# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:45:19 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (5R)-2-amino-5-[4-fluoro-3-(pyrimidin-5-yl)phenyl]-3-methyl-5-[4-(trifluoromethoxy)phenyl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](C1=O)(c2ccc(OC(F)(F)F)cc2)c3ccc(F)c(c3)c4cncnc4)N
#
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
 569  569  (5R)-2-amino-5-[4-fluoro-3-(pyrimidin-5-yl)phenyl]-3-methyl-5-[4-(trifluoromethoxy)phenyl]-3,5-dihydro-4H-imidazol-4-one  ligand  47  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_569
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
 569  C1    C  CH3   0  -0.557  -0.2053   5.4805   0.1602
 569  F1    F  F     0  -0.299  -3.9954  -3.0519   1.2084
 569  N1    N  NR5   0  -0.521   0.0073   4.0591   0.2974
 569  O1    O  O     0  -0.436  -0.7151   3.3383  -1.7562
 569  C2    C  CR5   0   0.591  -0.2648   3.1263  -0.6544
 569  F2    F  F     0  -0.277  -5.8198  -3.1581   0.0651
 569  N2    N  N     0  -0.467   0.5021   2.1226   1.3427
 569  O2    O  O2    0  -0.523  -4.6612  -1.3528  -0.0658
 569  C3    C  CR5   0  -0.253   0.0859   1.7785   0.0022
 569  F3    F  F     0  -0.299  -3.9076  -3.2642  -0.9215
 569  N3    N  NH2   0  -0.844   0.7108   4.1150   2.5450
 569  C4    C  CR5   0   0.687   0.4431   3.3997   1.4418
 569  F4    F  F     0  -0.302   4.2771  -1.0849  -2.4410
 569  N4    N  N     0  -0.387   4.7660  -2.2513   2.2757
 569  C5    C  CR6   0   0.171  -1.1681   0.9107  -0.0063
 569  N5    N  N     0  -0.388   4.5270  -3.8621   0.5652
 569  C6    C  CR16  0  -0.279  -1.6481   0.3816  -1.2024
 569  C7    C  CR16  0  -0.289  -2.8002  -0.3865  -1.2285
 569  C8    C  CR6   0   0.304  -3.4732  -0.6286  -0.0423
 569  C9    C  CR16  0  -0.284  -3.0197  -0.1145   1.1572
 569  C10   C  CR16  0  -0.310  -1.8660   0.6581   1.1677
 569  C11   C  CT    0   1.072  -4.5852  -2.6817   0.0702
 569  C12   C  CR6   0   0.172   1.2230   1.0529  -0.7119
 569  C13   C  CR16  0  -0.306   1.5814   1.2754  -2.0353
 569  C14   C  CR16  0  -0.393   2.6104   0.5488  -2.6218
 569  C15   C  CR6   0   0.519   3.2682  -0.4038  -1.8779
 569  C16   C  CR6   0  -0.128   2.9375  -0.6668  -0.5535
 569  C17   C  CR16  0  -0.309   1.9107   0.0820   0.0107
 569  C18   C  CR6   0  -0.038   3.6603  -1.6678   0.2464
 569  C19   C  CR16  0  -0.035   4.1346  -1.3660   1.5188
 569  C20   C  CR16  0   0.055   4.9349  -3.4583   1.7588
 569  C21   C  CR16  0  -0.031   3.8925  -2.9712  -0.1827
 569  H1    H  HCH3  0   0.268  -0.9690   5.8296   0.8539
 569  H1A   H  HCH3  0   0.265   0.7189   6.0301   0.3336
 569  H1B   H  HCH3  0   0.278  -0.5368   5.6846  -0.8535
 569  HN3   H  HNH2  0   0.409   1.1660   3.6285   3.2995
 569  HN3A  H  HNH2  0   0.415   0.9301   5.0946   2.4759
 569  H6    H  HCR6  0   0.268  -1.1248   0.5575  -2.1324
 569  H7    H  HCR6  0   0.281  -3.1728  -0.7766  -2.1663
 569  H9    H  HCR6  0   0.279  -3.5618  -0.2956   2.0760
 569  H10   H  HCR6  0   0.267  -1.5061   1.0591   2.1044
 569  H13   H  HCR6  0   0.273   1.0732   2.0136  -2.6386
 569  H14   H  HCR6  0   0.285   2.8991   0.7327  -3.6481
 569  H17   H  HCR6  0   0.270   1.6342  -0.1054   1.0403
 569  H19   H  HCR6  0   0.280   4.0034  -0.3703   1.9306
 569  H20   H  HCR6  0   0.270   5.4535  -4.1867   2.3720
 569  H21   H  HCR6  0   0.278   3.5372  -3.3126  -1.1484

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
 569  N1   C1    single    1.444  0.020  1.444
 569  C1   H1    single    0.970  0.020  1.090
 569  C1   H1A   single    0.970  0.020  1.090
 569  C1   H1B   single    0.970  0.020  1.090
 569  F1   C11   single    1.334  0.020  1.334
 569  C4   N1    single    1.391  0.020  1.391
 569  N1   C2    single    1.360  0.020  1.360
 569  C2   O1    double    1.209  0.020  1.209
 569  C3   C2    single    1.540  0.020  1.540
 569  C11  F2    single    1.323  0.020  1.323
 569  N2   C4    double    1.282  0.020  1.282
 569  N2   C3    single    1.445  0.020  1.445
 569  C8   O2    single    1.391  0.020  1.391
 569  O2   C11   single    1.338  0.020  1.338
 569  C12  C3    single    1.526  0.020  1.526
 569  C3   C5    single    1.525  0.020  1.525
 569  F3   C11   single    1.335  0.020  1.335
 569  N3   C4    single    1.342  0.020  1.342
 569  N3   HN3   single    0.890  0.020  1.040
 569  N3   HN3A  single    0.890  0.020  1.040
 569  F4   C15   single    1.341  0.020  1.341
 569  N4   C19   aromatic  1.325  0.020  1.325
 569  N4   C20   aromatic  1.324  0.020  1.324
 569  C6   C5    aromatic  1.393  0.020  1.393
 569  C5   C10   aromatic  1.389  0.020  1.389
 569  C20  N5    aromatic  1.324  0.020  1.324
 569  N5   C21   aromatic  1.325  0.020  1.325
 569  C6   C7    aromatic  1.385  0.020  1.385
 569  C6   H6    single    0.930  0.020  1.080
 569  C7   C8    aromatic  1.385  0.020  1.385
 569  C7   H7    single    0.930  0.020  1.080
 569  C8   C9    aromatic  1.382  0.020  1.382
 569  C10  C9    aromatic  1.389  0.020  1.389
 569  C9   H9    single    0.930  0.020  1.080
 569  C10  H10   single    0.930  0.020  1.080
 569  C17  C12   aromatic  1.392  0.020  1.392
 569  C12  C13   aromatic  1.389  0.020  1.389
 569  C14  C13   aromatic  1.390  0.020  1.390
 569  C13  H13   single    0.930  0.020  1.080
 569  C15  C14   aromatic  1.376  0.020  1.376
 569  C14  H14   single    0.930  0.020  1.080
 569  C16  C15   aromatic  1.390  0.020  1.390
 569  C18  C16   single    1.471  0.020  1.471
 569  C16  C17   aromatic  1.390  0.020  1.390
 569  C17  H17   single    0.930  0.020  1.080
 569  C19  C18   aromatic  1.391  0.020  1.391
 569  C18  C21   aromatic  1.392  0.020  1.392
 569  C19  H19   single    0.930  0.020  1.080
 569  C20  H20   single    0.930  0.020  1.080
 569  C21  H21   single    0.930  0.020  1.080

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
 569  H1B   C1   H1A  108.22  3.000
 569  H1B   C1   H1   108.68  3.000
 569  H1A   C1   H1   109.38  3.000
 569  H1B   C1   N1   108.59  3.000
 569  H1A   C1   N1   110.90  3.000
 569  H1    C1   N1   111.00  3.000
 569  C4    N1   C2   108.26  3.000
 569  C2    N1   C1   125.40  3.000
 569  C4    N1   C1   126.23  3.000
 569  C3    C2   O1   128.83  3.000
 569  C3    C2   N1   104.85  3.000
 569  O1    C2   N1   126.29  3.000
 569  C4    N2   C3   107.19  3.000
 569  C11   O2   C8   117.82  3.000
 569  C12   C3   C5   109.84  3.000
 569  C5    C3   N2   112.18  3.000
 569  C12   C3   N2   109.43  3.000
 569  C5    C3   C2   107.97  3.000
 569  C12   C3   C2   112.73  3.000
 569  N2    C3   C2   104.64  3.000
 569  HN3A  N3   HN3  115.05  3.000
 569  HN3A  N3   C4   120.40  3.000
 569  HN3   N3   C4   116.67  3.000
 569  N3    C4   N2   125.83  3.000
 569  N3    C4   N1   119.10  3.000
 569  N2    C4   N1   115.02  3.000
 569  C20   N4   C19  116.55  3.000
 569  C10   C5   C6   118.92  3.000
 569  C10   C5   C3   120.79  3.000
 569  C6    C5   C3   120.28  3.000
 569  C21   N5   C20  116.82  3.000
 569  H6    C6   C7   118.46  3.000
 569  H6    C6   C5   120.64  3.000
 569  C7    C6   C5   120.89  3.000
 569  H7    C7   C8   120.80  3.000
 569  H7    C7   C6   120.18  3.000
 569  C8    C7   C6   119.01  3.000
 569  C9    C8   C7   121.27  3.000
 569  C9    C8   O2   119.24  3.000
 569  C7    C8   O2   119.43  3.000
 569  H9    C9   C10  120.19  3.000
 569  H9    C9   C8   120.70  3.000
 569  C10   C9   C8   119.10  3.000
 569  H10   C10  C9   119.33  3.000
 569  H10   C10  C5   119.86  3.000
 569  C9    C10  C5   120.81  3.000
 569  F3    C11  O2   112.75  3.000
 569  F3    C11  F2   108.28  3.000
 569  O2    C11  F2   107.71  3.000
 569  F3    C11  F1   106.75  3.000
 569  O2    C11  F1   112.79  3.000
 569  F2    C11  F1   108.41  3.000
 569  C17   C12  C13  118.61  3.000
 569  C13   C12  C3   124.18  3.000
 569  C17   C12  C3   117.18  3.000
 569  H13   C13  C14  118.03  3.000
 569  H13   C13  C12  121.34  3.000
 569  C14   C13  C12  120.63  3.000
 569  H14   C14  C15  120.20  3.000
 569  H14   C14  C13  120.61  3.000
 569  C15   C14  C13  119.20  3.000
 569  C16   C15  C14  122.16  3.000
 569  C16   C15  F4   118.87  3.000
 569  C14   C15  F4   118.96  3.000
 569  C18   C16  C17  120.57  3.000
 569  C17   C16  C15  117.41  3.000
 569  C18   C16  C15  122.00  3.000
 569  H17   C17  C16  118.78  3.000
 569  H17   C17  C12  119.23  3.000
 569  C16   C17  C12  121.99  3.000
 569  C21   C18  C19  115.36  3.000
 569  C21   C18  C16  123.47  3.000
 569  C19   C18  C16  121.14  3.000
 569  H19   C19  C18  120.32  3.000
 569  H19   C19  N4   116.99  3.000
 569  C18   C19  N4   122.69  3.000
 569  H20   C20  N5   116.89  3.000
 569  H20   C20  N4   116.92  3.000
 569  N5    C20  N4   126.20  3.000
 569  H21   C21  C18  120.99  3.000
 569  H21   C21  N5   116.62  3.000
 569  C18   C21  N5   122.38  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
 569  CONST_01  C16  C18  C19  N4   180.00   0.0  0
 569  CONST_02  C21  C18  C19  N4     0.00   0.0  0
 569  CONST_03  C21  N5   C20  N4     0.00   0.0  0
 569  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 569  CONST_05  C8   C9   C10  C5     0.00   0.0  0
 569  CONST_06  C19  N4   C20  N5     0.00   0.0  0
 569  CONST_07  C16  C18  C21  N5   180.00   0.0  0
 569  CONST_08  C19  C18  C21  N5     0.00   0.0  0
 569  CONST_09  C9   C10  C5   C6     0.00   0.0  0
 569  CONST_10  C9   C8   C7   C6     0.00   0.0  0
 569  CONST_11  C10  C5   C6   C7     0.00   0.0  0
 569  CONST_12  C10  C9   C8   C7     0.00   0.0  0
 569  CONST_13  C15  C16  C17  C12    0.00   0.0  0
 569  CONST_14  C18  C16  C17  C12  180.00   0.0  0
 569  CONST_15  C15  C14  C13  C12    0.00   0.0  0
 569  CONST_16  C16  C17  C12  C13    0.00   0.0  0
 569  CONST_17  C16  C15  C14  C13    0.00   0.0  0
 569  CONST_18  C17  C12  C13  C14    0.00   0.0  0
 569  CONST_19  C18  C16  C15  C14  180.00   0.0  0
 569  CONST_20  C17  C16  C15  C14    0.00   0.0  0
 569  CONST_25  C20  N4   C19  C18    0.00   0.0  0
 569  CONST_26  C20  N5   C21  C18    0.00   0.0  0
 569  CONST_27  C16  C17  C12  C3   180.00   0.0  0
 569  CONST_28  C14  C13  C12  C3   180.00   0.0  0
 569  CONST_29  C7   C6   C5   C3   180.00   0.0  0
 569  CONST_30  C9   C10  C5   C3   180.00   0.0  0
 569  CONST_31  C3   N2   C4   N1     0.00   0.0  0
 569  CONST_32  N2   C4   N1   C2     0.00   0.0  0
 569  CONST_33  C4   N1   C2   C3     0.00   0.0  0
 569  CONST_34  C6   C7   C8   O2   180.00   0.0  0
 569  CONST_35  C10  C9   C8   O2   180.00   0.0  0
 569  CONST_36  C13  C14  C15  F4   180.00   0.0  0
 569  CONST_37  C18  C16  C15  F4     0.00   0.0  0
 569  CONST_38  C17  C16  C15  F4   180.00   0.0  0
 569  CONST_39  N2   C4   N1   C1   180.00   0.0  0
 569  CONST_40  C3   C2   N1   C1   180.00   0.0  0
 569  CONST_41  C4   N1   C2   O1   180.00   0.0  0
 569  CONST_42  N3   C4   N1   C2   180.00   0.0  0
 569  CONST_43  N3   C4   N2   C3   180.00   0.0  0
 569  CONST_44  H17  C17  C12  C3     0.00   0.0  0
 569  CONST_45  H13  C13  C12  C3     0.00   0.0  0
 569  CONST_46  H6   C6   C5   C3     0.00   0.0  0
 569  CONST_47  H10  C10  C5   C3     0.00   0.0  0
 569  CONST_48  H7   C7   C6   C5   180.00   0.0  0
 569  CONST_49  H9   C9   C10  C5   180.00   0.0  0
 569  CONST_50  H14  C14  C13  C12  180.00   0.0  0
 569  CONST_51  H19  C19  C18  C16    0.00   0.0  0
 569  CONST_52  H21  C21  C18  C16    0.00   0.0  0
 569  CONST_53  H20  C20  N4   C19  180.00   0.0  0
 569  CONST_54  N3   C4   N1   C1     0.00   0.0  0
 569  CONST_55  O1   C2   N1   C1     0.00   0.0  0
 569  CONST_56  HN3  N3   C4   N1   180.00   0.0  0
 569  Var_01    H1   C1   N1   C2   114.67  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
 569  chir_01  C3  N2  C12  C5  negativ

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
 569  plan-1  N4    0.020
 569  plan-1  N5    0.020
 569  plan-1  C16   0.020
 569  plan-1  C18   0.020
 569  plan-1  C19   0.020
 569  plan-1  C20   0.020
 569  plan-1  C21   0.020
 569  plan-1  H19   0.020
 569  plan-1  H20   0.020
 569  plan-1  H21   0.020
 569  plan-2  O2    0.020
 569  plan-2  C3    0.020
 569  plan-2  C5    0.020
 569  plan-2  C6    0.020
 569  plan-2  C7    0.020
 569  plan-2  C8    0.020
 569  plan-2  C9    0.020
 569  plan-2  C10   0.020
 569  plan-2  H6    0.020
 569  plan-2  H7    0.020
 569  plan-2  H9    0.020
 569  plan-2  H10   0.020
 569  plan-3  C3    0.020
 569  plan-3  F4    0.020
 569  plan-3  C12   0.020
 569  plan-3  C13   0.020
 569  plan-3  C14   0.020
 569  plan-3  C15   0.020
 569  plan-3  C16   0.020
 569  plan-3  C17   0.020
 569  plan-3  C18   0.020
 569  plan-3  H13   0.020
 569  plan-3  H14   0.020
 569  plan-3  H17   0.020
 569  plan-4  C1    0.020
 569  plan-4  N1    0.020
 569  plan-4  O1    0.020
 569  plan-4  C2    0.020
 569  plan-4  N2    0.020
 569  plan-4  C3    0.020
 569  plan-4  N3    0.020
 569  plan-4  C4    0.020
 569  plan-4  HN3   0.020
 569  plan-4  HN3A  0.020

