# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:32:49 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: (2E,5R)-5-cyclopropyl-2-imino-3-methyl-5-{3-[5-(prop-1-yn-1-yl)pyridin-3-yl]phenyl}imidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#Cc1cncc(c1)c2cccc(c2)[C@]3(NC(=N)N(C)C3=O)C4CC4
#
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
 0KR  0KR  (2E,5R)-5-cyclopropyl-2-imino-3-methyl-5-{3-[5-(prop-1-yn-1-yl)pyridin-3-yl]phenyl}imidazolidin-4-one  ligand  46  26  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0KR
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
 0KR  C1   C  CT    0  -0.116  22.3735  10.6696  21.8331
 0KR  N1   N  NH1   0  -0.658  22.7440   9.5751  22.6939
 0KR  C2   C  C     0   0.601  23.1206   9.9830  23.9400
 0KR  N2   N  NT    0  -0.521  22.8786  11.3597  23.9978
 0KR  C3   C  C     0   0.575  22.4659  11.8520  22.8013
 0KR  C4   C  CH1   0  -0.245  20.9327  10.5880  21.3612
 0KR  O1   O  O     0  -0.430  22.2007  13.0020  22.5437
 0KR  C5   C  CR6   0   0.235  23.3716  10.8556  20.6981
 0KR  C6   C  CR16  0  -0.377  24.7312  10.8738  20.9975
 0KR  C7   C  CR6   0   0.111  25.6928  11.0412  20.0061
 0KR  C8   C  CR16  0  -0.319  25.2745  11.1894  18.6829
 0KR  C9   C  CR16  0  -0.220  23.9255  11.1720  18.3757
 0KR  C10  C  CR16  0  -0.329  22.9748  11.0066  19.3758
 0KR  N3   N  N     0  -0.677  23.5897   9.2269  24.8416
 0KR  C11  C  CH3   0  -0.555  23.0808  12.1441  25.1917
 0KR  C12  C  CH2   0  -0.482  19.8878   9.9511  22.2196
 0KR  C13  C  CH2   0  -0.477  20.3301   9.2833  20.9524
 0KR  C14  C  CR6   0   0.005  27.1260  11.0545  20.3517
 0KR  C15  C  CR16  0  -0.238  27.6461  10.2274  21.3401
 0KR  C16  C  CR6   0  -0.160  29.0058  10.2782  21.6391
 0KR  C17  C  CR16  0  -0.098  29.7973  11.1707  20.9107
 0KR  C19  C  CR16  0  -0.096  28.0167  11.9079  19.6994
 0KR  C21  C  CSP   0   0.200  29.5801   9.4489  22.6439
 0KR  N5   N  N     0  -0.388  29.3133  11.9626  19.9685
 0KR  C22  C  CSP   0  -0.043  30.0686   8.7539  23.4987
 0KR  C23  C  CH3   0  -0.823  30.6561   7.9154  24.5282
 0KR  H1   H  HCH1  0   0.278  20.6121  11.4616  20.8049
 0KR  H2   H  HCR6  0   0.256  25.0592  10.7739  22.0263
 0KR  H3   H  HCR6  0   0.262  26.0037  11.2927  17.8897
 0KR  H4   H  HCR6  0   0.264  23.6078  11.2766  17.3467
 0KR  H5   H  HCR6  0   0.265  21.9278  10.9877  19.1077
 0KR  H6   H  H     0   0.351  23.8120   9.7293  25.6916
 0KR  H8   H  HCH3  0   0.265  22.5001  11.7376  26.0183
 0KR  H9   H  HCH3  0   0.265  24.1340  12.1663  25.4694
 0KR  H10  H  HCH3  0   0.277  22.7498  13.1608  25.0038
 0KR  H11  H  HCH2  0   0.258  18.9117  10.4175  22.2425
 0KR  H12  H  HCH2  0   0.252  20.1919   9.4984  23.1552
 0KR  H13  H  HCH2  0   0.260  19.6587   9.2837  20.1036
 0KR  H14  H  HCH2  0   0.247  20.9311   8.3865  21.0401
 0KR  H15  H  HCR6  0   0.270  27.0074   9.5301  21.8674
 0KR  H16  H  HCR6  0   0.269  30.8611  11.2349  21.1106
 0KR  H17  H  HCR6  0   0.268  27.6561  12.5879  18.9349
 0KR  H18  H  HCH3  0   0.273  30.0311   7.0448  24.7264
 0KR  H19  H  HCH3  0   0.272  31.6421   7.5613  24.2273
 0KR  H20  H  HCH3  0   0.272  30.7693   8.4658  25.4627
 0KR  H21  H  HNH1  0   0.402  23.1092   8.7116  22.3263

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
 0KR  C9   C8   aromatic  1.384  0.020  1.384
 0KR  C9   C10  aromatic  1.390  0.020  1.390
 0KR  C8   C7   aromatic  1.396  0.020  1.396
 0KR  C10  C5   aromatic  1.389  0.020  1.389
 0KR  C19  N5   aromatic  1.325  0.020  1.325
 0KR  C19  C14  aromatic  1.395  0.020  1.395
 0KR  C7   C14  single    1.474  0.020  1.474
 0KR  C7   C6   aromatic  1.391  0.020  1.391
 0KR  N5   C17  aromatic  1.323  0.020  1.323
 0KR  C14  C15  aromatic  1.390  0.020  1.390
 0KR  C5   C6   aromatic  1.392  0.020  1.392
 0KR  C5   C1   single    1.523  0.020  1.523
 0KR  C17  C16  aromatic  1.398  0.020  1.398
 0KR  C13  C4   single    1.494  0.020  1.494
 0KR  C13  C12  single    1.499  0.020  1.499
 0KR  C15  C16  aromatic  1.393  0.020  1.393
 0KR  C4   C1   single    1.518  0.020  1.518
 0KR  C4   C12  single    1.495  0.020  1.495
 0KR  C16  C21  single    1.424  0.020  1.424
 0KR  C1   N1   single    1.441  0.020  1.441
 0KR  C1   C3   single    1.531  0.020  1.531
 0KR  O1   C3   double    1.208  0.020  1.208
 0KR  N1   C2   single    1.364  0.020  1.364
 0KR  C21  C22  triple    1.205  0.020  1.205
 0KR  C3   N2   single    1.358  0.020  1.358
 0KR  C22  C23  single    1.452  0.020  1.452
 0KR  C2   N2   single    1.399  0.020  1.399
 0KR  C2   N3   double    1.267  0.020  1.267
 0KR  N2   C11  single    1.443  0.020  1.443
 0KR  C4   H1   single    0.970  0.020  1.090
 0KR  C6   H2   single    0.930  0.020  1.080
 0KR  C8   H3   single    0.930  0.020  1.080
 0KR  C9   H4   single    0.930  0.020  1.080
 0KR  C10  H5   single    0.930  0.020  1.080
 0KR  N3   H6   single    0.890  0.020  1.040
 0KR  C11  H8   single    0.970  0.020  1.090
 0KR  C11  H9   single    0.970  0.020  1.090
 0KR  C11  H10  single    0.970  0.020  1.090
 0KR  C12  H11  single    0.970  0.020  1.090
 0KR  C12  H12  single    0.970  0.020  1.090
 0KR  C13  H13  single    0.970  0.020  1.090
 0KR  C13  H14  single    0.970  0.020  1.090
 0KR  C15  H15  single    0.930  0.020  1.080
 0KR  C17  H16  single    0.930  0.020  1.080
 0KR  C19  H17  single    0.930  0.020  1.080
 0KR  C23  H18  single    0.970  0.020  1.090
 0KR  C23  H19  single    0.970  0.020  1.090
 0KR  C23  H20  single    0.970  0.020  1.090
 0KR  N1   H21  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
 0KR  C5   C1   C4   113.38  3.000
 0KR  C4   C1   C3   107.18  3.000
 0KR  C5   C1   C3   109.72  3.000
 0KR  C3   C1   N1   101.15  3.000
 0KR  C4   C1   N1   112.88  3.000
 0KR  C5   C1   N1   111.69  3.000
 0KR  H21  N1   C2   119.32  3.000
 0KR  H21  N1   C1   121.77  3.000
 0KR  C2   N1   C1   112.93  3.000
 0KR  N3   C2   N2   128.47  3.000
 0KR  N3   C2   N1   125.02  3.000
 0KR  N2   C2   N1   106.51  3.000
 0KR  C11  N2   C3   125.07  3.000
 0KR  C11  N2   C2   123.02  3.000
 0KR  C3   N2   C2   111.90  3.000
 0KR  O1   C3   N2   126.85  3.000
 0KR  N2   C3   C1   107.19  3.000
 0KR  O1   C3   C1   125.95  3.000
 0KR  H1   C4   C13  116.36  3.000
 0KR  H1   C4   C12  115.55  3.000
 0KR  C13  C4   C12   60.21  3.000
 0KR  H1   C4   C1   113.37  3.000
 0KR  C12  C4   C1   120.51  3.000
 0KR  C13  C4   C1   120.98  3.000
 0KR  C10  C5   C6   118.84  3.000
 0KR  C6   C5   C1   118.77  3.000
 0KR  C10  C5   C1   122.39  3.000
 0KR  H2   C6   C7   118.56  3.000
 0KR  H2   C6   C5   119.88  3.000
 0KR  C7   C6   C5   121.55  3.000
 0KR  C14  C7   C8   120.84  3.000
 0KR  C14  C7   C6   120.39  3.000
 0KR  C8   C7   C6   118.77  3.000
 0KR  H3   C8   C9   119.70  3.000
 0KR  H3   C8   C7   120.20  3.000
 0KR  C9   C8   C7   120.09  3.000
 0KR  H4   C9   C10  119.67  3.000
 0KR  H4   C9   C8   119.74  3.000
 0KR  C10  C9   C8   120.58  3.000
 0KR  H5   C10  C9   119.10  3.000
 0KR  H5   C10  C5   120.73  3.000
 0KR  C9   C10  C5   120.17  3.000
 0KR  H6   N3   C2   112.50  3.000
 0KR  H10  C11  H9   108.66  3.000
 0KR  H10  C11  H8   108.56  3.000
 0KR  H9   C11  H8   109.25  3.000
 0KR  H10  C11  N2   108.86  3.000
 0KR  H9   C11  N2   110.95  3.000
 0KR  H8   C11  N2   110.51  3.000
 0KR  H12  C12  H11  114.53  3.000
 0KR  H12  C12  C13  117.47  3.000
 0KR  H11  C12  C13  118.42  3.000
 0KR  H12  C12  C4   118.56  3.000
 0KR  H11  C12  C4   117.33  3.000
 0KR  C13  C12  C4    59.87  3.000
 0KR  H14  C13  H13  114.09  3.000
 0KR  H14  C13  C12  117.65  3.000
 0KR  H13  C13  C12  118.67  3.000
 0KR  H14  C13  C4   118.49  3.000
 0KR  H13  C13  C4   117.68  3.000
 0KR  C12  C13  C4    59.91  3.000
 0KR  C19  C14  C15  117.23  3.000
 0KR  C15  C14  C7   121.68  3.000
 0KR  C19  C14  C7   121.09  3.000
 0KR  H15  C15  C16  119.66  3.000
 0KR  H15  C15  C14  120.59  3.000
 0KR  C16  C15  C14  119.75  3.000
 0KR  C21  C16  C17  120.75  3.000
 0KR  C21  C16  C15  121.59  3.000
 0KR  C17  C16  C15  117.66  3.000
 0KR  H16  C17  N5   117.06  3.000
 0KR  H16  C17  C16  119.82  3.000
 0KR  N5   C17  C16  123.12  3.000
 0KR  H17  C19  N5   116.26  3.000
 0KR  H17  C19  C14  120.04  3.000
 0KR  N5   C19  C14  123.70  3.000
 0KR  C22  C21  C16  180.00  3.000
 0KR  C19  N5   C17  118.55  3.000
 0KR  C23  C22  C21  180.00  3.000
 0KR  H20  C23  H19  107.86  3.000
 0KR  H20  C23  H18  107.87  3.000
 0KR  H19  C23  H18  108.02  3.000
 0KR  H20  C23  C22  110.99  3.000
 0KR  H19  C23  C22  110.97  3.000
 0KR  H18  C23  C22  110.99  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
 0KR  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 0KR  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 0KR  CONST_03  C14  C7   C6   C5   180.00   0.0  0
 0KR  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 0KR  CONST_07  C9   C10  C5   C6     0.00   0.0  0
 0KR  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 0KR  CONST_09  N5   C19  C14  C7   180.00   0.0  0
 0KR  CONST_10  C16  C15  C14  C7   180.00   0.0  0
 0KR  CONST_11  C10  C5   C6   C7     0.00   0.0  0
 0KR  CONST_14  C14  C7   C8   C9   180.00   0.0  0
 0KR  CONST_15  C17  N5   C19  C14    0.00   0.0  0
 0KR  CONST_16  C17  C16  C15  C14    0.00   0.0  0
 0KR  CONST_17  N5   C19  C14  C15    0.00   0.0  0
 0KR  CONST_18  N5   C17  C16  C15    0.00   0.0  0
 0KR  CONST_19  C19  N5   C17  C16    0.00   0.0  0
 0KR  CONST_20  C19  C14  C15  C16    0.00   0.0  0
 0KR  CONST_21  C9   C10  C5   C1   180.00   0.0  0
 0KR  CONST_22  C7   C6   C5   C1   180.00   0.0  0
 0KR  CONST_23  N2   C2   N1   C1     0.00   0.0  0
 0KR  CONST_24  C2   N2   C3   C1     0.00   0.0  0
 0KR  CONST_25  C3   N2   C2   N1     0.00   0.0  0
 0KR  CONST_26  C21  C16  C15  C14  180.00   0.0  0
 0KR  CONST_27  N5   C17  C16  C21  180.00   0.0  0
 0KR  CONST_28  N3   C2   N1   C1   180.00   0.0  0
 0KR  CONST_29  C11  N2   C3   C1   180.00   0.0  0
 0KR  CONST_30  C11  N2   C2   N1   180.00   0.0  0
 0KR  CONST_31  O1   C3   N2   C2   180.00   0.0  0
 0KR  CONST_32  N3   C2   N2   C3   180.00   0.0  0
 0KR  CONST_33  H5   C10  C5   C1     0.00   0.0  0
 0KR  CONST_34  H2   C6   C5   C1     0.00   0.0  0
 0KR  CONST_35  H4   C9   C10  C5   180.00   0.0  0
 0KR  CONST_36  H3   C8   C7   C6   180.00   0.0  0
 0KR  CONST_37  H17  C19  C14  C7     0.00   0.0  0
 0KR  CONST_38  H15  C15  C14  C7     0.00   0.0  0
 0KR  CONST_39  H16  C17  C16  C15  180.00   0.0  0
 0KR  CONST_41  C11  N2   C3   O1     0.00   0.0  0
 0KR  CONST_42  C11  N2   C2   N3     0.00   0.0  0
 0KR  CONST_43  H6   N3   C2   N1   180.00   0.0  0
 0KR  Var_01    C12  C13  C4   C1   109.80  30.0  1
 0KR  Var_02    H8   C11  N2   C2   -56.39  30.0  3
 0KR  Var_03    H18  C23  C22  C21  -11.36  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
 0KR  chir_01  C1  C4   N1  C3   positiv
 0KR  chir_02  C4  C13  C1  C12  both

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
 0KR  plan-1  C1   0.020
 0KR  plan-1  C5   0.020
 0KR  plan-1  C6   0.020
 0KR  plan-1  C7   0.020
 0KR  plan-1  C8   0.020
 0KR  plan-1  C9   0.020
 0KR  plan-1  C10  0.020
 0KR  plan-1  C14  0.020
 0KR  plan-1  H2   0.020
 0KR  plan-1  H3   0.020
 0KR  plan-1  H4   0.020
 0KR  plan-1  H5   0.020
 0KR  plan-2  C7   0.020
 0KR  plan-2  C14  0.020
 0KR  plan-2  C15  0.020
 0KR  plan-2  C16  0.020
 0KR  plan-2  C17  0.020
 0KR  plan-2  C19  0.020
 0KR  plan-2  C21  0.020
 0KR  plan-2  N5   0.020
 0KR  plan-2  C22  0.020
 0KR  plan-2  H15  0.020
 0KR  plan-2  H16  0.020
 0KR  plan-2  H17  0.020
 0KR  plan-3  C1   0.020
 0KR  plan-3  N1   0.020
 0KR  plan-3  C2   0.020
 0KR  plan-3  N2   0.020
 0KR  plan-3  C3   0.020
 0KR  plan-3  O1   0.020
 0KR  plan-3  N3   0.020
 0KR  plan-3  C11  0.020
 0KR  plan-3  H6   0.020
 0KR  plan-3  H21  0.020

