# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 18:50:39 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](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
 PPD  PPD  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-aspartic acid'  ligand  41  24  .  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_PPD
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
 PPD  N1    N  N     0  -0.408   3.6449   0.8001   0.4766
 PPD  C2    C  CR6   0   0.129   3.2800   0.9662  -0.7825
 PPD  C2A   C  CH3   0  -0.720   4.2524   1.5969  -1.7309
 PPD  C3    C  CR6   0   0.262   2.0137   0.5607  -1.2357
 PPD  O3    O  OH1   0  -0.646   1.7249   0.7472  -2.5299
 PPD  C4    C  CR6   0   0.023   1.1201  -0.0260  -0.3381
 PPD  C4A   C  CH2   0  -0.333  -0.2243  -0.5268  -0.8056
 PPD  C5    C  CR6   0  -0.070   1.5329  -0.1888   0.9885
 PPD  C6    C  CR16  0  -0.145   2.8009   0.2420   1.3399
 PPD  C5A   C  CH2   0  -0.217   0.6019  -0.8263   1.9826
 PPD  O4P   O  O2    0  -0.591   1.2740  -1.0029   3.2247
 PPD  P     P  P     0   1.459   0.4172  -1.2244   4.5557
 PPD  O1P   O  O     0  -0.707  -0.6490  -2.2401   4.4906
 PPD  O2P   O  OH1   0  -0.728   1.6496  -1.4927   5.5269
 PPD  O3P   O  OH1   0  -0.738  -0.2136   0.1932   4.9337
 PPD  N     N  NH1   0  -0.672  -0.7743   0.3119  -1.8691
 PPD  CA    C  CH1   0  -0.156  -1.9465  -0.2625  -2.5037
 PPD  CB    C  CH2   0  -0.611  -2.6666   0.7802  -3.3581
 PPD  CG    C  C     0   0.562  -3.3864   1.8219  -2.5405
 PPD  OD1   O  O     0  -0.438  -3.3933   1.8717  -1.3358
 PPD  OD2   O  OH1   0  -0.587  -4.0239   2.6845  -3.3160
 PPD  C     C  C     0   0.534  -1.5921  -1.4266  -3.4175
 PPD  O     O  O     0  -0.431  -2.3692  -2.3121  -3.6686
 PPD  OXT   O  OH1   0  -0.576  -0.3815  -1.3338  -3.9373
 PPD  H2A1  H  HCH3  0   0.244   4.4747   0.9461  -2.5784
 PPD  H2A2  H  HCH3  0   0.245   3.8626   2.5298  -2.1429
 PPD  H2A3  H  HCH3  0   0.245   5.1851   1.8148  -1.2147
 PPD  HO3   H  HOH1  0   0.479   0.7476   0.5981  -2.6359
 PPD  H4A1  H  HCH2  0   0.281  -0.0940  -1.5441  -1.1882
 PPD  H4A2  H  HCH2  0   0.263  -0.9301  -0.6054   0.0272
 PPD  H6    H  HCR6  0   0.254   3.1614   0.1388   2.3550
 PPD  H5A1  H  HCH2  0   0.256  -0.2863  -0.1963   2.1057
 PPD  H5A2  H  HCH2  0   0.265   0.2609  -1.7994   1.6199
 PPD  HOP2  H  HOH1  0   0.506   1.3968  -1.8340   6.3954
 PPD  HOP3  H  HOH1  0   0.497   0.4150   0.9175   5.0554
 PPD  HN    H  HNH1  0   0.389  -1.0267   1.2057  -1.4621
 PPD  HA    H  HCH1  0   0.282  -2.6531  -0.6640  -1.7665
 PPD  HB1   H  HCH2  0   0.309  -1.9586   1.2785  -4.0270
 PPD  HB2   H  HCH2  0   0.316  -3.4049   0.2943  -4.0011
 PPD  HOD   H  HOH1  0   0.486  -4.4828   3.3469  -2.7773
 PPD  HXT   H  HOH1  0   0.489  -0.2132  -2.0830  -4.5296

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
 PPD  N1   C2    aromatic  1.321  0.020  1.321
 PPD  N1   C6    aromatic  1.330  0.020  1.330
 PPD  C2   C2A   single    1.498  0.020  1.498
 PPD  C2   C3    aromatic  1.405  0.020  1.405
 PPD  C2A  H2A1  single    0.970  0.020  1.090
 PPD  C2A  H2A2  single    0.970  0.020  1.090
 PPD  C2A  H2A3  single    0.970  0.020  1.090
 PPD  C3   O3    single    1.339  0.020  1.339
 PPD  C3   C4    aromatic  1.396  0.020  1.396
 PPD  O3   HO3   single    0.850  0.020  0.980
 PPD  C4   C4A   single    1.509  0.020  1.509
 PPD  C4   C5    aromatic  1.399  0.020  1.399
 PPD  C4A  N     single    1.462  0.020  1.462
 PPD  C4A  H4A1  single    0.970  0.020  1.090
 PPD  C4A  H4A2  single    0.970  0.020  1.090
 PPD  C5   C6    aromatic  1.385  0.020  1.385
 PPD  C5   C5A   single    1.504  0.020  1.504
 PPD  C6   H6    single    0.930  0.020  1.080
 PPD  C5A  O4P   single    1.423  0.020  1.423
 PPD  C5A  H5A1  single    0.970  0.020  1.090
 PPD  C5A  H5A2  single    0.970  0.020  1.090
 PPD  O4P  P     single    1.598  0.020  1.598
 PPD  P    O1P   double    1.474  0.020  1.474
 PPD  P    O2P   single    1.592  0.020  1.592
 PPD  P    O3P   single    1.597  0.020  1.597
 PPD  O2P  HOP2  single    0.850  0.020  0.980
 PPD  O3P  HOP3  single    0.850  0.020  0.980
 PPD  N    CA    single    1.451  0.020  1.451
 PPD  N    HN    single    0.890  0.020  1.040
 PPD  CA   CB    single    1.528  0.020  1.528
 PPD  CA   C     single    1.522  0.020  1.522
 PPD  CA   HA    single    0.970  0.020  1.090
 PPD  CB   CG    single    1.507  0.020  1.507
 PPD  CB   HB1   single    0.970  0.020  1.090
 PPD  CB   HB2   single    0.970  0.020  1.090
 PPD  CG   OD1   double    1.206  0.020  1.206
 PPD  CG   OD2   single    1.324  0.020  1.324
 PPD  OD2  HOD   single    0.850  0.020  0.980
 PPD  C    O     double    1.205  0.020  1.205
 PPD  C    OXT   single    1.321  0.020  1.321
 PPD  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
 PPD  C6    N1   C2    119.74  3.000
 PPD  C3    C2   C2A   120.17  3.000
 PPD  C3    C2   N1    121.34  3.000
 PPD  C2A   C2   N1    118.50  3.000
 PPD  H2A3  C2A  H2A2  108.30  3.000
 PPD  H2A3  C2A  H2A1  108.25  3.000
 PPD  H2A2  C2A  H2A1  106.81  3.000
 PPD  H2A3  C2A  C2    109.91  3.000
 PPD  H2A2  C2A  C2    111.53  3.000
 PPD  H2A1  C2A  C2    111.89  3.000
 PPD  C4    C3   O3    122.82  3.000
 PPD  C4    C3   C2    119.40  3.000
 PPD  O3    C3   C2    117.78  3.000
 PPD  HO3   O3   C3    107.11  3.000
 PPD  C5    C4   C4A   121.21  3.000
 PPD  C5    C4   C3    118.03  3.000
 PPD  C4A   C4   C3    120.71  3.000
 PPD  H4A2  C4A  H4A1  106.02  3.000
 PPD  H4A2  C4A  N     110.62  3.000
 PPD  H4A1  C4A  N     108.89  3.000
 PPD  H4A2  C4A  C4    111.26  3.000
 PPD  H4A1  C4A  C4    108.10  3.000
 PPD  N     C4A  C4    111.73  3.000
 PPD  C5A   C5   C6    122.09  3.000
 PPD  C5A   C5   C4    119.57  3.000
 PPD  C6    C5   C4    118.34  3.000
 PPD  H6    C6   C5    120.90  3.000
 PPD  H6    C6   N1    115.94  3.000
 PPD  C5    C6   N1    123.16  3.000
 PPD  H5A2  C5A  H5A1  107.23  3.000
 PPD  H5A2  C5A  O4P   109.06  3.000
 PPD  H5A1  C5A  O4P   110.85  3.000
 PPD  H5A2  C5A  C5    110.56  3.000
 PPD  H5A1  C5A  C5    109.41  3.000
 PPD  O4P   C5A  C5    109.70  3.000
 PPD  P     O4P  C5A   119.39  3.000
 PPD  O3P   P    O2P   108.12  3.000
 PPD  O3P   P    O1P   109.66  3.000
 PPD  O2P   P    O1P   118.08  3.000
 PPD  O3P   P    O4P   106.61  3.000
 PPD  O2P   P    O4P    96.68  3.000
 PPD  O1P   P    O4P   116.52  3.000
 PPD  HOP2  O2P  P     113.90  3.000
 PPD  HOP3  O3P  P     115.98  3.000
 PPD  HN    N    CA    108.86  3.000
 PPD  HN    N    C4A   107.90  3.000
 PPD  CA    N    C4A   113.26  3.000
 PPD  HA    CA   C     105.87  3.000
 PPD  HA    CA   CB    108.78  3.000
 PPD  C     CA   CB    107.21  3.000
 PPD  HA    CA   N     111.79  3.000
 PPD  C     CA   N     112.16  3.000
 PPD  CB    CA   N     110.79  3.000
 PPD  HB2   CB   HB1   106.25  3.000
 PPD  HB2   CB   CG    107.69  3.000
 PPD  HB1   CB   CG    109.02  3.000
 PPD  HB2   CB   CA    110.11  3.000
 PPD  HB1   CB   CA    110.34  3.000
 PPD  CG    CB   CA    113.16  3.000
 PPD  OD2   CG   OD1   123.76  3.000
 PPD  OD2   CG   CB    111.26  3.000
 PPD  OD1   CG   CB    124.98  3.000
 PPD  HOD   OD2  CG    110.35  3.000
 PPD  OXT   C    O     124.13  3.000
 PPD  OXT   C    CA    113.33  3.000
 PPD  O     C    CA    122.50  3.000
 PPD  HXT   OXT  C     110.19  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
 PPD  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PPD  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PPD  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PPD  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PPD  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PPD  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PPD  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PPD  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PPD  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PPD  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PPD  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PPD  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PPD  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 PPD  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 PPD  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PPD  CONST_16  HXT   OXT  C    CA   180.00   0.0  0
 PPD  CONST_17  HOD   OD2  CG   CB   180.00   0.0  0
 PPD  Var_01    N     C4A  C4   C3   -34.63  30.0  2
 PPD  Var_02    O4P   C5A  C5   C4   174.50  30.0  2
 PPD  Var_03    H2A1  C2A  C2   N1   121.89  30.0  2
 PPD  Var_04    CA    N    C4A  C4   169.88  30.0  3
 PPD  Var_05    O1P   P    O4P  C5A   48.78  30.0  3
 PPD  Var_06    OD1   CG   CB   CA     1.32  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
 PPD  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
 PPD  plan-1  N1   0.020
 PPD  plan-1  C2   0.020
 PPD  plan-1  C2A  0.020
 PPD  plan-1  C3   0.020
 PPD  plan-1  O3   0.020
 PPD  plan-1  C4   0.020
 PPD  plan-1  C4A  0.020
 PPD  plan-1  C5   0.020
 PPD  plan-1  C6   0.020
 PPD  plan-1  C5A  0.020
 PPD  plan-1  H6   0.020
 PPD  plan-2  CB   0.020
 PPD  plan-2  CG   0.020
 PPD  plan-2  OD1  0.020
 PPD  plan-2  OD2  0.020
 PPD  plan-2  HOD  0.020
 PPD  plan-3  CA   0.020
 PPD  plan-3  C    0.020
 PPD  plan-3  O    0.020
 PPD  plan-3  OXT  0.020
 PPD  plan-3  HXT  0.020

