# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:30:06 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(naphthalen-2-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)Nc2ccc3ccccc3c2)[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
 179  179  N-[(naphthalen-2-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine  ligand  47  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_179
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
 179  C18  C  CR16  0  -0.434  -4.2270  -0.2166  -0.8722
 179  C17  C  CR66  0   0.141  -5.6093  -0.2363  -0.5997
 179  C16  C  CR16  0  -0.314  -6.5645  -0.5299  -1.6031
 179  C15  C  CR16  0  -0.256  -7.9001  -0.5408  -1.3085
 179  C14  C  CR16  0  -0.261  -8.3480  -0.2589   0.0006
 179  C13  C  CR16  0  -0.305  -7.4471   0.0277   0.9896
 179  C12  C  CR66  0   0.103  -6.0600   0.0452   0.7150
 179  C11  C  CR16  0  -0.302  -5.0963   0.3351   1.7058
 179  C10  C  CR16  0  -0.311  -3.7579   0.3509   1.4281
 179  C9   C  CR6   0   0.399  -3.3113   0.0706   0.1128
 179  N2   N  NH1   0  -0.738  -1.9618   0.0751  -0.2546
 179  C8   C  C     0   0.439  -0.8705   0.2765   0.4952
 179  O8   O  O     0  -0.447  -0.8235   0.5023   1.6900
 179  C7   C  C     0   0.472   0.4173   0.1916  -0.3451
 179  O7   O  O     0  -0.454   0.3784  -0.0559  -1.5357
 179  N1   N  NH1   0  -0.680   1.5192   0.4303   0.3743
 179  C1   C  CH1   0   0.214   2.8423   0.3788  -0.1617
 179  O5   O  O2    0  -0.486   3.4004  -0.8670   0.1705
 179  C5   C  CH1   0  -0.017   4.6781  -1.0773  -0.3984
 179  C6   C  CH2   0  -0.156   5.1094  -2.4851  -0.0471
 179  O6   O  OH1   0  -0.670   4.2050  -3.3943  -0.6258
 179  C4   C  CH1   0   0.034   5.6600  -0.0324   0.1345
 179  O4   O  OH1   0  -0.671   6.8952  -0.2314  -0.5061
 179  C3   C  CH1   0  -0.004   5.1166   1.3660  -0.1359
 179  O3   O  OH1   0  -0.671   6.0031   2.2862   0.4509
 179  C2   C  CH1   0  -0.033   3.7017   1.5100   0.4076
 179  O2   O  OH1   0  -0.662   3.2173   2.7681   0.0142
 179  H18  H  HCR6  0   0.272  -3.8896  -0.4358  -1.8794
 179  H16  H  HCR6  0   0.256  -6.2234  -0.7475  -2.6079
 179  H15  H  HCR6  0   0.260  -8.6224  -0.7663  -2.0823
 179  H14  H  HCR6  0   0.259  -9.4082  -0.2700   0.2166
 179  H13  H  HCR6  0   0.257  -7.7867   0.2467   1.9949
 179  H11  H  HCR6  0   0.262  -5.4286   0.5531   2.7134
 179  H10  H  HCR6  0   0.286  -3.0549   0.5765   2.2129
 179  HN2  H  HNH1  0   0.427  -1.7747  -0.1031  -1.2336
 179  HN1  H  HNH1  0   0.417   1.4033   0.5698   1.3697
 179  H1   H  HCH1  0   0.238   2.7763   0.4946  -1.2512
 179  H5   H  HCH1  0   0.227   4.6212  -0.9772  -1.4947
 179  H6   H  HCH2  0   0.215   6.1291  -2.6360  -0.4155
 179  H6A  H  HCH2  0   0.197   5.1435  -2.5812   1.0473
 179  HO6  H  HOH1  0   0.457   4.5262  -4.2835  -0.4527
 179  H4   H  HCH1  0   0.215   5.7515  -0.1675   1.2245
 179  HO4  H  HOH1  0   0.455   7.5164   0.4236  -0.1714
 179  H3   H  HCH1  0   0.219   5.0751   1.5031  -1.2289
 179  HO3  H  HOH1  0   0.457   5.7669   3.1711   0.1553
 179  H2   H  HCH1  0   0.235   3.7291   1.4119   1.5033
 179  HO2  H  HOH1  0   0.459   2.4773   3.0122   0.5780

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
 179  C18  C17  aromatic  1.409  0.020  1.409
 179  C18  C9   aromatic  1.375  0.020  1.375
 179  C17  C16  aromatic  1.416  0.020  1.416
 179  C17  C12  aromatic  1.418  0.020  1.418
 179  C16  C15  aromatic  1.368  0.020  1.368
 179  C15  C14  aromatic  1.412  0.020  1.412
 179  C14  C13  aromatic  1.368  0.020  1.368
 179  C13  C12  aromatic  1.414  0.020  1.414
 179  C12  C11  aromatic  1.412  0.020  1.412
 179  C11  C10  aromatic  1.367  0.020  1.367
 179  C10  C9   aromatic  1.417  0.020  1.417
 179  C9   N2   single    1.399  0.020  1.399
 179  N2   C8   single    1.339  0.020  1.339
 179  C8   O8   double    1.217  0.020  1.217
 179  C8   C7   single    1.540  0.020  1.540
 179  C7   O7   double    1.217  0.020  1.217
 179  C7   N1   single    1.337  0.020  1.337
 179  N1   C1   single    1.428  0.020  1.428
 179  C1   O5   single    1.405  0.020  1.405
 179  C1   C2   single    1.530  0.020  1.530
 179  O5   C5   single    1.414  0.020  1.414
 179  C5   C6   single    1.514  0.020  1.514
 179  C5   C4   single    1.530  0.020  1.530
 179  C6   O6   single    1.407  0.020  1.407
 179  C4   O4   single    1.406  0.020  1.406
 179  C4   C3   single    1.524  0.020  1.524
 179  C3   O3   single    1.406  0.020  1.406
 179  C3   C2   single    1.523  0.020  1.523
 179  C2   O2   single    1.404  0.020  1.404
 179  C18  H18  single    0.930  0.020  1.080
 179  C16  H16  single    0.930  0.020  1.080
 179  C15  H15  single    0.930  0.020  1.080
 179  C14  H14  single    0.930  0.020  1.080
 179  C13  H13  single    0.930  0.020  1.080
 179  C11  H11  single    0.930  0.020  1.080
 179  C10  H10  single    0.930  0.020  1.080
 179  N2   HN2  single    0.860  0.020  1.020
 179  N1   HN1  single    0.860  0.020  1.020
 179  C1   H1   single    0.970  0.020  1.090
 179  C5   H5   single    0.970  0.020  1.090
 179  C6   H6   single    0.970  0.020  1.090
 179  C6   H6A  single    0.970  0.020  1.090
 179  O6   HO6  single    0.850  0.020  0.980
 179  C4   H4   single    0.970  0.020  1.090
 179  O4   HO4  single    0.850  0.020  0.980
 179  C3   H3   single    0.970  0.020  1.090
 179  O3   HO3  single    0.850  0.020  0.980
 179  C2   H2   single    0.970  0.020  1.090
 179  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
 179  H18  C18  C9   120.01  3.000
 179  H18  C18  C17  118.81  3.000
 179  C9   C18  C17  121.17  3.000
 179  C12  C17  C16  118.93  3.000
 179  C12  C17  C18  119.23  3.000
 179  C16  C17  C18  121.84  3.000
 179  H16  C16  C15  120.38  3.000
 179  H16  C16  C17  119.11  3.000
 179  C15  C16  C17  120.51  3.000
 179  H15  C15  C14  119.52  3.000
 179  H15  C15  C16  119.96  3.000
 179  C14  C15  C16  120.52  3.000
 179  H14  C14  C13  120.20  3.000
 179  H14  C14  C15  119.59  3.000
 179  C13  C14  C15  120.21  3.000
 179  H13  C13  C12  119.01  3.000
 179  H13  C13  C14  120.45  3.000
 179  C12  C13  C14  120.54  3.000
 179  C11  C12  C13  122.39  3.000
 179  C11  C12  C17  118.32  3.000
 179  C13  C12  C17  119.29  3.000
 179  H11  C11  C10  119.15  3.000
 179  H11  C11  C12  118.98  3.000
 179  C10  C11  C12  121.86  3.000
 179  H10  C10  C9   120.79  3.000
 179  H10  C10  C11  119.55  3.000
 179  C9   C10  C11  119.66  3.000
 179  N2   C9   C10  123.18  3.000
 179  N2   C9   C18  117.06  3.000
 179  C10  C9   C18  119.75  3.000
 179  HN2  N2   C8   114.66  3.000
 179  HN2  N2   C9   115.58  3.000
 179  C8   N2   C9   129.76  3.000
 179  C7   C8   O8   120.91  3.000
 179  C7   C8   N2   111.57  3.000
 179  O8   C8   N2   127.52  3.000
 179  N1   C7   O7   126.09  3.000
 179  N1   C7   C8   112.68  3.000
 179  O7   C7   C8   121.22  3.000
 179  HN1  N1   C1   118.70  3.000
 179  HN1  N1   C7   117.35  3.000
 179  C1   N1   C7   123.70  3.000
 179  H1   C1   C2   108.97  3.000
 179  H1   C1   O5   110.62  3.000
 179  C2   C1   O5   110.14  3.000
 179  H1   C1   N1   108.24  3.000
 179  C2   C1   N1   110.73  3.000
 179  O5   C1   N1   108.13  3.000
 179  C5   O5   C1   113.30  3.000
 179  H5   C5   C4   108.51  3.000
 179  H5   C5   C6   109.26  3.000
 179  C4   C5   C6   111.81  3.000
 179  H5   C5   O5   109.87  3.000
 179  C4   C5   O5   109.77  3.000
 179  C6   C5   O5   107.60  3.000
 179  H6A  C6   H6   107.10  3.000
 179  H6A  C6   O6   111.89  3.000
 179  H6   C6   O6   111.79  3.000
 179  H6A  C6   C5   108.74  3.000
 179  H6   C6   C5   108.40  3.000
 179  O6   C6   C5   108.81  3.000
 179  HO6  O6   C6   107.99  3.000
 179  H4   C4   C3   108.51  3.000
 179  H4   C4   O4   111.12  3.000
 179  C3   C4   O4   111.24  3.000
 179  H4   C4   C5   108.30  3.000
 179  C3   C4   C5   109.64  3.000
 179  O4   C4   C5   107.98  3.000
 179  HO4  O4   C4   108.20  3.000
 179  H3   C3   C2   107.89  3.000
 179  H3   C3   O3   110.86  3.000
 179  C2   C3   O3   112.03  3.000
 179  H3   C3   C4   107.65  3.000
 179  C2   C3   C4   110.78  3.000
 179  O3   C3   C4   107.56  3.000
 179  HO3  O3   C3   108.59  3.000
 179  H2   C2   O2   111.56  3.000
 179  H2   C2   C3   108.89  3.000
 179  O2   C2   C3   107.78  3.000
 179  H2   C2   C1   108.57  3.000
 179  O2   C2   C1   111.36  3.000
 179  C3   C2   C1   108.61  3.000
 179  HO2  O2   C2   109.18  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
 179  CONST_01  C15  C16  C17  C18  180.00  0.0  0
 179  CONST_02  C13  C12  C17  C18  180.00  0.0  0
 179  CONST_03  C11  C12  C17  C18    0.00  0.0  0
 179  CONST_04  C11  C10  C9   C18    0.00  0.0  0
 179  CONST_05  C10  C9   C18  C17    0.00  0.0  0
 179  CONST_06  C14  C15  C16  C17    0.00  0.0  0
 179  CONST_07  C14  C13  C12  C17    0.00  0.0  0
 179  CONST_08  C10  C11  C12  C17    0.00  0.0  0
 179  CONST_09  C9   C18  C17  C16  180.00  0.0  0
 179  CONST_10  C13  C12  C17  C16    0.00  0.0  0
 179  CONST_11  C11  C12  C17  C16  180.00  0.0  0
 179  CONST_12  C13  C14  C15  C16    0.00  0.0  0
 179  CONST_13  C12  C17  C16  C15    0.00  0.0  0
 179  CONST_14  C12  C13  C14  C15    0.00  0.0  0
 179  CONST_15  C11  C12  C13  C14  180.00  0.0  0
 179  CONST_16  C10  C11  C12  C13  180.00  0.0  0
 179  CONST_17  C9   C18  C17  C12    0.00  0.0  0
 179  CONST_18  C9   C10  C11  C12    0.00  0.0  0
 179  CONST_19  N2   C9   C18  C17  180.00  0.0  0
 179  CONST_20  N2   C9   C10  C11  180.00  0.0  0
 179  CONST_21  H16  C16  C17  C18    0.00  0.0  0
 179  CONST_22  H10  C10  C9   C18  180.00  0.0  0
 179  CONST_23  H15  C15  C16  C17  180.00  0.0  0
 179  CONST_24  H13  C13  C12  C17  180.00  0.0  0
 179  CONST_25  H11  C11  C12  C17  180.00  0.0  0
 179  CONST_26  H18  C18  C17  C16    0.00  0.0  0
 179  CONST_27  H14  C14  C15  C16  180.00  0.0  0
 179  CONST_28  C8   N2   C9   C18  180.00  0.0  0
 179  CONST_29  C8   N2   C9   C10    0.00  0.0  0
 179  CONST_30  HN2  N2   C9   C18    0.00  0.0  0
 179  CONST_31  O8   C8   N2   C9     0.00  0.0  0
 179  CONST_32  C7   C8   N2   C9   180.00  0.0  0
 179  CONST_33  C1   N1   C7   C8   180.00  0.0  0
 179  CONST_34  C1   N1   C7   O7     0.00  0.0  0
 179  CONST_35  N1   C7   C8   N2   180.00  0.0  0
 179  CONST_36  N1   C7   C8   O8     0.00  0.0  0
 179  CONST_37  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
 179  chir_01  C1  N1  O5  C2  positiv
 179  chir_02  C5  O5  C6  C4  positiv
 179  chir_03  C4  O4  C5  C3  positiv
 179  chir_04  C3  O3  C2  C4  positiv
 179  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
 179  plan-1  C18  0.020
 179  plan-1  C17  0.020
 179  plan-1  C16  0.020
 179  plan-1  C15  0.020
 179  plan-1  C14  0.020
 179  plan-1  C13  0.020
 179  plan-1  C12  0.020
 179  plan-1  C11  0.020
 179  plan-1  C10  0.020
 179  plan-1  C9   0.020
 179  plan-1  N2   0.020
 179  plan-1  H18  0.020
 179  plan-1  H16  0.020
 179  plan-1  H15  0.020
 179  plan-1  H14  0.020
 179  plan-1  H13  0.020
 179  plan-1  H11  0.020
 179  plan-1  H10  0.020
 179  plan-2  C9   0.020
 179  plan-2  N2   0.020
 179  plan-2  C8   0.020
 179  plan-2  O8   0.020
 179  plan-2  C7   0.020
 179  plan-2  O7   0.020
 179  plan-2  N1   0.020
 179  plan-2  C1   0.020
 179  plan-2  HN2  0.020
 179  plan-2  HN1  0.020

