# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 10:17:14 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNCCCC(O)=O)c1O
#
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
 PLZ  PLZ  '4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]butanoic acid'  ligand  41  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PLZ
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
 PLZ  N1    N  N     0  -0.409   5.3094  -6.8563   0.2866
 PLZ  C2A   C  CH3   0  -0.721   6.9213  -5.4806   1.4581
 PLZ  O3    O  OH1   0  -0.622   5.0675  -3.4597   1.3176
 PLZ  C4A   C  CH2   0  -0.370   2.3832  -3.7129   0.0948
 PLZ  C5    C  CH2   0  -0.461  -0.9333  -3.5289   1.8742
 PLZ  C6    C  CH2   0  -0.561  -1.3820  -4.9687   1.6577
 PLZ  P     P  P     0   1.482   0.6438  -5.6474  -3.3351
 PLZ  N9    N  NH1   0  -0.575   1.3212  -4.0194   1.0315
 PLZ  C8    C  CH2   0  -0.279   0.2075  -3.0927   0.9639
 PLZ  C1    C  C     0   0.548  -1.9329  -5.2297   0.2827
 PLZ  O2    O  OH1   0  -0.595  -1.6858  -6.4685  -0.1337
 PLZ  O4    O  O     0  -0.452  -2.5613  -4.4324  -0.3702
 PLZ  C19   C  CR6   0   0.068   3.4327  -4.7946   0.1307
 PLZ  C13   C  CR6   0   0.251   4.6674  -4.6107   0.7439
 PLZ  C12   C  CR6   0   0.145   5.5898  -5.6720   0.8006
 PLZ  C16   C  CR16  0  -0.134   4.1310  -7.0440  -0.2984
 PLZ  C15   C  CR6   0  -0.013   3.1640  -6.0628  -0.4021
 PLZ  C5M   C  CH2   0  -0.302   1.8721  -6.3787  -1.0884
 PLZ  O4P   O  O2    0  -0.586   1.9381  -5.8601  -2.4324
 PLZ  O2P   O  O     0  -0.698   1.0168  -5.3175  -4.7228
 PLZ  O1P   O  OH1   0  -0.741  -0.1510  -4.5465  -2.5021
 PLZ  O3P   O  OH1   0  -0.749  -0.2951  -6.9300  -3.1454
 PLZ  H2A1  H  HCH3  0   0.249   7.5041  -4.6997   0.9658
 PLZ  H2A2  H  HCH3  0   0.249   6.8164  -5.1861   2.5038
 PLZ  H2A3  H  HCH3  0   0.248   7.4896  -6.4073   1.4192
 PLZ  HO3   H  HOH1  0   0.476   4.4173  -2.7583   1.2016
 PLZ  H4A1  H  HCH2  0   0.213   2.8175  -2.7124   0.2502
 PLZ  H4A2  H  HCH2  0   0.265   1.9522  -3.6630  -0.9066
 PLZ  H51   H  HCH2  0   0.240  -1.7720  -2.8438   1.7380
 PLZ  H52   H  HCH2  0   0.241  -0.6251  -3.4273   2.9181
 PLZ  H61   H  HCH2  0   0.286  -2.1818  -5.2095   2.3664
 PLZ  H62   H  HCH2  0   0.263  -0.5681  -5.6608   1.8681
 PLZ  HN9   H  HNH1  0   0.347   1.6952  -4.0376   1.9736
 PLZ  H81   H  HCH2  0   0.211   0.4941  -2.0624   1.2237
 PLZ  H82   H  HCH2  0   0.230  -0.1376  -3.0607  -0.0725
 PLZ  HO2   H  HOH1  0   0.470  -2.0646  -6.6073  -1.0146
 PLZ  H16   H  HCR6  0   0.256   3.9442  -8.0335  -0.7037
 PLZ  H5M1  H  HCH2  0   0.260   1.7290  -7.4597  -1.1331
 PLZ  H5M2  H  HCH2  0   0.271   1.0347  -5.9424  -0.5436
 PLZ  HO1P  H  HOH1  0   0.499  -1.0217  -4.3020  -2.8420
 PLZ  HO3P  H  HOH1  0   0.500  -0.0917  -7.6637  -3.7415

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
 PLZ  N1   C12   aromatic  1.321  0.020  1.321
 PLZ  N1   C16   aromatic  1.329  0.020  1.329
 PLZ  C2A  C12   single    1.497  0.020  1.497
 PLZ  C2A  H2A1  single    0.970  0.020  1.090
 PLZ  C2A  H2A2  single    0.970  0.020  1.090
 PLZ  C2A  H2A3  single    0.970  0.020  1.090
 PLZ  O3   C13   single    1.347  0.020  1.347
 PLZ  O3   HO3   single    0.850  0.020  0.980
 PLZ  C4A  C19   single    1.508  0.020  1.508
 PLZ  C4A  N9    single    1.449  0.020  1.449
 PLZ  C4A  H4A1  single    0.970  0.020  1.090
 PLZ  C4A  H4A2  single    0.970  0.020  1.090
 PLZ  C5   C8    single    1.523  0.020  1.523
 PLZ  C5   C6    single    1.524  0.020  1.524
 PLZ  C5   H51   single    0.970  0.020  1.090
 PLZ  C5   H52   single    0.970  0.020  1.090
 PLZ  C6   C1    single    1.504  0.020  1.504
 PLZ  C6   H61   single    0.970  0.020  1.090
 PLZ  C6   H62   single    0.970  0.020  1.090
 PLZ  P    O4P   single    1.592  0.020  1.592
 PLZ  P    O2P   double    1.474  0.020  1.474
 PLZ  P    O1P   single    1.593  0.020  1.593
 PLZ  P    O3P   single    1.601  0.020  1.601
 PLZ  N9   C8    single    1.450  0.020  1.450
 PLZ  N9   HN9   single    0.890  0.020  1.040
 PLZ  C8   H81   single    0.970  0.020  1.090
 PLZ  C8   H82   single    0.970  0.020  1.090
 PLZ  C1   O4    double    1.207  0.020  1.207
 PLZ  C1   O2    single    1.330  0.020  1.330
 PLZ  O2   HO2   single    0.850  0.020  0.980
 PLZ  C19  C13   aromatic  1.391  0.020  1.391
 PLZ  C19  C15   aromatic  1.402  0.020  1.402
 PLZ  C13  C12   aromatic  1.407  0.020  1.407
 PLZ  C16  C15   aromatic  1.381  0.020  1.381
 PLZ  C16  H16   single    0.930  0.020  1.080
 PLZ  C15  C5M   single    1.497  0.020  1.497
 PLZ  C5M  O4P   single    1.442  0.020  1.442
 PLZ  C5M  H5M1  single    0.970  0.020  1.090
 PLZ  C5M  H5M2  single    0.970  0.020  1.090
 PLZ  O1P  HO1P  single    0.850  0.020  0.980
 PLZ  O3P  HO3P  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
 PLZ  C16   N1   C12   119.08  3.000
 PLZ  H2A3  C2A  H2A2  108.32  3.000
 PLZ  H2A3  C2A  H2A1  108.32  3.000
 PLZ  H2A2  C2A  H2A1  106.88  3.000
 PLZ  H2A3  C2A  C12   109.87  3.000
 PLZ  H2A2  C2A  C12   111.70  3.000
 PLZ  H2A1  C2A  C12   111.60  3.000
 PLZ  HO3   O3   C13   111.74  3.000
 PLZ  H4A2  C4A  H4A1  104.10  3.000
 PLZ  H4A2  C4A  C19   109.24  3.000
 PLZ  H4A1  C4A  C19   111.95  3.000
 PLZ  H4A2  C4A  N9    108.27  3.000
 PLZ  H4A1  C4A  N9    112.95  3.000
 PLZ  C19   C4A  N9    110.06  3.000
 PLZ  H52   C5   H51   106.11  3.000
 PLZ  H52   C5   C8    109.44  3.000
 PLZ  H51   C5   C8    108.74  3.000
 PLZ  H52   C5   C6    107.85  3.000
 PLZ  H51   C5   C6    110.43  3.000
 PLZ  C8    C5   C6    113.97  3.000
 PLZ  H62   C6   H61   106.32  3.000
 PLZ  H62   C6   C1    109.88  3.000
 PLZ  H61   C6   C1    106.61  3.000
 PLZ  H62   C6   C5    110.68  3.000
 PLZ  H61   C6   C5    109.32  3.000
 PLZ  C1    C6   C5    113.69  3.000
 PLZ  O3P   P    O1P   101.48  3.000
 PLZ  O3P   P    O2P   116.05  3.000
 PLZ  O1P   P    O2P   117.63  3.000
 PLZ  O3P   P    O4P   107.62  3.000
 PLZ  O1P   P    O4P   101.62  3.000
 PLZ  O2P   P    O4P   110.97  3.000
 PLZ  HN9   N9   C8    109.76  3.000
 PLZ  HN9   N9   C4A   109.52  3.000
 PLZ  C8    N9   C4A   113.42  3.000
 PLZ  H82   C8   H81   106.18  3.000
 PLZ  H82   C8   N9    107.78  3.000
 PLZ  H81   C8   N9    112.78  3.000
 PLZ  H82   C8   C5    109.79  3.000
 PLZ  H81   C8   C5    108.79  3.000
 PLZ  N9    C8   C5    111.36  3.000
 PLZ  O4    C1   O2    122.87  3.000
 PLZ  O2    C1   C6    112.32  3.000
 PLZ  O4    C1   C6    124.79  3.000
 PLZ  HO2   O2   C1    110.21  3.000
 PLZ  C15   C19  C13   117.22  3.000
 PLZ  C15   C19  C4A   120.45  3.000
 PLZ  C13   C19  C4A   122.25  3.000
 PLZ  C12   C13  C19   120.00  3.000
 PLZ  C12   C13  O3    115.64  3.000
 PLZ  C19   C13  O3    124.37  3.000
 PLZ  C13   C12  C2A   120.27  3.000
 PLZ  C13   C12  N1    121.42  3.000
 PLZ  C2A   C12  N1    118.31  3.000
 PLZ  H16   C16  C15   119.93  3.000
 PLZ  H16   C16  N1    116.47  3.000
 PLZ  C15   C16  N1    123.60  3.000
 PLZ  C5M   C15  C16   119.26  3.000
 PLZ  C5M   C15  C19   122.06  3.000
 PLZ  C16   C15  C19   118.68  3.000
 PLZ  H5M2  C5M  H5M1  108.43  3.000
 PLZ  H5M2  C5M  O4P   110.92  3.000
 PLZ  H5M1  C5M  O4P   108.90  3.000
 PLZ  H5M2  C5M  C15   110.46  3.000
 PLZ  H5M1  C5M  C15   109.94  3.000
 PLZ  O4P   C5M  C15   108.18  3.000
 PLZ  C5M   O4P  P     122.63  3.000
 PLZ  HO1P  O1P  P     116.14  3.000
 PLZ  HO3P  O3P  P     114.30  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
 PLZ  CONST_01  C19   C13  C12  N1      0.00   0.0  0
 PLZ  CONST_02  C19   C15  C16  N1      0.00   0.0  0
 PLZ  CONST_03  C16   C15  C19  C13     0.00   0.0  0
 PLZ  CONST_04  C16   N1   C12  C13     0.00   0.0  0
 PLZ  CONST_05  C15   C16  N1   C12     0.00   0.0  0
 PLZ  CONST_06  C15   C19  C13  C12     0.00   0.0  0
 PLZ  CONST_07  O3    C13  C12  N1    180.00   0.0  0
 PLZ  CONST_08  C5M   C15  C16  N1    180.00   0.0  0
 PLZ  CONST_09  C16   N1   C12  C2A   180.00   0.0  0
 PLZ  CONST_10  C19   C13  C12  C2A   180.00   0.0  0
 PLZ  CONST_11  C15   C19  C13  O3    180.00   0.0  0
 PLZ  CONST_12  C12   C13  C19  C4A   180.00   0.0  0
 PLZ  CONST_13  C16   C15  C19  C4A   180.00   0.0  0
 PLZ  CONST_14  C5M   C15  C19  C13   180.00   0.0  0
 PLZ  CONST_15  H16   C16  C15  C19   180.00   0.0  0
 PLZ  CONST_16  HO2   O2   C1   C6    180.00   0.0  0
 PLZ  Var_01    C13   C19  C4A  N9   -105.37  30.0  2
 PLZ  Var_02    O4P   C5M  C15  C19    79.59  30.0  2
 PLZ  Var_03    H2A1  C2A  C12  N1    119.61  30.0  2
 PLZ  Var_04    C15   C5M  O4P  P    -163.02  30.0  2
 PLZ  Var_05    C19   C4A  N9   C8   -174.34  30.0  2
 PLZ  Var_06    C5    C8   N9   C4A   174.83  30.0  3
 PLZ  Var_07    O4    C1   C6   C5    -34.02  30.0  3
 PLZ  Var_08    N9    C8   C5   C6    -52.41  30.0  3
 PLZ  Var_09    C1    C6   C5   C8    -62.57  30.0  3
 PLZ  Var_10    O2P   P    O4P  C5M  -170.80  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
 PLZ  plan-1  N1   0.020
 PLZ  plan-1  C2A  0.020
 PLZ  plan-1  O3   0.020
 PLZ  plan-1  C4A  0.020
 PLZ  plan-1  C19  0.020
 PLZ  plan-1  C13  0.020
 PLZ  plan-1  C12  0.020
 PLZ  plan-1  C16  0.020
 PLZ  plan-1  C15  0.020
 PLZ  plan-1  C5M  0.020
 PLZ  plan-1  H16  0.020
 PLZ  plan-2  C6   0.020
 PLZ  plan-2  C1   0.020
 PLZ  plan-2  O2   0.020
 PLZ  plan-2  O4   0.020
 PLZ  plan-2  HO2  0.020

