# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:53:31 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N~6~-[(R)-[(1-carboxyethenyl)amino]{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([C@H](NCCCC[C@H](N)C(O)=O)NC(=C)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
 EXA  EXA  N~6~-[(R)-[(1-carboxyethenyl)amino]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl]-L-lysine  peptide  58  31  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_EXA
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
 EXA  N    N  NH2   0  -0.785  -6.5540   2.0376  -1.2348
 EXA  CA   C  CH1   0  -0.217  -6.7321   0.8327  -0.4530
 EXA  CB   C  CH2   0  -0.436  -5.5605   0.4659   0.4795
 EXA  CG   C  CH2   0  -0.426  -4.2539   0.2644  -0.2761
 EXA  CD   C  CH2   0  -0.442  -3.0994  -0.1126   0.6437
 EXA  CE   C  CH2   0  -0.263  -1.8075  -0.3319  -0.1259
 EXA  NZ   N  NH1   0  -0.587  -0.7034  -0.6249   0.7723
 EXA  C4'  C  CH1   0  -0.036   0.5520  -0.8396   0.0955
 EXA  C4   C  CR6   0   0.147   1.6861  -0.9077   1.1055
 EXA  C3   C  CR6   0   0.262   1.7636  -1.9520   2.0213
 EXA  O3   O  OH1   0  -0.635   0.8053  -2.9007   1.9739
 EXA  C2   C  CR6   0   0.141   2.8112  -2.0006   2.9481
 EXA  C2'  C  CH3   0  -0.787   2.8960  -3.1172   3.9452
 EXA  C5   C  CR6   0  -0.089   2.6875   0.0654   1.1471
 EXA  C6   C  CR16  0  -0.130   3.6894  -0.0629   2.0980
 EXA  N1   N  N     0  -0.407   3.7443  -1.0631   2.9683
 EXA  C5'  C  CH2   0  -0.214   2.6665   1.2113   0.1716
 EXA  OP4  O  O2    0  -0.593   3.7763   2.0653   0.4142
 EXA  P    P  P     0   1.465   4.1440   3.2035  -0.6492
 EXA  OP1  O  O     0  -0.706   4.2396   2.7714  -2.0550
 EXA  OP2  O  OH1   0  -0.742   3.0348   4.3434  -0.5113
 EXA  OP3  O  OH1   0  -0.728   5.4654   3.7089   0.0792
 EXA  C    C  C     0   0.546  -7.9987   0.9604   0.3681
 EXA  O1   O  O     0  -0.440  -8.5505   2.0004   0.6243
 EXA  N3   N  NH1   0  -0.687   0.6151  -1.9695  -0.8091
 EXA  C7   C  C     0   0.258   0.7053  -1.8602  -2.1707
 EXA  C8   C  C     0   0.512   1.1711  -3.1347  -2.8074
 EXA  C9   C  C2    0  -0.631   0.4173  -0.7844  -2.9211
 EXA  O10  O  O     0  -0.443   1.4470  -4.1177  -2.1615
 EXA  O11  O  OH1   0  -0.583   1.2427  -3.0813  -4.1240
 EXA  OXT  O  OH1   0  -0.595  -8.4245  -0.2182   0.8102
 EXA  H1   H  HNH2  0   0.344  -6.2529   2.8018  -0.6415
 EXA  H2   H  HNH2  0   0.359  -5.8141   1.8932  -1.9088
 EXA  H4   H  HCH1  0   0.268  -6.8757   0.0024  -1.1527
 EXA  H5   H  HCH2  0   0.229  -5.4352   1.2578   1.2263
 EXA  H6   H  HCH2  0   0.234  -5.8003  -0.4481   1.0286
 EXA  H7   H  HCH2  0   0.222  -4.3906  -0.5137  -1.0349
 EXA  H8   H  HCH2  0   0.215  -3.9894   1.1797  -0.8136
 EXA  H9   H  HCH2  0   0.222  -2.9477   0.6739   1.3891
 EXA  H10  H  HCH2  0   0.220  -3.3522  -1.0238   1.1967
 EXA  H11  H  HCH2  0   0.203  -1.9619  -1.1203  -0.8775
 EXA  H12  H  HCH2  0   0.218  -1.5593   0.5795  -0.6802
 EXA  H13  H  HNH1  0   0.352  -0.9348  -1.4313   1.3396
 EXA  H15  H  HCH1  0   0.243   0.7037   0.0451  -0.5245
 EXA  H16  H  HOH1  0   0.492   0.9592  -3.5961   2.6237
 EXA  H17  H  HCH3  0   0.258   2.9901  -4.0942   3.4641
 EXA  H18  H  HCH3  0   0.273   3.7677  -2.9810   4.5806
 EXA  H19  H  HCH3  0   0.261   2.0153  -3.1529   4.5910
 EXA  H20  H  HCR6  0   0.262   4.4852   0.6664   2.1680
 EXA  H21  H  HCH2  0   0.253   2.7091   0.8291  -0.8532
 EXA  H22  H  HCH2  0   0.262   1.7366   1.7801   0.2726
 EXA  H23  H  HOH1  0   0.497   2.9417   4.7391   0.3658
 EXA  H24  H  HOH1  0   0.506   5.9701   4.3615  -0.4248
 EXA  H25  H  H     0   0.263   0.5494  -0.7989  -3.9903
 EXA  H26  H  H     0   0.254   0.0356   0.1343  -2.4992
 EXA  H28  H  HOH1  0   0.491   1.5517  -3.9307  -4.4729
 EXA  H29  H  HOH1  0   0.481  -9.2089  -0.1014   1.3669
 EXA  H3   H  HNH1  0   0.390   0.8898  -2.8595  -0.4256

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
 EXA  O10  C8   double    1.208  0.020  1.208
 EXA  O11  C8   single    1.320  0.020  1.320
 EXA  C8   C7   single    1.499  0.020  1.499
 EXA  C7   C9   double    1.343  0.020  1.343
 EXA  C7   N3   single    1.369  0.020  1.369
 EXA  OP1  P    double    1.474  0.020  1.474
 EXA  N3   C4'  single    1.449  0.020  1.449
 EXA  C4'  NZ   single    1.442  0.020  1.442
 EXA  C4'  C4   single    1.520  0.020  1.520
 EXA  P    OP2  single    1.596  0.020  1.596
 EXA  P    OP3  single    1.591  0.020  1.591
 EXA  P    OP4  single    1.600  0.020  1.600
 EXA  CE   NZ   single    1.453  0.020  1.453
 EXA  CE   CD   single    1.520  0.020  1.520
 EXA  C5'  OP4  single    1.421  0.020  1.421
 EXA  C5'  C5   single    1.505  0.020  1.505
 EXA  C4   C5   aromatic  1.397  0.020  1.397
 EXA  C4   C3   aromatic  1.391  0.020  1.391
 EXA  CG   CD   single    1.523  0.020  1.523
 EXA  CG   CB   single    1.523  0.020  1.523
 EXA  C5   C6   aromatic  1.387  0.020  1.387
 EXA  O3   C3   single    1.349  0.020  1.349
 EXA  C3   C2   aromatic  1.400  0.020  1.400
 EXA  O1   C    double    1.205  0.020  1.205
 EXA  CA   CB   single    1.530  0.020  1.530
 EXA  CA   N    single    1.458  0.019  1.458
 EXA  CA   C    single    1.525  0.021  1.525
 EXA  C6   N1   aromatic  1.327  0.020  1.327
 EXA  C2   N1   aromatic  1.323  0.020  1.323
 EXA  C2   C2'  single    1.499  0.020  1.499
 EXA  C    OXT  single    1.329  0.020  1.329
 EXA  N    H1   single    0.890  0.020  1.040
 EXA  N    H2   single    0.890  0.020  1.040
 EXA  CA   H4   single    0.970  0.020  1.090
 EXA  CB   H5   single    0.970  0.020  1.090
 EXA  CB   H6   single    0.970  0.020  1.090
 EXA  CG   H7   single    0.970  0.020  1.090
 EXA  CG   H8   single    0.970  0.020  1.090
 EXA  CD   H9   single    0.970  0.020  1.090
 EXA  CD   H10  single    0.970  0.020  1.090
 EXA  CE   H11  single    0.970  0.020  1.090
 EXA  CE   H12  single    0.970  0.020  1.090
 EXA  NZ   H13  single    0.890  0.020  1.040
 EXA  C4'  H15  single    0.970  0.020  1.090
 EXA  O3   H16  single    0.850  0.020  0.980
 EXA  C2'  H17  single    0.970  0.020  1.090
 EXA  C2'  H18  single    0.970  0.020  1.090
 EXA  C2'  H19  single    0.970  0.020  1.090
 EXA  C6   H20  single    0.930  0.020  1.080
 EXA  C5'  H21  single    0.970  0.020  1.090
 EXA  C5'  H22  single    0.970  0.020  1.090
 EXA  OP2  H23  single    0.850  0.020  0.980
 EXA  OP3  H24  single    0.850  0.020  0.980
 EXA  C9   H25  single    0.930  0.020  1.080
 EXA  C9   H26  single    0.930  0.020  1.080
 EXA  O11  H28  single    0.850  0.020  0.980
 EXA  OXT  H29  single    0.850  0.020  0.980
 EXA  N3   H3   single    0.860  0.020  1.020

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
 EXA  H2   N    H1   106.29  3.000
 EXA  H2   N    CA   109.34  3.000
 EXA  H1   N    CA   110.37  3.000
 EXA  H4   CA   C    107.49  3.000
 EXA  H4   CA   CB   107.80  3.000
 EXA  C    CA   CB   110.10  1.900
 EXA  H4   CA   N    107.59  3.000
 EXA  C    CA   N    111.00  2.800
 EXA  CB   CA   N    110.50  1.700
 EXA  H6   CB   H5   106.68  3.000
 EXA  H6   CB   CG   109.08  3.000
 EXA  H5   CB   CG   109.61  3.000
 EXA  H6   CB   CA   109.64  3.000
 EXA  H5   CB   CA   109.10  3.000
 EXA  CG   CB   CA   112.55  3.000
 EXA  H8   CG   H7   106.51  3.000
 EXA  H8   CG   CD   108.70  3.000
 EXA  H7   CG   CD   109.70  3.000
 EXA  H8   CG   CB   109.91  3.000
 EXA  H7   CG   CB   109.31  3.000
 EXA  CD   CG   CB   112.55  3.000
 EXA  H10  CD   H9   106.62  3.000
 EXA  H10  CD   CE   109.38  3.000
 EXA  H9   CD   CE   109.32  3.000
 EXA  H10  CD   CG   109.61  3.000
 EXA  H9   CD   CG   109.79  3.000
 EXA  CE   CD   CG   111.97  3.000
 EXA  H12  CE   H11  106.40  3.000
 EXA  H12  CE   NZ   107.96  3.000
 EXA  H11  CE   NZ   112.61  3.000
 EXA  H12  CE   CD   109.20  3.000
 EXA  H11  CE   CD   109.28  3.000
 EXA  NZ   CE   CD   111.22  3.000
 EXA  H13  NZ   C4'  110.08  3.000
 EXA  H13  NZ   CE   109.46  3.000
 EXA  C4'  NZ   CE   113.66  3.000
 EXA  H15  C4'  N3   105.76  3.000
 EXA  H15  C4'  C4   108.07  3.000
 EXA  N3   C4'  C4   110.32  3.000
 EXA  H15  C4'  NZ   105.49  3.000
 EXA  C4   C4'  NZ   110.14  3.000
 EXA  N3   C4'  NZ   116.55  3.000
 EXA  C5   C4   C3   117.61  3.000
 EXA  C3   C4   C4'  120.84  3.000
 EXA  C5   C4   C4'  121.56  3.000
 EXA  C2   C3   O3   122.03  3.000
 EXA  C2   C3   C4   120.25  3.000
 EXA  O3   C3   C4   117.72  3.000
 EXA  H16  O3   C3   111.72  3.000
 EXA  N1   C2   C2'  118.54  3.000
 EXA  C2'  C2   C3   120.57  3.000
 EXA  N1   C2   C3   120.89  3.000
 EXA  H19  C2'  H18  107.76  3.000
 EXA  H19  C2'  H17  107.47  3.000
 EXA  H18  C2'  H17  107.47  3.000
 EXA  H19  C2'  C2   111.83  3.000
 EXA  H18  C2'  C2   109.92  3.000
 EXA  H17  C2'  C2   112.20  3.000
 EXA  C5'  C5   C6   121.65  3.000
 EXA  C6   C5   C4   118.27  3.000
 EXA  C5'  C5   C4   120.07  3.000
 EXA  H20  C6   N1   115.81  3.000
 EXA  H20  C6   C5   120.88  3.000
 EXA  N1   C6   C5   123.31  3.000
 EXA  C6   N1   C2   119.67  3.000
 EXA  H22  C5'  H21  107.50  3.000
 EXA  H22  C5'  OP4  109.59  3.000
 EXA  H21  C5'  OP4  109.83  3.000
 EXA  H22  C5'  C5   110.35  3.000
 EXA  H21  C5'  C5   109.91  3.000
 EXA  OP4  C5'  C5   109.64  3.000
 EXA  P    OP4  C5'  119.56  3.000
 EXA  OP3  P    OP2  108.10  3.000
 EXA  OP3  P    OP1  118.42  3.000
 EXA  OP2  P    OP1  109.68  3.000
 EXA  OP3  P    OP4   96.46  3.000
 EXA  OP2  P    OP4  106.90  3.000
 EXA  OP1  P    OP4  116.11  3.000
 EXA  H23  OP2  P    115.94  3.000
 EXA  H24  OP3  P    114.15  3.000
 EXA  OXT  C    O1   123.24  3.000
 EXA  OXT  C    CA   111.93  3.000
 EXA  O1   C    CA   124.81  3.000
 EXA  H3   N3   C7   115.55  3.000
 EXA  H3   N3   C4'  117.60  3.000
 EXA  C7   N3   C4'  124.17  3.000
 EXA  C9   C7   C8   120.69  3.000
 EXA  C9   C7   N3   127.28  3.000
 EXA  C8   C7   N3   112.03  3.000
 EXA  O11  C8   O10  123.63  3.000
 EXA  O11  C8   C7   113.97  3.000
 EXA  O10  C8   C7   122.39  3.000
 EXA  H26  C9   H25  116.25  3.000
 EXA  H26  C9   C7   122.58  3.000
 EXA  H25  C9   C7   121.16  3.000
 EXA  H28  O11  C8   109.95  3.000
 EXA  H29  OXT  C    110.09  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
 EXA  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 EXA  CONST_02  N1   C2   C3   C4      0.00   0.0  0
 EXA  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 EXA  CONST_04  C6   N1   C2   C3      0.00   0.0  0
 EXA  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 EXA  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 EXA  CONST_07  C6   C5   C4   C4'   180.00   0.0  0
 EXA  CONST_08  C2   C3   C4   C4'   180.00   0.0  0
 EXA  CONST_09  C2'  C2   C3   C4    180.00   0.0  0
 EXA  CONST_10  C5'  C5   C4   C3    180.00   0.0  0
 EXA  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 EXA  CONST_12  N1   C2   C3   O3    180.00   0.0  0
 EXA  CONST_13  C6   N1   C2   C2'   180.00   0.0  0
 EXA  CONST_14  C5'  C5   C6   N1    180.00   0.0  0
 EXA  CONST_15  H20  C6   C5   C4    180.00   0.0  0
 EXA  CONST_16  H29  OXT  C    CA    180.00   0.0  0
 EXA  CONST_17  H28  O11  C8   C7    180.00   0.0  0
 EXA  Var_01    OP4  C5'  C5   C4    179.76  30.0  1
 EXA  Var_02    H17  C2'  C2   C3     60.87  30.0  2
 EXA  Var_03    CD   CG   CB   CA   -179.39  30.0  1
 EXA  Var_04    CE   CD   CG   CB    179.10  30.0  3
 EXA  Var_05    NZ   CE   CD   CG    177.15  30.0  1
 EXA  Var_06    C4'  NZ   CE   CD   -179.86  30.0  3
 EXA  Var_07    C8   C7   N3   C4'   162.44  30.0  2
 EXA  Var_08    OP1  P    OP4  C5'   -49.67  30.0  2
 EXA  Var_09    O10  C8   C7   N3     -1.13  30.0  2
 EXA  Var_10    H25  C9   C7   N3    178.36   0.0  2

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
 EXA  chir_01  CA   CB  N   C   positiv
 EXA  chir_02  C4'  N3  NZ  C4  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
 EXA  plan-1  C4'  0.020
 EXA  plan-1  C4   0.020
 EXA  plan-1  C3   0.020
 EXA  plan-1  O3   0.020
 EXA  plan-1  C2   0.020
 EXA  plan-1  C2'  0.020
 EXA  plan-1  C5   0.020
 EXA  plan-1  C6   0.020
 EXA  plan-1  N1   0.020
 EXA  plan-1  C5'  0.020
 EXA  plan-1  H20  0.020
 EXA  plan-2  CA   0.020
 EXA  plan-2  C    0.020
 EXA  plan-2  O1   0.020
 EXA  plan-2  OXT  0.020
 EXA  plan-2  H29  0.020
 EXA  plan-3  C7   0.020
 EXA  plan-3  C8   0.020
 EXA  plan-3  O10  0.020
 EXA  plan-3  O11  0.020
 EXA  plan-3  H28  0.020
 EXA  plan-4  N3   0.020
 EXA  plan-4  C7   0.020
 EXA  plan-4  C8   0.020
 EXA  plan-4  C9   0.020
 EXA  plan-4  H25  0.020
 EXA  plan-4  H26  0.020

