# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 05:12:37 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@H]1CCCO1)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
 6SV  6SV  1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea  ligand  38  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6SV
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
 6SV  C1   C  CH2   0  -0.430  -5.4254  -0.0022  -0.2341
 6SV  C2   C  CH2   0  -0.436  -4.8408  -1.2531   0.4135
 6SV  C3   C  CH2   0  -0.442  -3.3970  -1.4878  -0.0200
 6SV  C4   C  CH1   0  -0.051  -2.5244  -0.2679   0.2623
 6SV  C5   C  CH2   0  -0.427  -3.1164   0.9861  -0.3845
 6SV  C6   C  CH2   0  -0.439  -4.5585   1.2183   0.0541
 6SV  N1   N  NH1   0  -0.685  -1.1703  -0.5287  -0.1872
 6SV  C7   C  C     0   0.733  -0.1055   0.1817   0.2786
 6SV  O1   O  O     0  -0.552  -0.1635   0.8832   1.2846
 6SV  N2   N  NH1   0  -0.685   1.0456   0.0140  -0.4263
 6SV  C8   C  CH2   0  -0.247   2.2248   0.7982  -0.1487
 6SV  C9   C  CH1   0   0.005   3.4458   0.2077  -0.8380
 6SV  C10  C  CH2   0  -0.502   4.7218   0.9823  -0.4991
 6SV  C11  C  CH2   0  -0.496   5.2939   0.1825   0.6665
 6SV  C12  C  CH2   0  -0.154   4.9093  -1.2339   0.2737
 6SV  O2   O  O2    0  -0.503   3.6641  -1.1276  -0.4012
 6SV  H1   H  HCH2  0   0.209  -5.4907  -0.1517  -1.3175
 6SV  H2   H  HCH2  0   0.228  -6.4462   0.1640   0.1184
 6SV  H3   H  HCH2  0   0.213  -4.8797  -1.1466   1.5031
 6SV  H4   H  HCH2  0   0.231  -5.4464  -2.1281   0.1670
 6SV  H5   H  HCH2  0   0.237  -2.9829  -2.3623   0.4880
 6SV  H6   H  HCH2  0   0.213  -3.3741  -1.7061  -1.0946
 6SV  H7   H  HCH1  0   0.229  -2.4900  -0.1178   1.3449
 6SV  H8   H  HCH2  0   0.232  -2.4984   1.8522  -0.1355
 6SV  H9   H  HCH2  0   0.208  -3.0770   0.8701  -1.4739
 6SV  H10  H  HCH2  0   0.230  -4.9624   2.1013  -0.4464
 6SV  H11  H  HCH2  0   0.212  -4.5816   1.4337   1.1279
 6SV  H12  H  HNH1  0   0.379  -1.0861  -0.9698  -1.0908
 6SV  H13  H  HNH1  0   0.385   0.9849  -0.4025  -1.3422
 6SV  H14  H  HCH2  0   0.223   2.1087   1.8340  -0.4904
 6SV  H15  H  HCH2  0   0.235   2.3901   0.8344   0.9297
 6SV  H16  H  HCH1  0   0.232   3.2708   0.1994  -1.9212
 6SV  H17  H  HCH2  0   0.248   5.4108   0.9664  -1.3455
 6SV  H18  H  HCH2  0   0.252   4.5249   2.0264  -0.2539
 6SV  H19  H  HCH2  0   0.250   6.3702   0.3051   0.7824
 6SV  H20  H  HCH2  0   0.238   4.8219   0.4701   1.6082
 6SV  H21  H  HCH2  0   0.202   5.6670  -1.6691  -0.3897
 6SV  H22  H  HCH2  0   0.225   4.7941  -1.9017   1.1300

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
 6SV  O1   C7   double  1.228  0.020  1.228
 6SV  C5   C6   single  1.525  0.020  1.525
 6SV  C5   C4   single  1.530  0.020  1.530
 6SV  C7   N2   single  1.360  0.020  1.360
 6SV  C7   N1   single  1.362  0.020  1.362
 6SV  N2   C8   single  1.443  0.020  1.443
 6SV  C8   C9   single  1.521  0.020  1.521
 6SV  C6   C1   single  1.525  0.020  1.525
 6SV  C1   C2   single  1.525  0.020  1.525
 6SV  N1   C4   single  1.450  0.020  1.450
 6SV  O2   C9   single  1.422  0.020  1.422
 6SV  O2   C12  single  1.420  0.020  1.420
 6SV  C4   C3   single  1.526  0.020  1.526
 6SV  C9   C10  single  1.531  0.020  1.531
 6SV  C2   C3   single  1.526  0.020  1.526
 6SV  C12  C11  single  1.519  0.020  1.519
 6SV  C10  C11  single  1.525  0.020  1.525
 6SV  C1   H1   single  0.970  0.020  1.090
 6SV  C1   H2   single  0.970  0.020  1.090
 6SV  C2   H3   single  0.970  0.020  1.090
 6SV  C2   H4   single  0.970  0.020  1.090
 6SV  C3   H5   single  0.970  0.020  1.090
 6SV  C3   H6   single  0.970  0.020  1.090
 6SV  C4   H7   single  0.970  0.020  1.090
 6SV  C5   H8   single  0.970  0.020  1.090
 6SV  C5   H9   single  0.970  0.020  1.090
 6SV  C6   H10  single  0.970  0.020  1.090
 6SV  C6   H11  single  0.970  0.020  1.090
 6SV  N1   H12  single  0.890  0.020  1.040
 6SV  N2   H13  single  0.890  0.020  1.040
 6SV  C8   H14  single  0.970  0.020  1.090
 6SV  C8   H15  single  0.970  0.020  1.090
 6SV  C9   H16  single  0.970  0.020  1.090
 6SV  C10  H17  single  0.970  0.020  1.090
 6SV  C10  H18  single  0.970  0.020  1.090
 6SV  C11  H19  single  0.970  0.020  1.090
 6SV  C11  H20  single  0.970  0.020  1.090
 6SV  C12  H21  single  0.970  0.020  1.090
 6SV  C12  H22  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
 6SV  H2   C1   H1   106.50  3.000
 6SV  H2   C1   C6   110.39  3.000
 6SV  H1   C1   C6   109.27  3.000
 6SV  H2   C1   C2   110.24  3.000
 6SV  H1   C1   C2   109.32  3.000
 6SV  C6   C1   C2   111.00  3.000
 6SV  H4   C2   H3   106.41  3.000
 6SV  H4   C2   C3   109.72  3.000
 6SV  H3   C2   C3   109.34  3.000
 6SV  H4   C2   C1   110.41  3.000
 6SV  H3   C2   C1   109.21  3.000
 6SV  C3   C2   C1   111.61  3.000
 6SV  H6   C3   H5   106.75  3.000
 6SV  H6   C3   C4   109.17  3.000
 6SV  H5   C3   C4   109.69  3.000
 6SV  H6   C3   C2   109.20  3.000
 6SV  H5   C3   C2   110.47  3.000
 6SV  C4   C3   C2   111.44  3.000
 6SV  H7   C4   N1   107.59  3.000
 6SV  H7   C4   C5   108.55  3.000
 6SV  N1   C4   C5   112.18  3.000
 6SV  H7   C4   C3   108.11  3.000
 6SV  N1   C4   C3   109.44  3.000
 6SV  C5   C4   C3   110.83  3.000
 6SV  H9   C5   H8   106.86  3.000
 6SV  H9   C5   C6   109.63  3.000
 6SV  H8   C5   C6   110.40  3.000
 6SV  H9   C5   C4   108.63  3.000
 6SV  H8   C5   C4   109.53  3.000
 6SV  C6   C5   C4   111.66  3.000
 6SV  H11  C6   H10  106.41  3.000
 6SV  H11  C6   C5   109.38  3.000
 6SV  H10  C6   C5   109.93  3.000
 6SV  H11  C6   C1   109.31  3.000
 6SV  H10  C6   C1   110.51  3.000
 6SV  C5   C6   C1   111.18  3.000
 6SV  H12  N1   C7   117.97  3.000
 6SV  H12  N1   C4   115.72  3.000
 6SV  C7   N1   C4   122.01  3.000
 6SV  N2   C7   O1   122.35  3.000
 6SV  N2   C7   N1   114.84  3.000
 6SV  O1   C7   N1   122.77  3.000
 6SV  H13  N2   C8   116.64  3.000
 6SV  H13  N2   C7   118.09  3.000
 6SV  C8   N2   C7   121.66  3.000
 6SV  H15  C8   H14  107.00  3.000
 6SV  H15  C8   C9   109.81  3.000
 6SV  H14  C8   C9   108.08  3.000
 6SV  H15  C8   N2   109.38  3.000
 6SV  H14  C8   N2   111.52  3.000
 6SV  C9   C8   N2   110.96  3.000
 6SV  H16  C9   O2   108.70  3.000
 6SV  H16  C9   C10  110.81  3.000
 6SV  O2   C9   C10  106.22  3.000
 6SV  H16  C9   C8   108.80  3.000
 6SV  C10  C9   C8   111.86  3.000
 6SV  O2   C9   C8   110.40  3.000
 6SV  H18  C10  H17  107.59  3.000
 6SV  H18  C10  C11  113.46  3.000
 6SV  H17  C10  C11  110.38  3.000
 6SV  H18  C10  C9   112.57  3.000
 6SV  H17  C10  C9   110.31  3.000
 6SV  C11  C10  C9   102.51  3.000
 6SV  H20  C11  H19  107.80  3.000
 6SV  H20  C11  C12  111.05  3.000
 6SV  H19  C11  C12  112.49  3.000
 6SV  H20  C11  C10  111.03  3.000
 6SV  H19  C11  C10  113.13  3.000
 6SV  C12  C11  C10  101.32  3.000
 6SV  H22  C12  H21  107.72  3.000
 6SV  H22  C12  O2   109.02  3.000
 6SV  H21  C12  O2   110.35  3.000
 6SV  H22  C12  C11  113.21  3.000
 6SV  H21  C12  C11  110.57  3.000
 6SV  O2   C12  C11  105.96  3.000
 6SV  C12  O2   C9   110.54  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
 6SV  CONST_02  N2   C7   N1   C4   180.00   0.0  0
 6SV  CONST_03  C8   N2   C7   O1     0.00   0.0  0
 6SV  CONST_04  C8   N2   C7   N1   180.00   0.0  0
 6SV  CONST_05  H13  N2   C7   O1   180.00   0.0  0
 6SV  CONST_06  H12  N1   C7   O1   180.00   0.0  0
 6SV  Var_01    C4   C5   C6   C1   -55.60  30.0  1
 6SV  Var_02    C4   C3   C2   C1    55.31  30.0  1
 6SV  Var_03    C5   C6   C1   C2    55.36  30.0  1
 6SV  Var_04    C6   C1   C2   C3   -55.37  30.0  1
 6SV  Var_05    C11  C12  O2   C9    18.51  30.0  1
 6SV  Var_06    C12  C11  C10  C9    35.17  30.0  1
 6SV  Var_07    O2   C12  C11  C10  -33.59  30.0  1
 6SV  Var_08    C9   C8   N2   C7   166.87  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
 6SV  chir_01  C4  C5  N1  C3   positiv
 6SV  chir_02  C9  O2  C8  C10  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
 6SV  plan-1  C4   0.020
 6SV  plan-1  N1   0.020
 6SV  plan-1  C7   0.020
 6SV  plan-1  O1   0.020
 6SV  plan-1  N2   0.020
 6SV  plan-1  C8   0.020
 6SV  plan-1  H12  0.020
 6SV  plan-1  H13  0.020

