# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:18:25 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-(4-methoxyphenyl)prop-2-yn-1-yl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C#CCO[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O
#
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
 HNV  HNV  '3-(4-methoxyphenyl)prop-2-yn-1-yl alpha-D-mannopyranoside'  D-saccharide  43  23  .  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_HNV
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
 HNV  O6    O  OH1   0  -0.628   3.1844   3.3496   0.6871
 HNV  C6    C  CH2   0  -0.148   4.0125   2.2821   1.0825
 HNV  C5    C  CH1   0  -0.056   3.3754   0.9845   0.6369
 HNV  O5    O  O2    0  -0.508   3.3208   1.0032  -0.7801
 HNV  C4    C  CH1   0   0.062   4.1589  -0.2392   1.1126
 HNV  O4    O  OH1   0  -0.653   4.1100  -0.2624   2.5188
 HNV  C3    C  CH1   0  -0.008   3.5352  -1.5005   0.5245
 HNV  O3    O  OH1   0  -0.680   4.3177  -2.5928   0.9446
 HNV  C2    C  CH1   0  -0.005   3.4303  -1.4015  -0.9955
 HNV  O2    O  OH1   0  -0.585   4.7265  -1.4065  -1.5323
 HNV  C1    C  CH1   0   0.263   2.7068  -0.1022  -1.3666
 HNV  O1    O  O2    0  -0.444   1.3728  -0.2424  -0.9831
 HNV  C7    C  CH2   0  -0.279   0.5443   0.8311  -1.3951
 HNV  C8    C  CSP   0  -0.088  -0.8279   0.5450  -1.0064
 HNV  C9    C  CSP   0   0.209  -1.9696   0.3550  -0.6702
 HNV  C10   C  CR6   0  -0.120  -3.3178   0.1411  -0.2618
 HNV  C15   C  CR16  0  -0.238  -3.8763   0.9011   0.7749
 HNV  C14   C  CR16  0  -0.319  -5.1809   0.6997   1.1718
 HNV  C13   C  CR6   0   0.459  -5.9687  -0.2703   0.5422
 HNV  O7    O  O2    0  -0.492  -7.2262  -0.3926   0.9928
 HNV  C16   C  CH3   0  -0.455  -8.0746  -1.3578   0.3986
 HNV  C12   C  CR16  0  -0.381  -5.4246  -1.0326  -0.4918
 HNV  C11   C  CR16  0  -0.237  -4.1113  -0.8222  -0.8847
 HNV  H6    H  HOH1  0   0.436   3.5304   4.1532   1.0848
 HNV  H61C  H  HCH2  0   0.224   5.0183   2.3611   0.6457
 HNV  H62C  H  HCH2  0   0.199   4.1354   2.2485   2.1702
 HNV  H5    H  HCH1  0   0.230   2.3621   0.9325   1.0600
 HNV  H4    H  HCH1  0   0.207   5.1971  -0.1539   0.7585
 HNV  H1    H  HCH1  0   0.234   2.7768   0.0755  -2.4500
 HNV  HA    H  HOH1  0   0.422   4.5104  -1.0868   2.8148
 HNV  H3    H  HCH1  0   0.230   2.5134  -1.5842   0.9212
 HNV  HB    H  HOH1  0   0.423   3.7859  -3.3924   0.9027
 HNV  H2    H  HCH1  0   0.180   2.8387  -2.2489  -1.3749
 HNV  HC    H  HOH1  0   0.430   4.6627  -1.4954  -2.4875
 HNV  H71C  H  HCH2  0   0.202   0.8381   1.7719  -0.9341
 HNV  H72C  H  HCH2  0   0.213   0.6075   0.9701  -2.4812
 HNV  H15   H  HCR6  0   0.246  -3.2769   1.6547   1.2679
 HNV  H11   H  HCR6  0   0.236  -3.6985  -1.3950  -1.7011
 HNV  H14   H  HCR6  0   0.247  -5.6053   1.2929   1.9726
 HNV  H12   H  HCR6  0   0.238  -6.0084  -1.7860  -1.0024
 HNV  H161  H  HCH3  0   0.224  -7.6783  -2.3706   0.5060
 HNV  H162  H  HCH3  0   0.256  -9.0258  -1.2956   0.9223
 HNV  H163  H  HCH3  0   0.251  -8.2411  -1.1540  -0.6624

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
 HNV  O6   C6    single    1.408  0.020  1.408
 HNV  C6   C5    single    1.513  0.020  1.513
 HNV  C5   O5    single    1.418  0.020  1.418
 HNV  C5   C4    single    1.529  0.020  1.529
 HNV  O5   C1    single    1.394  0.020  1.394
 HNV  C4   O4    single    1.407  0.020  1.407
 HNV  C4   C3    single    1.525  0.020  1.525
 HNV  C3   O3    single    1.408  0.020  1.408
 HNV  C3   C2    single    1.527  0.020  1.527
 HNV  C2   O2    single    1.403  0.020  1.403
 HNV  C2   C1    single    1.533  0.020  1.533
 HNV  C1   O1    single    1.395  0.020  1.395
 HNV  O1   C7    single    1.417  0.020  1.417
 HNV  C7   C8    single    1.455  0.020  1.455
 HNV  C8   C9    triple    1.205  0.020  1.205
 HNV  C9   C10   single    1.425  0.020  1.425
 HNV  C10  C15   aromatic  1.401  0.020  1.401
 HNV  C10  C11   aromatic  1.395  0.020  1.395
 HNV  C15  C14   aromatic  1.378  0.020  1.378
 HNV  C14  C13   aromatic  1.399  0.020  1.399
 HNV  C13  O7    single    1.341  0.020  1.341
 HNV  C13  C12   aromatic  1.395  0.020  1.395
 HNV  O7   C16   single    1.416  0.020  1.416
 HNV  C12  C11   aromatic  1.387  0.020  1.387
 HNV  O6   H6    single    0.850  0.020  0.980
 HNV  C6   H61C  single    0.970  0.020  1.090
 HNV  C6   H62C  single    0.970  0.020  1.090
 HNV  C5   H5    single    0.970  0.020  1.090
 HNV  C4   H4    single    0.970  0.020  1.090
 HNV  C1   H1    single    0.970  0.020  1.090
 HNV  O4   HA    single    0.850  0.020  0.980
 HNV  C3   H3    single    0.970  0.020  1.090
 HNV  O3   HB    single    0.850  0.020  0.980
 HNV  C2   H2    single    0.970  0.020  1.090
 HNV  O2   HC    single    0.850  0.020  0.980
 HNV  C7   H71C  single    0.970  0.020  1.090
 HNV  C7   H72C  single    0.970  0.020  1.090
 HNV  C15  H15   single    0.930  0.020  1.080
 HNV  C11  H11   single    0.930  0.020  1.080
 HNV  C14  H14   single    0.930  0.020  1.080
 HNV  C12  H12   single    0.930  0.020  1.080
 HNV  C16  H161  single    0.970  0.020  1.090
 HNV  C16  H162  single    0.970  0.020  1.090
 HNV  C16  H163  single    0.970  0.020  1.090

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
 HNV  H6    O6   C6    107.82  3.000
 HNV  H62C  C6   H61C  107.10  3.000
 HNV  H62C  C6   C5    108.27  3.000
 HNV  H61C  C6   C5    109.26  3.000
 HNV  H62C  C6   O6    111.61  3.000
 HNV  H61C  C6   O6    111.85  3.000
 HNV  C5    C6   O6    108.66  3.000
 HNV  H5    C5   C4    108.34  3.000
 HNV  H5    C5   O5    110.47  3.000
 HNV  C4    C5   O5    109.95  3.000
 HNV  H5    C5   C6    108.39  3.000
 HNV  C4    C5   C6    112.28  3.000
 HNV  O5    C5   C6    107.41  3.000
 HNV  C1    O5   C5    115.27  3.000
 HNV  H4    C4   C3    109.02  3.000
 HNV  H4    C4   O4    110.83  3.000
 HNV  C3    C4   O4    110.95  3.000
 HNV  H4    C4   C5    108.74  3.000
 HNV  C3    C4   C5    109.41  3.000
 HNV  O4    C4   C5    107.84  3.000
 HNV  HA    O4   C4    107.87  3.000
 HNV  H3    C3   C2    107.47  3.000
 HNV  H3    C3   O3    110.48  3.000
 HNV  C2    C3   O3    112.68  3.000
 HNV  H3    C3   C4    107.70  3.000
 HNV  C2    C3   C4    111.00  3.000
 HNV  O3    C3   C4    107.42  3.000
 HNV  HB    O3   C3    108.96  3.000
 HNV  H2    C2   C1    108.39  3.000
 HNV  H2    C2   O2    111.21  3.000
 HNV  C1    C2   O2    110.27  3.000
 HNV  H2    C2   C3    109.27  3.000
 HNV  C1    C2   C3    109.17  3.000
 HNV  O2    C2   C3    108.49  3.000
 HNV  HC    O2   C2    108.61  3.000
 HNV  H1    C1   O1    110.35  3.000
 HNV  H1    C1   C2    110.20  3.000
 HNV  O1    C1   C2    107.43  3.000
 HNV  H1    C1   O5    104.96  3.000
 HNV  O1    C1   O5    112.66  3.000
 HNV  C2    C1   O5    111.25  3.000
 HNV  C7    O1   C1    113.76  3.000
 HNV  H72C  C7   H71C  107.13  3.000
 HNV  H72C  C7   C8    110.11  3.000
 HNV  H71C  C7   C8    108.16  3.000
 HNV  H72C  C7   O1    110.50  3.000
 HNV  H71C  C7   O1    111.96  3.000
 HNV  C8    C7   O1    108.95  3.000
 HNV  C9    C8   C7    180.00  3.000
 HNV  C10   C9   C8    180.00  3.000
 HNV  C11   C10  C15   118.56  3.000
 HNV  C11   C10  C9    120.93  3.000
 HNV  C15   C10  C9    120.51  3.000
 HNV  H15   C15  C14   119.66  3.000
 HNV  H15   C15  C10   119.61  3.000
 HNV  C14   C15  C10   120.72  3.000
 HNV  H14   C14  C13   119.45  3.000
 HNV  H14   C14  C15   120.24  3.000
 HNV  C13   C14  C15   120.31  3.000
 HNV  C12   C13  O7    124.39  3.000
 HNV  C12   C13  C14   119.51  3.000
 HNV  O7    C13  C14   116.09  3.000
 HNV  C16   O7   C13   118.87  3.000
 HNV  H163  C16  H162  108.88  3.000
 HNV  H163  C16  H161  108.87  3.000
 HNV  H162  C16  H161  108.83  3.000
 HNV  H163  C16  O7    111.81  3.000
 HNV  H162  C16  O7    106.43  3.000
 HNV  H161  C16  O7    111.92  3.000
 HNV  H12   C12  C11   118.90  3.000
 HNV  H12   C12  C13   121.34  3.000
 HNV  C11   C12  C13   119.76  3.000
 HNV  H11   C11  C12   119.73  3.000
 HNV  H11   C11  C10   119.12  3.000
 HNV  C12   C11  C10   121.13  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
 HNV  CONST_01  C13   C14  C15  C10    0.00   0.0  0
 HNV  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 HNV  CONST_03  C12   C11  C10  C15    0.00   0.0  0
 HNV  CONST_04  C12   C13  C14  C15    0.00   0.0  0
 HNV  CONST_05  C11   C10  C15  C14    0.00   0.0  0
 HNV  CONST_06  C11   C12  C13  C14    0.00   0.0  0
 HNV  CONST_07  C14   C15  C10  C9   180.00   0.0  0
 HNV  CONST_08  C12   C11  C10  C9   180.00   0.0  0
 HNV  CONST_09  O7    C13  C14  C15  180.00   0.0  0
 HNV  CONST_10  C11   C12  C13  O7   180.00   0.0  0
 HNV  CONST_11  H14   C14  C15  C10  180.00   0.0  0
 HNV  CONST_12  H12   C12  C11  C10  180.00   0.0  0
 HNV  CONST_13  H11   C11  C10  C15  180.00   0.0  0
 HNV  CONST_14  H15   C15  C14  C13  180.00   0.0  0
 HNV  Var_01    C12   C13  O7   C16    0.31  30.0  2
 HNV  Var_02    C8    C7   O1   C1   176.96  30.0  3
 HNV  Var_03    H161  C16  O7   C13   60.29  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
 HNV  chir_01  C5  C6  O5  C4  negativ
 HNV  chir_02  C4  O4  C5  C3  positiv
 HNV  chir_03  C3  O3  C2  C4  positiv
 HNV  chir_04  C2  O2  C3  C1  negativ
 HNV  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
 HNV  plan-1  C8   0.020
 HNV  plan-1  C9   0.020
 HNV  plan-1  C10  0.020
 HNV  plan-1  C15  0.020
 HNV  plan-1  C14  0.020
 HNV  plan-1  C13  0.020
 HNV  plan-1  O7   0.020
 HNV  plan-1  C12  0.020
 HNV  plan-1  C11  0.020
 HNV  plan-1  H15  0.020
 HNV  plan-1  H11  0.020
 HNV  plan-1  H14  0.020
 HNV  plan-1  H12  0.020

