# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 21:26:32 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CO)C(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
 PLS  PLS  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-serine  ligand  39  22  .  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_PLS
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
 PLS  N     N  NH1   0  -0.671  -0.5784   0.5986  -2.0780
 PLS  CA    C  CH1   0  -0.186  -1.6908   0.2144  -2.9287
 PLS  CB    C  CH2   0  -0.162  -1.9910   1.3639  -3.8897
 PLS  OG    O  OH1   0  -0.665  -2.9557   0.9189  -4.8066
 PLS  C     C  C     0   0.532  -1.3694  -1.0360  -3.7304
 PLS  O     O  O     0  -0.428  -2.1227  -1.9676  -3.8489
 PLS  OXT   O  OH1   0  -0.582  -0.1777  -0.9718  -4.3033
 PLS  N1    N  N     0  -0.408   3.3405   0.5395   1.0354
 PLS  C2    C  CR6   0   0.130   3.2550   0.6493  -0.2789
 PLS  C2A   C  CH3   0  -0.720   4.4806   1.0406  -1.0454
 PLS  C3    C  CR6   0   0.265   2.0487   0.4015  -0.9530
 PLS  O3    O  OH1   0  -0.646   2.0399   0.5179  -2.2873
 PLS  C4    C  CR6   0   0.029   0.9172   0.0331  -0.2233
 PLS  C4A   C  CH2   0  -0.339  -0.3682  -0.2954  -0.9412
 PLS  C5    C  CR6   0  -0.075   1.0347  -0.0700   1.1663
 PLS  C6    C  CR16  0  -0.145   2.2673   0.1942   1.7407
 PLS  C5A   C  CH2   0  -0.213  -0.1586  -0.4743   1.9870
 PLS  O4P   O  O2    0  -0.593   0.2054  -0.5255   3.3615
 PLS  P     P  P     0   1.463  -0.9274  -0.7436   4.4687
 PLS  O1P   O  O     0  -0.708  -1.8642  -1.8583   4.2378
 PLS  O2P   O  OH1   0  -0.728   0.0549  -0.8340   5.7178
 PLS  O3P   O  OH1   0  -0.740  -1.7399   0.6274   4.5735
 PLS  HN    H  HNH1  0   0.388  -0.7449   1.5359  -1.7258
 PLS  HA    H  HCH1  0   0.269  -2.5936  -0.0081  -2.3459
 PLS  HB1   H  HCH2  0   0.229  -2.3457   2.2183  -3.2993
 PLS  HB2   H  HCH2  0   0.217  -1.0597   1.6695  -4.3808
 PLS  HOG   H  HOH1  0   0.466  -3.1115   1.6199  -5.4464
 PLS  HXT   H  HOH1  0   0.487  -0.0121  -1.7737  -4.8222
 PLS  H2A1  H  HCH3  0   0.245   4.7406   0.2979  -1.8015
 PLS  H2A2  H  HCH3  0   0.245   4.3412   1.9887  -1.5686
 PLS  H2A3  H  HCH3  0   0.245   5.3246   1.1469  -0.3670
 PLS  HO3   H  HOH1  0   0.477   1.0884   0.5604  -2.5703
 PLS  H4A1  H  HCH2  0   0.281  -0.2972  -1.3230  -1.3139
 PLS  H4A2  H  HCH2  0   0.264  -1.2262  -0.2777  -0.2631
 PLS  H6    H  HCR6  0   0.254   2.4065   0.1293   2.8119
 PLS  H5A1  H  HCH2  0   0.256  -0.9708   0.2449   1.8350
 PLS  H5A2  H  HCH2  0   0.264  -0.5264  -1.4542   1.6687
 PLS  HOP2  H  HOH1  0   0.506  -0.3801  -1.0776   6.5462
 PLS  HOP3  H  HOH1  0   0.497  -1.2144   1.4151   4.7676

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
 PLS  N    CA    single    1.452  0.020  1.452
 PLS  N    C4A   single    1.461  0.020  1.461
 PLS  N    HN    single    0.890  0.020  1.040
 PLS  CA   CB    single    1.528  0.020  1.528
 PLS  CA   C     single    1.520  0.020  1.520
 PLS  CA   HA    single    0.970  0.020  1.090
 PLS  CB   OG    single    1.403  0.020  1.403
 PLS  CB   HB1   single    0.970  0.020  1.090
 PLS  CB   HB2   single    0.970  0.020  1.090
 PLS  OG   HOG   single    0.850  0.020  0.980
 PLS  C    O     double    1.204  0.020  1.204
 PLS  C    OXT   single    1.324  0.020  1.324
 PLS  OXT  HXT   single    0.850  0.020  0.980
 PLS  N1   C2    aromatic  1.322  0.020  1.322
 PLS  N1   C6    aromatic  1.330  0.020  1.330
 PLS  C2   C2A   single    1.498  0.020  1.498
 PLS  C2   C3    aromatic  1.404  0.020  1.404
 PLS  C2A  H2A1  single    0.970  0.020  1.090
 PLS  C2A  H2A2  single    0.970  0.020  1.090
 PLS  C2A  H2A3  single    0.970  0.020  1.090
 PLS  C3   O3    single    1.339  0.020  1.339
 PLS  C3   C4    aromatic  1.396  0.020  1.396
 PLS  O3   HO3   single    0.850  0.020  0.980
 PLS  C4   C4A   single    1.509  0.020  1.509
 PLS  C4   C5    aromatic  1.398  0.020  1.398
 PLS  C4A  H4A1  single    0.970  0.020  1.090
 PLS  C4A  H4A2  single    0.970  0.020  1.090
 PLS  C5   C6    aromatic  1.385  0.020  1.385
 PLS  C5   C5A   single    1.504  0.020  1.504
 PLS  C6   H6    single    0.930  0.020  1.080
 PLS  C5A  O4P   single    1.423  0.020  1.423
 PLS  C5A  H5A1  single    0.970  0.020  1.090
 PLS  C5A  H5A2  single    0.970  0.020  1.090
 PLS  O4P  P     single    1.599  0.020  1.599
 PLS  P    O1P   double    1.474  0.020  1.474
 PLS  P    O2P   single    1.592  0.020  1.592
 PLS  P    O3P   single    1.597  0.020  1.597
 PLS  O2P  HOP2  single    0.850  0.020  0.980
 PLS  O3P  HOP3  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
 PLS  HN    N    C4A   108.58  3.000
 PLS  HN    N    CA    108.78  3.000
 PLS  C4A   N    CA    113.83  3.000
 PLS  HA    CA   C     106.70  3.000
 PLS  HA    CA   CB    108.96  3.000
 PLS  C     CA   CB    109.19  3.000
 PLS  HA    CA   N     111.88  3.000
 PLS  C     CA   N     111.39  3.000
 PLS  CB    CA   N     108.66  3.000
 PLS  HB2   CB   HB1   107.37  3.000
 PLS  HB2   CB   OG    112.31  3.000
 PLS  HB1   CB   OG    112.10  3.000
 PLS  HB2   CB   CA    108.93  3.000
 PLS  HB1   CB   CA    108.11  3.000
 PLS  OG    CB   CA    107.91  3.000
 PLS  HOG   OG   CB    108.36  3.000
 PLS  OXT   C    O     123.93  3.000
 PLS  OXT   C    CA    112.26  3.000
 PLS  O     C    CA    123.80  3.000
 PLS  HXT   OXT  C     110.20  3.000
 PLS  C6    N1   C2    119.79  3.000
 PLS  C3    C2   C2A   120.24  3.000
 PLS  C3    C2   N1    121.22  3.000
 PLS  C2A   C2   N1    118.54  3.000
 PLS  H2A3  C2A  H2A2  108.24  3.000
 PLS  H2A3  C2A  H2A1  108.28  3.000
 PLS  H2A2  C2A  H2A1  106.82  3.000
 PLS  H2A3  C2A  C2    109.95  3.000
 PLS  H2A2  C2A  C2    111.57  3.000
 PLS  H2A1  C2A  C2    111.82  3.000
 PLS  C4    C3   O3    122.58  3.000
 PLS  C4    C3   C2    119.48  3.000
 PLS  O3    C3   C2    117.94  3.000
 PLS  HO3   O3   C3    107.08  3.000
 PLS  C5    C4   C4A   121.90  3.000
 PLS  C5    C4   C3    118.09  3.000
 PLS  C4A   C4   C3    119.96  3.000
 PLS  H4A2  C4A  H4A1  106.08  3.000
 PLS  H4A2  C4A  C4    111.71  3.000
 PLS  H4A1  C4A  C4    108.11  3.000
 PLS  H4A2  C4A  N     111.07  3.000
 PLS  H4A1  C4A  N     108.58  3.000
 PLS  C4    C4A  N     111.07  3.000
 PLS  C5A   C5   C6    122.08  3.000
 PLS  C5A   C5   C4    119.70  3.000
 PLS  C6    C5   C4    118.21  3.000
 PLS  H6    C6   C5    120.89  3.000
 PLS  H6    C6   N1    115.90  3.000
 PLS  C5    C6   N1    123.21  3.000
 PLS  H5A2  C5A  H5A1  107.36  3.000
 PLS  H5A2  C5A  O4P   109.56  3.000
 PLS  H5A1  C5A  O4P   110.32  3.000
 PLS  H5A2  C5A  C5    110.42  3.000
 PLS  H5A1  C5A  C5    109.64  3.000
 PLS  O4P   C5A  C5    109.51  3.000
 PLS  P     O4P  C5A   119.51  3.000
 PLS  O3P   P    O2P   108.13  3.000
 PLS  O3P   P    O1P   109.63  3.000
 PLS  O2P   P    O1P   118.17  3.000
 PLS  O3P   P    O4P   106.79  3.000
 PLS  O2P   P    O4P    96.55  3.000
 PLS  O1P   P    O4P   116.41  3.000
 PLS  HOP2  O2P  P     114.15  3.000
 PLS  HOP3  O3P  P     115.86  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
 PLS  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PLS  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PLS  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PLS  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PLS  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PLS  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PLS  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PLS  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PLS  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PLS  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PLS  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PLS  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PLS  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 PLS  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 PLS  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PLS  CONST_16  HXT   OXT  C    CA   180.00   0.0  0
 PLS  Var_01    C3    C4   C4A  N    -38.68  30.0  1
 PLS  Var_02    O4P   C5A  C5   C4   179.31  30.0  2
 PLS  Var_03    H2A1  C2A  C2   N1   122.60  30.0  2
 PLS  Var_04    C4    C4A  N    CA   171.36  30.0  3
 PLS  Var_05    O1P   P    O4P  C5A   49.54  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
 PLS  chir_01  CA  N  CB  C  negativ

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
 PLS  plan-1  N1   0.020
 PLS  plan-1  C2   0.020
 PLS  plan-1  C2A  0.020
 PLS  plan-1  C3   0.020
 PLS  plan-1  O3   0.020
 PLS  plan-1  C4   0.020
 PLS  plan-1  C4A  0.020
 PLS  plan-1  C5   0.020
 PLS  plan-1  C6   0.020
 PLS  plan-1  C5A  0.020
 PLS  plan-1  H6   0.020
 PLS  plan-2  CA   0.020
 PLS  plan-2  C    0.020
 PLS  plan-2  O    0.020
 PLS  plan-2  OXT  0.020
 PLS  plan-2  HXT  0.020

