# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:35:56 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-[2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-6'-(trifluoromethyl)[1,1'-biphenyl]-3-yl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@H]1Oc2cccc(c2c3cccc(N[S](C)(=O)=O)c3)C(F)(F)F
#
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
 JC7  JC7  N-[2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-6'-(trifluoromethyl)[1,1'-biphenyl]-3-yl]methanesulfonamide  ligand  61  36  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JC7
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
 JC7  C10  C  CR16  0  -0.309   0.0204  -4.4882   0.2676
 JC7  C17  C  CR6   0   0.057   1.3548  -0.9662   0.8151
 JC7  C26  C  CR16  0  -0.240   2.1910   0.5783   2.4550
 JC7  C28  C  CH1   0  -0.148  -2.4331   1.3287   0.3218
 JC7  C03  C  CH1   0  -0.019  -4.4162   0.0216  -1.2875
 JC7  O04  O  O2    0  -0.489  -3.0414  -0.3149  -1.3234
 JC7  C05  C  CH1   0   0.309  -2.4151  -0.1439  -0.0911
 JC7  C07  C  CR6   0   0.351  -0.7781  -1.8512  -0.0737
 JC7  C08  C  CR16  0  -0.333  -1.6402  -2.8868  -0.4228
 JC7  C09  C  CR16  0  -0.240  -1.2355  -4.1978  -0.2384
 JC7  C11  C  CR6   0  -0.238   0.8827  -3.4502   0.5984
 JC7  C12  C  CT    0   1.063   2.2427  -3.7717   1.1480
 JC7  F13  F  F     0  -0.312   2.3712  -3.3919   2.4276
 JC7  F14  F  F     0  -0.303   2.5039  -5.0827   1.1142
 JC7  F15  F  F     0  -0.309   3.2232  -3.1698   0.4640
 JC7  C16  C  CR6   0  -0.036   0.4924  -2.1180   0.4436
 JC7  C18  C  CR16  0  -0.310   2.0922  -0.3092  -0.1600
 JC7  C19  C  CR6   0   0.297   2.8898   0.7788   0.1726
 JC7  N20  N  NC1   0  -0.822   3.6586   1.4109  -0.8379
 JC7  S21  S  S     0   1.320   3.3060   2.9789  -1.2855
 JC7  O22  O  OS    0  -0.668   4.1164   3.2298  -2.4664
 JC7  C23  C  CH3   0  -0.820   1.5890   2.9885  -1.7394
 JC7  O24  O  OS    0  -0.655   3.4753   3.8222  -0.1148
 JC7  C25  C  CR16  0  -0.264   2.9518   1.2187   1.4904
 JC7  C27  C  CR16  0  -0.267   1.3913  -0.5056   2.1252
 JC7  C31  C  CH3   0  -0.788  -0.5408   2.5509   3.3511
 JC7  O32  O  O     0  -0.491  -0.3867   3.1500   1.0431
 JC7  C33  C  CH1   0   0.053  -3.8825   1.8268   0.3189
 JC7  O34  O  OH1   0  -0.656  -3.8646   3.1912   0.6269
 JC7  C35  C  CH1   0  -0.024  -4.5647   1.5192  -1.0166
 JC7  O36  O  OH1   0  -0.670  -3.9671   2.2994  -2.0216
 JC7  H1   H  HCR6  0   0.272   0.3140  -5.5203   0.3901
 JC7  H2   H  HCR6  0   0.260   2.2326   0.9216   3.4800
 JC7  H3   H  HCH1  0   0.279  -1.8482   1.8989  -0.4031
 JC7  H4   H  HOH1  0   0.458  -5.2918  -2.1010  -3.5229
 JC7  H7   H  HCH1  0   0.227  -4.9131  -0.5210  -0.4665
 JC7  H8   H  HCH1  0   0.207  -2.9208  -0.7560   0.6785
 JC7  H9   H  HCR6  0   0.294  -2.6078  -2.6835  -0.8611
 JC7  H10  H  HCR6  0   0.273  -1.9048  -5.0040  -0.5066
 JC7  H11  H  HCR6  0   0.260   2.0480  -0.6472  -1.1888
 JC7  H12  H  HNC1  0   0.419   3.8088   0.8319  -1.6581
 JC7  H13  H  HCH3  0   0.314   0.9793   2.7265  -0.8765
 JC7  H14  H  HCH3  0   0.307   1.3444   3.9969  -2.0698
 JC7  H15  H  HCH3  0   0.291   1.4327   2.2818  -2.5512
 JC7  H16  H  HCR6  0   0.267   3.5935   2.0432   1.7641
 JC7  H17  H  HCR6  0   0.252   0.7990  -0.9940   2.8875
 JC7  H19  H  HCH3  0   0.248  -0.7288   1.6389   3.9155
 JC7  H20  H  HCH3  0   0.259   0.5048   2.8262   3.4627
 JC7  H21  H  HCH3  0   0.271  -1.1448   3.3459   3.7929
 JC7  H22  H  HCH1  0   0.216  -4.4335   1.2589   1.0852
 JC7  H23  H  HOH1  0   0.454  -4.7644   3.4737   0.8184
 JC7  H24  H  HCH1  0   0.245  -5.6350   1.7466  -0.9145
 JC7  H25  H  HOH1  0   0.459  -4.6077   2.4541  -2.7207
 JC7  O06  O  O2    0  -0.474  -1.0890  -0.5406  -0.2179
 JC7  N29  N  NH1   0  -0.625  -1.8286   1.5004   1.6137
 JC7  C02  C  CH2   0  -0.165  -5.0393  -0.4229  -2.5903
 JC7  C30  C  C     0   0.548  -0.8905   2.4279   1.8899
 JC7  O01  O  OH1   0  -0.664  -4.9780  -1.8274  -2.6565
 JC7  H5   H  HCH2  0   0.205  -4.5129   0.0462  -3.4304
 JC7  H6   H  HCH2  0   0.207  -6.0750  -0.0594  -2.6108
 JC7  H18  H  HNH1  0   0.397  -2.2287   0.9926   2.3875

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
 JC7  F15  C12  single    1.338  0.020  1.338
 JC7  C10  C09  aromatic  1.385  0.020  1.385
 JC7  C10  C11  aromatic  1.389  0.020  1.389
 JC7  C09  C08  aromatic  1.384  0.020  1.384
 JC7  C12  C11  single    1.502  0.020  1.502
 JC7  C12  F14  single    1.337  0.020  1.337
 JC7  C12  F13  single    1.341  0.020  1.341
 JC7  C11  C16  aromatic  1.397  0.020  1.397
 JC7  C08  C07  aromatic  1.392  0.020  1.392
 JC7  C16  C07  aromatic  1.397  0.020  1.397
 JC7  C16  C17  single    1.486  0.020  1.486
 JC7  C07  O06  single    1.355  0.020  1.355
 JC7  C02  C03  single    1.511  0.020  1.511
 JC7  C02  O01  single    1.407  0.020  1.407
 JC7  O04  C03  single    1.416  0.020  1.416
 JC7  O04  C05  single    1.393  0.020  1.393
 JC7  C03  C35  single    1.529  0.020  1.529
 JC7  O06  C05  single    1.390  0.020  1.390
 JC7  C17  C18  aromatic  1.388  0.020  1.388
 JC7  C17  C27  aromatic  1.389  0.020  1.389
 JC7  C05  C28  single    1.530  0.020  1.530
 JC7  C23  S21  single    1.776  0.020  1.776
 JC7  C18  C19  aromatic  1.389  0.020  1.389
 JC7  C27  C26  aromatic  1.387  0.020  1.387
 JC7  C35  C33  single    1.531  0.020  1.531
 JC7  C35  O36  single    1.406  0.020  1.406
 JC7  C28  N29  single    1.437  0.020  1.437
 JC7  C28  C33  single    1.533  0.020  1.533
 JC7  C19  N20  single    1.418  0.020  1.418
 JC7  C19  C25  aromatic  1.391  0.020  1.391
 JC7  N29  C30  single    1.348  0.020  1.348
 JC7  C33  O34  single    1.399  0.020  1.399
 JC7  S21  N20  single    1.668  0.020  1.668
 JC7  S21  O22  double    1.454  0.020  1.454
 JC7  S21  O24  double    1.453  0.020  1.453
 JC7  C26  C25  aromatic  1.385  0.020  1.385
 JC7  C30  C31  single    1.508  0.020  1.508
 JC7  C30  O32  double    1.222  0.020  1.222
 JC7  C10  H1   single    0.930  0.020  1.080
 JC7  C26  H2   single    0.930  0.020  1.080
 JC7  C28  H3   single    0.970  0.020  1.090
 JC7  O01  H4   single    0.850  0.020  0.980
 JC7  C02  H5   single    0.970  0.020  1.090
 JC7  C02  H6   single    0.970  0.020  1.090
 JC7  C03  H7   single    0.970  0.020  1.090
 JC7  C05  H8   single    0.970  0.020  1.090
 JC7  C08  H9   single    0.930  0.020  1.080
 JC7  C09  H10  single    0.930  0.020  1.080
 JC7  C18  H11  single    0.930  0.020  1.080
 JC7  N20  H12  single    0.890  0.020  1.040
 JC7  C23  H13  single    0.970  0.020  1.090
 JC7  C23  H14  single    0.970  0.020  1.090
 JC7  C23  H15  single    0.970  0.020  1.090
 JC7  C25  H16  single    0.930  0.020  1.080
 JC7  C27  H17  single    0.930  0.020  1.080
 JC7  N29  H18  single    0.860  0.020  1.020
 JC7  C31  H19  single    0.970  0.020  1.090
 JC7  C31  H20  single    0.970  0.020  1.090
 JC7  C31  H21  single    0.970  0.020  1.090
 JC7  C33  H22  single    0.970  0.020  1.090
 JC7  O34  H23  single    0.850  0.020  0.980
 JC7  C35  H24  single    0.970  0.020  1.090
 JC7  O36  H25  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
 JC7  H1   C10  C11  121.21  3.000
 JC7  H1   C10  C09  119.24  3.000
 JC7  C11  C10  C09  119.55  3.000
 JC7  C27  C17  C18  119.45  3.000
 JC7  C27  C17  C16  120.53  3.000
 JC7  C18  C17  C16  119.98  3.000
 JC7  H2   C26  C27  119.71  3.000
 JC7  H2   C26  C25  119.47  3.000
 JC7  C27  C26  C25  120.82  3.000
 JC7  H3   C28  C33  109.60  3.000
 JC7  H3   C28  N29  108.01  3.000
 JC7  C33  C28  N29  111.15  3.000
 JC7  H3   C28  C05  108.49  3.000
 JC7  C33  C28  C05  108.87  3.000
 JC7  N29  C28  C05  110.67  3.000
 JC7  H7   C03  C35  107.83  3.000
 JC7  H7   C03  O04  109.85  3.000
 JC7  C35  C03  O04  109.37  3.000
 JC7  H7   C03  C02  108.14  3.000
 JC7  C35  C03  C02  113.63  3.000
 JC7  O04  C03  C02  107.98  3.000
 JC7  C05  O04  C03  112.64  3.000
 JC7  H8   C05  O06  109.99  3.000
 JC7  H8   C05  O04  110.01  3.000
 JC7  O06  C05  O04  108.25  3.000
 JC7  H8   C05  C28  109.86  3.000
 JC7  O06  C05  C28  108.10  3.000
 JC7  O04  C05  C28  110.60  3.000
 JC7  C16  C07  C08  120.92  3.000
 JC7  C16  C07  O06  115.64  3.000
 JC7  C08  C07  O06  123.43  3.000
 JC7  H9   C08  C09  119.57  3.000
 JC7  H9   C08  C07  121.06  3.000
 JC7  C09  C08  C07  119.35  3.000
 JC7  H10  C09  C08  119.47  3.000
 JC7  H10  C09  C10  119.70  3.000
 JC7  C08  C09  C10  120.82  3.000
 JC7  C16  C11  C12  119.86  3.000
 JC7  C16  C11  C10  120.85  3.000
 JC7  C12  C11  C10  119.29  3.000
 JC7  F15  C12  F14  106.55  3.000
 JC7  F14  C12  F13  106.45  3.000
 JC7  F15  C12  F13  106.86  3.000
 JC7  F13  C12  C11  112.05  3.000
 JC7  F14  C12  C11  112.18  3.000
 JC7  F15  C12  C11  112.34  3.000
 JC7  C11  C16  C07  118.50  3.000
 JC7  C07  C16  C17  118.18  3.000
 JC7  C11  C16  C17  123.32  3.000
 JC7  H11  C18  C19  119.66  3.000
 JC7  H11  C18  C17  119.84  3.000
 JC7  C19  C18  C17  120.50  3.000
 JC7  C25  C19  N20  120.66  3.000
 JC7  C25  C19  C18  120.01  3.000
 JC7  N20  C19  C18  119.31  3.000
 JC7  H12  N20  S21  110.52  3.000
 JC7  H12  N20  C19  113.68  3.000
 JC7  S21  N20  C19  119.70  3.000
 JC7  O24  S21  C23  108.39  3.000
 JC7  O24  S21  O22  119.30  3.000
 JC7  C23  S21  O22  109.28  3.000
 JC7  O24  S21  N20  107.74  3.000
 JC7  O22  S21  N20  105.21  3.000
 JC7  C23  S21  N20  106.14  3.000
 JC7  H15  C23  H14  110.05  3.000
 JC7  H15  C23  H13  110.78  3.000
 JC7  H14  C23  H13  109.72  3.000
 JC7  H15  C23  S21  109.04  3.000
 JC7  H14  C23  S21  107.44  3.000
 JC7  H13  C23  S21  109.73  3.000
 JC7  H16  C25  C19  120.54  3.000
 JC7  H16  C25  C26  120.18  3.000
 JC7  C19  C25  C26  119.28  3.000
 JC7  H17  C27  C26  120.07  3.000
 JC7  H17  C27  C17  120.03  3.000
 JC7  C26  C27  C17  119.91  3.000
 JC7  H21  C31  H20  107.83  3.000
 JC7  H21  C31  H19  107.74  3.000
 JC7  H20  C31  H19  108.97  3.000
 JC7  H21  C31  C30  108.86  3.000
 JC7  H20  C31  C30  110.07  3.000
 JC7  H19  C31  C30  113.21  3.000
 JC7  H22  C33  C35  106.28  3.000
 JC7  H22  C33  O34  110.86  3.000
 JC7  C35  C33  O34  113.19  3.000
 JC7  H22  C33  C28  107.71  3.000
 JC7  O34  C33  C28  107.73  3.000
 JC7  C35  C33  C28  110.97  3.000
 JC7  H23  O34  C33  108.55  3.000
 JC7  H24  C35  O36  111.45  3.000
 JC7  H24  C35  C33  108.14  3.000
 JC7  O36  C35  C33  108.82  3.000
 JC7  H24  C35  C03  108.29  3.000
 JC7  O36  C35  C03  112.06  3.000
 JC7  C33  C35  C03  107.94  3.000
 JC7  H25  O36  C35  109.03  3.000
 JC7  C07  O06  C05  119.04  3.000
 JC7  H18  N29  C30  117.74  3.000
 JC7  H18  N29  C28  117.58  3.000
 JC7  C30  N29  C28  124.02  3.000
 JC7  H6   C02  H5   107.27  3.000
 JC7  H6   C02  C03  107.92  3.000
 JC7  H5   C02  C03  109.67  3.000
 JC7  H6   C02  O01  111.76  3.000
 JC7  H5   C02  O01  111.71  3.000
 JC7  C03  C02  O01  108.43  3.000
 JC7  O32  C30  C31  121.87  3.000
 JC7  O32  C30  N29  123.49  3.000
 JC7  C31  C30  N29  114.60  3.000
 JC7  H4   O01  C02  108.19  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
 JC7  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 JC7  CONST_02  C07  C16  C11  C10    0.00   0.0  0
 JC7  CONST_03  C17  C16  C11  C10  180.00   0.0  0
 JC7  CONST_04  C08  C07  C16  C17  180.00   0.0  0
 JC7  CONST_05  C25  C19  C18  C17    0.00   0.0  0
 JC7  CONST_06  C25  C26  C27  C17    0.00   0.0  0
 JC7  CONST_07  C16  C17  C27  C26  180.00   0.0  0
 JC7  CONST_08  C18  C17  C27  C26    0.00   0.0  0
 JC7  CONST_09  C18  C19  C25  C26    0.00   0.0  0
 JC7  CONST_12  C11  C10  C09  C08    0.00   0.0  0
 JC7  CONST_13  C11  C16  C07  C08    0.00   0.0  0
 JC7  CONST_14  C16  C11  C10  C09    0.00   0.0  0
 JC7  CONST_15  C16  C07  C08  C09    0.00   0.0  0
 JC7  CONST_18  C19  C18  C17  C16  180.00   0.0  0
 JC7  CONST_19  C27  C17  C18  C19    0.00   0.0  0
 JC7  CONST_20  C27  C26  C25  C19    0.00   0.0  0
 JC7  CONST_21  C12  C11  C16  C17    0.00   0.0  0
 JC7  CONST_22  O06  C07  C16  C17    0.00   0.0  0
 JC7  CONST_23  N20  C19  C18  C17  180.00   0.0  0
 JC7  CONST_24  N20  C19  C25  C26  180.00   0.0  0
 JC7  CONST_25  C09  C08  C07  O06  180.00   0.0  0
 JC7  CONST_26  C11  C16  C07  O06  180.00   0.0  0
 JC7  CONST_27  C12  C11  C16  C07  180.00   0.0  0
 JC7  CONST_28  C12  C11  C10  C09  180.00   0.0  0
 JC7  CONST_29  H9   C08  C09  C10  180.00   0.0  0
 JC7  CONST_30  H2   C26  C27  C17  180.00   0.0  0
 JC7  CONST_31  H10  C09  C08  C07  180.00   0.0  0
 JC7  CONST_32  H1   C10  C09  C08  180.00   0.0  0
 JC7  CONST_33  H11  C18  C17  C16    0.00   0.0  0
 JC7  CONST_34  H17  C27  C17  C16    0.00   0.0  0
 JC7  CONST_35  H16  C25  C19  C18  180.00   0.0  0
 JC7  CONST_39  C31  C30  N29  C28  180.00   0.0  0
 JC7  CONST_40  O32  C30  N29  C28    0.00   0.0  0
 JC7  CONST_41  H18  N29  C30  C31    0.00   0.0  0
 JC7  Var_01    C08  C07  O06  C05   31.36  30.0  2
 JC7  Var_02    F15  C12  C11  C10  126.77  30.0  3
 JC7  Var_03    C23  S21  N20  C19  -55.11  30.0  1
 JC7  Var_04    H13  C23  S21  N20   62.73  30.0  3
 JC7  Var_05    H19  C31  C30  N29   25.50  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
 JC7  chir_01  C28  C05  N29  C33  positiv
 JC7  chir_02  C03  O04  C35  C02  negativ
 JC7  chir_03  C05  O04  O06  C28  negativ
 JC7  chir_04  C33  O34  C28  C35  positiv
 JC7  chir_05  C35  O36  C03  C33  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
 JC7  plan-1  C10  0.020
 JC7  plan-1  C17  0.020
 JC7  plan-1  C07  0.020
 JC7  plan-1  C08  0.020
 JC7  plan-1  C09  0.020
 JC7  plan-1  C11  0.020
 JC7  plan-1  C12  0.020
 JC7  plan-1  C16  0.020
 JC7  plan-1  H1   0.020
 JC7  plan-1  H9   0.020
 JC7  plan-1  H10  0.020
 JC7  plan-1  O06  0.020
 JC7  plan-2  C17  0.020
 JC7  plan-2  C26  0.020
 JC7  plan-2  C16  0.020
 JC7  plan-2  C18  0.020
 JC7  plan-2  C19  0.020
 JC7  plan-2  N20  0.020
 JC7  plan-2  C25  0.020
 JC7  plan-2  C27  0.020
 JC7  plan-2  H2   0.020
 JC7  plan-2  H11  0.020
 JC7  plan-2  H16  0.020
 JC7  plan-2  H17  0.020
 JC7  plan-3  C28  0.020
 JC7  plan-3  C31  0.020
 JC7  plan-3  O32  0.020
 JC7  plan-3  N29  0.020
 JC7  plan-3  C30  0.020
 JC7  plan-3  H18  0.020
 JC7  plan-4  C19  0.020
 JC7  plan-4  N20  0.020
 JC7  plan-4  S21  0.020
 JC7  plan-4  H12  0.020

