# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:34:41 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[4-[(4~{S})-4-methyl-2-oxidanylidene-imidazolidin-4-yl]phenyl]-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CNC(=O)N1)c2ccc(cc2)C3=Nc4ccccc4C(=O)N3
#
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
 KC8  KC8  2-[4-[(4~{S})-4-methyl-2-oxidanylidene-imidazolidin-4-yl]phenyl]-3~{H}-quinazolin-4-one  ligand  40  24  .  2022-07-25  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_KC8
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
 KC8  O    O  O     0  -0.514   6.5872  -2.0491   0.2322
 KC8  C2   C  CR5   0   0.630   5.7871  -1.1294   0.2058
 KC8  N1   N  NR15  0  -0.650   5.8875   0.0544   0.8708
 KC8  C3   C  CH2   0  -0.245   4.6599   0.8073   0.7780
 KC8  N    N  NR15  0  -0.667   4.6165  -1.0995  -0.5082
 KC8  C1   C  CR5   0   0.022   4.0374   0.2329  -0.5181
 KC8  C    C  CH3   0  -0.636   4.4965   1.0162  -1.7516
 KC8  C4   C  CR6   0   0.144   2.5266   0.2114  -0.4333
 KC8  C5   C  CR16  0  -0.297   1.8017  -0.9759  -0.4341
 KC8  C6   C  CR16  0  -0.250   0.4186  -0.9636  -0.3658
 KC8  C9   C  CR16  0  -0.283   1.8276   1.4135  -0.3460
 KC8  C8   C  CR16  0  -0.285   0.4458   1.4317  -0.2746
 KC8  C7   C  CR6   0   0.005  -0.2783   0.2400  -0.2940
 KC8  C10  C  CR6   0   0.491  -1.7503   0.2143  -0.2303
 KC8  N3   N  NR16  0  -0.728  -2.4201   1.3279  -0.6487
 KC8  C17  C  CR6   0   0.538  -3.7914   1.4651  -0.6416
 KC8  O2   O  O     0  -0.450  -4.3219   2.4902  -1.0289
 KC8  N2   N  N     0  -0.472  -2.3518  -0.8377   0.2030
 KC8  C11  C  CR66  0   0.265  -3.7235  -0.8310   0.2414
 KC8  C12  C  CR66  0  -0.106  -4.4847   0.2812  -0.1526
 KC8  C16  C  CR16  0  -0.322  -4.3894  -1.9779   0.6972
 KC8  C15  C  CR16  0  -0.237  -5.7656  -2.0037   0.7512
 KC8  C14  C  CR16  0  -0.260  -6.5188  -0.8919   0.3565
 KC8  C13  C  CR16  0  -0.276  -5.8803   0.2433  -0.0924
 KC8  H1   H  HCH2  0   0.251   4.0064   0.6302   1.6378
 KC8  H2   H  HNR5  0   0.396   4.5589  -1.6765  -1.3347
 KC8  H3   H  HCH3  0   0.245   5.5858   1.0421  -1.8022
 KC8  H4   H  HCH3  0   0.246   4.1202   0.5526  -2.6641
 KC8  H5   H  HCH3  0   0.238   4.1392   2.0451  -1.7248
 KC8  H6   H  HCR6  0   0.259   2.3153  -1.9261  -0.4897
 KC8  H7   H  HCR6  0   0.262  -0.1277  -1.8970  -0.3768
 KC8  H8   H  HCR6  0   0.261   2.3596   2.3565  -0.3224
 KC8  H9   H  HCR6  0   0.263  -0.0496   2.3894  -0.1767
 KC8  H10  H  HNR6  0   0.432  -1.8997   2.1050  -1.0347
 KC8  H11  H  HCR6  0   0.266  -3.8039  -2.8347   1.0042
 KC8  H12  H  HCR6  0   0.270  -6.2694  -2.8941   1.1038
 KC8  H13  H  HCR6  0   0.267  -7.5987  -0.9254   0.4049
 KC8  H14  H  HCR6  0   0.269  -6.4524   1.1080  -0.4020
 KC8  H15  H  HNR5  0   0.401   6.4754   0.1194   1.6863
 KC8  H16  H  HCH2  0   0.255   4.8402   1.8795   0.6995

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
 KC8  O    C2   double    1.219  0.020  1.219
 KC8  N1   C2   single    1.361  0.020  1.361
 KC8  N1   C3   single    1.443  0.020  1.443
 KC8  C2   N    single    1.371  0.020  1.371
 KC8  C3   C1   single    1.548  0.020  1.548
 KC8  N    C1   single    1.453  0.020  1.453
 KC8  C    C1   single    1.532  0.020  1.532
 KC8  C1   C4   single    1.513  0.020  1.513
 KC8  C4   C5   aromatic  1.391  0.020  1.391
 KC8  C4   C9   aromatic  1.393  0.020  1.393
 KC8  C5   C6   aromatic  1.385  0.020  1.385
 KC8  C9   C8   aromatic  1.384  0.020  1.384
 KC8  C6   C7   aromatic  1.393  0.020  1.393
 KC8  C8   C7   aromatic  1.395  0.020  1.395
 KC8  C7   C10  single    1.474  0.020  1.474
 KC8  C10  N2   double    1.287  0.020  1.287
 KC8  C10  N3   single    1.365  0.020  1.365
 KC8  N2   C11  single    1.372  0.020  1.372
 KC8  N3   C17  single    1.378  0.020  1.378
 KC8  C11  C16  aromatic  1.402  0.020  1.402
 KC8  C11  C12  aromatic  1.404  0.020  1.404
 KC8  C16  C15  aromatic  1.377  0.020  1.377
 KC8  C17  C12  single    1.456  0.020  1.456
 KC8  C17  O2   double    1.217  0.020  1.217
 KC8  C12  C13  aromatic  1.397  0.020  1.397
 KC8  C15  C14  aromatic  1.400  0.020  1.400
 KC8  C13  C14  aromatic  1.378  0.020  1.378
 KC8  C3   H1   single    0.970  0.020  1.090
 KC8  N    H2   single    0.890  0.020  1.040
 KC8  C    H3   single    0.970  0.020  1.090
 KC8  C    H4   single    0.970  0.020  1.090
 KC8  C    H5   single    0.970  0.020  1.090
 KC8  C5   H6   single    0.930  0.020  1.080
 KC8  C6   H7   single    0.930  0.020  1.080
 KC8  C9   H8   single    0.930  0.020  1.080
 KC8  C8   H9   single    0.930  0.020  1.080
 KC8  N3   H10  single    0.860  0.020  1.020
 KC8  C16  H11  single    0.930  0.020  1.080
 KC8  C15  H12  single    0.930  0.020  1.080
 KC8  C14  H13  single    0.930  0.020  1.080
 KC8  C13  H14  single    0.930  0.020  1.080
 KC8  N1   H15  single    0.890  0.020  1.040
 KC8  C3   H16  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
 KC8  N    C2   N1   107.36  3.000
 KC8  N    C2   O    126.00  3.000
 KC8  N1   C2   O    126.65  3.000
 KC8  H15  N1   C3   120.98  3.000
 KC8  H15  N1   C2   119.64  3.000
 KC8  C3   N1   C2   111.07  3.000
 KC8  H16  C3   H1   108.33  3.000
 KC8  H16  C3   C1   111.79  3.000
 KC8  H1   C3   C1   110.95  3.000
 KC8  H16  C3   N1   112.15  3.000
 KC8  H1   C3   N1   111.90  3.000
 KC8  C1   C3   N1   101.67  3.000
 KC8  H2   N    C1   119.72  3.000
 KC8  H2   N    C2   117.55  3.000
 KC8  C1   N    C2   111.33  3.000
 KC8  C4   C1   C    110.58  3.000
 KC8  C4   C1   N    112.62  3.000
 KC8  C    C1   N    110.80  3.000
 KC8  C4   C1   C3   111.09  3.000
 KC8  C    C1   C3   111.34  3.000
 KC8  N    C1   C3   100.04  3.000
 KC8  H5   C    H4   107.99  3.000
 KC8  H5   C    H3   107.83  3.000
 KC8  H4   C    H3   108.41  3.000
 KC8  H5   C    C1   111.40  3.000
 KC8  H4   C    C1   110.67  3.000
 KC8  H3   C    C1   110.42  3.000
 KC8  C9   C4   C5   118.36  3.000
 KC8  C9   C4   C1   119.48  3.000
 KC8  C5   C4   C1   122.16  3.000
 KC8  H6   C5   C6   118.99  3.000
 KC8  H6   C5   C4   120.16  3.000
 KC8  C6   C5   C4   120.85  3.000
 KC8  H7   C6   C7   119.58  3.000
 KC8  H7   C6   C5   119.76  3.000
 KC8  C7   C6   C5   120.66  3.000
 KC8  H8   C9   C8   118.55  3.000
 KC8  H8   C9   C4   120.41  3.000
 KC8  C8   C9   C4   121.04  3.000
 KC8  H9   C8   C7   121.30  3.000
 KC8  H9   C8   C9   118.25  3.000
 KC8  C7   C8   C9   120.43  3.000
 KC8  C10  C7   C8   122.21  3.000
 KC8  C10  C7   C6   119.14  3.000
 KC8  C8   C7   C6   118.65  3.000
 KC8  N2   C10  N3   122.73  3.000
 KC8  N3   C10  C7   117.55  3.000
 KC8  N2   C10  C7   119.71  3.000
 KC8  H10  N3   C17  115.93  3.000
 KC8  H10  N3   C10  119.42  3.000
 KC8  C17  N3   C10  124.60  3.000
 KC8  C12  C17  O2   125.72  3.000
 KC8  O2   C17  N3   121.05  3.000
 KC8  C12  C17  N3   113.23  3.000
 KC8  C11  N2   C10  118.21  3.000
 KC8  C16  C11  C12  118.79  3.000
 KC8  C12  C11  N2   122.54  3.000
 KC8  C16  C11  N2   118.67  3.000
 KC8  C13  C12  C11  120.52  3.000
 KC8  C13  C12  C17  120.79  3.000
 KC8  C11  C12  C17  118.69  3.000
 KC8  H11  C16  C15  120.97  3.000
 KC8  H11  C16  C11  118.87  3.000
 KC8  C15  C16  C11  120.16  3.000
 KC8  H12  C15  C14  119.66  3.000
 KC8  H12  C15  C16  119.56  3.000
 KC8  C14  C15  C16  120.77  3.000
 KC8  H13  C14  C13  120.19  3.000
 KC8  H13  C14  C15  120.00  3.000
 KC8  C13  C14  C15  119.81  3.000
 KC8  H14  C13  C14  120.45  3.000
 KC8  H14  C13  C12  119.60  3.000
 KC8  C14  C13  C12  119.95  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
 KC8  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 KC8  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 KC8  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 KC8  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 KC8  CONST_05  C9   C4   C5   C6     0.00   0.0  0
 KC8  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 KC8  CONST_07  C14  C15  C16  C11    0.00   0.0  0
 KC8  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 KC8  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 KC8  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 KC8  CONST_11  C13  C12  C11  C16    0.00   0.0  0
 KC8  CONST_12  C13  C14  C15  C16    0.00   0.0  0
 KC8  CONST_13  C6   C5   C4   C1   180.00   0.0  0
 KC8  CONST_14  C8   C9   C4   C1   180.00   0.0  0
 KC8  CONST_15  C10  C7   C6   C5   180.00   0.0  0
 KC8  CONST_16  C10  C7   C8   C9   180.00   0.0  0
 KC8  CONST_18  C1   N    C2   N1     0.00   0.0  0
 KC8  CONST_19  N    C2   N1   C3     0.00   0.0  0
 KC8  CONST_20  C11  N2   C10  C7   180.00   0.0  0
 KC8  CONST_21  C17  N3   C10  C7   180.00   0.0  0
 KC8  CONST_22  C12  C17  N3   C10    0.00   0.0  0
 KC8  CONST_23  C11  N2   C10  N3     0.00   0.0  0
 KC8  CONST_24  N2   C10  N3   C17    0.00   0.0  0
 KC8  CONST_25  C3   N1   C2   O    180.00   0.0  0
 KC8  CONST_26  C1   N    C2   O    180.00   0.0  0
 KC8  CONST_27  O2   C17  N3   C10  180.00   0.0  0
 KC8  CONST_28  H6   C5   C4   C1     0.00   0.0  0
 KC8  CONST_29  H8   C9   C4   C1     0.00   0.0  0
 KC8  CONST_30  H7   C6   C5   C4   180.00   0.0  0
 KC8  CONST_31  H9   C8   C9   C4   180.00   0.0  0
 KC8  CONST_32  H14  C13  C12  C17    0.00   0.0  0
 KC8  CONST_33  H11  C16  C11  N2     0.00   0.0  0
 KC8  CONST_34  H12  C15  C16  C11  180.00   0.0  0
 KC8  CONST_35  H13  C14  C13  C12  180.00   0.0  0
 KC8  CONST_38  H10  N3   C10  C7     0.00   0.0  0
 KC8  Var_01    N2   C10  C7   C6    23.31  30.0  2
 KC8  Var_02    H1   C3   N1   C2    94.30  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
 KC8  chir_01  C1  N  C3  C4  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
 KC8  plan-1  C1   0.020
 KC8  plan-1  C4   0.020
 KC8  plan-1  C5   0.020
 KC8  plan-1  C6   0.020
 KC8  plan-1  C9   0.020
 KC8  plan-1  C8   0.020
 KC8  plan-1  C7   0.020
 KC8  plan-1  C10  0.020
 KC8  plan-1  H6   0.020
 KC8  plan-1  H7   0.020
 KC8  plan-1  H8   0.020
 KC8  plan-1  H9   0.020
 KC8  plan-2  C7   0.020
 KC8  plan-2  C10  0.020
 KC8  plan-2  N3   0.020
 KC8  plan-2  C17  0.020
 KC8  plan-2  O2   0.020
 KC8  plan-2  N2   0.020
 KC8  plan-2  C11  0.020
 KC8  plan-2  C12  0.020
 KC8  plan-2  C16  0.020
 KC8  plan-2  C15  0.020
 KC8  plan-2  C14  0.020
 KC8  plan-2  C13  0.020
 KC8  plan-2  H10  0.020
 KC8  plan-2  H11  0.020
 KC8  plan-2  H12  0.020
 KC8  plan-2  H13  0.020
 KC8  plan-2  H14  0.020
 KC8  plan-3  O    0.020
 KC8  plan-3  C2   0.020
 KC8  plan-3  N1   0.020
 KC8  plan-3  C3   0.020
 KC8  plan-3  N    0.020
 KC8  plan-3  C1   0.020
 KC8  plan-3  H2   0.020
 KC8  plan-3  H15  0.020

