# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:50:07 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol
#   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)c2[nH]nc(n2)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
 KS3  KS3  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol  ligand  45  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KS3
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
 KS3  O6'  O  OH1   0  -0.670   4.0151   3.4098  -0.1004
 KS3  C6'  C  CH2   0  -0.157   4.3892   2.3268  -0.9179
 KS3  C5'  C  CH1   0  -0.018   4.1588   1.0405  -0.1542
 KS3  C4'  C  CH1   0   0.040   4.6487  -0.1841  -0.9291
 KS3  O4'  O  OH1   0  -0.673   6.0386  -0.0678  -1.1013
 KS3  O5'  O  O2    0  -0.492   2.7682   0.9315   0.0828
 KS3  C1'  C  CH1   0  -0.060   2.4161  -0.1809   0.8633
 KS3  C2'  C  CH1   0   0.013   2.7988  -1.4786   0.1514
 KS3  O2'  O  OH1   0  -0.669   2.4486  -2.5387   1.0053
 KS3  C3'  C  CH1   0  -0.026   4.2902  -1.4507  -0.1592
 KS3  O3'  O  OH1   0  -0.674   4.6795  -2.5559  -0.9454
 KS3  C1   C  CR5   0   0.499   0.9427  -0.1198   1.0784
 KS3  N2   N  NR15  0  -0.469   0.3434  -0.0916   2.2690
 KS3  N3   N  N     0  -0.266  -0.9785  -0.0453   2.1302
 KS3  C4   C  CR5   0   0.309  -1.1351  -0.0418   0.8217
 KS3  N5   N  N     0  -0.473   0.0291  -0.0892   0.1359
 KS3  C6   C  CR6   0   0.012  -2.4429   0.0105   0.1676
 KS3  C7   C  CR16  0  -0.371  -3.6054   0.0443   0.8989
 KS3  C8   C  CR66  0   0.150  -4.8644   0.0953   0.2633
 KS3  C12  C  CR16  0  -0.315  -6.0712   0.1300   1.0028
 KS3  C13  C  CR16  0  -0.257  -7.2791   0.1794   0.3627
 KS3  C14  C  CR16  0  -0.257  -7.3389   0.1967  -1.0475
 KS3  C15  C  CR16  0  -0.307  -6.1887   0.1642  -1.7881
 KS3  C9   C  CR66  0   0.107  -4.9260   0.1128  -1.1542
 KS3  C10  C  CR16  0  -0.298  -3.7162   0.0776  -1.8858
 KS3  C11  C  CR16  0  -0.297  -2.5104   0.0278  -1.2471
 KS3  H1   H  HOH1  0   0.457   4.1881   4.2211  -0.5858
 KS3  H2   H  HCH2  0   0.199   3.8050   2.2950  -1.8481
 KS3  H3   H  HCH2  0   0.214   5.4455   2.3785  -1.2007
 KS3  H4   H  HCH1  0   0.225   4.7012   1.0877   0.8043
 KS3  H5   H  HCH1  0   0.212   4.1300  -0.2075  -1.9013
 KS3  H6   H  HOH1  0   0.453   6.3561  -0.8808  -1.5095
 KS3  H7   H  HCH1  0   0.254   2.9245  -0.1516   1.8400
 KS3  H8   H  HCH1  0   0.232   2.2388  -1.5248  -0.7926
 KS3  H9   H  HOH1  0   0.461   2.3509  -3.3396   0.4824
 KS3  H10  H  HCH1  0   0.223   4.8446  -1.4382   0.7915
 KS3  H11  H  HOH1  0   0.460   4.8784  -3.2959  -0.3649
 KS3  H12  H  HNR5  0   0.434   0.7627  -0.1026   3.1876
 KS3  H13  H  HCR6  0   0.252  -3.5695   0.0324   1.9817
 KS3  H14  H  HCR6  0   0.256  -6.0241   0.1175   2.0850
 KS3  H15  H  HCR6  0   0.260  -8.1957   0.2060   0.9374
 KS3  H16  H  HCR6  0   0.260  -8.3012   0.2365  -1.5412
 KS3  H17  H  HCR6  0   0.257  -6.2332   0.1772  -2.8705
 KS3  H18  H  HCR6  0   0.257  -3.7558   0.0903  -2.9683
 KS3  H19  H  HCR6  0   0.255  -1.5952   0.0012  -1.8230

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
 KS3  O3'  C3'  single    1.411  0.020  1.411
 KS3  O4'  C4'  single    1.405  0.020  1.405
 KS3  C3'  C4'  single    1.525  0.020  1.525
 KS3  C3'  C2'  single    1.524  0.020  1.524
 KS3  C4'  C5'  single    1.530  0.020  1.530
 KS3  O2'  C2'  single    1.406  0.020  1.406
 KS3  C2'  C1'  single    1.529  0.020  1.529
 KS3  O6'  C6'  single    1.408  0.020  1.408
 KS3  C5'  C6'  single    1.514  0.020  1.514
 KS3  C5'  O5'  single    1.415  0.020  1.415
 KS3  C1'  O5'  single    1.404  0.020  1.404
 KS3  C1'  C1   single    1.490  0.020  1.490
 KS3  N2   C1   aromatic  1.333  0.020  1.333
 KS3  N2   N3   aromatic  1.330  0.020  1.330
 KS3  C1   N5   aromatic  1.313  0.020  1.313
 KS3  N3   C4   aromatic  1.318  0.020  1.318
 KS3  N5   C4   aromatic  1.352  0.020  1.352
 KS3  C4   C6   single    1.463  0.020  1.463
 KS3  C6   C7   aromatic  1.374  0.020  1.374
 KS3  C6   C11  aromatic  1.416  0.020  1.416
 KS3  C7   C8   aromatic  1.411  0.020  1.411
 KS3  C11  C10  aromatic  1.365  0.020  1.365
 KS3  C8   C12  aromatic  1.416  0.020  1.416
 KS3  C8   C9   aromatic  1.419  0.020  1.419
 KS3  C12  C13  aromatic  1.368  0.020  1.368
 KS3  C10  C9   aromatic  1.414  0.020  1.414
 KS3  C9   C15  aromatic  1.414  0.020  1.414
 KS3  C13  C14  aromatic  1.412  0.020  1.412
 KS3  C15  C14  aromatic  1.368  0.020  1.368
 KS3  O6'  H1   single    0.850  0.020  0.980
 KS3  C6'  H2   single    0.970  0.020  1.090
 KS3  C6'  H3   single    0.970  0.020  1.090
 KS3  C5'  H4   single    0.970  0.020  1.090
 KS3  C4'  H5   single    0.970  0.020  1.090
 KS3  O4'  H6   single    0.850  0.020  0.980
 KS3  C1'  H7   single    0.970  0.020  1.090
 KS3  C2'  H8   single    0.970  0.020  1.090
 KS3  O2'  H9   single    0.850  0.020  0.980
 KS3  C3'  H10  single    0.970  0.020  1.090
 KS3  O3'  H11  single    0.850  0.020  0.980
 KS3  N2   H12  single    0.860  0.020  1.020
 KS3  C7   H13  single    0.930  0.020  1.080
 KS3  C12  H14  single    0.930  0.020  1.080
 KS3  C13  H15  single    0.930  0.020  1.080
 KS3  C14  H16  single    0.930  0.020  1.080
 KS3  C15  H17  single    0.930  0.020  1.080
 KS3  C10  H18  single    0.930  0.020  1.080
 KS3  C11  H19  single    0.930  0.020  1.080

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
 KS3  H1   O6'  C6'  107.96  3.000
 KS3  H3   C6'  H2   107.19  3.000
 KS3  H3   C6'  C5'  108.50  3.000
 KS3  H2   C6'  C5'  108.76  3.000
 KS3  H3   C6'  O6'  111.73  3.000
 KS3  H2   C6'  O6'  111.88  3.000
 KS3  C5'  C6'  O6'  108.69  3.000
 KS3  H4   C5'  O5'  109.96  3.000
 KS3  H4   C5'  C4'  108.49  3.000
 KS3  O5'  C5'  C4'  109.75  3.000
 KS3  H4   C5'  C6'  109.11  3.000
 KS3  O5'  C5'  C6'  107.43  3.000
 KS3  C4'  C5'  C6'  112.09  3.000
 KS3  H5   C4'  C3'  108.49  3.000
 KS3  H5   C4'  O4'  111.04  3.000
 KS3  C3'  C4'  O4'  111.29  3.000
 KS3  H5   C4'  C5'  108.25  3.000
 KS3  C3'  C4'  C5'  109.50  3.000
 KS3  O4'  C4'  C5'  108.21  3.000
 KS3  H6   O4'  C4'  107.94  3.000
 KS3  C1'  O5'  C5'  113.62  3.000
 KS3  H7   C1'  C1   109.10  3.000
 KS3  H7   C1'  C2'  108.66  3.000
 KS3  C1   C1'  C2'  110.46  3.000
 KS3  H7   C1'  O5'  110.86  3.000
 KS3  C1   C1'  O5'  107.20  3.000
 KS3  C2'  C1'  O5'  110.54  3.000
 KS3  H8   C2'  C3'  108.94  3.000
 KS3  H8   C2'  O2'  111.30  3.000
 KS3  C3'  C2'  O2'  112.43  3.000
 KS3  H8   C2'  C1'  107.95  3.000
 KS3  O2'  C2'  C1'  107.15  3.000
 KS3  C3'  C2'  C1'  108.93  3.000
 KS3  H9   O2'  C2'  108.85  3.000
 KS3  H10  C3'  O3'  110.57  3.000
 KS3  H10  C3'  C2'  108.49  3.000
 KS3  O3'  C3'  C2'  111.67  3.000
 KS3  H10  C3'  C4'  107.95  3.000
 KS3  C2'  C3'  C4'  110.38  3.000
 KS3  O3'  C3'  C4'  107.72  3.000
 KS3  H11  O3'  C3'  108.87  3.000
 KS3  N5   C1   N2   109.13  3.000
 KS3  N5   C1   C1'  125.83  3.000
 KS3  N2   C1   C1'  125.04  3.000
 KS3  H12  N2   N3   120.52  3.000
 KS3  H12  N2   C1   128.72  3.000
 KS3  N3   N2   C1   110.76  3.000
 KS3  C4   N3   N2   102.81  3.000
 KS3  C6   C4   N5   122.97  3.000
 KS3  C6   C4   N3   123.38  3.000
 KS3  N5   C4   N3   113.66  3.000
 KS3  C4   N5   C1   103.64  3.000
 KS3  C11  C6   C7   119.41  3.000
 KS3  C11  C6   C4   119.31  3.000
 KS3  C7   C6   C4   121.28  3.000
 KS3  H13  C7   C8   118.68  3.000
 KS3  H13  C7   C6   120.24  3.000
 KS3  C8   C7   C6   121.07  3.000
 KS3  C9   C8   C12  118.98  3.000
 KS3  C9   C8   C7   119.27  3.000
 KS3  C12  C8   C7   121.74  3.000
 KS3  H14  C12  C13  120.42  3.000
 KS3  H14  C12  C8   118.98  3.000
 KS3  C13  C12  C8   120.61  3.000
 KS3  H15  C13  C14  119.62  3.000
 KS3  H15  C13  C12  120.02  3.000
 KS3  C14  C13  C12  120.35  3.000
 KS3  H16  C14  C15  120.09  3.000
 KS3  H16  C14  C13  119.59  3.000
 KS3  C15  C14  C13  120.32  3.000
 KS3  H17  C15  C9   119.02  3.000
 KS3  H17  C15  C14  120.39  3.000
 KS3  C9   C15  C14  120.59  3.000
 KS3  C10  C9   C15  122.20  3.000
 KS3  C15  C9   C8   119.15  3.000
 KS3  C10  C9   C8   118.65  3.000
 KS3  H18  C10  C11  120.01  3.000
 KS3  H18  C10  C9   119.04  3.000
 KS3  C11  C10  C9   120.95  3.000
 KS3  H19  C11  C10  119.94  3.000
 KS3  H19  C11  C6   119.42  3.000
 KS3  C10  C11  C6   120.64  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
 KS3  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 KS3  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 KS3  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 KS3  CONST_04  C4   N5   C1   N2     0.00  0.0  0
 KS3  CONST_05  N5   C4   N3   N2     0.00  0.0  0
 KS3  CONST_06  C6   C4   N3   N2   180.00  0.0  0
 KS3  CONST_07  N5   C1   N2   N3     0.00  0.0  0
 KS3  CONST_08  C7   C6   C4   N3     0.00  0.0  0
 KS3  CONST_09  C11  C6   C4   N3   180.00  0.0  0
 KS3  CONST_10  C8   C7   C6   C4   180.00  0.0  0
 KS3  CONST_11  C10  C11  C6   C4   180.00  0.0  0
 KS3  CONST_12  C7   C6   C4   N5   180.00  0.0  0
 KS3  CONST_13  C11  C6   C4   N5     0.00  0.0  0
 KS3  CONST_14  C12  C8   C7   C6   180.00  0.0  0
 KS3  CONST_15  C9   C8   C7   C6     0.00  0.0  0
 KS3  CONST_16  C9   C10  C11  C6     0.00  0.0  0
 KS3  CONST_17  C10  C11  C6   C7     0.00  0.0  0
 KS3  CONST_18  C13  C12  C8   C7   180.00  0.0  0
 KS3  CONST_19  C10  C9   C8   C7     0.00  0.0  0
 KS3  CONST_20  C15  C9   C8   C7   180.00  0.0  0
 KS3  CONST_21  C11  C6   C7   C8     0.00  0.0  0
 KS3  CONST_22  C14  C13  C12  C8     0.00  0.0  0
 KS3  CONST_23  C11  C10  C9   C8     0.00  0.0  0
 KS3  CONST_24  C14  C15  C9   C8     0.00  0.0  0
 KS3  CONST_25  C10  C9   C8   C12  180.00  0.0  0
 KS3  CONST_26  C15  C9   C8   C12    0.00  0.0  0
 KS3  CONST_27  C15  C14  C13  C12    0.00  0.0  0
 KS3  CONST_28  C9   C8   C12  C13    0.00  0.0  0
 KS3  CONST_29  C9   C15  C14  C13    0.00  0.0  0
 KS3  CONST_30  C10  C9   C15  C14  180.00  0.0  0
 KS3  CONST_31  C11  C10  C9   C15  180.00  0.0  0
 KS3  CONST_32  N3   N2   C1   C1'  180.00  0.0  0
 KS3  CONST_33  C4   N5   C1   C1'  180.00  0.0  0
 KS3  CONST_34  H12  N2   C1   C1'    0.00  0.0  0
 KS3  CONST_35  H13  C7   C6   C4     0.00  0.0  0
 KS3  CONST_36  H19  C11  C6   C4     0.00  0.0  0
 KS3  CONST_37  H18  C10  C11  C6   180.00  0.0  0
 KS3  CONST_38  H14  C12  C8   C7     0.00  0.0  0
 KS3  CONST_39  H15  C13  C12  C8   180.00  0.0  0
 KS3  CONST_40  H17  C15  C9   C8   180.00  0.0  0
 KS3  CONST_41  H16  C14  C13  C12  180.00  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
 KS3  chir_01  C5'  C4'  C6'  O5'  negativ
 KS3  chir_02  C4'  O4'  C5'  C3'  positiv
 KS3  chir_03  C1'  O5'  C2'  C1   positiv
 KS3  chir_04  C2'  O2'  C1'  C3'  negativ
 KS3  chir_05  C3'  O3'  C2'  C4'  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
 KS3  plan-1  C1'  0.020
 KS3  plan-1  C1   0.020
 KS3  plan-1  N2   0.020
 KS3  plan-1  N3   0.020
 KS3  plan-1  C4   0.020
 KS3  plan-1  N5   0.020
 KS3  plan-1  C6   0.020
 KS3  plan-1  H12  0.020
 KS3  plan-2  C4   0.020
 KS3  plan-2  C6   0.020
 KS3  plan-2  C7   0.020
 KS3  plan-2  C8   0.020
 KS3  plan-2  C12  0.020
 KS3  plan-2  C13  0.020
 KS3  plan-2  C14  0.020
 KS3  plan-2  C15  0.020
 KS3  plan-2  C9   0.020
 KS3  plan-2  C10  0.020
 KS3  plan-2  C11  0.020
 KS3  plan-2  H13  0.020
 KS3  plan-2  H14  0.020
 KS3  plan-2  H15  0.020
 KS3  plan-2  H16  0.020
 KS3  plan-2  H17  0.020
 KS3  plan-2  H18  0.020
 KS3  plan-2  H19  0.020

