# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:56:29 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: methyl {5-[(S)-propylsulfinyl]-1H-benzimidazol-2-yl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[S@](=O)c1ccc2[nH]c(NC(=O)OC)nc2c1
#
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
 ALW  ALW  'methyl {5-[(S)-propylsulfinyl]-1H-benzimidazol-2-yl}carbamate'  ligand  34  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ALW
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
 ALW  S1    S  S3    0   0.755  -0.2257   0.8801   3.7229
 ALW  C11   C  CH2   0  -0.587   0.1451  -0.8250   4.2370
 ALW  CX5   C  CH2   0  -0.432   0.5081  -0.8663   5.7126
 ALW  C     C  CH3   0  -0.658   0.8582  -2.2807   6.1550
 ALW  N     N  N     0  -0.510   1.1117   0.4538  -1.3310
 ALW  C7    C  CR5   0   0.683   0.3477   0.1280  -2.3366
 ALW  N1    N  NR15  0  -0.715  -0.9382  -0.1251  -1.9921
 ALW  C3A   C  CR56  0   0.358  -1.0212   0.0498  -0.6347
 ALW  C7A   C  CR56  0   0.175   0.2789   0.4137  -0.2396
 ALW  C1    C  CR16  0  -0.296  -2.0762  -0.0626   0.2571
 ALW  C2    C  CR16  0  -0.264  -1.7976   0.2010   1.5880
 ALW  C3    C  CR6   0  -0.225  -0.5028   0.5460   1.9878
 ALW  C4    C  CR16  0  -0.310   0.5497   0.6737   1.0987
 ALW  C5    C  C     0   0.763   0.0904  -0.2723  -4.7245
 ALW  O     O  O2    0  -0.463   0.8586  -0.2598  -5.7977
 ALW  C6    C  CH3   0  -0.423   0.2383  -0.5815  -7.0446
 ALW  O1    O  O     0  -0.491  -1.0916  -0.5299  -4.7118
 ALW  O2    O  O     0  -0.771   1.0745   1.6390   3.8439
 ALW  H111  H  HCH2  0   0.285   0.9634  -1.1850   3.6077
 ALW  H112  H  HCH2  0   0.278  -0.7456  -1.4208   4.0253
 ALW  H3'1  H  HCH2  0   0.239  -0.3256  -0.4866   6.3086
 ALW  H3'2  H  HCH2  0   0.238   1.3561  -0.2041   5.8964
 ALW  HC1   H  HCH3  0   0.237   1.1383  -2.2989   7.2080
 ALW  HC2   H  HCH3  0   0.225   0.0145  -2.9589   6.0227
 ALW  HC3   H  HCH3  0   0.226   1.6966  -2.6756   5.5799
 ALW  H1    H  HNR5  0   0.430  -1.6779  -0.3827  -2.6275
 ALW  H2    H  HCR6  0   0.277  -3.0733  -0.3309  -0.0645
 ALW  HB    H  HCR6  0   0.274  -2.5929   0.1425   2.3208
 ALW  H4    H  HCR6  0   0.273   1.5383   0.9645   1.4300
 ALW  HA    H  HNH1  0   0.432   1.8106   0.2478  -3.7238
 ALW  H6C1  H  HCH3  0   0.259   1.0236  -0.5082  -7.7899
 ALW  H6C2  H  HCH3  0   0.246  -0.1618  -1.5944  -7.0372
 ALW  H6C3  H  HCH3  0   0.246  -0.5566   0.1228  -7.2860
 ALW  N2    N  NH1   0  -0.755   0.8253   0.0496  -3.6183

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
 ALW  S1   C11   single    1.819  0.020  1.819
 ALW  S1   C3    single    1.789  0.020  1.789
 ALW  S1   O2    double    1.510  0.020  1.510
 ALW  C11  CX5   single    1.520  0.020  1.520
 ALW  C11  H111  single    0.970  0.020  1.090
 ALW  C11  H112  single    0.970  0.020  1.090
 ALW  CX5  C     single    1.523  0.020  1.523
 ALW  CX5  H3'1  single    0.970  0.020  1.090
 ALW  CX5  H3'2  single    0.970  0.020  1.090
 ALW  C    HC1   single    0.970  0.020  1.090
 ALW  C    HC2   single    0.970  0.020  1.090
 ALW  C    HC3   single    0.970  0.020  1.090
 ALW  N    C7    aromatic  1.304  0.020  1.304
 ALW  N    C7A   aromatic  1.373  0.020  1.373
 ALW  C7   N1    aromatic  1.355  0.020  1.355
 ALW  C7   N2    single    1.370  0.020  1.370
 ALW  N1   C3A   aromatic  1.371  0.020  1.371
 ALW  N1   H1    single    0.860  0.020  1.020
 ALW  C3A  C7A   aromatic  1.407  0.020  1.407
 ALW  C3A  C1    aromatic  1.386  0.020  1.386
 ALW  C7A  C4    aromatic  1.390  0.020  1.390
 ALW  C1   C2    aromatic  1.385  0.020  1.385
 ALW  C1   H2    single    0.930  0.020  1.080
 ALW  C2   C3    aromatic  1.398  0.020  1.398
 ALW  C2   HB    single    0.930  0.020  1.080
 ALW  C3   C4    aromatic  1.384  0.020  1.384
 ALW  C4   H4    single    0.930  0.020  1.080
 ALW  N2   C5    single    1.367  0.020  1.367
 ALW  N2   HA    single    0.860  0.020  1.020
 ALW  C5   O     single    1.320  0.020  1.320
 ALW  C5   O1    double    1.210  0.020  1.210
 ALW  O    C6    single    1.429  0.020  1.429
 ALW  C6   H6C1  single    0.970  0.020  1.090
 ALW  C6   H6C2  single    0.970  0.020  1.090
 ALW  C6   H6C3  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
 ALW  O2    S1   C3    107.75  3.000
 ALW  O2    S1   C11   105.83  3.000
 ALW  C3    S1   C11    97.51  3.000
 ALW  H112  C11  H111  108.61  3.000
 ALW  H112  C11  CX5   111.60  3.000
 ALW  H111  C11  CX5   111.79  3.000
 ALW  H112  C11  S1    106.87  3.000
 ALW  H111  C11  S1    107.37  3.000
 ALW  CX5   C11  S1    110.39  3.000
 ALW  H3'2  CX5  H3'1  106.86  3.000
 ALW  H3'2  CX5  C     109.63  3.000
 ALW  H3'1  CX5  C     109.85  3.000
 ALW  H3'2  CX5  C11   109.42  3.000
 ALW  H3'1  CX5  C11   109.74  3.000
 ALW  C     CX5  C11   111.23  3.000
 ALW  HC3   C    HC2   107.79  3.000
 ALW  HC3   C    HC1   107.81  3.000
 ALW  HC2   C    HC1   107.80  3.000
 ALW  HC3   C    CX5   111.09  3.000
 ALW  HC2   C    CX5   111.38  3.000
 ALW  HC1   C    CX5   110.82  3.000
 ALW  C7A   N    C7    104.49  3.000
 ALW  N2    C7   N1    123.91  3.000
 ALW  N2    C7   N     122.10  3.000
 ALW  N1    C7   N     113.99  3.000
 ALW  H1    N1   C3A   127.72  3.000
 ALW  H1    N1   C7    125.70  3.000
 ALW  C3A   N1   C7    106.58  3.000
 ALW  C1    C3A  C7A   122.94  3.000
 ALW  C1    C3A  N1    132.28  3.000
 ALW  C7A   C3A  N1    104.78  3.000
 ALW  C4    C7A  C3A   119.92  3.000
 ALW  C4    C7A  N     129.91  3.000
 ALW  C3A   C7A  N     110.17  3.000
 ALW  H2    C1   C2    121.23  3.000
 ALW  H2    C1   C3A   122.04  3.000
 ALW  C2    C1   C3A   116.72  3.000
 ALW  HB    C2   C3    119.99  3.000
 ALW  HB    C2   C1    119.48  3.000
 ALW  C3    C2   C1    120.53  3.000
 ALW  C4    C3   C2    122.91  3.000
 ALW  C4    C3   S1    119.23  3.000
 ALW  C2    C3   S1    117.83  3.000
 ALW  H4    C4   C3    121.53  3.000
 ALW  H4    C4   C7A   121.52  3.000
 ALW  C3    C4   C7A   116.95  3.000
 ALW  O1    C5   O     125.39  3.000
 ALW  O1    C5   N2    124.55  3.000
 ALW  O     C5   N2    110.06  3.000
 ALW  C6    O    C5    117.04  3.000
 ALW  H6C3  C6   H6C2  109.56  3.000
 ALW  H6C3  C6   H6C1  109.41  3.000
 ALW  H6C2  C6   H6C1  109.47  3.000
 ALW  H6C3  C6   O     111.38  3.000
 ALW  H6C2  C6   O     111.27  3.000
 ALW  H6C1  C6   O     105.65  3.000
 ALW  HA    N2   C5    119.08  3.000
 ALW  HA    N2   C7    115.24  3.000
 ALW  C5    N2   C7    125.68  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
 ALW  CONST_01  C3A   N1   C7   N       0.00   0.0  0
 ALW  CONST_02  N1    C3A  C7A  N       0.00   0.0  0
 ALW  CONST_03  C1    C3A  C7A  N     180.00   0.0  0
 ALW  CONST_04  C3    C4   C7A  N     180.00   0.0  0
 ALW  CONST_05  C3A   C7A  N    C7      0.00   0.0  0
 ALW  CONST_06  C4    C7A  N    C7    180.00   0.0  0
 ALW  CONST_07  C7A   C3A  N1   C7      0.00   0.0  0
 ALW  CONST_08  C1    C3A  N1   C7    180.00   0.0  0
 ALW  CONST_09  C7A   N    C7   N1      0.00   0.0  0
 ALW  CONST_10  C4    C7A  C3A  N1    180.00   0.0  0
 ALW  CONST_11  C2    C1   C3A  N1    180.00   0.0  0
 ALW  CONST_12  C3    C4   C7A  C3A     0.00   0.0  0
 ALW  CONST_13  C3    C2   C1   C3A     0.00   0.0  0
 ALW  CONST_14  C2    C1   C3A  C7A     0.00   0.0  0
 ALW  CONST_15  C2    C3   C4   C7A     0.00   0.0  0
 ALW  CONST_16  C4    C7A  C3A  C1      0.00   0.0  0
 ALW  CONST_17  C4    C3   C2   C1      0.00   0.0  0
 ALW  CONST_18  C1    C2   C3   S1    180.00   0.0  0
 ALW  CONST_19  C7A   C4   C3   S1    180.00   0.0  0
 ALW  CONST_20  N2    C7   N1   C3A   180.00   0.0  0
 ALW  CONST_21  N2    C7   N    C7A   180.00   0.0  0
 ALW  CONST_22  H1    N1   C7   N     180.00   0.0  0
 ALW  CONST_23  H4    C4   C7A  N       0.00   0.0  0
 ALW  CONST_24  H2    C1   C3A  N1      0.00   0.0  0
 ALW  CONST_25  HB    C2   C1   C3A   180.00   0.0  0
 ALW  CONST_26  C5    N2   C7   N     180.00   0.0  0
 ALW  CONST_27  C5    N2   C7   N1      0.00   0.0  0
 ALW  CONST_28  HA    N2   C7   N       0.00   0.0  0
 ALW  CONST_29  O     C5   N2   C7    180.00   0.0  0
 ALW  CONST_30  O1    C5   N2   C7      0.00   0.0  0
 ALW  Var_01    C2    C3   S1   C11    88.52  30.0  2
 ALW  Var_02    C3    S1   C11  CX5   177.06  30.0  2
 ALW  Var_03    C     CX5  C11  S1   -178.50  30.0  3
 ALW  Var_04    HC1   C    CX5  C11   178.76  30.0  3
 ALW  Var_05    H6C1  C6   O    C5    179.54  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
 ALW  plan-1  S1   0.020
 ALW  plan-1  N    0.020
 ALW  plan-1  C7   0.020
 ALW  plan-1  N1   0.020
 ALW  plan-1  C3A  0.020
 ALW  plan-1  C7A  0.020
 ALW  plan-1  C1   0.020
 ALW  plan-1  C2   0.020
 ALW  plan-1  C3   0.020
 ALW  plan-1  C4   0.020
 ALW  plan-1  H1   0.020
 ALW  plan-1  H2   0.020
 ALW  plan-1  HB   0.020
 ALW  plan-1  H4   0.020
 ALW  plan-1  N2   0.020
 ALW  plan-2  C7   0.020
 ALW  plan-2  C5   0.020
 ALW  plan-2  HA   0.020
 ALW  plan-2  N2   0.020
 ALW  plan-3  S1   0.020
 ALW  plan-3  C11  0.020
 ALW  plan-3  C3   0.020
 ALW  plan-3  O2   0.020
 ALW  plan-4  C5   0.020
 ALW  plan-4  O    0.020
 ALW  plan-4  O1   0.020
 ALW  plan-4  N2   0.020

