# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 12 18:47:07 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-nitrophenyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](O[C@@H]2CO)Oc3ccc(cc3)[N+]([O-])=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
 NPJ  NPJ  '4-nitrophenyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside'  ligand  57  32  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPJ
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
 NPJ  C1A   C  CH1    0   0.197  -3.4034  -0.5654   0.4859
 NPJ  C2A   C  CH1    0   0.021  -4.2673  -0.8701  -0.7414
 NPJ  C3A   C  CH1    0  -0.014  -4.4023   0.3734  -1.6105
 NPJ  C4A   C  CH1    0   0.041  -4.9153   1.5379  -0.7729
 NPJ  C5A   C  CH1    0  -0.020  -3.9898   1.7455   0.4245
 NPJ  C6A   C  CH2    0  -0.161  -4.4996   2.8169   1.3639
 NPJ  O1A   O  O2     0  -0.510  -2.0794  -0.3769   0.0763
 NPJ  O2A   O  OH1    0  -0.698  -3.7666  -1.9279  -1.5180
 NPJ  O3A   O  OH1    0  -0.677  -5.3185   0.1787  -2.6652
 NPJ  O4A   O  OH1    0  -0.674  -4.9499   2.7328  -1.5135
 NPJ  O5A   O  O2     0  -0.493  -3.8932   0.5426   1.1728
 NPJ  O6A   O  OH1    0  -0.664  -3.5505   3.0140   2.3849
 NPJ  C1B   C  CH1    0   0.200   1.6989  -1.7547   1.0189
 NPJ  C2B   C  CH1    0  -0.012   0.6249  -2.8266   0.8267
 NPJ  C3B   C  CH1    0   0.017  -0.5733  -2.2337   0.0986
 NPJ  C4B   C  CH1    0   0.012  -1.0642  -0.9926   0.8350
 NPJ  C5B   C  CH1    0  -0.018   0.0829   0.0017   1.0295
 NPJ  C6B   C  CH2    0  -0.177  -0.3123   1.1566   1.9252
 NPJ  O2B   O  OH1    0  -0.661   1.0897  -3.9239   0.0906
 NPJ  O3B   O  OH1    0  -0.674  -1.6426  -3.1552   0.0454
 NPJ  O5B   O  O2     0  -0.487   1.1824  -0.6427   1.6608
 NPJ  O6B   O  OH1    0  -0.666   0.7611   2.0646   1.9822
 NPJ  C1C   C  CR6    0   0.230   5.7031   0.6086  -0.8959
 NPJ  C2C   C  CR16   0  -0.255   5.2238   0.5178   0.4024
 NPJ  C3C   C  CR16   0  -0.356   4.0426  -0.1540   0.6567
 NPJ  C4C   C  CR6    0   0.425   3.3463  -0.7513  -0.3956
 NPJ  C5C   C  CR16   0  -0.346   3.8363  -0.6437  -1.7008
 NPJ  C6C   C  CR16   0  -0.252   5.0090   0.0313  -1.9544
 NPJ  O2C   O  O     -1  -0.388   7.5128   1.8217  -0.2154
 NPJ  O3C   O  O      0  -0.388   7.3378   1.3706  -2.2932
 NPJ  H1A   H  HCH1   0   0.255  -3.4713  -1.3961   1.1973
 NPJ  H2A   H  HCH1   0   0.212  -5.2660  -1.1234  -0.3535
 NPJ  H3A   H  HCH1   0   0.217  -3.4114   0.6408  -2.0065
 NPJ  H4A   H  HCH1   0   0.209  -5.9183   1.2785  -0.3962
 NPJ  H5A   H  HCH1   0   0.227  -2.9990   2.0448   0.0542
 NPJ  H6A1  H  HCH2   0   0.195  -5.4745   2.5063   1.7655
 NPJ  H6A2  H  HCH2   0   0.211  -4.6661   3.7312   0.7853
 NPJ  HO2A  H  HOH1   0   0.454  -3.1195  -2.4405  -1.0079
 NPJ  HO3A  H  HOH1   0   0.457  -4.9103  -0.3917  -3.3233
 NPJ  HO4A  H  HOH1   0   0.454  -5.4856   2.5789  -2.2988
 NPJ  HO6A  H  HOH1   0   0.455  -3.8687   3.7228   2.9507
 NPJ  H1B   H  HCH1   0   0.277   2.5050  -2.1330   1.6578
 NPJ  H2B   H  HCH1   0   0.251   0.3035  -3.1250   1.8337
 NPJ  H3B   H  HCH1   0   0.237  -0.2731  -1.9395  -0.9166
 NPJ  H4B   H  HCH1   0   0.245  -1.4423  -1.2924   1.8233
 NPJ  H5B   H  HCH1   0   0.243   0.3802   0.3987   0.0490
 NPJ  H6B1  H  HCH2   0   0.230  -1.2142   1.6258   1.5225
 NPJ  H6B2  H  HCH2   0   0.198  -0.5725   0.7634   2.9180
 NPJ  HO2B  H  HOH1   0   0.465   1.5787  -4.5115   0.6747
 NPJ  HO3B  H  HOH1   0   0.468  -1.3551  -3.9302  -0.4515
 NPJ  HO6B  H  HOH1   0   0.456   0.4758   2.8278   2.4921
 NPJ  H2C   H  HCR6   0   0.301   5.7548   0.9728   1.2256
 NPJ  H3C   H  HCR6   0   0.301   3.6822  -0.1861   1.6735
 NPJ  H5C   H  HCR6   0   0.286   3.2894  -1.1022  -2.5140
 NPJ  H6C   H  HCR6   0   0.299   5.3733   0.1005  -2.9688
 NPJ  O1B   O  O2     0  -0.482   2.2071  -1.4449  -0.2622
 NPJ  N1C   N  N      1   0.328   6.9366   1.3162  -1.1524

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
 NPJ  C1A  C2A   single    1.531  0.020  1.531
 NPJ  C1A  O1A   single    1.399  0.020  1.399
 NPJ  C1A  O5A   single    1.393  0.020  1.393
 NPJ  C1A  H1A   single    0.970  0.020  1.090
 NPJ  C2A  C3A   single    1.523  0.020  1.523
 NPJ  C2A  O2A   single    1.405  0.020  1.405
 NPJ  C2A  H2A   single    0.970  0.020  1.090
 NPJ  C3A  C4A   single    1.523  0.020  1.523
 NPJ  C3A  O3A   single    1.411  0.020  1.411
 NPJ  C3A  H3A   single    0.970  0.020  1.090
 NPJ  C4A  C5A   single    1.528  0.020  1.528
 NPJ  C4A  O4A   single    1.406  0.020  1.406
 NPJ  C4A  H4A   single    0.970  0.020  1.090
 NPJ  C5A  C6A   single    1.513  0.020  1.513
 NPJ  C5A  O5A   single    1.420  0.020  1.420
 NPJ  C5A  H5A   single    0.970  0.020  1.090
 NPJ  C6A  O6A   single    1.408  0.020  1.408
 NPJ  C6A  H6A1  single    0.970  0.020  1.090
 NPJ  C6A  H6A2  single    0.970  0.020  1.090
 NPJ  O1A  C4B   single    1.409  0.020  1.409
 NPJ  O2A  HO2A  single    0.850  0.020  0.980
 NPJ  O3A  HO3A  single    0.850  0.020  0.980
 NPJ  O4A  HO4A  single    0.850  0.020  0.980
 NPJ  O6A  HO6A  single    0.850  0.020  0.980
 NPJ  C1B  C2B   single    1.530  0.020  1.530
 NPJ  C1B  O1B   single    1.413  0.020  1.413
 NPJ  C1B  O5B   single    1.384  0.020  1.384
 NPJ  C1B  H1B   single    0.970  0.020  1.090
 NPJ  C2B  C3B   single    1.522  0.020  1.522
 NPJ  C2B  O2B   single    1.401  0.020  1.401
 NPJ  C2B  H2B   single    0.970  0.020  1.090
 NPJ  C3B  C4B   single    1.524  0.020  1.524
 NPJ  C3B  O3B   single    1.413  0.020  1.413
 NPJ  C3B  H3B   single    0.970  0.020  1.090
 NPJ  C4B  C5B   single    1.530  0.020  1.530
 NPJ  C4B  H4B   single    0.970  0.020  1.090
 NPJ  C5B  C6B   single    1.514  0.020  1.514
 NPJ  C5B  O5B   single    1.422  0.020  1.422
 NPJ  C5B  H5B   single    0.970  0.020  1.090
 NPJ  C6B  O6B   single    1.407  0.020  1.407
 NPJ  C6B  H6B1  single    0.970  0.020  1.090
 NPJ  C6B  H6B2  single    0.970  0.020  1.090
 NPJ  O1B  C4C   single    1.340  0.020  1.340
 NPJ  O2B  HO2B  single    0.850  0.020  0.980
 NPJ  O3B  HO3B  single    0.850  0.020  0.980
 NPJ  O6B  HO6B  single    0.850  0.020  0.980
 NPJ  C1C  C2C   aromatic  1.387  0.020  1.387
 NPJ  C1C  C6C   aromatic  1.391  0.020  1.391
 NPJ  C1C  N1C   single    1.445  0.020  1.445
 NPJ  C2C  C3C   aromatic  1.382  0.020  1.382
 NPJ  C2C  H2C   single    0.930  0.020  1.080
 NPJ  C3C  C4C   aromatic  1.396  0.020  1.396
 NPJ  C3C  H3C   single    0.930  0.020  1.080
 NPJ  C4C  C5C   aromatic  1.398  0.020  1.398
 NPJ  C5C  C6C   aromatic  1.377  0.020  1.377
 NPJ  C5C  H5C   single    0.930  0.020  1.080
 NPJ  C6C  H6C   single    0.930  0.020  1.080
 NPJ  N1C  O2C   single    1.211  0.020  1.211
 NPJ  N1C  O3C   double    1.211  0.020  1.211

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
 NPJ  H1A   C1A  O5A   105.13  3.000
 NPJ  H1A   C1A  O1A   110.54  3.000
 NPJ  O5A   C1A  O1A   111.72  3.000
 NPJ  H1A   C1A  C2A   109.54  3.000
 NPJ  O5A   C1A  C2A   110.81  3.000
 NPJ  O1A   C1A  C2A   109.04  3.000
 NPJ  H2A   C2A  O2A   110.18  3.000
 NPJ  H2A   C2A  C3A   107.97  3.000
 NPJ  O2A   C2A  C3A   109.32  3.000
 NPJ  H2A   C2A  C1A   105.98  3.000
 NPJ  O2A   C2A  C1A   113.07  3.000
 NPJ  C3A   C2A  C1A   110.17  3.000
 NPJ  H3A   C3A  O3A   110.46  3.000
 NPJ  H3A   C3A  C4A   108.39  3.000
 NPJ  O3A   C3A  C4A   107.32  3.000
 NPJ  H3A   C3A  C2A   108.91  3.000
 NPJ  O3A   C3A  C2A   111.81  3.000
 NPJ  C4A   C3A  C2A   109.89  3.000
 NPJ  H4A   C4A  O4A   110.95  3.000
 NPJ  H4A   C4A  C5A   108.38  3.000
 NPJ  O4A   C4A  C5A   108.19  3.000
 NPJ  H4A   C4A  C3A   108.33  3.000
 NPJ  O4A   C4A  C3A   111.61  3.000
 NPJ  C5A   C4A  C3A   109.32  3.000
 NPJ  H5A   C5A  O5A   110.29  3.000
 NPJ  H5A   C5A  C6A   108.67  3.000
 NPJ  O5A   C5A  C6A   107.19  3.000
 NPJ  H5A   C5A  C4A   108.60  3.000
 NPJ  O5A   C5A  C4A   109.82  3.000
 NPJ  C6A   C5A  C4A   112.25  3.000
 NPJ  H6A2  C6A  H6A1  107.10  3.000
 NPJ  H6A2  C6A  O6A   111.65  3.000
 NPJ  H6A1  C6A  O6A   111.87  3.000
 NPJ  H6A2  C6A  C5A   108.33  3.000
 NPJ  H6A1  C6A  C5A   109.00  3.000
 NPJ  O6A   C6A  C5A   108.79  3.000
 NPJ  C4B   O1A  C1A   117.74  3.000
 NPJ  HO2A  O2A  C2A   110.17  3.000
 NPJ  HO3A  O3A  C3A   108.53  3.000
 NPJ  HO4A  O4A  C4A   107.90  3.000
 NPJ  C5A   O5A  C1A   115.98  3.000
 NPJ  HO6A  O6A  C6A   107.87  3.000
 NPJ  H1B   C1B  O5B   106.35  3.000
 NPJ  H1B   C1B  O1B   109.86  3.000
 NPJ  O5B   C1B  O1B   112.25  3.000
 NPJ  H1B   C1B  C2B   110.36  3.000
 NPJ  O5B   C1B  C2B   111.06  3.000
 NPJ  O1B   C1B  C2B   107.00  3.000
 NPJ  H2B   C2B  O2B   111.48  3.000
 NPJ  H2B   C2B  C3B   108.30  3.000
 NPJ  O2B   C2B  C3B   108.36  3.000
 NPJ  H2B   C2B  C1B   106.30  3.000
 NPJ  O2B   C2B  C1B   112.46  3.000
 NPJ  C3B   C2B  C1B   109.87  3.000
 NPJ  H3B   C3B  O3B   110.28  3.000
 NPJ  H3B   C3B  C4B   108.44  3.000
 NPJ  O3B   C3B  C4B   107.79  3.000
 NPJ  H3B   C3B  C2B   109.34  3.000
 NPJ  O3B   C3B  C2B   111.08  3.000
 NPJ  C4B   C3B  C2B   109.85  3.000
 NPJ  H4B   C4B  C5B   108.70  3.000
 NPJ  H4B   C4B  C3B   108.84  3.000
 NPJ  C5B   C4B  C3B   110.43  3.000
 NPJ  H4B   C4B  O1A   110.81  3.000
 NPJ  C5B   C4B  O1A   108.94  3.000
 NPJ  C3B   C4B  O1A   109.13  3.000
 NPJ  H5B   C5B  O5B   110.53  3.000
 NPJ  H5B   C5B  C6B   108.84  3.000
 NPJ  O5B   C5B  C6B   106.55  3.000
 NPJ  H5B   C5B  C4B   108.91  3.000
 NPJ  O5B   C5B  C4B   109.96  3.000
 NPJ  C6B   C5B  C4B   112.03  3.000
 NPJ  H6B2  C6B  H6B1  106.92  3.000
 NPJ  H6B2  C6B  O6B   112.01  3.000
 NPJ  H6B1  C6B  O6B   111.55  3.000
 NPJ  H6B2  C6B  C5B   108.86  3.000
 NPJ  H6B1  C6B  C5B   108.95  3.000
 NPJ  O6B   C6B  C5B   108.48  3.000
 NPJ  HO2B  O2B  C2B   109.16  3.000
 NPJ  HO3B  O3B  C3B   108.54  3.000
 NPJ  C5B   O5B  C1B   116.53  3.000
 NPJ  HO6B  O6B  C6B   107.90  3.000
 NPJ  N1C   C1C  C6C   119.61  3.000
 NPJ  N1C   C1C  C2C   119.55  3.000
 NPJ  C6C   C1C  C2C   120.84  3.000
 NPJ  H2C   C2C  C3C   118.98  3.000
 NPJ  H2C   C2C  C1C   121.06  3.000
 NPJ  C3C   C2C  C1C   119.95  3.000
 NPJ  H3C   C3C  C4C   122.06  3.000
 NPJ  H3C   C3C  C2C   118.23  3.000
 NPJ  C4C   C3C  C2C   119.70  3.000
 NPJ  C5C   C4C  C3C   119.73  3.000
 NPJ  C5C   C4C  O1B   115.50  3.000
 NPJ  C3C   C4C  O1B   124.77  3.000
 NPJ  H5C   C5C  C6C   119.99  3.000
 NPJ  H5C   C5C  C4C   119.46  3.000
 NPJ  C6C   C5C  C4C   120.54  3.000
 NPJ  H6C   C6C  C5C   119.46  3.000
 NPJ  H6C   C6C  C1C   121.31  3.000
 NPJ  C5C   C6C  C1C   119.23  3.000
 NPJ  C4C   O1B  C1B   120.63  3.000
 NPJ  O3C   N1C  O2C   123.56  3.000
 NPJ  O3C   N1C  C1C   118.18  3.000
 NPJ  O2C   N1C  C1C   118.26  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
 NPJ  CONST_01  C4C  C3C  C2C  C1C    0.00   0.0  0
 NPJ  CONST_02  C4C  C5C  C6C  C1C    0.00   0.0  0
 NPJ  CONST_03  C5C  C6C  C1C  C2C    0.00   0.0  0
 NPJ  CONST_04  C5C  C4C  C3C  C2C    0.00   0.0  0
 NPJ  CONST_05  C6C  C1C  C2C  C3C    0.00   0.0  0
 NPJ  CONST_06  C6C  C5C  C4C  C3C    0.00   0.0  0
 NPJ  CONST_07  C2C  C3C  C4C  O1B  180.00   0.0  0
 NPJ  CONST_08  C6C  C5C  C4C  O1B  180.00   0.0  0
 NPJ  CONST_09  N1C  C1C  C2C  C3C  180.00   0.0  0
 NPJ  CONST_10  N1C  C1C  C6C  C5C  180.00   0.0  0
 NPJ  CONST_11  H3C  C3C  C2C  C1C  180.00   0.0  0
 NPJ  CONST_12  H5C  C5C  C6C  C1C  180.00   0.0  0
 NPJ  CONST_13  H6C  C6C  C1C  C2C  180.00   0.0  0
 NPJ  CONST_14  H2C  C2C  C3C  C4C  180.00   0.0  0
 NPJ  CONST_15  O2C  N1C  C1C  C2C    0.00   0.0  0
 NPJ  CONST_16  O3C  N1C  C1C  C2C  180.00   0.0  0
 NPJ  CONST_17  O2C  N1C  C1C  C6C  180.00   0.0  0
 NPJ  CONST_18  O3C  N1C  C1C  C6C    0.00   0.0  0
 NPJ  Var_01    C3C  C4C  O1B  C1B   -7.45  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
 NPJ  chir_01  C1A  C2A  O1A  O5A  negativ
 NPJ  chir_02  C2A  O2A  C1A  C3A  negativ
 NPJ  chir_03  C3A  O3A  C2A  C4A  positiv
 NPJ  chir_04  C4A  O4A  C5A  C3A  positiv
 NPJ  chir_05  C5A  O5A  C4A  C6A  negativ
 NPJ  chir_06  C1B  C2B  O1B  O5B  negativ
 NPJ  chir_07  C2B  O2B  C1B  C3B  negativ
 NPJ  chir_08  C3B  O3B  C2B  C4B  positiv
 NPJ  chir_09  C4B  O1A  C5B  C3B  positiv
 NPJ  chir_10  C5B  O5B  C4B  C6B  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
 NPJ  plan-1  C1C  0.020
 NPJ  plan-1  C2C  0.020
 NPJ  plan-1  C3C  0.020
 NPJ  plan-1  C4C  0.020
 NPJ  plan-1  C5C  0.020
 NPJ  plan-1  C6C  0.020
 NPJ  plan-1  H2C  0.020
 NPJ  plan-1  H3C  0.020
 NPJ  plan-1  H5C  0.020
 NPJ  plan-1  H6C  0.020
 NPJ  plan-1  O1B  0.020
 NPJ  plan-1  N1C  0.020
 NPJ  plan-2  C1C  0.020
 NPJ  plan-2  O2C  0.020
 NPJ  plan-2  O3C  0.020
 NPJ  plan-2  N1C  0.020

