# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 18:36:49 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5-(1,1-dioxido-1,2-thiazinan-2-yl)-N-(4-fluorobenzyl)-8-hydroxy-1,6-naphthyridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(nc(N2CCCC[S]2(=O)=O)c3cccnc13)C(=O)NCc4ccc(F)cc4
#
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
 ZYP  ZYP  5-(1,1-dioxido-1,2-thiazinan-2-yl)-N-(4-fluorobenzyl)-8-hydroxy-1,6-naphthyridine-7-carboxamide  ligand  49  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZYP
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
 ZYP  OAA   O  O     0  -0.485   0.8322   3.7017   0.4405
 ZYP  OAB   O  OS    0  -0.647  -2.6257  -1.7832   1.6697
 ZYP  OAC   O  OS    0  -0.656  -2.4540  -3.7380   0.1031
 ZYP  CAF   C  CR16  0  -0.331  -5.4916   0.6786  -0.2948
 ZYP  CAG   C  CR16  0  -0.036  -5.3837   2.0508   0.0052
 ZYP  CAH   C  CR16  0  -0.396   5.2547  -0.7214  -1.5878
 ZYP  CAI   C  CR16  0  -0.393   4.4487  -1.4020   0.5884
 ZYP  CAJ   C  CR16  0  -0.277   4.5707   0.4799  -1.4528
 ZYP  CAK   C  CR16  0  -0.264   3.7795  -0.1940   0.7057
 ZYP  CAL   C  CR16  0  -0.160  -4.3532  -0.0678  -0.4300
 ZYP  CAM   C  CH2   0  -0.450   0.5459  -2.2195  -1.2752
 ZYP  CAN   C  CH2   0  -0.469   0.5886  -3.2259  -0.1310
 ZYP  CAO   C  CH2   0  -0.340  -0.8703  -1.9122  -1.7461
 ZYP  CAP   C  CH2   0  -0.309   3.0416   2.0342  -0.1866
 ZYP  CAQ   C  CH2   0  -0.602  -0.2124  -2.7544   1.0787
 ZYP  NAR   N  N     0  -0.469  -4.2373   2.6649   0.1468
 ZYP  NAS   N  N     0  -0.433  -0.7369   0.6073  -0.2809
 ZYP  CAU   C  C     0   0.566   0.6468   2.5518   0.0678
 ZYP  CAV   C  CR6   0   0.517   5.1762  -1.6422  -0.5630
 ZYP  CAW   C  CR6   0   0.034   3.8307   0.7595  -0.3103
 ZYP  CAX   C  CR6   0   0.327  -1.8802   2.6509   0.1351
 ZYP  CAY   C  CR6   0  -0.059  -0.7129   1.9369  -0.0338
 ZYP  CAZ   C  CR6   0   0.371  -1.8370  -0.0609  -0.3885
 ZYP  CBA   C  CR66  0   0.034  -3.1072   0.5677  -0.2713
 ZYP  CBB   C  CR66  0   0.231  -3.1135   1.9418   0.0052
 ZYP  NBC   N  N     0  -0.663  -1.7785  -1.4428  -0.6808
 ZYP  SBD   S  S     0   1.341  -1.9157  -2.4894   0.6166
 ZYP  HOAD  H  HOH1  0   0.477  -2.8677   4.1960   0.4536
 ZYP  HAF   H  HCR6  0   0.290  -6.4695   0.2348  -0.4146
 ZYP  HAG   H  HCR6  0   0.288  -6.2794   2.6489   0.1243
 ZYP  HAH   H  HCR6  0   0.281   5.8331  -0.9359  -2.4768
 ZYP  HAI   H  HCR6  0   0.282   4.4084  -2.1407   1.3780
 ZYP  HAJ   H  HCR6  0   0.267   4.6179   1.2052  -2.2556
 ZYP  HAK   H  HCR6  0   0.268   3.2103   0.0081   1.6052
 ZYP  HAL   H  HCR6  0   0.278  -4.4050  -1.1212  -0.6678
 ZYP  HAM   H  HCH2  0   0.238   1.0418  -1.2979  -0.9664
 ZYP  HAMA  H  HCH2  0   0.264   1.1084  -2.6102  -2.1248
 ZYP  HAN   H  HCH2  0   0.257   0.2193  -4.1990  -0.4610
 ZYP  HANA  H  HCH2  0   0.274   1.6191  -3.3791   0.1931
 ZYP  HAO   H  HCH2  0   0.285  -0.8628  -1.1427  -2.5161
 ZYP  HAOA  H  HCH2  0   0.275  -1.3204  -2.8004  -2.1928
 ZYP  HAP   H  HCH2  0   0.257   3.3373   2.7416  -0.9658
 ZYP  HAPA  H  HCH2  0   0.259   3.2416   2.5143   0.7741
 ZYP  HAQ   H  HCH2  0   0.325  -0.2157  -3.4846   1.8898
 ZYP  HAQA  H  HCH2  0   0.294   0.1559  -1.8018   1.4655
 ZYP  HNAT  H  HNH1  0   0.422   1.3655   0.7975  -0.5956
 ZYP  OAD   O  OH1   0  -0.586  -1.9273   3.9476   0.3939
 ZYP  NAT   N  NH1   0  -0.665   1.6335   1.7167  -0.2823
 ZYP  FAE   F  F     0  -0.315   5.8303  -2.8084  -0.6855

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
 ZYP  OAA  CAU   double    1.223  0.020  1.223
 ZYP  OAB  SBD   double    1.453  0.020  1.453
 ZYP  OAC  SBD   double    1.453  0.020  1.453
 ZYP  OAD  CAX   single    1.323  0.020  1.323
 ZYP  FAE  CAV   single    1.343  0.020  1.343
 ZYP  CAF  CAG   aromatic  1.409  0.020  1.409
 ZYP  CAF  CAL   aromatic  1.368  0.020  1.368
 ZYP  CAG  NAR   aromatic  1.308  0.020  1.308
 ZYP  CAH  CAJ   aromatic  1.389  0.020  1.389
 ZYP  CAH  CAV   aromatic  1.380  0.020  1.380
 ZYP  CAI  CAK   aromatic  1.386  0.020  1.386
 ZYP  CAI  CAV   aromatic  1.383  0.020  1.383
 ZYP  CAJ  CAW   aromatic  1.390  0.020  1.390
 ZYP  CAK  CAW   aromatic  1.394  0.020  1.394
 ZYP  CAL  CBA   aromatic  1.408  0.020  1.408
 ZYP  CAM  CAN   single    1.524  0.020  1.524
 ZYP  CAM  CAO   single    1.524  0.020  1.524
 ZYP  CAN  CAQ   single    1.525  0.020  1.525
 ZYP  CAO  NBC   single    1.476  0.020  1.476
 ZYP  CAP  NAT   single    1.447  0.020  1.447
 ZYP  CAP  CAW   single    1.504  0.020  1.504
 ZYP  CAQ  SBD   single    1.785  0.020  1.785
 ZYP  NAR  CBB   aromatic  1.344  0.020  1.344
 ZYP  NAS  CAY   aromatic  1.353  0.020  1.353
 ZYP  NAS  CAZ   aromatic  1.292  0.020  1.292
 ZYP  NAT  CAU   single    1.339  0.020  1.339
 ZYP  CAU  CAY   single    1.496  0.020  1.496
 ZYP  CAX  CAY   aromatic  1.379  0.020  1.379
 ZYP  CAX  CBB   aromatic  1.428  0.020  1.428
 ZYP  CAZ  CBA   aromatic  1.422  0.020  1.422
 ZYP  CAZ  NBC   single    1.414  0.020  1.414
 ZYP  CBA  CBB   aromatic  1.402  0.020  1.402
 ZYP  NBC  SBD   single    1.672  0.020  1.672
 ZYP  OAD  HOAD  single    0.850  0.020  0.980
 ZYP  CAF  HAF   single    0.930  0.020  1.080
 ZYP  CAG  HAG   single    0.930  0.020  1.080
 ZYP  CAH  HAH   single    0.930  0.020  1.080
 ZYP  CAI  HAI   single    0.930  0.020  1.080
 ZYP  CAJ  HAJ   single    0.930  0.020  1.080
 ZYP  CAK  HAK   single    0.930  0.020  1.080
 ZYP  CAL  HAL   single    0.930  0.020  1.080
 ZYP  CAM  HAM   single    0.970  0.020  1.090
 ZYP  CAM  HAMA  single    0.970  0.020  1.090
 ZYP  CAN  HAN   single    0.970  0.020  1.090
 ZYP  CAN  HANA  single    0.970  0.020  1.090
 ZYP  CAO  HAO   single    0.970  0.020  1.090
 ZYP  CAO  HAOA  single    0.970  0.020  1.090
 ZYP  CAP  HAP   single    0.970  0.020  1.090
 ZYP  CAP  HAPA  single    0.970  0.020  1.090
 ZYP  CAQ  HAQ   single    0.970  0.020  1.090
 ZYP  CAQ  HAQA  single    0.970  0.020  1.090
 ZYP  NAT  HNAT  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
 ZYP  HAF   CAF  CAL  121.20  3.000
 ZYP  HAF   CAF  CAG  119.54  3.000
 ZYP  CAL   CAF  CAG  119.26  3.000
 ZYP  HAG   CAG  NAR  116.96  3.000
 ZYP  HAG   CAG  CAF  119.85  3.000
 ZYP  NAR   CAG  CAF  123.19  3.000
 ZYP  HAH   CAH  CAV  120.55  3.000
 ZYP  HAH   CAH  CAJ  120.96  3.000
 ZYP  CAV   CAH  CAJ  118.48  3.000
 ZYP  HAI   CAI  CAV  120.57  3.000
 ZYP  HAI   CAI  CAK  121.02  3.000
 ZYP  CAV   CAI  CAK  118.41  3.000
 ZYP  HAJ   CAJ  CAW  119.87  3.000
 ZYP  HAJ   CAJ  CAH  119.06  3.000
 ZYP  CAW   CAJ  CAH  121.08  3.000
 ZYP  HAK   CAK  CAW  119.78  3.000
 ZYP  HAK   CAK  CAI  119.11  3.000
 ZYP  CAW   CAK  CAI  121.11  3.000
 ZYP  HAL   CAL  CBA  120.47  3.000
 ZYP  HAL   CAL  CAF  120.90  3.000
 ZYP  CBA   CAL  CAF  118.63  3.000
 ZYP  HAMA  CAM  HAM  106.76  3.000
 ZYP  HAMA  CAM  CAO  108.10  3.000
 ZYP  HAM   CAM  CAO  109.85  3.000
 ZYP  HAMA  CAM  CAN  109.49  3.000
 ZYP  HAM   CAM  CAN  109.42  3.000
 ZYP  CAO   CAM  CAN  113.03  3.000
 ZYP  HANA  CAN  HAN  106.50  3.000
 ZYP  HANA  CAN  CAQ  107.69  3.000
 ZYP  HAN   CAN  CAQ  109.72  3.000
 ZYP  HANA  CAN  CAM  110.01  3.000
 ZYP  HAN   CAN  CAM  110.61  3.000
 ZYP  CAQ   CAN  CAM  112.11  3.000
 ZYP  HAOA  CAO  HAO  106.77  3.000
 ZYP  HAOA  CAO  NBC  107.48  3.000
 ZYP  HAO   CAO  NBC  106.85  3.000
 ZYP  HAOA  CAO  CAM  110.22  3.000
 ZYP  HAO   CAO  CAM  110.78  3.000
 ZYP  NBC   CAO  CAM  114.38  3.000
 ZYP  HAPA  CAP  HAP  107.03  3.000
 ZYP  HAPA  CAP  CAW  110.41  3.000
 ZYP  HAP   CAP  CAW  110.36  3.000
 ZYP  HAPA  CAP  NAT  109.44  3.000
 ZYP  HAP   CAP  NAT  110.99  3.000
 ZYP  CAW   CAP  NAT  108.61  3.000
 ZYP  HAQA  CAQ  HAQ  108.75  3.000
 ZYP  HAQA  CAQ  SBD  106.50  3.000
 ZYP  HAQ   CAQ  SBD  106.79  3.000
 ZYP  HAQA  CAQ  CAN  111.93  3.000
 ZYP  HAQ   CAQ  CAN  112.59  3.000
 ZYP  SBD   CAQ  CAN  109.98  3.000
 ZYP  CBB   NAR  CAG  117.96  3.000
 ZYP  CAZ   NAS  CAY  122.61  3.000
 ZYP  CAY   CAU  NAT  113.30  3.000
 ZYP  CAY   CAU  OAA  123.03  3.000
 ZYP  NAT   CAU  OAA  123.66  3.000
 ZYP  CAI   CAV  CAH  122.16  3.000
 ZYP  CAI   CAV  FAE  118.88  3.000
 ZYP  CAH   CAV  FAE  118.95  3.000
 ZYP  CAP   CAW  CAK  120.02  3.000
 ZYP  CAP   CAW  CAJ  121.16  3.000
 ZYP  CAK   CAW  CAJ  118.76  3.000
 ZYP  CBB   CAX  CAY  117.56  3.000
 ZYP  CBB   CAX  OAD  118.27  3.000
 ZYP  CAY   CAX  OAD  124.17  3.000
 ZYP  CAX   CAY  CAU  123.26  3.000
 ZYP  CAX   CAY  NAS  121.09  3.000
 ZYP  CAU   CAY  NAS  115.64  3.000
 ZYP  NBC   CAZ  CBA  119.08  3.000
 ZYP  NBC   CAZ  NAS  119.19  3.000
 ZYP  CBA   CAZ  NAS  121.68  3.000
 ZYP  CBB   CBA  CAZ  116.98  3.000
 ZYP  CBB   CBA  CAL  117.44  3.000
 ZYP  CAZ   CBA  CAL  125.58  3.000
 ZYP  CBA   CBB  CAX  120.05  3.000
 ZYP  CBA   CBB  NAR  123.51  3.000
 ZYP  CAX   CBB  NAR  116.44  3.000
 ZYP  SBD   NBC  CAZ  116.61  3.000
 ZYP  SBD   NBC  CAO  114.28  3.000
 ZYP  CAZ   NBC  CAO  119.03  3.000
 ZYP  NBC   SBD  CAQ  102.44  3.000
 ZYP  NBC   SBD  OAC  107.09  3.000
 ZYP  CAQ   SBD  OAC  108.50  3.000
 ZYP  NBC   SBD  OAB  107.35  3.000
 ZYP  CAQ   SBD  OAB  110.54  3.000
 ZYP  OAC   SBD  OAB  119.51  3.000
 ZYP  HOAD  OAD  CAX  107.23  3.000
 ZYP  HNAT  NAT  CAU  117.02  3.000
 ZYP  HNAT  NAT  CAP  118.66  3.000
 ZYP  CAU   NAT  CAP  124.26  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
 ZYP  CONST_01  CBB   NAR  CAG  CAF     0.00   0.0  0
 ZYP  CONST_02  CAZ   CBA  CAL  CAF   180.00   0.0  0
 ZYP  CONST_03  CBB   CBA  CAL  CAF     0.00   0.0  0
 ZYP  CONST_04  CBA   CAL  CAF  CAG     0.00   0.0  0
 ZYP  CONST_05  CAX   CBB  NAR  CAG   180.00   0.0  0
 ZYP  CONST_06  CBA   CBB  NAR  CAG     0.00   0.0  0
 ZYP  CONST_07  CAK   CAW  CAJ  CAH     0.00   0.0  0
 ZYP  CONST_08  CAK   CAI  CAV  CAH     0.00   0.0  0
 ZYP  CONST_09  CAJ   CAW  CAK  CAI     0.00   0.0  0
 ZYP  CONST_10  CAJ   CAH  CAV  CAI     0.00   0.0  0
 ZYP  CONST_11  NAR   CAG  CAF  CAL     0.00   0.0  0
 ZYP  CONST_12  NAS   CAZ  CBA  CAL   180.00   0.0  0
 ZYP  CONST_13  NAR   CBB  CBA  CAL     0.00   0.0  0
 ZYP  CONST_14  CAX   CBB  CBA  CAL   180.00   0.0  0
 ZYP  CONST_15  CAY   CAX  CBB  NAR   180.00   0.0  0
 ZYP  CONST_16  CAZ   CBA  CBB  NAR   180.00   0.0  0
 ZYP  CONST_17  CBB   CAX  CAY  NAS     0.00   0.0  0
 ZYP  CONST_18  CBB   CBA  CAZ  NAS     0.00   0.0  0
 ZYP  CONST_19  CAW   CAJ  CAH  CAV     0.00   0.0  0
 ZYP  CONST_20  CAW   CAK  CAI  CAV     0.00   0.0  0
 ZYP  CONST_21  CAZ   NAS  CAY  CAX     0.00   0.0  0
 ZYP  CONST_22  CAZ   CBA  CBB  CAX     0.00   0.0  0
 ZYP  CONST_23  CBA   CAZ  NAS  CAY     0.00   0.0  0
 ZYP  CONST_24  CBA   CBB  CAX  CAY     0.00   0.0  0
 ZYP  CONST_25  NBC   CAZ  CBA  CAL     0.00   0.0  0
 ZYP  CONST_26  NBC   CAZ  NAS  CAY   180.00   0.0  0
 ZYP  CONST_27  NBC   CAZ  CBA  CBB   180.00   0.0  0
 ZYP  CONST_28  NAS   CAY  CAX  OAD   180.00   0.0  0
 ZYP  CONST_29  NAR   CBB  CAX  OAD     0.00   0.0  0
 ZYP  CONST_30  CBA   CBB  CAX  OAD   180.00   0.0  0
 ZYP  CONST_31  CAJ   CAH  CAV  FAE   180.00   0.0  0
 ZYP  CONST_32  CAK   CAI  CAV  FAE   180.00   0.0  0
 ZYP  CONST_33  CAP   CAW  CAJ  CAH   180.00   0.0  0
 ZYP  CONST_34  CAP   CAW  CAK  CAI   180.00   0.0  0
 ZYP  CONST_35  CAZ   NAS  CAY  CAU   180.00   0.0  0
 ZYP  CONST_36  CBB   CAX  CAY  CAU   180.00   0.0  0
 ZYP  CONST_37  HAL   CAL  CAF  CAG   180.00   0.0  0
 ZYP  CONST_38  HAI   CAI  CAV  CAH   180.00   0.0  0
 ZYP  CONST_39  HAH   CAH  CAV  CAI   180.00   0.0  0
 ZYP  CONST_40  HAK   CAK  CAW  CAJ   180.00   0.0  0
 ZYP  CONST_41  HAJ   CAJ  CAW  CAK   180.00   0.0  0
 ZYP  CONST_42  HAG   CAG  CAF  CAL   180.00   0.0  0
 ZYP  CONST_43  HAF   CAF  CAG  NAR   180.00   0.0  0
 ZYP  CONST_44  CAY   CAU  NAT  CAP   180.00   0.0  0
 ZYP  CONST_45  HNAT  NAT  CAU  CAY     0.00   0.0  0
 ZYP  CONST_46  CAP   NAT  CAU  OAA     0.00   0.0  0
 ZYP  Var_01    SBD   CAQ  CAN  CAM    59.05  30.0  1
 ZYP  Var_02    CAZ   NBC  CAO  CAM    87.94  30.0  1
 ZYP  Var_03    NBC   CAO  CAM  CAN    55.40  30.0  1
 ZYP  Var_04    NBC   SBD  CAQ  CAN   -54.08  30.0  1
 ZYP  Var_05    CAQ   CAN  CAM  CAO   -57.94  30.0  1
 ZYP  Var_06    NAS   CAZ  NBC  CAO   -45.39  30.0  2
 ZYP  Var_07    CAQ   SBD  NBC  CAO    52.97  30.0  1
 ZYP  Var_08    NAS   CAY  CAU  OAA  -171.14  30.0  2
 ZYP  Var_09    NAT   CAP  CAW  CAJ   108.30  30.0  2
 ZYP  Var_10    CAW   CAP  NAT  CAU   165.04  30.0  1

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
 ZYP  plan-1  CAH   0.020
 ZYP  plan-1  CAI   0.020
 ZYP  plan-1  CAJ   0.020
 ZYP  plan-1  CAK   0.020
 ZYP  plan-1  CAP   0.020
 ZYP  plan-1  CAV   0.020
 ZYP  plan-1  CAW   0.020
 ZYP  plan-1  HAH   0.020
 ZYP  plan-1  HAI   0.020
 ZYP  plan-1  HAJ   0.020
 ZYP  plan-1  HAK   0.020
 ZYP  plan-1  FAE   0.020
 ZYP  plan-2  CAF   0.020
 ZYP  plan-2  CAG   0.020
 ZYP  plan-2  CAL   0.020
 ZYP  plan-2  NAR   0.020
 ZYP  plan-2  NAS   0.020
 ZYP  plan-2  CAU   0.020
 ZYP  plan-2  CAX   0.020
 ZYP  plan-2  CAY   0.020
 ZYP  plan-2  CAZ   0.020
 ZYP  plan-2  CBA   0.020
 ZYP  plan-2  CBB   0.020
 ZYP  plan-2  NBC   0.020
 ZYP  plan-2  HAF   0.020
 ZYP  plan-2  HAG   0.020
 ZYP  plan-2  HAL   0.020
 ZYP  plan-2  OAD   0.020
 ZYP  plan-3  OAA   0.020
 ZYP  plan-3  CAP   0.020
 ZYP  plan-3  CAU   0.020
 ZYP  plan-3  CAY   0.020
 ZYP  plan-3  HNAT  0.020
 ZYP  plan-3  NAT   0.020
 ZYP  plan-4  CAO   0.020
 ZYP  plan-4  CAZ   0.020
 ZYP  plan-4  NBC   0.020
 ZYP  plan-4  SBD   0.020

