# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 13:16:43 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2S)-2-amino-6-{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]amino}hexanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNCC(=O)[C@H](O)[C@H](O)CO[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
 L5P  L5P  '(2S)-2-amino-6-{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]amino}hexanoic acid (non-preferred name)'  L-peptide  46  23  .  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_L5P
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
 L5P  N    N  NH2   0  -0.776   7.2879   2.2394   0.4138
 L5P  CA   C  CH1   0  -0.208   7.4995   0.8118   0.4154
 L5P  CB   C  CH2   0  -0.429   6.3154   0.0852  -0.2368
 L5P  CG   C  CH2   0  -0.412   5.0041   0.2925   0.5091
 L5P  CD   C  CH2   0  -0.444   3.8446  -0.4288  -0.1652
 L5P  CE   C  CH2   0  -0.250   2.5384  -0.2847   0.5985
 L5P  NZ   N  NH1   0  -0.602   1.4581  -0.9687  -0.0881
 L5P  C1   C  C     0   0.521   8.7882   0.3888  -0.2776
 L5P  O    O  O     0  -0.442   9.4269   1.0879  -1.0244
 L5P  O4   O  O     0  -0.390  -0.7806  -2.1792  -1.1333
 L5P  C3   C  C     0   0.364  -0.9187  -1.5663  -0.1012
 L5P  C2   C  CH2   0  -0.370   0.2082  -0.8829   0.6131
 L5P  C5   C  CH1   0  -0.102  -2.3038  -1.4772   0.5427
 L5P  O13  O  OH1   0  -0.650  -2.9319  -2.7296   0.5385
 L5P  C6   C  CH1   0  -0.029  -3.1324  -0.4182  -0.2097
 L5P  O14  O  OH1   0  -0.653  -2.4187   0.7830  -0.3534
 L5P  C7   C  CH2   0  -0.186  -4.4745  -0.2213   0.4695
 L5P  O8   O  O2    0  -0.587  -5.2284   0.7098  -0.3110
 L5P  P9   P  P     0   1.453  -6.8078   0.8120  -0.1092
 L5P  O12  O  OH1   0  -0.740  -7.4582  -0.4293  -0.8776
 L5P  O11  O  O     0  -0.711  -7.2948   0.8378   1.2824
 L5P  O10  O  OH1   0  -0.731  -7.0241   2.1113  -1.0058
 L5P  H1   H  HNH2  0   0.353   8.0464   2.7091   0.8913
 L5P  H2   H  HNH2  0   0.342   7.2916   2.5903  -0.5363
 L5P  H4   H  HCH1  0   0.264   7.5682   0.4771   1.4561
 L5P  H5   H  HCH2  0   0.228   6.2117   0.4301  -1.2718
 L5P  H6   H  HCH2  0   0.239   6.5286  -0.9850  -0.2894
 L5P  H7   H  HCH2  0   0.214   5.1170  -0.0717   1.5361
 L5P  H8   H  HCH2  0   0.224   4.7875   1.3602   0.5829
 L5P  H9   H  HCH2  0   0.217   3.7151  -0.0372  -1.1806
 L5P  H10  H  HCH2  0   0.218   4.0768  -1.4928  -0.2714
 L5P  H11  H  HCH2  0   0.218   2.6505  -0.7297   1.5925
 L5P  H12  H  HCH2  0   0.192   2.3234   0.7834   0.7638
 L5P  H13  H  HNH1  0   0.345   1.3549  -0.5762  -1.0163
 L5P  OXT  O  OH1   0  -0.594   9.1321  -0.8590   0.0232
 L5P  H16  H  HCH2  0   0.272   0.3001  -1.3748   1.5909
 L5P  H17  H  HCH2  0   0.233  -0.1215   0.1429   0.8512
 L5P  H18  H  HCH1  0   0.267  -2.1995  -1.1791   1.5922
 L5P  H19  H  HOH1  0   0.451  -2.9382  -3.0646  -0.3666
 L5P  H20  H  HCH1  0   0.256  -3.3045  -0.7874  -1.2272
 L5P  H21  H  HOH1  0   0.454  -2.3424   1.2172   0.5042
 L5P  H22  H  HCH2  0   0.251  -4.9890  -1.1813   0.5495
 L5P  H23  H  HCH2  0   0.247  -4.3381   0.1739   1.4812
 L5P  H24  H  HOH1  0   0.496  -7.2322  -0.5089  -1.8142
 L5P  H25  H  HOH1  0   0.504  -7.9365   2.4290  -1.0304
 L5P  HXT  H  HOH1  0   0.480   9.9356  -1.1101  -0.4569

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
 L5P  O11  P9   double  1.475  0.020  1.475
 L5P  P9   O8   single  1.596  0.020  1.596
 L5P  P9   O10  single  1.593  0.020  1.593
 L5P  P9   O12  single  1.598  0.020  1.598
 L5P  O8   C7   single  1.430  0.020  1.430
 L5P  O14  C6   single  1.405  0.020  1.405
 L5P  C6   C7   single  1.517  0.020  1.517
 L5P  C6   C5   single  1.541  0.020  1.541
 L5P  N    CA   single  1.458  0.019  1.458
 L5P  CD   CG   single  1.523  0.020  1.523
 L5P  CD   CE   single  1.520  0.020  1.520
 L5P  O4   C3   double  1.208  0.020  1.208
 L5P  NZ   CE   single  1.451  0.020  1.451
 L5P  NZ   C2   single  1.436  0.020  1.436
 L5P  CG   CB   single  1.523  0.020  1.523
 L5P  O    C1   double  1.206  0.020  1.206
 L5P  CB   CA   single  1.530  0.020  1.530
 L5P  C3   C5   single  1.530  0.020  1.530
 L5P  C3   C2   single  1.499  0.020  1.499
 L5P  C5   O13  single  1.401  0.020  1.401
 L5P  CA   C1   single  1.523  0.020  1.523
 L5P  N    H1   single  0.890  0.020  1.040
 L5P  N    H2   single  0.890  0.020  1.040
 L5P  CA   H4   single  0.970  0.020  1.090
 L5P  CB   H5   single  0.970  0.020  1.090
 L5P  CB   H6   single  0.970  0.020  1.090
 L5P  CG   H7   single  0.970  0.020  1.090
 L5P  CG   H8   single  0.970  0.020  1.090
 L5P  CD   H9   single  0.970  0.020  1.090
 L5P  CD   H10  single  0.970  0.020  1.090
 L5P  CE   H11  single  0.970  0.020  1.090
 L5P  CE   H12  single  0.970  0.020  1.090
 L5P  NZ   H13  single  0.890  0.020  1.040
 L5P  C1   OXT  single  1.329  0.020  1.329
 L5P  C2   H16  single  0.970  0.020  1.090
 L5P  C2   H17  single  0.970  0.020  1.090
 L5P  C5   H18  single  0.970  0.020  1.090
 L5P  O13  H19  single  0.850  0.020  0.980
 L5P  C6   H20  single  0.970  0.020  1.090
 L5P  O14  H21  single  0.850  0.020  0.980
 L5P  C7   H22  single  0.970  0.020  1.090
 L5P  C7   H23  single  0.970  0.020  1.090
 L5P  O12  H24  single  0.850  0.020  0.980
 L5P  O10  H25  single  0.850  0.020  0.980
 L5P  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
 L5P  H2   N    H1   106.20  3.000
 L5P  H2   N    CA   110.07  3.000
 L5P  H1   N    CA   110.41  3.000
 L5P  H4   CA   C1   107.12  3.000
 L5P  H4   CA   CB   107.91  3.000
 L5P  C1   CA   CB   109.15  3.000
 L5P  H4   CA   N    108.21  3.000
 L5P  C1   CA   N    113.47  3.000
 L5P  CB   CA   N    110.50  1.700
 L5P  H6   CB   H5   106.34  3.000
 L5P  H6   CB   CG   108.96  3.000
 L5P  H5   CB   CG   109.78  3.000
 L5P  H6   CB   CA   109.49  3.000
 L5P  H5   CB   CA   108.99  3.000
 L5P  CG   CB   CA   113.06  3.000
 L5P  H8   CG   H7   106.39  3.000
 L5P  H8   CG   CD   109.99  3.000
 L5P  H7   CG   CD   109.64  3.000
 L5P  H8   CG   CB   109.70  3.000
 L5P  H7   CG   CB   108.98  3.000
 L5P  CD   CG   CB   111.98  3.000
 L5P  H10  CD   H9   106.42  3.000
 L5P  H10  CD   CE   108.86  3.000
 L5P  H9   CD   CE   109.28  3.000
 L5P  H10  CD   CG   109.99  3.000
 L5P  H9   CD   CG   109.33  3.000
 L5P  CE   CD   CG   112.76  3.000
 L5P  H12  CE   H11  106.13  3.000
 L5P  H12  CE   NZ   112.49  3.000
 L5P  H11  CE   NZ   108.31  3.000
 L5P  H12  CE   CD   109.56  3.000
 L5P  H11  CE   CD   109.25  3.000
 L5P  NZ   CE   CD   110.94  3.000
 L5P  H13  NZ   C2   109.61  3.000
 L5P  H13  NZ   CE   109.07  3.000
 L5P  C2   NZ   CE   112.88  3.000
 L5P  OXT  C1   O    123.19  3.000
 L5P  OXT  C1   CA   112.13  3.000
 L5P  O    C1   CA   124.67  3.000
 L5P  C5   C3   C2   116.97  3.000
 L5P  C2   C3   O4   123.53  3.000
 L5P  C5   C3   O4   119.50  3.000
 L5P  H17  C2   H16  104.43  3.000
 L5P  H17  C2   C3   107.58  3.000
 L5P  H16  C2   C3   106.43  3.000
 L5P  H17  C2   NZ   114.90  3.000
 L5P  H16  C2   NZ   109.58  3.000
 L5P  C3   C2   NZ   113.24  3.000
 L5P  H18  C5   C6   109.38  3.000
 L5P  H18  C5   O13  106.77  3.000
 L5P  C6   C5   O13  111.83  3.000
 L5P  H18  C5   C3   109.43  3.000
 L5P  O13  C5   C3   110.64  3.000
 L5P  C6   C5   C3   108.75  3.000
 L5P  H19  O13  C5   108.42  3.000
 L5P  H20  C6   C7   108.69  3.000
 L5P  H20  C6   O14  105.84  3.000
 L5P  C7   C6   O14  112.60  3.000
 L5P  H20  C6   C5   107.84  3.000
 L5P  C7   C6   C5   110.26  3.000
 L5P  O14  C6   C5   111.38  3.000
 L5P  H21  O14  C6   109.53  3.000
 L5P  H23  C7   H22  107.96  3.000
 L5P  H23  C7   O8   109.57  3.000
 L5P  H22  C7   O8   111.35  3.000
 L5P  H23  C7   C6   110.52  3.000
 L5P  H22  C7   C6   109.60  3.000
 L5P  O8   C7   C6   107.85  3.000
 L5P  P9   O8   C7   119.64  3.000
 L5P  O10  P9   O11  118.16  3.000
 L5P  O10  P9   O12  107.91  3.000
 L5P  O11  P9   O12  109.45  3.000
 L5P  O12  P9   O8   107.00  3.000
 L5P  O10  P9   O8    96.62  3.000
 L5P  O11  P9   O8   116.58  3.000
 L5P  H24  O12  P9   115.76  3.000
 L5P  H25  O10  P9   114.24  3.000
 L5P  HXT  OXT  C1   110.23  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
 L5P  CONST_01  HXT  OXT  C1  CA  180.00   0.0  0
 L5P  Var_01    CD   CG   CB  CA  179.51  30.0  1
 L5P  Var_02    CE   CD   CG  CB  177.46  30.0  1
 L5P  Var_03    NZ   CE   CD  CG  179.14  30.0  3
 L5P  Var_04    C2   NZ   CE  CD  178.77  30.0  1
 L5P  Var_05    C3   C2   NZ  CE  178.99  30.0  3
 L5P  Var_06    O4   C3   C2  NZ    3.10  30.0  1
 L5P  Var_07    O11  P9   O8  C7   44.87  30.0  2
 L5P  Var_08    H22  C7   O8  P9   42.24  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
 L5P  chir_01  CA  N    CB  C1   negativ
 L5P  chir_02  C5  C6   C3  O13  positiv
 L5P  chir_03  C6  O14  C5  C7   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
 L5P  plan-1  O4   0.020
 L5P  plan-1  C3   0.020
 L5P  plan-1  C2   0.020
 L5P  plan-1  C5   0.020
 L5P  plan-2  CA   0.020
 L5P  plan-2  C1   0.020
 L5P  plan-2  O    0.020
 L5P  plan-2  OXT  0.020
 L5P  plan-2  HXT  0.020

