# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:29:04 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [2-amino-1-(piperidin-4-ylmethyl)-1H-benzimidazol-6-yl](phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2ccc(cc2n1CC3CCNCC3)C(=O)c4ccccc4
#
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
 B6A  B6A  '[2-amino-1-(piperidin-4-ylmethyl)-1H-benzimidazol-6-yl](phenyl)methanone'  ligand  47  25  .  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_B6A
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
 B6A  CAM  C  CH2   0  -0.433  -2.7616   2.5230   0.3765
 B6A  CAK  C  CH2   0  -0.316  -3.3160   3.3213  -0.8030
 B6A  NAQ  N  NH1   0  -0.575  -4.4967   2.7340  -1.4131
 B6A  CAL  C  CH2   0  -0.310  -4.2733   1.3474  -1.7834
 B6A  CAN  C  CH2   0  -0.452  -3.7573   0.4716  -0.6425
 B6A  CAX  C  CH1   0  -0.242  -2.4982   1.0711  -0.0204
 B6A  CAO  C  CH2   0  -0.338  -2.0021   0.2799   1.1874
 B6A  NAY  N  NR5   0  -0.561  -1.5805  -1.0667   0.8603
 B6A  CAW  C  CR56  0   0.376  -0.3506  -1.4079   0.3379
 B6A  CAJ  C  CR16  0  -0.350   0.7644  -0.6540   0.0475
 B6A  CAU  C  CR5   0   0.635  -2.2858  -2.2306   0.9600
 B6A  NAA  N  NH2   0  -0.857  -3.5210  -2.2868   1.4981
 B6A  NAP  N  N     0  -0.522  -1.6154  -3.2871   0.5486
 B6A  CAV  C  CR56  0   0.165  -0.4024  -2.8024   0.1549
 B6A  CAI  C  CR16  0  -0.332   0.7084  -3.4635  -0.3675
 B6A  CAH  C  CR16  0  -0.289   1.8267  -2.7156  -0.6858
 B6A  CAT  C  CR6   0  -0.067   1.8775  -1.3279  -0.4688
 B6A  CAR  C  C     0   0.358   3.1039  -0.5932  -0.8399
 B6A  OAB  O  O     0  -0.406   3.8577  -1.0102  -1.7014
 B6A  CAS  C  CR6   0  -0.042   3.4284   0.6792  -0.1331
 B6A  CAF  C  CR16  0  -0.279   3.2102   0.8296   1.2359
 B6A  CAD  C  CR16  0  -0.240   3.5983   1.9944   1.8830
 B6A  CAC  C  CR16  0  -0.251   4.1890   3.0246   1.1645
 B6A  CAE  C  CR16  0  -0.245   4.4081   2.8820  -0.2009
 B6A  CAG  C  CR16  0  -0.276   4.0449   1.7095  -0.8435
 B6A  H1   H  HCH2  0   0.233  -1.8424   2.9914   0.7399
 B6A  H2   H  HCH2  0   0.218  -3.4818   2.5503   1.2031
 B6A  H3   H  HCH2  0   0.236  -3.5525   4.3397  -0.4883
 B6A  H4   H  HCH2  0   0.216  -2.5417   3.4042  -1.5743
 B6A  H5   H  HNH1  0   0.339  -5.2660   2.7798  -0.7538
 B6A  H7   H  HCH2  0   0.237  -5.2031   0.9339  -2.1789
 B6A  H8   H  HCH2  0   0.217  -3.5478   1.3268  -2.6044
 B6A  H9   H  HCH2  0   0.215  -4.5386   0.3913   0.1238
 B6A  H10  H  HCH2  0   0.237  -3.5726  -0.5356  -1.0259
 B6A  H11  H  HCH1  0   0.236  -1.7041   1.0649  -0.7799
 B6A  H12  H  HCH2  0   0.273  -1.1510   0.7894   1.6460
 B6A  H13  H  HCH2  0   0.270  -2.7708   0.2301   1.9615
 B6A  H14  H  HCR6  0   0.276   0.7770   0.4187   0.1916
 B6A  H15  H  HNH2  0   0.408  -4.1152  -1.4754   1.4769
 B6A  H16  H  HNH2  0   0.406  -4.0106  -3.1571   1.3715
 B6A  H17  H  HCR6  0   0.254   0.6957  -4.5351  -0.5180
 B6A  H18  H  HCR6  0   0.255   2.6969  -3.2144  -1.0915
 B6A  H19  H  HCR6  0   0.270   2.7587   0.0287   1.8069
 B6A  H20  H  HCR6  0   0.263   3.4382   2.0960   2.9482
 B6A  H21  H  HCR6  0   0.265   4.4836   3.9367   1.6671
 B6A  H22  H  HCR6  0   0.263   4.8685   3.6843  -0.7621
 B6A  H23  H  HCR6  0   0.262   4.2271   1.5987  -1.9047

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
 B6A  CAK  NAQ  single    1.453  0.020  1.453
 B6A  CAK  CAM  single    1.528  0.020  1.528
 B6A  NAQ  CAL  single    1.452  0.020  1.452
 B6A  CAM  CAX  single    1.528  0.020  1.528
 B6A  CAL  CAN  single    1.528  0.020  1.528
 B6A  CAX  CAN  single    1.527  0.020  1.527
 B6A  CAX  CAO  single    1.527  0.020  1.527
 B6A  NAA  CAU  single    1.348  0.020  1.348
 B6A  NAP  CAU  aromatic  1.317  0.020  1.317
 B6A  NAP  CAV  aromatic  1.364  0.020  1.364
 B6A  CAU  NAY  aromatic  1.365  0.020  1.365
 B6A  CAV  CAI  aromatic  1.394  0.020  1.394
 B6A  CAV  CAW  aromatic  1.407  0.020  1.407
 B6A  NAY  CAO  single    1.449  0.020  1.449
 B6A  NAY  CAW  aromatic  1.379  0.020  1.379
 B6A  CAI  CAH  aromatic  1.382  0.020  1.382
 B6A  CAW  CAJ  aromatic  1.377  0.020  1.377
 B6A  CAH  CAT  aromatic  1.406  0.020  1.406
 B6A  OAB  CAR  double    1.218  0.020  1.218
 B6A  CAJ  CAT  aromatic  1.400  0.020  1.400
 B6A  CAT  CAR  single    1.477  0.020  1.477
 B6A  CAR  CAS  single    1.491  0.020  1.491
 B6A  CAF  CAS  aromatic  1.394  0.020  1.394
 B6A  CAF  CAD  aromatic  1.388  0.020  1.388
 B6A  CAS  CAG  aromatic  1.395  0.020  1.395
 B6A  CAD  CAC  aromatic  1.388  0.020  1.388
 B6A  CAG  CAE  aromatic  1.385  0.020  1.385
 B6A  CAC  CAE  aromatic  1.390  0.020  1.390
 B6A  CAM  H1   single    0.970  0.020  1.090
 B6A  CAM  H2   single    0.970  0.020  1.090
 B6A  CAK  H3   single    0.970  0.020  1.090
 B6A  CAK  H4   single    0.970  0.020  1.090
 B6A  NAQ  H5   single    0.890  0.020  1.040
 B6A  CAL  H7   single    0.970  0.020  1.090
 B6A  CAL  H8   single    0.970  0.020  1.090
 B6A  CAN  H9   single    0.970  0.020  1.090
 B6A  CAN  H10  single    0.970  0.020  1.090
 B6A  CAX  H11  single    0.970  0.020  1.090
 B6A  CAO  H12  single    0.970  0.020  1.090
 B6A  CAO  H13  single    0.970  0.020  1.090
 B6A  CAJ  H14  single    0.930  0.020  1.080
 B6A  NAA  H15  single    0.890  0.020  1.040
 B6A  NAA  H16  single    0.890  0.020  1.040
 B6A  CAI  H17  single    0.930  0.020  1.080
 B6A  CAH  H18  single    0.930  0.020  1.080
 B6A  CAF  H19  single    0.930  0.020  1.080
 B6A  CAD  H20  single    0.930  0.020  1.080
 B6A  CAC  H21  single    0.930  0.020  1.080
 B6A  CAE  H22  single    0.930  0.020  1.080
 B6A  CAG  H23  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
 B6A  H2   CAM  H1   106.91  3.000
 B6A  H2   CAM  CAX  109.43  3.000
 B6A  H1   CAM  CAX  110.38  3.000
 B6A  H2   CAM  CAK  109.30  3.000
 B6A  H1   CAM  CAK  109.72  3.000
 B6A  CAX  CAM  CAK  111.00  3.000
 B6A  H4   CAK  H3   106.58  3.000
 B6A  H4   CAK  NAQ  108.01  3.000
 B6A  H3   CAK  NAQ  108.78  3.000
 B6A  H4   CAK  CAM  109.05  3.000
 B6A  H3   CAK  CAM  110.08  3.000
 B6A  NAQ  CAK  CAM  114.06  3.000
 B6A  H5   NAQ  CAL  108.99  3.000
 B6A  H5   NAQ  CAK  108.97  3.000
 B6A  CAL  NAQ  CAK  111.59  3.000
 B6A  H8   CAL  H7   106.58  3.000
 B6A  H8   CAL  CAN  108.97  3.000
 B6A  H7   CAL  CAN  109.94  3.000
 B6A  H8   CAL  NAQ  108.11  3.000
 B6A  H7   CAL  NAQ  108.84  3.000
 B6A  CAN  CAL  NAQ  114.13  3.000
 B6A  H10  CAN  H9   107.32  3.000
 B6A  H10  CAN  CAX  111.42  3.000
 B6A  H9   CAN  CAX  109.35  3.000
 B6A  H10  CAN  CAL  108.86  3.000
 B6A  H9   CAN  CAL  108.84  3.000
 B6A  CAX  CAN  CAL  110.95  3.000
 B6A  H11  CAX  CAO  108.00  3.000
 B6A  H11  CAX  CAN  108.18  3.000
 B6A  CAO  CAX  CAN  112.76  3.000
 B6A  H11  CAX  CAM  108.03  3.000
 B6A  CAO  CAX  CAM  110.06  3.000
 B6A  CAN  CAX  CAM  109.68  3.000
 B6A  H13  CAO  H12  105.78  3.000
 B6A  H13  CAO  NAY  108.82  3.000
 B6A  H12  CAO  NAY  107.55  3.000
 B6A  H13  CAO  CAX  110.83  3.000
 B6A  H12  CAO  CAX  110.09  3.000
 B6A  NAY  CAO  CAX  113.43  3.000
 B6A  CAU  NAY  CAW  106.12  3.000
 B6A  CAW  NAY  CAO  125.10  3.000
 B6A  CAU  NAY  CAO  128.76  3.000
 B6A  CAV  CAW  CAJ  123.01  3.000
 B6A  CAJ  CAW  NAY  131.81  3.000
 B6A  CAV  CAW  NAY  105.16  3.000
 B6A  H14  CAJ  CAT  121.12  3.000
 B6A  H14  CAJ  CAW  121.59  3.000
 B6A  CAT  CAJ  CAW  117.27  3.000
 B6A  NAP  CAU  NAA  123.88  3.000
 B6A  NAP  CAU  NAY  113.47  3.000
 B6A  NAA  CAU  NAY  122.56  3.000
 B6A  H16  NAA  H15  114.04  3.000
 B6A  H16  NAA  CAU  115.56  3.000
 B6A  H15  NAA  CAU  119.93  3.000
 B6A  CAV  NAP  CAU  104.93  3.000
 B6A  CAI  CAV  NAP  130.39  3.000
 B6A  CAI  CAV  CAW  119.29  3.000
 B6A  NAP  CAV  CAW  110.32  3.000
 B6A  H17  CAI  CAH  120.88  3.000
 B6A  H17  CAI  CAV  120.82  3.000
 B6A  CAH  CAI  CAV  118.31  3.000
 B6A  H18  CAH  CAT  118.94  3.000
 B6A  H18  CAH  CAI  119.18  3.000
 B6A  CAT  CAH  CAI  121.86  3.000
 B6A  CAR  CAT  CAH  118.84  3.000
 B6A  CAR  CAT  CAJ  120.90  3.000
 B6A  CAH  CAT  CAJ  120.23  3.000
 B6A  CAS  CAR  OAB  119.51  3.000
 B6A  CAS  CAR  CAT  119.08  3.000
 B6A  OAB  CAR  CAT  121.41  3.000
 B6A  CAG  CAS  CAF  119.30  3.000
 B6A  CAG  CAS  CAR  119.01  3.000
 B6A  CAF  CAS  CAR  121.56  3.000
 B6A  H19  CAF  CAD  119.46  3.000
 B6A  H19  CAF  CAS  120.22  3.000
 B6A  CAD  CAF  CAS  120.30  3.000
 B6A  H20  CAD  CAC  120.19  3.000
 B6A  H20  CAD  CAF  119.77  3.000
 B6A  CAC  CAD  CAF  120.04  3.000
 B6A  H21  CAC  CAE  119.98  3.000
 B6A  H21  CAC  CAD  120.07  3.000
 B6A  CAE  CAC  CAD  119.95  3.000
 B6A  H22  CAE  CAG  119.91  3.000
 B6A  H22  CAE  CAC  120.02  3.000
 B6A  CAG  CAE  CAC  120.07  3.000
 B6A  H23  CAG  CAE  119.81  3.000
 B6A  H23  CAG  CAS  119.87  3.000
 B6A  CAE  CAG  CAS  120.31  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
 B6A  CONST_01  CAV  NAP  CAU  NAY    0.00   0.0  0
 B6A  CONST_02  NAP  CAV  CAW  NAY    0.00   0.0  0
 B6A  CONST_03  CAI  CAV  CAW  NAY  180.00   0.0  0
 B6A  CONST_04  CAT  CAJ  CAW  NAY  180.00   0.0  0
 B6A  CONST_05  CAU  NAP  CAV  CAW    0.00   0.0  0
 B6A  CONST_06  CAH  CAI  CAV  CAW    0.00   0.0  0
 B6A  CONST_07  NAP  CAU  NAY  CAW    0.00   0.0  0
 B6A  CONST_08  CAH  CAT  CAJ  CAW    0.00   0.0  0
 B6A  CONST_09  NAP  CAV  CAW  CAJ  180.00   0.0  0
 B6A  CONST_10  CAI  CAV  CAW  CAJ    0.00   0.0  0
 B6A  CONST_11  CAU  NAY  CAW  CAJ  180.00   0.0  0
 B6A  CONST_12  CAI  CAH  CAT  CAJ    0.00   0.0  0
 B6A  CONST_13  CAI  CAV  NAP  CAU  180.00   0.0  0
 B6A  CONST_14  CAV  CAW  NAY  CAU    0.00   0.0  0
 B6A  CONST_15  CAH  CAI  CAV  NAP  180.00   0.0  0
 B6A  CONST_16  CAT  CAH  CAI  CAV    0.00   0.0  0
 B6A  CONST_17  CAT  CAJ  CAW  CAV    0.00   0.0  0
 B6A  CONST_18  CAC  CAD  CAF  CAS    0.00   0.0  0
 B6A  CONST_19  CAC  CAE  CAG  CAS    0.00   0.0  0
 B6A  CONST_20  CAE  CAG  CAS  CAF    0.00   0.0  0
 B6A  CONST_21  CAE  CAC  CAD  CAF    0.00   0.0  0
 B6A  CONST_22  CAG  CAS  CAF  CAD    0.00   0.0  0
 B6A  CONST_23  CAG  CAE  CAC  CAD    0.00   0.0  0
 B6A  CONST_24  NAP  CAU  NAY  CAO  180.00   0.0  0
 B6A  CONST_25  CAV  CAW  NAY  CAO  180.00   0.0  0
 B6A  CONST_26  CAJ  CAW  NAY  CAO    0.00   0.0  0
 B6A  CONST_27  NAA  CAU  NAY  CAW  180.00   0.0  0
 B6A  CONST_28  CAR  CAT  CAJ  CAW  180.00   0.0  0
 B6A  CONST_29  CAV  NAP  CAU  NAA  180.00   0.0  0
 B6A  CONST_30  CAR  CAT  CAH  CAI  180.00   0.0  0
 B6A  CONST_31  CAD  CAF  CAS  CAR  180.00   0.0  0
 B6A  CONST_32  CAE  CAG  CAS  CAR  180.00   0.0  0
 B6A  CONST_33  H14  CAJ  CAW  NAY    0.00   0.0  0
 B6A  CONST_34  H17  CAI  CAV  CAW  180.00   0.0  0
 B6A  CONST_35  H18  CAH  CAT  CAJ  180.00   0.0  0
 B6A  CONST_36  H20  CAD  CAF  CAS  180.00   0.0  0
 B6A  CONST_37  H22  CAE  CAG  CAS  180.00   0.0  0
 B6A  CONST_38  H23  CAG  CAS  CAF  180.00   0.0  0
 B6A  CONST_39  H21  CAC  CAD  CAF  180.00   0.0  0
 B6A  CONST_40  H19  CAF  CAD  CAC  180.00   0.0  0
 B6A  CONST_42  H16  NAA  CAU  NAY  180.00   0.0  0
 B6A  Var_01    CAL  NAQ  CAK  CAM  -53.28  30.0  1
 B6A  Var_02    CAN  CAL  NAQ  CAK   53.34  30.0  1
 B6A  Var_03    CAX  CAM  CAK  NAQ   54.16  30.0  1
 B6A  Var_04    CAX  CAN  CAL  NAQ  -54.24  30.0  1
 B6A  Var_05    CAU  NAY  CAO  CAX  -96.65  30.0  2
 B6A  Var_06    CAS  CAR  CAT  CAJ   28.02  30.0  2
 B6A  Var_07    CAF  CAS  CAR  CAT   39.18  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 B6A  chir_01  CAX  CAM  CAN  CAO  positiv

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
 B6A  plan-1  CAR  0.020
 B6A  plan-1  CAS  0.020
 B6A  plan-1  CAF  0.020
 B6A  plan-1  CAD  0.020
 B6A  plan-1  CAC  0.020
 B6A  plan-1  CAE  0.020
 B6A  plan-1  CAG  0.020
 B6A  plan-1  H19  0.020
 B6A  plan-1  H20  0.020
 B6A  plan-1  H21  0.020
 B6A  plan-1  H22  0.020
 B6A  plan-1  H23  0.020
 B6A  plan-2  CAO  0.020
 B6A  plan-2  NAY  0.020
 B6A  plan-2  CAW  0.020
 B6A  plan-2  CAJ  0.020
 B6A  plan-2  CAU  0.020
 B6A  plan-2  NAA  0.020
 B6A  plan-2  NAP  0.020
 B6A  plan-2  CAV  0.020
 B6A  plan-2  CAI  0.020
 B6A  plan-2  CAH  0.020
 B6A  plan-2  CAT  0.020
 B6A  plan-2  CAR  0.020
 B6A  plan-2  H14  0.020
 B6A  plan-2  H17  0.020
 B6A  plan-2  H18  0.020
 B6A  plan-3  CAU  0.020
 B6A  plan-3  NAA  0.020
 B6A  plan-3  H15  0.020
 B6A  plan-3  H16  0.020
 B6A  plan-4  CAT  0.020
 B6A  plan-4  CAR  0.020
 B6A  plan-4  OAB  0.020
 B6A  plan-4  CAS  0.020

