# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:13:22 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 4-amino-1-(5-{[3-(1H-benzimidazol-2-yl)propanoyl]amino}-5-deoxy-alpha-L-lyxofuranosyl)pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@@H](CNC(=O)CCc3[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
 NVG  NVG  4-amino-1-(5-{[3-(1H-benzimidazol-2-yl)propanoyl]amino}-5-deoxy-alpha-L-lyxofuranosyl)pyrimidin-2(1H)-one  ligand  52  30  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NVG
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
 NVG  OAC   O  O     0  -0.510  -2.8553   0.5267  -1.6381
 NVG  CAV   C  CR6   0   0.601  -3.5890   1.2270  -0.9541
 NVG  NAO   N  N     0  -0.540  -3.8811   2.5023  -1.2788
 NVG  CAT   C  CR6   0   0.514  -4.6902   3.2309  -0.5349
 NVG  NAA   N  NH2   0  -0.808  -4.9384   4.4838  -0.9123
 NVG  CAF   C  CR16  0  -0.477  -5.2941   2.7189   0.6541
 NVG  CAG   C  CR16  0   0.098  -4.9838   1.4499   0.9807
 NVG  NBD   N  NR6   0  -0.559  -4.1594   0.6928   0.2163
 NVG  CBC   C  CR15  0   0.231  -3.8755  -0.6744   0.6296
 NVG  OAS   O  O     0  -0.496  -2.5108  -0.8744   0.8314
 NVG  CBA   C  CR15  0  -0.064  -4.3533  -1.7562  -0.3487
 NVG  OAE   O  OH1   0  -0.659  -5.6737  -2.1081  -0.0382
 NVG  CAZ   C  CR15  0  -0.023  -3.3264  -2.8638  -0.0955
 NVG  OAD   O  OH1   0  -0.674  -3.6346  -3.5724   1.0773
 NVG  CBB   C  CR15  0   0.026  -2.0733  -2.0324   0.1164
 NVG  CAN   C  CH2   0  -0.313  -0.9654  -2.7161   0.8965
 NVG  NAQ   N  NH1   0  -0.637   0.2241  -1.9020   0.9944
 NVG  CAU   C  C     0   0.570   1.1531  -1.8430   0.0264
 NVG  OAB   O  O     0  -0.504   1.0979  -2.5307  -0.9850
 NVG  CAL   C  CH2   0  -0.579   2.2653  -0.8437   0.2618
 NVG  CAM   C  CH2   0  -0.541   3.5993  -1.3490  -0.2642
 NVG  CAW   C  CR5   0   0.478   4.6818  -0.3342  -0.1422
 NVG  NAR   N  NR15  0  -0.705   5.9842  -0.6588  -0.3609
 NVG  CAY   C  CR56  0   0.327   6.7284   0.4792  -0.1992
 NVG  CAK   C  CR16  0  -0.308   8.0893   0.7422  -0.2967
 NVG  CAI   C  CR16  0  -0.281   8.4894   2.0469  -0.0586
 NVG  CAH   C  CR16  0  -0.272   7.5642   3.0500   0.2651
 NVG  CAJ   C  CR16  0  -0.338   6.2101   2.7776   0.3613
 NVG  CAX   C  CR56  0   0.136   5.7873   1.4707   0.1247
 NVG  NAP   N  N     0  -0.484   4.5234   0.9272   0.1524
 NVG  HAA1  H  HNH2  0   0.403  -4.5133   4.8558  -1.7445
 NVG  HAA2  H  HNH2  0   0.414  -5.5628   5.0763  -0.3944
 NVG  HAF   H  HCR6  0   0.289  -5.9545   3.3112   1.2687
 NVG  HAG   H  HCR6  0   0.319  -5.3795   0.9799   1.8703
 NVG  HBC   H  HCR5  0   0.248  -4.4100  -0.8034   1.5778
 NVG  HBA   H  HCR5  0   0.265  -4.2598  -1.4131  -1.3815
 NVG  HBB   H  HCR5  0   0.243  -1.6889  -1.7302  -0.8644
 NVG  HAE   H  HOH1  0   0.468  -6.0807  -2.4966  -0.8186
 NVG  HAZ   H  HCR5  0   0.243  -3.2177  -3.5323  -0.9593
 NVG  HAD   H  HOH1  0   0.449  -4.5824  -3.7519   1.0701
 NVG  HAN1  H  HCH2  0   0.264  -1.2980  -2.9499   1.9065
 NVG  HAN2  H  HCH2  0   0.256  -0.7163  -3.6583   0.4072
 NVG  HAQ   H  HNH1  0   0.403   0.3119  -1.2904   1.7891
 NVG  HAL1  H  HCH2  0   0.280   1.9877   0.0795  -0.2544
 NVG  HAL2  H  HCH2  0   0.262   2.3440  -0.5888   1.3198
 NVG  HAM1  H  HCH2  0   0.272   3.8982  -2.2546   0.2701
 NVG  HAM2  H  HCH2  0   0.278   3.5043  -1.6364  -1.3145
 NVG  HAR   H  HNR5  0   0.417   6.3320  -1.5743  -0.5982
 NVG  HAK   H  HCR6  0   0.264   8.8050  -0.0308  -0.5450
 NVG  HAI   H  HCR6  0   0.253   9.5404   2.2971  -0.1233
 NVG  HAH   H  HCR6  0   0.250   7.9194   4.0565   0.4445
 NVG  HAJ   H  HCR6  0   0.252   5.4982   3.5540   0.6117

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
 NVG  OAC  CAV   double    1.223  0.020  1.223
 NVG  CAV  NAO   single    1.348  0.020  1.348
 NVG  CAV  NBD   single    1.407  0.020  1.407
 NVG  NAO  CAT   double    1.319  0.020  1.319
 NVG  CAT  NAA   single    1.332  0.020  1.332
 NVG  CAT  CAF   single    1.429  0.020  1.429
 NVG  NAA  HAA1  single    0.860  0.020  1.020
 NVG  NAA  HAA2  single    0.860  0.020  1.020
 NVG  CAF  CAG   double    1.347  0.020  1.347
 NVG  CAF  HAF   single    0.930  0.020  1.080
 NVG  CAG  NBD   single    1.355  0.020  1.355
 NVG  CAG  HAG   single    0.930  0.020  1.080
 NVG  NBD  CBC   single    1.456  0.020  1.456
 NVG  CBC  OAS   single    1.394  0.020  1.394
 NVG  CBC  CBA   single    1.535  0.020  1.535
 NVG  CBC  HBC   single    0.970  0.020  1.090
 NVG  OAS  CBB   single    1.430  0.020  1.430
 NVG  CBA  OAE   single    1.401  0.020  1.401
 NVG  CBA  CAZ   single    1.531  0.020  1.531
 NVG  CBA  HBA   single    0.970  0.020  1.090
 NVG  OAE  HAE   single    0.850  0.020  0.980
 NVG  CAZ  OAD   single    1.404  0.020  1.404
 NVG  CAZ  CBB   single    1.519  0.020  1.519
 NVG  CAZ  HAZ   single    0.970  0.020  1.090
 NVG  OAD  HAD   single    0.850  0.020  0.980
 NVG  CBB  CAN   single    1.518  0.020  1.518
 NVG  CBB  HBB   single    0.970  0.020  1.090
 NVG  CAN  NAQ   single    1.445  0.020  1.445
 NVG  CAN  HAN1  single    0.970  0.020  1.090
 NVG  CAN  HAN2  single    0.970  0.020  1.090
 NVG  NAQ  CAU   single    1.343  0.020  1.343
 NVG  NAQ  HAQ   single    0.860  0.020  1.020
 NVG  CAU  OAB   double    1.224  0.020  1.224
 NVG  CAU  CAL   single    1.514  0.020  1.514
 NVG  CAL  CAM   single    1.520  0.020  1.520
 NVG  CAL  HAL1  single    0.970  0.020  1.090
 NVG  CAL  HAL2  single    0.970  0.020  1.090
 NVG  CAM  CAW   single    1.489  0.020  1.489
 NVG  CAM  HAM1  single    0.970  0.020  1.090
 NVG  CAM  HAM2  single    0.970  0.020  1.090
 NVG  CAW  NAR   aromatic  1.360  0.020  1.360
 NVG  CAW  NAP   aromatic  1.305  0.020  1.305
 NVG  NAR  CAY   aromatic  1.369  0.020  1.369
 NVG  NAR  HAR   single    0.860  0.020  1.020
 NVG  CAY  CAK   aromatic  1.389  0.020  1.389
 NVG  CAY  CAX   aromatic  1.405  0.020  1.405
 NVG  CAK  CAI   aromatic  1.385  0.020  1.385
 NVG  CAK  HAK   single    0.930  0.020  1.080
 NVG  CAI  CAH   aromatic  1.403  0.020  1.403
 NVG  CAI  HAI   single    0.930  0.020  1.080
 NVG  CAH  CAJ   aromatic  1.385  0.020  1.385
 NVG  CAH  HAH   single    0.930  0.020  1.080
 NVG  CAJ  CAX   aromatic  1.394  0.020  1.394
 NVG  CAJ  HAJ   single    0.930  0.020  1.080
 NVG  CAX  NAP   aromatic  1.376  0.020  1.376

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
 NVG  NBD   CAV  NAO   118.14  3.000
 NVG  NBD   CAV  OAC   119.39  3.000
 NVG  NAO   CAV  OAC   122.47  3.000
 NVG  CAT   NAO  CAV   121.32  3.000
 NVG  CAF   CAT  NAA   119.62  3.000
 NVG  CAF   CAT  NAO   122.07  3.000
 NVG  NAA   CAT  NAO   118.31  3.000
 NVG  HAA2  NAA  HAA1  118.11  3.000
 NVG  HAA2  NAA  CAT   121.64  3.000
 NVG  HAA1  NAA  CAT   120.23  3.000
 NVG  HAF   CAF  CAG   121.34  3.000
 NVG  HAF   CAF  CAT   122.41  3.000
 NVG  CAG   CAF  CAT   116.25  3.000
 NVG  HAG   CAG  NBD   116.35  3.000
 NVG  HAG   CAG  CAF   121.66  3.000
 NVG  NBD   CAG  CAF   121.99  3.000
 NVG  CBC   NBD  CAG   118.87  3.000
 NVG  CBC   NBD  CAV   120.89  3.000
 NVG  CAG   NBD  CAV   120.24  3.000
 NVG  HBC   CBC  CBA   108.46  3.000
 NVG  HBC   CBC  OAS   109.59  3.000
 NVG  CBA   CBC  OAS   107.21  3.000
 NVG  HBC   CBC  NBD   105.13  3.000
 NVG  CBA   CBC  NBD   114.84  3.000
 NVG  OAS   CBC  NBD   111.51  3.000
 NVG  CBB   OAS  CBC   110.09  3.000
 NVG  HBA   CBA  CAZ   109.03  3.000
 NVG  HBA   CBA  OAE   111.66  3.000
 NVG  CAZ   CBA  OAE   114.42  3.000
 NVG  HBA   CBA  CBC   110.78  3.000
 NVG  CAZ   CBA  CBC   101.28  3.000
 NVG  OAE   CBA  CBC   109.21  3.000
 NVG  HAE   OAE  CBA   108.68  3.000
 NVG  HAZ   CAZ  CBB   111.19  3.000
 NVG  HAZ   CAZ  OAD   111.82  3.000
 NVG  CBB   CAZ  OAD   109.92  3.000
 NVG  HAZ   CAZ  CBA   112.13  3.000
 NVG  CBB   CAZ  CBA   100.39  3.000
 NVG  OAD   CAZ  CBA   110.84  3.000
 NVG  HAD   OAD  CAZ   107.65  3.000
 NVG  HBB   CBB  CAN   109.16  3.000
 NVG  HBB   CBB  CAZ   108.39  3.000
 NVG  CAN   CBB  CAZ   115.31  3.000
 NVG  HBB   CBB  OAS   109.36  3.000
 NVG  CAN   CBB  OAS   109.34  3.000
 NVG  CAZ   CBB  OAS   105.11  3.000
 NVG  HAN2  CAN  HAN1  107.48  3.000
 NVG  HAN2  CAN  NAQ   109.22  3.000
 NVG  HAN1  CAN  NAQ   108.04  3.000
 NVG  HAN2  CAN  CBB   108.99  3.000
 NVG  HAN1  CAN  CBB   110.52  3.000
 NVG  NAQ   CAN  CBB   112.46  3.000
 NVG  HAQ   NAQ  CAU   118.82  3.000
 NVG  HAQ   NAQ  CAN   117.89  3.000
 NVG  CAU   NAQ  CAN   123.05  3.000
 NVG  CAL   CAU  OAB   122.17  3.000
 NVG  CAL   CAU  NAQ   115.16  3.000
 NVG  OAB   CAU  NAQ   122.66  3.000
 NVG  HAL2  CAL  HAL1  106.19  3.000
 NVG  HAL2  CAL  CAM   110.48  3.000
 NVG  HAL1  CAL  CAM   109.88  3.000
 NVG  HAL2  CAL  CAU   110.98  3.000
 NVG  HAL1  CAL  CAU   107.30  3.000
 NVG  CAM   CAL  CAU   111.81  3.000
 NVG  HAM2  CAM  HAM1  106.00  3.000
 NVG  HAM2  CAM  CAW   108.73  3.000
 NVG  HAM1  CAM  CAW   109.01  3.000
 NVG  HAM2  CAM  CAL   110.09  3.000
 NVG  HAM1  CAM  CAL   110.25  3.000
 NVG  CAW   CAM  CAL   112.52  3.000
 NVG  NAP   CAW  NAR   112.54  3.000
 NVG  NAP   CAW  CAM   126.09  3.000
 NVG  NAR   CAW  CAM   121.36  3.000
 NVG  HAR   NAR  CAY   126.53  3.000
 NVG  HAR   NAR  CAW   125.82  3.000
 NVG  CAY   NAR  CAW   107.65  3.000
 NVG  CAX   CAY  CAK   122.60  3.000
 NVG  CAX   CAY  NAR   104.46  3.000
 NVG  CAK   CAY  NAR   132.94  3.000
 NVG  HAK   CAK  CAI   121.41  3.000
 NVG  HAK   CAK  CAY   121.91  3.000
 NVG  CAI   CAK  CAY   116.68  3.000
 NVG  HAI   CAI  CAH   119.28  3.000
 NVG  HAI   CAI  CAK   119.20  3.000
 NVG  CAH   CAI  CAK   121.52  3.000
 NVG  HAH   CAH  CAJ   119.50  3.000
 NVG  HAH   CAH  CAI   119.14  3.000
 NVG  CAJ   CAH  CAI   121.36  3.000
 NVG  HAJ   CAJ  CAX   120.81  3.000
 NVG  HAJ   CAJ  CAH   121.20  3.000
 NVG  CAX   CAJ  CAH   117.99  3.000
 NVG  NAP   CAX  CAJ   130.21  3.000
 NVG  NAP   CAX  CAY   109.95  3.000
 NVG  CAJ   CAX  CAY   119.84  3.000
 NVG  CAX   NAP  CAW   105.41  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
 NVG  CONST_01  CAK   CAY  NAR  CAW  180.00   0.0  0
 NVG  CONST_02  CAX   CAY  NAR  CAW    0.00   0.0  0
 NVG  CONST_03  CAY   CAX  NAP  CAW    0.00   0.0  0
 NVG  CONST_04  CAJ   CAX  NAP  CAW  180.00   0.0  0
 NVG  CONST_05  CAX   NAP  CAW  NAR    0.00   0.0  0
 NVG  CONST_06  CAI   CAK  CAY  NAR  180.00   0.0  0
 NVG  CONST_07  CAJ   CAX  CAY  NAR  180.00   0.0  0
 NVG  CONST_08  NAP   CAX  CAY  NAR    0.00   0.0  0
 NVG  CONST_09  NAP   CAW  NAR  CAY    0.00   0.0  0
 NVG  CONST_10  CAH   CAI  CAK  CAY    0.00   0.0  0
 NVG  CONST_11  CAH   CAJ  CAX  CAY    0.00   0.0  0
 NVG  CONST_12  CAJ   CAX  CAY  CAK    0.00   0.0  0
 NVG  CONST_13  NAP   CAX  CAY  CAK  180.00   0.0  0
 NVG  CONST_14  CAJ   CAH  CAI  CAK    0.00   0.0  0
 NVG  CONST_15  CAX   CAY  CAK  CAI    0.00   0.0  0
 NVG  CONST_16  CAX   CAJ  CAH  CAI    0.00   0.0  0
 NVG  CONST_17  NAP   CAX  CAJ  CAH  180.00   0.0  0
 NVG  CONST_18  CAF   CAT  NAO  CAV    0.00   0.0  0
 NVG  CONST_19  CAG   NBD  CAV  NAO    0.00   0.0  0
 NVG  CONST_20  CBC   NBD  CAV  NAO  180.00   0.0  0
 NVG  CONST_21  NBD   CAV  NAO  CAT    0.00   0.0  0
 NVG  CONST_22  CAY   NAR  CAW  CAM  180.00   0.0  0
 NVG  CONST_23  CAX   NAP  CAW  CAM  180.00   0.0  0
 NVG  CONST_24  CAT   NAO  CAV  OAC  180.00   0.0  0
 NVG  CONST_25  CAG   NBD  CAV  OAC  180.00   0.0  0
 NVG  CONST_26  CBC   NBD  CAV  OAC    0.00   0.0  0
 NVG  CONST_27  NAA   CAT  NAO  CAV  180.00   0.0  0
 NVG  CONST_28  HAK   CAK  CAY  NAR    0.00   0.0  0
 NVG  CONST_29  HAI   CAI  CAK  CAY  180.00   0.0  0
 NVG  CONST_30  HAJ   CAJ  CAX  CAY  180.00   0.0  0
 NVG  CONST_31  HAR   NAR  CAY  CAK    0.00   0.0  0
 NVG  CONST_32  HAH   CAH  CAI  CAK  180.00   0.0  0
 NVG  CONST_33  HAA1  NAA  CAT  NAO    0.00   0.0  0
 NVG  CONST_34  HAA2  NAA  CAT  NAO  180.00   0.0  0
 NVG  CONST_35  OAB   CAU  NAQ  CAN    0.00   0.0  0
 NVG  CONST_36  CAL   CAU  NAQ  CAN  180.00   0.0  0
 NVG  CONST_37  HAQ   NAQ  CAU  OAB  180.00   0.0  0
 NVG  Var_01    NAR   CAW  CAM  CAL  169.63  30.0  2
 NVG  Var_02    CAU   NAQ  CAN  CBB  -83.05  30.0  3
 NVG  Var_03    CAW   CAM  CAL  CAU  175.30  30.0  3
 NVG  Var_04    CAM   CAL  CAU  NAQ  144.46  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
 NVG  chir_01  CBC  NBD  OAS  CBA  positiv
 NVG  chir_02  CBA  OAE  CBC  CAZ  negativ
 NVG  chir_03  CAZ  OAD  CBA  CBB  negativ
 NVG  chir_04  CBB  OAS  CAZ  CAN  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
 NVG  plan-1  OAC   0.020
 NVG  plan-1  CAV   0.020
 NVG  plan-1  NAO   0.020
 NVG  plan-1  CAT   0.020
 NVG  plan-1  NAA   0.020
 NVG  plan-1  CAF   0.020
 NVG  plan-1  CAG   0.020
 NVG  plan-1  NBD   0.020
 NVG  plan-1  CBC   0.020
 NVG  plan-1  HAA1  0.020
 NVG  plan-1  HAA2  0.020
 NVG  plan-1  HAF   0.020
 NVG  plan-1  HAG   0.020
 NVG  plan-2  CAM   0.020
 NVG  plan-2  CAW   0.020
 NVG  plan-2  NAR   0.020
 NVG  plan-2  CAY   0.020
 NVG  plan-2  CAK   0.020
 NVG  plan-2  CAI   0.020
 NVG  plan-2  CAH   0.020
 NVG  plan-2  CAJ   0.020
 NVG  plan-2  CAX   0.020
 NVG  plan-2  NAP   0.020
 NVG  plan-2  HAR   0.020
 NVG  plan-2  HAK   0.020
 NVG  plan-2  HAI   0.020
 NVG  plan-2  HAH   0.020
 NVG  plan-2  HAJ   0.020
 NVG  plan-3  CAN   0.020
 NVG  plan-3  NAQ   0.020
 NVG  plan-3  CAU   0.020
 NVG  plan-3  OAB   0.020
 NVG  plan-3  CAL   0.020
 NVG  plan-3  HAQ   0.020

