# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 23:38:28 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@](C)(CC(O)=O)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
 PLA  PLA  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-L-aspartic acid'  ligand  44  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_PLA
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
 PLA  N1    N  N     0  -0.408   2.9427   0.8112   2.6323
 PLA  C2    C  CR6   0   0.130   3.3014   0.8309   1.3606
 PLA  C2A   C  CH3   0  -0.721   4.7028   1.2341   1.0190
 PLA  C3    C  CR6   0   0.260   2.4012   0.4745   0.3435
 PLA  O3    O  OH1   0  -0.646   2.8424   0.5003  -0.9210
 PLA  C4    C  CR6   0   0.039   1.1008   0.0949   0.6789
 PLA  C4A   C  CH2   0  -0.347   0.1289  -0.3518  -0.3871
 PLA  C5    C  CR6   0  -0.075   0.7489   0.0824   2.0328
 PLA  C6    C  CR16  0  -0.146   1.7063   0.4505   2.9634
 PLA  C5A   C  CH2   0  -0.213  -0.6356  -0.3432   2.4363
 PLA  O4P   O  O2    0  -0.593  -0.7351  -0.3613   3.8552
 PLA  P     P  P     0   1.464  -2.1470  -0.6797   4.5353
 PLA  O1P   O  O     0  -0.708  -2.8896  -1.8269   3.9828
 PLA  O2P   O  OH1   0  -0.728  -1.6115  -0.7728   6.0314
 PLA  O3P   O  OH1   0  -0.739  -3.0313   0.6442   4.4091
 PLA  N     N  NH1   0  -0.677   0.3123   0.4122  -1.6203
 PLA  CA    C  CT    0  -0.003  -0.3788  -0.0985  -2.8143
 PLA  CB1   C  CH2   0  -0.598  -0.2139   0.9939  -3.8774
 PLA  CB2   C  CH3   0  -0.666  -1.8572  -0.3850  -2.5715
 PLA  CG    C  C     0   0.563  -0.6070   0.5701  -5.2641
 PLA  OD1   O  O     0  -0.435  -0.7129  -0.5756  -5.6262
 PLA  OD2   O  OH1   0  -0.588  -0.7935   1.6105  -6.0612
 PLA  C     C  C     0   0.578   0.3532  -1.3817  -3.2291
 PLA  O     O  O     0  -0.425  -0.1168  -2.4868  -3.1543
 PLA  OXT   O  OH1   0  -0.588   1.5946  -1.1365  -3.6190
 PLA  H2A1  H  HCH3  0   0.246   5.2507   0.4217   0.5375
 PLA  H2A2  H  HCH3  0   0.245   4.7229   2.0806   0.3305
 PLA  H2A3  H  HCH3  0   0.245   5.2386   1.5152   1.9235
 PLA  HO3   H  HOH1  0   0.476   2.0395   0.4624  -1.5056
 PLA  H4A1  H  HCH2  0   0.283   0.3101  -1.4118  -0.5917
 PLA  H4A2  H  HCH2  0   0.267  -0.8986  -0.2831  -0.0235
 PLA  H6    H  HCR6  0   0.254   1.4797   0.4568   4.0215
 PLA  H5A1  H  HCH2  0   0.257  -1.3728   0.3487   2.0137
 PLA  H5A2  H  HCH2  0   0.263  -0.8565  -1.3382   2.0394
 PLA  HOP2  H  HOH1  0   0.506  -2.2834  -1.0296   6.6774
 PLA  HOP3  H  HOH1  0   0.497  -2.6555   1.4421   4.8050
 PLA  HN    H  HNH1  0   0.388   0.0087   1.3674  -1.4558
 PLA  HB11  H  HCH2  0   0.301  -0.8015   1.8664  -3.5804
 PLA  HB12  H  HCH2  0   0.318   0.8255   1.3344  -3.9172
 PLA  HB21  H  HCH3  0   0.245  -2.3510   0.5227  -2.2212
 PLA  HB22  H  HCH3  0   0.255  -2.3579  -0.7082  -3.4827
 PLA  HB23  H  HCH3  0   0.254  -2.0129  -1.1621  -1.8259
 PLA  HOD   H  HOH1  0   0.485  -1.0065   1.3109  -6.9584
 PLA  HXT   H  HOH1  0   0.486   2.0447  -1.9650  -3.8435

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
 PLA  N1   C2    aromatic  1.321  0.020  1.321
 PLA  N1   C6    aromatic  1.330  0.020  1.330
 PLA  C2   C2A   single    1.498  0.020  1.498
 PLA  C2   C3    aromatic  1.404  0.020  1.404
 PLA  C2A  H2A1  single    0.970  0.020  1.090
 PLA  C2A  H2A2  single    0.970  0.020  1.090
 PLA  C2A  H2A3  single    0.970  0.020  1.090
 PLA  C3   O3    single    1.340  0.020  1.340
 PLA  C3   C4    aromatic  1.396  0.020  1.396
 PLA  O3   HO3   single    0.850  0.020  0.980
 PLA  C4   C4A   single    1.510  0.020  1.510
 PLA  C4   C5    aromatic  1.399  0.020  1.399
 PLA  C4A  N     single    1.462  0.020  1.462
 PLA  C4A  H4A1  single    0.970  0.020  1.090
 PLA  C4A  H4A2  single    0.970  0.020  1.090
 PLA  C5   C6    aromatic  1.385  0.020  1.385
 PLA  C5   C5A   single    1.504  0.020  1.504
 PLA  C6   H6    single    0.930  0.020  1.080
 PLA  C5A  O4P   single    1.423  0.020  1.423
 PLA  C5A  H5A1  single    0.970  0.020  1.090
 PLA  C5A  H5A2  single    0.970  0.020  1.090
 PLA  O4P  P     single    1.599  0.020  1.599
 PLA  P    O1P   double    1.474  0.020  1.474
 PLA  P    O2P   single    1.592  0.020  1.592
 PLA  P    O3P   single    1.597  0.020  1.597
 PLA  O2P  HOP2  single    0.850  0.020  0.980
 PLA  O3P  HOP3  single    0.850  0.020  0.980
 PLA  N    CA    single    1.471  0.020  1.471
 PLA  N    HN    single    0.890  0.020  1.040
 PLA  CA   CB1   single    1.533  0.020  1.533
 PLA  CA   CB2   single    1.525  0.020  1.525
 PLA  CA   C     single    1.534  0.020  1.534
 PLA  CB1  CG    single    1.502  0.020  1.502
 PLA  CB1  HB11  single    0.970  0.020  1.090
 PLA  CB1  HB12  single    0.970  0.020  1.090
 PLA  CB2  HB21  single    0.970  0.020  1.090
 PLA  CB2  HB22  single    0.970  0.020  1.090
 PLA  CB2  HB23  single    0.970  0.020  1.090
 PLA  CG   OD1   double    1.206  0.020  1.206
 PLA  CG   OD2   single    1.324  0.020  1.324
 PLA  OD2  HOD   single    0.850  0.020  0.980
 PLA  C    O     double    1.203  0.020  1.203
 PLA  C    OXT   single    1.324  0.020  1.324
 PLA  OXT  HXT   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
 PLA  C6    N1   C2    119.74  3.000
 PLA  C3    C2   C2A   120.20  3.000
 PLA  C3    C2   N1    121.28  3.000
 PLA  C2A   C2   N1    118.52  3.000
 PLA  H2A3  C2A  H2A2  108.36  3.000
 PLA  H2A3  C2A  H2A1  108.16  3.000
 PLA  H2A2  C2A  H2A1  106.85  3.000
 PLA  H2A3  C2A  C2    109.91  3.000
 PLA  H2A2  C2A  C2    111.71  3.000
 PLA  H2A1  C2A  C2    111.70  3.000
 PLA  C4    C3   O3    122.62  3.000
 PLA  C4    C3   C2    119.49  3.000
 PLA  O3    C3   C2    117.88  3.000
 PLA  HO3   O3   C3    106.76  3.000
 PLA  C5    C4   C4A   121.24  3.000
 PLA  C5    C4   C3    118.00  3.000
 PLA  C4A   C4   C3    120.70  3.000
 PLA  H4A2  C4A  H4A1  106.19  3.000
 PLA  H4A2  C4A  N     111.46  3.000
 PLA  H4A1  C4A  N     109.12  3.000
 PLA  H4A2  C4A  C4    110.61  3.000
 PLA  H4A1  C4A  C4    108.18  3.000
 PLA  N     C4A  C4    111.10  3.000
 PLA  C5A   C5   C6    122.10  3.000
 PLA  C5A   C5   C4    119.59  3.000
 PLA  C6    C5   C4    118.30  3.000
 PLA  H6    C6   C5    120.92  3.000
 PLA  H6    C6   N1    115.89  3.000
 PLA  C5    C6   N1    123.19  3.000
 PLA  H5A2  C5A  H5A1  107.37  3.000
 PLA  H5A2  C5A  O4P   109.65  3.000
 PLA  H5A1  C5A  O4P   110.22  3.000
 PLA  H5A2  C5A  C5    110.25  3.000
 PLA  H5A1  C5A  C5    109.72  3.000
 PLA  O4P   C5A  C5    109.61  3.000
 PLA  P     O4P  C5A   119.24  3.000
 PLA  O3P   P    O2P   108.00  3.000
 PLA  O3P   P    O1P   109.67  3.000
 PLA  O2P   P    O1P   118.45  3.000
 PLA  O3P   P    O4P   106.87  3.000
 PLA  O2P   P    O4P    96.57  3.000
 PLA  O1P   P    O4P   116.13  3.000
 PLA  HOP2  O2P  P     114.19  3.000
 PLA  HOP3  O3P  P     115.89  3.000
 PLA  HN    N    CA    108.51  3.000
 PLA  HN    N    C4A   108.50  3.000
 PLA  CA    N    C4A   116.37  3.000
 PLA  C     CA   CB2   110.38  3.000
 PLA  C     CA   CB1   110.92  3.000
 PLA  CB2   CA   CB1   110.39  3.000
 PLA  C     CA   N     106.60  3.000
 PLA  CB2   CA   N     113.04  3.000
 PLA  CB1   CA   N     105.36  3.000
 PLA  HB12  CB1  HB11  105.79  3.000
 PLA  HB12  CB1  CG    107.62  3.000
 PLA  HB11  CB1  CG    109.59  3.000
 PLA  HB12  CB1  CA    110.43  3.000
 PLA  HB11  CB1  CA    108.81  3.000
 PLA  CG    CB1  CA    114.26  3.000
 PLA  HB23  CB2  HB22  107.19  3.000
 PLA  HB23  CB2  HB21  108.02  3.000
 PLA  HB22  CB2  HB21  107.91  3.000
 PLA  HB23  CB2  CA    112.45  3.000
 PLA  HB22  CB2  CA    111.61  3.000
 PLA  HB21  CB2  CA    109.48  3.000
 PLA  OD2   CG   OD1   123.60  3.000
 PLA  OD2   CG   CB1   111.77  3.000
 PLA  OD1   CG   CB1   124.61  3.000
 PLA  HOD   OD2  CG    110.20  3.000
 PLA  OXT   C    O     123.69  3.000
 PLA  OXT   C    CA    111.83  3.000
 PLA  O     C    CA    124.40  3.000
 PLA  HXT   OXT  C     110.20  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
 PLA  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PLA  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PLA  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PLA  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PLA  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PLA  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PLA  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PLA  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PLA  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PLA  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PLA  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PLA  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PLA  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 PLA  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 PLA  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PLA  CONST_16  HXT   OXT  C    CA   180.00   0.0  0
 PLA  CONST_17  HOD   OD2  CG   CB1  180.00   0.0  0
 PLA  Var_01    N     C4A  C4   C3   -36.43  30.0  2
 PLA  Var_02    O4P   C5A  C5   C4   176.20  30.0  2
 PLA  Var_03    H2A1  C2A  C2   N1   117.18  30.0  2
 PLA  Var_04    CA    N    C4A  C4   168.16  30.0  3
 PLA  Var_05    O1P   P    O4P  C5A   46.03  30.0  3
 PLA  Var_06    OD1   CG   CB1  CA   -18.54  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
 PLA  chir_01  CA  CB1  CB2  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
 PLA  plan-1  N1   0.020
 PLA  plan-1  C2   0.020
 PLA  plan-1  C2A  0.020
 PLA  plan-1  C3   0.020
 PLA  plan-1  O3   0.020
 PLA  plan-1  C4   0.020
 PLA  plan-1  C4A  0.020
 PLA  plan-1  C5   0.020
 PLA  plan-1  C6   0.020
 PLA  plan-1  C5A  0.020
 PLA  plan-1  H6   0.020
 PLA  plan-2  CB1  0.020
 PLA  plan-2  CG   0.020
 PLA  plan-2  OD1  0.020
 PLA  plan-2  OD2  0.020
 PLA  plan-2  HOD  0.020
 PLA  plan-3  CA   0.020
 PLA  plan-3  C    0.020
 PLA  plan-3  O    0.020
 PLA  plan-3  OXT  0.020
 PLA  plan-3  HXT  0.020

