# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:56:54 2020
#   Inital geometry file: a 114 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@@H]2OCC=C3C[N@]4CC[C@@]56[C@@H]4C[C@@H]3[C@@H]2[C@@H]5N1c7ccccc67
#
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
 SY9  SY9  'None                     '  ligand  47  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SY9
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
 SY9  CAV   C  CR15   0  -0.100  -0.1648  -2.0116  -0.7370
 SY9  CAU   C  CH2    0  -0.464  -0.9139  -1.3662  -1.8862
 SY9  CAT   C  CH1    0  -0.321  -1.8745  -0.3280  -1.3067
 SY9  CAN   C  CH1    0  -0.273  -0.9957   0.8394  -0.8682
 SY9  CAK   C  CH1    0  -0.047  -0.0944   0.4362   0.2858
 SY9  NAH   N  NT     0  -0.580   1.0637   1.3363   0.2619
 SY9  CAA   C  CR6    0   0.357   2.2453   0.6049   0.1039
 SY9  CAF   C  CR16   0  -0.306   3.5532   1.0587  -0.0148
 SY9  CAE   C  CR16   0  -0.265   4.5576   0.1124  -0.1985
 SY9  CAD   C  CR16   0  -0.261   4.2697  -1.2445  -0.2555
 SY9  CAC   C  CR16   0  -0.336   2.9549  -1.6823  -0.1212
 SY9  CAB   C  CR6    0   0.092   1.9448  -0.7560   0.0587
 SY9  CAG   C  CR5    0  -0.140   0.4793  -1.0047   0.2926
 SY9  CAW   C  CH2    0  -0.446   0.2189  -1.6999   1.6585
 SY9  CAX   C  CH2    0  -0.318  -0.3991  -3.0529   1.2961
 SY9  NAY   N  NR5    0  -0.401  -1.0566  -2.8776   0.0167
 SY9  CAS   C  CH2   -1  -0.362  -2.4477  -2.4223   0.0437
 SY9  CAR   C  C      0   0.138  -2.6491  -0.9408  -0.1578
 SY9  CAQ   C  C1     0  -0.324  -3.4680  -0.2142   0.5987
 SY9  CAP   C  CH2    0  -0.231  -3.6943   1.2570   0.3793
 SY9  OAO   O  O2     0  -0.491  -2.5427   2.0447   0.6221
 SY9  CAM   C  CH1    0   0.053  -1.6503   2.1561  -0.4645
 SY9  CAL   C  CH2    0  -0.606  -0.5504   3.1548  -0.0454
 SY9  CAI   C  C      0   0.511   0.8872   2.6628   0.0485
 SY9  OAJ   O  O      0  -0.479   1.8184   3.4466  -0.0484
 SY9  HAV   H  HCR5   0   0.252   0.6509  -2.6264  -1.1328
 SY9  HAU1  H  HCH2   0   0.254  -0.2207  -0.8912  -2.5826
 SY9  HAU2  H  HCH2   0   0.262  -1.4407  -2.1387  -2.4514
 SY9  HAT   H  HCH1   0   0.268  -2.5706   0.0147  -2.0809
 SY9  HAN   H  HCH1   0   0.261  -0.3681   1.0859  -1.7338
 SY9  HAK   H  HCH1   0   0.272  -0.6382   0.5966   1.2176
 SY9  HAM   H  HCH1   0   0.246  -2.1881   2.5621  -1.3327
 SY9  HAF   H  HCR6   0   0.271   3.7940   2.1084   0.0315
 SY9  HAE   H  HCR6   0   0.255   5.5820   0.4480  -0.2972
 SY9  HAD   H  HCR6   0   0.253   5.0663  -1.9628  -0.3970
 SY9  HAC   H  HCR6   0   0.249   2.7327  -2.7425  -0.1514
 SY9  HAW1  H  HCH2   0   0.249   1.1295  -1.8015   2.2496
 SY9  HAW2  H  HCH2   0   0.245  -0.4823  -1.1116   2.2535
 SY9  HAX1  H  HCH2   0   0.235   0.3900  -3.8035   1.1816
 SY9  HAX2  H  HCH2   0   0.246  -1.0892  -3.4283   2.0520
 SY9  HAS1  H  HCH2   0   0.243  -2.9948  -2.9384  -0.7552
 SY9  HAS2  H  HCH2   0   0.252  -2.9099  -2.7428   0.9786
 SY9  HAQ   H  H      0   0.243  -3.9964  -0.6839   1.4226
 SY9  HAP1  H  HCH2   0   0.217  -4.0683   1.4397  -0.6387
 SY9  HAP2  H  HCH2   0   0.246  -4.4617   1.6187   1.0647
 SY9  HAL1  H  HCH2   0   0.286  -0.5282   4.0005  -0.7328
 SY9  HAL2  H  HCH2   0   0.294  -0.8077   3.5718   0.9328

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
 SY9  CAV  CAU   single    1.516  0.020  1.516
 SY9  CAV  CAG   single    1.578  0.020  1.578
 SY9  CAV  NAY   single    1.454  0.020  1.454
 SY9  CAU  CAT   single    1.529  0.020  1.529
 SY9  CAT  CAN   single    1.526  0.020  1.526
 SY9  CAT  CAR   single    1.515  0.020  1.515
 SY9  CAN  CAK   single    1.519  0.020  1.519
 SY9  CAN  CAM   single    1.525  0.020  1.525
 SY9  CAK  NAH   single    1.467  0.020  1.467
 SY9  CAK  CAG   single    1.551  0.020  1.551
 SY9  NAH  CAA   single    1.399  0.020  1.399
 SY9  NAH  CAI   single    1.355  0.020  1.355
 SY9  CAA  CAF   aromatic  1.389  0.020  1.389
 SY9  CAA  CAB   aromatic  1.394  0.020  1.394
 SY9  CAF  CAE   aromatic  1.392  0.020  1.392
 SY9  CAE  CAD   aromatic  1.388  0.020  1.388
 SY9  CAD  CAC   aromatic  1.392  0.020  1.392
 SY9  CAC  CAB   aromatic  1.382  0.020  1.382
 SY9  CAB  CAG   single    1.505  0.020  1.505
 SY9  CAG  CAW   single    1.555  0.020  1.555
 SY9  CAW  CAX   single    1.531  0.020  1.531
 SY9  CAX  NAY   single    1.449  0.020  1.449
 SY9  NAY  CAS   single    1.464  0.020  1.464
 SY9  CAS  CAR   single    1.509  0.020  1.509
 SY9  CAR  CAQ   double    1.331  0.020  1.331
 SY9  CAQ  CAP   single    1.505  0.020  1.505
 SY9  CAP  OAO   single    1.416  0.020  1.416
 SY9  OAO  CAM   single    1.411  0.020  1.411
 SY9  CAM  CAL   single    1.544  0.020  1.544
 SY9  CAL  CAI   single    1.522  0.020  1.522
 SY9  CAI  OAJ   double    1.221  0.020  1.221
 SY9  CAV  HAV   single    0.970  0.020  1.090
 SY9  CAU  HAU1  single    0.970  0.020  1.090
 SY9  CAU  HAU2  single    0.970  0.020  1.090
 SY9  CAT  HAT   single    0.970  0.020  1.090
 SY9  CAN  HAN   single    0.970  0.020  1.090
 SY9  CAK  HAK   single    0.970  0.020  1.090
 SY9  CAM  HAM   single    0.970  0.020  1.090
 SY9  CAF  HAF   single    0.930  0.020  1.080
 SY9  CAE  HAE   single    0.930  0.020  1.080
 SY9  CAD  HAD   single    0.930  0.020  1.080
 SY9  CAC  HAC   single    0.930  0.020  1.080
 SY9  CAW  HAW1  single    0.970  0.020  1.090
 SY9  CAW  HAW2  single    0.970  0.020  1.090
 SY9  CAX  HAX1  single    0.970  0.020  1.090
 SY9  CAX  HAX2  single    0.970  0.020  1.090
 SY9  CAS  HAS1  single    0.970  0.020  1.090
 SY9  CAS  HAS2  single    0.970  0.020  1.090
 SY9  CAQ  HAQ   single    0.930  0.020  1.080
 SY9  CAP  HAP1  single    0.970  0.020  1.090
 SY9  CAP  HAP2  single    0.970  0.020  1.090
 SY9  CAL  HAL1  single    0.970  0.020  1.090
 SY9  CAL  HAL2  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
 SY9  HAV   CAV  NAY   108.05  3.000
 SY9  HAV   CAV  CAG   106.86  3.000
 SY9  NAY   CAV  CAG   107.00  3.000
 SY9  HAV   CAV  CAU   109.45  3.000
 SY9  NAY   CAV  CAU   110.09  3.000
 SY9  CAG   CAV  CAU   115.13  3.000
 SY9  HAU2  CAU  HAU1  106.49  3.000
 SY9  HAU2  CAU  CAT   111.93  3.000
 SY9  HAU1  CAU  CAT   110.21  3.000
 SY9  HAU2  CAU  CAV   109.23  3.000
 SY9  HAU1  CAU  CAV   110.80  3.000
 SY9  CAT   CAU  CAV   108.20  3.000
 SY9  HAT   CAT  CAR   109.72  3.000
 SY9  HAT   CAT  CAN   109.25  3.000
 SY9  CAR   CAT  CAN   112.71  3.000
 SY9  HAT   CAT  CAU   110.10  3.000
 SY9  CAR   CAT  CAU   109.51  3.000
 SY9  CAN   CAT  CAU   105.47  3.000
 SY9  HAN   CAN  CAM   105.09  3.000
 SY9  HAN   CAN  CAK   108.64  3.000
 SY9  CAM   CAN  CAK   106.43  3.000
 SY9  HAN   CAN  CAT   105.94  3.000
 SY9  CAM   CAN  CAT   119.31  3.000
 SY9  CAK   CAN  CAT   110.92  3.000
 SY9  HAK   CAK  CAG   108.50  3.000
 SY9  HAK   CAK  NAH   108.50  3.000
 SY9  CAG   CAK  NAH   106.15  3.000
 SY9  HAK   CAK  CAN   108.31  3.000
 SY9  CAG   CAK  CAN   118.00  3.000
 SY9  NAH   CAK  CAN   107.05  3.000
 SY9  CAI   NAH  CAA   127.17  3.000
 SY9  CAI   NAH  CAK   120.02  3.000
 SY9  CAA   NAH  CAK   110.36  3.000
 SY9  CAB   CAA  CAF   121.25  3.000
 SY9  CAB   CAA  NAH   109.39  3.000
 SY9  CAF   CAA  NAH   129.36  3.000
 SY9  HAF   CAF  CAE   120.43  3.000
 SY9  HAF   CAF  CAA   121.64  3.000
 SY9  CAE   CAF  CAA   117.93  3.000
 SY9  HAE   CAE  CAD   119.70  3.000
 SY9  HAE   CAE  CAF   118.96  3.000
 SY9  CAD   CAE  CAF   121.35  3.000
 SY9  HAD   CAD  CAC   119.94  3.000
 SY9  HAD   CAD  CAE   120.11  3.000
 SY9  CAC   CAD  CAE   119.95  3.000
 SY9  HAC   CAC  CAB   120.63  3.000
 SY9  HAC   CAC  CAD   119.91  3.000
 SY9  CAB   CAC  CAD   119.47  3.000
 SY9  CAG   CAB  CAC   128.40  3.000
 SY9  CAG   CAB  CAA   111.48  3.000
 SY9  CAC   CAB  CAA   120.05  3.000
 SY9  CAW   CAG  CAB   111.94  3.000
 SY9  CAW   CAG  CAK   110.94  3.000
 SY9  CAB   CAG  CAK   101.89  3.000
 SY9  CAW   CAG  CAV   102.69  3.000
 SY9  CAB   CAG  CAV   113.68  3.000
 SY9  CAK   CAG  CAV   116.05  3.000
 SY9  HAW2  CAW  HAW1  106.92  3.000
 SY9  HAW2  CAW  CAX   110.24  3.000
 SY9  HAW1  CAW  CAX   112.53  3.000
 SY9  HAW2  CAW  CAG   110.21  3.000
 SY9  HAW1  CAW  CAG   112.22  3.000
 SY9  CAX   CAW  CAG   104.76  3.000
 SY9  HAX2  CAX  HAX1  107.01  3.000
 SY9  HAX2  CAX  NAY   111.51  3.000
 SY9  HAX1  CAX  NAY   108.51  3.000
 SY9  HAX2  CAX  CAW   113.31  3.000
 SY9  HAX1  CAX  CAW   109.85  3.000
 SY9  NAY   CAX  CAW   106.58  3.000
 SY9  CAS   NAY  CAX   116.90  3.000
 SY9  CAS   NAY  CAV   114.03  3.000
 SY9  CAX   NAY  CAV   104.56  3.000
 SY9  HAS2  CAS  HAS1  105.94  3.000
 SY9  HAS2  CAS  CAR   110.26  3.000
 SY9  HAS1  CAS  CAR   107.35  3.000
 SY9  HAS2  CAS  NAY   109.09  3.000
 SY9  HAS1  CAS  NAY   108.31  3.000
 SY9  CAR   CAS  NAY   115.45  3.000
 SY9  CAQ   CAR  CAS   122.85  3.000
 SY9  CAQ   CAR  CAT   121.65  3.000
 SY9  CAS   CAR  CAT   115.48  3.000
 SY9  HAQ   CAQ  CAP   117.42  3.000
 SY9  HAQ   CAQ  CAR   119.65  3.000
 SY9  CAP   CAQ  CAR   122.93  3.000
 SY9  HAP2  CAP  HAP1  106.69  3.000
 SY9  HAP2  CAP  OAO   106.26  3.000
 SY9  HAP1  CAP  OAO   110.05  3.000
 SY9  HAP2  CAP  CAQ   109.79  3.000
 SY9  HAP1  CAP  CAQ   110.40  3.000
 SY9  OAO   CAP  CAQ   113.36  3.000
 SY9  CAM   OAO  CAP   115.24  3.000
 SY9  HAM   CAM  CAL   108.92  3.000
 SY9  HAM   CAM  OAO   109.15  3.000
 SY9  CAL   CAM  OAO   107.02  3.000
 SY9  HAM   CAM  CAN   108.66  3.000
 SY9  CAL   CAM  CAN   108.95  3.000
 SY9  OAO   CAM  CAN   114.03  3.000
 SY9  HAL2  CAL  HAL1  105.84  3.000
 SY9  HAL2  CAL  CAI   106.87  3.000
 SY9  HAL1  CAL  CAI   105.69  3.000
 SY9  HAL2  CAL  CAM   108.77  3.000
 SY9  HAL1  CAL  CAM   110.19  3.000
 SY9  CAI   CAL  CAM   118.72  3.000
 SY9  OAJ   CAI  CAL   120.52  3.000
 SY9  OAJ   CAI  NAH   122.79  3.000
 SY9  CAL   CAI  NAH   116.68  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
 SY9  CONST_01  CAD  CAE  CAF  CAA    0.00   0.0  0
 SY9  CONST_02  CAD  CAC  CAB  CAA    0.00   0.0  0
 SY9  CONST_03  CAC  CAB  CAA  CAF    0.00   0.0  0
 SY9  CONST_04  CAC  CAD  CAE  CAF    0.00   0.0  0
 SY9  CONST_05  CAB  CAA  CAF  CAE    0.00   0.0  0
 SY9  CONST_06  CAB  CAC  CAD  CAE    0.00   0.0  0
 SY9  CONST_07  CAL  CAI  NAH  CAK    0.00   0.0  0
 SY9  CONST_08  CAL  CAI  NAH  CAA  180.00   0.0  0
 SY9  CONST_09  OAJ  CAI  NAH  CAK  180.00   0.0  0
 SY9  CONST_11  HAF  CAF  CAA  NAH    0.00   0.0  0
 SY9  CONST_12  HAE  CAE  CAF  CAA  180.00   0.0  0
 SY9  CONST_13  HAC  CAC  CAB  CAA  180.00   0.0  0
 SY9  CONST_14  HAD  CAD  CAE  CAF  180.00   0.0  0
 SY9  Var_01    CAF  CAA  NAH  CAK  177.56  30.0  1
 SY9  Var_02    CAM  CAL  CAI  NAH  -24.41  30.0  1
 SY9  Var_03    NAY  CAX  CAW  CAG  -26.90  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
 SY9  chir_01  CAV  CAU  CAG  NAY  negativ
 SY9  chir_02  CAT  CAU  CAN  CAR  positiv
 SY9  chir_03  CAN  CAM  CAK  CAT  negativ
 SY9  chir_04  CAK  NAH  CAG  CAN  positiv
 SY9  chir_05  CAG  CAB  CAK  CAV  negativ
 SY9  chir_06  NAY  CAS  CAX  CAV  positiv
 SY9  chir_07  CAM  OAO  CAL  CAN  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
 SY9  plan-1  CAK  0.020
 SY9  plan-1  NAH  0.020
 SY9  plan-1  CAA  0.020
 SY9  plan-1  CAL  0.020
 SY9  plan-1  CAI  0.020
 SY9  plan-1  OAJ  0.020
 SY9  plan-2  NAH  0.020
 SY9  plan-2  CAA  0.020
 SY9  plan-2  CAF  0.020
 SY9  plan-2  CAE  0.020
 SY9  plan-2  CAD  0.020
 SY9  plan-2  CAC  0.020
 SY9  plan-2  CAB  0.020
 SY9  plan-2  CAG  0.020
 SY9  plan-2  HAF  0.020
 SY9  plan-2  HAE  0.020
 SY9  plan-2  HAD  0.020
 SY9  plan-2  HAC  0.020

