# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:20:51 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(1H-benzimidazol-2-yl)methyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)NCc1[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
 W0A  W0A  N-[(1H-benzimidazol-2-yl)methyl]butanamide  ligand  31  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W0A
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
 W0A  N1   N  NR15  0  -0.688  14.0672   6.1034  11.2339
 W0A  C4   C  CH2   0  -0.383  14.5567   8.5245  11.5854
 W0A  C5   C  CR5   0   0.446  14.7866   7.2086  10.9159
 W0A  C6   C  CR56  0   0.335  14.4837   5.0928  10.4083
 W0A  C7   C  CR16  0  -0.308  14.1123   3.7597  10.2835
 W0A  C8   C  CR16  0  -0.280  14.7671   3.0204   9.3124
 W0A  C10  C  CR16  0  -0.336  16.1218   4.9195   8.6315
 W0A  O    O  O     0  -0.489  16.2309   7.5452  13.5247
 W0A  C3   C  C     0   0.555  15.1199   7.9184  13.8722
 W0A  C2   C  CH2   0  -0.568  14.6525   7.8525  15.3080
 W0A  C1   C  CH2   0  -0.429  15.6989   8.3838  16.2825
 W0A  C    C  CH3   0  -0.667  15.9564   9.8757  16.1244
 W0A  N    N  NH1   0  -0.644  14.2272   8.3929  12.9815
 W0A  N2   N  N     0  -0.481  15.6361   7.0034   9.9490
 W0A  C11  C  CR56  0   0.133  15.4723   5.6818   9.6015
 W0A  C9   C  CR16  0  -0.272  15.7571   3.5909   8.4989
 W0A  H1   H  HNR5  0   0.415  13.3570   6.0449  11.9463
 W0A  H2   H  HCH2  0   0.272  15.4426   9.1443  11.4364
 W0A  H3   H  HCH2  0   0.295  13.7231   9.0334  11.0993
 W0A  H4   H  HCR6  0   0.265  13.3488   3.3166  10.9096
 W0A  H5   H  HCR6  0   0.254  14.5084   1.9783   9.1776
 W0A  H6   H  HCR6  0   0.253  16.8870   5.3574   8.0029
 W0A  H7   H  HCH2  0   0.247  13.7102   8.3896  15.4382
 W0A  H8   H  HCH2  0   0.276  14.4426   6.8014  15.5290
 W0A  H9   H  HCH2  0   0.234  15.3575   8.1768  17.2987
 W0A  H10  H  HCH2  0   0.227  16.6287   7.8269  16.1528
 W0A  H11  H  HCH3  0   0.233  16.6882  10.2275  16.8519
 W0A  H12  H  HCH3  0   0.222  16.3429  10.1164  15.1325
 W0A  H13  H  HCH3  0   0.220  15.0406  10.4511  16.2704
 W0A  H14  H  HNH1  0   0.411  13.3382   8.7413  13.2989
 W0A  H16  H  HCR6  0   0.251  16.2437   2.9759   7.7533

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
 W0A  C10  C9   aromatic  1.384  0.020  1.384
 W0A  C10  C11  aromatic  1.394  0.020  1.394
 W0A  C9   C8   aromatic  1.403  0.020  1.403
 W0A  C11  N2   aromatic  1.376  0.020  1.376
 W0A  C11  C6   aromatic  1.405  0.020  1.405
 W0A  N2   C5   aromatic  1.303  0.020  1.303
 W0A  C8   C7   aromatic  1.385  0.020  1.385
 W0A  C6   C7   aromatic  1.389  0.020  1.389
 W0A  C6   N1   aromatic  1.370  0.020  1.370
 W0A  C5   C4   single    1.494  0.020  1.494
 W0A  C5   N1   aromatic  1.356  0.020  1.356
 W0A  C4   N    single    1.441  0.020  1.441
 W0A  N    C3   single    1.347  0.020  1.347
 W0A  O    C3   double    1.222  0.020  1.222
 W0A  C3   C2   single    1.511  0.020  1.511
 W0A  C2   C1   single    1.525  0.020  1.525
 W0A  C1   C    single    1.522  0.020  1.522
 W0A  N1   H1   single    0.860  0.020  1.020
 W0A  C4   H2   single    0.970  0.020  1.090
 W0A  C4   H3   single    0.970  0.020  1.090
 W0A  C7   H4   single    0.930  0.020  1.080
 W0A  C8   H5   single    0.930  0.020  1.080
 W0A  C10  H6   single    0.930  0.020  1.080
 W0A  C2   H7   single    0.970  0.020  1.090
 W0A  C2   H8   single    0.970  0.020  1.090
 W0A  C1   H9   single    0.970  0.020  1.090
 W0A  C1   H10  single    0.970  0.020  1.090
 W0A  C    H11  single    0.970  0.020  1.090
 W0A  C    H12  single    0.970  0.020  1.090
 W0A  C    H13  single    0.970  0.020  1.090
 W0A  N    H14  single    0.860  0.020  1.020
 W0A  C9   H16  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
 W0A  H1   N1   C6   126.69  3.000
 W0A  H1   N1   C5   125.93  3.000
 W0A  C6   N1   C5   107.37  3.000
 W0A  H3   C4   H2   107.12  3.000
 W0A  H3   C4   N    107.44  3.000
 W0A  H2   C4   N    111.71  3.000
 W0A  H3   C4   C5   109.19  3.000
 W0A  H2   C4   C5   108.30  3.000
 W0A  N    C4   C5   112.89  3.000
 W0A  N2   C5   C4   124.84  3.000
 W0A  C4   C5   N1   122.06  3.000
 W0A  N2   C5   N1   113.04  3.000
 W0A  C11  C6   C7   122.59  3.000
 W0A  C7   C6   N1   132.90  3.000
 W0A  C11  C6   N1   104.51  3.000
 W0A  H4   C7   C8   121.37  3.000
 W0A  H4   C7   C6   121.97  3.000
 W0A  C8   C7   C6   116.66  3.000
 W0A  H5   C8   C9   119.22  3.000
 W0A  H5   C8   C7   119.24  3.000
 W0A  C9   C8   C7   121.55  3.000
 W0A  H6   C10  C9   121.25  3.000
 W0A  H6   C10  C11  120.80  3.000
 W0A  C9   C10  C11  117.95  3.000
 W0A  N    C3   C2   116.00  3.000
 W0A  C2   C3   O    122.53  3.000
 W0A  N    C3   O    121.45  3.000
 W0A  H8   C2   H7   106.42  3.000
 W0A  H8   C2   C1   109.70  3.000
 W0A  H7   C2   C1   110.14  3.000
 W0A  H8   C2   C3   107.04  3.000
 W0A  H7   C2   C3   111.01  3.000
 W0A  C1   C2   C3   112.30  3.000
 W0A  H10  C1   H9   106.27  3.000
 W0A  H10  C1   C    110.10  3.000
 W0A  H9   C1   C    109.60  3.000
 W0A  H10  C1   C2   109.31  3.000
 W0A  H9   C1   C2   108.30  3.000
 W0A  C    C1   C2   113.02  3.000
 W0A  H13  C    H12  107.61  3.000
 W0A  H13  C    H11  107.68  3.000
 W0A  H12  C    H11  107.31  3.000
 W0A  H13  C    C1   111.16  3.000
 W0A  H12  C    C1   111.75  3.000
 W0A  H11  C    C1   111.13  3.000
 W0A  H14  N    C3   119.93  3.000
 W0A  H14  N    C4   118.43  3.000
 W0A  C3   N    C4   121.42  3.000
 W0A  C11  N2   C5   105.13  3.000
 W0A  N2   C11  C10  130.19  3.000
 W0A  N2   C11  C6   109.95  3.000
 W0A  C10  C11  C6   119.86  3.000
 W0A  H16  C9   C10  119.54  3.000
 W0A  H16  C9   C8   119.07  3.000
 W0A  C10  C9   C8   121.39  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
 W0A  CONST_01  C10  C11  C6   N1  180.00   0.0  0
 W0A  CONST_02  N2   C11  C6   N1    0.00   0.0  0
 W0A  CONST_03  C8   C7   C6   N1  180.00   0.0  0
 W0A  CONST_04  C11  N2   C5   N1    0.00   0.0  0
 W0A  CONST_05  C10  C11  N2   C5  180.00   0.0  0
 W0A  CONST_06  C6   C11  N2   C5    0.00   0.0  0
 W0A  CONST_07  C11  C6   N1   C5    0.00   0.0  0
 W0A  CONST_08  C7   C6   N1   C5  180.00   0.0  0
 W0A  CONST_09  C9   C10  C11  C6    0.00   0.0  0
 W0A  CONST_10  C9   C8   C7   C6    0.00   0.0  0
 W0A  CONST_11  N2   C5   N1   C6    0.00   0.0  0
 W0A  CONST_12  C10  C9   C8   C7    0.00   0.0  0
 W0A  CONST_13  C10  C11  C6   C7    0.00   0.0  0
 W0A  CONST_14  N2   C11  C6   C7  180.00   0.0  0
 W0A  CONST_15  C11  C10  C9   C8    0.00   0.0  0
 W0A  CONST_16  C11  C6   C7   C8    0.00   0.0  0
 W0A  CONST_17  C9   C10  C11  N2  180.00   0.0  0
 W0A  CONST_18  C11  N2   C5   C4  180.00   0.0  0
 W0A  CONST_19  C6   N1   C5   C4  180.00   0.0  0
 W0A  CONST_20  H4   C7   C6   N1    0.00   0.0  0
 W0A  CONST_21  H6   C10  C11  C6  180.00   0.0  0
 W0A  CONST_22  H5   C8   C7   C6  180.00   0.0  0
 W0A  CONST_23  H16  C9   C8   C7  180.00   0.0  0
 W0A  CONST_24  H1   N1   C6   C7    0.00   0.0  0
 W0A  CONST_25  O    C3   N    C4    0.00   0.0  0
 W0A  CONST_26  C2   C3   N    C4  180.00   0.0  0
 W0A  CONST_27  H14  N    C3   O   180.00   0.0  0
 W0A  Var_01    N    C4   C5   N1   36.27  30.0  2
 W0A  Var_02    C3   N    C4   C5   66.09  30.0  3
 W0A  Var_03    C1   C2   C3   O    46.23  30.0  3
 W0A  Var_04    C    C1   C2   C3   66.31  30.0  3
 W0A  Var_05    H11  C    C1   C2  178.48  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
 W0A  plan-1  N1   0.020
 W0A  plan-1  C4   0.020
 W0A  plan-1  C5   0.020
 W0A  plan-1  C6   0.020
 W0A  plan-1  C7   0.020
 W0A  plan-1  C8   0.020
 W0A  plan-1  C10  0.020
 W0A  plan-1  N2   0.020
 W0A  plan-1  C11  0.020
 W0A  plan-1  C9   0.020
 W0A  plan-1  H1   0.020
 W0A  plan-1  H4   0.020
 W0A  plan-1  H5   0.020
 W0A  plan-1  H6   0.020
 W0A  plan-1  H16  0.020
 W0A  plan-2  C4   0.020
 W0A  plan-2  O    0.020
 W0A  plan-2  C3   0.020
 W0A  plan-2  C2   0.020
 W0A  plan-2  N    0.020
 W0A  plan-2  H14  0.020

