# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:58:39 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5-[(pyridin-2-ylmethyl)amino]-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ccc(NCc3ccccn3)cc2N1
#
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
 47Q  47Q  5-[(pyridin-2-ylmethyl)amino]-1,3-dihydro-2H-benzimidazol-2-one  ligand  30  18  .  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_47Q
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
 47Q  C4   C  CR6   0   0.358   0.3219   0.2214  -0.0309
 47Q  C5   C  CH2   0  -0.328  -2.0215   0.9533   0.1692
 47Q  C6   C  CR6   0   0.213  -3.3967   0.3481   0.0924
 47Q  N1   N  NH1   0  -0.691  -1.0289  -0.0839  -0.0079
 47Q  C7   C  CR16  0  -0.335  -4.1465   0.1308   1.2419
 47Q  C8   C  CR16  0  -0.149  -5.3979  -0.4577   1.1273
 47Q  N2   N  N     0  -0.407  -3.8365   0.0119  -1.1184
 47Q  C9   C  CR16  0  -0.325  -5.8545  -0.8086  -0.1322
 47Q  C10  C  CR16  0  -0.079  -5.0332  -0.5494  -1.2213
 47Q  C11  C  CR16  0  -0.416   1.2456  -0.8257   0.1287
 47Q  C12  C  CR56  0   0.347   2.5883  -0.5280   0.0515
 47Q  N3   N  NR15  0  -0.742   3.7079  -1.3220   0.1628
 47Q  O    O  O     0  -0.505   6.0047  -0.9867   0.0470
 47Q  C    C  CR5   0   0.603   4.8561  -0.5796   0.0080
 47Q  C1   C  CR56  0   0.296   3.0478   0.7732  -0.1789
 47Q  N    N  NR15  0  -0.738   4.4310   0.7044  -0.1977
 47Q  C3   C  CR16  0  -0.369   0.7902   1.5248  -0.2478
 47Q  C2   C  CR16  0  -0.300   2.1533   1.8084  -0.3287
 47Q  H1   H  HCH2  0   0.250  -1.9239   1.6882  -0.6324
 47Q  H2   H  HCH2  0   0.232  -1.9022   1.4933   1.1178
 47Q  H3   H  HNH1  0   0.377  -1.2403  -0.9280   0.5031
 47Q  H4   H  HCR6  0   0.270  -3.7556   0.4164   2.2096
 47Q  H5   H  HCR6  0   0.275  -6.0024  -0.6373   2.0066
 47Q  H6   H  HCR6  0   0.271  -6.8216  -1.2704  -0.2760
 47Q  H7   H  HCR6  0   0.263  -5.3614  -0.8055  -2.2227
 47Q  H8   H  HCR6  0   0.268   0.9067  -1.8397   0.3042
 47Q  H9   H  HNR5  0   0.416   3.7151  -2.3166   0.3205
 47Q  H10  H  HNR5  0   0.415   5.0613   1.4740  -0.3524
 47Q  H11  H  HCR6  0   0.264   0.0942   2.3442  -0.3578
 47Q  H12  H  HCR6  0   0.266   2.4870   2.8233  -0.5004

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
 47Q  O    C    double    1.219  0.020  1.219
 47Q  C    N3   single    1.376  0.020  1.376
 47Q  C    N    single    1.368  0.020  1.368
 47Q  N3   C12  single    1.377  0.020  1.377
 47Q  C12  C11  aromatic  1.378  0.020  1.378
 47Q  C12  C1   aromatic  1.399  0.020  1.399
 47Q  N    C1   single    1.385  0.020  1.385
 47Q  C11  C4   aromatic  1.405  0.020  1.405
 47Q  C1   C2   aromatic  1.376  0.020  1.376
 47Q  C4   N1   single    1.385  0.020  1.385
 47Q  C4   C3   aromatic  1.402  0.020  1.402
 47Q  C2   C3   aromatic  1.395  0.020  1.395
 47Q  N1   C5   single    1.446  0.020  1.446
 47Q  C5   C6   single    1.504  0.020  1.504
 47Q  C6   C7   aromatic  1.389  0.020  1.389
 47Q  C6   N2   aromatic  1.331  0.020  1.331
 47Q  C7   C8   aromatic  1.388  0.020  1.388
 47Q  N2   C10  aromatic  1.326  0.020  1.326
 47Q  C8   C9   aromatic  1.385  0.020  1.385
 47Q  C10  C9   aromatic  1.389  0.020  1.389
 47Q  C5   H1   single    0.970  0.020  1.090
 47Q  C5   H2   single    0.970  0.020  1.090
 47Q  N1   H3   single    0.890  0.020  1.040
 47Q  C7   H4   single    0.930  0.020  1.080
 47Q  C8   H5   single    0.930  0.020  1.080
 47Q  C9   H6   single    0.930  0.020  1.080
 47Q  C10  H7   single    0.930  0.020  1.080
 47Q  C11  H8   single    0.930  0.020  1.080
 47Q  N3   H9   single    0.860  0.020  1.020
 47Q  N    H10  single    0.860  0.020  1.020
 47Q  C3   H11  single    0.930  0.020  1.080
 47Q  C2   H12  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
 47Q  C3   C4   C11  119.39  3.000
 47Q  C3   C4   N1   122.23  3.000
 47Q  C11  C4   N1   118.35  3.000
 47Q  H2   C5   H1   107.07  3.000
 47Q  H2   C5   N1   112.57  3.000
 47Q  H1   C5   N1   109.35  3.000
 47Q  H2   C5   C6   109.95  3.000
 47Q  H1   C5   C6   108.36  3.000
 47Q  N1   C5   C6   109.43  3.000
 47Q  N2   C6   C7   122.32  3.000
 47Q  N2   C6   C5   116.74  3.000
 47Q  C7   C6   C5   120.93  3.000
 47Q  H3   N1   C5   113.21  3.000
 47Q  H3   N1   C4   113.40  3.000
 47Q  C5   N1   C4   120.88  3.000
 47Q  H4   C7   C8   120.77  3.000
 47Q  H4   C7   C6   120.24  3.000
 47Q  C8   C7   C6   118.99  3.000
 47Q  H5   C8   C9   120.85  3.000
 47Q  H5   C8   C7   120.47  3.000
 47Q  C9   C8   C7   118.68  3.000
 47Q  C10  N2   C6   118.41  3.000
 47Q  H6   C9   C10  120.30  3.000
 47Q  H6   C9   C8   121.60  3.000
 47Q  C10  C9   C8   118.10  3.000
 47Q  H7   C10  C9   120.08  3.000
 47Q  H7   C10  N2   116.42  3.000
 47Q  C9   C10  N2   123.51  3.000
 47Q  H8   C11  C12  121.08  3.000
 47Q  H8   C11  C4   120.67  3.000
 47Q  C12  C11  C4   118.24  3.000
 47Q  C1   C12  N3   106.41  3.000
 47Q  C1   C12  C11  122.03  3.000
 47Q  N3   C12  C11  131.55  3.000
 47Q  H9   N3   C    122.99  3.000
 47Q  H9   N3   C12  126.01  3.000
 47Q  C    N3   C12  110.99  3.000
 47Q  N    C    O    127.65  3.000
 47Q  N    C    N3   105.31  3.000
 47Q  O    C    N3   127.04  3.000
 47Q  C2   C1   N    133.23  3.000
 47Q  C2   C1   C12  120.27  3.000
 47Q  N    C1   C12  106.50  3.000
 47Q  H10  N    C1   126.11  3.000
 47Q  H10  N    C    123.09  3.000
 47Q  C1   N    C    110.79  3.000
 47Q  H11  C3   C2   117.99  3.000
 47Q  H11  C3   C4   120.37  3.000
 47Q  C2   C3   C4   121.64  3.000
 47Q  H12  C2   C3   120.09  3.000
 47Q  H12  C2   C1   121.49  3.000
 47Q  C3   C2   C1   118.42  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
 47Q  CONST_01  C1   C12  C11  C4     0.00   0.0  0
 47Q  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 47Q  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 47Q  CONST_04  C9   C10  N2   C6     0.00   0.0  0
 47Q  CONST_05  C10  N2   C6   C7     0.00   0.0  0
 47Q  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 47Q  CONST_07  N2   C6   C7   C8     0.00   0.0  0
 47Q  CONST_08  N2   C10  C9   C8     0.00   0.0  0
 47Q  CONST_09  C2   C1   C12  C11    0.00   0.0  0
 47Q  CONST_10  C2   C3   C4   C11    0.00   0.0  0
 47Q  CONST_11  C3   C4   C11  C12    0.00   0.0  0
 47Q  CONST_12  C3   C2   C1   C12    0.00   0.0  0
 47Q  CONST_13  N    C    N3   C12    0.00   0.0  0
 47Q  CONST_14  C    N    C1   C12    0.00   0.0  0
 47Q  CONST_15  C1   N    C    N3     0.00   0.0  0
 47Q  CONST_16  N    C1   C12  N3     0.00   0.0  0
 47Q  CONST_17  C1   C12  N3   C      0.00   0.0  0
 47Q  CONST_18  C8   C7   C6   C5   180.00   0.0  0
 47Q  CONST_19  C10  N2   C6   C5   180.00   0.0  0
 47Q  CONST_20  C12  C11  C4   N1   180.00   0.0  0
 47Q  CONST_21  C2   C3   C4   N1   180.00   0.0  0
 47Q  CONST_22  O    C    N3   C12  180.00   0.0  0
 47Q  CONST_23  C1   N    C    O    180.00   0.0  0
 47Q  CONST_24  H12  C2   C3   C4   180.00   0.0  0
 47Q  CONST_25  H5   C8   C7   C6   180.00   0.0  0
 47Q  CONST_26  H7   C10  N2   C6   180.00   0.0  0
 47Q  CONST_27  H6   C9   C8   C7   180.00   0.0  0
 47Q  CONST_28  H4   C7   C6   N2   180.00   0.0  0
 47Q  CONST_29  H11  C3   C4   C11  180.00   0.0  0
 47Q  CONST_30  H8   C11  C12  N3     0.00   0.0  0
 47Q  CONST_31  H10  N    C1   C12  180.00   0.0  0
 47Q  CONST_32  H9   N3   C12  C1   180.00   0.0  0
 47Q  Var_01    C6   C5   N1   C4   177.48  30.0  3
 47Q  Var_02    C7   C6   C5   N1   103.47  30.0  2

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
 47Q  plan-1  C5   0.020
 47Q  plan-1  C6   0.020
 47Q  plan-1  C7   0.020
 47Q  plan-1  C8   0.020
 47Q  plan-1  N2   0.020
 47Q  plan-1  C9   0.020
 47Q  plan-1  C10  0.020
 47Q  plan-1  H4   0.020
 47Q  plan-1  H5   0.020
 47Q  plan-1  H6   0.020
 47Q  plan-1  H7   0.020
 47Q  plan-2  C4   0.020
 47Q  plan-2  N1   0.020
 47Q  plan-2  C11  0.020
 47Q  plan-2  C12  0.020
 47Q  plan-2  N3   0.020
 47Q  plan-2  O    0.020
 47Q  plan-2  C    0.020
 47Q  plan-2  C1   0.020
 47Q  plan-2  N    0.020
 47Q  plan-2  C3   0.020
 47Q  plan-2  C2   0.020
 47Q  plan-2  H8   0.020
 47Q  plan-2  H9   0.020
 47Q  plan-2  H10  0.020
 47Q  plan-2  H11  0.020
 47Q  plan-2  H12  0.020
 47Q  plan-3  C4   0.020
 47Q  plan-3  C5   0.020
 47Q  plan-3  N1   0.020
 47Q  plan-3  H3   0.020

