# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:39:50 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-hydroxy-6-[2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1C2=CC(=O)C(=C(N2)C(O)=O)O)C3=NOC(=O)N3
#
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
 HRJ  HRJ  '3-hydroxy-6-[2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid'  ligand  34  24  .  2022-07-25  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_HRJ
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
 HRJ  OAB  O  O      0  -0.597   3.4040   2.6700  -1.0549
 HRJ  CAO  C  C      0   0.422   4.2378   1.7827  -0.7809
 HRJ  OAE  O  OC    -1  -0.560   5.4715   1.8469  -0.8306
 HRJ  CAV  C  CR6    0   0.016   3.6203   0.4656  -0.3323
 HRJ  NAL  N  NR16   0  -0.676   2.2567   0.4853  -0.2793
 HRJ  CAT  C  CR6    0   0.193   4.2594  -0.6902   0.0033
 HRJ  OAF  O  OH1    0  -0.616   5.5879  -0.8374  -0.0025
 HRJ  CAW  C  CR6    0   0.363   3.5121  -1.8791   0.3962
 HRJ  OAC  O  O      0  -0.543   4.1505  -2.9110   0.6807
 HRJ  CAJ  C  CR16   0  -0.508   2.0968  -1.7416   0.4250
 HRJ  CAR  C  CR6    0   0.323   1.5003  -0.5550   0.0845
 HRJ  CAU  C  CR6    0   0.008   0.0347  -0.3659   0.1030
 HRJ  CAP  C  CR6    0   0.111  -0.5633   0.6023   0.9238
 HRJ  CAA  C  CH3    0  -0.748   0.2411   1.4812   1.8385
 HRJ  CAI  C  CR16   0  -0.320  -1.9451   0.7259   0.8917
 HRJ  CAH  C  CR16   0  -0.251  -0.7508  -1.1860  -0.7002
 HRJ  CAG  C  CR16   0  -0.290  -2.1277  -1.0501  -0.7235
 HRJ  CAQ  C  CR6    0   0.062  -2.7300  -0.0839   0.0741
 HRJ  CAS  C  CR5    0   0.482  -4.1796   0.0809   0.0833
 HRJ  NAK  N  N      0  -0.169  -4.8311   0.6836   1.0158
 HRJ  OAN  O  O      0  -0.364  -6.1611   0.6274   0.6375
 HRJ  CAX  C  CR5    0   0.666  -6.2931  -0.0270  -0.5349
 HRJ  OAD  O  O      0  -0.451  -7.3390  -0.2169  -1.0916
 HRJ  NAM  N  NR15   0  -0.721  -5.0227  -0.3781  -0.8815
 HRJ  H2   H  HOH1   0   0.456   5.7367  -1.7620   0.2680
 HRJ  H3   H  HCR6   0   0.268   1.4847  -2.5789   0.7320
 HRJ  H5   H  HCH3   0   0.256   0.7237   2.2975   1.2982
 HRJ  H6   H  HCH3   0   0.262  -0.3965   1.9307   2.5977
 HRJ  H7   H  HCH3   0   0.255   1.0246   0.9211   2.3494
 HRJ  H8   H  HCR6   0   0.267  -2.4186   1.4714   1.5183
 HRJ  H9   H  HCR6   0   0.273  -0.2794  -1.9353  -1.3226
 HRJ  H10  H  HCR6   0   0.265  -2.7100  -1.7092  -1.3539
 HRJ  H11  H  HNR5   0   0.451  -4.7796  -0.8456  -1.7419
 HRJ  H12  H  HNR6   0   0.413   1.8507   1.3645  -0.5834

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
 HRJ  OAC  CAW  double    1.246  0.020  1.246
 HRJ  OAF  CAT  single    1.337  0.020  1.337
 HRJ  CAW  CAT  single    1.458  0.020  1.458
 HRJ  CAW  CAJ  single    1.422  0.020  1.422
 HRJ  CAT  CAV  double    1.363  0.020  1.363
 HRJ  CAJ  CAR  double    1.371  0.020  1.371
 HRJ  OAB  CAO  deloc     1.248  0.020  1.248
 HRJ  CAV  CAO  single    1.522  0.020  1.522
 HRJ  CAV  NAL  single    1.365  0.020  1.365
 HRJ  CAA  CAP  single    1.502  0.020  1.502
 HRJ  CAO  OAE  deloc     1.236  0.020  1.236
 HRJ  CAR  NAL  single    1.337  0.020  1.337
 HRJ  CAR  CAU  single    1.478  0.020  1.478
 HRJ  CAP  CAU  aromatic  1.403  0.020  1.403
 HRJ  CAP  CAI  aromatic  1.388  0.020  1.388
 HRJ  CAU  CAH  aromatic  1.391  0.020  1.391
 HRJ  CAI  CAQ  aromatic  1.393  0.020  1.393
 HRJ  CAH  CAG  aromatic  1.384  0.020  1.384
 HRJ  CAQ  CAG  aromatic  1.390  0.020  1.390
 HRJ  CAQ  CAS  single    1.459  0.020  1.459
 HRJ  NAM  CAS  single    1.361  0.020  1.361
 HRJ  NAM  CAX  single    1.363  0.020  1.363
 HRJ  CAS  NAK  double    1.287  0.020  1.287
 HRJ  OAD  CAX  double    1.200  0.020  1.200
 HRJ  CAX  OAN  single    1.349  0.020  1.349
 HRJ  NAK  OAN  single    1.384  0.020  1.384
 HRJ  OAF  H2   single    0.850  0.020  0.980
 HRJ  CAJ  H3   single    0.930  0.020  1.080
 HRJ  CAA  H5   single    0.970  0.020  1.090
 HRJ  CAA  H6   single    0.970  0.020  1.090
 HRJ  CAA  H7   single    0.970  0.020  1.090
 HRJ  CAI  H8   single    0.930  0.020  1.080
 HRJ  CAH  H9   single    0.930  0.020  1.080
 HRJ  CAG  H10  single    0.930  0.020  1.080
 HRJ  NAM  H11  single    0.860  0.020  1.020
 HRJ  NAL  H12  single    0.860  0.020  1.020

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
 HRJ  CAV  CAO  OAE  117.48  3.000
 HRJ  OAE  CAO  OAB  128.38  3.000
 HRJ  CAV  CAO  OAB  114.13  3.000
 HRJ  CAT  CAV  NAL  118.12  3.000
 HRJ  NAL  CAV  CAO  113.84  3.000
 HRJ  CAT  CAV  CAO  128.04  3.000
 HRJ  H12  NAL  CAR  121.96  3.000
 HRJ  H12  NAL  CAV  113.62  3.000
 HRJ  CAR  NAL  CAV  124.38  3.000
 HRJ  CAW  CAT  OAF  114.88  3.000
 HRJ  CAW  CAT  CAV  121.17  3.000
 HRJ  OAF  CAT  CAV  123.95  3.000
 HRJ  H2   OAF  CAT  104.77  3.000
 HRJ  CAJ  CAW  OAC  125.82  3.000
 HRJ  CAJ  CAW  CAT  115.89  3.000
 HRJ  OAC  CAW  CAT  118.29  3.000
 HRJ  H3   CAJ  CAR  119.62  3.000
 HRJ  H3   CAJ  CAW  119.61  3.000
 HRJ  CAR  CAJ  CAW  120.77  3.000
 HRJ  CAU  CAR  CAJ  122.63  3.000
 HRJ  CAU  CAR  NAL  117.71  3.000
 HRJ  CAJ  CAR  NAL  119.67  3.000
 HRJ  CAH  CAU  CAP  120.26  3.000
 HRJ  CAH  CAU  CAR  118.51  3.000
 HRJ  CAP  CAU  CAR  121.22  3.000
 HRJ  CAI  CAP  CAA  119.68  3.000
 HRJ  CAI  CAP  CAU  118.19  3.000
 HRJ  CAA  CAP  CAU  122.12  3.000
 HRJ  H7   CAA  H6   107.83  3.000
 HRJ  H7   CAA  H5   107.36  3.000
 HRJ  H6   CAA  H5   107.19  3.000
 HRJ  H7   CAA  CAP  111.69  3.000
 HRJ  H6   CAA  CAP  110.65  3.000
 HRJ  H5   CAA  CAP  111.90  3.000
 HRJ  H8   CAI  CAQ  119.57  3.000
 HRJ  H8   CAI  CAP  118.91  3.000
 HRJ  CAQ  CAI  CAP  121.52  3.000
 HRJ  H9   CAH  CAG  119.46  3.000
 HRJ  H9   CAH  CAU  119.62  3.000
 HRJ  CAG  CAH  CAU  120.92  3.000
 HRJ  H10  CAG  CAQ  121.63  3.000
 HRJ  H10  CAG  CAH  119.05  3.000
 HRJ  CAQ  CAG  CAH  119.32  3.000
 HRJ  CAS  CAQ  CAG  120.84  3.000
 HRJ  CAS  CAQ  CAI  119.37  3.000
 HRJ  CAG  CAQ  CAI  119.78  3.000
 HRJ  NAM  CAS  NAK  110.97  3.000
 HRJ  NAK  CAS  CAQ  124.08  3.000
 HRJ  NAM  CAS  CAQ  124.95  3.000
 HRJ  OAN  NAK  CAS  105.62  3.000
 HRJ  CAX  OAN  NAK  110.57  3.000
 HRJ  NAM  CAX  OAD  130.82  3.000
 HRJ  OAD  CAX  OAN  124.42  3.000
 HRJ  NAM  CAX  OAN  104.76  3.000
 HRJ  H11  NAM  CAX  124.12  3.000
 HRJ  H11  NAM  CAS  127.70  3.000
 HRJ  CAX  NAM  CAS  108.08  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
 HRJ  CONST_01  CAQ  CAI  CAP  CAU    0.00   0.0  0
 HRJ  CONST_02  CAQ  CAG  CAH  CAU    0.00   0.0  0
 HRJ  CONST_03  CAG  CAH  CAU  CAP    0.00   0.0  0
 HRJ  CONST_04  CAG  CAQ  CAI  CAP    0.00   0.0  0
 HRJ  CONST_05  CAH  CAU  CAP  CAI    0.00   0.0  0
 HRJ  CONST_06  CAH  CAG  CAQ  CAI    0.00   0.0  0
 HRJ  CONST_07  CAI  CAP  CAU  CAR  180.00   0.0  0
 HRJ  CONST_08  CAG  CAH  CAU  CAR  180.00   0.0  0
 HRJ  CONST_09  CAS  CAQ  CAI  CAP  180.00   0.0  0
 HRJ  CONST_10  CAS  CAQ  CAG  CAH  180.00   0.0  0
 HRJ  CONST_11  CAX  NAM  CAS  CAQ  180.00   0.0  0
 HRJ  CONST_12  OAN  NAK  CAS  CAQ  180.00   0.0  0
 HRJ  CONST_13  OAN  CAX  NAM  CAS    0.00   0.0  0
 HRJ  CONST_14  CAX  OAN  NAK  CAS    0.00   0.0  0
 HRJ  CONST_15  CAX  NAM  CAS  NAK    0.00   0.0  0
 HRJ  CONST_16  NAM  CAX  OAN  NAK    0.00   0.0  0
 HRJ  CONST_17  NAM  CAS  NAK  OAN    0.00   0.0  0
 HRJ  CONST_18  CAA  CAP  CAU  CAR    0.00   0.0  0
 HRJ  CONST_19  CAH  CAU  CAP  CAA  180.00   0.0  0
 HRJ  CONST_20  CAQ  CAI  CAP  CAA  180.00   0.0  0
 HRJ  CONST_21  H9   CAH  CAU  CAR    0.00   0.0  0
 HRJ  CONST_22  H8   CAI  CAP  CAU  180.00   0.0  0
 HRJ  CONST_23  H10  CAG  CAH  CAU  180.00   0.0  0
 HRJ  CONST_24  H11  NAM  CAS  CAQ    0.00   0.0  0
 HRJ  Var_01    CAP  CAU  CAR  NAL  -60.09  30.0  2
 HRJ  Var_02    NAM  CAS  CAQ  CAI  162.23  30.0  2
 HRJ  Var_03    CAT  CAV  CAO  OAB  178.41  30.0  2
 HRJ  Var_04    H5   CAA  CAP  CAU   78.22  30.0  2

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
 HRJ  plan-1  CAQ  0.020
 HRJ  plan-1  CAS  0.020
 HRJ  plan-1  NAK  0.020
 HRJ  plan-1  OAN  0.020
 HRJ  plan-1  CAX  0.020
 HRJ  plan-1  OAD  0.020
 HRJ  plan-1  NAM  0.020
 HRJ  plan-1  H11  0.020
 HRJ  plan-2  CAO  0.020
 HRJ  plan-2  CAV  0.020
 HRJ  plan-2  NAL  0.020
 HRJ  plan-2  CAT  0.020
 HRJ  plan-2  OAF  0.020
 HRJ  plan-2  CAW  0.020
 HRJ  plan-2  OAC  0.020
 HRJ  plan-2  CAJ  0.020
 HRJ  plan-2  CAR  0.020
 HRJ  plan-2  CAU  0.020
 HRJ  plan-2  H3   0.020
 HRJ  plan-2  H12  0.020
 HRJ  plan-3  CAR  0.020
 HRJ  plan-3  CAU  0.020
 HRJ  plan-3  CAP  0.020
 HRJ  plan-3  CAA  0.020
 HRJ  plan-3  CAI  0.020
 HRJ  plan-3  CAH  0.020
 HRJ  plan-3  CAG  0.020
 HRJ  plan-3  CAQ  0.020
 HRJ  plan-3  CAS  0.020
 HRJ  plan-3  H8   0.020
 HRJ  plan-3  H9   0.020
 HRJ  plan-3  H10  0.020
 HRJ  plan-4  OAB  0.020
 HRJ  plan-4  CAO  0.020
 HRJ  plan-4  OAE  0.020
 HRJ  plan-4  CAV  0.020

