# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:46:31 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(5-methyl-1H-benzimidazol-2-yl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2[nH]c(nc2c1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
#
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
 IMK  IMK  (1S)-1,5-anhydro-1-(5-methyl-1H-benzimidazol-2-yl)-D-glucitol  ligand  39  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IMK
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
 IMK  C1    C  CH1   0  -0.068   0.8721  -0.1493   0.5557
 IMK  C2    C  CH1   0   0.018   1.4090  -1.4569  -0.0249
 IMK  O2    O  OH1   0  -0.669   0.8088  -2.5079   0.6901
 IMK  C3    C  CH1   0  -0.026   2.9287  -1.4634   0.0997
 IMK  O3    O  OH1   0  -0.676   3.4995  -2.5809  -0.5480
 IMK  C4    C  CH1   0   0.038   3.5188  -0.2072  -0.5314
 IMK  O4    O  OH1   0  -0.673   4.9035  -0.1228  -0.3060
 IMK  C5    C  CH1   0  -0.016   2.8550   1.0308   0.0727
 IMK  O5    O  O2    0  -0.492   1.4537   0.9498  -0.0997
 IMK  C6    C  CH2   0  -0.158   3.3259   2.3076  -0.5901
 IMK  O6    O  OH1   0  -0.670   2.7275   3.4024   0.0615
 IMK  C7    C  CR16  0  -0.396  -3.6652   0.1336  -1.3124
 IMK  C8    C  CR56  0   0.149  -2.5539   0.0669  -0.4691
 IMK  C9    C  CR56  0   0.315  -2.7284   0.0949   0.9222
 IMK  C10   C  CR16  0  -0.295  -3.9860   0.1858   1.5091
 IMK  C11   C  CR16  0  -0.311  -5.0684   0.2500   0.6530
 IMK  C12   C  CR6   0   0.085  -4.9274   0.2253  -0.7506
 IMK  N1    N  NR15  0  -0.706  -1.4595   0.0176   1.4309
 IMK  C13   C  CR5   0   0.465  -0.6077  -0.0531   0.3801
 IMK  N2    N  N     0  -0.467  -1.2175  -0.0282  -0.7728
 IMK  H1    H  HCH1  0   0.248   1.1048  -0.1246   1.6328
 IMK  H2    H  HCH1  0   0.226   1.1369  -1.4936  -1.0892
 IMK  HO2   H  HOH1  0   0.459   0.9022  -3.3194   0.1825
 IMK  H3    H  HCH1  0   0.223   3.1874  -1.4631   1.1693
 IMK  HO3   H  HOH1  0   0.462   3.5934  -3.2979   0.0849
 IMK  H4    H  HCH1  0   0.212   3.2961  -0.2221  -1.6109
 IMK  HO4   H  HOH1  0   0.453   5.3058  -0.9326  -0.6386
 IMK  H5    H  HCH1  0   0.222   3.0989   1.0749   1.1470
 IMK  H61   H  HCH2  0   0.214   4.4182   2.3460  -0.5272
 IMK  H62   H  HCH2  0   0.197   3.0655   2.2731  -1.6573
 IMK  HO6   H  HOH1  0   0.457   3.0905   4.2081  -0.3168
 IMK  H7    H  HCR6  0   0.246  -3.5382   0.1145  -2.3885
 IMK  H10   H  HCR6  0   0.264  -4.1166   0.2084   2.5831
 IMK  H11   H  HCR6  0   0.247  -6.0646   0.3232   1.0733
 IMK  HN1   H  HNR5  0   0.421  -1.2011   0.0224   2.4053
 IMK  H141  H  HCH3  0   0.242  -6.8162  -0.5517  -1.4408
 IMK  H142  H  HCH3  0   0.242  -6.7324   1.2000  -1.4141
 IMK  H143  H  HCH3  0   0.242  -5.8947   0.3007  -2.6745
 IMK  C14   C  CH3   0  -0.723  -6.1534   0.2975  -1.6164

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
 IMK  C1   C2    single    1.528  0.020  1.528
 IMK  C1   O5    single    1.406  0.020  1.406
 IMK  C1   C13   single    1.493  0.020  1.493
 IMK  C1   H1    single    0.970  0.020  1.090
 IMK  C2   O2    single    1.406  0.020  1.406
 IMK  C2   C3    single    1.525  0.020  1.525
 IMK  C2   H2    single    0.970  0.020  1.090
 IMK  O2   HO2   single    0.850  0.020  0.980
 IMK  C3   O3    single    1.412  0.020  1.412
 IMK  C3   C4    single    1.525  0.020  1.525
 IMK  C3   H3    single    0.970  0.020  1.090
 IMK  O3   HO3   single    0.850  0.020  0.980
 IMK  C4   O4    single    1.405  0.020  1.405
 IMK  C4   C5    single    1.529  0.020  1.529
 IMK  C4   H4    single    0.970  0.020  1.090
 IMK  O4   HO4   single    0.850  0.020  0.980
 IMK  C5   O5    single    1.414  0.020  1.414
 IMK  C5   C6    single    1.514  0.020  1.514
 IMK  C5   H5    single    0.970  0.020  1.090
 IMK  C6   O6    single    1.408  0.020  1.408
 IMK  C6   H61   single    0.970  0.020  1.090
 IMK  C6   H62   single    0.970  0.020  1.090
 IMK  O6   HO6   single    0.850  0.020  0.980
 IMK  C7   C8    aromatic  1.397  0.020  1.397
 IMK  C7   C12   aromatic  1.385  0.020  1.385
 IMK  C7   H7    single    0.930  0.020  1.080
 IMK  C8   C9    aromatic  1.402  0.020  1.402
 IMK  C8   N2    aromatic  1.374  0.020  1.374
 IMK  C9   C10   aromatic  1.391  0.020  1.391
 IMK  C9   N1    aromatic  1.369  0.020  1.369
 IMK  C10  C11   aromatic  1.382  0.020  1.382
 IMK  C10  H10   single    0.930  0.020  1.080
 IMK  C11  C12   aromatic  1.411  0.020  1.411
 IMK  C11  H11   single    0.930  0.020  1.080
 IMK  C12  C14   single    1.503  0.020  1.503
 IMK  N1   C13   aromatic  1.355  0.020  1.355
 IMK  N1   HN1   single    0.860  0.020  1.020
 IMK  C13  N2    aromatic  1.305  0.020  1.305
 IMK  C14  H141  single    0.970  0.020  1.090
 IMK  C14  H142  single    0.970  0.020  1.090
 IMK  C14  H143  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
 IMK  H1    C1   C13   108.83  3.000
 IMK  H1    C1   O5    110.53  3.000
 IMK  C13   C1   O5    107.75  3.000
 IMK  H1    C1   C2    108.44  3.000
 IMK  C13   C1   C2    111.01  3.000
 IMK  O5    C1   C2    110.28  3.000
 IMK  H2    C2   C3    109.01  3.000
 IMK  H2    C2   O2    111.21  3.000
 IMK  C3    C2   O2    112.38  3.000
 IMK  H2    C2   C1    108.03  3.000
 IMK  C3    C2   C1    108.83  3.000
 IMK  O2    C2   C1    107.24  3.000
 IMK  HO2   O2   C2    108.73  3.000
 IMK  H3    C3   C4    108.13  3.000
 IMK  H3    C3   O3    110.55  3.000
 IMK  C4    C3   O3    107.80  3.000
 IMK  H3    C3   C2    108.29  3.000
 IMK  C4    C3   C2    110.39  3.000
 IMK  O3    C3   C2    111.64  3.000
 IMK  HO3   O3   C3    109.14  3.000
 IMK  H4    C4   C5    108.07  3.000
 IMK  H4    C4   O4    110.91  3.000
 IMK  C5    C4   O4    108.40  3.000
 IMK  H4    C4   C3    108.42  3.000
 IMK  C5    C4   C3    109.60  3.000
 IMK  O4    C4   C3    111.37  3.000
 IMK  HO4   O4   C4    107.79  3.000
 IMK  H5    C5   C6    108.91  3.000
 IMK  H5    C5   O5    109.89  3.000
 IMK  C6    C5   O5    107.65  3.000
 IMK  H5    C5   C4    108.74  3.000
 IMK  C6    C5   C4    112.02  3.000
 IMK  O5    C5   C4    109.61  3.000
 IMK  C5    O5   C1    113.45  3.000
 IMK  H62   C6   H61   107.05  3.000
 IMK  H62   C6   O6    111.91  3.000
 IMK  H61   C6   O6    111.73  3.000
 IMK  H62   C6   C5    108.96  3.000
 IMK  H61   C6   C5    108.35  3.000
 IMK  O6    C6   C5    108.73  3.000
 IMK  HO6   O6   C6    108.02  3.000
 IMK  H7    C7   C12   120.72  3.000
 IMK  H7    C7   C8    120.36  3.000
 IMK  C12   C7   C8    118.92  3.000
 IMK  N2    C8   C9    109.99  3.000
 IMK  N2    C8   C7    130.08  3.000
 IMK  C9    C8   C7    119.93  3.000
 IMK  N1    C9   C10   133.22  3.000
 IMK  N1    C9   C8    104.60  3.000
 IMK  C10   C9   C8    122.18  3.000
 IMK  H10   C10  C11   121.30  3.000
 IMK  H10   C10  C9    121.96  3.000
 IMK  C11   C10  C9    116.74  3.000
 IMK  H11   C11  C12   118.61  3.000
 IMK  H11   C11  C10   118.89  3.000
 IMK  C12   C11  C10   122.51  3.000
 IMK  C14   C12  C11   119.40  3.000
 IMK  C14   C12  C7    120.87  3.000
 IMK  C11   C12  C7    119.73  3.000
 IMK  HN1   N1   C13   126.08  3.000
 IMK  HN1   N1   C9    126.61  3.000
 IMK  C13   N1   C9    107.31  3.000
 IMK  N2    C13  N1    113.00  3.000
 IMK  N2    C13  C1    124.64  3.000
 IMK  N1    C13  C1    122.37  3.000
 IMK  C13   N2   C8    105.11  3.000
 IMK  H143  C14  H142  107.68  3.000
 IMK  H143  C14  H141  107.63  3.000
 IMK  H142  C14  H141  106.94  3.000
 IMK  H143  C14  C12   111.48  3.000
 IMK  H142  C14  C12   111.46  3.000
 IMK  H141  C14  C12   111.43  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
 IMK  CONST_01  C10   C9   C8   C7     0.00   0.0  0
 IMK  CONST_02  N1    C9   C8   C7   180.00   0.0  0
 IMK  CONST_03  C13   N2   C8   C7   180.00   0.0  0
 IMK  CONST_04  C10   C11  C12  C7     0.00   0.0  0
 IMK  CONST_05  C11   C12  C7   C8     0.00   0.0  0
 IMK  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 IMK  CONST_07  C13   N1   C9   C8     0.00   0.0  0
 IMK  CONST_08  N1    C13  N2   C8     0.00   0.0  0
 IMK  CONST_09  C12   C7   C8   C9     0.00   0.0  0
 IMK  CONST_10  C13   N2   C8   C9     0.00   0.0  0
 IMK  CONST_11  C12   C11  C10  C9     0.00   0.0  0
 IMK  CONST_12  N2    C13  N1   C9     0.00   0.0  0
 IMK  CONST_13  N2    C8   C9   C10  180.00   0.0  0
 IMK  CONST_14  C13   N1   C9   C10  180.00   0.0  0
 IMK  CONST_15  N1    C9   C10  C11  180.00   0.0  0
 IMK  CONST_16  N2    C8   C7   C12  180.00   0.0  0
 IMK  CONST_17  N2    C8   C9   N1     0.00   0.0  0
 IMK  CONST_18  C9    N1   C13  C1   180.00   0.0  0
 IMK  CONST_19  C8    N2   C13  C1   180.00   0.0  0
 IMK  CONST_20  C14   C12  C7   C8   180.00   0.0  0
 IMK  CONST_21  C14   C12  C11  C10  180.00   0.0  0
 IMK  CONST_22  HN1   N1   C13  C1     0.00   0.0  0
 IMK  CONST_23  H11   C11  C12  C7   180.00   0.0  0
 IMK  CONST_24  H10   C10  C9   C8   180.00   0.0  0
 IMK  CONST_25  H7    C7   C8   C9   180.00   0.0  0
 IMK  Var_01    H141  C14  C12  C7   118.38  30.0  2

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
 IMK  chir_01  C1  C2  O5  C13  negativ
 IMK  chir_02  C2  O2  C1  C3   negativ
 IMK  chir_03  C3  O3  C2  C4   positiv
 IMK  chir_04  C4  O4  C5  C3   positiv
 IMK  chir_05  C5  O5  C4  C6   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
 IMK  plan-1  C1   0.020
 IMK  plan-1  C7   0.020
 IMK  plan-1  C8   0.020
 IMK  plan-1  C9   0.020
 IMK  plan-1  C10  0.020
 IMK  plan-1  C11  0.020
 IMK  plan-1  C12  0.020
 IMK  plan-1  N1   0.020
 IMK  plan-1  C13  0.020
 IMK  plan-1  N2   0.020
 IMK  plan-1  H7   0.020
 IMK  plan-1  H10  0.020
 IMK  plan-1  H11  0.020
 IMK  plan-1  HN1  0.020
 IMK  plan-1  C14  0.020

