# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:37:45 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 5-[(2S)-3-benzoyl-4-hydroxy-2-(4-nitrophenyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]-2-hydroxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(ccc1O)N2[C@@H](c3ccc(cc3)[N+]([O-])=O)C(=C(O)C2=O)C(=O)c4ccccc4
#
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
 YR1  YR1  '5-[(2S)-3-benzoyl-4-hydroxy-2-(4-nitrophenyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]-2-hydroxybenzoic acid'  ligand  49  34  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YR1
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
 YR1  OAA   O  O      0  -0.629   5.9714   1.2839   0.4428
 YR1  OAB   O  O      0  -0.383  -3.4809  -2.1639  -2.1498
 YR1  OAD   O  O      0  -0.378  -1.9050   4.8690   1.0492
 YR1  OAE   O  OC    -1  -0.545   4.8675   1.1747  -1.4861
 YR1  OAF   O  OH1    0  -0.559  -0.9095  -3.3857  -2.9076
 YR1  OAG   O  OH1    0  -0.651   5.1325   0.2080   2.4671
 YR1  OAH   O  O     -1  -0.378  -1.3178   4.9659  -0.9991
 YR1  CAI   C  CR16   0  -0.247  -5.0053  -0.2835   2.2227
 YR1  CAJ   C  CR16   0  -0.240  -5.1970   0.2500   0.9539
 YR1  CAK   C  CR16   0  -0.240  -4.1350  -1.3499   2.4045
 YR1  CAL   C  CR16   0  -0.270  -4.5223  -0.2821  -0.1334
 YR1  CAM   C  CR16   0  -0.285  -3.4357  -1.8647   1.3227
 YR1  CAN   C  CR16   0  -0.358   3.1105  -1.0042   2.4045
 YR1  CAO   C  CR16   0  -0.288  -1.2392   0.8403   1.1828
 YR1  CAP   C  CR16   0  -0.288  -0.6074   0.9480  -1.1312
 YR1  CAQ   C  CR16   0  -0.276   2.0266  -1.4730   1.6901
 YR1  CAR   C  CR16   0  -0.250  -1.4727   2.2051   1.1954
 YR1  CAS   C  CR16   0  -0.253  -0.8283   2.3117  -1.1382
 YR1  CAT   C  CR16   0  -0.309   2.8494  -0.3968  -0.2917
 YR1  CAU   C  C      0   0.497   5.0031   0.9081  -0.2906
 YR1  CAV   C  CR5    0   0.238  -0.6182  -2.6478  -1.8640
 YR1  CAW   C  C      0   0.373  -2.8918  -1.8764  -1.1253
 YR1  CAX   C  CR5    0   0.471   0.8002  -2.4427  -1.4517
 YR1  CAY   C  CR5    0  -0.133  -1.4390  -2.0001  -1.0168
 YR1  CAZ   C  CR6    0   0.364   4.0920  -0.2323   1.7726
 YR1  CBA   C  CR6    0  -0.045  -3.6238  -1.3299   0.0508
 YR1  CBB   C  CR6    0   0.198  -0.8168   0.2031   0.0251
 YR1  CBC   C  CR6    0  -0.282   3.9577   0.0702   0.4024
 YR1  CBD   C  CR6    0   0.332   1.8876  -1.1691   0.3378
 YR1  CBE   C  CR6    0   0.242  -1.2652   2.9240   0.0297
 YR1  CBF   C  CR15   0  -0.216  -0.5978  -1.2921   0.0173
 YR1  NBG   N  NR5    0  -0.596   0.7589  -1.6337  -0.3748
 YR1  NBH   N  N      1   0.331  -1.5134   4.3577   0.0267
 YR1  HOAF  H  HOH1   0   0.488  -0.0938  -3.7404  -3.2953
 YR1  HOAG  H  HOH1   0   0.461   5.6758   0.7364   1.7695
 YR1  HAI   H  HCR6   0   0.264  -5.5387   0.1300   3.0687
 YR1  HAJ   H  HCR6   0   0.263  -5.8760   1.0806   0.8138
 YR1  HAK   H  HCR6   0   0.264  -3.9966  -1.7785   3.3883
 YR1  HAL   H  HCR6   0   0.263  -4.6729   0.1347  -1.1210
 YR1  HAM   H  HCR6   0   0.275  -2.7620  -2.7003   1.4690
 YR1  HAN   H  HCR6   0   0.261   3.2123  -1.2398   3.4563
 YR1  HAO   H  HCR6   0   0.273  -1.4018   0.2680   2.0866
 YR1  HAP   H  HCR6   0   0.271  -0.2764   0.4677  -2.0432
 YR1  HAQ   H  HCR6   0   0.270   1.2831  -2.0812   2.1905
 YR1  HAR   H  HCR6   0   0.298  -1.8100   2.6845   2.1022
 YR1  HAS   H  HCR6   0   0.300  -0.6641   2.8797  -2.0420
 YR1  HAT   H  HCR6   0   0.256   2.7401  -0.1388  -1.3374
 YR1  HBF   H  HCR5   0   0.301  -0.7926  -1.6849   1.0199
 YR1  OAC   O  O      0  -0.454   1.7649  -2.9289  -2.0073

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
 YR1  OAA  CAU   deloc     1.272  0.020  1.272
 YR1  OAB  CAW   double    1.216  0.020  1.216
 YR1  OAC  CAX   double    1.215  0.020  1.215
 YR1  OAD  NBH   double    1.208  0.020  1.208
 YR1  OAE  CAU   deloc     1.232  0.020  1.232
 YR1  OAF  CAV   single    1.311  0.020  1.311
 YR1  OAG  CAZ   single    1.326  0.020  1.326
 YR1  OAH  NBH   single    1.209  0.020  1.209
 YR1  CAI  CAJ   aromatic  1.390  0.020  1.390
 YR1  CAI  CAK   aromatic  1.388  0.020  1.388
 YR1  CAJ  CAL   aromatic  1.386  0.020  1.386
 YR1  CAK  CAM   aromatic  1.387  0.020  1.387
 YR1  CAL  CBA   aromatic  1.392  0.020  1.392
 YR1  CAM  CBA   aromatic  1.393  0.020  1.393
 YR1  CAN  CAQ   aromatic  1.380  0.020  1.380
 YR1  CAN  CAZ   aromatic  1.400  0.020  1.400
 YR1  CAO  CAR   aromatic  1.385  0.020  1.385
 YR1  CAO  CBB   aromatic  1.387  0.020  1.387
 YR1  CAP  CAS   aromatic  1.381  0.020  1.381
 YR1  CAP  CBB   aromatic  1.391  0.020  1.391
 YR1  CAQ  CBD   aromatic  1.393  0.020  1.393
 YR1  CAR  CBE   aromatic  1.385  0.020  1.385
 YR1  CAS  CBE   aromatic  1.389  0.020  1.389
 YR1  CAT  CBC   aromatic  1.389  0.020  1.389
 YR1  CAT  CBD   aromatic  1.385  0.020  1.385
 YR1  CAU  CBC   single    1.508  0.020  1.508
 YR1  CAV  CAX   single    1.491  0.020  1.491
 YR1  CAV  CAY   double    1.346  0.020  1.346
 YR1  CAW  CAY   single    1.462  0.020  1.462
 YR1  CAW  CBA   single    1.489  0.020  1.489
 YR1  CAX  NBG   single    1.348  0.020  1.348
 YR1  CAY  CBF   single    1.509  0.020  1.509
 YR1  CAZ  CBC   aromatic  1.410  0.020  1.410
 YR1  CBB  CBF   single    1.511  0.020  1.511
 YR1  CBD  NBG   single    1.413  0.020  1.413
 YR1  CBE  NBH   single    1.455  0.020  1.455
 YR1  CBF  NBG   single    1.453  0.020  1.453
 YR1  OAF  HOAF  single    0.850  0.020  0.980
 YR1  OAG  HOAG  single    0.850  0.020  0.980
 YR1  CAI  HAI   single    0.930  0.020  1.080
 YR1  CAJ  HAJ   single    0.930  0.020  1.080
 YR1  CAK  HAK   single    0.930  0.020  1.080
 YR1  CAL  HAL   single    0.930  0.020  1.080
 YR1  CAM  HAM   single    0.930  0.020  1.080
 YR1  CAN  HAN   single    0.930  0.020  1.080
 YR1  CAO  HAO   single    0.930  0.020  1.080
 YR1  CAP  HAP   single    0.930  0.020  1.080
 YR1  CAQ  HAQ   single    0.930  0.020  1.080
 YR1  CAR  HAR   single    0.930  0.020  1.080
 YR1  CAS  HAS   single    0.930  0.020  1.080
 YR1  CAT  HAT   single    0.930  0.020  1.080
 YR1  CBF  HBF   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
 YR1  HOAF  OAF  CAV  109.70  3.000
 YR1  HOAG  OAG  CAZ  103.27  3.000
 YR1  HAI   CAI  CAK  120.00  3.000
 YR1  HAI   CAI  CAJ  119.94  3.000
 YR1  CAK   CAI  CAJ  120.06  3.000
 YR1  HAJ   CAJ  CAL  119.91  3.000
 YR1  HAJ   CAJ  CAI  119.97  3.000
 YR1  CAL   CAJ  CAI  120.12  3.000
 YR1  HAK   CAK  CAM  119.84  3.000
 YR1  HAK   CAK  CAI  120.23  3.000
 YR1  CAM   CAK  CAI  119.92  3.000
 YR1  HAL   CAL  CBA  120.01  3.000
 YR1  HAL   CAL  CAJ  120.01  3.000
 YR1  CBA   CAL  CAJ  119.95  3.000
 YR1  HAM   CAM  CBA  120.24  3.000
 YR1  HAM   CAM  CAK  119.63  3.000
 YR1  CBA   CAM  CAK  120.11  3.000
 YR1  HAN   CAN  CAZ  119.52  3.000
 YR1  HAN   CAN  CAQ  120.18  3.000
 YR1  CAZ   CAN  CAQ  120.30  3.000
 YR1  HAO   CAO  CBB  120.00  3.000
 YR1  HAO   CAO  CAR  119.23  3.000
 YR1  CBB   CAO  CAR  120.77  3.000
 YR1  HAP   CAP  CBB  120.57  3.000
 YR1  HAP   CAP  CAS  118.86  3.000
 YR1  CBB   CAP  CAS  120.57  3.000
 YR1  HAQ   CAQ  CBD  120.17  3.000
 YR1  HAQ   CAQ  CAN  119.39  3.000
 YR1  CBD   CAQ  CAN  120.45  3.000
 YR1  HAR   CAR  CBE  121.54  3.000
 YR1  HAR   CAR  CAO  119.86  3.000
 YR1  CBE   CAR  CAO  118.60  3.000
 YR1  HAS   CAS  CBE  121.30  3.000
 YR1  HAS   CAS  CAP  119.94  3.000
 YR1  CBE   CAS  CAP  118.76  3.000
 YR1  HAT   CAT  CBD  120.12  3.000
 YR1  HAT   CAT  CBC  118.90  3.000
 YR1  CBD   CAT  CBC  120.98  3.000
 YR1  CBC   CAU  OAE  119.31  3.000
 YR1  CBC   CAU  OAA  115.27  3.000
 YR1  OAE   CAU  OAA  125.41  3.000
 YR1  CAY   CAV  CAX  109.87  3.000
 YR1  CAY   CAV  OAF  129.54  3.000
 YR1  CAX   CAV  OAF  120.59  3.000
 YR1  CBA   CAW  CAY  117.44  3.000
 YR1  CBA   CAW  OAB  120.92  3.000
 YR1  CAY   CAW  OAB  121.59  3.000
 YR1  NBG   CAX  CAV  105.92  3.000
 YR1  NBG   CAX  OAC  129.06  3.000
 YR1  CAV   CAX  OAC  125.01  3.000
 YR1  CBF   CAY  CAW  124.40  3.000
 YR1  CBF   CAY  CAV  108.49  3.000
 YR1  CAW   CAY  CAV  126.87  3.000
 YR1  CBC   CAZ  CAN  119.37  3.000
 YR1  CBC   CAZ  OAG  120.84  3.000
 YR1  CAN   CAZ  OAG  119.80  3.000
 YR1  CAW   CBA  CAM  120.93  3.000
 YR1  CAW   CBA  CAL  119.27  3.000
 YR1  CAM   CBA  CAL  119.80  3.000
 YR1  CBF   CBB  CAP  120.24  3.000
 YR1  CBF   CBB  CAO  120.19  3.000
 YR1  CAP   CBB  CAO  119.57  3.000
 YR1  CAZ   CBC  CAU  119.98  3.000
 YR1  CAZ   CBC  CAT  119.33  3.000
 YR1  CAU   CBC  CAT  120.69  3.000
 YR1  NBG   CBD  CAT  120.58  3.000
 YR1  NBG   CBD  CAQ  119.83  3.000
 YR1  CAT   CBD  CAQ  119.58  3.000
 YR1  NBH   CBE  CAS  119.10  3.000
 YR1  NBH   CBE  CAR  119.18  3.000
 YR1  CAS   CBE  CAR  121.72  3.000
 YR1  HBF   CBF  NBG  109.22  3.000
 YR1  HBF   CBF  CBB  108.94  3.000
 YR1  NBG   CBF  CBB  111.67  3.000
 YR1  HBF   CBF  CAY  111.11  3.000
 YR1  NBG   CBF  CAY  103.02  3.000
 YR1  CBB   CBF  CAY  112.76  3.000
 YR1  CBF   NBG  CBD  122.16  3.000
 YR1  CBF   NBG  CAX  112.67  3.000
 YR1  CBD   NBG  CAX  125.16  3.000
 YR1  CBE   NBH  OAH  118.03  3.000
 YR1  CBE   NBH  OAD  118.07  3.000
 YR1  OAH   NBH  OAD  123.90  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
 YR1  CONST_01  CBA  CAL  CAJ  CAI     0.00   0.0  0
 YR1  CONST_02  CBA  CAM  CAK  CAI     0.00   0.0  0
 YR1  CONST_03  CAM  CAK  CAI  CAJ     0.00   0.0  0
 YR1  CONST_04  CAM  CBA  CAL  CAJ     0.00   0.0  0
 YR1  CONST_05  CAL  CAJ  CAI  CAK     0.00   0.0  0
 YR1  CONST_06  CAL  CBA  CAM  CAK     0.00   0.0  0
 YR1  CONST_07  CAT  CBD  CAQ  CAN     0.00   0.0  0
 YR1  CONST_08  CAT  CBC  CAZ  CAN     0.00   0.0  0
 YR1  CONST_09  CAS  CBE  CAR  CAO     0.00   0.0  0
 YR1  CONST_10  CAS  CAP  CBB  CAO     0.00   0.0  0
 YR1  CONST_11  CAR  CBE  CAS  CAP     0.00   0.0  0
 YR1  CONST_12  CAR  CAO  CBB  CAP     0.00   0.0  0
 YR1  CONST_13  CBC  CAZ  CAN  CAQ     0.00   0.0  0
 YR1  CONST_14  CBC  CAT  CBD  CAQ     0.00   0.0  0
 YR1  CONST_15  CBD  CAQ  CAN  CAZ     0.00   0.0  0
 YR1  CONST_16  CBD  CAT  CBC  CAZ     0.00   0.0  0
 YR1  CONST_17  CBE  CAR  CAO  CBB     0.00   0.0  0
 YR1  CONST_18  CBE  CAS  CAP  CBB     0.00   0.0  0
 YR1  CONST_19  NBG  CBD  CAQ  CAN   180.00   0.0  0
 YR1  CONST_20  CBF  CBB  CAO  CAR   180.00   0.0  0
 YR1  CONST_21  CBF  CBB  CAP  CAS   180.00   0.0  0
 YR1  CONST_22  NBG  CBD  CAT  CBC   180.00   0.0  0
 YR1  CONST_23  CBD  NBG  CAX  CAV   180.00   0.0  0
 YR1  CONST_24  CBF  NBG  CAX  CAV     0.00   0.0  0
 YR1  CONST_25  CAQ  CAN  CAZ  OAG   180.00   0.0  0
 YR1  CONST_26  CAT  CBC  CAZ  OAG   180.00   0.0  0
 YR1  CONST_27  CAW  CBA  CAL  CAJ   180.00   0.0  0
 YR1  CONST_28  CAW  CBA  CAM  CAK   180.00   0.0  0
 YR1  CONST_29  CAU  CBC  CAZ  CAN   180.00   0.0  0
 YR1  CONST_30  NBH  CBE  CAR  CAO   180.00   0.0  0
 YR1  CONST_31  NBH  CBE  CAS  CAP   180.00   0.0  0
 YR1  CONST_32  CBD  CAT  CBC  CAU   180.00   0.0  0
 YR1  CONST_33  CBD  NBG  CAX  OAC     0.00   0.0  0
 YR1  CONST_34  CBF  NBG  CAX  OAC   180.00   0.0  0
 YR1  CONST_35  HAL  CAL  CAJ  CAI   180.00   0.0  0
 YR1  CONST_36  HAM  CAM  CAK  CAI   180.00   0.0  0
 YR1  CONST_37  HAK  CAK  CAI  CAJ   180.00   0.0  0
 YR1  CONST_38  HAJ  CAJ  CAI  CAK   180.00   0.0  0
 YR1  CONST_39  HAI  CAI  CAJ  CAL   180.00   0.0  0
 YR1  CONST_40  HAP  CAP  CBB  CAO   180.00   0.0  0
 YR1  CONST_41  HAO  CAO  CBB  CAP   180.00   0.0  0
 YR1  CONST_42  HAT  CAT  CBD  CAQ   180.00   0.0  0
 YR1  CONST_43  HAS  CAS  CBE  CAR   180.00   0.0  0
 YR1  CONST_44  HAR  CAR  CBE  CAS   180.00   0.0  0
 YR1  CONST_45  HAQ  CAQ  CBD  CAT   180.00   0.0  0
 YR1  CONST_46  HAN  CAN  CAZ  CBC   180.00   0.0  0
 YR1  CONST_47  CAR  CBE  NBH  OAD     0.00   0.0  0
 YR1  CONST_48  CAS  CBE  NBH  OAD   180.00   0.0  0
 YR1  CONST_49  CAR  CBE  NBH  OAH   180.00   0.0  0
 YR1  CONST_50  CAS  CBE  NBH  OAH     0.00   0.0  0
 YR1  Var_01    CAX  NBG  CBD  CAQ  -120.06  30.0  2
 YR1  Var_02    CBF  CAY  CAV  CAX     0.95  30.0  1
 YR1  Var_03    NBG  CAX  CAV  CAY    -1.67  30.0  1
 YR1  Var_04    CAY  CAW  CBA  CAL   129.20  30.0  2
 YR1  Var_05    CBA  CAW  CAY  CAV   169.08  30.0  2
 YR1  Var_06    CAT  CBC  CAU  OAA   179.78  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
 YR1  chir_01  CBF  CAY  CBB  NBG  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
 YR1  plan-1  CAI  0.020
 YR1  plan-1  CAJ  0.020
 YR1  plan-1  CAK  0.020
 YR1  plan-1  CAL  0.020
 YR1  plan-1  CAM  0.020
 YR1  plan-1  CAW  0.020
 YR1  plan-1  CBA  0.020
 YR1  plan-1  HAI  0.020
 YR1  plan-1  HAJ  0.020
 YR1  plan-1  HAK  0.020
 YR1  plan-1  HAL  0.020
 YR1  plan-1  HAM  0.020
 YR1  plan-2  OAG  0.020
 YR1  plan-2  CAN  0.020
 YR1  plan-2  CAQ  0.020
 YR1  plan-2  CAT  0.020
 YR1  plan-2  CAU  0.020
 YR1  plan-2  CAZ  0.020
 YR1  plan-2  CBC  0.020
 YR1  plan-2  CBD  0.020
 YR1  plan-2  NBG  0.020
 YR1  plan-2  HAN  0.020
 YR1  plan-2  HAQ  0.020
 YR1  plan-2  HAT  0.020
 YR1  plan-3  CAO  0.020
 YR1  plan-3  CAP  0.020
 YR1  plan-3  CAR  0.020
 YR1  plan-3  CAS  0.020
 YR1  plan-3  CBB  0.020
 YR1  plan-3  CBE  0.020
 YR1  plan-3  CBF  0.020
 YR1  plan-3  NBH  0.020
 YR1  plan-3  HAO  0.020
 YR1  plan-3  HAP  0.020
 YR1  plan-3  HAR  0.020
 YR1  plan-3  HAS  0.020
 YR1  plan-4  OAD  0.020
 YR1  plan-4  OAH  0.020
 YR1  plan-4  CBE  0.020
 YR1  plan-4  NBH  0.020
 YR1  plan-5  OAB  0.020
 YR1  plan-5  CAW  0.020
 YR1  plan-5  CAY  0.020
 YR1  plan-5  CBA  0.020
 YR1  plan-6  CAV  0.020
 YR1  plan-6  CAX  0.020
 YR1  plan-6  CBD  0.020
 YR1  plan-6  CBF  0.020
 YR1  plan-6  NBG  0.020
 YR1  plan-6  OAC  0.020
 YR1  plan-7  OAA  0.020
 YR1  plan-7  OAE  0.020
 YR1  plan-7  CAU  0.020
 YR1  plan-7  CBC  0.020

