# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 07:04:17 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(CO[C@@H]2C=CO[C@H](CO)[C@@H]2O)nc3ccc(cc13)C(O)=O
#
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
 4IU  4IU  "2-[[(2R,3R,4R)-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2H-pyran-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid"  ligand  41  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4IU
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
 4IU  O4   O  OC    -1  -0.589   4.8495  -0.3384   6.6456
 4IU  C15  C  C      0   0.397   4.5804  -1.2898   5.8862
 4IU  O5   O  O      0  -0.588   3.7139  -1.3108   4.9914
 4IU  C12  C  CR6    0  -0.118   5.3993  -2.5646   6.0730
 4IU  C11  C  CR16   0  -0.306   5.2310  -3.6532   5.1952
 4IU  C10  C  CR16   0  -0.324   5.9575  -4.8216   5.3192
 4IU  C8   C  CR56   0   0.124   6.8790  -4.9135   6.3628
 4IU  N    N  N      0  -0.479   7.7270  -5.9322   6.7198
 4IU  C13  C  CR16   0  -0.373   6.3158  -2.6502   7.1114
 4IU  C9   C  CR56   0   0.371   7.0337  -3.8320   7.2424
 4IU  N1   N  NR5    0  -0.532   7.9817  -4.2401   8.1485
 4IU  C14  C  CH3    0  -0.529   8.4871  -3.4591   9.2541
 4IU  C7   C  CR5    0   0.411   8.3595  -5.4932   7.7751
 4IU  C6   C  CH2    0  -0.252   9.3910  -6.2671   8.5195
 4IU  O3   O  O2     0  -0.491  10.5820  -5.5194   8.5157
 4IU  C1   C  CH1    0   0.090  11.6296  -6.0975   9.2619
 4IU  C2   C  C1     0  -0.413  11.4511  -5.9351  10.7458
 4IU  C3   C  C1     0   0.057  12.4778  -5.6430  11.5396
 4IU  O    O  O2     0  -0.461  13.7562  -5.5090  11.1415
 4IU  C4   C  CH1    0   0.002  14.0293  -5.9052   9.8010
 4IU  C    C  CH1    0  -0.073  12.9351  -5.4230   8.8478
 4IU  O2   O  OH1    0  -0.660  12.7622  -4.0297   8.9189
 4IU  C5   C  CH2    0  -0.169  15.3978  -5.3816   9.4279
 4IU  O1   O  OH1    0  -0.663  16.3548  -5.9716  10.2725
 4IU  H2   H  HCR6   0   0.236   4.5081  -3.5605   4.3961
 4IU  H3   H  HCR6   0   0.242   5.8176  -5.6440   4.6285
 4IU  H4   H  HCR6   0   0.253   6.4556  -1.8163   7.7868
 4IU  H5   H  HCH3   0   0.264   8.7190  -4.1024  10.0993
 4IU  H6   H  HCH3   0   0.256   9.3821  -2.9052   8.9758
 4IU  H7   H  HCH3   0   0.261   7.7212  -2.7563   9.5717
 4IU  H8   H  HCH2   0   0.237   9.0356  -6.4654   9.5399
 4IU  H9   H  HCH2   0   0.252   9.5158  -7.2386   8.0272
 4IU  H10  H  HCH1   0   0.233  11.7108  -7.1638   9.0031
 4IU  H11  H  H      0   0.259  10.4741  -6.0510  11.1963
 4IU  H12  H  H      0   0.266  12.3658  -5.4915  12.6068
 4IU  H13  H  HCH1   0   0.238  14.0521  -7.0041   9.7594
 4IU  H14  H  HCH1   0   0.248  13.1960  -5.7466   7.8322
 4IU  H15  H  HOH1   0   0.457  13.3899  -3.6077   8.3260
 4IU  H16  H  HCH2   0   0.207  15.5703  -5.6343   8.3736
 4IU  H17  H  HCH2   0   0.203  15.4096  -4.2870   9.5054
 4IU  H18  H  HOH1   0   0.456  17.2162  -5.6078  10.0494

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
 4IU  O5   C15  deloc     1.246  0.020  1.246
 4IU  C11  C10  aromatic  1.381  0.020  1.381
 4IU  C11  C12  aromatic  1.408  0.020  1.408
 4IU  C10  C8   aromatic  1.395  0.020  1.395
 4IU  C15  C12  single    1.527  0.020  1.527
 4IU  C15  O4   deloc     1.247  0.020  1.247
 4IU  C12  C13  aromatic  1.388  0.020  1.388
 4IU  C8   N    aromatic  1.373  0.020  1.373
 4IU  C8   C9   aromatic  1.403  0.020  1.403
 4IU  N    C7   aromatic  1.306  0.020  1.306
 4IU  C13  C9   aromatic  1.389  0.020  1.389
 4IU  C9   N1   aromatic  1.373  0.020  1.373
 4IU  C7   N1   aromatic  1.361  0.020  1.361
 4IU  C7   C6   single    1.489  0.020  1.489
 4IU  N1   C14  single    1.445  0.020  1.445
 4IU  C6   O3   single    1.406  0.020  1.406
 4IU  O3   C1   single    1.410  0.020  1.410
 4IU  O2   C    single    1.406  0.020  1.406
 4IU  C    C1   single    1.527  0.020  1.527
 4IU  C    C4   single    1.529  0.020  1.529
 4IU  C5   C4   single    1.512  0.020  1.512
 4IU  C5   O1   single    1.406  0.020  1.406
 4IU  C1   C2   single    1.503  0.020  1.503
 4IU  C4   O    single    1.424  0.020  1.424
 4IU  C2   C3   double    1.330  0.020  1.330
 4IU  O    C3   single    1.346  0.020  1.346
 4IU  C11  H2   single    0.930  0.020  1.080
 4IU  C10  H3   single    0.930  0.020  1.080
 4IU  C13  H4   single    0.930  0.020  1.080
 4IU  C14  H5   single    0.970  0.020  1.090
 4IU  C14  H6   single    0.970  0.020  1.090
 4IU  C14  H7   single    0.970  0.020  1.090
 4IU  C6   H8   single    0.970  0.020  1.090
 4IU  C6   H9   single    0.970  0.020  1.090
 4IU  C1   H10  single    0.970  0.020  1.090
 4IU  C2   H11  single    0.930  0.020  1.080
 4IU  C3   H12  single    0.930  0.020  1.080
 4IU  C4   H13  single    0.970  0.020  1.090
 4IU  C    H14  single    0.970  0.020  1.090
 4IU  O2   H15  single    0.850  0.020  0.980
 4IU  C5   H16  single    0.970  0.020  1.090
 4IU  C5   H17  single    0.970  0.020  1.090
 4IU  O1   H18  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
 4IU  C12  C15  O5   116.55  3.000
 4IU  C12  C15  O4   116.54  3.000
 4IU  O5   C15  O4   126.91  3.000
 4IU  C13  C12  C11  119.84  3.000
 4IU  C13  C12  C15  119.83  3.000
 4IU  C11  C12  C15  120.33  3.000
 4IU  H2   C11  C10  119.35  3.000
 4IU  H2   C11  C12  118.31  3.000
 4IU  C10  C11  C12  122.34  3.000
 4IU  H3   C10  C8   120.82  3.000
 4IU  H3   C10  C11  121.14  3.000
 4IU  C8   C10  C11  118.05  3.000
 4IU  C9   C8   N    109.94  3.000
 4IU  C9   C8   C10  119.41  3.000
 4IU  N    C8   C10  130.65  3.000
 4IU  C7   N    C8   105.06  3.000
 4IU  H4   C13  C9   122.00  3.000
 4IU  H4   C13  C12  120.32  3.000
 4IU  C9   C13  C12  117.68  3.000
 4IU  N1   C9   C13  132.21  3.000
 4IU  N1   C9   C8   105.11  3.000
 4IU  C13  C9   C8   122.67  3.000
 4IU  C7   N1   C14  127.62  3.000
 4IU  C14  N1   C9   125.85  3.000
 4IU  C7   N1   C9   106.52  3.000
 4IU  H7   C14  H6   108.97  3.000
 4IU  H7   C14  H5   107.80  3.000
 4IU  H6   C14  H5   108.93  3.000
 4IU  H7   C14  N1   109.06  3.000
 4IU  H6   C14  N1   111.53  3.000
 4IU  H5   C14  N1   110.47  3.000
 4IU  C6   C7   N1   122.26  3.000
 4IU  C6   C7   N    124.37  3.000
 4IU  N1   C7   N    113.37  3.000
 4IU  H9   C6   H8   107.10  3.000
 4IU  H9   C6   O3   111.94  3.000
 4IU  H8   C6   O3   111.87  3.000
 4IU  H9   C6   C7   108.36  3.000
 4IU  H8   C6   C7   109.52  3.000
 4IU  O3   C6   C7   108.00  3.000
 4IU  C1   O3   C6   114.19  3.000
 4IU  H10  C1   C    107.53  3.000
 4IU  H10  C1   C2   110.22  3.000
 4IU  C    C1   C2   108.75  3.000
 4IU  H10  C1   O3   109.13  3.000
 4IU  C2   C1   O3   112.94  3.000
 4IU  C    C1   O3   108.10  3.000
 4IU  H11  C2   C3   118.16  3.000
 4IU  H11  C2   C1   120.43  3.000
 4IU  C3   C2   C1   121.40  3.000
 4IU  H12  C3   O    112.06  3.000
 4IU  H12  C3   C2   122.59  3.000
 4IU  O    C3   C2   125.36  3.000
 4IU  C4   O    C3   115.65  3.000
 4IU  H13  C4   C5   108.53  3.000
 4IU  H13  C4   C    107.84  3.000
 4IU  C5   C4   C    112.62  3.000
 4IU  H13  C4   O    108.51  3.000
 4IU  C5   C4   O    108.02  3.000
 4IU  C    C4   O    111.21  3.000
 4IU  H14  C    O2   111.61  3.000
 4IU  H14  C    C4   108.29  3.000
 4IU  O2   C    C4   111.66  3.000
 4IU  H14  C    C1   108.91  3.000
 4IU  C4   C    C1   107.67  3.000
 4IU  O2   C    C1   108.60  3.000
 4IU  H15  O2   C    108.89  3.000
 4IU  H17  C5   H16  107.19  3.000
 4IU  H17  C5   O1   111.64  3.000
 4IU  H16  C5   O1   111.92  3.000
 4IU  H17  C5   C4   109.74  3.000
 4IU  H16  C5   C4   107.43  3.000
 4IU  O1   C5   C4   108.82  3.000
 4IU  H18  O1   C5   108.16  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
 4IU  CONST_01  C8   C10  C11  C12     0.00   0.0  0
 4IU  CONST_02  C8   C9   C13  C12     0.00   0.0  0
 4IU  CONST_03  N1   C9   C13  C12   180.00   0.0  0
 4IU  CONST_04  N    C8   C10  C11   180.00   0.0  0
 4IU  CONST_05  C9   C8   C10  C11     0.00   0.0  0
 4IU  CONST_06  C9   C13  C12  C11     0.00   0.0  0
 4IU  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 4IU  CONST_08  C7   N    C8   C10   180.00   0.0  0
 4IU  CONST_09  C13  C9   C8   C10     0.00   0.0  0
 4IU  CONST_10  N1   C9   C8   C10   180.00   0.0  0
 4IU  CONST_11  N1   C7   N    C8      0.00   0.0  0
 4IU  CONST_12  C7   N1   C9   C8      0.00   0.0  0
 4IU  CONST_13  C13  C9   C8   N     180.00   0.0  0
 4IU  CONST_14  N1   C9   C8   N       0.00   0.0  0
 4IU  CONST_15  C9   N1   C7   N       0.00   0.0  0
 4IU  CONST_16  C7   N1   C9   C13   180.00   0.0  0
 4IU  CONST_17  C7   N    C8   C9      0.00   0.0  0
 4IU  CONST_18  C10  C11  C12  C15   180.00   0.0  0
 4IU  CONST_19  C9   C13  C12  C15   180.00   0.0  0
 4IU  CONST_20  C6   C7   N    C8    180.00   0.0  0
 4IU  CONST_21  C14  N1   C9   C8    180.00   0.0  0
 4IU  CONST_22  C14  N1   C7   N     180.00   0.0  0
 4IU  CONST_23  C14  N1   C9   C13     0.00   0.0  0
 4IU  CONST_24  C6   C7   N1   C9    180.00   0.0  0
 4IU  CONST_25  H3   C10  C11  C12   180.00   0.0  0
 4IU  CONST_26  H4   C13  C12  C11   180.00   0.0  0
 4IU  CONST_27  H2   C11  C10  C8    180.00   0.0  0
 4IU  CONST_28  H4   C13  C9   C8    180.00   0.0  0
 4IU  CONST_29  H3   C10  C8   N       0.00   0.0  0
 4IU  CONST_30  H2   C11  C12  C13   180.00   0.0  0
 4IU  CONST_31  H3   C10  C8   C9    180.00   0.0  0
 4IU  CONST_32  H4   C13  C9   N1      0.00   0.0  0
 4IU  Var_01    O    C3   C2   C1     -2.41  30.0  1
 4IU  Var_02    C4   O    C3   C2     -9.48  30.0  1
 4IU  Var_03    H12  C3   C2   C1    178.06  30.0  1
 4IU  Var_04    H11  C2   C3   O     177.79  30.0  1
 4IU  Var_05    H12  C3   O    C4    170.09  30.0  1
 4IU  Var_06    C11  C12  C15  O4   -175.29  30.0  2
 4IU  Var_07    C13  C12  C15  O4      4.59  30.0  2
 4IU  Var_08    C11  C12  C15  O5      4.73  30.0  2
 4IU  Var_09    C13  C12  C15  O5   -175.38  30.0  2
 4IU  Var_10    O3   C6   C7   N     121.67  30.0  2
 4IU  Var_11    O3   C6   C7   N1    -58.64  30.0  2
 4IU  Var_12    C1   O3   C6   C7    176.23  30.0  3
 4IU  Var_13    H8   C6   C7   N    -116.28  30.0  2
 4IU  Var_14    H9   C6   C7   N       0.22  30.0  2
 4IU  Var_15    H5   C14  N1   C9    146.22  30.0  2
 4IU  Var_16    H6   C14  N1   C9    -92.49  30.0  2
 4IU  Var_17    H7   C14  N1   C9     27.91  30.0  2
 4IU  Var_18    H8   C6   C7   N1     63.41  30.0  2
 4IU  Var_19    H9   C6   C7   N1    179.91  30.0  2
 4IU  Var_20    H5   C14  N1   C7    -35.49  30.0  2
 4IU  Var_21    H6   C14  N1   C7     85.80  30.0  2
 4IU  Var_22    H7   C14  N1   C7   -153.80  30.0  2
 4IU  Var_23    H8   C6   O3   C1     55.64  30.0  1
 4IU  Var_24    H9   C6   O3   C1    -64.57  30.0  1

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
 4IU  chir_01  C1  O3  C   C2  negativ
 4IU  chir_02  C4  O   C5  C   positiv
 4IU  chir_03  C   O2  C4  C1  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
 4IU  plan-1  C15  0.020
 4IU  plan-1  C12  0.020
 4IU  plan-1  C11  0.020
 4IU  plan-1  C10  0.020
 4IU  plan-1  C8   0.020
 4IU  plan-1  N    0.020
 4IU  plan-1  C13  0.020
 4IU  plan-1  C9   0.020
 4IU  plan-1  N1   0.020
 4IU  plan-1  C14  0.020
 4IU  plan-1  C7   0.020
 4IU  plan-1  C6   0.020
 4IU  plan-1  H2   0.020
 4IU  plan-1  H3   0.020
 4IU  plan-1  H4   0.020
 4IU  plan-2  O4   0.020
 4IU  plan-2  C15  0.020
 4IU  plan-2  O5   0.020
 4IU  plan-2  C12  0.020

