# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 08:49:59 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-deoxy-1-[methyl(octanoyl)amino]hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)N(C)CC(O)C(O)C(O)C(O)CO
#
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
 MG8  MG8  1-deoxy-1-[methyl(octanoyl)amino]hexitol  ligand  53  22  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MG8
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
 MG8  C1    C  CH3   0  -0.663  14.4260  13.4409  -2.5683
 MG8  C2    C  CH2   0  -0.418  14.0613  12.0221  -2.1541
 MG8  C3    C  CH2   0  -0.406  15.2250  11.0482  -2.2914
 MG8  C4    C  CH2   0  -0.412  14.8722   9.6201  -1.8956
 MG8  C5    C  CH2   0  -0.414  16.0522   8.6635  -2.0081
 MG8  C6    C  CH2   0  -0.406  15.6920   7.2191  -1.6823
 MG8  C7    C  CH2   0  -0.592  16.9131   6.3151  -1.7429
 MG8  C8    C  C     0   0.574  16.6040   4.8440  -1.5649
 MG8  O8    O  O     0  -0.512  15.4491   4.4369  -1.4985
 MG8  N     N  NT    0  -0.448  17.6671   4.0101  -1.4811
 MG8  C9    C  CH2   0  -0.361  17.4598   2.5769  -1.4212
 MG8  C10   C  CH1   0   0.020  17.5614   1.9215  -2.7999
 MG8  O10   O  OH1   0  -0.666  16.6779   2.5386  -3.7203
 MG8  C11   C  CH1   0  -0.028  17.3339   0.4035  -2.7195
 MG8  O11   O  OH1   0  -0.670  18.3154  -0.0959  -1.8346
 MG8  C12   C  CH1   0  -0.004  17.4639  -0.2707  -4.1035
 MG8  O12   O  OH1   0  -0.690  16.4348   0.1204  -4.9787
 MG8  C13   C  CH1   0  -0.002  17.4629  -1.8025  -4.0325
 MG8  O13   O  OH1   0  -0.672  17.7816  -2.3645  -5.2862
 MG8  C14   C  CH2   0  -0.170  16.1160  -2.3687  -3.6040
 MG8  O14   O  OH1   0  -0.666  16.1446  -3.7634  -3.4077
 MG8  C15   C  CH3   0  -0.544  19.0280   4.4556  -1.7158
 MG8  H11A  H  HCH3  0   0.226  13.5831  14.1230  -2.4521
 MG8  H12A  H  HCH3  0   0.215  15.2491  13.8274  -1.9643
 MG8  H13A  H  HCH3  0   0.215  14.7403  13.4790  -3.6131
 MG8  H21   H  HCH2  0   0.210  13.7106  12.0218  -1.1175
 MG8  H22   H  HCH2  0   0.210  13.2190  11.6683  -2.7570
 MG8  H31   H  HCH2  0   0.206  15.5844  11.0576  -3.3264
 MG8  H32   H  HCH2  0   0.206  16.0638  11.3987  -1.6793
 MG8  H41   H  HCH2  0   0.207  14.0495   9.2623  -2.5249
 MG8  H42   H  HCH2  0   0.207  14.4926   9.6095  -0.8681
 MG8  H51   H  HCH2  0   0.209  16.8557   9.0024  -1.3448
 MG8  H52   H  HCH2  0   0.210  16.4614   8.7115  -3.0234
 MG8  H61   H  HCH2  0   0.219  15.2424   7.1693  -0.6865
 MG8  H62   H  HCH2  0   0.220  14.9284   6.8712  -2.3818
 MG8  H71   H  HCH2  0   0.263  17.4191   6.4424  -2.7071
 MG8  H72   H  HCH2  0   0.263  17.6430   6.6346  -0.9934
 MG8  H91   H  HCH2  0   0.270  18.2054   2.1467  -0.7537
 MG8  H92   H  HCH2  0   0.262  16.4818   2.3720  -0.9843
 MG8  H10   H  HCH1  0   0.245  18.5675   2.0881  -3.2033
 MG8  HO10  H  HOH1  0   0.456  15.8185   2.6555  -3.2963
 MG8  H11   H  HCH1  0   0.230  16.3202   0.2291  -2.3300
 MG8  HO11  H  HOH1  0   0.460  17.9442  -0.8170  -1.3202
 MG8  H12   H  HCH1  0   0.202  18.4531   0.0234  -4.5006
 MG8  HO12  H  HOH1  0   0.447  16.3542   1.0821  -4.9079
 MG8  H13   H  HCH1  0   0.207  18.2136  -2.0986  -3.2854
 MG8  HO13  H  HOH1  0   0.448  18.7008  -2.1604  -5.4840
 MG8  H141  H  HCH2  0   0.227  15.3705  -2.1775  -4.3773
 MG8  H142  H  HCH2  0   0.202  15.7778  -1.8460  -2.7002
 MG8  HO14  H  HOH1  0   0.445  16.7480  -3.9544  -2.6834
 MG8  H151  H  HCH3  0   0.258  19.2811   5.3224  -1.1080
 MG8  H152  H  HCH3  0   0.245  19.2142   4.7047  -2.7626
 MG8  H153  H  HCH3  0   0.263  19.7106   3.6562  -1.4356

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
 MG8  C1   C2    single  1.522  0.020  1.522
 MG8  C1   H11A  single  0.970  0.020  1.090
 MG8  C1   H12A  single  0.970  0.020  1.090
 MG8  C1   H13A  single  0.970  0.020  1.090
 MG8  C2   C3    single  1.524  0.020  1.524
 MG8  C2   H21   single  0.970  0.020  1.090
 MG8  C2   H22   single  0.970  0.020  1.090
 MG8  C3   C4    single  1.523  0.020  1.523
 MG8  C3   H31   single  0.970  0.020  1.090
 MG8  C3   H32   single  0.970  0.020  1.090
 MG8  C4   C5    single  1.523  0.020  1.523
 MG8  C4   H41   single  0.970  0.020  1.090
 MG8  C4   H42   single  0.970  0.020  1.090
 MG8  C5   C6    single  1.524  0.020  1.524
 MG8  C5   H51   single  0.970  0.020  1.090
 MG8  C5   H52   single  0.970  0.020  1.090
 MG8  C6   C7    single  1.521  0.020  1.521
 MG8  C6   H61   single  0.970  0.020  1.090
 MG8  C6   H62   single  0.970  0.020  1.090
 MG8  C7   C8    single  1.514  0.020  1.514
 MG8  C7   H71   single  0.970  0.020  1.090
 MG8  C7   H72   single  0.970  0.020  1.090
 MG8  C8   O8    double  1.226  0.020  1.226
 MG8  C8   N     single  1.354  0.020  1.354
 MG8  N    C9    single  1.449  0.020  1.449
 MG8  N    C15   single  1.451  0.020  1.451
 MG8  C9   C10   single  1.530  0.020  1.530
 MG8  C9   H91   single  0.970  0.020  1.090
 MG8  C9   H92   single  0.970  0.020  1.090
 MG8  C10  O10   single  1.417  0.020  1.417
 MG8  C10  C11   single  1.537  0.020  1.537
 MG8  C10  H10   single  0.970  0.020  1.090
 MG8  O10  HO10  single  0.850  0.020  0.980
 MG8  C11  O11   single  1.413  0.020  1.413
 MG8  C11  C12   single  1.545  0.020  1.545
 MG8  C11  H11   single  0.970  0.020  1.090
 MG8  O11  HO11  single  0.850  0.020  0.980
 MG8  C12  O12   single  1.406  0.020  1.406
 MG8  C12  C13   single  1.533  0.020  1.533
 MG8  C12  H12   single  0.970  0.020  1.090
 MG8  O12  HO12  single  0.850  0.020  0.980
 MG8  C13  O13   single  1.410  0.020  1.410
 MG8  C13  C14   single  1.523  0.020  1.523
 MG8  C13  H13   single  0.970  0.020  1.090
 MG8  O13  HO13  single  0.850  0.020  0.980
 MG8  C14  O14   single  1.409  0.020  1.409
 MG8  C14  H141  single  0.970  0.020  1.090
 MG8  C14  H142  single  0.970  0.020  1.090
 MG8  O14  HO14  single  0.850  0.020  0.980
 MG8  C15  H151  single  0.970  0.020  1.090
 MG8  C15  H152  single  0.970  0.020  1.090
 MG8  C15  H153  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
 MG8  H13A  C1   H12A  107.46  3.000
 MG8  H13A  C1   H11A  107.62  3.000
 MG8  H12A  C1   H11A  107.60  3.000
 MG8  H13A  C1   C2    111.22  3.000
 MG8  H12A  C1   C2    111.10  3.000
 MG8  H11A  C1   C2    111.64  3.000
 MG8  H22   C2   H21   105.97  3.000
 MG8  H22   C2   C3    109.36  3.000
 MG8  H21   C2   C3    109.27  3.000
 MG8  H22   C2   C1    109.62  3.000
 MG8  H21   C2   C1    109.56  3.000
 MG8  C3    C2   C1    112.84  3.000
 MG8  H32   C3   H31   105.89  3.000
 MG8  H32   C3   C4    109.38  3.000
 MG8  H31   C3   C4    109.24  3.000
 MG8  H32   C3   C2    109.26  3.000
 MG8  H31   C3   C2    109.28  3.000
 MG8  C4    C3   C2    113.51  3.000
 MG8  H42   C4   H41   105.98  3.000
 MG8  H42   C4   C5    109.37  3.000
 MG8  H41   C4   C5    109.52  3.000
 MG8  H42   C4   C3    109.45  3.000
 MG8  H41   C4   C3    109.31  3.000
 MG8  C5    C4   C3    112.97  3.000
 MG8  H52   C5   H51   105.87  3.000
 MG8  H52   C5   C6    109.14  3.000
 MG8  H51   C5   C6    109.70  3.000
 MG8  H52   C5   C4    109.28  3.000
 MG8  H51   C5   C4    109.22  3.000
 MG8  C6    C5   C4    113.35  3.000
 MG8  H62   C6   H61   106.32  3.000
 MG8  H62   C6   C7    110.27  3.000
 MG8  H61   C6   C7    109.84  3.000
 MG8  H62   C6   C5    109.28  3.000
 MG8  H61   C6   C5    109.57  3.000
 MG8  C7    C6   C5    111.42  3.000
 MG8  H72   C7   H71   105.11  3.000
 MG8  H72   C7   C8    109.85  3.000
 MG8  H71   C7   C8    108.09  3.000
 MG8  H72   C7   C6    109.57  3.000
 MG8  H71   C7   C6    109.67  3.000
 MG8  C8    C7   C6    114.15  3.000
 MG8  N     C8   O8    122.12  3.000
 MG8  N     C8   C7    116.46  3.000
 MG8  O8    C8   C7    121.42  3.000
 MG8  C15   N    C9    116.39  3.000
 MG8  C15   N    C8    122.50  3.000
 MG8  C9    N    C8    119.96  3.000
 MG8  H92   C9   H91   107.10  3.000
 MG8  H92   C9   C10   109.88  3.000
 MG8  H91   C9   C10   109.73  3.000
 MG8  H92   C9   N     109.31  3.000
 MG8  H91   C9   N     108.54  3.000
 MG8  C10   C9   N     112.14  3.000
 MG8  H10   C10  C11   107.76  3.000
 MG8  H10   C10  O10   105.48  3.000
 MG8  C11   C10  O10   111.82  3.000
 MG8  H10   C10  C9    109.11  3.000
 MG8  C11   C10  C9    111.48  3.000
 MG8  O10   C10  C9    110.94  3.000
 MG8  HO10  O10  C10   108.81  3.000
 MG8  H11   C11  C12   109.00  3.000
 MG8  H11   C11  O11   111.25  3.000
 MG8  C12   C11  O11   110.39  3.000
 MG8  H11   C11  C10   108.15  3.000
 MG8  C12   C11  C10   111.82  3.000
 MG8  O11   C11  C10   106.20  3.000
 MG8  HO11  O11  C11   109.41  3.000
 MG8  H12   C12  C13   106.43  3.000
 MG8  H12   C12  O12   110.93  3.000
 MG8  C13   C12  O12   107.83  3.000
 MG8  H12   C12  C11   106.31  3.000
 MG8  C13   C12  C11   113.23  3.000
 MG8  O12   C12  C11   111.99  3.000
 MG8  HO12  O12  C12   106.97  3.000
 MG8  H13   C13  C14   108.21  3.000
 MG8  H13   C13  O13   110.02  3.000
 MG8  C14   C13  O13   107.57  3.000
 MG8  H13   C13  C12   107.46  3.000
 MG8  C14   C13  C12   112.65  3.000
 MG8  O13   C13  C12   110.90  3.000
 MG8  HO13  O13  C13   108.31  3.000
 MG8  H142  C14  H141  106.84  3.000
 MG8  H142  C14  O14   111.29  3.000
 MG8  H141  C14  O14   106.62  3.000
 MG8  H142  C14  C13   109.10  3.000
 MG8  H141  C14  C13   109.87  3.000
 MG8  O14   C14  C13   112.92  3.000
 MG8  HO14  O14  C14   108.31  3.000
 MG8  H153  C15  H152  107.91  3.000
 MG8  H153  C15  H151  107.18  3.000
 MG8  H152  C15  H151  108.29  3.000
 MG8  H153  C15  N     108.74  3.000
 MG8  H152  C15  N     112.65  3.000
 MG8  H151  C15  N     111.86  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
 MG8  CONST_01  C9    N    C8  C7   180.00   0.0  0
 MG8  CONST_02  C15   N    C8  C7     0.00   0.0  0
 MG8  CONST_03  C9    N    C8  O8     0.00   0.0  0
 MG8  CONST_04  C15   N    C8  O8   180.00   0.0  0
 MG8  Var_01    C4    C3   C2  C1  -179.35  30.0  3
 MG8  Var_02    C5    C4   C3  C2  -178.72  30.0  3
 MG8  Var_03    C6    C5   C4  C3  -177.07  30.0  3
 MG8  Var_04    C7    C6   C5  C4  -177.27  30.0  3
 MG8  Var_05    C8    C7   C6  C5  -174.23  30.0  3
 MG8  Var_06    O8    C8   C7  C6     6.06  30.0  3
 MG8  Var_07    C10   C9   N   C8    95.15  30.0  3
 MG8  Var_08    H11A  C1   C2  C3  -179.38  30.0  3
 MG8  Var_09    H151  C15  N   C8    52.78  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
 MG8  chir_01  C10  C9   O10  C11  positiv
 MG8  chir_02  C11  O11  C10  C12  negativ
 MG8  chir_03  C12  O12  C11  C13  negativ
 MG8  chir_04  C13  O13  C12  C14  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
 MG8  plan-1  C7   0.020
 MG8  plan-1  C8   0.020
 MG8  plan-1  O8   0.020
 MG8  plan-1  N    0.020
 MG8  plan-1  C9   0.020
 MG8  plan-1  C15  0.020

