0   0.407   0.4670   1.2418   0.9842
 H0D  H15  H   HCR6  0   0.277  -1.5812   1.4243   1.9384

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
 H0D  C8   C7   aromatic  1.387  0.020  1.387
 H0D  C8   C9   aromatic  1.385  0.020  1.385
 H0D  C7   C6   aromatic  1.397  0.020  1.397
 H0D  CL1  C9   single    1.735  0.020  1.735
 H0D  C9   C10  aromatic  1.386  0.020  1.386
 H0D  C6   N2   single    1.391  0.020  1.391
 H0D  C6   C11  aromatic  1.397  0.020  1.397
 H0D  N2   C5   single    1.379  0.020  1.379
 H0D  O1   C4   single    1.410  0.020  1.410
 H0D  C5   N1   single    1.351  0.020  1.351
 H0D  C5   O2   double    1.222  0.020  1.222
 H0D  N1   C3   single    1.449  0.020  1.449
 H0D  C10  C11  aromatic  1.383  0.020  1.383
 H0D  C4   C3   single    1.521  0.020  1.521
 H0D  C3   C2   single    1.530  0.020  1.530
 H0D  C2   C1   single    1.522  0.020  1.522
 H0D  N1   H1   single    0.860  0.020  1.020
 H0D  C4   H2   single    0.970  0.020  1.090
 H0D  C4   H3   single    0.970  0.020  1.090
 H0D  C7   H4   single    0.930  0.020  1.080
 H0D  C8   H5   single    0.930  0.020  1.080
 H0D  C10  H6   single    0.930  0.020  1.080
 H0D  C1   H7   single    0.970  0.020  1.090
 H0D  C1   H8   single    0.970  0.020  1.090
 H0D  C1   H9   single    0.970  0.020  1.090
 H0D  C2   H10  single    0.970  0.020  1.090
 H0D  C2   H11  single    0.970  0.020  1.090
 H0D  C3   H12  single    0.970  0.020  1.090
 H0D  O1   H13  single    0.850  0.020  0.980
 H0D  N2   H14  single    0.860  0.020  1.020
 H0D  C11  H15  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
 H0D  H1   N1   C3   116.51  3.000
 H0D  H1   N1   C5   119.35  3.000
 H0D  C3   N1   C5   124.13  3.000
 H0D  H3   C4   H2   107.20  3.000
 H0D  H3   C4   O1   111.57  3.000
 H0D  H2   C4   O1   111.76  3.000
 H0D  H3   C4   C3   108.68  3.000
 H0D  H2   C4   C3   108.65  3.000
 H0D  O1   C4   C3   108.90  3.000
 H0D  N2   C5   O2   122.95  3.000
 H0D  O2   C5   N1   123.99  3.000
 H0D  N2   C5   N1   113.05  3.000
 H0D  C11  C6   N2   117.47  3.000
 H0D  C11  C6   C7   118.47  3.000
 H0D  N2   C6   C7   124.02  3.000
 H0D  H4   C7   C8   118.59  3.000
 H0D  H4   C7   C6   121.17  3.000
 H0D  C8   C7   C6   120.24  3.000
 H0D  H5   C8   C9   120.43  3.000
 H0D  H5   C8   C7   119.26  3.000
 H0D  C9   C8   C7   120.31  3.000
 H0D  H6   C10  C11  119.77  3.000
 H0D  H6   C10  C9   120.89  3.000
 H0D  C11  C10  C9   119.34  3.000
 H0D  H9   C1   H8   107.73  3.000
 H0D  H9   C1   H7   107.63  3.000
 H0D  H8   C1   H7   107.51  3.000
 H0D  H9   C1   C2   111.38  3.000
 H0D  H8   C1   C2   111.54  3.000
 H0D  H7   C1   C2   110.86  3.000
 H0D  H11  C2   H10  106.29  3.000
 H0D  H11  C2   C3   108.19  3.000
 H0D  H10  C2   C3   109.65  3.000
 H0D  H11  C2   C1   109.53  3.000
 H0D  H10  C2   C1   109.84  3.000
 H0D  C3   C2   C1   113.11  3.000
 H0D  H12  C3   C2   108.53  3.000
 H0D  H12  C3   C4   106.78  3.000
 H0D  C2   C3   C4   112.78  3.000
 H0D  H12  C3   N1   107.23  3.000
 H0D  C2   C3   N1   110.87  3.000
 H0D  C4   C3   N1   110.39  3.000
 H0D  H13  O1   C4   108.49  3.000
 H0D  H14  N2   C6   114.80  3.000
 H0D  H14  N2   C5   116.90  3.000
 H0D  C6   N2   C5   126.96  3.000
 H0D  CL1  C9   C10  119.84  3.000
 H0D  C10  C9   C8   120.29  3.000
 H0D  CL1  C9   C8   119.88  3.000
 H0D  H15  C11  C10  118.88  3.000
 H0D  H15  C11  C6   119.77  3.000
 H0D  C10  C11  C6   121.35  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
 H0D  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 H0D  CONST_02  C9   C10  C11  C6      0.00   0.0  0
 H0D  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 H0D  CONST_04  C10  C11  C6   C7      0.00   0.0  0
 H0D  CONST_05  C11  C6   C7   C8      0.00   0.0  0
 H0D  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 H0D  CONST_07  CL1  C9   C8   C7    180.00   0.0  0
 H0D  CONST_08  N2   C6   C7   C8    180.00   0.0  0
 H0D  CONST_09  N2   C6   C11  C10   180.00   0.0  0
 H0D  CONST_10  CL1  C9   C10  C11   180.00   0.0  0
 H0D  CONST_11  H5   C8   C7   C6    180.00   0.0  0
 H0D  CONST_12  H6   C10  C11  C6    180.00   0.0  0
 H0D  CONST_13  H15  C11  C6   C7    180.00   0.0  0
 H0D  CONST_14  H4   C7   C8   C9    180.00   0.0  0
 H0D  CONST_17  H14  N2   C6   C7    180.00   0.0  0
 H0D  CONST_18  O2   C5   N2   C6      0.00   0.0  0
 H0D  CONST_19  C6   N2   C5   N1    180.00   0.0  0
 H0D  CONST_20  O2   C5   N1   C3      0.00   0.0  0
 H0D  CONST_21  N2   C5   N1   C3    180.00   0.0  0
 H0D  CONST_22  H1   N1   C5   O2    180.00   0.0  0
 H0D  Var_01    H7   C1   C2   C3   -178.55  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
 H0D  chir_01  C3  N1  C4  C2  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
 H0D  plan-1  C6   0.020
 H0D  plan-1  C7   0.020
 H0D  plan-1  C8   0.020
 H0D  plan-1  C10  0.020
 H0D  plan-1  N2   0.020
 H0D  plan-1  C9   0.020
 H0D  plan-1  C11  0.020
 H0D  plan-1  CL1  0.020
 H0D  plan-1  H4   0.020
 H0D  plan-1  H5   0.020
 H0D  plan-1  H6   0.020
 H0D  plan-1  H15  0.020
 H0D  plan-2  N1   0.020
 H0D  plan-2  C5   0.020
 H0D  plan-2  C6   0.020
 H0D  plan-2  C3   0.020
 H0D  plan-2  O2   0.020
 H0D  plan-2  N2   0.020
 H0D  plan-2  H1   0.020
 H0D  plan-2  H14  0.020

