# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 03:00:55 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-methoxy-5-(4-pyridin-3-yl-1,2,3-triazol-1-yl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1n2cc(nn2)c3cccnc3
#
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
 UH8  UH8  "Methyl 2-deoxy-2-(4-(pyridine-3-yl))-1,2,3-triazol-1-yl)-alpha-D-mannopyranoside"  ligand  41  23  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UH8
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
 UH8  C1   C  CH1   0  -0.009  15.2173  -10.0789  25.1836
 UH8  C2   C  CH1   0   0.292  17.4452   -9.2041  25.2053
 UH8  C3   C  CH3   0  -0.413  17.7573   -9.1815  22.8715
 UH8  C4   C  CH1   0  -0.209  17.8352  -10.0542  26.4152
 UH8  C5   C  CR15  0  -0.084  16.8054   -8.4391  28.0883
 UH8  C6   C  CR5   0   0.150  17.2564   -8.0483  29.3262
 UH8  C7   C  CR6   0  -0.020  16.6474   -7.1354  30.2861
 UH8  N    N  NR5   0  -0.272  17.7571   -9.2765  27.6398
 UH8  C    C  CH2   0  -0.182  13.7982   -9.5529  25.1285
 UH8  O    O  OH1   0  -0.664  13.5223   -8.8231  26.2999
 UH8  C10  C  CR16  0  -0.305  14.9855   -5.5321  30.9238
 UH8  C11  C  CR16  0  -0.225  15.5181   -6.3825  29.9714
 UH8  C12  C  CH1   0   0.039  16.9687  -11.3215  26.4824
 UH8  C13  C  CH1   0   0.019  15.4851  -10.9861  26.3888
 UH8  C8   C  CR16  0  -0.082  17.1813   -6.9796  31.5662
 UH8  C9   C  CR16  0  -0.074  15.6006   -5.4545  32.1645
 UH8  N1   N  N     0  -0.394  16.6778   -6.1636  32.4809
 UH8  N2   N  N     0  -0.322  18.4365   -8.6720  29.5478
 UH8  N3   N  N     0  -0.080  18.7265   -9.4040  28.5349
 UH8  O1   O  O2    0  -0.500  16.0744   -8.9442  25.1971
 UH8  O2   O  O2    0  -0.491  17.8751   -9.8978  24.0859
 UH8  O3   O  OH1   0  -0.657  17.1708  -12.0326  27.6733
 UH8  O4   O  OH1   0  -0.667  14.7156  -12.1476  26.2004
 UH8  H    H  HCH1  0   0.245  15.3777  -10.6694  24.2709
 UH8  H1   H  HCH1  0   0.256  17.9229   -8.2162  25.2654
 UH8  H9   H  HCH3  0   0.242  18.2874   -9.7507  22.1107
 UH8  H8   H  HCH3  0   0.222  16.7178   -9.0635  22.5564
 UH8  H10  H  HCH3  0   0.217  18.2137   -8.1892  22.9462
 UH8  H2   H  HCH1  0   0.310  18.8863  -10.3343  26.3257
 UH8  H11  H  HCR5  0   0.321  15.9166   -8.1908  27.5355
 UH8  H6   H  HCH2  0   0.217  13.6996   -8.9316  24.2288
 UH8  H7   H  HCH2  0   0.213  13.1205  -10.4038  25.0024
 UH8  H5   H  HOH1  0   0.459  12.6092   -8.5249  26.2659
 UH8  H14  H  HCR6  0   0.273  14.1100   -4.9350  30.7091
 UH8  H15  H  HCR6  0   0.267  15.0591   -6.4524  28.9930
 UH8  H3   H  HCH1  0   0.241  17.2327  -11.9279  25.6063
 UH8  H4   H  HCH1  0   0.227  15.1822  -10.4705  27.3102
 UH8  H12  H  HCR6  0   0.262  18.0575   -7.5474  31.8588
 UH8  H13  H  HCR6  0   0.264  15.2089   -4.7949  32.9309
 UH8  H16  H  HOH1  0   0.459  18.0141  -12.4949  27.6273
 UH8  H17  H  HOH1  0   0.454  14.7785  -12.6861  26.9958

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
 UH8  C3   O2   single    1.415  0.020  1.415
 UH8  O2   C2   single    1.385  0.020  1.385
 UH8  C    C1   single    1.514  0.020  1.514
 UH8  C    O    single    1.407  0.020  1.407
 UH8  C1   O1   single    1.422  0.020  1.422
 UH8  C1   C13  single    1.532  0.020  1.532
 UH8  O1   C2   single    1.395  0.020  1.395
 UH8  C2   C4   single    1.529  0.020  1.529
 UH8  O4   C13  single    1.406  0.020  1.406
 UH8  C13  C12  single    1.524  0.020  1.524
 UH8  C4   C12  single    1.537  0.020  1.537
 UH8  C4   N    single    1.453  0.020  1.453
 UH8  C12  O3   single    1.402  0.020  1.402
 UH8  N    C5   aromatic  1.345  0.020  1.345
 UH8  N    N3   aromatic  1.326  0.020  1.326
 UH8  C5   C6   aromatic  1.374  0.020  1.374
 UH8  N3   N2   aromatic  1.283  0.020  1.283
 UH8  C6   N2   aromatic  1.353  0.020  1.353
 UH8  C6   C7   single    1.458  0.020  1.458
 UH8  C11  C7   aromatic  1.393  0.020  1.393
 UH8  C11  C10  aromatic  1.383  0.020  1.383
 UH8  C7   C8   aromatic  1.396  0.020  1.396
 UH8  C10  C9   aromatic  1.387  0.020  1.387
 UH8  C8   N1   aromatic  1.325  0.020  1.325
 UH8  C9   N1   aromatic  1.328  0.020  1.328
 UH8  C1   H    single    0.970  0.020  1.090
 UH8  C2   H1   single    0.970  0.020  1.090
 UH8  C3   H9   single    0.970  0.020  1.090
 UH8  C3   H8   single    0.970  0.020  1.090
 UH8  C3   H10  single    0.970  0.020  1.090
 UH8  C4   H2   single    0.970  0.020  1.090
 UH8  C5   H11  single    0.930  0.020  1.080
 UH8  C    H6   single    0.970  0.020  1.090
 UH8  C    H7   single    0.970  0.020  1.090
 UH8  O    H5   single    0.850  0.020  0.980
 UH8  C10  H14  single    0.930  0.020  1.080
 UH8  C11  H15  single    0.930  0.020  1.080
 UH8  C12  H3   single    0.970  0.020  1.090
 UH8  C13  H4   single    0.970  0.020  1.090
 UH8  C8   H12  single    0.930  0.020  1.080
 UH8  C9   H13  single    0.930  0.020  1.080
 UH8  O3   H16  single    0.850  0.020  0.980
 UH8  O4   H17  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
 UH8  H    C1   O1   110.41  3.000
 UH8  H    C1   C13  108.04  3.000
 UH8  O1   C1   C13  111.08  3.000
 UH8  H    C1   C    107.05  3.000
 UH8  C13  C1   C    113.46  3.000
 UH8  O1   C1   C    106.73  3.000
 UH8  H1   C2   O2   111.06  3.000
 UH8  H1   C2   O1   105.07  3.000
 UH8  O2   C2   O1   113.17  3.000
 UH8  H1   C2   C4   110.22  3.000
 UH8  O1   C2   C4   111.02  3.000
 UH8  O2   C2   C4   106.37  3.000
 UH8  H10  C3   H8   108.57  3.000
 UH8  H10  C3   H9   108.59  3.000
 UH8  H8   C3   H9   108.57  3.000
 UH8  H10  C3   O2   111.44  3.000
 UH8  H8   C3   O2   112.42  3.000
 UH8  H9   C3   O2   107.14  3.000
 UH8  H2   C4   C12  109.57  3.000
 UH8  H2   C4   N    104.97  3.000
 UH8  C12  C4   N    111.99  3.000
 UH8  H2   C4   C2   108.87  3.000
 UH8  N    C4   C2   110.83  3.000
 UH8  C12  C4   C2   110.44  3.000
 UH8  H11  C5   N    123.86  3.000
 UH8  H11  C5   C6   131.94  3.000
 UH8  N    C5   C6   104.20  3.000
 UH8  N2   C6   C7   123.03  3.000
 UH8  C7   C6   C5   129.35  3.000
 UH8  N2   C6   C5   107.62  3.000
 UH8  C8   C7   C11  117.18  3.000
 UH8  C8   C7   C6   120.94  3.000
 UH8  C11  C7   C6   121.88  3.000
 UH8  N3   N    C5   110.63  3.000
 UH8  N3   N    C4   118.58  3.000
 UH8  C5   N    C4   130.74  3.000
 UH8  H7   C    H6   106.85  3.000
 UH8  H7   C    O    112.17  3.000
 UH8  H6   C    O    111.78  3.000
 UH8  H7   C    C1   108.31  3.000
 UH8  H6   C    C1   108.10  3.000
 UH8  O    C    C1   109.48  3.000
 UH8  H5   O    C    108.52  3.000
 UH8  H14  C10  C9   120.38  3.000
 UH8  H14  C10  C11  120.96  3.000
 UH8  C9   C10  C11  118.65  3.000
 UH8  H15  C11  C10  119.90  3.000
 UH8  H15  C11  C7   120.84  3.000
 UH8  C10  C11  C7   119.26  3.000
 UH8  H3   C12  O3   111.30  3.000
 UH8  H3   C12  C13  107.86  3.000
 UH8  O3   C12  C13  107.71  3.000
 UH8  H3   C12  C4   106.57  3.000
 UH8  O3   C12  C4   111.97  3.000
 UH8  C13  C12  C4   111.39  3.000
 UH8  H4   C13  O4   110.45  3.000
 UH8  H4   C13  C12  108.68  3.000
 UH8  O4   C13  C12  111.05  3.000
 UH8  H4   C13  C1   109.49  3.000
 UH8  C12  C13  C1   110.41  3.000
 UH8  O4   C13  C1   106.75  3.000
 UH8  H12  C8   N1   116.31  3.000
 UH8  H12  C8   C7   119.87  3.000
 UH8  N1   C8   C7   123.82  3.000
 UH8  H13  C9   N1   116.70  3.000
 UH8  H13  C9   C10  120.41  3.000
 UH8  N1   C9   C10  122.89  3.000
 UH8  C9   N1   C8   118.20  3.000
 UH8  N3   N2   C6   109.32  3.000
 UH8  N2   N3   N    108.23  3.000
 UH8  C2   O1   C1   116.33  3.000
 UH8  C3   O2   C2   114.47  3.000
 UH8  H16  O3   C12  109.23  3.000
 UH8  H17  O4   C13  108.40  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
 UH8  CONST_01  N2   N3   N    C5     0.00   0.0  0
 UH8  CONST_02  N3   N2   C6   C5     0.00   0.0  0
 UH8  CONST_03  C11  C7   C6   C5     0.00   0.0  0
 UH8  CONST_04  C8   C7   C6   C5   180.00   0.0  0
 UH8  CONST_05  N3   N    C5   C6     0.00   0.0  0
 UH8  CONST_06  N    N3   N2   C6     0.00   0.0  0
 UH8  CONST_07  C10  C11  C7   C6   180.00   0.0  0
 UH8  CONST_08  N1   C8   C7   C6   180.00   0.0  0
 UH8  CONST_09  N    C5   C6   C7   180.00   0.0  0
 UH8  CONST_10  N3   N2   C6   C7   180.00   0.0  0
 UH8  CONST_11  C9   C10  C11  C7     0.00   0.0  0
 UH8  CONST_12  C9   N1   C8   C7     0.00   0.0  0
 UH8  CONST_13  N2   C6   C5   N      0.00   0.0  0
 UH8  CONST_14  C8   C7   C11  C10    0.00   0.0  0
 UH8  CONST_15  C8   N1   C9   C10    0.00   0.0  0
 UH8  CONST_16  N2   C6   C7   C11  180.00   0.0  0
 UH8  CONST_17  N1   C8   C7   C11    0.00   0.0  0
 UH8  CONST_18  N1   C9   C10  C11    0.00   0.0  0
 UH8  CONST_19  N2   C6   C7   C8     0.00   0.0  0
 UH8  CONST_20  C6   C5   N    C4   180.00   0.0  0
 UH8  CONST_21  N2   N3   N    C4   180.00   0.0  0
 UH8  CONST_22  H11  C5   N    C4     0.00   0.0  0
 UH8  CONST_23  H15  C11  C7   C6     0.00   0.0  0
 UH8  CONST_24  H12  C8   C7   C6     0.00   0.0  0
 UH8  CONST_25  H11  C5   C6   C7     0.00   0.0  0
 UH8  CONST_26  H14  C10  C11  C7   180.00   0.0  0
 UH8  CONST_27  H12  C8   C7   C11  180.00   0.0  0
 UH8  CONST_28  H13  C9   C10  C11  180.00   0.0  0
 UH8  CONST_29  H15  C11  C7   C8   180.00   0.0  0
 UH8  CONST_30  H13  C9   N1   C8   180.00   0.0  0
 UH8  CONST_31  H15  C11  C10  C9   180.00   0.0  0
 UH8  CONST_32  H12  C8   N1   C9   180.00   0.0  0
 UH8  CONST_33  H14  C10  C9   N1   180.00   0.0  0
 UH8  CONST_34  H11  C5   C6   N2   180.00   0.0  0
 UH8  CONST_35  H11  C5   N    N3   180.00   0.0  0
 UH8  Var_01    H9   C3   O2   C2   169.83  30.0  3
 UH8  Var_02    H8   C3   O2   C2   -70.97  30.0  3
 UH8  Var_03    H10  C3   O2   C2    51.18  30.0  3

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
 UH8  chir_01  C1   C   O1   C13  negativ
 UH8  chir_02  C2   O2  O1   C4   negativ
 UH8  chir_03  C4   N   C12  C2   negativ
 UH8  chir_04  C12  O3  C4   C13  positiv
 UH8  chir_05  C13  O4  C1   C12  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
 UH8  plan-1  C4   0.020
 UH8  plan-1  C5   0.020
 UH8  plan-1  C6   0.020
 UH8  plan-1  C7   0.020
 UH8  plan-1  N    0.020
 UH8  plan-1  N2   0.020
 UH8  plan-1  N3   0.020
 UH8  plan-1  H11  0.020
 UH8  plan-2  C6   0.020
 UH8  plan-2  C7   0.020
 UH8  plan-2  C10  0.020
 UH8  plan-2  C11  0.020
 UH8  plan-2  C8   0.020
 UH8  plan-2  C9   0.020
 UH8  plan-2  N1   0.020
 UH8  plan-2  H14  0.020
 UH8  plan-2  H15  0.020
 UH8  plan-2  H12  0.020
 UH8  plan-2  H13  0.020

