# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:29:51 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2S)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CON=C1c2ccccc2c3ccccc13)C(O)=O
#
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
 6BD  6BD  '(2S)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methylpropanoic acid'  ligand  35  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6BD
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
 6BD  CAQ   C  CR56   0   0.032  -2.1083   1.1454   0.0073
 6BD  CAH   C  CR16   0  -0.297  -2.3384   2.5097   0.0355
 6BD  CAD   C  CR16   0  -0.262  -3.6554   2.9572   0.0641
 6BD  CAF   C  CR16   0  -0.249  -4.7154   2.0539   0.0642
 6BD  CAJ   C  CR16   0  -0.346  -4.4827   0.6825   0.0358
 6BD  CAS   C  CR56   0   0.105  -3.1721   0.2354   0.0073
 6BD  CAT   C  CR56   0   0.082  -2.6187  -1.1199  -0.0253
 6BD  CAK   C  CR16   0  -0.341  -3.2613  -2.3448  -0.0331
 6BD  CAG   C  CR16   0  -0.244  -2.4904  -3.5027  -0.0639
 6BD  CAE   C  CR16   0  -0.257  -1.1026  -3.4294  -0.0884
 6BD  CAI   C  CR16   0  -0.299  -0.4498  -2.1995  -0.0809
 6BD  CAR   C  CR56   0   0.042  -1.2134  -1.0409  -0.0481
 6BD  CAP   C  CR5    0   0.094  -0.8481   0.3866  -0.0250
 6BD  NAM   N  N      0  -0.084   0.2778   0.9868  -0.0232
 6BD  OAN   O  O2     0  -0.394   1.3351   0.1616  -0.0554
 6BD  CAL   C  CH2    0  -0.107   2.5637   0.8964  -0.0283
 6BD  CAU   C  CH1    0  -0.441   3.7057  -0.1001  -0.0629
 6BD  CAA   C  CH3    0  -0.661   3.6675  -1.0707   1.1163
 6BD  CAO   C  C      0   0.434   5.0716   0.6266  -0.1344
 6BD  OAC   O  O      0  -0.603   5.0560   1.8698  -0.2313
 6BD  OAB   O  OC    -1  -0.613   6.0831  -0.0998  -0.0962
 6BD  HAH   H  HCR6   0   0.256  -1.5173   3.2146   0.0356
 6BD  HAD   H  HCR6   0   0.261  -3.8579   4.0199   0.0864
 6BD  HAF   H  HCR6   0   0.262  -5.7324   2.4232   0.0869
 6BD  HAJ   H  HCR6   0   0.252  -5.3122  -0.0138   0.0359
 6BD  HAK   H  HCR6   0   0.253  -4.3420  -2.4093  -0.0146
 6BD  HAG   H  HCR6   0   0.264  -2.9765  -4.4696  -0.0691
 6BD  HAE   H  HCR6   0   0.262  -0.5179  -4.3394  -0.1141
 6BD  HAI   H  HCR6   0   0.269   0.6287  -2.1679  -0.1033
 6BD  HAL   H  HCH2   0   0.223   2.6000   1.5666  -0.8896
 6BD  HALA  H  HCH2   0   0.209   2.6018   1.5051   0.8805
 6BD  HAU   H  HCH1   0   0.233   3.6155  -0.6896  -0.9852
 6BD  HAA   H  HCH3   0   0.212   3.7113  -0.5360   2.0684
 6BD  HAAA  H  HCH3   0   0.225   2.7623  -1.6782   1.1209
 6BD  HAAB  H  HCH3   0   0.229   4.5195  -1.7459   1.0737

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
 6BD  CAQ  CAS   aromatic  1.400  0.020  1.400
 6BD  CAH  CAQ   aromatic  1.384  0.020  1.384
 6BD  CAH  CAD   aromatic  1.391  0.020  1.391
 6BD  CAH  HAH   single    0.930  0.020  1.080
 6BD  CAD  CAF   aromatic  1.393  0.020  1.393
 6BD  CAD  HAD   single    0.930  0.020  1.080
 6BD  CAF  CAJ   aromatic  1.391  0.020  1.391
 6BD  CAF  HAF   single    0.930  0.020  1.080
 6BD  CAJ  HAJ   single    0.930  0.020  1.080
 6BD  CAS  CAJ   aromatic  1.385  0.020  1.385
 6BD  CAT  CAS   aromatic  1.464  0.020  1.464
 6BD  CAT  CAK   aromatic  1.383  0.020  1.383
 6BD  CAK  HAK   single    0.930  0.020  1.080
 6BD  CAG  CAK   aromatic  1.391  0.020  1.391
 6BD  CAG  HAG   single    0.930  0.020  1.080
 6BD  CAE  CAG   aromatic  1.390  0.020  1.390
 6BD  CAE  HAE   single    0.930  0.020  1.080
 6BD  CAI  CAE   aromatic  1.392  0.020  1.392
 6BD  CAI  CAR   aromatic  1.388  0.020  1.388
 6BD  CAI  HAI   single    0.930  0.020  1.080
 6BD  CAR  CAT   aromatic  1.408  0.020  1.408
 6BD  CAP  CAQ   single    1.471  0.020  1.471
 6BD  CAP  CAR   single    1.474  0.020  1.474
 6BD  NAM  CAP   double    1.276  0.020  1.276
 6BD  OAN  NAM   single    1.342  0.020  1.342
 6BD  CAL  OAN   single    1.432  0.020  1.432
 6BD  CAL  HAL   single    0.970  0.020  1.090
 6BD  CAL  HALA  single    0.970  0.020  1.090
 6BD  CAU  CAL   single    1.516  0.020  1.516
 6BD  CAU  CAO   single    1.549  0.020  1.549
 6BD  CAU  HAU   single    0.970  0.020  1.090
 6BD  CAA  CAU   single    1.528  0.020  1.528
 6BD  CAA  HAA   single    0.970  0.020  1.090
 6BD  CAA  HAAA  single    0.970  0.020  1.090
 6BD  CAA  HAAB  single    0.970  0.020  1.090
 6BD  CAO  OAB   deloc     1.246  0.020  1.246
 6BD  OAC  CAO   deloc     1.247  0.020  1.247

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
 6BD  CAP   CAQ  CAS   108.40  3.000
 6BD  CAP   CAQ  CAH   130.64  3.000
 6BD  CAS   CAQ  CAH   120.96  3.000
 6BD  HAH   CAH  CAD   120.58  3.000
 6BD  HAH   CAH  CAQ   121.07  3.000
 6BD  CAD   CAH  CAQ   118.35  3.000
 6BD  HAD   CAD  CAF   119.64  3.000
 6BD  HAD   CAD  CAH   119.57  3.000
 6BD  CAF   CAD  CAH   120.79  3.000
 6BD  HAF   CAF  CAJ   119.60  3.000
 6BD  HAF   CAF  CAD   119.60  3.000
 6BD  CAJ   CAF  CAD   120.80  3.000
 6BD  HAJ   CAJ  CAS   121.15  3.000
 6BD  CAS   CAJ  CAF   118.48  3.000
 6BD  HAJ   CAJ  CAF   120.37  3.000
 6BD  CAT   CAS  CAJ   131.06  3.000
 6BD  CAT   CAS  CAQ   108.32  3.000
 6BD  CAJ   CAS  CAQ   120.62  3.000
 6BD  CAR   CAT  CAK   120.89  3.000
 6BD  CAR   CAT  CAS   109.01  3.000
 6BD  CAK   CAT  CAS   130.10  3.000
 6BD  HAK   CAK  CAG   120.25  3.000
 6BD  CAG   CAK  CAT   118.66  3.000
 6BD  HAK   CAK  CAT   121.09  3.000
 6BD  HAG   CAG  CAE   119.70  3.000
 6BD  CAE   CAG  CAK   120.65  3.000
 6BD  HAG   CAG  CAK   119.65  3.000
 6BD  HAE   CAE  CAI   119.32  3.000
 6BD  CAI   CAE  CAG   120.97  3.000
 6BD  HAE   CAE  CAG   119.71  3.000
 6BD  HAI   CAI  CAR   121.72  3.000
 6BD  HAI   CAI  CAE   119.62  3.000
 6BD  CAR   CAI  CAE   118.66  3.000
 6BD  CAP   CAR  CAI   132.27  3.000
 6BD  CAP   CAR  CAT   107.55  3.000
 6BD  CAI   CAR  CAT   120.18  3.000
 6BD  NAM   CAP  CAR   132.41  3.000
 6BD  NAM   CAP  CAQ   120.87  3.000
 6BD  CAR   CAP  CAQ   106.71  3.000
 6BD  OAN   NAM  CAP   113.95  3.000
 6BD  CAL   OAN  NAM   111.10  3.000
 6BD  HALA  CAL  HAL   108.21  3.000
 6BD  HALA  CAL  CAU   110.99  3.000
 6BD  HAL   CAL  CAU   111.12  3.000
 6BD  CAU   CAL  OAN   107.97  3.000
 6BD  HALA  CAL  OAN   109.33  3.000
 6BD  HAL   CAL  OAN   109.19  3.000
 6BD  HAU   CAU  CAO   106.58  3.000
 6BD  HAU   CAU  CAA   107.77  3.000
 6BD  CAO   CAU  CAA   110.84  3.000
 6BD  CAA   CAU  CAL   112.41  3.000
 6BD  HAU   CAU  CAL   108.07  3.000
 6BD  CAO   CAU  CAL   110.91  3.000
 6BD  HAAB  CAA  HAAA  107.73  3.000
 6BD  HAAB  CAA  HAA   107.84  3.000
 6BD  HAAA  CAA  HAA   107.59  3.000
 6BD  HAAB  CAA  CAU   110.15  3.000
 6BD  HAAA  CAA  CAU   112.21  3.000
 6BD  HAA   CAA  CAU   111.14  3.000
 6BD  OAB   CAO  OAC   126.42  3.000
 6BD  OAC   CAO  CAU   117.41  3.000
 6BD  OAB   CAO  CAU   116.17  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
 6BD  CONST_01  CAF  CAJ  CAS  CAQ    0.00   0.0  0
 6BD  CONST_02  CAK  CAT  CAS  CAQ  180.00   0.0  0
 6BD  CONST_03  CAR  CAT  CAS  CAQ    0.00   0.0  0
 6BD  CONST_04  CAF  CAD  CAH  CAQ    0.00   0.0  0
 6BD  CONST_05  CAJ  CAS  CAQ  CAH    0.00   0.0  0
 6BD  CONST_06  CAT  CAS  CAQ  CAH  180.00   0.0  0
 6BD  CONST_07  CAJ  CAF  CAD  CAH    0.00   0.0  0
 6BD  CONST_08  CAS  CAQ  CAH  CAD    0.00   0.0  0
 6BD  CONST_09  CAS  CAJ  CAF  CAD    0.00   0.0  0
 6BD  CONST_10  CAT  CAS  CAJ  CAF  180.00   0.0  0
 6BD  CONST_11  CAK  CAT  CAS  CAJ    0.00   0.0  0
 6BD  CONST_12  CAR  CAT  CAS  CAJ  180.00   0.0  0
 6BD  CONST_13  CAG  CAK  CAT  CAS  180.00   0.0  0
 6BD  CONST_14  CAI  CAR  CAT  CAS  180.00   0.0  0
 6BD  CONST_15  CAE  CAG  CAK  CAT    0.00   0.0  0
 6BD  CONST_16  CAE  CAI  CAR  CAT    0.00   0.0  0
 6BD  CONST_17  CAI  CAR  CAT  CAK    0.00   0.0  0
 6BD  CONST_18  CAI  CAE  CAG  CAK    0.00   0.0  0
 6BD  CONST_19  CAR  CAT  CAK  CAG    0.00   0.0  0
 6BD  CONST_20  CAR  CAI  CAE  CAG    0.00   0.0  0
 6BD  CONST_21  HAJ  CAJ  CAS  CAQ  180.00   0.0  0
 6BD  CONST_22  HAD  CAD  CAH  CAQ  180.00   0.0  0
 6BD  CONST_23  HAF  CAF  CAD  CAH  180.00   0.0  0
 6BD  CONST_24  HAH  CAH  CAD  CAF  180.00   0.0  0
 6BD  CONST_25  HAK  CAK  CAT  CAS    0.00   0.0  0
 6BD  CONST_26  HAG  CAG  CAK  CAT  180.00   0.0  0
 6BD  CONST_27  HAI  CAI  CAR  CAT  180.00   0.0  0
 6BD  CONST_28  HAE  CAE  CAG  CAK  180.00   0.0  0
 6BD  Var_01    NAM  CAP  CAQ  CAH    0.39  30.0  1
 6BD  Var_02    CAU  CAL  OAN  NAM  179.83  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
 6BD  chir_01  CAU  CAL  CAO  CAA  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
 6BD  plan-1  CAU  0.020
 6BD  plan-1  CAO  0.020
 6BD  plan-1  OAC  0.020
 6BD  plan-1  OAB  0.020
 6BD  plan-2  CAQ  0.020
 6BD  plan-2  CAH  0.020
 6BD  plan-2  CAD  0.020
 6BD  plan-2  CAF  0.020
 6BD  plan-2  CAJ  0.020
 6BD  plan-2  CAS  0.020
 6BD  plan-2  CAT  0.020
 6BD  plan-2  CAK  0.020
 6BD  plan-2  CAG  0.020
 6BD  plan-2  CAE  0.020
 6BD  plan-2  CAI  0.020
 6BD  plan-2  CAR  0.020
 6BD  plan-2  CAP  0.020
 6BD  plan-2  HAH  0.020
 6BD  plan-2  HAD  0.020
 6BD  plan-2  HAF  0.020
 6BD  plan-2  HAJ  0.020
 6BD  plan-2  HAK  0.020
 6BD  plan-2  HAG  0.020
 6BD  plan-2  HAE  0.020
 6BD  plan-2  HAI  0.020

