# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 01:50:20 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-5-methylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CC(O)=O)NCc1c(O)c(C)ncc1CO[P](O)(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
 PLK  PLK  '(3R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-5-methylhexanoic acid'  ligand  50  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PLK
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
 PLK  C11   C  CH3   0  -0.658   0.5456  -3.6153  -2.0266
 PLK  C12   C  CH1   0  -0.246   0.1916  -3.3529  -0.5664
 PLK  C13   C  CH3   0  -0.644  -0.6260  -4.5088   0.0022
 PLK  C14   C  CH2   0  -0.413   1.4367  -3.1298   0.2951
 PLK  C15   C  CH1   0  -0.086   2.2907  -1.9097  -0.0490
 PLK  C16   C  CH2   0  -0.530   3.5818  -1.9212   0.7780
 PLK  C17   C  C     0   0.553   4.4066  -0.7149   0.4233
 PLK  O11   O  OH1   0  -0.592   4.6540   0.0777   1.4598
 PLK  O12   O  O     0  -0.458   4.8192  -0.4874  -0.6881
 PLK  N11   N  NH1   0  -0.597   1.6268  -0.6313   0.1763
 PLK  C21   C  CH2   0  -0.354   1.0960   0.0432  -0.9916
 PLK  C22   C  CR6   0   0.073   0.5632   1.3943  -0.5924
 PLK  C23   C  CR6   0   0.266   1.4238   2.4803  -0.4639
 PLK  O21   O  OH1   0  -0.609   2.7260   2.2905  -0.7359
 PLK  C24   C  CR6   0   0.123   0.9180   3.7262  -0.0671
 PLK  C25   C  CH3   0  -0.785   1.8270   4.9120   0.0650
 PLK  N21   N  N     0  -0.408  -0.3675   3.8882   0.2024
 PLK  C26   C  CR16  0  -0.135  -1.1971   2.8566   0.1024
 PLK  C27   C  CR6   0  -0.066  -0.7839   1.5902  -0.2828
 PLK  C28   C  CH2   0  -0.214  -1.7364   0.4314  -0.3788
 PLK  O22   O  O2    0  -0.592  -2.9828   0.7812   0.2100
 PLK  P     P  P     0   1.463  -4.1597  -0.3037   0.2214
 PLK  O1P   O  OH1   0  -0.729  -5.1491   0.5129   1.1642
 PLK  O2P   O  OH1   0  -0.740  -4.7832  -0.3252  -1.2485
 PLK  O3P   O  O     0  -0.702  -3.7766  -1.6699   0.6199
 PLK  H111  H  HCH3  0   0.227   1.0376  -2.7626  -2.4961
 PLK  H112  H  HCH3  0   0.217   1.2180  -4.4727  -2.1131
 PLK  H113  H  HCH3  0   0.229  -0.3490  -3.8347  -2.6112
 PLK  H12   H  HCH1  0   0.212  -0.4415  -2.4592  -0.5210
 PLK  H131  H  HCH3  0   0.212  -0.0423  -5.4328   0.0109
 PLK  H132  H  HCH3  0   0.225  -0.9424  -4.3060   1.0267
 PLK  H133  H  HCH3  0   0.226  -1.5239  -4.6891  -0.5909
 PLK  H141  H  HCH2  0   0.222   1.1357  -3.0534   1.3468
 PLK  H142  H  HCH2  0   0.219   2.0641  -4.0259   0.2283
 PLK  H15   H  HCH1  0   0.239   2.5783  -1.9600  -1.1030
 PLK  H161  H  HCH2  0   0.248   3.3419  -1.9313   1.8426
 PLK  H162  H  HCH2  0   0.269   4.1675  -2.8184   0.5607
 PLK  H11   H  HNH1  0   0.347   0.9256  -0.7158   0.9021
 PLK  HA    H  HOH1  0   0.472   5.1689   0.8446   1.1671
 PLK  H211  H  HCH2  0   0.262   1.9067   0.1688  -1.7107
 PLK  H212  H  HCH2  0   0.219   0.3168  -0.5218  -1.5220
 PLK  H21   H  HOH1  0   0.484   3.2242   3.1106  -0.6521
 PLK  H251  H  HCH3  0   0.256   2.3081   5.1686  -0.8827
 PLK  H252  H  HCH3  0   0.271   1.2586   5.7802   0.3900
 PLK  H253  H  HCH3  0   0.257   2.6189   4.7422   0.7990
 PLK  H26   H  HCR6  0   0.256  -2.2329   3.0567   0.3447
 PLK  H281  H  HCH2  0   0.261  -1.8794   0.1474  -1.4267
 PLK  H282  H  HCH2  0   0.247  -1.3214  -0.4365   0.1410
 PLK  H1P   H  HOH1  0   0.506  -5.9436   0.0257   1.4213
 PLK  H2P   H  HOH1  0   0.497  -5.1099   0.5223  -1.5797

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
 PLK  C11  C12   single    1.525  0.020  1.525
 PLK  C12  C13   single    1.526  0.020  1.526
 PLK  C12  C14   single    1.530  0.020  1.530
 PLK  C14  C15   single    1.529  0.020  1.529
 PLK  C15  C16   single    1.533  0.020  1.533
 PLK  C15  N11   single    1.458  0.020  1.458
 PLK  C16  C17   single    1.504  0.020  1.504
 PLK  C17  O11   single    1.328  0.020  1.328
 PLK  C17  O12   double    1.207  0.020  1.207
 PLK  N11  C21   single    1.449  0.020  1.449
 PLK  C21  C22   single    1.506  0.020  1.506
 PLK  C22  C23   aromatic  1.392  0.020  1.392
 PLK  C22  C27   aromatic  1.396  0.020  1.396
 PLK  C23  O21   single    1.344  0.020  1.344
 PLK  C23  C24   aromatic  1.402  0.020  1.402
 PLK  C24  C25   single    1.500  0.020  1.500
 PLK  C24  N21   aromatic  1.323  0.020  1.323
 PLK  N21  C26   aromatic  1.328  0.020  1.328
 PLK  C26  C27   aromatic  1.387  0.020  1.387
 PLK  C27  C28   single    1.503  0.020  1.503
 PLK  C28  O22   single    1.422  0.020  1.422
 PLK  O22  P     single    1.601  0.020  1.601
 PLK  P    O1P   single    1.592  0.020  1.592
 PLK  P    O2P   single    1.597  0.020  1.597
 PLK  P    O3P   double    1.474  0.020  1.474
 PLK  C11  H111  single    0.970  0.020  1.090
 PLK  C11  H112  single    0.970  0.020  1.090
 PLK  C11  H113  single    0.970  0.020  1.090
 PLK  C12  H12   single    0.970  0.020  1.090
 PLK  C13  H131  single    0.970  0.020  1.090
 PLK  C13  H132  single    0.970  0.020  1.090
 PLK  C13  H133  single    0.970  0.020  1.090
 PLK  C14  H141  single    0.970  0.020  1.090
 PLK  C14  H142  single    0.970  0.020  1.090
 PLK  C15  H15   single    0.970  0.020  1.090
 PLK  C16  H161  single    0.970  0.020  1.090
 PLK  C16  H162  single    0.970  0.020  1.090
 PLK  N11  H11   single    0.890  0.020  1.040
 PLK  O11  HA    single    0.850  0.020  0.980
 PLK  C21  H211  single    0.970  0.020  1.090
 PLK  C21  H212  single    0.970  0.020  1.090
 PLK  O21  H21   single    0.850  0.020  0.980
 PLK  C25  H251  single    0.970  0.020  1.090
 PLK  C25  H252  single    0.970  0.020  1.090
 PLK  C25  H253  single    0.970  0.020  1.090
 PLK  C26  H26   single    0.930  0.020  1.080
 PLK  C28  H281  single    0.970  0.020  1.090
 PLK  C28  H282  single    0.970  0.020  1.090
 PLK  O1P  H1P   single    0.850  0.020  0.980
 PLK  O2P  H2P   single    0.850  0.020  0.980

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
 PLK  H113  C11  H112  107.71  3.000
 PLK  H113  C11  H111  107.25  3.000
 PLK  H112  C11  H111  107.56  3.000
 PLK  H113  C11  C12   110.93  3.000
 PLK  H112  C11  C12   110.70  3.000
 PLK  H111  C11  C12   112.48  3.000
 PLK  H12   C12  C14   109.12  3.000
 PLK  H12   C12  C13   107.03  3.000
 PLK  C14   C12  C13   109.67  3.000
 PLK  H12   C12  C11   108.30  3.000
 PLK  C14   C12  C11   112.03  3.000
 PLK  C13   C12  C11   110.54  3.000
 PLK  H133  C13  H132  107.60  3.000
 PLK  H133  C13  H131  107.70  3.000
 PLK  H132  C13  H131  107.72  3.000
 PLK  H133  C13  C12   111.32  3.000
 PLK  H132  C13  C12   111.38  3.000
 PLK  H131  C13  C12   110.94  3.000
 PLK  H142  C14  H141  105.82  3.000
 PLK  H142  C14  C15   108.60  3.000
 PLK  H141  C14  C15   108.28  3.000
 PLK  H142  C14  C12   108.19  3.000
 PLK  H141  C14  C12   109.07  3.000
 PLK  C15   C14  C12   116.37  3.000
 PLK  H15   C15  N11   108.00  3.000
 PLK  H15   C15  C16   107.34  3.000
 PLK  N11   C15  C16   107.86  3.000
 PLK  H15   C15  C14   109.10  3.000
 PLK  N11   C15  C14   114.24  3.000
 PLK  C16   C15  C14   110.06  3.000
 PLK  H162  C16  H161  107.70  3.000
 PLK  H162  C16  C17   108.51  3.000
 PLK  H161  C16  C17   110.98  3.000
 PLK  H162  C16  C15   110.49  3.000
 PLK  H161  C16  C15   109.95  3.000
 PLK  C17   C16  C15   109.18  3.000
 PLK  O12   C17  O11   122.85  3.000
 PLK  O12   C17  C16   123.77  3.000
 PLK  O11   C17  C16   113.38  3.000
 PLK  HA    O11  C17   109.60  3.000
 PLK  H11   N11  C21   111.27  3.000
 PLK  H11   N11  C15   110.66  3.000
 PLK  C21   N11  C15   116.76  3.000
 PLK  H212  C21  H211  105.55  3.000
 PLK  H212  C21  C22   109.78  3.000
 PLK  H211  C21  C22   109.53  3.000
 PLK  H212  C21  N11   114.16  3.000
 PLK  H211  C21  N11   108.21  3.000
 PLK  C22   C21  N11   109.47  3.000
 PLK  C27   C22  C23   117.82  3.000
 PLK  C27   C22  C21   121.73  3.000
 PLK  C23   C22  C21   120.38  3.000
 PLK  C24   C23  O21   122.17  3.000
 PLK  C24   C23  C22   119.77  3.000
 PLK  O21   C23  C22   118.05  3.000
 PLK  H21   O21  C23   111.31  3.000
 PLK  N21   C24  C25   118.29  3.000
 PLK  N21   C24  C23   121.12  3.000
 PLK  C25   C24  C23   120.59  3.000
 PLK  H253  C25  H252  107.58  3.000
 PLK  H253  C25  H251  107.44  3.000
 PLK  H252  C25  H251  107.56  3.000
 PLK  H253  C25  C24   112.05  3.000
 PLK  H252  C25  C24   109.92  3.000
 PLK  H251  C25  C24   112.08  3.000
 PLK  C26   N21  C24   119.77  3.000
 PLK  H26   C26  C27   121.07  3.000
 PLK  H26   C26  N21   115.95  3.000
 PLK  C27   C26  N21   122.98  3.000
 PLK  C28   C27  C26   122.20  3.000
 PLK  C28   C27  C22   119.29  3.000
 PLK  C26   C27  C22   118.51  3.000
 PLK  H282  C28  H281  107.37  3.000
 PLK  H282  C28  O22   109.33  3.000
 PLK  H281  C28  O22   110.21  3.000
 PLK  H282  C28  C27   109.95  3.000
 PLK  H281  C28  C27   110.11  3.000
 PLK  O22   C28  C27   109.84  3.000
 PLK  P     O22  C28   118.73  3.000
 PLK  O3P   P    O2P   109.75  3.000
 PLK  O3P   P    O1P   118.49  3.000
 PLK  O2P   P    O1P   108.02  3.000
 PLK  O3P   P    O22   116.04  3.000
 PLK  O2P   P    O22   106.83  3.000
 PLK  O1P   P    O22    96.52  3.000
 PLK  H1P   O1P  P     114.19  3.000
 PLK  H2P   O2P  P     115.82  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
 PLK  CONST_01  N21   C24  C23  C22     0.00   0.0  0
 PLK  CONST_02  N21   C26  C27  C22     0.00   0.0  0
 PLK  CONST_03  C26   C27  C22  C23     0.00   0.0  0
 PLK  CONST_04  C26   N21  C24  C23     0.00   0.0  0
 PLK  CONST_05  C27   C22  C23  C24     0.00   0.0  0
 PLK  CONST_06  C27   C26  N21  C24     0.00   0.0  0
 PLK  CONST_07  C24   C23  C22  C21   180.00   0.0  0
 PLK  CONST_08  C26   C27  C22  C21   180.00   0.0  0
 PLK  CONST_09  C25   C24  C23  C22   180.00   0.0  0
 PLK  CONST_10  C28   C27  C22  C23   180.00   0.0  0
 PLK  CONST_11  C27   C22  C23  O21   180.00   0.0  0
 PLK  CONST_12  N21   C24  C23  O21   180.00   0.0  0
 PLK  CONST_13  C26   N21  C24  C25   180.00   0.0  0
 PLK  CONST_14  C28   C27  C26  N21   180.00   0.0  0
 PLK  CONST_15  H26   C26  C27  C22   180.00   0.0  0
 PLK  CONST_16  HA    O11  C17  C16   180.00   0.0  0
 PLK  Var_01    C23   C22  C21  N11    82.49  30.0  2
 PLK  Var_02    O22   C28  C27  C22   169.24  30.0  2
 PLK  Var_03    H251  C25  C24  C23    61.00  30.0  2
 PLK  Var_04    C22   C21  N11  C15  -174.85  30.0  3
 PLK  Var_05    C15   C14  C12  C11    63.19  30.0  3
 PLK  Var_06    O11   C17  C16  C15   120.73  30.0  3
 PLK  Var_07    O1P   P    O22  C28   171.39  30.0  3
 PLK  Var_08    H131  C13  C12  C11    63.73  30.0  3
 PLK  Var_09    H111  C11  C12  C13   173.85  30.0  3

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
 PLK  chir_01  C15  C14  C16  N11  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
 PLK  plan-1  C21  0.020
 PLK  plan-1  C22  0.020
 PLK  plan-1  C23  0.020
 PLK  plan-1  O21  0.020
 PLK  plan-1  C24  0.020
 PLK  plan-1  C25  0.020
 PLK  plan-1  N21  0.020
 PLK  plan-1  C26  0.020
 PLK  plan-1  C27  0.020
 PLK  plan-1  C28  0.020
 PLK  plan-1  H26  0.020
 PLK  plan-2  C16  0.020
 PLK  plan-2  C17  0.020
 PLK  plan-2  O11  0.020
 PLK  plan-2  O12  0.020
 PLK  plan-2  HA   0.020

