# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:48:37 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-amino-1,3,6-trimethyl-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(N)c(C)cc12
#
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
 39O  39O  5-amino-1,3,6-trimethyl-1,3-dihydro-2H-benzimidazol-2-one  ligand  27  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_39O
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
 39O  CAA  C  CH3   0  -0.745   3.5213   1.4452   0.0225
 39O  CAH  C  CR6   0   0.036   2.2176   0.7018   0.0090
 39O  CAF  C  CR16  0  -0.372   1.0112   1.4029  -0.0193
 39O  CAK  C  CR56  0   0.318  -0.1753   0.6997  -0.0110
 39O  NAM  N  NR5   0  -0.580  -1.4996   1.1032  -0.0289
 39O  CAB  C  CH3   0  -0.533  -1.9474   2.4694  -0.0597
 39O  CAJ  C  CR5   0   0.646  -2.3197   0.0051  -0.0121
 39O  OAE  O  O     0  -0.514  -3.5408  -0.0022  -0.0217
 39O  NAN  N  NR5   0  -0.583  -1.4918  -1.0959   0.0182
 39O  CAC  C  CH3   0  -0.534  -1.9400  -2.4628   0.0430
 39O  CAL  C  CR56  0   0.334  -0.1743  -0.6918   0.0204
 39O  CAG  C  CR16  0  -0.404   1.0020  -1.4135   0.0396
 39O  CAI  C  CR6   0   0.244   2.2121  -0.7068   0.0370
 39O  NAD  N  NH2   0  -0.861   3.4138  -1.4002   0.1249
 39O  H1   H  HCH3  0   0.242   4.1226   1.1941   0.8996
 39O  H2   H  HCH3  0   0.238   4.1352   1.2240  -0.8554
 39O  H3   H  HCH3  0   0.253   3.3565   2.5216   0.0335
 39O  H4   H  HCR6  0   0.262   1.0215   2.4861  -0.0420
 39O  H5   H  HCH3  0   0.250  -1.6001   2.9718  -0.9631
 39O  H6   H  HCH3  0   0.265  -3.0333   2.4914  -0.0463
 39O  H7   H  HCH3  0   0.250  -1.5776   3.0159   0.8082
 39O  H8   H  HCH3  0   0.266  -3.0259  -2.4833   0.0368
 39O  H9   H  HCH3  0   0.251  -1.5766  -3.0051  -0.8302
 39O  H10  H  HCH3  0   0.251  -1.5873  -2.9691   0.9418
 39O  H11  H  HCR6  0   0.269   1.0006  -2.4968   0.0556
 39O  H12  H  HNH2  0   0.375   3.3427  -2.3784  -0.1085
 39O  H13  H  HNH2  0   0.376   4.1854  -0.9819  -0.3714

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
 39O  NAD  CAI  single    1.390  0.020  1.390
 39O  CAI  CAG  aromatic  1.401  0.020  1.401
 39O  CAI  CAH  aromatic  1.409  0.020  1.409
 39O  CAG  CAL  aromatic  1.380  0.020  1.380
 39O  CAC  NAN  single    1.439  0.020  1.439
 39O  CAA  CAH  single    1.501  0.020  1.501
 39O  CAH  CAF  aromatic  1.396  0.020  1.396
 39O  CAL  NAN  single    1.378  0.020  1.378
 39O  CAL  CAK  aromatic  1.392  0.020  1.392
 39O  NAN  CAJ  single    1.378  0.020  1.378
 39O  CAF  CAK  aromatic  1.379  0.020  1.379
 39O  CAK  NAM  single    1.385  0.020  1.385
 39O  CAJ  NAM  single    1.371  0.020  1.371
 39O  CAJ  OAE  double    1.221  0.020  1.221
 39O  NAM  CAB  single    1.438  0.020  1.438
 39O  CAA  H1   single    0.970  0.020  1.090
 39O  CAA  H2   single    0.970  0.020  1.090
 39O  CAA  H3   single    0.970  0.020  1.090
 39O  CAF  H4   single    0.930  0.020  1.080
 39O  CAB  H5   single    0.970  0.020  1.090
 39O  CAB  H6   single    0.970  0.020  1.090
 39O  CAB  H7   single    0.970  0.020  1.090
 39O  CAC  H8   single    0.970  0.020  1.090
 39O  CAC  H9   single    0.970  0.020  1.090
 39O  CAC  H10  single    0.970  0.020  1.090
 39O  CAG  H11  single    0.930  0.020  1.080
 39O  NAD  H12  single    0.890  0.020  1.040
 39O  NAD  H13  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
 39O  H3   CAA  H2   107.04  3.000
 39O  H3   CAA  H1   107.60  3.000
 39O  H2   CAA  H1   106.79  3.000
 39O  H3   CAA  CAH  110.99  3.000
 39O  H2   CAA  CAH  112.34  3.000
 39O  H1   CAA  CAH  111.80  3.000
 39O  CAI  CAH  CAF  119.96  3.000
 39O  CAF  CAH  CAA  120.14  3.000
 39O  CAI  CAH  CAA  119.90  3.000
 39O  H4   CAF  CAK  121.20  3.000
 39O  H4   CAF  CAH  119.64  3.000
 39O  CAK  CAF  CAH  119.16  3.000
 39O  CAL  CAK  NAM  106.99  3.000
 39O  NAM  CAK  CAF  132.39  3.000
 39O  CAL  CAK  CAF  120.61  3.000
 39O  CAJ  NAM  CAB  125.10  3.000
 39O  CAB  NAM  CAK  125.10  3.000
 39O  CAJ  NAM  CAK  109.80  3.000
 39O  H7   CAB  H6   108.61  3.000
 39O  H7   CAB  H5   108.70  3.000
 39O  H6   CAB  H5   108.62  3.000
 39O  H7   CAB  NAM  110.71  3.000
 39O  H6   CAB  NAM  109.28  3.000
 39O  H5   CAB  NAM  110.87  3.000
 39O  NAN  CAJ  OAE  126.60  3.000
 39O  OAE  CAJ  NAM  127.09  3.000
 39O  NAN  CAJ  NAM  106.31  3.000
 39O  CAL  NAN  CAC  125.20  3.000
 39O  CAL  NAN  CAJ  109.89  3.000
 39O  CAC  NAN  CAJ  124.91  3.000
 39O  H10  CAC  H9   108.75  3.000
 39O  H10  CAC  H8   108.62  3.000
 39O  H9   CAC  H8   108.61  3.000
 39O  H10  CAC  NAN  110.78  3.000
 39O  H9   CAC  NAN  110.79  3.000
 39O  H8   CAC  NAN  109.23  3.000
 39O  CAG  CAL  NAN  131.42  3.000
 39O  NAN  CAL  CAK  107.00  3.000
 39O  CAG  CAL  CAK  121.58  3.000
 39O  H11  CAG  CAI  120.36  3.000
 39O  H11  CAG  CAL  121.46  3.000
 39O  CAI  CAG  CAL  118.19  3.000
 39O  NAD  CAI  CAG  119.66  3.000
 39O  CAG  CAI  CAH  120.50  3.000
 39O  NAD  CAI  CAH  119.77  3.000
 39O  H13  NAD  H12  110.03  3.000
 39O  H13  NAD  CAI  115.05  3.000
 39O  H12  NAD  CAI  114.10  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
 39O  CONST_01  CAL  CAG  CAI  CAH    0.00   0.0  0
 39O  CONST_02  CAL  CAK  CAF  CAH    0.00   0.0  0
 39O  CONST_03  CAG  CAI  CAH  CAF    0.00   0.0  0
 39O  CONST_04  CAG  CAL  CAK  CAF    0.00   0.0  0
 39O  CONST_05  CAI  CAG  CAL  CAK    0.00   0.0  0
 39O  CONST_06  CAI  CAH  CAF  CAK    0.00   0.0  0
 39O  CONST_07  CAJ  NAN  CAL  CAK    0.00   0.0  0
 39O  CONST_08  NAN  CAJ  NAM  CAK    0.00   0.0  0
 39O  CONST_09  NAN  CAL  CAK  NAM    0.00   0.0  0
 39O  CONST_10  CAL  NAN  CAJ  NAM    0.00   0.0  0
 39O  CONST_11  CAL  CAK  NAM  CAJ    0.00   0.0  0
 39O  CONST_12  CAG  CAI  CAH  CAA  180.00   0.0  0
 39O  CONST_13  CAK  CAF  CAH  CAA  180.00   0.0  0
 39O  CONST_14  NAD  CAI  CAH  CAF  180.00   0.0  0
 39O  CONST_15  NAD  CAI  CAG  CAL  180.00   0.0  0
 39O  CONST_16  CAC  NAN  CAL  CAK  180.00   0.0  0
 39O  CONST_17  OAE  CAJ  NAM  CAK  180.00   0.0  0
 39O  CONST_18  CAC  NAN  CAJ  NAM  180.00   0.0  0
 39O  CONST_19  CAL  CAK  NAM  CAB  180.00   0.0  0
 39O  CONST_20  NAN  CAJ  NAM  CAB  180.00   0.0  0
 39O  CONST_21  CAL  NAN  CAJ  OAE  180.00   0.0  0
 39O  CONST_22  H11  CAG  CAI  CAH  180.00   0.0  0
 39O  CONST_23  H4   CAF  CAK  NAM    0.00   0.0  0
 39O  CONST_24  OAE  CAJ  NAM  CAB    0.00   0.0  0
 39O  CONST_25  CAC  NAN  CAJ  OAE    0.00   0.0  0
 39O  Var_01    H1   CAA  CAH  CAF  121.62  30.0  2
 39O  Var_02    H5   CAB  NAM  CAK   61.53  30.0  3
 39O  Var_03    H8   CAC  NAN  CAJ   -0.15  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
 39O  plan-1  CAA  0.020
 39O  plan-1  CAH  0.020
 39O  plan-1  CAF  0.020
 39O  plan-1  CAK  0.020
 39O  plan-1  NAM  0.020
 39O  plan-1  CAB  0.020
 39O  plan-1  CAJ  0.020
 39O  plan-1  OAE  0.020
 39O  plan-1  NAN  0.020
 39O  plan-1  CAC  0.020
 39O  plan-1  CAL  0.020
 39O  plan-1  CAG  0.020
 39O  plan-1  CAI  0.020
 39O  plan-1  NAD  0.020
 39O  plan-1  H4   0.020
 39O  plan-1  H11  0.020
 39O  plan-2  CAI  0.020
 39O  plan-2  NAD  0.020
 39O  plan-2  H12  0.020
 39O  plan-2  H13  0.020

