# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 18:48:36 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-(3-hydroxyprop-1-yn-1-yl)phenyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC#Cc1ccc(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)cc1
#
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
 HNW  HNW  '4-(3-hydroxyprop-1-yn-1-yl)phenyl alpha-D-mannopyranoside'  D-saccharide  40  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 PERFECT
;

data_comp_HNW
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
 HNW  O6    O  OH1   0  -0.667  -1.2040   3.2662   0.2238
 HNW  C6    C  CH2   0  -0.159  -2.5029   2.7329   0.1287
 HNW  C5    C  CH1   0  -0.013  -2.4035   1.2510  -0.1656
 HNW  O5    O  O2    0  -0.487  -1.7856   0.6445   0.9604
 HNW  C4    C  CH1   0   0.027  -3.7766   0.6310  -0.4263
 HNW  O4    O  OH1   0  -0.674  -4.2659   1.1811  -1.6257
 HNW  C3    C  CH1   0   0.003  -3.6520  -0.8856  -0.5305
 HNW  O3    O  OH1   0  -0.671  -4.9483  -1.4070  -0.6978
 HNW  C2    C  CH1   0  -0.024  -2.9518  -1.4569   0.7001
 HNW  O2    O  OH1   0  -0.665  -3.7755  -1.2527   1.8177
 HNW  O7    O  OH1   0  -0.666   7.9789  -0.4401   0.7107
 HNW  C7    C  CH2   0  -0.338   7.3463   0.2170  -0.3645
 HNW  C8    C  CSP   0  -0.062   5.9102  -0.0243  -0.2986
 HNW  C10   C  CR6   0  -0.121   3.3124  -0.4260  -0.2103
 HNW  C15   C  CR16  0  -0.271   2.6684  -1.1753  -1.2011
 HNW  C14   C  CR16  0  -0.344   1.3050  -1.3827  -1.1528
 HNW  C13   C  CR6   0   0.393   0.5456  -0.8492  -0.1106
 HNW  O1    O  O2    0  -0.498  -0.7755  -1.1278  -0.1504
 HNW  C1    C  CH1   0   0.202  -1.6199  -0.7289   0.9062
 HNW  C12   C  CR16  0  -0.352   1.1708  -0.0915   0.8778
 HNW  C11   C  CR16  0  -0.275   2.5412   0.1074   0.8225
 HNW  H6    H  HOH1  0   0.456  -1.2830   4.2196   0.3179
 HNW  H61C  H  HCH2  0   0.195  -3.0737   2.8750   1.0574
 HNW  H62C  H  HCH2  0   0.213  -3.0759   3.2044  -0.6763
 HNW  H5    H  HCH1  0   0.231  -1.7825   1.1154  -1.0623
 HNW  H4    H  HCH1  0   0.215  -4.4406   0.8766   0.4160
 HNW  H1    H  HCH1  0   0.264  -1.1786  -1.0184   1.8681
 HNW  HA    H  HOH1  0   0.453  -5.1175   0.7725  -1.8131
 HNW  H3    H  HCH1  0   0.232  -3.0289  -1.1116  -1.4063
 HNW  HB    H  HOH1  0   0.458  -4.8845  -2.2658  -1.1260
 HNW  H2    H  HCH1  0   0.242  -2.7473  -2.5245   0.5420
 HNW  HC    H  HOH1  0   0.459  -3.4479  -1.7901   2.5454
 HNW  HD    H  HOH1  0   0.463   8.9196  -0.2439   0.6557
 HNW  H71C  H  HCH2  0   0.237   7.5206   1.3001  -0.3410
 HNW  H72C  H  HCH2  0   0.236   7.7142  -0.1365  -1.3358
 HNW  H11   H  HCR6  0   0.265   3.0178   0.6947   1.5962
 HNW  H14   H  HCR6  0   0.271   0.8162  -1.9653  -1.9232
 HNW  H12   H  HCR6  0   0.288   0.6176   0.3620   1.6865
 HNW  H15   H  HCR6  0   0.263   3.2428  -1.5988  -2.0142
 HNW  C9    C  CSP   0   0.225   4.7198  -0.2077  -0.2586

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
 HNW  O6   C6    single    1.407  0.020  1.407
 HNW  C6   C5    single    1.514  0.020  1.514
 HNW  C5   O5    single    1.420  0.020  1.420
 HNW  C5   C4    single    1.529  0.020  1.529
 HNW  O5   C1    single    1.384  0.020  1.384
 HNW  C4   O4    single    1.407  0.020  1.407
 HNW  C4   C3    single    1.525  0.020  1.525
 HNW  C3   O3    single    1.407  0.020  1.407
 HNW  C3   C2    single    1.527  0.020  1.527
 HNW  C2   O2    single    1.403  0.020  1.403
 HNW  C2   C1    single    1.532  0.020  1.532
 HNW  O7   C7    single    1.410  0.020  1.410
 HNW  C7   C8    single    1.458  0.020  1.458
 HNW  C8   C9    triple    1.205  0.020  1.205
 HNW  C9   C10   single    1.425  0.020  1.425
 HNW  C10  C15   aromatic  1.399  0.020  1.399
 HNW  C10  C11   aromatic  1.395  0.020  1.395
 HNW  C15  C14   aromatic  1.380  0.020  1.380
 HNW  C14  C13   aromatic  1.396  0.020  1.396
 HNW  C13  O1    single    1.351  0.020  1.351
 HNW  C13  C12   aromatic  1.394  0.020  1.394
 HNW  O1   C1    single    1.410  0.020  1.410
 HNW  C12  C11   aromatic  1.386  0.020  1.386
 HNW  O6   H6    single    0.850  0.020  0.980
 HNW  C6   H61C  single    0.970  0.020  1.090
 HNW  C6   H62C  single    0.970  0.020  1.090
 HNW  C5   H5    single    0.970  0.020  1.090
 HNW  C4   H4    single    0.970  0.020  1.090
 HNW  C1   H1    single    0.970  0.020  1.090
 HNW  O4   HA    single    0.850  0.020  0.980
 HNW  C3   H3    single    0.970  0.020  1.090
 HNW  O3   HB    single    0.850  0.020  0.980
 HNW  C2   H2    single    0.970  0.020  1.090
 HNW  O2   HC    single    0.850  0.020  0.980
 HNW  O7   HD    single    0.850  0.020  0.980
 HNW  C7   H71C  single    0.970  0.020  1.090
 HNW  C7   H72C  single    0.970  0.020  1.090
 HNW  C15  H15   single    0.930  0.020  1.080
 HNW  C11  H11   single    0.930  0.020  1.080
 HNW  C14  H14   single    0.930  0.020  1.080
 HNW  C12  H12   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
 HNW  H6    O6   C6    107.86  3.000
 HNW  H62C  C6   H61C  107.08  3.000
 HNW  H62C  C6   C5    108.24  3.000
 HNW  H61C  C6   C5    108.95  3.000
 HNW  H62C  C6   O6    111.68  3.000
 HNW  H61C  C6   O6    111.91  3.000
 HNW  C5    C6   O6    108.87  3.000
 HNW  H5    C5   C4    108.56  3.000
 HNW  H5    C5   O5    110.38  3.000
 HNW  C4    C5   O5    110.65  3.000
 HNW  H5    C5   C6    108.44  3.000
 HNW  C4    C5   C6    111.78  3.000
 HNW  O5    C5   C6    107.00  3.000
 HNW  C1    O5   C5    116.40  3.000
 HNW  H4    C4   C3    108.88  3.000
 HNW  H4    C4   O4    110.82  3.000
 HNW  C3    C4   O4    111.03  3.000
 HNW  H4    C4   C5    108.72  3.000
 HNW  C3    C4   C5    109.97  3.000
 HNW  O4    C4   C5    107.40  3.000
 HNW  HA    O4   C4    107.91  3.000
 HNW  H3    C3   C2    107.79  3.000
 HNW  H3    C3   O3    110.59  3.000
 HNW  C2    C3   O3    112.31  3.000
 HNW  H3    C3   C4    107.79  3.000
 HNW  C2    C3   C4    110.76  3.000
 HNW  O3    C3   C4    107.54  3.000
 HNW  HB    O3   C3    108.82  3.000
 HNW  H2    C2   C1    108.63  3.000
 HNW  H2    C2   O2    111.43  3.000
 HNW  C1    C2   O2    109.51  3.000
 HNW  H2    C2   C3    109.45  3.000
 HNW  C1    C2   C3    109.23  3.000
 HNW  O2    C2   C3    108.56  3.000
 HNW  HC    O2   C2    108.73  3.000
 HNW  HD    O7   C7    107.45  3.000
 HNW  H72C  C7   H71C  106.48  3.000
 HNW  H72C  C7   C8    108.49  3.000
 HNW  H71C  C7   C8    108.60  3.000
 HNW  H72C  C7   O7    111.99  3.000
 HNW  H71C  C7   O7    111.87  3.000
 HNW  C8    C7   O7    109.29  3.000
 HNW  C9    C8   C7    180.00  3.000
 HNW  C11   C10  C15   118.33  3.000
 HNW  C11   C10  C9    120.83  3.000
 HNW  C15   C10  C9    120.84  3.000
 HNW  H15   C15  C14   119.48  3.000
 HNW  H15   C15  C10   119.83  3.000
 HNW  C14   C15  C10   120.69  3.000
 HNW  H14   C14  C13   119.44  3.000
 HNW  H14   C14  C15   120.14  3.000
 HNW  C13   C14  C15   120.42  3.000
 HNW  C12   C13  O1    124.88  3.000
 HNW  C12   C13  C14   119.57  3.000
 HNW  O1    C13  C14   115.56  3.000
 HNW  C1    O1   C13   120.35  3.000
 HNW  H1    C1   O1    109.96  3.000
 HNW  H1    C1   C2    110.02  3.000
 HNW  O1    C1   C2    106.58  3.000
 HNW  H1    C1   O5    106.00  3.000
 HNW  O1    C1   O5    112.43  3.000
 HNW  C2    C1   O5    111.88  3.000
 HNW  H12   C12  C11   118.44  3.000
 HNW  H12   C12  C13   121.99  3.000
 HNW  C11   C12  C13   119.56  3.000
 HNW  H11   C11  C12   119.01  3.000
 HNW  H11   C11  C10   119.57  3.000
 HNW  C12   C11  C10   121.42  3.000
 HNW  C10   C9   C8    180.00  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
 HNW  CONST_01  C13   C14  C15  C10    0.00   0.0  0
 HNW  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 HNW  CONST_03  C12   C11  C10  C15    0.00   0.0  0
 HNW  CONST_04  C12   C13  C14  C15    0.00   0.0  0
 HNW  CONST_05  C11   C10  C15  C14    0.00   0.0  0
 HNW  CONST_06  C11   C12  C13  C14    0.00   0.0  0
 HNW  CONST_07  C14   C15  C10  C9   180.00   0.0  0
 HNW  CONST_08  C12   C11  C10  C9   180.00   0.0  0
 HNW  CONST_09  O1    C13  C14  C15  180.00   0.0  0
 HNW  CONST_10  C11   C12  C13  O1   180.00   0.0  0
 HNW  CONST_11  H14   C14  C15  C10  180.00   0.0  0
 HNW  CONST_12  H12   C12  C11  C10  180.00   0.0  0
 HNW  CONST_13  H11   C11  C10  C15  180.00   0.0  0
 HNW  CONST_14  H15   C15  C14  C13  180.00   0.0  0
 HNW  Var_01    C12   C13  O1   C1    -4.75  30.0  2
 HNW  Var_02    H71C  C7   C8   C9    43.84  30.0  1

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
 HNW  chir_01  C5  C6  O5  C4  negativ
 HNW  chir_02  C4  O4  C5  C3  positiv
 HNW  chir_03  C3  O3  C4  C2  negativ
 HNW  chir_04  C2  O2  C3  C1  negativ
 HNW  chir_05  C1  O1  O5  C2  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
 HNW  plan-1  C8   0.020
 HNW  plan-1  C10  0.020
 HNW  plan-1  C15  0.020
 HNW  plan-1  C14  0.020
 HNW  plan-1  C13  0.020
 HNW  plan-1  O1   0.020
 HNW  plan-1  C12  0.020
 HNW  plan-1  C11  0.020
 HNW  plan-1  H11  0.020
 HNW  plan-1  H14  0.020
 HNW  plan-1  H12  0.020
 HNW  plan-1  H15  0.020
 HNW  plan-1  C9   0.020

