# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:18:22 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(2-methyl-1H-benzimidazol-1-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccccc2n1CCC(N)=O
#
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
 UVJ  UVJ  3-(2-methyl-1H-benzimidazol-1-yl)propanamide  ligand  28  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UVJ
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
 UVJ  N1   N  NR5   0  -0.538  -19.2768  13.2202  25.7766
 UVJ  C4   C  CR16  0  -0.275  -23.0507  11.9483  26.6856
 UVJ  C5   C  CR16  0  -0.278  -22.3083  12.4615  27.7589
 UVJ  C6   C  CR16  0  -0.312  -21.0169  12.9328  27.5867
 UVJ  C7   C  CR56  0   0.341  -20.4960  12.8683  26.2998
 UVJ  C8   C  CH2   0  -0.318  -18.1989  13.8599  26.4973
 UVJ  C10  C  C     0   0.535  -17.2367  16.0512  27.2761
 UVJ  N    N  N     0  -0.484  -20.4615  12.4160  24.0721
 UVJ  O    O  O     0  -0.495  -16.1054  15.5861  27.2609
 UVJ  C1   C  CR5   0   0.432  -19.3211  12.9342  24.4420
 UVJ  C2   C  CR56  0   0.132  -21.2244  12.3586  25.2137
 UVJ  C3   C  CR16  0  -0.334  -22.5228  11.8901  25.4070
 UVJ  C9   C  CH2   0  -0.590  -18.3876  15.3701  26.5646
 UVJ  N2   N  NH2   0  -0.802  -17.5498  17.1984  27.8918
 UVJ  H1   H  HCR6  0   0.251  -24.0558  11.5898  26.8658
 UVJ  H2   H  HCR6  0   0.254  -22.7539  12.4894  28.7447
 UVJ  H3   H  HCR6  0   0.266  -20.4511  13.3283  28.4210
 UVJ  H4   H  HCH2  0   0.279  -18.1592  13.4324  27.4995
 UVJ  H5   H  HCH2  0   0.281  -17.2566  13.6083  26.0149
 UVJ  H6   H  HCH3  0   0.274  -18.4228  12.8648  22.5328
 UVJ  H7   H  HCH3  0   0.263  -17.9159  14.2506  23.4995
 UVJ  H8   H  HCH3  0   0.267  -17.2799  12.6508  23.8614
 UVJ  H9   H  HCR6  0   0.252  -23.0979  11.4929  24.5800
 UVJ  H10  H  HCH2  0   0.272  -19.3394  15.6150  27.0406
 UVJ  H11  H  HCH2  0   0.288  -18.4396  15.7776  25.5503
 UVJ  H12  H  HNH2  0   0.401  -16.8353  17.7528  28.3353
 UVJ  H13  H  HNH2  0   0.409  -18.4881  17.5585  27.8999
 UVJ  C    C  CH3   0  -0.769  -18.1715  13.1905  23.5386

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
 UVJ  C    C1   single    1.484  0.020  1.484
 UVJ  N    C1   aromatic  1.306  0.020  1.306
 UVJ  N    C2   aromatic  1.374  0.020  1.374
 UVJ  C1   N1   aromatic  1.366  0.020  1.366
 UVJ  C2   C3   aromatic  1.394  0.020  1.394
 UVJ  C2   C7   aromatic  1.403  0.020  1.403
 UVJ  C3   C4   aromatic  1.385  0.020  1.385
 UVJ  O    C10  double    1.223  0.020  1.223
 UVJ  N1   C7   aromatic  1.373  0.020  1.373
 UVJ  N1   C8   single    1.446  0.020  1.446
 UVJ  C9   C10  single    1.515  0.020  1.515
 UVJ  C9   C8   single    1.523  0.020  1.523
 UVJ  C7   C6   aromatic  1.390  0.020  1.390
 UVJ  C4   C5   aromatic  1.402  0.020  1.402
 UVJ  C10  N2   single    1.339  0.020  1.339
 UVJ  C6   C5   aromatic  1.385  0.020  1.385
 UVJ  C4   H1   single    0.930  0.020  1.080
 UVJ  C5   H2   single    0.930  0.020  1.080
 UVJ  C6   H3   single    0.930  0.020  1.080
 UVJ  C8   H4   single    0.970  0.020  1.090
 UVJ  C8   H5   single    0.970  0.020  1.090
 UVJ  C    H6   single    0.970  0.020  1.090
 UVJ  C    H7   single    0.970  0.020  1.090
 UVJ  C    H8   single    0.970  0.020  1.090
 UVJ  C3   H9   single    0.930  0.020  1.080
 UVJ  C9   H10  single    0.970  0.020  1.090
 UVJ  C9   H11  single    0.970  0.020  1.090
 UVJ  N2   H12  single    0.860  0.020  1.020
 UVJ  N2   H13  single    0.860  0.020  1.020

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
 UVJ  C1   N1   C8   127.16  3.000
 UVJ  C8   N1   C7   125.85  3.000
 UVJ  C1   N1   C7   106.86  3.000
 UVJ  H1   C4   C3   119.60  3.000
 UVJ  H1   C4   C5   119.05  3.000
 UVJ  C3   C4   C5   121.36  3.000
 UVJ  H2   C5   C6   119.22  3.000
 UVJ  H2   C5   C4   119.25  3.000
 UVJ  C6   C5   C4   121.52  3.000
 UVJ  H3   C6   C7   122.31  3.000
 UVJ  H3   C6   C5   121.03  3.000
 UVJ  C7   C6   C5   116.66  3.000
 UVJ  C2   C7   C6   122.61  3.000
 UVJ  C6   C7   N1   132.37  3.000
 UVJ  C2   C7   N1   105.02  3.000
 UVJ  H5   C8   H4   106.57  3.000
 UVJ  H5   C8   C9   110.85  3.000
 UVJ  H4   C8   C9   110.65  3.000
 UVJ  H5   C8   N1   108.80  3.000
 UVJ  H4   C8   N1   108.17  3.000
 UVJ  C9   C8   N1   111.61  3.000
 UVJ  N2   C10  C9   115.06  3.000
 UVJ  N2   C10  O    123.21  3.000
 UVJ  C9   C10  O    121.72  3.000
 UVJ  C2   N    C1   105.42  3.000
 UVJ  C    C1   N    124.91  3.000
 UVJ  N    C1   N1   112.84  3.000
 UVJ  C    C1   N1   122.24  3.000
 UVJ  C3   C2   N    130.26  3.000
 UVJ  C3   C2   C7   119.88  3.000
 UVJ  N    C2   C7   109.85  3.000
 UVJ  H9   C3   C2   120.81  3.000
 UVJ  H9   C3   C4   121.21  3.000
 UVJ  C2   C3   C4   117.98  3.000
 UVJ  H11  C9   H10  106.20  3.000
 UVJ  H11  C9   C10  107.70  3.000
 UVJ  H10  C9   C10  110.89  3.000
 UVJ  H11  C9   C8   109.52  3.000
 UVJ  H10  C9   C8   110.46  3.000
 UVJ  C10  C9   C8   111.86  3.000
 UVJ  H13  N2   H12  117.48  3.000
 UVJ  H13  N2   C10  121.93  3.000
 UVJ  H12  N2   C10  120.54  3.000
 UVJ  H8   C    H7   107.44  3.000
 UVJ  H8   C    H6   108.34  3.000
 UVJ  H7   C    H6   108.19  3.000
 UVJ  H8   C    C1   111.56  3.000
 UVJ  H7   C    C1   111.78  3.000
 UVJ  H6   C    C1   109.42  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
 UVJ  CONST_01  C2   N    C1   N1     0.00   0.0  0
 UVJ  CONST_02  N    C2   C7   N1     0.00   0.0  0
 UVJ  CONST_03  C3   C2   C7   N1   180.00   0.0  0
 UVJ  CONST_04  C5   C6   C7   N1   180.00   0.0  0
 UVJ  CONST_05  N    C2   C3   C4   180.00   0.0  0
 UVJ  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 UVJ  CONST_07  C7   C6   C5   C4     0.00   0.0  0
 UVJ  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 UVJ  CONST_09  C2   C7   C6   C5     0.00   0.0  0
 UVJ  CONST_10  N    C2   C7   C6   180.00   0.0  0
 UVJ  CONST_11  C3   C2   C7   C6     0.00   0.0  0
 UVJ  CONST_12  C1   N1   C7   C6   180.00   0.0  0
 UVJ  CONST_13  C3   C4   C5   C6     0.00   0.0  0
 UVJ  CONST_14  C1   N    C2   C7     0.00   0.0  0
 UVJ  CONST_15  N    C1   N1   C7     0.00   0.0  0
 UVJ  CONST_16  C3   C2   N    C1   180.00   0.0  0
 UVJ  CONST_17  C2   C7   N1   C1     0.00   0.0  0
 UVJ  CONST_18  C8   N1   C7   C6     0.00   0.0  0
 UVJ  CONST_19  C    C1   N1   C7   180.00   0.0  0
 UVJ  CONST_20  N    C1   N1   C8   180.00   0.0  0
 UVJ  CONST_21  C2   C7   N1   C8   180.00   0.0  0
 UVJ  CONST_22  C2   N    C1   C    180.00   0.0  0
 UVJ  CONST_23  H3   C6   C7   N1     0.00   0.0  0
 UVJ  CONST_24  H9   C3   C4   C5   180.00   0.0  0
 UVJ  CONST_25  H1   C4   C5   C6   180.00   0.0  0
 UVJ  CONST_26  H2   C5   C6   C7   180.00   0.0  0
 UVJ  CONST_27  H12  N2   C10  O      0.00   0.0  0
 UVJ  CONST_28  H13  N2   C10  O    180.00   0.0  0
 UVJ  Var_01    C9   C8   N1   C7   -83.27  30.0  2
 UVJ  Var_02    H6   C    C1   N1   178.61  30.0  2
 UVJ  Var_03    C10  C9   C8   N1  -177.99  30.0  1
 UVJ  Var_04    O    C10  C9   C8    29.40  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
 UVJ  plan-1  N1   0.020
 UVJ  plan-1  C4   0.020
 UVJ  plan-1  C5   0.020
 UVJ  plan-1  C6   0.020
 UVJ  plan-1  C7   0.020
 UVJ  plan-1  C8   0.020
 UVJ  plan-1  N    0.020
 UVJ  plan-1  C1   0.020
 UVJ  plan-1  C2   0.020
 UVJ  plan-1  C3   0.020
 UVJ  plan-1  H1   0.020
 UVJ  plan-1  H2   0.020
 UVJ  plan-1  H3   0.020
 UVJ  plan-1  H9   0.020
 UVJ  plan-1  C    0.020
 UVJ  plan-2  C10  0.020
 UVJ  plan-2  O    0.020
 UVJ  plan-2  C9   0.020
 UVJ  plan-2  N2   0.020
 UVJ  plan-2  H12  0.020
 UVJ  plan-2  H13  0.020

