# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:24:06 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-[(2S)-6-amino-1-oxo-1-(pyrrolidin-1-yl)hexan-2-yl]-4-(beta-D-galactopyranosyloxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NC(=O)c1ccc(O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)cc1)C(=O)N3CCCC3
#
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
 G0P  G0P  N-[(2S)-6-amino-1-oxo-1-(pyrrolidin-1-yl)hexan-2-yl]-4-(beta-D-galactopyranosyloxy)benzamide  ligand  69  34  .  2021-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G0P
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
 G0P  C12   C  CH2   0  -0.281  -6.4712   1.2509  -1.2138
 G0P  C13   C  CH2   0  -0.471  -7.2678   2.4440  -1.7284
 G0P  C14   C  CH2   0  -0.486  -7.3040   3.3812  -0.5262
 G0P  C15   C  CH2   0  -0.258  -5.9164   3.2245   0.0835
 G0P  N16   N  NT    0  -0.474  -5.5441   1.8529  -0.2575
 G0P  C17   C  C     0   0.564  -4.4486   1.2913   0.2703
 G0P  O18   O  O     0  -0.503  -3.7034   1.9010   1.0266
 G0P  C19   C  CH1   0  -0.196  -4.1876  -0.1817  -0.0625
 G0P  C20   C  CH2   0  -0.456  -5.0179  -1.0825   0.8549
 G0P  C21   C  CH2   0  -0.417  -4.8968  -2.5615   0.5082
 G0P  C22   C  CH2   0  -0.428  -5.8079  -3.4365   1.3588
 G0P  C23   C  CH2   0  -0.272  -5.6817  -4.9126   1.0144
 G0P  N24   N  NH2   0  -0.800  -6.5690  -5.7211   1.8387
 G0P  N25   N  NH1   0  -0.650  -2.7878  -0.4816   0.0847
 G0P  C26   C  C     0   0.548  -1.8792   0.0293  -0.7694
 G0P  O27   O  O     0  -0.484  -2.2071   0.6879  -1.7471
 G0P  C28   C  CR6   0  -0.061  -0.4504  -0.2617  -0.4673
 G0P  C29   C  CR16  0  -0.258   0.5248   0.5692  -1.0094
 G0P  C30   C  CR16  0  -0.341   1.8721   0.3610  -0.7630
 G0P  C31   C  CR6   0   0.372   2.2609  -0.7041   0.0460
 G0P  C32   C  CR16  0  -0.330   1.2984  -1.5647   0.5688
 G0P  C33   C  CR16  0  -0.277  -0.0413  -1.3442   0.3120
 G0P  O34   O  O2    0  -0.495   3.5456  -0.9862   0.3663
 G0P  C35   C  CH1   0   0.263   4.5142   0.0110   0.2617
 G0P  O36   O  O2    0  -0.489   4.9510   0.0511  -1.0615
 G0P  C37   C  CH1   0  -0.019   5.9229   1.0591  -1.2797
 G0P  C38   C  CH2   0  -0.153   6.1989   1.1362  -2.7647
 G0P  O39   O  OH1   0  -0.665   5.0390   1.6109  -3.4057
 G0P  C40   C  CH1   0   0.002   7.1729   0.7875  -0.4526
 G0P  O41   O  OH1   0  -0.670   7.7829  -0.3880  -0.9231
 G0P  C42   C  CH1   0   0.004   6.7732   0.6764   1.0176
 G0P  O43   O  OH1   0  -0.676   7.9240   0.3507   1.7547
 G0P  C44   C  CH1   0  -0.026   5.6652  -0.3561   1.1955
 G0P  O45   O  OH1   0  -0.674   5.2673  -0.3282   2.5429
 G0P  H121  H  HCH2  0   0.242  -7.1277   0.5269  -0.7213
 G0P  H122  H  HCH2  0   0.256  -5.9454   0.7331  -2.0162
 G0P  H132  H  HCH2  0   0.241  -6.7397   2.9134  -2.5609
 G0P  H131  H  HCH2  0   0.253  -8.2560   2.1530  -2.0812
 G0P  H141  H  HCH2  0   0.253  -7.5207   4.4145  -0.7936
 G0P  H142  H  HCH2  0   0.239  -8.0660   3.0558   0.1852
 G0P  H151  H  HCH2  0   0.236  -5.2046   3.9310  -0.3527
 G0P  H152  H  HCH2  0   0.247  -5.9110   3.3738   1.1633
 G0P  H191  H  HCH1  0   0.267  -4.4700  -0.3865  -1.0971
 G0P  H201  H  HCH2  0   0.242  -4.7219  -0.9102   1.8950
 G0P  H202  H  HCH2  0   0.252  -6.0661  -0.7806   0.7852
 G0P  H211  H  HCH2  0   0.221  -5.1389  -2.7011  -0.5504
 G0P  H212  H  HCH2  0   0.220  -3.8611  -2.8922   0.6310
 G0P  H222  H  HCH2  0   0.216  -5.5790  -3.2948   2.4195
 G0P  H221  H  HCH2  0   0.214  -6.8478  -3.1199   1.2192
 G0P  H231  H  HCH2  0   0.188  -5.8499  -5.0395  -0.0652
 G0P  H232  H  HCH2  0   0.212  -4.6537  -5.2357   1.2020
 G0P  H242  H  HNH2  0   0.336  -7.5300  -5.5148   1.5940
 G0P  H241  H  HNH2  0   0.345  -6.4387  -6.6993   1.6141
 G0P  H251  H  HNH1  0   0.400  -2.4788  -0.7923   0.9921
 G0P  H291  H  HCR6  0   0.264   0.2331   1.4015  -1.6361
 G0P  H301  H  HCR6  0   0.293   2.5961   1.0172  -1.2259
 G0P  H321  H  HCR6  0   0.273   1.6053  -2.4063   1.1765
 G0P  H331  H  HCR6  0   0.257  -0.7603  -2.0429   0.7211
 G0P  H351  H  HCH1  0   0.211   4.0920   0.9864   0.5632
 G0P  H371  H  HCH1  0   0.234   5.5290   2.0358  -0.9557
 G0P  H381  H  HCH2  0   0.201   7.0515   1.8113  -2.9137
 G0P  H382  H  HCH2  0   0.209   6.4969   0.1505  -3.1386
 G0P  H391  H  HOH1  0   0.455   5.1966   1.5967  -4.3538
 G0P  H401  H  HCH1  0   0.234   7.8402   1.6552  -0.5619
 G0P  H411  H  HOH1  0   0.453   8.5130  -0.6035  -0.3330
 G0P  H421  H  HCH1  0   0.215   6.3744   1.6565   1.3230
 G0P  H431  H  HOH1  0   0.461   7.6684   0.1889   2.6691
 G0P  H441  H  HCH1  0   0.248   6.0432  -1.3463   0.9053
 G0P  H451  H  HOH1  0   0.468   4.7492  -1.1171   2.7298

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
 G0P  O41  C40   single    1.405  0.020  1.405
 G0P  C38  O39   single    1.408  0.020  1.408
 G0P  C38  C37   single    1.512  0.020  1.512
 G0P  C40  C37   single    1.523  0.020  1.523
 G0P  C40  C42   single    1.528  0.020  1.528
 G0P  O43  C42   single    1.405  0.020  1.405
 G0P  C37  O36   single    1.417  0.020  1.417
 G0P  C42  C44   single    1.525  0.020  1.525
 G0P  O36  C35   single    1.394  0.020  1.394
 G0P  C44  C35   single    1.527  0.020  1.527
 G0P  C44  O45   single    1.405  0.020  1.405
 G0P  C35  O34   single    1.394  0.020  1.394
 G0P  O34  C31   single    1.354  0.020  1.354
 G0P  C31  C32   aromatic  1.393  0.020  1.393
 G0P  C31  C30   aromatic  1.393  0.020  1.393
 G0P  C32  C33   aromatic  1.382  0.020  1.382
 G0P  C30  C29   aromatic  1.385  0.020  1.385
 G0P  C33  C28   aromatic  1.395  0.020  1.395
 G0P  C29  C28   aromatic  1.391  0.020  1.391
 G0P  C28  C26   single    1.489  0.020  1.489
 G0P  C14  C13   single    1.525  0.020  1.525
 G0P  C14  C15   single    1.524  0.020  1.524
 G0P  C13  C12   single    1.524  0.020  1.524
 G0P  O27  C26   double    1.224  0.020  1.224
 G0P  C15  N16   single    1.462  0.020  1.462
 G0P  C26  N25   single    1.348  0.020  1.348
 G0P  N25  C19   single    1.439  0.020  1.439
 G0P  N16  C12   single    1.462  0.020  1.462
 G0P  N16  C17   single    1.339  0.020  1.339
 G0P  C19  C17   single    1.532  0.020  1.532
 G0P  C19  C20   single    1.530  0.020  1.530
 G0P  C17  O18   double    1.224  0.020  1.224
 G0P  C20  C21   single    1.524  0.020  1.524
 G0P  C21  C22   single    1.523  0.020  1.523
 G0P  C22  C23   single    1.521  0.020  1.521
 G0P  C23  N24   single    1.456  0.020  1.456
 G0P  C12  H121  single    0.970  0.020  1.090
 G0P  C12  H122  single    0.970  0.020  1.090
 G0P  C13  H132  single    0.970  0.020  1.090
 G0P  C13  H131  single    0.970  0.020  1.090
 G0P  C14  H141  single    0.970  0.020  1.090
 G0P  C14  H142  single    0.970  0.020  1.090
 G0P  C15  H151  single    0.970  0.020  1.090
 G0P  C15  H152  single    0.970  0.020  1.090
 G0P  C19  H191  single    0.970  0.020  1.090
 G0P  C20  H201  single    0.970  0.020  1.090
 G0P  C20  H202  single    0.970  0.020  1.090
 G0P  C21  H211  single    0.970  0.020  1.090
 G0P  C21  H212  single    0.970  0.020  1.090
 G0P  C22  H222  single    0.970  0.020  1.090
 G0P  C22  H221  single    0.970  0.020  1.090
 G0P  C23  H231  single    0.970  0.020  1.090
 G0P  C23  H232  single    0.970  0.020  1.090
 G0P  N24  H242  single    0.890  0.020  1.040
 G0P  N24  H241  single    0.890  0.020  1.040
 G0P  N25  H251  single    0.890  0.020  1.040
 G0P  C29  H291  single    0.930  0.020  1.080
 G0P  C30  H301  single    0.930  0.020  1.080
 G0P  C32  H321  single    0.930  0.020  1.080
 G0P  C33  H331  single    0.930  0.020  1.080
 G0P  C35  H351  single    0.970  0.020  1.090
 G0P  C37  H371  single    0.970  0.020  1.090
 G0P  C38  H381  single    0.970  0.020  1.090
 G0P  C38  H382  single    0.970  0.020  1.090
 G0P  O39  H391  single    0.850  0.020  0.980
 G0P  C40  H401  single    0.970  0.020  1.090
 G0P  O41  H411  single    0.850  0.020  0.980
 G0P  C42  H421  single    0.970  0.020  1.090
 G0P  O43  H431  single    0.850  0.020  0.980
 G0P  C44  H441  single    0.970  0.020  1.090
 G0P  O45  H451  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
 G0P  H122  C12  H121  107.84  3.000
 G0P  H122  C12  N16   111.80  3.000
 G0P  H121  C12  N16   111.01  3.000
 G0P  H122  C12  C13   112.05  3.000
 G0P  H121  C12  C13   110.87  3.000
 G0P  N16   C12  C13   103.30  3.000
 G0P  H131  C13  H132  107.86  3.000
 G0P  H131  C13  C14   113.47  3.000
 G0P  H132  C13  C14   110.39  3.000
 G0P  H131  C13  C12   112.00  3.000
 G0P  H132  C13  C12   109.95  3.000
 G0P  C14   C13  C12   103.14  3.000
 G0P  H142  C14  H141  107.68  3.000
 G0P  H142  C14  C15   110.13  3.000
 G0P  H141  C14  C15   112.15  3.000
 G0P  H142  C14  C13   110.30  3.000
 G0P  H141  C14  C13   113.22  3.000
 G0P  C15   C14  C13   103.33  3.000
 G0P  H152  C15  H151  107.66  3.000
 G0P  H152  C15  N16   111.00  3.000
 G0P  H151  C15  N16   110.33  3.000
 G0P  H152  C15  C14   112.75  3.000
 G0P  H151  C15  C14   111.51  3.000
 G0P  N16   C15  C14   103.60  3.000
 G0P  C17   N16  C15   120.66  3.000
 G0P  C17   N16  C12   127.15  3.000
 G0P  C15   N16  C12   112.18  3.000
 G0P  C19   C17  O18   120.61  3.000
 G0P  O18   C17  N16   122.17  3.000
 G0P  C19   C17  N16   117.18  3.000
 G0P  H191  C19  N25   108.02  3.000
 G0P  H191  C19  C20   108.50  3.000
 G0P  N25   C19  C20   110.10  3.000
 G0P  H191  C19  C17   110.01  3.000
 G0P  C20   C19  C17   110.07  3.000
 G0P  N25   C19  C17   110.11  3.000
 G0P  H202  C20  H201  106.04  3.000
 G0P  H202  C20  C21   109.25  3.000
 G0P  H201  C20  C21   110.33  3.000
 G0P  H202  C20  C19   108.63  3.000
 G0P  H201  C20  C19   109.28  3.000
 G0P  C21   C20  C19   113.07  3.000
 G0P  H212  C21  H211  106.22  3.000
 G0P  H212  C21  C22   109.27  3.000
 G0P  H211  C21  C22   109.54  3.000
 G0P  H212  C21  C20   110.06  3.000
 G0P  H211  C21  C20   109.04  3.000
 G0P  C22   C21  C20   112.52  3.000
 G0P  H221  C22  H222  106.53  3.000
 G0P  H221  C22  C23   109.29  3.000
 G0P  H222  C22  C23   109.14  3.000
 G0P  H221  C22  C21   109.30  3.000
 G0P  H222  C22  C21   109.98  3.000
 G0P  C23   C22  C21   112.43  3.000
 G0P  H232  C23  H231  106.14  3.000
 G0P  H232  C23  N24   108.16  3.000
 G0P  H231  C23  N24   113.47  3.000
 G0P  H232  C23  C22   109.02  3.000
 G0P  H231  C23  C22   108.75  3.000
 G0P  N24   C23  C22   111.11  3.000
 G0P  H241  N24  H242  105.39  3.000
 G0P  H241  N24  C23   109.43  3.000
 G0P  H242  N24  C23   109.17  3.000
 G0P  H251  N25  C26   118.74  3.000
 G0P  H251  N25  C19   117.04  3.000
 G0P  C26   N25  C19   120.79  3.000
 G0P  C28   C26  O27   121.63  3.000
 G0P  O27   C26  N25   122.00  3.000
 G0P  C28   C26  N25   116.37  3.000
 G0P  C33   C28  C29   118.40  3.000
 G0P  C29   C28  C26   118.48  3.000
 G0P  C33   C28  C26   123.12  3.000
 G0P  H291  C29  C30   118.74  3.000
 G0P  H291  C29  C28   119.75  3.000
 G0P  C30   C29  C28   121.51  3.000
 G0P  H301  C30  C31   121.72  3.000
 G0P  H301  C30  C29   118.94  3.000
 G0P  C31   C30  C29   119.33  3.000
 G0P  O34   C31  C32   115.99  3.000
 G0P  C32   C31  C30   119.83  3.000
 G0P  O34   C31  C30   124.18  3.000
 G0P  H321  C32  C33   120.22  3.000
 G0P  H321  C32  C31   119.67  3.000
 G0P  C33   C32  C31   120.10  3.000
 G0P  H331  C33  C32   118.07  3.000
 G0P  H331  C33  C28   121.13  3.000
 G0P  C32   C33  C28   120.79  3.000
 G0P  C35   O34  C31   119.51  3.000
 G0P  H351  C35  C44   109.48  3.000
 G0P  H351  C35  O36   110.69  3.000
 G0P  C44   C35  O36   110.56  3.000
 G0P  H351  C35  O34   110.22  3.000
 G0P  C44   C35  O34   107.81  3.000
 G0P  O36   C35  O34   108.03  3.000
 G0P  C37   O36  C35   112.43  3.000
 G0P  H371  C37  C40   106.96  3.000
 G0P  H371  C37  C38   107.99  3.000
 G0P  C40   C37  C38   113.11  3.000
 G0P  H371  C37  O36   109.88  3.000
 G0P  C40   C37  O36   110.63  3.000
 G0P  C38   C37  O36   108.22  3.000
 G0P  H382  C38  H381  107.20  3.000
 G0P  H382  C38  O39   111.85  3.000
 G0P  H381  C38  O39   111.77  3.000
 G0P  H382  C38  C37   109.81  3.000
 G0P  H381  C38  C37   107.84  3.000
 G0P  O39   C38  C37   108.30  3.000
 G0P  H391  O39  C38   108.00  3.000
 G0P  H401  C40  C42   108.16  3.000
 G0P  H401  C40  O41   111.30  3.000
 G0P  C42   C40  O41   112.02  3.000
 G0P  H401  C40  C37   107.65  3.000
 G0P  C42   C40  C37   108.71  3.000
 G0P  O41   C40  C37   108.87  3.000
 G0P  H411  O41  C40   108.12  3.000
 G0P  H421  C42  C44   107.88  3.000
 G0P  H421  C42  O43   110.94  3.000
 G0P  C44   C42  O43   112.15  3.000
 G0P  H421  C42  C40   107.27  3.000
 G0P  C44   C42  C40   110.59  3.000
 G0P  O43   C42  C40   107.91  3.000
 G0P  H431  O43  C42   108.65  3.000
 G0P  H441  C44  O45   111.63  3.000
 G0P  H441  C44  C42   109.23  3.000
 G0P  O45   C44  C42   107.70  3.000
 G0P  H441  C44  C35   108.33  3.000
 G0P  O45   C44  C35   111.60  3.000
 G0P  C42   C44  C35   108.28  3.000
 G0P  H451  O45  C44   108.81  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
 G0P  CONST_01  C31   C32  C33  C28     0.00   0.0  0
 G0P  CONST_02  C31   C30  C29  C28     0.00   0.0  0
 G0P  CONST_03  C32   C31  C30  C29     0.00   0.0  0
 G0P  CONST_04  C32   C33  C28  C29     0.00   0.0  0
 G0P  CONST_05  C33   C32  C31  C30     0.00   0.0  0
 G0P  CONST_06  C33   C28  C29  C30     0.00   0.0  0
 G0P  CONST_07  C32   C33  C28  C26   180.00   0.0  0
 G0P  CONST_08  C30   C29  C28  C26   180.00   0.0  0
 G0P  CONST_09  O34   C31  C30  C29   180.00   0.0  0
 G0P  CONST_10  O34   C31  C32  C33   180.00   0.0  0
 G0P  CONST_11  H321  C32  C33  C28   180.00   0.0  0
 G0P  CONST_12  H301  C30  C29  C28   180.00   0.0  0
 G0P  CONST_13  H331  C33  C28  C29   180.00   0.0  0
 G0P  CONST_14  H291  C29  C30  C31   180.00   0.0  0
 G0P  CONST_15  C19   C17  N16  C12     0.00   0.0  0
 G0P  CONST_16  O18   C17  N16  C12   180.00   0.0  0
 G0P  CONST_17  C19   C17  N16  C15   180.00   0.0  0
 G0P  CONST_18  O18   C17  N16  C15     0.00   0.0  0
 G0P  CONST_19  C28   C26  N25  C19   180.00   0.0  0
 G0P  CONST_21  O27   C26  N25  C19     0.00   0.0  0
 G0P  Var_01    C15   C14  C13  C12    38.26  30.0  1
 G0P  Var_02    C14   C15  N16  C12    10.19  30.0  1
 G0P  Var_03    N16   C15  C14  C13   -29.76  30.0  1
 G0P  Var_04    C15   N16  C12  C13    13.60  30.0  1
 G0P  Var_05    N16   C12  C13  C14   -31.71  30.0  1
 G0P  Var_06    C33   C28  C26  N25    22.52  30.0  2
 G0P  Var_07    C22   C21  C20  C19  -175.65  30.0  3
 G0P  Var_08    C23   C22  C21  C20  -179.79  30.0  3
 G0P  Var_09    N24   C23  C22  C21  -179.70  30.0  3
 G0P  Var_10    H242  N24  C23  C22    67.31  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
 G0P  chir_01  C19  N25  C17  C20  positiv
 G0P  chir_02  C35  O36  C44  O34  positiv
 G0P  chir_03  C37  O36  C38  C40  positiv
 G0P  chir_04  C40  O41  C37  C42  negativ
 G0P  chir_05  C42  O43  C44  C40  positiv
 G0P  chir_06  C44  O45  C42  C35  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
 G0P  plan-1  C26   0.020
 G0P  plan-1  C28   0.020
 G0P  plan-1  C29   0.020
 G0P  plan-1  C30   0.020
 G0P  plan-1  C31   0.020
 G0P  plan-1  C32   0.020
 G0P  plan-1  C33   0.020
 G0P  plan-1  O34   0.020
 G0P  plan-1  H291  0.020
 G0P  plan-1  H301  0.020
 G0P  plan-1  H321  0.020
 G0P  plan-1  H331  0.020
 G0P  plan-2  C19   0.020
 G0P  plan-2  N25   0.020
 G0P  plan-2  C26   0.020
 G0P  plan-2  O27   0.020
 G0P  plan-2  C28   0.020
 G0P  plan-2  H251  0.020
 G0P  plan-3  C12   0.020
 G0P  plan-3  C15   0.020
 G0P  plan-3  N16   0.020
 G0P  plan-3  C17   0.020
 G0P  plan-3  O18   0.020
 G0P  plan-3  C19   0.020

