# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 23:41:09 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-{cis-4-[(2,6-difluorophenyl)methoxy]cyclohexyl}-N'-(3-phenylpropyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(F)c1CO[C@@H]2CC[C@@H](CC2)NC(=O)NCCCc3ccccc3
#
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
 K9V  K9V  N-{cis-4-[(2,6-difluorophenyl)methoxy]cyclohexyl}-N'-(3-phenylpropyl)urea  ligand  57  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_K9V
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
 K9V  C10  C  CR16  0  -0.274  -9.2280   2.2548  -1.1645
 K9V  C15  C  CH2   0  -0.465   1.2633  -2.8641  -1.6407
 K9V  C17  C  CH1   0   0.097   2.9829  -1.6074  -0.3029
 K9V  C20  C  CR6   0  -0.316   5.6155   0.8324   0.4054
 K9V  C21  C  CR6   0   0.552   5.3553   2.0205   1.0746
 K9V  C24  C  CR16  0  -0.231   7.0871   3.1738  -0.0737
 K9V  C26  C  CR6   0   0.550   6.6389   0.8855  -0.5318
 K9V  C28  C  CH2   0  -0.480   2.0634  -1.6808   0.9138
 K9V  O01  O  O     0  -0.554  -2.1254  -3.0229   0.8829
 K9V  C02  C  C     0   0.735  -1.8173  -2.0225   0.2395
 K9V  N03  N  NH1   0  -0.688  -2.6277  -0.9320   0.1438
 K9V  C04  C  CH2   0  -0.249  -3.8310  -0.7872   0.9286
 K9V  C05  C  CH2   0  -0.442  -4.9017  -0.0173   0.1703
 K9V  C06  C  CH2   0  -0.514  -6.1690   0.1458   1.0104
 K9V  C07  C  CR6   0   0.140  -7.2514   0.8823   0.2722
 K9V  C08  C  CR16  0  -0.308  -8.0449   0.2196  -0.6633
 K9V  C09  C  CR16  0  -0.240  -9.0240   0.8967  -1.3769
 K9V  C11  C  CR16  0  -0.240  -8.4450   2.9259  -0.2350
 K9V  C12  C  CR16  0  -0.318  -7.4649   2.2433   0.4752
 K9V  N13  N  NH1   0  -0.684  -0.6589  -1.9375  -0.4623
 K9V  C14  C  CH1   0  -0.080   0.3493  -2.9794  -0.4224
 K9V  C16  C  CH2   0  -0.481   2.1729  -1.6372  -1.5906
 K9V  O18  O  O2    0  -0.496   3.7684  -0.4298  -0.3242
 K9V  C19  C  CH2   0  -0.193   4.8059  -0.4104   0.6285
 K9V  F22  F  F     0  -0.305   4.3652   2.0347   1.9780
 K9V  C23  C  CR16  0  -0.419   6.0668   3.1860   0.8655
 K9V  C25  C  CR16  0  -0.420   7.3846   2.0199  -0.7842
 K9V  F27  F  F     0  -0.304   6.9211  -0.2292  -1.2198
 K9V  C29  C  CH2   0  -0.439   1.1881  -2.9289   0.8569
 K9V  H1   H  HCR6  0   0.252  -9.9936   2.7851  -1.7158
 K9V  H2   H  HCH2  0   0.239   1.8816  -3.7658  -1.6758
 K9V  H3   H  HCH2  0   0.249   0.6710  -2.8581  -2.5587
 K9V  H4   H  HCH1  0   0.195   3.6458  -2.4888  -0.2874
 K9V  H5   H  HCR6  0   0.281   7.6575   4.0746  -0.2542
 K9V  H6   H  HCH2  0   0.242   2.6431  -1.6895   1.8401
 K9V  H7   H  HCH2  0   0.222   1.4362  -0.7831   0.9430
 K9V  H8   H  HNH1  0   0.385  -2.2492  -0.0868  -0.2540
 K9V  H9   H  HCH2  0   0.240  -4.2032  -1.7810   1.1743
 K9V  H10  H  HCH2  0   0.219  -3.6228  -0.2840   1.8808
 K9V  H11  H  HCH2  0   0.231  -4.5248   0.9704  -0.1137
 K9V  H12  H  HCH2  0   0.233  -5.1380  -0.5432  -0.7587
 K9V  H13  H  HCH2  0   0.242  -6.5319  -0.8438   1.3031
 K9V  H14  H  HCH2  0   0.243  -5.9235   0.6742   1.9353
 K9V  H15  H  HCR6  0   0.245  -7.8953  -0.8408  -0.8335
 K9V  H16  H  HCR6  0   0.252  -9.6304   0.3619  -2.0970
 K9V  H17  H  HCR6  0   0.253  -8.5990   3.9828  -0.0582
 K9V  H18  H  HCR6  0   0.245  -6.8612   2.7764   1.2008
 K9V  H19  H  HNH1  0   0.388  -0.4385  -1.0797  -0.9418
 K9V  H20  H  HCH1  0   0.250  -0.1642  -3.9419  -0.4679
 K9V  H21  H  HCH2  0   0.247   2.8439  -1.6459  -2.4527
 K9V  H22  H  HCH2  0   0.223   1.5859  -0.7147  -1.6650
 K9V  H23  H  HCH2  0   0.226   5.4409  -1.2984   0.5293
 K9V  H24  H  HCH2  0   0.228   4.4197  -0.4202   1.6517
 K9V  H25  H  HCR6  0   0.285   5.8263   4.0804   1.4241
 K9V  H26  H  HCR6  0   0.285   8.1763   2.0010  -1.5205
 K9V  H27  H  HCH2  0   0.224   1.8190  -3.8237   0.8898
 K9V  H28  H  HCH2  0   0.242   0.5380  -2.9769   1.7321

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
 K9V  C24  C25  aromatic  1.387  0.020  1.387
 K9V  C24  C23  aromatic  1.387  0.020  1.387
 K9V  C25  C26  aromatic  1.381  0.020  1.381
 K9V  C23  C21  aromatic  1.381  0.020  1.381
 K9V  C26  F27  single    1.340  0.020  1.340
 K9V  C26  C20  aromatic  1.389  0.020  1.389
 K9V  C21  C20  aromatic  1.388  0.020  1.388
 K9V  C21  F22  single    1.340  0.020  1.340
 K9V  C20  C19  single    1.500  0.020  1.500
 K9V  C19  O18  single    1.409  0.020  1.409
 K9V  O18  C17  single    1.416  0.020  1.416
 K9V  C28  C17  single    1.527  0.020  1.527
 K9V  C28  C29  single    1.526  0.020  1.526
 K9V  C17  C16  single    1.522  0.020  1.522
 K9V  C16  C15  single    1.528  0.020  1.528
 K9V  C29  C14  single    1.531  0.020  1.531
 K9V  C15  C14  single    1.527  0.020  1.527
 K9V  C14  N13  single    1.450  0.020  1.450
 K9V  N13  C02  single    1.357  0.020  1.357
 K9V  C02  O01  double    1.229  0.020  1.229
 K9V  C02  N03  single    1.362  0.020  1.362
 K9V  C12  C11  aromatic  1.390  0.020  1.390
 K9V  C12  C07  aromatic  1.393  0.020  1.393
 K9V  N03  C04  single    1.444  0.020  1.444
 K9V  C06  C07  single    1.503  0.020  1.503
 K9V  C06  C05  single    1.529  0.020  1.529
 K9V  C11  C10  aromatic  1.388  0.020  1.388
 K9V  C07  C08  aromatic  1.394  0.020  1.394
 K9V  C04  C05  single    1.521  0.020  1.521
 K9V  C10  C09  aromatic  1.390  0.020  1.390
 K9V  C08  C09  aromatic  1.388  0.020  1.388
 K9V  C10  H1   single    0.930  0.020  1.080
 K9V  C15  H2   single    0.970  0.020  1.090
 K9V  C15  H3   single    0.970  0.020  1.090
 K9V  C17  H4   single    0.970  0.020  1.090
 K9V  C24  H5   single    0.930  0.020  1.080
 K9V  C28  H6   single    0.970  0.020  1.090
 K9V  C28  H7   single    0.970  0.020  1.090
 K9V  N03  H8   single    0.860  0.020  1.020
 K9V  C04  H9   single    0.970  0.020  1.090
 K9V  C04  H10  single    0.970  0.020  1.090
 K9V  C05  H11  single    0.970  0.020  1.090
 K9V  C05  H12  single    0.970  0.020  1.090
 K9V  C06  H13  single    0.970  0.020  1.090
 K9V  C06  H14  single    0.970  0.020  1.090
 K9V  C08  H15  single    0.930  0.020  1.080
 K9V  C09  H16  single    0.930  0.020  1.080
 K9V  C11  H17  single    0.930  0.020  1.080
 K9V  C12  H18  single    0.930  0.020  1.080
 K9V  N13  H19  single    0.860  0.020  1.020
 K9V  C14  H20  single    0.970  0.020  1.090
 K9V  C16  H21  single    0.970  0.020  1.090
 K9V  C16  H22  single    0.970  0.020  1.090
 K9V  C19  H23  single    0.970  0.020  1.090
 K9V  C19  H24  single    0.970  0.020  1.090
 K9V  C23  H25  single    0.930  0.020  1.080
 K9V  C25  H26  single    0.930  0.020  1.080
 K9V  C29  H27  single    0.970  0.020  1.090
 K9V  C29  H28  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
 K9V  H1   C10  C11  120.21  3.000
 K9V  H1   C10  C09  120.32  3.000
 K9V  C11  C10  C09  119.47  3.000
 K9V  H3   C15  H2   106.51  3.000
 K9V  H3   C15  C16  110.23  3.000
 K9V  H2   C15  C16  109.05  3.000
 K9V  H3   C15  C14  110.25  3.000
 K9V  H2   C15  C14  107.56  3.000
 K9V  C16  C15  C14  112.99  3.000
 K9V  H4   C17  O18  109.36  3.000
 K9V  H4   C17  C16  108.43  3.000
 K9V  O18  C17  C16  107.39  3.000
 K9V  H4   C17  C28  108.20  3.000
 K9V  C16  C17  C28  110.66  3.000
 K9V  O18  C17  C28  112.71  3.000
 K9V  C19  C20  C26  122.00  3.000
 K9V  C19  C20  C21  122.43  3.000
 K9V  C26  C20  C21  115.51  3.000
 K9V  C23  C21  F22  118.26  3.000
 K9V  F22  C21  C20  118.20  3.000
 K9V  C23  C21  C20  123.54  3.000
 K9V  H5   C24  C25  119.62  3.000
 K9V  H5   C24  C23  119.59  3.000
 K9V  C25  C24  C23  120.79  3.000
 K9V  F27  C26  C25  118.41  3.000
 K9V  F27  C26  C20  118.03  3.000
 K9V  C25  C26  C20  123.56  3.000
 K9V  H7   C28  H6   106.72  3.000
 K9V  H7   C28  C29  110.06  3.000
 K9V  H6   C28  C29  109.24  3.000
 K9V  H7   C28  C17  109.07  3.000
 K9V  H6   C28  C17  110.88  3.000
 K9V  C29  C28  C17  110.80  3.000
 K9V  N13  C02  N03  114.92  3.000
 K9V  N03  C02  O01  122.65  3.000
 K9V  N13  C02  O01  122.40  3.000
 K9V  H8   N03  C04  116.32  3.000
 K9V  H8   N03  C02  118.40  3.000
 K9V  C04  N03  C02  122.54  3.000
 K9V  H10  C04  H9   106.72  3.000
 K9V  H10  C04  C05  109.52  3.000
 K9V  H9   C04  C05  109.49  3.000
 K9V  H10  C04  N03  111.08  3.000
 K9V  H9   C04  N03  108.41  3.000
 K9V  C05  C04  N03  111.49  3.000
 K9V  H12  C05  H11  106.73  3.000
 K9V  H12  C05  C06  109.81  3.000
 K9V  H11  C05  C06  109.37  3.000
 K9V  H12  C05  C04  109.41  3.000
 K9V  H11  C05  C04  110.10  3.000
 K9V  C06  C05  C04  111.31  3.000
 K9V  H14  C06  H13  106.58  3.000
 K9V  H14  C06  C07  109.91  3.000
 K9V  H13  C06  C07  109.62  3.000
 K9V  H14  C06  C05  109.28  3.000
 K9V  H13  C06  C05  108.99  3.000
 K9V  C07  C06  C05  112.29  3.000
 K9V  C12  C07  C08  118.37  3.000
 K9V  C08  C07  C06  120.43  3.000
 K9V  C12  C07  C06  121.18  3.000
 K9V  H15  C08  C09  119.59  3.000
 K9V  H15  C08  C07  119.44  3.000
 K9V  C09  C08  C07  120.97  3.000
 K9V  H16  C09  C08  119.74  3.000
 K9V  H16  C09  C10  120.14  3.000
 K9V  C08  C09  C10  120.12  3.000
 K9V  H17  C11  C12  119.76  3.000
 K9V  H17  C11  C10  120.07  3.000
 K9V  C12  C11  C10  120.17  3.000
 K9V  H18  C12  C11  119.56  3.000
 K9V  H18  C12  C07  119.53  3.000
 K9V  C11  C12  C07  120.91  3.000
 K9V  H19  N13  C14  118.22  3.000
 K9V  H19  N13  C02  119.10  3.000
 K9V  C14  N13  C02  122.29  3.000
 K9V  H20  C14  C29  108.76  3.000
 K9V  H20  C14  N13  107.77  3.000
 K9V  C29  C14  N13  112.35  3.000
 K9V  H20  C14  C15  108.34  3.000
 K9V  N13  C14  C15  109.87  3.000
 K9V  C29  C14  C15  109.65  3.000
 K9V  H22  C16  H21  106.38  3.000
 K9V  H22  C16  C17  109.03  3.000
 K9V  H21  C16  C17  109.94  3.000
 K9V  H22  C16  C15  110.78  3.000
 K9V  H21  C16  C15  109.47  3.000
 K9V  C17  C16  C15  111.12  3.000
 K9V  C19  O18  C17  114.20  3.000
 K9V  H24  C19  H23  106.37  3.000
 K9V  H24  C19  O18  111.87  3.000
 K9V  H23  C19  O18  110.75  3.000
 K9V  H24  C19  C20  109.70  3.000
 K9V  H23  C19  C20  110.18  3.000
 K9V  O18  C19  C20  107.96  3.000
 K9V  H25  C23  C24  121.37  3.000
 K9V  H25  C23  C21  120.33  3.000
 K9V  C24  C23  C21  118.30  3.000
 K9V  H26  C25  C26  120.37  3.000
 K9V  H26  C25  C24  121.35  3.000
 K9V  C26  C25  C24  118.29  3.000
 K9V  H28  C29  H27  106.45  3.000
 K9V  H28  C29  C14  110.02  3.000
 K9V  H27  C29  C14  108.29  3.000
 K9V  H28  C29  C28  110.36  3.000
 K9V  H27  C29  C28  109.68  3.000
 K9V  C14  C29  C28  111.87  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
 K9V  CONST_01  C07  C12  C11  C10     0.00   0.0  0
 K9V  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 K9V  CONST_03  C24  C25  C26  C20     0.00   0.0  0
 K9V  CONST_04  C24  C23  C21  C20     0.00   0.0  0
 K9V  CONST_05  C25  C24  C23  C21     0.00   0.0  0
 K9V  CONST_06  C25  C26  C20  C21     0.00   0.0  0
 K9V  CONST_07  C23  C24  C25  C26     0.00   0.0  0
 K9V  CONST_08  C23  C21  C20  C26     0.00   0.0  0
 K9V  CONST_09  C11  C12  C07  C08     0.00   0.0  0
 K9V  CONST_10  C11  C10  C09  C08     0.00   0.0  0
 K9V  CONST_11  C12  C11  C10  C09     0.00   0.0  0
 K9V  CONST_12  C12  C07  C08  C09     0.00   0.0  0
 K9V  CONST_13  F27  C26  C20  C21   180.00   0.0  0
 K9V  CONST_14  F27  C26  C25  C24   180.00   0.0  0
 K9V  CONST_15  F22  C21  C23  C24   180.00   0.0  0
 K9V  CONST_16  F22  C21  C20  C26   180.00   0.0  0
 K9V  CONST_17  C11  C12  C07  C06   180.00   0.0  0
 K9V  CONST_18  C09  C08  C07  C06   180.00   0.0  0
 K9V  CONST_19  C25  C26  C20  C19   180.00   0.0  0
 K9V  CONST_20  C23  C21  C20  C19   180.00   0.0  0
 K9V  CONST_21  H18  C12  C11  C10   180.00   0.0  0
 K9V  CONST_22  H15  C08  C09  C10   180.00   0.0  0
 K9V  CONST_23  H26  C25  C26  C20   180.00   0.0  0
 K9V  CONST_24  H25  C23  C21  C20   180.00   0.0  0
 K9V  CONST_25  H5   C24  C23  C21   180.00   0.0  0
 K9V  CONST_26  H17  C11  C12  C07   180.00   0.0  0
 K9V  CONST_27  H16  C09  C08  C07   180.00   0.0  0
 K9V  CONST_28  H1   C10  C09  C08   180.00   0.0  0
 K9V  CONST_29  C14  N13  C02  O01     0.00   0.0  0
 K9V  CONST_30  C14  N13  C02  N03   180.00   0.0  0
 K9V  CONST_31  C04  N03  C02  O01     0.00   0.0  0
 K9V  CONST_32  N13  C02  N03  C04   180.00   0.0  0
 K9V  CONST_33  H19  N13  C02  O01   180.00   0.0  0
 K9V  CONST_34  H8   N03  C02  O01   180.00   0.0  0
 K9V  Var_01    C14  C29  C28  C17   -57.45  30.0  1
 K9V  Var_02    C14  C15  C16  C17    54.74  30.0  1
 K9V  Var_03    C20  C19  O18  C17   175.13  30.0  2
 K9V  Var_04    O18  C19  C20  C21    92.46  30.0  2
 K9V  Var_05    C12  C07  C06  C05   -98.36  30.0  2
 K9V  Var_06    C07  C06  C05  C04  -178.95  30.0  2
 K9V  Var_07    C05  C04  N03  C02  -147.56  30.0  3
 K9V  Var_08    C06  C05  C04  N03  -179.43  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
 K9V  chir_01  C17  O18  C28  C16  negativ
 K9V  chir_02  C14  N13  C29  C15  positiv

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
 K9V  plan-1  C20  0.020
 K9V  plan-1  C21  0.020
 K9V  plan-1  C24  0.020
 K9V  plan-1  C26  0.020
 K9V  plan-1  C19  0.020
 K9V  plan-1  F22  0.020
 K9V  plan-1  C23  0.020
 K9V  plan-1  C25  0.020
 K9V  plan-1  F27  0.020
 K9V  plan-1  H5   0.020
 K9V  plan-1  H25  0.020
 K9V  plan-1  H26  0.020
 K9V  plan-2  C10  0.020
 K9V  plan-2  C06  0.020
 K9V  plan-2  C07  0.020
 K9V  plan-2  C08  0.020
 K9V  plan-2  C09  0.020
 K9V  plan-2  C11  0.020
 K9V  plan-2  C12  0.020
 K9V  plan-2  H1   0.020
 K9V  plan-2  H15  0.020
 K9V  plan-2  H16  0.020
 K9V  plan-2  H17  0.020
 K9V  plan-2  H18  0.020
 K9V  plan-3  O01  0.020
 K9V  plan-3  C02  0.020
 K9V  plan-3  N03  0.020
 K9V  plan-3  C04  0.020
 K9V  plan-3  N13  0.020
 K9V  plan-3  C14  0.020
 K9V  plan-3  H8   0.020
 K9V  plan-3  H19  0.020

