# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 14:27:52 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: (5~{S})-5-(cyclohexylmethyl)-3-(5-fluoranylpyridin-3-yl)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cncc(c1)N2C(=O)N[C@@H](CC3CCCCC3)C2=O
#
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
 SQ5  SQ5  "(5S)-5-(cyclohexylmethyl)-3-(5-fluoropyridin-3-yl)imidazolidine-2,4-dione"
  ligand  39  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SQ5
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
 SQ5  C4   C  CH1   0  -0.239  -2.9669  -0.1685  12.2581
 SQ5  C14  C  CR6   0   0.437  -0.1277  -2.4845  19.2418
 SQ5  C5   C  CH2   0  -0.415  -2.2099   0.5433  11.1353
 SQ5  C6   C  CH2   0  -0.430  -2.3520  -0.1814   9.8013
 SQ5  C11  C  CR6   0   0.263  -0.8943  -1.4493  17.2694
 SQ5  C7   C  CH2   0  -0.428  -3.8177  -0.3606   9.4225
 SQ5  C8   C  CH2   0  -0.427  -4.5826  -1.0717  10.5325
 SQ5  C9   C  CH2   0  -0.425  -4.4348  -0.3451  11.8661
 SQ5  C10  C  CR5   0   0.547  -2.3554  -1.1761  15.2986
 SQ5  C12  C  CR16  0  -0.072   0.3463  -1.7271  16.7062
 SQ5  C13  C  CR16  0  -0.198   1.0789  -2.7397  18.6158
 SQ5  N1   N  NR15  0  -0.671  -3.3135   0.7941  15.9691
 SQ5  N2   N  NR5   0  -0.679  -1.8708  -0.7698  16.5209
 SQ5  C3   C  CH2   0  -0.430  -2.8045   0.6129  13.5603
 SQ5  N3   N  N     0  -0.380   1.3007  -2.3654  17.3639
 SQ5  C1   C  CR5   0   0.700  -2.4515   0.4477  16.9357
 SQ5  C15  C  CR16  0  -0.311  -1.1491  -1.8418  18.5750
 SQ5  C2   C  CR15  0  -0.183  -3.3036  -0.0902  14.8293
 SQ5  O2   O  O     0  -0.409  -2.0618  -2.1958  14.7293
 SQ5  H1   H  HCH1  0   0.226  -2.5225  -1.1633  12.3769
 SQ5  H2   H  HCH2  0   0.226  -1.1533   0.6342  11.4029
 SQ5  H3   H  HCH2  0   0.207  -2.5944   1.5660  11.0366
 SQ5  H4   H  HCH2  0   0.208  -1.8742  -1.1645   9.8735
 SQ5  H5   H  HCH2  0   0.225  -1.8199   0.3663   9.0196
 SQ5  H6   H  HCH2  0   0.207  -4.2676   0.6225   9.2446
 SQ5  H7   H  HCH2  0   0.224  -3.9028  -0.9158   8.4852
 SQ5  H8   H  HCH2  0   0.225  -5.6400  -1.1578  10.2708
 SQ5  H9   H  HCH2  0   0.209  -4.2043  -2.0947  10.6352
 SQ5  H10  H  HCH2  0   0.208  -4.9016   0.6447  11.7940
 SQ5  H11  H  HCH2  0   0.230  -4.9831  -0.8903  12.6391
 SQ5  H12  H  HCR6  0   0.285   0.5690  -1.4148  15.6927
 SQ5  H13  H  HCR6  0   0.291   1.8771  -3.2518  19.1418
 SQ5  H14  H  HNR5  0   0.418  -3.8219   1.6640  15.9912
 SQ5  H15  H  HCH2  0   0.247  -1.7547   0.8856  13.7079
 SQ5  H16  H  HCH2  0   0.250  -3.3563   1.5550  13.4759
 SQ5  H17  H  HCR6  0   0.312  -2.1039  -1.6613  19.0506
 SQ5  H18  H  HCR5  0   0.308  -4.2934  -0.5281  14.6699
 SQ5  O1   O  O     0  -0.460  -2.1881   1.0138  17.9695
 SQ5  F1   F  F     0  -0.296  -0.3056  -2.8737  20.5071

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
 SQ5  C7   C6   single    1.524  0.020  1.524
 SQ5  C7   C8   single    1.524  0.020  1.524
 SQ5  C6   C5   single    1.525  0.020  1.525
 SQ5  C8   C9   single    1.526  0.020  1.526
 SQ5  C5   C4   single    1.530  0.020  1.530
 SQ5  C9   C4   single    1.530  0.020  1.530
 SQ5  C4   C3   single    1.527  0.020  1.527
 SQ5  C3   C2   single    1.534  0.020  1.534
 SQ5  O2   C10  double    1.204  0.020  1.204
 SQ5  C2   C10  single    1.516  0.020  1.516
 SQ5  C2   N1   single    1.443  0.020  1.443
 SQ5  C10  N2   single    1.376  0.020  1.376
 SQ5  N1   C1   single    1.341  0.020  1.341
 SQ5  N2   C1   single    1.411  0.020  1.411
 SQ5  N2   C11  single    1.406  0.020  1.406
 SQ5  C1   O1   double    1.208  0.020  1.208
 SQ5  C12  C11  aromatic  1.390  0.020  1.390
 SQ5  C12  N3   aromatic  1.323  0.020  1.323
 SQ5  C11  C15  aromatic  1.387  0.020  1.387
 SQ5  N3   C13  aromatic  1.325  0.020  1.325
 SQ5  C15  C14  aromatic  1.379  0.020  1.379
 SQ5  C13  C14  aromatic  1.383  0.020  1.383
 SQ5  C14  F1   single    1.336  0.020  1.336
 SQ5  C4   H1   single    0.970  0.020  1.090
 SQ5  C5   H2   single    0.970  0.020  1.090
 SQ5  C5   H3   single    0.970  0.020  1.090
 SQ5  C6   H4   single    0.970  0.020  1.090
 SQ5  C6   H5   single    0.970  0.020  1.090
 SQ5  C7   H6   single    0.970  0.020  1.090
 SQ5  C7   H7   single    0.970  0.020  1.090
 SQ5  C8   H8   single    0.970  0.020  1.090
 SQ5  C8   H9   single    0.970  0.020  1.090
 SQ5  C9   H10  single    0.970  0.020  1.090
 SQ5  C9   H11  single    0.970  0.020  1.090
 SQ5  C12  H12  single    0.930  0.020  1.080
 SQ5  C13  H13  single    0.930  0.020  1.080
 SQ5  N1   H14  single    0.860  0.020  1.020
 SQ5  C3   H15  single    0.970  0.020  1.090
 SQ5  C3   H16  single    0.970  0.020  1.090
 SQ5  C15  H17  single    0.930  0.020  1.080
 SQ5  C2   H18  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
 SQ5  H1   C4   C3   109.20  3.000
 SQ5  H1   C4   C9   108.19  3.000
 SQ5  C3   C4   C9   112.31  3.000
 SQ5  H1   C4   C5   107.53  3.000
 SQ5  C3   C4   C5   109.58  3.000
 SQ5  C9   C4   C5   109.90  3.000
 SQ5  F1   C14  C15  119.69  3.000
 SQ5  F1   C14  C13  119.42  3.000
 SQ5  C15  C14  C13  120.89  3.000
 SQ5  H3   C5   H2   106.45  3.000
 SQ5  H3   C5   C6   109.37  3.000
 SQ5  H2   C5   C6   110.10  3.000
 SQ5  H3   C5   C4   109.05  3.000
 SQ5  H2   C5   C4   109.69  3.000
 SQ5  C6   C5   C4   112.02  3.000
 SQ5  H5   C6   H4   106.53  3.000
 SQ5  H5   C6   C7   110.44  3.000
 SQ5  H4   C6   C7   109.28  3.000
 SQ5  H5   C6   C5   110.01  3.000
 SQ5  H4   C6   C5   109.16  3.000
 SQ5  C7   C6   C5   111.28  3.000
 SQ5  C15  C11  N2   120.69  3.000
 SQ5  C15  C11  C12  119.25  3.000
 SQ5  N2   C11  C12  120.05  3.000
 SQ5  H7   C7   H6   106.54  3.000
 SQ5  H7   C7   C8   110.40  3.000
 SQ5  H6   C7   C8   109.31  3.000
 SQ5  H7   C7   C6   110.35  3.000
 SQ5  H6   C7   C6   109.25  3.000
 SQ5  C8   C7   C6   110.88  3.000
 SQ5  H9   C8   H8   106.44  3.000
 SQ5  H9   C8   C9   109.23  3.000
 SQ5  H8   C8   C9   109.91  3.000
 SQ5  H9   C8   C7   109.31  3.000
 SQ5  H8   C8   C7   110.36  3.000
 SQ5  C9   C8   C7   111.45  3.000
 SQ5  H11  C9   H10  106.45  3.000
 SQ5  H11  C9   C8   109.38  3.000
 SQ5  H10  C9   C8   109.34  3.000
 SQ5  H11  C9   C4   110.95  3.000
 SQ5  H10  C9   C4   108.73  3.000
 SQ5  C8   C9   C4   111.84  3.000
 SQ5  O2   C10  C2   127.78  3.000
 SQ5  C2   C10  N2   106.48  3.000
 SQ5  O2   C10  N2   125.74  3.000
 SQ5  H12  C12  N3   117.11  3.000
 SQ5  H12  C12  C11  120.31  3.000
 SQ5  N3   C12  C11  122.59  3.000
 SQ5  H13  C13  N3   117.92  3.000
 SQ5  H13  C13  C14  120.64  3.000
 SQ5  N3   C13  C14  121.43  3.000
 SQ5  H14  N1   C2   123.36  3.000
 SQ5  H14  N1   C1   122.11  3.000
 SQ5  C2   N1   C1   114.01  3.000
 SQ5  C1   N2   C10  111.77  3.000
 SQ5  C1   N2   C11  123.12  3.000
 SQ5  C10  N2   C11  125.09  3.000
 SQ5  H16  C3   H15  106.23  3.000
 SQ5  H16  C3   C2   107.10  3.000
 SQ5  H15  C3   C2   108.34  3.000
 SQ5  H16  C3   C4   108.71  3.000
 SQ5  H15  C3   C4   110.14  3.000
 SQ5  C2   C3   C4   115.85  3.000
 SQ5  C13  N3   C12  119.01  3.000
 SQ5  O1   C1   N2   124.49  3.000
 SQ5  O1   C1   N1   129.52  3.000
 SQ5  N2   C1   N1   105.99  3.000
 SQ5  H17  C15  C11  121.92  3.000
 SQ5  H17  C15  C14  121.26  3.000
 SQ5  C11  C15  C14  116.81  3.000
 SQ5  H18  C2   C3   110.94  3.000
 SQ5  H18  C2   N1   110.75  3.000
 SQ5  C3   C2   N1   112.01  3.000
 SQ5  H18  C2   C10  108.92  3.000
 SQ5  N1   C2   C10  101.46  3.000
 SQ5  C3   C2   C10  112.38  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
 SQ5  CONST_01  C12  C11  C15  C14     0.00   0.0  0
 SQ5  CONST_02  C12  N3   C13  C14     0.00   0.0  0
 SQ5  CONST_03  C13  N3   C12  C11     0.00   0.0  0
 SQ5  CONST_04  C13  C14  C15  C11     0.00   0.0  0
 SQ5  CONST_05  C15  C11  C12  N3      0.00   0.0  0
 SQ5  CONST_06  C15  C14  C13  N3      0.00   0.0  0
 SQ5  CONST_07  N2   C11  C15  C14   180.00   0.0  0
 SQ5  CONST_08  N3   C12  C11  N2    180.00   0.0  0
 SQ5  CONST_09  C2   C10  N2   C11   180.00   0.0  0
 SQ5  CONST_10  N1   C1   N2   C11   180.00   0.0  0
 SQ5  CONST_11  N1   C1   N2   C10     0.00   0.0  0
 SQ5  CONST_12  C2   N1   C1   N2      0.00   0.0  0
 SQ5  CONST_13  C2   C10  N2   C1      0.00   0.0  0
 SQ5  CONST_14  F1   C14  C15  C11   180.00   0.0  0
 SQ5  CONST_15  F1   C14  C13  N3    180.00   0.0  0
 SQ5  CONST_16  O2   C10  N2   C11     0.00   0.0  0
 SQ5  CONST_17  O1   C1   N2   C11     0.00   0.0  0
 SQ5  CONST_18  O1   C1   N2   C10   180.00   0.0  0
 SQ5  CONST_19  O2   C10  N2   C1    180.00   0.0  0
 SQ5  CONST_20  O1   C1   N1   C2    180.00   0.0  0
 SQ5  CONST_21  H17  C15  C11  C12   180.00   0.0  0
 SQ5  CONST_22  H13  C13  N3   C12   180.00   0.0  0
 SQ5  CONST_23  H12  C12  N3   C13   180.00   0.0  0
 SQ5  CONST_24  H17  C15  C14  C13   180.00   0.0  0
 SQ5  CONST_25  H12  C12  C11  N2      0.00   0.0  0
 SQ5  CONST_26  H17  C15  C11  N2      0.00   0.0  0
 SQ5  CONST_27  H12  C12  C11  C15   180.00   0.0  0
 SQ5  CONST_28  H13  C13  C14  C15   180.00   0.0  0
 SQ5  CONST_29  H14  N1   C1   N2    180.00   0.0  0
 SQ5  CONST_30  H14  N1   C1   O1      0.00   0.0  0
 SQ5  Var_01    C7   C6   C5   C4     55.92  30.0  1
 SQ5  Var_02    C7   C8   C9   C4    -55.86  30.0  1
 SQ5  Var_03    C8   C7   C6   C5    -55.11  30.0  1
 SQ5  Var_04    C9   C8   C7   C6     55.17  30.0  1
 SQ5  Var_05    C12  C11  N2   C10    56.35  30.0  2
 SQ5  Var_06    C15  C11  N2   C10  -124.09  30.0  2
 SQ5  Var_07    C1   N2   C11  C12  -122.07  30.0  3
 SQ5  Var_08    C15  C11  N2   C1     57.49  30.0  2
 SQ5  Var_09    H4   C6   C5   C4    -64.78  30.0  1
 SQ5  Var_10    H5   C6   C5   C4    178.66  30.0  1
 SQ5  Var_11    H8   C8   C9   C4   -178.54  30.0  1
 SQ5  Var_12    H9   C8   C9   C4     65.02  30.0  1
 SQ5  Var_13    H6   C7   C6   C5     65.43  30.0  1
 SQ5  Var_14    H7   C7   C6   C5   -177.75  30.0  1
 SQ5  Var_15    H8   C8   C7   C6    177.60  30.0  1
 SQ5  Var_16    H9   C8   C7   C6    -65.66  30.0  1
 SQ5  Var_17    H2   C5   C6   C7    178.27  30.0  1
 SQ5  Var_18    H3   C5   C6   C7    -65.10  30.0  1
 SQ5  Var_19    H10  C9   C8   C7     64.62  30.0  1
 SQ5  Var_20    H11  C9   C8   C7   -179.18  30.0  1
 SQ5  Var_21    H4   C6   C7   C8     65.52  30.0  1
 SQ5  Var_22    H5   C6   C7   C8   -177.60  30.0  1
 SQ5  Var_23    H6   C7   C8   C9    -65.33  30.0  1
 SQ5  Var_24    H7   C7   C8   C9    177.79  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
 SQ5  chir_01  C4  C5  C9   C3  positiv
 SQ5  chir_02  C2  N1  C10  C3  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
 SQ5  plan-1  C11  0.020
 SQ5  plan-1  C10  0.020
 SQ5  plan-1  N1   0.020
 SQ5  plan-1  N2   0.020
 SQ5  plan-1  C1   0.020
 SQ5  plan-1  C2   0.020
 SQ5  plan-1  O2   0.020
 SQ5  plan-1  H14  0.020
 SQ5  plan-1  O1   0.020
 SQ5  plan-2  C14  0.020
 SQ5  plan-2  C11  0.020
 SQ5  plan-2  C12  0.020
 SQ5  plan-2  C13  0.020
 SQ5  plan-2  N2   0.020
 SQ5  plan-2  N3   0.020
 SQ5  plan-2  C15  0.020
 SQ5  plan-2  H12  0.020
 SQ5  plan-2  H13  0.020
 SQ5  plan-2  H17  0.020
 SQ5  plan-2  F1   0.020

