# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 22:46:26 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}-alpha-D-ribofuranosylamine
#   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
 8L7  8L7  N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine  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_8L7
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
 8L7  C1   C   CR6   0   0.133  -5.1599   0.3947   0.2783
 8L7  C10  C   C     0   0.748  -1.8909   2.1129  -0.0011
 8L7  C11  C   CT    0   0.071  -4.3528   1.6264  -0.1348
 8L7  C12  C   CH3   0  -0.644  -4.4539   1.7478  -1.6620
 8L7  C13  C   CH3   0  -0.670  -4.8674   2.9123   0.5144
 8L7  C17  C   CR6   0   0.413   0.5410   2.1680   0.4475
 8L7  C18  C   CR16  0  -0.351   0.8010   3.5259   0.2661
 8L7  C19  C   CR16  0  -0.205   2.1164   3.9415   0.1413
 8L7  C2   C   CR16  0  -0.344  -6.3464   0.4823   0.9981
 8L7  C20  C   CR6   0  -0.164   3.1621   3.0424   0.2139
 8L7  C21  C   CR6   0   0.479   2.9314   1.6727   0.4118
 8L7  C22  C   CR16  0  -0.466   1.5991   1.2627   0.5068
 8L7  C24  C   CH1   0   0.195   3.8219  -0.5955   0.6890
 8L7  C25  C   CH1   0  -0.044   5.1227  -1.2928   1.0668
 8L7  C26  C   CH1   0  -0.054   4.8324  -2.7145   0.5854
 8L7  C27  C   CH1   0   0.027   4.0461  -2.4672  -0.7030
 8L7  C29  C   CH2   0  -0.158   3.0731  -3.5819  -1.0051
 8L7  C3   C   CR16  0  -0.214  -7.0490  -0.6688   1.3311
 8L7  C4   C   CR16  0  -0.331  -6.5839  -1.9161   0.9503
 8L7  C5   C   CR6   0   0.123  -5.4047  -2.0333   0.2102
 8L7  C6   C   CR16  0  -0.364  -4.7068  -0.8672  -0.1014
 8L7  C7   C   C     0   0.101  -4.9069  -3.3587  -0.2266
 8L7  C8   C   CH3   0  -0.733  -5.2291  -4.5409   0.6419
 8L7  C9   C   C2    0  -0.579  -4.2093  -3.5036  -1.3556
 8L7  N3   N   NH1   0  -0.706  -2.9762   1.3546   0.2930
 8L7  N34  N   NH1   0  -0.731   3.9840   0.7989   0.5179
 8L7  N4   N   NH1   0  -0.791  -0.7434   1.6511   0.6122
 8L7  O2   O   O     0  -0.512  -1.9020   3.0879  -0.7344
 8L7  O3   O   O2    0  -0.508   3.3668  -1.2406  -0.5021
 8L7  O4   O   OH1   0  -0.674   6.1862  -0.7231   0.3506
 8L7  O5   O   OH1   0  -0.658   5.9819  -3.4692   0.3160
 8L7  CL   CL  CL    0  -0.135   4.7958   3.6226   0.0742
 8L7  H1   H   HCH3  0   0.233  -5.5042   1.8036  -1.9500
 8L7  H2   H   HCH3  0   0.247  -3.9552   2.6416  -2.0283
 8L7  H3   H   HCH3  0   0.233  -4.0178   0.8795  -2.1567
 8L7  H4   H   HCH3  0   0.235  -4.8466   2.8475   1.6030
 8L7  H5   H   HCH3  0   0.254  -4.2447   3.7516   0.2096
 8L7  H6   H   HCH3  0   0.232  -5.8887   3.1334   0.2036
 8L7  H7   H   HCR6  0   0.268   0.0093   4.2560   0.2320
 8L7  H8   H   HCR6  0   0.275   2.3287   4.9931   0.0004
 8L7  H9   H   HCR6  0   0.257  -6.7341   1.4403   1.3144
 8L7  H10  H   HCR6  0   0.284   1.3676   0.2095   0.6029
 8L7  H11  H   HCH1  0   0.238   3.0896  -0.7675   1.4858
 8L7  H12  H   HCH1  0   0.250   5.2937  -1.2424   2.1489
 8L7  H13  H   HCH1  0   0.244   4.1884  -3.2104   1.3240
 8L7  H14  H   HCH1  0   0.226   4.7497  -2.3682  -1.5422
 8L7  H15  H   HCH2  0   0.203   3.6350  -4.5254  -1.0201
 8L7  H16  H   HCH2  0   0.196   2.3460  -3.6539  -0.1843
 8L7  H17  H   HCR6  0   0.257  -7.9678  -0.5887   1.8976
 8L7  H18  H   HCR6  0   0.253  -7.1521  -2.7964   1.2221
 8L7  H19  H   HCR6  0   0.253  -3.7704  -0.9472  -0.6411
 8L7  H20  H   HCH3  0   0.244  -6.2998  -4.7536   0.6514
 8L7  H21  H   HCH3  0   0.249  -4.7227  -5.4368   0.2864
 8L7  H22  H   HCH3  0   0.243  -4.9326  -4.3660   1.6776
 8L7  H23  H   H     0   0.241  -3.8369  -4.4728  -1.6616
 8L7  H24  H   H     0   0.238  -3.9981  -2.6759  -2.0205
 8L7  H25  H   HNH1  0   0.397  -2.8895   0.7166   1.0685
 8L7  H26  H   HNH1  0   0.382   4.8614   1.0978   0.1206
 8L7  H27  H   HNH1  0   0.405  -0.7789   0.7243   1.0086
 8L7  H28  H   HOH1  0   0.455   6.8242  -1.4212   0.1581
 8L7  H29  H   HOH1  0   0.467   6.3039  -3.8496   1.1397
 8L7  H30  H   HOH1  0   0.456   1.8431  -4.0523  -2.4232
 8L7  O6   O   OH1   0  -0.671   2.4472  -3.3276  -2.2396

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
 8L7  C13  C11  single    1.530  0.020  1.530
 8L7  C8   C7   single    1.502  0.020  1.502
 8L7  C11  C1   single    1.529  0.020  1.529
 8L7  C11  C12  single    1.535  0.020  1.535
 8L7  C11  N3   single    1.467  0.020  1.467
 8L7  C6   C1   aromatic  1.393  0.020  1.393
 8L7  C6   C5   aromatic  1.394  0.020  1.394
 8L7  C7   C5   single    1.482  0.020  1.482
 8L7  C7   C9   double    1.335  0.020  1.335
 8L7  C1   C2   aromatic  1.390  0.020  1.390
 8L7  C5   C4   aromatic  1.397  0.020  1.397
 8L7  C2   C3   aromatic  1.389  0.020  1.389
 8L7  C4   C3   aromatic  1.385  0.020  1.385
 8L7  N3   C10  single    1.356  0.020  1.356
 8L7  C10  N4   single    1.381  0.020  1.381
 8L7  C10  O2   double    1.220  0.020  1.220
 8L7  N4   C17  single    1.394  0.020  1.394
 8L7  C17  C18  aromatic  1.394  0.020  1.394
 8L7  C17  C22  aromatic  1.394  0.020  1.394
 8L7  C18  C19  aromatic  1.385  0.020  1.385
 8L7  C22  C21  aromatic  1.397  0.020  1.397
 8L7  C19  C20  aromatic  1.381  0.020  1.381
 8L7  C21  C20  aromatic  1.403  0.020  1.403
 8L7  C21  N34  single    1.372  0.020  1.372
 8L7  C20  CL   single    1.739  0.020  1.739
 8L7  N34  C24  single    1.414  0.020  1.414
 8L7  O4   C25  single    1.403  0.020  1.403
 8L7  C25  C24  single    1.524  0.020  1.524
 8L7  C25  C26  single    1.529  0.020  1.529
 8L7  C24  O3   single    1.429  0.020  1.429
 8L7  O5   C26  single    1.401  0.020  1.401
 8L7  C26  C27  single    1.529  0.020  1.529
 8L7  O3   C27  single    1.416  0.020  1.416
 8L7  C27  C29  single    1.510  0.020  1.510
 8L7  C29  O6   single    1.407  0.020  1.407
 8L7  C12  H1   single    0.970  0.020  1.090
 8L7  C12  H2   single    0.970  0.020  1.090
 8L7  C12  H3   single    0.970  0.020  1.090
 8L7  C13  H4   single    0.970  0.020  1.090
 8L7  C13  H5   single    0.970  0.020  1.090
 8L7  C13  H6   single    0.970  0.020  1.090
 8L7  C18  H7   single    0.930  0.020  1.080
 8L7  C19  H8   single    0.930  0.020  1.080
 8L7  C2   H9   single    0.930  0.020  1.080
 8L7  C22  H10  single    0.930  0.020  1.080
 8L7  C24  H11  single    0.970  0.020  1.090
 8L7  C25  H12  single    0.970  0.020  1.090
 8L7  C26  H13  single    0.970  0.020  1.090
 8L7  C27  H14  single    0.970  0.020  1.090
 8L7  C29  H15  single    0.970  0.020  1.090
 8L7  C29  H16  single    0.970  0.020  1.090
 8L7  C3   H17  single    0.930  0.020  1.080
 8L7  C4   H18  single    0.930  0.020  1.080
 8L7  C6   H19  single    0.930  0.020  1.080
 8L7  C8   H20  single    0.970  0.020  1.090
 8L7  C8   H21  single    0.970  0.020  1.090
 8L7  C8   H22  single    0.970  0.020  1.090
 8L7  C9   H23  single    0.930  0.020  1.080
 8L7  C9   H24  single    0.930  0.020  1.080
 8L7  N3   H25  single    0.860  0.020  1.020
 8L7  N34  H26  single    0.890  0.020  1.040
 8L7  N4   H27  single    0.860  0.020  1.020
 8L7  O4   H28  single    0.850  0.020  0.980
 8L7  O5   H29  single    0.850  0.020  0.980
 8L7  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
 8L7  C6   C1   C2   118.40  3.000
 8L7  C2   C1   C11  122.64  3.000
 8L7  C6   C1   C11  118.95  3.000
 8L7  O2   C10  N4   122.81  3.000
 8L7  O2   C10  N3   124.74  3.000
 8L7  N4   C10  N3   112.44  3.000
 8L7  N3   C11  C13  110.34  3.000
 8L7  N3   C11  C12  111.50  3.000
 8L7  C13  C11  C12  109.48  3.000
 8L7  N3   C11  C1   105.50  3.000
 8L7  C12  C11  C1   107.31  3.000
 8L7  C13  C11  C1   112.63  3.000
 8L7  H3   C12  H2   108.57  3.000
 8L7  H3   C12  H1   107.82  3.000
 8L7  H2   C12  H1   108.11  3.000
 8L7  H3   C12  C11  111.22  3.000
 8L7  H2   C12  C11  111.72  3.000
 8L7  H1   C12  C11  109.28  3.000
 8L7  H6   C13  H5   107.44  3.000
 8L7  H6   C13  H4   108.33  3.000
 8L7  H5   C13  H4   108.33  3.000
 8L7  H6   C13  C11  111.38  3.000
 8L7  H5   C13  C11  109.68  3.000
 8L7  H4   C13  C11  111.54  3.000
 8L7  N4   C17  C22  116.97  3.000
 8L7  C22  C17  C18  119.77  3.000
 8L7  N4   C17  C18  123.24  3.000
 8L7  H7   C18  C19  119.45  3.000
 8L7  H7   C18  C17  121.80  3.000
 8L7  C19  C18  C17  118.75  3.000
 8L7  H8   C19  C20  119.41  3.000
 8L7  H8   C19  C18  119.32  3.000
 8L7  C20  C19  C18  121.26  3.000
 8L7  H9   C2   C3   118.88  3.000
 8L7  H9   C2   C1   120.89  3.000
 8L7  C3   C2   C1   120.23  3.000
 8L7  CL   C20  C21  119.44  3.000
 8L7  CL   C20  C19  119.33  3.000
 8L7  C21  C20  C19  121.23  3.000
 8L7  N34  C21  C22  122.64  3.000
 8L7  N34  C21  C20  120.43  3.000
 8L7  C22  C21  C20  116.93  3.000
 8L7  H10  C22  C21  119.70  3.000
 8L7  H10  C22  C17  118.25  3.000
 8L7  C21  C22  C17  122.03  3.000
 8L7  H11  C24  O3   108.81  3.000
 8L7  H11  C24  N34  108.62  3.000
 8L7  O3   C24  N34  112.38  3.000
 8L7  H11  C24  C25  108.57  3.000
 8L7  O3   C24  C25  105.79  3.000
 8L7  N34  C24  C25  112.55  3.000
 8L7  H12  C25  O4   111.52  3.000
 8L7  H12  C25  C26  112.53  3.000
 8L7  O4   C25  C26  111.15  3.000
 8L7  H12  C25  C24  110.90  3.000
 8L7  C26  C25  C24  100.68  3.000
 8L7  O4   C25  C24  109.55  3.000
 8L7  H13  C26  O5   111.54  3.000
 8L7  H13  C26  C27  109.76  3.000
 8L7  O5   C26  C27  110.30  3.000
 8L7  H13  C26  C25  108.63  3.000
 8L7  C27  C26  C25  102.27  3.000
 8L7  O5   C26  C25  113.93  3.000
 8L7  H14  C27  O3   109.70  3.000
 8L7  H14  C27  C29  109.03  3.000
 8L7  O3   C27  C29  111.02  3.000
 8L7  H14  C27  C26  109.18  3.000
 8L7  C29  C27  C26  112.35  3.000
 8L7  O3   C27  C26  105.49  3.000
 8L7  H16  C29  H15  107.01  3.000
 8L7  H16  C29  O6   111.88  3.000
 8L7  H15  C29  O6   111.77  3.000
 8L7  H16  C29  C27  108.98  3.000
 8L7  H15  C29  C27  107.89  3.000
 8L7  O6   C29  C27  109.18  3.000
 8L7  H17  C3   C4   119.72  3.000
 8L7  H17  C3   C2   119.57  3.000
 8L7  C4   C3   C2   120.71  3.000
 8L7  H18  C4   C5   120.52  3.000
 8L7  H18  C4   C3   119.16  3.000
 8L7  C5   C4   C3   120.32  3.000
 8L7  C7   C5   C6   120.94  3.000
 8L7  C7   C5   C4   120.99  3.000
 8L7  C6   C5   C4   118.08  3.000
 8L7  H19  C6   C5   118.82  3.000
 8L7  H19  C6   C1   118.91  3.000
 8L7  C5   C6   C1   122.26  3.000
 8L7  C9   C7   C8   121.05  3.000
 8L7  C9   C7   C5   121.46  3.000
 8L7  C8   C7   C5   117.49  3.000
 8L7  H22  C8   H21  108.38  3.000
 8L7  H22  C8   H20  106.82  3.000
 8L7  H21  C8   H20  107.38  3.000
 8L7  H22  C8   C7   111.37  3.000
 8L7  H21  C8   C7   111.04  3.000
 8L7  H20  C8   C7   111.64  3.000
 8L7  H24  C9   H23  116.35  3.000
 8L7  H24  C9   C7   122.57  3.000
 8L7  H23  C9   C7   121.07  3.000
 8L7  H25  N3   C11  114.98  3.000
 8L7  H25  N3   C10  116.87  3.000
 8L7  C11  N3   C10  125.74  3.000
 8L7  H26  N34  C24  116.08  3.000
 8L7  H26  N34  C21  116.63  3.000
 8L7  C24  N34  C21  123.32  3.000
 8L7  H27  N4   C17  114.80  3.000
 8L7  H27  N4   C10  116.92  3.000
 8L7  C17  N4   C10  126.10  3.000
 8L7  C27  O3   C24  110.88  3.000
 8L7  H28  O4   C25  108.00  3.000
 8L7  H29  O5   C26  108.83  3.000
 8L7  H30  O6   C29  108.11  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
 8L7  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 8L7  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 8L7  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 8L7  CONST_04  C20  C21  C22  C17    0.00   0.0  0
 8L7  CONST_05  C21  C22  C17  C18    0.00   0.0  0
 8L7  CONST_06  C21  C20  C19  C18    0.00   0.0  0
 8L7  CONST_07  C22  C17  C18  C19    0.00   0.0  0
 8L7  CONST_08  C22  C21  C20  C19    0.00   0.0  0
 8L7  CONST_09  C5   C6   C1   C2     0.00   0.0  0
 8L7  CONST_10  C5   C4   C3   C2     0.00   0.0  0
 8L7  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 8L7  CONST_12  C6   C5   C4   C3     0.00   0.0  0
 8L7  CONST_13  C7   C5   C6   C1   180.00   0.0  0
 8L7  CONST_14  C5   C6   C1   C11  180.00   0.0  0
 8L7  CONST_15  C3   C2   C1   C11  180.00   0.0  0
 8L7  CONST_16  N34  C21  C22  C17  180.00   0.0  0
 8L7  CONST_17  CL   C20  C19  C18  180.00   0.0  0
 8L7  CONST_18  N4   C17  C18  C19  180.00   0.0  0
 8L7  CONST_19  N34  C21  C20  C19  180.00   0.0  0
 8L7  CONST_20  N4   C17  C22  C21  180.00   0.0  0
 8L7  CONST_21  CL   C20  C21  C22  180.00   0.0  0
 8L7  CONST_22  C7   C5   C4   C3   180.00   0.0  0
 8L7  CONST_23  C24  N34  C21  C20  180.00   0.0  0
 8L7  CONST_24  C24  N34  C21  C22    0.00   0.0  0
 8L7  CONST_25  H17  C3   C2   C1   180.00   0.0  0
 8L7  CONST_26  H8   C19  C18  C17  180.00   0.0  0
 8L7  CONST_27  H10  C22  C17  C18  180.00   0.0  0
 8L7  CONST_28  H19  C6   C1   C2   180.00   0.0  0
 8L7  CONST_29  H18  C4   C3   C2   180.00   0.0  0
 8L7  CONST_30  H7   C18  C19  C20  180.00   0.0  0
 8L7  CONST_31  H9   C2   C3   C4   180.00   0.0  0
 8L7  CONST_36  O2   C10  N4   C17    0.00   0.0  0
 8L7  CONST_37  N3   C10  N4   C17  180.00   0.0  0
 8L7  CONST_38  O2   C10  N3   C11    0.00   0.0  0
 8L7  CONST_39  N4   C10  N3   C11  180.00   0.0  0
 8L7  CONST_40  H25  N3   C10  O2   180.00   0.0  0
 8L7  Var_01    C6   C1   C11  C12   67.32  30.0  2
 8L7  Var_02    C8   C7   C5   C4   -29.96  30.0  2
 8L7  Var_03    C10  N3   C11  C1   172.27  30.0  3
 8L7  Var_04    H23  C9   C7   C5   179.14   0.0  2
 8L7  Var_05    H4   C13  C11  C1    58.49  30.0  3
 8L7  Var_06    H1   C12  C11  C1    56.76  30.0  3
 8L7  Var_07    H20  C8   C7   C5    66.56  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
 8L7  chir_01  C24  N34  C25  O3   positiv
 8L7  chir_02  C25  O4   C26  C24  positiv
 8L7  chir_03  C26  O5   C25  C27  negativ
 8L7  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
 8L7  plan-1  C17  0.020
 8L7  plan-1  C18  0.020
 8L7  plan-1  C19  0.020
 8L7  plan-1  C20  0.020
 8L7  plan-1  C21  0.020
 8L7  plan-1  C22  0.020
 8L7  plan-1  N34  0.020
 8L7  plan-1  N4   0.020
 8L7  plan-1  CL   0.020
 8L7  plan-1  H7   0.020
 8L7  plan-1  H8   0.020
 8L7  plan-1  H10  0.020
 8L7  plan-2  C1   0.020
 8L7  plan-2  C11  0.020
 8L7  plan-2  C2   0.020
 8L7  plan-2  C3   0.020
 8L7  plan-2  C4   0.020
 8L7  plan-2  C5   0.020
 8L7  plan-2  C6   0.020
 8L7  plan-2  C7   0.020
 8L7  plan-2  H9   0.020
 8L7  plan-2  H17  0.020
 8L7  plan-2  H18  0.020
 8L7  plan-2  H19  0.020
 8L7  plan-3  C10  0.020
 8L7  plan-3  C11  0.020
 8L7  plan-3  C17  0.020
 8L7  plan-3  N3   0.020
 8L7  plan-3  N4   0.020
 8L7  plan-3  O2   0.020
 8L7  plan-3  H25  0.020
 8L7  plan-3  H27  0.020
 8L7  plan-4  C21  0.020
 8L7  plan-4  C24  0.020
 8L7  plan-4  N34  0.020
 8L7  plan-4  H26  0.020
 8L7  plan-5  C5   0.020
 8L7  plan-5  C7   0.020
 8L7  plan-5  C8   0.020
 8L7  plan-5  C9   0.020
 8L7  plan-5  H23  0.020
 8L7  plan-5  H24  0.020

