# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 05:17:50 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)Nc1ccc2NC(=O)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
 1FE  1FE  N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide  ligand  25  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1FE
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
 1FE  O2   O  O     0  -0.500  -4.7891  -1.1850  -0.1377
 1FE  C6   C  CR5   0   0.606  -3.6949  -0.6510  -0.1022
 1FE  N2   N  NR15  0  -0.737  -3.4220   0.6862   0.0306
 1FE  N3   N  NR15  0  -0.740  -2.4667  -1.2622  -0.1875
 1FE  C7   C  CR56  0   0.359  -1.4497  -0.3373  -0.1111
 1FE  C5   C  CR56  0   0.310  -2.0605   0.9105   0.0281
 1FE  C4   C  CR16  0  -0.298  -1.2957   2.0547   0.1275
 1FE  C3   C  CR16  0  -0.371   0.0855   1.9140   0.0893
 1FE  C8   C  CR16  0  -0.394  -0.0777  -0.4948  -0.1557
 1FE  C2   C  CR6   0   0.366   0.6991   0.6633  -0.0511
 1FE  N1   N  NH1   0  -0.743   2.0990   0.6567  -0.0994
 1FE  C1   C  C     0   0.521   2.9590  -0.3881   0.0012
 1FE  O1   O  O     0  -0.469   2.6166  -1.5474   0.1372
 1FE  C9   C  CH2   0  -0.416   4.4161   0.0313  -0.1083
 1FE  N4   N  NH2   0  -0.789   5.3018  -1.0853   0.1228
 1FE  H1   H  HNR5  0   0.418  -4.1385   1.3881   0.1197
 1FE  H2   H  HNR5  0   0.419  -2.3539  -2.2581  -0.2868
 1FE  H3   H  HCR6  0   0.273  -1.7447   3.0325   0.2370
 1FE  H4   H  HCR6  0   0.270   0.7033   2.7998   0.1719
 1FE  H5   H  HCR6  0   0.289   0.3611  -1.4722  -0.2724
 1FE  H6   H  HNH1  0   0.414   2.5212   1.5705  -0.1749
 1FE  H7   H  HCH2  0   0.244   4.5402   0.5246  -1.0841
 1FE  H8   H  HCH2  0   0.265   4.6121   0.8029   0.6412
 1FE  H9   H  HNH2  0   0.347   5.2233  -1.7482  -0.6371
 1FE  H10  H  HNH2  0   0.356   6.2555  -0.7499   0.1016

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
 1FE  N4  C9   single    1.444  0.020  1.444
 1FE  O1  C1   double    1.216  0.020  1.216
 1FE  C9  C1   single    1.520  0.020  1.520
 1FE  C1  N1   single    1.357  0.020  1.357
 1FE  N1  C2   single    1.401  0.020  1.401
 1FE  C8  C2   aromatic  1.398  0.020  1.398
 1FE  C8  C7   aromatic  1.382  0.020  1.382
 1FE  C2  C3   aromatic  1.400  0.020  1.400
 1FE  N3  C7   single    1.377  0.020  1.377
 1FE  N3  C6   single    1.375  0.020  1.375
 1FE  C7  C5   aromatic  1.396  0.020  1.396
 1FE  C3  C4   aromatic  1.389  0.020  1.389
 1FE  C6  O2   double    1.218  0.020  1.218
 1FE  C6  N2   single    1.371  0.020  1.371
 1FE  C5  C4   aromatic  1.380  0.020  1.380
 1FE  C5  N2   single    1.380  0.020  1.380
 1FE  N2  H1   single    0.860  0.020  1.020
 1FE  N3  H2   single    0.860  0.020  1.020
 1FE  C4  H3   single    0.930  0.020  1.080
 1FE  C3  H4   single    0.930  0.020  1.080
 1FE  C8  H5   single    0.930  0.020  1.080
 1FE  N1  H6   single    0.860  0.020  1.020
 1FE  C9  H7   single    0.970  0.020  1.090
 1FE  C9  H8   single    0.970  0.020  1.090
 1FE  N4  H9   single    0.890  0.020  1.040
 1FE  N4  H10  single    0.890  0.020  1.040

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
 1FE  N3   C6  N2  105.17  3.000
 1FE  N2   C6  O2  127.53  3.000
 1FE  N3   C6  O2  127.30  3.000
 1FE  H1   N2  C5  126.09  3.000
 1FE  H1   N2  C6  123.14  3.000
 1FE  C5   N2  C6  110.78  3.000
 1FE  H2   N3  C7  125.94  3.000
 1FE  H2   N3  C6  123.08  3.000
 1FE  C7   N3  C6  110.98  3.000
 1FE  C8   C7  C5  122.65  3.000
 1FE  C5   C7  N3  106.42  3.000
 1FE  C8   C7  N3  130.93  3.000
 1FE  C4   C5  C7  120.38  3.000
 1FE  C4   C5  N2  132.97  3.000
 1FE  C7   C5  N2  106.65  3.000
 1FE  H3   C4  C3  120.48  3.000
 1FE  H3   C4  C5  121.79  3.000
 1FE  C3   C4  C5  117.72  3.000
 1FE  H4   C3  C2  119.22  3.000
 1FE  H4   C3  C4  118.84  3.000
 1FE  C2   C3  C4  121.94  3.000
 1FE  H5   C8  C2  122.21  3.000
 1FE  H5   C8  C7  120.74  3.000
 1FE  C2   C8  C7  117.05  3.000
 1FE  N1   C2  C8  123.28  3.000
 1FE  C8   C2  C3  120.25  3.000
 1FE  N1   C2  C3  116.46  3.000
 1FE  H6   N1  C1  115.94  3.000
 1FE  H6   N1  C2  114.61  3.000
 1FE  C1   N1  C2  129.38  3.000
 1FE  C9   C1  O1  122.74  3.000
 1FE  C9   C1  N1  112.93  3.000
 1FE  O1   C1  N1  124.31  3.000
 1FE  H8   C9  H7  105.74  3.000
 1FE  H8   C9  N4  109.03  3.000
 1FE  H7   C9  N4  114.80  3.000
 1FE  H8   C9  C1  108.49  3.000
 1FE  H7   C9  C1  107.20  3.000
 1FE  N4   C9  C1  111.29  3.000
 1FE  H10  N4  H9  105.95  3.000
 1FE  H10  N4  C9  108.59  3.000
 1FE  H9   N4  C9  109.82  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
 1FE  CONST_01  C3  C2  C8  C7    0.00   0.0  0
 1FE  CONST_02  C3  C4  C5  C7    0.00   0.0  0
 1FE  CONST_03  C2  C8  C7  C5    0.00   0.0  0
 1FE  CONST_04  C2  C3  C4  C5    0.00   0.0  0
 1FE  CONST_05  C8  C2  C3  C4    0.00   0.0  0
 1FE  CONST_06  C8  C7  C5  C4    0.00   0.0  0
 1FE  CONST_07  C5  C7  N3  C6    0.00   0.0  0
 1FE  CONST_08  C7  C5  N2  C6    0.00   0.0  0
 1FE  CONST_09  C7  N3  C6  N2    0.00   0.0  0
 1FE  CONST_10  N3  C7  C5  N2    0.00   0.0  0
 1FE  CONST_11  C5  N2  C6  N3    0.00   0.0  0
 1FE  CONST_12  N1  C2  C8  C7  180.00   0.0  0
 1FE  CONST_13  N1  C2  C3  C4  180.00   0.0  0
 1FE  CONST_14  C7  N3  C6  O2  180.00   0.0  0
 1FE  CONST_15  C5  N2  C6  O2  180.00   0.0  0
 1FE  CONST_16  H3  C4  C5  N2    0.00   0.0  0
 1FE  CONST_17  H5  C8  C7  N3    0.00   0.0  0
 1FE  CONST_18  H4  C3  C4  C5  180.00   0.0  0
 1FE  CONST_19  H2  N3  C6  N2  180.00   0.0  0
 1FE  CONST_20  H1  N2  C6  N3  180.00   0.0  0
 1FE  CONST_21  C1  N1  C2  C3  180.00   0.0  0
 1FE  CONST_22  C1  N1  C2  C8    0.00   0.0  0
 1FE  CONST_23  H6  N1  C2  C3    0.00   0.0  0
 1FE  CONST_24  O1  C1  N1  C2    0.00   0.0  0
 1FE  CONST_25  C9  C1  N1  C2  180.00   0.0  0
 1FE  Var_01    N4  C9  C1  N1  174.83  30.0  1
 1FE  Var_02    H9  N4  C9  C1   68.29  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
 1FE  plan-1  O2  0.020
 1FE  plan-1  C6  0.020
 1FE  plan-1  N2  0.020
 1FE  plan-1  N3  0.020
 1FE  plan-1  C7  0.020
 1FE  plan-1  C5  0.020
 1FE  plan-1  C4  0.020
 1FE  plan-1  C3  0.020
 1FE  plan-1  C8  0.020
 1FE  plan-1  C2  0.020
 1FE  plan-1  N1  0.020
 1FE  plan-1  H1  0.020
 1FE  plan-1  H2  0.020
 1FE  plan-1  H3  0.020
 1FE  plan-1  H4  0.020
 1FE  plan-1  H5  0.020
 1FE  plan-2  C2  0.020
 1FE  plan-2  N1  0.020
 1FE  plan-2  C1  0.020
 1FE  plan-2  O1  0.020
 1FE  plan-2  C9  0.020
 1FE  plan-2  H6  0.020

