# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 00:13:20 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(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
 PP3  PP3  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-alanine  ligand  38  21  .  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_PP3
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
 PP3  N1    N  N     0  -0.409   3.4167   0.5041  -0.1233
 PP3  C2    C  CR6   0   0.129   3.1374   0.4647   1.1688
 PP3  C2A   C  CH3   0  -0.720   4.2348   0.7478   2.1476
 PP3  C3    C  CR6   0   0.266   1.8462   0.1569   1.6235
 PP3  O3    O  OH1   0  -0.649   1.6256   0.1274   2.9448
 PP3  C4    C  CR6   0   0.029   0.8388  -0.1196   0.6972
 PP3  C4A   C  CH2   0  -0.340  -0.5241  -0.5422   1.1853
 PP3  C5    C  CR6   0  -0.076   1.1571  -0.0549  -0.6622
 PP3  C6    C  CR16  0  -0.146   2.4603   0.2600  -1.0138
 PP3  C5A   C  CH2   0  -0.212   0.0977  -0.3353  -1.6918
 PP3  O4P   O  O2    0  -0.592   0.6293  -0.1098  -2.9925
 PP3  P     P  P     0   1.463  -0.2484  -0.4767  -4.2771
 PP3  O1P   O  O     0  -0.708  -1.6425   0.0021  -4.2732
 PP3  O2P   O  OH1   0  -0.729   0.7530   0.1243  -5.3588
 PP3  O3P   O  OH1   0  -0.739  -0.2271  -2.0677  -4.4147
 PP3  N     N  NH1   0  -0.672  -0.9198   0.2185   2.3685
 PP3  CA    C  CH1   0  -0.174  -2.0747  -0.3408   3.0571
 PP3  C     C  C     0   0.546  -2.7858   0.7665   3.8098
 PP3  O     O  O     0  -0.435  -2.4817   1.9315   3.7587
 PP3  CB    C  CH3   0  -0.664  -1.6555  -1.4710   3.9947
 PP3  OXT   O  OH1   0  -0.585  -3.8001   0.3015   4.5195
 PP3  H2A1  H  HCH3  0   0.244   4.3970  -0.0910   2.8271
 PP3  H2A2  H  HCH3  0   0.244   5.1650   0.9418   1.6176
 PP3  H2A3  H  HCH3  0   0.245   4.0064   1.6168   2.7676
 PP3  HO3   H  HOH1  0   0.474   0.6334   0.1731   3.0622
 PP3  H4A1  H  HCH2  0   0.278  -0.4724  -1.6022   1.4514
 PP3  H4A2  H  HCH2  0   0.264  -1.2792  -0.4648   0.3977
 PP3  H6    H  HCR6  0   0.254   2.7558   0.3210  -2.0530
 PP3  H5A1  H  HCH2  0   0.257  -0.2504  -1.3695  -1.5984
 PP3  H5A2  H  HCH2  0   0.261  -0.7657   0.3172  -1.5312
 PP3  HOP2  H  HOH1  0   0.506   0.4075   0.1199  -6.2617
 PP3  HOP3  H  HOH1  0   0.496   0.6465  -2.4726  -4.5004
 PP3  HN2   H  HNH1  0   0.386  -1.1108   1.1755   2.0925
 PP3  HA    H  HCH1  0   0.278  -2.8054  -0.7412   2.3381
 PP3  HB1   H  HCH3  0   0.241  -1.0277  -1.0972   4.8038
 PP3  HB2   H  HCH3  0   0.253  -2.5198  -1.9710   4.4261
 PP3  HB3   H  HCH3  0   0.249  -1.0885  -2.2226   3.4470
 PP3  HXT   H  HOH1  0   0.488  -4.2457   1.0277   4.9816

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
 PP3  N1   C2    aromatic  1.323  0.020  1.323
 PP3  N1   C6    aromatic  1.329  0.020  1.329
 PP3  C2   C2A   single    1.497  0.020  1.497
 PP3  C2   C3    aromatic  1.403  0.020  1.403
 PP3  C2A  H2A1  single    0.970  0.020  1.090
 PP3  C2A  H2A2  single    0.970  0.020  1.090
 PP3  C2A  H2A3  single    0.970  0.020  1.090
 PP3  C3   O3    single    1.340  0.020  1.340
 PP3  C3   C4    aromatic  1.396  0.020  1.396
 PP3  O3   HO3   single    0.850  0.020  0.980
 PP3  C4   C4A   single    1.508  0.020  1.508
 PP3  C4   C5    aromatic  1.398  0.020  1.398
 PP3  C4A  N     single    1.461  0.020  1.461
 PP3  C4A  H4A1  single    0.970  0.020  1.090
 PP3  C4A  H4A2  single    0.970  0.020  1.090
 PP3  C5   C6    aromatic  1.386  0.020  1.386
 PP3  C5   C5A   single    1.504  0.020  1.504
 PP3  C6   H6    single    0.930  0.020  1.080
 PP3  C5A  O4P   single    1.423  0.020  1.423
 PP3  C5A  H5A1  single    0.970  0.020  1.090
 PP3  C5A  H5A2  single    0.970  0.020  1.090
 PP3  O4P  P     single    1.598  0.020  1.598
 PP3  P    O1P   double    1.474  0.020  1.474
 PP3  P    O2P   single    1.592  0.020  1.592
 PP3  P    O3P   single    1.597  0.020  1.597
 PP3  O2P  HOP2  single    0.850  0.020  0.980
 PP3  O3P  HOP3  single    0.850  0.020  0.980
 PP3  N    CA    single    1.456  0.020  1.456
 PP3  N    HN2   single    0.890  0.020  1.040
 PP3  CA   C     single    1.516  0.020  1.516
 PP3  CA   CB    single    1.527  0.020  1.527
 PP3  CA   HA    single    0.970  0.020  1.090
 PP3  C    O     double    1.205  0.020  1.205
 PP3  C    OXT   single    1.322  0.020  1.322
 PP3  CB   HB1   single    0.970  0.020  1.090
 PP3  CB   HB2   single    0.970  0.020  1.090
 PP3  CB   HB3   single    0.970  0.020  1.090
 PP3  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
 PP3  C6    N1   C2    119.80  3.000
 PP3  C3    C2   C2A   120.27  3.000
 PP3  C3    C2   N1    121.17  3.000
 PP3  C2A   C2   N1    118.56  3.000
 PP3  H2A3  C2A  H2A2  108.27  3.000
 PP3  H2A3  C2A  H2A1  106.81  3.000
 PP3  H2A2  C2A  H2A1  108.26  3.000
 PP3  H2A3  C2A  C2    111.61  3.000
 PP3  H2A2  C2A  C2    109.99  3.000
 PP3  H2A1  C2A  C2    111.75  3.000
 PP3  C4    C3   O3    122.08  3.000
 PP3  C4    C3   C2    119.50  3.000
 PP3  O3    C3   C2    118.42  3.000
 PP3  HO3   O3   C3    106.15  3.000
 PP3  C5    C4   C4A   122.25  3.000
 PP3  C5    C4   C3    118.15  3.000
 PP3  C4A   C4   C3    119.53  3.000
 PP3  H4A2  C4A  H4A1  106.04  3.000
 PP3  H4A2  C4A  N     111.05  3.000
 PP3  H4A1  C4A  N     108.68  3.000
 PP3  H4A2  C4A  C4    111.78  3.000
 PP3  H4A1  C4A  C4    107.91  3.000
 PP3  N     C4A  C4    111.16  3.000
 PP3  C5A   C5   C6    122.08  3.000
 PP3  C5A   C5   C4    119.79  3.000
 PP3  C6    C5   C4    118.12  3.000
 PP3  H6    C6   C5    120.88  3.000
 PP3  H6    C6   N1    115.88  3.000
 PP3  C5    C6   N1    123.25  3.000
 PP3  H5A2  C5A  H5A1  107.45  3.000
 PP3  H5A2  C5A  O4P   109.53  3.000
 PP3  H5A1  C5A  O4P   110.27  3.000
 PP3  H5A2  C5A  C5    110.14  3.000
 PP3  H5A1  C5A  C5    109.98  3.000
 PP3  O4P   C5A  C5    109.46  3.000
 PP3  P     O4P  C5A   119.54  3.000
 PP3  O3P   P    O2P   108.01  3.000
 PP3  O3P   P    O1P   109.66  3.000
 PP3  O2P   P    O1P   118.30  3.000
 PP3  O3P   P    O4P   106.90  3.000
 PP3  O2P   P    O4P    96.54  3.000
 PP3  O1P   P    O4P   116.27  3.000
 PP3  HOP2  O2P  P     114.09  3.000
 PP3  HOP3  O3P  P     115.91  3.000
 PP3  HN2   N    CA    109.98  3.000
 PP3  HN2   N    C4A   108.78  3.000
 PP3  CA    N    C4A   113.43  3.000
 PP3  HA    CA   CB    108.30  3.000
 PP3  HA    CA   C     106.19  3.000
 PP3  CB    CA   C     111.38  3.000
 PP3  HA    CA   N     110.94  3.000
 PP3  CB    CA   N     110.91  3.000
 PP3  C     CA   N     109.04  3.000
 PP3  OXT   C    O     123.79  3.000
 PP3  OXT   C    CA    111.68  3.000
 PP3  O     C    CA    124.52  3.000
 PP3  HB3   CB   HB2   107.21  3.000
 PP3  HB3   CB   HB1   108.06  3.000
 PP3  HB2   CB   HB1   108.72  3.000
 PP3  HB3   CB   CA    110.17  3.000
 PP3  HB2   CB   CA    111.44  3.000
 PP3  HB1   CB   CA    111.10  3.000
 PP3  HXT   OXT  C     110.18  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
 PP3  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PP3  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PP3  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PP3  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PP3  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PP3  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PP3  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PP3  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PP3  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PP3  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PP3  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PP3  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PP3  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PP3  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PP3  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PP3  CONST_16  HXT   OXT  C    CA    180.00   0.0  0
 PP3  Var_01    N     C4A  C4   C3     39.88  30.0  2
 PP3  Var_02    O4P   C5A  C5   C4    175.60  30.0  2
 PP3  Var_03    H2A1  C2A  C2   N1   -121.20  30.0  2
 PP3  Var_04    CA    N    C4A  C4   -167.03  30.0  3
 PP3  Var_05    O1P   P    O4P  C5A    47.96  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
 PP3  chir_01  CA  N  C  CB  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
 PP3  plan-1  N1   0.020
 PP3  plan-1  C2   0.020
 PP3  plan-1  C2A  0.020
 PP3  plan-1  C3   0.020
 PP3  plan-1  O3   0.020
 PP3  plan-1  C4   0.020
 PP3  plan-1  C4A  0.020
 PP3  plan-1  C5   0.020
 PP3  plan-1  C6   0.020
 PP3  plan-1  C5A  0.020
 PP3  plan-1  H6   0.020
 PP3  plan-2  CA   0.020
 PP3  plan-2  C    0.020
 PP3  plan-2  O    0.020
 PP3  plan-2  OXT  0.020
 PP3  plan-2  HXT  0.020

