# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:23:07 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-azanylidene-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1C(=O)[C@@H](C(=O)NCc2ccc(F)cc2F)C(=N)c3cccnc13
#
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
 WA5  WA5  4-azanylidene-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide  ligand  37  25  .  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_WA5
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
 WA5  NAA   N  N     0  -0.533   2.8857   2.5500  -1.2702
 WA5  OAC   O  O     0  -0.421   0.5253  -1.2626  -1.9884
 WA5  OAD   O  OH1   0  -0.520   2.4816  -2.7210  -0.9868
 WA5  CAG   C  CR16  0  -0.329   5.5103   0.2341   1.3998
 WA5  CAH   C  CR16  0  -0.054   5.2534  -1.1242   1.3236
 WA5  CAI   C  CR16  0  -0.411  -4.8365  -1.4738   0.8169
 WA5  CAJ   C  CR16  0  -0.255  -3.5879  -1.0040   1.1950
 WA5  CAK   C  CR16  0  -0.191   4.6661   1.0927   0.7150
 WA5  CAL   C  CR16  0  -0.553  -5.1978   0.5694  -0.4328
 WA5  CAM   C  CH2   0  -0.307  -1.7654   0.7393   1.2095
 WA5  NAN   N  N     0  -0.420   4.2416  -1.6411   0.6353
 WA5  NAO   N  NH1   0  -0.629  -0.8154   0.6125   0.1161
 WA5  CAP   C  C     0   0.603   0.4618   0.9794   0.2482
 WA5  CAQ   C  CR6   0   0.539  -5.6180  -0.6714   0.0094
 WA5  CAR   C  C     0   0.259   2.6711   1.4005  -0.7910
 WA5  CAS   C  CR6   0   0.563  -3.9486   0.9941  -0.0260
 WA5  CAT   C  CR6   0  -0.167  -3.1161   0.2399   0.7890
 WA5  CAU   C  CH1   0  -0.684   1.3250   0.7689  -1.0113
 WA5  CAV   C  C     0   0.566   1.3721  -0.7147  -1.3209
 WA5  CAW   C  CR6   0  -0.056   3.6061   0.5771  -0.0135
 WA5  CAX   C  CR6   0   0.486   3.4469  -0.8130  -0.0073
 WA5  NAY   N  NT    0  -0.286   2.4005  -1.3929  -0.7351
 WA5  HNAA  H  H     0   0.350   3.8230   2.8839  -1.0566
 WA5  HOAD  H  HOH1  0   0.487   2.0730  -3.1723  -0.2336
 WA5  HAG   H  HCR6  0   0.282   6.3422   0.6064   1.9796
 WA5  HAH   H  HCR6  0   0.280   5.8869  -1.8328   1.8436
 WA5  HAI   H  HCR6  0   0.289  -5.1920  -2.4404   1.1462
 WA5  HAJ   H  HCR6  0   0.281  -2.9639  -1.6184   1.8309
 WA5  HAK   H  HCR6  0   0.284   4.8279   2.1626   0.7595
 WA5  HAL   H  HCR6  0   0.307  -5.8205   1.1857  -1.0677
 WA5  HAM   H  HCH2  0   0.270  -1.4214   0.1592   2.0677
 WA5  HAMA  H  HCH2  0   0.268  -1.8178   1.7807   1.5333
 WA5  HNAO  H  HNH1  0   0.412  -1.1348   0.2232  -0.7574
 WA5  HAU   H  HCH1  0   0.355   0.8335   1.2580  -1.8548
 WA5  OAB   O  O     0  -0.460   0.9315   1.4525   1.2666
 WA5  FAE   F  F     0  -0.307  -6.8294  -1.1037  -0.3597
 WA5  FAF   F  F     0  -0.300  -3.5258   2.1960  -0.4380

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
 WA5  NAA  CAR   double    1.264  0.020  1.264
 WA5  NAA  HNAA  single    0.890  0.020  1.040
 WA5  OAB  CAP   double    1.217  0.020  1.217
 WA5  CAV  OAC   double    1.209  0.020  1.209
 WA5  NAY  OAD   single    1.354  0.020  1.354
 WA5  OAD  HOAD  single    0.850  0.020  0.980
 WA5  CAQ  FAE   single    1.338  0.020  1.338
 WA5  CAS  FAF   single    1.339  0.020  1.339
 WA5  CAK  CAG   aromatic  1.385  0.020  1.385
 WA5  CAG  CAH   aromatic  1.384  0.020  1.384
 WA5  CAG  HAG   single    0.930  0.020  1.080
 WA5  CAH  NAN   aromatic  1.328  0.020  1.328
 WA5  CAH  HAH   single    0.930  0.020  1.080
 WA5  CAJ  CAI   aromatic  1.387  0.020  1.387
 WA5  CAI  CAQ   aromatic  1.381  0.020  1.381
 WA5  CAI  HAI   single    0.930  0.020  1.080
 WA5  CAJ  CAT   aromatic  1.391  0.020  1.391
 WA5  CAJ  HAJ   single    0.930  0.020  1.080
 WA5  CAK  CAW   aromatic  1.386  0.020  1.386
 WA5  CAK  HAK   single    0.930  0.020  1.080
 WA5  CAQ  CAL   aromatic  1.383  0.020  1.383
 WA5  CAS  CAL   aromatic  1.381  0.020  1.381
 WA5  CAL  HAL   single    0.930  0.020  1.080
 WA5  CAM  CAT   single    1.500  0.020  1.500
 WA5  CAM  NAO   single    1.454  0.020  1.454
 WA5  CAM  HAM   single    0.970  0.020  1.090
 WA5  CAM  HAMA  single    0.970  0.020  1.090
 WA5  CAX  NAN   aromatic  1.315  0.020  1.315
 WA5  CAP  NAO   single    1.335  0.020  1.335
 WA5  NAO  HNAO  single    0.860  0.020  1.020
 WA5  CAP  CAU   single    1.541  0.020  1.541
 WA5  CAR  CAU   single    1.503  0.020  1.503
 WA5  CAR  CAW   single    1.469  0.020  1.469
 WA5  CAT  CAS   aromatic  1.388  0.020  1.388
 WA5  CAU  CAV   single    1.516  0.020  1.516
 WA5  CAU  HAU   single    0.970  0.020  1.090
 WA5  CAV  NAY   single    1.364  0.020  1.364
 WA5  CAW  CAX   aromatic  1.399  0.020  1.399
 WA5  CAX  NAY   single    1.400  0.020  1.400

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
 WA5  HNAA  NAA  CAR  112.04  3.000
 WA5  HOAD  OAD  NAY  106.69  3.000
 WA5  HAG   CAG  CAK  121.40  3.000
 WA5  HAG   CAG  CAH  120.71  3.000
 WA5  CAK   CAG  CAH  117.89  3.000
 WA5  HAH   CAH  NAN  116.08  3.000
 WA5  HAH   CAH  CAG  120.45  3.000
 WA5  NAN   CAH  CAG  123.48  3.000
 WA5  HAI   CAI  CAQ  120.76  3.000
 WA5  HAI   CAI  CAJ  121.06  3.000
 WA5  CAQ   CAI  CAJ  118.17  3.000
 WA5  HAJ   CAJ  CAT  118.93  3.000
 WA5  HAJ   CAJ  CAI  119.14  3.000
 WA5  CAT   CAJ  CAI  121.93  3.000
 WA5  HAK   CAK  CAW  120.23  3.000
 WA5  HAK   CAK  CAG  120.06  3.000
 WA5  CAW   CAK  CAG  119.70  3.000
 WA5  HAL   CAL  CAS  121.22  3.000
 WA5  HAL   CAL  CAQ  121.60  3.000
 WA5  CAS   CAL  CAQ  117.18  3.000
 WA5  HAMA  CAM  HAM  106.79  3.000
 WA5  HAMA  CAM  CAT  110.94  3.000
 WA5  HAM   CAM  CAT  109.10  3.000
 WA5  HAMA  CAM  NAO  109.73  3.000
 WA5  HAM   CAM  NAO  109.81  3.000
 WA5  CAT   CAM  NAO  110.40  3.000
 WA5  CAX   NAN  CAH  117.93  3.000
 WA5  HNAO  NAO  CAP  119.65  3.000
 WA5  HNAO  NAO  CAM  118.56  3.000
 WA5  CAP   NAO  CAM  121.78  3.000
 WA5  CAU   CAP  NAO  114.66  3.000
 WA5  CAU   CAP  OAB  121.38  3.000
 WA5  NAO   CAP  OAB  123.96  3.000
 WA5  CAL   CAQ  CAI  122.45  3.000
 WA5  CAL   CAQ  FAE  118.48  3.000
 WA5  CAI   CAQ  FAE  119.07  3.000
 WA5  CAW   CAR  CAU  114.34  3.000
 WA5  CAW   CAR  NAA  127.06  3.000
 WA5  CAU   CAR  NAA  118.60  3.000
 WA5  CAT   CAS  CAL  123.27  3.000
 WA5  CAT   CAS  FAF  118.62  3.000
 WA5  CAL   CAS  FAF  118.11  3.000
 WA5  CAS   CAT  CAM  121.59  3.000
 WA5  CAS   CAT  CAJ  117.00  3.000
 WA5  CAM   CAT  CAJ  121.42  3.000
 WA5  HAU   CAU  CAV  107.13  3.000
 WA5  HAU   CAU  CAR  109.16  3.000
 WA5  CAV   CAU  CAR  114.41  3.000
 WA5  HAU   CAU  CAP  108.54  3.000
 WA5  CAV   CAU  CAP  108.53  3.000
 WA5  CAR   CAU  CAP  108.92  3.000
 WA5  NAY   CAV  CAU  114.97  3.000
 WA5  NAY   CAV  OAC  122.66  3.000
 WA5  CAU   CAV  OAC  122.29  3.000
 WA5  CAX   CAW  CAR  119.14  3.000
 WA5  CAX   CAW  CAK  117.03  3.000
 WA5  CAR   CAW  CAK  123.83  3.000
 WA5  NAY   CAX  CAW  119.62  3.000
 WA5  NAY   CAX  NAN  116.40  3.000
 WA5  CAW   CAX  NAN  123.98  3.000
 WA5  CAX   NAY  CAV  125.50  3.000
 WA5  CAX   NAY  OAD  117.26  3.000
 WA5  CAV   NAY  OAD  116.93  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
 WA5  CONST_01  CAX   CAW  CAK  CAG     0.00   0.0  0
 WA5  CONST_02  CAX   NAN  CAH  CAG     0.00   0.0  0
 WA5  CONST_03  CAW   CAK  CAG  CAH     0.00   0.0  0
 WA5  CONST_04  CAW   CAX  NAN  CAH     0.00   0.0  0
 WA5  CONST_05  CAS   CAT  CAJ  CAI     0.00   0.0  0
 WA5  CONST_06  CAS   CAL  CAQ  CAI     0.00   0.0  0
 WA5  CONST_07  CAL   CAQ  CAI  CAJ     0.00   0.0  0
 WA5  CONST_08  CAL   CAS  CAT  CAJ     0.00   0.0  0
 WA5  CONST_09  NAN   CAH  CAG  CAK     0.00   0.0  0
 WA5  CONST_10  NAN   CAX  CAW  CAK     0.00   0.0  0
 WA5  CONST_11  CAT   CAJ  CAI  CAQ     0.00   0.0  0
 WA5  CONST_12  CAT   CAS  CAL  CAQ     0.00   0.0  0
 WA5  CONST_13  CAX   NAY  CAV  CAU     0.00   0.0  0
 WA5  CONST_14  CAJ   CAI  CAQ  FAE   180.00   0.0  0
 WA5  CONST_15  CAS   CAL  CAQ  FAE   180.00   0.0  0
 WA5  CONST_16  CAQ   CAL  CAS  FAF   180.00   0.0  0
 WA5  CONST_17  CAJ   CAT  CAS  FAF   180.00   0.0  0
 WA5  CONST_18  CAM   CAT  CAJ  CAI   180.00   0.0  0
 WA5  CONST_19  CAM   CAT  CAS  CAL   180.00   0.0  0
 WA5  CONST_20  CAX   NAY  CAV  OAC   180.00   0.0  0
 WA5  CONST_21  CAU   CAV  NAY  OAD   180.00   0.0  0
 WA5  CONST_22  HAK   CAK  CAG  CAH   180.00   0.0  0
 WA5  CONST_23  HAL   CAL  CAQ  CAI   180.00   0.0  0
 WA5  CONST_24  HAH   CAH  CAG  CAK   180.00   0.0  0
 WA5  CONST_25  HAI   CAI  CAQ  CAL   180.00   0.0  0
 WA5  CONST_26  HAG   CAG  CAH  NAN   180.00   0.0  0
 WA5  CONST_27  HAJ   CAJ  CAI  CAQ   180.00   0.0  0
 WA5  CONST_28  OAD   NAY  CAV  OAC     0.00   0.0  0
 WA5  CONST_29  CAU   CAP  NAO  CAM   180.00   0.0  0
 WA5  CONST_30  HNAO  NAO  CAP  CAU     0.00   0.0  0
 WA5  CONST_31  CAM   NAO  CAP  OAB     0.00   0.0  0
 WA5  Var_01    CAU   CAR  CAW  CAK  -155.55  30.0  1
 WA5  Var_02    CAV   NAY  CAX  NAN   170.92  30.0  1
 WA5  Var_03    NAO   CAM  CAT  CAJ   103.11  30.0  2
 WA5  Var_04    CAT   CAM  NAO  CAP  -179.36  30.0  1

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
 WA5  chir_01  CAU  CAP  CAR  CAV  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
 WA5  plan-1  CAI   0.020
 WA5  plan-1  CAJ   0.020
 WA5  plan-1  CAL   0.020
 WA5  plan-1  CAM   0.020
 WA5  plan-1  CAQ   0.020
 WA5  plan-1  CAS   0.020
 WA5  plan-1  CAT   0.020
 WA5  plan-1  HAI   0.020
 WA5  plan-1  HAJ   0.020
 WA5  plan-1  HAL   0.020
 WA5  plan-1  FAE   0.020
 WA5  plan-1  FAF   0.020
 WA5  plan-2  CAG   0.020
 WA5  plan-2  CAH   0.020
 WA5  plan-2  CAK   0.020
 WA5  plan-2  NAN   0.020
 WA5  plan-2  CAR   0.020
 WA5  plan-2  CAW   0.020
 WA5  plan-2  CAX   0.020
 WA5  plan-2  NAY   0.020
 WA5  plan-2  HAG   0.020
 WA5  plan-2  HAH   0.020
 WA5  plan-2  HAK   0.020
 WA5  plan-3  CAM   0.020
 WA5  plan-3  NAO   0.020
 WA5  plan-3  CAP   0.020
 WA5  plan-3  CAU   0.020
 WA5  plan-3  HNAO  0.020
 WA5  plan-3  OAB   0.020
 WA5  plan-4  OAC   0.020
 WA5  plan-4  OAD   0.020
 WA5  plan-4  CAU   0.020
 WA5  plan-4  CAV   0.020
 WA5  plan-4  CAX   0.020
 WA5  plan-4  NAY   0.020

