# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 01:14:36 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)c1cccc(c1)C(C)(C)NC(=O)Nc2ccc(Cl)c(N[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
 8N1  8N1  N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine  ligand  63  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_8N1
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
 8N1  C1   C   CR6   0   0.128   4.9333  -0.0357   0.5807
 8N1  C2   C   CR16  0  -0.306   4.4346  -1.0906   1.3492
 8N1  C3   C   CR16  0  -0.220   5.1500  -2.2692   1.4700
 8N1  C4   C   CR16  0  -0.335   6.3716  -2.4205   0.8285
 8N1  C5   C   CR6   0   0.138   6.8893  -1.3897   0.0467
 8N1  C6   C   CR16  0  -0.407   6.1567  -0.2012  -0.0519
 8N1  C7   C   C     0   0.108   8.1842  -1.5480  -0.6558
 8N1  C8   C   C2    0  -0.584   8.4758  -0.8596  -1.7622
 8N1  C10  C   C     0   0.748   1.6988   1.7258   0.2028
 8N1  C11  C   CT    0   0.080   4.1500   1.2754   0.5121
 8N1  C12  C   CH3   0  -0.644   4.2581   1.9443   1.8901
 8N1  C13  C   CH3   0  -0.674   4.6823   2.2258  -0.5620
 8N1  C17  C   CR6   0   0.411  -0.7277   1.6833  -0.2565
 8N1  C18  C   CR16  0  -0.347  -0.9357   3.0113  -0.6279
 8N1  C19  C   CR16  0  -0.204  -2.2329   3.4904  -0.6952
 8N1  C20  C   CR6   0  -0.165  -3.3117   2.6779  -0.4045
 8N1  C21  C   CR6   0   0.483  -3.1337   1.3351  -0.0431
 8N1  C22  C   CR16  0  -0.464  -1.8203   0.8626   0.0164
 8N1  C24  C   CH1   0   0.179  -4.1214  -0.8309   0.5800
 8N1  C25  C   CH1   0  -0.046  -5.4119  -1.3780   1.1832
 8N1  C26  C   CH1   0  -0.012  -5.2923  -2.8540   0.8434
 8N1  C27  C   CH1   0  -0.024  -4.6711  -2.8106  -0.5583
 8N1  C29  C   CH2   0  -0.145  -5.6896  -2.7834  -1.6845
 8N1  C9   C   CH3   0  -0.736   9.1643  -2.5338  -0.0858
 8N1  N1   N   NH1   0  -0.732  -4.2172   0.5507   0.2780
 8N1  N3   N   NH1   0  -0.707   2.7674   0.8911   0.2061
 8N1  N4   N   NH1   0  -0.791   0.5381   1.0994  -0.2061
 8N1  O2   O   O     0  -0.512   1.7329   2.9003   0.5321
 8N1  O3   O   O2    0  -0.499  -3.8799  -1.6266  -0.5746
 8N1  O4   O   OH1   0  -0.657  -5.5334  -1.1833   2.5618
 8N1  O5   O   OH1   0  -0.661  -6.4955  -3.5679   0.8497
 8N1  O6   O   OH1   0  -0.671  -4.9822  -2.6707  -2.8975
 8N1  CL1  CL  CL    0  -0.134  -4.9187   3.3379  -0.4867
 8N1  H1   H   HCR6  0   0.260   3.4872  -0.9901   1.8639
 8N1  H2   H   HCR6  0   0.257   4.7549  -3.0780   2.0708
 8N1  H3   H   HCR6  0   0.253   6.9094  -3.3535   0.9338
 8N1  H4   H   HCR6  0   0.247   6.5770   0.6134  -0.6251
 8N1  H5   H   H     0   0.242   9.4345  -0.9735  -2.2512
 8N1  H6   H   H     0   0.238   7.7812  -0.1721  -2.2268
 8N1  H7   H   HCH3  0   0.234   5.3108   2.0774   2.1415
 8N1  H8   H   HCH3  0   0.247   3.7816   2.9210   1.8987
 8N1  H9   H   HCH3  0   0.234   3.8008   1.3300   2.6664
 8N1  H10  H   HCH3  0   0.235   4.6917   1.7533  -1.5450
 8N1  H11  H   HCH3  0   0.255   4.0489   3.1090  -0.6162
 8N1  H12  H   HCH3  0   0.233   5.6927   2.5641  -0.3313
 8N1  H13  H   HCR6  0   0.268  -0.1163   3.6648  -0.8792
 8N1  H14  H   HCR6  0   0.276  -2.4055   4.5183  -0.9852
 8N1  H15  H   HCR6  0   0.287  -1.6344  -0.1713   0.2772
 8N1  H16  H   HCH1  0   0.232  -3.3065  -0.9746   1.2996
 8N1  H17  H   HCH1  0   0.227  -6.2733  -0.9563   0.6420
 8N1  H18  H   HCH1  0   0.240  -4.5645  -3.3022   1.5365
 8N1  H19  H   HCH1  0   0.244  -4.0088  -3.6689  -0.7158
 8N1  H20  H   HCH2  0   0.206  -6.2789  -3.7061  -1.6470
 8N1  H21  H   HCH2  0   0.191  -6.3889  -1.9472  -1.5474
 8N1  H22  H   HCH3  0   0.243   9.3456  -2.3484   0.9746
 8N1  H23  H   HCH3  0   0.244   8.7979  -3.5593  -0.1707
 8N1  H24  H   HCH3  0   0.250  10.1175  -2.4840  -0.6100
 8N1  H25  H   HNH1  0   0.380  -5.1061   0.8611  -0.0857
 8N1  H26  H   HNH1  0   0.397   2.6667   0.0168  -0.2862
 8N1  H27  H   HNH1  0   0.406   0.5444   0.0907  -0.2219
 8N1  H28  H   HOH1  0   0.459  -5.7058  -0.2509   2.7283
 8N1  H29  H   HOH1  0   0.460  -6.8063  -3.6326   1.7582
 8N1  H30  H   HOH1  0   0.456  -5.6142  -2.7431  -3.6178

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
 8N1  CL1  C20  single    1.739  0.020  1.739
 8N1  O5   C26  single    1.399  0.020  1.399
 8N1  C25  C26  single    1.519  0.020  1.519
 8N1  C25  O4   single    1.398  0.020  1.398
 8N1  C25  C24  single    1.526  0.020  1.526
 8N1  C26  C27  single    1.534  0.020  1.534
 8N1  O6   C29  single    1.409  0.020  1.409
 8N1  N1   C24  single    1.417  0.020  1.417
 8N1  N1   C21  single    1.376  0.020  1.376
 8N1  C20  C19  aromatic  1.381  0.020  1.381
 8N1  C20  C21  aromatic  1.402  0.020  1.402
 8N1  C29  C27  single    1.519  0.020  1.519
 8N1  C24  O3   single    1.423  0.020  1.423
 8N1  C19  C18  aromatic  1.385  0.020  1.385
 8N1  C27  O3   single    1.424  0.020  1.424
 8N1  C21  C22  aromatic  1.397  0.020  1.397
 8N1  C18  C17  aromatic  1.395  0.020  1.395
 8N1  C22  C17  aromatic  1.393  0.020  1.393
 8N1  C17  N4   single    1.395  0.020  1.395
 8N1  N4   C10  single    1.381  0.020  1.381
 8N1  O2   C10  double    1.220  0.020  1.220
 8N1  C10  N3   single    1.356  0.020  1.356
 8N1  N3   C11  single    1.467  0.020  1.467
 8N1  C9   C7   single    1.502  0.020  1.502
 8N1  C13  C11  single    1.530  0.020  1.530
 8N1  C11  C1   single    1.529  0.020  1.529
 8N1  C11  C12  single    1.536  0.020  1.536
 8N1  C6   C1   aromatic  1.387  0.020  1.387
 8N1  C6   C5   aromatic  1.400  0.020  1.400
 8N1  C7   C8   double    1.335  0.020  1.335
 8N1  C7   C5   single    1.482  0.020  1.482
 8N1  C1   C2   aromatic  1.397  0.020  1.397
 8N1  C5   C4   aromatic  1.393  0.020  1.393
 8N1  C2   C3   aromatic  1.384  0.020  1.384
 8N1  C4   C3   aromatic  1.388  0.020  1.388
 8N1  C2   H1   single    0.930  0.020  1.080
 8N1  C3   H2   single    0.930  0.020  1.080
 8N1  C4   H3   single    0.930  0.020  1.080
 8N1  C6   H4   single    0.930  0.020  1.080
 8N1  C8   H5   single    0.930  0.020  1.080
 8N1  C8   H6   single    0.930  0.020  1.080
 8N1  C12  H7   single    0.970  0.020  1.090
 8N1  C12  H8   single    0.970  0.020  1.090
 8N1  C12  H9   single    0.970  0.020  1.090
 8N1  C13  H10  single    0.970  0.020  1.090
 8N1  C13  H11  single    0.970  0.020  1.090
 8N1  C13  H12  single    0.970  0.020  1.090
 8N1  C18  H13  single    0.930  0.020  1.080
 8N1  C19  H14  single    0.930  0.020  1.080
 8N1  C22  H15  single    0.930  0.020  1.080
 8N1  C24  H16  single    0.970  0.020  1.090
 8N1  C25  H17  single    0.970  0.020  1.090
 8N1  C26  H18  single    0.970  0.020  1.090
 8N1  C27  H19  single    0.970  0.020  1.090
 8N1  C29  H20  single    0.970  0.020  1.090
 8N1  C29  H21  single    0.970  0.020  1.090
 8N1  C9   H22  single    0.970  0.020  1.090
 8N1  C9   H23  single    0.970  0.020  1.090
 8N1  C9   H24  single    0.970  0.020  1.090
 8N1  N1   H25  single    0.890  0.020  1.040
 8N1  N3   H26  single    0.860  0.020  1.020
 8N1  N4   H27  single    0.860  0.020  1.020
 8N1  O4   H28  single    0.850  0.020  0.980
 8N1  O5   H29  single    0.850  0.020  0.980
 8N1  O6   H30  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
 8N1  C11  C1   C6   122.26  3.000
 8N1  C6   C1   C2   118.40  3.000
 8N1  C11  C1   C2   119.29  3.000
 8N1  H1   C2   C3   119.33  3.000
 8N1  H1   C2   C1   120.25  3.000
 8N1  C3   C2   C1   120.43  3.000
 8N1  H2   C3   C4   119.76  3.000
 8N1  H2   C3   C2   119.75  3.000
 8N1  C4   C3   C2   120.49  3.000
 8N1  H3   C4   C5   120.51  3.000
 8N1  H3   C4   C3   119.11  3.000
 8N1  C5   C4   C3   120.37  3.000
 8N1  C7   C5   C6   120.98  3.000
 8N1  C7   C5   C4   120.78  3.000
 8N1  C6   C5   C4   118.24  3.000
 8N1  H4   C6   C5   118.27  3.000
 8N1  H4   C6   C1   119.65  3.000
 8N1  C5   C6   C1   122.06  3.000
 8N1  C9   C7   C8   120.68  3.000
 8N1  C8   C7   C5   121.91  3.000
 8N1  C9   C7   C5   117.41  3.000
 8N1  H6   C8   H5   116.20  3.000
 8N1  H6   C8   C7   122.90  3.000
 8N1  H5   C8   C7   120.90  3.000
 8N1  O2   C10  N4   122.68  3.000
 8N1  O2   C10  N3   124.74  3.000
 8N1  N4   C10  N3   112.58  3.000
 8N1  N3   C11  C13  110.13  3.000
 8N1  C13  C11  C12  109.57  3.000
 8N1  N3   C11  C12  111.57  3.000
 8N1  C12  C11  C1   107.29  3.000
 8N1  C13  C11  C1   112.71  3.000
 8N1  N3   C11  C1   105.51  3.000
 8N1  H9   C12  H8   108.47  3.000
 8N1  H9   C12  H7   108.03  3.000
 8N1  H8   C12  H7   108.16  3.000
 8N1  H9   C12  C11  111.34  3.000
 8N1  H8   C12  C11  111.58  3.000
 8N1  H7   C12  C11  109.15  3.000
 8N1  H12  C13  H11  107.35  3.000
 8N1  H12  C13  H10  108.49  3.000
 8N1  H11  C13  H10  108.16  3.000
 8N1  H12  C13  C11  111.51  3.000
 8N1  H11  C13  C11  109.67  3.000
 8N1  H10  C13  C11  111.51  3.000
 8N1  N4   C17  C22  117.26  3.000
 8N1  N4   C17  C18  122.92  3.000
 8N1  C22  C17  C18  119.74  3.000
 8N1  H13  C18  C19  119.42  3.000
 8N1  H13  C18  C17  121.74  3.000
 8N1  C19  C18  C17  118.83  3.000
 8N1  H14  C19  C20  119.38  3.000
 8N1  H14  C19  C18  119.42  3.000
 8N1  C20  C19  C18  121.20  3.000
 8N1  CL1  C20  C21  119.54  3.000
 8N1  C21  C20  C19  121.22  3.000
 8N1  CL1  C20  C19  119.24  3.000
 8N1  N1   C21  C22  122.53  3.000
 8N1  C22  C21  C20  117.02  3.000
 8N1  N1   C21  C20  120.42  3.000
 8N1  H15  C22  C21  119.66  3.000
 8N1  H15  C22  C17  118.36  3.000
 8N1  C21  C22  C17  121.98  3.000
 8N1  H16  C24  O3   109.45  3.000
 8N1  H16  C24  N1   108.53  3.000
 8N1  O3   C24  N1   112.56  3.000
 8N1  H16  C24  C25  108.79  3.000
 8N1  O3   C24  C25  105.30  3.000
 8N1  N1   C24  C25  112.12  3.000
 8N1  H17  C25  O4   111.31  3.000
 8N1  H17  C25  C26  108.88  3.000
 8N1  O4   C25  C26  111.27  3.000
 8N1  H17  C25  C24  109.27  3.000
 8N1  O4   C25  C24  114.43  3.000
 8N1  C26  C25  C24  101.15  3.000
 8N1  H18  C26  O5   110.99  3.000
 8N1  H18  C26  C27  108.62  3.000
 8N1  O5   C26  C27  111.53  3.000
 8N1  H18  C26  C25  107.87  3.000
 8N1  C27  C26  C25  102.05  3.000
 8N1  O5   C26  C25  115.28  3.000
 8N1  H19  C27  O3   108.30  3.000
 8N1  H19  C27  C29  108.23  3.000
 8N1  O3   C27  C29  110.44  3.000
 8N1  H19  C27  C26  110.74  3.000
 8N1  O3   C27  C26  105.01  3.000
 8N1  C29  C27  C26  113.98  3.000
 8N1  H21  C29  H20  107.13  3.000
 8N1  H21  C29  O6   111.48  3.000
 8N1  H20  C29  O6   111.53  3.000
 8N1  H21  C29  C27  110.37  3.000
 8N1  H20  C29  C27  108.68  3.000
 8N1  O6   C29  C27  107.65  3.000
 8N1  H24  C9   H23  107.41  3.000
 8N1  H24  C9   H22  108.33  3.000
 8N1  H23  C9   H22  106.90  3.000
 8N1  H24  C9   C7   111.00  3.000
 8N1  H23  C9   C7   111.57  3.000
 8N1  H22  C9   C7   111.43  3.000
 8N1  H25  N1   C24  115.85  3.000
 8N1  H25  N1   C21  115.74  3.000
 8N1  C24  N1   C21  123.52  3.000
 8N1  H26  N3   C11  115.03  3.000
 8N1  H26  N3   C10  116.99  3.000
 8N1  C11  N3   C10  125.58  3.000
 8N1  H27  N4   C17  115.06  3.000
 8N1  H27  N4   C10  116.93  3.000
 8N1  C17  N4   C10  125.71  3.000
 8N1  C27  O3   C24  111.18  3.000
 8N1  H28  O4   C25  108.73  3.000
 8N1  H29  O5   C26  108.44  3.000
 8N1  H30  O6   C29  108.01  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
 8N1  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 8N1  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 8N1  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 8N1  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 8N1  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 8N1  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 8N1  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 8N1  CONST_08  C20  C21  C22  C17    0.00   0.0  0
 8N1  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 8N1  CONST_10  C21  C22  C17  C18    0.00   0.0  0
 8N1  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 8N1  CONST_12  C22  C17  C18  C19    0.00   0.0  0
 8N1  CONST_13  C7   C5   C6   C1   180.00   0.0  0
 8N1  CONST_14  C11  C1   C2   C3   180.00   0.0  0
 8N1  CONST_15  C7   C5   C4   C3   180.00   0.0  0
 8N1  CONST_16  C11  C1   C6   C5   180.00   0.0  0
 8N1  CONST_17  N1   C21  C22  C17  180.00   0.0  0
 8N1  CONST_18  CL1  C20  C19  C18  180.00   0.0  0
 8N1  CONST_19  N1   C21  C20  C19  180.00   0.0  0
 8N1  CONST_20  N4   C17  C18  C19  180.00   0.0  0
 8N1  CONST_21  N4   C17  C22  C21  180.00   0.0  0
 8N1  CONST_22  CL1  C20  C21  C22  180.00   0.0  0
 8N1  CONST_23  C24  N1   C21  C20  180.00   0.0  0
 8N1  CONST_24  C24  N1   C21  C22    0.00   0.0  0
 8N1  CONST_25  H2   C3   C2   C1   180.00   0.0  0
 8N1  CONST_26  H4   C6   C1   C2   180.00   0.0  0
 8N1  CONST_27  H3   C4   C3   C2   180.00   0.0  0
 8N1  CONST_28  H1   C2   C3   C4   180.00   0.0  0
 8N1  CONST_29  H14  C19  C18  C17  180.00   0.0  0
 8N1  CONST_30  H15  C22  C17  C18  180.00   0.0  0
 8N1  CONST_31  H13  C18  C19  C20  180.00   0.0  0
 8N1  CONST_36  O2   C10  N4   C17    0.00   0.0  0
 8N1  CONST_37  N3   C10  N4   C17  180.00   0.0  0
 8N1  CONST_38  O2   C10  N3   C11    0.00   0.0  0
 8N1  CONST_39  N4   C10  N3   C11  180.00   0.0  0
 8N1  CONST_40  H26  N3   C10  O2   180.00   0.0  0
 8N1  Var_01    N3   C11  C1   C2   -49.09  30.0  2
 8N1  Var_02    C9   C7   C5   C4   -24.97  30.0  2
 8N1  Var_03    C10  N3   C11  C1   172.07  30.0  2
 8N1  Var_04    H5   C8   C7   C5   178.78   0.0  2
 8N1  Var_05    H10  C13  C11  C1    56.23  30.0  3
 8N1  Var_06    H7   C12  C11  C1    56.50  30.0  3
 8N1  Var_07    H22  C9   C7   C5   -52.61  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
 8N1  chir_01  C24  C25  N1   O3   positiv
 8N1  chir_02  C25  O4   C26  C24  positiv
 8N1  chir_03  C26  O5   C25  C27  positiv
 8N1  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
 8N1  plan-1  C5   0.020
 8N1  plan-1  C7   0.020
 8N1  plan-1  C8   0.020
 8N1  plan-1  C9   0.020
 8N1  plan-1  H5   0.020
 8N1  plan-1  H6   0.020
 8N1  plan-2  C1   0.020
 8N1  plan-2  C2   0.020
 8N1  plan-2  C3   0.020
 8N1  plan-2  C4   0.020
 8N1  plan-2  C5   0.020
 8N1  plan-2  C6   0.020
 8N1  plan-2  C7   0.020
 8N1  plan-2  C11  0.020
 8N1  plan-2  H1   0.020
 8N1  plan-2  H2   0.020
 8N1  plan-2  H3   0.020
 8N1  plan-2  H4   0.020
 8N1  plan-3  C17  0.020
 8N1  plan-3  C18  0.020
 8N1  plan-3  C19  0.020
 8N1  plan-3  C20  0.020
 8N1  plan-3  C21  0.020
 8N1  plan-3  C22  0.020
 8N1  plan-3  N1   0.020
 8N1  plan-3  N4   0.020
 8N1  plan-3  CL1  0.020
 8N1  plan-3  H13  0.020
 8N1  plan-3  H14  0.020
 8N1  plan-3  H15  0.020
 8N1  plan-4  C21  0.020
 8N1  plan-4  C24  0.020
 8N1  plan-4  N1   0.020
 8N1  plan-4  H25  0.020
 8N1  plan-5  C10  0.020
 8N1  plan-5  C11  0.020
 8N1  plan-5  C17  0.020
 8N1  plan-5  N3   0.020
 8N1  plan-5  N4   0.020
 8N1  plan-5  O2   0.020
 8N1  plan-5  H26  0.020
 8N1  plan-5  H27  0.020

