# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:18:40 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-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
 PDD  PDD  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-alanine  D-peptide  35  21  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PDD
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
 PDD  N     N  NH1    0  -0.589  24.0497  15.9025  69.2108
 PDD  N1    N  N      0  -0.410  23.9882  10.9242  69.4526
 PDD  C2    C  CR6    0   0.119  25.1196  11.5953  69.3077
 PDD  C2A   C  CH3    0  -0.717  26.4048  10.8824  69.6035
 PDD  C3    C  CR6    0   0.256  25.1365  12.9369  68.8795
 PDD  O3A   O  OH1    0  -0.676  26.3313  13.5231  68.7803
 PDD  C4    C  CR6    0   0.048  23.9273  13.5603  68.5563
 PDD  C4A   C  CH2    0  -0.404  23.9343  14.9845  68.0779
 PDD  C5    C  CR6    0  -0.025  22.7425  12.8378  68.7305
 PDD  C5A   C  CH2    0  -0.229  21.3974  13.4140  68.3807
 PDD  OP4   O  O2     0  -0.651  21.2574  13.4412  66.9897
 PDD  P     P  P      0   1.234  20.1588  14.5842  66.3278
 PDD  OP1   O  O      0  -0.897  18.7930  14.1730  66.8715
 PDD  OP2   O  OP    -1  -0.885  20.3687  14.3420  64.8402
 PDD  OP3   O  OP    -1  -0.889  20.6498  15.9409  66.8379
 PDD  C6    C  CR16   0  -0.166  22.8378  11.5317  69.1805
 PDD  CA    C  CH1    0  -0.238  24.6649  17.1776  68.8911
 PDD  CB    C  CH3    0  -0.663  23.8603  17.9236  67.8303
 PDD  C     C  C      0   0.451  26.1702  17.1200  68.5235
 PDD  O     O  O      0  -0.570  26.7033  18.1842  68.1852
 PDD  OXT   O  OC    -1  -0.612  26.7729  16.0159  68.6384
 PDD  H     H  HNH1   0   0.340  24.5803  15.4683  69.9542
 PDD  H2A1  H  HCH3   0   0.237  27.0591  10.8536  68.7300
 PDD  H2A2  H  HCH3   0   0.237  26.9679  11.3703  70.4014
 PDD  H2A3  H  HCH3   0   0.236  26.1999   9.8578  69.9077
 PDD  HO3   H  HOH1   0   0.485  26.3331  14.5332  68.7110
 PDD  H4A1  H  HCH2   0   0.207  24.7491  15.1054  67.3504
 PDD  H4A2  H  HCH2   0   0.268  23.0156  15.2029  67.5357
 PDD  H5A1  H  HCH2   0   0.179  21.3043  14.4154  68.8199
 PDD  H5A2  H  HCH2   0   0.185  20.6207  12.7963  68.8562
 PDD  H6    H  HCR6   0   0.234  21.9354  10.9437  69.3220
 PDD  HA    H  HCH1   0   0.236  24.6162  17.7774  69.8093
 PDD  HB1   H  HCH3   0   0.219  22.8050  17.9532  68.1041
 PDD  HB2   H  HCH3   0   0.230  24.2137  18.9472  67.7296
 PDD  HB3   H  HCH3   0   0.220  23.9346  17.4513  66.8493

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
 PDD  N    C4A   single    1.463  0.020  1.463
 PDD  N    CA    single    1.458  0.019  1.458
 PDD  N    H     single    0.860  0.020  0.860
 PDD  N1   C2    aromatic  1.323  0.020  1.323
 PDD  N1   C6    aromatic  1.329  0.020  1.329
 PDD  C2   C2A   single    1.499  0.020  1.499
 PDD  C2   C3    aromatic  1.408  0.020  1.408
 PDD  C2A  H2A1  single    0.970  0.020  1.090
 PDD  C2A  H2A2  single    0.970  0.020  1.090
 PDD  C2A  H2A3  single    0.970  0.020  1.090
 PDD  C3   O3A   single    1.335  0.020  1.335
 PDD  C3   C4    aromatic  1.398  0.020  1.398
 PDD  O3A  HO3   single    0.850  0.020  0.980
 PDD  C4   C4A   single    1.502  0.020  1.502
 PDD  C4   C5    aromatic  1.399  0.020  1.399
 PDD  C4A  H4A1  single    0.970  0.020  1.090
 PDD  C4A  H4A2  single    0.970  0.020  1.090
 PDD  C5   C5A   single    1.505  0.020  1.505
 PDD  C5   C6    aromatic  1.385  0.020  1.385
 PDD  C5A  OP4   single    1.398  0.020  1.398
 PDD  C5A  H5A1  single    0.970  0.020  1.090
 PDD  C5A  H5A2  single    0.970  0.020  1.090
 PDD  OP4  P     single    1.718  0.020  1.718
 PDD  P    OP1   deloc     1.526  0.020  1.526
 PDD  P    OP2   deloc     1.522  0.020  1.522
 PDD  P    OP3   deloc     1.530  0.020  1.530
 PDD  C6   H6    single    0.930  0.020  1.080
 PDD  CA   CB    single    1.521  0.033  1.521
 PDD  CA   C     single    1.525  0.021  1.525
 PDD  CA   HA    single    0.970  0.020  0.970
 PDD  CB   HB1   single    0.970  0.020  1.090
 PDD  CB   HB2   single    0.970  0.020  1.090
 PDD  CB   HB3   single    0.970  0.020  1.090
 PDD  C    O     deloc     1.231  0.020  1.231
 PDD  C    OXT   deloc     1.263  0.020  1.263

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
 PDD  H     N    CA    114.00  3.000
 PDD  H     N    C4A   109.95  3.000
 PDD  CA    N    C4A   114.47  3.000
 PDD  C6    N1   C2    119.06  3.000
 PDD  C3    C2   C2A   120.18  3.000
 PDD  C3    C2   N1    121.78  3.000
 PDD  C2A   C2   N1    118.04  3.000
 PDD  H2A3  C2A  H2A2  108.27  3.000
 PDD  H2A3  C2A  H2A1  108.15  3.000
 PDD  H2A2  C2A  H2A1  106.70  3.000
 PDD  H2A3  C2A  C2    109.97  3.000
 PDD  H2A2  C2A  C2    111.96  3.000
 PDD  H2A1  C2A  C2    111.63  3.000
 PDD  C4    C3   O3A   124.14  3.000
 PDD  C4    C3   C2    118.98  3.000
 PDD  O3A   C3   C2    116.86  3.000
 PDD  HO3   O3A  C3    116.42  3.000
 PDD  C5    C4   C4A   122.23  3.000
 PDD  C5    C4   C3    118.26  3.000
 PDD  C4A   C4   C3    119.48  3.000
 PDD  H4A2  C4A  H4A1  105.89  3.000
 PDD  H4A2  C4A  C4    110.17  3.000
 PDD  H4A1  C4A  C4    108.57  3.000
 PDD  H4A2  C4A  N     109.05  3.000
 PDD  H4A1  C4A  N     112.65  3.000
 PDD  C4    C4A  N     110.41  3.000
 PDD  C6    C5   C5A   119.89  3.000
 PDD  C6    C5   C4    118.00  3.000
 PDD  C5A   C5   C4    122.04  3.000
 PDD  H5A2  C5A  H5A1  106.22  3.000
 PDD  H5A2  C5A  OP4   111.72  3.000
 PDD  H5A1  C5A  OP4   111.83  3.000
 PDD  H5A2  C5A  C5    108.40  3.000
 PDD  H5A1  C5A  C5    109.41  3.000
 PDD  OP4   C5A  C5    109.17  3.000
 PDD  P     OP4  C5A   117.40  3.000
 PDD  OP3   P    OP2   115.00  3.000
 PDD  OP3   P    OP1   114.03  3.000
 PDD  OP2   P    OP1   115.38  3.000
 PDD  OP3   P    OP4   104.85  3.000
 PDD  OP2   P    OP4   100.51  3.000
 PDD  OP1   P    OP4   104.82  3.000
 PDD  H6    C6   C5    119.72  3.000
 PDD  H6    C6   N1    116.42  3.000
 PDD  C5    C6   N1    123.86  3.000
 PDD  HA    CA   C     110.00  3.000
 PDD  HA    CA   CB    109.00  3.000
 PDD  C     CA   CB    110.50  1.500
 PDD  HA    CA   N     110.00  3.000
 PDD  C     CA   N     111.00  2.800
 PDD  CB    CA   N     110.40  1.500
 PDD  HB3   CB   HB2   107.58  3.000
 PDD  HB3   CB   HB1   107.66  3.000
 PDD  HB2   CB   HB1   108.19  3.000
 PDD  HB3   CB   CA    112.17  3.000
 PDD  HB2   CB   CA    110.68  3.000
 PDD  HB1   CB   CA    110.42  3.000
 PDD  OXT   C    O     124.83  3.000
 PDD  OXT   C    CA    120.80  1.700
 PDD  O     C    CA    120.80  1.700

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
 PDD  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PDD  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PDD  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PDD  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PDD  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PDD  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PDD  CONST_07  O3A   C3   C2   N1   180.00   0.0  0
 PDD  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PDD  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PDD  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PDD  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PDD  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PDD  CONST_13  C5    C4   C3   O3A  180.00   0.0  0
 PDD  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 PDD  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PDD  Var_01    C3    C4   C4A  N    -80.19  30.0  1
 PDD  Var_02    OP4   C5A  C5   C4    73.80  30.0  2
 PDD  Var_03    H2A1  C2A  C2   N1   120.25  30.0  2
 PDD  Var_04    CA    N    C4A  C4   153.06  30.0  1
 PDD  Var_05    OP1   P    OP4  C5A  -63.15  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
 PDD  chir_01  CA  N  CB  C  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
 PDD  plan-1  N1   0.020
 PDD  plan-1  C2   0.020
 PDD  plan-1  C2A  0.020
 PDD  plan-1  C3   0.020
 PDD  plan-1  O3A  0.020
 PDD  plan-1  C4   0.020
 PDD  plan-1  C4A  0.020
 PDD  plan-1  C5   0.020
 PDD  plan-1  C5A  0.020
 PDD  plan-1  C6   0.020
 PDD  plan-1  H6   0.020
 PDD  plan-2  CA   0.020
 PDD  plan-2  C    0.020
 PDD  plan-2  O    0.020
 PDD  plan-2  OXT  0.020

