# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 04:36:11 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2E,5R)-2-imino-3-methyl-5-phenyl-5-[3-(pyridin-3-yl)phenyl]imidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@](C1=O)(c2ccccc2)c3cccc(c3)c4cccnc4
#
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
 0KP  0KP  (2E,5R)-2-imino-3-methyl-5-phenyl-5-[3-(pyridin-3-yl)phenyl]imidazolidin-4-one  ligand  44  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0KP
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
 0KP  O1   O  O     0  -0.422  -2.1062   0.6591  -2.2647
 0KP  C1   C  C     0   0.567  -1.8913   0.9821  -1.1217
 0KP  C2   C  CT    0  -0.138  -1.3503   0.0721  -0.0082
 0KP  N1   N  NH1   0  -0.658  -1.1666   1.0272   1.0600
 0KP  C3   C  C     0   0.612  -1.7244   2.2404   0.7769
 0KP  N2   N  NT    0  -0.522  -2.0788   2.2088  -0.5750
 0KP  N3   N  N     0  -0.675  -1.8587   3.1894   1.6038
 0KP  C4   C  CH3   0  -0.555  -2.5928   3.3603  -1.2779
 0KP  C5   C  CR6   0   0.181  -2.3693  -0.9872   0.3983
 0KP  C6   C  CR16  0  -0.276  -1.9411  -2.0838   1.1434
 0KP  C7   C  CR16  0  -0.245  -2.8520  -3.0158   1.6180
 0KP  C8   C  CR16  0  -0.261  -4.2063  -2.8670   1.3503
 0KP  C9   C  CR16  0  -0.241  -4.6409  -1.7763   0.6116
 0KP  C10  C  CR16  0  -0.316  -3.7292  -0.8396   0.1419
 0KP  C11  C  CR6   0   0.137  -0.0457  -0.5411  -0.4918
 0KP  C12  C  CR16  0  -0.282  -0.0747  -1.5726  -1.4277
 0KP  C13  C  CR16  0  -0.230   1.1103  -2.1104  -1.9026
 0KP  C14  C  CR16  0  -0.318   2.3310  -1.6324  -1.4486
 0KP  C15  C  CR6   0   0.112   2.3768  -0.6012  -0.5136
 0KP  C16  C  CR16  0  -0.368   1.1764  -0.0597  -0.0486
 0KP  C17  C  CR16  0  -0.071   6.0137   0.8568   1.0129
 0KP  N4   N  N     0  -0.398   4.9708   0.7326   1.8257
 0KP  C18  C  CR16  0  -0.100   3.8371   0.2699   1.3190
 0KP  C19  C  CR6   0  -0.008   3.6683  -0.0921  -0.0184
 0KP  C20  C  CR16  0  -0.195   4.7756   0.0429  -0.8533
 0KP  C21  C  CR16  0  -0.315   5.9653   0.5220  -0.3319
 0KP  H1   H  H     0   0.352  -2.2908   4.0059   1.1894
 0KP  H3   H  HCH3  0   0.266  -3.5412   3.6794  -0.8478
 0KP  H4   H  HCH3  0   0.268  -1.8826   4.1843  -1.2324
 0KP  H5   H  HCH3  0   0.278  -2.7540   3.0946  -2.3178
 0KP  H6   H  HCR6  0   0.262  -0.8877  -2.2192   1.3552
 0KP  H7   H  HCR6  0   0.261  -2.5009  -3.8618   2.1944
 0KP  H8   H  HCR6  0   0.261  -4.9174  -3.5966   1.7148
 0KP  H9   H  HCR6  0   0.262  -5.6936  -1.6495   0.3956
 0KP  H10  H  HCR6  0   0.258  -4.1059   0.0034  -0.4235
 0KP  H11  H  HCR6  0   0.258  -1.0184  -1.9678  -1.7792
 0KP  H12  H  HCR6  0   0.262   1.0840  -2.9162  -2.6239
 0KP  H13  H  HCR6  0   0.259   3.2478  -2.0822  -1.8089
 0KP  H14  H  HCR6  0   0.259   1.1961   0.7599   0.6577
 0KP  H16  H  HCR6  0   0.261   3.0126   0.1615   2.0163
 0KP  H17  H  HCR6  0   0.271   4.7045  -0.2060  -1.9046
 0KP  H18  H  HCR6  0   0.274   6.8386   0.6434  -0.9578
 0KP  H19  H  HNH1  0   0.405  -1.1394   0.7198   2.0199
 0KP  H15  H  HCR6  0   0.267   6.9292   1.2389   1.4501

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
 0KP  C13  C14  aromatic  1.387  0.020  1.387
 0KP  C13  C12  aromatic  1.385  0.020  1.385
 0KP  C14  C15  aromatic  1.393  0.020  1.393
 0KP  C12  C11  aromatic  1.393  0.020  1.393
 0KP  C15  C19  single    1.474  0.020  1.474
 0KP  C15  C16  aromatic  1.397  0.020  1.397
 0KP  C8   C9   aromatic  1.387  0.020  1.387
 0KP  C8   C7   aromatic  1.388  0.020  1.388
 0KP  C20  C19  aromatic  1.393  0.020  1.393
 0KP  C20  C21  aromatic  1.384  0.020  1.384
 0KP  C9   C10  aromatic  1.389  0.020  1.389
 0KP  C7   C6   aromatic  1.387  0.020  1.387
 0KP  C19  C18  aromatic  1.396  0.020  1.396
 0KP  C11  C16  aromatic  1.386  0.020  1.386
 0KP  C11  C2   single    1.520  0.020  1.520
 0KP  C21  C17  aromatic  1.387  0.020  1.387
 0KP  C10  C5   aromatic  1.392  0.020  1.392
 0KP  C6   C5   aromatic  1.393  0.020  1.393
 0KP  C5   C2   single    1.525  0.020  1.525
 0KP  C18  N4   aromatic  1.325  0.020  1.325
 0KP  C17  N4   aromatic  1.328  0.020  1.328
 0KP  C2   N1   single    1.445  0.020  1.445
 0KP  C2   C1   single    1.537  0.020  1.537
 0KP  O1   C1   double    1.207  0.020  1.207
 0KP  N1   C3   single    1.365  0.020  1.365
 0KP  C1   N2   single    1.356  0.020  1.356
 0KP  C3   N2   single    1.398  0.020  1.398
 0KP  C3   N3   double    1.266  0.020  1.266
 0KP  N2   C4   single    1.444  0.020  1.444
 0KP  N3   H1   single    0.890  0.020  1.040
 0KP  C4   H3   single    0.970  0.020  1.090
 0KP  C4   H4   single    0.970  0.020  1.090
 0KP  C4   H5   single    0.970  0.020  1.090
 0KP  C6   H6   single    0.930  0.020  1.080
 0KP  C7   H7   single    0.930  0.020  1.080
 0KP  C8   H8   single    0.930  0.020  1.080
 0KP  C9   H9   single    0.930  0.020  1.080
 0KP  C10  H10  single    0.930  0.020  1.080
 0KP  C12  H11  single    0.930  0.020  1.080
 0KP  C13  H12  single    0.930  0.020  1.080
 0KP  C14  H13  single    0.930  0.020  1.080
 0KP  C16  H14  single    0.930  0.020  1.080
 0KP  C17  H15  single    0.930  0.020  1.080
 0KP  C18  H16  single    0.930  0.020  1.080
 0KP  C20  H17  single    0.930  0.020  1.080
 0KP  C21  H18  single    0.930  0.020  1.080
 0KP  N1   H19  single    0.890  0.020  1.040

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
 0KP  N2   C1   C2   107.00  3.000
 0KP  N2   C1   O1   126.82  3.000
 0KP  C2   C1   O1   126.19  3.000
 0KP  C11  C2   C5   112.21  3.000
 0KP  C5   C2   N1   110.31  3.000
 0KP  C11  C2   N1   113.12  3.000
 0KP  N1   C2   C1   100.90  3.000
 0KP  C5   C2   C1   111.67  3.000
 0KP  C11  C2   C1   108.09  3.000
 0KP  H19  N1   C3   118.65  3.000
 0KP  H19  N1   C2   120.38  3.000
 0KP  C3   N1   C2   112.48  3.000
 0KP  N3   C3   N2   128.45  3.000
 0KP  N3   C3   N1   125.04  3.000
 0KP  N2   C3   N1   106.50  3.000
 0KP  C4   N2   C3   122.89  3.000
 0KP  C4   N2   C1   125.06  3.000
 0KP  C3   N2   C1   112.04  3.000
 0KP  H1   N3   C3   112.49  3.000
 0KP  H5   C4   H4   108.80  3.000
 0KP  H5   C4   H3   108.72  3.000
 0KP  H4   C4   H3   109.26  3.000
 0KP  H5   C4   N2   108.90  3.000
 0KP  H4   C4   N2   110.55  3.000
 0KP  H3   C4   N2   110.57  3.000
 0KP  C10  C5   C6   118.84  3.000
 0KP  C6   C5   C2   118.94  3.000
 0KP  C10  C5   C2   122.01  3.000
 0KP  H6   C6   C7   119.20  3.000
 0KP  H6   C6   C5   120.13  3.000
 0KP  C7   C6   C5   120.67  3.000
 0KP  H7   C7   C8   120.19  3.000
 0KP  H7   C7   C6   119.64  3.000
 0KP  C8   C7   C6   120.17  3.000
 0KP  H8   C8   C9   120.24  3.000
 0KP  H8   C8   C7   120.25  3.000
 0KP  C9   C8   C7   119.51  3.000
 0KP  H9   C9   C10  119.48  3.000
 0KP  H9   C9   C8   120.21  3.000
 0KP  C10  C9   C8   120.31  3.000
 0KP  H10  C10  C9   118.25  3.000
 0KP  H10  C10  C5   121.25  3.000
 0KP  C9   C10  C5   120.50  3.000
 0KP  C16  C11  C12  119.36  3.000
 0KP  C16  C11  C2   120.98  3.000
 0KP  C12  C11  C2   119.63  3.000
 0KP  H11  C12  C13  119.54  3.000
 0KP  H11  C12  C11  120.46  3.000
 0KP  C13  C12  C11  119.99  3.000
 0KP  H12  C13  C14  119.75  3.000
 0KP  H12  C13  C12  119.80  3.000
 0KP  C14  C13  C12  120.45  3.000
 0KP  H13  C14  C15  120.20  3.000
 0KP  H13  C14  C13  119.53  3.000
 0KP  C15  C14  C13  120.25  3.000
 0KP  C19  C15  C16  120.49  3.000
 0KP  C16  C15  C14  118.84  3.000
 0KP  C19  C15  C14  120.67  3.000
 0KP  H14  C16  C15  119.69  3.000
 0KP  H14  C16  C11  119.19  3.000
 0KP  C15  C16  C11  121.11  3.000
 0KP  H15  C17  C21  120.38  3.000
 0KP  H15  C17  N4   116.70  3.000
 0KP  C21  C17  N4   122.92  3.000
 0KP  C18  N4   C17  118.06  3.000
 0KP  H16  C18  C19  119.86  3.000
 0KP  H16  C18  N4   116.05  3.000
 0KP  C19  C18  N4   124.09  3.000
 0KP  C20  C19  C18  116.93  3.000
 0KP  C18  C19  C15  121.17  3.000
 0KP  C20  C19  C15  121.91  3.000
 0KP  H17  C20  C21  120.11  3.000
 0KP  H17  C20  C19  120.49  3.000
 0KP  C21  C20  C19  119.40  3.000
 0KP  H18  C21  C20  121.00  3.000
 0KP  H18  C21  C17  120.40  3.000
 0KP  C20  C21  C17  118.60  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
 0KP  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 0KP  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 0KP  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 0KP  CONST_04  C9   C10  C5   C6     0.00   0.0  0
 0KP  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 0KP  CONST_06  C10  C5   C6   C7     0.00   0.0  0
 0KP  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 0KP  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 0KP  CONST_09  C19  C15  C16  C11  180.00   0.0  0
 0KP  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 0KP  CONST_11  C15  C16  C11  C12    0.00   0.0  0
 0KP  CONST_12  C19  C15  C14  C13  180.00   0.0  0
 0KP  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 0KP  CONST_14  C16  C11  C12  C13    0.00   0.0  0
 0KP  CONST_17  C21  C20  C19  C15  180.00   0.0  0
 0KP  CONST_18  N4   C18  C19  C15  180.00   0.0  0
 0KP  CONST_21  C19  C20  C21  C17    0.00   0.0  0
 0KP  CONST_22  C19  C18  N4   C17    0.00   0.0  0
 0KP  CONST_23  C20  C19  C18  N4     0.00   0.0  0
 0KP  CONST_24  C20  C21  C17  N4     0.00   0.0  0
 0KP  CONST_25  C21  C20  C19  C18    0.00   0.0  0
 0KP  CONST_26  C21  C17  N4   C18    0.00   0.0  0
 0KP  CONST_27  C13  C12  C11  C2   180.00   0.0  0
 0KP  CONST_28  C15  C16  C11  C2   180.00   0.0  0
 0KP  CONST_29  C9   C10  C5   C2   180.00   0.0  0
 0KP  CONST_30  C7   C6   C5   C2   180.00   0.0  0
 0KP  CONST_31  N1   C3   N2   C1     0.00   0.0  0
 0KP  CONST_32  N2   C3   N1   C2     0.00   0.0  0
 0KP  CONST_33  C3   N2   C1   C2     0.00   0.0  0
 0KP  CONST_34  C3   N2   C1   O1   180.00   0.0  0
 0KP  CONST_35  N3   C3   N2   C1   180.00   0.0  0
 0KP  CONST_36  N3   C3   N1   C2   180.00   0.0  0
 0KP  CONST_37  C4   N2   C1   C2   180.00   0.0  0
 0KP  CONST_38  C4   N2   C3   N1   180.00   0.0  0
 0KP  CONST_39  H11  C12  C11  C2     0.00   0.0  0
 0KP  CONST_40  H14  C16  C11  C2     0.00   0.0  0
 0KP  CONST_41  H10  C10  C5   C2     0.00   0.0  0
 0KP  CONST_42  H6   C6   C5   C2     0.00   0.0  0
 0KP  CONST_43  H9   C9   C10  C5   180.00   0.0  0
 0KP  CONST_44  H7   C7   C6   C5   180.00   0.0  0
 0KP  CONST_45  H8   C8   C7   C6   180.00   0.0  0
 0KP  CONST_46  H12  C13  C12  C11  180.00   0.0  0
 0KP  CONST_47  H13  C14  C13  C12  180.00   0.0  0
 0KP  CONST_48  H17  C20  C19  C15    0.00   0.0  0
 0KP  CONST_49  H16  C18  C19  C15    0.00   0.0  0
 0KP  CONST_50  H18  C21  C17  N4   180.00   0.0  0
 0KP  CONST_51  H15  C17  N4   C18  180.00   0.0  0
 0KP  CONST_53  C4   N2   C1   O1     0.00   0.0  0
 0KP  CONST_54  C4   N2   C3   N3     0.00   0.0  0
 0KP  CONST_55  H1   N3   C3   N1   180.00   0.0  0
 0KP  Var_01    H3   C4   N2   C1   116.57  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
 0KP  chir_01  C2  C5  N1  C1  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
 0KP  plan-1  C2   0.020
 0KP  plan-1  C5   0.020
 0KP  plan-1  C6   0.020
 0KP  plan-1  C7   0.020
 0KP  plan-1  C8   0.020
 0KP  plan-1  C9   0.020
 0KP  plan-1  C10  0.020
 0KP  plan-1  H6   0.020
 0KP  plan-1  H7   0.020
 0KP  plan-1  H8   0.020
 0KP  plan-1  H9   0.020
 0KP  plan-1  H10  0.020
 0KP  plan-2  C2   0.020
 0KP  plan-2  C11  0.020
 0KP  plan-2  C12  0.020
 0KP  plan-2  C13  0.020
 0KP  plan-2  C14  0.020
 0KP  plan-2  C15  0.020
 0KP  plan-2  C16  0.020
 0KP  plan-2  C19  0.020
 0KP  plan-2  H11  0.020
 0KP  plan-2  H12  0.020
 0KP  plan-2  H13  0.020
 0KP  plan-2  H14  0.020
 0KP  plan-3  C15  0.020
 0KP  plan-3  C17  0.020
 0KP  plan-3  N4   0.020
 0KP  plan-3  C18  0.020
 0KP  plan-3  C19  0.020
 0KP  plan-3  C20  0.020
 0KP  plan-3  C21  0.020
 0KP  plan-3  H16  0.020
 0KP  plan-3  H17  0.020
 0KP  plan-3  H18  0.020
 0KP  plan-3  H15  0.020
 0KP  plan-4  O1   0.020
 0KP  plan-4  C1   0.020
 0KP  plan-4  C2   0.020
 0KP  plan-4  N1   0.020
 0KP  plan-4  C3   0.020
 0KP  plan-4  N2   0.020
 0KP  plan-4  N3   0.020
 0KP  plan-4  C4   0.020
 0KP  plan-4  H1   0.020
 0KP  plan-4  H19  0.020

