# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 06:30:02 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-[(biphenyl-4-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccc(cc2)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 F59  F59  N-[(biphenyl-4-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  ligand  51  29  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F59
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
 F59  C16  C  CR16  0  -0.308  -6.7528  -0.2080  -1.8096
 F59  C17  C  CR16  0  -0.239  -8.0325  -0.5492  -2.2210
 F59  C18  C  CR16  0  -0.263  -8.9954  -0.9060  -1.2859
 F59  C19  C  CR16  0  -0.239  -8.6683  -0.9186   0.0637
 F59  C20  C  CR16  0  -0.309  -7.3890  -0.5757   0.4752
 F59  C15  C  CR6   0   0.091  -6.4126  -0.2153  -0.4555
 F59  C12  C  CR6   0   0.095  -5.0520   0.1524  -0.0188
 F59  C13  C  CR16  0  -0.298  -4.8438   0.8550   1.1706
 F59  C14  C  CR16  0  -0.243  -3.5699   1.2097   1.5740
 F59  C11  C  CR16  0  -0.295  -3.9376  -0.1846  -0.7875
 F59  C10  C  CR16  0  -0.271  -2.6596   0.1564  -0.3792
 F59  C9   C  CR6   0  -0.069  -2.4598   0.8533   0.8110
 F59  C8   C  C     0   0.547  -1.1130   1.2790   1.2899
 F59  O8   O  O     0  -0.420  -0.9684   2.2479   2.0004
 F59  N2   N  NH1   0  -0.761  -0.0800   0.4726   0.8697
 F59  C7   C  C     0   0.771   1.2793   0.6989   1.0705
 F59  O7   O  O     0  -0.469   1.7245   1.6606   1.6534
 F59  N1   N  NH1   0  -0.738   2.0474  -0.2983   0.5502
 F59  C1   C  CH1   0   0.209   3.4687  -0.2098   0.5163
 F59  O5   O  O2    0  -0.487   3.8518   0.4702  -0.6558
 F59  C5   C  CH1   0  -0.014   5.2442   0.6905  -0.7464
 F59  C6   C  CH2   0  -0.157   5.5032   1.5364  -1.9745
 F59  O6   O  OH1   0  -0.669   4.8690   2.7825  -1.8112
 F59  C4   C  CH1   0   0.037   5.9670  -0.6555  -0.8145
 F59  O4   O  OH1   0  -0.672   7.3502  -0.4119  -0.8622
 F59  C3   C  CH1   0  -0.007   5.5965  -1.4932   0.4037
 F59  O3   O  OH1   0  -0.671   6.2127  -2.7495   0.2572
 F59  C2   C  CH1   0  -0.029   4.0845  -1.6121   0.5392
 F59  O2   O  OH1   0  -0.663   3.8153  -2.2715   1.7493
 F59  H16  H  HCR6  0   0.257  -6.0189   0.0858  -2.5499
 F59  H17  H  HCR6  0   0.260  -8.2784  -0.5306  -3.2748
 F59  H18  H  HCR6  0   0.260  -9.9934  -1.1739  -1.6068
 F59  H19  H  HCR6  0   0.260  -9.4095  -1.2019   0.7999
 F59  H20  H  HCR6  0   0.258  -7.1448  -0.6087   1.5298
 F59  H13  H  HCR6  0   0.263  -5.6883   1.1504   1.7800
 F59  H14  H  HCR6  0   0.267  -3.4386   1.7659   2.4925
 F59  H11  H  HCR6  0   0.266  -4.0620  -0.7338  -1.7119
 F59  H10  H  HCR6  0   0.266  -1.8304  -0.1127  -1.0219
 F59  HN2  H  HNH1  0   0.425  -0.3374  -0.3810   0.3980
 F59  HN1  H  HNH1  0   0.407   1.6188  -0.9830  -0.0566
 F59  H1   H  HCH1  0   0.235   3.8054   0.3403   1.4038
 F59  H5   H  HCH1  0   0.223   5.6001   1.2342   0.1444
 F59  H6   H  HCH2  0   0.215   6.5854   1.6455  -2.0953
 F59  H6A  H  HCH2  0   0.195   5.1309   1.0026  -2.8601
 F59  HO6  H  HOH1  0   0.457   5.1608   3.3577  -2.5237
 F59  H4   H  HCH1  0   0.213   5.6253  -1.1829  -1.7198
 F59  HO4  H  HOH1  0   0.454   7.8029  -1.2605  -0.9104
 F59  H3   H  HCH1  0   0.220   5.9773  -0.9726   1.2967
 F59  HO3  H  HOH1  0   0.458   6.2020  -3.2004   1.1071
 F59  H2   H  HCH1  0   0.228   3.6969  -2.1765  -0.3233
 F59  HO2  H  HOH1  0   0.457   2.8919  -2.5420   1.7598

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
 F59  C16  C17  aromatic  1.387  0.020  1.387
 F59  C16  C15  aromatic  1.396  0.020  1.396
 F59  C17  C18  aromatic  1.389  0.020  1.389
 F59  C18  C19  aromatic  1.389  0.020  1.389
 F59  C19  C20  aromatic  1.387  0.020  1.387
 F59  C20  C15  aromatic  1.396  0.020  1.396
 F59  C15  C12  single    1.476  0.020  1.476
 F59  C12  C13  aromatic  1.397  0.020  1.397
 F59  C12  C11  aromatic  1.395  0.020  1.395
 F59  C13  C14  aromatic  1.382  0.020  1.382
 F59  C14  C9   aromatic  1.393  0.020  1.393
 F59  C11  C10  aromatic  1.384  0.020  1.384
 F59  C10  C9   aromatic  1.394  0.020  1.394
 F59  C9   C8   single    1.491  0.020  1.491
 F59  C8   O8   double    1.210  0.020  1.210
 F59  C8   N2   single    1.376  0.020  1.376
 F59  N2   C7   single    1.393  0.020  1.393
 F59  C7   O7   double    1.209  0.020  1.209
 F59  C7   N1   single    1.362  0.020  1.362
 F59  N1   C1   single    1.424  0.020  1.424
 F59  C1   O5   single    1.408  0.020  1.408
 F59  C1   C2   single    1.532  0.020  1.532
 F59  O5   C5   single    1.413  0.020  1.413
 F59  C5   C6   single    1.514  0.020  1.514
 F59  C5   C4   single    1.529  0.020  1.529
 F59  C6   O6   single    1.408  0.020  1.408
 F59  C4   O4   single    1.405  0.020  1.405
 F59  C4   C3   single    1.524  0.020  1.524
 F59  C3   O3   single    1.407  0.020  1.407
 F59  C3   C2   single    1.523  0.020  1.523
 F59  C2   O2   single    1.404  0.020  1.404
 F59  C16  H16  single    0.930  0.020  1.080
 F59  C17  H17  single    0.930  0.020  1.080
 F59  C18  H18  single    0.930  0.020  1.080
 F59  C19  H19  single    0.930  0.020  1.080
 F59  C20  H20  single    0.930  0.020  1.080
 F59  C13  H13  single    0.930  0.020  1.080
 F59  C14  H14  single    0.930  0.020  1.080
 F59  C11  H11  single    0.930  0.020  1.080
 F59  C10  H10  single    0.930  0.020  1.080
 F59  N2   HN2  single    0.860  0.020  1.020
 F59  N1   HN1  single    0.860  0.020  1.020
 F59  C1   H1   single    0.970  0.020  1.090
 F59  C5   H5   single    0.970  0.020  1.090
 F59  C6   H6   single    0.970  0.020  1.090
 F59  C6   H6A  single    0.970  0.020  1.090
 F59  O6   HO6  single    0.850  0.020  0.980
 F59  C4   H4   single    0.970  0.020  1.090
 F59  O4   HO4  single    0.850  0.020  0.980
 F59  C3   H3   single    0.970  0.020  1.090
 F59  O3   HO3  single    0.850  0.020  0.980
 F59  C2   H2   single    0.970  0.020  1.090
 F59  O2   HO2  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
 F59  H16  C16  C15  119.95  3.000
 F59  H16  C16  C17  119.29  3.000
 F59  C15  C16  C17  120.75  3.000
 F59  H17  C17  C18  120.16  3.000
 F59  H17  C17  C16  119.62  3.000
 F59  C18  C17  C16  120.22  3.000
 F59  H18  C18  C19  120.21  3.000
 F59  H18  C18  C17  120.23  3.000
 F59  C19  C18  C17  119.56  3.000
 F59  H19  C19  C20  119.64  3.000
 F59  H19  C19  C18  120.14  3.000
 F59  C20  C19  C18  120.22  3.000
 F59  H20  C20  C15  119.96  3.000
 F59  H20  C20  C19  119.29  3.000
 F59  C15  C20  C19  120.74  3.000
 F59  C12  C15  C20  120.79  3.000
 F59  C12  C15  C16  120.69  3.000
 F59  C20  C15  C16  118.52  3.000
 F59  C11  C12  C13  118.14  3.000
 F59  C11  C12  C15  120.88  3.000
 F59  C13  C12  C15  120.98  3.000
 F59  H13  C13  C14  118.99  3.000
 F59  H13  C13  C12  120.02  3.000
 F59  C14  C13  C12  120.98  3.000
 F59  H14  C14  C9   119.98  3.000
 F59  H14  C14  C13  119.44  3.000
 F59  C9   C14  C13  120.58  3.000
 F59  H11  C11  C10  118.88  3.000
 F59  H11  C11  C12  120.09  3.000
 F59  C10  C11  C12  121.02  3.000
 F59  H10  C10  C9   121.42  3.000
 F59  H10  C10  C11  118.07  3.000
 F59  C9   C10  C11  120.50  3.000
 F59  C8   C9   C10  123.12  3.000
 F59  C8   C9   C14  118.07  3.000
 F59  C10  C9   C14  118.77  3.000
 F59  N2   C8   O8   123.97  3.000
 F59  N2   C8   C9   114.36  3.000
 F59  O8   C8   C9   121.67  3.000
 F59  HN2  N2   C7   117.00  3.000
 F59  HN2  N2   C8   116.56  3.000
 F59  C7   N2   C8   126.40  3.000
 F59  N1   C7   O7   123.96  3.000
 F59  N1   C7   N2   112.11  3.000
 F59  O7   C7   N2   123.92  3.000
 F59  HN1  N1   C1   116.82  3.000
 F59  HN1  N1   C7   119.10  3.000
 F59  C1   N1   C7   121.75  3.000
 F59  H1   C1   C2   108.88  3.000
 F59  H1   C1   O5   110.35  3.000
 F59  C2   C1   O5   110.19  3.000
 F59  H1   C1   N1   108.55  3.000
 F59  C2   C1   N1   110.11  3.000
 F59  O5   C1   N1   108.74  3.000
 F59  C5   O5   C1   113.38  3.000
 F59  H5   C5   C4   108.51  3.000
 F59  H5   C5   C6   108.94  3.000
 F59  C4   C5   C6   112.02  3.000
 F59  H5   C5   O5   110.08  3.000
 F59  C4   C5   O5   109.36  3.000
 F59  C6   C5   O5   107.93  3.000
 F59  H6A  C6   H6   107.12  3.000
 F59  H6A  C6   O6   111.76  3.000
 F59  H6   C6   O6   111.72  3.000
 F59  H6A  C6   C5   108.93  3.000
 F59  H6   C6   C5   108.33  3.000
 F59  O6   C6   C5   108.88  3.000
 F59  HO6  O6   C6   107.88  3.000
 F59  H4   C4   C3   108.56  3.000
 F59  H4   C4   O4   111.12  3.000
 F59  C3   C4   O4   111.20  3.000
 F59  H4   C4   C5   108.13  3.000
 F59  C3   C4   C5   109.47  3.000
 F59  O4   C4   C5   108.31  3.000
 F59  HO4  O4   C4   108.16  3.000
 F59  H3   C3   C2   107.94  3.000
 F59  H3   C3   O3   110.80  3.000
 F59  C2   C3   O3   111.99  3.000
 F59  H3   C3   C4   107.71  3.000
 F59  C2   C3   C4   110.82  3.000
 F59  O3   C3   C4   107.52  3.000
 F59  HO3  O3   C3   108.76  3.000
 F59  H2   C2   O2   111.51  3.000
 F59  H2   C2   C3   108.65  3.000
 F59  O2   C2   C3   107.68  3.000
 F59  H2   C2   C1   108.42  3.000
 F59  O2   C2   C1   111.45  3.000
 F59  C3   C2   C1   109.05  3.000
 F59  HO2  O2   C2   108.99  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
 F59  CONST_01  C19  C18  C17  C16    0.00   0.0  0
 F59  CONST_02  C19  C20  C15  C16    0.00   0.0  0
 F59  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 F59  CONST_06  C12  C15  C16  C17  180.00   0.0  0
 F59  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 F59  CONST_08  C15  C16  C17  C18    0.00   0.0  0
 F59  CONST_09  C15  C20  C19  C18    0.00   0.0  0
 F59  CONST_10  C12  C15  C20  C19  180.00   0.0  0
 F59  CONST_13  C14  C13  C12  C15  180.00   0.0  0
 F59  CONST_14  C10  C11  C12  C15  180.00   0.0  0
 F59  CONST_15  C9   C14  C13  C12    0.00   0.0  0
 F59  CONST_16  C9   C10  C11  C12    0.00   0.0  0
 F59  CONST_17  C10  C11  C12  C13    0.00   0.0  0
 F59  CONST_18  C10  C9   C14  C13    0.00   0.0  0
 F59  CONST_19  C11  C12  C13  C14    0.00   0.0  0
 F59  CONST_20  C11  C10  C9   C14    0.00   0.0  0
 F59  CONST_21  C8   C9   C14  C13  180.00   0.0  0
 F59  CONST_22  C8   C9   C10  C11  180.00   0.0  0
 F59  CONST_23  H18  C18  C17  C16  180.00   0.0  0
 F59  CONST_24  H20  C20  C15  C16  180.00   0.0  0
 F59  CONST_25  H19  C19  C18  C17  180.00   0.0  0
 F59  CONST_26  H16  C16  C17  C18  180.00   0.0  0
 F59  CONST_27  H17  C17  C18  C19  180.00   0.0  0
 F59  CONST_28  H13  C13  C12  C15    0.00   0.0  0
 F59  CONST_29  H11  C11  C12  C15    0.00   0.0  0
 F59  CONST_30  H14  C14  C13  C12  180.00   0.0  0
 F59  CONST_31  H10  C10  C11  C12  180.00   0.0  0
 F59  CONST_32  C7   N2   C8   C9   180.00   0.0  0
 F59  CONST_33  C1   N1   C7   O7     0.00   0.0  0
 F59  CONST_34  C1   N1   C7   N2   180.00   0.0  0
 F59  CONST_35  HN2  N2   C8   C9     0.00   0.0  0
 F59  CONST_36  O7   C7   N2   C8     0.00   0.0  0
 F59  CONST_37  C7   N2   C8   O8     0.00   0.0  0
 F59  CONST_38  N1   C7   N2   C8   180.00   0.0  0
 F59  CONST_39  HN1  N1   C7   O7   180.00   0.0  0
 F59  Var_01    O8   C8   C9   C14  -25.45  30.0  2

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
 F59  chir_01  C1  N1  O5  C2  positiv
 F59  chir_02  C5  O5  C6  C4  positiv
 F59  chir_03  C4  O4  C5  C3  positiv
 F59  chir_04  C3  O3  C2  C4  positiv
 F59  chir_05  C2  O2  C3  C1  positiv

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
 F59  plan-1  C16  0.020
 F59  plan-1  C17  0.020
 F59  plan-1  C18  0.020
 F59  plan-1  C19  0.020
 F59  plan-1  C20  0.020
 F59  plan-1  C15  0.020
 F59  plan-1  C12  0.020
 F59  plan-1  H16  0.020
 F59  plan-1  H17  0.020
 F59  plan-1  H18  0.020
 F59  plan-1  H19  0.020
 F59  plan-1  H20  0.020
 F59  plan-2  C15  0.020
 F59  plan-2  C12  0.020
 F59  plan-2  C13  0.020
 F59  plan-2  C14  0.020
 F59  plan-2  C11  0.020
 F59  plan-2  C10  0.020
 F59  plan-2  C9   0.020
 F59  plan-2  C8   0.020
 F59  plan-2  H13  0.020
 F59  plan-2  H14  0.020
 F59  plan-2  H11  0.020
 F59  plan-2  H10  0.020
 F59  plan-3  C9   0.020
 F59  plan-3  C8   0.020
 F59  plan-3  O8   0.020
 F59  plan-3  N2   0.020
 F59  plan-3  C7   0.020
 F59  plan-3  O7   0.020
 F59  plan-3  N1   0.020
 F59  plan-3  C1   0.020
 F59  plan-3  HN2  0.020
 F59  plan-3  HN1  0.020

