# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:32:02 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(1-oxo-1H-inden-5-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc2C(=O)C=Cc2c1
#
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
 3VX  3VX  N-(1-oxo-1H-inden-5-yl)acetamide  ligand  23  14  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3VX
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
 3VX  CAA  C  CH3   0  -0.782   4.7882  -0.0984  -0.0776
 3VX  CAJ  C  C     0   0.523   3.3714   0.4128  -0.1035
 3VX  OAB  O  O     0  -0.465   3.1178   1.6029  -0.1203
 3VX  NAI  N  NH1   0  -0.739   2.4214  -0.5649  -0.0962
 3VX  CAL  C  CR6   0   0.396   1.0348  -0.4562  -0.0903
 3VX  CAF  C  CR16  0  -0.389   0.3483   0.7758  -0.1187
 3VX  CAM  C  CR56  0   0.143  -1.0255   0.7393  -0.1101
 3VX  CAH  C  CR15  0  -0.230  -2.0025   1.8499  -0.1348
 3VX  CAG  C  CR15  0  -0.362  -3.2487   1.3633  -0.1162
 3VX  CAK  C  CR5   0   0.342  -3.1821  -0.1283  -0.0772
 3VX  OAC  O  O     0  -0.371  -4.1117  -0.9010  -0.0535
 3VX  CAN  C  CR56  0  -0.074  -1.7346  -0.4605  -0.0749
 3VX  CAE  C  CR16  0  -0.261  -1.0728  -1.6661  -0.0473
 3VX  CAD  C  CR16  0  -0.361   0.3184  -1.6557  -0.0550
 3VX  H1   H  HCH3  0   0.257   4.8711  -1.1812  -0.1407
 3VX  H2   H  HCH3  0   0.274   5.3441   0.3411  -0.9051
 3VX  H3   H  HCH3  0   0.276   5.2666   0.2294   0.8458
 3VX  H4   H  HNH1  0   0.420   2.7675  -1.5123  -0.0840
 3VX  H5   H  HCR6  0   0.291   0.8800   1.7128  -0.1474
 3VX  H6   H  HCR5  0   0.282  -1.7217   2.8933  -0.1640
 3VX  H7   H  HCR5  0   0.280  -4.1705   1.9255  -0.1275
 3VX  H8   H  HCR6  0   0.270  -1.6070  -2.6073  -0.0191
 3VX  H9   H  HCR6  0   0.279   0.8577  -2.5949  -0.0315

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
 3VX  OAB  CAJ  double    1.217  0.020  1.217
 3VX  CAA  CAJ  single    1.506  0.020  1.506
 3VX  CAJ  NAI  single    1.363  0.020  1.363
 3VX  NAI  CAL  single    1.391  0.020  1.391
 3VX  CAL  CAD  aromatic  1.398  0.020  1.398
 3VX  CAL  CAF  aromatic  1.411  0.020  1.411
 3VX  CAD  CAE  aromatic  1.391  0.020  1.391
 3VX  CAF  CAM  aromatic  1.374  0.020  1.374
 3VX  CAE  CAN  aromatic  1.376  0.020  1.376
 3VX  CAM  CAN  aromatic  1.394  0.020  1.394
 3VX  CAM  CAH  single    1.479  0.020  1.479
 3VX  CAN  CAK  single    1.485  0.020  1.485
 3VX  CAH  CAG  double    1.338  0.020  1.338
 3VX  CAK  OAC  double    1.209  0.020  1.209
 3VX  CAK  CAG  single    1.494  0.020  1.494
 3VX  CAA  H1   single    0.970  0.020  1.090
 3VX  CAA  H2   single    0.970  0.020  1.090
 3VX  CAA  H3   single    0.970  0.020  1.090
 3VX  NAI  H4   single    0.860  0.020  1.020
 3VX  CAF  H5   single    0.930  0.020  1.080
 3VX  CAH  H6   single    0.930  0.020  1.080
 3VX  CAG  H7   single    0.930  0.020  1.080
 3VX  CAE  H8   single    0.930  0.020  1.080
 3VX  CAD  H9   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
 3VX  H3   CAA  H2   107.35  3.000
 3VX  H3   CAA  H1   108.36  3.000
 3VX  H2   CAA  H1   108.58  3.000
 3VX  H3   CAA  CAJ  108.97  3.000
 3VX  H2   CAA  CAJ  109.27  3.000
 3VX  H1   CAA  CAJ  114.11  3.000
 3VX  NAI  CAJ  OAB  123.79  3.000
 3VX  NAI  CAJ  CAA  114.33  3.000
 3VX  OAB  CAJ  CAA  121.88  3.000
 3VX  H4   NAI  CAL  114.54  3.000
 3VX  H4   NAI  CAJ  115.76  3.000
 3VX  CAL  NAI  CAJ  129.70  3.000
 3VX  CAD  CAL  CAF  120.04  3.000
 3VX  CAF  CAL  NAI  123.60  3.000
 3VX  CAD  CAL  NAI  116.37  3.000
 3VX  H5   CAF  CAM  121.10  3.000
 3VX  H5   CAF  CAL  121.31  3.000
 3VX  CAM  CAF  CAL  117.59  3.000
 3VX  CAN  CAM  CAH  108.09  3.000
 3VX  CAH  CAM  CAF  129.80  3.000
 3VX  CAN  CAM  CAF  122.10  3.000
 3VX  H6   CAH  CAG  126.40  3.000
 3VX  H6   CAH  CAM  123.61  3.000
 3VX  CAG  CAH  CAM  109.99  3.000
 3VX  H7   CAG  CAK  123.94  3.000
 3VX  H7   CAG  CAH  127.27  3.000
 3VX  CAK  CAG  CAH  108.78  3.000
 3VX  CAN  CAK  OAC  127.33  3.000
 3VX  OAC  CAK  CAG  127.19  3.000
 3VX  CAN  CAK  CAG  105.48  3.000
 3VX  CAE  CAN  CAK  131.68  3.000
 3VX  CAK  CAN  CAM  107.65  3.000
 3VX  CAE  CAN  CAM  120.67  3.000
 3VX  H8   CAE  CAD  120.01  3.000
 3VX  H8   CAE  CAN  121.67  3.000
 3VX  CAD  CAE  CAN  118.32  3.000
 3VX  H9   CAD  CAE  119.42  3.000
 3VX  H9   CAD  CAL  119.30  3.000
 3VX  CAE  CAD  CAL  121.28  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
 3VX  CONST_01  CAN  CAE  CAD  CAL     0.00   0.0  0
 3VX  CONST_02  CAN  CAM  CAF  CAL     0.00   0.0  0
 3VX  CONST_03  CAE  CAD  CAL  CAF     0.00   0.0  0
 3VX  CONST_04  CAE  CAN  CAM  CAF     0.00   0.0  0
 3VX  CONST_05  CAD  CAL  CAF  CAM     0.00   0.0  0
 3VX  CONST_06  CAD  CAE  CAN  CAM     0.00   0.0  0
 3VX  CONST_07  CAE  CAD  CAL  NAI   180.00   0.0  0
 3VX  CONST_08  CAM  CAF  CAL  NAI   180.00   0.0  0
 3VX  CONST_09  H8   CAE  CAD  CAL   180.00   0.0  0
 3VX  CONST_10  H9   CAD  CAL  CAF   180.00   0.0  0
 3VX  CONST_11  H5   CAF  CAM  CAH     0.00   0.0  0
 3VX  CONST_12  CAD  CAL  NAI  CAJ   180.00   0.0  0
 3VX  CONST_13  CAF  CAL  NAI  CAJ     0.00   0.0  0
 3VX  CONST_14  H4   NAI  CAL  CAF   180.00   0.0  0
 3VX  CONST_15  CAL  NAI  CAJ  CAA   180.00   0.0  0
 3VX  CONST_16  CAL  NAI  CAJ  OAB     0.00   0.0  0
 3VX  Var_01    H1   CAA  CAJ  OAB  -175.60  30.0  3

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
 3VX  plan-1  CAA  0.020
 3VX  plan-1  CAJ  0.020
 3VX  plan-1  OAB  0.020
 3VX  plan-1  NAI  0.020
 3VX  plan-1  CAL  0.020
 3VX  plan-1  H4   0.020
 3VX  plan-2  NAI  0.020
 3VX  plan-2  CAL  0.020
 3VX  plan-2  CAF  0.020
 3VX  plan-2  CAM  0.020
 3VX  plan-2  CAH  0.020
 3VX  plan-2  CAG  0.020
 3VX  plan-2  CAK  0.020
 3VX  plan-2  OAC  0.020
 3VX  plan-2  CAN  0.020
 3VX  plan-2  CAE  0.020
 3VX  plan-2  CAD  0.020
 3VX  plan-2  H5   0.020
 3VX  plan-2  H6   0.020
 3VX  plan-2  H7   0.020
 3VX  plan-2  H8   0.020
 3VX  plan-2  H9   0.020

