# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 19:27:57 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)c1cccc(c1)C(C)(C)NC(=O)Nc2ccc(Cl)c(O[C@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2
#
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
 8LA  8LA  N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea  ligand  62  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8LA
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
 8LA  C1   C   CR6   0   0.129   5.1631  -0.6497  -0.0298
 8LA  C2   C   CR16  0  -0.342   6.3349  -0.8436   0.6945
 8LA  C3   C   CR16  0  -0.214   7.1440   0.2374   1.0180
 8LA  C4   C   CR16  0  -0.329   6.7967   1.5211   0.6322
 8LA  C5   C   CR6   0   0.122   5.6178   1.7487  -0.0815
 8LA  C6   C   CR16  0  -0.365   4.8281   0.6473  -0.4123
 8LA  C10  C   C     0   0.755   1.7748  -2.0854  -0.4556
 8LA  C11  C   CT    0   0.073   4.2704  -1.8094  -0.4719
 8LA  C12  C   CH3   0  -0.645   4.4392  -1.9611  -1.9901
 8LA  C13  C   CH3   0  -0.671   4.6307  -3.1237   0.2225
 8LA  C17  C   CR6   0   0.412  -0.6678  -1.9785  -0.0551
 8LA  C18  C   CR16  0  -0.336  -1.0251  -3.2912  -0.3609
 8LA  C19  C   CR16  0  -0.203  -2.3648  -3.6163  -0.5051
 8LA  C20  C   CR6   0  -0.180  -3.3519  -2.6654  -0.3316
 8LA  C21  C   CR6   0   0.476  -3.0077  -1.3519  -0.0121
 8LA  C22  C   CR16  0  -0.477  -1.6677  -1.0159   0.1112
 8LA  C24  C   CH1   0   0.280  -3.8389   0.7197   0.8254
 8LA  C25  C   CH1   0  -0.089  -5.2167   1.2515   1.2413
 8LA  C26  C   CH1   0   0.006  -4.9633   2.7569   1.1713
 8LA  C27  C   CH1   0   0.007  -4.0592   2.8644  -0.0550
 8LA  C29  C   CH2   0  -0.156  -3.1844   4.0931  -0.0335
 8LA  C7   C   C     0   0.105   5.2255   3.1191  -0.4859
 8LA  C8   C   CH3   0  -0.738   6.3260   4.1215  -0.6888
 8LA  C9   C   C2    0  -0.583   3.9451   3.4614  -0.6476
 8LA  N3   N   NH1   0  -0.706   2.9022  -1.4125  -0.1167
 8LA  N4   N   NH1   0  -0.793   0.6448  -1.5590   0.1381
 8LA  O1   O   O2    0  -0.493  -4.0255  -0.4809   0.1297
 8LA  O2   O   O     0  -0.511   1.7364  -3.0410  -1.2131
 8LA  O3   O   O2    0  -0.507  -3.2556   1.6899   0.0011
 8LA  O4   O   OH1   0  -0.658  -6.2159   0.9326   0.3160
 8LA  O5   O   OH1   0  -0.658  -6.0951   3.5559   1.0193
 8LA  O6   O   OH1   0  -0.670  -2.4291   4.1459  -1.2195
 8LA  CL   CL  CL    0  -0.116  -5.0210  -3.0892  -0.4953
 8LA  H1   H   HCR6  0   0.257   6.6373  -1.8332   1.0074
 8LA  H2   H   HCR6  0   0.257   8.0543   0.0737   1.5803
 8LA  H3   H   HCR6  0   0.253   7.4441   2.3455   0.9009
 8LA  H4   H   HCR6  0   0.253   3.9362   0.8055  -1.0073
 8LA  H5   H   HCH3  0   0.234   5.4936  -2.1159  -2.2196
 8LA  H6   H   HCH3  0   0.248   3.8807  -2.8102  -2.3754
 8LA  H7   H   HCH3  0   0.234   4.1099  -1.0632  -2.5132
 8LA  H8   H   HCH3  0   0.236   4.5829  -3.0264   1.3078
 8LA  H9   H   HCH3  0   0.254   3.9338  -3.9029  -0.0807
 8LA  H10  H   HCH3  0   0.233   5.6322  -3.4614  -0.0468
 8LA  H11  H   HCR6  0   0.276  -0.2828  -4.0628  -0.4780
 8LA  H12  H   HCR6  0   0.281  -2.6412  -4.6352  -0.7406
 8LA  H13  H   HCR6  0   0.300  -1.3764   0.0068   0.3151
 8LA  H14  H   HCH1  0   0.240  -3.1971   0.5426   1.6974
 8LA  H15  H   HCH1  0   0.252  -5.4702   0.9128   2.2532
 8LA  H16  H   HCH1  0   0.234  -4.3839   3.0419   2.0620
 8LA  H17  H   HCH1  0   0.233  -4.6689   2.8634  -0.9687
 8LA  H18  H   HCH2  0   0.207  -3.8400   4.9670   0.0707
 8LA  H19  H   HCH2  0   0.197  -2.5465   4.0592   0.8603
 8LA  H20  H   HCH3  0   0.243   7.1100   3.7272  -1.3377
 8LA  H21  H   HCH3  0   0.251   5.9433   5.0392  -1.1324
 8LA  H22  H   HCH3  0   0.245   6.8041   4.3895   0.2560
 8LA  H23  H   H     0   0.242   3.6691   4.4599  -0.9605
 8LA  H24  H   H     0   0.239   3.1299   2.7744  -0.4615
 8LA  H25  H   HNH1  0   0.397   2.8362  -0.7729   0.6599
 8LA  H26  H   HNH1  0   0.408   0.7408  -0.6672   0.5994
 8LA  H27  H   HOH1  0   0.453  -6.2810  -0.0263   0.2528
 8LA  H28  H   HOH1  0   0.461  -6.5342   3.6353   1.8716
 8LA  H29  H   HOH1  0   0.458  -1.9055   4.9520  -1.2058

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
 8LA  O6   C29  single    1.407  0.020  1.407
 8LA  CL   C20  single    1.730  0.020  1.730
 8LA  C29  C27  single    1.508  0.020  1.508
 8LA  O3   C24  single    1.400  0.020  1.400
 8LA  O3   C27  single    1.424  0.020  1.424
 8LA  C24  C25  single    1.534  0.020  1.534
 8LA  C24  O1   single    1.400  0.020  1.400
 8LA  C25  O4   single    1.399  0.020  1.399
 8LA  C25  C26  single    1.528  0.020  1.528
 8LA  C27  C26  single    1.527  0.020  1.527
 8LA  C20  C19  aromatic  1.382  0.020  1.382
 8LA  C20  C21  aromatic  1.395  0.020  1.395
 8LA  C19  C18  aromatic  1.386  0.020  1.386
 8LA  C26  O5   single    1.394  0.020  1.394
 8LA  O1   C21  single    1.347  0.020  1.347
 8LA  C21  C22  aromatic  1.387  0.020  1.387
 8LA  C18  C17  aromatic  1.394  0.020  1.394
 8LA  C22  C17  aromatic  1.398  0.020  1.398
 8LA  C17  N4   single    1.391  0.020  1.391
 8LA  C8   C7   single    1.502  0.020  1.502
 8LA  C9   C7   double    1.335  0.020  1.335
 8LA  C7   C5   single    1.482  0.020  1.482
 8LA  N4   C10  single    1.381  0.020  1.381
 8LA  C5   C6   aromatic  1.395  0.020  1.395
 8LA  C5   C4   aromatic  1.397  0.020  1.397
 8LA  C10  O2   double    1.220  0.020  1.220
 8LA  C10  N3   single    1.356  0.020  1.356
 8LA  C6   C1   aromatic  1.393  0.020  1.393
 8LA  C4   C3   aromatic  1.385  0.020  1.385
 8LA  N3   C11  single    1.468  0.020  1.468
 8LA  C1   C11  single    1.529  0.020  1.529
 8LA  C1   C2   aromatic  1.391  0.020  1.391
 8LA  C3   C2   aromatic  1.388  0.020  1.388
 8LA  C11  C12  single    1.535  0.020  1.535
 8LA  C11  C13  single    1.529  0.020  1.529
 8LA  C2   H1   single    0.930  0.020  1.080
 8LA  C3   H2   single    0.930  0.020  1.080
 8LA  C4   H3   single    0.930  0.020  1.080
 8LA  C6   H4   single    0.930  0.020  1.080
 8LA  C12  H5   single    0.970  0.020  1.090
 8LA  C12  H6   single    0.970  0.020  1.090
 8LA  C12  H7   single    0.970  0.020  1.090
 8LA  C13  H8   single    0.970  0.020  1.090
 8LA  C13  H9   single    0.970  0.020  1.090
 8LA  C13  H10  single    0.970  0.020  1.090
 8LA  C18  H11  single    0.930  0.020  1.080
 8LA  C19  H12  single    0.930  0.020  1.080
 8LA  C22  H13  single    0.930  0.020  1.080
 8LA  C24  H14  single    0.970  0.020  1.090
 8LA  C25  H15  single    0.970  0.020  1.090
 8LA  C26  H16  single    0.970  0.020  1.090
 8LA  C27  H17  single    0.970  0.020  1.090
 8LA  C29  H18  single    0.970  0.020  1.090
 8LA  C29  H19  single    0.970  0.020  1.090
 8LA  C8   H20  single    0.970  0.020  1.090
 8LA  C8   H21  single    0.970  0.020  1.090
 8LA  C8   H22  single    0.970  0.020  1.090
 8LA  C9   H23  single    0.930  0.020  1.080
 8LA  C9   H24  single    0.930  0.020  1.080
 8LA  N3   H25  single    0.890  0.020  1.040
 8LA  N4   H26  single    0.860  0.020  1.020
 8LA  O4   H27  single    0.850  0.020  0.980
 8LA  O5   H28  single    0.850  0.020  0.980
 8LA  O6   H29  single    0.850  0.020  0.980

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
 8LA  C11  C1   C6   119.10  3.000
 8LA  C11  C1   C2   122.46  3.000
 8LA  C6   C1   C2   118.38  3.000
 8LA  H1   C2   C3   118.84  3.000
 8LA  H1   C2   C1   120.93  3.000
 8LA  C3   C2   C1   120.24  3.000
 8LA  H2   C3   C4   119.73  3.000
 8LA  H2   C3   C2   119.56  3.000
 8LA  C4   C3   C2   120.71  3.000
 8LA  H3   C4   C5   120.51  3.000
 8LA  H3   C4   C3   119.15  3.000
 8LA  C5   C4   C3   120.34  3.000
 8LA  C7   C5   C6   121.04  3.000
 8LA  C6   C5   C4   118.06  3.000
 8LA  C7   C5   C4   120.91  3.000
 8LA  H4   C6   C5   118.74  3.000
 8LA  H4   C6   C1   118.98  3.000
 8LA  C5   C6   C1   122.26  3.000
 8LA  O2   C10  N4   122.68  3.000
 8LA  O2   C10  N3   124.75  3.000
 8LA  N4   C10  N3   112.57  3.000
 8LA  N3   C11  C13  110.00  3.000
 8LA  C13  C11  C12  109.77  3.000
 8LA  N3   C11  C12  111.62  3.000
 8LA  C13  C11  C1   112.52  3.000
 8LA  C12  C11  C1   107.26  3.000
 8LA  N3   C11  C1   105.61  3.000
 8LA  H7   C12  H6   108.55  3.000
 8LA  H7   C12  H5   107.94  3.000
 8LA  H6   C12  H5   108.15  3.000
 8LA  H7   C12  C11  111.10  3.000
 8LA  H6   C12  C11  111.80  3.000
 8LA  H5   C12  C11  109.19  3.000
 8LA  H10  C13  H9   107.30  3.000
 8LA  H10  C13  H8   108.27  3.000
 8LA  H9   C13  H8   108.24  3.000
 8LA  H10  C13  C11  111.74  3.000
 8LA  H9   C13  C11  109.74  3.000
 8LA  H8   C13  C11  111.40  3.000
 8LA  N4   C17  C22  116.78  3.000
 8LA  N4   C17  C18  123.78  3.000
 8LA  C22  C17  C18  119.41  3.000
 8LA  H11  C18  C19  119.13  3.000
 8LA  H11  C18  C17  121.45  3.000
 8LA  C19  C18  C17  119.42  3.000
 8LA  H12  C19  C20  119.54  3.000
 8LA  H12  C19  C18  119.38  3.000
 8LA  C20  C19  C18  121.07  3.000
 8LA  CL   C20  C21  119.37  3.000
 8LA  C21  C20  C19  120.04  3.000
 8LA  CL   C20  C19  120.59  3.000
 8LA  O1   C21  C22  124.33  3.000
 8LA  C22  C21  C20  119.14  3.000
 8LA  O1   C21  C20  116.52  3.000
 8LA  H13  C22  C21  120.36  3.000
 8LA  H13  C22  C17  118.72  3.000
 8LA  C21  C22  C17  120.91  3.000
 8LA  H14  C24  O3   109.63  3.000
 8LA  H14  C24  O1   109.54  3.000
 8LA  O3   C24  O1   110.93  3.000
 8LA  H14  C24  C25  111.46  3.000
 8LA  O1   C24  C25  108.20  3.000
 8LA  O3   C24  C25  107.07  3.000
 8LA  H15  C25  O4   112.01  3.000
 8LA  H15  C25  C26  112.63  3.000
 8LA  O4   C25  C26  108.23  3.000
 8LA  H15  C25  C24  110.53  3.000
 8LA  C26  C25  C24  100.37  3.000
 8LA  O4   C25  C24  112.53  3.000
 8LA  H16  C26  O5   111.56  3.000
 8LA  H16  C26  C27  108.67  3.000
 8LA  O5   C26  C27  110.65  3.000
 8LA  H16  C26  C25  107.79  3.000
 8LA  O5   C26  C25  115.79  3.000
 8LA  C27  C26  C25  101.79  3.000
 8LA  H17  C27  O3   110.19  3.000
 8LA  H17  C27  C29  109.55  3.000
 8LA  O3   C27  C29  110.12  3.000
 8LA  H17  C27  C26  109.83  3.000
 8LA  O3   C27  C26  104.14  3.000
 8LA  C29  C27  C26  112.90  3.000
 8LA  H19  C29  H18  107.12  3.000
 8LA  H19  C29  O6   112.04  3.000
 8LA  H18  C29  O6   111.76  3.000
 8LA  H19  C29  C27  108.86  3.000
 8LA  H18  C29  C27  107.67  3.000
 8LA  O6   C29  C27  109.25  3.000
 8LA  C9   C7   C8   121.00  3.000
 8LA  C9   C7   C5   121.61  3.000
 8LA  C8   C7   C5   117.39  3.000
 8LA  H22  C8   H21  107.43  3.000
 8LA  H22  C8   H20  106.76  3.000
 8LA  H21  C8   H20  108.35  3.000
 8LA  H22  C8   C7   111.56  3.000
 8LA  H21  C8   C7   111.10  3.000
 8LA  H20  C8   C7   111.43  3.000
 8LA  H24  C9   H23  116.31  3.000
 8LA  H24  C9   C7   122.60  3.000
 8LA  H23  C9   C7   121.08  3.000
 8LA  H25  N3   C11  114.76  3.000
 8LA  H25  N3   C10  116.93  3.000
 8LA  C11  N3   C10  125.46  3.000
 8LA  H26  N4   C17  114.83  3.000
 8LA  H26  N4   C10  117.12  3.000
 8LA  C17  N4   C10  126.68  3.000
 8LA  C24  O1   C21  120.41  3.000
 8LA  C27  O3   C24  111.07  3.000
 8LA  H27  O4   C25  108.58  3.000
 8LA  H28  O5   C26  108.75  3.000
 8LA  H29  O6   C29  108.16  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
 8LA  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 8LA  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 8LA  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 8LA  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 8LA  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 8LA  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 8LA  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 8LA  CONST_08  C20  C21  C22  C17     0.00   0.0  0
 8LA  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 8LA  CONST_10  C21  C22  C17  C18     0.00   0.0  0
 8LA  CONST_11  C22  C21  C20  C19     0.00   0.0  0
 8LA  CONST_12  C22  C17  C18  C19     0.00   0.0  0
 8LA  CONST_13  C7   C5   C6   C1    180.00   0.0  0
 8LA  CONST_14  C7   C5   C4   C3    180.00   0.0  0
 8LA  CONST_15  C11  C1   C2   C3    180.00   0.0  0
 8LA  CONST_16  C11  C1   C6   C5    180.00   0.0  0
 8LA  CONST_17  O1   C21  C22  C17   180.00   0.0  0
 8LA  CONST_18  CL   C20  C19  C18   180.00   0.0  0
 8LA  CONST_19  O1   C21  C20  C19   180.00   0.0  0
 8LA  CONST_20  N4   C17  C18  C19   180.00   0.0  0
 8LA  CONST_21  N4   C17  C22  C21   180.00   0.0  0
 8LA  CONST_22  CL   C20  C21  C22   180.00   0.0  0
 8LA  CONST_23  H2   C3   C2   C1    180.00   0.0  0
 8LA  CONST_24  H4   C6   C1   C2    180.00   0.0  0
 8LA  CONST_25  H3   C4   C3   C2    180.00   0.0  0
 8LA  CONST_26  H1   C2   C3   C4    180.00   0.0  0
 8LA  CONST_27  H12  C19  C18  C17   180.00   0.0  0
 8LA  CONST_28  H13  C22  C17  C18   180.00   0.0  0
 8LA  CONST_29  H11  C18  C19  C20   180.00   0.0  0
 8LA  CONST_33  O2   C10  N4   C17     0.00   0.0  0
 8LA  CONST_34  N3   C10  N4   C17   180.00   0.0  0
 8LA  CONST_35  O2   C10  N3   C11     0.00   0.0  0
 8LA  CONST_36  N4   C10  N3   C11   180.00   0.0  0
 8LA  CONST_37  H25  N3   C10  O2    180.00   0.0  0
 8LA  Var_01    N3   C11  C1   C2    132.80  30.0  2
 8LA  Var_02    C8   C7   C5   C4     27.33  30.0  2
 8LA  Var_03    C10  N3   C11  C1    172.68  30.0  1
 8LA  Var_04    H23  C9   C7   C5   -178.89   0.0  2
 8LA  Var_05    H5   C12  C11  C1     56.81  30.0  3
 8LA  Var_06    H8   C13  C11  C1     56.92  30.0  3
 8LA  Var_07    H20  C8   C7   C5     50.10  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
 8LA  chir_01  C24  O3  C25  O1   negativ
 8LA  chir_02  C25  O4  C24  C26  negativ
 8LA  chir_03  C26  O5  C27  C25  positiv
 8LA  chir_04  C27  O3  C26  C29  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
 8LA  plan-1  C1   0.020
 8LA  plan-1  C2   0.020
 8LA  plan-1  C3   0.020
 8LA  plan-1  C4   0.020
 8LA  plan-1  C5   0.020
 8LA  plan-1  C6   0.020
 8LA  plan-1  C11  0.020
 8LA  plan-1  C7   0.020
 8LA  plan-1  H1   0.020
 8LA  plan-1  H2   0.020
 8LA  plan-1  H3   0.020
 8LA  plan-1  H4   0.020
 8LA  plan-2  C17  0.020
 8LA  plan-2  C18  0.020
 8LA  plan-2  C19  0.020
 8LA  plan-2  C20  0.020
 8LA  plan-2  C21  0.020
 8LA  plan-2  C22  0.020
 8LA  plan-2  N4   0.020
 8LA  plan-2  O1   0.020
 8LA  plan-2  CL   0.020
 8LA  plan-2  H11  0.020
 8LA  plan-2  H12  0.020
 8LA  plan-2  H13  0.020
 8LA  plan-3  C10  0.020
 8LA  plan-3  C11  0.020
 8LA  plan-3  C17  0.020
 8LA  plan-3  N3   0.020
 8LA  plan-3  N4   0.020
 8LA  plan-3  O2   0.020
 8LA  plan-3  H25  0.020
 8LA  plan-3  H26  0.020
 8LA  plan-4  C5   0.020
 8LA  plan-4  C7   0.020
 8LA  plan-4  C8   0.020
 8LA  plan-4  C9   0.020
 8LA  plan-4  H23  0.020
 8LA  plan-4  H24  0.020

