# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:29:20 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2ccccc2n1Cc3ccc(Cl)c(Cl)c3
#
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
 AX8  AX8  1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine  ligand  30  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AX8
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
 AX8  CAJ   C   CR16  0  -0.248  -1.1381  -0.6185   0.1706
 AX8  CAO   C   CR6   0   0.024  -2.2446  -0.0366  -0.4236
 AX8  CLAC  CL  CL    0  -0.094  -3.0804  -0.8883  -1.6657
 AX8  CAN   C   CR6   0  -0.016  -2.6769   1.2225  -0.0154
 AX8  CLAB  CL  CL    0  -0.094  -4.0492   1.9601  -0.7480
 AX8  CAG   C   CR16  0  -0.199  -1.9956   1.8884   0.9895
 AX8  CAF   C   CR16  0  -0.313  -0.8862   1.3022   1.5795
 AX8  CAM   C   CR6   0   0.137  -0.4477   0.0484   1.1767
 AX8  CAK   C   CH2   0  -0.438   0.7658  -0.5872   1.8085
 AX8  NAS   N   NR5   0  -0.551   1.8143  -0.8357   0.8466
 AX8  CAR   C   CR56  0   0.354   2.6184   0.1353   0.2844
 AX8  CAI   C   CR16  0  -0.310   2.7577   1.4883   0.5405
 AX8  CAE   C   CR16  0  -0.284   3.6927   2.1784  -0.2235
 AX8  CAD   C   CR16  0  -0.274   4.4514   1.5282  -1.1997
 AX8  CAH   C   CR16  0  -0.343   4.3010   0.1697  -1.4478
 AX8  CAQ   C   CR56  0   0.152   3.3684  -0.5354  -0.6951
 AX8  NAL   N   N     0  -0.519   3.0255  -1.8674  -0.7271
 AX8  CAP   C   CR5   0   0.623   2.1004  -2.0010   0.1875
 AX8  NAA   N   NH2   0  -0.856   1.4144  -3.1479   0.4320
 AX8  HAJ   H   HCR6  0   0.284  -0.8245  -1.6032  -0.1535
 AX8  HAG   H   HCR6  0   0.292  -2.3272   2.8679   1.3051
 AX8  HAF   H   HCR6  0   0.274  -0.3629   1.8380   2.3615
 AX8  HAK   H   HCH2  0   0.298   1.1605   0.0554   2.5967
 AX8  HAKA  H   HCH2  0   0.296   0.4956  -1.5241   2.2955
 AX8  HAI   H   HCR6  0   0.258   2.1720   1.9984   1.2946
 AX8  HAE   H   HCR6  0   0.251   3.8332   3.2383  -0.0569
 AX8  HAD   H   HCR6  0   0.248   5.1713   2.0974  -1.7735
 AX8  HAH   H   HCR6  0   0.248   4.8912  -0.3291  -2.2063
 AX8  HNAA  H   HNH2  0   0.400   1.1185  -3.3267   1.3787
 AX8  HNAB  H   HNH2  0   0.400   1.8179  -3.9643   0.0001

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
 AX8  CAJ  CAO   aromatic  1.384  0.020  1.384
 AX8  CAJ  CAM   aromatic  1.391  0.020  1.391
 AX8  CAO  CLAC  single    1.722  0.020  1.722
 AX8  CAO  CAN   aromatic  1.392  0.020  1.392
 AX8  CAN  CLAB  single    1.722  0.020  1.722
 AX8  CAN  CAG   aromatic  1.385  0.020  1.385
 AX8  CAG  CAF   aromatic  1.387  0.020  1.387
 AX8  CAF  CAM   aromatic  1.388  0.020  1.388
 AX8  CAM  CAK   single    1.509  0.020  1.509
 AX8  CAK  NAS   single    1.444  0.020  1.444
 AX8  NAS  CAR   aromatic  1.380  0.020  1.380
 AX8  NAS  CAP   aromatic  1.369  0.020  1.369
 AX8  CAR  CAI   aromatic  1.384  0.020  1.384
 AX8  CAR  CAQ   aromatic  1.404  0.020  1.404
 AX8  CAI  CAE   aromatic  1.391  0.020  1.391
 AX8  CAE  CAD   aromatic  1.397  0.020  1.397
 AX8  CAD  CAH   aromatic  1.389  0.020  1.389
 AX8  CAH  CAQ   aromatic  1.391  0.020  1.391
 AX8  CAQ  NAL   aromatic  1.376  0.020  1.376
 AX8  NAL  CAP   aromatic  1.308  0.020  1.308
 AX8  CAP  NAA   single    1.359  0.020  1.359
 AX8  CAJ  HAJ   single    0.930  0.020  1.080
 AX8  CAG  HAG   single    0.930  0.020  1.080
 AX8  CAF  HAF   single    0.930  0.020  1.080
 AX8  CAK  HAK   single    0.970  0.020  1.090
 AX8  CAK  HAKA  single    0.970  0.020  1.090
 AX8  CAI  HAI   single    0.930  0.020  1.080
 AX8  CAE  HAE   single    0.930  0.020  1.080
 AX8  CAD  HAD   single    0.930  0.020  1.080
 AX8  CAH  HAH   single    0.930  0.020  1.080
 AX8  NAA  HNAA  single    0.890  0.020  1.040
 AX8  NAA  HNAB  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
 AX8  HAJ   CAJ  CAM   120.58  3.000
 AX8  HAJ   CAJ  CAO   119.03  3.000
 AX8  CAM   CAJ  CAO   120.39  3.000
 AX8  CAN   CAO  CLAC  120.53  3.000
 AX8  CAN   CAO  CAJ   120.16  3.000
 AX8  CLAC  CAO  CAJ   119.31  3.000
 AX8  CAG   CAN  CLAB  119.67  3.000
 AX8  CAG   CAN  CAO   119.66  3.000
 AX8  CLAB  CAN  CAO   120.67  3.000
 AX8  HAG   CAG  CAF   120.28  3.000
 AX8  HAG   CAG  CAN   119.78  3.000
 AX8  CAF   CAG  CAN   119.94  3.000
 AX8  HAF   CAF  CAM   120.26  3.000
 AX8  HAF   CAF  CAG   119.00  3.000
 AX8  CAM   CAF  CAG   120.74  3.000
 AX8  CAK   CAM  CAF   120.88  3.000
 AX8  CAK   CAM  CAJ   120.03  3.000
 AX8  CAF   CAM  CAJ   119.10  3.000
 AX8  HAKA  CAK  HAK   105.85  3.000
 AX8  HAKA  CAK  NAS   109.25  3.000
 AX8  HAK   CAK  NAS   108.66  3.000
 AX8  HAKA  CAK  CAM   110.48  3.000
 AX8  HAK   CAK  CAM   110.21  3.000
 AX8  NAS   CAK  CAM   112.18  3.000
 AX8  CAP   NAS  CAR   106.31  3.000
 AX8  CAP   NAS  CAK   128.23  3.000
 AX8  CAR   NAS  CAK   124.97  3.000
 AX8  CAQ   CAR  CAI   122.84  3.000
 AX8  CAQ   CAR  NAS   105.03  3.000
 AX8  CAI   CAR  NAS   132.13  3.000
 AX8  HAI   CAI  CAE   120.84  3.000
 AX8  HAI   CAI  CAR   122.35  3.000
 AX8  CAE   CAI  CAR   116.81  3.000
 AX8  HAE   CAE  CAD   119.54  3.000
 AX8  HAE   CAE  CAI   119.26  3.000
 AX8  CAD   CAE  CAI   121.20  3.000
 AX8  HAD   CAD  CAH   119.44  3.000
 AX8  HAD   CAD  CAE   119.14  3.000
 AX8  CAH   CAD  CAE   121.42  3.000
 AX8  HAH   CAH  CAQ   120.75  3.000
 AX8  HAH   CAH  CAD   121.10  3.000
 AX8  CAQ   CAH  CAD   118.15  3.000
 AX8  NAL   CAQ  CAH   130.20  3.000
 AX8  NAL   CAQ  CAR   110.21  3.000
 AX8  CAH   CAQ  CAR   119.58  3.000
 AX8  CAP   NAL  CAQ   105.01  3.000
 AX8  NAA   CAP  NAL   124.70  3.000
 AX8  NAA   CAP  NAS   121.76  3.000
 AX8  NAL   CAP  NAS   113.43  3.000
 AX8  HNAB  NAA  HNAA  112.11  3.000
 AX8  HNAB  NAA  CAP   113.86  3.000
 AX8  HNAA  NAA  CAP   117.85  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
 AX8  CONST_01  CAG   CAN  CAO  CAJ     0.00   0.0  0
 AX8  CONST_02  CAG   CAF  CAM  CAJ     0.00   0.0  0
 AX8  CONST_03  CAF   CAM  CAJ  CAO     0.00   0.0  0
 AX8  CONST_04  CAF   CAG  CAN  CAO     0.00   0.0  0
 AX8  CONST_05  CAM   CAJ  CAO  CAN     0.00   0.0  0
 AX8  CONST_06  CAM   CAF  CAG  CAN     0.00   0.0  0
 AX8  CONST_07  CAE   CAI  CAR  NAS   180.00   0.0  0
 AX8  CONST_08  CAH   CAQ  CAR  NAS   180.00   0.0  0
 AX8  CONST_09  NAL   CAQ  CAR  NAS     0.00   0.0  0
 AX8  CONST_10  CAQ   NAL  CAP  NAS     0.00   0.0  0
 AX8  CONST_11  NAL   CAP  NAS  CAR     0.00   0.0  0
 AX8  CONST_12  CAD   CAE  CAI  CAR     0.00   0.0  0
 AX8  CONST_13  CAD   CAH  CAQ  CAR     0.00   0.0  0
 AX8  CONST_14  CAP   NAL  CAQ  CAR     0.00   0.0  0
 AX8  CONST_15  CAP   NAS  CAR  CAI   180.00   0.0  0
 AX8  CONST_16  CAH   CAQ  CAR  CAI     0.00   0.0  0
 AX8  CONST_17  NAL   CAQ  CAR  CAI   180.00   0.0  0
 AX8  CONST_18  CAH   CAD  CAE  CAI     0.00   0.0  0
 AX8  CONST_19  CAQ   CAR  CAI  CAE     0.00   0.0  0
 AX8  CONST_20  CAQ   CAH  CAD  CAE     0.00   0.0  0
 AX8  CONST_21  NAL   CAQ  CAH  CAD   180.00   0.0  0
 AX8  CONST_22  CAP   NAL  CAQ  CAH   180.00   0.0  0
 AX8  CONST_23  CAP   NAS  CAR  CAQ     0.00   0.0  0
 AX8  CONST_24  CLAB  CAN  CAO  CAJ   180.00   0.0  0
 AX8  CONST_25  CAK   CAM  CAJ  CAO   180.00   0.0  0
 AX8  CONST_26  CAM   CAJ  CAO  CLAC  180.00   0.0  0
 AX8  CONST_27  CAG   CAN  CAO  CLAC  180.00   0.0  0
 AX8  CONST_28  CAF   CAG  CAN  CLAB  180.00   0.0  0
 AX8  CONST_29  CAK   CAM  CAF  CAG   180.00   0.0  0
 AX8  CONST_30  CAI   CAR  NAS  CAK     0.00   0.0  0
 AX8  CONST_31  CAQ   CAR  NAS  CAK   180.00   0.0  0
 AX8  CONST_32  NAL   CAP  NAS  CAK   180.00   0.0  0
 AX8  CONST_33  NAA   CAP  NAS  CAR   180.00   0.0  0
 AX8  CONST_34  NAA   CAP  NAL  CAQ   180.00   0.0  0
 AX8  CONST_35  HAF   CAF  CAM  CAJ   180.00   0.0  0
 AX8  CONST_36  HAG   CAG  CAN  CAO   180.00   0.0  0
 AX8  CONST_37  HAJ   CAJ  CAO  CAN   180.00   0.0  0
 AX8  CONST_38  HAI   CAI  CAR  NAS     0.00   0.0  0
 AX8  CONST_39  HAE   CAE  CAI  CAR   180.00   0.0  0
 AX8  CONST_40  HAH   CAH  CAQ  CAR   180.00   0.0  0
 AX8  CONST_41  HAD   CAD  CAE  CAI   180.00   0.0  0
 AX8  CONST_43  HNAB  NAA  CAP  NAS   180.00   0.0  0
 AX8  Var_01    NAS   CAK  CAM  CAJ    60.66  30.0  2
 AX8  Var_02    CAR   NAS  CAK  CAM    73.56  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
 AX8  plan-1  CAJ   0.020
 AX8  plan-1  CAO   0.020
 AX8  plan-1  CLAC  0.020
 AX8  plan-1  CAN   0.020
 AX8  plan-1  CLAB  0.020
 AX8  plan-1  CAG   0.020
 AX8  plan-1  CAF   0.020
 AX8  plan-1  CAM   0.020
 AX8  plan-1  CAK   0.020
 AX8  plan-1  HAJ   0.020
 AX8  plan-1  HAG   0.020
 AX8  plan-1  HAF   0.020
 AX8  plan-2  CAK   0.020
 AX8  plan-2  NAS   0.020
 AX8  plan-2  CAR   0.020
 AX8  plan-2  CAI   0.020
 AX8  plan-2  CAE   0.020
 AX8  plan-2  CAD   0.020
 AX8  plan-2  CAH   0.020
 AX8  plan-2  CAQ   0.020
 AX8  plan-2  NAL   0.020
 AX8  plan-2  CAP   0.020
 AX8  plan-2  NAA   0.020
 AX8  plan-2  HAI   0.020
 AX8  plan-2  HAE   0.020
 AX8  plan-2  HAD   0.020
 AX8  plan-2  HAH   0.020
 AX8  plan-3  CAP   0.020
 AX8  plan-3  NAA   0.020
 AX8  plan-3  HNAA  0.020
 AX8  plan-3  HNAB  0.020

