# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 01:21:55 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 1-cyclohexyl-3-(pyridin-3-ylmethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)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
 9VW  9VW  1-cyclohexyl-3-(pyridin-3-ylmethyl)urea  ligand  36  17  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9VW
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
 9VW  C13  C  CR16  0  -0.071   5.0379   1.4110   0.0824
 9VW  C20  C  CH1   0  -0.056  -2.5165   0.1859  -0.0564
 9VW  C22  C  CH2   0  -0.437  -3.1477   1.2642  -0.9325
 9VW  C28  C  CH2   0  -0.431  -5.4487   0.5033  -0.2319
 9VW  O01  O  O     0  -0.550  -0.2468  -0.6386   1.3981
 9VW  C02  C  C     0   0.748  -0.2214  -0.6755   0.1709
 9VW  N03  N  NH1   0  -0.671   0.8303  -1.1939  -0.5245
 9VW  C05  C  CH2   0  -0.386   2.0605  -1.5990   0.1114
 9VW  C08  C  CR6   0   0.030   3.1028  -0.5102   0.1454
 9VW  C09  C  CR16  0  -0.182   2.9590   0.6220   0.9423
 9VW  C11  C  CR16  0  -0.318   3.9404   1.5982   0.9122
 9VW  N15  N  N     0  -0.401   5.1929   0.3380  -0.6819
 9VW  C16  C  CR16  0  -0.104   4.2444  -0.5917  -0.6429
 9VW  N18  N  NH1   0  -0.684  -1.2311  -0.2000  -0.6044
 9VW  C25  C  CH2   0  -0.437  -4.5080   1.6933  -0.3904
 9VW  C31  C  CH2   0  -0.439  -4.8198  -0.5776   0.6406
 9VW  C34  C  CH2   0  -0.425  -3.4605  -1.0077   0.0974
 9VW  H1   H  HCR6  0   0.263   5.8220   2.1585   0.0363
 9VW  H2   H  HCH1  0   0.232  -2.3309   0.6141   0.9321
 9VW  H3   H  HCH2  0   0.236  -2.4750   2.1226  -0.9999
 9VW  H4   H  HCH2  0   0.213  -3.2692   0.8751  -1.9509
 9VW  H5   H  HCH2  0   0.229  -6.4003   0.8275   0.1960
 9VW  H6   H  HCH2  0   0.210  -5.6774   0.0872  -1.2190
 9VW  H7   H  HNH1  0   0.390   0.8629  -1.0619  -1.5227
 9VW  H8   H  HCH2  0   0.267   1.8339  -1.9344   1.1225
 9VW  H9   H  HCH2  0   0.266   2.4546  -2.4636  -0.4251
 9VW  H10  H  HCR6  0   0.269   2.0919   0.7350   1.5811
 9VW  H11  H  HCR6  0   0.270   3.8636   2.4887   1.5211
 9VW  H12  H  HCR6  0   0.257   4.3975  -1.4604  -1.2769
 9VW  H13  H  HNH1  0   0.382  -1.2171  -0.4197  -1.5891
 9VW  H14  H  HCH2  0   0.213  -4.3727   2.1780   0.5828
 9VW  H15  H  HCH2  0   0.232  -4.9493   2.4433  -1.0507
 9VW  H16  H  HCH2  0   0.212  -4.6976  -0.1938   1.6594
 9VW  H17  H  HCH2  0   0.230  -5.4831  -1.4424   0.7139
 9VW  H18  H  HCH2  0   0.208  -3.5896  -1.4814  -0.8830
 9VW  H19  H  HCH2  0   0.232  -3.0041  -1.7528   0.7534

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
 9VW  O01  C02  double    1.228  0.020  1.228
 9VW  C25  C28  single    1.525  0.020  1.525
 9VW  C25  C22  single    1.526  0.020  1.526
 9VW  C31  C28  single    1.525  0.020  1.525
 9VW  C31  C34  single    1.526  0.020  1.526
 9VW  C20  C22  single    1.526  0.020  1.526
 9VW  C20  C34  single    1.530  0.020  1.530
 9VW  C20  N18  single    1.450  0.020  1.450
 9VW  C02  N18  single    1.359  0.020  1.359
 9VW  C02  N03  single    1.363  0.020  1.363
 9VW  C05  N03  single    1.443  0.020  1.443
 9VW  C05  C08  single    1.508  0.020  1.508
 9VW  C08  C09  aromatic  1.392  0.020  1.392
 9VW  C08  C16  aromatic  1.390  0.020  1.390
 9VW  C09  C11  aromatic  1.385  0.020  1.385
 9VW  C16  N15  aromatic  1.329  0.020  1.329
 9VW  C11  C13  aromatic  1.389  0.020  1.389
 9VW  C13  N15  aromatic  1.326  0.020  1.326
 9VW  C13  H1   single    0.930  0.020  1.080
 9VW  C20  H2   single    0.970  0.020  1.090
 9VW  C22  H3   single    0.970  0.020  1.090
 9VW  C22  H4   single    0.970  0.020  1.090
 9VW  C28  H5   single    0.970  0.020  1.090
 9VW  C28  H6   single    0.970  0.020  1.090
 9VW  N03  H7   single    0.860  0.020  1.020
 9VW  C05  H8   single    0.970  0.020  1.090
 9VW  C05  H9   single    0.970  0.020  1.090
 9VW  C09  H10  single    0.930  0.020  1.080
 9VW  C11  H11  single    0.930  0.020  1.080
 9VW  C16  H12  single    0.930  0.020  1.080
 9VW  N18  H13  single    0.890  0.020  1.040
 9VW  C25  H14  single    0.970  0.020  1.090
 9VW  C25  H15  single    0.970  0.020  1.090
 9VW  C31  H16  single    0.970  0.020  1.090
 9VW  C31  H17  single    0.970  0.020  1.090
 9VW  C34  H18  single    0.970  0.020  1.090
 9VW  C34  H19  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
 9VW  H1   C13  N15  116.66  3.000
 9VW  H1   C13  C11  120.26  3.000
 9VW  N15  C13  C11  123.08  3.000
 9VW  H2   C20  C34  108.64  3.000
 9VW  H2   C20  N18  107.19  3.000
 9VW  C34  C20  N18  112.18  3.000
 9VW  H2   C20  C22  108.22  3.000
 9VW  N18  C20  C22  109.74  3.000
 9VW  C34  C20  C22  110.72  3.000
 9VW  H4   C22  H3   106.83  3.000
 9VW  H4   C22  C25  109.32  3.000
 9VW  H3   C22  C25  110.48  3.000
 9VW  H4   C22  C20  109.16  3.000
 9VW  H3   C22  C20  109.63  3.000
 9VW  C25  C22  C20  111.31  3.000
 9VW  H6   C28  H5   106.49  3.000
 9VW  H6   C28  C31  109.42  3.000
 9VW  H5   C28  C31  110.21  3.000
 9VW  H6   C28  C25  109.36  3.000
 9VW  H5   C28  C25  110.26  3.000
 9VW  C31  C28  C25  110.99  3.000
 9VW  N18  C02  N03  114.54  3.000
 9VW  N03  C02  O01  122.49  3.000
 9VW  N18  C02  O01  122.97  3.000
 9VW  H7   N03  C05  116.47  3.000
 9VW  H7   N03  C02  118.73  3.000
 9VW  C05  N03  C02  122.67  3.000
 9VW  H9   C05  H8   106.70  3.000
 9VW  H9   C05  C08  109.49  3.000
 9VW  H8   C05  C08  110.20  3.000
 9VW  H9   C05  N03  108.29  3.000
 9VW  H8   C05  N03  108.55  3.000
 9VW  C08  C05  N03  113.37  3.000
 9VW  C16  C08  C09  117.21  3.000
 9VW  C16  C08  C05  120.85  3.000
 9VW  C09  C08  C05  121.93  3.000
 9VW  H10  C09  C11  120.45  3.000
 9VW  H10  C09  C08  120.35  3.000
 9VW  C11  C09  C08  119.20  3.000
 9VW  H11  C11  C09  121.19  3.000
 9VW  H11  C11  C13  120.24  3.000
 9VW  C09  C11  C13  118.56  3.000
 9VW  C16  N15  C13  117.75  3.000
 9VW  H12  C16  N15  116.22  3.000
 9VW  H12  C16  C08  119.59  3.000
 9VW  N15  C16  C08  124.19  3.000
 9VW  H13  N18  C02  118.05  3.000
 9VW  H13  N18  C20  116.05  3.000
 9VW  C02  N18  C20  122.43  3.000
 9VW  H15  C25  H14  106.44  3.000
 9VW  H15  C25  C28  110.45  3.000
 9VW  H14  C25  C28  109.21  3.000
 9VW  H15  C25  C22  109.78  3.000
 9VW  H14  C25  C22  109.26  3.000
 9VW  C28  C25  C22  111.55  3.000
 9VW  H17  C31  H16  106.42  3.000
 9VW  H17  C31  C34  109.98  3.000
 9VW  H16  C31  C34  109.30  3.000
 9VW  H17  C31  C28  110.44  3.000
 9VW  H16  C31  C28  109.26  3.000
 9VW  C34  C31  C28  111.32  3.000
 9VW  H19  C34  H18  106.94  3.000
 9VW  H19  C34  C31  110.53  3.000
 9VW  H18  C34  C31  109.59  3.000
 9VW  H19  C34  C20  109.55  3.000
 9VW  H18  C34  C20  108.66  3.000
 9VW  C31  C34  C20  111.45  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
 9VW  CONST_01  C08  C09  C11  C13    0.00   0.0  0
 9VW  CONST_02  C08  C16  N15  C13    0.00   0.0  0
 9VW  CONST_03  N15  C16  C08  C09    0.00   0.0  0
 9VW  CONST_04  N15  C13  C11  C09    0.00   0.0  0
 9VW  CONST_05  C16  C08  C09  C11    0.00   0.0  0
 9VW  CONST_06  C16  N15  C13  C11    0.00   0.0  0
 9VW  CONST_07  C11  C09  C08  C05  180.00   0.0  0
 9VW  CONST_08  N15  C16  C08  C05  180.00   0.0  0
 9VW  CONST_09  H10  C09  C11  C13  180.00   0.0  0
 9VW  CONST_10  H12  C16  N15  C13  180.00   0.0  0
 9VW  CONST_11  H11  C11  C09  C08  180.00   0.0  0
 9VW  CONST_12  H1   C13  C11  C09  180.00   0.0  0
 9VW  CONST_13  O01  C02  N18  C20    0.00   0.0  0
 9VW  CONST_14  N03  C02  N18  C20  180.00   0.0  0
 9VW  CONST_15  C05  N03  C02  O01    0.00   0.0  0
 9VW  CONST_16  N18  C02  N03  C05  180.00   0.0  0
 9VW  CONST_17  H13  N18  C02  O01  180.00   0.0  0
 9VW  CONST_18  H7   N03  C02  O01  180.00   0.0  0
 9VW  Var_01    C28  C25  C22  C20  -55.61  30.0  1
 9VW  Var_02    C28  C31  C34  C20   55.66  30.0  1
 9VW  Var_03    C31  C28  C25  C22   55.22  30.0  1
 9VW  Var_04    C34  C31  C28  C25  -55.17  30.0  1
 9VW  Var_05    C09  C08  C05  N03   69.41  30.0  2
 9VW  Var_06    C08  C05  N03  C02  -92.45  30.0  1

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
 9VW  chir_01  C20  C22  C34  N18  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
 9VW  plan-1  C13  0.020
 9VW  plan-1  C05  0.020
 9VW  plan-1  C08  0.020
 9VW  plan-1  C09  0.020
 9VW  plan-1  C11  0.020
 9VW  plan-1  N15  0.020
 9VW  plan-1  C16  0.020
 9VW  plan-1  H1   0.020
 9VW  plan-1  H10  0.020
 9VW  plan-1  H11  0.020
 9VW  plan-1  H12  0.020
 9VW  plan-2  C20  0.020
 9VW  plan-2  O01  0.020
 9VW  plan-2  C02  0.020
 9VW  plan-2  N03  0.020
 9VW  plan-2  C05  0.020
 9VW  plan-2  N18  0.020
 9VW  plan-2  H7   0.020
 9VW  plan-2  H13  0.020

