# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:59:29 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 7-(aminomethyl)-6-(2-chlorophenyl)-1-methyl-1H-benzimidazole-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2cc(C#N)c(c(CN)c12)c3ccccc3Cl
#
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
 7AC  7AC  7-(aminomethyl)-6-(2-chlorophenyl)-1-methyl-1H-benzimidazole-5-carbonitrile  ligand  34  21  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7AC
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
 7AC  C5    C   CR56  0   0.128   2.4283  -1.2477   0.1328
 7AC  C6    C   CR16  0  -0.328   1.3932  -2.1533   0.3107
 7AC  C7    C   CR6   0   0.005   0.1071  -1.6416   0.3572
 7AC  C8    C   CSP   0   0.006  -0.9833  -2.5421   0.5413
 7AC  C10   C   CR6   0   0.058  -0.1623  -0.2574   0.2302
 7AC  C13   C   CR16  0  -0.230  -3.3821   1.0632   1.6902
 7AC  C15   C   CR16  0  -0.197  -3.7574   0.5842  -0.6365
 7AC  C21   C   CR56  0   0.361   2.1614   0.1305   0.0051
 7AC  N2    N   NR5   0  -0.508   3.3955   0.7036  -0.1531
 7AC  C3    C   CR15  0   0.106   4.2992  -0.3097  -0.1119
 7AC  N4    N   N     0  -0.455   3.7750  -1.4867   0.0570
 7AC  N9    N   NS    0  -0.252  -1.8545  -3.2824   0.6906
 7AC  C11   C   CR6   0   0.036  -1.5718   0.1933   0.3400
 7AC  C12   C   CR16  0  -0.287  -2.0670   0.6431   1.5613
 7AC  C14   C   CR16  0  -0.268  -4.2260   1.0338   0.5891
 7AC  C16   C   CR6   0  -0.085  -2.4399   0.1688  -0.7475
 7AC  CL17  CL  CL    0  -0.122  -1.8609  -0.3868  -2.2826
 7AC  C18   C   CR6   0   0.083   0.8618   0.6578   0.0343
 7AC  C19   C   CH2   0  -0.402   0.5796   2.1318  -0.0846
 7AC  N20   N   NH2   0  -0.783   0.9322   2.8141   1.1525
 7AC  H6    H   HCR6  0   0.282   1.5828  -3.2135   0.4097
 7AC  H13   H   HCR6  0   0.268  -3.7462   1.4094   2.6479
 7AC  H15   H   HCR6  0   0.284  -4.4106   0.5601  -1.4980
 7AC  H1    H   HCH3  0   0.274   3.2748   2.7121   0.4058
 7AC  H1A   H   HCH3  0   0.273   4.8236   2.1921  -0.2788
 7AC  H1B   H   HCH3  0   0.263   3.4354   2.4351  -1.3430
 7AC  H3    H   HCR5  0   0.295   5.3564  -0.1089  -0.2113
 7AC  H12   H   HCR6  0   0.265  -1.4087   0.6519   2.4210
 7AC  H14   H   HCR6  0   0.272  -5.2536   1.3599   0.6781
 7AC  H19   H   HCH2  0   0.255   1.1778   2.5543  -0.8927
 7AC  H19A  H   HCH2  0   0.246  -0.4640   2.2742  -0.3830
 7AC  HN20  H   HNH2  0   0.359   0.7919   3.8096   1.0308
 7AC  HN2A  H   HNH2  0   0.348   0.2966   2.5324   1.8899
 7AC  C1    C   CH3   0  -0.548   3.7438   2.0953  -0.3561

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
 7AC  C5   C6    aromatic  1.387  0.020  1.387
 7AC  C5   C21   aromatic  1.410  0.020  1.410
 7AC  C5   N4    aromatic  1.370  0.020  1.370
 7AC  C6   C7    aromatic  1.385  0.020  1.385
 7AC  C7   C8    single    1.426  0.020  1.426
 7AC  C7   C10   aromatic  1.416  0.020  1.416
 7AC  C8   N9    triple    1.153  0.020  1.153
 7AC  C10  C11   single    1.484  0.020  1.484
 7AC  C10  C18   aromatic  1.387  0.020  1.387
 7AC  C13  C12   aromatic  1.387  0.020  1.387
 7AC  C13  C14   aromatic  1.388  0.020  1.388
 7AC  C15  C14   aromatic  1.387  0.020  1.387
 7AC  C15  C16   aromatic  1.386  0.020  1.386
 7AC  C21  N2    aromatic  1.370  0.020  1.370
 7AC  C21  C18   aromatic  1.403  0.020  1.403
 7AC  C1   N2    single    1.449  0.020  1.449
 7AC  N2   C3    aromatic  1.358  0.020  1.358
 7AC  C3   N4    aromatic  1.299  0.020  1.299
 7AC  C11  C12   aromatic  1.392  0.020  1.392
 7AC  C11  C16   aromatic  1.392  0.020  1.392
 7AC  C16  CL17  single    1.732  0.020  1.732
 7AC  C18  C19   single    1.506  0.020  1.506
 7AC  C19  N20   single    1.456  0.020  1.456
 7AC  C6   H6    single    0.930  0.020  1.080
 7AC  C13  H13   single    0.930  0.020  1.080
 7AC  C15  H15   single    0.930  0.020  1.080
 7AC  C1   H1    single    0.970  0.020  1.090
 7AC  C1   H1A   single    0.970  0.020  1.090
 7AC  C1   H1B   single    0.970  0.020  1.090
 7AC  C3   H3    single    0.930  0.020  1.080
 7AC  C12  H12   single    0.930  0.020  1.080
 7AC  C14  H14   single    0.930  0.020  1.080
 7AC  C19  H19   single    0.970  0.020  1.090
 7AC  C19  H19A  single    0.970  0.020  1.090
 7AC  N20  HN20  single    0.890  0.020  1.040
 7AC  N20  HN2A  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
 7AC  N4    C5   C21   110.59  3.000
 7AC  N4    C5   C6    128.83  3.000
 7AC  C21   C5   C6    120.58  3.000
 7AC  H6    C6   C7    121.46  3.000
 7AC  H6    C6   C5    121.40  3.000
 7AC  C7    C6   C5    117.14  3.000
 7AC  C10   C7   C8    118.91  3.000
 7AC  C10   C7   C6    122.34  3.000
 7AC  C8    C7   C6    118.75  3.000
 7AC  N9    C8   C7    180.00  3.000
 7AC  C18   C10  C11   120.75  3.000
 7AC  C18   C10  C7    121.14  3.000
 7AC  C11   C10  C7    118.10  3.000
 7AC  H13   C13  C14   120.32  3.000
 7AC  H13   C13  C12   119.91  3.000
 7AC  C14   C13  C12   119.77  3.000
 7AC  H15   C15  C16   120.25  3.000
 7AC  H15   C15  C14   120.48  3.000
 7AC  C16   C15  C14   119.28  3.000
 7AC  C18   C21  N2    132.82  3.000
 7AC  C18   C21  C5    122.76  3.000
 7AC  N2    C21  C5    104.42  3.000
 7AC  C3    N2   C1    124.11  3.000
 7AC  C3    N2   C21   106.48  3.000
 7AC  C1    N2   C21   129.39  3.000
 7AC  H3    C3   N4    125.09  3.000
 7AC  H3    C3   N2    120.63  3.000
 7AC  N4    C3   N2    114.28  3.000
 7AC  C3    N4   C5    104.23  3.000
 7AC  C16   C11  C12   117.98  3.000
 7AC  C16   C11  C10   121.96  3.000
 7AC  C12   C11  C10   120.05  3.000
 7AC  H12   C12  C11   118.87  3.000
 7AC  H12   C12  C13   120.02  3.000
 7AC  C11   C12  C13   121.11  3.000
 7AC  H14   C14  C15   119.43  3.000
 7AC  H14   C14  C13   120.40  3.000
 7AC  C15   C14  C13   120.18  3.000
 7AC  CL17  C16  C11   119.32  3.000
 7AC  CL17  C16  C15   119.01  3.000
 7AC  C11   C16  C15   121.68  3.000
 7AC  C19   C18  C21   122.69  3.000
 7AC  C19   C18  C10   121.24  3.000
 7AC  C21   C18  C10   116.03  3.000
 7AC  H19A  C19  H19   105.70  3.000
 7AC  H19A  C19  N20   113.68  3.000
 7AC  H19   C19  N20   108.37  3.000
 7AC  H19A  C19  C18   109.12  3.000
 7AC  H19   C19  C18   109.57  3.000
 7AC  N20   C19  C18   110.26  3.000
 7AC  HN2A  N20  HN20  105.89  3.000
 7AC  HN2A  N20  C19   109.63  3.000
 7AC  HN20  N20  C19   108.96  3.000
 7AC  H1B   C1   H1A   108.56  3.000
 7AC  H1B   C1   H1    109.65  3.000
 7AC  H1A   C1   H1    109.17  3.000
 7AC  H1B   C1   N2    111.03  3.000
 7AC  H1A   C1   N2    108.32  3.000
 7AC  H1    C1   N2    110.07  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
 7AC  CONST_01  C10   C7   C6   C5     0.00   0.0  0
 7AC  CONST_02  C3    N2   C21  C5     0.00   0.0  0
 7AC  CONST_03  C10   C18  C21  C5     0.00   0.0  0
 7AC  CONST_04  N2    C3   N4   C5     0.00   0.0  0
 7AC  CONST_05  N2    C21  C5   C6   180.00   0.0  0
 7AC  CONST_06  C18   C21  C5   C6     0.00   0.0  0
 7AC  CONST_07  C3    N4   C5   C6   180.00   0.0  0
 7AC  CONST_08  C11   C10  C7   C6   180.00   0.0  0
 7AC  CONST_09  C18   C10  C7   C6     0.00   0.0  0
 7AC  CONST_10  C21   C5   C6   C7     0.00   0.0  0
 7AC  CONST_11  N4    C5   C6   C7   180.00   0.0  0
 7AC  CONST_14  C21   C18  C10  C7     0.00   0.0  0
 7AC  CONST_15  C13   C12  C11  C10  180.00   0.0  0
 7AC  CONST_16  C15   C16  C11  C10  180.00   0.0  0
 7AC  CONST_17  N2    C21  C18  C10  180.00   0.0  0
 7AC  CONST_18  C16   C11  C12  C13    0.00   0.0  0
 7AC  CONST_19  C16   C15  C14  C13    0.00   0.0  0
 7AC  CONST_20  C12   C13  C14  C15    0.00   0.0  0
 7AC  CONST_21  C12   C11  C16  C15    0.00   0.0  0
 7AC  CONST_22  C3    N4   C5   C21    0.00   0.0  0
 7AC  CONST_23  N4    C3   N2   C21    0.00   0.0  0
 7AC  CONST_24  C11   C10  C18  C21  180.00   0.0  0
 7AC  CONST_25  N4    C5   C21  N2     0.00   0.0  0
 7AC  CONST_26  C18   C21  N2   C3   180.00   0.0  0
 7AC  CONST_27  C18   C21  C5   N4   180.00   0.0  0
 7AC  CONST_28  C14   C13  C12  C11    0.00   0.0  0
 7AC  CONST_29  C14   C15  C16  C11    0.00   0.0  0
 7AC  CONST_32  C8    C7   C6   C5   180.00   0.0  0
 7AC  CONST_33  C1    N2   C21  C5   180.00   0.0  0
 7AC  CONST_34  C19   C18  C21  C5   180.00   0.0  0
 7AC  CONST_35  C19   C18  C10  C7   180.00   0.0  0
 7AC  CONST_36  C11   C10  C7   C8     0.00   0.0  0
 7AC  CONST_37  C18   C10  C7   C8   180.00   0.0  0
 7AC  CONST_38  CL17  C16  C11  C10    0.00   0.0  0
 7AC  CONST_39  C18   C21  N2   C1     0.00   0.0  0
 7AC  CONST_40  N4    C3   N2   C1   180.00   0.0  0
 7AC  CONST_41  C19   C18  C21  N2     0.00   0.0  0
 7AC  CONST_42  C19   C18  C10  C11    0.00   0.0  0
 7AC  CONST_43  CL17  C16  C11  C12  180.00   0.0  0
 7AC  CONST_44  CL17  C16  C15  C14  180.00   0.0  0
 7AC  CONST_45  H3    C3   N4   C5   180.00   0.0  0
 7AC  CONST_46  H6    C6   C7   C10  180.00   0.0  0
 7AC  CONST_47  H12   C12  C11  C10    0.00   0.0  0
 7AC  CONST_48  H15   C15  C14  C13  180.00   0.0  0
 7AC  CONST_49  H13   C13  C14  C15  180.00   0.0  0
 7AC  CONST_50  H14   C14  C13  C12  180.00   0.0  0
 7AC  Var_01    N20   C19  C18  C10  103.58  30.0  2
 7AC  Var_02    H1    C1   N2   C21   51.68  30.0  2
 7AC  Var_03    HN20  N20  C19  C18  176.35  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
 7AC  plan-1  C10   0.020
 7AC  plan-1  C13   0.020
 7AC  plan-1  C15   0.020
 7AC  plan-1  C11   0.020
 7AC  plan-1  C12   0.020
 7AC  plan-1  C14   0.020
 7AC  plan-1  C16   0.020
 7AC  plan-1  CL17  0.020
 7AC  plan-1  H13   0.020
 7AC  plan-1  H15   0.020
 7AC  plan-1  H12   0.020
 7AC  plan-1  H14   0.020
 7AC  plan-2  C5    0.020
 7AC  plan-2  C6    0.020
 7AC  plan-2  C7    0.020
 7AC  plan-2  C8    0.020
 7AC  plan-2  C10   0.020
 7AC  plan-2  C21   0.020
 7AC  plan-2  N2    0.020
 7AC  plan-2  C3    0.020
 7AC  plan-2  N4    0.020
 7AC  plan-2  N9    0.020
 7AC  plan-2  C11   0.020
 7AC  plan-2  C18   0.020
 7AC  plan-2  C19   0.020
 7AC  plan-2  H6    0.020
 7AC  plan-2  H3    0.020
 7AC  plan-2  C1    0.020

