# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:27:42 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: N-cyclopentyl-N'-{[(2R)-oxolan-2-yl]methyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@H]1CCCO1)NC2CCCC2
#
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
 TBJ  TBJ  N-cyclopentyl-N'-{[(2R)-oxolan-2-yl]methyl}urea  ligand  35  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TBJ
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
 TBJ  C4   C  CH2   0  -0.454  23.5788   7.5920  55.0908
 TBJ  C5   C  C     0   0.739  23.5471   3.8572  55.0230
 TBJ  C6   C  CH2   0  -0.329  22.7592   1.5387  55.2087
 TBJ  N1   N  NH1   0  -0.683  22.5803   2.9612  55.3576
 TBJ  C7   C  CH1   0   0.082  23.5656   0.9263  56.3485
 TBJ  C8   C  CH2   0  -0.500  22.9148   1.0743  57.7224
 TBJ  C9   C  CH2   0  -0.494  23.3606  -0.2002  58.4287
 TBJ  C10  C  CH2   0  -0.156  23.3329  -1.2022  57.2850
 TBJ  O    O  O     0  -0.550  24.5884   3.5216  54.4661
 TBJ  N    N  NH1   0  -0.687  23.2487   5.1535  55.3093
 TBJ  C3   C  CH1   0  -0.058  24.2220   6.2103  55.1835
 TBJ  C2   C  CH2   0  -0.440  25.1856   6.3661  56.3623
 TBJ  C1   C  CH2   0  -0.454  25.7887   7.7609  56.1636
 TBJ  C    C  CH2   0  -0.451  24.7436   8.5570  55.3400
 TBJ  O1   O  O2    0  -0.513  23.7004  -0.4732  56.1225
 TBJ  H1   H  HCH2  0   0.222  22.8242   7.6941  55.8779
 TBJ  H2   H  HCH2  0   0.240  23.0781   7.7609  54.1366
 TBJ  H3   H  HCH2  0   0.245  21.7686   1.0795  55.1805
 TBJ  H4   H  HCH2  0   0.249  23.2379   1.3275  54.2514
 TBJ  H5   H  HNH1  0   0.392  21.7755   3.2758  55.8733
 TBJ  H6   H  HCH1  0   0.213  24.5645   1.3809  56.3590
 TBJ  H7   H  HCH2  0   0.252  23.2264   1.9854  58.2316
 TBJ  H8   H  HCH2  0   0.231  21.8241   1.0972  57.6330
 TBJ  H9   H  HCH2  0   0.248  22.7101  -0.4893  59.2540
 TBJ  H10  H  HCH2  0   0.237  24.3734  -0.0892  58.8228
 TBJ  H11  H  HCH2  0   0.202  22.3281  -1.6259  57.1665
 TBJ  H12  H  HCH2  0   0.222  24.0306  -2.0309  57.4246
 TBJ  H13  H  HNH1  0   0.382  22.4592   5.3429  55.9079
 TBJ  H14  H  HCH1  0   0.238  24.7992   6.0313  54.2732
 TBJ  H15  H  HCH2  0   0.235  25.9333   5.5729  56.4022
 TBJ  H16  H  HCH2  0   0.217  24.6104   6.3239  57.2923
 TBJ  H17  H  HCH2  0   0.228  26.7311   7.6961  55.6169
 TBJ  H18  H  HCH2  0   0.232  26.0150   8.2414  57.1157
 TBJ  H19  H  HCH2  0   0.230  25.1766   8.8794  54.3921
 TBJ  H20  H  HCH2  0   0.233  24.4141   9.4596  55.8546

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
 TBJ  O    C5   double  1.228  0.020  1.228
 TBJ  C    C4   single  1.533  0.020  1.533
 TBJ  C    C1   single  1.551  0.020  1.551
 TBJ  C4   C3   single  1.527  0.020  1.527
 TBJ  C1   C2   single  1.533  0.020  1.533
 TBJ  C3   C2   single  1.530  0.020  1.530
 TBJ  C3   N    single  1.442  0.020  1.442
 TBJ  C5   N    single  1.361  0.020  1.361
 TBJ  C5   N1   single  1.360  0.020  1.360
 TBJ  C6   N1   single  1.441  0.020  1.441
 TBJ  C6   C7   single  1.525  0.020  1.525
 TBJ  O1   C10  single  1.421  0.020  1.421
 TBJ  O1   C7   single  1.424  0.020  1.424
 TBJ  C10  C9   single  1.521  0.020  1.521
 TBJ  C7   C8   single  1.527  0.020  1.527
 TBJ  C9   C8   single  1.524  0.020  1.524
 TBJ  C4   H1   single  0.970  0.020  1.090
 TBJ  C4   H2   single  0.970  0.020  1.090
 TBJ  C6   H3   single  0.970  0.020  1.090
 TBJ  C6   H4   single  0.970  0.020  1.090
 TBJ  N1   H5   single  0.860  0.020  1.020
 TBJ  C7   H6   single  0.970  0.020  1.090
 TBJ  C8   H7   single  0.970  0.020  1.090
 TBJ  C8   H8   single  0.970  0.020  1.090
 TBJ  C9   H9   single  0.970  0.020  1.090
 TBJ  C9   H10  single  0.970  0.020  1.090
 TBJ  C10  H11  single  0.970  0.020  1.090
 TBJ  C10  H12  single  0.970  0.020  1.090
 TBJ  N    H13  single  0.890  0.020  1.040
 TBJ  C3   H14  single  0.970  0.020  1.090
 TBJ  C2   H15  single  0.970  0.020  1.090
 TBJ  C2   H16  single  0.970  0.020  1.090
 TBJ  C1   H17  single  0.970  0.020  1.090
 TBJ  C1   H18  single  0.970  0.020  1.090
 TBJ  C    H19  single  0.970  0.020  1.090
 TBJ  C    H20  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
 TBJ  H2   C4   H1   107.34  3.000
 TBJ  H2   C4   C    113.17  3.000
 TBJ  H1   C4   C    110.36  3.000
 TBJ  H2   C4   C3   112.74  3.000
 TBJ  H1   C4   C3   109.34  3.000
 TBJ  C    C4   C3   103.87  3.000
 TBJ  N    C5   O    122.81  3.000
 TBJ  N    C5   N1   114.83  3.000
 TBJ  O    C5   N1   122.31  3.000
 TBJ  H4   C6   H3   107.09  3.000
 TBJ  H4   C6   C7   110.25  3.000
 TBJ  H3   C6   C7   109.27  3.000
 TBJ  H4   C6   N1   109.64  3.000
 TBJ  H3   C6   N1   107.76  3.000
 TBJ  C7   C6   N1   112.63  3.000
 TBJ  H5   N1   C6   117.43  3.000
 TBJ  H5   N1   C5   119.26  3.000
 TBJ  C6   N1   C5   122.45  3.000
 TBJ  H6   C7   O1   108.81  3.000
 TBJ  H6   C7   C8   109.82  3.000
 TBJ  O1   C7   C8   106.16  3.000
 TBJ  H6   C7   C6   108.79  3.000
 TBJ  C8   C7   C6   114.09  3.000
 TBJ  O1   C7   C6   109.04  3.000
 TBJ  H8   C8   H7   107.80  3.000
 TBJ  H8   C8   C9   110.30  3.000
 TBJ  H7   C8   C9   113.53  3.000
 TBJ  H8   C8   C7   110.68  3.000
 TBJ  H7   C8   C7   112.31  3.000
 TBJ  C9   C8   C7   102.19  3.000
 TBJ  H10  C9   H9   107.89  3.000
 TBJ  H10  C9   C10  110.80  3.000
 TBJ  H9   C9   C10  112.57  3.000
 TBJ  H10  C9   C8   110.70  3.000
 TBJ  H9   C9   C8   113.46  3.000
 TBJ  C10  C9   C8   101.37  3.000
 TBJ  H12  C10  H11  107.81  3.000
 TBJ  H12  C10  O1   109.19  3.000
 TBJ  H11  C10  O1   110.29  3.000
 TBJ  H12  C10  C9   113.09  3.000
 TBJ  H11  C10  C9   110.64  3.000
 TBJ  O1   C10  C9   105.82  3.000
 TBJ  H13  N    C3   116.25  3.000
 TBJ  H13  N    C5   118.38  3.000
 TBJ  C3   N    C5   122.12  3.000
 TBJ  H14  C3   C2   109.02  3.000
 TBJ  H14  C3   N    108.00  3.000
 TBJ  C2   C3   N    115.61  3.000
 TBJ  H14  C3   C4   108.68  3.000
 TBJ  N    C3   C4   112.58  3.000
 TBJ  C2   C3   C4   102.70  3.000
 TBJ  H16  C2   H15  107.53  3.000
 TBJ  H16  C2   C1   110.62  3.000
 TBJ  H15  C2   C1   113.37  3.000
 TBJ  H16  C2   C3   108.65  3.000
 TBJ  H15  C2   C3   112.69  3.000
 TBJ  C1   C2   C3   103.92  3.000
 TBJ  H18  C1   H17  106.52  3.000
 TBJ  H18  C1   C    112.18  3.000
 TBJ  H17  C1   C    110.27  3.000
 TBJ  H18  C1   C2   111.69  3.000
 TBJ  H17  C1   C2   110.53  3.000
 TBJ  C    C1   C2   105.72  3.000
 TBJ  H20  C    H19  106.59  3.000
 TBJ  H20  C    C1   112.22  3.000
 TBJ  H19  C    C1   110.23  3.000
 TBJ  H20  C    C4   111.61  3.000
 TBJ  H19  C    C4   110.27  3.000
 TBJ  C1   C    C4   105.98  3.000
 TBJ  C10  O1   C7   110.49  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
 TBJ  CONST_01  C3   N    C5  O     0.00   0.0  0
 TBJ  CONST_02  C3   N    C5  N1  180.00   0.0  0
 TBJ  CONST_03  O    C5   N1  C6    0.00   0.0  0
 TBJ  CONST_04  N    C5   N1  C6  180.00   0.0  0
 TBJ  CONST_05  H13  N    C5  O   180.00   0.0  0
 TBJ  CONST_06  H5   N1   C5  O   180.00   0.0  0
 TBJ  Var_01    C2   C1   C   C4   -0.15  30.0  1
 TBJ  Var_02    C9   C10  O1  C7  -17.29  30.0  1
 TBJ  Var_03    O1   C10  C9  C8   33.50  30.0  1
 TBJ  Var_04    C1   C    C4  C3  -24.88  30.0  1
 TBJ  Var_05    C    C1   C2  C3   25.07  30.0  1
 TBJ  Var_06    C7   C6   N1  C5   80.10  30.0  2

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
 TBJ  chir_01  C7  C6  O1  C8  positiv
 TBJ  chir_02  C3  N   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
 TBJ  plan-1  C5   0.020
 TBJ  plan-1  C6   0.020
 TBJ  plan-1  N1   0.020
 TBJ  plan-1  O    0.020
 TBJ  plan-1  N    0.020
 TBJ  plan-1  C3   0.020
 TBJ  plan-1  H5   0.020
 TBJ  plan-1  H13  0.020

