# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:29:05 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2C(=O)c3cccc(CC(O)=O)c3Oc2c1C
#
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
 1YE  1YE  '(5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid'  ligand  34  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1YE
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
 1YE  OAD  O  O      0  -0.436   1.1238  -3.4427  -0.4269
 1YE  CAQ  C  CR6    0   0.422   0.7634  -2.2892  -0.2412
 1YE  CAS  C  CR66   0  -0.059   1.7015  -1.1689  -0.1618
 1YE  CAJ  C  CR16   0  -0.221   3.0744  -1.3688  -0.3294
 1YE  CAH  C  CR16   0  -0.324   3.9392  -0.3007  -0.2668
 1YE  CAN  C  CR6    0  -0.105   3.4618   0.9964  -0.0377
 1YE  CAA  C  CH3    0  -0.671   4.4335   2.1400   0.0230
 1YE  CAO  C  CR6    0   0.041   2.0965   1.2278   0.1312
 1YE  CAB  C  CH3    0  -0.715   1.5905   2.6159   0.3945
 1YE  CAT  C  CR66   0   0.290   1.2375   0.1266   0.0708
 1YE  OAL  O  O      0  -0.466  -0.0756   0.3751   0.2558
 1YE  CAU  C  CR66   0   0.316  -1.0008  -0.5996   0.1615
 1YE  CAR  C  CR66   0  -0.153  -0.6481  -1.9244  -0.0849
 1YE  CAI  C  CR16   0  -0.293  -1.6570  -2.8925  -0.1600
 1YE  CAF  C  CR16   0  -0.275  -2.9719  -2.5291   0.0169
 1YE  CAG  C  CR16   0  -0.323  -3.2923  -1.1971   0.2922
 1YE  CAP  C  CR6    0   0.133  -2.3309  -0.2074   0.3797
 1YE  CAK  C  CH2    0  -0.666  -2.6724   1.1917   0.7759
 1YE  CAM  C  C      0   0.443  -2.4550   2.2883  -0.2904
 1YE  OAE  O  OC    -1  -0.680  -2.3646   3.4529   0.1477
 1YE  OAC  O  O      0  -0.521  -2.4351   1.9356  -1.4745
 1YE  H1   H  HCR6   0   0.267   3.4471  -2.3690  -0.5040
 1YE  H2   H  HCR6   0   0.226   5.0036  -0.4589  -0.3880
 1YE  H3   H  HCH3   0   0.281   4.2484   2.8520  -0.7840
 1YE  H4   H  HCH3   0   0.231   4.3505   2.6950   0.9585
 1YE  H5   H  HCH3   0   0.286   5.4589   1.7897  -0.0696
 1YE  H6   H  HCH3   0   0.231   0.5118   2.7040   0.2842
 1YE  H7   H  HCH3   0   0.259   1.8467   2.9395   1.4054
 1YE  H8   H  HCH3   0   0.248   2.0456   3.3275  -0.2956
 1YE  H9   H  HCR6   0   0.243  -1.3841  -3.9199  -0.3455
 1YE  H10  H  HCR6   0   0.258  -3.7579  -3.2714  -0.0440
 1YE  H11  H  HCR6   0   0.242  -4.3268  -0.9206   0.4472
 1YE  H12  H  HCH2   0   0.256  -3.7322   1.2247   1.0487
 1YE  H13  H  HCH2   0   0.235  -2.1321   1.4747   1.6822

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
 1YE  CAG  CAF  aromatic  1.397  0.020  1.397
 1YE  CAG  CAP  aromatic  1.383  0.020  1.383
 1YE  CAK  CAM  single    1.545  0.020  1.545
 1YE  CAK  CAP  single    1.494  0.020  1.494
 1YE  CAF  CAI  aromatic  1.376  0.020  1.376
 1YE  CAM  OAC  deloc     1.236  0.020  1.236
 1YE  CAM  OAE  deloc     1.247  0.020  1.247
 1YE  CAP  CAU  aromatic  1.404  0.020  1.404
 1YE  CAI  CAR  aromatic  1.400  0.020  1.400
 1YE  CAU  CAR  aromatic  1.393  0.020  1.393
 1YE  CAU  OAL  single    1.347  0.020  1.347
 1YE  CAR  CAQ  single    1.466  0.020  1.466
 1YE  OAL  CAT  single    1.349  0.020  1.349
 1YE  CAQ  OAD  double    1.223  0.020  1.223
 1YE  CAQ  CAS  single    1.463  0.020  1.463
 1YE  CAT  CAS  aromatic  1.396  0.020  1.396
 1YE  CAT  CAO  aromatic  1.398  0.020  1.398
 1YE  CAB  CAO  single    1.501  0.020  1.501
 1YE  CAS  CAJ  aromatic  1.398  0.020  1.398
 1YE  CAO  CAN  aromatic  1.395  0.020  1.395
 1YE  CAJ  CAH  aromatic  1.376  0.020  1.376
 1YE  CAN  CAH  aromatic  1.401  0.020  1.401
 1YE  CAN  CAA  single    1.502  0.020  1.502
 1YE  CAJ  H1   single    0.930  0.020  1.080
 1YE  CAH  H2   single    0.930  0.020  1.080
 1YE  CAA  H3   single    0.970  0.020  1.090
 1YE  CAA  H4   single    0.970  0.020  1.090
 1YE  CAA  H5   single    0.970  0.020  1.090
 1YE  CAB  H6   single    0.970  0.020  1.090
 1YE  CAB  H7   single    0.970  0.020  1.090
 1YE  CAB  H8   single    0.970  0.020  1.090
 1YE  CAI  H9   single    0.930  0.020  1.080
 1YE  CAF  H10  single    0.930  0.020  1.080
 1YE  CAG  H11  single    0.930  0.020  1.080
 1YE  CAK  H12  single    0.970  0.020  1.090
 1YE  CAK  H13  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
 1YE  CAR  CAQ  CAS  114.89  3.000
 1YE  CAS  CAQ  OAD  122.79  3.000
 1YE  CAR  CAQ  OAD  122.32  3.000
 1YE  CAT  CAS  CAJ  118.65  3.000
 1YE  CAJ  CAS  CAQ  120.91  3.000
 1YE  CAT  CAS  CAQ  120.44  3.000
 1YE  H1   CAJ  CAH  120.58  3.000
 1YE  H1   CAJ  CAS  119.35  3.000
 1YE  CAH  CAJ  CAS  120.07  3.000
 1YE  H2   CAH  CAN  119.24  3.000
 1YE  H2   CAH  CAJ  119.96  3.000
 1YE  CAN  CAH  CAJ  120.80  3.000
 1YE  CAO  CAN  CAA  120.13  3.000
 1YE  CAA  CAN  CAH  119.41  3.000
 1YE  CAO  CAN  CAH  120.46  3.000
 1YE  H5   CAA  H4   107.97  3.000
 1YE  H5   CAA  H3   107.87  3.000
 1YE  H4   CAA  H3   106.80  3.000
 1YE  H5   CAA  CAN  111.18  3.000
 1YE  H4   CAA  CAN  111.89  3.000
 1YE  H3   CAA  CAN  110.91  3.000
 1YE  CAT  CAO  CAB  121.94  3.000
 1YE  CAB  CAO  CAN  120.31  3.000
 1YE  CAT  CAO  CAN  117.74  3.000
 1YE  H8   CAB  H7   107.12  3.000
 1YE  H8   CAB  H6   107.26  3.000
 1YE  H7   CAB  H6   107.61  3.000
 1YE  H8   CAB  CAO  110.59  3.000
 1YE  H7   CAB  CAO  110.94  3.000
 1YE  H6   CAB  CAO  113.05  3.000
 1YE  OAL  CAT  CAO  116.55  3.000
 1YE  CAO  CAT  CAS  122.29  3.000
 1YE  OAL  CAT  CAS  121.16  3.000
 1YE  CAU  OAL  CAT  121.70  3.000
 1YE  CAP  CAU  CAR  122.22  3.000
 1YE  CAR  CAU  OAL  121.78  3.000
 1YE  CAP  CAU  OAL  115.96  3.000
 1YE  CAI  CAR  CAU  118.98  3.000
 1YE  CAU  CAR  CAQ  119.95  3.000
 1YE  CAI  CAR  CAQ  121.06  3.000
 1YE  H9   CAI  CAF  121.02  3.000
 1YE  H9   CAI  CAR  119.03  3.000
 1YE  CAF  CAI  CAR  119.95  3.000
 1YE  H10  CAF  CAG  119.87  3.000
 1YE  H10  CAF  CAI  120.37  3.000
 1YE  CAG  CAF  CAI  119.76  3.000
 1YE  H11  CAG  CAP  118.22  3.000
 1YE  H11  CAG  CAF  119.41  3.000
 1YE  CAP  CAG  CAF  122.36  3.000
 1YE  CAK  CAP  CAG  121.89  3.000
 1YE  CAK  CAP  CAU  121.30  3.000
 1YE  CAG  CAP  CAU  116.69  3.000
 1YE  H13  CAK  H12  105.32  3.000
 1YE  H13  CAK  CAM  108.61  3.000
 1YE  H12  CAK  CAM  106.67  3.000
 1YE  H13  CAK  CAP  110.46  3.000
 1YE  H12  CAK  CAP  108.40  3.000
 1YE  CAM  CAK  CAP  116.72  3.000
 1YE  OAC  CAM  OAE  127.00  3.000
 1YE  OAE  CAM  CAK  115.49  3.000
 1YE  OAC  CAM  CAK  117.45  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
 1YE  CONST_01  CAN  CAO  CAT  CAS     0.00   0.0  0
 1YE  CONST_02  CAN  CAH  CAJ  CAS     0.00   0.0  0
 1YE  CONST_03  CAO  CAT  CAS  CAJ     0.00   0.0  0
 1YE  CONST_04  CAO  CAN  CAH  CAJ     0.00   0.0  0
 1YE  CONST_05  CAT  CAS  CAJ  CAH     0.00   0.0  0
 1YE  CONST_06  CAT  CAO  CAN  CAH     0.00   0.0  0
 1YE  CONST_07  CAF  CAG  CAP  CAU     0.00   0.0  0
 1YE  CONST_08  CAF  CAI  CAR  CAU     0.00   0.0  0
 1YE  CONST_09  CAG  CAF  CAI  CAR     0.00   0.0  0
 1YE  CONST_10  CAG  CAP  CAU  CAR     0.00   0.0  0
 1YE  CONST_11  CAP  CAG  CAF  CAI     0.00   0.0  0
 1YE  CONST_12  CAP  CAU  CAR  CAI     0.00   0.0  0
 1YE  CONST_13  CAB  CAO  CAT  CAS   180.00   0.0  0
 1YE  CONST_14  CAA  CAN  CAH  CAJ   180.00   0.0  0
 1YE  CONST_15  CAB  CAO  CAN  CAH   180.00   0.0  0
 1YE  CONST_16  CAT  CAO  CAN  CAA   180.00   0.0  0
 1YE  CONST_17  OAL  CAT  CAO  CAB     0.00   0.0  0
 1YE  CONST_18  CAK  CAP  CAU  OAL     0.00   0.0  0
 1YE  CONST_19  CAK  CAP  CAU  CAR   180.00   0.0  0
 1YE  CONST_20  CAK  CAP  CAG  CAF   180.00   0.0  0
 1YE  CONST_21  H9   CAI  CAR  CAQ     0.00   0.0  0
 1YE  CONST_22  H1   CAJ  CAS  CAQ     0.00   0.0  0
 1YE  CONST_23  H2   CAH  CAJ  CAS   180.00   0.0  0
 1YE  CONST_24  H11  CAG  CAP  CAU   180.00   0.0  0
 1YE  CONST_25  H10  CAF  CAI  CAR   180.00   0.0  0
 1YE  Var_01    CAI  CAR  CAQ  CAS   178.98  30.0  1
 1YE  Var_02    CAR  CAQ  CAS  CAJ  -178.28  30.0  1
 1YE  Var_03    CAP  CAU  OAL  CAT   179.85  30.0  1
 1YE  Var_04    CAM  CAK  CAP  CAU    68.80  30.0  3
 1YE  Var_05    H3   CAA  CAN  CAH   116.68  30.0  2
 1YE  Var_06    H6   CAB  CAO  CAN   166.98  30.0  2
 1YE  Var_07    OAC  CAM  CAK  CAP    22.46  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
 1YE  plan-1  OAD  0.020
 1YE  plan-1  CAQ  0.020
 1YE  plan-1  CAS  0.020
 1YE  plan-1  CAR  0.020
 1YE  plan-2  CAQ  0.020
 1YE  plan-2  CAS  0.020
 1YE  plan-2  CAJ  0.020
 1YE  plan-2  CAH  0.020
 1YE  plan-2  CAN  0.020
 1YE  plan-2  CAA  0.020
 1YE  plan-2  CAO  0.020
 1YE  plan-2  CAB  0.020
 1YE  plan-2  CAT  0.020
 1YE  plan-2  OAL  0.020
 1YE  plan-2  H1   0.020
 1YE  plan-2  H2   0.020
 1YE  plan-3  CAQ  0.020
 1YE  plan-3  OAL  0.020
 1YE  plan-3  CAU  0.020
 1YE  plan-3  CAR  0.020
 1YE  plan-3  CAI  0.020
 1YE  plan-3  CAF  0.020
 1YE  plan-3  CAG  0.020
 1YE  plan-3  CAP  0.020
 1YE  plan-3  CAK  0.020
 1YE  plan-3  H9   0.020
 1YE  plan-3  H10  0.020
 1YE  plan-3  H11  0.020
 1YE  plan-4  CAK  0.020
 1YE  plan-4  CAM  0.020
 1YE  plan-4  OAE  0.020
 1YE  plan-4  OAC  0.020

