# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 01:31:36 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (3S)-3-[2-(1,3-benzodioxol-5-yl)-2-oxoethyl]-4-bromo-3-hydroxy-5-methyl-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2NC(=O)[C@](O)(CC(=O)c3ccc4OCOc4c3)c2c1Br
#
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
 9VU  9VU  (3S)-3-[2-(1,3-benzodioxol-5-yl)-2-oxoethyl]-4-bromo-3-hydroxy-5-methyl-1,3-dihydro-2H-indol-2-one  ligand  39  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9VU
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
 9VU  OAN   O   O     0  -0.432  -0.0294   3.2116  -0.2850
 9VU  CAH   C   CR5   0   0.539   0.8742   2.4660   0.0164
 9VU  NAG   N   NR15  0  -0.738   1.8176   2.6786   0.9661
 9VU  CAC   C   CR56  0   0.360   2.7553   1.6538   1.0107
 9VU  CAB   C   CR16  0  -0.284   3.8732   1.5547   1.8109
 9VU  CAA   C   CR16  0  -0.326   4.6800   0.4350   1.6457
 9VU  CAF   C   CR6   0   0.136   4.4113  -0.5658   0.7147
 9VU  CAJ   C   CH3   0  -0.721   5.3391  -1.7361   0.5809
 9VU  CAE   C   CR6   0  -0.282   3.2598  -0.4167  -0.0717
 9VU  BRA   BR  BR    0  -0.036   2.8538  -1.7247  -1.3713
 9VU  CAD   C   CR56  0   0.175   2.4289   0.6739   0.0772
 9VU  CAI   C   CR5   0   0.045   1.1422   1.0669  -0.6054
 9VU  OAL   O   OH1   0  -0.661   1.3139   1.1484  -1.9833
 9VU  CAM   C   CH2   0  -0.629  -0.0106   0.1482  -0.1569
 9VU  CAO   C   C     0   0.412  -1.3382   0.4379  -0.8257
 9VU  OAP   O   O     0  -0.426  -1.3746   0.9055  -1.9523
 9VU  CAQ   C   CR6   0  -0.025  -2.5909   0.0909  -0.1247
 9VU  CAV   C   CR16  0  -0.359  -3.8101   0.4501  -0.7403
 9VU  CAU   C   CR56  0   0.324  -4.9609   0.1015  -0.0951
 9VU  OAY   O   O     0  -0.483  -6.2404   0.3351  -0.4644
 9VU  CAX   C   CH2   0   0.072  -7.0734  -0.2326   0.5368
 9VU  OAW   O   O     0  -0.472  -6.2113  -0.8033   1.5196
 9VU  CAT   C   CR56  0   0.321  -4.9510  -0.5906   1.1114
 9VU  CAS   C   CR16  0  -0.325  -3.7796  -0.9609   1.7255
 9VU  CAR   C   CR16  0  -0.301  -2.5934  -0.6015   1.0836
 9VU  HAG   H   HNR5  0   0.417   1.8743   3.5209   1.5197
 9VU  HAB   H   HCR6  0   0.277   4.1233   2.3185   2.5347
 9VU  HAA   H   HCR6  0   0.266   5.5639   0.3394   2.2639
 9VU  HAJ1  H   HCH3  0   0.251   4.8289  -2.6851   0.7520
 9VU  HAJ2  H   HCH3  0   0.251   5.7912  -1.7850  -0.4111
 9VU  HAJ3  H   HCH3  0   0.254   6.1474  -1.6621   1.3063
 9VU  HAL   H   HOH1  0   0.460   0.4252   1.2032  -2.3714
 9VU  HAM1  H   HCH2  0   0.320   0.2285  -0.8954  -0.3886
 9VU  HAM2  H   HCH2  0   0.290  -0.0943   0.1999   0.9289
 9VU  HAV   H   HCR6  0   0.281  -3.8291   0.9840  -1.6803
 9VU  HAR   H   HCR6  0   0.271  -1.6646  -0.8904   1.5537
 9VU  HAX1  H   HCH2  0   0.247  -7.6889   0.5434   0.9962
 9VU  HAX2  H   HCH2  0   0.247  -7.7006  -1.0138   0.1024
 9VU  HAS   H   HCR6  0   0.285  -3.7703  -1.5033   2.6605

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
 9VU  OAN  CAH   double    1.210  0.020  1.210
 9VU  CAH  NAG   single    1.355  0.020  1.355
 9VU  CAH  CAI   single    1.554  0.020  1.554
 9VU  NAG  CAC   single    1.390  0.020  1.390
 9VU  CAC  CAB   aromatic  1.378  0.020  1.378
 9VU  CAC  CAD   aromatic  1.392  0.020  1.392
 9VU  CAB  CAA   aromatic  1.390  0.020  1.390
 9VU  CAA  CAF   aromatic  1.393  0.020  1.393
 9VU  CAF  CAJ   single    1.499  0.020  1.499
 9VU  CAF  CAE   aromatic  1.402  0.020  1.402
 9VU  CAE  BRA   single    1.888  0.020  1.888
 9VU  CAE  CAD   aromatic  1.379  0.020  1.379
 9VU  CAD  CAI   single    1.509  0.020  1.509
 9VU  CAI  OAL   single    1.391  0.020  1.391
 9VU  CAI  CAM   single    1.541  0.020  1.541
 9VU  CAM  CAO   single    1.514  0.020  1.514
 9VU  CAO  OAP   double    1.220  0.020  1.220
 9VU  CAO  CAQ   single    1.477  0.020  1.477
 9VU  CAQ  CAV   aromatic  1.412  0.020  1.412
 9VU  CAQ  CAR   aromatic  1.393  0.020  1.393
 9VU  CAV  CAU   aromatic  1.365  0.020  1.365
 9VU  CAU  OAY   single    1.352  0.020  1.352
 9VU  CAU  CAT   aromatic  1.391  0.020  1.391
 9VU  OAY  CAX   single    1.421  0.020  1.421
 9VU  CAX  OAW   single    1.427  0.020  1.427
 9VU  OAW  CAT   single    1.342  0.020  1.342
 9VU  CAT  CAS   aromatic  1.374  0.020  1.374
 9VU  CAS  CAR   aromatic  1.396  0.020  1.396
 9VU  NAG  HAG   single    0.860  0.020  1.020
 9VU  CAB  HAB   single    0.930  0.020  1.080
 9VU  CAA  HAA   single    0.930  0.020  1.080
 9VU  CAJ  HAJ1  single    0.970  0.020  1.090
 9VU  CAJ  HAJ2  single    0.970  0.020  1.090
 9VU  CAJ  HAJ3  single    0.970  0.020  1.090
 9VU  OAL  HAL   single    0.850  0.020  0.980
 9VU  CAM  HAM1  single    0.970  0.020  1.090
 9VU  CAM  HAM2  single    0.970  0.020  1.090
 9VU  CAV  HAV   single    0.930  0.020  1.080
 9VU  CAR  HAR   single    0.930  0.020  1.080
 9VU  CAX  HAX1  single    0.970  0.020  1.090
 9VU  CAX  HAX2  single    0.970  0.020  1.090
 9VU  CAS  HAS   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
 9VU  CAI   CAH  NAG   107.54  3.000
 9VU  CAI   CAH  OAN   125.73  3.000
 9VU  NAG   CAH  OAN   126.71  3.000
 9VU  HAG   NAG  CAC   124.04  3.000
 9VU  HAG   NAG  CAH   123.65  3.000
 9VU  CAC   NAG  CAH   112.11  3.000
 9VU  CAD   CAC  CAB   121.92  3.000
 9VU  CAD   CAC  NAG   109.84  3.000
 9VU  CAB   CAC  NAG   128.23  3.000
 9VU  HAB   CAB  CAA   120.94  3.000
 9VU  HAB   CAB  CAC   121.69  3.000
 9VU  CAA   CAB  CAC   117.37  3.000
 9VU  HAA   CAA  CAF   118.40  3.000
 9VU  HAA   CAA  CAB   118.49  3.000
 9VU  CAF   CAA  CAB   123.11  3.000
 9VU  CAE   CAF  CAJ   122.75  3.000
 9VU  CAE   CAF  CAA   117.18  3.000
 9VU  CAJ   CAF  CAA   120.07  3.000
 9VU  HAJ3  CAJ  HAJ2  107.52  3.000
 9VU  HAJ3  CAJ  HAJ1  107.58  3.000
 9VU  HAJ2  CAJ  HAJ1  107.30  3.000
 9VU  HAJ3  CAJ  CAF   110.30  3.000
 9VU  HAJ2  CAJ  CAF   111.86  3.000
 9VU  HAJ1  CAJ  CAF   112.06  3.000
 9VU  CAD   CAE  BRA   119.51  3.000
 9VU  CAD   CAE  CAF   121.21  3.000
 9VU  BRA   CAE  CAF   119.27  3.000
 9VU  CAI   CAD  CAE   132.14  3.000
 9VU  CAI   CAD  CAC   108.66  3.000
 9VU  CAE   CAD  CAC   119.20  3.000
 9VU  CAM   CAI  OAL   114.56  3.000
 9VU  CAM   CAI  CAD   110.56  3.000
 9VU  OAL   CAI  CAD   110.99  3.000
 9VU  CAM   CAI  CAH   106.93  3.000
 9VU  OAL   CAI  CAH   111.39  3.000
 9VU  CAD   CAI  CAH   101.57  3.000
 9VU  HAL   OAL  CAI   106.63  3.000
 9VU  HAM2  CAM  HAM1  105.81  3.000
 9VU  HAM2  CAM  CAO   111.31  3.000
 9VU  HAM1  CAM  CAO   106.28  3.000
 9VU  HAM2  CAM  CAI   108.60  3.000
 9VU  HAM1  CAM  CAI   110.07  3.000
 9VU  CAO   CAM  CAI   114.41  3.000
 9VU  CAQ   CAO  OAP   120.19  3.000
 9VU  CAQ   CAO  CAM   119.28  3.000
 9VU  OAP   CAO  CAM   120.47  3.000
 9VU  CAR   CAQ  CAV   120.20  3.000
 9VU  CAR   CAQ  CAO   122.02  3.000
 9VU  CAV   CAQ  CAO   117.75  3.000
 9VU  HAV   CAV  CAU   121.49  3.000
 9VU  HAV   CAV  CAQ   121.31  3.000
 9VU  CAU   CAV  CAQ   117.19  3.000
 9VU  CAT   CAU  OAY   109.24  3.000
 9VU  CAT   CAU  CAV   122.09  3.000
 9VU  OAY   CAU  CAV   128.67  3.000
 9VU  CAX   OAY  CAU   107.06  3.000
 9VU  HAX2  CAX  HAX1  110.61  3.000
 9VU  HAX2  CAX  OAW   109.57  3.000
 9VU  HAX1  CAX  OAW   109.58  3.000
 9VU  HAX2  CAX  OAY   110.02  3.000
 9VU  HAX1  CAX  OAY   110.06  3.000
 9VU  OAW   CAX  OAY   106.92  3.000
 9VU  CAT   OAW  CAX   107.13  3.000
 9VU  CAS   CAT  OAW   128.49  3.000
 9VU  CAS   CAT  CAU   121.87  3.000
 9VU  OAW   CAT  CAU   109.64  3.000
 9VU  HAS   CAS  CAR   121.31  3.000
 9VU  HAS   CAS  CAT   121.96  3.000
 9VU  CAR   CAS  CAT   116.73  3.000
 9VU  HAR   CAR  CAS   117.49  3.000
 9VU  HAR   CAR  CAQ   120.59  3.000
 9VU  CAS   CAR  CAQ   121.91  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
 9VU  CONST_01  CAF   CAA  CAB  CAC     0.00   0.0  0
 9VU  CONST_02  CAF   CAE  CAD  CAC     0.00   0.0  0
 9VU  CONST_03  CAE   CAD  CAC  CAB     0.00   0.0  0
 9VU  CONST_04  CAE   CAF  CAA  CAB     0.00   0.0  0
 9VU  CONST_05  CAD   CAC  CAB  CAA     0.00   0.0  0
 9VU  CONST_06  CAD   CAE  CAF  CAA     0.00   0.0  0
 9VU  CONST_07  CAT   CAU  CAV  CAQ     0.00   0.0  0
 9VU  CONST_08  CAT   CAS  CAR  CAQ     0.00   0.0  0
 9VU  CONST_09  CAS   CAR  CAQ  CAV     0.00   0.0  0
 9VU  CONST_10  CAS   CAT  CAU  CAV     0.00   0.0  0
 9VU  CONST_11  CAR   CAQ  CAV  CAU     0.00   0.0  0
 9VU  CONST_12  CAR   CAS  CAT  CAU     0.00   0.0  0
 9VU  CONST_13  CAI   CAH  NAG  CAC     0.00   0.0  0
 9VU  CONST_14  BRA   CAE  CAD  CAC   180.00   0.0  0
 9VU  CONST_15  CAJ   CAF  CAA  CAB   180.00   0.0  0
 9VU  CONST_16  BRA   CAE  CAF  CAA   180.00   0.0  0
 9VU  CONST_17  CAD   CAE  CAF  CAJ   180.00   0.0  0
 9VU  CONST_18  CAI   CAD  CAE  BRA     0.00   0.0  0
 9VU  CONST_19  CAU   CAV  CAQ  CAO   180.00   0.0  0
 9VU  CONST_20  CAS   CAR  CAQ  CAO   180.00   0.0  0
 9VU  CONST_21  CAC   NAG  CAH  OAN   180.00   0.0  0
 9VU  CONST_22  HAB   CAB  CAC  NAG     0.00   0.0  0
 9VU  CONST_23  HAA   CAA  CAB  CAC   180.00   0.0  0
 9VU  CONST_24  HAS   CAS  CAR  CAQ   180.00   0.0  0
 9VU  CONST_25  HAR   CAR  CAQ  CAV   180.00   0.0  0
 9VU  CONST_26  HAV   CAV  CAU  OAY     0.00   0.0  0
 9VU  CONST_27  HAG   NAG  CAH  CAI   180.00   0.0  0
 9VU  Var_01    OAW   CAX  OAY  CAU     0.44  30.0  1
 9VU  Var_02    CAT   CAU  OAY  CAX    -0.28  30.0  1
 9VU  Var_03    CAS   CAT  OAW  CAX  -179.81  30.0  1
 9VU  Var_04    CAQ   CAO  CAM  CAI  -153.49  30.0  3
 9VU  Var_05    CAV   CAQ  CAO  CAM   176.15  30.0  2
 9VU  Var_06    HAJ1  CAJ  CAF  CAA   121.77  30.0  2

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
 9VU  chir_01  CAI  CAD  CAH  CAM  positiv

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
 9VU  plan-1  CAO  0.020
 9VU  plan-1  CAQ  0.020
 9VU  plan-1  CAV  0.020
 9VU  plan-1  CAU  0.020
 9VU  plan-1  OAY  0.020
 9VU  plan-1  OAW  0.020
 9VU  plan-1  CAT  0.020
 9VU  plan-1  CAS  0.020
 9VU  plan-1  CAR  0.020
 9VU  plan-1  HAV  0.020
 9VU  plan-1  HAR  0.020
 9VU  plan-1  HAS  0.020
 9VU  plan-2  CAM  0.020
 9VU  plan-2  CAO  0.020
 9VU  plan-2  OAP  0.020
 9VU  plan-2  CAQ  0.020
 9VU  plan-3  OAN  0.020
 9VU  plan-3  CAH  0.020
 9VU  plan-3  NAG  0.020
 9VU  plan-3  CAC  0.020
 9VU  plan-3  CAB  0.020
 9VU  plan-3  CAA  0.020
 9VU  plan-3  CAF  0.020
 9VU  plan-3  CAJ  0.020
 9VU  plan-3  CAE  0.020
 9VU  plan-3  BRA  0.020
 9VU  plan-3  CAD  0.020
 9VU  plan-3  CAI  0.020
 9VU  plan-3  HAG  0.020
 9VU  plan-3  HAB  0.020
 9VU  plan-3  HAA  0.020

