# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 16:47:35 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-(1,3-benzodioxol-5-yloxy)-2-[4-(1H-imidazol-1-yl)phenoxy]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Oc2ccc(Oc3ccnc(Oc4ccc(cc4)n5ccnc5)n3)cc2O1
#
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
 333  333  4-(1,3-benzodioxol-5-yloxy)-2-[4-(1H-imidazol-1-yl)phenoxy]pyrimidine  ligand  42  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_333
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
 333  C36   C  CR16  0  -0.361  -1.3335  -1.9774  -1.0855
 333  C35   C  CR56  0   0.314  -2.2306  -2.9615  -0.7637
 333  O39   O  O     0  -0.486  -2.8387  -3.8462  -1.5882
 333  C38   C  CH2   0   0.060  -3.8200  -4.5060  -0.7987
 333  O37   O  O     0  -0.486  -3.5037  -4.2389   0.5597
 333  C34   C  CR56  0   0.306  -2.6320  -3.2007   0.5428
 333  C33   C  CR16  0  -0.347  -2.1527  -2.4598   1.5921
 333  C32   C  CR16  0  -0.325  -1.2231  -1.4551   1.2913
 333  C31   C  CR6   0   0.335  -0.8346  -1.2321  -0.0129
 333  O28   O  O2    0  -0.504   0.0622  -0.2022  -0.2586
 333  C23   C  CR6   0   0.559   1.3094  -0.5271  -0.6074
 333  N22   N  N     0  -0.467   1.6231  -1.7969  -0.7034
 333  C24   C  CR16  0  -0.418   2.2351   0.4856  -0.8551
 333  C25   C  CR16  0  -0.021   3.4952   0.0490  -1.2058
 333  N26   N  N     0  -0.447   3.8270  -1.2383  -1.3291
 333  C21   C  CR6   0   0.588   2.8516  -2.0834  -1.0767
 333  O17   O  O2    0  -0.498   3.1639  -3.3812  -1.2219
 333  C14   C  CR6   0   0.343   2.1239  -4.2840  -1.1073
 333  C15   C  CR16  0  -0.295   1.9955  -5.0224   0.0536
 333  C16   C  CR16  0  -0.299   0.9459  -5.9200   0.1775
 333  C13   C  CR16  0  -0.277   1.2263  -4.4338  -2.1509
 333  C12   C  CR16  0  -0.288   0.1623  -5.3066  -2.0153
 333  C11   C  CR6   0   0.363   0.0187  -6.0464  -0.8477
 333  N3    N  NR5   0  -0.525  -1.0763  -6.9229  -0.7032
 333  C4    C  CR15  0  -0.111  -1.7921  -7.1572   0.4438
 333  C5    C  CR15  0  -0.216  -2.7521  -8.0593   0.0963
 333  NFE   N  N     0  -0.445  -2.6417  -8.3847  -1.2282
 333  C2    C  CR15  0   0.083  -1.6331  -7.6893  -1.6765
 333  H36   H  HCR6  0   0.284  -1.0185  -1.7966  -2.1038
 333  H381  H  HCH2  0   0.243  -3.7842  -5.5796  -0.9819
 333  H382  H  HCH2  0   0.240  -4.8135  -4.1082  -1.0344
 333  H33   H  HCR6  0   0.278  -2.4641  -2.6419   2.6113
 333  H32   H  HCR6  0   0.272  -0.8110  -0.8491   2.0871
 333  H24   H  HCR6  0   0.290   1.9903   1.5341  -0.7757
 333  H25   H  HCR6  0   0.288   4.2809   0.7674  -1.4061
 333  H15   H  HCR6  0   0.279   2.7064  -4.9025   0.8603
 333  H16   H  HCR6  0   0.283   0.8567  -6.5142   1.0774
 333  H13   H  HCR6  0   0.280   1.3314  -3.8482  -3.0550
 333  H12   H  HCR6  0   0.281  -0.5689  -5.3823  -2.8083
 333  H4    H  HCR5  0   0.297  -1.5759  -6.6561   1.3717
 333  H5    H  HCR5  0   0.258  -3.5167  -8.4845   0.7276
 333  H2    H  HCR5  0   0.292  -1.2437  -7.7134  -2.6831

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
 333  C36  C31   aromatic  1.398  0.020  1.398
 333  C36  C35   aromatic  1.370  0.020  1.370
 333  C36  H36   single    0.930  0.020  1.080
 333  C35  O39   single    1.354  0.020  1.354
 333  C35  C34   aromatic  1.388  0.020  1.388
 333  O39  C38   single    1.422  0.020  1.422
 333  C38  O37   single    1.420  0.020  1.420
 333  C38  H381  single    0.970  0.020  1.090
 333  C38  H382  single    0.970  0.020  1.090
 333  O37  C34   single    1.356  0.020  1.356
 333  C34  C33   aromatic  1.371  0.020  1.371
 333  C33  C32   aromatic  1.401  0.020  1.401
 333  C33  H33   single    0.930  0.020  1.080
 333  C32  C31   aromatic  1.379  0.020  1.379
 333  C32  H32   single    0.930  0.020  1.080
 333  C31  O28   single    1.388  0.020  1.388
 333  O28  C23   single    1.335  0.020  1.335
 333  C23  C24   aromatic  1.394  0.020  1.394
 333  C23  N22   aromatic  1.312  0.020  1.312
 333  N22  C21   aromatic  1.316  0.020  1.316
 333  C24  C25   aromatic  1.379  0.020  1.379
 333  C24  H24   single    0.930  0.020  1.080
 333  C25  N26   aromatic  1.335  0.020  1.335
 333  C25  H25   single    0.930  0.020  1.080
 333  N26  C21   aromatic  1.315  0.020  1.315
 333  C21  O17   single    1.343  0.020  1.343
 333  O17  C14   single    1.382  0.020  1.382
 333  C14  C15   aromatic  1.382  0.020  1.382
 333  C14  C13   aromatic  1.385  0.020  1.385
 333  C15  C16   aromatic  1.387  0.020  1.387
 333  C15  H15   single    0.930  0.020  1.080
 333  C16  C11   aromatic  1.388  0.020  1.388
 333  C16  H16   single    0.930  0.020  1.080
 333  C13  C12   aromatic  1.383  0.020  1.383
 333  C13  H13   single    0.930  0.020  1.080
 333  C12  C11   aromatic  1.390  0.020  1.390
 333  C12  H12   single    0.930  0.020  1.080
 333  C11  N3    single    1.410  0.020  1.410
 333  N3   C4    aromatic  1.372  0.020  1.372
 333  N3   C2    aromatic  1.358  0.020  1.358
 333  C4   C5    aromatic  1.362  0.020  1.362
 333  C4   H4    single    0.930  0.020  1.080
 333  C5   NFE   aromatic  1.368  0.020  1.368
 333  C5   H5    single    0.930  0.020  1.080
 333  NFE  C2    aromatic  1.305  0.020  1.305
 333  C2   H2    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
 333  H36   C36  C31   121.97  3.000
 333  H36   C36  C35   122.15  3.000
 333  C31   C36  C35   115.88  3.000
 333  C34   C35  O39   109.33  3.000
 333  C34   C35  C36   122.30  3.000
 333  O39   C35  C36   128.36  3.000
 333  C38   O39  C35   105.97  3.000
 333  H382  C38  H381  110.56  3.000
 333  H382  C38  O37   109.85  3.000
 333  H381  C38  O37   109.81  3.000
 333  H382  C38  O39   109.74  3.000
 333  H381  C38  O39   109.94  3.000
 333  O37   C38  O39   106.87  3.000
 333  C34   O37  C38   105.98  3.000
 333  C33   C34  O37   128.98  3.000
 333  C33   C34  C35   121.77  3.000
 333  O37   C34  C35   109.25  3.000
 333  H33   C33  C32   120.94  3.000
 333  H33   C33  C34   121.99  3.000
 333  C32   C33  C34   117.07  3.000
 333  H32   C32  C31   119.86  3.000
 333  H32   C32  C33   119.76  3.000
 333  C31   C32  C33   120.38  3.000
 333  O28   C31  C32   118.01  3.000
 333  O28   C31  C36   119.37  3.000
 333  C32   C31  C36   122.60  3.000
 333  C23   O28  C31   118.00  3.000
 333  C24   C23  N22   122.10  3.000
 333  N22   C23  O28   118.56  3.000
 333  C24   C23  O28   119.33  3.000
 333  C21   N22  C23   117.06  3.000
 333  H24   C24  C25   122.24  3.000
 333  H24   C24  C23   122.81  3.000
 333  C25   C24  C23   114.95  3.000
 333  H25   C25  N26   116.24  3.000
 333  H25   C25  C24   119.98  3.000
 333  N26   C25  C24   123.78  3.000
 333  C21   N26  C25   114.68  3.000
 333  O17   C21  N26   115.33  3.000
 333  O17   C21  N22   117.28  3.000
 333  N26   C21  N22   127.39  3.000
 333  C14   O17  C21   116.57  3.000
 333  C13   C14  C15   121.01  3.000
 333  C13   C14  O17   119.74  3.000
 333  C15   C14  O17   119.25  3.000
 333  H15   C15  C16   120.16  3.000
 333  H15   C15  C14   120.41  3.000
 333  C16   C15  C14   119.43  3.000
 333  H16   C16  C11   120.61  3.000
 333  H16   C16  C15   119.49  3.000
 333  C11   C16  C15   119.91  3.000
 333  H13   C13  C12   119.88  3.000
 333  H13   C13  C14   120.54  3.000
 333  C12   C13  C14   119.55  3.000
 333  H12   C12  C11   120.60  3.000
 333  H12   C12  C13   119.51  3.000
 333  C11   C12  C13   119.87  3.000
 333  N3    C11  C12   119.82  3.000
 333  N3    C11  C16   119.98  3.000
 333  C12   C11  C16   120.20  3.000
 333  C2    N3   C4    106.79  3.000
 333  C2    N3   C11   126.57  3.000
 333  C4    N3   C11   126.65  3.000
 333  H4    C4   C5    132.04  3.000
 333  H4    C4   N3    122.43  3.000
 333  C5    C4   N3    105.51  3.000
 333  H5    C5   NFE   121.99  3.000
 333  H5    C5   C4    127.67  3.000
 333  NFE   C5   C4    110.33  3.000
 333  C2    NFE  C5    105.56  3.000
 333  H2    C2   NFE   125.98  3.000
 333  H2    C2   N3    122.20  3.000
 333  NFE   C2   N3    111.81  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
 333  CONST_01  C33  C32  C31  C36     0.00   0.0  0
 333  CONST_02  C33  C34  C35  C36     0.00   0.0  0
 333  CONST_03  C32  C31  C36  C35     0.00   0.0  0
 333  CONST_04  C32  C33  C34  C35     0.00   0.0  0
 333  CONST_05  C31  C36  C35  C34     0.00   0.0  0
 333  CONST_06  C31  C32  C33  C34     0.00   0.0  0
 333  CONST_07  N26  C25  C24  C23     0.00   0.0  0
 333  CONST_08  N26  C21  N22  C23     0.00   0.0  0
 333  CONST_09  C25  C24  C23  N22     0.00   0.0  0
 333  CONST_10  C25  N26  C21  N22     0.00   0.0  0
 333  CONST_11  C21  N22  C23  C24     0.00   0.0  0
 333  CONST_12  C21  N26  C25  C24     0.00   0.0  0
 333  CONST_13  C11  C16  C15  C14     0.00   0.0  0
 333  CONST_14  C11  C12  C13  C14     0.00   0.0  0
 333  CONST_15  C12  C13  C14  C15     0.00   0.0  0
 333  CONST_16  C12  C11  C16  C15     0.00   0.0  0
 333  CONST_17  N3   C11  C16  C15   180.00   0.0  0
 333  CONST_18  C13  C14  C15  C16     0.00   0.0  0
 333  CONST_19  C13  C12  C11  C16     0.00   0.0  0
 333  CONST_22  N3   C11  C12  C13   180.00   0.0  0
 333  CONST_25  C5   C4   N3   C11   180.00   0.0  0
 333  CONST_26  NFE  C2   N3   C11   180.00   0.0  0
 333  CONST_27  NFE  C5   C4   N3      0.00   0.0  0
 333  CONST_28  C5   NFE  C2   N3      0.00   0.0  0
 333  CONST_29  NFE  C2   N3   C4      0.00   0.0  0
 333  CONST_30  C2   NFE  C5   C4      0.00   0.0  0
 333  CONST_31  C2   N3   C4   C5      0.00   0.0  0
 333  CONST_32  O28  C31  C36  C35   180.00   0.0  0
 333  CONST_33  O28  C31  C32  C33   180.00   0.0  0
 333  CONST_34  C25  C24  C23  O28   180.00   0.0  0
 333  CONST_35  C21  N22  C23  O28   180.00   0.0  0
 333  CONST_36  O17  C21  N22  C23   180.00   0.0  0
 333  CONST_37  O17  C21  N26  C25   180.00   0.0  0
 333  CONST_38  C16  C15  C14  O17   180.00   0.0  0
 333  CONST_39  C12  C13  C14  O17   180.00   0.0  0
 333  CONST_40  H32  C32  C31  C36   180.00   0.0  0
 333  CONST_41  H33  C33  C34  C35   180.00   0.0  0
 333  CONST_42  H36  C36  C35  O39     0.00   0.0  0
 333  CONST_43  H25  C25  C24  C23   180.00   0.0  0
 333  CONST_44  H24  C24  C23  N22   180.00   0.0  0
 333  CONST_45  H16  C16  C15  C14   180.00   0.0  0
 333  CONST_46  H12  C12  C13  C14   180.00   0.0  0
 333  CONST_47  H13  C13  C14  C15   180.00   0.0  0
 333  CONST_48  H15  C15  C14  C13   180.00   0.0  0
 333  CONST_49  H4   C4   N3   C11     0.00   0.0  0
 333  CONST_50  H2   C2   N3   C11     0.00   0.0  0
 333  CONST_51  H5   C5   C4   N3    180.00   0.0  0
 333  Var_01    O37  C38  O39  C35   -15.76  30.0  1
 333  Var_02    C34  C35  O39  C38     9.98  30.0  1
 333  Var_03    C33  C34  O37  C38   171.15  30.0  1
 333  Var_04    C24  C23  O28  C31  -179.72  30.0  2
 333  Var_05    C15  C14  O17  C21  -103.75  30.0  2

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
 333  plan-1  C11  0.020
 333  plan-1  N3   0.020
 333  plan-1  C4   0.020
 333  plan-1  C5   0.020
 333  plan-1  NFE  0.020
 333  plan-1  C2   0.020
 333  plan-1  H4   0.020
 333  plan-1  H5   0.020
 333  plan-1  H2   0.020
 333  plan-2  O28  0.020
 333  plan-2  C23  0.020
 333  plan-2  N22  0.020
 333  plan-2  C24  0.020
 333  plan-2  C25  0.020
 333  plan-2  N26  0.020
 333  plan-2  C21  0.020
 333  plan-2  O17  0.020
 333  plan-2  H24  0.020
 333  plan-2  H25  0.020
 333  plan-3  C36  0.020
 333  plan-3  C35  0.020
 333  plan-3  O39  0.020
 333  plan-3  O37  0.020
 333  plan-3  C34  0.020
 333  plan-3  C33  0.020
 333  plan-3  C32  0.020
 333  plan-3  C31  0.020
 333  plan-3  O28  0.020
 333  plan-3  H36  0.020
 333  plan-3  H33  0.020
 333  plan-3  H32  0.020
 333  plan-4  O17  0.020
 333  plan-4  C14  0.020
 333  plan-4  C15  0.020
 333  plan-4  C16  0.020
 333  plan-4  C13  0.020
 333  plan-4  C12  0.020
 333  plan-4  C11  0.020
 333  plan-4  N3   0.020
 333  plan-4  H15  0.020
 333  plan-4  H16  0.020
 333  plan-4  H13  0.020
 333  plan-4  H12  0.020

