# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:04:58 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(1H-benzimidazol-2-yl)methyl]-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=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
 W0V  W0V  N-[(1H-benzimidazol-2-yl)methyl]-2-methylpropanamide  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 PERFECT
;

data_comp_W0V
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
 W0V  N1   N  NR15  0  -0.701   -7.0427  14.6799  -0.0757
 W0V  C4   C  CH2   0  -0.395   -8.6303  13.7714   1.6184
 W0V  C5   C  CR5   0   0.444   -7.3025  14.3349   1.2121
 W0V  C6   C  CR56  0   0.333   -5.7513  15.1360  -0.1244
 W0V  C7   C  CR16  0  -0.308   -4.9537  15.6107  -1.1581
 W0V  C8   C  CR16  0  -0.280   -3.6633  15.9883  -0.8242
 W0V  C10  C  CR16  0  -0.335   -3.9935  15.4253   1.5167
 W0V  O    O  O     0  -0.498   -9.2581  15.7667   3.4261
 W0V  C3   C  C     0   0.579   -8.9786  14.6560   3.8530
 W0V  C1   C  CH1   0  -0.376   -8.8802  14.3645   5.3377
 W0V  C2   C  CH3   0  -0.650   -7.6934  15.1329   5.9175
 W0V  C    C  CH3   0  -0.650  -10.1835  14.7346   6.0390
 W0V  N    N  NH1   0  -0.621   -8.7380  13.6116   3.0380
 W0V  N2   N  N     0  -0.460   -6.2889  14.5296   2.0059
 W0V  C11  C  CR56  0   0.132   -5.2943  15.0365   1.2006
 W0V  C9   C  CR16  0  -0.273   -3.1903  15.8984   0.4932
 W0V  H1   H  HNR5  0   0.419   -7.6836  14.6101  -0.8504
 W0V  H2   H  HCH2  0   0.278   -9.4292  14.4178   1.2508
 W0V  H3   H  HCH2  0   0.296   -8.7768  12.7990   1.1444
 W0V  H4   H  HCR6  0   0.265   -5.3159  15.6807  -2.1755
 W0V  H5   H  HCR6  0   0.254   -3.0042  16.3599  -1.5982
 W0V  H6   H  HCR6  0   0.252   -3.6265  15.3581   2.5331
 W0V  H7   H  HCH1  0   0.248   -8.6993  13.2959   5.4842
 W0V  H8   H  HCH3  0   0.235   -7.6131  14.9496   6.9895
 W0V  H9   H  HCH3  0   0.235   -6.7553  14.8262   5.4531
 W0V  H10  H  HCH3  0   0.227   -7.8103  16.2067   5.7683
 W0V  H11  H  HCH3  0   0.235  -10.1187  14.4947   7.1005
 W0V  H12  H  HCH3  0   0.226  -10.3901  15.8014   5.9487
 W0V  H13  H  HCH3  0   0.234  -11.0334  14.1894   5.6263
 W0V  H14  H  HNH1  0   0.405   -8.4175  12.7449   3.4365
 W0V  H16  H  HCR6  0   0.251   -2.1766  16.2082   0.7112

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
 W0V  C7   C8   aromatic  1.385  0.020  1.385
 W0V  C7   C6   aromatic  1.389  0.020  1.389
 W0V  C8   C9   aromatic  1.403  0.020  1.403
 W0V  C6   N1   aromatic  1.370  0.020  1.370
 W0V  C6   C11  aromatic  1.405  0.020  1.405
 W0V  N1   C5   aromatic  1.358  0.020  1.358
 W0V  C9   C10  aromatic  1.384  0.020  1.384
 W0V  C11  C10  aromatic  1.394  0.020  1.394
 W0V  C11  N2   aromatic  1.376  0.020  1.376
 W0V  C5   C4   single    1.499  0.020  1.499
 W0V  C5   N2   aromatic  1.302  0.020  1.302
 W0V  C4   N    single    1.433  0.020  1.433
 W0V  N    C3   single    1.346  0.020  1.346
 W0V  O    C3   double    1.222  0.020  1.222
 W0V  C3   C1   single    1.516  0.020  1.516
 W0V  C1   C    single    1.526  0.020  1.526
 W0V  C1   C2   single    1.528  0.020  1.528
 W0V  N1   H1   single    0.860  0.020  1.020
 W0V  C4   H2   single    0.970  0.020  1.090
 W0V  C4   H3   single    0.970  0.020  1.090
 W0V  C7   H4   single    0.930  0.020  1.080
 W0V  C8   H5   single    0.930  0.020  1.080
 W0V  C10  H6   single    0.930  0.020  1.080
 W0V  C1   H7   single    0.970  0.020  1.090
 W0V  C2   H8   single    0.970  0.020  1.090
 W0V  C2   H9   single    0.970  0.020  1.090
 W0V  C2   H10  single    0.970  0.020  1.090
 W0V  C    H11  single    0.970  0.020  1.090
 W0V  C    H12  single    0.970  0.020  1.090
 W0V  C    H13  single    0.970  0.020  1.090
 W0V  N    H14  single    0.860  0.020  1.020
 W0V  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
 W0V  H1   N1   C6   126.51  3.000
 W0V  H1   N1   C5   126.13  3.000
 W0V  C6   N1   C5   107.36  3.000
 W0V  H3   C4   H2   106.44  3.000
 W0V  H3   C4   N    108.71  3.000
 W0V  H2   C4   N    110.17  3.000
 W0V  H3   C4   C5   109.64  3.000
 W0V  H2   C4   C5   109.55  3.000
 W0V  N    C4   C5   112.16  3.000
 W0V  N2   C5   C4   125.50  3.000
 W0V  N2   C5   N1   113.02  3.000
 W0V  C4   C5   N1   121.47  3.000
 W0V  C11  C6   C7   122.62  3.000
 W0V  C11  C6   N1   104.44  3.000
 W0V  C7   C6   N1   132.93  3.000
 W0V  H4   C7   C8   121.38  3.000
 W0V  H4   C7   C6   121.96  3.000
 W0V  C8   C7   C6   116.65  3.000
 W0V  H5   C8   C9   119.23  3.000
 W0V  H5   C8   C7   119.23  3.000
 W0V  C9   C8   C7   121.53  3.000
 W0V  H6   C10  C9   121.25  3.000
 W0V  H6   C10  C11  120.78  3.000
 W0V  C9   C10  C11  117.97  3.000
 W0V  N    C3   C1   115.59  3.000
 W0V  C1   C3   O    122.11  3.000
 W0V  N    C3   O    122.30  3.000
 W0V  H7   C1   C    108.47  3.000
 W0V  H7   C1   C2   108.18  3.000
 W0V  C    C1   C2   111.53  3.000
 W0V  H7   C1   C3   109.26  3.000
 W0V  C2   C1   C3   108.98  3.000
 W0V  C    C1   C3   110.37  3.000
 W0V  H10  C2   H9   108.12  3.000
 W0V  H10  C2   H8   107.94  3.000
 W0V  H9   C2   H8   107.94  3.000
 W0V  H10  C2   C1   111.10  3.000
 W0V  H9   C2   C1   111.40  3.000
 W0V  H8   C2   C1   110.22  3.000
 W0V  H13  C    H12  108.06  3.000
 W0V  H13  C    H11  107.74  3.000
 W0V  H12  C    H11  107.89  3.000
 W0V  H13  C    C1   111.74  3.000
 W0V  H12  C    C1   111.18  3.000
 W0V  H11  C    C1   110.09  3.000
 W0V  H14  N    C3   119.03  3.000
 W0V  H14  N    C4   117.67  3.000
 W0V  C3   N    C4   121.78  3.000
 W0V  C11  N2   C5   105.12  3.000
 W0V  N2   C11  C10  130.11  3.000
 W0V  N2   C11  C6   110.05  3.000
 W0V  C10  C11  C6   119.84  3.000
 W0V  H16  C9   C10  119.49  3.000
 W0V  H16  C9   C8   119.13  3.000
 W0V  C10  C9   C8   121.38  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
 W0V  CONST_01  C8   C7   C6   N1   180.00   0.0  0
 W0V  CONST_02  C10  C11  C6   N1   180.00   0.0  0
 W0V  CONST_03  N2   C11  C6   N1     0.00   0.0  0
 W0V  CONST_04  C11  N2   C5   N1     0.00   0.0  0
 W0V  CONST_05  C7   C6   N1   C5   180.00   0.0  0
 W0V  CONST_06  C11  C6   N1   C5     0.00   0.0  0
 W0V  CONST_07  C6   C11  N2   C5     0.00   0.0  0
 W0V  CONST_08  C10  C11  N2   C5   180.00   0.0  0
 W0V  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 W0V  CONST_10  N2   C5   N1   C6     0.00   0.0  0
 W0V  CONST_11  C9   C10  C11  C6     0.00   0.0  0
 W0V  CONST_12  C10  C9   C8   C7     0.00   0.0  0
 W0V  CONST_13  C10  C11  C6   C7     0.00   0.0  0
 W0V  CONST_14  N2   C11  C6   C7   180.00   0.0  0
 W0V  CONST_15  C11  C6   C7   C8     0.00   0.0  0
 W0V  CONST_16  C11  C10  C9   C8     0.00   0.0  0
 W0V  CONST_17  C9   C10  C11  N2   180.00   0.0  0
 W0V  CONST_18  C6   N1   C5   C4   180.00   0.0  0
 W0V  CONST_19  C11  N2   C5   C4   180.00   0.0  0
 W0V  CONST_20  H4   C7   C6   N1     0.00   0.0  0
 W0V  CONST_21  H5   C8   C7   C6   180.00   0.0  0
 W0V  CONST_22  H6   C10  C11  C6   180.00   0.0  0
 W0V  CONST_23  H16  C9   C8   C7   180.00   0.0  0
 W0V  CONST_24  H1   N1   C6   C7     0.00   0.0  0
 W0V  CONST_25  O    C3   N    C4     0.00   0.0  0
 W0V  CONST_26  C1   C3   N    C4   180.00   0.0  0
 W0V  CONST_27  H14  N    C3   O    180.00   0.0  0
 W0V  Var_01    N    C4   C5   N1  -173.79  30.0  2
 W0V  Var_02    C3   N    C4   C5    77.68  30.0  3
 W0V  Var_03    C    C1   C3   O     56.32  30.0  3
 W0V  Var_04    H11  C    C1   C3   178.26  30.0  3
 W0V  Var_05    H8   C2   C1   C3   179.13  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
 W0V  plan-1  N1   0.020
 W0V  plan-1  C4   0.020
 W0V  plan-1  C5   0.020
 W0V  plan-1  C6   0.020
 W0V  plan-1  C7   0.020
 W0V  plan-1  C8   0.020
 W0V  plan-1  C10  0.020
 W0V  plan-1  N2   0.020
 W0V  plan-1  C11  0.020
 W0V  plan-1  C9   0.020
 W0V  plan-1  H1   0.020
 W0V  plan-1  H4   0.020
 W0V  plan-1  H5   0.020
 W0V  plan-1  H6   0.020
 W0V  plan-1  H16  0.020
 W0V  plan-2  C4   0.020
 W0V  plan-2  O    0.020
 W0V  plan-2  C3   0.020
 W0V  plan-2  C1   0.020
 W0V  plan-2  N    0.020
 W0V  plan-2  H14  0.020

