# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:49:50 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-(1H-benzimidazol-2-ylsulfanyl)ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCSc1[nH]c2ccccc2n1
#
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
 6N4  6N4  2-(1H-benzimidazol-2-ylsulfanyl)ethanol  ligand  23  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6N4
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
 6N4  C1    C  CR16  0  -0.251  -3.8558   1.3835   0.0160
 6N4  C2    C  CR16  0  -0.261  -4.2781   0.0489   0.0620
 6N4  C3    C  CR16  0  -0.279  -3.3705  -0.9977   0.0611
 6N4  C4    C  CR56  0   0.342  -2.0269  -0.6553   0.0135
 6N4  C5    C  CR56  0   0.150  -1.5840   0.6764  -0.0301
 6N4  C6    C  CR16  0  -0.315  -2.5122   1.7145  -0.0299
 6N4  N7    N  N     0  -0.457  -0.2076   0.7187  -0.0699
 6N4  C8    C  CR5   0   0.310   0.1654  -0.5273  -0.0508
 6N4  N9    N  NR15  0  -0.696  -0.8751  -1.4023  -0.0013
 6N4  S10   S  S2    0   0.049   1.7979  -1.1227  -0.0873
 6N4  C11   C  CH2   0  -0.557   2.7058   0.4472  -0.0122
 6N4  C12   C  CH2   0  -0.122   4.1901   0.1275  -0.0326
 6N4  O13   O  OH1   0  -0.642   4.8738   1.3532   0.0377
 6N4  H1    H  HCR6  0   0.235  -4.5982   2.1698   0.0165
 6N4  H2    H  HCR6  0   0.236  -5.3368  -0.1689   0.0995
 6N4  H6    H  HCR6  0   0.235  -2.1893   2.7464  -0.0668
 6N4  H3    H  HCR6  0   0.239  -3.6998  -2.0272   0.0997
 6N4  H9    H  HNR5  0   0.390  -0.8127  -2.4052   0.0295
 6N4  H111  H  HCH2  0   0.281   2.4290   1.0614  -0.8676
 6N4  H112  H  HCH2  0   0.279   2.4331   0.9703   0.9034
 6N4  H121  H  HCH2  0   0.199   4.4383  -0.5258   0.8131
 6N4  H122  H  HCH2  0   0.203   4.4363  -0.4236  -0.9485
 6N4  H13   H  HOH1  0   0.436   5.8141   1.1636   0.0605

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
 6N4  C1   C2    aromatic  1.401  0.020  1.401
 6N4  C1   C6    aromatic  1.385  0.020  1.385
 6N4  C2   C3    aromatic  1.385  0.020  1.385
 6N4  C3   C4    aromatic  1.387  0.020  1.387
 6N4  C4   C5    aromatic  1.404  0.020  1.404
 6N4  C4   N9    aromatic  1.373  0.020  1.373
 6N4  C5   C6    aromatic  1.393  0.020  1.393
 6N4  C5   N7    aromatic  1.378  0.020  1.378
 6N4  N7   C8    aromatic  1.301  0.020  1.301
 6N4  C8   N9    aromatic  1.360  0.020  1.360
 6N4  C8   S10   single    1.738  0.020  1.738
 6N4  S10  C11   single    1.815  0.020  1.815
 6N4  C11  C12   single    1.518  0.020  1.518
 6N4  C12  O13   single    1.405  0.020  1.405
 6N4  C1   H1    single    0.930  0.020  1.080
 6N4  C2   H2    single    0.930  0.020  1.080
 6N4  C6   H6    single    0.930  0.020  1.080
 6N4  C3   H3    single    0.930  0.020  1.080
 6N4  N9   H9    single    0.860  0.020  1.020
 6N4  C11  H111  single    0.970  0.020  1.090
 6N4  C11  H112  single    0.970  0.020  1.090
 6N4  C12  H121  single    0.970  0.020  1.090
 6N4  C12  H122  single    0.970  0.020  1.090
 6N4  O13  H13   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
 6N4  H1    C1   C6    119.49  3.000
 6N4  H1    C1   C2    119.07  3.000
 6N4  C6    C1   C2    121.43  3.000
 6N4  H2    C2   C3    119.29  3.000
 6N4  H2    C2   C1    119.23  3.000
 6N4  C3    C2   C1    121.49  3.000
 6N4  H3    C3   C4    122.07  3.000
 6N4  H3    C3   C2    121.31  3.000
 6N4  C4    C3   C2    116.62  3.000
 6N4  N9    C4   C5    104.54  3.000
 6N4  N9    C4   C3    132.73  3.000
 6N4  C5    C4   C3    122.73  3.000
 6N4  N7    C5   C6    130.02  3.000
 6N4  N7    C5   C4    110.19  3.000
 6N4  C6    C5   C4    119.78  3.000
 6N4  H6    C6   C5    120.80  3.000
 6N4  H6    C6   C1    121.25  3.000
 6N4  C5    C6   C1    117.95  3.000
 6N4  C8    N7   C5    104.88  3.000
 6N4  S10   C8   N9    119.92  3.000
 6N4  S10   C8   N7    126.67  3.000
 6N4  N9    C8   N7    113.41  3.000
 6N4  H9    N9   C8    126.54  3.000
 6N4  H9    N9   C4    126.47  3.000
 6N4  C8    N9   C4    106.98  3.000
 6N4  C11   S10  C8     99.94  3.000
 6N4  H112  C11  H111  109.01  3.000
 6N4  H112  C11  C12   110.93  3.000
 6N4  H111  C11  C12   110.90  3.000
 6N4  H112  C11  S10   108.96  3.000
 6N4  H111  C11  S10   109.16  3.000
 6N4  C12   C11  S10   107.84  3.000
 6N4  H122  C12  H121  107.08  3.000
 6N4  H122  C12  O13   111.77  3.000
 6N4  H121  C12  O13   111.76  3.000
 6N4  H122  C12  C11   109.66  3.000
 6N4  H121  C12  C11   109.64  3.000
 6N4  O13   C12  C11   106.93  3.000
 6N4  H13   O13  C12   107.79  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
 6N4  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 6N4  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 6N4  CONST_03  N7   C5   C6   C1    180.00   0.0  0
 6N4  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 6N4  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 6N4  CONST_06  N9   C4   C3   C2    180.00   0.0  0
 6N4  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 6N4  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 6N4  CONST_09  N7   C5   C4   C3    180.00   0.0  0
 6N4  CONST_10  C8   N9   C4   C3    180.00   0.0  0
 6N4  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 6N4  CONST_12  N7   C8   N9   C4      0.00   0.0  0
 6N4  CONST_13  C8   N9   C4   C5      0.00   0.0  0
 6N4  CONST_14  N9   C8   N7   C5      0.00   0.0  0
 6N4  CONST_15  N9   C4   C5   C6    180.00   0.0  0
 6N4  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 6N4  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 6N4  CONST_18  S10  C8   N9   C4    180.00   0.0  0
 6N4  CONST_19  S10  C8   N7   C5    180.00   0.0  0
 6N4  CONST_20  H3   C3   C2   C1    180.00   0.0  0
 6N4  CONST_21  H6   C6   C1   C2    180.00   0.0  0
 6N4  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 6N4  CONST_23  H9   N9   C4   C3      0.00   0.0  0
 6N4  CONST_24  H2   C2   C3   C4    180.00   0.0  0
 6N4  Var_01    C12  C11  S10  C8    179.94  30.0  3
 6N4  Var_02    O13  C12  C11  S10  -179.50  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
 6N4  plan-1  C1   0.020
 6N4  plan-1  C2   0.020
 6N4  plan-1  C3   0.020
 6N4  plan-1  C4   0.020
 6N4  plan-1  C5   0.020
 6N4  plan-1  C6   0.020
 6N4  plan-1  N7   0.020
 6N4  plan-1  C8   0.020
 6N4  plan-1  N9   0.020
 6N4  plan-1  S10  0.020
 6N4  plan-1  H1   0.020
 6N4  plan-1  H2   0.020
 6N4  plan-1  H6   0.020
 6N4  plan-1  H3   0.020
 6N4  plan-1  H9   0.020

