# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:56:07 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  43  23  .  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_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  -0.786   7.3200   2.1836   0.4822
 L5P  CA   C  CH1    0  -0.211   7.5137   0.7412   0.4693
 L5P  CB   C  CH2    0  -0.414   6.3237   0.0567  -0.2072
 L5P  CG   C  CH2    0  -0.407   4.9928   0.2887   0.4956
 L5P  CD   C  CH2    0  -0.440   3.8326  -0.4099  -0.2011
 L5P  CE   C  CH2    0  -0.248   2.5143  -0.2490   0.5384
 L5P  NZ   N  NH1    0  -0.601   1.4388  -0.9316  -0.1566
 L5P  C1   C  C      0   0.383   8.8306   0.2526  -0.1838
 L5P  O    O  O      0  -0.609   9.4775   1.0704  -0.8682
 L5P  O4   O  O      0  -0.398  -0.7794  -2.1699  -1.2064
 L5P  C3   C  C      0   0.371  -0.9346  -1.5505  -0.1795
 L5P  C2   C  CH2    0  -0.372   0.1817  -0.8443   0.5318
 L5P  C5   C  CH1    0  -0.101  -2.3199  -1.4719   0.4607
 L5P  O13  O  OH1    0  -0.653  -2.9092  -2.7447   0.5078
 L5P  C6   C  CH1    0  -0.028  -3.1793  -0.4616  -0.3218
 L5P  O14  O  OH1    0  -0.664  -2.4432   0.7163  -0.5736
 L5P  C7   C  CH2    0  -0.139  -4.4955  -0.1928   0.3883
 L5P  O8   O  O2     0  -0.656  -5.3025   0.6202  -0.4035
 L5P  P9   P  P      0   1.220  -6.9566   0.7154   0.0202
 L5P  O12  O  OP    -1  -0.904  -7.4797  -0.7088  -0.1359
 L5P  O11  O  O      0  -0.906  -6.9611   1.2270   1.4567
 L5P  O10  O  OP    -1  -0.896  -7.4570   1.7051  -1.0222
 L5P  H1   H  HNH2   0   0.333   8.0598   2.6039   1.0320
 L5P  H2   H  HNH2   0   0.321   7.4828   2.5286  -0.4570
 L5P  H4   H  HCH1   0   0.204   7.5276   0.4061   1.5139
 L5P  H5   H  HCH2   0   0.201   6.2526   0.4012  -1.2469
 L5P  H6   H  HCH2   0   0.214   6.5206  -1.0171  -0.2552
 L5P  H7   H  HCH2   0   0.201   5.0697  -0.0735   1.5273
 L5P  H8   H  HCH2   0   0.213   4.7970   1.3616   0.5640
 L5P  H9   H  HCH2   0   0.211   3.7270  -0.0155  -1.2186
 L5P  H10  H  HCH2   0   0.212   4.0494  -1.4777  -0.3058
 L5P  H11  H  HCH2   0   0.215   2.6074  -0.6858   1.5382
 L5P  H12  H  HCH2   0   0.189   2.3055   0.8223   0.6915
 L5P  H13  H  HNH1   0   0.343   1.3445  -0.5425  -1.0871
 L5P  OXT  O  OC    -1  -0.626   9.1278  -0.9449   0.0150
 L5P  H16  H  HCH2   0   0.267   0.2714  -1.3179   1.5188
 L5P  H17  H  HCH2   0   0.232  -0.1603   0.1825   0.7476
 L5P  H18  H  HCH1   0   0.252  -2.2205  -1.1372   1.5000
 L5P  H19  H  HOH1   0   0.447  -2.9918  -3.0734  -0.3952
 L5P  H20  H  HCH1   0   0.227  -3.3884  -0.8984  -1.3063
 L5P  H21  H  HOH1   0   0.448  -2.4413   1.2588   0.2226
 L5P  H22  H  HCH2   0   0.187  -4.9722  -1.1566   0.6075
 L5P  H23  H  HCH2   0   0.170  -4.2750   0.2707   1.3652

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   deloc   1.525  0.020  1.525
 L5P  P9   O8   single  1.710  0.020  1.710
 L5P  P9   O10  deloc   1.522  0.020  1.522
 L5P  P9   O12  deloc   1.525  0.020  1.525
 L5P  O8   C7   single  1.393  0.020  1.393
 L5P  O14  C6   single  1.412  0.020  1.412
 L5P  C6   C7   single  1.519  0.020  1.519
 L5P  C6   C5   single  1.540  0.020  1.540
 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  1.209  0.020  1.209
 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   deloc   1.247  0.020  1.247
 L5P  CB   CA   single  1.530  0.020  1.530
 L5P  C3   C5   single  1.528  0.020  1.528
 L5P  C3   C2   single  1.500  0.020  1.500
 L5P  C5   O13  single  1.403  0.020  1.403
 L5P  CA   C1   single  1.549  0.020  1.549
 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  deloc   1.250  0.020  1.250
 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

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   104.14  3.000
 L5P  H2   N    CA   107.92  3.000
 L5P  H1   N    CA   108.59  3.000
 L5P  H4   CA   C1   107.12  3.000
 L5P  H4   CA   CB   107.11  3.000
 L5P  C1   CA   CB   109.48  3.000
 L5P  H4   CA   N    107.22  3.000
 L5P  C1   CA   N    115.44  3.000
 L5P  CB   CA   N    110.50  1.700
 L5P  H6   CB   H5   106.17  3.000
 L5P  H6   CB   CG   109.11  3.000
 L5P  H5   CB   CG   109.43  3.000
 L5P  H6   CB   CA   108.59  3.000
 L5P  H5   CB   CA   109.20  3.000
 L5P  CG   CB   CA   114.04  3.000
 L5P  H8   CG   H7   106.15  3.000
 L5P  H8   CG   CD   110.03  3.000
 L5P  H7   CG   CD   109.42  3.000
 L5P  H8   CG   CB   109.58  3.000
 L5P  H7   CG   CB   108.83  3.000
 L5P  CD   CG   CB   112.63  3.000
 L5P  H10  CD   H9   106.34  3.000
 L5P  H10  CD   CE   108.75  3.000
 L5P  H9   CD   CE   109.26  3.000
 L5P  H10  CD   CG   109.90  3.000
 L5P  H9   CD   CG   109.45  3.000
 L5P  CE   CD   CG   112.93  3.000
 L5P  H12  CE   H11  106.08  3.000
 L5P  H12  CE   NZ   112.54  3.000
 L5P  H11  CE   NZ   108.22  3.000
 L5P  H12  CE   CD   109.56  3.000
 L5P  H11  CE   CD   109.17  3.000
 L5P  NZ   CE   CD   111.10  3.000
 L5P  H13  NZ   C2   109.60  3.000
 L5P  H13  NZ   CE   109.16  3.000
 L5P  C2   NZ   CE   112.99  3.000
 L5P  OXT  C1   O    126.31  3.000
 L5P  OXT  C1   CA   115.93  3.000
 L5P  O    C1   CA   117.74  3.000
 L5P  C5   C3   C2   116.85  3.000
 L5P  C2   C3   O4   123.24  3.000
 L5P  C5   C3   O4   119.90  3.000
 L5P  H17  C2   H16  104.53  3.000
 L5P  H17  C2   C3   107.46  3.000
 L5P  H16  C2   C3   106.49  3.000
 L5P  H17  C2   NZ   114.94  3.000
 L5P  H16  C2   NZ   109.46  3.000
 L5P  C3   C2   NZ   113.29  3.000
 L5P  H18  C5   C6   109.39  3.000
 L5P  H18  C5   O13  106.45  3.000
 L5P  C6   C5   O13  112.19  3.000
 L5P  H18  C5   C3   109.31  3.000
 L5P  O13  C5   C3   110.37  3.000
 L5P  C6   C5   C3   109.07  3.000
 L5P  H19  O13  C5   108.28  3.000
 L5P  H20  C6   C7   108.95  3.000
 L5P  H20  C6   O14  105.76  3.000
 L5P  C7   C6   O14  112.80  3.000
 L5P  H20  C6   C5   107.52  3.000
 L5P  C7   C6   C5   111.22  3.000
 L5P  O14  C6   C5   110.31  3.000
 L5P  H21  O14  C6   108.88  3.000
 L5P  H23  C7   H22  106.19  3.000
 L5P  H23  C7   O8   111.96  3.000
 L5P  H22  C7   O8   112.00  3.000
 L5P  H23  C7   C6   108.35  3.000
 L5P  H22  C7   C6   108.32  3.000
 L5P  O8   C7   C6   109.85  3.000
 L5P  P9   O8   C7   116.88  3.000
 L5P  O10  P9   O11  115.22  3.000
 L5P  O10  P9   O12  115.11  3.000
 L5P  O11  P9   O12  114.12  3.000
 L5P  O12  P9   O8   104.74  3.000
 L5P  O10  P9   O8   100.63  3.000
 L5P  O11  P9   O8   104.77  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  Var_01  CD   CG  CB  CA  -179.80  30.0  1
 L5P  Var_02  CE   CD  CG  CB   176.71  30.0  1
 L5P  Var_03  NZ   CE  CD  CG  -179.85  30.0  3
 L5P  Var_04  C2   NZ  CE  CD   178.00  30.0  1
 L5P  Var_05  C3   C2  NZ  CE  -179.87  30.0  3
 L5P  Var_06  O4   C3  C2  NZ     2.41  30.0  1
 L5P  Var_07  O11  P9  O8  C7    58.29  30.0  2
 L5P  Var_08  H22  C7  O8  P9    44.47  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

