# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:08:39 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-ethyl-3-{6-(pyrimidin-5-yl)-5-[(3R)-tetrahydrofuran-3-ylmethoxy][1,3]thiazolo[5,4-b]pyridin-2-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1sc2nc(OC[C@@H]3CCOC3)c(cc2n1)c4cncnc4
#
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
 28F  28F  1-ethyl-3-{6-(pyrimidin-5-yl)-5-[(3R)-tetrahydrofuran-3-ylmethoxy][1,3]thiazolo[5,4-b]pyridin-2-yl}urea  ligand  48  28  .  2022-07-22  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_28F
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
 28F  C1   C  CH3   0  -0.704   9.2019   0.4066   0.2912
 28F  C2   C  CH2   0  -0.258   7.8566   1.0765   0.0888
 28F  O5   O  O     0  -0.512   5.1082   1.5589  -0.2093
 28F  N6   N  NH1   0  -0.744   4.6200  -0.6349   0.0924
 28F  C7   C  CR5   0   0.312   3.2677  -0.5108   0.0031
 28F  C9   C  CR56  0   0.291   1.1785  -1.1486   0.0002
 28F  C10  C  CR16  0  -0.240   0.0472  -1.9577   0.0806
 28F  C11  C  CR6   0  -0.100  -1.2021  -1.3762  -0.0337
 28F  C12  C  CR6   0   0.486  -1.2674   0.0229  -0.2478
 28F  C14  C  CR56  0  -0.049   0.9689   0.2130  -0.1988
 28F  C19  C  CH2   0  -0.505  -4.3437   3.7916  -0.6863
 28F  C20  C  CH2   0  -0.165  -5.5699   4.0130   0.2173
 28F  C22  C  CH2   0  -0.150  -4.8266   1.9081   0.6861
 28F  C24  C  CR16  0  -0.038  -2.5833  -3.3437  -0.7129
 28F  N25  N  N     0  -0.388  -3.6658  -4.1063  -0.6380
 28F  N3   N  NH1   0  -0.675   6.7959   0.0861   0.1365
 28F  C4   C  C     0   0.773   5.5086   0.4214  -0.0056
 28F  N8   N  N     0  -0.457   2.4895  -1.5340   0.1115
 28F  N13  N  N     0  -0.471  -0.2100   0.7976  -0.3271
 28F  S15  S  S2    0   0.212   2.4986   1.0462  -0.2534
 28F  O16  O  O2    0  -0.472  -2.4820   0.5506  -0.3855
 28F  C17  C  CH2   0  -0.166  -2.6068   1.9615  -0.5539
 28F  C18  C  CR15  0  -0.319  -4.0821   2.2809  -0.5932
 28F  O21  O  O     0  -0.495  -5.9642   2.7394   0.6983
 28F  C23  C  CR6   0  -0.042  -2.4232  -2.1911   0.0475
 28F  C26  C  CR16  0   0.053  -4.6086  -3.7154   0.2036
 28F  N27  N  N     0  -0.391  -4.5657  -2.6453   0.9844
 28F  C28  C  CR16  0  -0.022  -3.4785  -1.8938   0.9063
 28F  H1   H  HCH3  0   0.249   9.9949   1.1513   0.2543
 28F  H2   H  HCH3  0   0.237   9.2543  -0.0915   1.2600
 28F  H3   H  HCH3  0   0.237   9.3996  -0.3323  -0.4861
 28F  H4   H  HCH2  0   0.239   7.6978   1.8308   0.8626
 28F  H5   H  HCH2  0   0.240   7.8375   1.5928  -0.8733
 28F  H6   H  HNH1  0   0.426   4.9548  -1.5738   0.2598
 28F  H7   H  HCR6  0   0.278   0.1462  -3.0228   0.2507
 28F  H9   H  HCH2  0   0.245  -3.4871   4.3613  -0.3186
 28F  H10  H  HCH2  0   0.209  -5.3182   4.6791   1.0500
 28F  H11  H  HCH2  0   0.226  -6.4137   4.4529  -0.3164
 28F  H12  H  HCH2  0   0.236  -5.1577   0.8690   0.7166
 28F  H13  H  HCH2  0   0.197  -4.1863   2.0881   1.5646
 28F  H14  H  HCR6  0   0.278  -1.8120  -3.6527  -1.4111
 28F  H15  H  HNH1  0   0.409   7.0467  -0.8688   0.3382
 28F  H16  H  HCH2  0   0.228  -2.1283   2.4840   0.2810
 28F  H17  H  HCH2  0   0.245  -2.1076   2.2780  -1.4736
 28F  H18  H  HCR5  0   0.260  -4.5449   1.7729  -1.4445
 28F  H19  H  HCR6  0   0.268  -5.4998  -4.3301   0.2625
 28F  H20  H  HCR6  0   0.273  -3.4327  -1.0325   1.5627
 28F  H8   H  HCH2  0   0.258  -4.5250   4.1057  -1.7132

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
 28F  C1   C2   single    1.516  0.020  1.516
 28F  C2   N3   single    1.452  0.020  1.452
 28F  N3   C4   single    1.338  0.020  1.338
 28F  C4   O5   double    1.223  0.020  1.223
 28F  C4   N6   single    1.384  0.020  1.384
 28F  N6   C7   single    1.361  0.020  1.361
 28F  C7   S15  aromatic  1.755  0.020  1.755
 28F  C7   N8   aromatic  1.290  0.020  1.290
 28F  S15  C14  aromatic  1.743  0.020  1.743
 28F  N8   C9   aromatic  1.371  0.020  1.371
 28F  C9   C14  aromatic  1.392  0.020  1.392
 28F  C9   C10  aromatic  1.393  0.020  1.393
 28F  C14  N13  aromatic  1.322  0.020  1.322
 28F  C10  C11  aromatic  1.383  0.020  1.383
 28F  N13  C12  aromatic  1.313  0.020  1.313
 28F  C12  C11  aromatic  1.417  0.020  1.417
 28F  C12  O16  single    1.331  0.020  1.331
 28F  C11  C23  single    1.470  0.020  1.470
 28F  O16  C17  single    1.426  0.020  1.426
 28F  C23  C24  aromatic  1.390  0.020  1.390
 28F  C23  C28  aromatic  1.393  0.020  1.393
 28F  C17  C18  single    1.510  0.020  1.510
 28F  C24  N25  aromatic  1.326  0.020  1.326
 28F  C22  O21  single    1.409  0.020  1.409
 28F  C22  C18  single    1.526  0.020  1.526
 28F  O21  C20  single    1.417  0.020  1.417
 28F  C28  N27  aromatic  1.324  0.020  1.324
 28F  C18  C19  single    1.536  0.020  1.536
 28F  N25  C26  aromatic  1.323  0.020  1.323
 28F  C20  C19  single    1.539  0.020  1.539
 28F  N27  C26  aromatic  1.325  0.020  1.325
 28F  C1   H1   single    0.970  0.020  1.090
 28F  C1   H2   single    0.970  0.020  1.090
 28F  C1   H3   single    0.970  0.020  1.090
 28F  C2   H4   single    0.970  0.020  1.090
 28F  C2   H5   single    0.970  0.020  1.090
 28F  N6   H6   single    0.860  0.020  1.020
 28F  C10  H7   single    0.930  0.020  1.080
 28F  C19  H8   single    0.970  0.020  1.090
 28F  C19  H9   single    0.970  0.020  1.090
 28F  C20  H10  single    0.970  0.020  1.090
 28F  C20  H11  single    0.970  0.020  1.090
 28F  C22  H12  single    0.970  0.020  1.090
 28F  C22  H13  single    0.970  0.020  1.090
 28F  C24  H14  single    0.930  0.020  1.080
 28F  N3   H15  single    0.860  0.020  1.020
 28F  C17  H16  single    0.970  0.020  1.090
 28F  C17  H17  single    0.970  0.020  1.090
 28F  C18  H18  single    0.970  0.020  1.090
 28F  C26  H19  single    0.930  0.020  1.080
 28F  C28  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
 28F  H3   C1   H2   108.36  3.000
 28F  H3   C1   H1   107.90  3.000
 28F  H2   C1   H1   107.91  3.000
 28F  H3   C1   C2   111.41  3.000
 28F  H2   C1   C2   111.28  3.000
 28F  H1   C1   C2   109.85  3.000
 28F  H5   C2   H4   107.16  3.000
 28F  H5   C2   N3   109.80  3.000
 28F  H4   C2   N3   109.97  3.000
 28F  H5   C2   C1   110.00  3.000
 28F  H4   C2   C1   109.85  3.000
 28F  N3   C2   C1   110.02  3.000
 28F  H6   N6   C4   120.54  3.000
 28F  H6   N6   C7   115.13  3.000
 28F  C4   N6   C7   124.32  3.000
 28F  S15  C7   N8   116.84  3.000
 28F  N8   C7   N6   121.44  3.000
 28F  S15  C7   N6   121.72  3.000
 28F  N8   C9   C14  115.51  3.000
 28F  C14  C9   C10  117.00  3.000
 28F  N8   C9   C10  127.48  3.000
 28F  H7   C10  C11  120.61  3.000
 28F  H7   C10  C9   120.39  3.000
 28F  C11  C10  C9   118.99  3.000
 28F  C23  C11  C12  121.15  3.000
 28F  C23  C11  C10  120.84  3.000
 28F  C12  C11  C10  118.00  3.000
 28F  O16  C12  N13  119.63  3.000
 28F  O16  C12  C11  116.69  3.000
 28F  N13  C12  C11  123.68  3.000
 28F  S15  C14  N13  124.63  3.000
 28F  N13  C14  C9   125.50  3.000
 28F  S15  C14  C9   109.87  3.000
 28F  H9   C19  H8   107.30  3.000
 28F  H9   C19  C18  111.03  3.000
 28F  H8   C19  C18  111.66  3.000
 28F  H9   C19  C20  110.61  3.000
 28F  H8   C19  C20  112.30  3.000
 28F  C18  C19  C20  103.98  3.000
 28F  H11  C20  H10  107.72  3.000
 28F  H11  C20  O21  108.24  3.000
 28F  H10  C20  O21  110.63  3.000
 28F  H11  C20  C19  112.76  3.000
 28F  H10  C20  C19  110.53  3.000
 28F  O21  C20  C19  106.96  3.000
 28F  H13  C22  H12  108.04  3.000
 28F  H13  C22  O21  111.46  3.000
 28F  H12  C22  O21  108.47  3.000
 28F  H13  C22  C18  110.17  3.000
 28F  H12  C22  C18  113.83  3.000
 28F  O21  C22  C18  104.89  3.000
 28F  H14  C24  C23  120.41  3.000
 28F  H14  C24  N25  116.91  3.000
 28F  C23  C24  N25  122.68  3.000
 28F  C26  N25  C24  116.59  3.000
 28F  H15  N3   C4   119.89  3.000
 28F  H15  N3   C2   118.10  3.000
 28F  C4   N3   C2   121.91  3.000
 28F  N3   C4   N6   114.78  3.000
 28F  N6   C4   O5   120.76  3.000
 28F  N3   C4   O5   124.46  3.000
 28F  C9   N8   C7   110.30  3.000
 28F  C14  N13  C12  116.83  3.000
 28F  C14  S15  C7    87.47  3.000
 28F  C17  O16  C12  118.96  3.000
 28F  H17  C17  H16  107.68  3.000
 28F  H17  C17  C18  111.28  3.000
 28F  H16  C17  C18  110.23  3.000
 28F  H17  C17  O16  110.23  3.000
 28F  H16  C17  O16  110.11  3.000
 28F  C18  C17  O16  107.33  3.000
 28F  H18  C18  C17  109.59  3.000
 28F  H18  C18  C22  109.41  3.000
 28F  C17  C18  C22  113.77  3.000
 28F  H18  C18  C19  109.72  3.000
 28F  C22  C18  C19  102.00  3.000
 28F  C17  C18  C19  112.09  3.000
 28F  C22  O21  C20  107.61  3.000
 28F  C28  C23  C24  115.28  3.000
 28F  C28  C23  C11  123.03  3.000
 28F  C24  C23  C11  121.67  3.000
 28F  H19  C26  N27  116.90  3.000
 28F  H19  C26  N25  116.92  3.000
 28F  N27  C26  N25  126.18  3.000
 28F  C28  N27  C26  116.75  3.000
 28F  H20  C28  N27  116.75  3.000
 28F  H20  C28  C23  120.73  3.000
 28F  N27  C28  C23  122.51  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
 28F  CONST_01  C9   C14  S15  C7      0.00   0.0  0
 28F  CONST_02  N13  C14  S15  C7    180.00   0.0  0
 28F  CONST_03  C14  C9   N8   C7      0.00   0.0  0
 28F  CONST_04  C10  C9   N8   C7    180.00   0.0  0
 28F  CONST_05  S15  C7   N8   C9      0.00   0.0  0
 28F  CONST_06  C12  N13  C14  C9      0.00   0.0  0
 28F  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 28F  CONST_08  C23  C11  C10  C9    180.00   0.0  0
 28F  CONST_09  S15  C14  C9   C10   180.00   0.0  0
 28F  CONST_10  N13  C14  C9   C10     0.00   0.0  0
 28F  CONST_11  N13  C12  C11  C10     0.00   0.0  0
 28F  CONST_14  N8   C9   C10  C11   180.00   0.0  0
 28F  CONST_15  C14  C9   C10  C11     0.00   0.0  0
 28F  CONST_16  C14  N13  C12  C11     0.00   0.0  0
 28F  CONST_17  N25  C24  C23  C11   180.00   0.0  0
 28F  CONST_18  N27  C28  C23  C11   180.00   0.0  0
 28F  CONST_19  S15  C14  N13  C12   180.00   0.0  0
 28F  CONST_22  N8   C7   S15  C14     0.00   0.0  0
 28F  CONST_23  N27  C28  C23  C24     0.00   0.0  0
 28F  CONST_24  N27  C26  N25  C24     0.00   0.0  0
 28F  CONST_25  C28  C23  C24  N25     0.00   0.0  0
 28F  CONST_26  C28  N27  C26  N25     0.00   0.0  0
 28F  CONST_27  S15  C14  C9   N8      0.00   0.0  0
 28F  CONST_28  N13  C14  C9   N8    180.00   0.0  0
 28F  CONST_29  C23  C11  C12  N13   180.00   0.0  0
 28F  CONST_30  C26  N25  C24  C23     0.00   0.0  0
 28F  CONST_31  C26  N27  C28  C23     0.00   0.0  0
 28F  CONST_32  C14  S15  C7   N6    180.00   0.0  0
 28F  CONST_33  C9   N8   C7   N6    180.00   0.0  0
 28F  CONST_34  O16  C12  C11  C10   180.00   0.0  0
 28F  CONST_35  O16  C12  N13  C14   180.00   0.0  0
 28F  CONST_36  C23  C11  C12  O16     0.00   0.0  0
 28F  CONST_37  H14  C24  C23  C11     0.00   0.0  0
 28F  CONST_38  H20  C28  C23  C11     0.00   0.0  0
 28F  CONST_39  H7   C10  C11  C12   180.00   0.0  0
 28F  CONST_40  H19  C26  N25  C24   180.00   0.0  0
 28F  CONST_41  S15  C7   N6   C4      0.00   0.0  0
 28F  CONST_42  N8   C7   N6   C4    180.00   0.0  0
 28F  CONST_43  H6   N6   C7   N8      0.00   0.0  0
 28F  CONST_44  C7   N6   C4   O5      0.00   0.0  0
 28F  CONST_45  N3   C4   N6   C7    180.00   0.0  0
 28F  CONST_46  O5   C4   N3   C2      0.00   0.0  0
 28F  CONST_47  N6   C4   N3   C2    180.00   0.0  0
 28F  CONST_48  H15  N3   C4   O5    180.00   0.0  0
 28F  Var_01    C18  C22  O21  C20   -38.85  30.0  1
 28F  Var_02    O21  C20  C19  C18    -2.39  30.0  1
 28F  Var_03    H10  C20  O21  C22   -94.71  30.0  1
 28F  Var_04    C18  C17  O16  C12  -176.40  30.0  3
 28F  Var_05    C4   N3   C2   C1    179.51  30.0  3
 28F  Var_06    H1   C1   C2   N3    179.97  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
 28F  chir_01  C18  C17  C22  C19  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
 28F  plan-1  C11  0.020
 28F  plan-1  C24  0.020
 28F  plan-1  N25  0.020
 28F  plan-1  C23  0.020
 28F  plan-1  C26  0.020
 28F  plan-1  N27  0.020
 28F  plan-1  C28  0.020
 28F  plan-1  H14  0.020
 28F  plan-1  H19  0.020
 28F  plan-1  H20  0.020
 28F  plan-2  N6   0.020
 28F  plan-2  C7   0.020
 28F  plan-2  C9   0.020
 28F  plan-2  C10  0.020
 28F  plan-2  C11  0.020
 28F  plan-2  C12  0.020
 28F  plan-2  C14  0.020
 28F  plan-2  N8   0.020
 28F  plan-2  N13  0.020
 28F  plan-2  S15  0.020
 28F  plan-2  O16  0.020
 28F  plan-2  C23  0.020
 28F  plan-2  H7   0.020
 28F  plan-3  C2   0.020
 28F  plan-3  O5   0.020
 28F  plan-3  N6   0.020
 28F  plan-3  C7   0.020
 28F  plan-3  N3   0.020
 28F  plan-3  C4   0.020
 28F  plan-3  H6   0.020
 28F  plan-3  H15  0.020

