# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:18:39 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: heptyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[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
 KGM  KGM  'heptyl alpha-D-mannopyranoside'  D-saccharide  45  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KGM
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
 KGM  O6    O  OH1   0  -0.671   1.6048  -3.3148   0.9437
 KGM  C6    C  CH2   0  -0.159   2.7357  -2.6284   0.4614
 KGM  C5    C  CH1   0  -0.011   2.3150  -1.2428   0.0186
 KGM  C10   C  CH2   0  -0.411  -4.5775   0.5807  -0.4382
 KGM  O5    O  O2    0  -0.500   1.8522  -0.5599   1.1706
 KGM  C4    C  CH1   0   0.031   3.4721  -0.4811  -0.6299
 KGM  O4    O  OH1   0  -0.676   3.8071  -1.1499  -1.8235
 KGM  C3    C  CH1   0   0.003   3.0429   0.9550  -0.9083
 KGM  O3    O  OH1   0  -0.673   4.1491   1.6285  -1.4607
 KGM  C2    C  CH1   0  -0.030   2.5258   1.6192   0.3639
 KGM  O2    O  OH1   0  -0.669   3.5958   1.7429   1.2662
 KGM  C1    C  CH1   0   0.242   1.4163   0.7525   0.9681
 KGM  O1    O  O2    0  -0.507   0.3108   0.8363   0.1300
 KGM  C7    C  CH2   0  -0.134  -0.8618   0.2087   0.6205
 KGM  C8    C  CH2   0  -0.462  -2.0559   0.7086  -0.1663
 KGM  C9    C  CH2   0  -0.425  -3.3524   0.0579   0.3010
 KGM  C13   C  CH3   0  -0.662  -8.4056  -0.1477  -0.2043
 KGM  C12   C  CH2   0  -0.419  -7.1081   0.4860  -0.6867
 KGM  C11   C  CH2   0  -0.407  -5.8788  -0.0570   0.0315
 KGM  H131  H  HCH3  0   0.216  -8.4035  -1.2268  -0.3691
 KGM  H132  H  HCH3  0   0.215  -8.5511   0.0198   0.8646
 KGM  H133  H  HCH3  0   0.226  -9.2711   0.2638  -0.7248
 KGM  H121  H  HCH2  0   0.210  -6.9993   0.3248  -1.7638
 KGM  H122  H  HCH2  0   0.210  -7.1568   1.5705  -0.5473
 KGM  H111  H  HCH2  0   0.207  -5.8248  -1.1421  -0.1105
 KGM  H112  H  HCH2  0   0.206  -5.9900   0.1011   1.1101
 KGM  H101  H  HCH2  0   0.209  -4.6401   1.6668  -0.3099
 KGM  H102  H  HCH2  0   0.209  -4.4562   0.4096  -1.5135
 KGM  H91C  H  HCH2  0   0.213  -3.4789   0.2284   1.3756
 KGM  H92C  H  HCH2  0   0.215  -3.2849  -1.0276   0.1718
 KGM  H81C  H  HCH2  0   0.221  -2.1317   1.7949  -0.0585
 KGM  H82C  H  HCH2  0   0.224  -1.9076   0.5047  -1.2312
 KGM  H71C  H  HCH2  0   0.208  -0.7830  -0.8814   0.5338
 KGM  H72C  H  HCH2  0   0.202  -0.9937   0.4382   1.6868
 KGM  H1    H  HCH1  0   0.233   1.1613   1.1184   1.9742
 KGM  H2    H  HCH1  0   0.231   2.1004   2.6012   0.1126
 KGM  HA    H  HOH1  0   0.455   3.3008   2.2568   2.0244
 KGM  H3    H  HCH1  0   0.226   2.2120   0.9187  -1.6257
 KGM  HB    H  HOH1  0   0.457   3.8371   2.4181  -1.9130
 KGM  H4    H  HCH1  0   0.212   4.3254  -0.4731   0.0649
 KGM  HC    H  HOH1  0   0.452   4.4943  -0.6389  -2.2638
 KGM  H5    H  HCH1  0   0.223   1.5092  -1.3402  -0.7239
 KGM  H61C  H  HCH2  0   0.195   3.5148  -2.5324   1.2304
 KGM  H62C  H  HCH2  0   0.210   3.1874  -3.1441  -0.3922
 KGM  H6    H  HOH1  0   0.456   1.8788  -4.2033   1.1872

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
 KGM  C13  C12   single  1.522  0.020  1.522
 KGM  C12  C11   single  1.524  0.020  1.524
 KGM  C11  C10   single  1.523  0.020  1.523
 KGM  C10  C9    single  1.523  0.020  1.523
 KGM  C9   C8    single  1.524  0.020  1.524
 KGM  C8   C7    single  1.515  0.020  1.515
 KGM  C7   O1    single  1.418  0.020  1.418
 KGM  O1   C1    single  1.390  0.020  1.390
 KGM  C1   C2    single  1.532  0.020  1.532
 KGM  C1   O5    single  1.398  0.020  1.398
 KGM  C2   O2    single  1.405  0.020  1.405
 KGM  C2   C3    single  1.525  0.020  1.525
 KGM  C3   O3    single  1.408  0.020  1.408
 KGM  C3   C4    single  1.525  0.020  1.525
 KGM  C4   O4    single  1.409  0.020  1.409
 KGM  C4   C5    single  1.530  0.020  1.530
 KGM  C5   O5    single  1.417  0.020  1.417
 KGM  C5   C6    single  1.514  0.020  1.514
 KGM  C6   O6    single  1.408  0.020  1.408
 KGM  C13  H131  single  0.970  0.020  1.090
 KGM  C13  H132  single  0.970  0.020  1.090
 KGM  C13  H133  single  0.970  0.020  1.090
 KGM  C12  H121  single  0.970  0.020  1.090
 KGM  C12  H122  single  0.970  0.020  1.090
 KGM  C11  H111  single  0.970  0.020  1.090
 KGM  C11  H112  single  0.970  0.020  1.090
 KGM  C10  H101  single  0.970  0.020  1.090
 KGM  C10  H102  single  0.970  0.020  1.090
 KGM  C9   H91C  single  0.970  0.020  1.090
 KGM  C9   H92C  single  0.970  0.020  1.090
 KGM  C8   H81C  single  0.970  0.020  1.090
 KGM  C8   H82C  single  0.970  0.020  1.090
 KGM  C7   H71C  single  0.970  0.020  1.090
 KGM  C7   H72C  single  0.970  0.020  1.090
 KGM  C1   H1    single  0.970  0.020  1.090
 KGM  C2   H2    single  0.970  0.020  1.090
 KGM  O2   HA    single  0.850  0.020  0.980
 KGM  C3   H3    single  0.970  0.020  1.090
 KGM  O3   HB    single  0.850  0.020  0.980
 KGM  C4   H4    single  0.970  0.020  1.090
 KGM  O4   HC    single  0.850  0.020  0.980
 KGM  C5   H5    single  0.970  0.020  1.090
 KGM  C6   H61C  single  0.970  0.020  1.090
 KGM  C6   H62C  single  0.970  0.020  1.090
 KGM  O6   H6    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
 KGM  H6    O6   C6    107.96  3.000
 KGM  H62C  C6   H61C  107.11  3.000
 KGM  H62C  C6   C5    108.52  3.000
 KGM  H61C  C6   C5    108.77  3.000
 KGM  H62C  C6   O6    111.64  3.000
 KGM  H61C  C6   O6    111.86  3.000
 KGM  C5    C6   O6    108.85  3.000
 KGM  H5    C5   C4    108.18  3.000
 KGM  H5    C5   O5    110.63  3.000
 KGM  C4    C5   O5    110.60  3.000
 KGM  H5    C5   C6    108.65  3.000
 KGM  O5    C5   C6    107.10  3.000
 KGM  C4    C5   C6    111.68  3.000
 KGM  H102  C10  H101  106.03  3.000
 KGM  H102  C10  C11   109.38  3.000
 KGM  H101  C10  C11   109.27  3.000
 KGM  H102  C10  C9    109.49  3.000
 KGM  H101  C10  C9    109.23  3.000
 KGM  C11   C10  C9    113.18  3.000
 KGM  C1    O5   C5    115.89  3.000
 KGM  H4    C4   C3    109.07  3.000
 KGM  H4    C4   O4    110.73  3.000
 KGM  C3    C4   O4    111.07  3.000
 KGM  H4    C4   C5    108.82  3.000
 KGM  O4    C4   C5    107.63  3.000
 KGM  C3    C4   C5    109.48  3.000
 KGM  HC    O4   C4    107.77  3.000
 KGM  H3    C3   C2    107.63  3.000
 KGM  H3    C3   O3    110.72  3.000
 KGM  C2    C3   O3    112.66  3.000
 KGM  H3    C3   C4    107.52  3.000
 KGM  O3    C3   C4    107.52  3.000
 KGM  C2    C3   C4    110.69  3.000
 KGM  HB    O3   C3    108.80  3.000
 KGM  H2    C2   C1    108.38  3.000
 KGM  H2    C2   O2    111.28  3.000
 KGM  C1    C2   O2    110.37  3.000
 KGM  H2    C2   C3    109.23  3.000
 KGM  O2    C2   C3    108.41  3.000
 KGM  C1    C2   C3    109.15  3.000
 KGM  HA    O2   C2    108.64  3.000
 KGM  H1    C1   O1    110.30  3.000
 KGM  H1    C1   C2    109.89  3.000
 KGM  O1    C1   C2    107.70  3.000
 KGM  H1    C1   O5    104.60  3.000
 KGM  C2    C1   O5    111.25  3.000
 KGM  O1    C1   O5    113.08  3.000
 KGM  C7    O1   C1    115.00  3.000
 KGM  H72C  C7   H71C  107.04  3.000
 KGM  H72C  C7   C8    109.91  3.000
 KGM  H71C  C7   C8    110.10  3.000
 KGM  H72C  C7   O1    110.04  3.000
 KGM  H71C  C7   O1    110.69  3.000
 KGM  C8    C7   O1    109.04  3.000
 KGM  H82C  C8   H81C  106.87  3.000
 KGM  H82C  C8   C9    109.52  3.000
 KGM  H81C  C8   C9    109.55  3.000
 KGM  H82C  C8   C7    109.70  3.000
 KGM  H81C  C8   C7    109.33  3.000
 KGM  C9    C8   C7    111.74  3.000
 KGM  H92C  C9   H91C  106.09  3.000
 KGM  H92C  C9   C8    109.55  3.000
 KGM  H91C  C9   C8    109.42  3.000
 KGM  H92C  C9   C10   109.42  3.000
 KGM  H91C  C9   C10   109.26  3.000
 KGM  C8    C9   C10   112.88  3.000
 KGM  H133  C13  H132  107.67  3.000
 KGM  H133  C13  H131  107.60  3.000
 KGM  H132  C13  H131  107.44  3.000
 KGM  H133  C13  C12   111.60  3.000
 KGM  H132  C13  C12   111.10  3.000
 KGM  H131  C13  C12   111.22  3.000
 KGM  H122  C12  H121  106.00  3.000
 KGM  H122  C12  C11   109.20  3.000
 KGM  H121  C12  C11   109.34  3.000
 KGM  H122  C12  C13   109.52  3.000
 KGM  H121  C12  C13   109.59  3.000
 KGM  C11   C12  C13   112.95  3.000
 KGM  H112  C11  H111  105.99  3.000
 KGM  H112  C11  C12   109.31  3.000
 KGM  H111  C11  C12   109.36  3.000
 KGM  H112  C11  C10   109.26  3.000
 KGM  H111  C11  C10   109.42  3.000
 KGM  C12   C11  C10   113.24  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
 KGM  Var_01  C8    C7   O1   C1    163.69  30.0  1
 KGM  Var_02  C13   C12  C11  C10  -179.54  30.0  1
 KGM  Var_03  C7    C8   C9   C10   177.85  30.0  3
 KGM  Var_04  C9    C8   C7   O1    179.30  30.0  1
 KGM  Var_05  C11   C10  C9   C8   -179.52  30.0  1
 KGM  Var_06  C12   C11  C10  C9    178.80  30.0  2
 KGM  Var_07  H131  C13  C12  C11   -60.42  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
 KGM  chir_01  C5  C4  O5  C6  positiv
 KGM  chir_02  C4  O4  C5  C3  positiv
 KGM  chir_03  C3  O3  C2  C4  positiv
 KGM  chir_04  C2  O2  C3  C1  negativ
 KGM  chir_05  C1  O5  O1  C2  positiv

