# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:14:51 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)[n+]2cc(CCc3ccccc3)[nH]c12
#
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
 VGB  VGB  (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  52  26  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VGB
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
 VGB  CBA   C  CH3   0  -0.661  -1.3546   5.2540   0.3994
 VGB  CAN   C  CH2   0  -0.572  -2.4416   4.1929   0.4154
 VGB  CAL   C  C     0   0.581  -2.0054   2.8865  -0.1996
 VGB  OAM   O  O     0  -0.505  -1.1205   2.8054  -1.0430
 VGB  NAK   N  NH1   0  -0.642  -2.6703   1.7958   0.2303
 VGB  CAC   C  CH1   0  -0.199  -2.5372   0.4980  -0.3862
 VGB  CAB   C  CH1   0   0.032  -3.7343  -0.3754  -0.0302
 VGB  OAG   O  OH1   0  -0.654  -4.8321   0.1434  -0.7163
 VGB  CAA   C  CH1   0  -0.026  -3.4604  -1.8324  -0.4056
 VGB  OAH   O  OH1   0  -0.660  -4.6324  -2.5596  -0.1480
 VGB  CAF   C  CH1   0  -0.119  -2.3200  -2.4075   0.4456
 VGB  CAI   C  CH2   0  -0.161  -1.9212  -3.7922  -0.0356
 VGB  OAJ   O  OH1   0  -0.661  -1.1393  -4.4177   0.9520
 VGB  NAE   N  NR5   1  -0.484  -1.1856  -1.4748   0.3995
 VGB  CAQ   C  CR15  0  -0.140   0.1304  -1.7469   0.7138
 VGB  CAD   C  CR5   0   0.684  -1.2833  -0.2031   0.0334
 VGB  NAO   N  NR15  0  -0.660  -0.0706   0.3274   0.0922
 VGB  CAP   C  CR5   0   0.316   0.8383  -0.6080   0.5195
 VGB  CAR   C  CH2   0  -0.522   2.2874  -0.3232   0.6736
 VGB  CAS   C  CH2   0  -0.518   2.9897  -0.0748  -0.6699
 VGB  CAT   C  CR6   0   0.125   4.4532   0.2039  -0.4715
 VGB  CAU   C  CR16  0  -0.307   5.3803  -0.8357  -0.4629
 VGB  CAV   C  CR16  0  -0.240   6.7275  -0.5843  -0.2387
 VGB  CAW   C  CR16  0  -0.270   7.1671   0.7146  -0.0179
 VGB  CAX   C  CR16  0  -0.240   6.2509   1.7586  -0.0229
 VGB  CAY   C  CR16  0  -0.306   4.9049   1.5027  -0.2474
 VGB  HBA   H  HCH3  0   0.233  -1.0388   5.4901  -0.6151
 VGB  HBAA  H  HCH3  0   0.240  -1.7236   6.1719   0.8545
 VGB  HBAB  H  HCH3  0   0.232  -0.4767   4.9349   0.9612
 VGB  HAN   H  HCH2  0   0.263  -2.7984   4.0218   1.4333
 VGB  HANA  H  HCH2  0   0.283  -3.3135   4.5354  -0.1507
 VGB  HNAK  H  HNH1  0   0.420  -3.3428   1.8935   0.9756
 VGB  HAC   H  HCH1  0   0.328  -2.5019   0.6121  -1.4761
 VGB  HAB   H  HCH1  0   0.248  -3.8842  -0.3338   1.0617
 VGB  HOAG  H  HOH1  0   0.461  -5.6033  -0.3911  -0.4951
 VGB  HAA   H  HCH1  0   0.268  -3.1824  -1.8841  -1.4672
 VGB  HOAH  H  HOH1  0   0.473  -4.8511  -3.0985  -0.9128
 VGB  HAF   H  HCH1  0   0.307  -2.6560  -2.4674   1.4852
 VGB  HAI   H  HCH2  0   0.236  -2.8422  -4.3545  -0.2205
 VGB  HAIA  H  HCH2  0   0.228  -1.3939  -3.7036  -0.9931
 VGB  HOAJ  H  HOH1  0   0.467  -0.7792  -5.2302   0.5842
 VGB  HAQ   H  HCR5  0   0.333   0.4560  -2.7151   1.0481
 VGB  HNAO  H  HNR5  0   0.447   0.1270   1.2817  -0.1887
 VGB  HAR   H  HCH2  0   0.280   2.4220   0.5431   1.3264
 VGB  HARA  H  HCH2  0   0.281   2.7475  -1.1733   1.1789
 VGB  HAS   H  HCH2  0   0.265   2.8554  -0.9489  -1.3101
 VGB  HASA  H  HCH2  0   0.256   2.5210   0.7684  -1.1836
 VGB  HAU   H  HCR6  0   0.249   5.0465  -1.8516  -0.6396
 VGB  HAV   H  HCR6  0   0.255   7.4353  -1.4031  -0.2394
 VGB  HAW   H  HCR6  0   0.255   8.2173   0.9124   0.1531
 VGB  HAX   H  HCR6  0   0.255   6.5847   2.7745   0.1454
 VGB  HAY   H  HCR6  0   0.249   4.1963   2.3229  -0.2532

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
 VGB  CBA  CAN   single    1.519  0.020  1.519
 VGB  CAN  CAL   single    1.508  0.020  1.508
 VGB  CAL  OAM   double    1.225  0.020  1.225
 VGB  CAL  NAK   single    1.348  0.020  1.348
 VGB  NAK  CAC   single    1.443  0.020  1.443
 VGB  CAC  CAB   single    1.524  0.020  1.524
 VGB  CAC  CAD   single    1.497  0.020  1.497
 VGB  CAB  OAG   single    1.395  0.020  1.395
 VGB  CAB  CAA   single    1.529  0.020  1.529
 VGB  CAA  OAH   single    1.403  0.020  1.403
 VGB  CAA  CAF   single    1.535  0.020  1.535
 VGB  CAF  CAI   single    1.519  0.020  1.519
 VGB  CAF  NAE   single    1.469  0.020  1.469
 VGB  CAI  OAJ   single    1.406  0.020  1.406
 VGB  NAE  CAQ   aromatic  1.380  0.020  1.380
 VGB  NAE  CAD   aromatic  1.327  0.020  1.327
 VGB  CAQ  CAP   aromatic  1.355  0.020  1.355
 VGB  CAD  NAO   aromatic  1.325  0.020  1.325
 VGB  NAO  CAP   aromatic  1.372  0.020  1.372
 VGB  CAP  CAR   single    1.485  0.020  1.485
 VGB  CAR  CAS   single    1.536  0.020  1.536
 VGB  CAS  CAT   single    1.503  0.020  1.503
 VGB  CAT  CAU   aromatic  1.393  0.020  1.393
 VGB  CAT  CAY   aromatic  1.393  0.020  1.393
 VGB  CAU  CAV   aromatic  1.389  0.020  1.389
 VGB  CAV  CAW   aromatic  1.389  0.020  1.389
 VGB  CAW  CAX   aromatic  1.389  0.020  1.389
 VGB  CAX  CAY   aromatic  1.388  0.020  1.388
 VGB  CBA  HBA   single    0.970  0.020  1.090
 VGB  CBA  HBAA  single    0.970  0.020  1.090
 VGB  CBA  HBAB  single    0.970  0.020  1.090
 VGB  CAN  HAN   single    0.970  0.020  1.090
 VGB  CAN  HANA  single    0.970  0.020  1.090
 VGB  NAK  HNAK  single    0.860  0.020  1.020
 VGB  CAC  HAC   single    0.970  0.020  1.090
 VGB  CAB  HAB   single    0.970  0.020  1.090
 VGB  OAG  HOAG  single    0.850  0.020  0.980
 VGB  CAA  HAA   single    0.970  0.020  1.090
 VGB  OAH  HOAH  single    0.850  0.020  0.980
 VGB  CAF  HAF   single    0.970  0.020  1.090
 VGB  CAI  HAI   single    0.970  0.020  1.090
 VGB  CAI  HAIA  single    0.970  0.020  1.090
 VGB  OAJ  HOAJ  single    0.850  0.020  0.980
 VGB  CAQ  HAQ   single    0.930  0.020  1.080
 VGB  NAO  HNAO  single    0.860  0.020  1.020
 VGB  CAR  HAR   single    0.970  0.020  1.090
 VGB  CAR  HARA  single    0.970  0.020  1.090
 VGB  CAS  HAS   single    0.970  0.020  1.090
 VGB  CAS  HASA  single    0.970  0.020  1.090
 VGB  CAU  HAU   single    0.930  0.020  1.080
 VGB  CAV  HAV   single    0.930  0.020  1.080
 VGB  CAW  HAW   single    0.930  0.020  1.080
 VGB  CAX  HAX   single    0.930  0.020  1.080
 VGB  CAY  HAY   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
 VGB  HBAB  CBA  HBAA  107.72  3.000
 VGB  HBAB  CBA  HBA   108.08  3.000
 VGB  HBAA  CBA  HBA   107.76  3.000
 VGB  HBAB  CBA  CAN   111.49  3.000
 VGB  HBAA  CBA  CAN   109.99  3.000
 VGB  HBA   CBA  CAN   111.65  3.000
 VGB  HANA  CAN  HAN   105.72  3.000
 VGB  HANA  CAN  CAL   106.88  3.000
 VGB  HAN   CAN  CAL   109.80  3.000
 VGB  HANA  CAN  CBA   110.25  3.000
 VGB  HAN   CAN  CBA   110.68  3.000
 VGB  CAL   CAN  CBA   113.19  3.000
 VGB  NAK   CAL  OAM   121.49  3.000
 VGB  NAK   CAL  CAN   115.35  3.000
 VGB  OAM   CAL  CAN   123.16  3.000
 VGB  HNAK  NAK  CAC   117.67  3.000
 VGB  HNAK  NAK  CAL   119.09  3.000
 VGB  CAC   NAK  CAL   123.10  3.000
 VGB  HAC   CAC  CAD   107.49  3.000
 VGB  HAC   CAC  CAB   108.49  3.000
 VGB  CAD   CAC  CAB   108.92  3.000
 VGB  HAC   CAC  NAK   109.51  3.000
 VGB  CAD   CAC  NAK   112.26  3.000
 VGB  CAB   CAC  NAK   110.07  3.000
 VGB  HAB   CAB  CAA   107.65  3.000
 VGB  HAB   CAB  OAG   111.47  3.000
 VGB  CAA   CAB  OAG   112.00  3.000
 VGB  HAB   CAB  CAC   108.45  3.000
 VGB  CAA   CAB  CAC   110.36  3.000
 VGB  OAG   CAB  CAC   106.87  3.000
 VGB  HOAG  OAG  CAB   108.09  3.000
 VGB  HAA   CAA  CAF   109.28  3.000
 VGB  HAA   CAA  OAH   111.37  3.000
 VGB  CAF   CAA  OAH   108.94  3.000
 VGB  HAA   CAA  CAB   109.11  3.000
 VGB  CAF   CAA  CAB   110.73  3.000
 VGB  OAH   CAA  CAB   107.40  3.000
 VGB  HOAH  OAH  CAA   109.55  3.000
 VGB  HAF   CAF  NAE   107.55  3.000
 VGB  HAF   CAF  CAI   109.37  3.000
 VGB  NAE   CAF  CAI   111.47  3.000
 VGB  HAF   CAF  CAA   108.62  3.000
 VGB  NAE   CAF  CAA   108.56  3.000
 VGB  CAI   CAF  CAA   111.16  3.000
 VGB  HAIA  CAI  HAI   107.37  3.000
 VGB  HAIA  CAI  OAJ   112.44  3.000
 VGB  HAI   CAI  OAJ   110.97  3.000
 VGB  HAIA  CAI  CAF   109.21  3.000
 VGB  HAI   CAI  CAF   107.51  3.000
 VGB  OAJ   CAI  CAF   109.20  3.000
 VGB  HOAJ  OAJ  CAI   108.38  3.000
 VGB  CAD   NAE  CAQ   108.78  3.000
 VGB  CAD   NAE  CAF   124.07  3.000
 VGB  CAQ   NAE  CAF   127.15  3.000
 VGB  HAQ   CAQ  CAP   130.05  3.000
 VGB  HAQ   CAQ  NAE   122.51  3.000
 VGB  CAP   CAQ  NAE   107.44  3.000
 VGB  NAO   CAD  NAE   107.70  3.000
 VGB  NAO   CAD  CAC   126.28  3.000
 VGB  NAE   CAD  CAC   126.01  3.000
 VGB  HNAO  NAO  CAP   126.76  3.000
 VGB  HNAO  NAO  CAD   122.87  3.000
 VGB  CAP   NAO  CAD   110.31  3.000
 VGB  CAR   CAP  NAO   123.22  3.000
 VGB  CAR   CAP  CAQ   131.01  3.000
 VGB  NAO   CAP  CAQ   105.75  3.000
 VGB  HARA  CAR  HAR   106.80  3.000
 VGB  HARA  CAR  CAS   109.78  3.000
 VGB  HAR   CAR  CAS   109.74  3.000
 VGB  HARA  CAR  CAP   108.08  3.000
 VGB  HAR   CAR  CAP   109.53  3.000
 VGB  CAS   CAR  CAP   112.73  3.000
 VGB  HASA  CAS  HAS   106.82  3.000
 VGB  HASA  CAS  CAT   109.67  3.000
 VGB  HAS   CAS  CAT   110.22  3.000
 VGB  HASA  CAS  CAR   109.86  3.000
 VGB  HAS   CAS  CAR   109.09  3.000
 VGB  CAT   CAS  CAR   111.08  3.000
 VGB  CAY   CAT  CAU   118.61  3.000
 VGB  CAY   CAT  CAS   120.65  3.000
 VGB  CAU   CAT  CAS   120.70  3.000
 VGB  HAU   CAU  CAV   119.66  3.000
 VGB  HAU   CAU  CAT   119.57  3.000
 VGB  CAV   CAU  CAT   120.77  3.000
 VGB  HAV   CAV  CAW   120.04  3.000
 VGB  HAV   CAV  CAU   119.82  3.000
 VGB  CAW   CAV  CAU   120.13  3.000
 VGB  HAW   CAW  CAX   120.21  3.000
 VGB  HAW   CAW  CAV   120.21  3.000
 VGB  CAX   CAW  CAV   119.58  3.000
 VGB  HAX   CAX  CAY   119.80  3.000
 VGB  HAX   CAX  CAW   120.10  3.000
 VGB  CAY   CAX  CAW   120.10  3.000
 VGB  HAY   CAY  CAX   119.68  3.000
 VGB  HAY   CAY  CAT   119.51  3.000
 VGB  CAX   CAY  CAT   120.81  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
 VGB  CONST_01  NAO   CAP  CAQ  NAE     0.00   0.0  0
 VGB  CONST_02  CAP   NAO  CAD  NAE     0.00   0.0  0
 VGB  CONST_03  NAO   CAD  NAE  CAQ     0.00   0.0  0
 VGB  CONST_04  CAD   NAO  CAP  CAQ     0.00   0.0  0
 VGB  CONST_05  CAP   CAQ  NAE  CAD     0.00   0.0  0
 VGB  CONST_06  CAW   CAV  CAU  CAT     0.00   0.0  0
 VGB  CONST_07  CAW   CAX  CAY  CAT     0.00   0.0  0
 VGB  CONST_08  CAX   CAY  CAT  CAU     0.00   0.0  0
 VGB  CONST_09  CAX   CAW  CAV  CAU     0.00   0.0  0
 VGB  CONST_10  CAY   CAT  CAU  CAV     0.00   0.0  0
 VGB  CONST_11  CAY   CAX  CAW  CAV     0.00   0.0  0
 VGB  CONST_12  CAR   CAP  CAQ  NAE   180.00   0.0  0
 VGB  CONST_13  CAR   CAP  NAO  CAD   180.00   0.0  0
 VGB  CONST_14  CAV   CAU  CAT  CAS   180.00   0.0  0
 VGB  CONST_15  CAX   CAY  CAT  CAS   180.00   0.0  0
 VGB  CONST_16  HNAO  NAO  CAD  CAC     0.00   0.0  0
 VGB  CONST_17  HAQ   CAQ  NAE  CAF     0.00   0.0  0
 VGB  CONST_18  HAV   CAV  CAU  CAT   180.00   0.0  0
 VGB  CONST_19  HAX   CAX  CAY  CAT   180.00   0.0  0
 VGB  CONST_20  HAY   CAY  CAT  CAU   180.00   0.0  0
 VGB  CONST_21  HAW   CAW  CAV  CAU   180.00   0.0  0
 VGB  CONST_22  HAU   CAU  CAV  CAW   180.00   0.0  0
 VGB  CONST_23  CAC   NAK  CAL  CAN   180.00   0.0  0
 VGB  CONST_24  CAC   NAK  CAL  OAM     0.00   0.0  0
 VGB  CONST_25  HNAK  NAK  CAL  CAN     0.00   0.0  0
 VGB  Var_01    CAS   CAR  CAP  CAQ   110.76  30.0  2
 VGB  Var_02    CAT   CAS  CAR  CAP  -179.78  30.0  3
 VGB  Var_03    CAU   CAT  CAS  CAR    89.61  30.0  2
 VGB  Var_04    OAM   CAL  CAN  CBA   -25.74  30.0  3
 VGB  Var_05    HBA   CBA  CAN  CAL    60.45  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
 VGB  chir_01  CAC  NAK  CAB  CAD  positiv
 VGB  chir_02  CAB  OAG  CAC  CAA  positiv
 VGB  chir_03  CAA  OAH  CAB  CAF  negativ
 VGB  chir_04  CAF  NAE  CAA  CAI  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
 VGB  plan-1  CAS   0.020
 VGB  plan-1  CAT   0.020
 VGB  plan-1  CAU   0.020
 VGB  plan-1  CAV   0.020
 VGB  plan-1  CAW   0.020
 VGB  plan-1  CAX   0.020
 VGB  plan-1  CAY   0.020
 VGB  plan-1  HAU   0.020
 VGB  plan-1  HAV   0.020
 VGB  plan-1  HAW   0.020
 VGB  plan-1  HAX   0.020
 VGB  plan-1  HAY   0.020
 VGB  plan-2  CAC   0.020
 VGB  plan-2  CAF   0.020
 VGB  plan-2  NAE   0.020
 VGB  plan-2  CAQ   0.020
 VGB  plan-2  CAD   0.020
 VGB  plan-2  NAO   0.020
 VGB  plan-2  CAP   0.020
 VGB  plan-2  CAR   0.020
 VGB  plan-2  HAQ   0.020
 VGB  plan-2  HNAO  0.020
 VGB  plan-3  CAN   0.020
 VGB  plan-3  CAL   0.020
 VGB  plan-3  OAM   0.020
 VGB  plan-3  NAK   0.020
 VGB  plan-3  CAC   0.020
 VGB  plan-3  HNAK  0.020

