# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:06:17 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(naphthalen-1-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)C(=O)Nc2cccc3ccccc23)[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
 376  376  N-[(naphthalen-1-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine  ligand  47  27  .  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_376
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
 376  C18  C  CR66  0   0.067   4.5575  -0.2137   0.1129
 376  C17  C  CR16  0  -0.305   4.2765  -1.4879   0.6617
 376  C16  C  CR16  0  -0.248   5.2781  -2.3968   0.8726
 376  C15  C  CR16  0  -0.255   6.6110  -2.0838   0.5410
 376  C14  C  CR16  0  -0.309   6.9093  -0.8691  -0.0114
 376  C13  C  CR66  0   0.099   5.8976   0.0914  -0.2450
 376  C12  C  CR16  0  -0.320   6.1966   1.3398  -0.8373
 376  C11  C  CR16  0  -0.261   5.2061   2.2550  -1.0540
 376  C10  C  CR16  0  -0.300   3.8788   1.9815  -0.6740
 376  C9   C  CR6   0   0.322   3.5561   0.7779  -0.1004
 376  N2   N  NH1   0  -0.740   2.2460   0.4929   0.3183
 376  C8   C  C     0   0.437   1.1165   0.7918  -0.3388
 376  O8   O  O     0  -0.441   1.0231   1.3820  -1.3970
 376  C7   C  C     0   0.464  -0.1300   0.2793   0.4050
 376  O7   O  O     0  -0.454  -0.0272  -0.3601   1.4351
 376  N1   N  NH1   0  -0.678  -1.2708   0.6247  -0.2007
 376  C1   C  CH1   0   0.211  -2.5678   0.2403   0.2603
 376  O5   O  O2    0  -0.487  -3.0161  -0.8201  -0.5449
 376  C5   C  CH1   0  -0.016  -4.2630  -1.3506  -0.1387
 376  C6   C  CH2   0  -0.157  -4.5672  -2.5363  -1.0293
 376  O6   O  OH1   0  -0.670  -3.5860  -3.5239  -0.8219
 376  C4   C  CH1   0   0.033  -5.3429  -0.2717  -0.2352
 376  O4   O  OH1   0  -0.671  -6.5483  -0.8196   0.2359
 376  C3   C  CH1   0  -0.002  -4.9267   0.9424   0.5871
 376  O3   O  OH1   0  -0.671  -5.9010   1.9389   0.3999
 376  C2   C  CH1   0  -0.031  -3.5405   1.4182   0.1742
 376  O2   O  OH1   0  -0.663  -3.1657   2.4543   1.0447
 376  H17  H  HCR6  0   0.246   3.2608  -1.7688   0.9064
 376  H16  H  HCR6  0   0.264   5.0420  -3.3656   1.2923
 376  H15  H  HCR6  0   0.262   7.3940  -2.8093   0.7180
 376  H14  H  HCR6  0   0.260   7.9298  -0.6239  -0.2791
 376  H12  H  HCR6  0   0.260   7.2202   1.5600  -1.1136
 376  H11  H  HCR6  0   0.265   5.4359   3.2104  -1.5061
 376  H10  H  HCR6  0   0.275   3.1247   2.7407  -0.8194
 376  HN2  H  HNH1  0   0.422   2.1256  -0.0275   1.1772
 376  HN1  H  HNH1  0   0.418  -1.1981   1.1281  -1.0756
 376  H1   H  HCH1  0   0.239  -2.4791  -0.0769   1.3071
 376  H5   H  HCH1  0   0.227  -4.2031  -1.6923   0.9078
 376  H6   H  HCH2  0   0.215  -5.5690  -2.9034  -0.7847
 376  H6A  H  HCH2  0   0.198  -4.5930  -2.1971  -2.0745
 376  HO6  H  HOH1  0   0.457  -3.8264  -4.2935  -1.3449
 376  H4   H  HCH1  0   0.216  -5.4327   0.0361  -1.2892
 376  HO4  H  HOH1  0   0.456  -7.2401  -0.1575   0.1360
 376  H3   H  HCH1  0   0.217  -4.8802   0.6324   1.6438
 376  HO3  H  HOH1  0   0.457  -5.7254   2.6576   1.0156
 376  H2   H  HCH1  0   0.234  -3.5808   1.7624  -0.8704
 376  HO2  H  HOH1  0   0.460  -2.4552   2.9629   0.6426

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
 376  C18  C17  aromatic  1.416  0.020  1.416
 376  C18  C13  aromatic  1.420  0.020  1.420
 376  C18  C9   aromatic  1.425  0.020  1.425
 376  C17  C16  aromatic  1.369  0.020  1.369
 376  C16  C15  aromatic  1.409  0.020  1.409
 376  C15  C14  aromatic  1.367  0.020  1.367
 376  C14  C13  aromatic  1.414  0.020  1.414
 376  C13  C12  aromatic  1.414  0.020  1.414
 376  C12  C11  aromatic  1.366  0.020  1.366
 376  C11  C10  aromatic  1.407  0.020  1.407
 376  C10  C9   aromatic  1.372  0.020  1.372
 376  C9   N2   single    1.405  0.020  1.405
 376  N2   C8   single    1.340  0.020  1.340
 376  C8   O8   double    1.215  0.020  1.215
 376  C8   C7   single    1.539  0.020  1.539
 376  C7   O7   double    1.217  0.020  1.217
 376  C7   N1   single    1.337  0.020  1.337
 376  N1   C1   single    1.429  0.020  1.429
 376  C1   O5   single    1.405  0.020  1.405
 376  C1   C2   single    1.530  0.020  1.530
 376  O5   C5   single    1.415  0.020  1.415
 376  C5   C6   single    1.514  0.020  1.514
 376  C5   C4   single    1.530  0.020  1.530
 376  C6   O6   single    1.408  0.020  1.408
 376  C4   O4   single    1.405  0.020  1.405
 376  C4   C3   single    1.524  0.020  1.524
 376  C3   O3   single    1.406  0.020  1.406
 376  C3   C2   single    1.523  0.020  1.523
 376  C2   O2   single    1.404  0.020  1.404
 376  C17  H17  single    0.930  0.020  1.080
 376  C16  H16  single    0.930  0.020  1.080
 376  C15  H15  single    0.930  0.020  1.080
 376  C14  H14  single    0.930  0.020  1.080
 376  C12  H12  single    0.930  0.020  1.080
 376  C11  H11  single    0.930  0.020  1.080
 376  C10  H10  single    0.930  0.020  1.080
 376  N2   HN2  single    0.860  0.020  1.020
 376  N1   HN1  single    0.860  0.020  1.020
 376  C1   H1   single    0.970  0.020  1.090
 376  C5   H5   single    0.970  0.020  1.090
 376  C6   H6   single    0.970  0.020  1.090
 376  C6   H6A  single    0.970  0.020  1.090
 376  O6   HO6  single    0.850  0.020  0.980
 376  C4   H4   single    0.970  0.020  1.090
 376  O4   HO4  single    0.850  0.020  0.980
 376  C3   H3   single    0.970  0.020  1.090
 376  O3   HO3  single    0.850  0.020  0.980
 376  C2   H2   single    0.970  0.020  1.090
 376  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
 376  C9   C18  C13  118.41  3.000
 376  C9   C18  C17  123.01  3.000
 376  C13  C18  C17  118.58  3.000
 376  H17  C17  C16  118.67  3.000
 376  H17  C17  C18  120.52  3.000
 376  C16  C17  C18  120.81  3.000
 376  H16  C16  C15  119.79  3.000
 376  H16  C16  C17  119.64  3.000
 376  C15  C16  C17  120.57  3.000
 376  H15  C15  C14  120.26  3.000
 376  H15  C15  C16  119.82  3.000
 376  C14  C15  C16  119.92  3.000
 376  H14  C14  C13  118.64  3.000
 376  H14  C14  C15  120.43  3.000
 376  C13  C14  C15  120.93  3.000
 376  C12  C13  C14  121.17  3.000
 376  C12  C13  C18  119.66  3.000
 376  C14  C13  C18  119.17  3.000
 376  H12  C12  C11  120.58  3.000
 376  H12  C12  C13  119.11  3.000
 376  C11  C12  C13  120.32  3.000
 376  H11  C11  C10  119.00  3.000
 376  H11  C11  C12  120.27  3.000
 376  C10  C11  C12  120.72  3.000
 376  H10  C10  C9   120.59  3.000
 376  H10  C10  C11  119.05  3.000
 376  C9   C10  C11  120.35  3.000
 376  N2   C9   C10  121.48  3.000
 376  N2   C9   C18  118.00  3.000
 376  C10  C9   C18  120.51  3.000
 376  HN2  N2   C8   115.51  3.000
 376  HN2  N2   C9   117.95  3.000
 376  C8   N2   C9   126.48  3.000
 376  C7   C8   O8   121.34  3.000
 376  C7   C8   N2   111.79  3.000
 376  O8   C8   N2   126.87  3.000
 376  N1   C7   O7   126.25  3.000
 376  N1   C7   C8   112.71  3.000
 376  O7   C7   C8   121.04  3.000
 376  HN1  N1   C1   118.54  3.000
 376  HN1  N1   C7   117.31  3.000
 376  C1   N1   C7   123.97  3.000
 376  H1   C1   C2   109.12  3.000
 376  H1   C1   O5   110.76  3.000
 376  C2   C1   O5   110.24  3.000
 376  H1   C1   N1   108.18  3.000
 376  C2   C1   N1   110.59  3.000
 376  O5   C1   N1   107.93  3.000
 376  C5   O5   C1   113.57  3.000
 376  H5   C5   C4   108.47  3.000
 376  H5   C5   C6   109.06  3.000
 376  C4   C5   C6   111.93  3.000
 376  H5   C5   O5   109.94  3.000
 376  C4   C5   O5   109.86  3.000
 376  C6   C5   O5   107.57  3.000
 376  H6A  C6   H6   107.12  3.000
 376  H6A  C6   O6   111.90  3.000
 376  H6   C6   O6   111.70  3.000
 376  H6A  C6   C5   108.81  3.000
 376  H6   C6   C5   108.37  3.000
 376  O6   C6   C5   108.83  3.000
 376  HO6  O6   C6   107.89  3.000
 376  H4   C4   C3   108.41  3.000
 376  H4   C4   O4   111.08  3.000
 376  C3   C4   O4   111.34  3.000
 376  H4   C4   C5   108.36  3.000
 376  C3   C4   C5   109.57  3.000
 376  O4   C4   C5   108.03  3.000
 376  HO4  O4   C4   108.27  3.000
 376  H3   C3   C2   108.03  3.000
 376  H3   C3   O3   110.87  3.000
 376  C2   C3   O3   111.92  3.000
 376  H3   C3   C4   107.74  3.000
 376  C2   C3   C4   110.56  3.000
 376  O3   C3   C4   107.66  3.000
 376  HO3  O3   C3   108.52  3.000
 376  H2   C2   O2   111.55  3.000
 376  H2   C2   C3   108.77  3.000
 376  O2   C2   C3   107.79  3.000
 376  H2   C2   C1   108.51  3.000
 376  O2   C2   C1   111.31  3.000
 376  C3   C2   C1   108.84  3.000
 376  HO2  O2   C2   109.16  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
 376  CONST_01  C15  C16  C17  C18    0.00  0.0  0
 376  CONST_02  C15  C14  C13  C18    0.00  0.0  0
 376  CONST_03  C11  C12  C13  C18    0.00  0.0  0
 376  CONST_04  C11  C10  C9   C18    0.00  0.0  0
 376  CONST_05  C14  C13  C18  C17    0.00  0.0  0
 376  CONST_06  C12  C13  C18  C17  180.00  0.0  0
 376  CONST_07  C10  C9   C18  C17  180.00  0.0  0
 376  CONST_08  C14  C15  C16  C17    0.00  0.0  0
 376  CONST_09  C13  C18  C17  C16    0.00  0.0  0
 376  CONST_10  C9   C18  C17  C16  180.00  0.0  0
 376  CONST_11  C13  C14  C15  C16    0.00  0.0  0
 376  CONST_12  C12  C13  C14  C15  180.00  0.0  0
 376  CONST_13  C9   C18  C13  C14  180.00  0.0  0
 376  CONST_14  C11  C12  C13  C14  180.00  0.0  0
 376  CONST_15  C10  C9   C18  C13    0.00  0.0  0
 376  CONST_16  C10  C11  C12  C13    0.00  0.0  0
 376  CONST_17  C9   C18  C13  C12    0.00  0.0  0
 376  CONST_18  C9   C10  C11  C12    0.00  0.0  0
 376  CONST_19  N2   C9   C18  C17    0.00  0.0  0
 376  CONST_20  N2   C9   C18  C13  180.00  0.0  0
 376  CONST_21  N2   C9   C10  C11  180.00  0.0  0
 376  CONST_22  H16  C16  C17  C18  180.00  0.0  0
 376  CONST_23  H14  C14  C13  C18  180.00  0.0  0
 376  CONST_24  H12  C12  C13  C18  180.00  0.0  0
 376  CONST_25  H10  C10  C9   C18  180.00  0.0  0
 376  CONST_26  H15  C15  C16  C17  180.00  0.0  0
 376  CONST_27  H17  C17  C16  C15  180.00  0.0  0
 376  CONST_28  H11  C11  C12  C13  180.00  0.0  0
 376  CONST_32  O8   C8   N2   C9     0.00  0.0  0
 376  CONST_33  C7   C8   N2   C9   180.00  0.0  0
 376  CONST_34  C1   N1   C7   C8   180.00  0.0  0
 376  CONST_35  C1   N1   C7   O7     0.00  0.0  0
 376  CONST_36  N1   C7   C8   N2   180.00  0.0  0
 376  CONST_37  N1   C7   C8   O8     0.00  0.0  0
 376  CONST_38  HN1  N1   C7   C8     0.00  0.0  0

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
 376  chir_01  C1  N1  O5  C2  positiv
 376  chir_02  C5  O5  C6  C4  positiv
 376  chir_03  C4  O4  C5  C3  positiv
 376  chir_04  C3  O3  C2  C4  positiv
 376  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
 376  plan-1  C18  0.020
 376  plan-1  C17  0.020
 376  plan-1  C16  0.020
 376  plan-1  C15  0.020
 376  plan-1  C14  0.020
 376  plan-1  C13  0.020
 376  plan-1  C12  0.020
 376  plan-1  C11  0.020
 376  plan-1  C10  0.020
 376  plan-1  C9   0.020
 376  plan-1  N2   0.020
 376  plan-1  H17  0.020
 376  plan-1  H16  0.020
 376  plan-1  H15  0.020
 376  plan-1  H14  0.020
 376  plan-1  H12  0.020
 376  plan-1  H11  0.020
 376  plan-1  H10  0.020
 376  plan-2  C9   0.020
 376  plan-2  N2   0.020
 376  plan-2  C8   0.020
 376  plan-2  O8   0.020
 376  plan-2  C7   0.020
 376  plan-2  O7   0.020
 376  plan-2  N1   0.020
 376  plan-2  C1   0.020
 376  plan-2  HN2  0.020
 376  plan-2  HN1  0.020

