# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 23:11:29 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->2)-beta-D-galactofuranosyl-(1->6)-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO[C@@H]2O[C@@H]([C@H](O)CO)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3NC(C)=O)[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
 3PV  3PV  'methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->2)-beta-D-galactofuranosyl-(1->6)-alpha-D-glucopyranoside'  ligand  75  38  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3PV
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
 3PV  C1   C  CH1   0   0.260  -4.1909   0.0656   1.4018
 3PV  C2   C  CH1   0  -0.024  -5.1747  -0.0739   0.2351
 3PV  C3   C  CH1   0  -0.013  -4.4604   0.0011  -1.1112
 3PV  C4   C  CH1   0   0.038  -3.5726   1.2378  -1.1719
 3PV  C5   C  CH1   0  -0.017  -2.6386   1.2295   0.0335
 3PV  C11  C  CR15  0   0.298   0.4840   2.1676   0.8824
 3PV  C13  C  CR15  0   0.003   2.1257   1.4701  -0.6726
 3PV  C12  C  CR15  0  -0.092   0.8418   0.9798  -0.0223
 3PV  C14  C  CR15  0  -0.006   1.7758   2.9389  -0.9065
 3PV  C15  C  CH1   0  -0.033   2.9776   3.8649  -1.0406
 3PV  C16  C  CH2   0  -0.156   2.5352   5.2920  -1.3255
 3PV  O2   O  OH1   0  -0.664  -5.8955  -1.2778   0.2820
 3PV  O3   O  OH1   0  -0.673  -5.3788   0.0824  -2.1754
 3PV  C6   C  CH2   0  -0.225  -1.7632   2.4647   0.1071
 3PV  O1   O  O2    0  -0.514  -3.4319  -1.0978   1.5214
 3PV  O4   O  OH1   0  -0.670  -2.7743   1.2484  -2.3289
 3PV  O5   O  O2    0  -0.498  -3.4003   1.2034   1.2285
 3PV  O11  O  O2    0  -0.481  -0.8505   2.3500   1.1845
 3PV  O13  O  OH1   0  -0.658   2.4231   0.7563  -1.8405
 3PV  O14  O  O     0  -0.514   1.0111   3.3066   0.2349
 3PV  O15  O  OH1   0  -0.654   3.8381   3.7756   0.0678
 3PV  C21  C  CH1   0   0.344   0.9734  -1.3909   0.1128
 3PV  O21  O  O2    0  -0.496   0.9515  -0.1723   0.7705
 3PV  C22  C  CH1   0  -0.166   2.1719  -2.2064   0.6136
 3PV  N22  N  NH1   0  -0.625   3.4010  -1.5191   0.3220
 3PV  C27  C  C     0   0.518   4.2058  -0.9666   1.2504
 3PV  O27  O  O     0  -0.497   4.0289  -1.0872   2.4536
 3PV  C28  C  CH3   0  -0.792   5.3581  -0.1669   0.6941
 3PV  C23  C  CH1   0   0.044   2.1436  -3.5866  -0.0296
 3PV  O23  O  OH1   0  -0.663   3.1882  -4.3477   0.5140
 3PV  C24  C  CH1   0  -0.002   0.7843  -4.2383   0.1969
 3PV  O24  O  OH1   0  -0.673   0.7804  -5.4475  -0.5301
 3PV  C25  C  CH1   0  -0.027  -0.3395  -3.3002  -0.2590
 3PV  C26  C  CH2   0  -0.190  -1.7086  -3.8790   0.0568
 3PV  O26  O  OH1   0  -0.691  -2.7734  -3.1022  -0.4219
 3PV  O25  O  O2    0  -0.482  -0.2215  -2.0574   0.4090
 3PV  H1   H  HCH1  0   0.238  -4.7406   0.2416   2.3371
 3PV  H2   H  HCH1  0   0.235  -5.8466   0.7931   0.3017
 3PV  H3   H  HCH1  0   0.214  -3.8105  -0.8777  -1.2313
 3PV  H4   H  HCH1  0   0.215  -4.2104   2.1348  -1.1194
 3PV  H5   H  HCH1  0   0.236  -1.9987   0.3381  -0.0339
 3PV  H6   H  HCR5  0   0.243   0.9728   2.0393   1.8550
 3PV  H7   H  HCR5  0   0.237   2.9404   1.4063   0.0607
 3PV  H8   H  HCR5  0   0.245   0.0866   0.8404  -0.8101
 3PV  H9   H  HCR5  0   0.232   1.1648   3.0183  -1.8178
 3PV  H10  H  HCH1  0   0.242   3.5536   3.5142  -1.9050
 3PV  H11  H  HCH2  0   0.200   1.8378   5.2748  -2.1737
 3PV  H12  H  HCH2  0   0.202   1.9782   5.6842  -0.4637
 3PV  H13  H  HCH3  0   0.229  -1.7023  -0.4219   2.4821
 3PV  H14  H  HCH3  0   0.217  -3.0731  -0.8147   3.5481
 3PV  H15  H  HCH3  0   0.236  -2.1652  -2.1078   2.7451
 3PV  H16  H  HOH1  0   0.460  -6.6036  -1.1905   0.9273
 3PV  H17  H  HOH1  0   0.456  -5.8538  -0.7529  -2.2319
 3PV  H18  H  HCH2  0   0.241  -1.2635   2.6279  -0.8509
 3PV  H19  H  HCH2  0   0.249  -2.3873   3.3452   0.2865
 3PV  H20  H  HOH1  0   0.456  -3.3528   1.2351  -3.0985
 3PV  H21  H  HOH1  0   0.461   3.2997   1.0045  -2.1504
 3PV  H22  H  HOH1  0   0.444   3.3650   4.0907   0.8463
 3PV  H23  H  HOH1  0   0.456   3.3874   6.9798  -1.7299
 3PV  H24  H  HCH1  0   0.203   1.0550  -1.2560  -0.9783
 3PV  H25  H  HCH1  0   0.276   2.0885  -2.3110   1.6981
 3PV  H26  H  HNH1  0   0.393   3.6115  -1.3469  -0.6489
 3PV  H27  H  HCH3  0   0.248   5.4612  -0.2413  -0.3870
 3PV  H28  H  HCH3  0   0.265   5.2224   0.8849   0.9509
 3PV  H29  H  HCH3  0   0.274   6.2899  -0.4942   1.1535
 3PV  H30  H  HCH1  0   0.209   2.2753  -3.4624  -1.1186
 3PV  H31  H  HOH1  0   0.451   3.1570  -5.2215   0.1097
 3PV  H32  H  HCH1  0   0.227   0.6666  -4.4242   1.2747
 3PV  H33  H  HOH1  0   0.464   0.2237  -6.0870  -0.0778
 3PV  H34  H  HCH1  0   0.220  -0.2539  -3.1501  -1.3479
 3PV  H35  H  HCH2  0   0.225  -1.7825  -4.8582  -0.4212
 3PV  H36  H  HCH2  0   0.204  -1.7823  -4.0477   1.1403
 3PV  H37  H  HOH1  0   0.463  -2.9404  -2.3791   0.1990
 3PV  O16  O  OH1   0  -0.669   3.6735   6.0710  -1.6026
 3PV  C7   C  CH3   0  -0.405  -2.5466  -1.0958   2.6311

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
 3PV  C7   O1   single  1.420  0.020  1.420
 3PV  O2   C2   single  1.404  0.020  1.404
 3PV  O1   C1   single  1.394  0.020  1.394
 3PV  C1   C2   single  1.533  0.020  1.533
 3PV  C1   O5   single  1.396  0.020  1.396
 3PV  C2   C3   single  1.526  0.020  1.526
 3PV  C26  O26  single  1.402  0.020  1.402
 3PV  C26  C25  single  1.520  0.020  1.520
 3PV  O5   C5   single  1.417  0.020  1.417
 3PV  O13  C13  single  1.401  0.020  1.401
 3PV  C3   O3   single  1.408  0.020  1.408
 3PV  C3   C4   single  1.524  0.020  1.524
 3PV  C25  O25  single  1.416  0.020  1.416
 3PV  C25  C24  single  1.533  0.020  1.533
 3PV  O16  C16  single  1.407  0.020  1.407
 3PV  C4   C5   single  1.525  0.020  1.525
 3PV  C4   O4   single  1.406  0.020  1.406
 3PV  C5   C6   single  1.516  0.020  1.516
 3PV  O25  C21  single  1.400  0.020  1.400
 3PV  O24  C24  single  1.411  0.020  1.411
 3PV  O11  C6   single  1.417  0.020  1.417
 3PV  O11  C11  single  1.380  0.020  1.380
 3PV  C13  C12  single  1.520  0.020  1.520
 3PV  C13  C14  single  1.528  0.020  1.528
 3PV  C12  C11  single  1.535  0.020  1.535
 3PV  C12  O21  single  1.403  0.020  1.403
 3PV  C14  O14  single  1.422  0.020  1.422
 3PV  C14  C15  single  1.523  0.020  1.523
 3PV  C24  C23  single  1.524  0.020  1.524
 3PV  C21  O21  single  1.385  0.020  1.385
 3PV  C21  C22  single  1.534  0.020  1.534
 3PV  C11  O14  single  1.412  0.020  1.412
 3PV  C16  C15  single  1.521  0.020  1.521
 3PV  C15  O15  single  1.406  0.020  1.406
 3PV  C23  C22  single  1.523  0.020  1.523
 3PV  C23  O23  single  1.402  0.020  1.402
 3PV  C22  N22  single  1.438  0.020  1.438
 3PV  N22  C27  single  1.347  0.020  1.347
 3PV  C27  O27  double  1.222  0.020  1.222
 3PV  C27  C28  single  1.509  0.020  1.509
 3PV  C1   H1   single  0.970  0.020  1.090
 3PV  C2   H2   single  0.970  0.020  1.090
 3PV  C3   H3   single  0.970  0.020  1.090
 3PV  C4   H4   single  0.970  0.020  1.090
 3PV  C5   H5   single  0.970  0.020  1.090
 3PV  C11  H6   single  0.970  0.020  1.090
 3PV  C13  H7   single  0.970  0.020  1.090
 3PV  C12  H8   single  0.970  0.020  1.090
 3PV  C14  H9   single  0.970  0.020  1.090
 3PV  C15  H10  single  0.970  0.020  1.090
 3PV  C16  H11  single  0.970  0.020  1.090
 3PV  C16  H12  single  0.970  0.020  1.090
 3PV  C7   H13  single  0.970  0.020  1.090
 3PV  C7   H14  single  0.970  0.020  1.090
 3PV  C7   H15  single  0.970  0.020  1.090
 3PV  O2   H16  single  0.850  0.020  0.980
 3PV  O3   H17  single  0.850  0.020  0.980
 3PV  C6   H18  single  0.970  0.020  1.090
 3PV  C6   H19  single  0.970  0.020  1.090
 3PV  O4   H20  single  0.850  0.020  0.980
 3PV  O13  H21  single  0.850  0.020  0.980
 3PV  O15  H22  single  0.850  0.020  0.980
 3PV  O16  H23  single  0.850  0.020  0.980
 3PV  C21  H24  single  0.970  0.020  1.090
 3PV  C22  H25  single  0.970  0.020  1.090
 3PV  N22  H26  single  0.860  0.020  1.020
 3PV  C28  H27  single  0.970  0.020  1.090
 3PV  C28  H28  single  0.970  0.020  1.090
 3PV  C28  H29  single  0.970  0.020  1.090
 3PV  C23  H30  single  0.970  0.020  1.090
 3PV  O23  H31  single  0.850  0.020  0.980
 3PV  C24  H32  single  0.970  0.020  1.090
 3PV  O24  H33  single  0.850  0.020  0.980
 3PV  C25  H34  single  0.970  0.020  1.090
 3PV  C26  H35  single  0.970  0.020  1.090
 3PV  C26  H36  single  0.970  0.020  1.090
 3PV  O26  H37  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
 3PV  H1   C1   O5   104.97  3.000
 3PV  H1   C1   O1   109.45  3.000
 3PV  O5   C1   O1   112.49  3.000
 3PV  H1   C1   C2   109.96  3.000
 3PV  O5   C1   C2   110.07  3.000
 3PV  O1   C1   C2   109.80  3.000
 3PV  H2   C2   O2   111.14  3.000
 3PV  H2   C2   C3   107.51  3.000
 3PV  O2   C2   C3   108.18  3.000
 3PV  H2   C2   C1   105.93  3.000
 3PV  C3   C2   C1   111.52  3.000
 3PV  O2   C2   C1   112.47  3.000
 3PV  H3   C3   O3   110.43  3.000
 3PV  H3   C3   C4   107.46  3.000
 3PV  O3   C3   C4   107.65  3.000
 3PV  H3   C3   C2   109.50  3.000
 3PV  C4   C3   C2   110.35  3.000
 3PV  O3   C3   C2   111.37  3.000
 3PV  H4   C4   O4   111.21  3.000
 3PV  H4   C4   C5   108.74  3.000
 3PV  O4   C4   C5   107.63  3.000
 3PV  H4   C4   C3   108.76  3.000
 3PV  O4   C4   C3   111.71  3.000
 3PV  C5   C4   C3   108.72  3.000
 3PV  H5   C5   O5   110.47  3.000
 3PV  H5   C5   C6   109.12  3.000
 3PV  O5   C5   C6   106.53  3.000
 3PV  H5   C5   C4   108.20  3.000
 3PV  C6   C5   C4   112.81  3.000
 3PV  O5   C5   C4   109.72  3.000
 3PV  H6   C11  O14  109.56  3.000
 3PV  H6   C11  O11  104.62  3.000
 3PV  O14  C11  O11  110.77  3.000
 3PV  H6   C11  C12  109.17  3.000
 3PV  O14  C11  C12  105.48  3.000
 3PV  O11  C11  C12  117.16  3.000
 3PV  H7   C13  O13  111.70  3.000
 3PV  H7   C13  C14  109.15  3.000
 3PV  O13  C13  C14  114.26  3.000
 3PV  H7   C13  C12  108.80  3.000
 3PV  C14  C13  C12  100.49  3.000
 3PV  O13  C13  C12  111.81  3.000
 3PV  H8   C12  O21  110.75  3.000
 3PV  H8   C12  C13  108.32  3.000
 3PV  O21  C12  C13  116.14  3.000
 3PV  H8   C12  C11  111.10  3.000
 3PV  O21  C12  C11  108.70  3.000
 3PV  C13  C12  C11  101.50  3.000
 3PV  H9   C14  O14  110.34  3.000
 3PV  H9   C14  C15  108.75  3.000
 3PV  O14  C14  C15  109.74  3.000
 3PV  H9   C14  C13  108.87  3.000
 3PV  C15  C14  C13  114.66  3.000
 3PV  O14  C14  C13  104.41  3.000
 3PV  H10  C15  O15  106.25  3.000
 3PV  H10  C15  C16  107.78  3.000
 3PV  O15  C15  C16  112.66  3.000
 3PV  H10  C15  C14  106.82  3.000
 3PV  O15  C15  C14  112.01  3.000
 3PV  C16  C15  C14  110.94  3.000
 3PV  H12  C16  H11  106.83  3.000
 3PV  H12  C16  O16  111.53  3.000
 3PV  H11  C16  O16  111.73  3.000
 3PV  H12  C16  C15  109.61  3.000
 3PV  H11  C16  C15  108.34  3.000
 3PV  O16  C16  C15  108.73  3.000
 3PV  H16  O2   C2   108.82  3.000
 3PV  H17  O3   C3   108.44  3.000
 3PV  H19  C6   H18  106.53  3.000
 3PV  H19  C6   O11  107.94  3.000
 3PV  H18  C6   O11  112.59  3.000
 3PV  H19  C6   C5   109.53  3.000
 3PV  H18  C6   C5   110.07  3.000
 3PV  O11  C6   C5   110.06  3.000
 3PV  C7   O1   C1   113.91  3.000
 3PV  H20  O4   C4   108.45  3.000
 3PV  C5   O5   C1   115.08  3.000
 3PV  C6   O11  C11  117.85  3.000
 3PV  H21  O13  C13  109.30  3.000
 3PV  C14  O14  C11  111.10  3.000
 3PV  H22  O15  C15  108.40  3.000
 3PV  H24  C21  O25  109.32  3.000
 3PV  H24  C21  C22  109.29  3.000
 3PV  O25  C21  C22  110.17  3.000
 3PV  H24  C21  O21  111.32  3.000
 3PV  C22  C21  O21  108.98  3.000
 3PV  O25  C21  O21  107.75  3.000
 3PV  C21  O21  C12  117.10  3.000
 3PV  H25  C22  C23  109.33  3.000
 3PV  H25  C22  N22  108.19  3.000
 3PV  C23  C22  N22  111.31  3.000
 3PV  H25  C22  C21  108.38  3.000
 3PV  N22  C22  C21  110.34  3.000
 3PV  C23  C22  C21  109.24  3.000
 3PV  H26  N22  C27  117.95  3.000
 3PV  H26  N22  C22  117.09  3.000
 3PV  C27  N22  C22  124.53  3.000
 3PV  C28  C27  O27  121.72  3.000
 3PV  C28  C27  N22  114.81  3.000
 3PV  O27  C27  N22  123.47  3.000
 3PV  H29  C28  H28  107.27  3.000
 3PV  H29  C28  H27  108.50  3.000
 3PV  H28  C28  H27  108.15  3.000
 3PV  H29  C28  C27  109.78  3.000
 3PV  H28  C28  C27  109.21  3.000
 3PV  H27  C28  C27  113.72  3.000
 3PV  H30  C23  C24  107.52  3.000
 3PV  H30  C23  O23  110.78  3.000
 3PV  C24  C23  O23  112.00  3.000
 3PV  H30  C23  C22  108.20  3.000
 3PV  O23  C23  C22  108.32  3.000
 3PV  C24  C23  C22  109.95  3.000
 3PV  H31  O23  C23  107.79  3.000
 3PV  H32  C24  C25  108.44  3.000
 3PV  H32  C24  O24  111.09  3.000
 3PV  C25  C24  O24  111.66  3.000
 3PV  H32  C24  C23  108.25  3.000
 3PV  O24  C24  C23  107.00  3.000
 3PV  C25  C24  C23  110.35  3.000
 3PV  H33  O24  C24  109.23  3.000
 3PV  H34  C25  O25  109.88  3.000
 3PV  H34  C25  C26  109.09  3.000
 3PV  O25  C25  C26  108.14  3.000
 3PV  H34  C25  C24  108.67  3.000
 3PV  O25  C25  C24  109.61  3.000
 3PV  C26  C25  C24  111.44  3.000
 3PV  H36  C26  H35  106.82  3.000
 3PV  H36  C26  O26  111.76  3.000
 3PV  H35  C26  O26  107.21  3.000
 3PV  H36  C26  C25  108.89  3.000
 3PV  H35  C26  C25  108.15  3.000
 3PV  O26  C26  C25  113.71  3.000
 3PV  H37  O26  C26  109.02  3.000
 3PV  C25  O25  C21  112.91  3.000
 3PV  H23  O16  C16  107.98  3.000
 3PV  H15  C7   H14  108.66  3.000
 3PV  H15  C7   H13  108.53  3.000
 3PV  H14  C7   H13  109.16  3.000
 3PV  H15  C7   O1   107.43  3.000
 3PV  H14  C7   O1   110.82  3.000
 3PV  H13  C7   O1   112.14  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
 3PV  CONST_01  O27  C27  N22  C22    0.00   0.0  0
 3PV  CONST_02  C28  C27  N22  C22  180.00   0.0  0
 3PV  CONST_03  H26  N22  C27  O27  180.00   0.0  0
 3PV  Var_01    H13  C7   O1   C1   -72.21  30.0  3
 3PV  Var_02    H18  C6   O11  C11  -13.53  30.0  3
 3PV  Var_03    H27  C28  C27  N22   -7.15  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
 3PV  chir_01  C1   O1   C2   O5   positiv
 3PV  chir_02  C2   O2   C1   C3   negativ
 3PV  chir_03  C3   O3   C2   C4   positiv
 3PV  chir_04  C4   O4   C3   C5   negativ
 3PV  chir_05  C5   O5   C4   C6   negativ
 3PV  chir_06  C11  O11  O14  C12  positiv
 3PV  chir_07  C13  O13  C14  C12  negativ
 3PV  chir_08  C12  O21  C13  C11  positiv
 3PV  chir_09  C14  O14  C13  C15  positiv
 3PV  chir_10  C15  O15  C14  C16  negativ
 3PV  chir_11  C21  O25  O21  C22  negativ
 3PV  chir_12  C22  N22  C23  C21  positiv
 3PV  chir_13  C23  O23  C22  C24  positiv
 3PV  chir_14  C24  O24  C23  C25  negativ
 3PV  chir_15  C25  O25  C24  C26  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
 3PV  plan-1  C22  0.020
 3PV  plan-1  N22  0.020
 3PV  plan-1  C27  0.020
 3PV  plan-1  O27  0.020
 3PV  plan-1  C28  0.020
 3PV  plan-1  H26  0.020

