# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:25:37 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCCCN)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
 PE1  PE1  N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine  L-peptide  46  25  .  2012-08-28  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_PE1
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
 PE1  N1    N  N      0  -0.408   4.8978  62.6597  -10.1649
 PE1  C2    C  CR6    0   0.128   4.9441  61.3488  -10.0039
 PE1  C2A   C  CH3    0  -0.719   6.1908  60.7456   -9.4298
 PE1  C3    C  CR6    0   0.250   3.8516  60.5382  -10.3490
 PE1  O3    O  OH1    0  -0.630   4.0025  59.2138  -10.1292
 PE1  C4    C  CR6    0   0.076   2.6983  61.1131  -10.8724
 PE1  C4A   C  CH2    0  -0.400   1.4710  60.2888  -11.1709
 PE1  C5    C  CR6    0  -0.068   2.6725  62.5048  -11.0319
 PE1  C6    C  CR16   0  -0.156   3.7991  63.2211  -10.6660
 PE1  C5A   C  CH2    0  -0.171   1.4525  63.1819  -11.6016
 PE1  O4P   O  O2     0  -0.658   1.5963  64.5602  -11.6289
 PE1  P     P  P      0   1.224   0.1521  65.4890  -11.8066
 PE1  O1P   O  O      0  -0.896  -0.6711  65.1499  -10.5675
 PE1  O2P   O  OP    -1  -0.899  -0.4512  64.9980  -13.1194
 PE1  O3P   O  OP    -1  -0.885   0.7301  66.8963  -11.8391
 PE1  N     N  NH1    0  -0.585   0.5925  60.3052  -10.0212
 PE1  CA    C  CH1    0  -0.196  -0.7511  59.7980  -10.2295
 PE1  C     C  C      0   0.398  -1.5067  59.7031   -8.8802
 PE1  OXT   O  OC     0  -0.600  -0.8274  59.7281   -7.8344
 PE1  CB    C  CH2    0  -0.454  -0.8381  58.4500  -10.9653
 PE1  CG    C  CH2    0  -0.445  -0.1314  57.2958  -10.2632
 PE1  CD    C  CH2    0  -0.425  -0.2166  55.9754  -11.0225
 PE1  CE    C  CH2    0  -0.273   0.5100  55.9866  -12.3605
 PE1  O     O  O     -1  -0.610  -2.7443  59.5766   -8.9650
 PE1  NZ    N  NH2    0  -0.798   0.4716  54.6698  -12.9815
 PE1  H6    H  HCR6   0   0.241   3.8173  64.2982  -10.7713
 PE1  H2A1  H  HCH3   0   0.242   6.9185  61.5288   -9.2273
 PE1  H2A2  H  HCH3   0   0.241   5.9926  60.2164   -8.4958
 PE1  H2A3  H  HCH3   0   0.241   6.6460  60.0248  -10.1117
 PE1  H3    H  HOH1   0   0.476   3.2286  58.7176  -10.4181
 PE1  H4A1  H  HCH2   0   0.253   0.9371  60.7243  -12.0186
 PE1  H4A2  H  HCH2   0   0.208   1.7473  59.2806  -11.5211
 PE1  H     H  HNH1   0   0.336   1.0122  59.8407   -9.2265
 PE1  H5A1  H  HCH2   0   0.185   1.2750  62.7717  -12.6100
 PE1  H5A2  H  HCH2   0   0.189   0.5846  62.8703  -11.0022
 PE1  HA    H  HCH1   0   0.214  -1.2807  60.5301  -10.8534
 PE1  HB1C  H  HCH2   0   0.218  -1.8950  58.2022  -11.0981
 PE1  HB2C  H  HCH2   0   0.221  -0.4371  58.5711  -11.9763
 PE1  HG1C  H  HCH2   0   0.211   0.9235  57.5431  -10.0983
 PE1  HG2C  H  HCH2   0   0.225  -0.5616  57.1530   -9.2681
 PE1  HD1C  H  HCH2   0   0.215   0.2114  55.1816  -10.4008
 PE1  HD2C  H  HCH2   0   0.209  -1.2655  55.7073  -11.1845
 PE1  HE1C  H  HCH2   0   0.213   0.0246  56.6905  -13.0407
 PE1  HE2C  H  HCH2   0   0.183   1.5306  56.3694  -12.2027
 PE1  HZ1N  H  HNH2   0   0.342   0.9308  54.7071  -13.8826
 PE1  HZ2N  H  HNH2   0   0.334   1.0177  54.0232  -12.4249

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
 PE1  N1   C2    aromatic  1.322  0.020  1.322
 PE1  N1   C6    aromatic  1.332  0.020  1.332
 PE1  C2   C2A   single    1.499  0.020  1.499
 PE1  C2   C3    aromatic  1.403  0.020  1.403
 PE1  C3   O3    single    1.351  0.020  1.351
 PE1  C3   C4    aromatic  1.391  0.020  1.391
 PE1  C4   C4A   single    1.508  0.020  1.508
 PE1  C4   C5    aromatic  1.401  0.020  1.401
 PE1  C4A  N     single    1.447  0.020  1.447
 PE1  C5   C6    aromatic  1.384  0.020  1.384
 PE1  C5   C5A   single    1.507  0.020  1.507
 PE1  C5A  O4P   single    1.386  0.020  1.386
 PE1  O4P  P     single    1.726  0.020  1.726
 PE1  P    O1P   deloc     1.526  0.020  1.526
 PE1  P    O2P   deloc     1.526  0.020  1.526
 PE1  P    O3P   deloc     1.522  0.020  1.522
 PE1  N    CA    single    1.458  0.019  1.458
 PE1  CA   C     single    1.525  0.021  1.525
 PE1  CA   CB    single    1.530  0.020  1.530
 PE1  C    OXT   deloc     1.247  0.020  1.247
 PE1  C    O     deloc     1.231  0.020  1.231
 PE1  CB   CG    single    1.525  0.020  1.525
 PE1  CG   CD    single    1.526  0.020  1.526
 PE1  CD   CE    single    1.523  0.020  1.523
 PE1  CE   NZ    single    1.456  0.020  1.456
 PE1  C6   H6    single    0.930  0.020  1.080
 PE1  C2A  H2A1  single    0.970  0.020  1.090
 PE1  C2A  H2A2  single    0.970  0.020  1.090
 PE1  C2A  H2A3  single    0.970  0.020  1.090
 PE1  O3   H3    single    0.850  0.020  0.980
 PE1  C4A  H4A1  single    0.970  0.020  1.090
 PE1  C4A  H4A2  single    0.970  0.020  1.090
 PE1  N    H     single    0.860  0.020  0.860
 PE1  C5A  H5A1  single    0.970  0.020  1.090
 PE1  C5A  H5A2  single    0.970  0.020  1.090
 PE1  CA   HA    single    0.970  0.020  0.970
 PE1  CB   HB1C  single    0.970  0.020  1.090
 PE1  CB   HB2C  single    0.970  0.020  1.090
 PE1  CG   HG1C  single    0.970  0.020  1.090
 PE1  CG   HG2C  single    0.970  0.020  1.090
 PE1  CD   HD1C  single    0.970  0.020  1.090
 PE1  CD   HD2C  single    0.970  0.020  1.090
 PE1  CE   HE1C  single    0.970  0.020  1.090
 PE1  CE   HE2C  single    0.970  0.020  1.090
 PE1  NZ   HZ1N  single    0.890  0.020  1.040
 PE1  NZ   HZ2N  single    0.890  0.020  1.040

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
 PE1  C6    N1   C2    119.53  3.000
 PE1  C3    C2   C2A   120.61  3.000
 PE1  C3    C2   N1    121.04  3.000
 PE1  C2A   C2   N1    118.35  3.000
 PE1  H2A3  C2A  H2A2  106.86  3.000
 PE1  H2A3  C2A  H2A1  108.22  3.000
 PE1  H2A2  C2A  H2A1  108.12  3.000
 PE1  H2A3  C2A  C2    111.91  3.000
 PE1  H2A2  C2A  C2    111.82  3.000
 PE1  H2A1  C2A  C2    109.75  3.000
 PE1  C4    C3   O3    123.99  3.000
 PE1  C4    C3   C2    119.95  3.000
 PE1  O3    C3   C2    116.05  3.000
 PE1  H3    O3   C3    111.49  3.000
 PE1  C5    C4   C4A   120.36  3.000
 PE1  C5    C4   C3    117.95  3.000
 PE1  C4A   C4   C3    121.55  3.000
 PE1  H4A2  C4A  H4A1  103.92  3.000
 PE1  H4A2  C4A  N     114.52  3.000
 PE1  H4A1  C4A  N     108.38  3.000
 PE1  H4A2  C4A  C4    111.03  3.000
 PE1  H4A1  C4A  C4    109.47  3.000
 PE1  N     C4A  C4    109.30  3.000
 PE1  C5A   C5   C6    121.75  3.000
 PE1  C5A   C5   C4    120.28  3.000
 PE1  C6    C5   C4    117.97  3.000
 PE1  H6    C6   C5    120.20  3.000
 PE1  H6    C6   N1    116.24  3.000
 PE1  C5    C6   N1    123.56  3.000
 PE1  H5A2  C5A  H5A1  105.42  3.000
 PE1  H5A2  C5A  O4P   111.99  3.000
 PE1  H5A1  C5A  O4P   111.63  3.000
 PE1  H5A2  C5A  C5    107.78  3.000
 PE1  H5A1  C5A  C5    107.98  3.000
 PE1  O4P   C5A  C5    111.73  3.000
 PE1  P     O4P  C5A   116.76  3.000
 PE1  O3P   P    O2P   115.43  3.000
 PE1  O3P   P    O1P   115.33  3.000
 PE1  O2P   P    O1P   114.44  3.000
 PE1  O3P   P    O4P   100.49  3.000
 PE1  O2P   P    O4P   104.25  3.000
 PE1  O1P   P    O4P   104.37  3.000
 PE1  H     N    CA    114.00  3.000
 PE1  H     N    C4A   111.54  3.000
 PE1  CA    N    C4A   116.36  3.000
 PE1  HA    CA   CB    109.00  3.000
 PE1  HA    CA   C     109.00  3.000
 PE1  CB    CA   C     110.10  1.900
 PE1  HA    CA   N     110.00  3.000
 PE1  CB    CA   N     110.50  1.700
 PE1  C     CA   N     111.00  2.800
 PE1  O     C    OXT   126.84  3.000
 PE1  O     C    CA    120.80  1.700
 PE1  OXT   C    CA    117.61  3.000
 PE1  HB2C  CB   HB1C  105.49  3.000
 PE1  HB2C  CB   CG    109.84  3.000
 PE1  HB1C  CB   CG    109.41  3.000
 PE1  HB2C  CB   CA    108.92  3.000
 PE1  HB1C  CB   CA    108.14  3.000
 PE1  CG    CB   CA    114.64  3.000
 PE1  HG2C  CG   HG1C  105.74  3.000
 PE1  HG2C  CG   CD    108.53  3.000
 PE1  HG1C  CG   CD    108.90  3.000
 PE1  HG2C  CG   CB    109.61  3.000
 PE1  HG1C  CG   CB    110.16  3.000
 PE1  CD    CG   CB    113.59  3.000
 PE1  HD2C  CD   HD1C  106.31  3.000
 PE1  HD2C  CD   CE    109.20  3.000
 PE1  HD1C  CD   CE    108.52  3.000
 PE1  HD2C  CD   CG    109.83  3.000
 PE1  HD1C  CD   CG    108.84  3.000
 PE1  CE    CD   CG    113.85  3.000
 PE1  HE2C  CE   HE1C  106.07  3.000
 PE1  HE2C  CE   NZ    113.56  3.000
 PE1  HE1C  CE   NZ    107.78  3.000
 PE1  HE2C  CE   CD    108.59  3.000
 PE1  HE1C  CE   CD    109.87  3.000
 PE1  NZ    CE   CD    110.82  3.000
 PE1  HZ2N  NZ   HZ1N  105.56  3.000
 PE1  HZ2N  NZ   CE    109.19  3.000
 PE1  HZ1N  NZ   CE    109.53  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
 PE1  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PE1  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PE1  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PE1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PE1  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PE1  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PE1  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PE1  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PE1  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PE1  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PE1  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PE1  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PE1  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PE1  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PE1  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PE1  Var_01    N     C4A  C4   C3     92.58  30.0  2
 PE1  Var_02    O4P   C5A  C5   C4    177.47  30.0  2
 PE1  Var_03    H2A1  C2A  C2   N1     -0.49  30.0  2
 PE1  Var_04    CA    N    C4A  C4    167.64  30.0  3
 PE1  Var_05    O1P   P    O4P  C5A    62.10  30.0  3
 PE1  Var_06    CD    CG   CB   CA   -179.22  30.0  3
 PE1  Var_07    CE    CD   CG   CB     65.25  30.0  3
 PE1  Var_08    NZ    CE   CD   CG    175.77  30.0  3
 PE1  Var_09    HZ1N  NZ   CE   CD    178.02  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
 PE1  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
 PE1  plan-1  N1   0.020
 PE1  plan-1  C2   0.020
 PE1  plan-1  C2A  0.020
 PE1  plan-1  C3   0.020
 PE1  plan-1  O3   0.020
 PE1  plan-1  C4   0.020
 PE1  plan-1  C4A  0.020
 PE1  plan-1  C5   0.020
 PE1  plan-1  C6   0.020
 PE1  plan-1  C5A  0.020
 PE1  plan-1  H6   0.020
 PE1  plan-2  CA   0.020
 PE1  plan-2  C    0.020
 PE1  plan-2  OXT  0.020
 PE1  plan-2  O    0.020

