# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:08:49 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1[nH]c2ccccc2n1)c3occc3
#
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
 W0D  W0D  N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide  ligand  29  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W0D
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
 W0D  N1   N  NR15  0  -0.687  -5.7890  14.3630   1.5756
 W0D  C4   C  CR16  0  -0.307  -3.5387  15.1041   0.6926
 W0D  C5   C  CR16  0  -0.280  -2.9705  15.6380  -0.4518
 W0D  C6   C  CR16  0  -0.272  -3.7427  15.9311  -1.5857
 W0D  C7   C  CR16  0  -0.335  -5.1066  15.6971  -1.6102
 W0D  C8   C  CR56  0   0.134  -5.6975  15.1555  -0.4693
 W0D  C10  C  CR15  0  -0.320  -8.5537  16.6385   5.7769
 W0D  O    O  O     0  -0.472  -8.4608  16.3100   2.8348
 W0D  C    C  C     0   0.500  -8.3606  15.3424   3.5754
 W0D  C9   C  CR5   0   0.230  -8.3935  15.5137   5.0319
 W0D  O1   O  O     0  -0.409  -8.2521  14.4399   5.8408
 W0D  C12  C  CR15  0   0.018  -8.3220  14.8785   7.1082
 W0D  C11  C  CR15  0  -0.331  -8.5082  16.2218   7.1352
 W0D  N    N  NH1   0  -0.658  -8.2132  14.0858   3.1146
 W0D  C2   C  CR5   0   0.445  -7.0170  14.3622   0.9996
 W0D  N2   N  N     0  -0.480  -7.0103  14.8270  -0.2177
 W0D  C3   C  CR56  0   0.335  -4.9081  14.8710   0.6581
 W0D  H1   H  HNR5  0   0.416  -5.5696  14.0458   2.5069
 W0D  H2   H  HCR6  0   0.265  -2.9417  14.8773   1.5662
 W0D  H3   H  HCR6  0   0.254  -1.9062  15.8328  -0.4721
 W0D  H4   H  HCR6  0   0.252  -3.2583  16.3486  -2.4587
 W0D  H5   H  HCR6  0   0.253  -5.6989  15.9271  -2.4867
 W0D  H6   H  HCR5  0   0.276  -8.6899  17.6403   5.4039
 W0D  H7   H  HCR5  0   0.290  -8.2235  14.1360   7.8832
 W0D  H8   H  HCR5  0   0.275  -8.6032  16.8383   8.0136
 W0D  H9   H  HNH1  0   0.417  -8.1763  13.3052   3.7490
 W0D  H10  H  HCH2  0   0.278  -9.1112  14.2113   1.2149
 W0D  H11  H  HCH2  0   0.300  -8.2423  12.7298   1.5792
 W0D  C1   C  CH2   0  -0.388  -8.2183  13.8137   1.6995

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
 W0D  C7   C6   aromatic  1.384  0.020  1.384
 W0D  C7   C8   aromatic  1.394  0.020  1.394
 W0D  C6   C5   aromatic  1.403  0.020  1.403
 W0D  C8   N2   aromatic  1.376  0.020  1.376
 W0D  C8   C3   aromatic  1.405  0.020  1.405
 W0D  C5   C4   aromatic  1.385  0.020  1.385
 W0D  N2   C2   aromatic  1.303  0.020  1.303
 W0D  C3   C4   aromatic  1.390  0.020  1.390
 W0D  C3   N1   aromatic  1.370  0.020  1.370
 W0D  C2   N1   aromatic  1.356  0.020  1.356
 W0D  C2   C1   single    1.495  0.020  1.495
 W0D  C1   N    single    1.441  0.020  1.441
 W0D  N    C    single    1.347  0.020  1.347
 W0D  O    C    double    1.223  0.020  1.223
 W0D  C    C9   single    1.467  0.020  1.467
 W0D  C9   O1   aromatic  1.352  0.020  1.352
 W0D  C9   C10  aromatic  1.359  0.020  1.359
 W0D  O1   C12  aromatic  1.343  0.020  1.343
 W0D  C10  C11  aromatic  1.422  0.020  1.422
 W0D  C12  C11  aromatic  1.356  0.020  1.356
 W0D  N1   H1   single    0.860  0.020  1.020
 W0D  C4   H2   single    0.930  0.020  1.080
 W0D  C5   H3   single    0.930  0.020  1.080
 W0D  C6   H4   single    0.930  0.020  1.080
 W0D  C7   H5   single    0.930  0.020  1.080
 W0D  C10  H6   single    0.930  0.020  1.080
 W0D  C12  H7   single    0.930  0.020  1.080
 W0D  C11  H8   single    0.930  0.020  1.080
 W0D  N    H9   single    0.860  0.020  1.020
 W0D  C1   H10  single    0.970  0.020  1.090
 W0D  C1   H11  single    0.970  0.020  1.090

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
 W0D  H1   N1   C3   126.56  3.000
 W0D  H1   N1   C2   126.10  3.000
 W0D  C3   N1   C2   107.34  3.000
 W0D  H2   C4   C3   121.91  3.000
 W0D  H2   C4   C5   121.44  3.000
 W0D  C3   C4   C5   116.65  3.000
 W0D  H3   C5   C6   119.24  3.000
 W0D  H3   C5   C4   119.25  3.000
 W0D  C6   C5   C4   121.51  3.000
 W0D  H4   C6   C7   119.47  3.000
 W0D  H4   C6   C5   119.10  3.000
 W0D  C7   C6   C5   121.43  3.000
 W0D  H5   C7   C8   120.87  3.000
 W0D  H5   C7   C6   121.17  3.000
 W0D  C8   C7   C6   117.96  3.000
 W0D  C3   C8   N2   109.92  3.000
 W0D  C3   C8   C7   119.80  3.000
 W0D  N2   C8   C7   130.28  3.000
 W0D  H6   C10  C11  127.40  3.000
 W0D  H6   C10  C9   126.49  3.000
 W0D  C11  C10  C9   106.11  3.000
 W0D  N    C    C9   116.82  3.000
 W0D  C9   C    O    120.48  3.000
 W0D  N    C    O    122.70  3.000
 W0D  O1   C9   C    119.94  3.000
 W0D  O1   C9   C10  109.99  3.000
 W0D  C    C9   C10  130.08  3.000
 W0D  C12  O1   C9   107.45  3.000
 W0D  H7   C12  C11  132.88  3.000
 W0D  H7   C12  O1   116.68  3.000
 W0D  C11  C12  O1   110.45  3.000
 W0D  H8   C11  C12  126.51  3.000
 W0D  H8   C11  C10  127.48  3.000
 W0D  C12  C11  C10  106.01  3.000
 W0D  H9   N    C1   118.21  3.000
 W0D  H9   N    C    120.80  3.000
 W0D  C1   N    C    120.79  3.000
 W0D  N2   C2   C1   124.92  3.000
 W0D  C1   C2   N1   121.94  3.000
 W0D  N2   C2   N1   113.07  3.000
 W0D  C2   N2   C8   105.12  3.000
 W0D  C8   C3   C4   122.65  3.000
 W0D  C4   C3   N1   132.80  3.000
 W0D  C8   C3   N1   104.55  3.000
 W0D  H11  C1   H10  107.17  3.000
 W0D  H11  C1   C2   109.31  3.000
 W0D  H10  C1   C2   108.43  3.000
 W0D  H11  C1   N    107.22  3.000
 W0D  H10  C1   N    111.73  3.000
 W0D  C2   C1   N    112.81  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
 W0D  CONST_01  C7   C8   C3   N1    180.00   0.0  0
 W0D  CONST_02  N2   C8   C3   N1      0.00   0.0  0
 W0D  CONST_03  C5   C4   C3   N1    180.00   0.0  0
 W0D  CONST_04  C8   N2   C2   N1      0.00   0.0  0
 W0D  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 W0D  CONST_06  C7   C8   C3   C4      0.00   0.0  0
 W0D  CONST_07  N2   C8   C3   C4    180.00   0.0  0
 W0D  CONST_08  C2   N1   C3   C4    180.00   0.0  0
 W0D  CONST_09  C8   C7   C6   C5      0.00   0.0  0
 W0D  CONST_10  C8   C3   C4   C5      0.00   0.0  0
 W0D  CONST_11  N2   C8   C7   C6    180.00   0.0  0
 W0D  CONST_12  C3   C8   C7   C6      0.00   0.0  0
 W0D  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 W0D  CONST_14  C2   N2   C8   C7    180.00   0.0  0
 W0D  CONST_15  C2   N1   C3   C8      0.00   0.0  0
 W0D  CONST_16  C12  O1   C9   C10     0.00   0.0  0
 W0D  CONST_17  O1   C12  C11  C10     0.00   0.0  0
 W0D  CONST_18  C11  C12  O1   C9      0.00   0.0  0
 W0D  CONST_19  C12  C11  C10  C9      0.00   0.0  0
 W0D  CONST_20  C11  C10  C9   O1      0.00   0.0  0
 W0D  CONST_21  C3   C8   N2   C2      0.00   0.0  0
 W0D  CONST_22  C3   N1   C2   N2      0.00   0.0  0
 W0D  CONST_23  C1   C2   N2   C8    180.00   0.0  0
 W0D  CONST_24  C12  O1   C9   C     180.00   0.0  0
 W0D  CONST_25  C11  C10  C9   C     180.00   0.0  0
 W0D  CONST_26  C3   N1   C2   C1    180.00   0.0  0
 W0D  CONST_27  H2   C4   C3   N1      0.00   0.0  0
 W0D  CONST_28  H4   C6   C5   C4    180.00   0.0  0
 W0D  CONST_29  H1   N1   C3   C4      0.00   0.0  0
 W0D  CONST_30  H5   C7   C6   C5    180.00   0.0  0
 W0D  CONST_31  H3   C5   C6   C7    180.00   0.0  0
 W0D  CONST_32  H7   C12  C11  C10   180.00   0.0  0
 W0D  CONST_33  H8   C11  C10  C9    180.00   0.0  0
 W0D  CONST_34  H6   C10  C9   O1    180.00   0.0  0
 W0D  CONST_35  C1   N    C    C9    180.00   0.0  0
 W0D  CONST_36  H9   N    C    C9      0.00   0.0  0
 W0D  CONST_37  C1   N    C    O       0.00   0.0  0
 W0D  Var_01    N    C1   C2   N1     36.92  30.0  2
 W0D  Var_02    N    C    C9   C10  -178.62  30.0  2
 W0D  Var_03    C2   C1   N    C      68.31  30.0  1

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
 W0D  plan-1  C10  0.020
 W0D  plan-1  C    0.020
 W0D  plan-1  C9   0.020
 W0D  plan-1  O1   0.020
 W0D  plan-1  C12  0.020
 W0D  plan-1  C11  0.020
 W0D  plan-1  H6   0.020
 W0D  plan-1  H7   0.020
 W0D  plan-1  H8   0.020
 W0D  plan-2  N1   0.020
 W0D  plan-2  C4   0.020
 W0D  plan-2  C5   0.020
 W0D  plan-2  C6   0.020
 W0D  plan-2  C7   0.020
 W0D  plan-2  C8   0.020
 W0D  plan-2  C2   0.020
 W0D  plan-2  N2   0.020
 W0D  plan-2  C3   0.020
 W0D  plan-2  H1   0.020
 W0D  plan-2  H2   0.020
 W0D  plan-2  H3   0.020
 W0D  plan-2  H4   0.020
 W0D  plan-2  H5   0.020
 W0D  plan-2  C1   0.020
 W0D  plan-3  O    0.020
 W0D  plan-3  C    0.020
 W0D  plan-3  C9   0.020
 W0D  plan-3  N    0.020
 W0D  plan-3  H9   0.020
 W0D  plan-3  C1   0.020

