# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:24:27 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-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(CO)nn2
#
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
 M3N  M3N  4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-1H-1,2,3-triazole  D-saccharide  33  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M3N
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
 M3N  C1   C  CH1   0   0.140  -0.0843   0.6325  -1.1159
 M3N  C2   C  CH1   0   0.003  -1.0088   1.7684  -0.6678
 M3N  O2   O  OH1   0  -0.670  -1.8410   2.0152  -1.7735
 M3N  C3   C  CH1   0  -0.046  -1.8389   1.3818   0.5617
 M3N  O3   O  OH1   0  -0.671  -2.8985   2.3007   0.7388
 M3N  C4   C  CH1   0   0.047  -2.4564  -0.0015   0.4026
 M3N  O4   O  OH1   0  -0.673  -3.0709  -0.4233   1.5953
 M3N  C5   C  CH1   0  -0.023  -1.3615  -1.0069   0.0522
 M3N  O5   O  O2    0  -0.471  -0.7161  -0.6026  -1.1465
 M3N  C6   C  CH2   0  -0.157  -1.9177  -2.3944  -0.1908
 M3N  O6   O  OH1   0  -0.668  -0.8493  -3.2694  -0.4612
 M3N  C01  C  CR5   0   0.104   3.1089   0.1408   0.3932
 M3N  C02  C  CR15  0  -0.056   2.2972  -0.0141  -0.6970
 M3N  N03  N  NR5   0  -0.289   1.1409   0.5739  -0.3281
 M3N  N04  N  N     0  -0.100   1.2267   1.0483   0.9023
 M3N  N05  N  N     0  -0.304   2.4082   0.7984   1.3438
 M3N  O01  O  OH1   0  -0.665   4.9766  -0.8378  -0.6190
 M3N  H1   H  HCH1  0   0.299   0.2328   0.8339  -2.1405
 M3N  H2   H  HCH1  0   0.242  -0.4005   2.6513  -0.4285
 M3N  H3   H  HOH1  0   0.453  -2.5964   2.5245  -1.4562
 M3N  H4   H  HCH1  0   0.247  -1.1833   1.3671   1.4387
 M3N  H5   H  HOH1  0   0.465  -2.5672   3.0723   1.2098
 M3N  H6   H  HCH1  0   0.215  -3.1796   0.0220  -0.4270
 M3N  H7   H  HOH1  0   0.455  -3.7484   0.2213   1.8248
 M3N  H8   H  HCH1  0   0.232  -0.6381  -1.0587   0.8806
 M3N  H9   H  HCH2  0   0.216  -2.4762  -2.7000   0.6994
 M3N  H10  H  HCH2  0   0.197  -2.6327  -2.3516  -1.0242
 M3N  H11  H  HOH1  0   0.457  -1.2043  -4.1615  -0.5072
 M3N  H12  H  HCR5  0   0.312   2.4410  -0.4660  -1.6631
 M3N  H13  H  HCH2  0   0.223   5.1196   0.5620   0.9184
 M3N  H14  H  HCH2  0   0.227   4.5556  -1.0279   1.4103
 M3N  H15  H  HOH1  0   0.465   5.8593  -1.1903  -0.4755
 M3N  C03  C  CH2   0  -0.204   4.5180  -0.2967   0.5928

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
 M3N  C6   O6   single    1.407  0.020  1.407
 M3N  C6   C5   single    1.514  0.020  1.514
 M3N  O4   C4   single    1.406  0.020  1.406
 M3N  C5   C4   single    1.527  0.020  1.527
 M3N  C5   O5   single    1.420  0.020  1.420
 M3N  C4   C3   single    1.523  0.020  1.523
 M3N  O5   C1   single    1.388  0.020  1.388
 M3N  O01  C03  single    1.404  0.020  1.404
 M3N  C3   O3   single    1.414  0.020  1.414
 M3N  C3   C2   single    1.533  0.020  1.533
 M3N  C02  N03  aromatic  1.349  0.020  1.349
 M3N  C02  C01  aromatic  1.368  0.020  1.368
 M3N  C03  C01  single    1.489  0.020  1.489
 M3N  C1   C2   single    1.532  0.020  1.532
 M3N  C1   N03  single    1.458  0.020  1.458
 M3N  C2   O2   single    1.406  0.020  1.406
 M3N  N03  N04  aromatic  1.322  0.020  1.322
 M3N  C01  N05  aromatic  1.352  0.020  1.352
 M3N  N04  N05  aromatic  1.286  0.020  1.286
 M3N  C1   H1   single    0.970  0.020  1.090
 M3N  C2   H2   single    0.970  0.020  1.090
 M3N  O2   H3   single    0.850  0.020  0.980
 M3N  C3   H4   single    0.970  0.020  1.090
 M3N  O3   H5   single    0.850  0.020  0.980
 M3N  C4   H6   single    0.970  0.020  1.090
 M3N  O4   H7   single    0.850  0.020  0.980
 M3N  C5   H8   single    0.970  0.020  1.090
 M3N  C6   H9   single    0.970  0.020  1.090
 M3N  C6   H10  single    0.970  0.020  1.090
 M3N  O6   H11  single    0.850  0.020  0.980
 M3N  C02  H12  single    0.930  0.020  1.080
 M3N  C03  H13  single    0.970  0.020  1.090
 M3N  C03  H14  single    0.970  0.020  1.090
 M3N  O01  H15  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
 M3N  H1   C1   N03  105.70  3.000
 M3N  H1   C1   O5   106.01  3.000
 M3N  N03  C1   O5   111.02  3.000
 M3N  H1   C1   C2   108.26  3.000
 M3N  N03  C1   C2   112.27  3.000
 M3N  O5   C1   C2   113.06  3.000
 M3N  H2   C2   C3   109.14  3.000
 M3N  H2   C2   O2   110.98  3.000
 M3N  C3   C2   O2   110.76  3.000
 M3N  H2   C2   C1   109.00  3.000
 M3N  O2   C2   C1   104.92  3.000
 M3N  C3   C2   C1   111.99  3.000
 M3N  H3   O2   C2   107.31  3.000
 M3N  H4   C3   C4   108.31  3.000
 M3N  H4   C3   O3   110.93  3.000
 M3N  C4   C3   O3   107.43  3.000
 M3N  H4   C3   C2   108.75  3.000
 M3N  O3   C3   C2   110.02  3.000
 M3N  C4   C3   C2   111.39  3.000
 M3N  H5   O3   C3   108.92  3.000
 M3N  H6   C4   C5   108.19  3.000
 M3N  H6   C4   O4   111.00  3.000
 M3N  C5   C4   O4   108.09  3.000
 M3N  H6   C4   C3   109.00  3.000
 M3N  C5   C4   C3   109.34  3.000
 M3N  O4   C4   C3   111.15  3.000
 M3N  H7   O4   C4   107.98  3.000
 M3N  H8   C5   C6   108.59  3.000
 M3N  H8   C5   O5   110.48  3.000
 M3N  C6   C5   O5   107.00  3.000
 M3N  H8   C5   C4   109.23  3.000
 M3N  O5   C5   C4   109.40  3.000
 M3N  C6   C5   C4   112.13  3.000
 M3N  C5   O5   C1   116.21  3.000
 M3N  H10  C6   H9   107.20  3.000
 M3N  H10  C6   O6   111.87  3.000
 M3N  H9   C6   O6   111.72  3.000
 M3N  H10  C6   C5   108.96  3.000
 M3N  H9   C6   C5   108.22  3.000
 M3N  O6   C6   C5   108.77  3.000
 M3N  H11  O6   C6   107.82  3.000
 M3N  C03  C01  N05  122.63  3.000
 M3N  N05  C01  C02  107.93  3.000
 M3N  C03  C01  C02  129.43  3.000
 M3N  H12  C02  N03  122.90  3.000
 M3N  H12  C02  C01  133.13  3.000
 M3N  N03  C02  C01  103.97  3.000
 M3N  N04  N03  C02  110.82  3.000
 M3N  N04  N03  C1   122.91  3.000
 M3N  C02  N03  C1   126.18  3.000
 M3N  N05  N04  N03  108.03  3.000
 M3N  N04  N05  C01  109.23  3.000
 M3N  H15  O01  C03  108.20  3.000
 M3N  H14  C03  H13  106.35  3.000
 M3N  H14  C03  O01  112.02  3.000
 M3N  H13  C03  O01  112.23  3.000
 M3N  H14  C03  C01  109.15  3.000
 M3N  H13  C03  C01  109.18  3.000
 M3N  O01  C03  C01  107.85  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
 M3N  CONST_01  N04  N03  C02  C01    0.00   0.0  0
 M3N  CONST_02  N03  N04  N05  C01    0.00   0.0  0
 M3N  CONST_03  N05  N04  N03  C02    0.00   0.0  0
 M3N  CONST_04  N04  N05  C01  C02    0.00   0.0  0
 M3N  CONST_05  N05  C01  C02  N03    0.00   0.0  0
 M3N  CONST_06  C01  C02  N03  C1   180.00   0.0  0
 M3N  CONST_07  N05  N04  N03  C1   180.00   0.0  0
 M3N  CONST_08  C03  C01  C02  N03  180.00   0.0  0
 M3N  CONST_09  C03  C01  N05  N04  180.00   0.0  0
 M3N  CONST_10  H12  C02  N03  C1     0.00   0.0  0
 M3N  Var_01    O01  C03  C01  C02    5.02  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
 M3N  chir_01  C1  O5  C2  N03  negativ
 M3N  chir_02  C2  O2  C1  C3   positiv
 M3N  chir_03  C3  O3  C2  C4   positiv
 M3N  chir_04  C4  O4  C5  C3   positiv
 M3N  chir_05  C5  O5  C4  C6   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
 M3N  plan-1  C1   0.020
 M3N  plan-1  C01  0.020
 M3N  plan-1  C02  0.020
 M3N  plan-1  N03  0.020
 M3N  plan-1  N04  0.020
 M3N  plan-1  N05  0.020
 M3N  plan-1  H12  0.020
 M3N  plan-1  C03  0.020

