# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:14:31 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  54  31  .  2022-09-22  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_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  -0.801  -6.4862   2.0858  -1.2059
 EXA  CA   C  CH1    0  -0.204  -6.6292   0.8406  -0.4671
 EXA  CB   C  CH2    0  -0.424  -5.4322   0.4844   0.4313
 EXA  CG   C  CH2    0  -0.424  -4.1251   0.2780  -0.3243
 EXA  CD   C  CH2    0  -0.440  -2.9606  -0.0752   0.5928
 EXA  CE   C  CH2    0  -0.250  -1.6715  -0.3221  -0.1737
 EXA  NZ   N  NH1    0  -0.592  -0.5709  -0.6067   0.7314
 EXA  C4'  C  CH1    0  -0.052   0.6844  -0.8681   0.0590
 EXA  C4   C  CR6    0   0.150   1.8120  -0.9412   1.0754
 EXA  C3   C  CR6    0   0.255   1.8615  -1.9688   2.0128
 EXA  O3   O  OH1    0  -0.638   0.8789  -2.8982   1.9864
 EXA  C2   C  CR6    0   0.127   2.9004  -2.0219   2.9476
 EXA  C2'  C  CH3    0  -0.787   2.9532  -3.1168   3.9728
 EXA  C5   C  CR6    0  -0.088   2.8344   0.0114   1.0973
 EXA  C6   C  CR16   0  -0.146   3.8273  -0.1265   2.0582
 EXA  N1   N  N      0  -0.412   3.8574  -1.1063   2.9538
 EXA  C5'  C  CH2    0  -0.179   2.8681   1.1526   0.1073
 EXA  OP4  O  O2     0  -0.657   4.0063   1.9288   0.2691
 EXA  P    P  P      0   1.220   3.8885   3.5740  -0.2049
 EXA  OP1  O  O      0  -0.898   3.3909   3.5236  -1.6449
 EXA  OP2  O  OP    -1  -0.898   2.8972   4.1845   0.7783
 EXA  OP3  O  OP    -1  -0.892   5.3340   4.0157  -0.0283
 EXA  C    C  C      0   0.404  -7.9025   0.8683   0.4057
 EXA  O1   O  O     -1  -0.609  -8.3509   1.9857   0.7312
 EXA  N3   N  NH1    0  -0.665   0.7170  -2.0144  -0.8154
 EXA  C7   C  C      0   0.191   0.6250  -1.9774  -2.1803
 EXA  C8   C  C      0   0.386   0.3877  -3.3686  -2.7975
 EXA  C9   C  C2     0  -0.680   0.7339  -0.8939  -2.9683
 EXA  O10  O  O      0  -0.603   0.2216  -4.2982  -1.9809
 EXA  O11  O  OC    -1  -0.585   0.3730  -3.4517  -4.0359
 EXA  OXT  O  OC     0  -0.623  -8.3543  -0.2418   0.7537
 EXA  H1   H  HNH2   0   0.325  -6.5646   2.8555  -0.5529
 EXA  H2   H  HNH2   0   0.332  -5.5629   2.1466  -1.6167
 EXA  H4   H  HCH1   0   0.197  -6.7410   0.0275  -1.1956
 EXA  H5   H  HCH2   0   0.205  -5.3009   1.2750   1.1800
 EXA  H6   H  HCH2   0   0.210  -5.6679  -0.4307   0.9822
 EXA  H7   H  HCH2   0   0.211  -4.2603  -0.5144  -1.0691
 EXA  H8   H  HCH2   0   0.203  -3.8641   1.1826  -0.8843
 EXA  H9   H  HCH2   0   0.215  -2.8042   0.7295   1.3181
 EXA  H10  H  HCH2   0   0.212  -3.2126  -0.9705   1.1725
 EXA  H11  H  HCH2   0   0.197  -1.8359  -1.1239  -0.9085
 EXA  H12  H  HCH2   0   0.211  -1.4119   0.5718  -0.7508
 EXA  H13  H  HNH1   0   0.345  -0.8177  -1.3916   1.3224
 EXA  H15  H  HCH1   0   0.245   0.8611  -0.0003  -0.5742
 EXA  H16  H  HOH1   0   0.487   1.0101  -3.5684   2.6660
 EXA  H17  H  HCH3   0   0.254   3.0349  -4.1076   3.5178
 EXA  H18  H  HCH3   0   0.269   3.8208  -2.9808   4.6143
 EXA  H19  H  HCH3   0   0.255   2.0671  -3.1229   4.6129
 EXA  H20  H  HCR6   0   0.248   4.6347   0.5917   2.1086
 EXA  H21  H  HCH2   0   0.194   2.8138   0.7371  -0.9108
 EXA  H22  H  HCH2   0   0.194   1.9487   1.7442   0.2353
 EXA  H25  H  H      0   0.223   0.6652  -1.0096  -4.0381
 EXA  H26  H  H      0   0.216   0.8878   0.1106  -2.5965
 EXA  H3   H  HNH1   0   0.366   0.4991  -2.9187  -0.4240

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   deloc     1.248  0.020  1.248
 EXA  O11  C8   deloc     1.241  0.020  1.241
 EXA  C8   C7   single    1.540  0.020  1.540
 EXA  C7   C9   double    1.344  0.020  1.344
 EXA  C7   N3   single    1.368  0.020  1.368
 EXA  OP1  P    deloc     1.524  0.020  1.524
 EXA  N3   C4'  single    1.442  0.020  1.442
 EXA  C4'  NZ   single    1.448  0.020  1.448
 EXA  C4'  C4   single    1.520  0.020  1.520
 EXA  P    OP2  deloc     1.524  0.020  1.524
 EXA  P    OP3  deloc     1.522  0.020  1.522
 EXA  P    OP4  single    1.716  0.020  1.716
 EXA  CE   NZ   single    1.453  0.020  1.453
 EXA  CE   CD   single    1.520  0.020  1.520
 EXA  C5'  OP4  single    1.387  0.020  1.387
 EXA  C5'  C5   single    1.511  0.020  1.511
 EXA  C4   C5   aromatic  1.398  0.020  1.398
 EXA  C4   C3   aromatic  1.392  0.020  1.392
 EXA  CG   CD   single    1.524  0.020  1.524
 EXA  CG   CB   single    1.524  0.020  1.524
 EXA  C5   C6   aromatic  1.389  0.020  1.389
 EXA  O3   C3   single    1.353  0.020  1.353
 EXA  C3   C2   aromatic  1.399  0.020  1.399
 EXA  O1   C    deloc     1.247  0.020  1.247
 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  1.328  0.020  1.328
 EXA  C2   N1   aromatic  1.324  0.020  1.324
 EXA  C2   C2'  single    1.501  0.020  1.501
 EXA  C    OXT  deloc     1.248  0.020  1.248
 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  C9   H25  single    0.930  0.020  1.080
 EXA  C9   H26  single    0.930  0.020  1.080
 EXA  N3   H3   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
 EXA  H2   N    H1   106.66  3.000
 EXA  H2   N    CA   110.31  3.000
 EXA  H1   N    CA   108.39  3.000
 EXA  H4   CA   C    107.73  3.000
 EXA  H4   CA   CB   107.17  3.000
 EXA  C    CA   CB   110.10  1.900
 EXA  H4   CA   N    107.89  3.000
 EXA  C    CA   N    111.00  2.800
 EXA  CB   CA   N    110.50  1.700
 EXA  H6   CB   H5   106.56  3.000
 EXA  H6   CB   CG   108.75  3.000
 EXA  H5   CB   CG   109.48  3.000
 EXA  H6   CB   CA   108.67  3.000
 EXA  H5   CB   CA   108.96  3.000
 EXA  CG   CB   CA   114.15  3.000
 EXA  H8   CG   H7   106.21  3.000
 EXA  H8   CG   CD   108.48  3.000
 EXA  H7   CG   CD   109.62  3.000
 EXA  H8   CG   CB   110.24  3.000
 EXA  H7   CG   CB   109.22  3.000
 EXA  CD   CG   CB   112.86  3.000
 EXA  H10  CD   H9   106.44  3.000
 EXA  H10  CD   CE   109.21  3.000
 EXA  H9   CD   CE   109.41  3.000
 EXA  H10  CD   CG   109.39  3.000
 EXA  H9   CD   CG   109.73  3.000
 EXA  CE   CD   CG   112.47  3.000
 EXA  H12  CE   H11  106.16  3.000
 EXA  H12  CE   NZ   107.97  3.000
 EXA  H11  CE   NZ   112.74  3.000
 EXA  H12  CE   CD   109.52  3.000
 EXA  H11  CE   CD   109.18  3.000
 EXA  NZ   CE   CD   111.11  3.000
 EXA  H13  NZ   C4'  110.02  3.000
 EXA  H13  NZ   CE   109.30  3.000
 EXA  C4'  NZ   CE   113.75  3.000
 EXA  H15  C4'  N3   106.10  3.000
 EXA  H15  C4'  C4   107.87  3.000
 EXA  N3   C4'  C4   110.52  3.000
 EXA  H15  C4'  NZ   105.49  3.000
 EXA  C4   C4'  NZ   109.95  3.000
 EXA  N3   C4'  NZ   116.40  3.000
 EXA  C5   C4   C3   117.82  3.000
 EXA  C3   C4   C4'  120.82  3.000
 EXA  C5   C4   C4'  121.36  3.000
 EXA  C2   C3   O3   121.77  3.000
 EXA  C2   C3   C4   120.31  3.000
 EXA  O3   C3   C4   117.92  3.000
 EXA  H16  O3   C3   111.42  3.000
 EXA  N1   C2   C2'  118.41  3.000
 EXA  C2'  C2   C3   120.69  3.000
 EXA  N1   C2   C3   120.91  3.000
 EXA  H19  C2'  H18  107.58  3.000
 EXA  H19  C2'  H17  107.41  3.000
 EXA  H18  C2'  H17  107.41  3.000
 EXA  H19  C2'  C2   112.06  3.000
 EXA  H18  C2'  C2   109.86  3.000
 EXA  H17  C2'  C2   112.30  3.000
 EXA  C5'  C5   C6   120.83  3.000
 EXA  C6   C5   C4   117.79  3.000
 EXA  C5'  C5   C4   121.38  3.000
 EXA  H20  C6   N1   116.20  3.000
 EXA  H20  C6   C5   120.00  3.000
 EXA  N1   C6   C5   123.80  3.000
 EXA  C6   N1   C2   119.38  3.000
 EXA  H22  C5'  H21  105.62  3.000
 EXA  H22  C5'  OP4  111.78  3.000
 EXA  H21  C5'  OP4  111.07  3.000
 EXA  H22  C5'  C5   108.12  3.000
 EXA  H21  C5'  C5   108.65  3.000
 EXA  OP4  C5'  C5   111.37  3.000
 EXA  P    OP4  C5'  116.61  3.000
 EXA  OP3  P    OP2  115.26  3.000
 EXA  OP3  P    OP1  115.42  3.000
 EXA  OP2  P    OP1  114.23  3.000
 EXA  OP3  P    OP4  100.43  3.000
 EXA  OP2  P    OP4  104.51  3.000
 EXA  OP1  P    OP4  104.57  3.000
 EXA  OXT  C    O1   126.44  3.000
 EXA  OXT  C    CA   116.12  3.000
 EXA  O1   C    CA   117.39  3.000
 EXA  H3   N3   C7   113.37  3.000
 EXA  H3   N3   C4'  118.18  3.000
 EXA  C7   N3   C4'  125.57  3.000
 EXA  C9   C7   C8   120.37  3.000
 EXA  C9   C7   N3   126.95  3.000
 EXA  C8   C7   N3   112.68  3.000
 EXA  O11  C8   O10  126.95  3.000
 EXA  O11  C8   C7   117.52  3.000
 EXA  O10  C8   C7   115.53  3.000
 EXA  H26  C9   H25  116.71  3.000
 EXA  H26  C9   C7   123.95  3.000
 EXA  H25  C9   C7   119.34  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  Var_01    OP4  C5'  C5   C4   -176.75  30.0  1
 EXA  Var_02    H17  C2'  C2   C3     61.31  30.0  2
 EXA  Var_03    CD   CG   CB   CA   -179.92  30.0  1
 EXA  Var_04    CE   CD   CG   CB    178.19  30.0  3
 EXA  Var_05    NZ   CE   CD   CG    177.85  30.0  1
 EXA  Var_06    C4'  NZ   CE   CD    179.27  30.0  3
 EXA  Var_07    C8   C7   N3   C4'  -167.64  30.0  2
 EXA  Var_08    OP1  P    OP4  C5'   -53.95  30.0  3
 EXA  Var_09    O10  C8   C7   N3      4.77  30.0  2
 EXA  Var_10    H25  C9   C7   N3    178.47   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-3  C7   0.020
 EXA  plan-3  C8   0.020
 EXA  plan-3  O10  0.020
 EXA  plan-3  O11  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

