# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 18:09:29 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-[3-amino-6-(3-methoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cnc(N)c(n2)N3CCC(CC3)C(O)=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
 WI2  WI2  '1-[3-amino-6-(3-methoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid'  ligand  44  24  .  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_WI2
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
 WI2  CAL   C  CH2   0  -0.292  -1.9624  -0.7492   0.7135
 WI2  CAJ   C  CH2   0  -0.424  -3.3854  -0.9232   1.2216
 WI2  CAW   C  CH1   0  -0.394  -4.3798  -0.9426   0.0698
 WI2  CAQ   C  C     0   0.566  -5.8037  -1.0711   0.5494
 WI2  OAD   O  O     0  -0.439  -6.1558  -1.0302   1.7023
 WI2  OAC   O  OH1   0  -0.596  -6.6545  -1.2310  -0.4594
 WI2  CAK   C  CH2   0  -0.431  -4.2006   0.3077  -0.8012
 WI2  CAM   C  CH2   0  -0.327  -2.7514   0.4422  -1.2341
 WI2  NAX   N  NT    0  -0.510  -1.8633   0.4691  -0.0731
 WI2  CAV   C  CR6   0   0.380  -0.5808   0.9545  -0.3020
 WI2  NAO   N  N     0  -0.415   0.4574   0.1769  -0.1555
 WI2  CAR   C  CR6   0   0.384  -0.4017   2.3375  -0.6209
 WI2  NAB   N  NH2   0  -0.825  -1.4661   3.1834  -0.6787
 WI2  NAN   N  N     0  -0.408   0.8029   2.8035  -0.8772
 WI2  CAH   C  CR16  0  -0.142   1.8415   1.9746  -0.7640
 WI2  CAU   C  CR6   0   0.177   1.6932   0.6647  -0.3537
 WI2  CAT   C  CR6   0   0.083   2.8278  -0.2531  -0.1451
 WI2  CAI   C  CR16  0  -0.435   4.1023   0.2341   0.1247
 WI2  CAG   C  CR16  0  -0.321   2.6297  -1.6362  -0.2085
 WI2  CAE   C  CR16  0  -0.225   3.6981  -2.4923  -0.0184
 WI2  CAF   C  CR16  0  -0.395   4.9767  -2.0105   0.2427
 WI2  CAS   C  CR6   0   0.414   5.1771  -0.6347   0.3160
 WI2  OAP   O  O2    0  -0.474   6.3636  -0.0526   0.5782
 WI2  CAA   C  CH3   0  -0.436   7.4819  -0.8812   0.8248
 WI2  HAL1  H  HCH2  0   0.252  -1.2797  -0.6806   1.5602
 WI2  HAL2  H  HCH2  0   0.213  -1.6563  -1.6309   0.1329
 WI2  HAJ1  H  HCH2  0   0.247  -3.4420  -1.8501   1.7958
 WI2  HAJ2  H  HCH2  0   0.231  -3.6179  -0.1042   1.9065
 WI2  HAW   H  HCH1  0   0.275  -4.1754  -1.8151  -0.5640
 WI2  HAK1  H  HCH2  0   0.256  -4.8278   0.2566  -1.6921
 WI2  HAK2  H  HCH2  0   0.237  -4.5008   1.1992  -0.2425
 WI2  HAC   H  HOH1  0   0.480  -7.5610  -1.2896  -0.1223
 WI2  HAM1  H  HCH2  0   0.232  -2.4886  -0.3977  -1.8940
 WI2  HAM2  H  HCH2  0   0.268  -2.6300   1.3523  -1.8214
 WI2  HAB1  H  HNH2  0   0.391  -2.2633   2.9330  -0.1142
 WI2  HAB2  H  HNH2  0   0.390  -1.2411   4.1658  -0.6555
 WI2  HAH   H  HCR6  0   0.259   2.8131   2.3895  -1.0037
 WI2  HAI   H  HCR6  0   0.253   4.2810   1.2986   0.2157
 WI2  HAG   H  HCR6  0   0.249   1.6437  -2.0299  -0.4132
 WI2  HAE   H  HCR6  0   0.258   3.5437  -3.5623  -0.0739
 WI2  HAF   H  HCR6  0   0.279   5.7868  -2.7119   0.3870
 WI2  HAA1  H  HCH3  0   0.228   7.7355  -1.4959  -0.0430
 WI2  HAA2  H  HCH3  0   0.259   8.3169  -0.2181   1.0381
 WI2  HAA3  H  HCH3  0   0.228   7.3233  -1.5359   1.6859

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
 WI2  CAL  CAJ   single    1.521  0.020  1.521
 WI2  CAL  NAX   single    1.454  0.020  1.454
 WI2  CAJ  CAW   single    1.522  0.020  1.522
 WI2  CAW  CAQ   single    1.508  0.020  1.508
 WI2  CAW  CAK   single    1.534  0.020  1.534
 WI2  CAQ  OAD   double    1.206  0.020  1.206
 WI2  CAQ  OAC   single    1.329  0.020  1.329
 WI2  CAK  CAM   single    1.518  0.020  1.518
 WI2  CAM  NAX   single    1.462  0.020  1.462
 WI2  NAX  CAV   single    1.390  0.020  1.390
 WI2  CAV  NAO   aromatic  1.305  0.020  1.305
 WI2  CAV  CAR   aromatic  1.431  0.020  1.431
 WI2  NAO  CAU   aromatic  1.343  0.020  1.343
 WI2  CAR  NAB   single    1.361  0.020  1.361
 WI2  CAR  NAN   aromatic  1.317  0.020  1.317
 WI2  NAN  CAH   aromatic  1.334  0.020  1.334
 WI2  CAH  CAU   aromatic  1.381  0.020  1.381
 WI2  CAU  CAT   single    1.474  0.020  1.474
 WI2  CAT  CAI   aromatic  1.391  0.020  1.391
 WI2  CAT  CAG   aromatic  1.399  0.020  1.399
 WI2  CAI  CAS   aromatic  1.395  0.020  1.395
 WI2  CAG  CAE   aromatic  1.382  0.020  1.382
 WI2  CAE  CAF   aromatic  1.391  0.020  1.391
 WI2  CAF  CAS   aromatic  1.392  0.020  1.392
 WI2  CAS  OAP   single    1.347  0.020  1.347
 WI2  OAP  CAA   single    1.413  0.020  1.413
 WI2  CAL  HAL1  single    0.970  0.020  1.090
 WI2  CAL  HAL2  single    0.970  0.020  1.090
 WI2  CAJ  HAJ1  single    0.970  0.020  1.090
 WI2  CAJ  HAJ2  single    0.970  0.020  1.090
 WI2  CAW  HAW   single    0.970  0.020  1.090
 WI2  CAK  HAK1  single    0.970  0.020  1.090
 WI2  CAK  HAK2  single    0.970  0.020  1.090
 WI2  OAC  HAC   single    0.850  0.020  0.980
 WI2  CAM  HAM1  single    0.970  0.020  1.090
 WI2  CAM  HAM2  single    0.970  0.020  1.090
 WI2  NAB  HAB1  single    0.890  0.020  1.040
 WI2  NAB  HAB2  single    0.890  0.020  1.040
 WI2  CAH  HAH   single    0.930  0.020  1.080
 WI2  CAI  HAI   single    0.930  0.020  1.080
 WI2  CAG  HAG   single    0.930  0.020  1.080
 WI2  CAE  HAE   single    0.930  0.020  1.080
 WI2  CAF  HAF   single    0.930  0.020  1.080
 WI2  CAA  HAA1  single    0.970  0.020  1.090
 WI2  CAA  HAA2  single    0.970  0.020  1.090
 WI2  CAA  HAA3  single    0.970  0.020  1.090

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
 WI2  HAL2  CAL  HAL1  106.65  3.000
 WI2  HAL2  CAL  NAX   111.56  3.000
 WI2  HAL1  CAL  NAX   108.96  3.000
 WI2  HAL2  CAL  CAJ   110.20  3.000
 WI2  HAL1  CAL  CAJ   109.50  3.000
 WI2  NAX   CAL  CAJ   109.90  3.000
 WI2  HAJ2  CAJ  HAJ1  107.19  3.000
 WI2  HAJ2  CAJ  CAW   110.18  3.000
 WI2  HAJ1  CAJ  CAW   110.69  3.000
 WI2  HAJ2  CAJ  CAL   108.83  3.000
 WI2  HAJ1  CAJ  CAL   108.74  3.000
 WI2  CAW   CAJ  CAL   111.10  3.000
 WI2  HAW   CAW  CAK   107.35  3.000
 WI2  HAW   CAW  CAQ   106.96  3.000
 WI2  CAK   CAW  CAQ   111.12  3.000
 WI2  HAW   CAW  CAJ   108.99  3.000
 WI2  CAK   CAW  CAJ   110.05  3.000
 WI2  CAQ   CAW  CAJ   112.17  3.000
 WI2  OAC   CAQ  OAD   122.86  3.000
 WI2  OAC   CAQ  CAW   111.92  3.000
 WI2  OAD   CAQ  CAW   125.22  3.000
 WI2  HAC   OAC  CAQ   110.00  3.000
 WI2  HAK2  CAK  HAK1  107.31  3.000
 WI2  HAK2  CAK  CAM   109.59  3.000
 WI2  HAK1  CAK  CAM   108.67  3.000
 WI2  HAK2  CAK  CAW   110.00  3.000
 WI2  HAK1  CAK  CAW   110.99  3.000
 WI2  CAM   CAK  CAW   110.21  3.000
 WI2  HAM2  CAM  HAM1  106.72  3.000
 WI2  HAM2  CAM  NAX   110.18  3.000
 WI2  HAM1  CAM  NAX   110.20  3.000
 WI2  HAM2  CAM  CAK   109.50  3.000
 WI2  HAM1  CAM  CAK   109.35  3.000
 WI2  NAX   CAM  CAK   110.79  3.000
 WI2  CAV   NAX  CAM   115.85  3.000
 WI2  CAV   NAX  CAL   116.40  3.000
 WI2  CAM   NAX  CAL   111.90  3.000
 WI2  CAR   CAV  NAO   120.09  3.000
 WI2  CAR   CAV  NAX   119.33  3.000
 WI2  NAO   CAV  NAX   120.48  3.000
 WI2  CAU   NAO  CAV   119.92  3.000
 WI2  NAN   CAR  NAB   119.17  3.000
 WI2  NAN   CAR  CAV   120.01  3.000
 WI2  NAB   CAR  CAV   120.82  3.000
 WI2  HAB2  NAB  HAB1  113.93  3.000
 WI2  HAB2  NAB  CAR   115.48  3.000
 WI2  HAB1  NAB  CAR   116.12  3.000
 WI2  CAH   NAN  CAR   118.42  3.000
 WI2  HAH   CAH  CAU   121.70  3.000
 WI2  HAH   CAH  NAN   116.21  3.000
 WI2  CAU   CAH  NAN   122.09  3.000
 WI2  CAT   CAU  CAH   123.37  3.000
 WI2  CAT   CAU  NAO   117.45  3.000
 WI2  CAH   CAU  NAO   119.16  3.000
 WI2  CAG   CAT  CAI   119.01  3.000
 WI2  CAG   CAT  CAU   120.02  3.000
 WI2  CAI   CAT  CAU   120.97  3.000
 WI2  HAI   CAI  CAS   118.25  3.000
 WI2  HAI   CAI  CAT   120.77  3.000
 WI2  CAS   CAI  CAT   120.96  3.000
 WI2  HAG   CAG  CAE   120.36  3.000
 WI2  HAG   CAG  CAT   119.85  3.000
 WI2  CAE   CAG  CAT   119.78  3.000
 WI2  HAE   CAE  CAF   118.89  3.000
 WI2  HAE   CAE  CAG   119.66  3.000
 WI2  CAF   CAE  CAG   121.45  3.000
 WI2  HAF   CAF  CAS   121.75  3.000
 WI2  HAF   CAF  CAE   119.27  3.000
 WI2  CAS   CAF  CAE   118.98  3.000
 WI2  OAP   CAS  CAF   124.33  3.000
 WI2  OAP   CAS  CAI   115.85  3.000
 WI2  CAF   CAS  CAI   119.82  3.000
 WI2  CAA   OAP  CAS   118.52  3.000
 WI2  HAA3  CAA  HAA2  108.79  3.000
 WI2  HAA3  CAA  HAA1  108.79  3.000
 WI2  HAA2  CAA  HAA1  108.69  3.000
 WI2  HAA3  CAA  OAP   111.94  3.000
 WI2  HAA2  CAA  OAP   106.52  3.000
 WI2  HAA1  CAA  OAP   112.00  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
 WI2  CONST_01  CAH   CAU  NAO  CAV    0.00   0.0  0
 WI2  CONST_02  CAT   CAU  NAO  CAV  180.00   0.0  0
 WI2  CONST_03  CAH   NAN  CAR  CAV    0.00   0.0  0
 WI2  CONST_04  NAN   CAR  CAV  NAO    0.00   0.0  0
 WI2  CONST_05  NAN   CAH  CAU  NAO    0.00   0.0  0
 WI2  CONST_08  CAU   NAO  CAV  CAR    0.00   0.0  0
 WI2  CONST_09  CAU   CAH  NAN  CAR    0.00   0.0  0
 WI2  CONST_10  CAT   CAU  CAH  NAN  180.00   0.0  0
 WI2  CONST_13  CAS   CAI  CAT  CAU  180.00   0.0  0
 WI2  CONST_14  CAE   CAG  CAT  CAU  180.00   0.0  0
 WI2  CONST_15  CAF   CAS  CAI  CAT    0.00   0.0  0
 WI2  CONST_16  CAF   CAE  CAG  CAT    0.00   0.0  0
 WI2  CONST_17  CAE   CAG  CAT  CAI    0.00   0.0  0
 WI2  CONST_18  CAE   CAF  CAS  CAI    0.00   0.0  0
 WI2  CONST_19  CAS   CAI  CAT  CAG    0.00   0.0  0
 WI2  CONST_20  CAS   CAF  CAE  CAG    0.00   0.0  0
 WI2  CONST_21  CAU   NAO  CAV  NAX  180.00   0.0  0
 WI2  CONST_22  NAN   CAR  CAV  NAX  180.00   0.0  0
 WI2  CONST_23  NAB   CAR  CAV  NAX    0.00   0.0  0
 WI2  CONST_24  NAB   CAR  CAV  NAO  180.00   0.0  0
 WI2  CONST_25  CAH   NAN  CAR  NAB  180.00   0.0  0
 WI2  CONST_26  OAP   CAS  CAI  CAT  180.00   0.0  0
 WI2  CONST_27  OAP   CAS  CAF  CAE  180.00   0.0  0
 WI2  CONST_28  HAH   CAH  CAU  NAO  180.00   0.0  0
 WI2  CONST_29  HAI   CAI  CAT  CAU    0.00   0.0  0
 WI2  CONST_30  HAG   CAG  CAT  CAU    0.00   0.0  0
 WI2  CONST_31  HAE   CAE  CAG  CAT  180.00   0.0  0
 WI2  CONST_32  HAF   CAF  CAS  CAI  180.00   0.0  0
 WI2  CONST_35  HAC   OAC  CAQ  CAW  180.00   0.0  0
 WI2  Var_01    CAK   CAM  NAX  CAL   60.59  30.0  1
 WI2  Var_02    NAO   CAV  NAX  CAL   18.68  30.0  2
 WI2  Var_03    CAM   NAX  CAL  CAJ  -60.31  30.0  1
 WI2  Var_04    NAX   CAL  CAJ  CAW   57.07  30.0  1
 WI2  Var_05    NAX   CAM  CAK  CAW  -56.24  30.0  1
 WI2  Var_06    HAA1  CAA  OAP  CAS   62.83  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
 WI2  chir_01  CAW  CAJ  CAQ  CAK  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
 WI2  plan-1  NAX   0.020
 WI2  plan-1  CAV   0.020
 WI2  plan-1  NAO   0.020
 WI2  plan-1  CAR   0.020
 WI2  plan-1  NAB   0.020
 WI2  plan-1  NAN   0.020
 WI2  plan-1  CAH   0.020
 WI2  plan-1  CAU   0.020
 WI2  plan-1  CAT   0.020
 WI2  plan-1  HAH   0.020
 WI2  plan-2  CAU   0.020
 WI2  plan-2  CAT   0.020
 WI2  plan-2  CAI   0.020
 WI2  plan-2  CAG   0.020
 WI2  plan-2  CAE   0.020
 WI2  plan-2  CAF   0.020
 WI2  plan-2  CAS   0.020
 WI2  plan-2  OAP   0.020
 WI2  plan-2  HAI   0.020
 WI2  plan-2  HAG   0.020
 WI2  plan-2  HAE   0.020
 WI2  plan-2  HAF   0.020
 WI2  plan-3  CAR   0.020
 WI2  plan-3  NAB   0.020
 WI2  plan-3  HAB1  0.020
 WI2  plan-3  HAB2  0.020
 WI2  plan-4  CAW   0.020
 WI2  plan-4  CAQ   0.020
 WI2  plan-4  OAD   0.020
 WI2  plan-4  OAC   0.020
 WI2  plan-4  HAC   0.020

