# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:43:12 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[C@@H](CCC(O)=O)C(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
 SHR  SHR  'N-[(5S)-5-amino-5-carboxypentyl]-L-glutamic acid'  L-peptide  36  19  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_SHR
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
 SHR  N1   N  NH2    0  -0.797   0.2175   1.7063   5.1586
 SHR  C10  C  CH1    0  -0.244  -0.1386   0.3122   4.9419
 SHR  C9   C  CH2    0  -0.376   0.2958  -0.2552   3.5807
 SHR  C8   C  CH2    0  -0.446  -0.3633   0.4229   2.3857
 SHR  C7   C  CH2    0  -0.421   0.0502  -0.1904   1.0540
 SHR  C6   C  CH2    0  -0.283  -0.6209   0.4742  -0.1381
 SHR  N    N  NH1    0  -0.601  -0.2419  -0.1665  -1.3815
 SHR  C11  C  C      0   0.364   0.4579  -0.5756   6.0552
 SHR  O5   O  OC    -1  -0.648  -0.1247  -1.6580   6.2701
 SHR  O6   O  O      0  -0.561   1.4959  -0.1677   6.6143
 SHR  C4   C  CH1    0  -0.147  -0.7487   0.5030  -2.5643
 SHR  C3   C  CH2    0  -0.409  -0.1655  -0.1323  -3.8311
 SHR  C2   C  CH2    0  -0.573   1.3498  -0.0521  -3.9434
 SHR  C1   C  C      0   0.418   1.9446  -0.5631  -5.2702
 SHR  O1   O  OC    -1  -0.797   3.1779  -0.7642  -5.2735
 SHR  O2   O  O      0  -0.502   1.1723  -0.7188  -6.2365
 SHR  C5   C  C      0   0.425  -2.2895   0.4400  -2.6688
 SHR  O3   O  OC    -1  -0.761  -2.8685  -0.5466  -2.1766
 SHR  O4   O  O      0  -0.567  -2.8275   1.3790  -3.2942
 SHR  H12  H  HNH2   0   0.301   1.2184   1.7585   5.3027
 SHR  H11  H  HNH2   0   0.330   0.0110   2.2570   4.3347
 SHR  H10  H  HCH1   0   0.234  -1.2312   0.2291   4.9950
 SHR  H92  H  HCH2   0   0.261   1.3862  -0.1751   3.4930
 SHR  H91  H  HCH2   0   0.215   0.0602  -1.3234   3.5502
 SHR  H82  H  HCH2   0   0.176  -1.4522   0.3582   2.4918
 SHR  H81  H  HCH2   0   0.138  -0.1223   1.4916   2.3745
 SHR  H72  H  HCH2   0   0.266   1.1391  -0.1207   0.9468
 SHR  H71  H  HCH2   0   0.166  -0.1902  -1.2583   1.0498
 SHR  H62  H  HCH2   0   0.268  -1.7052   0.3995  -0.0236
 SHR  H61  H  HCH2   0   0.192  -0.3847   1.5529  -0.1296
 SHR  H    H  HNH1   0   0.335   0.7702  -0.1688  -1.4277
 SHR  H4   H  HCH1   0   0.172  -0.4666   1.5721  -2.5673
 SHR  H32  H  HCH2   0   0.202  -0.4853  -1.1788  -3.8755
 SHR  H31  H  HCH2   0   0.229  -0.6115   0.3634  -4.6947
 SHR  H22  H  HCH2   0   0.205   1.6702   0.9906  -3.8162
 SHR  H21  H  HCH2   0   0.235   1.8362  -0.6023  -3.1322

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
 SHR  N1   C10  single  1.455  0.020  1.455
 SHR  N1   H12  single  0.890  0.020  1.040
 SHR  N1   H11  single  0.890  0.020  1.040
 SHR  C10  C9   single  1.537  0.020  1.537
 SHR  C10  C11  single  1.544  0.020  1.544
 SHR  C10  H10  single  0.970  0.020  1.090
 SHR  C9   C8   single  1.524  0.020  1.524
 SHR  C9   H92  single  0.970  0.020  1.090
 SHR  C9   H91  single  0.970  0.020  1.090
 SHR  C8   C7   single  1.523  0.020  1.523
 SHR  C8   H82  single  0.970  0.020  1.090
 SHR  C8   H81  single  0.970  0.020  1.090
 SHR  C7   C6   single  1.521  0.020  1.521
 SHR  C7   H72  single  0.970  0.020  1.090
 SHR  C7   H71  single  0.970  0.020  1.090
 SHR  C6   N    single  1.449  0.020  1.449
 SHR  C6   H62  single  0.970  0.020  1.090
 SHR  C6   H61  single  0.970  0.020  1.090
 SHR  N    C4   single  1.451  0.020  1.451
 SHR  N    H    single  0.860  0.020  0.860
 SHR  C11  O5   deloc   1.248  0.020  1.248
 SHR  C11  O6   deloc   1.248  0.020  1.248
 SHR  C4   C3   single  1.532  0.020  1.532
 SHR  C4   C5   single  1.546  0.020  1.546
 SHR  C4   H4   single  0.970  0.020  1.090
 SHR  C3   C2   single  1.522  0.020  1.522
 SHR  C3   H32  single  0.970  0.020  1.090
 SHR  C3   H31  single  0.970  0.020  1.090
 SHR  C2   C1   single  1.541  0.020  1.541
 SHR  C2   H22  single  0.970  0.020  1.090
 SHR  C2   H21  single  0.970  0.020  1.090
 SHR  C1   O1   deloc   1.250  0.020  1.250
 SHR  C1   O2   deloc   1.247  0.020  1.247
 SHR  C5   O3   deloc   1.245  0.020  1.245
 SHR  C5   O4   deloc   1.250  0.020  1.250

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
 SHR  H11  N1   H12  106.82  3.000
 SHR  H11  N1   C10  110.49  3.000
 SHR  H12  N1   C10  108.21  3.000
 SHR  H10  C10  C11  107.84  3.000
 SHR  H10  C10  C9   107.23  3.000
 SHR  C11  C10  C9   108.48  3.000
 SHR  H10  C10  N1   108.01  3.000
 SHR  C11  C10  N1   110.43  3.000
 SHR  C9   C10  N1   114.60  3.000
 SHR  H91  C9   H92  106.45  3.000
 SHR  H91  C9   C8   108.62  3.000
 SHR  H92  C9   C8   109.56  3.000
 SHR  H91  C9   C10  108.91  3.000
 SHR  H92  C9   C10  108.95  3.000
 SHR  C8   C9   C10  114.07  3.000
 SHR  H81  C8   H82  106.09  3.000
 SHR  H81  C8   C7   108.91  3.000
 SHR  H82  C8   C7   109.31  3.000
 SHR  H81  C8   C9   110.30  3.000
 SHR  H82  C8   C9   109.12  3.000
 SHR  C7   C8   C9   112.89  3.000
 SHR  H71  C7   H72  106.24  3.000
 SHR  H71  C7   C6   109.05  3.000
 SHR  H72  C7   C6   109.50  3.000
 SHR  H71  C7   C8   109.66  3.000
 SHR  H72  C7   C8   109.24  3.000
 SHR  C6   C7   C8   112.93  3.000
 SHR  H61  C6   H62  106.15  3.000
 SHR  H61  C6   N    112.49  3.000
 SHR  H62  C6   N    108.61  3.000
 SHR  H61  C6   C7   109.05  3.000
 SHR  H62  C6   C7   109.01  3.000
 SHR  N    C6   C7   111.35  3.000
 SHR  H    N    C4   108.24  3.000
 SHR  H    N    C6   107.54  3.000
 SHR  C4   N    C6   113.85  3.000
 SHR  O6   C11  O5   126.50  3.000
 SHR  O6   C11  C10  117.17  3.000
 SHR  O5   C11  C10  116.27  3.000
 SHR  H4   C4   C5   107.07  3.000
 SHR  H4   C4   C3   107.55  3.000
 SHR  C5   C4   C3   107.85  3.000
 SHR  H4   C4   N    111.06  3.000
 SHR  C5   C4   N    112.62  3.000
 SHR  C3   C4   N    110.47  3.000
 SHR  H31  C3   H32  106.43  3.000
 SHR  H31  C3   C2   108.94  3.000
 SHR  H32  C3   C2   109.77  3.000
 SHR  H31  C3   C4   108.08  3.000
 SHR  H32  C3   C4   108.57  3.000
 SHR  C2   C3   C4   114.71  3.000
 SHR  H21  C2   H22  105.18  3.000
 SHR  H21  C2   C1   107.46  3.000
 SHR  H22  C2   C1   107.57  3.000
 SHR  H21  C2   C3   111.19  3.000
 SHR  H22  C2   C3   109.40  3.000
 SHR  C1   C2   C3   115.49  3.000
 SHR  O2   C1   O1   126.10  3.000
 SHR  O2   C1   C2   118.01  3.000
 SHR  O1   C1   C2   115.88  3.000
 SHR  O4   C5   O3   126.36  3.000
 SHR  O4   C5   C4   115.61  3.000
 SHR  O3   C5   C4   117.98  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
 SHR  Var_01  C7  C8  C9  C10  -178.08  30.0  3
 SHR  Var_02  C6  C7  C8  C9    179.26  30.0  3
 SHR  Var_03  N   C6  C7  C8   -177.89  30.0  3
 SHR  Var_04  C4  N   C6  C7   -174.40  30.0  3
 SHR  Var_05  C1  C2  C3  C4   -174.37  30.0  3
 SHR  Var_06  O1  C1  C2  C3   -165.64  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
 SHR  chir_01  C10  N1  C9  C11  negativ
 SHR  chir_02  C4   N   C3  C5   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
 SHR  plan-1  C10  0.020
 SHR  plan-1  C11  0.020
 SHR  plan-1  O5   0.020
 SHR  plan-1  O6   0.020
 SHR  plan-2  C2   0.020
 SHR  plan-2  C1   0.020
 SHR  plan-2  O1   0.020
 SHR  plan-2  O2   0.020
 SHR  plan-3  C4   0.020
 SHR  plan-3  C5   0.020
 SHR  plan-3  O3   0.020
 SHR  plan-3  O4   0.020

