# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:52:02 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(NC(=O)N[C@H]2c3ccccc3c4ccccc24)c(n1)c5ccccc5
#
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
 6UE  6UE  1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea  ligand  50  30  .  2022-07-23  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_6UE
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
 6UE  C2   C  CR16  0  -0.048  -2.6382   2.4109  -0.1771
 6UE  C3   C  CR6   0   0.213  -2.4521   1.0499   0.0349
 6UE  C5   C  CR6   0   0.032  -3.5717  -1.2108   0.1646
 6UE  C7   C  CR16  0  -0.236  -2.6469  -3.3906  -0.3037
 6UE  C9   C  CR16  0  -0.241  -4.5397  -3.1830   1.1621
 6UE  C10  C  CR16  0  -0.282  -4.5343  -1.8091   0.9765
 6UE  C11  C  C     0   0.747  -0.0797   0.7435  -0.3952
 6UE  C12  C  CR15  0  -0.209   2.3039   0.2173  -0.5800
 6UE  C13  C  CR56  0   0.080   3.2099   1.2447   0.0672
 6UE  C15  C  CR16  0  -0.261   3.9681   3.3467   0.9015
 6UE  C18  C  CR56  0   0.120   4.4237   0.6589   0.4344
 6UE  C20  C  CR56  0   0.053   3.1343  -1.0416  -0.4852
 6UE  C21  C  CR16  0  -0.308   2.8056  -2.3228  -0.8826
 6UE  C22  C  CR16  0  -0.262   3.7452  -3.3359  -0.7094
 6UE  O    O  O     0  -0.517  -0.0840   1.4701  -1.3762
 6UE  N2   N  NH1   0  -0.788  -1.2018   0.5271   0.3684
 6UE  N    N  N     0  -0.407  -3.8218   2.9368  -0.4389
 6UE  C4   C  CR6   0   0.223  -3.5981   0.2547  -0.0345
 6UE  C8   C  CR16  0  -0.256  -3.5951  -3.9769   0.5239
 6UE  C6   C  CR16  0  -0.296  -2.6303  -2.0147  -0.4790
 6UE  N1   N  N     0  -0.421  -4.7903   0.8042  -0.2504
 6UE  C1   C  CR6   0   0.336  -4.8650   2.1108  -0.4549
 6UE  C    C  CH3   0  -0.731  -6.2096   2.6924  -0.7517
 6UE  N3   N  NH1   0  -0.668   1.0110   0.0662   0.0374
 6UE  C23  C  CR16  0  -0.251   4.9889  -3.0596  -0.1491
 6UE  C24  C  CR16  0  -0.347   5.3167  -1.7705   0.2557
 6UE  C19  C  CR56  0   0.131   4.3773  -0.7634   0.0885
 6UE  C17  C  CR16  0  -0.345   5.4197   1.4162   1.0338
 6UE  C16  C  CR16  0  -0.252   5.1797   2.7661   1.2648
 6UE  C14  C  CR16  0  -0.316   2.9715   2.5863   0.2950
 6UE  H1   H  HCR6  0   0.282  -1.7998   3.0944  -0.1173
 6UE  H2   H  HCR6  0   0.263  -1.9197  -4.0047  -0.8182
 6UE  H3   H  HCR6  0   0.262  -5.2850  -3.6360   1.8027
 6UE  H4   H  HCR6  0   0.258  -5.2764  -1.1937   1.4682
 6UE  H5   H  HCR5  0   0.297   2.1434   0.4782  -1.6300
 6UE  H6   H  HCR6  0   0.258   3.7997   4.3986   1.0920
 6UE  H7   H  HCR6  0   0.252   1.8378  -2.5410  -1.3175
 6UE  H8   H  HCR6  0   0.260   3.5061  -4.3468  -1.0124
 6UE  H9   H  HNH1  0   0.409  -1.1896  -0.2229   1.0434
 6UE  H10  H  HCR6  0   0.263  -3.6021  -5.0496   0.6670
 6UE  H11  H  HCR6  0   0.265  -1.9018  -1.5746  -1.1476
 6UE  H12  H  HCH3  0   0.261  -6.3963   2.6717  -1.8278
 6UE  H13  H  HCH3  0   0.251  -7.0001   2.1204  -0.2706
 6UE  H14  H  HCH3  0   0.251  -6.2679   3.7302  -0.4303
 6UE  H15  H  HNH1  0   0.403   0.9891  -0.3804   0.9414
 6UE  H16  H  HCR6  0   0.260   5.7074  -3.8591  -0.0233
 6UE  H17  H  HCR6  0   0.250   6.2849  -1.5658   0.6959
 6UE  H18  H  HCR6  0   0.250   6.3642   0.9730   1.3242
 6UE  H19  H  HCR6  0   0.260   5.9443   3.3721   1.7334
 6UE  H20  H  HCR6  0   0.253   2.0326   3.0430   0.0064

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
 6UE  C15  C16  aromatic  1.392  0.020  1.392
 6UE  C15  C14  aromatic  1.393  0.020  1.393
 6UE  C16  C17  aromatic  1.390  0.020  1.390
 6UE  C14  C13  aromatic  1.382  0.020  1.382
 6UE  C    C1   single    1.495  0.020  1.495
 6UE  O    C11  double    1.221  0.020  1.221
 6UE  N    C1   aromatic  1.331  0.020  1.331
 6UE  N    C2   aromatic  1.321  0.020  1.321
 6UE  C17  C18  aromatic  1.387  0.020  1.387
 6UE  C1   N1   aromatic  1.325  0.020  1.325
 6UE  C13  C18  aromatic  1.397  0.020  1.397
 6UE  C13  C12  single    1.515  0.020  1.515
 6UE  C2   C3   aromatic  1.390  0.020  1.390
 6UE  N1   C4   aromatic  1.330  0.020  1.330
 6UE  C18  C19  aromatic  1.464  0.020  1.464
 6UE  C11  N2   single    1.374  0.020  1.374
 6UE  C11  N3   single    1.355  0.020  1.355
 6UE  C3   C4   aromatic  1.397  0.020  1.397
 6UE  C3   N2   single    1.396  0.020  1.396
 6UE  C4   C5   single    1.479  0.020  1.479
 6UE  C6   C7   aromatic  1.387  0.020  1.387
 6UE  C6   C5   aromatic  1.395  0.020  1.395
 6UE  C12  N3   single    1.441  0.020  1.441
 6UE  C12  C20  single    1.511  0.020  1.511
 6UE  C7   C8   aromatic  1.388  0.020  1.388
 6UE  C5   C10  aromatic  1.394  0.020  1.394
 6UE  C19  C20  aromatic  1.397  0.020  1.397
 6UE  C19  C24  aromatic  1.387  0.020  1.387
 6UE  C20  C21  aromatic  1.381  0.020  1.381
 6UE  C8   C9   aromatic  1.389  0.020  1.389
 6UE  C10  C9   aromatic  1.386  0.020  1.386
 6UE  C24  C23  aromatic  1.390  0.020  1.390
 6UE  C21  C22  aromatic  1.392  0.020  1.392
 6UE  C23  C22  aromatic  1.392  0.020  1.392
 6UE  C2   H1   single    0.930  0.020  1.080
 6UE  C7   H2   single    0.930  0.020  1.080
 6UE  C9   H3   single    0.930  0.020  1.080
 6UE  C10  H4   single    0.930  0.020  1.080
 6UE  C12  H5   single    0.970  0.020  1.090
 6UE  C15  H6   single    0.930  0.020  1.080
 6UE  C21  H7   single    0.930  0.020  1.080
 6UE  C22  H8   single    0.930  0.020  1.080
 6UE  N2   H9   single    0.860  0.020  1.020
 6UE  C8   H10  single    0.930  0.020  1.080
 6UE  C6   H11  single    0.930  0.020  1.080
 6UE  C    H12  single    0.970  0.020  1.090
 6UE  C    H13  single    0.970  0.020  1.090
 6UE  C    H14  single    0.970  0.020  1.090
 6UE  N3   H15  single    0.860  0.020  1.020
 6UE  C23  H16  single    0.930  0.020  1.080
 6UE  C24  H17  single    0.930  0.020  1.080
 6UE  C17  H18  single    0.930  0.020  1.080
 6UE  C16  H19  single    0.930  0.020  1.080
 6UE  C14  H20  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
 6UE  H1   C2   N    116.94  3.000
 6UE  H1   C2   C3   120.38  3.000
 6UE  N    C2   C3   122.68  3.000
 6UE  C4   C3   N2   122.26  3.000
 6UE  N2   C3   C2   121.55  3.000
 6UE  C4   C3   C2   116.11  3.000
 6UE  C6   C5   C4   121.39  3.000
 6UE  C6   C5   C10  119.16  3.000
 6UE  C4   C5   C10  119.42  3.000
 6UE  H2   C7   C6   119.65  3.000
 6UE  H2   C7   C8   120.19  3.000
 6UE  C6   C7   C8   120.16  3.000
 6UE  H3   C9   C8   120.07  3.000
 6UE  H3   C9   C10  119.78  3.000
 6UE  C8   C9   C10  120.15  3.000
 6UE  H4   C10  C9   120.00  3.000
 6UE  H4   C10  C5   119.61  3.000
 6UE  C9   C10  C5   120.39  3.000
 6UE  N3   C11  N2   113.65  3.000
 6UE  N3   C11  O    123.85  3.000
 6UE  N2   C11  O    122.50  3.000
 6UE  H5   C12  N3   107.74  3.000
 6UE  H5   C12  C20  109.85  3.000
 6UE  N3   C12  C20  112.27  3.000
 6UE  H5   C12  C13  109.64  3.000
 6UE  C20  C12  C13  102.10  3.000
 6UE  N3   C12  C13  115.13  3.000
 6UE  C14  C13  C18  120.92  3.000
 6UE  C18  C13  C12  110.33  3.000
 6UE  C14  C13  C12  128.74  3.000
 6UE  H6   C15  C14  119.74  3.000
 6UE  H6   C15  C16  119.67  3.000
 6UE  C14  C15  C16  120.59  3.000
 6UE  C17  C18  C19  130.92  3.000
 6UE  C19  C18  C13  108.52  3.000
 6UE  C17  C18  C13  120.56  3.000
 6UE  C19  C20  C21  120.97  3.000
 6UE  C21  C20  C12  128.61  3.000
 6UE  C19  C20  C12  110.41  3.000
 6UE  H7   C21  C22  120.42  3.000
 6UE  H7   C21  C20  120.99  3.000
 6UE  C22  C21  C20  118.59  3.000
 6UE  H8   C22  C23  119.71  3.000
 6UE  H8   C22  C21  119.72  3.000
 6UE  C23  C22  C21  120.57  3.000
 6UE  H9   N2   C11  118.61  3.000
 6UE  H9   N2   C3   116.68  3.000
 6UE  C11  N2   C3   122.66  3.000
 6UE  C1   N    C2   117.23  3.000
 6UE  N1   C4   C5   116.56  3.000
 6UE  C5   C4   C3   122.87  3.000
 6UE  N1   C4   C3   120.54  3.000
 6UE  H10  C8   C9   120.09  3.000
 6UE  H10  C8   C7   120.12  3.000
 6UE  C9   C8   C7   119.79  3.000
 6UE  H11  C6   C7   119.30  3.000
 6UE  H11  C6   C5   120.32  3.000
 6UE  C7   C6   C5   120.34  3.000
 6UE  C1   N1   C4   118.89  3.000
 6UE  C    C1   N1   117.73  3.000
 6UE  N1   C1   N    124.49  3.000
 6UE  C    C1   N    117.78  3.000
 6UE  H14  C    H13  109.39  3.000
 6UE  H14  C    H12  107.45  3.000
 6UE  H13  C    H12  107.54  3.000
 6UE  H14  C    C1   111.15  3.000
 6UE  H13  C    C1   111.17  3.000
 6UE  H12  C    C1   109.99  3.000
 6UE  H15  N3   C12  116.74  3.000
 6UE  H15  N3   C11  119.35  3.000
 6UE  C12  N3   C11  122.22  3.000
 6UE  H16  C23  C24  119.64  3.000
 6UE  H16  C23  C22  119.57  3.000
 6UE  C24  C23  C22  120.79  3.000
 6UE  H17  C24  C19  121.13  3.000
 6UE  H17  C24  C23  120.29  3.000
 6UE  C19  C24  C23  118.58  3.000
 6UE  C24  C19  C20  120.49  3.000
 6UE  C24  C19  C18  130.93  3.000
 6UE  C20  C19  C18  108.58  3.000
 6UE  H18  C17  C16  120.22  3.000
 6UE  H18  C17  C18  121.24  3.000
 6UE  C16  C17  C18  118.55  3.000
 6UE  H19  C16  C17  119.58  3.000
 6UE  H19  C16  C15  119.63  3.000
 6UE  C17  C16  C15  120.79  3.000
 6UE  H20  C14  C15  120.41  3.000
 6UE  H20  C14  C13  121.00  3.000
 6UE  C15  C14  C13  118.59  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
 6UE  CONST_01  N1   C1   N    C2     0.00   0.0  0
 6UE  CONST_02  N1   C4   C3   C2     0.00   0.0  0
 6UE  CONST_03  C5   C4   C3   C2   180.00   0.0  0
 6UE  CONST_04  C1   N    C2   C3     0.00   0.0  0
 6UE  CONST_05  C1   N1   C4   C3     0.00   0.0  0
 6UE  CONST_08  C1   N1   C4   C5   180.00   0.0  0
 6UE  CONST_09  C8   C7   C6   C5     0.00   0.0  0
 6UE  CONST_10  C8   C9   C10  C5     0.00   0.0  0
 6UE  CONST_11  C4   C5   C6   C7   180.00   0.0  0
 6UE  CONST_12  C10  C5   C6   C7     0.00   0.0  0
 6UE  CONST_13  C10  C9   C8   C7     0.00   0.0  0
 6UE  CONST_14  C6   C7   C8   C9     0.00   0.0  0
 6UE  CONST_15  C4   C5   C10  C9   180.00   0.0  0
 6UE  CONST_16  C6   C5   C10  C9     0.00   0.0  0
 6UE  CONST_18  C16  C15  C14  C13    0.00   0.0  0
 6UE  CONST_19  C16  C17  C18  C13    0.00   0.0  0
 6UE  CONST_20  C20  C19  C18  C13    0.00   0.0  0
 6UE  CONST_21  C24  C19  C18  C13  180.00   0.0  0
 6UE  CONST_22  C18  C17  C16  C15    0.00   0.0  0
 6UE  CONST_23  C18  C13  C14  C15    0.00   0.0  0
 6UE  CONST_24  C21  C20  C19  C18  180.00   0.0  0
 6UE  CONST_25  C23  C24  C19  C18  180.00   0.0  0
 6UE  CONST_26  C17  C18  C19  C20  180.00   0.0  0
 6UE  CONST_27  C23  C24  C19  C20    0.00   0.0  0
 6UE  CONST_28  C23  C22  C21  C20    0.00   0.0  0
 6UE  CONST_29  C24  C19  C20  C21    0.00   0.0  0
 6UE  CONST_30  C24  C23  C22  C21    0.00   0.0  0
 6UE  CONST_31  C19  C20  C21  C22    0.00   0.0  0
 6UE  CONST_32  C19  C24  C23  C22    0.00   0.0  0
 6UE  CONST_33  C4   N1   C1   N      0.00   0.0  0
 6UE  CONST_34  C4   C3   C2   N      0.00   0.0  0
 6UE  CONST_36  C17  C18  C19  C24    0.00   0.0  0
 6UE  CONST_37  C16  C17  C18  C19  180.00   0.0  0
 6UE  CONST_38  C14  C13  C18  C19  180.00   0.0  0
 6UE  CONST_39  C14  C15  C16  C17    0.00   0.0  0
 6UE  CONST_40  C14  C13  C18  C17    0.00   0.0  0
 6UE  CONST_41  C    C1   N    C2   180.00   0.0  0
 6UE  CONST_42  N2   C3   C4   C5     0.00   0.0  0
 6UE  CONST_43  N    C2   C3   N2   180.00   0.0  0
 6UE  CONST_44  N1   C4   C3   N2   180.00   0.0  0
 6UE  CONST_45  C    C1   N1   C4   180.00   0.0  0
 6UE  CONST_46  H2   C7   C6   C5   180.00   0.0  0
 6UE  CONST_47  H3   C9   C10  C5   180.00   0.0  0
 6UE  CONST_48  H11  C6   C5   C10  180.00   0.0  0
 6UE  CONST_49  H10  C8   C9   C10  180.00   0.0  0
 6UE  CONST_50  H20  C14  C13  C12    0.00   0.0  0
 6UE  CONST_51  H7   C21  C20  C12    0.00   0.0  0
 6UE  CONST_52  H6   C15  C14  C13  180.00   0.0  0
 6UE  CONST_53  H18  C17  C18  C13  180.00   0.0  0
 6UE  CONST_54  H19  C16  C17  C18  180.00   0.0  0
 6UE  CONST_55  H17  C24  C19  C18    0.00   0.0  0
 6UE  CONST_56  H8   C22  C21  C20  180.00   0.0  0
 6UE  CONST_57  H16  C23  C22  C21  180.00   0.0  0
 6UE  CONST_58  H1   C2   C3   C4   180.00   0.0  0
 6UE  CONST_59  H4   C10  C5   C4     0.00   0.0  0
 6UE  CONST_63  O    C11  N2   C3     0.00   0.0  0
 6UE  CONST_64  O    C11  N3   C12    0.00   0.0  0
 6UE  CONST_65  N3   C11  N2   C3   180.00   0.0  0
 6UE  CONST_66  N2   C11  N3   C12  180.00   0.0  0
 6UE  CONST_67  H15  N3   C11  O    180.00   0.0  0
 6UE  Var_01    H12  C    C1   N     89.88  30.0  2

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
 6UE  chir_01  C12  C13  N3  C20  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
 6UE  plan-1  C2   0.020
 6UE  plan-1  C3   0.020
 6UE  plan-1  C5   0.020
 6UE  plan-1  N2   0.020
 6UE  plan-1  N    0.020
 6UE  plan-1  C4   0.020
 6UE  plan-1  N1   0.020
 6UE  plan-1  C1   0.020
 6UE  plan-1  C    0.020
 6UE  plan-1  H1   0.020
 6UE  plan-2  C5   0.020
 6UE  plan-2  C7   0.020
 6UE  plan-2  C9   0.020
 6UE  plan-2  C10  0.020
 6UE  plan-2  C4   0.020
 6UE  plan-2  C8   0.020
 6UE  plan-2  C6   0.020
 6UE  plan-2  H2   0.020
 6UE  plan-2  H3   0.020
 6UE  plan-2  H4   0.020
 6UE  plan-2  H10  0.020
 6UE  plan-2  H11  0.020
 6UE  plan-3  C12  0.020
 6UE  plan-3  C13  0.020
 6UE  plan-3  C15  0.020
 6UE  plan-3  C18  0.020
 6UE  plan-3  C20  0.020
 6UE  plan-3  C21  0.020
 6UE  plan-3  C22  0.020
 6UE  plan-3  C23  0.020
 6UE  plan-3  C24  0.020
 6UE  plan-3  C19  0.020
 6UE  plan-3  C17  0.020
 6UE  plan-3  C16  0.020
 6UE  plan-3  C14  0.020
 6UE  plan-3  H6   0.020
 6UE  plan-3  H7   0.020
 6UE  plan-3  H8   0.020
 6UE  plan-3  H16  0.020
 6UE  plan-3  H17  0.020
 6UE  plan-3  H18  0.020
 6UE  plan-3  H19  0.020
 6UE  plan-3  H20  0.020
 6UE  plan-4  C3   0.020
 6UE  plan-4  C11  0.020
 6UE  plan-4  C12  0.020
 6UE  plan-4  O    0.020
 6UE  plan-4  N2   0.020
 6UE  plan-4  N3   0.020
 6UE  plan-4  H9   0.020
 6UE  plan-4  H15  0.020

