# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 10:19:56 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-phenyl-4~{H}-1,2,4-triazol-3-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]c(nn2)c3ccccc3
#
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
 73E  73E  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-phenyl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4,5-triol  D-saccharide  39  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_73E
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
 73E  O3'  O  OH1   0  -0.674  -3.9845   2.5270   0.0861
 73E  C3'  C  CH1   0  -0.020  -3.2513   1.3825   0.4614
 73E  C4'  C  CH1   0   0.036  -3.9829   0.1621  -0.0868
 73E  O4'  O  OH1   0  -0.672  -5.2532   0.0209   0.4975
 73E  C2'  C  CH1   0   0.014  -1.8226   1.4230  -0.0685
 73E  O2'  O  OH1   0  -0.670  -1.0615   2.4414   0.5311
 73E  C1'  C  CH1   0  -0.056  -1.1428   0.0926   0.2553
 73E  O5'  O  O2    0  -0.492  -1.8661  -0.9727  -0.3059
 73E  C5'  C  CH1   0  -0.017  -3.1746  -1.1001   0.2184
 73E  C6'  C  CH2   0  -0.157  -3.7954  -2.3347  -0.3992
 73E  O6'  O  OH1   0  -0.670  -3.0468  -3.4614  -0.0104
 73E  C1   C  CR5   0   0.431   0.2402   0.0521  -0.2977
 73E  N5   N  NR15  0  -0.675   1.3570  -0.0237   0.4551
 73E  C4   C  CR5   0   0.440   2.3923  -0.0238  -0.4184
 73E  N3   N  N     0  -0.332   1.9159   0.0455  -1.6353
 73E  N2   N  N     0  -0.317   0.5681   0.0954  -1.5580
 73E  C6   C  CR6   0   0.027   3.8037  -0.0883  -0.0536
 73E  C7   C  CR16  0  -0.284   4.7690  -0.1514  -1.0601
 73E  C8   C  CR16  0  -0.239   6.1137  -0.2113  -0.7346
 73E  C9   C  CR16  0  -0.256   6.5143  -0.2088   0.5963
 73E  C10  C  CR16  0  -0.237   5.5590  -0.1456   1.6011
 73E  C11  C  CR16  0  -0.306   4.2111  -0.0854   1.2797
 73E  H1   H  HOH1  0   0.460  -3.7933   3.2373   0.7058
 73E  H2   H  HCH1  0   0.220  -3.2099   1.2903   1.5577
 73E  H3   H  HCH1  0   0.214  -4.0596   0.2659  -1.1816
 73E  H4   H  HOH1  0   0.454  -5.7478   0.8300   0.3293
 73E  H5   H  HCH1  0   0.231  -1.8477   1.5342  -1.1612
 73E  H6   H  HOH1  0   0.462  -1.2165   3.2642   0.0586
 73E  H7   H  HCH1  0   0.254  -1.0827  -0.0111   1.3508
 73E  H8   H  HCH1  0   0.224  -3.1271  -1.2302   1.3120
 73E  H9   H  HCH2  0   0.216  -4.8351  -2.4034  -0.0637
 73E  H10  H  HCH2  0   0.197  -3.8158  -2.2148  -1.4915
 73E  H11  H  HOH1  0   0.457  -3.5078  -4.2452  -0.3216
 73E  H12  H  HNR5  0   0.438   1.3948  -0.0789   1.4617
 73E  H13  H  HCR6  0   0.259   4.4633  -0.1547  -2.0979
 73E  H14  H  HCR6  0   0.264   6.8526  -0.2613  -1.5231
 73E  H15  H  HCR6  0   0.264   7.5659  -0.2557   0.8469
 73E  H16  H  HCR6  0   0.265   5.8598  -0.1424   2.6404
 73E  H17  H  HCR6  0   0.249   3.4880  -0.0343   2.0838

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
 73E  O3'  C3'  single    1.410  0.020  1.410
 73E  O4'  C4'  single    1.405  0.020  1.405
 73E  C3'  C4'  single    1.525  0.020  1.525
 73E  C3'  C2'  single    1.524  0.020  1.524
 73E  C4'  C5'  single    1.530  0.020  1.530
 73E  O2'  C2'  single    1.406  0.020  1.406
 73E  C2'  C1'  single    1.529  0.020  1.529
 73E  O6'  C6'  single    1.408  0.020  1.408
 73E  C5'  C6'  single    1.514  0.020  1.514
 73E  C5'  O5'  single    1.415  0.020  1.415
 73E  C1'  O5'  single    1.405  0.020  1.405
 73E  C1'  C1   single    1.490  0.020  1.490
 73E  N2   C1   aromatic  1.303  0.020  1.303
 73E  N2   N3   aromatic  1.351  0.020  1.351
 73E  C1   N5   aromatic  1.349  0.020  1.349
 73E  N3   C4   aromatic  1.309  0.020  1.309
 73E  N5   C4   aromatic  1.355  0.020  1.355
 73E  C4   C6   single    1.459  0.020  1.459
 73E  C6   C7   aromatic  1.396  0.020  1.396
 73E  C6   C11  aromatic  1.394  0.020  1.394
 73E  C7   C8   aromatic  1.385  0.020  1.385
 73E  C11  C10  aromatic  1.387  0.020  1.387
 73E  C8   C9   aromatic  1.390  0.020  1.390
 73E  C10  C9   aromatic  1.388  0.020  1.388
 73E  O3'  H1   single    0.850  0.020  0.980
 73E  C3'  H2   single    0.970  0.020  1.090
 73E  C4'  H3   single    0.970  0.020  1.090
 73E  O4'  H4   single    0.850  0.020  0.980
 73E  C2'  H5   single    0.970  0.020  1.090
 73E  O2'  H6   single    0.850  0.020  0.980
 73E  C1'  H7   single    0.970  0.020  1.090
 73E  C5'  H8   single    0.970  0.020  1.090
 73E  C6'  H9   single    0.970  0.020  1.090
 73E  C6'  H10  single    0.970  0.020  1.090
 73E  O6'  H11  single    0.850  0.020  0.980
 73E  N5   H12  single    0.860  0.020  1.020
 73E  C7   H13  single    0.930  0.020  1.080
 73E  C8   H14  single    0.930  0.020  1.080
 73E  C9   H15  single    0.930  0.020  1.080
 73E  C10  H16  single    0.930  0.020  1.080
 73E  C11  H17  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
 73E  H1   O3'  C3'  108.94  3.000
 73E  H2   C3'  C2'  108.25  3.000
 73E  H2   C3'  C4'  108.00  3.000
 73E  C2'  C3'  C4'  110.24  3.000
 73E  H2   C3'  O3'  110.64  3.000
 73E  C2'  C3'  O3'  111.92  3.000
 73E  C4'  C3'  O3'  107.73  3.000
 73E  H3   C4'  C5'  108.22  3.000
 73E  H3   C4'  O4'  111.07  3.000
 73E  C5'  C4'  O4'  108.17  3.000
 73E  H3   C4'  C3'  108.36  3.000
 73E  C5'  C4'  C3'  109.58  3.000
 73E  O4'  C4'  C3'  111.38  3.000
 73E  H4   O4'  C4'  107.89  3.000
 73E  H5   C2'  C1'  107.99  3.000
 73E  H5   C2'  O2'  111.30  3.000
 73E  C1'  C2'  O2'  107.42  3.000
 73E  H5   C2'  C3'  109.09  3.000
 73E  C1'  C2'  C3'  108.67  3.000
 73E  O2'  C2'  C3'  112.24  3.000
 73E  H6   O2'  C2'  108.85  3.000
 73E  H7   C1'  C1   108.41  3.000
 73E  H7   C1'  O5'  110.72  3.000
 73E  C1   C1'  O5'  108.00  3.000
 73E  H7   C1'  C2'  108.46  3.000
 73E  C1   C1'  C2'  110.97  3.000
 73E  O5'  C1'  C2'  110.27  3.000
 73E  C5'  O5'  C1'  113.35  3.000
 73E  H8   C5'  C6'  109.03  3.000
 73E  H8   C5'  O5'  109.77  3.000
 73E  C6'  C5'  O5'  107.55  3.000
 73E  H8   C5'  C4'  108.55  3.000
 73E  O5'  C5'  C4'  109.90  3.000
 73E  C6'  C5'  C4'  112.02  3.000
 73E  H10  C6'  H9   107.09  3.000
 73E  H10  C6'  O6'  111.82  3.000
 73E  H9   C6'  O6'  111.73  3.000
 73E  H10  C6'  C5'  108.92  3.000
 73E  H9   C6'  C5'  108.40  3.000
 73E  O6'  C6'  C5'  108.79  3.000
 73E  H11  O6'  C6'  107.96  3.000
 73E  N2   C1   N5   109.47  3.000
 73E  N5   C1   C1'  124.25  3.000
 73E  N2   C1   C1'  126.27  3.000
 73E  H12  N5   C4   127.94  3.000
 73E  H12  N5   C1   126.22  3.000
 73E  C4   N5   C1   105.83  3.000
 73E  C6   C4   N3   125.94  3.000
 73E  C6   C4   N5   125.31  3.000
 73E  N3   C4   N5   108.75  3.000
 73E  N2   N3   C4   108.18  3.000
 73E  N3   N2   C1   107.77  3.000
 73E  C11  C6   C7   119.17  3.000
 73E  C11  C6   C4   121.45  3.000
 73E  C7   C6   C4   119.38  3.000
 73E  H13  C7   C8   119.98  3.000
 73E  H13  C7   C6   119.76  3.000
 73E  C8   C7   C6   120.26  3.000
 73E  H14  C8   C9   120.08  3.000
 73E  H14  C8   C7   119.60  3.000
 73E  C9   C8   C7   120.32  3.000
 73E  H15  C9   C10  120.21  3.000
 73E  H15  C9   C8   120.12  3.000
 73E  C10  C9   C8   119.66  3.000
 73E  H16  C10  C11  119.51  3.000
 73E  H16  C10  C9   120.28  3.000
 73E  C11  C10  C9   120.21  3.000
 73E  H17  C11  C10  118.62  3.000
 73E  H17  C11  C6   121.01  3.000
 73E  C10  C11  C6   120.37  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
 73E  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 73E  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 73E  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 73E  CONST_04  N3   N2   C1   N5     0.00  0.0  0
 73E  CONST_05  N2   N3   C4   N5     0.00  0.0  0
 73E  CONST_06  C7   C6   C4   N5   180.00  0.0  0
 73E  CONST_07  C11  C6   C4   N5     0.00  0.0  0
 73E  CONST_08  N2   C1   N5   C4     0.00  0.0  0
 73E  CONST_09  C8   C7   C6   C4   180.00  0.0  0
 73E  CONST_10  C10  C11  C6   C4   180.00  0.0  0
 73E  CONST_11  C7   C6   C4   N3     0.00  0.0  0
 73E  CONST_12  C11  C6   C4   N3   180.00  0.0  0
 73E  CONST_13  C6   C4   N3   N2   180.00  0.0  0
 73E  CONST_14  C9   C8   C7   C6     0.00  0.0  0
 73E  CONST_15  C9   C10  C11  C6     0.00  0.0  0
 73E  CONST_16  C10  C11  C6   C7     0.00  0.0  0
 73E  CONST_17  C10  C9   C8   C7     0.00  0.0  0
 73E  CONST_18  C11  C6   C7   C8     0.00  0.0  0
 73E  CONST_19  C11  C10  C9   C8     0.00  0.0  0
 73E  CONST_20  N3   N2   C1   C1'  180.00  0.0  0
 73E  CONST_21  C4   N5   C1   C1'  180.00  0.0  0
 73E  CONST_22  H12  N5   C1   C1'    0.00  0.0  0
 73E  CONST_23  H13  C7   C6   C4     0.00  0.0  0
 73E  CONST_24  H17  C11  C6   C4     0.00  0.0  0
 73E  CONST_25  H14  C8   C7   C6   180.00  0.0  0
 73E  CONST_26  H16  C10  C11  C6   180.00  0.0  0
 73E  CONST_27  H15  C9   C8   C7   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
 73E  chir_01  C3'  O3'  C4'  C2'  negativ
 73E  chir_02  C4'  O4'  C5'  C3'  positiv
 73E  chir_03  C2'  O2'  C3'  C1'  positiv
 73E  chir_04  C1'  O5'  C2'  C1   positiv
 73E  chir_05  C5'  O5'  C6'  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
 73E  plan-1  C1'  0.020
 73E  plan-1  C1   0.020
 73E  plan-1  N5   0.020
 73E  plan-1  C4   0.020
 73E  plan-1  N3   0.020
 73E  plan-1  N2   0.020
 73E  plan-1  C6   0.020
 73E  plan-1  H12  0.020
 73E  plan-2  C4   0.020
 73E  plan-2  C6   0.020
 73E  plan-2  C7   0.020
 73E  plan-2  C8   0.020
 73E  plan-2  C9   0.020
 73E  plan-2  C10  0.020
 73E  plan-2  C11  0.020
 73E  plan-2  H13  0.020
 73E  plan-2  H14  0.020
 73E  plan-2  H15  0.020
 73E  plan-2  H16  0.020
 73E  plan-2  H17  0.020

