# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:10:42 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-[(1H-benzimidazol-2-ylacetyl)amino]-5'-deoxycytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)Cc3[nH]c4ccccc4n3)[C@@H](O)[C@H]2O
#
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
 V12  V12  5'-[(1H-benzimidazol-2-ylacetyl)amino]-5'-deoxycytidine  ligand  49  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V12
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
 V12  OAC   O  O     0  -0.508   3.9394   0.5352   1.5413
 V12  CAV   C  CR6   0   0.604   4.5592   0.8528   0.5355
 V12  NAO   N  N     0  -0.541   5.4781   1.8381   0.5310
 V12  CAT   C  CR6   0   0.516   6.1460   2.1437  -0.5644
 V12  NAA   N  NH2   0  -0.808   7.0437   3.1252  -0.5028
 V12  CAF   C  CR16  0  -0.477   5.9300   1.4599  -1.8004
 V12  CAG   C  CR16  0   0.101   4.9965   0.4894  -1.7895
 V12  NBD   N  NR6   0  -0.556   4.3131   0.1654  -0.6641
 V12  CBC   C  CR15  0   0.204   3.2969  -0.8733  -0.7307
 V12  OAS   O  O     0  -0.493   2.0355  -0.3168  -0.4913
 V12  CBA   C  CR15  0  -0.042   3.4788  -2.0671   0.2233
 V12  OAE   O  OH1   0  -0.677   3.3467  -3.2439  -0.5329
 V12  CAZ   C  CR15  0  -0.033   2.3044  -1.9264   1.2097
 V12  OAD   O  OH1   0  -0.663   1.7354  -3.1642   1.5599
 V12  CB0   C  CR15  0   0.049   1.2884  -1.1026   0.4191
 V12  CAN   C  CH2   0  -0.318   0.4542  -0.1943   1.3033
 V12  NAQ   N  NH1   0  -0.637  -0.5293   0.5725   0.5763
 V12  CAU   C  C     0   0.566  -1.7502   0.1070   0.2757
 V12  OAB   O  O     0  -0.482  -2.1702  -0.9792   0.6412
 V12  CAL   C  CH2   0  -0.716  -2.5850   1.0428  -0.5868
 V12  CA0   C  CR5   0   0.460  -4.0282   0.6986  -0.5383
 V12  NAR   N  N     0  -0.470  -4.6984   0.1258  -1.4992
 V12  CAY   C  CR56  0   0.133  -5.9816  -0.0006  -1.0202
 V12  CAK   C  CR16  0  -0.334  -7.1180  -0.5402  -1.6220
 V12  CAI   C  CR16  0  -0.272  -8.2989  -0.5339  -0.9010
 V12  CAH   C  CR16  0  -0.279  -8.3603  -0.0015   0.3960
 V12  CAJ   C  CR16  0  -0.309  -7.2437   0.5385   1.0112
 V12  CAX   C  CR56  0   0.336  -6.0618   0.5265   0.2799
 V12  NAP   N  NR15  0  -0.685  -4.7943   0.9656   0.5508
 V12  HAA1  H  HNH2  0   0.404   7.1999   3.6146   0.3619
 V12  HAA2  H  HNH2  0   0.415   7.5930   3.3884  -1.3017
 V12  HAF   H  HCR6  0   0.289   6.4729   1.7057  -2.7003
 V12  HAG   H  HCR6  0   0.320   4.7535  -0.0762  -2.6788
 V12  HBC   H  HCR5  0   0.253   3.3524  -1.2551  -1.7545
 V12  HBA   H  HCR5  0   0.246   4.4497  -2.0389   0.7298
 V12  HB0   H  HCR5  0   0.237   0.6270  -1.7856  -0.1328
 V12  HAE   H  HOH1  0   0.447   2.7927  -3.8470  -0.0177
 V12  HAZ   H  HCR5  0   0.259   2.6329  -1.3797   2.0937
 V12  HAD   H  HOH1  0   0.469   2.1863  -3.5019   2.3405
 V12  HAN1  H  HCH2  0   0.257  -0.0469  -0.8027   2.0570
 V12  HAN2  H  HCH2  0   0.265   1.1116   0.5015   1.8255
 V12  HAQ   H  HNH1  0   0.409  -0.2473   1.4654   0.2060
 V12  HAL1  H  HCH2  0   0.301  -2.4258   2.0832  -0.2926
 V12  HAL2  H  HCH2  0   0.316  -2.2433   0.9503  -1.6198
 V12  HAP   H  HNR5  0   0.420  -4.4821   1.4043   1.4026
 V12  HAK   H  HCR6  0   0.253  -7.0736  -0.9513  -2.6225
 V12  HAI   H  HCR6  0   0.252  -9.1966  -0.9451  -1.3436
 V12  HAH   H  HCR6  0   0.255  -9.3032  -0.0105   0.9270
 V12  HAJ   H  HCR6  0   0.265  -7.2942   0.9509   2.0104

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
 V12  OAC  CAV   double    1.223  0.020  1.223
 V12  CAV  NAO   single    1.347  0.020  1.347
 V12  CAV  NBD   single    1.404  0.020  1.404
 V12  NAO  CAT   double    1.319  0.020  1.319
 V12  CAT  NAA   single    1.332  0.020  1.332
 V12  CAT  CAF   single    1.429  0.020  1.429
 V12  NAA  HAA1  single    0.860  0.020  1.020
 V12  NAA  HAA2  single    0.860  0.020  1.020
 V12  CAF  HAF   single    0.930  0.020  1.080
 V12  CAF  CAG   double    1.347  0.020  1.347
 V12  CAG  HAG   single    0.930  0.020  1.080
 V12  CAG  NBD   single    1.356  0.020  1.356
 V12  NBD  CBC   single    1.455  0.020  1.455
 V12  CBC  HBC   single    0.970  0.020  1.090
 V12  CBC  OAS   single    1.399  0.020  1.399
 V12  CBC  CBA   single    1.539  0.020  1.539
 V12  OAS  CB0   single    1.416  0.020  1.416
 V12  CBA  HBA   single    0.970  0.020  1.090
 V12  CBA  OAE   single    1.405  0.020  1.405
 V12  CBA  CAZ   single    1.540  0.020  1.540
 V12  OAE  HAE   single    0.850  0.020  0.980
 V12  CAZ  HAZ   single    0.970  0.020  1.090
 V12  CAZ  OAD   single    1.407  0.020  1.407
 V12  CAZ  CB0   single    1.528  0.020  1.528
 V12  OAD  HAD   single    0.850  0.020  0.980
 V12  CB0  CAN   single    1.517  0.020  1.517
 V12  CB0  HB0   single    0.970  0.020  1.090
 V12  CAN  NAQ   single    1.444  0.020  1.444
 V12  CAN  HAN1  single    0.970  0.020  1.090
 V12  CAN  HAN2  single    0.970  0.020  1.090
 V12  NAQ  CAU   single    1.341  0.020  1.341
 V12  NAQ  HAQ   single    0.860  0.020  1.020
 V12  CAU  OAB   double    1.221  0.020  1.221
 V12  CAU  CAL   single    1.522  0.020  1.522
 V12  CAL  CA0   single    1.484  0.020  1.484
 V12  CAL  HAL1  single    0.970  0.020  1.090
 V12  CAL  HAL2  single    0.970  0.020  1.090
 V12  CA0  NAR   aromatic  1.304  0.020  1.304
 V12  CA0  NAP   aromatic  1.358  0.020  1.358
 V12  NAR  CAY   aromatic  1.376  0.020  1.376
 V12  CAY  CAK   aromatic  1.395  0.020  1.395
 V12  CAY  CAX   aromatic  1.405  0.020  1.405
 V12  CAK  CAI   aromatic  1.384  0.020  1.384
 V12  CAK  HAK   single    0.930  0.020  1.080
 V12  CAI  CAH   aromatic  1.403  0.020  1.403
 V12  CAI  HAI   single    0.930  0.020  1.080
 V12  CAH  CAJ   aromatic  1.384  0.020  1.384
 V12  CAH  HAH   single    0.930  0.020  1.080
 V12  CAJ  CAX   aromatic  1.390  0.020  1.390
 V12  CAJ  HAJ   single    0.930  0.020  1.080
 V12  CAX  NAP   aromatic  1.368  0.020  1.368
 V12  NAP  HAP   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
 V12  NBD   CAV  NAO   118.33  3.000
 V12  NBD   CAV  OAC   119.11  3.000
 V12  NAO   CAV  OAC   122.56  3.000
 V12  CAT   NAO  CAV   121.18  3.000
 V12  CAF   CAT  NAA   119.65  3.000
 V12  CAF   CAT  NAO   122.07  3.000
 V12  NAA   CAT  NAO   118.28  3.000
 V12  HAA2  NAA  HAA1  118.11  3.000
 V12  HAA2  NAA  CAT   121.67  3.000
 V12  HAA1  NAA  CAT   120.21  3.000
 V12  HAF   CAF  CAG   121.30  3.000
 V12  CAG   CAF  CAT   116.27  3.000
 V12  HAF   CAF  CAT   122.42  3.000
 V12  HAG   CAG  NBD   116.38  3.000
 V12  NBD   CAG  CAF   121.89  3.000
 V12  HAG   CAG  CAF   121.73  3.000
 V12  CBC   NBD  CAG   119.00  3.000
 V12  CBC   NBD  CAV   120.73  3.000
 V12  CAG   NBD  CAV   120.25  3.000
 V12  HBC   CBC  CBA   107.66  3.000
 V12  CBA   CBC  OAS   108.00  3.000
 V12  HBC   CBC  OAS   110.16  3.000
 V12  CBA   CBC  NBD   116.29  3.000
 V12  OAS   CBC  NBD   109.75  3.000
 V12  HBC   CBC  NBD   104.86  3.000
 V12  CB0   OAS  CBC   111.40  3.000
 V12  HBA   CBA  CAZ   112.17  3.000
 V12  CAZ   CBA  OAE   110.45  3.000
 V12  HBA   CBA  OAE   110.72  3.000
 V12  CAZ   CBA  CBC   103.65  3.000
 V12  OAE   CBA  CBC   107.76  3.000
 V12  HBA   CBA  CBC   111.80  3.000
 V12  HAE   OAE  CBA   106.82  3.000
 V12  HAZ   CAZ  CB0   110.45  3.000
 V12  CB0   CAZ  OAD   109.52  3.000
 V12  HAZ   CAZ  OAD   111.18  3.000
 V12  CB0   CAZ  CBA   102.99  3.000
 V12  OAD   CAZ  CBA   112.80  3.000
 V12  HAZ   CAZ  CBA   109.60  3.000
 V12  HAD   OAD  CAZ   108.73  3.000
 V12  HB0   CB0  CAN   109.49  3.000
 V12  HB0   CB0  CAZ   108.95  3.000
 V12  CAN   CB0  CAZ   112.75  3.000
 V12  HB0   CB0  OAS   109.84  3.000
 V12  CAN   CB0  OAS   109.42  3.000
 V12  CAZ   CB0  OAS   106.32  3.000
 V12  HAN2  CAN  HAN1  107.58  3.000
 V12  HAN2  CAN  NAQ   108.24  3.000
 V12  HAN1  CAN  NAQ   109.35  3.000
 V12  HAN2  CAN  CB0   109.24  3.000
 V12  HAN1  CAN  CB0   108.74  3.000
 V12  NAQ   CAN  CB0   113.52  3.000
 V12  HAQ   NAQ  CAU   118.72  3.000
 V12  HAQ   NAQ  CAN   117.74  3.000
 V12  CAU   NAQ  CAN   123.29  3.000
 V12  CAL   CAU  OAB   121.88  3.000
 V12  CAL   CAU  NAQ   114.39  3.000
 V12  OAB   CAU  NAQ   123.73  3.000
 V12  HAL2  CAL  HAL1  106.85  3.000
 V12  HAL2  CAL  CA0   108.39  3.000
 V12  HAL1  CAL  CA0   110.70  3.000
 V12  HAL2  CAL  CAU   108.20  3.000
 V12  HAL1  CAL  CAU   110.67  3.000
 V12  CA0   CAL  CAU   111.85  3.000
 V12  NAP   CA0  NAR   112.79  3.000
 V12  NAP   CA0  CAL   121.94  3.000
 V12  NAR   CA0  CAL   125.27  3.000
 V12  CAY   NAR  CA0   105.26  3.000
 V12  CAX   CAY  CAK   119.86  3.000
 V12  CAX   CAY  NAR   109.93  3.000
 V12  CAK   CAY  NAR   130.20  3.000
 V12  HAK   CAK  CAI   121.22  3.000
 V12  HAK   CAK  CAY   120.82  3.000
 V12  CAI   CAK  CAY   117.96  3.000
 V12  HAI   CAI  CAH   119.07  3.000
 V12  HAI   CAI  CAK   119.55  3.000
 V12  CAH   CAI  CAK   121.38  3.000
 V12  HAH   CAH  CAJ   119.20  3.000
 V12  HAH   CAH  CAI   119.24  3.000
 V12  CAJ   CAH  CAI   121.56  3.000
 V12  HAJ   CAJ  CAX   121.93  3.000
 V12  HAJ   CAJ  CAH   121.42  3.000
 V12  CAX   CAJ  CAH   116.66  3.000
 V12  NAP   CAX  CAJ   132.90  3.000
 V12  NAP   CAX  CAY   104.51  3.000
 V12  CAJ   CAX  CAY   122.59  3.000
 V12  HAP   NAP  CAX   126.44  3.000
 V12  HAP   NAP  CA0   126.06  3.000
 V12  CAX   NAP  CA0   107.50  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
 V12  CONST_01  CAK   CAY  NAR  CA0   180.00   0.0  0
 V12  CONST_02  CAX   CAY  NAR  CA0     0.00   0.0  0
 V12  CONST_03  CAY   CAX  NAP  CA0     0.00   0.0  0
 V12  CONST_04  CAJ   CAX  NAP  CA0   180.00   0.0  0
 V12  CONST_05  CAX   NAP  CA0  NAR     0.00   0.0  0
 V12  CONST_06  CAI   CAK  CAY  NAR   180.00   0.0  0
 V12  CONST_07  CAJ   CAX  CAY  NAR   180.00   0.0  0
 V12  CONST_08  NAP   CAX  CAY  NAR     0.00   0.0  0
 V12  CONST_09  NAP   CA0  NAR  CAY     0.00   0.0  0
 V12  CONST_10  CAH   CAI  CAK  CAY     0.00   0.0  0
 V12  CONST_11  CAH   CAJ  CAX  CAY     0.00   0.0  0
 V12  CONST_12  CAJ   CAX  CAY  CAK     0.00   0.0  0
 V12  CONST_13  NAP   CAX  CAY  CAK   180.00   0.0  0
 V12  CONST_14  CAJ   CAH  CAI  CAK     0.00   0.0  0
 V12  CONST_15  CAX   CAY  CAK  CAI     0.00   0.0  0
 V12  CONST_16  CAX   CAJ  CAH  CAI     0.00   0.0  0
 V12  CONST_17  NAP   CAX  CAJ  CAH   180.00   0.0  0
 V12  CONST_18  CAF   CAT  NAO  CAV     0.00   0.0  0
 V12  CONST_19  CAG   NBD  CAV  NAO     0.00   0.0  0
 V12  CONST_20  CBC   NBD  CAV  NAO   180.00   0.0  0
 V12  CONST_21  NBD   CAV  NAO  CAT     0.00   0.0  0
 V12  CONST_22  CAY   NAR  CA0  CAL   180.00   0.0  0
 V12  CONST_23  CAX   NAP  CA0  CAL   180.00   0.0  0
 V12  CONST_24  CAT   NAO  CAV  OAC   180.00   0.0  0
 V12  CONST_25  CAG   NBD  CAV  OAC   180.00   0.0  0
 V12  CONST_26  CBC   NBD  CAV  OAC     0.00   0.0  0
 V12  CONST_27  NAA   CAT  NAO  CAV   180.00   0.0  0
 V12  CONST_28  HAP   NAP  CA0  NAR   180.00   0.0  0
 V12  CONST_29  HAK   CAK  CAY  NAR     0.00   0.0  0
 V12  CONST_30  HAI   CAI  CAK  CAY   180.00   0.0  0
 V12  CONST_31  HAJ   CAJ  CAX  CAY   180.00   0.0  0
 V12  CONST_32  HAH   CAH  CAI  CAK   180.00   0.0  0
 V12  CONST_33  HAA1  NAA  CAT  NAO     0.00   0.0  0
 V12  CONST_34  HAA2  NAA  CAT  NAO   180.00   0.0  0
 V12  CONST_35  OAB   CAU  NAQ  CAN     0.00   0.0  0
 V12  CONST_36  CAL   CAU  NAQ  CAN   180.00   0.0  0
 V12  CONST_37  HAQ   NAQ  CAU  OAB   180.00   0.0  0
 V12  Var_01    NAR   CA0  CAL  CAU  -106.44  30.0  2
 V12  Var_02    CAU   NAQ  CAN  CB0    85.74  30.0  3
 V12  Var_03    CA0   CAL  CAU  NAQ  -162.18  30.0  3

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
 V12  chir_01  CBC  NBD  OAS  CBA  positiv
 V12  chir_02  CBA  OAE  CBC  CAZ  negativ
 V12  chir_03  CAZ  OAD  CBA  CB0  negativ
 V12  chir_04  CB0  OAS  CAZ  CAN  negativ

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
 V12  plan-1  OAC   0.020
 V12  plan-1  CAV   0.020
 V12  plan-1  NAO   0.020
 V12  plan-1  CAT   0.020
 V12  plan-1  NAA   0.020
 V12  plan-1  CAF   0.020
 V12  plan-1  CAG   0.020
 V12  plan-1  NBD   0.020
 V12  plan-1  CBC   0.020
 V12  plan-1  HAA1  0.020
 V12  plan-1  HAA2  0.020
 V12  plan-1  HAF   0.020
 V12  plan-1  HAG   0.020
 V12  plan-2  CAL   0.020
 V12  plan-2  CA0   0.020
 V12  plan-2  NAR   0.020
 V12  plan-2  CAY   0.020
 V12  plan-2  CAK   0.020
 V12  plan-2  CAI   0.020
 V12  plan-2  CAH   0.020
 V12  plan-2  CAJ   0.020
 V12  plan-2  CAX   0.020
 V12  plan-2  NAP   0.020
 V12  plan-2  HAP   0.020
 V12  plan-2  HAK   0.020
 V12  plan-2  HAI   0.020
 V12  plan-2  HAH   0.020
 V12  plan-2  HAJ   0.020
 V12  plan-3  CAN   0.020
 V12  plan-3  NAQ   0.020
 V12  plan-3  CAU   0.020
 V12  plan-3  OAB   0.020
 V12  plan-3  CAL   0.020
 V12  plan-3  HAQ   0.020

