# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:19:24 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 1~{H}-benzimidazol-2-ylcyanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CNc1[nH]c2ccccc2n1
#
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
 AXV  AXV  1~{H}-benzimidazol-2-ylcyanamide  ligand  18  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AXV
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
 AXV  N1  N  NR15  0  -0.726   0.6102   0.7397   0.0446
 AXV  N3  N  NH1   0  -0.716   2.4379  -0.8026   0.0458
 AXV  C4  C  CR56  0   0.163  -1.0127  -0.7510   0.0151
 AXV  C5  C  CR56  0   0.349  -0.7632   0.6307   0.0303
 AXV  C6  C  CR16  0  -0.306  -1.7753   1.5771   0.0281
 AXV  C7  C  CR5   0   0.710   1.0873  -0.5262   0.0367
 AXV  C8  C  CSP   0   0.272   3.3709   0.1309   0.0461
 AXV  C1  C  CR16  0  -0.281  -3.0756   1.0947   0.0100
 AXV  C2  C  CR16  0  -0.269  -3.3452  -0.2792  -0.0050
 AXV  C3  C  CR16  0  -0.335  -2.3241  -1.2166  -0.0027
 AXV  N2  N  N     0  -0.500   0.1767  -1.4492   0.0196
 AXV  N4  N  NS    0  -0.289   4.1813   0.9543   0.0486
 AXV  H1  H  HNR5  0   0.431   1.1413   1.5973   0.0610
 AXV  H2  H  HNH1  0   0.462   2.7180  -1.7749   0.0374
 AXV  H3  H  HCR6  0   0.269  -1.5666   2.6386   0.0388
 AXV  H4  H  HCR6  0   0.257  -3.8986   1.7968   0.0068
 AXV  H5  H  HCR6  0   0.254  -4.3743  -0.6136  -0.0195
 AXV  H6  H  HCR6  0   0.256  -2.5353  -2.2780  -0.0148

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
 AXV  C1  C2  aromatic  1.400  0.020  1.400
 AXV  C1  C6  aromatic  1.387  0.020  1.387
 AXV  C2  C3  aromatic  1.386  0.020  1.386
 AXV  C6  C5  aromatic  1.386  0.020  1.386
 AXV  C3  C4  aromatic  1.392  0.020  1.392
 AXV  C5  C4  aromatic  1.404  0.020  1.404
 AXV  C5  N1  aromatic  1.378  0.020  1.378
 AXV  C4  N2  aromatic  1.379  0.020  1.379
 AXV  N1  C7  aromatic  1.353  0.020  1.353
 AXV  N2  C7  aromatic  1.297  0.020  1.297
 AXV  C7  N3  single    1.379  0.020  1.379
 AXV  N3  C8  single    1.320  0.020  1.320
 AXV  C8  N4  triple    1.155  0.020  1.155
 AXV  N1  H1  single    0.860  0.020  1.020
 AXV  N3  H2  single    0.860  0.020  1.020
 AXV  C6  H3  single    0.930  0.020  1.080
 AXV  C1  H4  single    0.930  0.020  1.080
 AXV  C2  H5  single    0.930  0.020  1.080
 AXV  C3  H6  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
 AXV  H1  N1  C7  127.58  3.000
 AXV  H1  N1  C5  126.31  3.000
 AXV  C7  N1  C5  106.11  3.000
 AXV  H2  N3  C8  118.95  3.000
 AXV  H2  N3  C7  117.63  3.000
 AXV  C8  N3  C7  123.41  3.000
 AXV  N2  C4  C3  130.04  3.000
 AXV  N2  C4  C5  110.17  3.000
 AXV  C3  C4  C5  119.78  3.000
 AXV  C6  C5  C4  122.84  3.000
 AXV  C4  C5  N1  104.78  3.000
 AXV  C6  C5  N1  132.38  3.000
 AXV  H3  C6  C1  121.48  3.000
 AXV  H3  C6  C5  121.96  3.000
 AXV  C1  C6  C5  116.56  3.000
 AXV  N2  C7  N3  123.05  3.000
 AXV  N3  C7  N1  122.21  3.000
 AXV  N2  C7  N1  114.74  3.000
 AXV  N4  C8  N3  180.00  3.000
 AXV  H4  C1  C2  119.37  3.000
 AXV  H4  C1  C6  119.18  3.000
 AXV  C2  C1  C6  121.46  3.000
 AXV  H5  C2  C3  119.45  3.000
 AXV  H5  C2  C1  119.10  3.000
 AXV  C3  C2  C1  121.45  3.000
 AXV  H6  C3  C2  121.30  3.000
 AXV  H6  C3  C4  120.80  3.000
 AXV  C2  C3  C4  117.90  3.000
 AXV  C7  N2  C4  104.20  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
 AXV  CONST_01  C1  C6  C5  N1  180.00  0.0  0
 AXV  CONST_02  C3  C4  C5  N1  180.00  0.0  0
 AXV  CONST_03  N2  C4  C5  N1    0.00  0.0  0
 AXV  CONST_04  C4  N2  C7  N1    0.00  0.0  0
 AXV  CONST_05  C1  C2  C3  C4    0.00  0.0  0
 AXV  CONST_06  C1  C6  C5  C4    0.00  0.0  0
 AXV  CONST_07  C7  N1  C5  C4    0.00  0.0  0
 AXV  CONST_08  C2  C1  C6  C5    0.00  0.0  0
 AXV  CONST_09  C2  C3  C4  C5    0.00  0.0  0
 AXV  CONST_10  C7  N2  C4  C5    0.00  0.0  0
 AXV  CONST_11  N2  C7  N1  C5    0.00  0.0  0
 AXV  CONST_12  C3  C2  C1  C6    0.00  0.0  0
 AXV  CONST_13  C3  C4  C5  C6    0.00  0.0  0
 AXV  CONST_14  N2  C4  C5  C6  180.00  0.0  0
 AXV  CONST_15  C7  N1  C5  C6  180.00  0.0  0
 AXV  CONST_16  C3  C4  N2  C7  180.00  0.0  0
 AXV  CONST_17  N2  C4  C3  C2  180.00  0.0  0
 AXV  CONST_18  C5  N1  C7  N3  180.00  0.0  0
 AXV  CONST_19  C4  N2  C7  N3  180.00  0.0  0
 AXV  CONST_20  H3  C6  C5  N1    0.00  0.0  0
 AXV  CONST_21  H5  C2  C3  C4  180.00  0.0  0
 AXV  CONST_22  H1  N1  C5  C4  180.00  0.0  0
 AXV  CONST_23  H4  C1  C6  C5  180.00  0.0  0
 AXV  CONST_24  H6  C3  C4  C5  180.00  0.0  0
 AXV  CONST_25  C8  N3  C7  N1    0.00  0.0  0
 AXV  CONST_26  N2  C7  N3  C8  180.00  0.0  0
 AXV  CONST_27  H2  N3  C7  N1  180.00  0.0  0

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
 AXV  plan-1  N1  0.020
 AXV  plan-1  N3  0.020
 AXV  plan-1  C4  0.020
 AXV  plan-1  C5  0.020
 AXV  plan-1  C6  0.020
 AXV  plan-1  C7  0.020
 AXV  plan-1  C1  0.020
 AXV  plan-1  C2  0.020
 AXV  plan-1  C3  0.020
 AXV  plan-1  N2  0.020
 AXV  plan-1  H1  0.020
 AXV  plan-1  H3  0.020
 AXV  plan-1  H4  0.020
 AXV  plan-1  H5  0.020
 AXV  plan-1  H6  0.020
 AXV  plan-2  N3  0.020
 AXV  plan-2  C7  0.020
 AXV  plan-2  C8  0.020
 AXV  plan-2  H2  0.020

