# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 23:31:43 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc([nH]c2c1)SCc3ncc(C)c(OC)c3C
#
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
 1C6  1C6  6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole  ligand  42  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1C6
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
 1C6  S    S  S2    0   0.060  -0.3343   0.8494  -0.6754
 1C6  CB   C  CH2   0  -0.630  -1.1972   0.2043   0.7968
 1C6  CG   C  CR6   0   0.181  -2.6711   0.3777   0.5686
 1C6  CD1  C  CR6   0  -0.023  -3.4178  -0.6109  -0.0792
 1C6  C3   C  CH3   0  -0.762  -2.7779  -1.8597  -0.6105
 1C6  CE1  C  CR6   0   0.397  -4.7854  -0.3718  -0.2193
 1C6  O2   O  O2    0  -0.482  -5.5870  -1.2785  -0.8330
 1C6  C2   C  CH3   0  -0.416  -5.9919  -2.3647  -0.0064
 1C6  CZ   C  CR6   0  -0.065  -5.3524   0.8181   0.2354
 1C6  C1   C  CH3   0  -0.717  -6.8105   1.1125   0.0682
 1C6  CE2  C  CR16  0  -0.129  -4.4906   1.7241   0.8373
 1C6  N1   N  N     0  -0.406  -3.1945   1.5146   1.0105
 1C6  CF1  C  CR5   0   0.298   1.3088   0.4448  -0.2637
 1C6  NV   N  NR15  0  -0.709   2.3279   0.7927  -1.0990
 1C6  CX2  C  CR56  0   0.353   3.4882   0.3491  -0.5183
 1C6  CS2  C  CR56  0   0.131   3.0758  -0.2616   0.6771
 1C6  NE1  N  N     0  -0.463   1.7032  -0.1829   0.8035
 1C6  CE3  C  CR16  0  -0.410   4.8126   0.4223  -0.9136
 1C6  CZ3  C  CR6   0   0.373   5.7553  -0.1467  -0.0603
 1C6  O3   O  O2    0  -0.478   7.0398  -0.0627  -0.4709
 1C6  C4   C  CH3   0  -0.435   8.0539  -0.5982   0.3535
 1C6  CH2  C  CR16  0  -0.393   5.3650  -0.7625   1.1412
 1C6  CZ2  C  CR16  0  -0.322   4.0302  -0.8232   1.5139
 1C6  H1   H  HCH2  0   0.304  -0.9169  -0.8377   0.9376
 1C6  H2   H  HCH2  0   0.312  -0.8808   0.7768   1.6664
 1C6  H3   H  HCH3  0   0.260  -2.6126  -2.5939   0.1814
 1C6  H4   H  HCH3  0   0.265  -3.3954  -2.3297  -1.3725
 1C6  H5   H  HCH3  0   0.255  -1.8092  -1.6445  -1.0608
 1C6  H6   H  HCH3  0   0.229  -6.5546  -2.0157   0.8629
 1C6  H7   H  HCH3  0   0.247  -6.6325  -3.0040  -0.6091
 1C6  H8   H  HCH3  0   0.231  -5.1384  -2.9505   0.3434
 1C6  H9   H  HCH3  0   0.248  -7.4367   0.3742   0.5710
 1C6  H10  H  HCH3  0   0.248  -7.0545   2.0885   0.4850
 1C6  H11  H  HCH3  0   0.252  -7.0990   1.1165  -0.9835
 1C6  H12  H  HCR6  0   0.258  -4.8802   2.6680   1.2055
 1C6  H13  H  HNR5  0   0.423   2.2456   1.2899  -1.9720
 1C6  H15  H  HCR6  0   0.272   5.1154   0.8950  -1.8392
 1C6  H16  H  HCH3  0   0.258   8.9963  -0.4131  -0.1565
 1C6  H17  H  HCH3  0   0.226   8.0842  -0.1141   1.3335
 1C6  H18  H  HCH3  0   0.226   7.9398  -1.6761   0.4976
 1C6  H19  H  HCR6  0   0.276   6.1032  -1.2025   1.7975
 1C6  H20  H  HCR6  0   0.259   3.7449  -1.3006   2.4423

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
 1C6  C4   O3   single    1.412  0.020  1.412
 1C6  O3   CZ3  single    1.351  0.020  1.351
 1C6  CZ3  CE3  aromatic  1.393  0.020  1.393
 1C6  CZ3  CH2  aromatic  1.405  0.020  1.405
 1C6  CE3  CX2  aromatic  1.384  0.020  1.384
 1C6  CH2  CZ2  aromatic  1.387  0.020  1.387
 1C6  CX2  NV   aromatic  1.371  0.020  1.371
 1C6  CX2  CS2  aromatic  1.404  0.020  1.404
 1C6  NV   CF1  aromatic  1.363  0.020  1.363
 1C6  CZ2  CS2  aromatic  1.388  0.020  1.388
 1C6  CS2  NE1  aromatic  1.381  0.020  1.381
 1C6  CF1  NE1  aromatic  1.299  0.020  1.299
 1C6  CF1  S    single    1.742  0.020  1.742
 1C6  S    CB   single    1.824  0.020  1.824
 1C6  CB   CG   single    1.502  0.020  1.502
 1C6  N1   CG   aromatic  1.327  0.020  1.327
 1C6  N1   CE2  aromatic  1.324  0.020  1.324
 1C6  CG   CD1  aromatic  1.398  0.020  1.398
 1C6  CE2  CZ   aromatic  1.388  0.020  1.388
 1C6  CD1  C3   single    1.500  0.020  1.500
 1C6  CD1  CE1  aromatic  1.395  0.020  1.395
 1C6  CZ   C1   single    1.497  0.020  1.497
 1C6  CZ   CE1  aromatic  1.394  0.020  1.394
 1C6  CE1  O2   single    1.357  0.020  1.357
 1C6  O2   C2   single    1.424  0.020  1.424
 1C6  CB   H1   single    0.970  0.020  1.090
 1C6  CB   H2   single    0.970  0.020  1.090
 1C6  C3   H3   single    0.970  0.020  1.090
 1C6  C3   H4   single    0.970  0.020  1.090
 1C6  C3   H5   single    0.970  0.020  1.090
 1C6  C2   H6   single    0.970  0.020  1.090
 1C6  C2   H7   single    0.970  0.020  1.090
 1C6  C2   H8   single    0.970  0.020  1.090
 1C6  C1   H9   single    0.970  0.020  1.090
 1C6  C1   H10  single    0.970  0.020  1.090
 1C6  C1   H11  single    0.970  0.020  1.090
 1C6  CE2  H12  single    0.930  0.020  1.080
 1C6  NV   H13  single    0.860  0.020  1.020
 1C6  CE3  H15  single    0.930  0.020  1.080
 1C6  C4   H16  single    0.970  0.020  1.090
 1C6  C4   H17  single    0.970  0.020  1.090
 1C6  C4   H18  single    0.970  0.020  1.090
 1C6  CH2  H19  single    0.930  0.020  1.080
 1C6  CZ2  H20  single    0.930  0.020  1.080

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
 1C6  CF1  S    CB    99.98  3.000
 1C6  H2   CB   H1   108.99  3.000
 1C6  H2   CB   CG   110.25  3.000
 1C6  H1   CB   CG   112.53  3.000
 1C6  H2   CB   S    108.74  3.000
 1C6  H1   CB   S    108.74  3.000
 1C6  CG   CB   S    107.51  3.000
 1C6  N1   CG   CD1  123.33  3.000
 1C6  CD1  CG   CB   120.86  3.000
 1C6  N1   CG   CB   115.81  3.000
 1C6  CE1  CD1  C3   121.67  3.000
 1C6  CE1  CD1  CG   116.67  3.000
 1C6  C3   CD1  CG   121.66  3.000
 1C6  H5   C3   H4   107.49  3.000
 1C6  H5   C3   H3   107.33  3.000
 1C6  H4   C3   H3   107.66  3.000
 1C6  H5   C3   CD1  111.17  3.000
 1C6  H4   C3   CD1  111.45  3.000
 1C6  H3   C3   CD1  111.54  3.000
 1C6  CZ   CE1  O2   118.52  3.000
 1C6  O2   CE1  CD1  120.66  3.000
 1C6  CZ   CE1  CD1  120.80  3.000
 1C6  C2   O2   CE1  114.53  3.000
 1C6  H8   C2   H7   108.81  3.000
 1C6  H8   C2   H6   108.59  3.000
 1C6  H7   C2   H6   108.99  3.000
 1C6  H8   C2   O2   111.89  3.000
 1C6  H7   C2   O2   107.11  3.000
 1C6  H6   C2   O2   111.39  3.000
 1C6  CE2  CZ   C1   121.67  3.000
 1C6  C1   CZ   CE1  121.84  3.000
 1C6  CE2  CZ   CE1  116.49  3.000
 1C6  H11  C1   H10  107.85  3.000
 1C6  H11  C1   H9   107.17  3.000
 1C6  H10  C1   H9   107.55  3.000
 1C6  H11  C1   CZ   111.47  3.000
 1C6  H10  C1   CZ   110.60  3.000
 1C6  H9   C1   CZ   112.00  3.000
 1C6  H12  CE2  N1   116.40  3.000
 1C6  H12  CE2  CZ   119.46  3.000
 1C6  N1   CE2  CZ   124.14  3.000
 1C6  CE2  N1   CG   118.55  3.000
 1C6  NE1  CF1  NV   113.56  3.000
 1C6  NE1  CF1  S    126.36  3.000
 1C6  NV   CF1  S    120.09  3.000
 1C6  H13  NV   CX2  126.54  3.000
 1C6  H13  NV   CF1  126.56  3.000
 1C6  CX2  NV   CF1  106.89  3.000
 1C6  CE3  CX2  CS2  123.17  3.000
 1C6  CS2  CX2  NV   104.64  3.000
 1C6  CE3  CX2  NV   132.19  3.000
 1C6  CZ2  CS2  NE1  130.65  3.000
 1C6  NE1  CS2  CX2  110.19  3.000
 1C6  CZ2  CS2  CX2  119.16  3.000
 1C6  CS2  NE1  CF1  104.73  3.000
 1C6  H15  CE3  CZ3  120.85  3.000
 1C6  H15  CE3  CX2  122.34  3.000
 1C6  CZ3  CE3  CX2  116.81  3.000
 1C6  CH2  CZ3  O3   123.43  3.000
 1C6  CH2  CZ3  CE3  120.98  3.000
 1C6  O3   CZ3  CE3  115.59  3.000
 1C6  C4   O3   CZ3  118.80  3.000
 1C6  H18  C4   H17  108.73  3.000
 1C6  H18  C4   H16  108.66  3.000
 1C6  H17  C4   H16  108.72  3.000
 1C6  H18  C4   O3   112.08  3.000
 1C6  H17  C4   O3   112.04  3.000
 1C6  H16  C4   O3   106.50  3.000
 1C6  H19  CH2  CZ2  118.43  3.000
 1C6  H19  CH2  CZ3  120.51  3.000
 1C6  CZ2  CH2  CZ3  121.07  3.000
 1C6  H20  CZ2  CH2  120.23  3.000
 1C6  H20  CZ2  CS2  120.96  3.000
 1C6  CH2  CZ2  CS2  118.81  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
 1C6  CONST_01  CZ   CE2  N1   CG      0.00   0.0  0
 1C6  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 1C6  CONST_03  CE2  N1   CG   CD1     0.00   0.0  0
 1C6  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 1C6  CONST_05  N1   CG   CD1  CE1     0.00   0.0  0
 1C6  CONST_06  N1   CE2  CZ   CE1     0.00   0.0  0
 1C6  CONST_07  CE3  CX2  NV   CF1   180.00   0.0  0
 1C6  CONST_08  CS2  CX2  NV   CF1     0.00   0.0  0
 1C6  CONST_09  CX2  CS2  NE1  CF1     0.00   0.0  0
 1C6  CONST_10  CZ2  CS2  NE1  CF1   180.00   0.0  0
 1C6  CONST_11  CZ3  CE3  CX2  NV    180.00   0.0  0
 1C6  CONST_12  CZ2  CS2  CX2  NV    180.00   0.0  0
 1C6  CONST_13  NE1  CS2  CX2  NV      0.00   0.0  0
 1C6  CONST_14  CS2  NE1  CF1  NV      0.00   0.0  0
 1C6  CONST_15  CH2  CZ3  CE3  CX2     0.00   0.0  0
 1C6  CONST_16  NE1  CF1  NV   CX2     0.00   0.0  0
 1C6  CONST_17  CH2  CZ2  CS2  CX2     0.00   0.0  0
 1C6  CONST_18  CZ3  CE3  CX2  CS2     0.00   0.0  0
 1C6  CONST_19  CZ3  CH2  CZ2  CS2     0.00   0.0  0
 1C6  CONST_20  CE3  CX2  CS2  NE1   180.00   0.0  0
 1C6  CONST_21  CH2  CZ2  CS2  NE1   180.00   0.0  0
 1C6  CONST_22  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 1C6  CONST_23  CZ2  CS2  CX2  CE3     0.00   0.0  0
 1C6  CONST_24  CX2  NV   CF1  S     180.00   0.0  0
 1C6  CONST_25  CS2  NE1  CF1  S     180.00   0.0  0
 1C6  CONST_26  CE2  N1   CG   CB    180.00   0.0  0
 1C6  CONST_27  CE1  CD1  CG   CB    180.00   0.0  0
 1C6  CONST_28  O2   CE1  CD1  CG    180.00   0.0  0
 1C6  CONST_29  C1   CZ   CE1  CD1   180.00   0.0  0
 1C6  CONST_30  N1   CG   CD1  C3    180.00   0.0  0
 1C6  CONST_31  CZ   CE1  CD1  C3    180.00   0.0  0
 1C6  CONST_32  CE2  CZ   CE1  O2    180.00   0.0  0
 1C6  CONST_33  N1   CE2  CZ   C1    180.00   0.0  0
 1C6  CONST_34  O3   CZ3  CE3  CX2   180.00   0.0  0
 1C6  CONST_35  CZ2  CH2  CZ3  O3    180.00   0.0  0
 1C6  CONST_36  H12  CE2  N1   CG    180.00   0.0  0
 1C6  CONST_37  H15  CE3  CX2  NV      0.00   0.0  0
 1C6  CONST_38  H20  CZ2  CS2  CX2   180.00   0.0  0
 1C6  CONST_39  H13  NV   CX2  CS2   180.00   0.0  0
 1C6  CONST_40  H19  CH2  CZ2  CS2   180.00   0.0  0
 1C6  Var_01    N1   CG   CB   S     -91.42  30.0  2
 1C6  Var_02    NV   CF1  S    CB   -178.07  30.0  2
 1C6  Var_03    CZ   CE1  O2   C2   -100.65  30.0  2
 1C6  Var_04    CH2  CZ3  O3   C4     -1.13  30.0  2
 1C6  Var_05    H3   C3   CD1  CG     80.24  30.0  2
 1C6  Var_06    H9   C1   CZ   CE1    60.20  30.0  2
 1C6  Var_07    H6   C2   O2   CE1    60.25  30.0  3
 1C6  Var_08    H16  C4   O3   CZ3  -179.31  30.0  3

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
 1C6  plan-1  CB   0.020
 1C6  plan-1  CG   0.020
 1C6  plan-1  CD1  0.020
 1C6  plan-1  C3   0.020
 1C6  plan-1  CE1  0.020
 1C6  plan-1  O2   0.020
 1C6  plan-1  CZ   0.020
 1C6  plan-1  C1   0.020
 1C6  plan-1  CE2  0.020
 1C6  plan-1  N1   0.020
 1C6  plan-1  H12  0.020
 1C6  plan-2  S    0.020
 1C6  plan-2  CF1  0.020
 1C6  plan-2  NV   0.020
 1C6  plan-2  CX2  0.020
 1C6  plan-2  CS2  0.020
 1C6  plan-2  NE1  0.020
 1C6  plan-2  CE3  0.020
 1C6  plan-2  CZ3  0.020
 1C6  plan-2  O3   0.020
 1C6  plan-2  CH2  0.020
 1C6  plan-2  CZ2  0.020
 1C6  plan-2  H13  0.020
 1C6  plan-2  H15  0.020
 1C6  plan-2  H19  0.020
 1C6  plan-2  H20  0.020

