# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 12:06:15 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{S},6~{S})-6-(3-azanylpropoxy)-2-(hydroxymethyl)-5-(4-phenyl-1,2,3-triazol-1-yl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1n2cc(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
 UH5  UH5  "3-Aminopropyl 2-deoxy-2-(4-phenyl-1,2,3-triazol-1-yl)-alpha-D-mannopyranoside"  ligand  50  26  .  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_UH5
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
 UH5  N1   N  NR5   0  -0.275  17.7516   -9.3970  27.6736
 UH5  C7   C  CR16  0   0.060  16.8054  -11.4144  26.5916
 UH5  C8   C  CR16  0  -0.194  17.7021  -10.1849  26.4536
 UH5  N2   N  N     0  -0.320  18.6458   -8.7373  29.4701
 UH5  C9   C  CR15  0  -0.087  16.8429   -8.5700  28.2214
 UH5  O1   O  O     0  -0.500  15.8933   -9.0123  25.3651
 UH5  C1   C  CH2   0  -0.471  17.7787  -10.1948  21.7534
 UH5  C5   C  CH2   0  -0.193  13.6007   -9.5746  25.4184
 UH5  C6   C  CR16  0  -0.013  15.3283  -11.0388  26.5870
 UH5  N3   N  N     0  -0.081  18.8276   -9.4833  28.4421
 UH5  C4   C  CR16  0  -0.017  15.0094  -10.1270  25.3950
 UH5  C3   C  CR16  0   0.298  17.2517   -9.3207  25.2726
 UH5  O3   O  OH1   0  -0.670  14.6042  -12.2461  26.4951
 UH5  N    N  NH2   0  -0.797  17.1941  -12.1746  20.4377
 UH5  C    C  CH2   0  -0.271  16.8573  -11.4001  21.6221
 UH5  O    O  O2    0  -0.497  17.5684  -10.0266  24.1247
 UH5  C10  C  CR5   0   0.155  17.4320   -8.1447  29.3885
 UH5  C11  C  CR6   0   0.064  16.9275   -7.2246  30.4050
 UH5  C12  C  CR16  0  -0.289  17.6549   -6.9892  31.5725
 UH5  C13  C  CR16  0  -0.237  17.1788   -6.1114  32.5345
 UH5  C14  C  CR16  0  -0.264  15.9704   -5.4530  32.3481
 UH5  C15  C  CR16  0  -0.233  15.2396   -5.6829  31.1896
 UH5  C16  C  CR16  0  -0.337  15.7132   -6.5603  30.2267
 UH5  O2   O  OH1   0  -0.663  13.4015   -8.8452  26.6049
 UH5  H15  H  HCR6  0   0.235  16.9915  -12.0322  25.7007
 UH5  H17  H  HCR6  0   0.311  18.7319  -10.5026  26.2845
 UH5  H18  H  HCR5  0   0.316  15.8928   -8.3440  27.7702
 UH5  H5   H  HCH2  0   0.227  18.8177  -10.5259  21.8327
 UH5  H4   H  HCH2  0   0.229  17.7127   -9.5880  20.8448
 UH5  H10  H  HCH2  0   0.221  13.4589   -8.9511  24.5263
 UH5  H11  H  HCH2  0   0.210  12.9020  -10.4149  25.3271
 UH5  H13  H  HCR6  0   0.236  15.0894  -10.5254  27.5259
 UH5  H9   H  HCR6  0   0.245  15.1042  -10.7203  24.4746
 UH5  H8   H  HCR6  0   0.255  17.7701   -8.3525  25.2988
 UH5  H14  H  HOH1  0   0.461  13.7517  -12.1377  26.9261
 UH5  H7   H  HCH2  0   0.228  18.0772   -8.4146  22.9341
 UH5  H6   H  HCH2  0   0.215  16.3943   -8.9338  22.8000
 UH5  H24  H  HNH2  0   0.345  16.6167  -13.0048  20.4017
 UH5  H1   H  HNH2  0   0.337  16.9574  -11.6413  19.6098
 UH5  H3   H  HCH2  0   0.187  15.8143  -11.0482  21.6374
 UH5  H2   H  HCH2  0   0.220  16.9744  -12.0465  22.4942
 UH5  H19  H  HCR6  0   0.252  18.5983   -7.4953  31.7311
 UH5  H20  H  HCR6  0   0.256  17.7561   -5.9415  33.4341
 UH5  H21  H  HCR6  0   0.256  15.6008   -4.7673  33.0992
 UH5  H22  H  HCR6  0   0.257  14.2966   -5.1755  31.0325
 UH5  H23  H  HCR6  0   0.250  15.1287   -6.7212  29.3291
 UH5  H12  H  HOH1  0   0.460  12.4877   -8.5483  26.6318
 UH5  O4   O  OH1   0  -0.657  17.1732  -12.0921  27.7616
 UH5  C2   C  CH2   0  -0.172  17.4225   -9.2950  22.9153
 UH5  H16  H  HOH1  0   0.454  16.6221  -12.8792  27.8307

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
 UH5  N    C    single    1.455  0.020  1.455
 UH5  C1   C    single    1.523  0.020  1.523
 UH5  C1   C2   single    1.512  0.020  1.512
 UH5  C2   O    single    1.421  0.020  1.421
 UH5  O    C3   single    1.384  0.020  1.384
 UH5  C5   C4   single    1.513  0.020  1.513
 UH5  C5   O2   single    1.407  0.020  1.407
 UH5  C4   O1   single    1.423  0.020  1.423
 UH5  C4   C6   single    1.534  0.020  1.534
 UH5  C3   O1   single    1.396  0.020  1.396
 UH5  C3   C8   single    1.531  0.020  1.531
 UH5  O3   C6   single    1.411  0.020  1.411
 UH5  C8   C7   single    1.528  0.020  1.528
 UH5  C8   N1   single    1.453  0.020  1.453
 UH5  C6   C7   single    1.524  0.020  1.524
 UH5  C7   O4   single    1.401  0.020  1.401
 UH5  N1   C9   aromatic  1.345  0.020  1.345
 UH5  N1   N3   aromatic  1.325  0.020  1.325
 UH5  C9   C10  aromatic  1.375  0.020  1.375
 UH5  N3   N2   aromatic  1.283  0.020  1.283
 UH5  C10  N2   aromatic  1.353  0.020  1.353
 UH5  C10  C11  single    1.461  0.020  1.461
 UH5  C16  C11  aromatic  1.396  0.020  1.396
 UH5  C16  C15  aromatic  1.386  0.020  1.386
 UH5  C11  C12  aromatic  1.396  0.020  1.396
 UH5  C15  C14  aromatic  1.389  0.020  1.389
 UH5  C12  C13  aromatic  1.387  0.020  1.387
 UH5  C14  C13  aromatic  1.389  0.020  1.389
 UH5  C7   H15  single    0.970  0.020  1.090
 UH5  C8   H17  single    0.970  0.020  1.090
 UH5  C9   H18  single    0.930  0.020  1.080
 UH5  C1   H5   single    0.970  0.020  1.090
 UH5  C1   H4   single    0.970  0.020  1.090
 UH5  C5   H10  single    0.970  0.020  1.090
 UH5  C5   H11  single    0.970  0.020  1.090
 UH5  C6   H13  single    0.970  0.020  1.090
 UH5  C4   H9   single    0.970  0.020  1.090
 UH5  O4   H16  single    0.850  0.020  0.980
 UH5  C3   H8   single    0.970  0.020  1.090
 UH5  O3   H14  single    0.850  0.020  0.980
 UH5  C2   H7   single    0.970  0.020  1.090
 UH5  C2   H6   single    0.970  0.020  1.090
 UH5  N    H24  single    0.890  0.020  1.040
 UH5  N    H1   single    0.890  0.020  1.040
 UH5  C    H3   single    0.970  0.020  1.090
 UH5  C    H2   single    0.970  0.020  1.090
 UH5  C12  H19  single    0.930  0.020  1.080
 UH5  C13  H20  single    0.930  0.020  1.080
 UH5  C14  H21  single    0.930  0.020  1.080
 UH5  C15  H22  single    0.930  0.020  1.080
 UH5  C16  H23  single    0.930  0.020  1.080
 UH5  O2   H12  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
 UH5  N3   N1   C9   110.63  3.000
 UH5  N3   N1   C8   118.64  3.000
 UH5  C9   N1   C8   130.70  3.000
 UH5  H15  C7   O4   111.11  3.000
 UH5  H15  C7   C6   107.46  3.000
 UH5  O4   C7   C6   112.10  3.000
 UH5  H15  C7   C8   106.23  3.000
 UH5  O4   C7   C8   108.09  3.000
 UH5  C6   C7   C8   111.73  3.000
 UH5  H17  C8   C3   108.81  3.000
 UH5  H17  C8   C7   109.49  3.000
 UH5  C3   C8   C7   110.56  3.000
 UH5  H17  C8   N1   104.83  3.000
 UH5  C7   C8   N1   112.36  3.000
 UH5  C3   C8   N1   110.58  3.000
 UH5  C10  N2   N3   109.47  3.000
 UH5  H18  C9   C10  132.02  3.000
 UH5  H18  C9   N1   123.71  3.000
 UH5  C10  C9   N1   104.27  3.000
 UH5  C3   O1   C4   115.64  3.000
 UH5  H4   C1   H5   106.58  3.000
 UH5  H4   C1   C    109.31  3.000
 UH5  H5   C1   C    109.97  3.000
 UH5  H4   C1   C2   107.08  3.000
 UH5  H5   C1   C2   110.38  3.000
 UH5  C    C1   C2   113.24  3.000
 UH5  H11  C5   H10  106.58  3.000
 UH5  H11  C5   O2   112.16  3.000
 UH5  H10  C5   O2   111.87  3.000
 UH5  H11  C5   C4   108.19  3.000
 UH5  H10  C5   C4   108.36  3.000
 UH5  O2   C5   C4   109.52  3.000
 UH5  H13  C6   O3   110.16  3.000
 UH5  H13  C6   C4   109.98  3.000
 UH5  O3   C6   C4   110.57  3.000
 UH5  H13  C6   C7   108.90  3.000
 UH5  O3   C6   C7   106.66  3.000
 UH5  C4   C6   C7   110.51  3.000
 UH5  N2   N3   N1   108.17  3.000
 UH5  H9   C4   C6   108.17  3.000
 UH5  H9   C4   C5   106.88  3.000
 UH5  C6   C4   C5   113.48  3.000
 UH5  H9   C4   O1   110.59  3.000
 UH5  C6   C4   O1   110.66  3.000
 UH5  C5   C4   O1   107.02  3.000
 UH5  H8   C3   O    111.18  3.000
 UH5  H8   C3   O1   105.24  3.000
 UH5  O    C3   O1   112.97  3.000
 UH5  H8   C3   C8   109.89  3.000
 UH5  O1   C3   C8   111.09  3.000
 UH5  O    C3   C8   106.53  3.000
 UH5  H14  O3   C6   109.24  3.000
 UH5  H1   N    H24  105.64  3.000
 UH5  H1   N    C    109.34  3.000
 UH5  H24  N    C    109.49  3.000
 UH5  H2   C    H3   106.25  3.000
 UH5  H2   C    N    108.08  3.000
 UH5  H3   C    N    113.63  3.000
 UH5  H2   C    C1   109.56  3.000
 UH5  H3   C    C1   108.61  3.000
 UH5  N    C    C1   110.58  3.000
 UH5  C2   O    C3   114.82  3.000
 UH5  C11  C10  C9   129.61  3.000
 UH5  C11  C10  N2   122.93  3.000
 UH5  C9   C10  N2   107.46  3.000
 UH5  C16  C11  C12  118.69  3.000
 UH5  C12  C11  C10  120.55  3.000
 UH5  C16  C11  C10  120.76  3.000
 UH5  H19  C12  C13  119.59  3.000
 UH5  H19  C12  C11  119.87  3.000
 UH5  C13  C12  C11  120.54  3.000
 UH5  H20  C13  C14  120.08  3.000
 UH5  H20  C13  C12  119.53  3.000
 UH5  C14  C13  C12  120.39  3.000
 UH5  H21  C14  C15  120.27  3.000
 UH5  H21  C14  C13  120.30  3.000
 UH5  C15  C14  C13  119.43  3.000
 UH5  H22  C15  C16  119.58  3.000
 UH5  H22  C15  C14  120.13  3.000
 UH5  C16  C15  C14  120.29  3.000
 UH5  H23  C16  C15  119.04  3.000
 UH5  H23  C16  C11  120.31  3.000
 UH5  C15  C16  C11  120.66  3.000
 UH5  H12  O2   C5   108.57  3.000
 UH5  H16  O4   C7   107.75  3.000
 UH5  H6   C2   H7   107.29  3.000
 UH5  H6   C2   O    110.83  3.000
 UH5  H7   C2   O    109.71  3.000
 UH5  H6   C2   C1   109.65  3.000
 UH5  H7   C2   C1   110.49  3.000
 UH5  O    C2   C1   108.87  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
 UH5  CONST_01  N2   C10  C9   N1      0.00   0.0  0
 UH5  CONST_02  C11  C10  C9   N1    180.00   0.0  0
 UH5  CONST_03  C10  N2   N3   N1      0.00   0.0  0
 UH5  CONST_04  C9   N1   N3   N2      0.00   0.0  0
 UH5  CONST_05  C16  C11  C10  N2    180.00   0.0  0
 UH5  CONST_06  C12  C11  C10  N2      0.00   0.0  0
 UH5  CONST_07  N3   N2   C10  C9      0.00   0.0  0
 UH5  CONST_08  C16  C11  C10  C9      0.00   0.0  0
 UH5  CONST_09  C12  C11  C10  C9    180.00   0.0  0
 UH5  CONST_10  C10  C9   N1   N3      0.00   0.0  0
 UH5  CONST_11  C11  C10  N2   N3    180.00   0.0  0
 UH5  CONST_12  C15  C16  C11  C10   180.00   0.0  0
 UH5  CONST_13  C13  C12  C11  C10   180.00   0.0  0
 UH5  CONST_14  C14  C15  C16  C11     0.00   0.0  0
 UH5  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 UH5  CONST_16  C15  C16  C11  C12     0.00   0.0  0
 UH5  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 UH5  CONST_18  C16  C11  C12  C13     0.00   0.0  0
 UH5  CONST_19  C16  C15  C14  C13     0.00   0.0  0
 UH5  CONST_20  C10  C9   N1   C8    180.00   0.0  0
 UH5  CONST_21  N2   N3   N1   C8    180.00   0.0  0
 UH5  CONST_22  H18  C9   N1   C8      0.00   0.0  0
 UH5  CONST_23  H18  C9   C10  N2    180.00   0.0  0
 UH5  CONST_24  H18  C9   N1   N3    180.00   0.0  0
 UH5  CONST_25  H23  C16  C11  C10     0.00   0.0  0
 UH5  CONST_26  H19  C12  C11  C10     0.00   0.0  0
 UH5  CONST_27  H18  C9   C10  C11     0.00   0.0  0
 UH5  CONST_28  H22  C15  C16  C11   180.00   0.0  0
 UH5  CONST_29  H20  C13  C12  C11   180.00   0.0  0
 UH5  CONST_30  H23  C16  C11  C12   180.00   0.0  0
 UH5  CONST_31  H21  C14  C13  C12   180.00   0.0  0
 UH5  CONST_32  H22  C15  C14  C13   180.00   0.0  0
 UH5  CONST_33  H23  C16  C15  C14   180.00   0.0  0
 UH5  CONST_34  H19  C12  C13  C14   180.00   0.0  0
 UH5  CONST_35  H20  C13  C14  C15   180.00   0.0  0
 UH5  CONST_36  H19  C12  C11  C16   180.00   0.0  0
 UH5  CONST_37  H21  C14  C15  C16   180.00   0.0  0
 UH5  Var_01    C3   O    C2   C1   -179.07  30.0  3
 UH5  Var_02    H7   C2   O    C3     59.91  30.0  1
 UH5  Var_03    H6   C2   O    C3    -58.38  30.0  1
 UH5  Var_04    N    C    C1   C2    176.15  30.0  3
 UH5  Var_05    O    C2   C1   C      62.63  30.0  3
 UH5  Var_06    H24  N    C    C1    176.03  30.0  3
 UH5  Var_07    H1   N    C    C1    -68.67  30.0  3
 UH5  Var_08    H3   C    C1   C2     50.83  30.0  3
 UH5  Var_09    H2   C    C1   C2    -64.82  30.0  3
 UH5  Var_10    H5   C1   C    N     -59.83  30.0  1
 UH5  Var_11    H4   C1   C    N      56.86  30.0  1
 UH5  Var_12    H7   C2   C1   C    -176.82  30.0  3
 UH5  Var_13    H6   C2   C1   C     -58.77  30.0  3
 UH5  Var_14    H5   C1   C2   O     -61.16  30.0  2
 UH5  Var_15    H4   C1   C2   O    -176.80  30.0  2

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
 UH5  chir_01  C7  C8  C6  O4  positiv
 UH5  chir_02  C8  N1  C7  C3  negativ
 UH5  chir_03  C6  O3  C4  C7  positiv
 UH5  chir_04  C4  O1  C6  C5  negativ
 UH5  chir_05  C3  O   O1  C8  negativ

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
 UH5  plan-1  N1   0.020
 UH5  plan-1  C8   0.020
 UH5  plan-1  N2   0.020
 UH5  plan-1  C9   0.020
 UH5  plan-1  N3   0.020
 UH5  plan-1  C10  0.020
 UH5  plan-1  C11  0.020
 UH5  plan-1  H18  0.020
 UH5  plan-2  C10  0.020
 UH5  plan-2  C11  0.020
 UH5  plan-2  C12  0.020
 UH5  plan-2  C13  0.020
 UH5  plan-2  C14  0.020
 UH5  plan-2  C15  0.020
 UH5  plan-2  C16  0.020
 UH5  plan-2  H19  0.020
 UH5  plan-2  H20  0.020
 UH5  plan-2  H21  0.020
 UH5  plan-2  H22  0.020
 UH5  plan-2  H23  0.020

