# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:58:35 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 1-cyclohexyl-3-methyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=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
 6NX  6NX  1-cyclohexyl-3-methyl-urea  ligand  27  11  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6NX
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
 6NX  C1    C  CH3   0  -0.506   4.2907  -0.1082  -0.0275
 6NX  N2    N  NH1   0  -0.673   2.9985   0.3621  -0.4610
 6NX  C3    C  C     0   0.726   1.8635  -0.0014   0.1888
 6NX  O4    O  O     0  -0.552   1.8702  -0.8407   1.0857
 6NX  N5    N  NH1   0  -0.684   0.7322   0.6399  -0.2165
 6NX  C6    C  CH1   0  -0.048  -0.5863   0.2135   0.2067
 6NX  C7    C  CH2   0  -0.440  -1.5620   1.3830   0.1138
 6NX  C8    C  CH2   0  -0.437  -2.9608   0.9739   0.5653
 6NX  C9    C  CH2   0  -0.429  -3.4765  -0.2296  -0.2171
 6NX  C10   C  CH2   0  -0.439  -2.4977  -1.3963  -0.1376
 6NX  C11   C  CH2   0  -0.427  -1.1025  -0.9826  -0.5951
 6NX  H11C  H  HCH3  0   0.243   5.0410   0.2797  -0.7117
 6NX  H12C  H  HCH3  0   0.224   4.5474   0.2243   0.9809
 6NX  H13C  H  HCH3  0   0.232   4.3488  -1.1962  -0.0509
 6NX  H2    H  HNH1  0   0.391   2.9778   1.1492  -1.0867
 6NX  H5    H  HNH1  0   0.380   0.7721   1.1772  -1.0695
 6NX  H6    H  HCH1  0   0.228  -0.5104  -0.0816   1.2568
 6NX  H71C  H  HCH2  0   0.236  -1.1958   2.2178   0.7168
 6NX  H72C  H  HCH2  0   0.213  -1.6040   1.7377  -0.9236
 6NX  H111  H  HCH2  0   0.207  -1.1280  -0.7102  -1.6565
 6NX  H112  H  HCH2  0   0.232  -0.4044  -1.8179  -0.4994
 6NX  H81C  H  HCH2  0   0.213  -2.9370   0.7265   1.6320
 6NX  H82C  H  HCH2  0   0.231  -3.6457   1.8184   0.4602
 6NX  H91C  H  HCH2  0   0.228  -4.4572  -0.5305   0.1591
 6NX  H92C  H  HCH2  0   0.210  -3.6200   0.0529  -1.2656
 6NX  H101  H  HCH2  0   0.212  -2.4472  -1.7567   0.8960
 6NX  H102  H  HCH2  0   0.230  -2.8548  -2.2360  -0.7385

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
 6NX  C1   N2    single  1.442  0.020  1.442
 6NX  N2   C3    single  1.357  0.020  1.357
 6NX  C3   O4    double  1.228  0.020  1.228
 6NX  C3   N5    single  1.362  0.020  1.362
 6NX  N5   C6    single  1.449  0.020  1.449
 6NX  C6   C7    single  1.526  0.020  1.526
 6NX  C6   C11   single  1.530  0.020  1.530
 6NX  C7   C8    single  1.526  0.020  1.526
 6NX  C8   C9    single  1.525  0.020  1.525
 6NX  C9   C10   single  1.525  0.020  1.525
 6NX  C10  C11   single  1.525  0.020  1.525
 6NX  C1   H11C  single  0.970  0.020  1.090
 6NX  C1   H12C  single  0.970  0.020  1.090
 6NX  C1   H13C  single  0.970  0.020  1.090
 6NX  N2   H2    single  0.860  0.020  1.020
 6NX  N5   H5    single  0.890  0.020  1.040
 6NX  C6   H6    single  0.970  0.020  1.090
 6NX  C7   H71C  single  0.970  0.020  1.090
 6NX  C7   H72C  single  0.970  0.020  1.090
 6NX  C11  H111  single  0.970  0.020  1.090
 6NX  C11  H112  single  0.970  0.020  1.090
 6NX  C8   H81C  single  0.970  0.020  1.090
 6NX  C8   H82C  single  0.970  0.020  1.090
 6NX  C9   H91C  single  0.970  0.020  1.090
 6NX  C9   H92C  single  0.970  0.020  1.090
 6NX  C10  H101  single  0.970  0.020  1.090
 6NX  C10  H102  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
 6NX  H13C  C1   H12C  108.13  3.000
 6NX  H13C  C1   H11C  107.82  3.000
 6NX  H12C  C1   H11C  108.07  3.000
 6NX  H13C  C1   N2    111.53  3.000
 6NX  H12C  C1   N2    112.88  3.000
 6NX  H11C  C1   N2    108.24  3.000
 6NX  H2    N2   C3    119.36  3.000
 6NX  H2    N2   C1    117.43  3.000
 6NX  C3    N2   C1    121.20  3.000
 6NX  N5    C3   O4    122.92  3.000
 6NX  N5    C3   N2    115.21  3.000
 6NX  O4    C3   N2    121.87  3.000
 6NX  H5    N5   C6    116.09  3.000
 6NX  H5    N5   C3    117.99  3.000
 6NX  C6    N5   C3    122.03  3.000
 6NX  H6    C6   C11   108.41  3.000
 6NX  H6    C6   C7    108.04  3.000
 6NX  C11   C6   C7    110.59  3.000
 6NX  H6    C6   N5    107.26  3.000
 6NX  C11   C6   N5    112.59  3.000
 6NX  C7    C6   N5    109.78  3.000
 6NX  H72C  C7   H71C  106.71  3.000
 6NX  H72C  C7   C8    109.36  3.000
 6NX  H71C  C7   C8    110.41  3.000
 6NX  H72C  C7   C6    109.26  3.000
 6NX  H71C  C7   C6    109.73  3.000
 6NX  C8    C7   C6    111.26  3.000
 6NX  H82C  C8   H81C  106.38  3.000
 6NX  H82C  C8   C9    110.40  3.000
 6NX  H81C  C8   C9    109.19  3.000
 6NX  H82C  C8   C7    109.82  3.000
 6NX  H81C  C8   C7    109.20  3.000
 6NX  C9    C8   C7    111.70  3.000
 6NX  H92C  C9   H91C  106.44  3.000
 6NX  H92C  C9   C10   109.35  3.000
 6NX  H91C  C9   C10   110.33  3.000
 6NX  H92C  C9   C8    109.38  3.000
 6NX  H91C  C9   C8    110.13  3.000
 6NX  C10   C9   C8    111.09  3.000
 6NX  H102  C10  H101  106.32  3.000
 6NX  H102  C10  C11   110.03  3.000
 6NX  H101  C10  C11   109.27  3.000
 6NX  H102  C10  C9    110.46  3.000
 6NX  H101  C10  C9    109.29  3.000
 6NX  C11   C10  C9    111.34  3.000
 6NX  H112  C11  H111  106.83  3.000
 6NX  H112  C11  C10   110.53  3.000
 6NX  H111  C11  C10   109.67  3.000
 6NX  H112  C11  C6    109.65  3.000
 6NX  H111  C11  C6    108.73  3.000
 6NX  C10   C11  C6    111.31  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
 6NX  CONST_01  C6    N5   C3   O4    0.00   0.0  0
 6NX  CONST_02  C6    N5   C3   N2  180.00   0.0  0
 6NX  CONST_03  O4    C3   N2   C1    0.00   0.0  0
 6NX  CONST_04  N5    C3   N2   C1  180.00   0.0  0
 6NX  CONST_05  H2    N2   C3   O4  180.00   0.0  0
 6NX  CONST_06  H5    N5   C3   O4  180.00   0.0  0
 6NX  Var_01    C9    C8   C7   C6  -55.42  30.0  1
 6NX  Var_02    C9    C10  C11  C6   55.90  30.0  1
 6NX  Var_03    C11   C10  C9   C8  -54.85  30.0  1
 6NX  Var_04    H11C  C1   N2   C3  178.04  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
 6NX  chir_01  C6  N5  C7  C11  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
 6NX  plan-1  C1  0.020
 6NX  plan-1  N2  0.020
 6NX  plan-1  C3  0.020
 6NX  plan-1  O4  0.020
 6NX  plan-1  N5  0.020
 6NX  plan-1  C6  0.020
 6NX  plan-1  H2  0.020
 6NX  plan-1  H5  0.020

