# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:21:32 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2[nH]c(nc2c1)c3ccc(cc3)c4ccc(cc4)C(N)=O
#
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
 D63  D63  4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide  ligand  44  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D63
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
 D63  NAA   N  NH2   0  -0.806   8.7250   0.1609  -0.5685
 D63  NAB   N  N     0  -0.645   7.9332   2.0632   0.4344
 D63  NAC   N  NH2   0  -0.813  -8.7832  -0.8198  -0.0574
 D63  OAD   O  O     0  -0.481  -8.6002   1.4236  -0.1498
 D63  CAE   C  CR16  0  -0.252  -5.8217   1.2658   0.3166
 D63  CAF   C  CR16  0  -0.267  -5.9341  -0.9883  -0.4884
 D63  CAG   C  CR16  0  -0.298  -4.4408   1.1872   0.3458
 D63  CAH   C  CR16  0  -0.294  -4.5518  -1.0637  -0.4665
 D63  CAI   C  CR16  0  -0.290  -1.6737  -1.2541   0.3549
 D63  CAJ   C  CR16  0  -0.291  -1.5161   1.0334  -0.3363
 D63  CAK   C  CR16  0  -0.287  -0.2932  -1.3400   0.3902
 D63  CAL   C  CR16  0  -0.273  -0.1372   0.9499  -0.3077
 D63  CAM   C  CR16  0  -0.301   6.3424  -1.2094   0.2340
 D63  CAN   C  CR16  0  -0.297   5.1425  -1.8888   0.3250
 D63  CAO   C  CR16  0  -0.391   5.2294   0.9288  -0.0562
 D63  NAP   N  NR15  0  -0.732   2.6571  -1.4493   0.2478
 D63  NAQ   N  N     0  -0.480   2.7337   0.7470  -0.0620
 D63  CAR   C  C     0   0.333   7.7111   0.8870  -0.0157
 D63  CAT   C  CR6   0  -0.049  -6.5872   0.1751  -0.0878
 D63  CAU   C  CR6   0  -0.007   6.3972   0.1866   0.0490
 D63  CAV   C  CR6   0   0.092  -3.7816   0.0197  -0.0428
 D63  CAW   C  CR6   0   0.085  -2.3108  -0.0677  -0.0088
 D63  CAX   C  CR6   0   0.006   0.4954  -0.2401   0.0549
 D63  CAY   C  CR5   0   0.486   1.9538  -0.2943   0.0775
 D63  CAZ   C  CR56  0   0.341   3.9837  -1.1310   0.2153
 D63  CBA   C  CR56  0   0.178   4.0112   0.2607   0.0217
 D63  HNAA  H  HNH2  0   0.383   9.5850   0.6592  -0.7345
 D63  HNAB  H  HNH2  0   0.391   8.4961  -0.5127  -1.2804
 D63  HNAC  H  H     0   0.331   7.1149   2.4244   0.9103
 D63  HNAD  H  HNH2  0   0.406  -9.7894  -0.7822  -0.0526
 D63  HNAE  H  HNH2  0   0.414  -8.3609  -1.7168   0.1061
 D63  HAE   H  HCR6  0   0.265  -6.3081   2.1797   0.6296
 D63  HAF   H  HCR6  0   0.262  -6.4885  -1.8442  -0.8519
 D63  HAG   H  HCR6  0   0.262  -3.8728   2.0394   0.6966
 D63  HAH   H  HCR6  0   0.264  -4.0698  -1.9702  -0.8089
 D63  HAI   H  HCR6  0   0.265  -2.2583  -2.1191   0.6408
 D63  HAJ   H  HCR6  0   0.263  -1.9782   1.9630  -0.6429
 D63  HAK   H  HCR6  0   0.252   0.1512  -2.2756   0.7039
 D63  HAL   H  HCR6  0   0.262   0.4576   1.8115  -0.5792
 D63  HAM   H  HCR6  0   0.263   7.2632  -1.7693   0.3303
 D63  HAN   H  HCR6  0   0.273   5.1155  -2.9592   0.4776
 D63  HAO   H  HCR6  0   0.263   5.2560   1.9994  -0.2165
 D63  HNAP  H  HNR5  0   0.427   2.2804  -2.3778   0.3539
 D63  CAS   C  C     0   0.488  -8.0761   0.3188  -0.1015

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
 D63  NAA  CAR   single    1.364  0.020  1.364
 D63  NAB  CAR   double    1.279  0.020  1.279
 D63  CAR  CAU   single    1.490  0.020  1.490
 D63  CAU  CAM   aromatic  1.409  0.020  1.409
 D63  CAU  CAO   aromatic  1.388  0.020  1.388
 D63  CAM  CAN   aromatic  1.382  0.020  1.382
 D63  CAO  CBA   aromatic  1.392  0.020  1.392
 D63  CAN  CAZ   aromatic  1.389  0.020  1.389
 D63  CBA  CAZ   aromatic  1.405  0.020  1.405
 D63  CBA  NAQ   aromatic  1.369  0.020  1.369
 D63  CAZ  NAP   aromatic  1.365  0.020  1.365
 D63  NAQ  CAY   aromatic  1.308  0.020  1.308
 D63  NAP  CAY   aromatic  1.363  0.020  1.363
 D63  CAY  CAX   single    1.460  0.020  1.460
 D63  CAX  CAL   aromatic  1.396  0.020  1.396
 D63  CAX  CAK   aromatic  1.394  0.020  1.394
 D63  CAL  CAJ   aromatic  1.382  0.020  1.382
 D63  CAK  CAI   aromatic  1.384  0.020  1.384
 D63  CAJ  CAW   aromatic  1.397  0.020  1.397
 D63  CAI  CAW   aromatic  1.395  0.020  1.395
 D63  CAW  CAV   single    1.474  0.020  1.474
 D63  CAV  CAG   aromatic  1.396  0.020  1.396
 D63  CAV  CAH   aromatic  1.395  0.020  1.395
 D63  CAG  CAE   aromatic  1.383  0.020  1.383
 D63  CAH  CAF   aromatic  1.385  0.020  1.385
 D63  CAE  CAT   aromatic  1.393  0.020  1.393
 D63  CAF  CAT   aromatic  1.393  0.020  1.393
 D63  CAT  CAS   single    1.496  0.020  1.496
 D63  CAS  NAC   single    1.341  0.020  1.341
 D63  CAS  OAD   double    1.224  0.020  1.224
 D63  NAA  HNAA  single    0.890  0.020  1.040
 D63  NAA  HNAB  single    0.890  0.020  1.040
 D63  NAB  HNAC  single    0.890  0.020  1.040
 D63  NAC  HNAD  single    0.860  0.020  1.020
 D63  NAC  HNAE  single    0.860  0.020  1.020
 D63  CAE  HAE   single    0.930  0.020  1.080
 D63  CAF  HAF   single    0.930  0.020  1.080
 D63  CAG  HAG   single    0.930  0.020  1.080
 D63  CAH  HAH   single    0.930  0.020  1.080
 D63  CAI  HAI   single    0.930  0.020  1.080
 D63  CAJ  HAJ   single    0.930  0.020  1.080
 D63  CAK  HAK   single    0.930  0.020  1.080
 D63  CAL  HAL   single    0.930  0.020  1.080
 D63  CAM  HAM   single    0.930  0.020  1.080
 D63  CAN  HAN   single    0.930  0.020  1.080
 D63  CAO  HAO   single    0.930  0.020  1.080
 D63  NAP  HNAP  single    0.860  0.020  1.020

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
 D63  HNAB  NAA  HNAA  114.11  3.000
 D63  HNAB  NAA  CAR   118.29  3.000
 D63  HNAA  NAA  CAR   115.97  3.000
 D63  HNAC  NAB  CAR   110.67  3.000
 D63  HNAE  NAC  HNAD  116.91  3.000
 D63  HNAE  NAC  CAS   122.80  3.000
 D63  HNAD  NAC  CAS   119.69  3.000
 D63  HAE   CAE  CAT   119.91  3.000
 D63  HAE   CAE  CAG   119.40  3.000
 D63  CAT   CAE  CAG   120.69  3.000
 D63  HAF   CAF  CAT   121.11  3.000
 D63  HAF   CAF  CAH   118.27  3.000
 D63  CAT   CAF  CAH   120.59  3.000
 D63  HAG   CAG  CAV   120.06  3.000
 D63  HAG   CAG  CAE   119.07  3.000
 D63  CAV   CAG  CAE   120.86  3.000
 D63  HAH   CAH  CAV   120.05  3.000
 D63  HAH   CAH  CAF   119.03  3.000
 D63  CAV   CAH  CAF   120.91  3.000
 D63  HAI   CAI  CAW   120.13  3.000
 D63  HAI   CAI  CAK   118.85  3.000
 D63  CAW   CAI  CAK   121.00  3.000
 D63  HAJ   CAJ  CAW   120.03  3.000
 D63  HAJ   CAJ  CAL   118.93  3.000
 D63  CAW   CAJ  CAL   121.02  3.000
 D63  HAK   CAK  CAX   121.30  3.000
 D63  HAK   CAK  CAI   118.08  3.000
 D63  CAX   CAK  CAI   120.61  3.000
 D63  HAL   CAL  CAX   119.68  3.000
 D63  HAL   CAL  CAJ   119.70  3.000
 D63  CAX   CAL  CAJ   120.61  3.000
 D63  HAM   CAM  CAU   119.42  3.000
 D63  HAM   CAM  CAN   118.60  3.000
 D63  CAU   CAM  CAN   121.97  3.000
 D63  HAN   CAN  CAZ   122.03  3.000
 D63  HAN   CAN  CAM   121.17  3.000
 D63  CAZ   CAN  CAM   116.81  3.000
 D63  HAO   CAO  CBA   120.30  3.000
 D63  HAO   CAO  CAU   121.28  3.000
 D63  CBA   CAO  CAU   118.41  3.000
 D63  HNAP  NAP  CAZ   125.52  3.000
 D63  HNAP  NAP  CAY   126.95  3.000
 D63  CAZ   NAP  CAY   107.51  3.000
 D63  CBA   NAQ  CAY   105.48  3.000
 D63  CAU   CAR  NAB   124.75  3.000
 D63  CAU   CAR  NAA   115.01  3.000
 D63  NAB   CAR  NAA   120.21  3.000
 D63  CAS   CAT  CAF   122.97  3.000
 D63  CAS   CAT  CAE   118.33  3.000
 D63  CAF   CAT  CAE   118.68  3.000
 D63  CAR   CAU  CAO   119.17  3.000
 D63  CAO   CAU  CAM   120.47  3.000
 D63  CAR   CAU  CAM   120.36  3.000
 D63  CAW   CAV  CAH   120.79  3.000
 D63  CAH   CAV  CAG   118.25  3.000
 D63  CAW   CAV  CAG   120.96  3.000
 D63  CAV   CAW  CAJ   121.04  3.000
 D63  CAV   CAW  CAI   120.81  3.000
 D63  CAJ   CAW  CAI   118.15  3.000
 D63  CAY   CAX  CAL   119.25  3.000
 D63  CAL   CAX  CAK   118.61  3.000
 D63  CAY   CAX  CAK   122.15  3.000
 D63  CAX   CAY  NAQ   124.36  3.000
 D63  CAX   CAY  NAP   123.30  3.000
 D63  NAQ   CAY  NAP   112.35  3.000
 D63  CBA   CAZ  NAP   104.68  3.000
 D63  NAP   CAZ  CAN   132.99  3.000
 D63  CBA   CAZ  CAN   122.33  3.000
 D63  CAZ   CBA  NAQ   109.99  3.000
 D63  NAQ   CBA  CAO   130.00  3.000
 D63  CAZ   CBA  CAO   120.02  3.000
 D63  CAT   CAS  OAD   120.89  3.000
 D63  OAD   CAS  NAC   122.82  3.000
 D63  CAT   CAS  NAC   116.29  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
 D63  CONST_01  CAW   CAV  CAG  CAE   180.00   0.0  0
 D63  CONST_02  CAH   CAV  CAG  CAE     0.00   0.0  0
 D63  CONST_03  CAH   CAF  CAT  CAE     0.00   0.0  0
 D63  CONST_04  CAW   CAV  CAH  CAF   180.00   0.0  0
 D63  CONST_05  CAG   CAV  CAH  CAF     0.00   0.0  0
 D63  CONST_06  CAG   CAE  CAT  CAF     0.00   0.0  0
 D63  CONST_11  CAY   CAX  CAK  CAI   180.00   0.0  0
 D63  CONST_12  CAL   CAX  CAK  CAI     0.00   0.0  0
 D63  CONST_13  CAL   CAJ  CAW  CAI     0.00   0.0  0
 D63  CONST_14  CAY   CAX  CAL  CAJ   180.00   0.0  0
 D63  CONST_15  CAK   CAX  CAL  CAJ     0.00   0.0  0
 D63  CONST_16  CAK   CAI  CAW  CAJ     0.00   0.0  0
 D63  CONST_17  NAQ   CAY  CAX  CAK   180.00   0.0  0
 D63  CONST_18  NAP   CAY  CAX  CAK     0.00   0.0  0
 D63  CONST_19  CAV   CAW  CAI  CAK   180.00   0.0  0
 D63  CONST_20  NAQ   CAY  CAX  CAL     0.00   0.0  0
 D63  CONST_21  NAP   CAY  CAX  CAL   180.00   0.0  0
 D63  CONST_22  CAV   CAW  CAJ  CAL   180.00   0.0  0
 D63  CONST_23  CBA   CAO  CAU  CAM     0.00   0.0  0
 D63  CONST_24  CBA   CAZ  CAN  CAM     0.00   0.0  0
 D63  CONST_25  NAP   CAZ  CAN  CAM   180.00   0.0  0
 D63  CONST_26  CAO   CAU  CAM  CAN     0.00   0.0  0
 D63  CONST_27  CAO   CBA  CAZ  CAN     0.00   0.0  0
 D63  CONST_28  NAQ   CBA  CAZ  CAN   180.00   0.0  0
 D63  CONST_29  CAY   NAP  CAZ  CAN   180.00   0.0  0
 D63  CONST_30  NAP   CAZ  CBA  CAO   180.00   0.0  0
 D63  CONST_31  CAY   NAQ  CBA  CAO   180.00   0.0  0
 D63  CONST_32  NAQ   CBA  CAZ  NAP     0.00   0.0  0
 D63  CONST_33  CBA   NAQ  CAY  NAP     0.00   0.0  0
 D63  CONST_34  CAU   CAO  CBA  NAQ   180.00   0.0  0
 D63  CONST_35  CAZ   NAP  CAY  NAQ     0.00   0.0  0
 D63  CONST_36  CAV   CAG  CAE  CAT     0.00   0.0  0
 D63  CONST_37  CAV   CAH  CAF  CAT     0.00   0.0  0
 D63  CONST_38  CAZ   CAN  CAM  CAU     0.00   0.0  0
 D63  CONST_39  CAZ   CBA  CAO  CAU     0.00   0.0  0
 D63  CONST_40  CAX   CAL  CAJ  CAW     0.00   0.0  0
 D63  CONST_41  CAX   CAK  CAI  CAW     0.00   0.0  0
 D63  CONST_42  CBA   NAQ  CAY  CAX   180.00   0.0  0
 D63  CONST_43  CAZ   NAP  CAY  CAX   180.00   0.0  0
 D63  CONST_44  CAZ   CBA  NAQ  CAY     0.00   0.0  0
 D63  CONST_45  CBA   CAZ  NAP  CAY     0.00   0.0  0
 D63  CONST_46  CAS   CAT  CAE  CAG   180.00   0.0  0
 D63  CONST_47  CAS   CAT  CAF  CAH   180.00   0.0  0
 D63  CONST_48  CAR   CAU  CAM  CAN   180.00   0.0  0
 D63  CONST_49  CBA   CAO  CAU  CAR   180.00   0.0  0
 D63  CONST_50  HAF   CAF  CAT  CAE   180.00   0.0  0
 D63  CONST_51  HAE   CAE  CAT  CAF   180.00   0.0  0
 D63  CONST_52  HAH   CAH  CAV  CAG   180.00   0.0  0
 D63  CONST_53  HAG   CAG  CAV  CAH   180.00   0.0  0
 D63  CONST_54  HAJ   CAJ  CAW  CAI   180.00   0.0  0
 D63  CONST_55  HAI   CAI  CAW  CAJ   180.00   0.0  0
 D63  CONST_56  HAL   CAL  CAX  CAK   180.00   0.0  0
 D63  CONST_57  HAK   CAK  CAX  CAL   180.00   0.0  0
 D63  CONST_58  HAO   CAO  CAU  CAM   180.00   0.0  0
 D63  CONST_59  HNAP  NAP  CAZ  CAN     0.00   0.0  0
 D63  CONST_60  HAM   CAM  CAU  CAO   180.00   0.0  0
 D63  CONST_61  HAN   CAN  CAZ  NAP     0.00   0.0  0
 D63  CONST_62  HNAD  NAC  CAS  CAT   180.00   0.0  0
 D63  CONST_63  HNAE  NAC  CAS  CAT     0.00   0.0  0
 D63  CONST_64  HNAA  NAA  CAR  CAU   180.00   0.0  0
 D63  CONST_66  HNAC  NAB  CAR  CAU     0.00   0.0  0
 D63  Var_01    CAM   CAU  CAR  NAA    32.58  30.0  2
 D63  Var_02    CAE   CAT  CAS  NAC  -158.68  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
 D63  plan-1  CAE   0.020
 D63  plan-1  CAF   0.020
 D63  plan-1  CAG   0.020
 D63  plan-1  CAH   0.020
 D63  plan-1  CAT   0.020
 D63  plan-1  CAV   0.020
 D63  plan-1  CAW   0.020
 D63  plan-1  HAE   0.020
 D63  plan-1  HAF   0.020
 D63  plan-1  HAG   0.020
 D63  plan-1  HAH   0.020
 D63  plan-1  CAS   0.020
 D63  plan-2  CAI   0.020
 D63  plan-2  CAJ   0.020
 D63  plan-2  CAK   0.020
 D63  plan-2  CAL   0.020
 D63  plan-2  CAV   0.020
 D63  plan-2  CAW   0.020
 D63  plan-2  CAX   0.020
 D63  plan-2  CAY   0.020
 D63  plan-2  HAI   0.020
 D63  plan-2  HAJ   0.020
 D63  plan-2  HAK   0.020
 D63  plan-2  HAL   0.020
 D63  plan-3  CAM   0.020
 D63  plan-3  CAN   0.020
 D63  plan-3  CAO   0.020
 D63  plan-3  NAP   0.020
 D63  plan-3  NAQ   0.020
 D63  plan-3  CAR   0.020
 D63  plan-3  CAU   0.020
 D63  plan-3  CAX   0.020
 D63  plan-3  CAY   0.020
 D63  plan-3  CAZ   0.020
 D63  plan-3  CBA   0.020
 D63  plan-3  HAM   0.020
 D63  plan-3  HAN   0.020
 D63  plan-3  HAO   0.020
 D63  plan-3  HNAP  0.020
 D63  plan-4  NAC   0.020
 D63  plan-4  OAD   0.020
 D63  plan-4  CAT   0.020
 D63  plan-4  HNAD  0.020
 D63  plan-4  HNAE  0.020
 D63  plan-4  CAS   0.020
 D63  plan-5  NAA   0.020
 D63  plan-5  NAB   0.020
 D63  plan-5  CAR   0.020
 D63  plan-5  CAU   0.020
 D63  plan-5  HNAA  0.020
 D63  plan-5  HNAB  0.020
 D63  plan-5  HNAC  0.020

