# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 14:30:33 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: pentyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 OPM  OPM  'pentyl alpha-D-mannopyranoside'  D-saccharide  39  17  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OPM
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
 OPM  C3'   C  CH2   0  -0.412  20.6857  59.1274  140.2908
 OPM  C4'   C  CH2   0  -0.425  21.9536  59.8569  140.7185
 OPM  C5'   C  CH3   0  -0.657  22.8354  59.0011  141.6171
 OPM  C1'   C  CH2   0  -0.192  20.2900  60.5220  138.1679
 OPM  C2'   C  CH2   0  -0.496  19.7164  59.9685  139.4655
 OPM  C2    C  CH1   0  -0.018  21.1343  57.4805  136.2743
 OPM  O2    O  OH1   0  -0.666  20.4271  56.3174  135.9221
 OPM  C3    C  CH1   0   0.029  21.8125  58.0286  135.0269
 OPM  O3    O  OH1   0  -0.668  22.6363  57.0287  134.4830
 OPM  C4    C  CH1   0   0.003  20.7659  58.5194  134.0321
 OPM  O4    O  OH1   0  -0.676  21.4574  59.1014  132.9467
 OPM  C5    C  CH1   0  -0.011  19.8618  59.5515  134.7180
 OPM  O5    O  O2    0  -0.499  19.2718  58.9902  135.8807
 OPM  C6    C  CH2   0  -0.195  18.7470  60.0728  133.8377
 OPM  O6    O  OH1   0  -0.667  17.9688  59.0009  133.3622
 OPM  O1    O  O2    0  -0.503  20.9604  59.5561  137.3739
 OPM  C1    C  CH1   0   0.246  20.1776  58.5354  136.8433
 OPM  H3'1  H  HCH2  0   0.217  20.9604  58.2212  139.7411
 OPM  H3'2  H  HCH2  0   0.219  20.1596  58.7799  141.1852
 OPM  H4'1  H  HCH2  0   0.217  22.5278  60.1607  139.8392
 OPM  H4'2  H  HCH2  0   0.210  21.6822  60.7806  141.2391
 OPM  H5'1  H  HCH3  0   0.225  23.7436  59.5289  141.9101
 OPM  H5'2  H  HCH3  0   0.215  22.3099  58.7147  142.5301
 OPM  H5'3  H  HCH3  0   0.215  23.1367  58.0824  141.1100
 OPM  H1'1  H  HCH2  0   0.225  19.4974  61.0182  137.5969
 OPM  H1'2  H  HCH2  0   0.230  21.0439  61.2805  138.3839
 OPM  H2'1  H  HCH2  0   0.235  18.8133  59.3855  139.2649
 OPM  H2'2  H  HCH2  0   0.236  19.3828  60.8291  140.0540
 OPM  H2    H  HCH1  0   0.233  21.8963  57.2663  137.0364
 OPM  HO2   H  HOH1  0   0.452  20.0809  55.9142  136.7245
 OPM  H3    H  HCH1  0   0.213  22.4110  58.8981  135.3384
 OPM  HO3   H  HOH1  0   0.445  23.0528  57.3931  133.6949
 OPM  H4    H  HCH1  0   0.226  20.1652  57.6654  133.7000
 OPM  HO4   H  HOH1  0   0.458  20.9192  59.0197  132.1543
 OPM  H5    H  HCH1  0   0.224  20.4786  60.4228  134.9818
 OPM  H61   H  HCH2  0   0.215  18.1485  60.7840  134.4226
 OPM  H62   H  HCH2  0   0.205  19.2003  60.6480  133.0211
 OPM  HO6   H  HOH1  0   0.456  17.3110  59.3515  132.7558
 OPM  H1    H  HCH1  0   0.234  19.5519  58.0694  137.6173

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
 OPM  C3'  C4'   single  1.524  0.020  1.524
 OPM  C3'  C2'   single  1.526  0.020  1.526
 OPM  C3'  H3'1  single  0.970  0.020  1.090
 OPM  C3'  H3'2  single  0.970  0.020  1.090
 OPM  C4'  C5'   single  1.522  0.020  1.522
 OPM  C4'  H4'1  single  0.970  0.020  1.090
 OPM  C4'  H4'2  single  0.970  0.020  1.090
 OPM  C5'  H5'1  single  0.970  0.020  1.090
 OPM  C5'  H5'2  single  0.970  0.020  1.090
 OPM  C5'  H5'3  single  0.970  0.020  1.090
 OPM  C1'  C2'   single  1.523  0.020  1.523
 OPM  C1'  O1    single  1.419  0.020  1.419
 OPM  C1'  H1'1  single  0.970  0.020  1.090
 OPM  C1'  H1'2  single  0.970  0.020  1.090
 OPM  C2'  H2'1  single  0.970  0.020  1.090
 OPM  C2'  H2'2  single  0.970  0.020  1.090
 OPM  C2   O2    single  1.406  0.020  1.406
 OPM  C2   C3    single  1.522  0.020  1.522
 OPM  C2   C1    single  1.534  0.020  1.534
 OPM  C2   H2    single  0.970  0.020  1.090
 OPM  O2   HO2   single  0.850  0.020  0.980
 OPM  C3   O3    single  1.405  0.020  1.405
 OPM  C3   C4    single  1.525  0.020  1.525
 OPM  C3   H3    single  0.970  0.020  1.090
 OPM  O3   HO3   single  0.850  0.020  0.980
 OPM  C4   O4    single  1.412  0.020  1.412
 OPM  C4   C5    single  1.534  0.020  1.534
 OPM  C4   H4    single  0.970  0.020  1.090
 OPM  O4   HO4   single  0.850  0.020  0.980
 OPM  C5   O5    single  1.419  0.020  1.419
 OPM  C5   C6    single  1.513  0.020  1.513
 OPM  C5   H5    single  0.970  0.020  1.090
 OPM  O5   C1    single  1.398  0.020  1.398
 OPM  C6   O6    single  1.407  0.020  1.407
 OPM  C6   H61   single  0.970  0.020  1.090
 OPM  C6   H62   single  0.970  0.020  1.090
 OPM  O6   HO6   single  0.850  0.020  0.980
 OPM  O1   C1    single  1.391  0.020  1.391
 OPM  C1   H1    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
 OPM  H3'2  C3'  H3'1  105.55  3.000
 OPM  H3'2  C3'  C2'   108.16  3.000
 OPM  H3'1  C3'  C2'   110.12  3.000
 OPM  H3'2  C3'  C4'   108.82  3.000
 OPM  H3'1  C3'  C4'   109.17  3.000
 OPM  C2'   C3'  C4'   114.61  3.000
 OPM  H4'2  C4'  H4'1  106.15  3.000
 OPM  H4'2  C4'  C5'   109.71  3.000
 OPM  H4'1  C4'  C5'   109.07  3.000
 OPM  H4'2  C4'  C3'   109.34  3.000
 OPM  H4'1  C4'  C3'   110.14  3.000
 OPM  C5'   C4'  C3'   112.24  3.000
 OPM  H5'3  C5'  H5'2  107.49  3.000
 OPM  H5'3  C5'  H5'1  107.59  3.000
 OPM  H5'2  C5'  H5'1  107.64  3.000
 OPM  H5'3  C5'  C4'   111.03  3.000
 OPM  H5'2  C5'  C4'   111.25  3.000
 OPM  H5'1  C5'  C4'   111.65  3.000
 OPM  H1'2  C1'  H1'1  106.75  3.000
 OPM  H1'2  C1'  O1    104.93  3.000
 OPM  H1'1  C1'  O1    111.01  3.000
 OPM  H1'2  C1'  C2'   110.14  3.000
 OPM  H1'1  C1'  C2'   109.64  3.000
 OPM  O1    C1'  C2'   114.04  3.000
 OPM  H2'2  C2'  H2'1  105.43  3.000
 OPM  H2'2  C2'  C1'   106.69  3.000
 OPM  H2'1  C2'  C1'   110.40  3.000
 OPM  H2'2  C2'  C3'   109.64  3.000
 OPM  H2'1  C2'  C3'   109.26  3.000
 OPM  C1'   C2'  C3'   114.96  3.000
 OPM  H2    C2   C1    108.02  3.000
 OPM  H2    C2   C3    109.25  3.000
 OPM  C1    C2   C3    109.53  3.000
 OPM  H2    C2   O2    111.18  3.000
 OPM  C1    C2   O2    110.38  3.000
 OPM  C3    C2   O2    108.46  3.000
 OPM  HO2   O2   C2    108.58  3.000
 OPM  H3    C3   C4    107.67  3.000
 OPM  H3    C3   O3    110.66  3.000
 OPM  C4    C3   O3    112.26  3.000
 OPM  H3    C3   C2    107.15  3.000
 OPM  C4    C3   C2    110.17  3.000
 OPM  O3    C3   C2    108.80  3.000
 OPM  HO3   O3   C3    107.53  3.000
 OPM  H4    C4   C5    109.69  3.000
 OPM  H4    C4   O4    110.90  3.000
 OPM  C5    C4   O4    110.79  3.000
 OPM  H4    C4   C3    108.84  3.000
 OPM  C5    C4   C3    109.23  3.000
 OPM  O4    C4   C3    107.33  3.000
 OPM  HO4   O4   C4    108.92  3.000
 OPM  H5    C5   C6    106.25  3.000
 OPM  H5    C5   O5    110.48  3.000
 OPM  C6    C5   O5    107.85  3.000
 OPM  H5    C5   C4    108.04  3.000
 OPM  C6    C5   C4    113.95  3.000
 OPM  O5    C5   C4    110.19  3.000
 OPM  C1    O5   C5    115.05  3.000
 OPM  H62   C6   H61   106.38  3.000
 OPM  H62   C6   O6    112.11  3.000
 OPM  H61   C6   O6    111.83  3.000
 OPM  H62   C6   C5    108.02  3.000
 OPM  H61   C6   C5    108.35  3.000
 OPM  O6    C6   C5    109.97  3.000
 OPM  HO6   O6   C6    108.29  3.000
 OPM  C1    O1   C1'   116.55  3.000
 OPM  H1    C1   O1    111.27  3.000
 OPM  H1    C1   O5    104.71  3.000
 OPM  O1    C1   O5    112.86  3.000
 OPM  H1    C1   C2    108.95  3.000
 OPM  O1    C1   C2    107.17  3.000
 OPM  O5    C1   C2    111.87  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
 OPM  Var_01  O1    C1'  C2'  C3'   48.87  30.0  1
 OPM  Var_02  C1'   C2'  C3'  C4'   59.05  30.0  3
 OPM  Var_03  C2'   C3'  C4'  C5'  176.06  30.0  1
 OPM  Var_04  H5'1  C5'  C4'  C3'  179.50  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
 OPM  chir_01  C2  O2  C3  C1  negativ
 OPM  chir_02  C3  O3  C2  C4  positiv
 OPM  chir_03  C4  O4  C5  C3  positiv
 OPM  chir_04  C5  O5  C4  C6  negativ
 OPM  chir_05  C1  O5  O1  C2  positiv

