# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:10:56 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[3-(hexyloxy)benzyl]-4-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCOc1cccc(CN2C=CC(=C(C(O)=O)C2=O)O)c1
#
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
 ZYL  ZYL  '1-[3-(hexyloxy)benzyl]-4-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxylic acid'  ligand  48  25  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZYL
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
 ZYL  CAA  C  CH3   0  -0.660  -22.7582  21.0353   9.9461
 ZYL  OAB  O  OH1   0  -0.586  -25.7045   8.2813   9.1921
 ZYL  OAD  O  O     0  -0.436  -25.3900   7.1460   7.3034
 ZYL  OAE  O  OH1   0  -0.584  -23.1518   8.6996  10.0436
 ZYL  CAF  C  CR16  0  -0.230  -25.2861  13.2045   3.9328
 ZYL  CAG  C  CR16  0  -0.312  -24.4927  12.0748   4.0474
 ZYL  CAH  C  CR16  0  -0.391  -24.9643  14.3829   4.5958
 ZYL  CAI  C  CR16  0  -0.514  -21.8918  10.0587   8.5537
 ZYL  CAJ  C  CR16  0   0.077  -21.7600  10.5515   7.2995
 ZYL  CAK  C  CR16  0  -0.400  -23.0114  13.2956   5.4920
 ZYL  CAL  C  CH2   0  -0.426  -23.3684  19.8331   9.2380
 ZYL  CAM  C  CH2   0  -0.415  -23.7178  20.1304   7.7836
 ZYL  CAN  C  CH2   0  -0.435  -24.4002  18.9806   7.0486
 ZYL  CAO  C  CH2   0  -0.463  -23.5293  17.7360   6.9087
 ZYL  CAP  C  CH2   0  -0.167  -24.2162  16.6792   6.0696
 ZYL  OAR  O  O2    0  -0.479  -23.3982  15.5187   6.0571
 ZYL  CAS  C  C     0   0.522  -25.0560   8.0219   8.0629
 ZYL  CAT  C  CR6   0   0.162  -23.3468  12.1199   4.8370
 ZYL  CAU  C  CR6   0   0.405  -23.8146  14.4312   5.3816
 ZYL  CAV  C  CR6   0   0.505  -23.0005   9.2278   8.8374
 ZYL  CAW  C  CR6   0  -0.398  -23.9085   8.9282   7.8398
 ZYL  CAX  C  CR6   0   0.581  -23.7510   9.4583   6.5090
 ZYL  NAY  N  NR6   0  -0.508  -22.6373  10.2801   6.3140
 ZYL  H1   H  HCH3  0   0.226  -22.4958  20.8018  10.9785
 ZYL  H2   H  HCH3  0   0.216  -21.8486  21.3663   9.4416
 ZYL  H3   H  HCH3  0   0.216  -23.4502  21.8793   9.9643
 ZYL  H4   H  HOH1  0   0.480  -26.4162   7.6349   9.3129
 ZYL  H5   H  HOH1  0   0.491  -22.4441   8.9838  10.6353
 ZYL  H6   H  HCR6  0   0.259  -26.1780  13.1759   3.3201
 ZYL  H7   H  HCR6  0   0.249  -24.7635  11.1625   3.5338
 ZYL  H8   H  HCR6  0   0.280  -25.6097  15.2434   4.4847
 ZYL  H9   H  HCR6  0   0.302  -21.1520  10.2930   9.3057
 ZYL  H10  H  HCR6  0   0.320  -20.9261  11.1868   7.0361
 ZYL  H11  H  HCR6  0   0.253  -22.1141  13.3508   6.0993
 ZYL  H12  H  HCH2  0   0.211  -24.2705  19.5111   9.7683
 ZYL  H13  H  HCH2  0   0.217  -22.6691  18.9944   9.2923
 ZYL  H14  H  HCH2  0   0.209  -22.8075  20.4151   7.2444
 ZYL  H15  H  HCH2  0   0.219  -24.3753  21.0047   7.7504
 ZYL  H16  H  HCH2  0   0.217  -25.3286  18.7174   7.5665
 ZYL  H17  H  HCH2  0   0.225  -24.6959  19.3262   6.0531
 ZYL  H18  H  HCH2  0   0.228  -22.5739  18.0049   6.4477
 ZYL  H19  H  HCH2  0   0.233  -23.3029  17.3205   7.8940
 ZYL  H20  H  HCH2  0   0.219  -25.2014  16.4418   6.4885
 ZYL  H21  H  HCH2  0   0.220  -24.3726  17.0502   5.0501
 ZYL  H22  H  HCH2  0   0.293  -22.6710  10.1666   4.2307
 ZYL  H23  H  HCH2  0   0.291  -21.4164  11.1821   4.9138
 ZYL  CAQ  C  CH2   0  -0.440  -22.4669  10.9065   5.0014
 ZYL  OAC  O  O     0  -0.483  -24.5191   9.2593   5.5780

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
 ZYL  OAC  CAX  double    1.223  0.020  1.223
 ZYL  OAD  CAS  double    1.207  0.020  1.207
 ZYL  CAQ  CAT  single    1.508  0.020  1.508
 ZYL  CAQ  NAY  single    1.464  0.020  1.464
 ZYL  CAG  CAT  aromatic  1.392  0.020  1.392
 ZYL  CAG  CAF  aromatic  1.385  0.020  1.385
 ZYL  CAX  NAY  single    1.398  0.020  1.398
 ZYL  CAX  CAW  single    1.441  0.020  1.441
 ZYL  CAT  CAK  aromatic  1.387  0.020  1.387
 ZYL  CAF  CAH  aromatic  1.390  0.020  1.390
 ZYL  CAS  CAW  single    1.479  0.020  1.479
 ZYL  CAS  OAB  single    1.328  0.020  1.328
 ZYL  NAY  CAJ  single    1.347  0.020  1.347
 ZYL  CAK  CAU  aromatic  1.395  0.020  1.395
 ZYL  CAW  CAV  double    1.382  0.020  1.382
 ZYL  CAH  CAU  aromatic  1.393  0.020  1.393
 ZYL  CAN  CAM  single    1.526  0.020  1.526
 ZYL  CAN  CAO  single    1.525  0.020  1.525
 ZYL  CAP  CAO  single    1.514  0.020  1.514
 ZYL  CAP  OAR  single    1.420  0.020  1.420
 ZYL  CAU  OAR  single    1.346  0.020  1.346
 ZYL  CAJ  CAI  double    1.354  0.020  1.354
 ZYL  CAM  CAL  single    1.525  0.020  1.525
 ZYL  CAA  CAL  single    1.523  0.020  1.523
 ZYL  CAV  CAI  single    1.414  0.020  1.414
 ZYL  CAV  OAE  single    1.326  0.020  1.326
 ZYL  CAA  H1   single    0.970  0.020  1.090
 ZYL  CAA  H2   single    0.970  0.020  1.090
 ZYL  CAA  H3   single    0.970  0.020  1.090
 ZYL  OAB  H4   single    0.850  0.020  0.980
 ZYL  OAE  H5   single    0.850  0.020  0.980
 ZYL  CAF  H6   single    0.930  0.020  1.080
 ZYL  CAG  H7   single    0.930  0.020  1.080
 ZYL  CAH  H8   single    0.930  0.020  1.080
 ZYL  CAI  H9   single    0.930  0.020  1.080
 ZYL  CAJ  H10  single    0.930  0.020  1.080
 ZYL  CAK  H11  single    0.930  0.020  1.080
 ZYL  CAL  H12  single    0.970  0.020  1.090
 ZYL  CAL  H13  single    0.970  0.020  1.090
 ZYL  CAM  H14  single    0.970  0.020  1.090
 ZYL  CAM  H15  single    0.970  0.020  1.090
 ZYL  CAN  H16  single    0.970  0.020  1.090
 ZYL  CAN  H17  single    0.970  0.020  1.090
 ZYL  CAO  H18  single    0.970  0.020  1.090
 ZYL  CAO  H19  single    0.970  0.020  1.090
 ZYL  CAP  H20  single    0.970  0.020  1.090
 ZYL  CAP  H21  single    0.970  0.020  1.090
 ZYL  CAQ  H22  single    0.970  0.020  1.090
 ZYL  CAQ  H23  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
 ZYL  H3   CAA  H2   107.55  3.000
 ZYL  H3   CAA  H1   107.60  3.000
 ZYL  H2   CAA  H1   107.58  3.000
 ZYL  H3   CAA  CAL  111.36  3.000
 ZYL  H2   CAA  CAL  111.00  3.000
 ZYL  H1   CAA  CAL  111.56  3.000
 ZYL  H4   OAB  CAS  109.54  3.000
 ZYL  H5   OAE  CAV  110.91  3.000
 ZYL  H6   CAF  CAH  118.90  3.000
 ZYL  H6   CAF  CAG  119.81  3.000
 ZYL  CAH  CAF  CAG  121.29  3.000
 ZYL  H7   CAG  CAT  120.18  3.000
 ZYL  H7   CAG  CAF  120.35  3.000
 ZYL  CAT  CAG  CAF  119.47  3.000
 ZYL  H8   CAH  CAU  121.52  3.000
 ZYL  H8   CAH  CAF  119.17  3.000
 ZYL  CAU  CAH  CAF  119.31  3.000
 ZYL  H9   CAI  CAV  121.63  3.000
 ZYL  H9   CAI  CAJ  119.94  3.000
 ZYL  CAV  CAI  CAJ  118.42  3.000
 ZYL  H10  CAJ  NAY  116.27  3.000
 ZYL  H10  CAJ  CAI  120.98  3.000
 ZYL  NAY  CAJ  CAI  122.75  3.000
 ZYL  H11  CAK  CAU  118.62  3.000
 ZYL  H11  CAK  CAT  120.49  3.000
 ZYL  CAU  CAK  CAT  120.89  3.000
 ZYL  H13  CAL  H12  106.10  3.000
 ZYL  H13  CAL  CAM  110.09  3.000
 ZYL  H12  CAL  CAM  109.29  3.000
 ZYL  H13  CAL  CAA  109.04  3.000
 ZYL  H12  CAL  CAA  109.70  3.000
 ZYL  CAM  CAL  CAA  112.42  3.000
 ZYL  H15  CAM  H14  106.06  3.000
 ZYL  H15  CAM  CAN  108.59  3.000
 ZYL  H14  CAM  CAN  109.29  3.000
 ZYL  H15  CAM  CAL  108.80  3.000
 ZYL  H14  CAM  CAL  109.24  3.000
 ZYL  CAN  CAM  CAL  114.52  3.000
 ZYL  H17  CAN  H16  106.08  3.000
 ZYL  H17  CAN  CAO  109.18  3.000
 ZYL  H16  CAN  CAO  109.35  3.000
 ZYL  H17  CAN  CAM  108.72  3.000
 ZYL  H16  CAN  CAM  109.42  3.000
 ZYL  CAO  CAN  CAM  113.81  3.000
 ZYL  H19  CAO  H18  106.99  3.000
 ZYL  H19  CAO  CAP  109.16  3.000
 ZYL  H18  CAO  CAP  109.51  3.000
 ZYL  H19  CAO  CAN  110.23  3.000
 ZYL  H18  CAO  CAN  109.67  3.000
 ZYL  CAP  CAO  CAN  111.18  3.000
 ZYL  H21  CAP  H20  107.48  3.000
 ZYL  H21  CAP  OAR  110.53  3.000
 ZYL  H20  CAP  OAR  110.12  3.000
 ZYL  H21  CAP  CAO  110.12  3.000
 ZYL  H20  CAP  CAO  110.30  3.000
 ZYL  OAR  CAP  CAO  108.30  3.000
 ZYL  CAU  OAR  CAP  119.11  3.000
 ZYL  CAW  CAS  OAD  124.38  3.000
 ZYL  CAW  CAS  OAB  112.80  3.000
 ZYL  OAD  CAS  OAB  122.82  3.000
 ZYL  CAQ  CAT  CAK  119.31  3.000
 ZYL  CAK  CAT  CAG  119.62  3.000
 ZYL  CAQ  CAT  CAG  121.07  3.000
 ZYL  OAR  CAU  CAK  116.09  3.000
 ZYL  OAR  CAU  CAH  124.49  3.000
 ZYL  CAK  CAU  CAH  119.43  3.000
 ZYL  CAW  CAV  CAI  119.85  3.000
 ZYL  CAI  CAV  OAE  120.41  3.000
 ZYL  CAW  CAV  OAE  119.71  3.000
 ZYL  CAX  CAW  CAV  121.01  3.000
 ZYL  CAV  CAW  CAS  122.26  3.000
 ZYL  CAX  CAW  CAS  116.71  3.000
 ZYL  NAY  CAX  CAW  115.60  3.000
 ZYL  CAW  CAX  OAC  125.06  3.000
 ZYL  NAY  CAX  OAC  119.32  3.000
 ZYL  CAX  NAY  CAQ  117.99  3.000
 ZYL  CAX  NAY  CAJ  122.36  3.000
 ZYL  CAQ  NAY  CAJ  119.59  3.000
 ZYL  H23  CAQ  H22  107.22  3.000
 ZYL  H23  CAQ  NAY  107.00  3.000
 ZYL  H22  CAQ  NAY  108.80  3.000
 ZYL  H23  CAQ  CAT  110.51  3.000
 ZYL  H22  CAQ  CAT  111.14  3.000
 ZYL  NAY  CAQ  CAT  111.96  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
 ZYL  CONST_01  CAK  CAT  CAG  CAF     0.00   0.0  0
 ZYL  CONST_02  CAK  CAU  CAH  CAF     0.00   0.0  0
 ZYL  CONST_03  CAU  CAK  CAT  CAG     0.00   0.0  0
 ZYL  CONST_04  CAU  CAH  CAF  CAG     0.00   0.0  0
 ZYL  CONST_05  CAT  CAG  CAF  CAH     0.00   0.0  0
 ZYL  CONST_06  CAT  CAK  CAU  CAH     0.00   0.0  0
 ZYL  CONST_07  CAW  CAX  NAY  CAJ     0.00   0.0  0
 ZYL  CONST_08  CAQ  CAT  CAG  CAF   180.00   0.0  0
 ZYL  CONST_09  OAR  CAU  CAH  CAF   180.00   0.0  0
 ZYL  CONST_10  CAU  CAK  CAT  CAQ   180.00   0.0  0
 ZYL  CONST_11  CAT  CAK  CAU  OAR   180.00   0.0  0
 ZYL  CONST_12  CAJ  NAY  CAX  OAC   180.00   0.0  0
 ZYL  CONST_13  CAW  CAX  NAY  CAQ   180.00   0.0  0
 ZYL  CONST_14  H11  CAK  CAT  CAG   180.00   0.0  0
 ZYL  CONST_15  H8   CAH  CAF  CAG   180.00   0.0  0
 ZYL  CONST_16  H7   CAG  CAF  CAH   180.00   0.0  0
 ZYL  CONST_17  H6   CAF  CAG  CAT   180.00   0.0  0
 ZYL  CONST_18  CAQ  NAY  CAX  OAC     0.00   0.0  0
 ZYL  CONST_19  H4   OAB  CAS  CAW   180.00   0.0  0
 ZYL  Var_01    NAY  CAQ  CAT  CAG  -105.01  30.0  3
 ZYL  Var_02    CAT  CAQ  NAY  CAJ   -98.05  30.0  2
 ZYL  Var_03    CAX  CAW  CAS  OAB  -136.03  30.0  2
 ZYL  Var_04    H20  CAP  OAR  CAU    58.52  30.0  1
 ZYL  Var_05    CAN  CAM  CAL  CAA  -176.94  30.0  1
 ZYL  Var_06    CAO  CAN  CAM  CAL   -63.61  30.0  1
 ZYL  Var_07    CAP  CAO  CAN  CAM  -175.08  30.0  3
 ZYL  Var_08    OAR  CAP  CAO  CAN  -175.97  30.0  1
 ZYL  Var_09    H1   CAA  CAL  CAM  -178.88  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
 ZYL  plan-1  CAF  0.020
 ZYL  plan-1  CAG  0.020
 ZYL  plan-1  CAH  0.020
 ZYL  plan-1  CAK  0.020
 ZYL  plan-1  OAR  0.020
 ZYL  plan-1  CAT  0.020
 ZYL  plan-1  CAU  0.020
 ZYL  plan-1  H6   0.020
 ZYL  plan-1  H7   0.020
 ZYL  plan-1  H8   0.020
 ZYL  plan-1  H11  0.020
 ZYL  plan-1  CAQ  0.020
 ZYL  plan-2  OAE  0.020
 ZYL  plan-2  CAI  0.020
 ZYL  plan-2  CAJ  0.020
 ZYL  plan-2  CAS  0.020
 ZYL  plan-2  CAV  0.020
 ZYL  plan-2  CAW  0.020
 ZYL  plan-2  CAX  0.020
 ZYL  plan-2  NAY  0.020
 ZYL  plan-2  H9   0.020
 ZYL  plan-2  H10  0.020
 ZYL  plan-2  CAQ  0.020
 ZYL  plan-2  OAC  0.020
 ZYL  plan-3  OAB  0.020
 ZYL  plan-3  OAD  0.020
 ZYL  plan-3  CAS  0.020
 ZYL  plan-3  CAW  0.020
 ZYL  plan-3  H4   0.020

