# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:01:11 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-beta-D-glucopyranosyl-4-naphthalen-2-yl-1H-1,2,3-triazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)n2cc(nn2)c3ccc4ccccc4c3
#
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
 SKY  SKY  1-beta-D-glucopyranosyl-4-naphthalen-2-yl-1H-1,2,3-triazole  ligand  45  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SKY
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
 SKY  C10  C  CR16  0  -0.368  -3.5593   0.2810   0.7250
 SKY  C11  C  CR66  0   0.150  -4.9372   0.0762   0.4973
 SKY  C12  C  CR16  0  -0.316  -5.9044   0.3492   1.4941
 SKY  C13  C  CR16  0  -0.256  -7.2346   0.1436   1.2486
 SKY  C14  C  CR16  0  -0.259  -7.6614  -0.3452  -0.0046
 SKY  C15  C  CR16  0  -0.308  -6.7481  -0.6188  -0.9869
 SKY  C16  C  CR66  0   0.101  -5.3677  -0.4156  -0.7616
 SKY  C17  C  CR16  0  -0.293  -4.3934  -0.6855  -1.7515
 SKY  C18  C  CR16  0  -0.329  -3.0671  -0.4784  -1.5054
 SKY  C9   C  CR6   0   0.064  -2.6285   0.0127  -0.2497
 SKY  C8   C  CR5   0   0.152  -1.2062   0.2278  -0.0031
 SKY  C7   C  CR15  0  -0.057  -0.1234  -0.0053  -0.8156
 SKY  N3   N  N     0  -0.308  -0.7338   0.7327   1.1642
 SKY  N2   N  N     0  -0.086   0.5433   0.8176   1.1118
 SKY  N1   N  NR5   0  -0.330   0.9311   0.3804  -0.0770
 SKY  C1   C  CH1   0   0.223   2.3290   0.3093  -0.4223
 SKY  O5   O  O2    0  -0.479   2.8514  -0.8286   0.1922
 SKY  C5   C  CH1   0  -0.021   4.1908  -1.0973  -0.1876
 SKY  C6   C  CH2   0  -0.156   4.6031  -2.3929   0.4770
 SKY  O6   O  OH1   0  -0.669   3.7974  -3.4326  -0.0216
 SKY  C4   C  CH1   0   0.034   5.0900   0.0706   0.2235
 SKY  O4   O  OH1   0  -0.669   6.3863  -0.2021  -0.2435
 SKY  C3   C  CH1   0  -0.003   4.5508   1.3732  -0.3609
 SKY  O3   O  OH1   0  -0.669   5.3537   2.4188   0.1239
 SKY  C2   C  CH1   0  -0.035   3.0881   1.5612   0.0227
 SKY  O2   O  OH1   0  -0.662   2.5990   2.7075  -0.6207
 SKY  H10  H  HCR6  0   0.255  -3.2414   0.6562   1.6900
 SKY  H12  H  HCR6  0   0.256  -5.5750   0.7240   2.4556
 SKY  H13  H  HCR6  0   0.260  -7.9670   0.3563   2.0163
 SKY  H14  H  HCR6  0   0.260  -8.7165  -0.5020  -0.1863
 SKY  H15  H  HCR6  0   0.257  -7.0746  -0.9947  -1.9490
 SKY  H17  H  HCR6  0   0.260  -4.7133  -1.0616  -2.7156
 SKY  H18  H  HCR6  0   0.250  -2.3454  -0.6911  -2.2838
 SKY  H7   H  HCR5  0   0.319  -0.0179  -0.3952  -1.8137
 SKY  H1   H  HCH1  0   0.256   2.3716   0.2271  -1.5172
 SKY  H5   H  HCH1  0   0.234   4.2494  -1.2169  -1.2813
 SKY  H6   H  HCH2  0   0.215   5.6644  -2.5617   0.2674
 SKY  H6A  H  HCH2  0   0.202   4.5012  -2.2814   1.5650
 SKY  HO6  H  HOH1  0   0.458   4.0480  -4.2439   0.4289
 SKY  H4   H  HCH1  0   0.220   5.0715   0.1518   1.3220
 SKY  HO4  H  HOH1  0   0.457   6.9687   0.5062   0.0496
 SKY  H3   H  HCH1  0   0.221   4.6162   1.3047  -1.4589
 SKY  HO3  H  HOH1  0   0.458   5.1379   3.2211  -0.3619
 SKY  H2   H  HCH1  0   0.250   3.0192   1.6472   1.1142
 SKY  HO2  H  HOH1  0   0.461   1.8791   3.0773  -0.1007

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
 SKY  C9   C10  aromatic  1.374  0.020  1.374
 SKY  C10  C11  aromatic  1.412  0.020  1.412
 SKY  C10  H10  single    0.930  0.020  1.080
 SKY  C16  C11  aromatic  1.418  0.020  1.418
 SKY  C11  C12  aromatic  1.415  0.020  1.415
 SKY  C12  C13  aromatic  1.368  0.020  1.368
 SKY  C12  H12  single    0.930  0.020  1.080
 SKY  C14  C13  aromatic  1.411  0.020  1.411
 SKY  C13  H13  single    0.930  0.020  1.080
 SKY  C15  C14  aromatic  1.369  0.020  1.369
 SKY  C14  H14  single    0.930  0.020  1.080
 SKY  C16  C15  aromatic  1.413  0.020  1.413
 SKY  C15  H15  single    0.930  0.020  1.080
 SKY  C17  C16  aromatic  1.415  0.020  1.415
 SKY  C18  C17  aromatic  1.365  0.020  1.365
 SKY  C17  H17  single    0.930  0.020  1.080
 SKY  C18  C9   aromatic  1.418  0.020  1.418
 SKY  C18  H18  single    0.930  0.020  1.080
 SKY  C8   C9   single    1.459  0.020  1.459
 SKY  C7   C8   aromatic  1.374  0.020  1.374
 SKY  C8   N3   aromatic  1.357  0.020  1.357
 SKY  N1   C7   aromatic  1.344  0.020  1.344
 SKY  C7   H7   single    0.930  0.020  1.080
 SKY  N2   N3   aromatic  1.281  0.020  1.281
 SKY  N1   N2   aromatic  1.325  0.020  1.325
 SKY  C1   N1   single    1.442  0.020  1.442
 SKY  C2   C1   single    1.530  0.020  1.530
 SKY  C1   O5   single    1.395  0.020  1.395
 SKY  C1   H1   single    0.970  0.020  1.090
 SKY  C5   O5   single    1.418  0.020  1.418
 SKY  C4   C5   single    1.530  0.020  1.530
 SKY  C5   C6   single    1.513  0.020  1.513
 SKY  C5   H5   single    0.970  0.020  1.090
 SKY  O6   C6   single    1.407  0.020  1.407
 SKY  C6   H6   single    0.970  0.020  1.090
 SKY  C6   H6A  single    0.970  0.020  1.090
 SKY  O6   HO6  single    0.850  0.020  0.980
 SKY  O4   C4   single    1.405  0.020  1.405
 SKY  C3   C4   single    1.526  0.020  1.526
 SKY  C4   H4   single    0.970  0.020  1.090
 SKY  O4   HO4  single    0.850  0.020  0.980
 SKY  O3   C3   single    1.405  0.020  1.405
 SKY  C3   C2   single    1.524  0.020  1.524
 SKY  C3   H3   single    0.970  0.020  1.090
 SKY  O3   HO3  single    0.850  0.020  0.980
 SKY  O2   C2   single    1.403  0.020  1.403
 SKY  C2   H2   single    0.970  0.020  1.090
 SKY  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
 SKY  H10  C10  C9   120.06  3.000
 SKY  H10  C10  C11  118.72  3.000
 SKY  C9   C10  C11  121.23  3.000
 SKY  C16  C11  C12  118.98  3.000
 SKY  C12  C11  C10  121.70  3.000
 SKY  C16  C11  C10  119.32  3.000
 SKY  H12  C12  C13  120.46  3.000
 SKY  H12  C12  C11  118.95  3.000
 SKY  C13  C12  C11  120.60  3.000
 SKY  H13  C13  C14  119.56  3.000
 SKY  H13  C13  C12  120.08  3.000
 SKY  C14  C13  C12  120.36  3.000
 SKY  H14  C14  C15  120.07  3.000
 SKY  H14  C14  C13  119.61  3.000
 SKY  C15  C14  C13  120.31  3.000
 SKY  H15  C15  C16  119.06  3.000
 SKY  H15  C15  C14  120.37  3.000
 SKY  C16  C15  C14  120.56  3.000
 SKY  C17  C16  C15  122.25  3.000
 SKY  C17  C16  C11  118.56  3.000
 SKY  C15  C16  C11  119.19  3.000
 SKY  H17  C17  C18  120.01  3.000
 SKY  H17  C17  C16  119.05  3.000
 SKY  C18  C17  C16  120.94  3.000
 SKY  H18  C18  C9   119.91  3.000
 SKY  H18  C18  C17  119.23  3.000
 SKY  C9   C18  C17  120.85  3.000
 SKY  C8   C9   C18  120.14  3.000
 SKY  C8   C9   C10  120.76  3.000
 SKY  C18  C9   C10  119.10  3.000
 SKY  N3   C8   C7   107.31  3.000
 SKY  N3   C8   C9   122.65  3.000
 SKY  C7   C8   C9   130.03  3.000
 SKY  H7   C7   N1   122.44  3.000
 SKY  H7   C7   C8   133.39  3.000
 SKY  N1   C7   C8   104.16  3.000
 SKY  N2   N3   C8   109.67  3.000
 SKY  N1   N2   N3   107.86  3.000
 SKY  C1   N1   N2   121.00  3.000
 SKY  C1   N1   C7   127.95  3.000
 SKY  N2   N1   C7   110.99  3.000
 SKY  H1   C1   C2   109.38  3.000
 SKY  H1   C1   O5   111.31  3.000
 SKY  C2   C1   O5   110.70  3.000
 SKY  H1   C1   N1   106.25  3.000
 SKY  O5   C1   N1   107.33  3.000
 SKY  C2   C1   N1   111.78  3.000
 SKY  C5   O5   C1   112.98  3.000
 SKY  H5   C5   C4   108.56  3.000
 SKY  H5   C5   C6   109.17  3.000
 SKY  C4   C5   C6   112.04  3.000
 SKY  H5   C5   O5   109.68  3.000
 SKY  C6   C5   O5   107.58  3.000
 SKY  C4   C5   O5   109.79  3.000
 SKY  H6A  C6   H6   107.17  3.000
 SKY  H6A  C6   O6   111.90  3.000
 SKY  H6   C6   O6   111.93  3.000
 SKY  H6A  C6   C5   108.83  3.000
 SKY  H6   C6   C5   108.18  3.000
 SKY  O6   C6   C5   108.72  3.000
 SKY  HO6  O6   C6   107.96  3.000
 SKY  H4   C4   C3   108.24  3.000
 SKY  H4   C4   O4   111.18  3.000
 SKY  C3   C4   O4   111.37  3.000
 SKY  H4   C4   C5   108.32  3.000
 SKY  C3   C4   C5   109.94  3.000
 SKY  O4   C4   C5   107.75  3.000
 SKY  HO4  O4   C4   108.32  3.000
 SKY  H3   C3   C2   108.39  3.000
 SKY  H3   C3   O3   110.87  3.000
 SKY  C2   C3   O3   111.71  3.000
 SKY  H3   C3   C4   107.91  3.000
 SKY  C2   C3   C4   110.37  3.000
 SKY  O3   C3   C4   107.54  3.000
 SKY  HO3  O3   C3   108.55  3.000
 SKY  H2   C2   O2   111.74  3.000
 SKY  H2   C2   C3   108.69  3.000
 SKY  O2   C2   C3   108.67  3.000
 SKY  H2   C2   C1   108.80  3.000
 SKY  O2   C2   C1   111.24  3.000
 SKY  C3   C2   C1   107.58  3.000
 SKY  HO2  O2   C2   109.09  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
 SKY  CONST_01  C17  C18  C9   C10    0.00  0.0  0
 SKY  CONST_02  C7   C8   C9   C10  180.00  0.0  0
 SKY  CONST_03  N3   C8   C9   C10    0.00  0.0  0
 SKY  CONST_04  C15  C16  C11  C10  180.00  0.0  0
 SKY  CONST_05  C17  C16  C11  C10    0.00  0.0  0
 SKY  CONST_06  C13  C12  C11  C10  180.00  0.0  0
 SKY  CONST_07  C18  C9   C10  C11    0.00  0.0  0
 SKY  CONST_08  C8   C9   C10  C11  180.00  0.0  0
 SKY  CONST_09  C14  C15  C16  C11    0.00  0.0  0
 SKY  CONST_10  C18  C17  C16  C11    0.00  0.0  0
 SKY  CONST_11  C14  C13  C12  C11    0.00  0.0  0
 SKY  CONST_12  C9   C10  C11  C12  180.00  0.0  0
 SKY  CONST_13  C15  C16  C11  C12    0.00  0.0  0
 SKY  CONST_14  C17  C16  C11  C12  180.00  0.0  0
 SKY  CONST_15  C15  C14  C13  C12    0.00  0.0  0
 SKY  CONST_16  C16  C11  C12  C13    0.00  0.0  0
 SKY  CONST_17  C16  C15  C14  C13    0.00  0.0  0
 SKY  CONST_18  C17  C16  C15  C14  180.00  0.0  0
 SKY  CONST_19  C18  C17  C16  C15  180.00  0.0  0
 SKY  CONST_20  C9   C10  C11  C16    0.00  0.0  0
 SKY  CONST_21  C9   C18  C17  C16    0.00  0.0  0
 SKY  CONST_22  C8   C9   C18  C17  180.00  0.0  0
 SKY  CONST_23  C7   C8   C9   C18    0.00  0.0  0
 SKY  CONST_24  N3   C8   C9   C18  180.00  0.0  0
 SKY  CONST_25  N1   C7   C8   C9   180.00  0.0  0
 SKY  CONST_26  N2   N3   C8   C9   180.00  0.0  0
 SKY  CONST_27  N2   N1   C7   C8     0.00  0.0  0
 SKY  CONST_28  N1   N2   N3   C8     0.00  0.0  0
 SKY  CONST_29  N2   N3   C8   C7     0.00  0.0  0
 SKY  CONST_30  N3   N2   N1   C7     0.00  0.0  0
 SKY  CONST_31  N1   C7   C8   N3     0.00  0.0  0
 SKY  CONST_32  C1   N1   C7   C8   180.00  0.0  0
 SKY  CONST_33  C1   N1   N2   N3   180.00  0.0  0
 SKY  CONST_34  H18  C18  C9   C10  180.00  0.0  0
 SKY  CONST_35  H12  C12  C11  C10    0.00  0.0  0
 SKY  CONST_36  H15  C15  C16  C11  180.00  0.0  0
 SKY  CONST_37  H17  C17  C16  C11  180.00  0.0  0
 SKY  CONST_38  H13  C13  C12  C11  180.00  0.0  0
 SKY  CONST_39  H10  C10  C11  C12    0.00  0.0  0
 SKY  CONST_40  H14  C14  C13  C12  180.00  0.0  0
 SKY  CONST_41  H7   C7   C8   C9     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
 SKY  chir_01  C1  N1  C2  O5  negativ
 SKY  chir_02  C5  O5  C6  C4  positiv
 SKY  chir_03  C4  O4  C5  C3  positiv
 SKY  chir_04  C3  O3  C2  C4  positiv
 SKY  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
 SKY  plan-1  C9   0.020
 SKY  plan-1  C8   0.020
 SKY  plan-1  C7   0.020
 SKY  plan-1  N3   0.020
 SKY  plan-1  N2   0.020
 SKY  plan-1  N1   0.020
 SKY  plan-1  C1   0.020
 SKY  plan-1  H7   0.020
 SKY  plan-2  C10  0.020
 SKY  plan-2  C11  0.020
 SKY  plan-2  C12  0.020
 SKY  plan-2  C13  0.020
 SKY  plan-2  C14  0.020
 SKY  plan-2  C15  0.020
 SKY  plan-2  C16  0.020
 SKY  plan-2  C17  0.020
 SKY  plan-2  C18  0.020
 SKY  plan-2  C9   0.020
 SKY  plan-2  C8   0.020
 SKY  plan-2  H10  0.020
 SKY  plan-2  H12  0.020
 SKY  plan-2  H13  0.020
 SKY  plan-2  H14  0.020
 SKY  plan-2  H15  0.020
 SKY  plan-2  H17  0.020
 SKY  plan-2  H18  0.020

