# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:30:35 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: ~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(Cc1ccccc1)Nc2[nH]c3ccccc3n2
#
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
 LUY  LUY  ~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine  ligand  33  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LUY
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
 LUY  N1   N  NR15  0  -0.738  -1.6411   0.5509   0.2160
 LUY  C4   C  CR16  0  -0.307   4.1521   0.0403   1.2011
 LUY  C5   C  CR16  0  -0.240   5.2863   0.8376   1.1239
 LUY  C6   C  CH2   0  -0.547   2.3082  -1.3001   0.1341
 LUY  C7   C  CH2   0  -0.269   1.0550  -0.4444  -0.0153
 LUY  C8   C  CR5   0   0.672  -1.3784  -0.7760   0.0499
 LUY  C10  C  CR16  0  -0.315  -3.8326   1.8098   0.2544
 LUY  C13  C  CR16  0  -0.351  -4.8715  -0.8000  -0.1752
 LUY  N    N  NH1   0  -0.688  -0.1253  -1.2758   0.0991
 LUY  C    C  CR16  0  -0.271   5.8379   1.1467  -0.1125
 LUY  C1   C  CR16  0  -0.240   5.2473   0.6532  -1.2690
 LUY  C11  C  CR16  0  -0.290  -5.2007   1.5879   0.1376
 LUY  C12  C  CR16  0  -0.272  -5.7091   0.3037  -0.0734
 LUY  C14  C  CR56  0   0.159  -3.4992  -0.5983  -0.0613
 LUY  C2   C  CR16  0  -0.305   4.1138  -0.1444  -1.1866
 LUY  C3   C  CR6   0   0.122   3.5532  -0.4626   0.0487
 LUY  C9   C  CR56  0   0.335  -3.0086   0.7032   0.1515
 LUY  N2   N  N     0  -0.536  -2.4615  -1.4976  -0.1221
 LUY  H1   H  HNR5  0   0.422  -0.9675   1.2871   0.3509
 LUY  H3   H  HCR6  0   0.255   5.7420   1.2130   2.0313
 LUY  H4   H  HCH2  0   0.260   2.2703  -1.8253   1.0914
 LUY  H5   H  HCH2  0   0.258   2.3173  -2.0625  -0.6500
 LUY  H6   H  HCH2  0   0.245   1.0477   0.3104   0.7756
 LUY  H7   H  HCH2  0   0.240   1.0854   0.0894  -0.9731
 LUY  H8   H  HCR6  0   0.260  -3.4368   2.8036   0.4197
 LUY  H9   H  HCR6  0   0.245  -5.2731  -1.7921  -0.3390
 LUY  H10  H  HNH1  0   0.396  -0.0477  -2.2190  -0.2495
 LUY  H11  H  HCR6  0   0.255   6.7241   1.7649  -0.1743
 LUY  H12  H  HCR6  0   0.255   5.6725   0.8835  -2.2374
 LUY  H13  H  HCR6  0   0.248  -5.8822   2.4250   0.2120
 LUY  H14  H  HCR6  0   0.246  -6.7797   0.1669  -0.1573
 LUY  H15  H  HCR6  0   0.249   3.6628  -0.5287  -2.0944
 LUY  H2   H  HCR6  0   0.249   3.7306  -0.1991   2.1705

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
 LUY  C    C5   aromatic  1.389  0.020  1.389
 LUY  C    C1   aromatic  1.389  0.020  1.389
 LUY  C5   C4   aromatic  1.389  0.020  1.389
 LUY  C1   C2   aromatic  1.388  0.020  1.388
 LUY  C4   C3   aromatic  1.393  0.020  1.393
 LUY  C2   C3   aromatic  1.393  0.020  1.393
 LUY  C3   C6   single    1.503  0.020  1.503
 LUY  C6   C7   single    1.525  0.020  1.525
 LUY  C7   N    single    1.448  0.020  1.448
 LUY  N2   C14  aromatic  1.374  0.020  1.374
 LUY  N2   C8   aromatic  1.313  0.020  1.313
 LUY  N    C8   single    1.350  0.020  1.350
 LUY  C13  C14  aromatic  1.392  0.020  1.392
 LUY  C13  C12  aromatic  1.389  0.020  1.389
 LUY  C14  C9   aromatic  1.407  0.020  1.407
 LUY  C8   N1   aromatic  1.363  0.020  1.363
 LUY  C12  C11  aromatic  1.397  0.020  1.397
 LUY  N1   C9   aromatic  1.377  0.020  1.377
 LUY  C9   C10  aromatic  1.384  0.020  1.384
 LUY  C11  C10  aromatic  1.391  0.020  1.391
 LUY  N1   H1   single    0.860  0.020  1.020
 LUY  C4   H2   single    0.930  0.020  1.080
 LUY  C5   H3   single    0.930  0.020  1.080
 LUY  C6   H4   single    0.970  0.020  1.090
 LUY  C6   H5   single    0.970  0.020  1.090
 LUY  C7   H6   single    0.970  0.020  1.090
 LUY  C7   H7   single    0.970  0.020  1.090
 LUY  C10  H8   single    0.930  0.020  1.080
 LUY  C13  H9   single    0.930  0.020  1.080
 LUY  N    H10  single    0.890  0.020  1.040
 LUY  C    H11  single    0.930  0.020  1.080
 LUY  C1   H12  single    0.930  0.020  1.080
 LUY  C11  H13  single    0.930  0.020  1.080
 LUY  C12  H14  single    0.930  0.020  1.080
 LUY  C2   H15  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
 LUY  H1   N1   C9   126.13  3.000
 LUY  H1   N1   C8   126.81  3.000
 LUY  C9   N1   C8   107.06  3.000
 LUY  H2   C4   C3   119.55  3.000
 LUY  H2   C4   C5   119.62  3.000
 LUY  C3   C4   C5   120.83  3.000
 LUY  H3   C5   C    120.12  3.000
 LUY  H3   C5   C4   119.76  3.000
 LUY  C    C5   C4   120.12  3.000
 LUY  H5   C6   H4   107.06  3.000
 LUY  H5   C6   C3   109.93  3.000
 LUY  H4   C6   C3   110.27  3.000
 LUY  H5   C6   C7   109.14  3.000
 LUY  H4   C6   C7   109.09  3.000
 LUY  C3   C6   C7   111.26  3.000
 LUY  H7   C7   H6   107.21  3.000
 LUY  H7   C7   N    111.77  3.000
 LUY  H6   C7   N    109.50  3.000
 LUY  H7   C7   C6   109.63  3.000
 LUY  H6   C7   C6   108.79  3.000
 LUY  N    C7   C6   109.87  3.000
 LUY  N2   C8   N    124.55  3.000
 LUY  N    C8   N1   122.35  3.000
 LUY  N2   C8   N1   113.08  3.000
 LUY  H8   C10  C9   121.87  3.000
 LUY  H8   C10  C11  121.26  3.000
 LUY  C9   C10  C11  116.87  3.000
 LUY  H9   C13  C14  120.73  3.000
 LUY  H9   C13  C12  121.02  3.000
 LUY  C14  C13  C12  118.25  3.000
 LUY  H10  N    C8   113.90  3.000
 LUY  H10  N    C7   116.54  3.000
 LUY  C8   N    C7   122.76  3.000
 LUY  H11  C    C1   120.23  3.000
 LUY  H11  C    C5   120.21  3.000
 LUY  C1   C    C5   119.56  3.000
 LUY  H12  C1   C2   119.73  3.000
 LUY  H12  C1   C    120.15  3.000
 LUY  C2   C1   C    120.12  3.000
 LUY  H13  C11  C12  119.49  3.000
 LUY  H13  C11  C10  119.36  3.000
 LUY  C12  C11  C10  121.15  3.000
 LUY  H14  C12  C11  119.19  3.000
 LUY  H14  C12  C13  119.35  3.000
 LUY  C11  C12  C13  121.46  3.000
 LUY  N2   C14  C9   110.40  3.000
 LUY  C9   C14  C13  119.36  3.000
 LUY  N2   C14  C13  130.24  3.000
 LUY  H15  C2   C3   119.61  3.000
 LUY  H15  C2   C1   119.58  3.000
 LUY  C3   C2   C1   120.81  3.000
 LUY  C2   C3   C6   120.72  3.000
 LUY  C6   C3   C4   120.69  3.000
 LUY  C2   C3   C4   118.57  3.000
 LUY  C14  C9   C10  122.92  3.000
 LUY  C10  C9   N1   132.55  3.000
 LUY  C14  C9   N1   104.54  3.000
 LUY  C14  N2   C8   104.92  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
 LUY  CONST_01  C14  N2   C8   N1      0.00   0.0  0
 LUY  CONST_02  N2   C14  C9   N1      0.00   0.0  0
 LUY  CONST_03  C13  C14  C9   N1    180.00   0.0  0
 LUY  CONST_04  C11  C10  C9   N1    180.00   0.0  0
 LUY  CONST_05  C1   C    C5   C4      0.00   0.0  0
 LUY  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 LUY  CONST_07  C2   C1   C    C5      0.00   0.0  0
 LUY  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 LUY  CONST_09  C13  C14  N2   C8    180.00   0.0  0
 LUY  CONST_10  C9   C14  N2   C8      0.00   0.0  0
 LUY  CONST_11  C14  C9   N1   C8      0.00   0.0  0
 LUY  CONST_12  C10  C9   N1   C8    180.00   0.0  0
 LUY  CONST_13  N2   C14  C9   C10   180.00   0.0  0
 LUY  CONST_14  C13  C14  C9   C10     0.00   0.0  0
 LUY  CONST_15  C13  C12  C11  C10     0.00   0.0  0
 LUY  CONST_16  C3   C4   C5   C       0.00   0.0  0
 LUY  CONST_17  C3   C2   C1   C       0.00   0.0  0
 LUY  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 LUY  CONST_19  C14  C9   C10  C11     0.00   0.0  0
 LUY  CONST_20  N2   C14  C13  C12   180.00   0.0  0
 LUY  CONST_21  C9   C14  C13  C12     0.00   0.0  0
 LUY  CONST_22  C9   C10  C11  C12     0.00   0.0  0
 LUY  CONST_23  N2   C8   N1   C9      0.00   0.0  0
 LUY  CONST_24  C6   C3   C4   C5    180.00   0.0  0
 LUY  CONST_25  C1   C2   C3   C6    180.00   0.0  0
 LUY  CONST_26  C14  N2   C8   N     180.00   0.0  0
 LUY  CONST_27  C9   N1   C8   N     180.00   0.0  0
 LUY  CONST_28  H8   C10  C9   N1      0.00   0.0  0
 LUY  CONST_29  H11  C    C5   C4    180.00   0.0  0
 LUY  CONST_30  H15  C2   C3   C4    180.00   0.0  0
 LUY  CONST_31  H12  C1   C    C5    180.00   0.0  0
 LUY  CONST_32  H1   N1   C9   C10     0.00   0.0  0
 LUY  CONST_33  H14  C12  C11  C10   180.00   0.0  0
 LUY  CONST_34  H13  C11  C12  C13   180.00   0.0  0
 LUY  CONST_35  H2   C4   C5   C     180.00   0.0  0
 LUY  CONST_36  H3   C5   C    C1    180.00   0.0  0
 LUY  CONST_37  H9   C13  C12  C11   180.00   0.0  0
 LUY  CONST_39  N2   C8   N    C7    180.00   0.0  0
 LUY  CONST_40  H10  N    C8   N1    180.00   0.0  0
 LUY  Var_01    C7   C6   C3   C4     93.35  30.0  2
 LUY  Var_02    C8   N    C7   C6    177.77  30.0  3
 LUY  Var_03    C3   C6   C7   N    -178.82  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
 LUY  plan-1  C4   0.020
 LUY  plan-1  C5   0.020
 LUY  plan-1  C6   0.020
 LUY  plan-1  C    0.020
 LUY  plan-1  C1   0.020
 LUY  plan-1  C2   0.020
 LUY  plan-1  C3   0.020
 LUY  plan-1  H3   0.020
 LUY  plan-1  H11  0.020
 LUY  plan-1  H12  0.020
 LUY  plan-1  H15  0.020
 LUY  plan-1  H2   0.020
 LUY  plan-2  N1   0.020
 LUY  plan-2  C8   0.020
 LUY  plan-2  C10  0.020
 LUY  plan-2  C13  0.020
 LUY  plan-2  N    0.020
 LUY  plan-2  C11  0.020
 LUY  plan-2  C12  0.020
 LUY  plan-2  C14  0.020
 LUY  plan-2  C9   0.020
 LUY  plan-2  N2   0.020
 LUY  plan-2  H1   0.020
 LUY  plan-2  H8   0.020
 LUY  plan-2  H9   0.020
 LUY  plan-2  H13  0.020
 LUY  plan-2  H14  0.020
 LUY  plan-3  C7   0.020
 LUY  plan-3  C8   0.020
 LUY  plan-3  N    0.020
 LUY  plan-3  H10  0.020

