# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:54:50 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{[3-(biphenyl-4-yl)propanoyl]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)CCc2ccc(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
 4D0  4D0  N-{[3-(biphenyl-4-yl)propanoyl]carbamoyl}-beta-D-glucopyranosylamine  ligand  57  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4D0
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
 4D0  C11  C  CR16  0  -0.294   5.8293  -1.3489   0.2088
 4D0  C13  C  CR16  0  -0.295   5.6008   1.0060   0.5550
 4D0  C14  C  CR16  0  -0.289   4.3949   0.7918   1.2027
 4D0  C15  C  CR6   0   0.089   7.6267   0.1670  -0.6458
 4D0  C16  C  CR16  0  -0.311   8.6927  -0.7211  -0.4888
 4D0  C17  C  CR16  0  -0.240   9.9004  -0.5049  -1.1365
 4D0  C20  C  CR16  0  -0.313   7.8068   1.2778  -1.4728
 4D0  C19  C  CR16  0  -0.239   9.0143   1.4951  -2.1203
 4D0  C18  C  CR16  0  -0.267  10.0668   0.6042  -1.9557
 4D0  C12  C  CR6   0   0.072   6.3411  -0.0614   0.0441
 4D0  C10  C  CR16  0  -0.296   4.6214  -1.5587   0.8573
 4D0  C9   C  CR6   0   0.113   3.8838  -0.4936   1.3658
 4D0  C8   C  CH2   0  -0.505   2.5577  -0.7142   2.0394
 4D0  C7   C  CH2   0  -0.599   1.4109  -0.5472   1.0477
 4D0  C5   C  C     0   0.576   0.0475  -0.7551   1.6687
 4D0  O6   O  O     0  -0.427  -0.1249  -1.3217   2.7215
 4D0  N4   N  NH1   0  -0.751  -0.9694  -0.2429   0.8910
 4D0  C2   C  C     0   0.760  -2.3326  -0.3037   1.1535
 4D0  O3   O  O     0  -0.474  -2.8084  -0.8494   2.1238
 4D0  N1   N  NH1   0  -0.733  -3.0689   0.3481   0.2099
 4D0  C1'  C  CH1   0   0.206  -4.4927   0.3285   0.2091
 4D0  O5'  O  O2    0  -0.487  -4.9320  -0.7130  -0.6303
 4D0  C5'  C  CH1   0  -0.015  -6.3338  -0.8873  -0.6174
 4D0  C6'  C  CH2   0  -0.157  -6.6573  -2.0988  -1.4654
 4D0  O6'  O  OH1   0  -0.670  -6.0648  -3.2338  -0.8812
 4D0  C4'  C  CH1   0   0.037  -7.0131   0.3759  -1.1498
 4D0  O4'  O  OH1   0  -0.672  -8.4046   0.1954  -1.0687
 4D0  C3'  C  CH1   0  -0.007  -6.5648   1.5827  -0.3338
 4D0  O3'  O  OH1   0  -0.671  -7.1435   2.7246  -0.9180
 4D0  C2'  C  CH1   0  -0.024  -5.0456   1.6673  -0.2868
 4D0  O2'  O  OH1   0  -0.663  -4.7053   2.7177   0.5805
 4D0  H1   H  HCR6  0   0.252   6.3693  -2.2002  -0.1875
 4D0  H2   H  HCR6  0   0.252   5.9790   2.0171   0.4679
 4D0  H3   H  HCR6  0   0.249   3.8492   1.6400   1.5998
 4D0  H4   H  HCR6  0   0.253   8.5868  -1.5799   0.1626
 4D0  H5   H  HCR6  0   0.257  10.7167  -1.2012  -0.9933
 4D0  H6   H  HCR6  0   0.254   6.9900   1.9719  -1.6304
 4D0  H7   H  HCR6  0   0.257   9.1295   2.3597  -2.7612
 4D0  H8   H  HCR6  0   0.257  11.0088   0.7729  -2.4613
 4D0  H9   H  HCR6  0   0.250   4.2474  -2.5699   0.9665
 4D0  H10  H  HCH2  0   0.256   2.5261  -1.7119   2.4794
 4D0  H11  H  HCH2  0   0.256   2.4391  -0.0003   2.8573
 4D0  H12  H  HCH2  0   0.278   1.4552   0.4405   0.5807
 4D0  H13  H  HCH2  0   0.296   1.5111  -1.2682   0.2290
 4D0  H14  H  HNH1  0   0.423  -0.6795   0.2335   0.0497
 4D0  H15  H  HNH1  0   0.408  -2.6151   0.6700  -0.6336
 4D0  H16  H  HCH1  0   0.236  -4.8371   0.1619   1.2373
 4D0  H17  H  HCH1  0   0.224  -6.6804  -1.0639   0.4143
 4D0  H18  H  HCH2  0   0.212  -7.7460  -2.1972  -1.5282
 4D0  H19  H  HCH2  0   0.197  -6.2900  -1.9246  -2.4866
 4D0  H20  H  HOH1  0   0.457  -6.2889  -3.9951  -1.4235
 4D0  H21  H  HCH1  0   0.212  -6.6928   0.5235  -2.1938
 4D0  H22  H  HOH1  0   0.455  -8.8295   1.0028  -1.3767
 4D0  H23  H  HCH1  0   0.218  -6.9272   1.4453   0.6979
 4D0  H24  H  HOH1  0   0.458  -7.0253   3.4695  -0.3203
 4D0  H25  H  HCH1  0   0.226  -4.6687   1.8469  -1.3059
 4D0  H26  H  HOH1  0   0.457  -3.7607   2.8880   0.5080

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
 4D0  O3'  C3'  single    1.407  0.020  1.407
 4D0  O4'  C4'  single    1.406  0.020  1.406
 4D0  C3'  C4'  single    1.524  0.020  1.524
 4D0  C3'  C2'  single    1.522  0.020  1.522
 4D0  C4'  C5'  single    1.530  0.020  1.530
 4D0  O2'  C2'  single    1.404  0.020  1.404
 4D0  C2'  C1'  single    1.531  0.020  1.531
 4D0  O6'  C6'  single    1.407  0.020  1.407
 4D0  C5'  C6'  single    1.514  0.020  1.514
 4D0  C5'  O5'  single    1.413  0.020  1.413
 4D0  C1'  O5'  single    1.408  0.020  1.408
 4D0  C1'  N1   single    1.424  0.020  1.424
 4D0  N1   C2   single    1.363  0.020  1.363
 4D0  C2   O3   double    1.211  0.020  1.211
 4D0  C2   N4   single    1.390  0.020  1.390
 4D0  N4   C5   single    1.379  0.020  1.379
 4D0  C5   O6   double    1.208  0.020  1.208
 4D0  C5   C7   single    1.512  0.020  1.512
 4D0  C7   C8   single    1.525  0.020  1.525
 4D0  C8   C9   single    1.504  0.020  1.504
 4D0  C14  C9   aromatic  1.393  0.020  1.393
 4D0  C14  C13  aromatic  1.385  0.020  1.385
 4D0  C9   C10  aromatic  1.392  0.020  1.392
 4D0  C13  C12  aromatic  1.396  0.020  1.396
 4D0  C10  C11  aromatic  1.387  0.020  1.387
 4D0  C12  C11  aromatic  1.395  0.020  1.395
 4D0  C12  C15  single    1.477  0.020  1.477
 4D0  C20  C15  aromatic  1.396  0.020  1.396
 4D0  C20  C19  aromatic  1.387  0.020  1.387
 4D0  C15  C16  aromatic  1.396  0.020  1.396
 4D0  C19  C18  aromatic  1.389  0.020  1.389
 4D0  C16  C17  aromatic  1.387  0.020  1.387
 4D0  C18  C17  aromatic  1.389  0.020  1.389
 4D0  C11  H1   single    0.930  0.020  1.080
 4D0  C13  H2   single    0.930  0.020  1.080
 4D0  C14  H3   single    0.930  0.020  1.080
 4D0  C16  H4   single    0.930  0.020  1.080
 4D0  C17  H5   single    0.930  0.020  1.080
 4D0  C20  H6   single    0.930  0.020  1.080
 4D0  C19  H7   single    0.930  0.020  1.080
 4D0  C18  H8   single    0.930  0.020  1.080
 4D0  C10  H9   single    0.930  0.020  1.080
 4D0  C8   H10  single    0.970  0.020  1.090
 4D0  C8   H11  single    0.970  0.020  1.090
 4D0  C7   H12  single    0.970  0.020  1.090
 4D0  C7   H13  single    0.970  0.020  1.090
 4D0  N4   H14  single    0.860  0.020  1.020
 4D0  N1   H15  single    0.860  0.020  1.020
 4D0  C1'  H16  single    0.970  0.020  1.090
 4D0  C5'  H17  single    0.970  0.020  1.090
 4D0  C6'  H18  single    0.970  0.020  1.090
 4D0  C6'  H19  single    0.970  0.020  1.090
 4D0  O6'  H20  single    0.850  0.020  0.980
 4D0  C4'  H21  single    0.970  0.020  1.090
 4D0  O4'  H22  single    0.850  0.020  0.980
 4D0  C3'  H23  single    0.970  0.020  1.090
 4D0  O3'  H24  single    0.850  0.020  0.980
 4D0  C2'  H25  single    0.970  0.020  1.090
 4D0  O2'  H26  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
 4D0  H1   C11  C10  119.10  3.000
 4D0  H1   C11  C12  119.94  3.000
 4D0  C10  C11  C12  120.95  3.000
 4D0  H2   C13  C12  119.95  3.000
 4D0  H2   C13  C14  119.08  3.000
 4D0  C12  C13  C14  120.96  3.000
 4D0  H3   C14  C9   119.64  3.000
 4D0  H3   C14  C13  119.23  3.000
 4D0  C9   C14  C13  121.12  3.000
 4D0  C12  C15  C20  120.80  3.000
 4D0  C20  C15  C16  118.30  3.000
 4D0  C12  C15  C16  120.91  3.000
 4D0  H4   C16  C17  119.30  3.000
 4D0  H4   C16  C15  119.83  3.000
 4D0  C17  C16  C15  120.86  3.000
 4D0  H5   C17  C18  120.09  3.000
 4D0  H5   C17  C16  119.64  3.000
 4D0  C18  C17  C16  120.27  3.000
 4D0  H6   C20  C19  119.21  3.000
 4D0  H6   C20  C15  119.90  3.000
 4D0  C19  C20  C15  120.88  3.000
 4D0  H7   C19  C18  120.12  3.000
 4D0  H7   C19  C20  119.62  3.000
 4D0  C18  C19  C20  120.26  3.000
 4D0  H8   C18  C19  120.28  3.000
 4D0  H8   C18  C17  120.29  3.000
 4D0  C19  C18  C17  119.43  3.000
 4D0  C15  C12  C13  120.95  3.000
 4D0  C15  C12  C11  121.15  3.000
 4D0  C13  C12  C11  117.90  3.000
 4D0  H9   C10  C9   119.63  3.000
 4D0  H9   C10  C11  119.26  3.000
 4D0  C9   C10  C11  121.11  3.000
 4D0  C8   C9   C10  121.25  3.000
 4D0  C10  C9   C14  117.96  3.000
 4D0  C8   C9   C14  120.76  3.000
 4D0  H11  C8   H10  107.01  3.000
 4D0  H11  C8   C7   109.49  3.000
 4D0  H10  C8   C7   109.91  3.000
 4D0  H11  C8   C9   109.60  3.000
 4D0  H10  C8   C9   109.91  3.000
 4D0  C7   C8   C9   110.84  3.000
 4D0  H13  C7   H12  105.76  3.000
 4D0  H13  C7   C5   107.39  3.000
 4D0  H12  C7   C5   109.64  3.000
 4D0  H13  C7   C8   110.18  3.000
 4D0  H12  C7   C8   110.25  3.000
 4D0  C5   C7   C8   113.31  3.000
 4D0  N4   C5   O6   124.09  3.000
 4D0  O6   C5   C7   123.43  3.000
 4D0  N4   C5   C7   112.47  3.000
 4D0  H14  N4   C2   117.38  3.000
 4D0  H14  N4   C5   115.70  3.000
 4D0  C2   N4   C5   126.92  3.000
 4D0  N1   C2   O3   123.93  3.000
 4D0  O3   C2   N4   123.83  3.000
 4D0  N1   C2   N4   112.23  3.000
 4D0  H15  N1   C1'  116.93  3.000
 4D0  H15  N1   C2   119.19  3.000
 4D0  C1'  N1   C2   122.28  3.000
 4D0  H16  C1'  C2'  108.85  3.000
 4D0  H16  C1'  O5'  110.39  3.000
 4D0  C2'  C1'  O5'  109.94  3.000
 4D0  H16  C1'  N1   108.39  3.000
 4D0  O5'  C1'  N1   108.81  3.000
 4D0  C2'  C1'  N1   110.45  3.000
 4D0  C5'  O5'  C1'  113.29  3.000
 4D0  H17  C5'  C4'  108.56  3.000
 4D0  H17  C5'  C6'  109.20  3.000
 4D0  C4'  C5'  C6'  111.77  3.000
 4D0  H17  C5'  O5'  109.89  3.000
 4D0  C6'  C5'  O5'  107.80  3.000
 4D0  C4'  C5'  O5'  109.60  3.000
 4D0  H19  C6'  H18  107.05  3.000
 4D0  H19  C6'  O6'  111.89  3.000
 4D0  H18  C6'  O6'  111.71  3.000
 4D0  H19  C6'  C5'  108.79  3.000
 4D0  H18  C6'  C5'  108.46  3.000
 4D0  O6'  C6'  C5'  108.84  3.000
 4D0  H20  O6'  C6'  107.84  3.000
 4D0  H21  C4'  C3'  108.40  3.000
 4D0  H21  C4'  O4'  111.08  3.000
 4D0  C3'  C4'  O4'  111.22  3.000
 4D0  H21  C4'  C5'  108.14  3.000
 4D0  C3'  C4'  C5'  109.68  3.000
 4D0  O4'  C4'  C5'  108.27  3.000
 4D0  H22  O4'  C4'  108.10  3.000
 4D0  H23  C3'  C2'  107.83  3.000
 4D0  H23  C3'  O3'  110.77  3.000
 4D0  C2'  C3'  O3'  112.22  3.000
 4D0  H23  C3'  C4'  107.80  3.000
 4D0  C2'  C3'  C4'  110.73  3.000
 4D0  O3'  C3'  C4'  107.41  3.000
 4D0  H24  O3'  C3'  108.64  3.000
 4D0  H25  C2'  O2'  111.51  3.000
 4D0  H25  C2'  C3'  108.79  3.000
 4D0  O2'  C2'  C3'  107.61  3.000
 4D0  H25  C2'  C1'  108.59  3.000
 4D0  O2'  C2'  C1'  111.50  3.000
 4D0  C3'  C2'  C1'  108.78  3.000
 4D0  H26  O2'  C2'  108.89  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
 4D0  CONST_01  C14  C9   C10  C11     0.00   0.0  0
 4D0  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 4D0  CONST_05  C10  C9   C14  C13     0.00   0.0  0
 4D0  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 4D0  CONST_09  C15  C12  C13  C14   180.00   0.0  0
 4D0  CONST_10  C10  C11  C12  C15   180.00   0.0  0
 4D0  CONST_11  C18  C19  C20  C15     0.00   0.0  0
 4D0  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 4D0  CONST_13  C19  C20  C15  C16     0.00   0.0  0
 4D0  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 4D0  CONST_15  C12  C15  C16  C17   180.00   0.0  0
 4D0  CONST_16  C20  C15  C16  C17     0.00   0.0  0
 4D0  CONST_17  C20  C19  C18  C17     0.00   0.0  0
 4D0  CONST_18  C12  C15  C20  C19   180.00   0.0  0
 4D0  CONST_19  C9   C14  C13  C12     0.00   0.0  0
 4D0  CONST_20  C9   C10  C11  C12     0.00   0.0  0
 4D0  CONST_21  C8   C9   C10  C11   180.00   0.0  0
 4D0  CONST_22  C8   C9   C14  C13   180.00   0.0  0
 4D0  CONST_23  H2   C13  C12  C11   180.00   0.0  0
 4D0  CONST_24  H1   C11  C12  C13   180.00   0.0  0
 4D0  CONST_25  H9   C10  C9   C14   180.00   0.0  0
 4D0  CONST_26  H7   C19  C20  C15   180.00   0.0  0
 4D0  CONST_27  H5   C17  C16  C15   180.00   0.0  0
 4D0  CONST_28  H6   C20  C15  C16   180.00   0.0  0
 4D0  CONST_29  H8   C18  C17  C16   180.00   0.0  0
 4D0  CONST_30  H4   C16  C15  C20   180.00   0.0  0
 4D0  CONST_31  H3   C14  C13  C12   180.00   0.0  0
 4D0  CONST_32  C1'  N1   C2   O3      0.00   0.0  0
 4D0  CONST_33  C1'  N1   C2   N4    180.00   0.0  0
 4D0  CONST_34  C2   N4   C5   C7    180.00   0.0  0
 4D0  CONST_35  O3   C2   N4   C5      0.00   0.0  0
 4D0  CONST_36  C2   N4   C5   O6      0.00   0.0  0
 4D0  CONST_37  N1   C2   N4   C5    180.00   0.0  0
 4D0  CONST_38  H14  N4   C5   C7      0.00   0.0  0
 4D0  CONST_39  H15  N1   C2   O3    180.00   0.0  0
 4D0  Var_01    C7   C8   C9   C14    84.05  30.0  2
 4D0  Var_02    C5   C7   C8   C9   -179.89  30.0  1
 4D0  Var_03    N4   C5   C7   C8    162.79  30.0  1

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
 4D0  chir_01  C1'  C2'  O5'  N1   negativ
 4D0  chir_02  C5'  O5'  C6'  C4'  positiv
 4D0  chir_03  C4'  O4'  C5'  C3'  positiv
 4D0  chir_04  C3'  O3'  C2'  C4'  positiv
 4D0  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
 4D0  plan-1  C11  0.020
 4D0  plan-1  C13  0.020
 4D0  plan-1  C14  0.020
 4D0  plan-1  C15  0.020
 4D0  plan-1  C12  0.020
 4D0  plan-1  C10  0.020
 4D0  plan-1  C9   0.020
 4D0  plan-1  C8   0.020
 4D0  plan-1  H1   0.020
 4D0  plan-1  H2   0.020
 4D0  plan-1  H3   0.020
 4D0  plan-1  H9   0.020
 4D0  plan-2  C15  0.020
 4D0  plan-2  C16  0.020
 4D0  plan-2  C17  0.020
 4D0  plan-2  C20  0.020
 4D0  plan-2  C19  0.020
 4D0  plan-2  C18  0.020
 4D0  plan-2  C12  0.020
 4D0  plan-2  H4   0.020
 4D0  plan-2  H5   0.020
 4D0  plan-2  H6   0.020
 4D0  plan-2  H7   0.020
 4D0  plan-2  H8   0.020
 4D0  plan-3  C7   0.020
 4D0  plan-3  C5   0.020
 4D0  plan-3  O6   0.020
 4D0  plan-3  N4   0.020
 4D0  plan-3  C2   0.020
 4D0  plan-3  O3   0.020
 4D0  plan-3  N1   0.020
 4D0  plan-3  C1'  0.020
 4D0  plan-3  H14  0.020
 4D0  plan-3  H15  0.020

